pangea.core.views package

Submodules

pangea.core.views.analysis_result_views module

class pangea.core.views.analysis_result_views.SampleAnalysisResultCreateView(**kwargs)

Bases: pangea.core.views.utils.PermissionedListCreateAPIView

filterset_fields = ['uuid', 'sample_id', 'module_name', 'replicate']

perform_create(serializer)

permission

alias of pangea.core.permissions.SampleAnalysisResultPermission

permission_classes = (<class 'rest_framework.permissions.IsAuthenticatedOrReadOnly'>,)

queryset

serializer_class

alias of pangea.core.serializers.SampleAnalysisResultSerializer

class pangea.core.views.analysis_result_views.SampleAnalysisResultDetailsView(**kwargs)

Bases: rest_framework.generics.RetrieveUpdateDestroyAPIView

permission_classes = (<class 'pangea.core.permissions.SampleAnalysisResultPermission'>,)

queryset

serializer_class

alias of pangea.core.serializers.SampleAnalysisResultSerializer

class pangea.core.views.analysis_result_views.SampleAnalysisResultFieldCreateView(**kwargs)

Bases: pangea.core.views.utils.PermissionedListCreateAPIView

filterset_fields = ['uuid', 'name', 'analysis_result_id']

perform_create(serializer)

permission

alias of pangea.core.permissions.SampleAnalysisResultFieldPermission

permission_classes = (<class 'rest_framework.permissions.IsAuthenticatedOrReadOnly'>,)

queryset

serializer_class

alias of pangea.core.serializers.SampleAnalysisResultFieldSerializer

class pangea.core.views.analysis_result_views.SampleAnalysisResultFieldDetailsView(**kwargs)

Bases: rest_framework.generics.RetrieveUpdateDestroyAPIView

permission_classes = (<class 'pangea.core.permissions.SampleAnalysisResultFieldPermission'>,)

queryset

serializer_class

alias of pangea.core.serializers.SampleAnalysisResultFieldSerializer

class pangea.core.views.analysis_result_views.SampleGroupAnalysisResultCreateView(**kwargs)

Bases: pangea.core.views.utils.PermissionedListCreateAPIView

filterset_fields = ['uuid', 'sample_group_id', 'module_name', 'replicate']

perform_create(serializer)

permission

alias of pangea.core.permissions.SampleGroupAnalysisResultPermission

permission_classes = (<class 'rest_framework.permissions.IsAuthenticatedOrReadOnly'>,)

queryset

serializer_class

alias of pangea.core.serializers.SampleGroupAnalysisResultSerializer

class pangea.core.views.analysis_result_views.SampleGroupAnalysisResultDetailsView(**kwargs)

Bases: rest_framework.generics.RetrieveUpdateDestroyAPIView

permission_classes = (<class 'pangea.core.permissions.SampleGroupAnalysisResultPermission'>,)

queryset

serializer_class

alias of pangea.core.serializers.SampleGroupAnalysisResultSerializer

class pangea.core.views.analysis_result_views.SampleGroupAnalysisResultFieldCreateView(**kwargs)

Bases: pangea.core.views.utils.PermissionedListCreateAPIView

filterset_fields = ['uuid', 'name', 'analysis_result_id']

perform_create(serializer)

permission

alias of pangea.core.permissions.SampleGroupAnalysisResultFieldPermission

permission_classes = (<class 'rest_framework.permissions.IsAuthenticatedOrReadOnly'>,)

queryset

serializer_class

alias of pangea.core.serializers.SampleGroupAnalysisResultFieldSerializer

class pangea.core.views.analysis_result_views.SampleGroupAnalysisResultFieldDetailsView(**kwargs)

Bases: rest_framework.generics.RetrieveUpdateDestroyAPIView

permission_classes = (<class 'pangea.core.permissions.SampleGroupAnalysisResultFieldPermission'>,)

queryset

serializer_class

alias of pangea.core.serializers.SampleGroupAnalysisResultFieldSerializer

pangea.core.views.analysis_result_views.authorize_sample_ar_upload_url(request, pk)

pangea.core.views.analysis_result_views.authorize_sample_group_ar_upload_url(request, pk)

pangea.core.views.analysis_result_views.post_sample_ar_complete_multipart_upload_url(self, request, *args, **kwargs)

Reply with a sample group manifest.

pangea.core.views.analysis_result_views.post_sample_ar_upload_url(self, request, *args, **kwargs)

Reply with a sample group manifest.

pangea.core.views.analysis_result_views.post_sample_group_ar_complete_multipart_upload_url(self, request, *args, **kwargs)

Reply with a sample group manifest.

pangea.core.views.analysis_result_views.post_sample_group_ar_upload_url(self, request, *args, **kwargs)

Reply with a sample group manifest.

pangea.core.views.organization_views module

class pangea.core.views.organization_views.OrganizationCreateView(**kwargs)

Bases: rest_framework.generics.ListCreateAPIView

filterset_fields = ['uuid', 'name']

perform_create(serializer)

Require valid session to create organization.

