MyTardis

Overview

MyTardis began at Monash University to solve the problem of users needing to store large datasets and share them with collaborators online. Its particular focus is on integration with scientific instruments, instrument facilities and research storage and computing infrastructure; to address the challenges of data storage, data access, collaboration and data publication.

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Key features for users

The MyTardis data management platform is a software solution that manages research data and the associated metadata. MyTardis handles the underlying storage to ensure that data is securely archived and provides access to the data through a web portal. Data hosted in MyTardis can also be accessed via SFTP.

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Key features for instrument facilities

MyTardis takes care of distributing data to your users. Its instrument integration technology takes care of securely and automatically shifting data from instrument to repository and makes it accessible by the right users.

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Developing for MyTardis

MyTardis is mostly written in the Python programming language and is built on top of the Django web framework. A complete installation of the service also includes an Elasticsearch index, a RabbitMQ-based task queue, an Nginx server, and a PostgreSQL database.

To set up and manage these services we employ the Kubernetes orchestration software and cloud technologies.

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Find out more

Project homepage http://mytardis.org

The source code is hosted at https://github.com/mytardis/mytardis

Documentation at http://mytardis.readthedocs.org includes

• User documentation
• Administrator documentation
• Developer documentation

The wiki at https://github.com/mytardis/mytardis/wiki includes

• Links to MyTardis add-ons, including apps and post-save filters
• Information about MyTardis community events

Known deployments

• Store.Synchrotron: https://store.synchrotron.org.au/
• Store.Monash: https://store.erc.monash.edu
• NIF ImageTrove: https://imagetrove.cai.uq.edu.au/
• MHTP Medical Genomics: https://mhtp-seq.erc.monash.edu/
• ANSTO: https://tardis.nbi.ansto.gov.au/
• Monash MyTardis Demo: https://mytardisdemo.erc.monash.edu/

Related projects and repositories

• MyData: https://github.com/mytardis/mydata
  • A desktop application for managing uploads to MyTardis
• NIF ImageTrove: https://github.com/NIF-au/imagetrove
  • A tool for ingesting and archiving NIF datasets, including
    • Web front end: MyTardis
    • A DICOM server: DICOM ToolKit
    • A dataset uploader: imagetrove-uploader
    • Federated authentication with the Australian Access Federation’s Rapid Connect service
• NIF ImageTrove Docker deployment: https://github.com/UWA-FoS/docker-mytardis
  • For ease of deployment, all of ImageTrove’s components are packaged into a Docker container.
• NIF Trusted Data Repositories: https://github.com/NIF-au/TDR
  • Delivering durable, reliable, high-quality image data

Releases

The default branch on GitHub is develop. This is the cutting edge development version. Please DO NOT use this in production, as it may have bugs that eat your data.

The master branch is the current stable release with all the latest bug fixes included. It will move to newer versions automatically. Follow this branch if you want to stay up to date in a production environment.

Each version has its own branch named by version number. At the time of writing, the latest release is 4.2.0, tagged from the series-4.2 branch. Follow this branch for your production installation and perform version upgrades manually.

Each bug fix or set of fixes bumps the minor version and each new release is tagged, eg. 4.2.1. Use tagged releases if you are paranoid about changes to the code you have not tested yourself.

To follow development, please see the contributing section below.

Reporting Bugs

Bug reports and feature requests can be made via our public issue tracker.

Contributing

New contributors are always welcome, however all developers should review the pull-request checklist before making pull requests.

For any wishes, comments, praise etc. either open a GitHub issue or contact us.

Active developers are also welcome to join our Slack team.

Contact details can be found on mytardis.org.

Documentation

User Guide

Basics

Organising Data

Data Structure Overview

Data in MyTardis is organised into a uniform hierarchy, which includes Experiments, Datasets and Data Files. Experiments are at the top of the hierarchy and can contain multiple Datasets. Similarly, Datasets can contain multiple Data Files. The hierarchy can be thought of like a directory structure on a typical PC (Fig. 1) in which a the Experiment directory contains multiple Dataset directories, which in turn contain multiple Data Files.

Fig. 1. Data hierarchy in MyTardis

Creating Experiments

1. Navigate to the My Data page.
2. Click on the Create button to the right of the page.

3. Fill in the ‘Create Experiment’ form. Requires at least a Title and one author.

4. Click Save.

Adding Datasets

Datasets always have at least one parent Experiment. To add a dataset to an Experiment:

1. Navigate to the Experiment page into which you would like to add a dataset.
2. Click the + Add New button to the right of the page.

3. Fill in the ‘Add new dataset’ form. Note: The ‘Description’ field is actually the name of the dataset.

4. Click Save.

Adding Data Files

Data Files can be added to a particular Dataset from the Dataset page.

1. Navigate to the Dataset into which you want to add new files.
2. Click the green Add files… button to the right of the page.

3. Select the files you want to add from the file selector dialog and Click Open. You can add multiple files by holding the “Shift” or “Ctrl” keys to select multiple files in the dialog.

Accessing Data

Download a Data File

Individual Data Files can be downloaded as follows:

1. Navigate to the Dataset containing the Data File you want to download.
2. Click the Download button on the Data File you want to download.

Download a Dataset

Entire Datasets can be downloaded as a tar archive.

1. Navigate to the Dataset you want to download.
2. Click the tar button to the right of the page.

Note: tar is an archive format like zip that may not be familiar to Windows users and a default Windows installation may not have the appropriate software to expand tar archives. We suggest that users install 7-zip to expand tar archives from MyTardis.

Download an Experiment

Entire Experiments can be downloaded as a tar archive.

1. Navigate to the Experiment you want to download.
2. Click the tar button under the ‘Description’ section of the page.

Note: tar is an archive format like zip that may not be familiar to Windows users and a default Windows installation may not have the appropriate software to expand tar archives. We suggest that users install 7-zip to expand tar archives from MyTardis.

Sharing and Publishing Data

MyTardis provides 3 primary mechanisms for sharing your data:

• Sharing with another MyTardis user.
• Sharing via a temporary (obfuscated) link.
• Making data public.

Data sharing is done at the Experiment level and you can find the options to share an Experiment under the Sharing tab on the left side of an Experiment page.

Sharing Data with Another MyTardis User

To share an Experiment with another MyTardis user:

1. Navigate to the Experiment you want to share.
2. Click on the Sharing tab on the left side of the page.
3. Click the Change User Sharing button.

4. Enter the Username of the user with which you want to share the data.

Note: Entering the users name or email address with activate autocomplete,

which helps to find the username of the user.

5. Select the permissions you’d like to give the user from the Permissions dropdown.
6. Click the +Add User button.
7. You should now see a new entry under the Current User Permissions section showing the user you’ve shared the Experiment with and the permissions you’ve given them.

Sharing Data via a Temporary Link

You can also share Data in an Experiment via a temporary (obfuscated) link. Temporary links expire after 1 month or can be deleted manually. Note: temporary links are not protected (i.e., anybody with the link can access the data); however, they are obfuscated and are thus difficult to find without prior knowledge of the link.

To share an Experiment via a temporary link:

1. Navigate to the Experiment you want to share.
2. Click on the Sharing tab on the left of the page.
3. Click the Create New Temporary Link button in the links section.

4. You should now see a new entry in the Links section. The new entry will provide links to both the Experiment page and a direct download link. These can be copied to the clipboard using the relevant buttons. These can then be shared with collaborators using email etc.

Publishing Data

Access to an Experiment in MyTardis is set to “private” by default and no license is attached to the data; however, MyTardis allows data from an Experiment to be made publicly available with an appropriate license. To make an Experiment publicly available:

1. Navigate to the Experiment you wish to publish and activate the Sharing tab to the left of the page.
2. Click the Change Public Access button. This will activate the Public Access dialog and display the current status of the data.
3. Select Public in the “Public access” dropdown menu.
4. Select an appropriate license from the list of licenses presented. In the following screenshot, a “Creative Commons Attribution” license is selected; however, your choices may be different as licenses are configured by your service provider.

5. Agree to the “Terms of Publishing” of your service provider.
6. Click Confirm

SFTP Access

SFTP is a secure and convenient way to access, browse and download large Experiments, Datasets and Files in MyTardis. Importantly, the SFTP interface to MyTardis is read only i.e., it is a mechanism to access data in MyTardis but does not allow adding data to MyTardis.

Prerequisites for accessing data via SFTP

In order to access data on MyTardis via SFTP, you will first need to install an SFTP client. There are many free and commercial SFTP clients for you to choose from; however, we recommend Cyberduck (Win & Mac), FileZilla (All platforms) or WinSCP (Win only) for the majority of users. The instructions here will focus on Cyberduck (Win & Mac).

Registering and managing SSH keys in MyTardis

MyTardis uses SSH key pairs to authenticate you when connecting via SFTP. Using SSH keys to authenticate is more secure and private than password-based authentication. SSH keys generally come in a pair: (1) a private part and (2) a public part. Key-based authentication typically requires you to share your public key with the service, again which you use your private key to authenticate. Never share your private key!

MyTardis provide to mechanism for registering a public key:

1. Adding an existing public SSH key to MyTardis
2. Have MyTardis to generate an SSH key pair

Adding an existing public SSH key to MyTardis

If you have an existing SSH keypair, you can register the public key in MyTardis. For instructions on how to create an SSH key pair, Gitlab provide some nice documentation on how to do so here.

To register a public key in MyTardis:

1. Navigate to the SSH key management page using the Manage SSH Keys link in the user menu.

2. Click the + Add Key button:

3. Fill in the Add SSH Keys form by entering a name for the key and the public key text. The public key text should be in OpenSSH format e.g., ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQDYZYnXpTP6e/BsQw+….

4. Click the Add Key button.

If successful you should get a new entry in the SSH keys table.

Have MyTardis to generate an SSH key pair

Creating SSH key pairs can be a bit of a challenge, particularly on Windows systems. For this reason, MyTardis provides another you another option for registering a public keys. In this case, MyTardis will generate the key pair for you, store the public part of the key and provide you with a one time opportunity to download the private part of the key.

It is important to note that MyTardis never stores your private key. If you lose/delete it, MyTardis cannot recover it for you. This isn’t really a problem, since MyTardis can always generate another key pair for you; however, you should revoke the public key associated to the lost private key in your account to ensure that no one who gains access to your private key can access your data. See Deleting previously registered public keys in MyTardis.

1. Navigate to the SSH key management page using the Manage SSH Keys link in the user menu.

2. Click the + Generate key button:

3. Give the key a name and click the Generate & Download button. The server will generate an SSH key pair, register the public key and trigger your browser to download the private key.

4. The SSH keys table will be updated with your newly registered public key.

Deleting previously registered public keys in MyTardis

Removing a previously registered public SSH key from MyTardis is straightforward.

1. Navigate to the SSH key management page using the Manage SSH Keys link in the user menu.

2. Click the Delete button on the key you wish to remove.

Attempting to connect to MyTardis via SFTP using the private sister key to the deleted key will no longer work.

Connecting to MyTardis via SFTP

1. Open your SFTP client and create a new connection with the following configuration:

Parameter	Value
Server:	URL for your MyTardis deployment e.g. https://store.erc.monash.edu
Port:	Port on which SFTP server is running
Username:	Your MyTardis username
Password:	Leave this blank
SSH Private Key	Path to a private SSH key [1]

Note: substitute your credentials and details for your MyTardis deployment for the italicised values. If you are unsure about any of these value, please contact your system admin should be able to provide these to you.

2. Click Connect
3. Upon successful connection you will be presented with a file browser showing all your data on MyTardis.

Data is organised according to the Experiment/Dataset/Data File hierarchy/structure described in the Organising Data section.

[1]	You must register the public key in MyTardis first, see Registering and managing SSH keys in MyTardis

Browse and/or Download a Specific Experiment or Dataset

MyTardis also provides a convenient way to access/browse a particular Experiment or Dataset via SFTP.

1. Navigate to the Experiment or Dataset page that you want to access via SFTP using your web browser.
2. There is an SFTP button in the Download section on both the Experiment and Dataset views.

3. Clicking the SFTP button at either of these two locations will redirect you to a page with instructions and links for starting an SFTP session for a specific experiment or dataset.

Configuration and Administration

Installation

The sections through to Extended Configuration below provide a Quick Start guide for getting a basic MyTardis installation up and running. The following section provides additional information on advanced configuration and add-on capabilities of MyTardis.

Prerequisites

Ubuntu (18.04 LTS is recommended)

Run this script for Python 3:

sudo bash install-ubuntu-py3-requirements.sh

It will install required packages with these commands:

# for Ubuntu 16.04 or 18.04
# sudo bash install-ubuntu-py3-requirements.sh

apt-get update
apt-get install \
   git libldap2-dev libmagickwand-dev libsasl2-dev \
   libssl-dev libxml2-dev libxslt1-dev libmagic-dev curl gnupg \
   python3-dev python3-pip python3-venv zlib1g-dev libfreetype6-dev libjpeg-dev    

curl -sL https://deb.nodesource.com/setup_12.x | sudo -E bash -
sudo apt-get install -y nodejs

Download

To get the most recent stable release:

git clone -b master https://github.com/mytardis/mytardis.git
cd mytardis

This clones the repository as read-only.

Or, to get the current development branch:

git clone -b develop git://github.com/mytardis/mytardis.git
cd mytardis

Quick configuration

If you want to use virtualenvwrapper, you can install it with sudo pip3 install virtualenvwrapper and set the export VIRTUALENV_PYTHON=/usr/bin/python3 in your ~/.bashrc or ~/.profile to ensure that mkvirtualenv will make a Python 3 virtual environment. For more information on configuring virtualenvwrapper, see https://virtualenvwrapper.readthedocs.io/en/latest/install.html#shell-startup-file

To activate virtualenvwrapper:

For Ubuntu 18.04 with Python 3 (using pip3 installed virtualenvwrapper):

source /usr/local/bin/virtualenvwrapper.sh

Then create the mytardis virtual environment

mkvirtualenv mytardis
pip install -U pip

Note: the next time you want to work with this virtualenv, run the appropriate source command and then use the command: workon mytardis

MyTardis dependencies are then installed with pip:

pip install -U -r requirements.txt

To install minimal Javascript dependencies for production:

npm install --production

To install Javascript dependencies for production and for testing:

npm install && npm test

Configuring MyTardis is done through a standard Django settings.py file. MyTardis comes with a set of default settings in its tardis/default_settings/ package. You can import this as the basis of your own config file - options defined here will override the relevant options in default_settings/*.py.

Create a new file tardis/settings.py containing the following:

from .default_settings import *

# Add site specific changes here.

# Turn on django debug mode.
DEBUG = True

# Use the built-in SQLite database for testing.
# The database needs to be named something other than "tardis" to avoid
# a conflict with a directory of the same name.
DATABASES['default']['ENGINE'] = 'django.db.backends.sqlite3'
DATABASES['default']['NAME'] = 'tardis_db'

In addition you will need to create a new SECRET_KEY for your installation. This is important for security reasons.

A convenient method is to run the following command in your mytardis installation location:

python -c "import os; from random import choice; key_line = '%sSECRET_KEY=\"%s\"  # generated from build.sh\n' % ('from .default_settings import * \n\n' if not os.path.isfile('tardis/settings.py') else '', ''.join([choice('abcdefghijklmnopqrstuvwxyz0123456789@#%^&*(-_=+)') for i in range(50)])); f=open('tardis/settings.py', 'a+'); f.write(key_line); f.close()"

This is the minimum set of changes required to successfully run the server in development mode. You can make any other site-specific changes as necessary.

Initialisation

Create and configure the database:

python manage.py migrate
python manage.py createcachetable default_cache
python manage.py createcachetable celery_lock_cache

This avoids creating a superuser before the MyTardis specific UserProfile table has been created. More information about the migrate commands can be found at Configuration and Administration.

Next, create a superuser:

python manage.py createsuperuser

MyTardis can now be executed in its simplest form using:

python manage.py runserver

This will start the Django web server at http://localhost:8000/.

Extended configuration

See below for some extra configuration options that are specific to MyTardis.

An automatically generated documentation of the settings can be found in tardis package.

Essential Production Settings

These settings are essential if you want to run MyTardis in production mode (DEBUG = False).

SECRET_KEY

This key needs to be unique per installation and, as the name implies, be kept secret.

A new one can be conveniently generated with the command:

echo "SECRET_KEY='`python manage.py generate_secret_key`'" >> tardis/settings.py

However, the more complex command shown above needs to be used at installation time.

ALLOWED_HOSTS

ALLOWED_HOSTS is a list of hostnames and/or IP addresses under which the server is accessible. If this is not set you will get a 500 Error for any request.

Database

tardis.default_settings.DATABASE_ENGINE

The database server engine that will be used to store the MyTardis metadata, possible values are postgresql_psycopg2, postgresql, mysql, sqlite3 or oracle.

tardis.default_settings.DATABASE_NAME

The name of the database to used to store the data, this is the path to the database if you are using the SQLite storage engine.

tardis.default_settings.DATABASE_USER

The user name used to authenticate to the database. If you are using SQLite this field is not used.

tardis.default_settings.DATABASE_PASSWORD

The password used to authenticate to the database. If you are using SQLite this field is not used.

tardis.default_settings.DATABASE_HOST

The host name of the machine hosting the database service. If this is empty then localhost will be used. If you are using SQLite then this field is ignored.

tardis.default_settings.DATABASE_PORT

The port the database is running on. If this is empty then the default port for the database engine will be used. If you are using SQLite then this field is ignored.

LDAP

For further information see LDAP authentication

Repository

tardis.default_settings.DEFAULT_STORAGE_BASE_DIR

The path to the default MyTardis storage location. This is where files will be stored to if you do not provide any other location explicitly through ``StorageBox``es.

tardis.default_settings.REQUIRE_DATAFILE_CHECKSUMS

If True, a Datafile requires an MD5 or SHA-512 checksum from the time it is first recorded in the MyTardis database. This enables a model-level constraint check each time a Datafile record is saved. Defaults to True. Datafile record is saved.

tardis.default_settings.REQUIRE_DATAFILE_SIZES

If True, a Datafile require a size from the time it is first recorded in the MyTardis database. This enables a model-level constraint check each time a Datafile record is saved. Defaults to True.

tardis.default_settings.REQUIRE_VALIDATION_ON_INGESTION

If True, ingestion of a Datafile is only permitted if the Datafile matches its supplied size and/or checksums. Defaults to True.

Access Rights & Licensing

Licences

By default, the Creative Commons Attribution 4.0 International licences are loaded.

You can use the admin interface to add other licences. Please ensure allows_distribution is set to the correct value to ensure the licence appears in conjunction with suitable public access types.

Legal Notice

When changing the public access rights or licence for an experiment, a legal notice is displayed. You can override it by specifying following settings in settings.py:

LEGAL_TEXT = "A sample legal Text"

Filters

tardis.default_settings.POST_SAVE_FILTERS

This contains a list of post save filters that are execute when a new data file is created.

The POST_SAVE_FILTERS variable is specified like:

POST_SAVE_FILTERS = [
    ("tardis.tardis_portal.filters.exif.EXIFFilter", ["EXIF", "http://exif.schema"]),
    ]

For further details please see the Filter Setup section.

Archive Organizations

tardis.default_settings.DEFAULT_ARCHIVE_FORMATS.

This is a prioritized list of download archive formats to be used in contexts where only one choice is offered to the user; e.g. the “download selected” buttons. (The list allows for using different archive formats depending on the user’s platform.)

tardis.default_settings.DEFAULT_PATH_MAPPER.

This gives the default archive “organization” to be used. Organizations are defined via the next attribute.

tardis.default_settings.DOWNLOAD_PATH_MAPPERS.

This is a hash that maps archive organization names to Datafile filename mapper functions. These functions are reponsible for generating the archive pathnames used for files written to “tar” and “zip” archives by the downloads module.

The DOWNLOAD_PATH_MAPPERS variable is specified like:

DOWNLOAD_PATH_MAPPERS = {
    'test': ('tardis.apps.example.ExampleMapper',),
    'test2': ('tardis.apps.example.ExampleMapper', {'foo': 1})
}

The key for each entry is the logical name for the organization, and the value is a tuple consisting of the function’s pathname and a set of optional keyword arguments to be passed to the function. At runtime, the function is called with each Datafile as a positional argument, and an additional ‘rootdir’ keyword argument. The function should compute and return a (unique) pathname based on the Datafile and associated objects. If the function returns None, this tells the archive builder to leave out the file.

By default, the archive builder uses the built-in “deep-storage” mapper which gives pathnames that try to use directory information to rebuild a file tree.

Storage Locations ( StorageBox es)

A MyTardis instance can be configured to support multiple locations ( StorageBox es) for storing data files. Each location holds copies ( DataFileObject s) of DataFile s that are recorded in the MyTardis database.

The StorageBox architecture is compatible with the Django File Storage API. This makes it relatively easy to support a number of different storage backends such as cloud storage or SFTP servers. Please refer to the StorageBox documentation for more detailed information.

Single Search

Instructions on installing and configuring Elasticsearch for advanced search are available from Setting Up Search.

Additional Tabs

Additional and custom tabs may be configured in MyTardis on a per-installation basis. The tabs are implemented as separate Django applications with a single view (index), listed in the TARDIS_APPS configuration item and either linked to, or installed in the TARDIS_APP_ROOT directory, by default tardis/apps.

Documentation on the additional tabs is available from Apps and Contextual Views.

Additional Views

Custom views may be configured in MyTardis on a per-installation basis. The tabs are implemented as separate Django applications with a single view function listed in the *_VIEWS configuration item and added to the INSTALLED_APPS list.

Refer to the views documentation for further information.

Site Customisations

Some settings that allow customised messages and styles.

PUBLICATION_INTRODUCTION = """
<p><strong>... introduction and publication agreement ...</strong></p>
"""
SITE_STYLES = ''  # should be CSS

# if either GA setting is empty, GA is disabled
GOOGLE_ANALYTICS_ID = ''  # whatever Google provides
GOOGLE_ANALYTICS_HOST = ''  # the host registered with Google

# these refer to any template finder findable location, e.g. APPDIR/templates/...
CUSTOM_ABOUT_SECTION_TEMPLATE = 'tardis_portal/about_include.html'
CUSTOM_USER_GUIDE = 'user_guide/index.html'

Deployment

Collecting Static Files

For performance reasons you should avoid static files being served via the application, and instead serve them directly through the webserver.

To collect all the static files to a single directory:

python manage.py collectstatic

tardis.default_settings.STATIC_ROOT

This contains the location to deposit static content for serving.

tardis.default_settings.STATIC_URL

The path static content will be served from. (eg. /static or http://mytardis-resources.example.com/)

See also

collectstatic, STATIC_ROOT, STATIC_URL

Serving with Nginx + Gunicorn

In this configuration, Nginx serves static files and proxies application requests to a Gunicorn server:

   HTTP  +-----------+       +-----------------+
+------->|   Nginx   +------>| Gunicorn Server |
         +-----------+       +-----------------+
           0.0.0.0:80         127.0.0.1:8000

Nginx should then be configured to send requests to the server. Here is an example configuration (SSL part from Mozilla SSL configurator). Please amend for your own needs and understand the settings before deploying it.:

upstream mytardis {
    server unix:/var/run/gunicorn/mytardis/socket;
    server 127.0.0.1:8000 backup;
}
server {
    listen 80 default_server;
    server_name demo.mytardis.org;
    return 301 https://$server_name$request_uri;
}

server {
    listen 443 default_server ssl;
    server_name demo.mytardis.org;

    # certs sent to the client in SERVER HELLO are concatenated in ssl_certificate
    ssl_certificate /path/to/signed_cert_plus_intermediates;
    ssl_certificate_key /path/to/private_key;
    ssl_session_timeout 5m;
    ssl_session_cache shared:SSL:50m;

    # Diffie-Hellman parameter for DHE ciphersuites, recommended 2048 bits
    ssl_dhparam /path/to/dhparam.pem;

    # intermediate configuration. tweak to your needs.
    ssl_protocols TLSv1.1 TLSv1.2;
    ssl_ciphers 'ECDHE-RSA-AES128-GCM-SHA256:ECDHE-ECDSA-AES128-GCM-SHA256:ECDHE-RSA-AES256-GCM-SHA384:ECDHE-ECDSA-AES256-GCM-SHA384:DHE-RSA-AES128-GCM-SHA256:DHE-DSS-AES128-GCM-SHA256:kEDH+AESGCM:ECDHE-RSA-AES128-SHA256:ECDHE-ECDSA-AES128-SHA256:ECDHE-RSA-AES128-SHA:ECDHE-ECDSA-AES128-SHA:ECDHE-RSA-AES256-SHA384:ECDHE-ECDSA-AES256-SHA384:ECDHE-RSA-AES256-SHA:ECDHE-ECDSA-AES256-SHA:DHE-RSA-AES128-SHA256:DHE-RSA-AES128-SHA:DHE-DSS-AES128-SHA256:DHE-RSA-AES256-SHA256:DHE-DSS-AES256-SHA:DHE-RSA-AES256-SHA:DES-CBC3-SHA:!aNULL:!eNULL:!EXPORT:!DES:!RC4:!MD5:!PSK:!aECDH:!EDH-DSS-DES-CBC3-SHA:!EDH-RSA-DES-CBC3-SHA:!KRB5-DES-CBC3-SHA';
    ssl_prefer_server_ciphers on;

    # HSTS (ngx_http_headers_module is required) (15768000 seconds = 6 months)
    add_header Strict-Transport-Security max-age=15768000;

    # OCSP Stapling ---
    # fetch OCSP records from URL in ssl_certificate and cache them
    ssl_stapling on;
    ssl_stapling_verify on;

    ## verify chain of trust of OCSP response using Root CA and Intermediate certs
    ssl_trusted_certificate /path/to/root_CA_cert_plus_intermediates;

    resolver <IP DNS resolver>;

    client_max_body_size 4G;
    keepalive_timeout 5;

    gzip off;  # security reasons
    gzip_proxied any;
    # MyTardis generates uncompressed archives, so compress them in transit
    gzip_types application/x-javascript text/css;
    gzip_min_length 1024;
    gzip_vary on;

    location / {
        proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
        proxy_set_header X-Forwarded-Proto $scheme;
        proxy_set_header Host $http_host;
        proxy_redirect off;
        proxy_pass http://mytardis;
        client_max_body_size 4G;
        client_body_buffer_size 8192k;
        proxy_connect_timeout 2000;
        proxy_send_timeout 2000;
        proxy_read_timeout 2000;
    }

    location /static/ {
        expires 7d;
        alias /srv/static_files/;
    }
}

The X-Forwarded-Proto header is explained in http://docs.gunicorn.org/en/stable/deploy.html#id5:

It is recommended to pass protocol information to Gunicorn. Many web frameworks use this information to generate URLs. Without this information, the application may mistakenly generate ‘http’ URLs in ‘https’ responses, leading to mixed content warnings or broken applications.

To tell MyTardis to set this header in its HTTP requests and redirects, you’ll need the following in your settings.py:

SECURE_PROXY_SSL_HEADER = ('HTTP_X_FORWARDED_PROTO', 'https')

For more information, including warnings on the risks of misconfiguring this setting, see: https://docs.djangoproject.com/en/2.2/ref/settings/#secure-proxy-ssl-header

Don’t forget to create the static files directory and give it appropriate permissions. The location is set in the settings.py file.

# Collect static files to ``settings.STATIC_ROOT``
python manage.py collectstatic
# Allow Nginx read permissions
setfacl -R -m user:nginx:rx static_dir

See also

Django with Gunicorn

Serving with Apache HTTPD + mod_wsgi

We do not support the use of Apache. If you need this and want to support this use case, we welcome your contribution of any relevant documentation.

Creating Systemd Services for Gunicorn and Celery

Gunicorn is a Python WSGI HTTP Server which is suitable for production (when combined with NGINX). Gunicorn is typically run from a Systemd service (on Ubuntu 16.04 or Ubuntu 18.04), saved in /etc/systemd/system/gunicorn.service:

[Unit]
Description=gunicorn daemon
After=network.target

[Service]
User=mytardis
Group=mytardis
WorkingDirectory=/home/mytardis/mytardis
ExecStart=/home/mytardis/.virtualenvs/mytardis/bin/gunicorn \
  -c gunicorn_settings.py -b unix:/tmp/gunicorn.socket \
  -b 127.0.0.1:8000 \
  --log-syslog \
  wsgi:application

[Install]
WantedBy=multi-user.target

On older systems (Ubuntu 14.04), Supervisor can be used instead of Systemd. In this case, the Gunicorn service would be configured in /etc/supervisor/conf.d/gunicorn.conf:

[program:gunicorn]
command=/home/mytardis/.virtualenvs/mytardis/bin/gunicorn
 -c /home/mytardis/mytardis/gunicorn_settings.py
 -b unix:/tmp/gunicorn.socket
 -b 127.0.0.1:8000
 --log-syslog
 wsgi:application
user=mytardis
stdout_logfile=/var/log/gunicorn.log
redirect_stderr=true

A single server MyTardis deployment requires only one Gunicorn service, but MyTardis can be installed on multiple web nodes, each running NGINX and Gunicorn to accomodate load balancing and high availability using HAProxy.

The Celery workers which run MyTardis asynchronous tasks also require a service configuration, which is typically implemented with Systemd (on Ubuntu 16.04 or Ubuntu 18.04), saved in /etc/systemd/system/celeryworker.service:

[Unit]
Description=celeryworker daemon
After=network.target

[Service]
User=mytardis
Group=mytardis
WorkingDirectory=/home/mytardis/mytardis
Environment=DJANGO_SETTINGS_MODULE=tardis.settings
ExecStart=/home/mytardis/.virtualenvs/mytardis/bin/celery worker \
  -A tardis.celery.tardis_app \
  -c 2 -Q celery,default -n "allqueues.%%h"

[Install]
WantedBy=multi-user.target

On older systems (Ubuntu 14.04), Supervisor can be used instead of Systemd. In this case, the Celery worker service would be configured in /etc/supervisor/conf.d/celeryworker.conf:

[program:celeryd]
environment=
  DJANGO_SETTINGS_MODULE=tardis.settings
command=/home/mytardis/.virtualenvs/mytardis/bin/celery worker
  -A tardis.celery.tardis_app
  -c 2 -Q celery,default -n "allqueues.%%h"
user=mytardis
directory=/home/mytardis/mytardis
stdout_logfile=/var/log/celeryd.log
redirect_stderr=true
killasgroup=true
stopwaitsecs=600

For tasks scheduled by Celerybeat, the Systemd service configuration (for Ubuntu 16.04 or Ubuntu 18.04), is saved in /etc/systemd/system/celerybeat.service:

[Unit]
Description=celerybeat daemon
After=network.target

[Service]
User=mytardis
Group=mytardis
WorkingDirectory=/home/mytardis/mytardis
Environment=DJANGO_SETTINGS_MODULE=tardis.settings
ExecStart=/home/mytardis/.virtualenvs/mytardis/bin/celery beat \
  -A tardis.celery.tardis_app --loglevel INFO

[Install]
WantedBy=multi-user.target

On older systems (Ubuntu 14.04), Supervisor can be used instead of Systemd. In this case, the Celerybeat service would be configured in /etc/supervisor/conf.d/celerybeat.conf:

[program:celerybeat]
environment=
  DJANGO_SETTINGS_MODULE=tardis.settings
command=/home/mytardis/.virtualenvs/mytardis/bin/celery beat
  -A tardis.celery.tardis_app --loglevel INFO
user=mytardis
directory=/home/mytardis/mytardis
stdout_logfile=/var/log/celerybeat.log
redirect_stderr=true

Authentication Methods

Users

MyTardis supports several sources of authentication and identity, referred to as user providers.

In the settings.py user providers are activated by specifying them within the USER_PROVIDERS variable:

USER_PROVIDERS = ('tardis.tardis_portal.auth.localdb_auth.DjangoUserProvider',)

Groups

MyTardis also supports several sources for group membership information, referred to as group providers.

In the settings.py group providers are activated by specifying them within the GROUP_PROVIDERS variable:

GROUP_PROVIDERS = ('tardis.tardis_portal.auth.localdb_auth.DjangoGroupProvider',
                   'tardis.tardis_portal.auth.vbl_auth.VblGroupProvider',)

Included Auth Plugins

HTTP Basic Endpoint Authentication

tardis.tardis_portal.auth.httpbasicendpoint_auth

HTTP Basic Endpoint authentication uses access to a HTTP resource (or endpoint) to determine if authentication should be allowed.

To use HTTP Basic Endpoint authentication, you’ll need a HTTP resource protected by HTTP Basic Auth which is accessible from the MyTardis server.

In the settings.py add the following to AUTH_PROVIDERS with an appropriate name. eg.

AUTH_PROVIDERS = (
    ('acls', 'acls', 'tardis.tardis_portal.auth.httpbasicendpoint_auth.HttpBasicEndpointAuth'),
)

On each request, MyTardis will attempt to use basic authentication with the provided credentials to access the HTTP resource. If it fails, access is denied.

Endpoint to use in HTTP Basic Endpoint Auth. eg.

HTTP_BASIC_AUTH_ENDPOINT = 'https://test.example/endpoint'

LDAP Authentication

tardis.tardis_portal.auth.ldap_auth

To enable LDAP you’ll need to specify which components of the LDAP authentication backend are enabled. In the settings.py add the following to either Authentication, User Provider, Group Provider slugs.:

'tardis.tardis_portal.auth.ldap_auth.ldap_auth'

This is a wrapper function that allows initialisation of the LDAP provider using settings.py values.

ldap_auth() Function

The following are configuration settings that are used when initialising the LDAP backend.

tardis.default_settings.LDAP_TLS

Enable TLS connections.

tardis.default_settings.LDAP_URL

Set the URL of the LDAP server, e.g. ldap://localhost:389/

tardis.default_settings.LDAP_USER_LOGIN_ATTR

Set the login attribute of the users, usually this will be either cn or uid

tardis.default_settings.LDAP_USER_ATTR_MAP

The LDAP user attribute map is used to map internal identifiers like first_name, last_name and email to their LDAP equivalents e.g. {“givenName”: “first_name”, “sn”: “last_name”, “mail”: “email”}

tardis.default_settings.LDAP_GROUP_ID_ATTR

This is where you specify the group identifier from LDAP, usually it will be cn.

tardis.default_settings.LDAP_GROUP_ATTR_MAP

This map is used to map internal identifiers like display e.g. {“description”: “display”}

tardis.default_settings.LDAP_BASE

Sets the search base of the LDAP queries dc=example, dc=com

tardis.default_settings.LDAP_USER_BASE

Sets the suffix to append to the user RDN (e.g. uid=jsmith) to construct the DN e.g. “ou=People, ” + LDAP_BASE

tardis.default_settings.LDAP_GROUP_BASE

Sets the suffix to append to the group RDN (e.g. cn=group1) to construct the DN e.g. “ou=Group, ” + LDAP_BASE

Temporary Token Authentication

tardis.tardis_portal.auth.token_auth

To use token authentication, you’ll need to specify the following settings.py

‘tardis.tardis_portal.auth.token_auth.TokenGroupProvider’,

TOKEN_EXPIRY_DAYS = 30

TOKEN_LENGTH = 30

TOKEN_USERNAME = ‘tokenuser’

and create a user with

bin/django createtokenuser

Cleaning up

bin/django cleanuptokens

It is recommended that you schedule regular purging of expired tokens. Set a cronjob to run bin/django cleanuptokens

Expiry

Token auth works by hijacking the group provider system.

MyTardis groups are calculated and cached when a user logs in.

This means that if a session is active, and a token becomes in valid (either through deletion or expiry) that access will still be granted. To mitigate this, when a token user logs in, an explicit expiry is set on their session - the earlier of 4am the next day, or the session expiry date (the end of the day)

This forces the user to attempt to log in again, and be denied access.

• tardis.tardis_portal.auth.ip_auth

The tardis.tardis_portal.auth package module contains the authentication specific code.

Filter Setup

With the USE_FILTERS option set to True in settings, filters will be called once a file object has been verified.

Filters allow post-processing of uploaded files and can be used to extract metadata from file headers and/or generate thumbnail images.

The DataFileObject’s verify method submits a task called “mytardis.apply_filters” to the message broker (RabbitMQ).

This task can be picked up by the “mytardis-filters” microservice: https://github.com/mytardis/mytardis-filters or by your own custom microservice.

Database

Initialising

When creating a new database the migrate command will need to be called to initialise the schema and insert the initial data fixtures.

Usage

python manage.py migrate

Migrating

Some of the upgrades to MyTardis will require that the database schema be upgraded to match the internal data model. The migrate command migrates data from old database schemas to the current one. It detects which version of the database you are currently running and will automatically migrate to the current version.

In certain cases it is also necessary to update the permissions table.

Usage

python manage.py migrate

If the model changes require it, run:

python manage.py update_permissions

creating superuser

After success of database initialization or migration, please use a command line utility called createsuperuser to create an administrator account using the admin site which is hooked to the URL /admin/.

Usage

python manage.py createsuperuser

Backup

Previous versions of MyTardis included a backupdb management command but it has been removed in 4.0. Please use the recommended backup tool for your database engine, e.g. pg_dump or mysqldump.

Schema and Parameter Sets

MyTardis stores metadata as Parameters, which are grouped in to Parameter Sets, which are defined by a Schema.

Managing Schema

Schema are managed through the Django administrative interface. The administrative interface is normally accesible from a link similar to:

http://domain.com:8000/admin/

Selecting “Schemas” in the adminstrative interface will display a list of the installed schemas. Clicking on a schema displays the editor for that schema.

Schema definitions are the combination of two tables, Schema and ParameterName.

The Schema fields are:

Namespace

The namespace uniquely identifies the schema. When exporting an experiment as a METS file the namespace is used as an XML Namespace, and thus must follow the XML standard, i.e. in the form of a URL.

The MyTardis naming convention is:

http://domain.com/localidentifiers/schemaname/version

Name

The display name of the schema.

Type

Experiment, Dataset or Datafile.

Subtype

Used to group and identify schema for forms based searching.

The ParameterName fields are:

Schema

The namespace of the schema which this parameter belongs to.

Name

The identifier used to ingest parameters.

Full Name

The display name of the parameter.

Units

The display name of the units for numerical values.

Data Type

One of:

• Numeric
• String
• Longstring
• URL
• Filename
• Datetime
• Link

Strings use the input field widget for editing, while longstrings use a textarea widget.

Immutable

If true, no user editing of the parameter is allowed, regardless of access.

Comparison Type

The type of search to be performed with Forms Based Search. Not used by Advanced Search.

Is Searchable

Flag whether this parameter is searchable.

Choices

If defined, a drop down list of values is displayed.

Order

The display order of the parameters within the schema. Sorting is by Order, then alphabetically.

Setting Up Search

Tardis comes with a single search option which provides users with a search field that returns a list of matching Experiments, Datasets and Datafiles.

The single search box uses Elasticsearch, and Django Elasticsearch DSL library that allows indexing of django models in elasticsearch, and accordingly requires some setup. The single search box is disabled by default.

Setting up Elasticsearch

Elasticsearch doesn’t work out of the box with MyTardis. It is not currently installed with pip and requires a number of manual steps to get working.

Elasticsearch can be found here: https://www.elastic.co/products/elasticsearch

The following are a very simple list of steps that will get everything up and running. It is advisable to follow up with the person responsible for overseeing security policy at your home institution to see if any extra setup is necessary.

Django Configuration

Enabling Single Search

A list of default settings for Single Search are already in default_settings.py in the MyTardis repository. Single search is enabled by setting the SINGLE_SEARCH_ENABLED option to True.

MyTardis comes with a search app that allows indexing Experiments, Dataset and Datafile models and also provides view and api to perform elasticsearch query on these models. This can be enabled by adding ‘tardis.apps.search’ to the list of installed apps.

Other settings are shown below:

ELASTICSEARCH_DSL Settings

The default value is

INSTALLED_APPS += ('django_elasticsearch_dsl','tardis.apps.search',)
ELASTICSEARCH_DSL = {
    'default': {
        'hosts': 'http://localhost:9200'
    },
}
ELASTICSEARCH_DSL_INDEX_SETTINGS = {
    'number_of_shards': 1
}

Updating Indexes

Once Elasticsearch is set up, and Single Search is enabled (i.e. the SINGLE_SEARCH_ENABLED option in settings is set to True) Elasticsearch DSL will automatically register the addition of and changes to models and reflect these in the search index. That is, as soon as a new instance of a model is added to the database, or changes are made to an existing instance, these changes will be searchable.

If you’re adding search to an existing deployment of Django then you’ll need to manually trigger a rebuild of the indexes (automatic indexing only happens through signals when models are added or changed).

Elasticsearch DSL registers a number of management commands with the Django framework, these commands can be listed by running the following command

python manage.py search_index --help

the important one here being the –rebuild command. To rebuild, navigate to your checkout and call the following command

python manage.py search_index --rebuild

Elasticsearch DSL will then ask you to confirm your decision (Note: Rebuilding will destroy your existing indexes, and will take a while for large datasets, so be sure), and then start rebuilding.

Storage Options and Architecture in MyTardis

Database layout for storage

The storage for each DataFile is configured individually. A “way to store data” is called StorageBox. Each file has one or many related DataFileObjects, which link a DataFile with a StorageBox. A DataFile can have several copies stored in different StorageBoxes via several DataFileObjects.

StorageBoxes

StorageBoxes contain all the information needed to store a file except an id unique to the file and storagebox.

Each StorageBox points to a class that implements the Django storage API via a python module path as string.

Optional instatiation parameters for each StorageBox can be stored in StorageBoxOptions. These are used as parameters to the storage class set in the django_storage_class attribute of a StorageBox

These parameters are string types by default. However, by setting the optional parameter value_type to 'pickle', any picklable object can be stored here and hence used for instantiation of the storage class.

Optional classification and other metadata can be stored in StorageBoxAttributes.

A special case is where someone registers a file and wants to put it into location themselves but needs to be given the place to put it (via the API). Such situation can only be resolved with StorageBoxes that implement the “build_save_location” function. Such StorageBoxes need to have a StorageBoxAttribute with key “staging” and value “True”.

DataFiles

DataFiles are the logical representation of the file. They contain information about the name, size, checksum, dates etc.

DataFileObjects

DataFileObjects point to the DataFile they belong to and the StorageBox they reside in. They also have an identifier that the StorageBox uses to find the actual file. DataFileObjects also have a date, and a state-flag.

Available backends

Django storage API compatible backends are available for example at https://github.com/jschneier/django-storages

We have tested the following backends with MyTardis:

• File on disk or any other system mounted storage
• SFTP
• SWIFT Object Storage

Documented backends

S3 compatible storage

S3 and S3 compatible storage backends are supported by the django-storages package.

The django-storages package is now included in MyTardis’s requirements-base.txt

It can be used to configure an S3 storage box, or it can be used to store static assets in S3, as described at https://django-storages.readthedocs.io/en/latest/backends/amazon-S3.html

Configuration

The following options can be set as StorageBoxOption on your S3 storage box or system wide in your Django settings (a default of * labels mandatory settings):

StorageBoxOption	Django Setting	Default
access_key	AWS_S3_ACCESS_KEY_ID AWS_ACCESS_KEY_ID	*
secret_key	AWS_S3_SECRET_ACCESS_KEY AWS_SECRET_ACCESS_KEY	*
file_overwrite	AWS_S3_FILE_OVERWRITE	True
headers	AWS_HEADERS	{}
bucket_name	AWS_STORAGE_BUCKET_NAME	*
auto_create_bucket	AWS_AUTO_CREATE_BUCKET	False
default_acl	AWS_DEFAULT_ACL	public-read
bucket_acl	AWS_BUCKET_ACL	default_acl
querystring_auth	AWS_QUERYSTRING_AUTH	True
querystring_expire	AWS_QUERYSTRING_EXPIRE	3600
reduced_redundancy	AWS_REDUCED_REDUNDANCY	False
location	AWS_LOCATION	''
encryption	AWS_S3_ENCRYPTION	False
custom_domain	AWS_S3_CUSTOM_DOMAIN	None
calling_format	AWS_S3_CALLING_FORMAT	SubdomainCallingFormat()
secure_urls	AWS_S3_SECURE_URLS	True
file_name_charset	AWS_S3_FILE_NAME_CHARSET	utf-8
gzip	AWS_IS_GZIPPED	False
preload_metadata	AWS_PRELOAD_METADATA	False
gzip_content_types	GZIP_CONTENT_TYPES	('text/css', 'text/javascript', 'application/javascript', 'application/x-javascript', 'image/svg+xml')
url_protocol	AWS_S3_URL_PROTOCOL	http:
host	AWS_S3_HOST	S3Connection.DefaultHost
use_ssl	AWS_S3_USE_SSL	True
port	AWS_S3_PORT	None
proxy	AWS_S3_PROXY_HOST	None
proxy_port	AWS_S3_PROXY_PORT	None
The max amount of memory a returned file can take up before being rolled over into a temporary file on disk. Default is 0: Do not roll over.
max_memory_size	AWS_S3_MAX_MEMORY_SIZE	0

Appendix: Conversion of ‘Replicas’

Replicas used to be the method of file storage abstraction in MyTardis versions 3.x. The StorageBoxes replace this. For pain-free upgrading, a conversion has been included with the database migrations that works as follows:

All ‘Locations’ that are local are converted to default (folder on disk) StorageBoxes. All ‘Locations’ that are not local are converted to dummy ‘link only’ StorageBoxes with the corresponding name. These can be upgraded manually to a StorageBox with an appropriate backend after the migration has taken place.

Max size is set to size of disk, hence for multiple locations on the same disk this number provides no protection. This also should be set to reasonable values manually after the migration.

Each ‘Replica’ of a file will be converted to a DataFileObject pointing to the relevant StorageBox.

All files are manually reverified, so that unverified entries can be checked for errors.

Facility Overview

Introduction

The Facility Overview included with MyTardis allows facility administrators to monitor the output of connected instruments, highlighting unverified files, dataset size, file counts and file listings.

Setup

In order for datasets to appear in the Facility Overview, each dataset must be associated with an Instrument, which is itself associated with a Facility. The Facility object will reference a facility administrator’s group, members of which may view the Facility Overview.

   +-------------------+   +------------------------+   +----------+
   | Facility Managers |-->| Facility Manager Group |-->| Facility |
   +-------------------+   +------------------------+   +----------+
|------------------------------------------------------------|
|
|  +------------+   +----------+   +-----------+
|->| Instrument |-->| Datasets |-->| Datafiles |
   +------------+   +----------+   +-----------+
                          ^
                          |  +-------------+
                          |--| Experiments |
                             +-------------+

The facility managers, facility manager groups, facilities and instruments may be configured via the django admin interface. MyData, the desktop uploader client for the MyTardis server, can be configured to assign the appropriate instrument to uploaded datasets at the point of ingestion.

It should be noted that the dataset visibility within the facility overview is limited to dataset and datafile listings only. Access to the experiment and dataset views, as well as raw data, is still controlled via the ACL framework.

Usage

Members of the facility manager groups for one or more facilities will see the “Facility Overview” menu item in the MyTardis web portal. After opening the facility overview, a list of recently ingested datasets will be displayed from the facility being managed. If a user manages multiple facilities, a blue drop-down selector will also appear on the right-hand side of the page. As the facility overview is designed to give a snapshot of recently uploaded datasets, older data is not immediately accessible; MyTardis’ search feature is better suited to this.

In addition to simply listing the most recent datasets, the datasets can be grouped by instrument or by owner, and filtered by username, experiment name and instrument name. Note that while filters are active, it may appear as though no new pages are loaded by clicking “Load more”, since the additional datasets fetched from the server might not match the active filters.

