tardis.tardis_portal package

Subpackages

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: TabularInline

extra = 0
form

alias of DataFileObjectInlineForm

property media
model

alias of 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: ModelForm

class Meta

Bases: object

fields = '__all__'
model

alias of 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 = {}
property media

Return all media required to render the widgets on this form.

class tardis.tardis_portal.admin.DatafileAdmin(model, admin_site)

Bases: ModelAdmin

form

alias of DatafileAdminForm

inlines = [<class 'tardis.tardis_portal.admin.DataFileObjectInline'>]
property 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: ModelForm

class Meta

Bases: object

fields = '__all__'
model

alias of 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 = {}
property media

Return all media required to render the widgets on this form.

class tardis.tardis_portal.admin.DatasetAdmin(model, admin_site)

Bases: ModelAdmin

property media
search_fields = ['description', 'id']
class tardis.tardis_portal.admin.ExperimentAdmin(model, admin_site)

Bases: ModelAdmin

inlines = [<class 'tardis.tardis_portal.admin.ObjectACLInline'>]
property media
search_fields = ['title', 'id']
class tardis.tardis_portal.admin.ExperimentParameterInline(parent_model, admin_site)

Bases: TabularInline

extra = 0
formfield_overrides = {<class 'django.db.models.fields.TextField'>: {'widget': <class 'django.forms.widgets.TextInput'>}}
property media
model

alias of ExperimentParameter

class tardis.tardis_portal.admin.ExperimentParameterSetAdmin(model, admin_site)

Bases: ModelAdmin

inlines = [<class 'tardis.tardis_portal.admin.ExperimentParameterInline'>]
property media
class tardis.tardis_portal.admin.FacilityAdmin(model, admin_site)

Bases: ModelAdmin

property media
search_fields = ['name']
class tardis.tardis_portal.admin.FreeTextSearchFieldAdmin(model, admin_site)

Bases: ModelAdmin

property media
class tardis.tardis_portal.admin.InstrumentAdmin(model, admin_site)

Bases: ModelAdmin

property media
search_fields = ['name']
class tardis.tardis_portal.admin.InstrumentParameterInline(parent_model, admin_site)

Bases: TabularInline

extra = 0
property media
model

alias of InstrumentParameter

class tardis.tardis_portal.admin.InstrumentParameterSetAdmin(model, admin_site)

Bases: ModelAdmin

inlines = [<class 'tardis.tardis_portal.admin.InstrumentParameterInline'>]
property media
class tardis.tardis_portal.admin.ObjectACLAdmin(model, admin_site)

Bases: ModelAdmin

list_display = ['__str__', 'pluginId', 'entityId', 'canRead', 'canWrite', 'canDelete', 'isOwner']
property media
search_fields = ['content_type', 'object_id']
class tardis.tardis_portal.admin.ObjectACLInline(parent_model, admin_site)

Bases: GenericTabularInline

extra = 0
property media
model

alias of ObjectACL

class tardis.tardis_portal.admin.ParameterNameAdmin(model, admin_site)

Bases: ModelAdmin

property media
search_fields = ['name', 'schema__id']
class tardis.tardis_portal.admin.ParameterNameInline(parent_model, admin_site)

Bases: TabularInline

extra = 0
property media
model

alias of ParameterName

class tardis.tardis_portal.admin.SchemaAdmin(model, admin_site)

Bases: ModelAdmin

inlines = [<class 'tardis.tardis_portal.admin.ParameterNameInline'>]
property media
search_fields = ['name', 'namespace']
class tardis.tardis_portal.admin.StorageBoxAdmin(model, admin_site)

Bases: ModelAdmin

form

alias of StorageBoxForm

inlines = [<class 'tardis.tardis_portal.admin.StorageBoxOptionInline'>, <class 'tardis.tardis_portal.admin.StorageBoxAttributeInline'>]
property media
search_fields = ['name']
class tardis.tardis_portal.admin.StorageBoxAttributeInline(parent_model, admin_site)

Bases: TabularInline

extra = 0
form

alias of StorageBoxAttributeInlineForm

property media
model

alias of 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: ModelForm

class Meta

Bases: object

fields = '__all__'
model

alias of 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 = {}
property media

Return all media required to render the widgets on this form.

