Publication Forms


MyTardis supports a simple, configurable, publication workflow allowing researchers to curate collections of data sets for public release. This workflow represents an alternative to simply setting an experiment to “public access” that encourages researchers to provide a higher standard of metadata and bibliographic information, including authorship and acknowledgements without altering the original experiment. Additional features include embargo support, admin publication approvals, and PDB metadata extraction from the Protein Data Bank. DOI minting is also supported but depends on a third-party DOI minting service. Set up of the minting service is beyond the scope of this document.

The publication workflow is a three-stage process:

  1. The user selects data sets to include in the publication, along with a title and description
  2. Based on the selected data sets, domain-specific fields are presented
  3. Authorship, acknowledgements and embargo information is collected

After stage one is started, the publication remains in draft until it is submitted.

Under the hood, this is achieved by creating a new experiment object that is differentiated from regular experiments by attaching a special publication schema. This new experiment links to the selected data sets, which may be from one or many original experiments. Publication related tasks (e.g. embargo processing) filter based on the publication schema and act accordingly.

Basic setup

A minimum setup requires the tardis.apps.publication_forms app to be added to INSTALLED_APPS and the following settings to be defined:

  • PUBLICATION_DATA_ADMIN set to the user name of the person responsible for research data management
  • PUBLICATION_NOTIFICATION_SENDER_EMAIL set to the email from which publication related notifications should be sent
  • PUBLICATION_INTRODUCTION set to an HTML formatted introductory text that is displayed to the user before begins the publication process
  • the apps.publication_forms.update_publication_records task should be added to CELERYBEAT_SCHEDULE and set to a reasonable interval for embargo processing

To disable the approval workflow and have publications automatically released, PUBLICATIONS_REQUIRE_APPROVAL can be set to False (defaults to True).

DOI support

These additional settings are required for DOI minting support:

  • MODC_DOI_ENABLED set to True to enable support
  • MODC_DOI_API_ID set to the API id assigned to this app by the minting service
  • MODC_DOI_API_PASSWORD set to the password corresponding to the API id
  • MODC_DOI_MINT_DEFINITION set to the WSDL file for DOI minting
  • MODC_DOI_ACTIVATE_DEFINITION set to the WSDL file for DOI activation
  • MODC_DOI_DEACTIVATE_DEFINITION set to the WSDL file for DOI deactivation
  • MODC_DOI_ENDPOINT set to the API SOAP endpoint
  • MODC_DOI_MINT_URL_ROOT set to the URL root for registered

DOIs, e.g.

Email configuration

There are a number of different notifications that are sent during the publication process. Very basic templates are preconfigured, but may be overridden by defining the PUBLICATION_EMAIL_MESSAGES dictionary in the file. Review the file for this app to see defaults. The following keys in the dictionary must be defined if

overriding the defaults:

  • PUBLICATION_DATA_ADMIN['requires_authorisation']
    • Sent to publication admins to authorise/approve a publication for release
    • {user_name}: the submitting user’s user name
    • {pub_url}: the direct link to the publication for review
    • {approvals_url}: the link to the admin approvals page
  • PUBLICATION_DATA_ADMIN['awaiting_approval']
    • Sent to all authors immediately after submission
    • {pub_title}: the title of the publication
    • Sent to all authors after the publication has been approved but before being released (e.g. by embargo expiry)
    • {pub_title}: the title of the publication
    • {pub_url}: the direct link to the publication
  • PUBLICATION_DATA_ADMIN['approved_with_doi']
    • As above, but contains a DOI
    • {doi}: the publication’s DOI
    • Sent to all authors if the publication is rejected
    • {pub_title}: the title of the publication
  • PUBLICATION_DATA_ADMIN['reverted_to_draft']
    • Sent to all authors when the publication requires amendments by the submitting user
    • {pub_title}: the title of the publication
    • Sent to all authors when the publication has been released following approval
    • {pub_title}: the title of the publication
  • PUBLICATION_DATA_ADMIN['released_with_doi']
    • As above, but contains a DOI
    • {doi}: the publication’s DOI

Domain-specific metadata

Domain-specific metadata is collected in stage two of the publication process. The forms to display are determined by inspecting the attached data set schemas. Schema to form mappings are defined in the PUBLICATION_FORM_MAPPINGS setting, an example of which is shown below:

 {'dataset_schema': r'^',
  'publication_schema': PDB_PUBLICATION_SCHEMA_ROOT,
  'form_template': '/static/publication-form/mx-pdb-template.html'},
 {'dataset_schema': r'^',
  'publication_schema': MX_PUBLICATION_DATASET_SCHEMA,

dataset_schema is a regular expression applied to each schema attached to each data set, and if matched, the corresponding publication_schema is added to the resulting publication, and its parameters are provided by the form template. Care could be taken in constructing the dataset_schema regex keeping in mind that the expression could match one or more data sets.

Constructing the form template HTML files are somewhat challenging; examples are provided in the static/publication-form directory. These forms require special syntax that is defined using AngularJs. All forms have access to a formTemplate variable, which includes the publication schema name ( a list of affected data sets (formTemplate.datasets). Each form will populate formData.extraInfo[x] with the user supplied data, where x is a unique key.

The forms themselves must be enclosed in a <tardis-form> tag, which requires a my-model attribute (set to formData.extraInfo[x], and a schema (set to Any form field tags must also include the tardis-form-field attribute, in addition to parameter-name, which is set to the publication schema’s parameter to populate. The value given to x as the formData.extraInfo[x] key must be unique over all included forms. In our example below, the form and data set indices are concatenated to form this unique key. Each entry in formData.extraInfo is given its own parameter set in the final publication metadata.

Here is an example that collects some information for each dataset that matches the dataset_schema regex:

<div ng-repeat="ds in formTemplate.datasets"
     ng-init="f = $parent.$index; formData.extraInfo[f+'.'+$index]['dataset'] = ds.description;">
     <h4>{{ ds.description }}</h4>
     <tardis-form my-model="formData.extraInfo[f+'.'+$index]" schema="">
              <textarea tardis-form-field parameter-name="additional-information"
                    placeholder="Information about this dataset.">

The above form works as follows:

  1. The code inside the outer <div> tag is repeated for each data set, which is provided by formTemplate.datasets. The outer <div> tag also initialises a form index, f, obtained from the parent scope’s $index variable, which is used in conjunction with the inner scope’s $index variable to form the unique key for formData.extraInfo; namely, formData.extraInfo[f+’.’+$index].
  2. ng-init in the outer <div> tag also saves a ‘dataset’ field, which is included in formData.extraInfo. This functions exactly as a hidden HTML input field would.
  3. The corresponding dataset name is displayed to the user in the <h4> tag
  4. A <tardis-form> is started, using formData.extraInfo[f+’.’+$index] as its model, linking it to the schema provided by
  5. A <textarea> collects a data set description that will be added to the parameter named ‘additional-information’, as defined in the corresponding schema

Please note that it is extremely important to ensure that the parameter-name attribute for each form field matches exactly the schema parameter. Any fields that do not match are silently ignored!