Task Priorities

Overview

From v4.1.0, MyTardis assumes the use of RabbitMQ as its message broker, and instructs Celery to create a “celery” queue with task priorites enabled. The queue’s maximum priority is set to 10 in tardis/default_settings/celery_settings.py which is used when setting up the Celery app in tardis/celery.py:

tardis/default_settings/celery_settings.py
------------------------------------------
...
MAX_TASK_PRIORITY = 10
DEFAULT_TASK_PRIORITY = 5
DEFAULT_EMAIL_TASK_PRIORITY = 10

CELERY_DEFAULT_QUEUE = 'celery'
# The 'x-max-priority' argument will only be respected by the RabbitMQ broker,
# which is the recommended broker for MyTardis:
CELERY_QUEUES = (
    Queue('celery', Exchange('celery'),
          routing_key='celery',
          queue_arguments={'x-max-priority': MAX_TASK_PRIORITY}),
)

tardis/celery.py
----------------
...
tardis_app = Celery('tardis')
tardis_app.config_from_object('django.conf:settings')
...

Celery’s apply_async method’s shadow argument is used to annotate storage box related task names with the location (storage box name) which they are running in, e.g. dfo_verify becomes dfo_verify location:default-storage:

tardis/tardis_portal/tasks.py
-----------------------------
...
def verify_dfos(**kwargs):
    ...
    for dfo in dfos_to_verify:
        kwargs['priority'] = dfo.priority
        kwargs['shadow'] = 'dfo_verify location:%s' % dfo.storage_box.name
        dfo_verify.apply_async(args=[dfo.id], **kwargs)
...

Monitoring

We can confirm that the x-max-priority argument was supplied when creating the queue by running rabbitmqctl report on our RabbitMQ server:

$ sudo rabbitmqctl report | grep 'x-max-priority'
...
Listing queues for vhost mytardis ...
name    durable auto_delete     arguments ...
...
celery        true    false   [{"x-max-priority",10}] ...

We can list the tasks currently running (and observe their priorities) by running celery inspect active from one of our Celery nodes:

(mytardis) mytardis@celery0 ~/mytardis$ DJANGO_SETTINGS_MODULE=tardis.settings celery -A tardis.celery.tardis_app inspect active
-> celery@allqueues.celery0: OK
    * {u'args': u'[32933203]', u'time_start': 1548368931.7151582, u'name': u'dfo_verify location:default-storage',
       u'delivery_info': {u'priority': 5, u'redelivered': False, u'routing_key': u'celery', u'exchange': u''},
       u'hostname': u'celery@allqueues.celery0', u'acknowledged': False, u'kwargs': u'{}',
       u'type': u'tardis_portal.dfo.verify', u'id': u'50c80b84-5d64-44c7-a6d4-c551b6d14e22', u'worker_pid': 3730}
-> celery@allqueues.celery2: OK
    - empty -
...
-> celery@allqueues.celery7: OK
    * {u'args': u'[30476811]', u'time_start': 1548368924.2799926, u'name': u'dfo_verify location:default-storage',
       u'delivery_info': {u'priority': 5, u'redelivered': False, u'routing_key': u'celery', u'exchange': u''},
       u'hostname': u'celery@allqueues.celery7', u'acknowledged': False, u'kwargs': u'{}',
       u'type': u'tardis_portal.dfo.verify', u'id': u'de7d0fe1-f386-4937-af7f-a693e7630fb5', u'worker_pid': 9051}
...
-> celery@allqueues.celery14: OK
    * {u'args': u'[289]', u'time_start': 1548368427.9639463, u'name': u'sbox_cache_files location:big-data1',
       u'delivery_info': {u'priority': 4, u'redelivered': False, u'routing_key': u'celery', u'exchange': u''},
       u'hostname': u'celery@allqueues.celery14', u'acknowledged': False, u'kwargs': u'{}',
       u'type': u'tardis_portal.storage_box.cache_files', u'id': u'8767709f-ae98-4735-9d29-21bb5b13e230', u'worker_pid': 15906}

Notice that most tasks have the default priority of 5 (defined in tardis/default_settings/celery_settings.py as DEFAULT_TASK_PRIORITY and that the task operating on a file from the big-data1 storage boxes has a lower priority of 4.

Default priorities for storage boxes can be configured via StorageBox Attributes. We can check which storage boxes have priorites specified in the Django shell as follows:

(mytardis) mytardis@celery0:~/mytardis$ ./manage.py shell_plus

>>> StorageBoxAttribute.objects.filter(key='priority')
<QuerySet [<StorageBoxAttribute: big-data1-> priority: 4>, <StorageBoxAttribute: big-data2-> priority: 4>]>

So in the example above, explicit priorities are only set for the “big-data1” and “big-data2” storage boxes.

Common Problems and Solutions

Celery workers time out when running celery inspect active

When running celery inspect active sometimes you will see this error:

Error: No nodes replied within time constraint.

Usually, running celery inspect active again will resolve the problem, i.e. it will just work without error on subsequent attempts.

If desired, you can specify a timeout e.g. timeout 10 but usually running celery inspect active again does the trick.

Non-priority queue already exists

If an attempt to submit a task to the queue (with apply_async triggers an error like this:

PreconditionFailed: Queue.declare: (406) PRECONDITION_FAILED - inequivalent arg 'x-max-priority' for queue 'celery' in vhost '/':
 received the value '10' of type 'signedint' but current is none

This means that the MyTardis process attempting to submit the task is expecting the queue to have the x-max-priority argument, but it doesn’t have that argument (see rabbitmqctl report above).

In this case, you can delete the celery queue, and allow Celery to recreate it with the x-max-priority argument:

(mytardis) mytardis@celery0 ~/mytardis$ DJANGO_SETTINGS_MODULE=tardis.settings celery -A tardis.celery.tardis_app amqp queue.delete celery

Development

Architecture

This page describes the architecture of MyTardis.

MyTardis is built on the Django web framework, which itself is built on Python, thus MyTardis follows the architectural model of Django.

Component Architecture

Web Server

MyTardis is typically deployed with the standard Nginx + Gunicorn + Django + Python stack.

RDBMS

Ideally, use PostgreSQL. MySQL or MariaDB may be usable but it is not as well tested.

Data Storage

Local disk, network mounted disks as well as S3 and SFTP are supported.

Ingestion

Ingestion is normally site specific. A desktop application is available (MyData).

Functional Architecture

MyTardis follows the standard Django architecture.

The major functional modules in MyTardis are:

API

A RESTful API provides anonymous and authenticated access to most of the stored data.

Auth

Authentication and Authorisation.

Download

Data download functionality.

Filters

Processing of metadata as data is uploaded, e.g. extract EXIF metadata from JPEG files.

Management

Additional commands for the Django CLI. The backup utility is implemented as a Django command.

Migrations

Database migration code.

Publish

RIF-CS metadata publication.

Search

Provides a searchable and authorisation enabled index for quickly finding data.

SFTP server

Provides read access to data in MyTardis via the SFTP protocol

Information on the individual modules is available from the Module Index.

Scalability Model

At the component / module level, performance and Scalability within MyTardis is achieved by:

• Allowing long lived or compute intensive operations to be hosted on separate machines from the main web server.
  • E.g. by running multiple web servers and sending long lived operations, such as ingestion, to a server reserved for such operations.
• Performance and Scalability of the database is achieved by a combination of 1) optimising the SQL requests issued by MyTardis, and 2) database specific scalability, please refer to the appropriate database documentation.
• Performance and Scalability of the web server is provided through the normal mechanisms for nginx / wsgi hosted python applications, e,g,:
  • Increasing individual Server capability
    • Individual Server performance / utilization may be managed by controlling the number of python (django) processes active at any one time.
  • Deploying multiple web servers
    • Multiple web servers may be deployed using standard mechanisms, e.g. load balancers. State (session) information is distributed using Django’s standard session model.
• The Data Archive is a normal file system, e.g. NFS, SAMBA, etc., with performance and scalability dependent on the implementation and deployment.
• Extraction and formatting of metadata for ingestion is up to the client and may be distributed across any number of machines.

SQL Scalability Notes

The datafileparameter table is expected to be the single largest table by an order of magnitude, in the hundreds of millions of records (at the Australian Synchrotron).

For Postgres, this will probably be addressed by table partioning. In this case using a date field to partition is often recommended. Dates may be introduced as part of the support for anotations, raw data, versioned data and derived data.

Persistance and Data Architecture

Django provides an Object-Relational-Model that maps Django Models to the underlying relational database.

The Django Models are defined in tardis.tardis_portal.models.

Security Model

Authentication

Access to data catalogued by MyTardis may be either public, i.e. anonymous access allowed, or private, requiring authentication. The Authentication Framework is documented in ref-authframework.

Authorisation

MyTardis includes an extensible authorisation engine, documented in ref-authframework and Authorisation Framework.

Class Diagram

Unless the application has a very rich business model (which MyTardis does not), a class diagram doesn’t convey much information in Django applications (it ends up being a flat list of classes). To understand the context in which the MyTardis classes are created, please refer to the Django documentation, http://docs.djangoproject.com/ on the responsibilities of models, views, managers and templates.

Source Code

This section describes the top level layout of the source code in the GitHub repository.

• docs
  • MyTardis User and Administrative documentation
• tardis
  • apps

    • Contains all the optional functionality and installation specific

      functionality. Examples include the optional ANDS Register (ands_register) and Related Info (related_info) tabs, and the ANSTO (mecat-ansto) and Australian Synchrotron (mecat-as) installation specific modules.

    • Some applications are part of the main code base, others can be added

      at installation time.

  • search
    • Search related code
  • tardis_portal
    • This is the main django application that contains most of the core MyTardis functionality

Authorisation Framework

Django Authorisation

Django has a built-in authorisation/permission mechanism that is in use by default. It is enabled in MyTardis in default_settings.py together with the custom object level permission framework described below.

AUTHENTICATION_BACKENDS = (
    'django.contrib.auth.backends.ModelBackend',
    'tardis.tardis_portal.auth.authorisation.ACLAwareBackend',
)

The Django default permissions are automatically available for each Model. The verbs are add, change, delete, and they can be queried on the user object as follows:

user.has_perm('tardis_portal.add_experiment')
user.has_perm('tardis_portal.add_dataset')
user.has_perm('tardis_portal.change_experiment')
user.has_perm('tardis_portal.delete_datasetparameterset')

There is a function in tardis.tardis_portal.auth.authservice called _set_user_from_dict that adds the following permissions for each new user created using custom methods:

'add_experiment'
'change_experiment'
'change_group'
'change_userauthentication'
'change_experimentacl'

These permissions apply in general and are augmented by ACLs

Object Level Permissions and Access Control Lists

The main purpose of the ACL system is to manage per experiment permissions. The architecture allows for future expansion to more find grained permission management. However, at this stage only the Experiment level is supported by the user interface.

Permissions are applied with a few predefined roles:

read

read permission allows individuals and groups access to view an experiment.

write

write permissions cover addition of new datasets and datafiles and also deletion of datafile.

delete

delete permission allows deletion of datasets and experiments.

Roles are applied through the web using the Control Panel and can be applied to either users or groups.

To make an experiment public requires an explicit publish action.

The ACL permissions can be queried on the user object just like standard permissions, however, with the addition of the object in question:

user.has_perm('tardis_acls.change_experiment', experiment)

Verbs currently available are change, view, delete, owns, share.

The translation of ACLs to has_perm verbs is defined in a function in tardis.tardis_portal.auth.authorisation.

To allow for querying on any object related to experiments, extra logic was added to some of the models. To support the logic, in addition to ACLs, has_perm calls model functions named _has_VERB_perm, which allows model-specific permission logic.

The current policy is that if those functions return True or False then that result is returned without further checking. If they return an object, permissions will be checked for this object thereby allowing delegation.

RESTful API for MyTardis

The data and metadata stored in MyTardis instances is made accessible through a RESTful API.

Not all functionality has been exposed via the API at this time. This documentation reflects what is available and tested.

The API version v1 is built on the Tastypie framework.

The RESTful API can also be explored via the automatically generated Swagger documentation at http://mytardis-example.com/api/v1/swagger/.

See swagger.io for details on the Swagger standard.

API accessible models

• Experiment
• ExperimentParameterSet
• ExperimentParameter

• Dataset
• DatasetParameterSet
• DatasetParameter

• DataFile
• DatafileParameterSet
• DatafileParameter

• StorageBox
• StorageBoxOption
• StorageBoxAttribute

• Schema
• ParameterName

• User
• Group

• Facility
• Instrument

• ObjectACL

Authentication

Currently implemented are Basic Auth, to be used via HTTPS only, and SessionAuth which queries Django sessions.

Due to our desire to provide information to users without any login, eg. for public data, the Basic Auth mechanism is slightly non-standard.

The standard sends an anonymous request, awaits a WWW-Authenticate header, then sends authentication credentials. Instead, this API sends public data for anonymous requests.

Using curl or the requests library this poses no problem. However, using urllib2 or web browser without a Django session is not going to work out of the box.

Here is a snippet (found here: http://stackoverflow.com/questions/4628610/does-urllib2-support-preemptive-authentication-authentication) that makes urllib2 work, should you want to use this library:

class PreemptiveBasicAuthHandler(urllib2.BaseHandler):

        def __init__(self, password_mgr=None):
                if password_mgr is None:
                    password_mgr = urllib2.HTTPPasswordMgrWithDefaultRealm()
                self.passwd = password_mgr
                self.add_password = self.passwd.add_password

        def http_request(self, req):
                uri = req.get_full_url()
                user, pw = self.passwd.find_user_password(None, uri)
                if pw is None:
                    return req

                raw = "%s:%s" % (user, pw)
                auth = 'Basic %s' % base64.b64encode(raw).strip()
                req.add_unredirected_header('Authorization', auth)
                return req

auth_handler = PreemptiveBasicAuthHandler()
auth_handler.add_password(realm=None,
                          uri=url,
                          user='mytardis',
                          passwd='mytardis')
opener = urllib2.build_opener(auth_handler)
# ...and install it globally so it can be used with urlopen.
urllib2.install_opener(opener)

Querying the database (GET)

All endpoints support querying lists and individual records via GET requests. Some support more complex queries via GET parameters as well.

Creating objects, adding files (POST)

The creation of Experiments, Datasets and Dataset_Files via POSTs with the option to include metadata/parametersets has been implemented and tested.

The following examples demonstrate how to go about it.

In all except the file attachment case the POST data should be a JSON string, the Content-Type header needs to be set to application/json and the Accept header as well. Other response formats may be made available in the future.

In all cases the URI of the created object is returned in the Location header of the response.

Experiments

Example JSON input

{
  "title": "API-created Experiment #1",
  "description": "Wow, all automatic!",
  "institution_name": "Monash University",
  "parameter_sets": [
    {
      "schema": "http://institution.com/my/schema",
      "parameters": [
         {
           "name": "important_parameter_1",
           "value": "Test16"
         },
         {
           "name": "important_parameter_3",
           "value": "57.136"
         }
      ]
    },
    {
      "schema": "http://company.com/some/other/schema",
      "parameters": [
         {
           "name": "meaningful_name",
           "value": "Test17"
         },
         {
           "name": "meaningless_name",
           "value": "1234"
         }
      ]
    }
  ]
}

This creates an experiment with two parametersets with two parameters each.

Alternative to Schema namespaces and Parameter names, you can also specify the URIs to each. Until the querying of Schemas and Parameters is documented this is discouraged.

Datasets

Example JSON input:

{
  "description": "API-created Dataset",
  "experiments": [
    "/api/v1/experiment/1/",
    "/api/v1/experiment/2/"
  ],
  "immutable": false,
  "parameter_sets": [
    {
      "parameters": [
        {
          "name": "obscure-instrument-setting-52",
          "value": "awesome dataset api POST"
        },
        {
          "name": "temperature",
          "value": "301"
        }
      ],
      "schema": "http://datasets.com/need/schemas/too"
    },
    {
      "parameters": [
        {
          "name": "someotherparameter",
          "value": "some other value"
        }
      ],
      "schema": "http://better-datasets.com/offers/better/schemas"
    }
  ]
}

DataFiles

There are three ways to add a file to MyTardis via the API.

Via multipart form POST

This works for single files at the moment.

The key is to send a multipart-form instead of ‘application/json’. This can be accomplished with the requests library as shown in the following example.

To use requests you need to install it first, eg. pip install requests.

Also, for this to work, the POST data needs to be sent with the JSON string called 'json_data' and the file called 'attached_file'.

Example JSON input:

{
    "dataset": "/api/v1/dataset/1/",
    "filename": "mytestfile.txt",
    "md5sum": "c858d6319609d6db3c091b09783c479c",
    "size": "12",
    "mimetype": "text/plain",
    "parameter_sets": [{
        "schema": "http://datafileshop.com/fileinfo/v1",
        "parameters": [{
            "name": "fileparameter1",
            "value": "123"
        },
        {
            "name": "fileparameter2",
            "value": "1234"
        }]
    }]
}

Example requests script:

import requests
from requests.auth import HTTPBasicAuth

url = "http://localhost:8000/api/v1/dataset_file/"
headers = {'Accept': 'application/json'}
response = requests.post(url, data={"json_data": data}, headers=headers,
                         files={'attached_file': open(filename, 'rb')},
                         auth=HTTPBasicAuth(username, password)
                         )

Via staging location

Another way to add a file is to create the database entry first without providing a storage location. This will return back a location on the server that you are assumed to have access to. Once the file appears there, for example when you copy it there, it will be moved to its permanent storage location managed by MyTardis.

The full file path that you should copy/move the file to is returned as the content of the response.

Example JSON input:

{
    "dataset": "/api/v1/dataset/1/",
    "filename": "mytestfile.txt",
    "md5sum": "c858d6319609d6db3c091b09783c479c",
    "size": "12",
    "mimetype": "text/plain",
    "parameter_sets": [{
        "schema": "http://datafileshop.com/fileinfo/v1",
        "parameters": [{
            "name": "fileparameter1",
            "value": "123"
        },
        {
            "name": "fileparameter2",
            "value": "1234"
        }]
    }]
}

Via shared permanent storage location

This method assumes that there exists a storage that is shared between MyTardis and you. The registered file will remain in this location.

For this to work you need to get a Location (internal MyTardis settings) name to submit with your metadata.

Examples JSON:

{
   "dataset": "/api/v1/dataset/1/",
   "filename": "mytestfile.txt",
   "md5sum": "c858d6319609d6db3c091b09783c479c",
   "size": "12",
   "mimetype": "text/plain",
   "replicas": [{
       "url": "mytestfile.txt",
       "location": "local",
       "protocol": "file"
   }],
   "parameter_sets": [{
       "schema": "http://datafileshop.com/fileinfo/2",
       "parameters": [{
           "name": "fileparameter1",
           "value": "123"
       },
       {
           "name": "fileparameter2",
           "value": "123"
       }]
   }]
}

urllib2 POST example script

Replace MODEL with one of the available model names in lower case. data is the JSON as a string.

import urllib2
url = "http://localhost:8000/api/v1/MODEL/"
headers = {'Accept': 'application/json',
           'Content-Type': 'application/json'}
auth_handler = urllib2.HTTPBasicAuthHandler()
auth_handler.add_password(realm="django-tastypie",
                          uri=url,
                          user=username,
                          passwd=password)
opener = urllib2.build_opener(auth_handler)
urllib2.install_opener(opener)
myrequest = urllib2.Request(url=url, data=data,
                            headers=headers)
myrequest.get_method = lambda: 'POST'
output = "error"
output = urllib2.urlopen(myrequest)
print output.headers["Location"]

Tests

Running the Test Suite

Run this command to run the unit tests:

./test.py

If you want to speciy any options or specific tests to run, the test argument is required first:

./test.py test –some-argument

You can choose to run the test suite with different options (e.g. with coverage, with different verbosity, etc.). To see the full list of options, run the same command with the –help flag.

Running Individual Unit Tests

The unit tests reside in the tardis/tardis_portal/tests directory. To run the unit tests individually, you can use this command:

./test.py test <test_module_name_here>

Note that the test module name argument should be the relative file path with “.” as folder separator. For example, if you want to run the test “test_authentication.py”, then your command to execute this test would be:

./test.py test tardis.tardis_portal.tests.test_authentication

Other options

You can choose to include different options when running the unit tests (e.g. run in verbose mode, print out a traceback, etc.). Run the test or django test command with –help flag to see the the full list of options:

./test.py test --help

Running BDD tests

To run BDD (Behaviour Driven Development) tests with the default settings and headless Chrome, download ChromeDriver from http://chromedriver.chromium.org/downloads and make it available in your PATH (e.g. in /usr/local/bin/) and run:

./test.py behave

Running QUnit tests

The QUnit tests reside in the js_tests/ directory.

package.json contains devDependencies required for running these tests.

Running npm install will install everything you need, whereas npm install --production will skip the devDependencies.

You can run the QUnit tests with:

npm test

Or by running a web server:

python -m SimpleHTTPServer

and opening http://127.0.0.1:8000/js_tests/tests.html in your browser.

tardis

tardis package

Subpackages

tardis.analytics package

Submodules

tardis.analytics.apps module

class tardis.analytics.apps.AnalyticsConfig(app_name, app_module)

Bases: django.apps.config.AppConfig

name = 'tardis.analytics'

verbose_name = 'Analytics framework'

tardis.analytics.ga module

Google analyitics tracking

tardis.analytics.ga.track_download(label, session_id, ip, user, total_size=None, num_files=None, ua=None)

tardis.analytics.ga.track_login(label, session_id, ip, user)

tardis.analytics.ga.track_logout(label, session_id, ip, user)

tardis.analytics.tracker module

Generic tracking and analytics interface Supports Google Analytics through ga.py, others may follow

class tardis.analytics.tracker.IteratorTracker(iterator, tracker_data=None)

Bases: object

wraps file iterator to track successful and incomplete downloads

close()

next()

tardis.analytics.tracker.service = <module 'tardis.analytics.ga' from '/home/docs/checkouts/readthedocs.org/user_builds/mytardis/checkouts/v4.2.0-rc3/tardis/analytics/ga.py'>

This can become a setting to other service in the future

Module contents

tardis.apps package

Subpackages

tardis.apps.deep_storage_download_mapper package

Submodules

tardis.apps.deep_storage_download_mapper.mapper module

File mapper that works for files stored in deep directory structures. It recreates the structure as stored in the datafile directory

tardis.apps.deep_storage_download_mapper.mapper.deep_storage_mapper(obj, rootdir=None)

If rootdir is None, just return a filesystem-safe representation of the object, e.g. “DatasetDescription_123” or “strange %2F filename.txt”

For now, only DataFiles are supported when rootdir is not None.

Parameters:

• obj (DataFile, Dataset or Experiment) – The model instance (DataFile, Dataset or Experiment) to generate a path for.
• rootdir (basestring) – The top-level directory name, or None

Returns:

Filesystem-safe path for the object in the archive or SFTP view.

Return type:

basestring

Raises:

• Exception –
• NotImplementedError –

tardis.apps.deep_storage_download_mapper.urls module

Module contents

tardis.apps.dl_mapper_df_dir_only package

Submodules

tardis.apps.dl_mapper_df_dir_only.mapper module

File mapper that works for files stored in deep directory structures. It recreates the structure as stored in the datafile directory

tardis.apps.dl_mapper_df_dir_only.mapper.df_dir_only(datafile, rootdir)

tardis.apps.dl_mapper_df_dir_only.urls module

Module contents

tardis.apps.filepicker package

Submodules

tardis.apps.filepicker.filepicker_settings module

tardis.apps.filepicker.urls module

tardis.apps.filepicker.utils module

taken from https://raw.github.com/Filepicker/django-filepicker/master/django_filepicker/utils.py on 11 Apr 2013

class tardis.apps.filepicker.utils.FilepickerFile(url)

Bases: object

cleanup()

Removes any downloaded objects and closes open files.

filepicker_url_regex = re.compile('https?:\\/\\/www.filepicker.io\\/api\\/file\\/.*')

get_file()

Downloads the file from filepicker.io and returns a Django File wrapper object

tardis.apps.filepicker.views module

Filepicker.io button view and upload handler

Module contents

tardis.apps.oaipmh package

Subpackages

tardis.apps.oaipmh.provider package

Submodules

tardis.apps.oaipmh.provider.base module

class tardis.apps.oaipmh.provider.base.BaseProvider(site)

Bases: oaipmh.interfaces.IOAI, object

A base provider which roughly implements the PyOAI interface for OAI-PMH servers.

Extend this if you’re writing your own provider for a new type or a different metadata format.

getRecord(metadataPrefix, identifier)

Get a record for a metadataPrefix and identifier.

Parameters:

• metadataPrefix (string) – identifies metadata set to retrieve
• identifier (string) –
  • repository-unique identifier of record

Raises:

• oaipmh.error.CannotDisseminateFormatError – if metadataPrefix is unknown or not supported by identifier.
• oaipmh.error.IdDoesNotExistError – if identifier is unknown or illegal.

Returns:

a header, metadata, about tuple describing the record.

identify()

Retrieve information about the repository.

Returns an Identify object describing the repository.

listIdentifiers(metadataPrefix, set=None, from_=None, until=None)

Get a list of header information on records.

Parameters:

• metadataPrefix (string) – identifies metadata set to retrieve
• set (string) – set identifier; only return headers in set
• from (datetime) – only retrieve headers from from_ date forward (in naive UTC)
• until (datetime) – only retrieve headers with dates up to and including until date (in naive UTC)

Raises:

• error.CannotDisseminateFormatError – if metadataPrefix is not supported by the repository.
• error.NoSetHierarchyError – if the repository does not support sets.

Returns:

an iterable of headers.

listMetadataFormats(identifier=None)

List metadata formats supported by repository or record.

Parameters:

identifier (string) – identify record for which we want to know all supported metadata formats. If absent, list all metadata formats supported by repository.

Raises:

• error.IdDoesNotExistError – if record with identifier does not exist.
• error.NoMetadataFormatsError – if no formats are available for the indicated record.

Returns:

an iterable of metadataPrefix, schema, metadataNamespace tuples (each entry in the tuple is a string).

listRecords(metadataPrefix, set=None, from_=None, until=None)

Get a list of header, metadata and about information on records.

Parameters:

• metadataPrefix (string) – identifies metadata set to retrieve
• set (string) – set identifier; only return records in set
• from (datetime) – only retrieve records from from_ date forward (in naive UTC)
• until (datetime) – only retrieve records with dates up to and including until date (in naive UTC)

Raises:

• oaipmh.error.CannotDisseminateFormatError – if metadataPrefix is not supported by the repository.
• oaipmh.error.NoSetHierarchyError – if the repository does not support sets.

Returns:

an iterable of header, metadata, about tuples.

listSets()

Get a list of sets in the repository.

Raises:error.NoSetHierarchyError – if the repository does not support sets. Returns:an iterable of setSpec, setName tuples (strings).

writeMetadata(element, metadata)

Create XML elements under the given element, using the provided metadata.

Should avoid doing any model-lookups, as they should be done when creating the metadata.

Parameters:

• element (lxml.etree.Element) – element to put all content under (as SubElements)
• metadata (oaipmh.common.Metadata) – metadata to turn into XML

Raises:

NotImplementedError – not implemented

tardis.apps.oaipmh.provider.experiment module

class tardis.apps.oaipmh.provider.experiment.AbstractExperimentProvider(site)

Bases: tardis.apps.oaipmh.provider.base.BaseProvider

NS_CC = 'http://www.tardis.edu.au/schemas/creative_commons/2011/05/17'

getRecord(metadataPrefix, identifier)

Return record if we handle it.

static get_id(obj)

listIdentifiers(metadataPrefix, set=None, from_=None, until=None)

Return identifiers in range, provided we handle this metadata prefix.

listRecords(metadataPrefix, set=None, from_=None, until=None)

Return records in range, provided we handle this metadata prefix.

listSets()

No support for sets.

class tardis.apps.oaipmh.provider.experiment.DcExperimentProvider(site)

Bases: tardis.apps.oaipmh.provider.experiment.AbstractExperimentProvider

listMetadataFormats(identifier=None)

Return metadata format if no identifier, or identifier is a valid experiment.

class tardis.apps.oaipmh.provider.experiment.RifCsExperimentProvider(site)

Bases: tardis.apps.oaipmh.provider.experiment.AbstractExperimentProvider

class ExperimentWriter(root, metadata, site)

Bases: object

write()

writeRegistryObjectsWrapper()

writeRelatedAuthor(element, obj, relation)

writeRelatedInfo(element, obj)

writeRelatedUser(element, obj, relation)

writeSubject(element, obj)

static get_rifcs_id(id_, site_=None)

listMetadataFormats(identifier=None)

Return metadata format if no identifier, or identifier is a valid experiment.

static writeExperimentMetadata(element, metadata, site=None, writer=None)

Wrapper around experiment writer.

static writeUserMetadata(element, metadata, site=None)

Module contents

tardis.apps.oaipmh.tests package

Subpackages

tardis.apps.oaipmh.tests.provider package

Submodules

tardis.apps.oaipmh.tests.provider.test_base module

class tardis.apps.oaipmh.tests.provider.test_base.BaseProviderTestCase(methodName='runTest')

Bases: django.test.testcases.TestCase

setUp()

Hook method for setting up the test fixture before exercising it.

tearDown()

Hook method for deconstructing the test fixture after testing it.

testGetRecord()

Default behaviour should be to not handle the identifier.

testIdentify()

There can be only one provider that responds. By default, don’t.

testListIdentifiers()

By default a provider cannot handle the given metadata prefix.

testListMetadataFormats()

By default a provider handles no metadata formats.

testListRecords()

By default a provider cannot handle the given metadata prefix.

testListSets()

By default a provider does not implement sets.

tardis.apps.oaipmh.tests.provider.test_experiment module

class tardis.apps.oaipmh.tests.provider.test_experiment.AbstractExperimentProviderTC

Bases: object

setUp()

tearDown()

testGetRecordHandlesInvalidIdentifiers()

testIdentify()

There can be only one provider that responds. This one does not.

testListIdentifiers()

testListIdentifiersDoesNotHandleSets()

testListMetadataFormats()

testListSets()

class tardis.apps.oaipmh.tests.provider.test_experiment.DcExperimentProviderTestCase(methodName='runTest')

Bases: tardis.apps.oaipmh.tests.provider.test_experiment.AbstractExperimentProviderTC, django.test.testcases.TestCase

testGetRecord()

testListRecords()

class tardis.apps.oaipmh.tests.provider.test_experiment.RifCsExperimentProviderTestCase(methodName='runTest')

Bases: tardis.apps.oaipmh.tests.provider.test_experiment.AbstractExperimentProviderTC, django.test.testcases.TestCase

tearDown()

Hook method for deconstructing the test fixture after testing it.

testGetRecord()

testListRecords()

Module contents

Submodules

tardis.apps.oaipmh.tests.test_oai module

class tardis.apps.oaipmh.tests.test_oai.EndpointTestCase(methodName='runTest')

Bases: django.test.testcases.TestCase

setUp()

Hook method for setting up the test fixture before exercising it.

tearDown()

Hook method for deconstructing the test fixture after testing it.

testGetRecord()

testIdentify()

testListIdentifiers()

testListMetadataFormats()

testListRecords()

Module contents

Submodules

tardis.apps.oaipmh.models module

tardis.apps.oaipmh.server module

class tardis.apps.oaipmh.server.ProxyingMetadataRegistry(providers)

Bases: oaipmh.metadata.MetadataRegistry

A registry that only writes, and does so by proxying to Providers.

hasReader(metadata_prefix)

hasWriter(metadata_prefix)

readMetadata(metadata_prefix, element)

Turn XML into metadata object.

element - element to read in

returns - metadata object

registerReader(metadata_prefix, reader)

registerWriter(metadata_prefix, writer)

writeMetadata(metadata_prefix, element, metadata)

Write metadata as XML.

element - ElementTree element to write under metadata - metadata object to write

class tardis.apps.oaipmh.server.ProxyingServer(providers)

Bases: oaipmh.interfaces.IOAI

getRecord(metadataPrefix, identifier)

Get a record for a metadataPrefix and identifier.

Raises:

• oaipmh.error.CannotDisseminateFormatError – if no provider returns a result, but at least one provider responds with oaipmh.error.CannotDisseminateFormatError (meaning the identifier exists)
• oaipmh.error.IdDoesNotExistError – if all providers fail with oaipmh.error.IdDoesNotExistError

Returns:

first successful provider response

Return type:

response

identify()

Retrieve information about the repository.

Returns:an oaipmh.common.Identify object describing the repository. Return type:oaipmh.common.Identify

listIdentifiers(metadataPrefix, **kwargs)

Lists identifiers from all providers as a single set.

Raises:

• error.CannotDisseminateFormatError – if metadataPrefix is not supported by the repository.
• error.NoSetHierarchyError – if a set is provided, as the repository does not support sets.

Returns:

a set.Set of headers.

Return type:

set

listMetadataFormats(**kwargs)

List metadata formats from all providers in a single set.

Raises:

• error.IdDoesNotExistError – if record with identifier does not exist.
• error.NoMetadataFormatsError – if no formats are available for the indicated record, but it does exist.

Returns:

a frozenset of metadataPrefix, schema, metadataNamespace tuples (each entry in the tuple is a string).

Return type:

frozenset

listRecords(metadataPrefix, **kwargs)

Lists records from all providers as a single set.

Raises:

• error.CannotDisseminateFormatError – if metadataPrefix is not supported by the repository.
• error.NoSetHierarchyError – if a set is provided, as the repository does not support sets.

Returns:

a set.Set of header, metadata, about tuples.

Return type:

set

listSets()

List sets.

Raises:oaipmh.error.NoSetHierarchyError – because set hierarchies are currrently not implemented

tardis.apps.oaipmh.server.get_server(current_site)

tardis.apps.oaipmh.urls module

tardis.apps.oaipmh.views module

tardis.apps.oaipmh.views.endpoint(request)

Module contents

tardis.apps.openid_migration package

Subpackages

tardis.apps.openid_migration.migrations package

Submodules

tardis.apps.openid_migration.migrations.0001_initial module

class tardis.apps.openid_migration.migrations.0001_initial.Migration(name, app_label)

Bases: django.db.migrations.migration.Migration

dependencies = [('tardis_portal', '0012_userauthentication_approved'), ('auth', '__first__')]

initial = True

operations = [<CreateModel name='OpenidACLMigration', fields=[('id', <django.db.models.fields.AutoField>), ('acl_id', <django.db.models.fields.related.ForeignKey>)]>, <CreateModel name='OpenidUserMigration', fields=[('id', <django.db.models.fields.AutoField>), ('old_user_auth_method', <django.db.models.fields.CharField>), ('new_user_auth_method', <django.db.models.fields.CharField>), ('migration_timestamp', <django.db.models.fields.DateTimeField>), ('migration_status', <django.db.models.fields.BooleanField>), ('new_user', <django.db.models.fields.related.ForeignKey>), ('old_user', <django.db.models.fields.related.ForeignKey>)]>, <AddField model_name='openidaclmigration', name='user_migration', field=<django.db.models.fields.related.ForeignKey>>]

Module contents

tardis.apps.openid_migration.tests package

Submodules

tardis.apps.openid_migration.tests.test_forms module

Tests related to OpenID migration forms

class tardis.apps.openid_migration.tests.test_forms.OpenIDMigrationFormTestCase(methodName='runTest')

Bases: django.test.testcases.TestCase

setUp()

Hook method for setting up the test fixture before exercising it.

test_init()

tardis.apps.openid_migration.tests.test_migration module

Tests related to OpenID migration

class tardis.apps.openid_migration.tests.test_migration.OpenIDMigrationTestCase(methodName='runTest')

Bases: django.test.testcases.TestCase

setUp()

Hook method for setting up the test fixture before exercising it.

test_do_migration()

tardis.apps.openid_migration.tests.test_models module

class tardis.apps.openid_migration.tests.test_models.ModelTestCase(methodName='runTest')

Bases: django.test.testcases.TestCase

create_OpenidUserMigration()

setUp()

Hook method for setting up the test fixture before exercising it.

test_OpenidUserMigration_creation()

tardis.apps.openid_migration.tests.test_views module

Tests related to OpenID migration views

class tardis.apps.openid_migration.tests.test_views.OpenIDMigrationViewTestCase(methodName='runTest')

Bases: django.test.testcases.TestCase

setUp()

Hook method for setting up the test fixture before exercising it.

test_migrate_accounts(mock_webpack_get_bundle)

Module contents

Submodules

tardis.apps.openid_migration.apps module

class tardis.apps.openid_migration.apps.OpenidMigrationConfig(app_name, app_module)

Bases: tardis.app_config.AbstractTardisAppConfig

name = 'tardis.apps.openid_migration'

verbose_name = 'OpenID migrations'

tardis.apps.openid_migration.context_processors module

tardis.apps.openid_migration.context_processors.openid_migration_processor(request)

adds context for openid_migration

tardis.apps.openid_migration.default_settings module

tardis.apps.openid_migration.email_text module

tardis.apps.openid_migration.email_text.email_migration_success(user, new_username, auth_method)

tardis.apps.openid_migration.email_text.interpolate_template(template_name, **kwargs)

tardis.apps.openid_migration.forms module

tardis.apps.openid_migration.forms.openid_user_migration_form()

Create a user migration form with username and password field.

tardis.apps.openid_migration.migration module

tardis.apps.openid_migration.migration.acl_migration(userIdToBeReplaced, replacementUserId, user_migration_record)

tardis.apps.openid_migration.migration.confirm_migration(request)

tardis.apps.openid_migration.migration.do_migration(request)

Migrating account from the account that the logged in user has provided in the Authentication Form. Migration involve relinking the UserAuthentication table entries, transferring ObjectACL entries to the migrated account, changing the Group memberships and making the old account inactive.

Parameters:request (Request) – the HTTP request object Returns:The HttpResponse which contains request.user’s new list of authentication methods Return type:HttpResponse

tardis.apps.openid_migration.migration.getSupportedAuthMethods()

Return the list of authentication methods.

tardis.apps.openid_migration.migration.get_api_key(user)

tardis.apps.openid_migration.migration.get_matching_auth_provider(backend)

tardis.apps.openid_migration.migration.migrate_api_key(old_user, new_user)

tardis.apps.openid_migration.migration.migrate_user_permissions(old_user, new_user)

tardis.apps.openid_migration.migration.openid_migration_method(request)

tardis.apps.openid_migration.models module

class tardis.apps.openid_migration.models.OpenidACLMigration(id, user_migration, acl_id)

Bases: django.db.models.base.Model

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

acl_id

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

acl_id_id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

objects = <django.db.models.manager.Manager object>

user_migration

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

user_migration_id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

class tardis.apps.openid_migration.models.OpenidACLMigrationAdmin(model, admin_site)

Bases: django.contrib.admin.options.ModelAdmin

list_display = ['user_migration_obj', 'acl_id']

media

user_migration_obj(obj)

class tardis.apps.openid_migration.models.OpenidUserMigration(id, old_user, old_user_auth_method, new_user, new_user_auth_method, migration_timestamp, migration_status)

Bases: django.db.models.base.Model

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

get_next_by_migration_timestamp(*, field=<django.db.models.fields.DateTimeField: migration_timestamp>, is_next=True, **kwargs)

get_previous_by_migration_timestamp(*, field=<django.db.models.fields.DateTimeField: migration_timestamp>, is_next=False, **kwargs)

id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

migration_status

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

migration_timestamp

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

new_user

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

new_user_auth_method

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

new_user_id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

objects = <django.db.models.manager.Manager object>

old_user

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

old_user_auth_method

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

old_user_id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

openidaclmigration_set

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

class tardis.apps.openid_migration.models.OpenidUserMigrationAdmin(model, admin_site)

Bases: django.contrib.admin.options.ModelAdmin

list_display = ['__str__', 'old_user', 'old_user_auth_method', 'new_user_id', 'new_user_auth_method', 'migration_timestamp', 'migration_status']

media

tardis.apps.openid_migration.tasks module

tardis.apps.openid_migration.urls module

tardis.apps.openid_migration.user_menu_modifiers module

tardis.apps.openid_migration.user_menu_modifiers.add_migrate_account_menu_item(request, user_menu)

Add a ‘Migrate My Account’ item to the user menu

Parameters:

• request (django.http.HttpRequest) – an HTTP Request instance
• user_menu (list) – user menu context to modify

Returns:

user_menu list

Return type:

list

tardis.apps.openid_migration.utils module

tardis.apps.openid_migration.utils.rollback_migration(user_migration_obj)

tardis.apps.openid_migration.views module

tardis.apps.openid_migration.views.migrate_accounts(request)

Manage user migration using AJAX.

Module contents

tardis.apps.push_to package

Subpackages

tardis.apps.push_to.migrations package

Submodules

tardis.apps.push_to.migrations.0001_initial module

class tardis.apps.push_to.migrations.0001_initial.Migration(name, app_label)

Bases: django.db.migrations.migration.Migration

dependencies = [('auth', '__first__'), ('auth', '0006_require_contenttypes_0002')]

operations = [<CreateModel name='Credential', fields=[('id', <django.db.models.fields.AutoField>), ('key_type', <django.db.models.fields.CharField>), ('public_key', <django.db.models.fields.TextField>), ('private_key', <django.db.models.fields.TextField>), ('remote_user', <django.db.models.fields.CharField>), ('password', <django.db.models.fields.CharField>)], options={'abstract': False}>, <CreateModel name='OAuthSSHCertSigningService', fields=[('id', <django.db.models.fields.AutoField>), ('nickname', <django.db.models.fields.CharField>), ('oauth_authorize_url', <django.db.models.fields.CharField>), ('oauth_token_url', <django.db.models.fields.CharField>), ('oauth_check_token_url', <django.db.models.fields.CharField>), ('oauth_client_id', <django.db.models.fields.CharField>), ('oauth_client_secret', <django.db.models.fields.CharField>), ('cert_signing_url', <django.db.models.fields.CharField>), ('allow_for_all', <django.db.models.fields.BooleanField>), ('allowed_groups', <django.db.models.fields.related.ManyToManyField>)], options={'verbose_name': 'OAuth2 SSH cert signing service', 'verbose_name_plural': 'OAuth2 SSH cert signing services'}>, <CreateModel name='RemoteHost', fields=[('id', <django.db.models.fields.AutoField>), ('key_type', <django.db.models.fields.CharField>), ('public_key', <django.db.models.fields.TextField>), ('private_key', <django.db.models.fields.TextField>), ('nickname', <django.db.models.fields.CharField>), ('logo_img', <django.db.models.fields.CharField>), ('host_name', <django.db.models.fields.CharField>), ('port', <django.db.models.fields.IntegerField>), ('administrator', <django.db.models.fields.related.ForeignKey>)], options={'abstract': False}>, <AddField model_name='oauthsshcertsigningservice', name='allowed_remote_hosts', field=<django.db.models.fields.related.ManyToManyField>>, <AddField model_name='oauthsshcertsigningservice', name='allowed_users', field=<django.db.models.fields.related.ManyToManyField>>, <AddField model_name='credential', name='remote_hosts', field=<django.db.models.fields.related.ManyToManyField>>, <AddField model_name='credential', name='user', field=<django.db.models.fields.related.ForeignKey>>]

tardis.apps.push_to.migrations.0002_auto_20160518_1953 module

class tardis.apps.push_to.migrations.0002_auto_20160518_1953.Migration(name, app_label)

Bases: django.db.migrations.migration.Migration

dependencies = [('push_to', '0001_initial')]

operations = [<AlterField model_name='credential', name='key_type', field=<django.db.models.fields.CharField>>, <AlterField model_name='remotehost', name='key_type', field=<django.db.models.fields.CharField>>]

Module contents

tardis.apps.push_to.tests package

Submodules

tardis.apps.push_to.tests.test_models module

class tardis.apps.push_to.tests.test_models.ModelsTestCase(methodName='runTest')

Bases: django.test.testcases.TestCase

setUp()

Hook method for setting up the test fixture before exercising it.

test_credential_generation()

test_get_allowed_signing_services()

test_keys_from_private_key_only()

test_pkey_to_credential()

Module contents

Submodules

tardis.apps.push_to.apps module

class tardis.apps.push_to.apps.PushToConfig(app_name, app_module)

Bases: tardis.app_config.AbstractTardisAppConfig

name = 'tardis.apps.push_to'

verbose_name = 'Push To'

tardis.apps.push_to.exceptions module

exception tardis.apps.push_to.exceptions.NoSuitableCredential

Bases: Exception

This exception is thrown when attempting to find a suitable credential for a remote host but none is found

tardis.apps.push_to.models module

class tardis.apps.push_to.models.Credential(*args, **kwargs)

Bases: tardis.apps.push_to.models.KeyPair

A credential that may contain a password and/or key. The auth method chosen depends on the credentials available, allowed auth methods, and priorities defined by the SSH client.

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

static generate_keypair_credential(tardis_user, remote_user, remote_hosts, bit_length=2048)

Generates and saves an RSA key pair credential. Credentials returned by this method are intended to be registered on remote systems before being used. @type tardis_user: User @type remote_user: str @type bit_length: int @type remote_hosts: list[RemoteHost] :return: the generated credential :rtype: object

get_client_for_host(remote_host)

Attempts to establish a connection with the remote_host using this credential object. The remote_host may be any host, but only those in the remote_hosts field are expected to work. @type remote_host: .RemoteHost :return: a connected SSH client :rtype: SSHClient

static get_suitable_credential(tardis_user, remote_host, remote_user=None)

id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

objects = <django.db.models.manager.Manager object>

password

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

remote_hosts

Accessor to the related objects manager on the forward and reverse sides of a many-to-many relation.

In the example:

class Pizza(Model):
    toppings = ManyToManyField(Topping, related_name='pizzas')

Pizza.toppings and Topping.pizzas are ManyToManyDescriptor instances.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

remote_user

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

user

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

user_id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

verify_remote_access(remote_host=None)

@type remote_host: RemoteHost

class tardis.apps.push_to.models.CredentialAdmin(model, admin_site)

Bases: django.contrib.admin.options.ModelAdmin

form

alias of CredentialForm

media

class tardis.apps.push_to.models.CredentialForm(data=None, files=None, auto_id='id_%s', prefix=None, initial=None, error_class=<class 'django.forms.utils.ErrorList'>, label_suffix=None, empty_permitted=False, instance=None, use_required_attribute=None, renderer=None)

Bases: django.forms.models.ModelForm

class Meta

Bases: object

fields = '__all__'

model

alias of Credential

widgets = {'password': <django.forms.widgets.PasswordInput object>}

base_fields = {'key_type': <django.forms.fields.CharField object>, 'password': <django.forms.fields.CharField object>, 'private_key': <django.forms.fields.CharField object>, 'public_key': <django.forms.fields.CharField object>, 'remote_hosts': <django.forms.models.ModelMultipleChoiceField object>, 'remote_user': <django.forms.fields.CharField object>, 'user': <django.forms.models.ModelChoiceField object>}

declared_fields = {}

media

class tardis.apps.push_to.models.DBHostKeyPolicy

Bases: paramiko.client.MissingHostKeyPolicy

Host key verification policy based on the host key stored in the database.

missing_host_key(client, hostname, key)

@type key: PKey

class tardis.apps.push_to.models.KeyPair(*args, **kwargs)

Bases: django.db.models.base.Model

A key pair

class Meta

Bases: object

abstract = False

key

Returns:a subclass of PKey of the appropriate key type Return type:PKey Raises:ValidationError –

key_type

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

private_key

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

public_key

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

save(*args, **kwargs)

Save the current instance. Override this in a subclass if you want to control the saving process.

The ‘force_insert’ and ‘force_update’ parameters can be used to insist that the “save” must be an SQL insert or update (or equivalent for non-SQL backends), respectively. Normally, they should not be set.

class tardis.apps.push_to.models.OAuthSSHCertSigningService(*args, **kwargs)

Bases: django.db.models.base.Model

Connection parameters for an OAuth2 SSH certificate signing service. Supports certificate signing server available here: https://github.com/monash-merc/ssh-authz

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

allow_for_all

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

allowed_groups

Accessor to the related objects manager on the forward and reverse sides of a many-to-many relation.