permission_classes = (<class 'rest_framework.permissions.IsAuthenticatedOrReadOnly'>,)

queryset

serializer_class

alias of pangea.core.serializers.OrganizationSerializer

class pangea.core.views.organization_views.OrganizationDetailsView(**kwargs)

Bases: rest_framework.generics.RetrieveUpdateDestroyAPIView

This class handles the http GET, PUT and DELETE requests.

permission_classes = (<class 'pangea.core.permissions.OrganizationPermission'>,)

queryset

serializer_class

alias of pangea.core.serializers.OrganizationSerializer

class pangea.core.views.organization_views.OrganizationUsersView(**kwargs)

Bases: rest_framework.generics.ListAPIView

This class handles managing membership of users within organizations.

get_queryset()

Limit sample queryset to samples in the specified sample group.

get_serializer_class()

Return the class to use for the serializer. Defaults to using self.serializer_class.

You may want to override this if you need to provide different serializations depending on the incoming request.

(Eg. admins get full serialization, others get basic serialization)

permission_classes = (<class 'rest_framework.permissions.IsAuthenticatedOrReadOnly'>,)

post(request, *args, **kwargs)

pangea.core.views.project_views module

class pangea.core.views.project_views.ProjectCreateView(**kwargs)

Bases: pangea.core.views.utils.PermissionedListCreateAPIView

filterset_fields = ['uuid', 'organization_id', 'name']

perform_create(serializer)

Require organization membership to create sample group.

permission

alias of pangea.core.permissions.ProjectPermission

permission_classes = (<class 'rest_framework.permissions.IsAuthenticatedOrReadOnly'>,)

queryset

serializer_class

alias of pangea.core.serializers.ProjectSerializer

class pangea.core.views.project_views.ProjectDetailsView(**kwargs)

Bases: rest_framework.generics.RetrieveUpdateDestroyAPIView

This class handles the http GET, PUT and DELETE requests.

permission_classes = (<class 'pangea.core.permissions.ProjectPermission'>,)

queryset

serializer_class

alias of pangea.core.serializers.ProjectSerializer

class pangea.core.views.project_views.ProjectSampleGroupsView(**kwargs)

Bases: rest_framework.generics.ListAPIView

This class handles managing membership of sample groups within projects.

filter_queryset(queryset)

Given a queryset, filter it with whichever filter backend is in use.

You are unlikely to want to override this method, although you may need to call it either from a list view, or from a custom get_object method if you want to apply the configured filtering backend to the default queryset.

get_serializer_class()

Return the class to use for the serializer. Defaults to using self.serializer_class.

You may want to override this if you need to provide different serializations depending on the incoming request.

(Eg. admins get full serialization, others get basic serialization)

permission_classes = (<class 'pangea.core.permissions.ProjectPermission'>,)

post(request, *args, **kwargs)

queryset

pangea.core.views.s3_views module

class pangea.core.views.s3_views.S3ApiKeyCreateView(**kwargs)

Bases: rest_framework.generics.ListCreateAPIView

get_queryset()

Get the list of items for this view. This must be an iterable, and may be a queryset. Defaults to using self.queryset.

This method should always be used rather than accessing self.queryset directly, as self.queryset gets evaluated only once, and those results are cached for all subsequent requests.

You may want to override this if you need to provide different querysets depending on the incoming request.

(Eg. return a list of items that is specific to the user)

perform_create(serializer)

Require organization membership to create S3 API Key.

permission_classes = (<class 'rest_framework.permissions.IsAuthenticated'>, <class 'pangea.core.permissions.S3ApiKeyPermission'>)

serializer_class

alias of pangea.core.serializers.S3ApiKeySerializer

class pangea.core.views.s3_views.S3ApiKeyDetailsView(**kwargs)

Bases: rest_framework.generics.RetrieveUpdateDestroyAPIView

get_queryset()

Get the list of items for this view. This must be an iterable, and may be a queryset. Defaults to using self.queryset.

This method should always be used rather than accessing self.queryset directly, as self.queryset gets evaluated only once, and those results are cached for all subsequent requests.

You may want to override this if you need to provide different querysets depending on the incoming request.

(Eg. return a list of items that is specific to the user)

permission_classes = (<class 'pangea.core.permissions.S3ApiKeyPermission'>, <class 'rest_framework.permissions.IsAuthenticated'>)

serializer_class

alias of pangea.core.serializers.S3ApiKeySerializer

class pangea.core.views.s3_views.S3BucketCreateView(**kwargs)

Bases: rest_framework.generics.ListCreateAPIView

get_queryset()

Get the list of items for this view. This must be an iterable, and may be a queryset. Defaults to using self.queryset.

This method should always be used rather than accessing self.queryset directly, as self.queryset gets evaluated only once, and those results are cached for all subsequent requests.

You may want to override this if you need to provide different querysets depending on the incoming request.