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: ModelForm

class Meta

Bases: object

fields = '__all__'
model

alias of 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 = {}
property media

Return all media required to render the widgets on this form.

class tardis.tardis_portal.admin.StorageBoxOptionInline(parent_model, admin_site)

Bases: TabularInline

extra = 0
form

alias of StorageBoxOptionInlineForm

property media
model

alias of 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: ModelForm

class Meta

Bases: object

fields = '__all__'
model

alias of 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 = {}
property media

Return all media required to render the widgets on this form.

class tardis.tardis_portal.admin.UserAuthenticationAdmin(model, admin_site)

Bases: ModelAdmin

property 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: 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: MyTardisModelResource

class Meta

Bases: Meta

filtering = {'dataset': 2, 'directory': ('exact', 'startswith'), 'filename': ('exact',)}
object_class

alias of 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: ParameterResource

class Meta

Bases: Meta

object_class

alias of 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: ParameterSetResource

class Meta

Bases: Meta

object_class

alias of 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: ParameterResource

class Meta

Bases: Meta

object_class

alias of 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: ParameterSetResource

class Meta

Bases: Meta

object_class

alias of 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: MyTardisModelResource

class Meta

Bases: Meta

always_return_data = True
filtering = {'description': ('exact',), 'directory': ('exact',), 'experiments': 2, 'id': ('exact',), 'instrument': 2}
object_class

alias of 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>}
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.

get_child_dir_files(request, **kwargs)

Return a list of datafile Ids within a child subdirectory :param request: a HTTP Request instance :type request: django.http.HttpRequest :param kwargs: :return: a list of datafile IDs :rtype: JsonResponse: :class: django.http.JsonResponse

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: MyTardisModelResource

API for ExperimentAuthors

class Meta

Bases: 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 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: ParameterResource

class Meta

Bases: Meta

object_class

alias of 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: ParameterSetResource

API for ExperimentParameterSets

class Meta

Bases: Meta

object_class

alias of 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: 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: Meta

always_return_data = True
filtering = {'id': ('exact',), 'title': ('exact',)}
object_class

alias of 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: MyTardisModelResource

class Meta

Bases: Meta

always_return_data = True
filtering = {'id': ('exact',), 'manager_group': 2, 'name': ('exact',)}
object_class

alias of 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: 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 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: MyTardisModelResource

class Meta

Bases: Meta

always_return_data = True
filtering = {'facility': 2, 'id': ('exact',), 'name': ('exact',)}
object_class

alias of 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: MyTardisModelResource

class Meta

Bases: 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: 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: 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 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: MyTardisModelResource

class Meta

Bases: Meta

filtering = {'schema': 2}
object_class

alias of 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: 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: 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: 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: MyTardisModelResource

class Meta

Bases: Meta

filtering = {'url': ('exact', 'startswith'), 'verified': ('exact',)}
object_class

alias of 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: MyTardisModelResource

class Meta

Bases: Meta

filtering = {'id': ('exact',), 'namespace': ('exact',)}
object_class

alias of 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: MyTardisModelResource

class Meta

Bases: Meta

object_class

alias of 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: MyTardisModelResource

class Meta

Bases: Meta

object_class

alias of 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: MyTardisModelResource

class Meta

Bases: Meta

object_class

alias of 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: 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 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

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: 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: 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>}
property media

Return all media required to render the widgets on this form.

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: 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>}
property media

Return all media required to render the widgets on this form.

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: ModelForm

class Meta

Bases: object

fields = ['description', 'directory', 'instrument']
model

alias of 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>}
property media

Return all media required to render the widgets on this form.

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: ModelForm

class Meta

Bases: object

fields = ['author', 'institution', 'email', 'order', 'url']
model

alias of 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 = {}
property media

Return all media required to render the widgets on this form.

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: 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(dict=None, /, **kwargs)

Bases: 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 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

property media

Return all media required to render the widgets on this form.

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: 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>}
property media

Return all media required to render the widgets on this form.

class tardis.tardis_portal.forms.LoginForm(*args, **kwargs)

Bases: 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>}
property media

Return all media required to render the widgets on this form.

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: ModelForm

Form for changing account details.

class Meta

Bases: object

fields = ('first_name', 'last_name', 'email')
model

alias of 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 = {}
property media

Return all media required to render the widgets on this form.

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: 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>}
property media

Return all media required to render the widgets on this form.

class tardis.tardis_portal.forms.NoInput(attrs=None)

Bases: Widget

property 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: 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>}
property media

Return all media required to render the widgets on this form.

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: 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>}
property media

Return all media required to render the widgets on this form.

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: ModelForm

Form for changing public access and licence.

class Meta

Bases: object

fields = ('public_access', 'license', 'legal_text')
model

alias of 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>}
property media

Return all media required to render the widgets on this form.

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: 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_parameter_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_parameter_add_form(schema, parentObject, request)
tardis.tardis_portal.forms.save_parameter_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(*args, **kwargs)

Bases: 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(*args, **kwargs)

Bases: 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(*args, **kwargs)

Bases: Manager

get_by_natural_key(namespace, name)
class tardis.tardis_portal.managers.SchemaManager(*args, **kwargs)

Bases: 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.

property schema

Use schema function to get the schema.

property 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.split_path(p)

tardis.tardis_portal.widgets module

class tardis.tardis_portal.widgets.CommaSeparatedInput(attrs=None)

Bases: TextInput

property 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: Widget

property media
render(name, value, attrs=None)

Render the widget as an HTML string.

tag = 'label'
class tardis.tardis_portal.widgets.Span(attrs=None)

Bases: Label

property 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