In the example:

class Pizza(Model):
    toppings = ManyToManyField(Topping, related_name='pizzas')

Pizza.toppings and Topping.pizzas are ManyToManyDescriptor instances.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

allowed_remote_hosts

Accessor to the related objects manager on the forward and reverse sides of a many-to-many relation.

In the example:

class Pizza(Model):
    toppings = ManyToManyField(Topping, related_name='pizzas')

Pizza.toppings and Topping.pizzas are ManyToManyDescriptor instances.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

allowed_users

Accessor to the related objects manager on the forward and reverse sides of a many-to-many relation.

In the example:

class Pizza(Model):
    toppings = ManyToManyField(Topping, related_name='pizzas')

Pizza.toppings and Topping.pizzas are ManyToManyDescriptor instances.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

cert_signing_url

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

static get_available_signing_services(user)

Gets all SSH cert signing services available for a given user :param User user: User :return: allowed signing services :rtype: User

static get_oauth_service(user, service_id)

@type user: User @type service_id: int

id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

nickname

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

oauth_authorize_url

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

oauth_check_token_url

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

oauth_client_id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

oauth_client_secret

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

oauth_token_url

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

objects = <django.db.models.manager.Manager object>

class tardis.apps.push_to.models.RemoteHost(*args, **kwargs)

Bases: tardis.apps.push_to.models.KeyPair

A remote host that may be connected to via SSH

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

administrator

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

administrator_id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

credential_set

Accessor to the related objects manager on the forward and reverse sides of a many-to-many relation.

In the example:

class Pizza(Model):
    toppings = ManyToManyField(Topping, related_name='pizzas')

Pizza.toppings and Topping.pizzas are ManyToManyDescriptor instances.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

host_name

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

logo_img

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

nickname

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

oauthsshcertsigningservice_set

Accessor to the related objects manager on the forward and reverse sides of a many-to-many relation.

In the example:

class Pizza(Model):
    toppings = ManyToManyField(Topping, related_name='pizzas')

Pizza.toppings and Topping.pizzas are ManyToManyDescriptor instances.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

objects = <django.db.models.manager.Manager object>

port

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

class tardis.apps.push_to.models.RemoteHostAdmin(model, admin_site)

Bases: django.contrib.admin.options.ModelAdmin

Hides the private key field, which is not necessary for host keys

fields = ['nickname', 'administrator', 'host_name', 'port', 'key_type', 'public_key', 'logo_img']

media

tardis.apps.push_to.oauth_tokens module

tardis.apps.push_to.oauth_tokens.get_token(request, oauth_service)

Returns the OAuth2 token from the current session :param Request request: django session object :param OAuthSSHCertSigningService oauth_service: an

OAuthSSHCertSigningService object

Returns: Return type:string

tardis.apps.push_to.oauth_tokens.get_token_data(oauth_service, token)

Gets the OAuth2 user attributes using the supplied token :param OAuthSSHCertSigningService oauth_service: an

OAuthSSHCertSigningService object

Parameters:token (basestring) – an OAuth2 token Returns:a json object of user attributes Return type:dict

tardis.apps.push_to.oauth_tokens.set_token(request, oauth_service, token)

Stores the OAuth2 token in the current session :param Request request: django request object :param OAuthSSHCertSigningService oauth_service: an

OAuthSSHCertSigningService object

Parameters:token (basestring) – the OAuth2 token

tardis.apps.push_to.ssh_authz module

tardis.apps.push_to.ssh_authz.sign_certificate(credential, token, url)

An interface to the OAuth2 SSH certificate signing service @type credential: models.Credential

tardis.apps.push_to.tasks module

tardis.apps.push_to.tasks.do_file_copy(credential_id, remote_host_id, datafile_map, base_dir=None)

tardis.apps.push_to.tasks.make_dirs(sftp_client, dir_list)

tardis.apps.push_to.tasks.notify_user(user_id, remote_host_id, success=True)

tardis.apps.push_to.urls module

tardis.apps.push_to.utils module

tardis.apps.push_to.utils.bytes_available(ssh_client, path)

tardis.apps.push_to.utils.can_copy(ssh_client, object_type, object_id, path)

tardis.apps.push_to.utils.get_default_push_location(sftp_client)

tardis.apps.push_to.utils.get_object_size(type, id)

tardis.apps.push_to.utils.is_directory(sftp_client, path)

tardis.apps.push_to.utils.list_subdirectories(sftp_client, path, show_hidden=False)

tardis.apps.push_to.utils.shell_escape(s)

tardis.apps.push_to.views module

tardis.apps.push_to.views.authorize_remote_access(request, remote_host_id, service_id=None)

Generates an SSH certificate using an OAuth2 SSH signing service :param Request request: request object :param basestring remote_host_id: remote host id :param basestring service_id: OAuth2 SSH certificate signing service id :return: an error message or OAuth2 redirects :rtype: HttpRedirect

tardis.apps.push_to.views.get_accessible_hosts(request, obj_type=None, push_obj_id=None)

Retrieves all accessible hosts (i.e. hosts for which the user already has credentials for) including push-to trigger URLs if the object type and id are supplied :param Request request: request object :param object obj_type: data type to be copied

(experiment, dataset or datafile)

Parameters:push_obj_id (int) – the database object id Returns:json object with accessible hosts Return type:HttpResponse

tardis.apps.push_to.views.get_credential(request, remote_host)

Fetches a suitable credential for the remote host, or raises an exception if none found :param Request request: request object :param RemoteHost remote_host: the RemoteHost for which a credential

should be found

Returns:the credential Return type:object Raises:NoSuitableCredential – raised when no credential is found

tardis.apps.push_to.views.get_push_url_for_host(remote_host, obj_type, push_obj_id)

Constructs a push-to URL to trigger data transfer :param RemoteHost remote_host: the RemoteHost to which data should be copied :param obj_type: data type to be copied (experiment, dataset or datafile) :type obj_type: object :param int push_obj_id: the database object id :return: a push-to URL :rtype: basestring

tardis.apps.push_to.views.get_signing_services(request, obj_type=None, push_obj_id=None)

Retrieves all certificate signing services and associated hosts including push-to trigger URLs if the object type and id are supplied :param Request request: request object :param class obj_type: data type to be copied (experiment, dataset or datafile) :param int push_obj_id: the database object id :return: json object with signing services and hosts :rtype: HttpResponse

tardis.apps.push_to.views.oauth_callback(request)

OAuth2 callback endpoint to continue the SSH certificate signing process :param Request request: request object :return: error message or redirect to the signing service with access token :rtype: HttpResponse

tardis.apps.push_to.views.oauth_callback_url(request)

Builds the oauth callback URL :param Request request: request object :return: callback URL :rtype: basestring

tardis.apps.push_to.views.render_error_message(request, message, status=500)

tardis.apps.push_to.views.render_success_message(request, message, status=200)

tardis.apps.push_to.views.validate_remote_path(request, remote_host_id)

Module contents

tardis.apps.related_info package

Subpackages

tardis.apps.related_info.tests package

Submodules

tardis.apps.related_info.tests.test_oaipmh module

class tardis.apps.related_info.tests.test_oaipmh.RifCSTestCase(methodName='runTest')

Bases: django.test.testcases.TransactionTestCase

setUp()

Hook method for setting up the test fixture before exercising it.

testExistsInOaipmh()

tardis.apps.related_info.tests.tests module

class tardis.apps.related_info.tests.tests.CreateTestCase(methodName='runTest')

Bases: django.test.testcases.TransactionTestCase

setUp()

Hook method for setting up the test fixture before exercising it.

testCanCreate()

testDetectsBadInput()

testMustHaveWrite(mock_webpack_get_bundle)

class tardis.apps.related_info.tests.tests.DeleteTestCase(methodName='runTest')

Bases: django.test.testcases.TransactionTestCase

setUp()

Hook method for setting up the test fixture before exercising it.

testCanDelete()

testMustHaveWrite(mock_webpack_get_bundle)

class tardis.apps.related_info.tests.tests.GetTestCase(methodName='runTest')

Bases: django.test.testcases.TransactionTestCase

setUp()

Hook method for setting up the test fixture before exercising it.

testHandlesFound()

testHandlesNotFound(mock_webpack_get_bundle)

class tardis.apps.related_info.tests.tests.ListTestCase(methodName='runTest')

Bases: django.test.testcases.TransactionTestCase

setUp()

Hook method for setting up the test fixture before exercising it.

testHandlesEmptySet()

testHandlesMultipleEntries()

testHandlesSingleEntry()

class tardis.apps.related_info.tests.tests.TabTestCase(methodName='runTest')

Bases: django.test.testcases.TestCase

setUp()

Hook method for setting up the test fixture before exercising it.

testAccessWithReadPerms(mock_webpack_get_bundle)

testAccessWithoutReadPerms(mock_webpack_get_bundle)

class tardis.apps.related_info.tests.tests.UpdateTestCase(methodName='runTest')

Bases: django.test.testcases.TransactionTestCase

setUp()

Hook method for setting up the test fixture before exercising it.

testDetectsBadInput()

testMustHaveWrite(mock_webpack_get_bundle)

Module contents

Submodules

tardis.apps.related_info.forms module

class tardis.apps.related_info.forms.RelatedInfoForm(data=None, files=None, auto_id='id_%s', prefix=None, initial=None, error_class=<class 'django.forms.utils.ErrorList'>, label_suffix=None, empty_permitted=False, field_order=None, use_required_attribute=None, renderer=None)

Bases: django.forms.forms.Form

base_fields = {'identifier': <django.forms.fields.URLField object>, 'notes': <django.forms.fields.CharField object>, 'title': <django.forms.fields.CharField object>, 'type': <django.forms.fields.CharField object>}

declared_fields = {'identifier': <django.forms.fields.URLField object>, 'notes': <django.forms.fields.CharField object>, 'title': <django.forms.fields.CharField object>, 'type': <django.forms.fields.CharField object>}

media

tardis.apps.related_info.models module

tardis.apps.related_info.settings module

tardis.apps.related_info.urls module

tardis.apps.related_info.views module

Module contents

tardis.apps.s3utils package

Subpackages

tardis.apps.s3utils.tests package

Submodules

tardis.apps.s3utils.tests.test_api module

Testing the s3util app’s extensions to the tastypie-based mytardis api

class tardis.apps.s3utils.tests.test_api.S3UtilsAppApiTestCase(methodName='runTest')

Bases: tardis.tardis_portal.tests.api.MyTardisResourceTestCase

setUp()

Hook method for setting up the test fixture before exercising it.

tearDown()

Hook method for deconstructing the test fixture after testing it.

test_download_dfo()

Test downloading a DataFileObject using the s3util app’s extensions to the MyTardis REST API.

tardis.apps.s3utils.tests.test_app_config module

class tardis.apps.s3utils.tests.test_app_config.S3UtilsConfigTestCase(methodName='runTest')

Bases: django.test.testcases.TestCase

test_app_config()

tardis.apps.s3utils.tests.test_checksums module

Testing the s3util app’s ability to calculate checksums for S3 objects

class tardis.apps.s3utils.tests.test_checksums.S3UtilsAppChecksumsTestCase(methodName='runTest')

Bases: django.test.testcases.TestCase

setUp()

Hook method for setting up the test fixture before exercising it.

tearDown()

Hook method for deconstructing the test fixture after testing it.

test_checksums()

Ensure that we can calculate an MD5 sum and a SHA512 sum for a file in S3 object storage

Module contents

Submodules

tardis.apps.s3utils.api module

Additions to MyTardis’s REST API

class tardis.apps.s3utils.api.ReplicaAppResource(api_name=None)

Bases: tardis.tardis_portal.api.ReplicaResource

Extends MyTardis’s API for DFOs, adding in a download method for S3 objects

class Meta

Bases: tardis.tardis_portal.api.Meta

authorization

Authorisation class for Tastypie.

queryset

resource_name = 'replica'

base_fields = {'created_time': <tastypie.fields.DateTimeField object>, 'datafile': <tastypie.fields.ForeignKey object>, 'id': <tastypie.fields.IntegerField object>, 'last_verified_time': <tastypie.fields.DateTimeField object>, 'resource_uri': <tastypie.fields.CharField object>, 'uri': <tastypie.fields.CharField object>, 'verified': <tastypie.fields.BooleanField object>}

declared_fields = {}

download_dfo(request, **kwargs)

Download DataFileObject from S3 Object Store

prepend_urls()

A hook for adding your own URLs or matching before the default URLs.

tardis.apps.s3utils.apps module

class tardis.apps.s3utils.apps.S3UtilsConfig(app_name, app_module)

Bases: django.apps.config.AppConfig

name = 's3utils'

tardis.apps.s3utils.default_settings module

Default settings for s3utils app

tardis.apps.s3utils.default_settings.S3_SIGNED_URL_EXPIRY = 30

A short expiry (30 seconds) is used, because it is only intended to provide access long enough for an authenticated MyTardis user to be redirected to the signed URL.

tardis.apps.s3utils.urls module

Minimal urls.py, so we can do a reverse lookup for the ‘s3_api_download_dfo’ URL pattern.

‘s3_api_download_dfo’ is defined in the prepend_urls method of the ReplicaAppResource class in api.py

The API endpoint defined in this app is mapped to a URL in tardis/urls/api.py (along with API endpoints defined by other MyTardis apps).

tardis.apps.s3utils.utils module

Utilities for S3 objects

tardis.apps.s3utils.utils.calculate_checksums(dfo, compute_md5=True, compute_sha512=False)

Calculates checksums for an S3 DataFileObject instance. For files in S3, using the django-storages abstraction is inefficient - we end up with a clash of chunking algorithms between the download from S3 and MyTardis’s Python-based checksum calculation. So for S3 files, we calculate checksums using external binaries (md5sum and shasum) instead.

:param dfo : The DataFileObject instance :type dfo: DataFileObject :param compute_md5: whether to compute md5 default=True :type compute_md5: bool :param compute_sha512: whether to compute sha512, default=True :type compute_sha512: bool

Returns:the checksums as {‘md5sum’: result, ‘sha512sum’: result} Return type:dict

tardis.apps.s3utils.utils.generate_presigned_url(dfo, expiry=None)

Generate a presigned URL for an S3 object

boto3 must be installed if you are using the storages.backends.s3boto3.S3Boto3Storage storage class, defined in the django-storages package

dfo : DataFileObject

The DataFileObject to generate the pre-signed URL for

expiry : int

The signed URL’s expiry in seconds

string

The pre-signed URL

Module contents

tardis.apps.search package

Subpackages

tardis.apps.search.tests package

Submodules

tardis.apps.search.tests.test_api module

class tardis.apps.search.tests.test_api.SimpleSearchTest(methodName='runTest')

Bases: tardis.tardis_portal.tests.api.MyTardisResourceTestCase

setUp()

Hook method for setting up the test fixture before exercising it.

test_advance_search_authenticated_user()

test_advance_search_unauthenticated_user()

test_simple_search_authenticated_user()

test_simple_search_unauthenticated_user()

tardis.apps.search.tests.test_index module

class tardis.apps.search.tests.test_index.IndexExperimentTestCase(methodName='runTest')

Bases: django.test.testcases.TestCase

setUp()

Hook method for setting up the test fixture before exercising it.

test_create_index()

Module contents

Submodules

tardis.apps.search.api module

RESTful API for MyTardis search. Implemented with Tastypie.

class tardis.apps.search.api.AdvanceSearchAppResource(api_name=None)

Bases: tastypie.resources.Resource

class Meta

Bases: object

always_return_data = True

authentication = <tardis.tardis_portal.api.MyTardisAuthentication object>

list_allowed_methods = ['post']

object_class

alias of SearchObject

resource_name = 'advance-search'

serializer = <tardis.apps.search.api.PrettyJSONSerializer object>

base_fields = {'hits': <tastypie.fields.ApiField object>, 'resource_uri': <tastypie.fields.CharField object>}

declared_fields = {'hits': <tastypie.fields.ApiField object>}

detail_uri_kwargs(bundle_or_obj)

Given a Bundle or an object (typically a Model instance), it returns the extra kwargs needed to generate a detail URI.

By default, it uses this resource’s detail_uri_name in order to create the URI.

get_object_list(request)

A hook to allow making returning the list of available objects.

This needs to be implemented at the user level.

ModelResource includes a full working version specific to Django’s Models.

obj_create(bundle, **kwargs)

Creates a new object based on the provided data.

This needs to be implemented at the user level.

ModelResource includes a full working version specific to Django’s Models.

obj_get_list(bundle, **kwargs)

Fetches the list of objects available on the resource.

This needs to be implemented at the user level.

ModelResource includes a full working version specific to Django’s Models.

class tardis.apps.search.api.PrettyJSONSerializer(formats=None, content_types=None, datetime_formatting=None)

Bases: tastypie.serializers.Serializer

json_indent = 2

to_json(data, options=None)

Given some Python data, produces JSON output.

class tardis.apps.search.api.SearchAppResource(api_name=None)

Bases: tastypie.resources.Resource

Tastypie resource for simple-search

class Meta

Bases: object

always_return_data = True

authentication = <tardis.tardis_portal.api.MyTardisAuthentication object>

list_allowed_methods = ['get']

object_class

alias of SearchObject

resource_name = 'simple-search'

serializer = <tardis.apps.search.api.PrettyJSONSerializer object>

base_fields = {'hits': <tastypie.fields.ApiField object>, 'resource_uri': <tastypie.fields.CharField object>}

declared_fields = {'hits': <tastypie.fields.ApiField object>}

detail_uri_kwargs(bundle_or_obj)

Given a Bundle or an object (typically a Model instance), it returns the extra kwargs needed to generate a detail URI.

By default, it uses this resource’s detail_uri_name in order to create the URI.

get_object_list(request)

A hook to allow making returning the list of available objects.

This needs to be implemented at the user level.

ModelResource includes a full working version specific to Django’s Models.

obj_get_list(bundle, **kwargs)

Fetches the list of objects available on the resource.

This needs to be implemented at the user level.

ModelResource includes a full working version specific to Django’s Models.

class tardis.apps.search.api.SearchObject(hits=None, id=None)

Bases: object

tardis.apps.search.api.simple_search_public_data(query_text)

tardis.apps.search.apps module

class tardis.apps.search.apps.SearchConfig(app_name, app_module)

Bases: tardis.app_config.AbstractTardisAppConfig

name = 'tardis.apps.search'

verbose_name = 'Search'

tardis.apps.search.documents module

class tardis.apps.search.documents.DataFileDocument(related_instance_to_ignore=None, **kwargs)

Bases: django_elasticsearch_dsl.documents.DocType

class Django

Bases: object

model

alias of tardis.tardis_portal.models.datafile.DataFile

queryset_pagination = 100000

related_models = [<class 'tardis.tardis_portal.models.dataset.Dataset'>, <class 'tardis.tardis_portal.models.experiment.Experiment'>]

class Index

Bases: object

name = 'datafile'

settings = {'number_of_replicas': 0, 'number_of_shards': 1}

django = {'model': <class 'tardis.tardis_portal.models.datafile.DataF...}

get_instances_from_related(related_instance)

class tardis.apps.search.documents.DatasetDocument(related_instance_to_ignore=None, **kwargs)

Bases: django_elasticsearch_dsl.documents.DocType

class Django

Bases: object

model

alias of tardis.tardis_portal.models.dataset.Dataset

related_models = [<class 'tardis.tardis_portal.models.experiment.Experiment'>, <class 'tardis.tardis_portal.models.instrument.Instrument'>]

class Index

Bases: object

name = 'dataset'

settings = {'number_of_replicas': 0, 'number_of_shards': 1}

django = {'model': <class 'tardis.tardis_portal.models.dataset.Datase...}

get_instances_from_related(related_instance)

class tardis.apps.search.documents.ExperimentDocument(related_instance_to_ignore=None, **kwargs)

Bases: django_elasticsearch_dsl.documents.DocType

class Django

Bases: object

model

alias of tardis.tardis_portal.models.experiment.Experiment

related_models = [<class 'django.contrib.auth.models.User'>, <class 'tardis.tardis_portal.models.access_control.ObjectACL'>]

class Index

Bases: object

name = 'experiments'

settings = {'number_of_replicas': 0, 'number_of_shards': 1}

django = {'model': <class 'tardis.tardis_portal.models.experiment.Exp...}

get_instances_from_related(related_instance)

tardis.apps.search.urls module

tardis.apps.search.views module

views relevant to search

class tardis.apps.search.views.SearchView(**kwargs)

Bases: django.views.generic.base.TemplateView

template_name = 'search.html'

Module contents

tardis.apps.sftp package

Subpackages

tardis.apps.sftp.management package

Subpackages

tardis.apps.sftp.management.commands package

Submodules

tardis.apps.sftp.management.commands.sftpd module

class tardis.apps.sftp.management.commands.sftpd.Command(stdout=None, stderr=None, no_color=False, force_color=False)

Bases: django.core.management.base.BaseCommand

add_arguments(parser)

Entry point for subclassed commands to add custom arguments.

handle(*args, **options)

The actual logic of the command. Subclasses must implement this method.

Module contents

Module contents

tardis.apps.sftp.migrations package

Submodules

tardis.apps.sftp.migrations.0001_initial module

class tardis.apps.sftp.migrations.0001_initial.Migration(name, app_label)

Bases: django.db.migrations.migration.Migration

dependencies = [('tardis_portal', '0011_auto_20160505_1643'), ('auth', '__first__')]

initial = True

operations = [<CreateModel name='SFTPPublicKey', fields=[('id', <django.db.models.fields.AutoField>), ('name', <django.db.models.fields.CharField>), ('key_type', <django.db.models.fields.CharField>), ('public_key', <django.db.models.fields.TextField>), ('added', <django.db.models.fields.DateField>), ('user', <django.db.models.fields.related.ForeignKey>)]>]

Module contents

tardis.apps.sftp.tests package

Submodules

tardis.apps.sftp.tests.test_sftp module

class tardis.apps.sftp.tests.test_sftp.SFTPDManagementTestCase(methodName='runTest')

Bases: django.test.testcases.TestCase

testSFTPDWithoutHostKey()

Attempting to start the SFTPD service without a host key should raise an SSHException

class tardis.apps.sftp.tests.test_sftp.SFTPTest(methodName='runTest')

Bases: django.test.testcases.TestCase

setUp()

Hook method for setting up the test fixture before exercising it.

test_cybderduck_connection_window()

test_sftp()

test_sftp_dynamic_docs_dataset(mock_webpack_get_bundle)

test_sftp_dynamic_docs_experiment(mock_webpack_get_bundle)

test_sftp_key_connect()

Module contents

Submodules

tardis.apps.sftp.admin module

tardis.apps.sftp.api module

class tardis.apps.sftp.api.SFTPACLAuthorization

Bases: tastypie.authorization.Authorization

create_detail(object_list, bundle)

Returns either True if the user is allowed to create the object in question or throw Unauthorized if they are not.

Returns True by default.

delete_detail(object_list, bundle)

Returns either True if the user is allowed to delete the object in question or throw Unauthorized if they are not.

Returns True by default.

read_detail(object_list, bundle)

Returns either True if the user is allowed to read the object in question or throw Unauthorized if they are not.

Returns True by default.

read_list(object_list, bundle)

Returns a list of all the objects a user is allowed to read.

Should return an empty list if none are allowed.

Returns the entire list by default.

class tardis.apps.sftp.api.SFTPPublicKeyAppResource(api_name=None)

Bases: tastypie.resources.ModelResource

Tastypie model resource for SFTPPublicKey model

class Meta

Bases: object

authentication = <tardis.tardis_portal.api.MyTardisAuthentication object>

authorization

detail_allowed_methods = ['get', 'delete']

filtering = {'id': ('exact',), 'name': ('exact',)}

list_allowed_methods = ['get', 'post']

object_class

alias of tardis.apps.sftp.models.SFTPPublicKey

queryset

resource_name = 'publickey'

validation = <tastypie.validation.FormValidation object>

base_fields = {'added': <tastypie.fields.DateField object>, 'id': <tastypie.fields.IntegerField object>, 'key_type': <tastypie.fields.CharField object>, 'name': <tastypie.fields.CharField object>, 'public_key': <tastypie.fields.CharField object>, 'resource_uri': <tastypie.fields.CharField object>}

declared_fields = {}

dehydrate(bundle)

A hook to allow a final manipulation of data once all fields/methods have built out the dehydrated data.

Useful if you need to access more than one dehydrated field or want to annotate on additional data.

Must return the modified bundle.

hydrate(bundle)

A hook to allow an initial manipulation of data before all methods/fields have built out the hydrated data.

Useful if you need to access more than one hydrated field or want to annotate on additional data.

Must return the modified bundle.

tardis.apps.sftp.apps module

class tardis.apps.sftp.apps.SFTPConfig(app_name, app_module)

Bases: tardis.app_config.AbstractTardisAppConfig

name = 'tardis.apps.sftp'

verbose_name = 'SFTP'

tardis.apps.sftp.default_settings module

tardis.apps.sftp.default_settings.REQUIRE_SSL_TO_GENERATE_KEY = True

Require a secure connection (i.e., HTTPS) to allow key generation.

tardis.apps.sftp.default_settings.SFTP_USERNAME_ATTRIBUTE = 'email'

The attribute from the User model (‘email’ or ‘username’) used to generate the SFTP login example on the sftp_access help page.

tardis.apps.sftp.forms module

class tardis.apps.sftp.forms.KeyAddForm(data=None, files=None, auto_id='id_%s', prefix=None, initial=None, error_class=<class 'django.forms.utils.ErrorList'>, label_suffix=None, empty_permitted=False, field_order=None, use_required_attribute=None, renderer=None)

Bases: django.forms.forms.Form

base_fields = {'key_type': <django.forms.fields.CharField object>, 'name': <django.forms.fields.CharField object>, 'public_key': <django.forms.fields.CharField object>}

clean()

Hook for doing any extra form-wide cleaning after Field.clean() has been called on every field. Any ValidationError raised by this method will not be associated with a particular field; it will have a special-case association with the field named ‘__all__’.

declared_fields = {'key_type': <django.forms.fields.CharField object>, 'name': <django.forms.fields.CharField object>, 'public_key': <django.forms.fields.CharField object>}

media

class tardis.apps.sftp.forms.KeyGenerateForm(data=None, files=None, auto_id='id_%s', prefix=None, initial=None, error_class=<class 'django.forms.utils.ErrorList'>, label_suffix=None, empty_permitted=False, field_order=None, use_required_attribute=None, renderer=None)

Bases: django.forms.forms.Form

base_fields = {'name': <django.forms.fields.CharField object>}

declared_fields = {'name': <django.forms.fields.CharField object>}

media

tardis.apps.sftp.models module

class tardis.apps.sftp.models.SFTPPublicKey(*args, **kwargs)

Bases: django.db.models.base.Model

Model for associated SFTP public keys with users

Parameters:

• user (ForeignKey for User) – user who owns this public key
• name (string) – name for this public key
• public_key (string) – OpenSSH formatted public key
• added (date) – date the public key was added (Optional)

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

added

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

get_next_by_added(*, field=<django.db.models.fields.DateField: added>, is_next=True, **kwargs)

get_previous_by_added(*, field=<django.db.models.fields.DateField: added>, is_next=False, **kwargs)

id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

key_type

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

name

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

objects = <django.db.models.manager.Manager object>

public_key

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

user

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

user_id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

tardis.apps.sftp.sftp module

SFTP Server

class tardis.apps.sftp.sftp.DynamicTree(host_obj=None)

Bases: object

add_child(name, obj=None)

add_path(path)

add_path_elems(elems)

clear_children()

get_leaf(path, update=False)

update_all_files()

update_dataset_files()

update_datasets()

update_experiments()

update_nothing()

class tardis.apps.sftp.sftp.MyTSFTPHandle(df, flags=0, optional_args=None)

Bases: paramiko.sftp_handle.SFTPHandle

SFTP File Handle

stat()

Return an L{SFTPAttributes} object referring to this open file, or an error code. This is equivalent to L{SFTPServerInterface.stat}, except it’s called on an open file instead of a path.

@return: an attributes object for the given file, or an SFTP error code (like L{SFTP_PERMISSION_DENIED}). @rtype: L{SFTPAttributes} I{or error code}

class tardis.apps.sftp.sftp.MyTSFTPRequestHandler(request, client_address, server)

Bases: socketserver.BaseRequestHandler

auth_timeout = 60

handle()

handle_timeout()

setup()

timeout = 60

class tardis.apps.sftp.sftp.MyTSFTPServer(*args, **kwargs)

Bases: paramiko.sftp_server.SFTPServer

override SFTPServer to provide channel information to the SFTP subsystem

class tardis.apps.sftp.sftp.MyTSFTPServerInterface(server, *args, **kwargs)

Bases: paramiko.sftp_si.SFTPServerInterface

MyTardis data via SFTP

canonicalize(path)

Return the canonical form of a path on the server.

experiments

list_folder(path)

Returns a list of files within a given folder. The C{path} will use posix notation (C{“/”} separates folder names) and may be an absolute or relative path.

The list of files is expected to be a list of L{SFTPAttributes} objects, which are similar in structure to the objects returned by C{os.stat}. In addition, each object should have its C{filename} field filled in, since this is important to a directory listing and not normally present in C{os.stat} results.

In case of an error, you should return one of the C{SFTP_*} error codes, such as L{SFTP_PERMISSION_DENIED}.

@param path: the requested path (relative or absolute) to be listed. @type path: str @return: a list of the files in the given folder, using L{SFTPAttributes} objects. @rtype: list of L{SFTPAttributes} I{or error code}

lstat(path)

symbolic links are not supported

open(path, flags, attr)

Open a file on the server and create a handle for future operations on that file. On success, a new object subclassed from L{SFTPHandle} should be returned. This handle will be used for future operations on the file (read, write, etc). On failure, an error code such as L{SFTP_PERMISSION_DENIED} should be returned.

C{flags} contains the requested mode for opening (read-only, write-append, etc) as a bitset of flags from the C{os} module:

• C{os.O_RDONLY}
• C{os.O_WRONLY}
• C{os.O_RDWR}
• C{os.O_APPEND}
• C{os.O_CREAT}
• C{os.O_TRUNC}
• C{os.O_EXCL}

(One of C{os.O_RDONLY}, C{os.O_WRONLY}, or C{os.O_RDWR} will always be set.)

The C{attr} object contains requested attributes of the file if it has to be created. Some or all attribute fields may be missing if the client didn’t specify them.

@note: The SFTP protocol defines all files to be in “binary” mode. There is no equivalent to python’s “text” mode.

Parameters:

• path (basestring) – the requested datafile path
• flags (int) – flags or’d together from the C{os} module indicating the requested mode for opening the file.
• attr (SFTPAttributes) – requested attributes of the file if it is newly created.

Returns:

a new L{SFTPHandle} I{or error code}.

Return type:

SFTPHandle

session_ended()

run cleanup on exceptions or disconnection. idea: collect stats and store them in this function

session_started()

run on connection initialisation

stat(path)

Return an L{SFTPAttributes} object for a path on the server, or an error code. If your server supports symbolic links (also known as “aliases”), you should follow them. (L{lstat} is the corresponding call that doesn’t follow symlinks/aliases.)

@param path: the requested path (relative or absolute) to fetch file statistics for. @type path: str

@return: an attributes object for the given file, or an SFTP error code (like L{SFTP_PERMISSION_DENIED}). @rtype: L{SFTPAttributes} I{or error code}

class tardis.apps.sftp.sftp.MyTSFTPTCPServer(address, host_key, RequestHandlerClass=None)

Bases: socketserver.TCPServer

allow_reuse_address = True

close_request(request)

Called to clean up an individual request.

shutdown_request(request)

Called to shutdown and close an individual request.

class tardis.apps.sftp.sftp.MyTServerInterface

Bases: paramiko.server.ServerInterface

check_auth_interactive(username, submethods)

Begin an interactive authentication challenge, if supported. You should override this method in server mode if you want to support the "keyboard-interactive" auth type, which requires you to send a series of questions for the client to answer.

Return AUTH_FAILED if this auth method isn’t supported. Otherwise, you should return an .InteractiveQuery object containing the prompts and instructions for the user. The response will be sent via a call to check_auth_interactive_response.

The default implementation always returns AUTH_FAILED.

Parameters:

• username (str) – the username of the authenticating client
• submethods (str) – a comma-separated list of methods preferred by the client (usually empty)

Returns:

AUTH_FAILED if this auth method isn’t supported; otherwise an object containing queries for the user

Return type:

int or .InteractiveQuery

check_auth_interactive_response(responses)

Continue or finish an interactive authentication challenge, if supported. You should override this method in server mode if you want to support the "keyboard-interactive" auth type.

Return AUTH_FAILED if the responses are not accepted, AUTH_SUCCESSFUL if the responses are accepted and complete the authentication, or AUTH_PARTIALLY_SUCCESSFUL if your authentication is stateful, and this set of responses is accepted for authentication, but more authentication is required. (In this latter case, get_allowed_auths will be called to report to the client what options it has for continuing the authentication.)

If you wish to continue interactive authentication with more questions, you may return an .InteractiveQuery object, which should cause the client to respond with more answers, calling this method again. This cycle can continue indefinitely.

The default implementation always returns AUTH_FAILED.

Parameters:responses – list of str responses from the client Returns:AUTH_FAILED if the authentication fails; AUTH_SUCCESSFUL if it succeeds; AUTH_PARTIALLY_SUCCESSFUL if the interactive auth is successful, but authentication must continue; otherwise an object containing queries for the user Return type:int or .InteractiveQuery

check_auth_password(username, password)

Determine if a given username and password supplied by the client is acceptable for use in authentication.

Return AUTH_FAILED if the password is not accepted, AUTH_SUCCESSFUL if the password is accepted and completes the authentication, or AUTH_PARTIALLY_SUCCESSFUL if your authentication is stateful, and this key is accepted for authentication, but more authentication is required. (In this latter case, get_allowed_auths will be called to report to the client what options it has for continuing the authentication.)

The default implementation always returns AUTH_FAILED.

Parameters:

• username (str) – the username of the authenticating client.
• password (str) – the password given by the client.

Returns:

AUTH_FAILED if the authentication fails; AUTH_SUCCESSFUL if it succeeds; AUTH_PARTIALLY_SUCCESSFUL if the password auth is successful, but authentication must continue.

Return type:

int

check_auth_publickey(username, key)

Determine if a given key supplied by the client is acceptable for use in authentication. You should override this method in server mode to check the username and key and decide if you would accept a signature made using this key.

Return AUTH_FAILED if the key is not accepted, AUTH_SUCCESSFUL if the key is accepted and completes the authentication, or AUTH_PARTIALLY_SUCCESSFUL if your authentication is stateful, and this password is accepted for authentication, but more authentication is required. (In this latter case, get_allowed_auths will be called to report to the client what options it has for continuing the authentication.)

Note that you don’t have to actually verify any key signtature here. If you’re willing to accept the key, Paramiko will do the work of verifying the client’s signature.

The default implementation always returns AUTH_FAILED.

Parameters:

• username (str) – the username of the authenticating client
• key (PKey) – the key object provided by the client

Returns:

AUTH_FAILED if the client can’t authenticate with this key; AUTH_SUCCESSFUL if it can; AUTH_PARTIALLY_SUCCESSFUL if it can authenticate with this key but must continue with authentication

Return type:

int

check_channel_request(kind, chanid)

Determine if a channel request of a given type will be granted, and return OPEN_SUCCEEDED or an error code. This method is called in server mode when the client requests a channel, after authentication is complete.

If you allow channel requests (and an ssh server that didn’t would be useless), you should also override some of the channel request methods below, which are used to determine which services will be allowed on a given channel:

• check_channel_pty_request
• check_channel_shell_request
• check_channel_subsystem_request
• check_channel_window_change_request
• check_channel_x11_request
• check_channel_forward_agent_request

The chanid parameter is a small number that uniquely identifies the channel within a .Transport. A .Channel object is not created unless this method returns OPEN_SUCCEEDED – once a .Channel object is created, you can call .Channel.get_id to retrieve the channel ID.

The return value should either be OPEN_SUCCEEDED (or 0) to allow the channel request, or one of the following error codes to reject it:

• OPEN_FAILED_ADMINISTRATIVELY_PROHIBITED
• OPEN_FAILED_CONNECT_FAILED
• OPEN_FAILED_UNKNOWN_CHANNEL_TYPE
• OPEN_FAILED_RESOURCE_SHORTAGE

The default implementation always returns OPEN_FAILED_ADMINISTRATIVELY_PROHIBITED.

Parameters:

• kind (str) – the kind of channel the client would like to open (usually "session").
• chanid (int) – ID of the channel

Returns:

an int success or failure code (listed above)

get_allowed_auths(username)

Return a list of authentication methods supported by the server. This list is sent to clients attempting to authenticate, to inform them of authentication methods that might be successful.

The “list” is actually a string of comma-separated names of types of authentication. Possible values are "password", "publickey", and "none".

The default implementation always returns "password".

Parameters:username (str) – the username requesting authentication. Returns:a comma-separated str of authentication types

myt_auth(username, password)

tardis.apps.sftp.sftp.start_server(host=None, port=None, keyfile=None)

The SFTP_HOST_KEY setting is required for configuring SFTP access. The SFTP_PORT setting defaults to 2200.

See: tardis/default_settings/sftp.py

tardis.apps.sftp.urls module

tardis.apps.sftp.user_menu_modifiers module

tardis.apps.sftp.user_menu_modifiers.add_ssh_keys_menu_item(request, user_menu)

Add a ‘Manage SSH Keys’ item to the user menu

Parameters:

• request (django.http.HttpRequest) – an HTTP Request instance
• user_menu (list) – user menu context to modify

Returns:

user_menu list

Return type:

list

tardis.apps.sftp.views module

tardis.apps.sftp.views.cybderduck_connection_window(request)

tardis.apps.sftp.views.sftp_access(request)

Show dynamically generated instructions on how to connect to SFTP :param Request request: HttpRequest :return: HttpResponse :rtype: HttpResponse

tardis.apps.sftp.views.sftp_keys(request)

Generate an RSA key pair for a user.

Generates a key pair, stores the public part of the key and provides a one time opportunity for the user to download the private part of the key.

Parameters:request (HttpRequest) – http request Returns:either returns form on GET request or private key download on POST request Return type:HttpResponse

Module contents

tardis.apps.social_auth package

Subpackages

tardis.apps.social_auth.auth package

Submodules

tardis.apps.social_auth.auth.authorisation module

tardis.apps.social_auth.auth.social_auth module

tardis.apps.social_auth.auth.social_auth.add_authentication_method(**kwargs)

Creates an authentication record for OpenID authenticated user

tardis.apps.social_auth.auth.social_auth.add_migration_permission(**kwargs)

Adds permission to migrate account for OpenID authenticated user

tardis.apps.social_auth.auth.social_auth.add_user_permissions(**kwargs)

Adds default permission to OpenID authenticated user

tardis.apps.social_auth.auth.social_auth.approve_user_auth(**kwargs)

Sets approved status to True in user authentication This will add user permissions as well.

tardis.apps.social_auth.auth.social_auth.configure_social_auth_user(**kwargs)

Applies configuration used for external (non-Django) accounts.

Adds user to settings.NEW_USER_INITIAL_GROUPS and sets isDjangoAccount to False in their UserProfile, so that MyTardis won’t allow them to change their password.

tardis.apps.social_auth.auth.social_auth.get_auth_method(authenticatedBackendName)

Return matching user authentication method from list of authentication methods in settings

tardis.apps.social_auth.auth.social_auth.is_openid_migration_enabled()

tardis.apps.social_auth.auth.social_auth.migrate_user_message(**kwargs)

Automatically detects if a user has an account with the same email address and prompts user to perform migration.

tardis.apps.social_auth.auth.social_auth.requires_admin_approval(authenticationBackend)

tardis.apps.social_auth.auth.social_auth.send_admin_email(**kwargs)

Sends MyTardis admins an email for approving account

Module contents

Submodules

tardis.apps.social_auth.apps module

class tardis.apps.social_auth.apps.SocialAuthConfig(app_name, app_module)

Bases: tardis.app_config.AbstractTardisAppConfig

name = 'tardis.apps.social_auth'

verbose_name = 'Social Auth'

tardis.apps.social_auth.default_settings module

tardis.apps.social_auth.urls module

Module contents

Module contents

tardis.default_settings package

Submodules

tardis.default_settings.admins module

tardis.default_settings.admins.ADMINS = []

A list of all the people who get code error notifications. When DEBUG=False and AdminEmailHandler is configured in LOGGING (done by default), Django emails these people the details of exceptions raised in the request/response cycle.

Each item in the list should be a tuple of (Full name, email address). Example:

[(‘John’, ‘john@example.com’), (‘Mary’, ‘mary@example.com’)]

tardis.default_settings.analytics module

tardis.default_settings.apps module

tardis.default_settings.apps.USER_MENU_MODIFIERS = ['tardis.apps.sftp.user_menu_modifiers.add_ssh_keys_menu_item', 'tardis.apps.openid_migration.user_menu_modifiers.add_migrate_account_menu_item']

A list of methods which can modify the user menu defined in tardis.tardis_portal.context_processors.user_menu_processor The modifications will be applied in order, so it is possible for one app to overwrite changes made by another app whose modifier method is earlier in the list.

Each modifier method should take a django.http.HttpRequest object and a list of user menu items, and return a modified list of user menu items.

An example from the SFTP app is below:

USER_MENU_MODIFIERS.extend([
    'tardis.apps.sftp.user_menu_modifiers.add_ssh_keys_menu_item'
])

tardis.default_settings.auth module

tardis.default_settings.auth.AUTOGENERATE_API_KEY = False

Generate a tastypie API key with user post_save (tardis/tardis_portal/models/hooks.py)

tardis.default_settings.auth.REGISTRATION_OPEN = True

Enable/disable the self-registration link and form in the UI. Note - this does not actually disable the URL endpoints for registration. You must also remove the registration app from INSTALLED_APPS to disable registration.

tardis.default_settings.caches module

tardis.default_settings.caches.CACHES = {'celery-locks': {'BACKEND': 'django.core.cache.backends.db.DatabaseCache', 'LOCATION': 'celery_lock_cache'}, 'default': {'BACKEND': 'django.core.cache.backends.db.DatabaseCache', 'LOCATION': 'default_cache'}}

change the CACHES setting to memcached if you prefer. Requires additional dependencies.

tardis.default_settings.celery_settings module

tardis.default_settings.custom_views module

tardis.default_settings.custom_views.DATASET_VIEWS = []

Dataset view overrides (‘contextual views’) are specified as tuples mapping a Schema namespace to a class-based view (or view function). See: https://mytardis.readthedocs.io/en/develop/apps/contextual_views.html#dataset-and-experiment-views

e.g.:

DATASET_VIEWS = [
    ('http://example.org/schemas/dataset/my_awesome_schema',
     'tardis.apps.my_awesome_app.views.CustomDatasetViewSubclass'),
]

tardis.default_settings.custom_views.EXPERIMENT_VIEWS = []

Experiment view overrides (‘contextual views’) are specified as tuples mapping a Schema namespace to a class-based view (or view function). See: https://mytardis.readthedocs.io/en/develop/apps/contextual_views.html#dataset-and-experiment-views

e.g.:

EXPERIMENT_VIEWS = [
    ('http://example.org/schemas/expt/my_awesome_schema',
     'tardis.apps.my_awesome_app.views.CustomExptViewSubclass'),
]

tardis.default_settings.custom_views.INDEX_VIEWS = {}

A custom index page override is defined in as dictionary mapping a class-based view (or view function) to a Django Site, specified by SITE_ID (an integer) or the domain name of the incoming request. See: https://mytardis.readthedocs.io/en/develop/apps/contextual_views.html#custom-index-view

e.g.:

INDEX_VIEWS = {
    1: 'tardis.apps.my_custom_app.views.MyCustomIndexSubclass',
    'store.example.com': 'tardis.apps.myapp.AnotherCustomIndexSubclass'
}

tardis.default_settings.custom_views.LOGIN_VIEWS = {}

A custom login page override is defined in as dictionary mapping a class-based view (or view function) to a Django Site, specified by SITE_ID (an integer) or the domain name of the incoming request. See: https://mytardis.readthedocs.io/en/develop/apps/contextual_views.html#custom-login-view

e.g.:

LOGIN_VIEWS = {
    1: 'tardis.apps.my_custom_app.views.MyCustomLoginSubclass',
    'store.example.com': 'tardis.apps.myapp.AnotherCustomLoginSubclass'
}

tardis.default_settings.database module

tardis.default_settings.debug module

tardis.default_settings.debug.ALLOWED_HOSTS = ['*']

For security reasons this needs to be set to your hostname and/or IP address in production.

tardis.default_settings.debug.DEBUG = True

Set to false for production use

tardis.default_settings.debug.INTERNAL_IPS = ('127.0.0.1',)

A list of IP addresses, as strings, that:

Allow the debug() context processor to add some variables to the template context.

tardis.default_settings.downloads module

tardis.default_settings.downloads.DEFAULT_ARCHIVE_FORMATS = ['tar']

Site’s preferred archive types, with the most preferred first other available option: ‘tgz’. Add to list if desired

tardis.default_settings.downloads.DOWNLOAD_URI_TEMPLATES = {}

When a file download is requested, by default, MyTardis will create a StreamingHttpResponse to serve the download which requires reading the file from a file-like object. For some storage backends, e.g. S3Boto3Storage provided by the django-storages package, it is more efficient to redirect the request directly to the storage provider.

Or the download request could be handled by an API which is aware of HSM (Hierarchical Storage Management) status for files which could be either on disk or on tape.

The DOWNLOAD_URI_TEMPLATES dictionary can be used to specify a URI template (e.g. ‘/api/v1/s3utils_replica/{dfo_id}/download/’ which can be used to download a DataFileObject, instead of using the default /api/v1/dataset_file/[datafile_id]/download/ endpoint.

For example,

DOWNLOAD_URI_TEMPLATES = {

‘storages.backends.s3boto3.S3Boto3Storage’: ‘/api/v1/s3utils_replica/{dfo_id}/download/’

}

The ‘/api/v1/s3utils_replica/{dfo_id}/download/’ endpoint is provided by the ‘s3utils’ tardis app which needs to be in your INSTALLED_APPS

tardis.default_settings.email module

tardis.default_settings.email.DEFAULT_FROM_EMAIL = 'webmaster@localhost'

This can be set as : “MyTardis Admins <admins@mytardis.org>”

tardis.default_settings.email.EMAIL_HOST = 'localhost'

Set this to your local SMTP server, e.g. ‘smtp.example.edu’ or to a remote SMTP server, e.g. ‘smtp.gmail.com’

tardis.default_settings.email.EMAIL_HOST_PASSWORD = ''

When using a local SMTP server, you probably don’t need to authenticate, so you can leave this blank.

If using a remote SMTP server, this can be set to the password used to authenticate.

tardis.default_settings.email.EMAIL_HOST_USER = ''

When using a local SMTP server, you probably don’t need to authenticate, so you can leave this blank.