(Eg. return a list of items that is specific to the user)

perform_create(serializer)

Require organization membership to create S3 bucket.

permission_classes = (<class 'rest_framework.permissions.IsAuthenticated'>, <class 'pangea.core.permissions.S3BucketPermission'>)

serializer_class

alias of pangea.core.serializers.S3BucketSerializer

class pangea.core.views.s3_views.S3BucketDetailsView(**kwargs)

Bases: rest_framework.generics.RetrieveUpdateDestroyAPIView

get_queryset()

Get the list of items for this view. This must be an iterable, and may be a queryset. Defaults to using self.queryset.

This method should always be used rather than accessing self.queryset directly, as self.queryset gets evaluated only once, and those results are cached for all subsequent requests.

You may want to override this if you need to provide different querysets depending on the incoming request.

(Eg. return a list of items that is specific to the user)

permission_classes = (<class 'pangea.core.permissions.S3BucketPermission'>, <class 'rest_framework.permissions.IsAuthenticated'>)

serializer_class

alias of pangea.core.serializers.S3BucketSerializer

pangea.core.views.sample_group_views module

exception pangea.core.views.sample_group_views.AnalysisResultFieldDownloadError

Bases: Exception

class pangea.core.views.sample_group_views.SampleGroupCreateView(**kwargs)

Bases: pangea.core.views.utils.PermissionedListCreateAPIView

filterset_fields = ['uuid', 'organization_id', 'name', 'is_public']

perform_create(serializer)

Require organization membership to create sample group.

permission

alias of pangea.core.permissions.SampleGroupPermission

permission_classes = (<class 'rest_framework.permissions.IsAuthenticatedOrReadOnly'>,)

queryset

serializer_class

alias of pangea.core.serializers.SampleGroupSerializer

class pangea.core.views.sample_group_views.SampleGroupDetailsView(**kwargs)

Bases: rest_framework.generics.RetrieveUpdateDestroyAPIView

This class handles the http GET, PUT and DELETE requests.

permission_classes = (<class 'pangea.core.permissions.SampleGroupPermission'>,)

queryset

serializer_class

alias of pangea.core.serializers.SampleGroupSerializer

class pangea.core.views.sample_group_views.SampleGroupSamplesView(**kwargs)

Bases: rest_framework.generics.ListAPIView

This class handles managing membership of samples within sample groups.

filter_queryset(queryset)

Given a queryset, filter it with whichever filter backend is in use.

You are unlikely to want to override this method, although you may need to call it either from a list view, or from a custom get_object method if you want to apply the configured filtering backend to the default queryset.

get_serializer_class()

Return the class to use for the serializer. Defaults to using self.serializer_class.

You may want to override this if you need to provide different serializations depending on the incoming request.

(Eg. admins get full serialization, others get basic serialization)

permission_classes = (<class 'rest_framework.permissions.IsAuthenticatedOrReadOnly'>,)

post(request, *args, **kwargs)

queryset

pangea.core.views.sample_group_views.clean_tarball_cache()

pangea.core.views.sample_group_views.download_file(ar_field, local_filepath)

pangea.core.views.sample_group_views.get_sample_ar_counts_in_group(self, request, *args, **kwargs)

Reply with counts for all types of sample analysis results in the group.

pangea.core.views.sample_group_views.get_sample_data_in_group(self, request, *args, **kwargs)

Reply with metadata for samples in group.

pangea.core.views.sample_group_views.get_sample_group_manifest(self, request, *args, **kwargs)

Reply with a sample group manifest.

pangea.core.views.sample_group_views.get_sample_metadata_in_group(self, request, *args, **kwargs)

Reply with metadata for samples in group.

pangea.core.views.sample_group_views.get_tarball(group_name, module_name, analysis_results)

pangea.core.views.sample_group_views.make_tarball(tarball_name, analysis_results)

pangea.core.views.sample_group_views.referenced_filename(arf)

pangea.core.views.sample_views module

class pangea.core.views.sample_views.SampleCreateView(**kwargs)

Bases: pangea.core.views.utils.PermissionedListCreateAPIView

filterset_fields = ['uuid', 'library_id', 'name']

perform_create(serializer)

permission

alias of pangea.core.permissions.SamplePermission

permission_classes = (<class 'rest_framework.permissions.IsAuthenticatedOrReadOnly'>,)

queryset

serializer_class

alias of pangea.core.serializers.SampleSerializer

class pangea.core.views.sample_views.SampleDetailsView(**kwargs)

Bases: rest_framework.generics.RetrieveUpdateDestroyAPIView

This class handles the http GET, PUT and DELETE requests.

permission_classes = (<class 'pangea.core.permissions.SamplePermission'>,)

queryset

serializer_class

alias of pangea.core.serializers.SampleSerializer

pangea.core.views.sample_views.get_sample_manifest(self, request, *args, **kwargs)

Reply with a sample group manifest.

pangea.core.views.utils module

class pangea.core.views.utils.PermissionedListCreateAPIView(**kwargs)

Bases: rest_framework.generics.ListCreateAPIView

filter_queryset(queryset)

Given a queryset, filter it with whichever filter backend is in use.

You are unlikely to want to override this method, although you may need to call it either from a list view, or from a custom get_object method if you want to apply the configured filtering backend to the default queryset.

Module contents