openapi: 3.2.0 info: title: Genialis base Modules API version: 0.0.0 description: Backend of the Genialis platform. servers: - url: https://app.genialis.com description: Base URL declared by the provider in apis.yml (roadmap#122). tags: - name: Modules paths: /api/_modules/differential_expression/geneset_search: get: operationId: api__modules_differential_expression_geneset_search_list description: 'View for geneset search endpoint. This endpoint returns combined list of Data objects of type ``data:differentialexpression:`` and ``data:geneset:``. Endpoint supports: * :drf:`Limit/Offset Pagination ` * filtering by list of genes (significant genes for differential expression objects and list of included genes fot geneset objects) * filtering differential expressions by basket ids provided in ``filter_de_by_basket`` parameter * same filtering as Data endpoint (~`resolwe.flow.views.DataViewSet`) * ordering by ``-number_of_genes`` which is the default * same ordering as Data endpoint (~`resolwe.flow.views.DataViewSet`)' parameters: - in: query name: basket schema: type: integer - in: query name: build schema: type: string - in: query name: collection schema: type: integer - in: query name: collection__in schema: type: array items: type: integer description: Multiple values may be separated by commas. explode: false style: form - in: query name: collection__isnull schema: type: boolean - in: query name: collection__name schema: type: string - in: query name: collection__name__contains schema: type: string - in: query name: collection__name__icontains schema: type: string - in: query name: collection__name__iexact schema: type: string - in: query name: collection__name__in schema: type: array items: type: string description: Multiple values may be separated by commas. explode: false style: form - in: query name: collection__name__isnull schema: type: boolean - in: query name: collection__name__istartswith schema: type: string - in: query name: collection__name__startswith schema: type: string - in: query name: collection__slug schema: type: string - in: query name: collection__slug__in schema: type: array items: type: string description: Multiple values may be separated by commas. explode: false style: form - in: query name: contributor schema: type: integer - in: query name: contributor__in schema: type: array items: type: integer description: Multiple values may be separated by commas. explode: false style: form - in: query name: contributor_name schema: type: string - in: query name: created schema: type: string format: date-time - in: query name: created__date schema: type: string format: date - in: query name: created__gt schema: type: string format: date-time - in: query name: created__gte schema: type: string format: date-time - in: query name: created__isnull schema: type: boolean - in: query name: created__lt schema: type: string format: date-time - in: query name: created__lte schema: type: string format: date-time - in: query name: created__time schema: type: string format: time - in: query name: entity schema: type: integer - in: query name: entity__in schema: type: array items: type: integer description: Multiple values may be separated by commas. explode: false style: form - in: query name: entity__isnull schema: type: boolean - in: query name: entity__name schema: type: string - in: query name: entity__name__contains schema: type: string - in: query name: entity__name__icontains schema: type: string - in: query name: entity__name__iexact schema: type: string - in: query name: entity__name__in schema: type: array items: type: string description: Multiple values may be separated by commas. explode: false style: form - in: query name: entity__name__isnull schema: type: boolean - in: query name: entity__name__istartswith schema: type: string - in: query name: entity__name__startswith schema: type: string - in: query name: entity__slug schema: type: string - in: query name: entity__slug__in schema: type: array items: type: string description: Multiple values may be separated by commas. explode: false style: form - in: query name: feature_type schema: type: string - in: query name: filter_de_by_basket schema: type: integer - in: query name: finished schema: type: string format: date-time - in: query name: finished__date schema: type: string format: date - in: query name: finished__gt schema: type: string format: date-time - in: query name: finished__gte schema: type: string format: date-time - in: query name: finished__isnull schema: type: boolean - in: query name: finished__lt schema: type: string format: date-time - in: query name: finished__lte schema: type: string format: date-time - in: query name: finished__time schema: type: string format: time - in: query name: gene_ids schema: type: array items: type: string - in: query name: group schema: type: string - in: query name: id schema: type: integer - in: query name: id__gt schema: type: integer - in: query name: id__gte schema: type: integer - in: query name: id__in schema: type: array items: type: integer description: Multiple values may be separated by commas. explode: false style: form - in: query name: id__isnull schema: type: boolean - in: query name: id__lt schema: type: integer - in: query name: id__lte schema: type: integer - name: limit required: false in: query description: Number of results to return per page. schema: type: integer - in: query name: modified schema: type: string format: date-time - in: query name: modified__date schema: type: string format: date - in: query name: modified__gt schema: type: string format: date-time - in: query name: modified__gte schema: type: string format: date-time - in: query name: modified__isnull schema: type: boolean - in: query name: modified__lt schema: type: string format: date-time - in: query name: modified__lte schema: type: string format: date-time - in: query name: modified__time schema: type: string format: time - in: query name: name schema: type: string - in: query name: name__contains schema: type: string - in: query name: name__icontains schema: type: string - in: query name: name__iexact schema: type: string - in: query name: name__in schema: type: array items: type: string description: Multiple values may be separated by commas. explode: false style: form - in: query name: name__isnull schema: type: boolean - in: query name: name__istartswith schema: type: string - in: query name: name__startswith schema: type: string - name: offset required: false in: query description: The initial index from which to return the results. schema: type: integer - name: ordering required: false in: query description: Which field to use when ordering the results. schema: type: string - in: query name: owners schema: type: integer - in: query name: owners_name schema: type: string - in: query name: permission schema: type: string - in: query name: process schema: type: integer - in: query name: process__in schema: type: array items: type: integer description: Multiple values may be separated by commas. explode: false style: form - in: query name: process__isnull schema: type: boolean - in: query name: process__name schema: type: string - in: query name: process__name__contains schema: type: string - in: query name: process__name__icontains schema: type: string - in: query name: process__name__iexact schema: type: string - in: query name: process__name__in schema: type: array items: type: string description: Multiple values may be separated by commas. explode: false style: form - in: query name: process__name__isnull schema: type: boolean - in: query name: process__name__istartswith schema: type: string - in: query name: process__name__startswith schema: type: string - in: query name: process__slug schema: type: string - in: query name: process__slug__in schema: type: array items: type: string description: Multiple values may be separated by commas. explode: false style: form - in: query name: relation_id schema: type: number - in: query name: shared_with_me schema: type: boolean - in: query name: slug schema: type: string - in: query name: slug__in schema: type: array items: type: string description: Multiple values may be separated by commas. explode: false style: form - in: query