If using a remote SMTP server, this can be set to the email address used to authenticate, e.g. ‘bob@bobmail.com’

tardis.default_settings.email.EMAIL_PORT = 25

Some SMTP servers require a different port, e.g. 587. Django’s default value for this setting is 25.

tardis.default_settings.email.EMAIL_USE_TLS = False

Some SMTP servers require this to be set to True. Django’s default value for this setting is False.

tardis.default_settings.filters module

tardis.default_settings.filters.FILTERS_TASK_PRIORITY = 4

The default RabbitMQ task priority for messages sent to the filters microservice. Priority 4 is slightly less than the overall default task priority of 5, defined in tardis/default_settings/celery_settings.py

tardis.default_settings.filters.USE_FILTERS = False

If enabled, a task will be sent to RabbitMQ after a file is saved and verified, requesting post-processing, e.g. extracting metadata from file headers and/or generating thumbnail images.

tardis.default_settings.frontend module

tardis.default_settings.frontend.BLEACH_ALLOWED_ATTRIBUTES = {'a': ['href', 'title'], 'abbr': ['title'], 'acronym': ['title']}

These are the default bleach values and shown here as an example.

tardis.default_settings.frontend.BLEACH_ALLOWED_TAGS = ['a', 'abbr', 'acronym', 'b', 'blockquote', 'code', 'em', 'i', 'li', 'ol', 'strong', 'ul']

These are the default bleach values and shown here as an example.

tardis.default_settings.frontend.MAX_IMAGES_IN_CAROUSEL = 100

Max number of images in dataset view’s carousel: zero means no limit

tardis.default_settings.frontend.RENDER_IMAGE_DATASET_SIZE_LIMIT = 0

Render image dataset size limit: zero means no limit

In order to display a dataset thumbnail image, MyTardis queries the dataset’s files for image MIME types. These queries can be very slow for large datasets, making page load times slow. In future versions, the dataset thumbnails will be generated asynchronously (not at response time), but for now, we can set RENDER_IMAGE_DATASET_SIZE_LIMIT to the maximum number of files a dataset can have for MyTardis to scan it for image files at response time.

tardis.default_settings.frontend.RENDER_IMAGE_SIZE_LIMIT = 0

Render image file size limit: zero means no limit

tardis.default_settings.i18n module

tardis.default_settings.localisation module

tardis.default_settings.logging module

tardis.default_settings.middlewares module

tardis.default_settings.publication module

tardis.default_settings.search module

Settings for search

tardis.default_settings.search.MAX_SEARCH_RESULTS = 100

Limits the maximum number of search results for each model (Experiment, Dataset and DataFile). The default value of 100 means that a query could potentially return 300 results in total, i.e. 100 experiments, 100 datasets and 100 datafiles.

tardis.default_settings.search.MIN_CUTOFF_SCORE = 0.0

Filters results based on this value. The default value of 0.0 means that nothing will be excluded from search results. Set it to any number greater than 0.0 to filter out results.

tardis.default_settings.search.SINGLE_SEARCH_ENABLED = False

To enable search:

SINGLE_SEARCH_ENABLED = True INSTALLED_APPS += (‘django_elasticsearch_dsl’, ‘tardis.app.search’) ELASTICSEARCH_DSL = {

‘default’: {

‘hosts’: os.environ.get(‘ELASTICSEARCH_URL’, ‘http://localhost:9200’)

}

} ELASTICSEARCH_DSL_INDEX_SETTINGS = {

‘number_of_shards’: 1

}

tardis.default_settings.sharing module

tardis.default_settings.site_customisations module

tardis.default_settings.site_customisations.SITE_TITLE = 'MyTardis'

customise the title of your site

tardis.default_settings.site_customisations.SPONSORED_TEXT = None

add text to the footer to acknowledge someone

tardis.default_settings.static_files module

tardis.default_settings.storage module

tardis.default_settings.storage.CALCULATE_CHECKSUMS_METHODS = {}

A custom method can be provided for calculating checksums for a storage class, e.g.

CALCULATE_CHECKSUMS_METHODS = {

‘storages.backends.s3boto3.S3Boto3Storage’:

‘tardis.apps.s3utils.utils.calculate_checksums’

}

The DataFileObject class’s calculate_checksums method checks for a storage class match in the CALCULATE_CHECKSUMS_METHODS dict, and if one is not found, it calls the classic compute_checksums method which uses the file_object to calculate the checksums one chunk at a time. For some storage backends (e.g. S3), representing the file as file-like object with Django’s file storage API is not the most efficient way to calculate the checksum.

tardis.default_settings.storage.METADATA_STORE_PATH = '/home/docs/checkouts/readthedocs.org/user_builds/mytardis/checkouts/v4.2.0-rc3/var/store'

storage path for image paths stored in parameters. Better to set to another location if possible

tardis.default_settings.storage.REUSE_DATASET_STORAGE_BOX = True

If a new DataFile is created in a Dataset whose files are all stored in the same storage box, then the new file will be stored in the same storage box, irrespective of the “default” StorageBoxAttribute.

The mytardis-app-mydata app has its own logic for determining the appropriate storage box for uploads from a MyData instance. When a MyData instance (an “Uploader”) is approved, it will be assigned a storage box which should be used for DataFileObjects created from MyData uploads.

tardis.default_settings.templates module

tardis.default_settings.uploads module

tardis.default_settings.uploads.UPLOAD_METHOD = False

Old version: UPLOAD_METHOD = “uploadify”. This can be changed to an app that provides an upload_button function, eg. “tardis.apps.filepicker.views.upload_button” to use a fancy commercial uploader. To use filepicker, please also get an API key at http://filepicker.io

tardis.default_settings.urls module

Module contents

tardis.default_settings.get_git_version()

tardis.tardis_portal package

Subpackages

tardis.tardis_portal.auth package

Submodules

tardis.tardis_portal.auth.authentication module

A module containing helper methods for the manage_auth_methods function in views.py.

tardis.tardis_portal.auth.authentication.add_auth_method(request)

Add a new authentication method to request.user’s existing list of authentication methods. This method will ask for a confirmation if the user wants to merge two accounts if the authentication method he provided already exists as a method for another user.

Parameters:request (Request) – the HTTP request object Returns:The HttpResponse which contains request.user’s new list of authentication methods Return type:HttpResponse

tardis.tardis_portal.auth.authentication.edit_auth_method(request)

Change the local DB (Django) password for request.user.

tardis.tardis_portal.auth.authentication.list_auth_methods(request)

Generate a list of authentication methods that request.user uses to authenticate to the system and send it back in a HttpResponse.

Parameters:request (Request) – the HTTP request object Returns:The HttpResponse which contains request.user’s list of authentication methods Return type:HttpResponse

tardis.tardis_portal.auth.authentication.merge_auth_method(request)

Merge the account that the user is logged in as and the account that he provided in the Authentication Form. Merging accounts involve relinking the UserAuthentication table entries, transferring ObjectACL entries to the merged account, changing the Group memberships and deleting the unneeded account.

Parameters:request (Request) – the HTTP request object Returns:The HttpResponse which contains request.user’s new list of authentication methods Return type:HttpResponse

tardis.tardis_portal.auth.authentication.remove_auth_method(request)

Removes the non-local DB auth method from the UserAuthentication model.

Parameters:request (Request) – the HTTP request object Returns:The HttpResponse which contains request.user’s new list of authentication methods Return type:HttpResponse

tardis.tardis_portal.auth.authorisation module

Object-level authorisation backend

class tardis.tardis_portal.auth.authorisation.ACLAwareBackend

Bases: object

app_label = 'tardis_acls'

authenticate(request)

do not use this backend for authentication

get_perm_bool(verb)

relates ACLs to permissions

has_perm(user_obj, perm, obj=None)

main method, calls other methods based on permission type queried

supports_anonymous_user = True

supports_object_permissions = True

tardis.tardis_portal.auth.authservice module

models.py

class tardis.tardis_portal.auth.authservice.AuthService(settings=<LazySettings "tardis.test_settings">)

Bases: object

The AuthService provides an interface for querying the auth(n|z) framework within MyTardis. The auth service works by reading the class path to plugins from the settings file.

Parameters:settings (django.conf.settings) – the settings object that contains the list of user and group plugins.

authenticate(authMethod, **credentials)

Try and authenticate the user using the auth type he/she specified to use and if authentication didn’t work using that

Parameters:

• authMethod (string) – the shortname of the auth method.
• credentials (kwargs) – the credentials as expected by the auth plugin

Returns:

authenticated User or None

Return type:

User or None

getGroups(user)

Parameters:user (User) – User Returns:a list of tuples containing pluginname and group id Return type:list

getGroupsForEntity(entity)

Return a list of the groups an entity belongs to

Parameters:entity (string) – the entity to earch for, user or group. Returns:groups Return type:Group

The groups will be reurned as a list similar to:

[{'name': 'Group 456', 'id': '2'},
{'name': 'Group 123', 'id': '1'}]

getUser(authMethod, user_id, force_user_create=False)

Return a user model based on the given auth method and user id.

This function is responsible for creating the user within the Django DB and returning the resulting user model.

getUsernameByEmail(authMethod, email)

Return a username given the auth method and email address of a user.

get_or_create_user(user_obj_or_dict, authMethod=None)

refactored out for external use by AAF and possibly others

searchEntities(filter)

Return a list of users and/or groups

searchGroups(**kw)

basestring id: the value of the id to search for basestring name: the value of the displayname to search for int max_results: the maximum number of elements to return basestring sort_by: the attribute the users should be sorted on basestring plugin: restrict the search to the specific group provider

returns: a list of users and/or groups rtype: list

searchUsers(filter)

Return a list of users and/or groups

tardis.tardis_portal.auth.decorators module

tardis.tardis_portal.auth.decorators.datafile_access_required(f)

tardis.tardis_portal.auth.decorators.dataset_access_required(f)

tardis.tardis_portal.auth.decorators.dataset_download_required(f)

tardis.tardis_portal.auth.decorators.dataset_write_permissions_required(f)

tardis.tardis_portal.auth.decorators.delete_permissions_required(f)

tardis.tardis_portal.auth.decorators.experiment_access_required(f)

tardis.tardis_portal.auth.decorators.experiment_download_required(f)

tardis.tardis_portal.auth.decorators.experiment_ownership_required(f)

A decorator for Django views that validates if a user is an owner of an experiment or ‘superuser’ prior to further processing the request. Unauthenticated requests are redirected to the login page. If the user making the request satisfies none of these criteria, an error response is returned.

Parameters:f (types.FunctionType) – A Django view function Returns:A Django view function Return type:types.FunctionType

tardis.tardis_portal.auth.decorators.get_accessible_datafiles_for_user(request)

tardis.tardis_portal.auth.decorators.get_accessible_experiments(request)

tardis.tardis_portal.auth.decorators.get_accessible_experiments_for_dataset(request, dataset_id)

tardis.tardis_portal.auth.decorators.get_owned_experiments(request)

tardis.tardis_portal.auth.decorators.get_shared_experiments(request)

tardis.tardis_portal.auth.decorators.group_ownership_required(f)

A decorator for Django views that validates if a user is a group admin or ‘superuser’ prior to further processing the request. Unauthenticated requests are redirected to the login page. If the user making the request satisfies none of these criteria, an error response is returned.

Parameters:f (types.FunctionType) – A Django view function Returns:A Django view function Return type:types.FunctionType

tardis.tardis_portal.auth.decorators.has_datafile_access(request, datafile_id)

tardis.tardis_portal.auth.decorators.has_datafile_download_access(request, datafile_id)

tardis.tardis_portal.auth.decorators.has_dataset_access(request, dataset_id)

tardis.tardis_portal.auth.decorators.has_dataset_download_access(request, dataset_id)

tardis.tardis_portal.auth.decorators.has_dataset_ownership(request, dataset_id)

tardis.tardis_portal.auth.decorators.has_dataset_write(request, dataset_id)

tardis.tardis_portal.auth.decorators.has_delete_permissions(request, experiment_id)

tardis.tardis_portal.auth.decorators.has_experiment_access(request, experiment_id)

tardis.tardis_portal.auth.decorators.has_experiment_download_access(request, experiment_id)

tardis.tardis_portal.auth.decorators.has_experiment_ownership(request, experiment_id)

tardis.tardis_portal.auth.decorators.has_experiment_write(request, experiment_id)

tardis.tardis_portal.auth.decorators.has_read_or_owner_ACL(request, experiment_id)

Check whether the user has read access to the experiment - this means either they have been granted read access, or that they are the owner.

NOTE: This does not check whether the experiment is public or not, which means even when the experiment is public, this method does not automatically returns true.

As such, this method should NOT be used to check whether the user has general read permission.

tardis.tardis_portal.auth.decorators.has_write_permissions(request, experiment_id)

tardis.tardis_portal.auth.decorators.is_group_admin(request, group_id)

tardis.tardis_portal.auth.decorators.upload_auth(f)

tardis.tardis_portal.auth.decorators.write_permissions_required(f)

tardis.tardis_portal.auth.fix_circular module

tardis.tardis_portal.auth.fix_circular.getGroups(user)

tardis.tardis_portal.auth.interfaces module

class tardis.tardis_portal.auth.interfaces.AuthProvider

Bases: object

authenticate(request)

from a request authenticate try to authenticate the user. return a user dict if successful.

getUsernameByEmail(email)

returns the username (format string) from the auth domain

Implementing this function is optional- it is needed for resolving experiment owner email addresses to usernames during ingestion.

get_user(user_id)

class tardis.tardis_portal.auth.interfaces.GroupProvider

Bases: object

getGroupById(id)

return the group associated with the id

getGroups(user)

return an iteration of the available groups.

getGroupsForEntity(id)

return a list of groups associated with a particular entity id

searchGroups(**filter)

return a list of groups that match the filter

class tardis.tardis_portal.auth.interfaces.UserProvider

Bases: object

getUserById(id)

return the user dictionary in the format of:

{"id": 123,
"first_name": "John",
"last_name": "Smith",
"email": "john@example.com"}

getUsernameByEmail(email)

returns the username (format string) from the auth domain needed for resolving experiment owners during ingestion

searchUsers(**filter)

return a list of user descriptions from the auth domain.

each user is in the format of:

{"id": 123,
"first_name": "John",
"last_name": "Smith",
"email": "john@example.com"}

tardis.tardis_portal.auth.ldap_auth module

tardis.tardis_portal.auth.localdb_auth module

Local DB Authentication module.

class tardis.tardis_portal.auth.localdb_auth.DjangoAuthBackend

Bases: tardis.tardis_portal.auth.interfaces.AuthProvider

Authenticate against Django’s Model Backend.

authenticate(request)

authenticate a user, this expect the user will be using form based auth and the username and password will be passed in as POST variables.

Parameters:request (django.http.HttpRequest) – a HTTP Request instance Returns:authenticated User Return type:User

get_user(user_id)

class tardis.tardis_portal.auth.localdb_auth.DjangoGroupProvider

Bases: tardis.tardis_portal.auth.interfaces.GroupProvider

getGroupById(id)

return the group associated with the id:

{"id": 123,

“display”: “Group Name”,}

getGroups(user)

return an iteration of the available groups.

name = 'django_group'

searchGroups(**filter)

return a list of groups that match the filter

class tardis.tardis_portal.auth.localdb_auth.DjangoUserProvider

Bases: tardis.tardis_portal.auth.interfaces.UserProvider

getUserById(id)

return the user dictionary in the format of:

{"id": 123,
"first_name": "John",
"last_name": "Smith",
"email": "john@example.com"}

name = 'django_user'

tardis.tardis_portal.auth.token_auth module

token authentication module

class tardis.tardis_portal.auth.token_auth.TokenAuthMiddleware(get_response)

Bases: object

adds tokens to the user object and the session from a GET query

process_request(request)

class tardis.tardis_portal.auth.token_auth.TokenGroupProvider

Bases: tardis.tardis_portal.auth.interfaces.GroupProvider

Transforms tokens into auth groups

getGroups(user)

return an iteration of the available groups.

name = 'token_group'

searchGroups(**kwargs)

return nothing because these are not groups in the standard sense

tardis.tardis_portal.auth.utils module

Created on 15/03/2011

@author: gerson

tardis.tardis_portal.auth.utils.configure_user(user)

Configure a user account that has just been created by adding the user to the default groups and marking it as a not a Django account.

Parameters:user (User) – the User instance for the newly created account Returns:User profile for user Return type:UserProfile

tardis.tardis_portal.auth.utils.create_user(auth_method, user_id, email='')

tardis.tardis_portal.auth.utils.get_or_create_user(auth_method, user_id, email='')

Module contents

tardis.tardis_portal.management package

Subpackages

tardis.tardis_portal.management.commands package

Submodules

tardis.tardis_portal.management.commands.createuser module

Management utility to create regular users.

class tardis.tardis_portal.management.commands.createuser.Command(stdout=None, stderr=None, no_color=False, force_color=False)

Bases: django.core.management.base.BaseCommand

add_arguments(parser)

Entry point for subclassed commands to add custom arguments.

handle(*args, **options)

The actual logic of the command. Subclasses must implement this method.

help = 'Used to create a MyTardis user.'

tardis.tardis_portal.management.commands.createuser.is_valid_email(value)

tardis.tardis_portal.management.commands.dumpschemas module

Command for dumping soft schema definitions

class tardis.tardis_portal.management.commands.dumpschemas.Command(stdout=None, stderr=None, no_color=False, force_color=False)

Bases: django.core.management.base.BaseCommand

add_arguments(parser)

Entry point for subclassed commands to add custom arguments.

args = '[namespace...]'

handle(*args, **options)

The actual logic of the command. Subclasses must implement this method.

help = 'Dump soft schema definitions. No namespace = dump all schemas'

tardis.tardis_portal.management.commands.loadschemas module

Command for loading soft schema definitions

class tardis.tardis_portal.management.commands.loadschemas.Command(stdout=None, stderr=None, no_color=False, force_color=False)

Bases: django.core.management.base.BaseCommand

add_arguments(parser)

Entry point for subclassed commands to add custom arguments.

args = 'schema [schema ...]'

handle(*args, **options)

The actual logic of the command. Subclasses must implement this method.

help = 'Load soft schema definitions'

tardis.tardis_portal.management.commands.rmexperiment module

Management command to delete the specified experiment and its associated datasets, datafiles and parameters.

The operation is atomic, either the entire experiment is deleted, or nothing.

rmexperiment was introduced due to the Oracle DISTINCT workaround causing sql delete cascading to fail. The current implementation of rmexperiment still relies on some cascading.

class tardis.tardis_portal.management.commands.rmexperiment.Command(stdout=None, stderr=None, no_color=False, force_color=False)

Bases: django.core.management.base.BaseCommand

add_arguments(parser)

Entry point for subclassed commands to add custom arguments.

args = '<MyTardis Exp ID>'

handle(*args, **options)

The actual logic of the command. Subclasses must implement this method.

help = 'Delete the supplied MyTardis Experiment ID'

Module contents

Module contents

tardis.tardis_portal.migrations package

Submodules

tardis.tardis_portal.migrations.0001_initial module

class tardis.tardis_portal.migrations.0001_initial.Migration(name, app_label)

Bases: django.db.migrations.migration.Migration

dependencies = [('contenttypes', '0002_remove_content_type_name'), ('auth', '__first__'), ('auth', '0006_require_contenttypes_0002')]

operations = [<CreateModel name='DataFile', fields=[('id', <django.db.models.fields.AutoField>), ('filename', <django.db.models.fields.CharField>), ('directory', <django.db.models.fields.TextField>), ('size', <django.db.models.fields.CharField>), ('created_time', <django.db.models.fields.DateTimeField>), ('modification_time', <django.db.models.fields.DateTimeField>), ('mimetype', <django.db.models.fields.CharField>), ('md5sum', <django.db.models.fields.CharField>), ('sha512sum', <django.db.models.fields.CharField>), ('deleted', <django.db.models.fields.BooleanField>), ('deleted_time', <django.db.models.fields.DateTimeField>), ('version', <django.db.models.fields.IntegerField>)], options={'ordering': ['filename']}>, <CreateModel name='DataFileObject', fields=[('id', <django.db.models.fields.AutoField>), ('uri', <django.db.models.fields.TextField>), ('created_time', <django.db.models.fields.DateTimeField>), ('verified', <django.db.models.fields.BooleanField>), ('last_verified_time', <django.db.models.fields.DateTimeField>), ('datafile', <django.db.models.fields.related.ForeignKey>)]>, <CreateModel name='DatafileParameter', fields=[('id', <django.db.models.fields.AutoField>), ('string_value', <django.db.models.fields.TextField>), ('numerical_value', <django.db.models.fields.FloatField>), ('datetime_value', <django.db.models.fields.DateTimeField>), ('link_id', <django.db.models.fields.PositiveIntegerField>), ('link_ct', <django.db.models.fields.related.ForeignKey>)], options={'ordering': ['name'], 'abstract': False}>, <CreateModel name='DatafileParameterSet', fields=[('id', <django.db.models.fields.AutoField>), ('datafile', <django.db.models.fields.related.ForeignKey>)], options={'ordering': ['id'], 'abstract': False}, bases=(<class 'django.db.models.base.Model'>, <class 'tardis.tardis_portal.models.parameters.ParameterSetManagerMixin'>)>, <CreateModel name='Dataset', fields=[('id', <django.db.models.fields.AutoField>), ('description', <django.db.models.fields.TextField>), ('directory', <django.db.models.fields.TextField>), ('immutable', <django.db.models.fields.BooleanField>)], options={'ordering': ['-id']}>, <CreateModel name='DatasetParameter', fields=[('id', <django.db.models.fields.AutoField>), ('string_value', <django.db.models.fields.TextField>), ('numerical_value', <django.db.models.fields.FloatField>), ('datetime_value', <django.db.models.fields.DateTimeField>), ('link_id', <django.db.models.fields.PositiveIntegerField>), ('link_ct', <django.db.models.fields.related.ForeignKey>)], options={'ordering': ['name'], 'abstract': False}>, <CreateModel name='DatasetParameterSet', fields=[('id', <django.db.models.fields.AutoField>), ('dataset', <django.db.models.fields.related.ForeignKey>)], options={'ordering': ['id'], 'abstract': False}, bases=(<class 'django.db.models.base.Model'>, <class 'tardis.tardis_portal.models.parameters.ParameterSetManagerMixin'>)>, <CreateModel name='Experiment', fields=[('id', <django.db.models.fields.AutoField>), ('url', <django.db.models.fields.URLField>), ('approved', <django.db.models.fields.BooleanField>), ('title', <django.db.models.fields.CharField>), ('institution_name', <django.db.models.fields.CharField>), ('description', <django.db.models.fields.TextField>), ('start_time', <django.db.models.fields.DateTimeField>), ('end_time', <django.db.models.fields.DateTimeField>), ('created_time', <django.db.models.fields.DateTimeField>), ('update_time', <django.db.models.fields.DateTimeField>), ('handle', <django.db.models.fields.TextField>), ('locked', <django.db.models.fields.BooleanField>), ('public_access', <django.db.models.fields.PositiveSmallIntegerField>), ('created_by', <django.db.models.fields.related.ForeignKey>)]>, <CreateModel name='ExperimentAuthor', fields=[('id', <django.db.models.fields.AutoField>), ('author', <django.db.models.fields.CharField>), ('institution', <django.db.models.fields.CharField>), ('email', <django.db.models.fields.CharField>), ('order', <django.db.models.fields.PositiveIntegerField>), ('url', <django.db.models.fields.URLField>), ('experiment', <django.db.models.fields.related.ForeignKey>)], options={'ordering': ['order']}>, <CreateModel name='ExperimentParameter', fields=[('id', <django.db.models.fields.AutoField>), ('string_value', <django.db.models.fields.TextField>), ('numerical_value', <django.db.models.fields.FloatField>), ('datetime_value', <django.db.models.fields.DateTimeField>), ('link_id', <django.db.models.fields.PositiveIntegerField>), ('link_ct', <django.db.models.fields.related.ForeignKey>)], options={'ordering': ['name'], 'abstract': False}>, <CreateModel name='ExperimentParameterSet', fields=[('id', <django.db.models.fields.AutoField>), ('experiment', <django.db.models.fields.related.ForeignKey>)], options={'ordering': ['id'], 'abstract': False}, bases=(<class 'django.db.models.base.Model'>, <class 'tardis.tardis_portal.models.parameters.ParameterSetManagerMixin'>)>, <CreateModel name='Facility', fields=[('id', <django.db.models.fields.AutoField>), ('name', <django.db.models.fields.CharField>), ('manager_group', <django.db.models.fields.related.ForeignKey>)], options={'verbose_name_plural': 'Facilities'}>, <CreateModel name='FreeTextSearchField', fields=[('id', <django.db.models.fields.AutoField>)]>, <CreateModel name='GroupAdmin', fields=[('id', <django.db.models.fields.AutoField>), ('group', <django.db.models.fields.related.ForeignKey>), ('user', <django.db.models.fields.related.ForeignKey>)]>, <CreateModel name='Instrument', fields=[('id', <django.db.models.fields.AutoField>), ('name', <django.db.models.fields.CharField>), ('facility', <django.db.models.fields.related.ForeignKey>)], options={'verbose_name_plural': 'Instruments'}>, <CreateModel name='InstrumentParameter', fields=[('id', <django.db.models.fields.AutoField>), ('string_value', <django.db.models.fields.TextField>), ('numerical_value', <django.db.models.fields.FloatField>), ('datetime_value', <django.db.models.fields.DateTimeField>), ('link_id', <django.db.models.fields.PositiveIntegerField>), ('link_ct', <django.db.models.fields.related.ForeignKey>)], options={'ordering': ['name'], 'abstract': False}>, <CreateModel name='InstrumentParameterSet', fields=[('id', <django.db.models.fields.AutoField>), ('instrument', <django.db.models.fields.related.ForeignKey>)], options={'ordering': ['id'], 'abstract': False}, bases=(<class 'django.db.models.base.Model'>, <class 'tardis.tardis_portal.models.parameters.ParameterSetManagerMixin'>)>, <CreateModel name='JTI', fields=[('id', <django.db.models.fields.AutoField>), ('jti', <django.db.models.fields.CharField>), ('created_time', <django.db.models.fields.DateTimeField>)]>, <CreateModel name='License', fields=[('id', <django.db.models.fields.AutoField>), ('name', <django.db.models.fields.CharField>), ('url', <django.db.models.fields.URLField>), ('internal_description', <django.db.models.fields.TextField>), ('image_url', <django.db.models.fields.URLField>), ('allows_distribution', <django.db.models.fields.BooleanField>), ('is_active', <django.db.models.fields.BooleanField>)]>, <CreateModel name='ObjectACL', fields=[('id', <django.db.models.fields.AutoField>), ('pluginId', <django.db.models.fields.CharField>), ('entityId', <django.db.models.fields.CharField>), ('object_id', <django.db.models.fields.PositiveIntegerField>), ('canRead', <django.db.models.fields.BooleanField>), ('canWrite', <django.db.models.fields.BooleanField>), ('canDelete', <django.db.models.fields.BooleanField>), ('isOwner', <django.db.models.fields.BooleanField>), ('effectiveDate', <django.db.models.fields.DateField>), ('expiryDate', <django.db.models.fields.DateField>), ('aclOwnershipType', <django.db.models.fields.IntegerField>), ('content_type', <django.db.models.fields.related.ForeignKey>)], options={'ordering': ['content_type', 'object_id'], 'verbose_name': 'Object ACL'}>, <CreateModel name='ParameterName', fields=[('id', <django.db.models.fields.AutoField>), ('name', <django.db.models.fields.CharField>), ('full_name', <django.db.models.fields.CharField>), ('units', <django.db.models.fields.CharField>), ('data_type', <django.db.models.fields.IntegerField>), ('immutable', <django.db.models.fields.BooleanField>), ('comparison_type', <django.db.models.fields.IntegerField>), ('is_searchable', <django.db.models.fields.BooleanField>), ('choices', <django.db.models.fields.CharField>), ('order', <django.db.models.fields.PositiveIntegerField>)], options={'ordering': ('order', 'name')}>, <CreateModel name='Schema', fields=[('id', <django.db.models.fields.AutoField>), ('namespace', <django.db.models.fields.URLField>), ('name', <django.db.models.fields.CharField>), ('type', <django.db.models.fields.IntegerField>), ('subtype', <django.db.models.fields.CharField>), ('immutable', <django.db.models.fields.BooleanField>), ('hidden', <django.db.models.fields.BooleanField>)]>, <CreateModel name='StorageBox', fields=[('id', <django.db.models.fields.AutoField>), ('django_storage_class', <django.db.models.fields.TextField>), ('max_size', <django.db.models.fields.BigIntegerField>), ('status', <django.db.models.fields.CharField>), ('name', <django.db.models.fields.TextField>), ('description', <django.db.models.fields.TextField>), ('master_box', <django.db.models.fields.related.ForeignKey>)], options={'verbose_name_plural': 'storage boxes'}>, <CreateModel name='StorageBoxAttribute', fields=[('id', <django.db.models.fields.AutoField>), ('key', <django.db.models.fields.TextField>), ('value', <django.db.models.fields.TextField>), ('storage_box', <django.db.models.fields.related.ForeignKey>)]>, <CreateModel name='StorageBoxOption', fields=[('id', <django.db.models.fields.AutoField>), ('key', <django.db.models.fields.TextField>), ('value', <django.db.models.fields.TextField>), ('storage_box', <django.db.models.fields.related.ForeignKey>)]>, <CreateModel name='Token', fields=[('id', <django.db.models.fields.AutoField>), ('token', <django.db.models.fields.CharField>), ('expiry_date', <django.db.models.fields.DateField>), ('experiment', <django.db.models.fields.related.ForeignKey>), ('user', <django.db.models.fields.related.ForeignKey>)]>, <CreateModel name='UserAuthentication', fields=[('id', <django.db.models.fields.AutoField>), ('username', <django.db.models.fields.CharField>), ('authenticationMethod', <django.db.models.fields.CharField>)]>, <CreateModel name='UserProfile', fields=[('id', <django.db.models.fields.AutoField>), ('isDjangoAccount', <django.db.models.fields.BooleanField>), ('rapidConnectEduPersonTargetedID', <django.db.models.fields.CharField>), ('user', <django.db.models.fields.related.ForeignKey>)]>, <AddField model_name='userauthentication', name='userProfile', field=<django.db.models.fields.related.ForeignKey>>, <AddField model_name='parametername', name='schema', field=<django.db.models.fields.related.ForeignKey>>, <AddField model_name='instrumentparameterset', name='schema', field=<django.db.models.fields.related.ForeignKey>>, <AddField model_name='instrumentparameterset', name='storage_box', field=<django.db.models.fields.related.ManyToManyField>>, <AddField model_name='instrumentparameter', name='name', field=<django.db.models.fields.related.ForeignKey>>, <AddField model_name='instrumentparameter', name='parameterset', field=<django.db.models.fields.related.ForeignKey>>, <AddField model_name='freetextsearchfield', name='parameter_name', field=<django.db.models.fields.related.ForeignKey>>, <AddField model_name='experimentparameterset', name='schema', field=<django.db.models.fields.related.ForeignKey>>, <AddField model_name='experimentparameterset', name='storage_box', field=<django.db.models.fields.related.ManyToManyField>>, <AddField model_name='experimentparameter', name='name', field=<django.db.models.fields.related.ForeignKey>>, <AddField model_name='experimentparameter', name='parameterset', field=<django.db.models.fields.related.ForeignKey>>, <AddField model_name='experiment', name='license', field=<django.db.models.fields.related.ForeignKey>>, <AddField model_name='datasetparameterset', name='schema', field=<django.db.models.fields.related.ForeignKey>>, <AddField model_name='datasetparameterset', name='storage_box', field=<django.db.models.fields.related.ManyToManyField>>, <AddField model_name='datasetparameter', name='name', field=<django.db.models.fields.related.ForeignKey>>, <AddField model_name='datasetparameter', name='parameterset', field=<django.db.models.fields.related.ForeignKey>>, <AddField model_name='dataset', name='experiments', field=<django.db.models.fields.related.ManyToManyField>>, <AddField model_name='dataset', name='instrument', field=<django.db.models.fields.related.ForeignKey>>, <AddField model_name='datafileparameterset', name='schema', field=<django.db.models.fields.related.ForeignKey>>, <AddField model_name='datafileparameterset', name='storage_box', field=<django.db.models.fields.related.ManyToManyField>>, <AddField model_name='datafileparameter', name='name', field=<django.db.models.fields.related.ForeignKey>>, <AddField model_name='datafileparameter', name='parameterset', field=<django.db.models.fields.related.ForeignKey>>, <AddField model_name='datafileobject', name='storage_box', field=<django.db.models.fields.related.ForeignKey>>, <AddField model_name='datafile', name='dataset', field=<django.db.models.fields.related.ForeignKey>>, <AlterUniqueTogether name='parametername', unique_together={('schema', 'name')}>, <AlterUniqueTogether name='experimentauthor', unique_together={('experiment', 'author')}>, <AlterUniqueTogether name='datafileobject', unique_together={('datafile', 'storage_box')}>, <AlterUniqueTogether name='datafile', unique_together={('dataset', 'directory', 'filename', 'version')}>]

tardis.tardis_portal.migrations.0001_squashed_0011_auto_20160505_1643 module

class tardis.tardis_portal.migrations.0001_squashed_0011_auto_20160505_1643.Migration(name, app_label)

Bases: django.db.migrations.migration.Migration

dependencies = [('contenttypes', '0002_remove_content_type_name'), ('auth', '__first__'), ('auth', '0006_require_contenttypes_0002')]

operations = [<CreateModel name='DataFile', fields=[('id', <django.db.models.fields.AutoField>), ('filename', <django.db.models.fields.CharField>), ('directory', <django.db.models.fields.CharField>), ('size', <django.db.models.fields.CharField>), ('created_time', <django.db.models.fields.DateTimeField>), ('modification_time', <django.db.models.fields.DateTimeField>), ('mimetype', <django.db.models.fields.CharField>), ('md5sum', <django.db.models.fields.CharField>), ('sha512sum', <django.db.models.fields.CharField>), ('deleted', <django.db.models.fields.BooleanField>), ('deleted_time', <django.db.models.fields.DateTimeField>), ('version', <django.db.models.fields.IntegerField>)], options={'ordering': ['filename']}>, <CreateModel name='DataFileObject', fields=[('id', <django.db.models.fields.AutoField>), ('uri', <django.db.models.fields.TextField>), ('created_time', <django.db.models.fields.DateTimeField>), ('verified', <django.db.models.fields.BooleanField>), ('last_verified_time', <django.db.models.fields.DateTimeField>), ('datafile', <django.db.models.fields.related.ForeignKey>)]>, <CreateModel name='DatafileParameter', fields=[('id', <django.db.models.fields.AutoField>), ('string_value', <django.db.models.fields.TextField>), ('numerical_value', <django.db.models.fields.FloatField>), ('datetime_value', <django.db.models.fields.DateTimeField>), ('link_id', <django.db.models.fields.PositiveIntegerField>), ('link_ct', <django.db.models.fields.related.ForeignKey>)], options={'ordering': ['name'], 'abstract': False}>, <CreateModel name='DatafileParameterSet', fields=[('id', <django.db.models.fields.AutoField>), ('datafile', <django.db.models.fields.related.ForeignKey>)], options={'ordering': ['id'], 'abstract': False}, bases=(<class 'django.db.models.base.Model'>, <class 'tardis.tardis_portal.models.parameters.ParameterSetManagerMixin'>)>, <CreateModel name='Dataset', fields=[('id', <django.db.models.fields.AutoField>), ('description', <django.db.models.fields.TextField>), ('directory', <django.db.models.fields.CharField>), ('immutable', <django.db.models.fields.BooleanField>)], options={'ordering': ['-id']}>, <CreateModel name='DatasetParameter', fields=[('id', <django.db.models.fields.AutoField>), ('string_value', <django.db.models.fields.TextField>), ('numerical_value', <django.db.models.fields.FloatField>), ('datetime_value', <django.db.models.fields.DateTimeField>), ('link_id', <django.db.models.fields.PositiveIntegerField>), ('link_ct', <django.db.models.fields.related.ForeignKey>)], options={'ordering': ['name'], 'abstract': False}>, <CreateModel name='DatasetParameterSet', fields=[('id', <django.db.models.fields.AutoField>), ('dataset', <django.db.models.fields.related.ForeignKey>)], options={'ordering': ['id'], 'abstract': False}, bases=(<class 'django.db.models.base.Model'>, <class 'tardis.tardis_portal.models.parameters.ParameterSetManagerMixin'>)>, <CreateModel name='Experiment', fields=[('id', <django.db.models.fields.AutoField>), ('url', <django.db.models.fields.URLField>), ('approved', <django.db.models.fields.BooleanField>), ('title', <django.db.models.fields.CharField>), ('institution_name', <django.db.models.fields.CharField>), ('description', <django.db.models.fields.TextField>), ('start_time', <django.db.models.fields.DateTimeField>), ('end_time', <django.db.models.fields.DateTimeField>), ('created_time', <django.db.models.fields.DateTimeField>), ('update_time', <django.db.models.fields.DateTimeField>), ('handle', <django.db.models.fields.TextField>), ('locked', <django.db.models.fields.BooleanField>), ('public_access', <django.db.models.fields.PositiveSmallIntegerField>), ('created_by', <django.db.models.fields.related.ForeignKey>)]>, <CreateModel name='ExperimentAuthor', fields=[('id', <django.db.models.fields.AutoField>), ('author', <django.db.models.fields.CharField>), ('institution', <django.db.models.fields.CharField>), ('email', <django.db.models.fields.CharField>), ('order', <django.db.models.fields.PositiveIntegerField>), ('url', <django.db.models.fields.URLField>), ('experiment', <django.db.models.fields.related.ForeignKey>)], options={'ordering': ['order']}>, <CreateModel name='ExperimentParameter', fields=[('id', <django.db.models.fields.AutoField>), ('string_value', <django.db.models.fields.TextField>), ('numerical_value', <django.db.models.fields.FloatField>), ('datetime_value', <django.db.models.fields.DateTimeField>), ('link_id', <django.db.models.fields.PositiveIntegerField>), ('link_ct', <django.db.models.fields.related.ForeignKey>)], options={'ordering': ['name'], 'abstract': False}>, <CreateModel name='ExperimentParameterSet', fields=[('id', <django.db.models.fields.AutoField>), ('experiment', <django.db.models.fields.related.ForeignKey>)], options={'ordering': ['id'], 'abstract': False}, bases=(<class 'django.db.models.base.Model'>, <class 'tardis.tardis_portal.models.parameters.ParameterSetManagerMixin'>)>, <CreateModel name='Facility', fields=[('id', <django.db.models.fields.AutoField>), ('name', <django.db.models.fields.CharField>), ('manager_group', <django.db.models.fields.related.ForeignKey>)], options={'verbose_name_plural': 'Facilities'}>, <CreateModel name='FreeTextSearchField', fields=[('id', <django.db.models.fields.AutoField>)]>, <CreateModel name='GroupAdmin', fields=[('id', <django.db.models.fields.AutoField>), ('group', <django.db.models.fields.related.ForeignKey>), ('user', <django.db.models.fields.related.ForeignKey>)]>, <CreateModel name='Instrument', fields=[('id', <django.db.models.fields.AutoField>), ('name', <django.db.models.fields.CharField>), ('facility', <django.db.models.fields.related.ForeignKey>)], options={'verbose_name_plural': 'Instruments'}>, <CreateModel name='InstrumentParameter', fields=[('id', <django.db.models.fields.AutoField>), ('string_value', <django.db.models.fields.TextField>), ('numerical_value', <django.db.models.fields.FloatField>), ('datetime_value', <django.db.models.fields.DateTimeField>), ('link_id', <django.db.models.fields.PositiveIntegerField>), ('link_ct', <django.db.models.fields.related.ForeignKey>)], options={'ordering': ['name'], 'abstract': False}>, <CreateModel name='InstrumentParameterSet', fields=[('id', <django.db.models.fields.AutoField>), ('instrument', <django.db.models.fields.related.ForeignKey>)], options={'ordering': ['id'], 'abstract': False}, bases=(<class 'django.db.models.base.Model'>, <class 'tardis.tardis_portal.models.parameters.ParameterSetManagerMixin'>)>, <CreateModel name='JTI', fields=[('id', <django.db.models.fields.AutoField>), ('jti', <django.db.models.fields.CharField>), ('created_time', <django.db.models.fields.DateTimeField>)]>, <CreateModel name='License', fields=[('id', <django.db.models.fields.AutoField>), ('name', <django.db.models.fields.CharField>), ('url', <django.db.models.fields.URLField>), ('internal_description', <django.db.models.fields.TextField>), ('image_url', <django.db.models.fields.URLField>), ('allows_distribution', <django.db.models.fields.BooleanField>), ('is_active', <django.db.models.fields.BooleanField>)]>, <CreateModel name='ObjectACL', fields=[('id', <django.db.models.fields.AutoField>), ('pluginId', <django.db.models.fields.CharField>), ('entityId', <django.db.models.fields.CharField>), ('object_id', <django.db.models.fields.PositiveIntegerField>), ('canRead', <django.db.models.fields.BooleanField>), ('canWrite', <django.db.models.fields.BooleanField>), ('canDelete', <django.db.models.fields.BooleanField>), ('isOwner', <django.db.models.fields.BooleanField>), ('effectiveDate', <django.db.models.fields.DateField>), ('expiryDate', <django.db.models.fields.DateField>), ('aclOwnershipType', <django.db.models.fields.IntegerField>), ('content_type', <django.db.models.fields.related.ForeignKey>)], options={'ordering': ['content_type', 'object_id'], 'verbose_name': 'Object ACL'}>, <CreateModel name='ParameterName', fields=[('id', <django.db.models.fields.AutoField>), ('name', <django.db.models.fields.CharField>), ('full_name', <django.db.models.fields.CharField>), ('units', <django.db.models.fields.CharField>), ('data_type', <django.db.models.fields.IntegerField>), ('immutable', <django.db.models.fields.BooleanField>), ('comparison_type', <django.db.models.fields.IntegerField>), ('is_searchable', <django.db.models.fields.BooleanField>), ('choices', <django.db.models.fields.CharField>), ('order', <django.db.models.fields.PositiveIntegerField>)], options={'ordering': ('order', 'name')}>, <CreateModel name='Schema', fields=[('id', <django.db.models.fields.AutoField>), ('namespace', <django.db.models.fields.URLField>), ('name', <django.db.models.fields.CharField>), ('type', <django.db.models.fields.IntegerField>), ('subtype', <django.db.models.fields.CharField>), ('immutable', <django.db.models.fields.BooleanField>), ('hidden', <django.db.models.fields.BooleanField>)]>, <CreateModel name='StorageBox', fields=[('id', <django.db.models.fields.AutoField>), ('django_storage_class', <django.db.models.fields.TextField>), ('max_size', <django.db.models.fields.BigIntegerField>), ('status', <django.db.models.fields.CharField>), ('name', <django.db.models.fields.CharField>), ('description', <django.db.models.fields.TextField>), ('master_box', <django.db.models.fields.related.ForeignKey>)], options={'verbose_name_plural': 'storage boxes'}>, <CreateModel name='StorageBoxAttribute', fields=[('id', <django.db.models.fields.AutoField>), ('key', <django.db.models.fields.TextField>), ('value', <django.db.models.fields.TextField>), ('storage_box', <django.db.models.fields.related.ForeignKey>)]>, <CreateModel name='StorageBoxOption', fields=[('id', <django.db.models.fields.AutoField>), ('key', <django.db.models.fields.TextField>), ('value', <django.db.models.fields.TextField>), ('storage_box', <django.db.models.fields.related.ForeignKey>), ('value_type', <django.db.models.fields.CharField>)]>, <CreateModel name='Token', fields=[('id', <django.db.models.fields.AutoField>), ('token', <django.db.models.fields.CharField>), ('expiry_date', <django.db.models.fields.DateField>), ('experiment', <django.db.models.fields.related.ForeignKey>), ('user', <django.db.models.fields.related.ForeignKey>)]>, <CreateModel name='UserAuthentication', fields=[('id', <django.db.models.fields.AutoField>), ('username', <django.db.models.fields.CharField>), ('authenticationMethod', <django.db.models.fields.CharField>)]>, <CreateModel name='UserProfile', fields=[('id', <django.db.models.fields.AutoField>), ('isDjangoAccount', <django.db.models.fields.BooleanField>), ('rapidConnectEduPersonTargetedID', <django.db.models.fields.CharField>), ('user', <django.db.models.fields.related.OneToOneField>)]>, <AddField model_name='userauthentication', name='userProfile', field=<django.db.models.fields.related.ForeignKey>>, <AddField model_name='parametername', name='schema', field=<django.db.models.fields.related.ForeignKey>>, <AddField model_name='instrumentparameterset', name='schema', field=<django.db.models.fields.related.ForeignKey>>, <AddField model_name='instrumentparameterset', name='storage_box', field=<django.db.models.fields.related.ManyToManyField>>, <AddField model_name='instrumentparameter', name='name', field=<django.db.models.fields.related.ForeignKey>>, <AddField model_name='instrumentparameter', name='parameterset', field=<django.db.models.fields.related.ForeignKey>>, <AddField model_name='freetextsearchfield', name='parameter_name', field=<django.db.models.fields.related.ForeignKey>>, <AddField model_name='experimentparameterset', name='schema', field=<django.db.models.fields.related.ForeignKey>>, <AddField model_name='experimentparameterset', name='storage_box', field=<django.db.models.fields.related.ManyToManyField>>, <AddField model_name='experimentparameter', name='name', field=<django.db.models.fields.related.ForeignKey>>, <AddField model_name='experimentparameter', name='parameterset', field=<django.db.models.fields.related.ForeignKey>>, <AddField model_name='experiment', name='license', field=<django.db.models.fields.related.ForeignKey>>, <AddField model_name='datasetparameterset', name='schema', field=<django.db.models.fields.related.ForeignKey>>, <AddField model_name='datasetparameterset', name='storage_box', field=<django.db.models.fields.related.ManyToManyField>>, <AddField model_name='datasetparameter', name='name', field=<django.db.models.fields.related.ForeignKey>>, <AddField model_name='datasetparameter', name='parameterset', field=<django.db.models.fields.related.ForeignKey>>, <AddField model_name='dataset', name='experiments', field=<django.db.models.fields.related.ManyToManyField>>, <AddField model_name='dataset', name='instrument', field=<django.db.models.fields.related.ForeignKey>>, <AddField model_name='datafileparameterset', name='schema', field=<django.db.models.fields.related.ForeignKey>>, <AddField model_name='datafileparameterset', name='storage_box', field=<django.db.models.fields.related.ManyToManyField>>, <AddField model_name='datafileparameter', name='name', field=<django.db.models.fields.related.ForeignKey>>, <AddField model_name='datafileparameter', name='parameterset', field=<django.db.models.fields.related.ForeignKey>>, <AddField model_name='datafileobject', name='storage_box', field=<django.db.models.fields.related.ForeignKey>>, <AddField model_name='datafile', name='dataset', field=<django.db.models.fields.related.ForeignKey>>, <AlterUniqueTogether name='parametername', unique_together={('schema', 'name')}>, <AlterUniqueTogether name='experimentauthor', unique_together={('experiment', 'author')}>, <AlterUniqueTogether name='datafileobject', unique_together={('datafile', 'storage_box')}>, <AlterUniqueTogether name='datafile', unique_together={('dataset', 'directory', 'filename', 'version')}>, <AlterField model_name='parametername', name='data_type', field=<django.db.models.fields.IntegerField>>, <AddField model_name='datafile', name='_size', field=<django.db.models.fields.BigIntegerField>>, <RunPython <function cast_string_to_integer>>, <RemoveField model_name='datafile', name='size'>, <RenameField model_name='datafile', old_name='_size', new_name='size'>, <AlterUniqueTogether name='instrument', unique_together={('name', 'facility')}>, <AlterField model_name='datafile', name='mimetype', field=<django.db.models.fields.CharField>>, <AlterField model_name='datafile', name='directory', field=<django.db.models.fields.CharField>>, <AlterField model_name='dataset', name='directory', field=<django.db.models.fields.CharField>>, <AlterField model_name='experimentauthor', name='url', field=<django.db.models.fields.URLField>>, <AlterField model_name='license', name='image_url', field=<django.db.models.fields.URLField>>, <AlterField model_name='license', name='name', field=<django.db.models.fields.CharField>>, <AlterField model_name='license', name='url', field=<django.db.models.fields.URLField>>, <AlterField model_name='storagebox', name='name', field=<django.db.models.fields.CharField>>]

replaces = [('tardis_portal', '0001_initial'), ('tardis_portal', '0002_auto_20150528_1128'), ('tardis_portal', '0003_auto_20150907_1315'), ('tardis_portal', '0004_storageboxoption_value_type'), ('tardis_portal', '0005_datafile_add_size_int_column'), ('tardis_portal', '0006_datafile_remove_size_string_column'), ('tardis_portal', '0007_remove_parameter_string_value_index'), ('tardis_portal', '0008_string_value_partial_index_postgres'), ('tardis_portal', '0009_auto_20160128_1119'), ('tardis_portal', '0010_auto_20160503_1443'), ('tardis_portal', '0011_auto_20160505_1643')]

tardis.tardis_portal.migrations.0001_squashed_0011_auto_20160505_1643.cast_string_to_integer(apps, schema_editor)

tardis.tardis_portal.migrations.0002_auto_20150528_1128 module

class tardis.tardis_portal.migrations.0002_auto_20150528_1128.Migration(name, app_label)

