Views¶
Phenopackets service¶
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class
chord_metadata_service.phenopackets.api_views.BiosampleBatchViewSet(**kwargs)¶ get: Return a list of all existing biosamples
post: Filter biosamples by a list of ids
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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)
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pagination_class¶ alias of
chord_metadata_service.restapi.pagination.BatchResultsSetPagination
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serializer_class¶ alias of
chord_metadata_service.phenopackets.serializers.BiosampleSerializer
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class
chord_metadata_service.phenopackets.api_views.BiosampleViewSet(**kwargs)¶ get: Return a list of all existing biosamples
post: Create a new biosample
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serializer_class¶ alias of
chord_metadata_service.phenopackets.serializers.BiosampleSerializer
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class
chord_metadata_service.phenopackets.api_views.DiagnosisViewSet(**kwargs)¶ get: Return a list of all existing diagnoses
post: Create a new diagnosis
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serializer_class¶ alias of
chord_metadata_service.phenopackets.serializers.DiagnosisSerializer
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class
chord_metadata_service.phenopackets.api_views.DiseaseViewSet(**kwargs)¶ get: Return a list of all existing diseases
post: Create a new disease
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serializer_class¶ alias of
chord_metadata_service.phenopackets.serializers.DiseaseSerializer
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class
chord_metadata_service.phenopackets.api_views.ExtendedPhenopacketsModelViewSet(**kwargs)¶
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class
chord_metadata_service.phenopackets.api_views.GeneViewSet(**kwargs)¶ get: Return a list of all existing genes
post: Create a new gene
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serializer_class¶ alias of
chord_metadata_service.phenopackets.serializers.GeneSerializer
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class
chord_metadata_service.phenopackets.api_views.GenomicInterpretationViewSet(**kwargs)¶ get: Return a list of all existing genomic interpretations
post: Create a new genomic interpretation
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serializer_class¶ alias of
chord_metadata_service.phenopackets.serializers.GenomicInterpretationSerializer
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class
chord_metadata_service.phenopackets.api_views.HtsFileViewSet(**kwargs)¶ get: Return a list of all existing HTS files
post: Create a new HTS file
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serializer_class¶ alias of
chord_metadata_service.phenopackets.serializers.HtsFileSerializer
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class
chord_metadata_service.phenopackets.api_views.InterpretationViewSet(**kwargs)¶ get: Return a list of all existing interpretations
post: Create a new interpretation
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serializer_class¶ alias of
chord_metadata_service.phenopackets.serializers.InterpretationSerializer
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class
chord_metadata_service.phenopackets.api_views.MetaDataViewSet(**kwargs)¶ get: Return a list of all existing metadata records
post: Create a new metadata record
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serializer_class¶ alias of
chord_metadata_service.phenopackets.serializers.MetaDataSerializer
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class
chord_metadata_service.phenopackets.api_views.PhenopacketViewSet(**kwargs)¶ get: Return a list of all existing phenopackets
post: Create a new phenopacket
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serializer_class¶ alias of
chord_metadata_service.phenopackets.serializers.PhenopacketSerializer
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class
chord_metadata_service.phenopackets.api_views.PhenopacketsModelViewSet(**kwargs)¶ -
dispatch(*args, **kwargs)¶ .dispatch() is pretty much the same as Django’s regular dispatch, but with extra hooks for startup, finalize, and exception handling.
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pagination_class¶ alias of
chord_metadata_service.restapi.pagination.LargeResultsSetPagination
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class
chord_metadata_service.phenopackets.api_views.PhenotypicFeatureViewSet(**kwargs)¶ get: Return a list of all existing phenotypic features
post: Create a new phenotypic feature
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serializer_class¶ alias of
chord_metadata_service.phenopackets.serializers.PhenotypicFeatureSerializer
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class
chord_metadata_service.phenopackets.api_views.ProcedureViewSet(**kwargs)¶ get: Return a list of all existing procedures
post: Create a new procedure
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serializer_class¶ alias of
chord_metadata_service.phenopackets.serializers.ProcedureSerializer
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class
chord_metadata_service.phenopackets.api_views.VariantViewSet(**kwargs)¶ get: Return a list of all existing variants
post: Create a new variant
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serializer_class¶ alias of
chord_metadata_service.phenopackets.serializers.VariantSerializer
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chord_metadata_service.phenopackets.api_views.get_chord_phenopacket_schema(request, *args, **kwargs)¶ get: Chord phenopacket schema that can be shared with data providers.
Patients service¶
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class
chord_metadata_service.patients.api_views.BatchViewSet(**kwargs)¶ A viewset that only implements the ‘list’ action. To be used with the BatchListRouter which maps the POST method to .list()
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class
chord_metadata_service.patients.api_views.BeaconListIndividuals(**kwargs)¶ View to return lists of individuals filtered using search terms from katsu’s config.json. Uncensored equivalent of PublicListIndividuals.
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class
chord_metadata_service.patients.api_views.IndividualBatchViewSet(**kwargs)¶ -
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)
-
pagination_class¶ alias of
chord_metadata_service.restapi.pagination.BatchResultsSetPagination
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serializer_class¶ alias of
chord_metadata_service.patients.serializers.IndividualSerializer
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class
chord_metadata_service.patients.api_views.IndividualViewSet(**kwargs)¶ get: Return a list of all existing individuals
post: Create a new individual
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dispatch(*args, **kwargs)¶ .dispatch() is pretty much the same as Django’s regular dispatch, but with extra hooks for startup, finalize, and exception handling.
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pagination_class¶ alias of
chord_metadata_service.restapi.pagination.LargeResultsSetPagination
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serializer_class¶ alias of
chord_metadata_service.patients.serializers.IndividualSerializer
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Mcode service¶
Experiments service¶
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class
chord_metadata_service.experiments.api_views.ExperimentViewSet(**kwargs)¶ get: Return a list of all existing experiments
post: Create a new experiment
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dispatch(*args, **kwargs)¶ .dispatch() is pretty much the same as Django’s regular dispatch, but with extra hooks for startup, finalize, and exception handling.
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pagination_class¶ alias of
chord_metadata_service.restapi.pagination.LargeResultsSetPagination
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serializer_class¶ alias of
chord_metadata_service.experiments.serializers.ExperimentSerializer
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chord_metadata_service.experiments.api_views.get_experiment_schema(request, *args, **kwargs)¶ get: Experiment schema
Resources service¶
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class
chord_metadata_service.resources.api_views.ResourceViewSet(**kwargs)¶ get: Return a list of all existing resources
post: Create a new resource
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pagination_class¶ alias of
chord_metadata_service.restapi.pagination.LargeResultsSetPagination
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serializer_class¶ alias of
chord_metadata_service.resources.serializers.ResourceSerializer
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