name: source schema: type: - string - 'null' minLength: 1 - in: query name: species schema: type: - string - 'null' minLength: 1 - in: query name: started schema: type: string format: date-time - in: query name: started__date schema: type: string format: date - in: query name: started__gt schema: type: string format: date-time - in: query name: started__gte schema: type: string format: date-time - in: query name: started__isnull schema: type: boolean - in: query name: started__lt schema: type: string format: date-time - in: query name: started__lte schema: type: string format: date-time - in: query name: started__time schema: type: string format: time - in: query name: status schema: type: string enum: - DR - ER - OK - PP - PR - RE - UP - WT description: '* `UP` - Uploading * `RE` - Resolving * `WT` - Waiting * `PP` - Preparing * `PR` - Processing * `OK` - Done * `ER` - Error * `DR` - Dirty' - in: query name: status__in schema: type: array items: type: string description: Multiple values may be separated by commas. explode: false style: form - in: query name: tags schema: type: array items: type: string description: Multiple values may be separated by commas. explode: false style: form - in: query name: type schema: type: string - in: query name: type__exact schema: type: string - in: query name: version schema: type: string - in: query name: version__gt schema: type: string - in: query name: version__gte schema: type: string - in: query name: version__in schema: type: array items: type: string description: Multiple values may be separated by commas. explode: false style: form - in: query name: version__isnull schema: type: boolean - in: query name: version__lt schema: type: string - in: query name: version__lte schema: type: string tags: - Modules security: - cookieAuth: [] responses: '200': content: application/json: schema: $ref: '#/components/schemas/PaginatedGenesetSearchSerializerWithPermissionsList' description: '' summary: Api modules differential expression geneset search list x-summary-source: derived post: operationId: api__modules_differential_expression_geneset_search_create description: Get list by POST request. tags: - Modules requestBody: content: application/json: schema: $ref: '#/components/schemas/GeneIds' application/x-www-form-urlencoded: schema: $ref: '#/components/schemas/GeneIds' multipart/form-data: schema: $ref: '#/components/schemas/GeneIds' security: - cookieAuth: [] responses: '200': content: application/json: schema: $ref: '#/components/schemas/GenesetSearchSerializerWithPermissions' description: '' summary: Api modules differential expression geneset search create x-summary-source: derived /api/_modules/differential_expression/list: get: operationId: api__modules_differential_expression_list_list description: 'Endpoint used for differential expression data. Endpoint used for retrieving differential expression data objects that derive from samples in the basket. Data objects contain some additional fields that are being calculated on the database side. Those additional fields are: - logfc_threshold - prob_field - prob_threshold - up_regulated - down_regulated Request accepts any standard filter for Data objects, plus: - basket (optional) - source (optional) - species (optional) - filter_de_by_basket (optional) Response: - a list of data objects with additional calculated fields' parameters: - in: query name: basket schema: type: string format: uuid - in: query name: build schema: type: string - in: query name: collection schema: type: integer - in: query name: collection__in schema: type: array items: type: integer description: Multiple values may be separated by commas. explode: false style: form - in: query name: collection__isnull schema: type: boolean - in: query name: collection__name schema: type: string - in: query name: collection__name__contains schema: type: string - in: query name: collection__name__icontains schema: type: string - in: query name: collection__name__iexact schema: type: string - in: query name: collection__name__in schema: type: array items: type: string description: Multiple values may be separated by commas. explode: false style: form - in: query name: collection__name__isnull schema: type: boolean - in: query name: collection__name__istartswith schema: type: string - in: query name: collection__name__startswith schema: type: string - in: query name: collection__slug schema: type: string - in: query name: collection__slug__in schema: type: array items: type: string description: Multiple values may be separated by commas. explode: false style: form - in: query name: contributor schema: type: integer - in: query name: contributor__in schema: type: array items: type: integer description: Multiple values may be separated by commas. explode: false style: form - in: query name: contributor_name schema: type: string - in: query name: created schema: type: string format: date-time - in: query name: created__date schema: type: string format: date - in: query name: created__gt schema: type: string format: date-time - in: query name: created__gte schema: type: string format: date-time - in: query name: created__isnull schema: type: boolean - in: query name: created__lt schema: type: string format: date-time - in: query name: created__lte schema: type: string format: date-time - in: query name: created__time schema: type: string format: time - in: query name: entity schema: type: integer - in: query name: entity__in schema: type: array items: type: integer description: Multiple values may be separated by commas. explode: false style: form - in: query name: entity__isnull schema: type: boolean - in: query name: entity__name schema: type: string - in: query name: entity__name__contains schema: type: string - in: query name: entity__name__icontains schema: type: string - in: query name: entity__name__iexact schema: type: string - in: query name: entity__name__in schema: type: array items: type: string description: Multiple values may be separated by commas. explode: false style: form - in: query name: entity__name__isnull schema: type: boolean - in: query name: entity__name__istartswith schema: type: string - in: query name: entity__name__startswith schema: type: string - in: query name: entity__slug schema: type: string - in: query name: entity__slug__in schema: type: array items: type: string description: Multiple values may be separated by commas. explode: false style: form - in: query name: feature_type schema: type: string - in: query name: filter_de_by_basket schema: type: boolean - in: query name: finished schema: type: string format: date-time - in: query name: finished__date schema: type: string format: date - in: query name: finished__gt schema: type: string format: date-time - in: query name: finished__gte schema: type: string format: date-time - in: query name: finished__isnull schema: type: boolean - in: query name: finished__lt schema: type: string format: date-time - in: query name: finished__lte schema: type: string format: date-time - in: query name: finished__time schema: type: string format: time - in: query name: group schema: type: string - in: query name: id schema: type: integer - in: query name: id__gt schema: type: integer - in: query name: id__gte schema: type: integer - in: query name: id__in schema: type: array items: type: integer description: Multiple values may be separated by commas. explode: false style: form - in: query name: id__isnull schema: type: boolean - in: query name: id__lt schema: type: integer - in: query name: id__lte schema: type: integer - name: limit required: false in: query description: Number of results to return per page. schema: type: integer - in: query name: modified schema: type: string format: date-time - in: query name: modified__date schema: type: string format: date - in: query name: modified__gt schema: type: string format: date-time - in: query name: modified__gte schema: type: string format: date-time - in: query name: modified__isnull schema: type: boolean - in: query name: modified__lt schema: type: string format: date-time - in: query name: modified__lte schema: type: string format: date-time - in: query name: modified__time schema: type: string format: time - in: query name: name schema: type: string - in: query name: name__contains schema: type: string - in: query name: name__icontains schema: type: string - in: query name: name__iexact schema: type: string - in: query name: name__in schema: type: array items: type: string description: Multiple values may be separated by commas. explode: false style: form - in: query name: name__isnull schema: type: boolean - in: query name: name__istartswith schema: type: string - in: query name: name__startswith schema: type: string - name: offset required: false in: query description: The initial index from which to return the results. schema: type: integer - name: ordering required: false in: query description: Which field to use when ordering the results. schema: type: string - in: query name: owners schema: type: integer - in: query name: owners_name schema: type: string - in: query name: permission schema: type: string - in: query name: process schema: type: integer - in: query name: process__in schema: type: array items: type: integer description: Multiple values may be separated by commas. explode: false style: form - in: query name: process__isnull schema: type: boolean - in: query name: process__name schema: type: string - in: query name: process__name__contains schema: type: string - in: query name: process__name__icontains schema: type: string - in: query name: process__name__iexact schema: type: string - in: query name: process__name__in schema: type: array items: type: string description: Multiple values may be separated by commas. explode: false style: form - in: query name: process__name__isnull schema: type: boolean - in: query name: process__name__istartswith schema: type: string - in: query name: process__name__startswith schema: type: string - in: query name: process__slug schema: type: string - in: query name: process__slug__in schema: type: array items: type: string description: Multiple values may be separated by commas. explode: false style: form - in: query name: relation_id schema: type: number - in: query name: shared_with_me schema: type: boolean - in: query name: slug schema: type: string - in: query name: slug__in schema: type: array items: type: string description: Multiple values may be separated by commas. explode: false style: form - in: query name: source schema: type: string minLength: 1 - in: query name: species schema: type: string minLength: 1 - in: query name: started schema: type: string format: date-time - in: query name: started__date schema: type: string format: date - in: query name: started__gt schema: type: string format: date-time - in: query name: started__gte schema: type: string format: date-time - in: query name: started__isnull schema: type: boolean - in: query name: started__lt schema: type: string format: date-time - in: query name: started__lte schema: type: string format: date-time - in: query name: started__time schema: type: string format: time - in: query name: status schema: type: string enum: - DR - ER - OK - PP - PR - RE - UP - WT description: '* `UP` - Uploading * `RE` - Resolving * `WT` - Waiting * `PP` - Preparing * `PR` - Processing * `OK` - Done * `ER` - Error * `DR` - Dirty' - in: query name: status__in schema: type: array items: type: string description: Multiple values may be separated by commas. explode: false style: form - in: query name: tags schema: type: array items: type: string description: Multiple values may be separated by commas. explode: false style: form - in: query name: type schema: type: string - in: query name: type__exact schema: type: string - in: query name: version schema: type: string - in: query name: version__gt schema: type: string - in: query name: version__gte schema: type: string - in: query name: version__in schema: type: array items: type: string description: Multiple values may be separated by commas. explode: false style: form - in: query name: version__isnull schema: type: boolean - in: query name: version__lt schema: type: string - in: query name: version__lte schema: type: string tags: - Modules security: - cookieAuth: [] responses: '200': content: application/json: schema: $ref: '#/components/schemas/PaginatedDifferentialExpressionsSerializerWithPermissionsList' description: '' summary: Api modules differential expression list list x-summary-source: derived post: operationId: api__modules_differential_expression_list_create description: Get list by POST request. tags: - Modules requestBody: content: application/json: schema: $ref: '#/components/schemas/DifferentialExpressionsDeserializer' application/x-www-form-urlencoded: schema: $ref: '#/components/schemas/DifferentialExpressionsDeserializer' multipart/form-data: schema: $ref: '#/components/schemas/DifferentialExpressionsDeserializer' security: - cookieAuth: [] responses: '200': content: application/json: schema: $ref: '#/components/schemas/DifferentialExpressionsSerializerWithPermissions' description: '' summary: Api modules differential expression list create x-summary-source: derived /api/_modules/gene_list/list: get: operationId: api__modules_gene_list_list_list description: Return a response. parameters: - in: query name: data schema: type: integer required: true - name: limit required: false in: query description: Number of results to return per page. schema: type: integer - name: offset required: false in: query description: The initial index from which to return the results. schema: type: integer - name: ordering required: false in: query description: Which field to use when ordering the results. schema: type: string tags: - Modules security: - cookieAuth: [] - {} responses: '200': content: application/json: schema: $ref: '#/components/schemas/PaginatedGeneListList' description: '' summary: Api modules gene list list list x-summary-source: derived /api/_modules/gene_list/list_by_ids: get: operationId: api__modules_gene_list_list_by_ids_list description: 'View for gene list by ids endpoint. This endpoint expects gene source and a list of gene ids and returns a list of features with additional metadata from the knowledge base. Endpoint supports LimitOffset pagination. When ''limit'' query parameter is provided, paginated response is returned.' parameters: - in: query name: gene_ids schema: type: array items: type: string - name: limit required: false in: query description: Number of results to return per page. schema: type: integer - name: offset required: false in: query description: The initial index from which to return the results. schema: type: integer - in: query name: source schema: type: - string - 'null' minLength: 1 - in: query name: species schema: type: - string - 'null' minLength: 1 tags: - Modules security: - cookieAuth: [] - {} responses: '200': content: application/json: schema: $ref: '#/components/schemas/PaginatedGeneListList' description: '' summary: Api modules gene list list by ids list x-summary-source: derived post: operationId: api__modules_gene_list_list_by_ids_create description: Return a response. tags: - Modules requestBody: content: application/json: schema: $ref: '#/components/schemas/GeneIds' application/x-www-form-urlencoded: schema: $ref: '#/components/schemas/GeneIds' multipart/form-data: schema: $ref: '#/components/schemas/GeneIds' security: - cookieAuth: [] - {} responses: '200': content: application/json: schema: $ref: '#/components/schemas/GeneList' description: '' summary: Api modules gene list list by ids create x-summary-source: derived /api/_modules/jbrowse/genome: get: operationId: api__modules_jbrowse_genome_list description: Return JBrowse reference sequence. parameters: - name: limit required: false in: query description: Number of results to return per page. schema: type: integer - name: offset required: false in: query description: The initial index from which to return the results. schema: type: integer - name: ordering required: false in: query description: Which field to use when ordering the results. schema: type: string - in: query name: sample_id schema: type: integer required: true tags: - Modules security: - cookieAuth: [] - {} responses: '200': content: application/json: schema: $ref: '#/components/schemas/PaginatedDataList' description: '' summary: Api modules jbrowse genome list x-summary-source: derived /api/_modules/process/list: get: operationId: api__modules_process_list_list description: Process viewset which returns reduced number of process fields for faster response time. parameters: - name: limit required: false in: query description: Number of results to return per page. schema: type: integer - name: offset required: false in: query description: The initial index from which to return the results. schema: type: integer - name: ordering required: false in: query description: Which field to use when ordering the results. schema: type: string tags: - Modules security: - cookieAuth: [] responses: '200': content: application/json: schema: $ref: '#/components/schemas/PaginatedProcessList' description: '' summary: Api modules process list list x-summary-source: derived /api/_modules/sample/table: post: operationId: api__modules_sample_table_create description: Return samples with column values. tags: - Modules requestBody: content: application/json: schema: $ref: '#/components/schemas/SampleTableDeserializer' application/x-www-form-urlencoded: schema: $ref: '#/components/schemas/SampleTableDeserializer' multipart/form-data: schema: $ref: '#/components/schemas/SampleTableDeserializer' required: true security: - cookieAuth: [] - {} responses: '200': content: application/json: schema: {} description: '' summary: Api modules sample table create x-summary-source: derived /api/_modules/species/collection: get: operationId: api__modules_species_collection_list description: Return collections' species. parameters: - in: query name: annotation_version schema: enum: - v2 type: string default: v2 minLength: 1 description: '* `v2` - v2' - in: query name: collection_ids schema: type: array items: type: integer required: true - name: limit required: false in: query description: Number of results to return per page. schema: type: integer - name: offset required: false in: query description: The initial index from which to return the results. schema: type: integer - name: ordering required: false in: query description: Which field to use when ordering the results. schema: type: string tags: - Modules security: - cookieAuth: [] - {} responses: '200': content: application/json: schema: $ref: '#/components/schemas/PaginatedCollectionSpeciesList' description: '' summary: Api modules species collection list x-summary-source: derived /api/_modules/visualizations/aggregated_expression_box_plot/get_last: get: operationId: api__modules_visualizations_aggregated_expression_box_plot_get_last_list description: 'Return aggregations appropriate for box plot. Aggregations are retrieved from last `data:aggregator:expression:` data object. If `diff_expr_id` parameter is provided, the first two elements of the response are aggregations from differential expression''s case and control data objects. Log transformation operation is log2(x + 1). Request: - feature symbol - source - species - group by - exp type - optional: differential expression - optional: log transform Response: - a list of aggregated expressions for box plot' parameters: - in: query name: diff_expr_id schema: type: - integer - 'null' - in: query name: exp_type schema: type: string minLength: 1 required: true - in: query name: gene_id schema: type: string minLength: 1 required: true - in: query name: group_by schema: type: string minLength: 1 required: true - name: limit required: false in: query description: Number of results to return per page. schema: type: integer - in: query name: log_transform schema: type: boolean default: false - name: offset required: false in: query description: The initial index from which to return the results. schema: type: integer - name: ordering required: false in: query description: Which field to use when ordering the results. schema: type: string - in: query name: source schema: type: string minLength: 1 required: true - in: query name: species schema: type: string minLength: 1 required: true tags: - Modules security: - cookieAuth: [] - {} responses: '200': content: application/json: schema: $ref: '#/components/schemas/PaginatedAggregatedExpressionBoxPlotList' description: '' summary: Api modules visualizations aggregated expression box plot get last list x-summary-source: derived /api/_modules/visualizations/attributes: post: operationId: api__modules_visualizations_attributes_create description: Attributes endpoint. tags: - Modules requestBody: content: application/json: schema: $ref: '#/components/schemas/AttributesDeserializer' application/x-www-form-urlencoded: schema: $ref: '#/components/schemas/AttributesDeserializer' multipart/form-data: schema: $ref: '#/components/schemas/AttributesDeserializer' security: - cookieAuth: [] - {} responses: '200': content: application/json: schema: $ref: '#/components/schemas/AttributeList' description: '' summary: Api modules visualizations attributes create x-summary-source: derived /api/_modules/visualizations/attributify: get: operationId: api__modules_visualizations_attributify_list description: 'Attributify endpoint. Returns a minimal set of sample fields and an resolved attribute field specified in the request. This can be used for visualizations to group samples by an attribute. The endpoint takes ``sample_ids`` or ``basket`` as a parameter where ``sample_ids`` takes precedence.' parameters: - in: query name: annotation_version schema: enum: - v2 type: string default: v2 minLength: 1 description: '* `v2` - v2' - in: query name: attribute schema: {} required: true - in: query name: basket schema: type: string format: uuid - name: limit required: false in: query description: Number of results to return per page. schema: type: integer - name: offset required: false in: query description: The initial index from which to return the results. schema: type: integer - name: ordering required: false in: query description: Which field to use when ordering the results. schema: type: string - in: query name: sample_ids schema: type: array items: type: integer tags: - Modules security: - cookieAuth: [] - {} responses: '200': content: application/json: schema: $ref: '#/components/schemas/PaginatedSampleList' description: '' summary: Api modules visualizations attributify list x-summary-source: derived post: operationId: api__modules_visualizations_attributify_create description: Attributify endpoint. tags: - Modules requestBody: content: application/json: schema: $ref: '#/components/schemas/AttributifyDeserializer' application/x-www-form-urlencoded: schema: $ref: '#/components/schemas/AttributifyDeserializer' multipart/form-data: schema: $ref: '#/components/schemas/AttributifyDeserializer' required: true security: - cookieAuth: [] - {} responses: '200': content: application/json: schema: $ref: '#/components/schemas/Sample' description: '' summary: Api modules visualizations attributify create x-summary-source: derived /api/_modules/visualizations/basket_expressions: get: operationId: api__modules_visualizations_basket_expressions_list description: 'Endpoint for retrieving basket expressions. Request: - basket id - tags (optional) Response: - a list of expressions' parameters: - in: query name: basket schema: type: string - name: limit required: false in: query description: Number of results to return per page. schema: type: integer - name: offset required: false in: query description: The initial index from which to return the results. schema: type: integer - name: ordering required: false in: query description: Which field to use when ordering the results. schema: type: string - in: query name: tags schema: type: array items: type: string description: Multiple values may be separated by commas. explode: false style: form tags: - Modules security: - cookieAuth: [] - {} responses: '200': content: application/json: schema: $ref: '#/components/schemas/PaginatedBasketExpressionsList' description: '' summary: Api modules visualizations basket expressions list x-summary-source: derived /api/_modules/visualizations/case_control_expressions: post: operationId: api__modules_visualizations_case_control_expressions_create description: Endpoint handler. tags: - Modules requestBody: content: application/json: schema: $ref: '#/components/schemas/CaseControlExpressionsDeserializer' application/x-www-form-urlencoded: schema: $ref: '#/components/schemas/CaseControlExpressionsDeserializer' multipart/form-data: schema: $ref: '#/components/schemas/CaseControlExpressionsDeserializer' required: true security: - cookieAuth: [] - {} responses: '200': content: application/json: schema: $ref: '#/components/schemas/CaseControlExpressions' description: '' summary: Api modules visualizations case control expressions create x-summary-source: derived /api/_modules/visualizations/expression_box_plot: get: operationId: api__modules_visualizations_expression_box_plot_list description: 'Endpoint for box plot. Statistics can be grouped by provided attribute or for each given gene if no attribute provided. Log transformation operation is log2(x + 1). Request: - basket id - a list of gene ids - source - species - optional: attribute the response is grouped by Response: - a list of aggregated statistics suitable for box plot' parameters: - in: query name: annotation_version schema: enum: - v2 type: string default: v2 minLength: 1 description: '* `v2` - v2' - in: query name: attribute schema: type: object additionalProperties: {} - in: query name: basket schema: type: string format: uuid required: true - in: query name: gene_ids schema: type: array items: type: string - name: limit required: false in: query description: Number of results to return per page. schema: type: integer - name: offset required: false in: query description: The initial index from which to return the results. schema: type: integer - name: ordering required: false in: query description: Which field to use when ordering the results. schema: type: string - in: query name: source schema: type: - string - 'null' minLength: 1 - in: query name: species schema: type: - string - 'null' minLength: 1 tags: - Modules security: - cookieAuth: [] - {} responses: '200': content: application/json: schema: $ref: '#/components/schemas/PaginatedExpressionBoxPlotList' description: '' summary: Api modules visualizations expression box plot list x-summary-source: derived post: operationId: api__modules_visualizations_expression_box_plot_create description: Endpoint handler. parameters: - name: limit required: false in: query description: Number of results to return per page. schema: type: integer - name: offset required: false in: query description: The initial index from which to return the results. schema: type: integer - name: ordering required: false in: query description: Which field to use when ordering the results. schema: type: string tags: - Modules requestBody: content: application/json: schema: $ref: '#/components/schemas/ExpressionBoxPlotDeserializer' application/x-www-form-urlencoded: schema: $ref: '#/components/schemas/ExpressionBoxPlotDeserializer' multipart/form-data: schema: $ref: '#/components/schemas/ExpressionBoxPlotDeserializer' required: true security: - cookieAuth: [] - {} responses: '200': content: application/json: schema: $ref: '#/components/schemas/PaginatedExpressionBoxPlotList' description: '' summary: Api modules visualizations expression box plot create x-summary-source: derived /api/_modules/visualizations/expressions: get: operationId: api__modules_visualizations_expressions_list description: 'Endpoint for retrieving expressions for provided genes. Request takes optional parameters: group_by and color_by which are descriptor or relation attributes. Request: - basket id - a list for gene ids - source - species - optional: group_by (serialized ```DescriptorAttribute``` or ```RelationAttribute```) - optional: color_by (same as group_by) Response: - a list of gene/expression/sample values' parameters: - in: query name: annotation_version schema: enum: - v2 type: string default: v2 minLength: 1 description: '* `v2` - v2' - in: query name: basket schema: type: string format: uuid required: true - in: query name: color_by schema: type: - object - 'null' additionalProperties: {} - in: query name: gene_ids schema: type: array items: type: string - in: query name: group_by schema: type: - object - 'null' additionalProperties: {} - name: limit required: false in: query description: Number of results to return per page. schema: type: integer - name: offset required: false in: query description: The initial index from which to return the results. schema: type: integer - name: ordering required: false in: query description: Which field to use when ordering the results. schema: type: string - in: query name: source schema: type: - string - 'null' minLength: 1 - in: query name: species schema: type: - string - 'null' minLength: 1 tags: - Modules security: - cookieAuth: [] - {} responses: '200': content: application/json: schema: $ref: '#/components/schemas/PaginatedExpressionsList' description: '' summary: Api modules visualizations expressions list x-summary-source: derived post: operationId: api__modules_visualizations_expressions_create description: Endpoint handler. parameters: - name: limit required: false in: query description: Number of results to return per page. schema: type: integer - name: offset required: false in: query description: The initial index from which to return the results. schema: type: integer - name: ordering required: false in: query description: Which field to use when ordering the results. schema: type: string tags: - Modules requestBody: content: application/json: schema: $ref: '#/components/schemas/ExpressionsDeserializer' application/x-www-form-urlencoded: schema: $ref: '#/components/schemas/ExpressionsDeserializer' multipart/form-data: schema: $ref: '#/components/schemas/ExpressionsDeserializer' required: true security: - cookieAuth: [] - {} responses: '200': content: application/json: schema: $ref: '#/components/schemas/PaginatedExpressionsList' description: '' summary: Api modules visualizations expressions create x-summary-source: derived /api/_modules/visualizations/heatmap: get: operationId: api__modules_visualizations_heatmap_list description: 'Endpoint used for heatmap visualization. Request: - gene_ids - source - species - sample_ids Response: - a list of objects containing heatmap related data: - sample name - gene - expression - expression type' parameters: - in: query name: gene_ids schema: type: array items: type: string - name: limit required: false in: query description: Number of results to return per page. schema: type: integer - name: offset required: false in: query description: The initial index from which to return the results. schema: type: integer - name: ordering required: false in: query description: Which field to use when ordering the results. schema: type: string - in: query name: sample_ids schema: type: array items: type: integer required: true - in: query name: source schema: type: - string - 'null' minLength: 1 - in: query name: species schema: type: - string - 'null' minLength: 1 tags: - Modules security: - cookieAuth: [] - {} responses: '200': content: application/json: schema: $ref: '#/components/schemas/PaginatedHeatmapList' description: '' summary: Api modules visualizations heatmap list x-summary-source: derived post: operationId: api__modules_visualizations_heatmap_create description: Return a response. parameters: - name: limit required: false in: query description: Number of results to return per page. schema: type: integer - name: offset required: false in: query description: The initial index from which to return the results. schema: type: integer - name: ordering required: false in: query description: Which field to use when ordering the results. schema: type: string tags: - Modules requestBody: content: application/json: schema: $ref: '#/components/schemas/HeatmapDeserializer' application/x-www-form-urlencoded: schema: $ref: '#/components/schemas/HeatmapDeserializer' multipart/form-data: schema: $ref: '#/components/schemas/HeatmapDeserializer' required: true security: - cookieAuth: [] - {} responses: '200': content: application/json: schema: $ref: '#/components/schemas/PaginatedHeatmapList' description: '' summary: Api modules visualizations heatmap create x-summary-source: derived /api/_modules/visualizations/rose2: get: operationId: api__modules_visualizations_rose2_list description: 'Endpoint returns Rose2 Data objects filtered by basket. Endpoint