Bases: django.db.migrations.migration.Migration

dependencies = [('tardis_portal', '0001_initial')]

operations = [<AlterField model_name='userprofile', name='user', field=<django.db.models.fields.related.OneToOneField>>]

tardis.tardis_portal.migrations.0003_auto_20150907_1315 module

class tardis.tardis_portal.migrations.0003_auto_20150907_1315.Migration(name, app_label)

Bases: django.db.migrations.migration.Migration

dependencies = [('tardis_portal', '0002_auto_20150528_1128')]

operations = [<AlterField model_name='parametername', name='data_type', field=<django.db.models.fields.IntegerField>>]

tardis.tardis_portal.migrations.0004_storageboxoption_value_type module

class tardis.tardis_portal.migrations.0004_storageboxoption_value_type.Migration(name, app_label)

Bases: django.db.migrations.migration.Migration

dependencies = [('tardis_portal', '0003_auto_20150907_1315')]

operations = [<AddField model_name='storageboxoption', name='value_type', field=<django.db.models.fields.CharField>>]

tardis.tardis_portal.migrations.0005_datafile_add_size_int_column module

class tardis.tardis_portal.migrations.0005_datafile_add_size_int_column.Migration(name, app_label)

Bases: django.db.migrations.migration.Migration

dependencies = [('tardis_portal', '0004_storageboxoption_value_type')]

operations = [<AddField model_name='datafile', name='_size', field=<django.db.models.fields.BigIntegerField>>, <RunPython <function cast_string_to_integer>>]

tardis.tardis_portal.migrations.0005_datafile_add_size_int_column.cast_string_to_integer(apps, schema_editor)

tardis.tardis_portal.migrations.0006_datafile_remove_size_string_column module

class tardis.tardis_portal.migrations.0006_datafile_remove_size_string_column.Migration(name, app_label)

Bases: django.db.migrations.migration.Migration

dependencies = [('tardis_portal', '0005_datafile_add_size_int_column')]

operations = [<RemoveField model_name='datafile', name='size'>, <RenameField model_name='datafile', old_name='_size', new_name='size'>]

tardis.tardis_portal.migrations.0007_remove_parameter_string_value_index module

class tardis.tardis_portal.migrations.0007_remove_parameter_string_value_index.Migration(name, app_label)

Bases: django.db.migrations.migration.Migration

dependencies = [('tardis_portal', '0006_datafile_remove_size_string_column')]

operations = [<AlterField model_name='datafileparameter', name='string_value', field=<django.db.models.fields.TextField>>, <AlterField model_name='datasetparameter', name='string_value', field=<django.db.models.fields.TextField>>, <AlterField model_name='experimentparameter', name='string_value', field=<django.db.models.fields.TextField>>, <AlterField model_name='instrumentparameter', name='string_value', field=<django.db.models.fields.TextField>>]

tardis.tardis_portal.migrations.0008_string_value_partial_index_postgres module

class tardis.tardis_portal.migrations.0008_string_value_partial_index_postgres.Migration(name, app_label)

Bases: django.db.migrations.migration.Migration

dependencies = [('tardis_portal', '0007_remove_parameter_string_value_index')]

operations = []

tardis.tardis_portal.migrations.0009_auto_20160128_1119 module

class tardis.tardis_portal.migrations.0009_auto_20160128_1119.Migration(name, app_label)

Bases: django.db.migrations.migration.Migration

dependencies = [('tardis_portal', '0008_string_value_partial_index_postgres')]

operations = [<AlterUniqueTogether name='instrument', unique_together={('name', 'facility')}>]

tardis.tardis_portal.migrations.0010_auto_20160503_1443 module

class tardis.tardis_portal.migrations.0010_auto_20160503_1443.Migration(name, app_label)

Bases: django.db.migrations.migration.Migration

dependencies = [('tardis_portal', '0009_auto_20160128_1119')]

operations = [<AlterField model_name='datafile', name='mimetype', field=<django.db.models.fields.CharField>>]

tardis.tardis_portal.migrations.0011_auto_20160505_1643 module

class tardis.tardis_portal.migrations.0011_auto_20160505_1643.Migration(name, app_label)

Bases: django.db.migrations.migration.Migration

dependencies = [('tardis_portal', '0010_auto_20160503_1443')]

operations = [<AlterField model_name='datafile', name='directory', field=<django.db.models.fields.CharField>>, <AlterField model_name='dataset', name='directory', field=<django.db.models.fields.CharField>>, <AlterField model_name='experimentauthor', name='url', field=<django.db.models.fields.URLField>>, <AlterField model_name='license', name='image_url', field=<django.db.models.fields.URLField>>, <AlterField model_name='license', name='name', field=<django.db.models.fields.CharField>>, <AlterField model_name='license', name='url', field=<django.db.models.fields.URLField>>, <AlterField model_name='storagebox', name='name', field=<django.db.models.fields.CharField>>]

tardis.tardis_portal.migrations.0012_userauthentication_approved module

class tardis.tardis_portal.migrations.0012_userauthentication_approved.Migration(name, app_label)

Bases: django.db.migrations.migration.Migration

dependencies = [('tardis_portal', '0011_auto_20160505_1643')]

operations = [<AddField model_name='userauthentication', name='approved', field=<django.db.models.fields.BooleanField>>]

tardis.tardis_portal.migrations.0013_auto_20181002_1136 module

class tardis.tardis_portal.migrations.0013_auto_20181002_1136.Migration(name, app_label)

Bases: django.db.migrations.migration.Migration

dependencies = [('tardis_portal', '0012_userauthentication_approved')]

operations = [<AlterModelOptions name='facility', options={'ordering': ('name',), 'verbose_name_plural': 'Facilities'}>, <AlterModelOptions name='instrument', options={'ordering': ('name',), 'verbose_name_plural': 'Instruments'}>, <AlterModelOptions name='storagebox', options={'ordering': ('name',), 'verbose_name_plural': 'storage boxes'}>]

tardis.tardis_portal.migrations.0014_auto_20181002_1154 module

class tardis.tardis_portal.migrations.0014_auto_20181002_1154.Migration(name, app_label)

Bases: django.db.migrations.migration.Migration

dependencies = [('tardis_portal', '0013_auto_20181002_1136')]

operations = [<AlterField model_name='storagebox', name='max_size', field=<django.db.models.fields.BigIntegerField>>, <AlterField model_name='storagebox', name='status', field=<django.db.models.fields.CharField>>]

tardis.tardis_portal.migrations.0015_dataset_created_time module

class tardis.tardis_portal.migrations.0015_dataset_created_time.Migration(name, app_label)

Bases: django.db.migrations.migration.Migration

dependencies = [('tardis_portal', '0014_auto_20181002_1154')]

operations = [<AddField model_name='dataset', name='created_time', field=<django.db.models.fields.DateTimeField>>, <AddField model_name='dataset', name='modified_time', field=<django.db.models.fields.DateTimeField>>]

tardis.tardis_portal.migrations.0016_add_timestamps module

class tardis.tardis_portal.migrations.0016_add_timestamps.Migration(name, app_label)

Bases: django.db.migrations.migration.Migration

dependencies = [('tardis_portal', '0015_dataset_created_time')]

operations = [<AddField model_name='facility', name='created_time', field=<django.db.models.fields.DateTimeField>>, <AddField model_name='facility', name='modified_time', field=<django.db.models.fields.DateTimeField>>, <AddField model_name='instrument', name='created_time', field=<django.db.models.fields.DateTimeField>>, <AddField model_name='instrument', name='modified_time', field=<django.db.models.fields.DateTimeField>>, <AlterField model_name='facility', name='created_time', field=<django.db.models.fields.DateTimeField>>, <AlterField model_name='instrument', name='created_time', field=<django.db.models.fields.DateTimeField>>, <AlterField model_name='dataset', name='created_time', field=<django.db.models.fields.DateTimeField>>]

tardis.tardis_portal.migrations.0017_add_cc_licenses module

class tardis.tardis_portal.migrations.0017_add_cc_licenses.Migration(name, app_label)

Bases: django.db.migrations.migration.Migration

dependencies = [('tardis_portal', '0016_add_timestamps'), ('auth', '0008_alter_user_username_max_length')]

operations = [<RunPython <function forwards_func>, <function reverse_func>>]

tardis.tardis_portal.migrations.0017_add_cc_licenses.forwards_func(apps, schema_editor)

tardis.tardis_portal.migrations.0017_add_cc_licenses.load_licenses(apps, schema_editor)

tardis.tardis_portal.migrations.0017_add_cc_licenses.remove_licenses(apps, schema_editor)

tardis.tardis_portal.migrations.0017_add_cc_licenses.reverse_func(apps, schema_editor)

tardis.tardis_portal.migrations.0018_make_default_storage_box_status_online module

class tardis.tardis_portal.migrations.0018_make_default_storage_box_status_online.Migration(name, app_label)

Bases: django.db.migrations.migration.Migration

dependencies = [('tardis_portal', '0017_add_cc_licenses')]

operations = [<AlterField model_name='storagebox', name='status', field=<django.db.models.fields.CharField>>]

Module contents

tardis.tardis_portal.models package

Submodules

tardis.tardis_portal.models.access_control module

class tardis.tardis_portal.models.access_control.GroupAdmin(*args, **kwargs)

Bases: django.db.models.base.Model

GroupAdmin links the Django User and Group tables for group administrators

Attribute user:a forign key to the django.contrib.auth.models.User Attribute group:  a forign key to the django.contrib.auth.models.Group

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

group

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

group_id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

objects = <django.db.models.manager.Manager object>

user

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

user_id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

class tardis.tardis_portal.models.access_control.ObjectACL(*args, **kwargs)

Bases: django.db.models.base.Model

The ObjectACL (formerly ExperimentACL) table is the core of the Tardis Authorisation framework

Attribute pluginId:  the the name of the auth plugin being used Attribute entityId:  a foreign key to auth plugins Attribute object_type:  a foreign key to ContentType Attribute object_id:  the primary key/id of the object_type Attribute canRead:  gives the user read access Attribute canWrite:  gives the user write access Attribute canDelete:  gives the user delete permission Attribute isOwner:  the experiment owner flag. Attribute effectiveDate:  the date when access takes into effect Attribute expiryDate:  the date when access ceases Attribute aclOwnershipType:  system-owned or user-owned.

System-owned ACLs will prevent users from removing or editing ACL entries to a particular experiment they own. User-owned ACLs will allow experiment owners to remove/add/edit ACL entries to the experiments they own.

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

OWNER_OWNED = 1

SYSTEM_OWNED = 2

aclOwnershipType

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

canDelete

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

canRead

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

canWrite

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

content_object

Provide a generic many-to-one relation through the content_type and object_id fields.

This class also doubles as an accessor to the related object (similar to ForwardManyToOneDescriptor) by adding itself as a model attribute.

content_type

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

content_type_id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

effectiveDate

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

entityId

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

expiryDate

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

get_aclOwnershipType_display(*, field=<django.db.models.fields.IntegerField: aclOwnershipType>)

classmethod get_effective_query()

get_related_object()

If possible, resolve the pluginId/entityId combination to a user or group object.

get_related_object_group()

If possible, resolve the pluginId/entityId combination to a user or group object.

id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

isOwner

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

object_id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

objects = <django.db.models.manager.Manager object>

openidaclmigration_set

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

pluginId

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

class tardis.tardis_portal.models.access_control.UserAuthentication(id, userProfile, username, authenticationMethod, approved)

Bases: django.db.models.base.Model

CHOICES = ()

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

approved

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

authenticationMethod

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

getAuthMethodDescription()

id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

objects = <django.db.models.manager.Manager object>

save(*args, **kwargs)

Save the current instance. Override this in a subclass if you want to control the saving process.

The ‘force_insert’ and ‘force_update’ parameters can be used to insist that the “save” must be an SQL insert or update (or equivalent for non-SQL backends), respectively. Normally, they should not be set.

userProfile

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

userProfile_id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

username

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

class tardis.tardis_portal.models.access_control.UserProfile(*args, **kwargs)

Bases: django.db.models.base.Model

UserProfile class is an extension to the Django standard user model.

Attribute isDjangoAccount:  is the user a local DB user Attribute user:a foreign key to the django.contrib.auth.models.User

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

ext_groups

getUserAuthentications()

id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

isDjangoAccount

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

isValidPublicContact()

Checks if there’s enough information on the user for it to be used as a public contact.

Note: Last name can’t be required, because people don’t necessarilly have a last (or family) name.

objects = <django.db.models.manager.Manager object>

rapidConnectEduPersonTargetedID

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

user

Accessor to the related object on the forward side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Restaurant.place is a ForwardOneToOneDescriptor instance.

user_id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

userauthentication_set

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

tardis.tardis_portal.models.access_control.create_user_api_key(sender, **kwargs)

Auto-create ApiKey objects using Tastypie’s create_api_key

tardis.tardis_portal.models.access_control.create_user_profile(sender, instance, created, **kwargs)

tardis.tardis_portal.models.datafile module

class tardis.tardis_portal.models.datafile.DataFile(*args, **kwargs)

Bases: django.db.models.base.Model

A DataFile is a record of a file which includes its filename, its size in bytes, its relative directory, and various other meta-data. Each DataFile belongs to a Dataset which usually represents the files from one folder on an instrument PC.

The physical copy (or copies) of a file are described by distinct DataFileObject records.

Attribute dataset:  The foreign key to the tardis.tardis_portal.models.Dataset the file belongs to. Attribute filename:  The name of the file, excluding the path. Attribute size:The size of the file. Attribute created_time:  Should be populated with the file’s creation time from the instrument PC. Attribute modification_time:  Should be populated with the file’s last modification time from the instrument PC. Attribute mimetype:  For example ‘application/pdf’ Attribute md5sum:  Digest of length 32, containing only hexadecimal digits Attribute sha512sum:  Digest of length 128, containing only hexadecimal digits

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

cache_file()

created_time

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

datafileparameterset_set

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

dataset

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

dataset_id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

deleted

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

deleted_time

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

directory

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

file_object

file_objects

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

filename

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

getParameterSets()

Return datafile parametersets associated with this datafile.

get_absolute_filepath()

get_as_temporary_file(directory=None)

Returns a traditional file-system-based file object that is a copy of the original data. The file is deleted when the context is destroyed.

Parameters:directory (basestring) – the directory in which to create the temp file Returns:the temporary file object Return type:NamedTemporaryFile

get_default_storage_box()

try to guess appropriate box from dataset or use global default

get_download_url()

get_file(verified_only=True)

Returns the file as a readable file-like object from the best avaiable storage box.

If verified_only=False, the return of files without a verified checksum is allowed, otherwise None is returned for unverified files.

Parameters:verified_only (bool) – if False return files without verified checksums Returns:Python file object Return type:Python File object

get_image_data()

get_mimetype()

get_preferred_dfo(verified_only=True)

get_receiving_storage_box()

get_size()

get_view_url()

has_image()

id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

is_image()

returns True if it’s an image and not an x-icon and not an img the image/img mimetype is made up though and may need revisiting if there is an official img mimetype that does not refer to diffraction images

is_local()

is_online

return False if a file is on tape. At this stage it checks it returns true for no file objects, because those files are offline through other checks

is_public()

md5sum

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

mimetype

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

modification_time

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

objects = <django.db.models.manager.Manager object>

save(*args, **kwargs)

Save the current instance. Override this in a subclass if you want to control the saving process.

The ‘force_insert’ and ‘force_update’ parameters can be used to insist that the “save” must be an SQL insert or update (or equivalent for non-SQL backends), respectively. Normally, they should not be set.

sha512sum

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

size

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

status

returns information about the status of the file. States are defined in StorageBox

classmethod sum_sizes(datafiles)

Takes a query set of datafiles and returns their total size.

update_mimetype(mimetype=None, force=False, save=True)

verified

Return True if at least one DataFileObject is verified

verify(reverify=False)

version

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

class tardis.tardis_portal.models.datafile.DataFileObject(*args, **kwargs)

Bases: django.db.models.base.Model

The physical copy (or copies) of a DataFile are described by distinct DataFileObject records.

Attribute datafile:  The DataFile record which this DataFileObject is storing a copy of. Attribute storage_box:  The StorageBox containing this copy of the file. The StorageBox could represent a directory on a mounted filesystem, or a bucket in an Object Store. Attribute uri:The relative path of the file location within the the StorageBox, e.g. dataset1-12345/file1.txt for a copy of a DataFile with filename file1.txt which belongs to a Dataset with a description of dataset1 and an ID of 12345.

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

apply_filters()

cache_file()

calculate_checksums(compute_md5=True, compute_sha512=False)

Calculates checksums for a DataFileObject instance

Parameters:

• compute_md5 (bool) – whether to compute md5 default=True
• compute_sha512 (bool) – whether to compute sha512, default=True

Returns:

the checksums as {‘md5sum’: result, ‘sha512sum’: result}

Return type:

dict

copy_file(dest_box=None, verify=True)

copies verified file to new storage box checks for existing copy triggers async verification if not disabled :param StorageBox dest_box: StorageBox instance :param bool verify: :returns: DataFileObject of copy :rtype: DataFileObject

create_set_uri(force=False, save=False)

sets the uri as well as building it :param bool force: :param book save: :return: :rtype: basestring

created_time

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

datafile

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

datafile_id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

delete_data()

file_object

A set of accessor functions that convert the file information to a standard Python file object for reading and copy the contents of an existing file_object into the storage backend.

Returns:a file object Return type:Python File object

get_full_path()

get_next_by_created_time(*, field=<django.db.models.fields.DateTimeField: created_time>, is_next=True, **kwargs)

get_previous_by_created_time(*, field=<django.db.models.fields.DateTimeField: created_time>, is_next=False, **kwargs)

id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

last_verified_time

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

modified_time

move_file(dest_box=None)

moves a file copies first, then synchronously verifies deletes file if copy is true copy and has been verified

Parameters:dest_box (StorageBox) – StorageBox instance Returns:moved file dfo Return type:DataFileObject

objects = <django.db.models.manager.Manager object>

priority

Default priority for tasks which take this DFO as an argument

save(*args, **kwargs)

Save the current instance. Override this in a subclass if you want to control the saving process.

The ‘force_insert’ and ‘force_update’ parameters can be used to insist that the “save” must be an SQL insert or update (or equivalent for non-SQL backends), respectively. Normally, they should not be set.

storage_box

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

storage_box_id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

storage_type

Returns:storage_box type Return type:StorageBox type constant

uri

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

verified

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

verify(add_checksums=True, add_size=True)

tardis.tardis_portal.models.datafile.compute_checksums(file_object, compute_md5=True, compute_sha512=False, close_file=True)

Computes checksums for a python file object

Parameters:

• file_object (object) – Python File object
• compute_md5 (bool) – whether to compute md5 default=True
• compute_sha512 (bool) – whether to compute sha512, default=True
• close_file (bool) – whether to close the file_object, default=True

Returns:

the checksums as {‘md5sum’: result, ‘sha512sum’: result}

Return type:

dict

tardis.tardis_portal.models.datafile.delete_dfo(sender, instance, **kwargs)

Deletes the actual file / object, before deleting the database record

tardis.tardis_portal.models.dataset module

class tardis.tardis_portal.models.dataset.Dataset(*args, **kwargs)

Bases: django.db.models.base.Model

A dataset represents a collection files usually associated with a folder on an instrument PC. Each file within the dataset is represented by a tardis.tardis_portal.models.DataFile record. A dataset can appear in one or more Experiment records. Access controls are configured at the Experiment level by creating ObjectACL records. Each dataset can be associated with an Instrument record, but it is possible to create a dataset without specifying an instrument.

Attribute experiment:  A foreign key to the one ore more Experiment records which contain this dataset Attribute instrument:  The foreign key to the instrument that generated this data Attribute description:  Description of this dataset, which usually corresponds to the folder name on the instrument PC Attribute immutable:  Whether this dataset is read-only

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

created_time

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

datafile_set

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

datasetparameterset_set

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

description

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

directory

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

experiments

Accessor to the related objects manager on the forward and reverse sides of a many-to-many relation.

In the example:

class Pizza(Model):
    toppings = ManyToManyField(Topping, related_name='pizzas')

Pizza.toppings and Topping.pizzas are ManyToManyDescriptor instances.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

getParameterSets()

Return the dataset parametersets associated with this experiment.

get_absolute_url()

Return the absolute url to the current Dataset

get_all_storage_boxes_used()

get_datafiles()

get_dir_nodes(dir_tuples)

Return child node’s subdirectories in format required for tree view

Given a list of (‘subdir’, ‘path/to/subdir’) tuples for a dataset directory node, return a list of {‘name’: ‘subdir’, ‘children’: []} dictionaries required for the tree view.

Like the get_dir_tuples method, the get_dir_nodes method only lists files and directories immediately within the supplied basedir, so any subdirectories will have an empty children array.

Continuing the example from the _dirs property method:

test files/subdir1/ test files/subdir2/ test files/subdir3/ test files/subdir3/subdir4/

List directories in the dataset’s top level directory: >>> dir_tuples = ds.get_dir_tuples(“”) >>> ds.get_dir_nodes(dir_tuples) [

{

‘name’: ‘test files’, ‘path’: ‘’, ‘children’: []

}

]

List directories within the dataset’s “test files” directory: >>> dir_tuples = ds.get_dir_tuples(“test files”) >>> ds.get_dir_nodes(dir_tuples) [

{

‘name’: ‘subdir1’, ‘path’: ‘test files/subdir1’, ‘children’: []

}, {

‘name’: ‘subdir2’, ‘path’: ‘test files/subdir2’, ‘children’: []

}, {

‘name’: ‘subdir3’, ‘path’: ‘test files/subdir3’, ‘children’: []

},

]

Request directories within a non-existent directory: >>> dir_tuples = ds.get_dir_tuples(“test file”) >>> ds.get_dir_nodes(dir_tuples) []

List directories within the dataset’s “test files/subdir3” directory: >>> dir_tuples = ds.get_dir_tuples(“test files3/subdir3”) >>> ds.get_dir_nodes(dir_tuples) [

‘name’: ‘subdir4’, ‘path’: ‘test files/subdir3/subdir4’, ‘children’: []

]

get_dir_tuples(basedir='')

List the directories immediately inside basedir.

If basedir is empty (the default), list directories with no separator, e.g. “subdir1”

If basedir is a string without a separator (e.g. “subdir1”), look for directory paths with one separator e.g. “subdir1/subdir2” and include a “..” for navigating back to the dataset’s top-level directory.

Continuing the example from the _dirs property method:

test files/subdir1/ test files/subdir2/ test files/subdir3/ test files/subdir3/subdir4/

List directories in the dataset’s top level directory: >>> ds.get_dir_tuples(“”) [(‘test files’)]

List directories within the dataset’s “test files” directory: >>> ds.get_dir_tuples(“test files”) [(‘..’, ‘test files’), (‘subdir1’, ‘test /filessubdir1’),

(‘subdir2’, ‘test files/subdir2’), (‘subdir3’, ‘test files/subdir3’)]

Request directories within a non-existent directory: >>> ds.get_dir_tuples(“test file”) []

List directories within the dataset’s “test files/subdir3” directory: >>> ds.get_dir_tuples(“test files/subdir3”) [(‘..’, ‘test files/subdir3’), (‘subdir4’, ‘test files/subdir3/subdir4’)]

List directories within the dataset’s “test files/subdir3/subdir4” directory: >>> ds.get_dir_tuples(“test files/subdir3/subdir4”) [(‘..’, ‘test files/subdir3/subdir4’)]

get_download_urls()

get_edit_url()

Return the absolute url to the edit view of the current Dataset

get_first_experiment()

get_images()

get_path()

get_size()

get_thumbnail_url()

id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

image

immutable

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

instrument

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

instrument_id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

is_online

modified_time

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

objects = <tardis.tardis_portal.managers.OracleSafeManager object>

save(force_insert=False, force_update=False, using=None, update_fields=None)

Save the current instance. Override this in a subclass if you want to control the saving process.

The ‘force_insert’ and ‘force_update’ parameters can be used to insist that the “save” must be an SQL insert or update (or equivalent for non-SQL backends), respectively. Normally, they should not be set.

tardis.tardis_portal.models.experiment module

class tardis.tardis_portal.models.experiment.Experiment(*args, **kwargs)

Bases: django.db.models.base.Model

An Experiment is a collection of Dataset records. A Dataset record can appear in multiple Experiment records. Access controls are configured at the Experiment level by creating ObjectACL records.

Attribute url:An optional URL associated with the data collection Attribute approved:  An optional field indicating whether the collection is approved Attribute title:  The title of the experiment. Attribute description:  The description of the experiment. Attribute institution_name:  The name of the institution who created the experiment. Attribute start_time:  Undocumented Attribute end_time:  Undocumented Attribute created_time:  Undocumented Attribute handle:  Undocumented Attribute public:  Whether the experiment is publicly accessible Attribute objects:  Default model manager Attribute safe:ACL aware model manager

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

PUBLICATION_DETAILS_SCHEMA = 'http://www.tardis.edu.au/schemas/publication/details/'

PUBLICATION_DRAFT_SCHEMA = 'http://www.tardis.edu.au/schemas/publication/draft/'

PUBLICATION_SCHEMA_ROOT = 'http://www.tardis.edu.au/schemas/publication/'

PUBLIC_ACCESS_CHOICES = ((1, 'No public access (hidden)'), (25, 'Ready to be released pending embargo expiry'), (50, 'Public Metadata only (no data file access)'), (100, 'Public'))

PUBLIC_ACCESS_EMBARGO = 25

PUBLIC_ACCESS_FULL = 100

PUBLIC_ACCESS_METADATA = 50

PUBLIC_ACCESS_NONE = 1

approved

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

created_by

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

created_by_id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

created_time

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

datasets

Accessor to the related objects manager on the forward and reverse sides of a many-to-many relation.

In the example:

class Pizza(Model):
    toppings = ManyToManyField(Topping, related_name='pizzas')

Pizza.toppings and Topping.pizzas are ManyToManyDescriptor instances.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

description

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

end_time

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

experimentauthor_set

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

experimentparameterset_set

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

getParameterSets()

Return the experiment parametersets associated with this experiment.

get_absolute_url()

Return the absolute url to the current Experiment

get_create_token_url()

Return the absolute url to the create token view of the current Experiment

get_ct()

get_datafiles()

get_download_urls()

get_edit_url()

Return the absolute url to the edit view of the current Experiment

get_groups()

get_images()

get_next_by_created_time(*, field=<django.db.models.fields.DateTimeField: created_time>, is_next=True, **kwargs)

get_next_by_update_time(*, field=<django.db.models.fields.DateTimeField: update_time>, is_next=True, **kwargs)

get_or_create_directory()

get_owners()

get_previous_by_created_time(*, field=<django.db.models.fields.DateTimeField: created_time>, is_next=False, **kwargs)

get_previous_by_update_time(*, field=<django.db.models.fields.DateTimeField: update_time>, is_next=False, **kwargs)

get_public_access_display(*, field=<django.db.models.fields.PositiveSmallIntegerField: public_access>)

get_size()

handle

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

institution_name

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

is_publication()

is_publication_draft()

license

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

license_id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

locked

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

objectacls

Accessor to the related objects manager on the one-to-many relation created by GenericRelation.

In the example:

class Post(Model):
    comments = GenericRelation(Comment)

post.comments is a ReverseGenericManyToOneDescriptor instance.

objects = <tardis.tardis_portal.managers.OracleSafeManager object>

public_access

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

classmethod public_access_implies_distribution(public_access_level)

Determines if a level of public access implies that distribution should be allowed, or alternately if it should not be allowed. Used to prevent free-distribution licences for essentially private data, and overly-restrictive licences for public data.

public_download_allowed()

instance method version of ‘public_access_implies_distribution’

safe = <tardis.tardis_portal.managers.ExperimentManager object>

save(*args, **kwargs)

Save the current instance. Override this in a subclass if you want to control the saving process.

The ‘force_insert’ and ‘force_update’ parameters can be used to insist that the “save” must be an SQL insert or update (or equivalent for non-SQL backends), respectively. Normally, they should not be set.

start_time

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

title

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

token_set

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

update_time

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

url

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

class tardis.tardis_portal.models.experiment.ExperimentAuthor(id, experiment, author, institution, email, order, url)

Bases: django.db.models.base.Model

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

author

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

email

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

experiment

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

experiment_id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

institution

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

objects = <django.db.models.manager.Manager object>

order

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

save(*args, **kwargs)

Save the current instance. Override this in a subclass if you want to control the saving process.

The ‘force_insert’ and ‘force_update’ parameters can be used to insist that the “save” must be an SQL insert or update (or equivalent for non-SQL backends), respectively. Normally, they should not be set.

url

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

tardis.tardis_portal.models.facility module

class tardis.tardis_portal.models.facility.Facility(*args, **kwargs)

Bases: django.db.models.base.Model

Represents a facility that produces data.

Each Instrument record must belong to exactly one facility. Many Instrument records can be associated with the same facility.

Attribute name:The name of the facility, e.g. “Test Facility” Attribute manager_group:  The group of users who can access the Facility Overview for this facility.

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

created_time

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

instrument_set

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

manager_group

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

manager_group_id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

modified_time

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

name

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

objects = <django.db.models.manager.Manager object>

save(*args, **kwargs)

Save the current instance. Override this in a subclass if you want to control the saving process.

The ‘force_insert’ and ‘force_update’ parameters can be used to insist that the “save” must be an SQL insert or update (or equivalent for non-SQL backends), respectively. Normally, they should not be set.

tardis.tardis_portal.models.facility.facilities_managed_by(user)

Returns a list of facilities managed by a user

tardis.tardis_portal.models.facility.is_facility_manager(user)

Returns true if the user manages one or more facilities

tardis.tardis_portal.models.hooks module

tardis.tardis_portal.models.hooks.post_save_experiment(sender, **kwargs)

tardis.tardis_portal.models.hooks.post_save_experiment_parameter(sender, **kwargs)

tardis.tardis_portal.models.hooks.post_save_experimentauthor(sender, **kwargs)

tardis.tardis_portal.models.hooks.publish_public_expt_rifcs(experiment)

tardis.tardis_portal.models.instrument module

class tardis.tardis_portal.models.instrument.Instrument(*args, **kwargs)

Bases: django.db.models.base.Model

Represents an instrument belonging to a facility that produces data

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

created_time

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

dataset_set

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

facility

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

facility_id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

getParameterSets()

Return the instrument parametersets associated with this instrument.

id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

instrumentparameterset_set

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

modified_time

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

name

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

objects = <django.db.models.manager.Manager object>

save(*args, **kwargs)

Save the current instance. Override this in a subclass if you want to control the saving process.

The ‘force_insert’ and ‘force_update’ parameters can be used to insist that the “save” must be an SQL insert or update (or equivalent for non-SQL backends), respectively. Normally, they should not be set.

tardis.tardis_portal.models.jti module

class tardis.tardis_portal.models.jti.JTI(id, jti, created_time)

Bases: django.db.models.base.Model

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

created_time

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

get_next_by_created_time(*, field=<django.db.models.fields.DateTimeField: created_time>, is_next=True, **kwargs)

get_previous_by_created_time(*, field=<django.db.models.fields.DateTimeField: created_time>, is_next=False, **kwargs)

id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

jti

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

objects = <django.db.models.manager.Manager object>

tardis.tardis_portal.models.license module

class tardis.tardis_portal.models.license.License(*args, **kwargs)

Bases: django.db.models.base.Model

Represents a licence for experiment content.

Instances should provide enough detail for both researchers to select the licence, and for the users of their data to divine correct usage of experiment content.

(Non-US developers: We’re using US spelling in the code.)

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

allows_distribution

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

experiment_set

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

classmethod get_none_option_license()

classmethod get_suitable_licenses(public_access_method=None)

id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

image_url

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

internal_description

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

is_active

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

name

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

objects = <django.db.models.manager.Manager object>

url

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

tardis.tardis_portal.models.parameters module

class tardis.tardis_portal.models.parameters.DatafileParameter(id, name, string_value, numerical_value, datetime_value, link_id, link_ct, parameterset)

Bases: tardis.tardis_portal.models.parameters.Parameter

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

link_ct

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

link_gfk

Provide a generic many-to-one relation through the content_type and object_id fields.

This class also doubles as an accessor to the related object (similar to ForwardManyToOneDescriptor) by adding itself as a model attribute.

name

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

parameter_type = 'Datafile'

parameterset

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

parameterset_id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

class tardis.tardis_portal.models.parameters.DatafileParameterSet(id, schema, datafile)

Bases: tardis.tardis_portal.models.parameters.ParameterSet

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

datafile

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

datafile_id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

datafileparameter_set

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

objects = <django.db.models.manager.Manager object>

parameter_class

alias of DatafileParameter

schema

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

storage_box

Accessor to the related objects manager on the forward and reverse sides of a many-to-many relation.

In the example:

class Pizza(Model):
    toppings = ManyToManyField(Topping, related_name='pizzas')

Pizza.toppings and Topping.pizzas are ManyToManyDescriptor instances.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

class tardis.tardis_portal.models.parameters.DatasetParameter(id, name, string_value, numerical_value, datetime_value, link_id, link_ct, parameterset)

Bases: tardis.tardis_portal.models.parameters.Parameter

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

link_ct

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

link_gfk

Provide a generic many-to-one relation through the content_type and object_id fields.

This class also doubles as an accessor to the related object (similar to ForwardManyToOneDescriptor) by adding itself as a model attribute.

name

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

parameter_type = 'Dataset'

parameterset

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

parameterset_id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

class tardis.tardis_portal.models.parameters.DatasetParameterSet(id, schema, dataset)

Bases: tardis.tardis_portal.models.parameters.ParameterSet

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

dataset

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

dataset_id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

datasetparameter_set

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

objects = <django.db.models.manager.Manager object>

parameter_class

alias of DatasetParameter

schema

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

storage_box

Accessor to the related objects manager on the forward and reverse sides of a many-to-many relation.

In the example:

class Pizza(Model):
    toppings = ManyToManyField(Topping, related_name='pizzas')

Pizza.toppings and Topping.pizzas are ManyToManyDescriptor instances.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

class tardis.tardis_portal.models.parameters.ExperimentParameter(id, name, string_value, numerical_value, datetime_value, link_id, link_ct, parameterset)

Bases: tardis.tardis_portal.models.parameters.Parameter

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

link_ct

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

link_gfk

Provide a generic many-to-one relation through the content_type and object_id fields.

This class also doubles as an accessor to the related object (similar to ForwardManyToOneDescriptor) by adding itself as a model attribute.

name

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

parameter_type = 'Experiment'

parameterset

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

parameterset_id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

save(*args, **kwargs)

Save the current instance. Override this in a subclass if you want to control the saving process.

The ‘force_insert’ and ‘force_update’ parameters can be used to insist that the “save” must be an SQL insert or update (or equivalent for non-SQL backends), respectively. Normally, they should not be set.

class tardis.tardis_portal.models.parameters.ExperimentParameterSet(id, schema, experiment)

Bases: tardis.tardis_portal.models.parameters.ParameterSet

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

experiment

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

experiment_id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

experimentparameter_set

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

objects = <django.db.models.manager.Manager object>

parameter_class

alias of ExperimentParameter

schema

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

storage_box

Accessor to the related objects manager on the forward and reverse sides of a many-to-many relation.

In the example:

class Pizza(Model):
    toppings = ManyToManyField(Topping, related_name='pizzas')

Pizza.toppings and Topping.pizzas are ManyToManyDescriptor instances.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

class tardis.tardis_portal.models.parameters.FreeTextSearchField(id, parameter_name)

Bases: django.db.models.base.Model

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

objects = <django.db.models.manager.Manager object>

parameter_name

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

parameter_name_id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

class tardis.tardis_portal.models.parameters.InstrumentParameter(id, name, string_value, numerical_value, datetime_value, link_id, link_ct, parameterset)

Bases: tardis.tardis_portal.models.parameters.Parameter

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

link_ct

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

link_gfk

Provide a generic many-to-one relation through the content_type and object_id fields.

This class also doubles as an accessor to the related object (similar to ForwardManyToOneDescriptor) by adding itself as a model attribute.

name

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

parameter_type = 'Instrument'

parameterset

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

parameterset_id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

class tardis.tardis_portal.models.parameters.InstrumentParameterSet(id, schema, instrument)

Bases: tardis.tardis_portal.models.parameters.ParameterSet

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

instrument

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

instrument_id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

instrumentparameter_set

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

objects = <django.db.models.manager.Manager object>

parameter_class

alias of InstrumentParameter

schema

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

storage_box

Accessor to the related objects manager on the forward and reverse sides of a many-to-many relation.

In the example:

class Pizza(Model):
    toppings = ManyToManyField(Topping, related_name='pizzas')

Pizza.toppings and Topping.pizzas are ManyToManyDescriptor instances.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

class tardis.tardis_portal.models.parameters.Parameter(*args, **kwargs)

Bases: django.db.models.base.Model

class Meta

Bases: object

abstract = False

app_label = 'tardis_portal'

ordering = ['name']

datetime_value

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

get()

link_ct

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

link_ct_id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

link_gfk

Provide a generic many-to-one relation through the content_type and object_id fields.

This class also doubles as an accessor to the related object (similar to ForwardManyToOneDescriptor) by adding itself as a model attribute.

link_id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

link_url

name

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

name_id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

numerical_value

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

objects

parameter_type = 'Abstract'

set_value(value)

Sets the parameter value, converting into the appropriate data type. Deals with date/time strings that are timezone naive or aware, based on the USE_TZ setting.

Parameters:value (basestring) – a string (or string-like) repr of the value Raises:SuspiciousOperation –

string_value

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

class tardis.tardis_portal.models.parameters.ParameterName(id, schema, name, full_name, units, data_type, immutable, comparison_type, is_searchable, choices, order)

Bases: django.db.models.base.Model

CONTAINS_COMPARISON = 8

DATETIME = 6

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

EXACT_VALUE_COMPARISON = 1

FILENAME = 5

GREATER_THAN_COMPARISON = 4

GREATER_THAN_EQUAL_COMPARISON = 5

JSON = 8

LESS_THAN_COMPARISON = 6

LESS_THAN_EQUAL_COMPARISON = 7

LINK = 4

LONGSTRING = 7

exception MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

NOT_EQUAL_COMPARISON = 2

NUMERIC = 1

RANGE_COMPARISON = 3

STRING = 2

URL = 3

choices

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

comparison_type

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

data_type

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

datafileparameter_set

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

datasetparameter_set

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

experimentparameter_set

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

freetextsearchfield_set

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

full_name

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

getUniqueShortName()

get_comparison_type_display(*, field=<django.db.models.fields.IntegerField: comparison_type>)

get_data_type_display(*, field=<django.db.models.fields.IntegerField: data_type>)

id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

immutable

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

instrumentparameter_set

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

isDateTime()

isFilename()

isLink()

isLongString()

isNumeric()

isString()

isURL()

is_json()

is_searchable

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

name

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

natural_key()

objects = <tardis.tardis_portal.managers.ParameterNameManager object>

order

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

schema

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

schema_id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

units

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

class tardis.tardis_portal.models.parameters.ParameterSet(*args, **kwargs)

Bases: django.db.models.base.Model, tardis.tardis_portal.models.parameters.ParameterSetManagerMixin

class Meta

Bases: object

abstract = False

app_label = 'tardis_portal'

ordering = ['id']

parameter_class = None

save(*args, **kwargs)

Save the current instance. Override this in a subclass if you want to control the saving process.

The ‘force_insert’ and ‘force_update’ parameters can be used to insist that the “save” must be an SQL insert or update (or equivalent for non-SQL backends), respectively. Normally, they should not be set.

schema

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

schema_id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

storage_box

Accessor to the related objects manager on the forward and reverse sides of a many-to-many relation.

In the example:

class Pizza(Model):
    toppings = ManyToManyField(Topping, related_name='pizzas')

Pizza.toppings and Topping.pizzas are ManyToManyDescriptor instances.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

class tardis.tardis_portal.models.parameters.ParameterSetManagerMixin(parameterset=None, parentObject=None, schema=None)

Bases: tardis.tardis_portal.ParameterSetManager.ParameterSetManager

for clarity’s sake and for future extension this class makes ParameterSetManager local to this file. At the moment its only function is increasing the line count

class tardis.tardis_portal.models.parameters.Schema(id, namespace, name, type, subtype, immutable, hidden)

Bases: django.db.models.base.Model

DATAFILE = 3

DATASET = 2

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

EXPERIMENT = 1

INSTRUMENT = 5

exception MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

NONE = 4

exception UnsupportedType(msg)

Bases: Exception

datafileparameterset_set

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

datasetparameterset_set

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

experimentparameterset_set

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

get_type_display(*, field=<django.db.models.fields.IntegerField: type>)

hidden

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

immutable

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

instrumentparameterset_set

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

name

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

namespace

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

natural_key()

objects = <tardis.tardis_portal.managers.SchemaManager object>

parametername_set

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

subtype

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

type

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

tardis.tardis_portal.models.storage module

class tardis.tardis_portal.models.storage.StorageBox(*args, **kwargs)

Bases: django.db.models.base.Model

table that holds storage boxes of any type. to extend to new types, add fields if necessary

Attribute max_size:  max size in bytes

BUNDLE = 6

CACHE = 3

DISK = 1

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

TAPE = 2

TEMPORARY = 4

TYPES = {'bundle': 6, 'cache': 3, 'disk': 1, 'receiving': 4, 'tape': 2}

TYPE_UNKNOWN = 5

attributes

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

autocache

Whether to automatically copy data into faster storage

Returns:True if data should be automatically cached Return type:bool

cache_box

Get cache box if set up

child_boxes

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

copy_files(dest_box=None)

copy_to_master()

classmethod create_local_box(location=None)

datafileparametersets

Accessor to the related objects manager on the forward and reverse sides of a many-to-many relation.

In the example:

class Pizza(Model):
    toppings = ManyToManyField(Topping, related_name='pizzas')

Pizza.toppings and Topping.pizzas are ManyToManyDescriptor instances.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

datasetparametersets

Accessor to the related objects manager on the forward and reverse sides of a many-to-many relation.

In the example:

class Pizza(Model):
    toppings = ManyToManyField(Topping, related_name='pizzas')

Pizza.toppings and Topping.pizzas are ManyToManyDescriptor instances.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

description

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

django_storage_class

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

experimentparametersets

Accessor to the related objects manager on the forward and reverse sides of a many-to-many relation.

In the example:

class Pizza(Model):
    toppings = ManyToManyField(Topping, related_name='pizzas')

Pizza.toppings and Topping.pizzas are ManyToManyDescriptor instances.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

file_objects

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

classmethod get_default_storage(location=None, user=None)

gets default storage box or get local storage box with given base location or create one if it doesn’t exist.

policies: Have a StorageBoxAttribute: key=’default’, value=True find a storage box where location is DEFAULT_STORAGE_BASE_DIR create a default storage box at DEFAULT_STORAGE_BASE_DIR lowest id storage box is default no storage box defined, use hard coded default for now TODO: consider removing this

Would be nice: get largest free space one, test for authorisation

get_initialised_storage_instance()

get_options_as_dict()

id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

instrumentparametersets

Accessor to the related objects manager on the forward and reverse sides of a many-to-many relation.

In the example:

class Pizza(Model):
    toppings = ManyToManyField(Topping, related_name='pizzas')

Pizza.toppings and Topping.pizzas are ManyToManyDescriptor instances.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

master_box

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

master_box_id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

max_size

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

move_files(dest_box=None)

move_to_master()

name

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

objects = <django.db.models.manager.Manager object>

offline_types = [2]

online_types = [3, 1, 4, 6]

options

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

priority

Default priority for tasks which take this box as an argument

status

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

storage_type

type_order = [3, 6, 1, 2, 4, 5]

class tardis.tardis_portal.models.storage.StorageBoxAttribute(*args, **kwargs)

Bases: django.db.models.base.Model

Can hold attributes/metadata about different storage locations.

Attribute key:The key used to look up the attribute (e.g. “type”). Attribute value:  The value of the attribute e.g. “cache”.

The “type” key has three values support by the core MyTardis code: “permanent”, “receiving” and “cache”.

Adding an attribute with key “type” and value “permanent” preserves the default behaviour of a storage box, i.e. it is equivalent to not adding the attribute.

Adding an attribute with key “type” and value “receiving” means that the storage box will be treated as a staging area which receives files intended to be transfered to a permanent storage box. If a storage box has the “type: receiving” attribute, it must link to a permanent storage box (via its master_box foreign key).

Adding an attribute with key “type” and value “cache” means that the storage box will be used to copy data from slow-access storage to fast-access storage. If a storage box has the “type: cache” attribute, it must link to a permanent storage box (via its master_box foreign key).

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

key

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

objects = <django.db.models.manager.Manager object>

storage_box

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

storage_box_id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

value

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

class tardis.tardis_portal.models.storage.StorageBoxOption(*args, **kwargs)

Bases: django.db.models.base.Model

holds the options passed to the storage class defined in StorageBox. key->value store with support for typed values through pickling when value_type is set to ‘pickle’

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

PICKLE = 'pickle'

STRING = 'string'

TYPE_CHOICES = (('string', 'String value'), ('pickle', 'Pickled value'))

get_value_type_display(*, field=<django.db.models.fields.CharField: value_type>)

id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

key

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

objects = <django.db.models.manager.Manager object>

storage_box

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

storage_box_id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

unpickled_value

value

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

value_type

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

tardis.tardis_portal.models.token module

class tardis.tardis_portal.models.token.Token(id, token, experiment, expiry_date, user)

Bases: django.db.models.base.Model

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

experiment

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

experiment_id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

expiry_date

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

get_next_by_expiry_date(*, field=<django.db.models.fields.DateField: expiry_date>, is_next=True, **kwargs)

get_previous_by_expiry_date(*, field=<django.db.models.fields.DateField: expiry_date>, is_next=False, **kwargs)

get_session_expiry()

A token login should expire at the earlier of a) tomorrow at 4am b) the (end of) the token’s expiry date

It is the responsibility of token_auth to set the session expiry

id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

is_expired()

objects = <tardis.tardis_portal.managers.OracleSafeManager object>

save_with_random_token()

token

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

user

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Child.parent is a ForwardManyToOneDescriptor instance.

user_id

A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

Module contents

models/__init__.py

tardis.tardis_portal.publish package

Subpackages

tardis.tardis_portal.publish.provider package

Submodules

tardis.tardis_portal.publish.provider.rifcsprovider module

class tardis.tardis_portal.publish.provider.rifcsprovider.RifCsProvider

Bases: object

can_publish(experiment)

get_rifcs_context(experiment)

get_template(experiment)

is_schema_valid(experiment)

Module contents

Submodules

tardis.tardis_portal.publish.publishservice module

class tardis.tardis_portal.publish.publishservice.PublishService(providers, experiment)

Bases: object

get_context()

get_template()

manage_rifcs(oaipath)

Module contents

tardis.tardis_portal.storage package

Submodules

tardis.tardis_portal.storage.file_system module

class tardis.tardis_portal.storage.file_system.MyTardisLocalFileSystemStorage(location=None, base_url=None)

Bases: django.core.files.storage.FileSystemStorage

Simply changes the FileSystemStorage default store location to the MyTardis file store location. Makes it easier to migrate 2.5 installations.

Module contents

class tardis.tardis_portal.storage.DummyStorage

Bases: django.core.files.storage.Storage

Does nothing except serve as a place holder for Storage classes not implemented yet

tardis.tardis_portal.templatetags package

Submodules

tardis.tardis_portal.templatetags.approved_user_tags module

tardis.tardis_portal.templatetags.approved_user_tags.check_if_user_not_approved(request)

Custom template filter to identify whether a user account is approved.

tardis.tardis_portal.templatetags.approved_user_tags.get_matching_authmethod(backend)

tardis.tardis_portal.templatetags.basiccomparisonfilters module

tardis.tardis_portal.templatetags.basiccomparisonfilters.gt(value, arg)

Returns a boolean of whether the value is greater than the argument.

tardis.tardis_portal.templatetags.basiccomparisonfilters.gte(value, arg)

Returns a boolean of whether the value is greater than or equal to the argument.

tardis.tardis_portal.templatetags.basiccomparisonfilters.length_gt(value, arg)

Returns a boolean of whether the value’s length is greater than the argument.

tardis.tardis_portal.templatetags.basiccomparisonfilters.length_gte(value, arg)

Returns a boolean of whether the value’s length is greater than or equal to the argument.

tardis.tardis_portal.templatetags.basiccomparisonfilters.length_lt(value, arg)

Returns a boolean of whether the value’s length is less than the argument.

tardis.tardis_portal.templatetags.basiccomparisonfilters.length_lte(value, arg)

Returns a boolean of whether the value’s length is less than or equal to the argument.

tardis.tardis_portal.templatetags.basiccomparisonfilters.lt(value, arg)

Returns a boolean of whether the value is less than the argument.

tardis.tardis_portal.templatetags.basiccomparisonfilters.lte(value, arg)

Returns a boolean of whether the value is less than or equal to the argument.

tardis.tardis_portal.templatetags.bleach_tag module

tardis.tardis_portal.templatetags.bleach_tag.bleach_value(value)

tardis.tardis_portal.templatetags.capture module

class tardis.tardis_portal.templatetags.capture.CaptureNode(nodelist, varname)

Bases: django.template.base.Node

render(context)

Return the node rendered as a string.

tardis.tardis_portal.templatetags.capture.capture(parser, token)

{% capture as [foo] %}

tardis.tardis_portal.templatetags.dataset_tags module

tardis.tardis_portal.templatetags.dataset_tags.dataset_datafiles_badge(dataset=None, count=None)

Displays an badge with the number of datafiles for this experiment

tardis.tardis_portal.templatetags.dataset_tags.dataset_experiments_badge(dataset)

Displays an badge with the number of datasets for this experiment

tardis.tardis_portal.templatetags.dataset_tags.dataset_size_badge(dataset=None, size=None)

Displays an badge with the total size of the files in this experiment

tardis.tardis_portal.templatetags.dataset_tags.dataset_tiles(experiment, include_thumbnails)

tardis.tardis_portal.templatetags.dynurl module

class tardis.tardis_portal.templatetags.dynurl.DynUrlNode(*args)

Bases: django.template.base.Node

render(context)

Return the node rendered as a string.

tardis.tardis_portal.templatetags.dynurl.dynurl(parser, token)

tardis.tardis_portal.templatetags.experiment_tags module

tardis.tardis_portal.templatetags.experiment_tags.experiment_authors(experiment, **kwargs)

Displays an experiment’s authors in an experiment list view

tardis.tardis_portal.templatetags.experiment_tags.experiment_badges(experiment, **kwargs)

Displays badges for an experiment for displaying in an experiment list view

tardis.tardis_portal.templatetags.experiment_tags.experiment_browse_item(experiment, **kwargs)

Displays an experiment for a browsing view.

tardis.tardis_portal.templatetags.experiment_tags.experiment_datafiles_badge(experiment)

Displays an badge with the number of datafiles for this experiment

tardis.tardis_portal.templatetags.experiment_tags.experiment_datasets_badge(experiment)

Displays an badge with the number of datasets for this experiment

tardis.tardis_portal.templatetags.experiment_tags.experiment_download_link(experiment, **kwargs)

Displays a download link for an experiment in a list view

tardis.tardis_portal.templatetags.experiment_tags.experiment_last_updated_badge(experiment)

tardis.tardis_portal.templatetags.experiment_tags.experiment_public_access_badge(experiment)

Displays an badge the level of public access for this experiment

tardis.tardis_portal.templatetags.experiment_tags.experiment_size_badge(experiment)

Displays an badge with the total size of the files in this experiment

tardis.tardis_portal.templatetags.experimentstats module

tardis.tardis_portal.templatetags.experimentstats.experiment_file_count(value)

tardis.tardis_portal.templatetags.facility_tags module

tardis.tardis_portal.templatetags.facility_tags.check_if_facility_manager(request)

Custom template filter to identify whether a user is a facility manager.

tardis.tardis_portal.templatetags.feed module

tardis.tardis_portal.templatetags.feed.todatetime(value)

tardis.tardis_portal.templatetags.formfieldfilters module

This module holds filters that can be used in postprocessing a form field.

@author: Gerson Galang

tardis.tardis_portal.templatetags.formfieldfilters.parametername_form(value)

Removes all values of arg from the given string

tardis.tardis_portal.templatetags.formfieldfilters.sanitize_html(html, bad_tags=['body'])

Removes identified malicious HTML content from the given string.

tardis.tardis_portal.templatetags.formfieldfilters.size(value, actualSize)

Add the size attribute to the text field.

tardis.tardis_portal.templatetags.lookupfilters module

tardis.tardis_portal.templatetags.lookupfilters.get_item(dictionary, key)

Returns a value from a dictionary.

tardis.tardis_portal.templatetags.pagination module

tardis.tardis_portal.templatetags.pagination.pagination(data_list, paginator, page_num, query_string)

Generates the series of links to the pages in a paginated list.

tardis.tardis_portal.templatetags.pagination.paginator_number(data_list, paginator, page_num, query_string, page_index)

Generates an individual page index link in a paginated list.

tardis.tardis_portal.templatetags.xmldate module

tardis.tardis_portal.templatetags.xmldate.toxmldatetime(value)

Module contents

tardis.tardis_portal.tests package

Subpackages

tardis.tardis_portal.tests.api package

Submodules

tardis.tardis_portal.tests.api.test_auth module

Testing authentication and authorization in the Tastypie-based MyTardis REST API

class tardis.tardis_portal.tests.api.test_auth.ACLAuthorizationTest(methodName='runTest')

Bases: django.test.testcases.TestCase

class tardis.tardis_portal.tests.api.test_auth.MyTardisAuthenticationTest(methodName='runTest')

Bases: tardis.tardis_portal.tests.api.MyTardisResourceTestCase

test_apikey_authentication()

test_bad_credentials()

tardis.tardis_portal.tests.api.test_datafile_metadata_resources module

Testing the DatafileParameter and DatafileParameterSet resources in MyTardis’s Tastypie-based REST API

class tardis.tardis_portal.tests.api.test_datafile_metadata_resources.DatafileParameterResourceTest(methodName='runTest')

Bases: tardis.tardis_portal.tests.api.MyTardisResourceTestCase

class tardis.tardis_portal.tests.api.test_datafile_metadata_resources.DatafileParameterSetResourceTest(methodName='runTest')

Bases: tardis.tardis_portal.tests.api.MyTardisResourceTestCase

tardis.tardis_portal.tests.api.test_datafile_resource module

Testing the DataFile resource in MyTardis’s Tastypie-based REST API

class tardis.tardis_portal.tests.api.test_datafile_resource.DataFileResourceTest(methodName='runTest')

Bases: tardis.tardis_portal.tests.api.MyTardisResourceTestCase

setUp()

Hook method for setting up the test fixture before exercising it.

test_create_df_for_staging()

test_download_file()

Re-run the upload test in order to create a verified file to download - it will be verified immediately becase CELERY_ALWAYS_EAGER is True in test_settings.py

Then download the file, check the HTTP status code and check the file content.

test_post_single_file()

test_shared_fs_many_files()

tests sending many files with known permanent location (useful for Australian Synchrotron ingestions)

test_shared_fs_single_file()

tardis.tardis_portal.tests.api.test_dataset_metadata_resources module

Testing the DatasetParameter and DatasetParameterSet resources in MyTardis’s Tastypie-based REST API

class tardis.tardis_portal.tests.api.test_dataset_metadata_resources.DatasetParameterResourceTest(methodName='runTest')

Bases: tardis.tardis_portal.tests.api.MyTardisResourceTestCase

class tardis.tardis_portal.tests.api.test_dataset_metadata_resources.DatasetParameterSetResourceTest(methodName='runTest')

Bases: tardis.tardis_portal.tests.api.MyTardisResourceTestCase

setUp()

Hook method for setting up the test fixture before exercising it.

tearDown()

Hook method for deconstructing the test fixture after testing it.

test_create_dataset_pset()

Test creating a dataset parameter set

test_create_dataset_pset_no_auth()

Test attempting to create a dataset parameter set without access

test_post_dataset_with_params()

Test creating a dataset with metadata

tardis.tardis_portal.tests.api.test_dataset_resource module

Testing the Dataset resource in MyTardis’s Tastypie-based REST API

class tardis.tardis_portal.tests.api.test_dataset_resource.DatasetResourceTest(methodName='runTest')

Bases: tardis.tardis_portal.tests.api.MyTardisResourceTestCase

setUp()

Hook method for setting up the test fixture before exercising it.

test_get_child_dir_nodes()

test_get_child_dir_nodes_no_files_in_root_dir()

test_get_dataset_files()

test_get_dataset_filter_instrument()

test_get_dataset_no_instrument()

test_get_dataset_with_instrument()

test_get_root_dir_nodes()

test_post_dataset()

tardis.tardis_portal.tests.api.test_experiment_metadata_resources module

Testing the ExperimentParameter and ExperimentParameterSet resources in MyTardis’s Tastypie-based REST API

class tardis.tardis_portal.tests.api.test_experiment_metadata_resources.ExperimentParameterResourceTest(methodName='runTest')

Bases: tardis.tardis_portal.tests.api.MyTardisResourceTestCase

class tardis.tardis_portal.tests.api.test_experiment_metadata_resources.ExperimentParameterSetResourceTest(methodName='runTest')

Bases: tardis.tardis_portal.tests.api.MyTardisResourceTestCase

tardis.tardis_portal.tests.api.test_experiment_resource module

Testing the Experiment resource in MyTardis’s Tastypie-based REST API

class tardis.tardis_portal.tests.api.test_experiment_resource.ExperimentResourceTest(methodName='runTest')

Bases: tardis.tardis_portal.tests.api.MyTardisResourceTestCase

setUp()

Hook method for setting up the test fixture before exercising it.

test_get_experiment()

test_get_experiment_author()

test_post_experiment()

tardis.tardis_portal.tests.api.test_facility_resource module

Testing the Facility resource in MyTardis’s Tastypie-based REST API

class tardis.tardis_portal.tests.api.test_facility_resource.FacilityResourceTest(methodName='runTest')

Bases: tardis.tardis_portal.tests.api.MyTardisResourceTestCase

test_get_facility_by_id()

test_get_facility_by_manager_group_id()

This type of query can be used to iterate through a user’s groups, and use each group’s id to determine which facilities a user manages, i.e. a way to obtain the functionality implemented by facilities_managed_by() via the API

test_get_facility_by_name()

tardis.tardis_portal.tests.api.test_group_resource module

Testing the Group resource in MyTardis’s Tastypie-based REST API

class tardis.tardis_portal.tests.api.test_group_resource.GroupResourceTest(methodName='runTest')

Bases: tardis.tardis_portal.tests.api.MyTardisResourceTestCase

test_get_group_by_id()

test_get_group_by_name()

tardis.tardis_portal.tests.api.test_instrument_resource module

Testing the Instrument resource in MyTardis’s Tastypie-based REST API

class tardis.tardis_portal.tests.api.test_instrument_resource.InstrumentResourceTest(methodName='runTest')

Bases: tardis.tardis_portal.tests.api.MyTardisResourceTestCase

test_get_instrument_by_id()

test_get_instrument_by_name()

test_post_instrument()

test_rename_instrument()

test_unauthorized_instrument_access_attempt()

tardis.tardis_portal.tests.api.test_list_api_endpoints module

Testing listing all of the endpoints in MyTardis’s Tastypie-based REST API

class tardis.tardis_portal.tests.api.test_list_api_endpoints.ListEndpointsTest(methodName='runTest')

Bases: tardis.tardis_portal.tests.api.MyTardisResourceTestCase

test_list_endpoints()

tardis.tardis_portal.tests.api.test_replica_resource module

Testing the Replica resource in MyTardis’s Tastypie-based REST API

“Replica” was the old name for what is now known as a DataFileObject in MyTardis. The API v1 endpoint is still /api/v1/replica/

class tardis.tardis_portal.tests.api.test_replica_resource.ReplicaResourceTest(methodName='runTest')

Bases: tardis.tardis_portal.tests.api.MyTardisResourceTestCase

tardis.tardis_portal.tests.api.test_schema_resource module

Testing the Schema resource in MyTardis’s Tastypie-based REST API

class tardis.tardis_portal.tests.api.test_schema_resource.SchemaResourceTest(methodName='runTest')

Bases: tardis.tardis_portal.tests.api.MyTardisResourceTestCase

setUp()

Hook method for setting up the test fixture before exercising it.

tearDown()

Hook method for deconstructing the test fixture after testing it.

test_get_schema_by_id()

test_get_schema_by_namespace()

tardis.tardis_portal.tests.api.test_serializer module

Testing the serializer in the Tastypie-based MyTardis REST API

class tardis.tardis_portal.tests.api.test_serializer.SerializerTest(methodName='runTest')

Bases: django.test.testcases.TestCase

test_debug_serializer()

test_pretty_serializer()

tardis.tardis_portal.tests.api.test_storagebox_resources module

Testing the StorageBox resources in MyTardis’s Tastypie-based REST API

class tardis.tardis_portal.tests.api.test_storagebox_resources.StorageBoxAttributeResourceTest(methodName='runTest')

Bases: tardis.tardis_portal.tests.api.MyTardisResourceTestCase

test_get_storage_box_attr_list_from_box_id()

class tardis.tardis_portal.tests.api.test_storagebox_resources.StorageBoxOptionResourceTest(methodName='runTest')

Bases: tardis.tardis_portal.tests.api.MyTardisResourceTestCase

test_get_storage_box_option_by_id()

test_get_storage_box_option_list_from_box_id()

class tardis.tardis_portal.tests.api.test_storagebox_resources.StorageBoxResourceTest(methodName='runTest')

Bases: tardis.tardis_portal.tests.api.MyTardisResourceTestCase

test_get_storage_box_by_id()

tardis.tardis_portal.tests.api.test_user_resource module

Testing the User resource in MyTardis’s Tastypie-based REST API

class tardis.tardis_portal.tests.api.test_user_resource.UserResourceTest(methodName='runTest')

Bases: tardis.tardis_portal.tests.api.MyTardisResourceTestCase

test_get_user_by_id()

test_get_user_by_username()

Module contents

Testing the tastypie-based mytardis api

class tardis.tardis_portal.tests.api.MyTardisResourceTestCase(methodName='runTest')

Bases: tastypie.test.ResourceTestCaseMixin, django.test.testcases.TestCase

abstract class without tests to combine common settings in one place

get_admin_credentials()

get_apikey_credentials()

get_credentials()

A convenience method for the user as a way to shorten up the often repetitious calls to create the same authentication.

Raises NotImplementedError by default.

Usage:

class MyResourceTestCase(ResourceTestCase):
    def get_credentials(self):
        return self.create_basic('daniel', 'pass')

    # Then the usual tests...

setUp()

Hook method for setting up the test fixture before exercising it.

tardis.tardis_portal.tests.auth package

Module contents

tardis.tardis_portal.tests.management package

Submodules

tardis.tardis_portal.tests.management.test_collectstatic module

class tardis.tardis_portal.tests.management.test_collectstatic.CollectstaticTest(methodName='runTest')

Bases: django.test.testcases.TestCase

setUp()

Hook method for setting up the test fixture before exercising it.

tearDown()

Hook method for deconstructing the test fixture after testing it.

test_collectstatic()

tardis.tardis_portal.tests.management.test_createuser module

class tardis.tardis_portal.tests.management.test_createuser.CreateUserTestCase(methodName='runTest')

Bases: django.test.testcases.TestCase

testInteractive()

Just test that we can run ./manage.py createuser without any runtime exceptions by mocking the raw_input username and email entry

testNoInput()

Just test that we can run ./manage.py createuser –username testuser1 –email testuser1@example.com –noinput without any runtime exceptions

tardis.tardis_portal.tests.management.test_dumpschemas module

class tardis.tardis_portal.tests.management.test_dumpschemas.DumpSchemasTestCase(methodName='runTest')

Bases: django.test.testcases.TestCase

setUp()

Hook method for setting up the test fixture before exercising it.

tearDown()

Hook method for deconstructing the test fixture after testing it.

testDumpSchemas()

Just test that we can run ./manage.py dumpschemas without any runtime exceptions

tardis.tardis_portal.tests.management.test_loadschemas module

class tardis.tardis_portal.tests.management.test_loadschemas.LoadSchemasTestCase(methodName='runTest')

Bases: django.test.testcases.TestCase

testLoadSchemas()

Test that we can run ./manage.py loadschemas tardis/tardis_portal/fixtures/jeol_metadata_schema.json

tardis.tardis_portal.tests.management.test_rmexperiment module

class tardis.tardis_portal.tests.management.test_rmexperiment.RmExperimentTestCase(methodName='runTest')

Bases: django.test.testcases.TestCase

testList()

testRemove()

Module contents

This package contains tests relating to management commands, i.e. command-line tools invoked with manage.py

tardis.tardis_portal.tests.models package

Submodules

tardis.tardis_portal.tests.models.test_authors module

test_authors.py

class tardis.tardis_portal.tests.models.test_authors.AuthorTestCase(methodName='runTest')

Bases: tardis.tardis_portal.tests.models.ModelTestCase

test_authors()

tardis.tardis_portal.tests.models.test_datafile module

test_datafile.py

class tardis.tardis_portal.tests.models.test_datafile.DataFileTestCase(methodName='runTest')

Bases: tardis.tardis_portal.tests.models.ModelTestCase

test_datafile(mock_send_task)

tardis.tardis_portal.tests.models.test_dataset module

test_dataset.py

class tardis.tardis_portal.tests.models.test_dataset.DatasetTestCase(methodName='runTest')

Bases: tardis.tardis_portal.tests.models.ModelTestCase

test_dataset()

test_get_dir_tuples()

tardis.tardis_portal.tests.models.test_dfo module

tests_datafileobject.py

class tardis.tardis_portal.tests.models.test_dfo.DataFileObjectTestCase(methodName='runTest')

Bases: tardis.tardis_portal.tests.models.ModelTestCase

test_deleting_dfo_without_uri()

tardis.tardis_portal.tests.models.test_experiment module

test_experiment.py

class tardis.tardis_portal.tests.models.test_experiment.ExperimentTestCase(methodName='runTest')

Bases: tardis.tardis_portal.tests.models.ModelTestCase

test_experiment()

tardis.tardis_portal.tests.models.test_generate_api_key module

test_generate_api_key.py

class tardis.tardis_portal.tests.models.test_generate_api_key.ApiKeyTestCase(methodName='runTest')

Bases: tardis.tardis_portal.tests.models.ModelTestCase

test_create_user_automatically_generate_api_key()

Verify that create a new user will generate an api_key automatically

tardis.tardis_portal.tests.models.test_instrument module

test_instrument.py

class tardis.tardis_portal.tests.models.test_instrument.InstrumentTestCase(methodName='runTest')

Bases: tardis.tardis_portal.tests.models.ModelTestCase

test_instrument()

tardis.tardis_portal.tests.models.test_parameter module

test_parameter.py

class tardis.tardis_portal.tests.models.test_parameter.ParameterTestCase(methodName='runTest')

Bases: tardis.tardis_portal.tests.models.ModelTestCase

test_parameter()

Module contents

tests/models/__init__.py http://docs.djangoproject.com/en/dev/topics/testing/

class tardis.tardis_portal.tests.models.ModelTestCase(methodName='runTest')

Bases: django.test.testcases.TestCase

setUp()

Hook method for setting up the test fixture before exercising it.

tardis.tardis_portal.tests.views package

Submodules

tardis.tardis_portal.tests.views.test_auth_views module

test_auth_views.py

Tests for view methods relating to users, groups, access controls and authorization

class tardis.tardis_portal.tests.views.test_auth_views.ManageAccountTestCase(methodName='runTest')

Bases: django.test.testcases.TestCase

test_manage_account(mock_webpack_get_bundle)

class tardis.tardis_portal.tests.views.test_auth_views.RightsTestCase(methodName='runTest')

Bases: django.test.testcases.TestCase

test_rights_require_valid_owner()

class tardis.tardis_portal.tests.views.test_auth_views.UserGroupListsTestCase(methodName='runTest')

Bases: django.test.testcases.TestCase

setUp()

Hook method for setting up the test fixture before exercising it.

tearDown()

Hook method for deconstructing the test fixture after testing it.

test_get_group_list()

test_get_user_list()

class tardis.tardis_portal.tests.views.test_auth_views.UserListTestCase(methodName='runTest')

Bases: django.test.testcases.TestCase

User lists are used for autocompleting the user-to-share-with field when granting access to an experiment

setUp()

Hook method for setting up the test fixture before exercising it.

tearDown()

Hook method for deconstructing the test fixture after testing it.

test_get_user_list()

tardis.tardis_portal.tests.views.test_contextual_views module

test_contextual_views.py

Tests for view methods supplying context data to templates

class tardis.tardis_portal.tests.views.test_contextual_views.ContextualViewTest(methodName='runTest')

Bases: django.test.testcases.TestCase

setUp()

setting up essential objects, copied from tests above

tearDown()

Hook method for deconstructing the test fixture after testing it.

test_details_display()

test display of view for an existing schema and no display for an undefined one.

tardis.tardis_portal.tests.views.test_experiment_views module

test_experiment_views.py

Tests for view methods relating to experiments

class tardis.tardis_portal.tests.views.test_experiment_views.ExperimentTestCase(methodName='runTest')

Bases: django.test.testcases.TestCase

setUp()

Hook method for setting up the test fixture before exercising it.

test_create_and_edit(mock_webpack_get_bundle)

test_dataset_json()

tardis.tardis_portal.tests.views.test_template_contexts module

test_template_contexts.py

Tests for view methods supplying context data to templates

class tardis.tardis_portal.tests.views.test_template_contexts.ExperimentListsTest(methodName='runTest')

Bases: django.test.testcases.TestCase

setUp()

setting up essential objects, copied from tests above

tearDown()

Hook method for deconstructing the test fixture after testing it.

test_mydata_view(mock_webpack_get_bundle)

Test My Data view

test_shared_view(mock_webpack_get_bundle)

Test Shared view

class tardis.tardis_portal.tests.views.test_template_contexts.ViewTemplateContextsTest(methodName='runTest')

Bases: django.test.testcases.TestCase

setUp()

setting up essential objects, copied from tests above

tearDown()

Hook method for deconstructing the test fixture after testing it.

test_dataset_view(mock_webpack_get_bundle)

test some context parameters for a dataset view

test_experiment_view(mock_webpack_get_bundle)

test some template context parameters for an experiment view

tardis.tardis_portal.tests.views.test_upload_views module

test_upload_views.py

Tests for view methods relating to uploads

class tardis.tardis_portal.tests.views.test_upload_views.UploadTestCase(methodName='runTest')

Bases: django.test.testcases.TestCase

setUp()

Hook method for setting up the test fixture before exercising it.

tearDown()

Hook method for deconstructing the test fixture after testing it.

test_file_upload()

test_upload_complete()

Module contents

Tests for view methods in tardis/tardis_portal/views/

Submodules

tardis.tardis_portal.tests.ldap_ldif module

tardis.tardis_portal.tests.slapd module

Utilities for starting up a test slapd server and talking to it with ldapsearch/ldapadd.

class tardis.tardis_portal.tests.slapd.Slapd

Bases: object

Controller class for a slapd instance, OpenLDAP’s server.

This class creates a temporary data store for slapd, runs it on a private port, and initialises it with a top-level dc and the root user.

When a reference to an instance of this class is lost, the slapd server is shut down.

PATH_LDAPADD = None

PATH_LDAPSEARCH = None

PATH_SCHEMA_DIR = '/home/docs/checkouts/readthedocs.org/user_builds/mytardis/checkouts/v4.2.0-rc3/tardis/tardis_portal/tests/ldap_schemas/'

PATH_SLAPD = None

PATH_SLAPTEST = None

PATH_TMPDIR = '/tmp/tmppm5ywalr'

TEST_UTILS_DIR = '/home/docs/checkouts/readthedocs.org/user_builds/mytardis/checkouts/v4.2.0-rc3/tardis/tardis_portal/tests'

classmethod check_paths()

Checks that the configured executable paths look valid. If they don’t, then logs warning messages (not errors).

configure(cfg)

Appends slapd.conf configuration lines to cfg. Also re-initializes any backing storage. Feel free to subclass and override this method.

get_address()

get_dn_suffix()

get_root_dn()

get_root_password()

get_tmpdir()

get_url()

ldapadd(ldif, extra_args=[])

Runs ldapadd on this slapd instance, passing it the ldif content

ldapsearch(base=None, filter='(objectClass=*)', attrs=[], scope='sub', extra_args=[])

restart()

Restarts the slapd server; ERASING previous content. Starts the server even it if isn’t already running.

set_debug()

set_dn_suffix(dn)

set_port(port)

set_root_cn(cn)

set_root_password(pw)

set_slapd_debug_level(level)

set_tmpdir(path)

start()

Starts the slapd server process running, and waits for it to come up.

started()

This method is called when the LDAP server has started up and is empty. By default, this method adds the two initial objects, the domain object and the root user object.

stop()

Stops the slapd server, and waits for it to terminate

wait()

Waits for the slapd process to terminate by itself.

tardis.tardis_portal.tests.slapd.delete_directory_content(path)

tardis.tardis_portal.tests.slapd.find_available_tcp_port(host='127.0.0.1')

tardis.tardis_portal.tests.slapd.mkdirs(path)

Creates the directory path unless it already exists

tardis.tardis_portal.tests.slapd.quote(s)

Quotes the ” and characters in a string and surrounds with “…”

tardis.tardis_portal.tests.slapd.which(executable)

tardis.tardis_portal.tests.test_authentication module

Created on 19/01/2011

class tardis.tardis_portal.tests.test_authentication.AuthenticationTestCase(methodName='runTest')

Bases: django.test.testcases.TestCase

setUp()

Hook method for setting up the test fixture before exercising it.

testManageAuthMethods(mock_webpack_get_bundle)

testSimpleAuthenticate()

test_djangoauth()

tardis.tardis_portal.tests.test_authorisation module

class tardis.tardis_portal.tests.test_authorisation.ObjectACLTestCase(methodName='runTest')

Bases: django.test.testcases.TestCase

setUp()

Hook method for setting up the test fixture before exercising it.

tearDown()

Hook method for deconstructing the test fixture after testing it.

testCantEditLockedExperiment(mock_webpack_get_bundle)

testChangeUserPermissions(mock_webpack_get_bundle)

testOwnedExperiments()

testReadAccess(mock_webpack_get_bundle)

testWriteAccess(mock_webpack_get_bundle)

urls = 'tardis.urls'

tardis.tardis_portal.tests.test_authservice module

class tardis.tardis_portal.tests.test_authservice.AuthServiceTestCase(methodName='runTest')

Bases: django.test.testcases.TestCase

setUp()

Hook method for setting up the test fixture before exercising it.

tearDown()

Hook method for deconstructing the test fixture after testing it.

testAuthenticate()

testGetGroupsForEntity()

testGroupProvider()

testGroupSearch()

testInitialisation()

class tardis.tardis_portal.tests.test_authservice.MockAuthProvider

Bases: object

authenticate(request)

class tardis.tardis_portal.tests.test_authservice.MockGroupProvider

Bases: tardis.tardis_portal.auth.interfaces.GroupProvider

getGroupById(id)

return the group associated with the id

getGroups(user)

return an iteration of the available groups.

getGroupsForEntity(id)

return a list of groups associated with a particular entity id

searchGroups(**filter)

return a list of groups that match the filter

class tardis.tardis_portal.tests.test_authservice.MockRequest

Bases: django.http.request.HttpRequest

setPost(field, value)

class tardis.tardis_portal.tests.test_authservice.MockSettings

Bases: object

tardis.tardis_portal.tests.test_copy_move module

test_copy_move.py

Test copying and moving a file to another storage box

class tardis.tardis_portal.tests.test_copy_move.CopyMoveTestCase(methodName='runTest')

Bases: django.test.testcases.TestCase

Test copying and moving files between storage boxes

setUp()

Hook method for setting up the test fixture before exercising it.

tearDown()

Hook method for deconstructing the test fixture after testing it.

test_cache()

Test caching a file from a slow-access storage box

test_copy()

Test copying a file to another storage box

test_move()

Test moving a file to another storage box

tardis.tardis_portal.tests.test_df_save_metadata module

class tardis.tardis_portal.tests.test_df_save_metadata.DatafileSaveMetadataTestCase(methodName='runTest')

Bases: django.test.testcases.TestCase

setUp()

Hook method for setting up the test fixture before exercising it.

tearDown()

Hook method for deconstructing the test fixture after testing it.

test_df_save_metadata()

Test the DataFile metadata saving task used by the post-save filters microservice

tardis.tardis_portal.tests.test_download module

class tardis.tardis_portal.tests.test_download.DownloadTestCase(methodName='runTest')

Bases: django.test.testcases.TestCase

setUp()

Hook method for setting up the test fixture before exercising it.

tearDown()

Hook method for deconstructing the test fixture after testing it.

testDatasetFile()

testDownload(mock_webpack_get_bundle)

testView(mock_webpack_get_bundle)

tardis.tardis_portal.tests.test_download.get_size_and_sha512sum(testfile)

tardis.tardis_portal.tests.test_download_apikey module

class tardis.tardis_portal.tests.test_download_apikey.ApiKeyDownloadTestCase(methodName='runTest')

Bases: tastypie.test.ResourceTestCaseMixin, django.test.testcases.TestCase

setUp()

Hook method for setting up the test fixture before exercising it.

tearDown()

Hook method for deconstructing the test fixture after testing it.

test_download_apikey()

tardis.tardis_portal.tests.test_facility_overview module

Tests relating to facility overview

class tardis.tardis_portal.tests.test_facility_overview.FacilityOverviewTestCase(methodName='runTest')

Bases: django.test.testcases.TestCase

setUp()

Hook method for setting up the test fixture before exercising it.

test_facility_overview_datafile_list()

test_facility_overview_experiments()

Despite the name of the test_facility_overview_experiments method, it actually returns a JSON list of datasets (not experiments)

tardis.tardis_portal.tests.test_forms module

test_models.py http://docs.djangoproject.com/en/dev/topics/testing/

class tardis.tardis_portal.tests.test_forms.RightsFormTestCase(methodName='runTest')

Bases: django.test.testcases.TestCase

setUp()

Hook method for setting up the test fixture before exercising it.

test_ensures_suitable_license()

test_needs_confirmation()

tardis.tardis_portal.tests.test_iiif module

class tardis.tardis_portal.tests.test_iiif.ExtraTestCases(methodName='runTest')

Bases: django.test.testcases.TestCase

As per: http://library.stanford.edu/iiif/image-api/compliance.html

setUp()

Hook method for setting up the test fixture before exercising it.

testImageCacheControl()

testImageHasEtags()

testInfoHasEtags()

class tardis.tardis_portal.tests.test_iiif.Level0TestCase(methodName='runTest')

Bases: django.test.testcases.TestCase

As per: http://library.stanford.edu/iiif/image-api/compliance.html

setUp()

Hook method for setting up the test fixture before exercising it.

testCanGetInfoAsJSON()

testCanGetInfoAsXML()

testCanGetOriginalImage()

class tardis.tardis_portal.tests.test_iiif.Level1TestCase(methodName='runTest')

Bases: django.test.testcases.TestCase

As per: http://library.stanford.edu/iiif/image-api/compliance.html

setUp()

Hook method for setting up the test fixture before exercising it.

testCanGetJpegFormat()

testHandleRegions()

testHandleRotation()

testHandleSizing()

class tardis.tardis_portal.tests.test_iiif.Level2TestCase(methodName='runTest')

Bases: django.test.testcases.TestCase

As per: http://library.stanford.edu/iiif/image-api/compliance.html

setUp()

Hook method for setting up the test fixture before exercising it.

testCanGetRequiredFormats()

testHandleSizing()

tardis.tardis_portal.tests.test_ldap module

class tardis.tardis_portal.tests.test_ldap.LDAPErrorTest(methodName='runTest')

Bases: django.test.testcases.TestCase

test_search()

class tardis.tardis_portal.tests.test_ldap.LDAPTest(methodName='runTest')

Bases: django.test.testcases.TestCase

setUp()

Hook method for setting up the test fixture before exercising it.

tearDown()

Hook method for deconstructing the test fixture after testing it.

test_authenticate()

test_getgroupbyid()

test_getgroups()

test_getgroupsforentity()

test_getuserbyid()

test_search()

test_searchgroups()

tardis.tardis_portal.tests.test_parameters module

test_parameters.py

class tardis.tardis_portal.tests.test_parameters.ParametersTestCase(methodName='runTest')

Bases: django.test.testcases.TestCase

Tests for the different parameter types, defined in the tardis.tardis_portal.models.parameters.ParameterName class:

NUMERIC, STRING, URL, LINK, FILENAME, DATETIME, LONGSTRING and JSON

setUp()

Hook method for setting up the test fixture before exercising it.

tearDown()

Hook method for deconstructing the test fixture after testing it.

test_experiment_parameter_get()

Test the Parameter class’s get() method which should return an appropriate string representation of the parameter which depends on the parameter’s data type:

NUMERIC, STRING, URL, LINK, FILENAME, DATETIME, LONGSTRING or JSON

test_image_filename_parameters()

When a FILENAME parameter refers to a thumbanil image file, MyTardis can generate a HTML for displaying that image.

This method tests the generation of the image HTML

test_link_urls()

Test URLs generated for parameters which link to MyTardis model records

test_permissions_checks()

Test permissions checks, used by tardis.tardis_portal.auth.authorisation

tardis.tardis_portal.tests.test_parametersets module

test_parametersets.py http://docs.djangoproject.com/en/dev/topics/testing/

class tardis.tardis_portal.tests.test_parametersets.EditParameterSetTestCase(methodName='runTest')

Bases: django.test.testcases.TestCase

setUp()

Hook method for setting up the test fixture before exercising it.

tearDown()

Hook method for deconstructing the test fixture after testing it.

test_add_datafile_params()

test_add_dataset_params()

test_add_experiment_params()

test_edit_datafile_params()

test_edit_dataset_params()

test_edit_experiment_params()

class tardis.tardis_portal.tests.test_parametersets.ParameterSetManagerTestCase(methodName='runTest')

Bases: django.test.testcases.TestCase

setUp()

Hook method for setting up the test fixture before exercising it.

tearDown()

Hook method for deconstructing the test fixture after testing it.

test_existing_parameterset()

test_link_parameter_type()

Test that Parameter.link_gfk (GenericForeignKey) is correctly assigned after using Parameter.set_value(some_url) for a LINK Parameter.

test_link_parameter_type_extra()

test_new_parameterset()

test_parameterset_as_string()

test_tz_aware_date_handling()

Ensure that dates are handling in a timezone-aware way.

test_tz_naive_date_handling()

Ensure that dates are handling in a timezone-aware way.

test_unresolvable_link_parameter()

Test that LINK Parameters that can’t be resolved to a model (including non-URL values) still work.

tardis.tardis_portal.tests.test_publishservice module

class tardis.tardis_portal.tests.test_publishservice.MockRifCsProvider

Bases: tardis.tardis_portal.publish.provider.rifcsprovider.RifCsProvider

get_beamline(experiment)

get_license_uri(experiment)

get_rifcs_context(experiment)

get_template(experiment)

tardis.test_settings adds this to the template dirs: tardis/tardis_portal/tests/rifcs/

is_schema_valid(experiment)

class tardis.tardis_portal.tests.test_publishservice.PublishServiceTestCase(methodName='runTest')

Bases: django.test.testcases.TestCase

setUp()

Hook method for setting up the test fixture before exercising it.

testContext()

testInitialisation()

testInitialisationNoProvider()

testManageRifCsCheckContent()

testManageRifCsCreateAndRemove()

tardis.tardis_portal.tests.test_storage module

test_storage.py http://docs.djangoproject.com/en/dev/topics/testing/

class tardis.tardis_portal.tests.test_storage.ModelTestCase(methodName='runTest')

Bases: django.test.testcases.TestCase

setUp()

Hook method for setting up the test fixture before exercising it.

tearDown()

Hook method for deconstructing the test fixture after testing it.

test_get_receiving_box()

test_storageboxoption()

tardis.tardis_portal.tests.test_tar_download module

class tardis.tardis_portal.tests.test_tar_download.TarDownloadTestCase(methodName='runTest')

Bases: django.test.testcases.TestCase

setUp()

Hook method for setting up the test fixture before exercising it.

tearDown()

Hook method for deconstructing the test fixture after testing it.

test_tar_experiment_download()

tardis.tardis_portal.tests.test_tasks module

class tardis.tardis_portal.tests.test_tasks.BackgroundTaskTestCase(methodName='runTest')

Bases: django.test.testcases.TestCase

As per: http://library.stanford.edu/iiif/image-api/compliance.html

setUp()

Hook method for setting up the test fixture before exercising it.

testLocalFile()

test_wrong_size_verification()

tardis.tardis_portal.tests.test_tokens module

test_tokens.py

class tardis.tardis_portal.tests.test_tokens.FrozenTime(*args, **kwargs)

Bases: object

classmethod freeze_time(time)

classmethod now()

class tardis.tardis_portal.tests.test_tokens.TokenTestCase(methodName='runTest')

Bases: django.test.testcases.TestCase

setUp()

Hook method for setting up the test fixture before exercising it.

tearDown()

Hook method for deconstructing the test fixture after testing it.

test_create_token(mock_webpack_get_bundle)

test_default_expiry()

test_get_session_expiry()

test_get_session_expiry_expired_token()

test_get_session_expiry_near_expiry()

test_is_expired()

test_retrieve_access_list_tokens()

test_save_with_random_token()

test_save_with_random_token_failures()

test_save_with_random_token_gives_up()

test_token_delete(mock_webpack_get_bundle)

urls = 'tardis.tardis_portal.tests.urls'

tardis.tardis_portal.tests.tests module

tests.py http://docs.djangoproject.com/en/dev/topics/testing/

class tardis.tardis_portal.tests.tests.UserInterfaceTestCase(methodName='runTest')

Bases: django.test.testcases.TestCase

test_login()

test_root(mock_webpack_get_bundle)

test_urls(mock_webpack_get_bundle)

test_urls_with_some_content(mock_webpack_get_bundle)

tardis.tardis_portal.tests.tests.suite()

tardis.tardis_portal.tests.urls module

Module contents

tardis.tardis_portal.views package

Submodules

tardis.tardis_portal.views.ajax_actions module

views that perform some action and don’t return anything very useful

tardis.tardis_portal.views.ajax_json module

views that return JSON data

tardis.tardis_portal.views.ajax_json.retrieve_licenses(request)

tardis.tardis_portal.views.ajax_pages module

views that return HTML that is injected into pages

tardis.tardis_portal.views.ajax_pages.experiment_public_access_badge(request, experiment_id)

tardis.tardis_portal.views.ajax_pages.retrieve_owned_exps_list(request, template_name='tardis_portal/ajax/exps_list.html')

tardis.tardis_portal.views.ajax_pages.retrieve_shared_exps_list(request, template_name='tardis_portal/ajax/exps_list.html')

tardis.tardis_portal.views.authentication module

views that have to do with authentication

tardis.tardis_portal.views.authentication.create_user(request)

tardis.tardis_portal.views.authentication.login(request)

handler for login page

tardis.tardis_portal.views.authentication.logout(request)

tardis.tardis_portal.views.authentication.manage_auth_methods(request)

Manage the user’s authentication methods using AJAX.

tardis.tardis_portal.views.authentication.manage_user_account(request)

tardis.tardis_portal.views.authentication.rcauth(request)

tardis.tardis_portal.views.authorisation module

views that have to do with authorisations

tardis.tardis_portal.views.authorisation.create_group(request)

tardis.tardis_portal.views.authorisation.manage_groups(request)

tardis.tardis_portal.views.authorisation.retrieve_access_list_group_readonly(request, experiment_id)

tardis.tardis_portal.views.authorisation.retrieve_access_list_user_readonly(request, experiment_id)

tardis.tardis_portal.views.authorisation.retrieve_group_list(request)

tardis.tardis_portal.views.authorisation.retrieve_group_list_by_user(request)

tardis.tardis_portal.views.authorisation.retrieve_group_userlist_readonly(request, group_id)

tardis.tardis_portal.views.authorisation.retrieve_user_list(request)

tardis.tardis_portal.views.authorisation.share(request, experiment_id)

Choose access rights and licence.

tardis.tardis_portal.views.authorisation.token_delete(request, token_id)

tardis.tardis_portal.views.facilities module

views relevant for facilities and the facility view

tardis.tardis_portal.views.facilities.dataset_aggregate_info(dataset)

tardis.tardis_portal.views.facilities.datetime_to_us(dt)

The datetime objects are kept as None if they aren’t set, otherwise they’re converted to milliseconds so AngularJS can format them nicely.

tardis.tardis_portal.views.facilities.facility_overview_data_count(request, facility_id)

returns the total number of datasets for pagination in json format

tardis.tardis_portal.views.facilities.facility_overview_datafile_list(dataset)

tardis.tardis_portal.views.facilities.facility_overview_dataset_detail(request, dataset_id)

tardis.tardis_portal.views.facilities.facility_overview_experiments(request, facility_id, start_index, end_index)

json facility datasets

tardis.tardis_portal.views.facilities.facility_overview_facilities_list(request)

json list of facilities managed by the current user

tardis.tardis_portal.views.images module

views that return images or route to images

tardis.tardis_portal.views.images.load_datafile_image(request, parameter_id)

tardis.tardis_portal.views.images.load_dataset_image(request, parameter_id)

tardis.tardis_portal.views.images.load_experiment_image(request, parameter_id)

tardis.tardis_portal.views.images.load_image(request, parameter)

tardis.tardis_portal.views.machine module

views that return data useful only to other machines (but not JSON)

tardis.tardis_portal.views.machine.site_settings(request)

tardis.tardis_portal.views.pages module

views that render full pages

class tardis.tardis_portal.views.pages.DatasetView(**kwargs)

Bases: django.views.generic.base.TemplateView

find_custom_view_override(request, dataset)

Determines if any custom view overrides have been defined in settings.DATASET_VIEWS and returns the view function if a match to one the schemas for the dataset is found. (DATASET_VIEWS is a list of (schema_namespace, view_function) tuples).

Parameters:

• request –
• dataset –

Returns:

Return type:

get(request, *args, **kwargs)

View an existing dataset.

This default view can be overriden by defining a dictionary DATASET_VIEWS in settings.

Parameters:

• request (django.http.HttpRequest) – a HTTP request object
• args (list) –
• kwargs (dict) –

Returns:

The Django response object

Return type:

django.http.HttpResponse

get_context_data(request, dataset, **kwargs)

Prepares the values to be passed to the default dataset view, respecting authorization rules. Returns a dict of values (the context).

Parameters:

• request (django.http.HttpRequest) – a HTTP request object
• dataset (tardis.tardis_portal.models.dataset.Dataset) – the Dataset model instance
• kwargs (dict) –

Returns:

A dictionary of values for the view/template.

Return type:

dict

template_name = 'tardis_portal/view_dataset.html'

class tardis.tardis_portal.views.pages.ExperimentView(**kwargs)

Bases: django.views.generic.base.TemplateView

find_custom_view_override(request, experiment)

get(request, *args, **kwargs)

View an existing experiment.

This default view can be overriden by defining a dictionary EXPERIMENT_VIEWS in settings.

Parameters:

• request (django.http.HttpRequest) – a HTTP Request instance
• args (list) –
• kwargs (dict) – In kwargs: param int experiment_id: the ID of the experiment

Returns:

an HttpResponse

Return type:

django.http.HttpResponse

get_context_data(request, experiment, **kwargs)

Prepares the values to be passed to the default experiment view, respecting authorization rules. Returns a dict of values (the context).

Parameters:

• request (django.http.HttpRequest) – a HTTP request object
• experiment (tardis.tardis_portal.models.experiment.Experiment) – the experiment model instance
• kwargs (dict) – kwargs

Returns:

A dictionary of values for the view/template.

Return type:

dict

template_name = 'tardis_portal/view_experiment.html'

class tardis.tardis_portal.views.pages.IndexView(**kwargs)

Bases: django.views.generic.base.TemplateView

get(request, *args, **kwargs)

The index view, intended to render the front page of the MyTardis site listing recent experiments.

This default view can be overriden by defining a dictionary INDEX_VIEWS in settings which maps SITE_ID’s or domain names to an alternative view function (similar to the DATASET_VIEWS or EXPERIMENT_VIEWS overrides).

Parameters:

• request (django.http.HttpRequest) – a HTTP request object
• args (list) –
• kwargs (dict) –

Returns:

The Django response object

Return type:

django.http.HttpResponse

get_context_data(*args, **kwargs)

template_name = 'tardis_portal/index.html'

tardis.tardis_portal.views.pages.about(request)

tardis.tardis_portal.views.pages.add_dataset(request, experiment_id)

tardis.tardis_portal.views.pages.create_experiment(request, template_name='tardis_portal/create_experiment.html')

Create a new experiment view.

Parameters:

• request (django.http.HttpRequest) – a HTTP Request instance
• template_name (string) – the path of the template to render

Returns:

an HttpResponse

Return type:

django.http.HttpResponse

tardis.tardis_portal.views.pages.edit_dataset(request, dataset_id)

tardis.tardis_portal.views.pages.facility_overview(request)

summary of experiments in a facility

tardis.tardis_portal.views.pages.healthz(request)

returns that the server is alive

tardis.tardis_portal.views.pages.my_data(request)

show owned data with credential-based access

tardis.tardis_portal.views.pages.public_data(request)

list of public experiments

tardis.tardis_portal.views.pages.shared(request)

show shared data with credential-based access

tardis.tardis_portal.views.pages.site_routed_view(request, _default_view, _site_mappings, *args, **kwargs)

Allows a view to be overriden based on the Site (eg domain) for the current request. Takes a default fallback view (_default_view) and a dictionary mapping Django Sites (domain name or int SITE_ID) to views. If the current request matches a Site in the dictionary, that view is used instead of the default.

The intention is to define {site: view} mappings in settings.py, and use this wrapper view in urls.py to allow a single URL to be routed to different views depending on the Site in the request.

Parameters:

• request (django.http.HttpRequest) – a HTTP request object
• _default_view (types.FunctionType | str) – The default view if no Site in _site_mappings matches the current Site.
• _site_mappings (dict) – A dictionary mapping Django sites to views (sites are specified as either a domain name str or int SITE_ID).
• args –
• kwargs –

Returns:

A view function

Return type:

types.FunctionType

tardis.tardis_portal.views.pages.stats(request)

tardis.tardis_portal.views.pages.use_rapid_connect(fn)

A decorator that adds AAF Rapid Connect settings to a get_context_data method.

Parameters:fn (types.FunctionType) – A get_context_data function/method. Returns:A get_context_data function that adds RAPID_CONNECT_* keys to its output context. Return type:types.FunctionType

tardis.tardis_portal.views.pages.user_guide(request)

tardis.tardis_portal.views.parameters module

views to do with metadata, parameters etc. Mostly ajax page inclusions

tardis.tardis_portal.views.parameters.add_datafile_par(request, datafile_id)

tardis.tardis_portal.views.parameters.add_dataset_par(request, dataset_id)

tardis.tardis_portal.views.parameters.add_experiment_par(request, experiment_id)

tardis.tardis_portal.views.parameters.add_par(request, parentObject, otype, stype)

tardis.tardis_portal.views.parameters.edit_datafile_par(request, parameterset_id)

tardis.tardis_portal.views.parameters.edit_dataset_par(request, parameterset_id)

tardis.tardis_portal.views.parameters.edit_experiment_par(request, parameterset_id)

tardis.tardis_portal.views.parameters.edit_parameters(request, parameterset, otype)

tardis.tardis_portal.views.upload module

views for uploading files via HTTP

tardis.tardis_portal.views.upload.upload_complete(request, template_name='tardis_portal/upload_complete.html')

The ajax-loaded result of a file being uploaded

Parameters:

• request (django.http.HttpRequest) – a HTTP Request instance
• template_name (string) – the path of the template to render

Returns:

an HttpResponse

Return type:

django.http.HttpResponse

tardis.tardis_portal.views.utils module

helper functions used by other views

class tardis.tardis_portal.views.utils.HttpResponseMethodNotAllowed(*args, **kwargs)

Bases: django.http.response.HttpResponse

status_code = 303

class tardis.tardis_portal.views.utils.HttpResponseSeeAlso(redirect_to, *args, **kwargs)

Bases: django.http.response.HttpResponseRedirect

status_code = 303

tardis.tardis_portal.views.utils.feedback(request)

tardis.tardis_portal.views.utils.get_dataset_info(dataset, include_thumbnail=False, exclude=None)

tardis.tardis_portal.views.utils.remove_csrf_token(request)

rather than fixing the form code that loops over all POST entries indiscriminately, I am removing the csrf token with this hack. This is only required in certain form code and can be removed should this ever be fixed

Module contents

importing all views files here, so that any old code will work as expected, when importing from tardis.tardis_portal.views

Submodules

tardis.tardis_portal.ParameterSetManager module

class tardis.tardis_portal.ParameterSetManager.ParameterSetManager(parameterset=None, parentObject=None, schema=None)

Bases: object

blank_param = None

delete_all_params()

delete_params(parname)

get_param(parname, value=False)

get_params(parname, value=False)

get_schema()

new_param(parname, value, fullparname=None)

parameters = None

parameterset = None

set_param(parname, value, fullparname=None, example_value=None)

set_param_list(parname, value_list, fullparname=None)

set_params_from_dict(params_dict)

tardis.tardis_portal.admin module

class tardis.tardis_portal.admin.DataFileObjectInline(parent_model, admin_site)

Bases: django.contrib.admin.options.TabularInline

extra = 0

form

alias of DataFileObjectInlineForm

media

model

alias of tardis.tardis_portal.models.datafile.DataFileObject

class tardis.tardis_portal.admin.DataFileObjectInlineForm(data=None, files=None, auto_id='id_%s', prefix=None, initial=None, error_class=<class 'django.forms.utils.ErrorList'>, label_suffix=None, empty_permitted=False, instance=None, use_required_attribute=None, renderer=None)

Bases: django.forms.models.ModelForm

class Meta

Bases: object

fields = '__all__'

model

alias of tardis.tardis_portal.models.datafile.DataFileObject

widgets = {'uri': <django.forms.widgets.TextInput object>}

base_fields = {'datafile': <django.forms.models.ModelChoiceField object>, 'last_verified_time': <django.forms.fields.DateTimeField object>, 'storage_box': <django.forms.models.ModelChoiceField object>, 'uri': <django.forms.fields.CharField object>, 'verified': <django.forms.fields.BooleanField object>}

declared_fields = {}

media

class tardis.tardis_portal.admin.DatafileAdmin(model, admin_site)

Bases: django.contrib.admin.options.ModelAdmin

form

alias of DatafileAdminForm

inlines = [<class 'tardis.tardis_portal.admin.DataFileObjectInline'>]

media

search_fields = ['filename', 'id']

class tardis.tardis_portal.admin.DatafileAdminForm(data=None, files=None, auto_id='id_%s', prefix=None, initial=None, error_class=<class 'django.forms.utils.ErrorList'>, label_suffix=None, empty_permitted=False, instance=None, use_required_attribute=None, renderer=None)

Bases: django.forms.models.ModelForm

class Meta

Bases: object

fields = '__all__'

model

alias of tardis.tardis_portal.models.datafile.DataFile

widgets = {'directory': <django.forms.widgets.TextInput object>}

base_fields = {'created_time': <django.forms.fields.DateTimeField object>, 'dataset': <django.forms.models.ModelChoiceField object>, 'deleted': <django.forms.fields.BooleanField object>, 'deleted_time': <django.forms.fields.DateTimeField object>, 'directory': <django.forms.fields.CharField object>, 'filename': <django.forms.fields.CharField object>, 'md5sum': <django.forms.fields.CharField object>, 'mimetype': <django.forms.fields.CharField object>, 'modification_time': <django.forms.fields.DateTimeField object>, 'sha512sum': <django.forms.fields.CharField object>, 'size': <django.forms.fields.IntegerField object>, 'version': <django.forms.fields.IntegerField object>}

declared_fields = {}

media

class tardis.tardis_portal.admin.DatasetAdmin(model, admin_site)

Bases: django.contrib.admin.options.ModelAdmin

media

search_fields = ['description', 'id']

class tardis.tardis_portal.admin.ExperimentAdmin(model, admin_site)

Bases: django.contrib.admin.options.ModelAdmin

inlines = [<class 'tardis.tardis_portal.admin.ObjectACLInline'>]

media

search_fields = ['title', 'id']

class tardis.tardis_portal.admin.ExperimentParameterInline(parent_model, admin_site)

Bases: django.contrib.admin.options.TabularInline

extra = 0

formfield_overrides = {<class 'django.db.models.fields.TextField'>: {'widget': <class 'django.forms.widgets.TextInput'>}}

media

model

alias of tardis.tardis_portal.models.parameters.ExperimentParameter

class tardis.tardis_portal.admin.ExperimentParameterSetAdmin(model, admin_site)

Bases: django.contrib.admin.options.ModelAdmin

inlines = [<class 'tardis.tardis_portal.admin.ExperimentParameterInline'>]

media

class tardis.tardis_portal.admin.FacilityAdmin(model, admin_site)

Bases: django.contrib.admin.options.ModelAdmin

media

search_fields = ['name']

class tardis.tardis_portal.admin.FreeTextSearchFieldAdmin(model, admin_site)

Bases: django.contrib.admin.options.ModelAdmin

media

class tardis.tardis_portal.admin.InstrumentAdmin(model, admin_site)

Bases: django.contrib.admin.options.ModelAdmin

media

search_fields = ['name']

class tardis.tardis_portal.admin.InstrumentParameterInline(parent_model, admin_site)

Bases: django.contrib.admin.options.TabularInline

extra = 0

media

model

alias of tardis.tardis_portal.models.parameters.InstrumentParameter

class tardis.tardis_portal.admin.InstrumentParameterSetAdmin(model, admin_site)

Bases: django.contrib.admin.options.ModelAdmin

inlines = [<class 'tardis.tardis_portal.admin.InstrumentParameterInline'>]

media

class tardis.tardis_portal.admin.ObjectACLAdmin(model, admin_site)

Bases: django.contrib.admin.options.ModelAdmin

list_display = ['__str__', 'pluginId', 'entityId', 'canRead', 'canWrite', 'canDelete', 'isOwner']

media

search_fields = ['content_type', 'object_id']

class tardis.tardis_portal.admin.ObjectACLInline(parent_model, admin_site)

Bases: django.contrib.contenttypes.admin.GenericTabularInline

extra = 0

media

model

alias of tardis.tardis_portal.models.access_control.ObjectACL

class tardis.tardis_portal.admin.ParameterNameAdmin(model, admin_site)

Bases: django.contrib.admin.options.ModelAdmin

media

search_fields = ['name', 'schema__id']

class tardis.tardis_portal.admin.ParameterNameInline(parent_model, admin_site)

Bases: django.contrib.admin.options.TabularInline

extra = 0

media

model

alias of tardis.tardis_portal.models.parameters.ParameterName

class tardis.tardis_portal.admin.SchemaAdmin(model, admin_site)

Bases: django.contrib.admin.options.ModelAdmin

inlines = [<class 'tardis.tardis_portal.admin.ParameterNameInline'>]

media

search_fields = ['name', 'namespace']

class tardis.tardis_portal.admin.StorageBoxAdmin(model, admin_site)

Bases: django.contrib.admin.options.ModelAdmin

form

alias of StorageBoxForm

inlines = [<class 'tardis.tardis_portal.admin.StorageBoxOptionInline'>, <class 'tardis.tardis_portal.admin.StorageBoxAttributeInline'>]

media

search_fields = ['name']

class tardis.tardis_portal.admin.StorageBoxAttributeInline(parent_model, admin_site)

Bases: django.contrib.admin.options.TabularInline

extra = 0

form

alias of StorageBoxAttributeInlineForm

media

model

alias of tardis.tardis_portal.models.storage.StorageBoxAttribute

class tardis.tardis_portal.admin.StorageBoxAttributeInlineForm(data=None, files=None, auto_id='id_%s', prefix=None, initial=None, error_class=<class 'django.forms.utils.ErrorList'>, label_suffix=None, empty_permitted=False, instance=None, use_required_attribute=None, renderer=None)

Bases: django.forms.models.ModelForm

class Meta

Bases: object

fields = '__all__'

model

alias of tardis.tardis_portal.models.storage.StorageBoxAttribute

widgets = {'key': <django.forms.widgets.TextInput object>, 'value': <django.forms.widgets.TextInput object>}

base_fields = {'key': <django.forms.fields.CharField object>, 'storage_box': <django.forms.models.ModelChoiceField object>, 'value': <django.forms.fields.CharField object>}

declared_fields = {}

media

class tardis.tardis_portal.admin.StorageBoxForm(data=None, files=None, auto_id='id_%s', prefix=None, initial=None, error_class=<class 'django.forms.utils.ErrorList'>, label_suffix=None, empty_permitted=False, instance=None, use_required_attribute=None, renderer=None)

Bases: django.forms.models.ModelForm

class Meta

Bases: object

fields = '__all__'

model

alias of tardis.tardis_portal.models.storage.StorageBox

widgets = {'description': <django.forms.widgets.TextInput object>, 'django_storage_class': <django.forms.widgets.TextInput object>, 'name': <django.forms.widgets.TextInput object>}

base_fields = {'description': <django.forms.fields.CharField object>, 'django_storage_class': <django.forms.fields.CharField object>, 'master_box': <django.forms.models.ModelChoiceField object>, 'max_size': <django.forms.fields.IntegerField object>, 'name': <django.forms.fields.CharField object>, 'status': <django.forms.fields.CharField object>}

declared_fields = {}

media

class tardis.tardis_portal.admin.StorageBoxOptionInline(parent_model, admin_site)

Bases: django.contrib.admin.options.TabularInline

extra = 0

form

alias of StorageBoxOptionInlineForm

media

model

alias of tardis.tardis_portal.models.storage.StorageBoxOption

class tardis.tardis_portal.admin.StorageBoxOptionInlineForm(data=None, files=None, auto_id='id_%s', prefix=None, initial=None, error_class=<class 'django.forms.utils.ErrorList'>, label_suffix=None, empty_permitted=False, instance=None, use_required_attribute=None, renderer=None)

Bases: django.forms.models.ModelForm

class Meta

Bases: object

fields = '__all__'

model

alias of tardis.tardis_portal.models.storage.StorageBoxOption

widgets = {'key': <django.forms.widgets.TextInput object>, 'value': <django.forms.widgets.TextInput object>}

base_fields = {'key': <django.forms.fields.CharField object>, 'storage_box': <django.forms.models.ModelChoiceField object>, 'value': <django.forms.fields.CharField object>, 'value_type': <django.forms.fields.TypedChoiceField object>}

declared_fields = {}

media

class tardis.tardis_portal.admin.UserAuthenticationAdmin(model, admin_site)

Bases: django.contrib.admin.options.ModelAdmin

media

search_fields = ['username', 'authenticationMethod', 'userProfile__user__username']

tardis.tardis_portal.api module

RESTful API for MyTardis models and data. Implemented with Tastypie.

class tardis.tardis_portal.api.ACLAuthorization

Bases: tastypie.authorization.Authorization

Authorisation class for Tastypie.

create_detail(object_list, bundle)

Returns either True if the user is allowed to create the object in question or throw Unauthorized if they are not.

Returns True by default.

create_list(object_list, bundle)

Unimplemented, as Tastypie never creates entire new lists, but present for consistency & possible extension.

delete_detail(object_list, bundle)

Returns either True if the user is allowed to delete the object in question or throw Unauthorized if they are not.

Returns True by default.

delete_list(object_list, bundle)

Returns a list of all the objects a user is allowed to delete.

Should return an empty list if none are allowed.

Returns the entire list by default.

read_detail(object_list, bundle)

Returns either True if the user is allowed to read the object in question or throw Unauthorized if they are not.

Returns True by default.

read_list(object_list, bundle)

Returns a list of all the objects a user is allowed to read.

Should return an empty list if none are allowed.

Returns the entire list by default.

update_detail(object_list, bundle)

Latest TastyPie requires update_detail permissions to be able to create objects. Rather than duplicating code here, we’ll just use the same authorization rules we use for create_detail.

update_list(object_list, bundle)

Returns a list of all the objects a user is allowed to update.

Should return an empty list if none are allowed.

Returns the entire list by default.

class tardis.tardis_portal.api.DataFileResource(api_name=None)

Bases: tardis.tardis_portal.api.MyTardisModelResource

class Meta

Bases: tardis.tardis_portal.api.Meta

filtering = {'dataset': 2, 'directory': ('exact', 'startswith'), 'filename': ('exact',)}

object_class

alias of tardis.tardis_portal.models.datafile.DataFile

ordering = ['id', 'filename', 'modification_time']

queryset

resource_name = 'dataset_file'

base_fields = {'created_time': <tastypie.fields.DateTimeField object>, 'datafile': <tastypie.fields.FileField object>, 'dataset': <tastypie.fields.ForeignKey object>, 'deleted': <tastypie.fields.BooleanField object>, 'deleted_time': <tastypie.fields.DateTimeField object>, 'directory': <tastypie.fields.CharField object>, 'filename': <tastypie.fields.CharField object>, 'id': <tastypie.fields.IntegerField object>, 'md5sum': <tastypie.fields.CharField object>, 'mimetype': <tastypie.fields.CharField object>, 'modification_time': <tastypie.fields.DateTimeField object>, 'parameter_sets': <tastypie.fields.ToManyField object>, 'replicas': <tastypie.fields.ToManyField object>, 'resource_uri': <tastypie.fields.CharField object>, 'sha512sum': <tastypie.fields.CharField object>, 'size': <tastypie.fields.IntegerField object>, 'version': <tastypie.fields.IntegerField object>}

declared_fields = {'datafile': <tastypie.fields.FileField object>, 'dataset': <tastypie.fields.ForeignKey object>, 'parameter_sets': <tastypie.fields.ToManyField object>, 'replicas': <tastypie.fields.ToManyField object>}

deserialize(request, data, format=None)

from https://github.com/toastdriven/django-tastypie/issues/42 modified to deserialize json sent via POST. Would fail if data is sent in a different format. uses a hack to get back pure json from request.POST

download_file(request, **kwargs)

curl needs the -J switch to get the filename right auth needs to be added manually here

hydrate(bundle)

A hook to allow an initial manipulation of data before all methods/fields have built out the hydrated data.

Useful if you need to access more than one hydrated field or want to annotate on additional data.

Must return the modified bundle.

obj_create(bundle, **kwargs)

Creates a new DataFile object from the provided bundle.data dict.

If a duplicate key error occurs, responds with HTTP Error 409: CONFLICT

post_list(request, **kwargs)

Creates a new resource/object with the provided data.

Calls obj_create with the provided data and returns a response with the new resource’s location.

If a new resource is created, return HttpCreated (201 Created). If Meta.always_return_data = True, there will be a populated body of serialized data.

prepend_urls()

A hook for adding your own URLs or matching before the default URLs.

put_detail(request, **kwargs)

from https://github.com/toastdriven/django-tastypie/issues/42

temp_url = None

verify_file(request, **kwargs)

triggers verification of file, e.g. after non-POST upload complete

class tardis.tardis_portal.api.DatafileParameterResource(api_name=None)

Bases: tardis.tardis_portal.api.ParameterResource

class Meta

Bases: tardis.tardis_portal.api.Meta

object_class

alias of tardis.tardis_portal.models.parameters.DatafileParameter

queryset

base_fields = {'datetime_value': <tastypie.fields.DateTimeField object>, 'id': <tastypie.fields.IntegerField object>, 'link_id': <tastypie.fields.IntegerField object>, 'name': <tastypie.fields.ForeignKey object>, 'numerical_value': <tastypie.fields.FloatField object>, 'parameterset': <tastypie.fields.ForeignKey object>, 'resource_uri': <tastypie.fields.CharField object>, 'string_value': <tastypie.fields.CharField object>, 'value': <tastypie.fields.CharField object>}

declared_fields = {'parameterset': <tastypie.fields.ForeignKey object>}

class tardis.tardis_portal.api.DatafileParameterSetResource(api_name=None)

Bases: tardis.tardis_portal.api.ParameterSetResource

class Meta

Bases: tardis.tardis_portal.api.Meta

object_class

alias of tardis.tardis_portal.models.parameters.DatafileParameterSet

queryset

base_fields = {'datafile': <tastypie.fields.ForeignKey object>, 'id': <tastypie.fields.IntegerField object>, 'parameters': <tastypie.fields.ToManyField object>, 'resource_uri': <tastypie.fields.CharField object>, 'schema': <tastypie.fields.ForeignKey object>}

declared_fields = {'datafile': <tastypie.fields.ForeignKey object>, 'parameters': <tastypie.fields.ToManyField object>}

class tardis.tardis_portal.api.DatasetParameterResource(api_name=None)

Bases: tardis.tardis_portal.api.ParameterResource

class Meta

Bases: tardis.tardis_portal.api.Meta

object_class

alias of tardis.tardis_portal.models.parameters.DatasetParameter

queryset

base_fields = {'datetime_value': <tastypie.fields.DateTimeField object>, 'id': <tastypie.fields.IntegerField object>, 'link_id': <tastypie.fields.IntegerField object>, 'name': <tastypie.fields.ForeignKey object>, 'numerical_value': <tastypie.fields.FloatField object>, 'parameterset': <tastypie.fields.ForeignKey object>, 'resource_uri': <tastypie.fields.CharField object>, 'string_value': <tastypie.fields.CharField object>, 'value': <tastypie.fields.CharField object>}

declared_fields = {'parameterset': <tastypie.fields.ForeignKey object>}

class tardis.tardis_portal.api.DatasetParameterSetResource(api_name=None)

Bases: tardis.tardis_portal.api.ParameterSetResource

class Meta

Bases: tardis.tardis_portal.api.Meta

object_class

alias of tardis.tardis_portal.models.parameters.DatasetParameterSet

queryset

base_fields = {'dataset': <tastypie.fields.ForeignKey object>, 'id': <tastypie.fields.IntegerField object>, 'parameters': <tastypie.fields.ToManyField object>, 'resource_uri': <tastypie.fields.CharField object>, 'schema': <tastypie.fields.ForeignKey object>}

declared_fields = {'dataset': <tastypie.fields.ForeignKey object>, 'parameters': <tastypie.fields.ToManyField object>}

class tardis.tardis_portal.api.DatasetResource(api_name=None)

Bases: tardis.tardis_portal.api.MyTardisModelResource

class Meta

Bases: tardis.tardis_portal.api.Meta

always_return_data = True

filtering = {'description': ('exact',), 'directory': ('exact',), 'experiments': 2, 'id': ('exact',), 'instrument': 2}

object_class

alias of tardis.tardis_portal.models.dataset.Dataset

ordering = ['id', 'description']

queryset

base_fields = {'created_time': <tastypie.fields.DateTimeField object>, 'description': <tastypie.fields.CharField object>, 'directory': <tastypie.fields.CharField object>, 'experiments': <tastypie.fields.ToManyField object>, 'id': <tastypie.fields.IntegerField object>, 'immutable': <tastypie.fields.BooleanField object>, 'instrument': <tastypie.fields.ForeignKey object>, 'modified_time': <tastypie.fields.DateTimeField object>, 'parameter_sets': <tastypie.fields.ToManyField object>, 'resource_uri': <tastypie.fields.CharField object>}

declared_fields = {'experiments': <tastypie.fields.ToManyField object>, 'instrument': <tastypie.fields.ForeignKey object>, 'parameter_sets': <tastypie.fields.ToManyField object>}

get_child_dir_nodes(request, **kwargs)

Return JSON-serialized list of filenames/folders within a child subdirectory

get_datafiles(request, **kwargs)

get_root_dir_nodes(request, **kwargs)

Return JSON-serialized list of filenames/folders in the dataset’s root directory

hydrate_m2m(bundle)

Create experiment-dataset associations first, because they affect authorization for adding other related resources, e.g. metadata

prepend_urls()

A hook for adding your own URLs or matching before the default URLs.

class tardis.tardis_portal.api.ExperimentAuthorResource(api_name=None)

Bases: tardis.tardis_portal.api.MyTardisModelResource

API for ExperimentAuthors

class Meta

Bases: tardis.tardis_portal.api.Meta

always_return_data = True

filtering = {'author': ('exact', 'iexact'), 'email': ('exact', 'iexact'), 'experiment': 2, 'id': ('exact',), 'institution': ('exact', 'iexact'), 'order': ('exact',), 'url': ('exact', 'iexact')}

object_class

alias of tardis.tardis_portal.models.experiment.ExperimentAuthor

ordering = ['id', 'author', 'email', 'order']

queryset

base_fields = {'author': <tastypie.fields.CharField object>, 'email': <tastypie.fields.CharField object>, 'experiment': <tastypie.fields.ForeignKey object>, 'id': <tastypie.fields.IntegerField object>, 'institution': <tastypie.fields.CharField object>, 'order': <tastypie.fields.IntegerField object>, 'resource_uri': <tastypie.fields.CharField object>, 'url': <tastypie.fields.CharField object>}

declared_fields = {'experiment': <tastypie.fields.ForeignKey object>}

class tardis.tardis_portal.api.ExperimentParameterResource(api_name=None)

Bases: tardis.tardis_portal.api.ParameterResource

class Meta

Bases: tardis.tardis_portal.api.Meta

object_class

alias of tardis.tardis_portal.models.parameters.ExperimentParameter

queryset

base_fields = {'datetime_value': <tastypie.fields.DateTimeField object>, 'id': <tastypie.fields.IntegerField object>, 'link_id': <tastypie.fields.IntegerField object>, 'name': <tastypie.fields.ForeignKey object>, 'numerical_value': <tastypie.fields.FloatField object>, 'parameterset': <tastypie.fields.ForeignKey object>, 'resource_uri': <tastypie.fields.CharField object>, 'string_value': <tastypie.fields.CharField object>, 'value': <tastypie.fields.CharField object>}

declared_fields = {'parameterset': <tastypie.fields.ForeignKey object>}

class tardis.tardis_portal.api.ExperimentParameterSetResource(api_name=None)

Bases: tardis.tardis_portal.api.ParameterSetResource

API for ExperimentParameterSets

class Meta

Bases: tardis.tardis_portal.api.Meta

object_class

alias of tardis.tardis_portal.models.parameters.ExperimentParameterSet

queryset

base_fields = {'experiment': <tastypie.fields.ForeignKey object>, 'id': <tastypie.fields.IntegerField object>, 'parameters': <tastypie.fields.ToManyField object>, 'resource_uri': <tastypie.fields.CharField object>, 'schema': <tastypie.fields.ForeignKey object>}

declared_fields = {'experiment': <tastypie.fields.ForeignKey object>, 'parameters': <tastypie.fields.ToManyField object>}

class tardis.tardis_portal.api.ExperimentResource(api_name=None)

Bases: tardis.tardis_portal.api.MyTardisModelResource

API for Experiments also creates a default ACL and allows ExperimentParameterSets to be read and written.

TODO: catch duplicate schema submissions for parameter sets

class Meta

Bases: tardis.tardis_portal.api.Meta

always_return_data = True

filtering = {'id': ('exact',), 'title': ('exact',)}

object_class

alias of tardis.tardis_portal.models.experiment.Experiment

ordering = ['id', 'title', 'created_time', 'update_time']

queryset

base_fields = {'approved': <tastypie.fields.BooleanField object>, 'created_by': <tastypie.fields.ForeignKey object>, 'created_time': <tastypie.fields.DateTimeField object>, 'description': <tastypie.fields.CharField object>, 'end_time': <tastypie.fields.DateTimeField object>, 'handle': <tastypie.fields.CharField object>, 'id': <tastypie.fields.IntegerField object>, 'institution_name': <tastypie.fields.CharField object>, 'locked': <tastypie.fields.BooleanField object>, 'parameter_sets': <tastypie.fields.ToManyField object>, 'public_access': <tastypie.fields.IntegerField object>, 'resource_uri': <tastypie.fields.CharField object>, 'start_time': <tastypie.fields.DateTimeField object>, 'title': <tastypie.fields.CharField object>, 'update_time': <tastypie.fields.DateTimeField object>, 'url': <tastypie.fields.CharField object>}

declared_fields = {'created_by': <tastypie.fields.ForeignKey object>, 'parameter_sets': <tastypie.fields.ToManyField object>}

dehydrate(bundle)

A hook to allow a final manipulation of data once all fields/methods have built out the dehydrated data.

Useful if you need to access more than one dehydrated field or want to annotate on additional data.

Must return the modified bundle.

hydrate_m2m(bundle)

create ACL before any related objects are created in order to use ACL permissions for those objects.

obj_create(bundle, **kwargs)

experiments need at least one ACL to be available through the ExperimentManager (Experiment.safe) Currently not tested for failed db transactions as sqlite does not enforce limits.

class tardis.tardis_portal.api.FacilityResource(api_name=None)

Bases: tardis.tardis_portal.api.MyTardisModelResource

class Meta

Bases: tardis.tardis_portal.api.Meta

always_return_data = True

filtering = {'id': ('exact',), 'manager_group': 2, 'name': ('exact',)}

object_class

alias of tardis.tardis_portal.models.facility.Facility

ordering = ['id', 'name']

queryset

base_fields = {'created_time': <tastypie.fields.DateTimeField object>, 'id': <tastypie.fields.IntegerField object>, 'manager_group': <tastypie.fields.ForeignKey object>, 'modified_time': <tastypie.fields.DateTimeField object>, 'name': <tastypie.fields.CharField object>, 'resource_uri': <tastypie.fields.CharField object>}

declared_fields = {'manager_group': <tastypie.fields.ForeignKey object>}

class tardis.tardis_portal.api.GroupResource(api_name=None)

Bases: tastypie.resources.ModelResource

class Meta

Bases: object

authentication = <tardis.tardis_portal.api.MyTardisAuthentication object>

authorization

Authorisation class for Tastypie.

filtering = {'id': ('exact',), 'name': ('exact',)}

object_class

alias of django.contrib.auth.models.Group

queryset

base_fields = {'id': <tastypie.fields.IntegerField object>, 'name': <tastypie.fields.CharField object>, 'resource_uri': <tastypie.fields.CharField object>}

declared_fields = {}

class tardis.tardis_portal.api.InstrumentResource(api_name=None)

Bases: tardis.tardis_portal.api.MyTardisModelResource

class Meta

Bases: tardis.tardis_portal.api.Meta

always_return_data = True

filtering = {'facility': 2, 'id': ('exact',), 'name': ('exact',)}

object_class

alias of tardis.tardis_portal.models.instrument.Instrument

ordering = ['id', 'name']

queryset

base_fields = {'created_time': <tastypie.fields.DateTimeField object>, 'facility': <tastypie.fields.ForeignKey object>, 'id': <tastypie.fields.IntegerField object>, 'modified_time': <tastypie.fields.DateTimeField object>, 'name': <tastypie.fields.CharField object>, 'resource_uri': <tastypie.fields.CharField object>}

declared_fields = {'facility': <tastypie.fields.ForeignKey object>}

class tardis.tardis_portal.api.LocationResource(api_name=None)

Bases: tardis.tardis_portal.api.MyTardisModelResource

class Meta

Bases: tardis.tardis_portal.api.Meta

queryset

base_fields = {'resource_uri': <tastypie.fields.CharField object>}

declared_fields = {}

class tardis.tardis_portal.api.MyTardisAuthentication

Bases: object

custom tastypie authentication that works with both anonymous use and a number of available auth mechanisms.

get_identifier(request)

is_authenticated(request, **kwargs)

handles backends explicitly so that it can return False when credentials are given but wrong and return Anonymous User when credentials are not given or the session has expired (web use).

class tardis.tardis_portal.api.MyTardisModelResource(api_name=None)

Bases: tastypie.resources.ModelResource

class Meta

Bases: object

authentication = <tardis.tardis_portal.api.MyTardisAuthentication object>

authorization

Authorisation class for Tastypie.

object_class = None

serializer = <tardis.tardis_portal.api.PrettyJSONSerializer object>

base_fields = {'resource_uri': <tastypie.fields.CharField object>}

declared_fields = {}

class tardis.tardis_portal.api.ObjectACLResource(api_name=None)

Bases: tardis.tardis_portal.api.MyTardisModelResource

class Meta

Bases: object

authentication = <tardis.tardis_portal.api.MyTardisAuthentication object>

authorization

Authorisation class for Tastypie.

filtering = {'entityId': ('exact',), 'pluginId': ('exact',)}

object_class

alias of tardis.tardis_portal.models.access_control.ObjectACL

ordering = ['id']

queryset

base_fields = {'aclOwnershipType': <tastypie.fields.IntegerField object>, 'canDelete': <tastypie.fields.BooleanField object>, 'canRead': <tastypie.fields.BooleanField object>, 'canWrite': <tastypie.fields.BooleanField object>, 'content_object': <tastypie.contrib.contenttypes.fields.GenericForeignKeyField object>, 'effectiveDate': <tastypie.fields.DateField object>, 'entityId': <tastypie.fields.CharField object>, 'expiryDate': <tastypie.fields.DateField object>, 'id': <tastypie.fields.IntegerField object>, 'isOwner': <tastypie.fields.BooleanField object>, 'object_id': <tastypie.fields.IntegerField object>, 'pluginId': <tastypie.fields.CharField object>, 'resource_uri': <tastypie.fields.CharField object>}

declared_fields = {'content_object': <tastypie.contrib.contenttypes.fields.GenericForeignKeyField object>}

hydrate(bundle)

A hook to allow an initial manipulation of data before all methods/fields have built out the hydrated data.

Useful if you need to access more than one hydrated field or want to annotate on additional data.

Must return the modified bundle.

class tardis.tardis_portal.api.ParameterNameResource(api_name=None)

Bases: tardis.tardis_portal.api.MyTardisModelResource

class Meta

Bases: tardis.tardis_portal.api.Meta

filtering = {'schema': 2}

object_class

alias of tardis.tardis_portal.models.parameters.ParameterName

queryset

base_fields = {'choices': <tastypie.fields.CharField object>, 'comparison_type': <tastypie.fields.IntegerField object>, 'data_type': <tastypie.fields.IntegerField object>, 'full_name': <tastypie.fields.CharField object>, 'id': <tastypie.fields.IntegerField object>, 'immutable': <tastypie.fields.BooleanField object>, 'is_searchable': <tastypie.fields.BooleanField object>, 'name': <tastypie.fields.CharField object>, 'order': <tastypie.fields.IntegerField object>, 'resource_uri': <tastypie.fields.CharField object>, 'schema': <tastypie.fields.ForeignKey object>, 'units': <tastypie.fields.CharField object>}

declared_fields = {'schema': <tastypie.fields.ForeignKey object>}

class tardis.tardis_portal.api.ParameterResource(api_name=None)

Bases: tardis.tardis_portal.api.MyTardisModelResource

base_fields = {'name': <tastypie.fields.ForeignKey object>, 'resource_uri': <tastypie.fields.CharField object>, 'value': <tastypie.fields.CharField object>}

declared_fields = {'name': <tastypie.fields.ForeignKey object>, 'value': <tastypie.fields.CharField object>}

hydrate(bundle)

sets the parametername by uri or name if untyped value is given, set value via parameter method, otherwise use modelresource automatisms

class tardis.tardis_portal.api.ParameterSetResource(api_name=None)

Bases: tardis.tardis_portal.api.MyTardisModelResource

base_fields = {'resource_uri': <tastypie.fields.CharField object>, 'schema': <tastypie.fields.ForeignKey object>}

declared_fields = {'schema': <tastypie.fields.ForeignKey object>}

hydrate_schema(bundle)

class tardis.tardis_portal.api.PrettyJSONSerializer(formats=None, content_types=None, datetime_formatting=None)

Bases: tastypie.serializers.Serializer

json_indent = 2

to_json(data, options=None)

Given some Python data, produces JSON output.

class tardis.tardis_portal.api.ReplicaResource(api_name=None)

Bases: tardis.tardis_portal.api.MyTardisModelResource

class Meta

Bases: tardis.tardis_portal.api.Meta

filtering = {'url': ('exact', 'startswith'), 'verified': ('exact',)}

object_class

alias of tardis.tardis_portal.models.datafile.DataFileObject

ordering = ['id']

queryset

base_fields = {'created_time': <tastypie.fields.DateTimeField object>, 'datafile': <tastypie.fields.ForeignKey object>, 'id': <tastypie.fields.IntegerField object>, 'last_verified_time': <tastypie.fields.DateTimeField object>, 'resource_uri': <tastypie.fields.CharField object>, 'uri': <tastypie.fields.CharField object>, 'verified': <tastypie.fields.BooleanField object>}

declared_fields = {'datafile': <tastypie.fields.ForeignKey object>}

dehydrate(bundle)

A hook to allow a final manipulation of data once all fields/methods have built out the dehydrated data.

Useful if you need to access more than one dehydrated field or want to annotate on additional data.

Must return the modified bundle.

hydrate(bundle)

A hook to allow an initial manipulation of data before all methods/fields have built out the hydrated data.

Useful if you need to access more than one hydrated field or want to annotate on additional data.

Must return the modified bundle.

class tardis.tardis_portal.api.SchemaResource(api_name=None)

Bases: tardis.tardis_portal.api.MyTardisModelResource

class Meta

Bases: tardis.tardis_portal.api.Meta

filtering = {'id': ('exact',), 'namespace': ('exact',)}

object_class

alias of tardis.tardis_portal.models.parameters.Schema

ordering = ['id']

queryset

base_fields = {'hidden': <tastypie.fields.BooleanField object>, 'id': <tastypie.fields.IntegerField object>, 'immutable': <tastypie.fields.BooleanField object>, 'name': <tastypie.fields.CharField object>, 'namespace': <tastypie.fields.CharField object>, 'resource_uri': <tastypie.fields.CharField object>, 'subtype': <tastypie.fields.CharField object>, 'type': <tastypie.fields.IntegerField object>}

declared_fields = {}

class tardis.tardis_portal.api.StorageBoxAttributeResource(api_name=None)

Bases: tardis.tardis_portal.api.MyTardisModelResource

class Meta

Bases: tardis.tardis_portal.api.Meta

object_class

alias of tardis.tardis_portal.models.storage.StorageBoxAttribute

ordering = ['id']

queryset

base_fields = {'id': <tastypie.fields.IntegerField object>, 'key': <tastypie.fields.CharField object>, 'resource_uri': <tastypie.fields.CharField object>, 'storage_box': <tastypie.fields.ForeignKey object>, 'value': <tastypie.fields.CharField object>}

declared_fields = {'storage_box': <tastypie.fields.ForeignKey object>}

class tardis.tardis_portal.api.StorageBoxOptionResource(api_name=None)

Bases: tardis.tardis_portal.api.MyTardisModelResource

class Meta

Bases: tardis.tardis_portal.api.Meta

object_class

alias of tardis.tardis_portal.models.storage.StorageBoxOption

ordering = ['id']

queryset

accessible_keys = ['location']

base_fields = {'id': <tastypie.fields.IntegerField object>, 'key': <tastypie.fields.CharField object>, 'resource_uri': <tastypie.fields.CharField object>, 'storage_box': <tastypie.fields.ForeignKey object>, 'value': <tastypie.fields.CharField object>, 'value_type': <tastypie.fields.CharField object>}

declared_fields = {'storage_box': <tastypie.fields.ForeignKey object>}

class tardis.tardis_portal.api.StorageBoxResource(api_name=None)

Bases: tardis.tardis_portal.api.MyTardisModelResource

class Meta

Bases: tardis.tardis_portal.api.Meta

object_class

alias of tardis.tardis_portal.models.storage.StorageBox

ordering = ['id']

queryset

base_fields = {'attributes': <tastypie.fields.ToManyField object>, 'description': <tastypie.fields.CharField object>, 'django_storage_class': <tastypie.fields.CharField object>, 'id': <tastypie.fields.IntegerField object>, 'max_size': <tastypie.fields.IntegerField object>, 'name': <tastypie.fields.CharField object>, 'options': <tastypie.fields.ToManyField object>, 'resource_uri': <tastypie.fields.CharField object>, 'status': <tastypie.fields.CharField object>}

declared_fields = {'attributes': <tastypie.fields.ToManyField object>, 'options': <tastypie.fields.ToManyField object>}

class tardis.tardis_portal.api.UserResource(api_name=None)

Bases: tastypie.resources.ModelResource

class Meta

Bases: object

allowed_methods = ['get']

authentication = <tardis.tardis_portal.api.MyTardisAuthentication object>

authorization

Authorisation class for Tastypie.

fields = ['username', 'first_name', 'last_name', 'email']

filtering = {'email': ('iexact',), 'username': ('exact',)}

object_class

alias of django.contrib.auth.models.User

queryset

serializer = <tardis.tardis_portal.api.PrettyJSONSerializer object>

base_fields = {'email': <tastypie.fields.CharField object>, 'first_name': <tastypie.fields.CharField object>, 'groups': <tastypie.fields.ManyToManyField object>, 'last_name': <tastypie.fields.CharField object>, 'resource_uri': <tastypie.fields.CharField object>, 'username': <tastypie.fields.CharField object>}

declared_fields = {'groups': <tastypie.fields.ManyToManyField object>}

dehydrate(bundle)

use cases:

public user:
  anonymous:
    name, uri, email, id
  authenticated:
    other user:
      name, uri, email, id [, username if facility manager]
    same user:
      name, uri, email, id, username
private user:
  anonymous:
    none
  authenticated:
    other user:
      name, uri, id [, username, email if facility manager]
    same user:
      name, uri, email, id, username

tardis.tardis_portal.context_processors module

tardis.tardis_portal.context_processors.global_contexts(request)

tardis.tardis_portal.context_processors.google_analytics(request)

adds context for portal_template.html

tardis.tardis_portal.context_processors.registration_processor(request)

tardis.tardis_portal.context_processors.single_search_processor(request)

tardis.tardis_portal.context_processors.user_details_processor(request)

tardis.tardis_portal.context_processors.user_menu_processor(request)

tardis.tardis_portal.deprecations module

Deprecation warnings

exception tardis.tardis_portal.deprecations.RemovedInMyTardis42Warning

Bases: DeprecationWarning

Used to raise warnings about deprecated functionality.

Usage:

import warnings

warnings.warn(
    "This method will be removed in MyTardis 4.2. "
    "Please use method2 instead.",
    RemovedInMyTardis42Warning
)

exception tardis.tardis_portal.deprecations.RemovedInMyTardis43Warning

Bases: PendingDeprecationWarning

Used to raise warnings about deprecated functionality.

Usage:

import warnings

warnings.warn(
    "This method will be removed in MyTardis 4.3. "
    "Please use method2 instead.",
    RemovedInMyTardis43Warning
)

tardis.tardis_portal.download module

download.py

class tardis.tardis_portal.download.UncachedTarStream(mapped_file_objs, filename, do_gzip=False, buffersize=131072, comp_level=6, http_buffersize=65535)

Bases: tarfile.TarFile

Stream files into a compressed tar stream on the fly

close_gzip()

compress(buf)

compute_size()

get_response(tracker_data=None)

make_tar()

main tar generator. until python 3 needs to be in one function because ‘yield’s don’t bubble up.

prepare_output(uc_buf, remainder)

tarinfo_for_df(df, name)

tardis.tardis_portal.download.classic_mapper(rootdir)

tardis.tardis_portal.download.download_api_key(request)

tardis.tardis_portal.download.download_datafile(request, datafile_id)

tardis.tardis_portal.download.get_download_organizations()

tardis.tardis_portal.download.make_mapper(organization, rootdir)

tardis.tardis_portal.download.streaming_download_datafiles(request)

takes string parameter “comptype” for compression method. Currently implemented: “tgz” and “tar” The datafiles to be downloaded are selected using “datafile”, “dataset” or “url” parameters. An “expid” parameter may be supplied for use in the download archive name. If “url” is used, the “expid” parameter is also used to limit the datafiles to be downloaded to a given experiment.

tardis.tardis_portal.download.view_datafile(request, datafile_id)

tardis.tardis_portal.email module

tardis.tardis_portal.email.build_template_html(template_filename, context)

tardis.tardis_portal.email.build_template_text(template_filename, context)

tardis.tardis_portal.email.email_user(subject, template_filename, context, user)

tardis.tardis_portal.fields module

class tardis.tardis_portal.fields.MultiValueCommaSeparatedField(fields, *, require_all_fields=True, **kwargs)

Bases: django.forms.fields.MultiValueField

compress(data_list)

Return a single value for the given list of values. The values can be assumed to be valid.

For example, if this MultiValueField was instantiated with fields=(DateField(), TimeField()), this might return a datetime object created by combining the date and time in data_list.

tardis.tardis_portal.forms module

forms module

class tardis.tardis_portal.forms.AddUserPermissionsForm(data=None, files=None, auto_id='id_%s', prefix=None, initial=None, error_class=<class 'django.forms.utils.ErrorList'>, label_suffix=None, empty_permitted=False, field_order=None, use_required_attribute=None, renderer=None)

Bases: django.forms.forms.Form

base_fields = {'authMethod': <django.forms.fields.CharField object>, 'autocomp_user': <django.forms.fields.CharField object>, 'delete': <django.forms.fields.BooleanField object>, 'entered_user': <django.forms.fields.CharField object>, 'read': <django.forms.fields.BooleanField object>, 'write': <django.forms.fields.BooleanField object>}

declared_fields = {'authMethod': <django.forms.fields.CharField object>, 'autocomp_user': <django.forms.fields.CharField object>, 'delete': <django.forms.fields.BooleanField object>, 'entered_user': <django.forms.fields.CharField object>, 'read': <django.forms.fields.BooleanField object>, 'write': <django.forms.fields.BooleanField object>}

media

class tardis.tardis_portal.forms.CreateUserPermissionsForm(data=None, files=None, auto_id='id_%s', prefix=None, initial=None, error_class=<class 'django.forms.utils.ErrorList'>, label_suffix=None, empty_permitted=False, field_order=None, use_required_attribute=None, renderer=None)

Bases: tardis.tardis_portal.forms.RegistrationForm

base_fields = {'authMethod': <django.forms.fields.CharField object>, 'email': <django.forms.fields.EmailField object>, 'password1': <django.forms.fields.CharField object>, 'password2': <django.forms.fields.CharField object>, 'username': <django.forms.fields.RegexField object>}

declared_fields = {'authMethod': <django.forms.fields.CharField object>, 'email': <django.forms.fields.EmailField object>, 'password1': <django.forms.fields.CharField object>, 'password2': <django.forms.fields.CharField object>, 'username': <django.forms.fields.RegexField object>}

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class tardis.tardis_portal.forms.DatasetForm(data=None, files=None, auto_id='id_%s', prefix=None, initial=None, error_class=<class 'django.forms.utils.ErrorList'>, label_suffix=None, empty_permitted=False, instance=None, use_required_attribute=None, renderer=None)

Bases: django.forms.models.ModelForm

class Meta

Bases: object

fields = ['description', 'directory', 'instrument']

model

alias of tardis.tardis_portal.models.dataset.Dataset

base_fields = {'description': <django.forms.fields.CharField object>, 'directory': <django.forms.fields.CharField object>, 'instrument': <django.forms.models.ModelChoiceField object>}

declared_fields = {'description': <django.forms.fields.CharField object>}

media

class tardis.tardis_portal.forms.ExperimentAuthor(data=None, files=None, auto_id='id_%s', prefix=None, initial=None, error_class=<class 'django.forms.utils.ErrorList'>, label_suffix=None, empty_permitted=False, instance=None, use_required_attribute=None, renderer=None)

Bases: django.forms.models.ModelForm

class Meta

Bases: object

fields = ['author', 'institution', 'email', 'order', 'url']

model

alias of tardis.tardis_portal.models.experiment.ExperimentAuthor

base_fields = {'author': <django.forms.fields.CharField object>, 'email': <django.forms.fields.CharField object>, 'institution': <django.forms.fields.CharField object>, 'order': <django.forms.fields.IntegerField object>, 'url': <django.forms.fields.URLField object>}

declared_fields = {}

media

class tardis.tardis_portal.forms.ExperimentForm(data=None, files=None, auto_id='%s', prefix=None, initial=None, error_class=<class 'django.forms.utils.ErrorList'>, label_suffix=':', empty_permitted=False, instance=None, extra=0)

Bases: django.forms.models.ModelForm

This handles the complex experiment forms.

All internal datasets forms are prefixed with dataset_, and all internal dataset file fields are prefixed with file_. These are parsed out of the post data and added to the form as internal lists.

class FullExperiment(**kwargs)

Bases: collections.UserDict

This is a dict wrapper that store the values returned from the tardis.tardis_portal.forms.ExperimentForm.save() function. It provides a convience method for saving the model objects.

save_m2m()

{‘experiment’: experiment, ‘experiment_authors’: experiment_authors, ‘authors’: authors, ‘datasets’: datasets, ‘datafiles’: datafiles}

class Meta

Bases: object

fields = ('title', 'institution_name', 'description')

model

alias of tardis.tardis_portal.models.experiment.Experiment

base_fields = {'description': <django.forms.fields.CharField object>, 'institution_name': <django.forms.fields.CharField object>, 'title': <django.forms.fields.CharField object>, 'url': <django.forms.fields.CharField object>}

declared_fields = {'url': <django.forms.fields.CharField object>}

is_valid()

Test the validity of the form, the form may be invalid even if the error attribute has no contents. This is because the returnd value is dependent on the validity of the nested forms.

This validity also takes into account forign keys that might be dependent on an unsaved model.

Returns:validity Return type:bool

media

save(commit=True)

Save this form’s self.instance object if commit=True. Otherwise, add a save_m2m() method to the form which can be called after the instance is saved manually at a later time. Return the model instance.

class tardis.tardis_portal.forms.ImportParamsForm(data=None, files=None, auto_id='id_%s', prefix=None, initial=None, error_class=<class 'django.forms.utils.ErrorList'>, label_suffix=None, empty_permitted=False, field_order=None, use_required_attribute=None, renderer=None)

Bases: django.forms.forms.Form

base_fields = {'params': <django.forms.fields.FileField object>, 'password': <django.forms.fields.CharField object>, 'username': <django.forms.fields.CharField object>}

declared_fields = {'params': <django.forms.fields.FileField object>, 'password': <django.forms.fields.CharField object>, 'username': <django.forms.fields.CharField object>}

media

class tardis.tardis_portal.forms.LoginForm(*args, **kwargs)

Bases: django.contrib.auth.forms.AuthenticationForm

base_fields = {'password': <django.forms.fields.CharField object>, 'username': <django.contrib.auth.forms.UsernameField object>}

declared_fields = {'password': <django.forms.fields.CharField object>, 'username': <django.contrib.auth.forms.UsernameField object>}

media

class tardis.tardis_portal.forms.ManageAccountForm(data=None, files=None, auto_id='id_%s', prefix=None, initial=None, error_class=<class 'django.forms.utils.ErrorList'>, label_suffix=None, empty_permitted=False, instance=None, use_required_attribute=None, renderer=None)

Bases: django.forms.models.ModelForm

Form for changing account details.

class Meta

Bases: object

fields = ('first_name', 'last_name', 'email')

model

alias of django.contrib.auth.models.User

base_fields = {'email': <django.forms.fields.EmailField object>, 'first_name': <django.forms.fields.CharField object>, 'last_name': <django.forms.fields.CharField object>}

declared_fields = {}

media

class tardis.tardis_portal.forms.ManageGroupPermissionsForm(data=None, files=None, auto_id='id_%s', prefix=None, initial=None, error_class=<class 'django.forms.utils.ErrorList'>, label_suffix=None, empty_permitted=False, field_order=None, use_required_attribute=None, renderer=None)

Bases: django.forms.forms.Form

base_fields = {'adduser': <django.forms.fields.CharField object>, 'admin': <django.forms.fields.BooleanField object>, 'authMethod': <django.forms.fields.CharField object>}

declared_fields = {'adduser': <django.forms.fields.CharField object>, 'admin': <django.forms.fields.BooleanField object>, 'authMethod': <django.forms.fields.CharField object>}

media

class tardis.tardis_portal.forms.NoInput(attrs=None)

Bases: django.forms.widgets.Widget

media

render(name, value, attrs=None)

Render the widget as an HTML string.

class tardis.tardis_portal.forms.RegisterExperimentForm(data=None, files=None, auto_id='id_%s', prefix=None, initial=None, error_class=<class 'django.forms.utils.ErrorList'>, label_suffix=None, empty_permitted=False, field_order=None, use_required_attribute=None, renderer=None)

Bases: django.forms.forms.Form

base_fields = {'experiment_owner': <django.forms.fields.CharField object>, 'from_url': <django.forms.fields.CharField object>, 'originid': <django.forms.fields.CharField object>, 'password': <django.forms.fields.CharField object>, 'username': <django.forms.fields.CharField object>, 'xml_filename': <django.forms.fields.CharField object>, 'xmldata': <django.forms.fields.FileField object>}

declared_fields = {'experiment_owner': <django.forms.fields.CharField object>, 'from_url': <django.forms.fields.CharField object>, 'originid': <django.forms.fields.CharField object>, 'password': <django.forms.fields.CharField object>, 'username': <django.forms.fields.CharField object>, 'xml_filename': <django.forms.fields.CharField object>, 'xmldata': <django.forms.fields.FileField object>}

media

class tardis.tardis_portal.forms.RegistrationForm(data=None, files=None, auto_id='id_%s', prefix=None, initial=None, error_class=<class 'django.forms.utils.ErrorList'>, label_suffix=None, empty_permitted=False, field_order=None, use_required_attribute=None, renderer=None)

Bases: django.forms.forms.Form

Form for registering a new user account.

Validates that the requested username is not already in use, and requires the password to be entered twice to catch typos.

Subclasses should feel free to add any additional validation they need, but should avoid defining a save() method – the actual saving of collected user data is delegated to the active registration backend.

base_fields = {'email': <django.forms.fields.EmailField object>, 'password1': <django.forms.fields.CharField object>, 'password2': <django.forms.fields.CharField object>, 'username': <django.forms.fields.RegexField object>}

clean()

Verifiy that the values entered into the two password fields match. Note that an error here will end up in non_field_errors() because it doesn’t apply to a single field.

clean_username()

Validate that the username is alphanumeric and is not already in use.

declared_fields = {'email': <django.forms.fields.EmailField object>, 'password1': <django.forms.fields.CharField object>, 'password2': <django.forms.fields.CharField object>, 'username': <django.forms.fields.RegexField object>}

media

save(profile_callback=None)

class tardis.tardis_portal.forms.RightsForm(data=None, files=None, auto_id='id_%s', prefix=None, initial=None, error_class=<class 'django.forms.utils.ErrorList'>, label_suffix=None, empty_permitted=False, instance=None, use_required_attribute=None, renderer=None)

Bases: django.forms.models.ModelForm

Form for changing public access and licence.

class Meta

Bases: object

fields = ('public_access', 'license', 'legal_text')

model

alias of tardis.tardis_portal.models.experiment.Experiment

widgets = {'license': <django.forms.widgets.HiddenInput object>}

base_fields = {'legal_text': <django.forms.fields.CharField object>, 'license': <django.forms.models.ModelChoiceField object>, 'public_access': <django.forms.fields.TypedChoiceField object>}

clean()

Hook for doing any extra form-wide cleaning after Field.clean() has been called on every field. Any ValidationError raised by this method will not be associated with a particular field; it will have a special-case association with the field named ‘__all__’.

declared_fields = {'legal_text': <django.forms.fields.CharField object>}

media

class tardis.tardis_portal.forms.StaticField(*, required=True, widget=None, label=None, initial=None, help_text='', error_messages=None, show_hidden_initial=False, validators=(), localize=False, disabled=False, label_suffix=None)

Bases: django.forms.fields.Field

clean(value)

Validate the given value and return its “cleaned” value as an appropriate Python object. Raise ValidationError for any errors.

widget

alias of NoInput

tardis.tardis_portal.forms.createLinkedUserAuthenticationForm(authMethods)

Create a LinkedUserAuthenticationForm and use the contents of authMethods to the list of options in the dropdown menu for authenticationMethod.

tardis.tardis_portal.forms.create_datafile_add_form(schema, parentObject, request=None)

tardis.tardis_portal.forms.create_parameterset_edit_form(parameterset, request=None)

tardis.tardis_portal.forms.getAuthMethodChoices()

tardis.tardis_portal.forms.save_datafile_add_form(schema, parentObject, request)

tardis.tardis_portal.forms.save_datafile_edit_form(parameterset, request)

tardis.tardis_portal.iiif module

tardis.tardis_portal.iiif.compliance_header(f)

tardis.tardis_portal.iiif.compute_etag(request, datafile_id, *args, **kwargs)

tardis.tardis_portal.iiif.download_image(*args, **kwargs)

tardis.tardis_portal.iiif.download_info(*args, **kwargs)

tardis.tardis_portal.logging_middleware module

class tardis.tardis_portal.logging_middleware.LoggingMiddleware(get_response)

Bases: object

process_exception(request, exception)

process_response(request, response)

tardis.tardis_portal.logging_middleware.get_client_ip(request)

tardis.tardis_portal.managers module

managers.py

class tardis.tardis_portal.managers.ExperimentManager

Bases: tardis.tardis_portal.managers.OracleSafeManager

Implements a custom manager for the Experiment model which checks the authorisation rules for the requesting user first

To make this work, the request must be passed to all class functions. The username and the group memberships are then resolved via the user.userprofile.ext_groups and user objects.

The tardis.tardis_portal.auth.AuthService is responsible for filling the request.groups object.

all(user)

Returns all experiments a user - either authenticated or anonymous - is allowed to see and search

Parameters:user (User) – a User instance Returns:QuerySet of Experiments Return type:QuerySet

external_users(experiment_id)

returns a list of groups which have external ACL rules

Parameters:experiment_id (int) – the ID of the experiment to be edited Returns:list of groups with external ACLs Return type:list

get(user, experiment_id)

Returns an experiment under the consideration of the ACL rules Raises PermissionDenied if the user does not have access.

Parameters:

• user (User) – a User instance
• experiment_id (int) – the ID of the experiment to be edited

Returns:

Experiment

Return type:

Experiment

Raises:

PermissionDenied –

group_acls_system_owned(experiment_id)

Returns a list of ACL rules associated with this experiment.

Parameters:experiment_id (int) – the ID of the experiment Returns:QuerySet of system-owned ACLs for experiment Return type:QuerySet

group_acls_user_owned(experiment_id)

Returns a list of ACL rules associated with this experiment.

Parameters:experiment_id (int) – the ID of the experiment Returns:QuerySet of ACLs Return type:QuerySet

owned(user)

Return all experiments which are owned by a particular user, including those shared with a group of which the user is a member.

Parameters:user (User) – a User instance Returns:QuerySet of Experiments owned by user Return type:QuerySet

owned_and_shared(user)

owned_by_group(group)

Return all experiments that are owned by a particular group

owned_by_user(user)

Return all experiments which are owned by a particular user id

Parameters:user (User) – a User Object Returns:QuerySet of Experiments owned by user Return type:QuerySet

owned_by_user_id(userId)

Return all experiments which are owned by a particular user id

Parameters:userId (int) – a User ID Returns:QuerySet of Experiments owned by user id Return type:QuerySet

public()

shared(user)

system_owned_groups(experiment_id)

returns a list of sytem-owned groups which have ACL rules associated with this experiment

Parameters:experiment_id (string) – the ID of the experiment to be edited Returns:system owned groups for experiment Return type:QuerySet

user_acls(experiment_id)

Returns a list of ACL rules associated with this experiment.

Parameters:experiment_id (string) – the ID of the experiment Returns:QuerySet of ACLs Return type:QuerySet

user_owned_groups(experiment_id)

returns a list of user owned-groups which have ACL rules associated with this experiment

Parameters:experiment_id (int) – the ID of the experiment to be edited Returns:QuerySet of non system Groups Return type:QuerySet

users(experiment_id)

Returns a list of users who have ACL rules associated with this experiment.

Parameters:experiment_id (int) – the ID of the experiment Returns:QuerySet of Users with experiment access Return type:QuerySet

class tardis.tardis_portal.managers.OracleSafeManager

Bases: django.db.models.manager.Manager

Implements a custom manager which automatically defers the retreival of any TextField fields on calls to get_queryset. This is to avoid the known issue that ‘distinct’ calls on query_sets containing TextFields fail when Oracle is being used as the backend.

get_queryset()

Return a new QuerySet object. Subclasses can override this method to customize the behavior of the Manager.

class tardis.tardis_portal.managers.ParameterNameManager

Bases: django.db.models.manager.Manager

get_by_natural_key(namespace, name)

class tardis.tardis_portal.managers.SchemaManager

Bases: django.db.models.manager.Manager

get_by_natural_key(namespace)

tardis.tardis_portal.rfc3339 module

The function rfc3339 formats dates according to the RFC 3339. rfc3339 tries to have as much as possible sensible defaults.

tardis.tardis_portal.rfc3339.rfc3339(date, utc=False, use_system_timezone=True)

Return a string formatted according to the RFC 3339. If called with utc=True, it normalizes date to the UTC date. If date does not have any timezone information, uses the local timezone:

>>> date = datetime.datetime(2008, 4, 2, 20)
>>> rfc3339(date, utc=True, use_system_timezone=False)
'2008-04-02T20:00:00Z'
>>> rfc3339(date) 
'2008-04-02T20:00:00...'

If called with user_system_time=False don’t use the local timezone and consider the offset to UTC to be zero:

>>> rfc3339(date, use_system_timezone=False)
'2008-04-02T20:00:00+00:00'

date must be a a datetime.datetime, datetime.date or a timestamp as returned by time.time():

>>> rfc3339(0, utc=True, use_system_timezone=False)
'1970-01-01T00:00:00Z'
>>> rfc3339(datetime.date(2008, 9, 6), use_system_timezone=False)
'2008-09-06T00:00:00+00:00'
>>> rfc3339('foo bar')
Traceback (most recent call last):
...
TypeError: excepted datetime, got str instead

tardis.tardis_portal.shortcuts module

class tardis.tardis_portal.shortcuts.RestfulExperimentParameterSet(schema_func, form_cls)

Bases: object

Helper class which enables a Backbone.sync-compatible interface to be created for a ExperimentParameterSet just by specifying a function which provides the schema and a form.

(A function for the schema is required rather than the actual schema, as to run unit tests effectively the object needs to be able to create the schema after instantiation.)

For UI consistency, it’s best to make sure the schema has hidden == true.

schema

Use schema function to get the schema.

view_functions

tardis.tardis_portal.shortcuts.get_experiment_referer(request, dataset_id)

tardis.tardis_portal.shortcuts.redirect_back_with_error(request, message)

tardis.tardis_portal.shortcuts.render_error_message(request, message, status=400)

Render a simple text error message in a generic error page. Any newlines are turned into <br>.

tardis.tardis_portal.shortcuts.render_response_index(request, *args, **kwargs)

tardis.tardis_portal.shortcuts.render_to_file(template, filename, context)

Write the output of render_to_string to a file.

The render_to_string() method returns a unicode string, which can be written to a file with locale.getpreferredencoding(), usually UTF-8.

tardis.tardis_portal.shortcuts.return_response_error(request)

tardis.tardis_portal.shortcuts.return_response_error_message(request, redirect_path, context)

tardis.tardis_portal.shortcuts.return_response_not_found(request)

tardis.tardis_portal.tasks module

tardis.tardis_portal.util module

tardis.tardis_portal.util.get_filesystem_safe_dataset_name(dataset)

Given a Dataset, return a filesystem safe string representing the dataset. Useful for filenames for dataset downloads, maybe URLs.

Parameters:dataset (tardis.tardis_portal.models.dataset.Dataset) – A Dataset object. Returns:A filesystem safe string as a Dataset name. Return type:basestring

tardis.tardis_portal.util.get_filesystem_safe_experiment_name(experiment)

Given an Experiment, return a filesystem safe string representing the experiment. Useful for filenames for experiment downloads, maybe URLs.

Parameters:experiment (tardis.tardis_portal.models.experiment.Experiment) – A Experiment object. Returns:A filesystem safe string as a Experiment name. Return type:basestring

tardis.tardis_portal.util.get_local_time(dt)

Ensure datetime is timezone-aware and in local time.

If the USE_TZ setting in the current dev version of Django comes in, this should keep providing correct behaviour.

tardis.tardis_portal.util.get_utc_time(dt)

Ensure datetime is timezone-aware and in UTC time.

If the USE_TZ setting in the current dev version of Django comes in, this should keep providing correct behaviour.

tardis.tardis_portal.util.render_mustache(template_name, data)

tardis.tardis_portal.util.render_public_access_badge(experiment)

tardis.tardis_portal.util.split_path(p)

tardis.tardis_portal.widgets module

class tardis.tardis_portal.widgets.CommaSeparatedInput(attrs=None)

Bases: django.forms.widgets.TextInput

media

render(name, value, attrs=None, renderer=None)

Render the widget as an HTML string.

value_from_datadict(data, files, name)

Given a dictionary of data and this widget’s name, return the value of this widget or None if it’s not provided.

class tardis.tardis_portal.widgets.Label(attrs=None)

Bases: django.forms.widgets.Widget

media

render(name, value, attrs=None)

Render the widget as an HTML string.

tag = 'label'

class tardis.tardis_portal.widgets.Span(attrs=None)

Bases: tardis.tardis_portal.widgets.Label

media

tag = 'span'

tardis.tardis_portal.xmlwriter module

class tardis.tardis_portal.xmlwriter.XMLWriter

Bases: object

static write_template_to_dir(dest_dir, dest_filename, template_path, context)

Parameters:

• dest_dir (string) – The directory to store the resulting document in
• dest_filename (string) – The name of the file to be output
• template_path (string) – The relative path to the Django template to be rendered
• context (django.template.context.Context) – The Context object (dictionary of variables for template output)

Returns:

The full path to the created file

Return type:

string

static write_template_to_file(prefix_dir, objectprefix, uniqueid, templatepath, context)

Parameters:

• prefix_dir (string) – The subdirectory off of the OAI_DOCS_PATH to store the resulting document in
• objectprefix (string) – The name prefix of the resulting file. Files are output in the format prefix-uniqueid.xml
• uniqueid (string) – The unique ID of the file to be output
• templatepath (string) – The relative path to the Django template to be rendered
• context (django.template.context.Context) – The Context object (dictionary of variables for template output)

Returns:

The full path to the created file

Return type:

string

static write_xml_to_file(prefix_dir, objectprefix, uniqueid, xmlstring)

Parameters:

• prefix_dir (string) – The subdirectory off of the OAI_DOCS_PATH to store the resulting document in
• objectprefix (string) – The name prefix of the resulting file. Files are output in the format prefix-uniqueid.xml
• uniqueid (string) – The unique ID of the file to be output
• xmlstring (string) – The relative path to the Django template to be rendered

Returns:

The full path to the created file

Return type:

string

tardis.tardis_portal.xmlwriter.logger = <Logger tardis.tardis_portal.xmlwriter (WARNING)>

XML Writer

A set of static methods for writing xml files.

Module contents

importing all views files here, so that any old code will work as expected, when importing from tardis.tardis_portal.views

models/__init__.py

tardis.urls package

Submodules

tardis.urls.accounts module

Accounts URLs

tardis.urls.ajax module

AJAX URLS

tardis.urls.api module

URLs for MyTardis’s RESTful API

tardis.urls.core module

Core URLs

tardis.urls.datafile module

DataFile URLs

tardis.urls.dataset module

Dataset URLs

tardis.urls.display module

Display URLs

tardis.urls.download module

Download URLs

tardis.urls.experiment module

URLs for experiments

tardis.urls.facility module

Facility URLs

tardis.urls.group module

Group URLs

tardis.urls.token module

Token URLs

Module contents

Submodules

tardis.app_config module

class tardis.app_config.AbstractTardisAppConfig(app_name, app_module)

Bases: django.apps.config.AppConfig

All MyTardis app configuration classes should extend this abstract class to have their APIs and URLs automatically added to URL routing.

app_dependencies = []

tardis.app_config.check_app_dependencies(app_configs, **kwargs)

Checks currently installed apps for dependencies required by installed apps as defined by the app_dependencies attribute of the AppConfig object, if present.

Parameters:

• app_configs (AppConfig) – a list of app_configs to check, or None for all apps to be checked
• kwargs (list of args) – unknown list of args

Returns:

a list of unsatisfied dependencies

Return type:

list of strings

tardis.app_config.format_app_name_for_url(name)

tardis.app_config.get_tardis_apps()

Gets a list of tuples where the first element is the app name, and the second is the module path

Returns:a list of tardis apps Return type:list of apps

tardis.app_config.is_tardis_app(app_config)

Determines whether the installed app is a MyTardis app

Parameters:app_config (AppConfig) – the AppConfig object of an installed app Returns:True if the app is a MyTardis app, False otherwise Return type:bool

tardis.celery module

tardis.test_on_mysql_settings module

tardis.test_on_postgresql_settings module

tardis.test_settings module

tardis.test_settings.get_all_tardis_apps()

tardis.views module

tardis.views.error_handler(request, **kwargs)

Module contents

importing all views files here, so that any old code will work as expected, when importing from tardis.tardis_portal.views

models/__init__.py

Documentation for included Apps

Apps and Contextual Views

Introduction

In order to better represent specific data types and facilities, MyTardis allows apps to override the default views for Experiments, Datasets, DataFile metadata, and the main index and login pages. The following sections detail settings and requirements of apps to make this happen.

Datafile Views

Rationale

By default there exists an option to show the metadata of individual DataFile s in the default Dataset view. Some kinds of files allow for rich and useful visualisation and/or processing. For this purpose there exist contextual views, views that are available depending on the type of file they refer to.

User Guide

A default installation has no contextual views. To enable them a few steps are needed:

• an app needs to be installed either in tardis/apps/, or the app’s configuration must subclass AbstractTardisAppConfig thereby enabling autodetection. AbstractTardisAppConfig replaces AppConfig as described in these django docs.
• DataFile s need to be manually or automatically tagged with a schema that identifies them as viewable with a particular view. Filters are a convenient way to do this. See below for an example.
• settings need to be added to settings.py. A list called DATAFILE_VIEWS holds a tuple for each available view. The first entry of the tuple is a schema namespace and is matched against all schemas attached to the DataFile. If a match occurs, a link to the url given as second entry of the tuple is added to the Datafile Detail section of the default Dataset view and loaded via AJAX on demand. Example:

DATAFILE_VIEWS = [("http://example.org/schemas/datafile/my_awesome_schema",
                   "/apps/my-awesome-app/view"),]

Currently, the default view is always DataFile metadata. This can be changed, for example, by developing a custom Dataset view, which is explained in the following section.

Dataset and Experiment Views

Rationale

For some specific uses the data available can be presented and/or processed in useful ways. MyTardis allows views for Experiments and Datasets to be overriden by apps on a per-schema basis, allowing custom views for specifc data types. The example that this feature was built for are single-image and many-image datasets from the Australian Synchrotron. Single images can be displayed large and for a many-image dataset it is more useful to show a couple of example images taken at regular intervals not from the beginning of the set of files. These different datasets can be detected via their schema namespace and displayed differently.

User Guide

Akin to DataFile contextual views, Dataset and Experiment contextual views rely on matching a specific schema namespace in an attached ParameterSet.

Existing schemas can be used, or a special schema intended only for tagging an Experiment or Dataset for contextual view override can be attached (via an otherwise empty ParameterSet).

Dataset and Experiment contextual views are configured in settings by

associating a schema namespace with a class-based view (or view function).

Unlike DataFile contextual views which inject content into the DOM via an AJAX call, these contextual views override the entire page.

Example:

DATASET_VIEWS = [
    ('http://example.org/schemas/dataset/my_awesome_schema',
     'tardis.apps.my_awesome_app.views.CustomDatasetViewSubclass'),
]

EXPERIMENT_VIEWS = [
    ('http://example.org/schemas/expt/my_awesome_schema',
     'tardis.apps.my_awesome_app.views.CustomExptViewSubclass'),
]

Custom Index View

Rationale

Specific sites or facilities often want to display a custom index page that presents recently ingested experiments in a way which is more meaningful for their particular domain or application. MyTardis support overriding the index page (/) on a per-domain or per-Site basis.

User Guide

Example:

INDEX_VIEWS = {
    1: 'tardis.apps.my_custom_app.views.MyCustomIndexSubclass',
    'facility.example.org': 'tardis.apps.myapp.AnotherCustomIndexSubclass'
}

A custom view override is defined in settings as dictionary mapping a class-based view (or view function) to a Django Site. A Site is specified by SITE_ID (an integer) or the domain name of the incoming request.

Developers creating custom contextual index views are encouraged to subclass tardis.tardis_portal.views.pages.IndexView.

Custom Login View

Rationale

Specific sites or facilities may want to display a custom login page that which is more meaningful to their particular domain or application. MyTardis supports overriding the login page (/login) on a per-domain or per-Site basis.

User Guide

Example:

LOGIN_VIEWS = {
    1: 'tardis.apps.my_custom_app.views.MyCustomLoginViewClass',
    'facility.example.org': 'tardis.apps.myapp.AnotherCustomLoginViewClass'
}

A custom view override is defined in settings as dictionary mapping a class-based view (or view function) to a Django Site. A Site is specified by SITE_ID (an integer) or the domain name of the incoming request.

For an example MyTardis app which provides a login view, see https://github.com/mytardis/mytardis-aaf-google-login

Good practice for app developers

In order to benefit from future bug and security fixes in core MyTardis, app developers are strongly encouraged to override IndexView, DatasetView and ExperimentView (from tardis.tardis_portal.pages) when creating custom contextual views.

The default and well-tested index.html, login.html, view_dataset.html and view_experiment.html templates can used as a basis for these custom contextual views.

New versions may change the default templates and view functions. If you copy and paste parts for your application, please check with each upgrade that you are still using up to date code.

OAI-PMH Producer

Using to provide RIF-CS

Minimal providers for Dublin Core and RIF-CS are included in the app.

To enable the app, include tardis.apps.oaipmh in settings.INSTALLED_APPS.

Your OAI-PMH query endpoint will be on: http://mytardis-example.com/apps/oaipmh/

Implementing your own providers

To allow multiple metadata formats (and types within them) the tardis.apps.oaipmh.server.ProxyingServer handles all requests and proxies them to the providers specified in settings.OAIPMH_PROVIDERS.

You should extend tardis.apps.oaipmh.provider.base.BaseProvider or one of the existing providers if you wish to extend the functionality in a site-specific way.

class tardis.apps.oaipmh.provider.base.BaseProvider(site)

A base provider which roughly implements the PyOAI interface for OAI-PMH servers.

Extend this if you’re writing your own provider for a new type or a different metadata format.

getRecord(metadataPrefix, identifier)

Get a record for a metadataPrefix and identifier.

Parameters:

• metadataPrefix (string) – identifies metadata set to retrieve
• identifier (string) –
  • repository-unique identifier of record

Raises:

• oaipmh.error.CannotDisseminateFormatError – if metadataPrefix is unknown or not supported by identifier.
• oaipmh.error.IdDoesNotExistError – if identifier is unknown or illegal.

Returns:

a header, metadata, about tuple describing the record.

identify()

Retrieve information about the repository.

Returns an Identify object describing the repository.

listIdentifiers(metadataPrefix, set=None, from_=None, until=None)

Get a list of header information on records.

Parameters:

• metadataPrefix (string) – identifies metadata set to retrieve
• set (string) – set identifier; only return headers in set
• from (datetime) – only retrieve headers from from_ date forward (in naive UTC)
• until (datetime) – only retrieve headers with dates up to and including until date (in naive UTC)

Raises:

• error.CannotDisseminateFormatError – if metadataPrefix is not supported by the repository.
• error.NoSetHierarchyError – if the repository does not support sets.

Returns:

an iterable of headers.

listMetadataFormats(identifier=None)

List metadata formats supported by repository or record.

Parameters:

identifier (string) – identify record for which we want to know all supported metadata formats. If absent, list all metadata formats supported by repository.

Raises:

• error.IdDoesNotExistError – if record with identifier does not exist.
• error.NoMetadataFormatsError – if no formats are available for the indicated record.

Returns:

an iterable of metadataPrefix, schema, metadataNamespace tuples (each entry in the tuple is a string).

listRecords(metadataPrefix, set=None, from_=None, until=None)

Get a list of header, metadata and about information on records.

Parameters:

• metadataPrefix (string) – identifies metadata set to retrieve
• set (string) – set identifier; only return records in set
• from (datetime) – only retrieve records from from_ date forward (in naive UTC)
• until (datetime) – only retrieve records with dates up to and including until date (in naive UTC)

Raises:

• oaipmh.error.CannotDisseminateFormatError – if metadataPrefix is not supported by the repository.
• oaipmh.error.NoSetHierarchyError – if the repository does not support sets.

Returns:

an iterable of header, metadata, about tuples.

listSets()

Get a list of sets in the repository.

Raises:error.NoSetHierarchyError – if the repository does not support sets. Returns:an iterable of setSpec, setName tuples (strings).

writeMetadata(element, metadata)

Create XML elements under the given element, using the provided metadata.

Should avoid doing any model-lookups, as they should be done when creating the metadata.

Parameters:

• element (lxml.etree.Element) – element to put all content under (as SubElements)
• metadata (oaipmh.common.Metadata) – metadata to turn into XML

Raises:

NotImplementedError – not implemented

class tardis.apps.oaipmh.server.ProxyingServer(providers)

getRecord(metadataPrefix, identifier)

Get a record for a metadataPrefix and identifier.

Raises:

• oaipmh.error.CannotDisseminateFormatError – if no provider returns a result, but at least one provider responds with oaipmh.error.CannotDisseminateFormatError (meaning the identifier exists)
• oaipmh.error.IdDoesNotExistError – if all providers fail with oaipmh.error.IdDoesNotExistError

Returns:

first successful provider response

Return type:

response

identify()

Retrieve information about the repository.

Returns:an oaipmh.common.Identify object describing the repository. Return type:oaipmh.common.Identify

listIdentifiers(metadataPrefix, **kwargs)

Lists identifiers from all providers as a single set.

Raises:

• error.CannotDisseminateFormatError – if metadataPrefix is not supported by the repository.
• error.NoSetHierarchyError – if a set is provided, as the repository does not support sets.

Returns:

a set.Set of headers.

Return type:

set

listMetadataFormats(**kwargs)

List metadata formats from all providers in a single set.

Raises:

• error.IdDoesNotExistError – if record with identifier does not exist.
• error.NoMetadataFormatsError – if no formats are available for the indicated record, but it does exist.

Returns:

a frozenset of metadataPrefix, schema, metadataNamespace tuples (each entry in the tuple is a string).

Return type:

frozenset

listRecords(metadataPrefix, **kwargs)

Lists records from all providers as a single set.

Raises:

• error.CannotDisseminateFormatError – if metadataPrefix is not supported by the repository.
• error.NoSetHierarchyError – if a set is provided, as the repository does not support sets.

Returns:

a set.Set of header, metadata, about tuples.

Return type:

set

listSets()

List sets.

Raises:oaipmh.error.NoSetHierarchyError – because set hierarchies are currrently not implemented

MyTardis Social Authentication

Overview

The MyTardis social auth app allows MyTardis deployments to accept logins using OAuth and OpenID Connect. It builds on the Python social auth package, and uses the Django social auth app.

Usage

To enable the app, include social_django and tardis.apps.social_auth in settings.INSTALLED_APPS:

INSTALLED_APPS += (
    'social_django',
    'tardis.apps.social_auth',
)

Adding backends

You will need to add authentication backends that you want to enable. To enable Google authentication add following AUTHENTICATION_BACKENDS to settings.py

AUTHENTICATION_BACKENDS += (
    'social_core.backends.open_id.OpenIdAuth',
    'social_core.backends.google.GoogleOpenId',
    'social_core.backends.google.GoogleOAuth2',
)

To enable Australian Access federation(AAF) OpenID connect Provider(OIDC) authentication add following AUTHENTICATION_BACKENDS to settings.py

AUTHENTICATION_BACKENDS += (
    'tardis.apps.social_auth.auth.authorisation.AAFOpenId',
)

Adding authentication providers

You will need add authentication providers that you want to enable.

AUTH_PROVIDERS += (
              ('Google', 'Google',
              'social_core.backends.google.GoogleOAuth2'),
              ('AAF','AAF',
              'tardis.apps.social_auth.auth.authorisation.AAFOpenId'),
              )

Adding Exception Middleware

You may want to add exception middleware provided by python-social-auth. To do this add following to settings.py

MIDDLEWARE += (
    'social_django.middleware.SocialAuthExceptionMiddleware',
)

Adding Context Processor

You will need to add following context processor to settings.py

TEMPLATES[0]['OPTIONS']['context_processors'].extend([
'social_django.context_processors.backends',
'social_django.context_processors.login_redirect'])

Application setup

Once the application is enabled and installed define the following settings to enable authentication behaviour.

SOCIAL_AUTH_AAF_PIPELINE = (
'social_core.pipeline.social_auth.social_details',
'social_core.pipeline.social_auth.social_uid',
'social_core.pipeline.social_auth.social_user',
'social_core.pipeline.user.get_username',
'social_core.pipeline.user.create_user',
'tardis.apps.social_auth.auth.social_auth.configure_social_auth_user',
'tardis.apps.social_auth.auth.social_auth.add_authentication_method',
'tardis.apps.social_auth.auth.social_auth.approve_user_auth',
'tardis.apps.social_auth.auth.social_auth.add_user_permissions',
'social_core.pipeline.social_auth.associate_user',
'social_core.pipeline.social_auth.load_extra_data',
'social_core.pipeline.user.user_details',
)

SOCIAL_AUTH_GOOGLE_OAUTH2_PIPELINE = (
'social_core.pipeline.social_auth.social_details',
'social_core.pipeline.social_auth.social_uid',
'social_core.pipeline.social_auth.social_user',
'social_core.pipeline.user.get_username',
'social_core.pipeline.user.create_user',
'tardis.apps.social_auth.auth.social_auth.configure_social_auth_user',
'tardis.apps.social_auth.auth.social_auth.add_authentication_method',
'social_core.pipeline.social_auth.associate_user',
'social_core.pipeline.social_auth.load_extra_data',
'social_core.pipeline.user.user_details',
'tardis.apps.social_auth.auth.social_auth.send_admin_email',
)

Get key and secrets from the OIDC provider that you want to enable and add following settings.

SOCIAL_AUTH_URL_NAMESPACE_BEGIN = 'social:begin',
SOCIAL_AUTH_GOOGLE_OAUTH2_KEY = 'Get this from Google'
SOCIAL_AUTH_GOOGLE_OAUTH2_SECRET = 'Get this from Google'
SOCIAL_AUTH_AAF_KEY = 'Get this from AAF'
SOCIAL_AUTH_AAF_SECRET = 'Get this from AAF'
SOCIAL_AUTH_AAF_AUTH_URL = 'Get this from AAF'
SOCIAL_AUTH_AAF_TOKEN_URL = 'Get this from AAF'
SOCIAL_AUTH_AAF_USER_INFO_URL = 'Get this from AAF'

To override MyTardis’s default login page (Username / Password) with a more appropriate page for AAF and Google authentication, you can use https://github.com/mytardis/mytardis-aaf-google-login

Releases

4.2.0

• Upgraded Django to 2.2.6
• Dropped support for Python 2
• Dataset view now includes a tree file browser
• Upgraded Bootstrap to 4.1.3

4.1.5

• Update AngularJS to address the SNYK-JS-ANGULAR-534884 vulnerability.
• Update the handlebars version in package-lock.json to avoid having “npm install” report high severity vulnerabilities.
• Fix the dataset metadata API test which was failing on Python 3.5.

4.1.4

• Fixed duplicate form submission bugs for create experiment/dataset
• Fixed search bug which restricted instrument drop-down to 20 records
• Fixed some byte string encoding issues with LDAP auth in Python 3
• Fixed Python 3.5 unit tests
• Fixed pickled StorageBoxOption values for Python 3

4.1.3

• Update the https-proxy-agent version in package-lock.json to avoid having “npm install” display “found 1 high severity vulnerability”.

4.1.2

• Allow .jsx files to be included in assets/js/tardis_portal/ and ensure that they won’t be linted using the jQuery ESLint configuration
• Switch back to the official version of the pyoai dependency

4.1.1

• Fix Python 3 bug with string encoding in deep download mapper which affected directory names in SFTP interface.

4.1

• Added React search components and django-elasticsearch-dsl backend
• Removed post-save filters middleware, replaced with microservice architecture
• Added RabbitMQ task priorities support, dropped support for Redis as a broker
• Upgraded Bootstrap CSS framework from v2.3.2 to v3.4.1
• Added Python 3 support
• Added webpack to collect static assets (JS / CSS), supporting ES6, JSX etc.
• Annotated storage box related tasks with their storage box name, visible in “celery inspect active”
• Added task for clearing Django sessions
• Added timestamps (created and modified) in facility and instrument models
• Updated built-in Creative Commons licenses to v4
• Added django-storages and boto3 to requirements to support S3 storage boxes and storing static assets in S3
• Improved efficiency of checksums and downloads for files in S3 storage
• COMPUTE_SHA512 now defaults to False. COMPUTE_MD5 still defaults to True.
• Legal text for publishing can now be specified in settings
• Now using Dataset created_time in facility overview instead of experiment created time
• Added a new setting to prevent large datasets (many files) from being scanned for image files at page load time
• API v1’s instrument resource now allows any authenticated user to list the instrument names, which is used in the new search interface
• The ExperimentAuthor model now exposed in API v1
• MyTardis no longer tries to guess an appropriate storage box for new DataFileObjects unless REUSE_DATASET_STORAGE_BOX is True
• Improved BDD test coverage, now measuring template coverage with django-coverage-plugin
• Bug fixes (GitHub Issue numbers below) - Fixed #1503 - Fixed #1568 - Removed bob@bobmail.com from default ADMINS, fixing #1613 - Fixed #1664 - Fixed #1708 - Fixed #1857 - Fixed #1853 - Fixed concatenated messages issue in user sharing and group sharing dialogs - Fixed #1790 - Fixed truncated TAR download issue with unverified files - Fixed sharing with AAF/Google issue - Fixed some broken Font Awesome icons

4.0.2

• Upgraded Django to 1.11.23
• Upgraded vulnerable dependencies of JS dev dependencies
• Fixed #1844 (remove a hard-coded LDAP attribute)

4.0.1

• Removed anzsrc_codes tardis app which contained a potentially insecure dependency (rdflib)
• Added created_time and modified_time fiels in the Instrument and Facility models
• Updated Python and Javascript dependencies which had vulnerabilities reported since the v4.0 release.
• Fixed token authentication (#1531, 615d9df)
• Fixed some Font Awesome icons (1ac549d)
• Fixed an incomplete database migration for the Dataset created_time field. This fix is included in the tardis/tardis_portal/migrations/0016_add_timestamps.py migration which also adds the created_time and modified_time fields to the Instrument and Facility models (ec238b4)
• Removed hard-coded LDAP attributes (#1664, 96a0fbf)
• Fixed issue with get_accessible_datafiles_for_user potentially returning an empty list instead of an empty QuerySet (a13cefc)
• Fixed issue with Add/Save Experiment Metadata - added a form attribute to the Save button. (fd2393a)
• In S3 storage documentation, removed reference to old fork of django-storages. (f0c62d5)
• Fixed issue where MyTardis could try to verify SHA512 sums even when COMPUTE_SHA512 was set to False (#1419, 1da1b3b)
• In S3 storage documentation, removed reference to old fork of django-storages. (f0c62d5)
• Fixed issue where MyTardis could try to verify SHA512 sums even when COMPUTE_SHA512 was set to False (#1419, 1da1b3b)
• Fixed issue where downloading a TAR of a dataset including unverified files could result in a “Truncated tar archive” error (#1425, b4fa17c)
• Fixed issue where MyTardis tried to retrieve thumbnail images for non-image files, resulting in 404 errors (e261065)
• Fixed issue where failing to set ADMINS in tardis/settings.py could cause MyTardis to attempt to send emails to bob@bobmail.com (#1613, f8ed6dd)
• Fixed issue where Facility Overview’s “Load more” button was enabled while content was still loading. (a28a253)

4.0

• Django 1.11
• jQuery 3.3.1
• Improved test coverage
• Continuous Integration tests run against Ubuntu 18.04 (MyTardis v3.x used 14.04)
• ChromeDriver is used for BDD (Behaviour Driven Development) tests
• Social Auth, including AAF and Google Auth via OpenID Connect
• Migrating user accounts from LDAP or localdb to OpenID Connect
• Customizable user menu
• Using message.level_tag instead of message.tags in portal_template, so that extra tags can be added to Django messages without interfering with the Bootstrap alert class.
• My Data page (which previously contained Owned and Shared experiments) has been split into two pages - “My Data” and “Shared” - Each page loads thumbnails asynchronously for faster initial page load time - An improved pagination widget allows for a very large number of pages.
• Index page’s thumbnails are loaded asynchronously for faster initial page load time.
• Login page can be replaced with a site-specific page
• SFTP can now be used with keys instead of passwords
• Upgraded Bootstrap from 2.0.4 to 2.3.2 (further upgrades coming soon)
• Fixed some bugs in single search
• jQuery code is being moved out of HTML templates and into JS files which can be linted (with ESLint) and tested (with QUnit).

• Removed old broken code and unnecessary code which is duplicated in other repositories.

  • Import via staging with jsTree
  • Uploadify

• Updated or removed (as appropriate) some out-of-date JS dependencies bundled within the MyTardis repository

  • Most JS dependences are installed by npm now, so we can run security checks with npm audit

• manage.py can now be used instead of mytardis.py and mytardis.py will soon be deprecated
• New support email setting can be used in email templates or HTML templates.
• Updating loadschemas management command for Django 1.11 and adding test for it
• Updated the dumpschemas management command for Django 1.11 and added a test for it

• Bug fixes (GitHub Issue numbers below)

  Fixed #243. Bug in tardis_acls.change_experiment permissions check Fixed #516 - only show “Add files” button if user has permission to upload files Fixed #636 Fixed #637 - “()” is added to “Author” line every time an experiment is edited Fixed #779 Fixed #868 Fixed #893 Fixed #988 Fixed #1083 Fixed #1185

• Added docs on X-Forwarded-Proto HTTP header for HTTPS deployments
• Added docs on configuring services in systemd or supervisor
• Removed password length restriction in linked user authentication form
• Removed settings_changeme - use default_settings instead
• Removed backslash from set of characters used to generate secret key.
• Removed django-celery - it is no longer necessary to run Celery via Django
• Improved forwards compatibility with Python 3, but we’re not fully Python 3 compatible yet.
• Switched to PEP 328 relative imports
• Tests no longer require the unmaintained “compare” module
• Added a default value for DATA_UPLOAD_MAX_MEMORY_SIZE (required by Django 1.10+) to default settings
• Removed some unused dependencies, e.g. PyYAML
• Removed the createmysuperuser which is no longer needed
• Removed the checkhashes management command
• Removed the diffraction image filter
• Removed the backupdb management command
• Removed the old publication form - a new publication workflow is coming soon.

3.9

• Added deprecation warnings for functionality which will be removed in 4.0
• Added INTERNAL_IPS to default settings for template debugging on localhost
• Disabled the old publication forms app in default settings, and ensured that MyTardis didn’t attempt to access its static content when disabled
• Removed apps code from ExperimentView’s get_context_data which assumed that each app would provide a views module with an index
• Fixed a bug where creating a group which already existed gave a 500 error
• Fixed a bug where non-ASCII characters in experiment names could break SFTP
• Made dataset thumbnails optional - disabling them can improve page load times
• Fixed a bug which had made it difficult to delete a DataFileObject without a URI from the Django shell
• Fixed a bug which made search indexing fail when there were users with non-ASCII characters in their first or last name

3.8.1

• Fix regression in Push To app

3.8

• Refactored settings
• Added pagination to My Data view
• BDD tests using behave and phantomjs
• Added download MD5 checksum buttons to Dataset View
• Add autocaching task that allows data from a StorageBox to be cached to another StorageBox
• Re-wrote user documentation and switched to hosting docs on RTD
• Switched to using NPM to manage JS deps.
• Facility and instrument are now visible on Experiment and dataset views - thanks @avrljk
• Added setting that allows datasets ordered by id on the Experiment page.
• Added setting to make sha512 checksums optional.

3.7 - 17 March 2016

• DataFile size is now a BigInteger field
• New settings for customisations, contextual view overrides (eg INDEX_VIEWS).
• A new AbstractTardisAppConfig class that all new tardis apps should subclass
• Third-party tardis app dependency checking
• Removed database index from Parameter.string_value to allow longer strings in Postgres. Migrations add a Postgres partial index for string_values shorter than 256 characters.
• Changed constraints on the instrument model; facility and instrument name are now unique together
• changed method tasks to task functions, pre-empting the removal of methods tasks in new celery versions
• RESTful API now supports ordering, e.g. &order_by=-title, for Experiments, Datasets and DataFiles.
• Allowed groups to be ‘owners’ of an Experiment. Enforce rule in views for web UI requiring every Experiment to have at least one user owner.
• Registration support updated for latest django-registration-redux package
• Speed-ups for dataset view page loading for datasets with large numbers of images. The carousel is now limited to a maximum of 100 preview images.
• Reorganised and updated documentation

3.6 - 16 March 2015

• removed legacy operations files (foreman, apache, uwsgi, etc)
• moved CI from Travis CI to Semaphore app
• removed buildout build system and setup.py dependency management
• build instructions in build.sh, using requirements.txt for dependencies now
• gunicorn instead of uwsgi
• updated Django to version 1.6.10
• removed migrations app
• renamed Dataset_File to DataFile
• DataFile have a deleted and a version flag, for upcoming support of these features.
• verifying files does not have side-effects anymore
• renamed Author_Experiment to ExperimentAuthor
• an ExperimentAuthor can now have an email and or a URL
• recoded Replica and Location as DataFileObject with associated StorageBox, based on the Django File API
• API v1 got some additions, largely or fully backwards-compatible
• a publication workflow app, guided publication of data
• download data via SFTP using a built-in SFTP server
• removed most traces of METS
• AAF authentication support
• parameters that can store a generic foreign key (link to any database object)
• new models Instrument and Facility
• basic support for SquashFS archives as StorageBox. Probably requires installation-specific code such as what is used at the Australian Synchrotron.
• error pages are no normal-sized
• new view “Facility Overview”, for facility administrators to have overview over data.
• “MyData” includes owned and shared data
• safely allowing HTML in descriptions now. Achieved by “bleaching” of tags
• stats page faster through DB-server-side aggregation
• layout improvements
• pep8 and pylint improvements
• bug fixes

3.5 - 26 August 2013

• REST API
• REST API keys
• Authorisation now supports object-level permissions
• Front page overview
• Contextual views for Datafiles, Datasets and Experiments
• Backwards incompatible database changes
• Replica multi file location support
• Migration of replicas
• Streaming downloads
• Django 1.5
• REDIS option for celery queue
• auto-verify files
• provisional directory support
• Pylint testing on Travis CI
• Some error pages are now functional
• optionally upload comfortably with Filepicker.io
• Experiment view page load speedup
• Removed ancient XML ingest format.

3.0 - unreleased

• Twitter Bootstrap
• javascript templates
• backbone.js rendering of datasets
• UI for transferring datasets
• bpython shell
• celery queue

2.0 - Unreleased

• Auth/Auth redesign [Gerson, Uli, Russel]

  • Authorisation. Support for several pluggable authorisation plugins (Django internal, LDAP, VBL). The added AuthService middleware provides a mechanism to query all available auth modules to determine what group memberships a users has.

  • Alternative authorisation. Rule based experiment access control engine was implemented with the following access attributes for indivdual users and groups: canRead, canWrite, canDelete, isOwner. Additionally, a time stamp can be specified for each access rule.

    Further information can be found at the wiki: Authorisation Engine design

• Metadata Editing [Steve, Grischa]

• New METS parser & METS exporter [Gerson]

• Dist/Buildout infrastructure [Russell]

• Through the web creation and editing of experiments [Steve, Russell]

• Through the web upload of files [Steve]

• Download protocol handler [Russel, Uli]

• Logging framework [Uli]

• Django 1.3

1.07 - 01/06/2010

• Publish to tardis.edu.au interface created, though not implemented, pending legal text

1.06 - 15/03/2010

• Parameter import interface for creation of new parameter/schema definitions
• iPhone Interface

1.05 - 01/03/2010

• Images as parameters supported
• Data / metadata transfer from synchrotron is now ‘threaded’ using asynchronous web service transfers.

1.0 - 01/02/2010

• MyTardis created from existin MyTardis python / django codebase
• Allows private data to be stored
• Open key/value parameter model, replacing current crystallography one
• Internal data store for data
• LDAP Login
• Pagination of files
• Creation of synchrotron-tardis from MyTardis codebase including specific code for the VBL login service and data transfer to MyTardis deployments.
• Web server changed to apache and mod_wsgi

0.5 - 2009

• Re-wrote federated index (python / django)
• Federated stores are now simple web server based with optional FTP access
• Runs on Jython / Tomcat

0.1 - 2007

• Federated index (php) running on Apache HTTP Server
• Crystallography data deposition and packaging tools for Fedora Commons (java swing desktop)
• Search Interface via web

Indices and tables

• Index
• Module Index
• Search Page