supports: * :drf:`Limit/Offset Pagination ` * filtering * ordering by `name` and `created`' parameters: - in: query name: basket schema: type: string format: uuid required: true - in: query name: build schema: type: string - in: query name: collection schema: type: integer - in: query name: collection__in schema: type: array items: type: integer description: Multiple values may be separated by commas. explode: false style: form - in: query name: collection__isnull schema: type: boolean - in: query name: collection__name schema: type: string - in: query name: collection__name__contains schema: type: string - in: query name: collection__name__icontains schema: type: string - in: query name: collection__name__iexact schema: type: string - in: query name: collection__name__in schema: type: array items: type: string description: Multiple values may be separated by commas. explode: false style: form - in: query name: collection__name__isnull schema: type: boolean - in: query name: collection__name__istartswith schema: type: string - in: query name: collection__name__startswith schema: type: string - in: query name: collection__slug schema: type: string - in: query name: collection__slug__in schema: type: array items: type: string description: Multiple values may be separated by commas. explode: false style: form - in: query name: contributor schema: type: integer - in: query name: contributor__in schema: type: array items: type: integer description: Multiple values may be separated by commas. explode: false style: form - in: query name: contributor_name schema: type: string - in: query name: created schema: type: string format: date-time - in: query name: created__date schema: type: string format: date - in: query name: created__gt schema: type: string format: date-time - in: query name: created__gte schema: type: string format: date-time - in: query name: created__isnull schema: type: boolean - in: query name: created__lt schema: type: string format: date-time - in: query name: created__lte schema: type: string format: date-time - in: query name: created__time schema: type: string format: time - in: query name: entity schema: type: integer - in: query name: entity__in schema: type: array items: type: integer description: Multiple values may be separated by commas. explode: false style: form - in: query name: entity__isnull schema: type: boolean - in: query name: entity__name schema: type: string - in: query name: entity__name__contains schema: type: string - in: query name: entity__name__icontains schema: type: string - in: query name: entity__name__iexact schema: type: string - in: query name: entity__name__in schema: type: array items: type: string description: Multiple values may be separated by commas. explode: false style: form - in: query name: entity__name__isnull schema: type: boolean - in: query name: entity__name__istartswith schema: type: string - in: query name: entity__name__startswith schema: type: string - in: query name: entity__slug schema: type: string - in: query name: entity__slug__in schema: type: array items: type: string description: Multiple values may be separated by commas. explode: false style: form - in: query name: feature_type schema: type: string - in: query name: finished schema: type: string format: date-time - in: query name: finished__date schema: type: string format: date - in: query name: finished__gt schema: type: string format: date-time - in: query name: finished__gte schema: type: string format: date-time - in: query name: finished__isnull schema: type: boolean - in: query name: finished__lt schema: type: string format: date-time - in: query name: finished__lte schema: type: string format: date-time - in: query name: finished__time schema: type: string format: time - in: query name: group schema: type: string - in: query name: id schema: type: integer - in: query name: id__gt schema: type: integer - in: query name: id__gte schema: type: integer - in: query name: id__in schema: type: array items: type: integer description: Multiple values may be separated by commas. explode: false style: form - in: query name: id__isnull schema: type: boolean - in: query name: id__lt schema: type: integer - in: query name: id__lte schema: type: integer - name: limit required: false in: query description: Number of results to return per page. schema: type: integer - in: query name: modified schema: type: string format: date-time - in: query name: modified__date schema: type: string format: date - in: query name: modified__gt schema: type: string format: date-time - in: query name: modified__gte schema: type: string format: date-time - in: query name: modified__isnull schema: type: boolean - in: query name: modified__lt schema: type: string format: date-time - in: query name: modified__lte schema: type: string format: date-time - in: query name: modified__time schema: type: string format: time - in: query name: name schema: type: string - in: query name: name__contains schema: type: string - in: query name: name__icontains schema: type: string - in: query name: name__iexact schema: type: string - in: query name: name__in schema: type: array items: type: string description: Multiple values may be separated by commas. explode: false style: form - in: query name: name__isnull schema: type: boolean - in: query name: name__istartswith schema: type: string - in: query name: name__startswith schema: type: string - name: offset required: false in: query description: The initial index from which to return the results. schema: type: integer - name: ordering required: false in: query description: Which field to use when ordering the results. schema: type: string - in: query name: owners schema: type: integer - in: query name: owners_name schema: type: string - in: query name: permission schema: type: string - in: query name: process schema: type: integer - in: query name: process__in schema: type: array items: type: integer description: Multiple values may be separated by commas. explode: false style: form - in: query name: process__isnull schema: type: boolean - in: query name: process__name schema: type: string - in: query name: process__name__contains schema: type: string - in: query name: process__name__icontains schema: type: string - in: query name: process__name__iexact schema: type: string - in: query name: process__name__in schema: type: array items: type: string description: Multiple values may be separated by commas. explode: false style: form - in: query name: process__name__isnull schema: type: boolean - in: query name: process__name__istartswith schema: type: string - in: query name: process__name__startswith schema: type: string - in: query name: process__slug schema: type: string - in: query name: process__slug__in schema: type: array items: type: string description: Multiple values may be separated by commas. explode: false style: form - in: query name: relation_id schema: type: number - in: query name: shared_with_me schema: type: boolean - in: query name: slug schema: type: string - in: query name: slug__in schema: type: array items: type: string description: Multiple values may be separated by commas. explode: false style: form - in: query name: source schema: type: string - in: query name: species schema: type: string - in: query name: started schema: type: string format: date-time - in: query name: started__date schema: type: string format: date - in: query name: started__gt schema: type: string format: date-time - in: query name: started__gte schema: type: string format: date-time - in: query name: started__isnull schema: type: boolean - in: query name: started__lt schema: type: string format: date-time - in: query name: started__lte schema: type: string format: date-time - in: query name: started__time schema: type: string format: time - in: query name: status schema: type: string enum: - DR - ER - OK - PP - PR - RE - UP - WT description: '* `UP` - Uploading * `RE` - Resolving * `WT` - Waiting * `PP` - Preparing * `PR` - Processing * `OK` - Done * `ER` - Error * `DR` - Dirty' - in: query name: status__in schema: type: array items: type: string description: Multiple values may be separated by commas. explode: false style: form - in: query name: tags schema: type: array items: type: string description: Multiple values may be separated by commas. explode: false style: form - in: query name: type schema: type: string - in: query name: type__exact schema: type: string - in: query name: version schema: type: string - in: query name: version__gt schema: type: string - in: query name: version__gte schema: type: string - in: query name: version__in schema: type: array items: type: string description: Multiple values may be separated by commas. explode: false style: form - in: query name: version__isnull schema: type: boolean - in: query name: version__lt schema: type: string - in: query name: version__lte schema: type: string tags: - Modules security: - cookieAuth: [] - {} responses: '200': content: application/json: schema: $ref: '#/components/schemas/PaginatedRose2List' description: '' summary: Api modules visualizations rose2 list x-summary-source: derived components: schemas: GeneList: type: object description: Gene list serializer. properties: feature_id: type: string name: type: string full_name: type: string required: - feature_id - full_name - name Rose2: type: object description: Rose2 serializer. properties: id: type: integer readOnly: true slug: type: string maxLength: 100 pattern: ^[-a-zA-Z0-9_]+$ name: type: string maxLength: 100 created: type: string format: date-time readOnly: true output: {} required: - created - id - name - slug ExpressionBoxPlotDeserializer: type: object description: ExpressionBoxPlot deserializer. properties: gene_ids: type: array items: type: string source: type: - string - 'null' species: type: - string - 'null' annotation_version: allOf: - $ref: '#/components/schemas/AnnotationVersionEnum' default: v2 attribute: type: object additionalProperties: {} basket: type: string format: uuid required: - basket AnnotationVersionEnum: enum: - v2 type: string description: '* `v2` - v2' HeatmapDeserializer: type: object description: Heatmap deserializer. properties: gene_ids: type: array items: type: string source: type: - string - 'null' species: type: - string - 'null' sample_ids: type: array items: type: integer required: - sample_ids PaginatedExpressionsList: type: object required: - count - results properties: count: type: integer example: 123 next: type: - string - 'null' format: uri example: http://api.example.org/accounts/?offset=400&limit=100 previous: type: - string - 'null' format: uri example: http://api.example.org/accounts/?offset=200&limit=100 results: type: array items: $ref: '#/components/schemas/Expressions' Expressions: type: object description: Expressions serializer. properties: gene: type: string expression: type: number format: double exp_type: type: string sample: type: string group_by: type: string color_by: type: string required: - exp_type - expression - gene - sample CollectionSpecies: type: object description: Species serializer. properties: collection_id: type: integer species: type: array items: type: string description: Return a list of species. readOnly: true required: - collection_id - species Statistics: type: object description: Statistics serializer. properties: name: type: string expression: type: number format: double sterr: type: number format: double type: type: string required: - expression - name - sterr - type PaginatedProcessList: type: object required: - count - results properties: count: type: integer example: 123 next: type: - string - 'null' format: uri example: http://api.example.org/accounts/?offset=400&limit=100 previous: type: - string - 'null' format: uri example: http://api.example.org/accounts/?offset=200&limit=100 results: type: array items: $ref: '#/components/schemas/Process' DataStatus: enum: - UP - RE - WT - PP - PR - OK - ER - DR type: string description: '* `UP` - Uploading * `RE` - Resolving * `WT` - Waiting * `PP` - Preparing * `PR` - Processing * `OK` - Done * `ER` - Error * `DR` - Dirty' DifferentialExpressionsSerializerWithPermissions: type: object description: Serialize ~`genesis.models.differential_expression.models.GeneSetSearch`. properties: checksum: type: string readOnly: true created: type: string format: date-time readOnly: true descriptor_dirty: type: boolean readOnly: true duplicated: type: - string - 'null' format: date-time readOnly: true finished: type: - string - 'null' format: date-time readOnly: true id: type: integer readOnly: true modified: type: string format: date-time readOnly: true process_cores: type: integer readOnly: true process_error: type: array items: type: string maxLength: 255 readOnly: true process_info: type: array items: type: string maxLength: 255 readOnly: true process_memory: type: integer readOnly: true process_progress: type: integer readOnly: true process_rc: type: - integer - 'null' readOnly: true process_warning: type: array items: type: string maxLength: 255 readOnly: true output: {} scheduled: type: - string - 'null' format: date-time readOnly: true size: type: integer readOnly: true started: type: - string - 'null' format: date-time readOnly: true status: allOf: - $ref: '#/components/schemas/DataStatus' readOnly: true contributor: $ref: '#/components/schemas/Contributor' input: {} process: $ref: '#/components/schemas/RelationshipDict' collection: allOf: - $ref: '#/components/schemas/RelationshipDict' descriptor: {} descriptor_schema: allOf: - $ref: '#/components/schemas/RelationshipDict' entity: allOf: - $ref: '#/components/schemas/RelationshipDict' name: type: string slug: type: - string - 'null' tags: type: array items: type: string maxLength: 255 process_resources: {} logfc_threshold: type: number format: double default: 0.0 prob_field: type: string default: '0' prob_threshold: type: number format: double default: 0.0 up_regulated: type: integer default: 0 down_regulated: type: integer default: 0 current_user_permissions: type: array items: $ref: '#/components/schemas/CurrentUserPermissions' readOnly: true required: - checksum - contributor - created - current_user_permissions - descriptor_dirty - duplicated - finished - id - modified - process - process_cores - process_error - process_info - process_memory - process_progress - process_rc - process_warning - scheduled - size - started - status DifferentialExpressionsDeserializer: type: object description: Deserialize ~`genesis.models.differential_expression.models.GeneSetSearch`. properties: basket: type: string format: uuid source: type: string species: type: string filter_de_by_basket: type: boolean PaginatedGenesetSearchSerializerWithPermissionsList: type: object required: - count - results properties: count: type: integer example: 123 next: type: - string - 'null' format: uri example: http://api.example.org/accounts/?offset=400&limit=100 previous: type: - string - 'null' format: uri example: http://api.example.org/accounts/?offset=200&limit=100 results: type: array items: $ref: '#/components/schemas/GenesetSearchSerializerWithPermissions' AttributeList: type: object description: Attribute serializer. properties: descriptor_attributes: type: array items: $ref: '#/components/schemas/DescriptorAttribute' relation_attributes: type: array items: $ref: '#/components/schemas/RelationAttribute' required: - descriptor_attributes - relation_attributes Process: type: object description: Process serializer. properties: id: type: integer readOnly: true slug: type: string maxLength: 100 pattern: ^[-a-zA-Z0-9_]+$ name: type: string maxLength: 100 description: type: string category: type: string pattern: ^([a-zA-Z0-9]+[:\-])*[a-zA-Z0-9]+:$ maxLength: 200 required: - id - name - slug PaginatedBasketExpressionsList: type: object required: - count - results properties: count: type: integer example: 123 next: type: - string - 'null' format: uri example: http://api.example.org/accounts/?offset=400&limit=100 previous: type: - string - 'null' format: uri example: http://api.example.org/accounts/?offset=200&limit=100 results: type: array items: $ref: '#/components/schemas/BasketExpressions' PaginatedExpressionBoxPlotList: type: object required: - count - results properties: count: type: integer example: 123 next: type: - string - 'null' format: uri example: http://api.example.org/accounts/?offset=400&limit=100 previous: type: - string - 'null' format: uri example: http://api.example.org/accounts/?offset=200&limit=100 results: type: array items: $ref: '#/components/schemas/ExpressionBoxPlot' SampleTableDeserializer: type: object description: Serializer for parsing sample table endpoint input. properties: annotation_version: allOf: - $ref: '#/components/schemas/AnnotationVersionEnum' default: v2 sample_ids: type: array items: type: integer table_column_ids: type: array items: type: integer required: - sample_ids - table_column_ids PermissionsEnum: enum: - none - view - edit - share - owner type: string description: '* `none` - none * `view` - view * `edit` - edit * `share` - share * `owner` - owner' PaginatedAggregatedExpressionBoxPlotList: type: object required: - count - results properties: count: type: integer example: 123 next: type: - string - 'null' format: uri example: http://api.example.org/accounts/?offset=400&limit=100 previous: type: - string - 'null' format: uri example: http://api.example.org/accounts/?offset=200&limit=100 results: type: array items: $ref: '#/components/schemas/AggregatedExpressionBoxPlot' PaginatedDifferentialExpressionsSerializerWithPermissionsList: type: object required: - count - results properties: count: type: integer example: 123 next: type: - string - 'null' format: uri example: http://api.example.org/accounts/?offset=400&limit=100 previous: type: - string - 'null' format: uri example: http://api.example.org/accounts/?offset=200&limit=100 results: type: array items: $ref: '#/components/schemas/DifferentialExpressionsSerializerWithPermissions' Contributor: type: object description: Serializer for contributor User objects. properties: first_name: type: string maxLength: 150 id: type: integer readOnly: true last_name: type: string maxLength: 150 username: type: string description: Required. 150 characters or fewer. Letters, digits and @/./+/-/_ only. pattern: ^[\w.@+-]+$ maxLength: 150 required: - id - username PaginatedHeatmapList: type: object required: - count - results properties: count: type: integer example: 123 next: type: - string - 'null' format: uri example: http://api.example.org/accounts/?offset=400&limit=100 previous: type: - string - 'null' format: uri example: http://api.example.org/accounts/?offset=200&limit=100 results: type: array items: $ref: '#/components/schemas/Heatmap' AttributesDeserializer: type: object description: Serializer for parsing attributes endpoint input. properties: annotation_version: allOf: - $ref: '#/components/schemas/AnnotationVersionEnum' default: v2 sample_ids: type: array items: type: integer basket: type: string format: uuid Sample: type: object description: Sample serializer. properties: sample_id: type: integer sample_name: type: string attribute: type: string required: - attribute - sample_id - sample_name PaginatedSampleList: type: object required: - count - results properties: count: type: integer example: 123 next: type: - string - 'null' format: uri example: http://api.example.org/accounts/?offset=400&limit=100 previous: type: - string - 'null' format: uri example: http://api.example.org/accounts/?offset=200&limit=100 results: type: array items: $ref: '#/components/schemas/Sample' DescriptorAttribute: type: object description: Descriptor attribute serializer. properties: attribute_type: type: string label: type: string field_path: type: string group_label: type: string default: '' field_type: type: string default: '' required: - attribute_type - field_path - label CurrentUserPermissionsTypeEnum: enum: - user - group - public type: string description: '* `user` - user * `group` - group * `public` - public' AggregatedExpressionBoxPlot: type: object description: Aggregated expression box plot serializer. properties: attribute: type: string gene: type: string exp_types: type: array items: {} min: type: number format: double max: type: number format: double median: type: number format: double q1: type: number format: double q3: type: number format: double lowerwhisker: type: number format: double upperwhisker: type: number format: double data_count: type: integer required: - attribute - data_count - exp_types - gene - lowerwhisker - max - median - min - q1 - q3 - upperwhisker PaginatedDataList: type: object required: - count - results properties: count: type: integer example: 123 next: type: - string - 'null' format: uri example: http://api.example.org/accounts/?offset=400&limit=100 previous: type: - string - 'null' format: uri example: http://api.example.org/accounts/?offset=200&limit=100 results: type: array items: $ref: '#/components/schemas/Data' PaginatedGeneListList: type: object required: - count - results properties: count: type: integer example: 123 next: type: - string - 'null' format: uri example: http://api.example.org/accounts/?offset=400&limit=100 previous: type: - string - 'null' format: uri example: http://api.example.org/accounts/?offset=200&limit=100 results: type: array items: $ref: '#/components/schemas/GeneList' GenesetSearchSerializerWithPermissions: type: object description: Serialize ~`genesis.models.differential_expression.models.GeneSetSearch`. properties: checksum: type: string readOnly: true created: type: string format: date-time readOnly: true descriptor_dirty: type: boolean readOnly: true duplicated: type: - string - 'null' format: date-time readOnly: true finished: type: - string - 'null' format: date-time readOnly: true id: type: integer readOnly: true modified: type: string format: date-time readOnly: true process_cores: type: integer readOnly: true process_error: type: array items: type: string maxLength: 255 readOnly: true process_info: type: array items: type: string maxLength: 255 readOnly: true process_memory: type: integer readOnly: true process_progress: type: integer readOnly: true process_rc: type: - integer - 'null' readOnly: true process_warning: type: array items: type: string maxLength: 255 readOnly: true output: {} scheduled: type: - string - 'null' format: date-time readOnly: true size: type: integer readOnly: true started: type: - string - 'null' format: date-time readOnly: true status: allOf: - $ref: '#/components/schemas/DataStatus' readOnly: true contributor: $ref: '#/components/schemas/Contributor' input: {} process: $ref: '#/components/schemas/RelationshipDict' collection: allOf: - $ref: '#/components/schemas/RelationshipDict' descriptor: {} descriptor_schema: allOf: - $ref: '#/components/schemas/RelationshipDict' entity: allOf: - $ref: '#/components/schemas/RelationshipDict' name: type: string slug: type: - string - 'null' tags: type: array items: type: string maxLength: 255 process_resources: {} logfc_threshold: type: number format: double default: 0.0 prob_field: type: string default: '0' prob_threshold: type: number format: double default: 0.0 up_regulated: type: integer default: 0 down_regulated: type: integer default: 0 number_of_genes: type: integer default: 0 source: type: string current_user_permissions: type: array items: $ref: '#/components/schemas/CurrentUserPermissions' readOnly: true required: - checksum - contributor - created - current_user_permissions - descriptor_dirty - duplicated - finished - id - modified - process - process_cores - process_error - process_info - process_memory - process_progress - process_rc - process_warning - scheduled - size - source - started - status ExpressionsDeserializer: type: object description: Expressions deserializer. properties: gene_ids: type: array items: type: string source: type: - string - 'null' species: type: - string - 'null' annotation_version: allOf: - $ref: '#/components/schemas/AnnotationVersionEnum' default: v2 basket: type: string format: uuid group_by: type: - object - 'null' additionalProperties: {} color_by: type: - object - 'null' additionalProperties: {} required: - basket Heatmap: type: object description: Heatmap serializer. properties: sample_id: type: integer description: Return sample id. readOnly: true sample_name: type: string description: Return sample name. readOnly: true gene: type: string expression: type: number format: double expression_type: type: - string - 'null' description: Return expression type. readOnly: true required: - expression - expression_type - gene - sample_id - sample_name Data: type: object description: Serializer for Data objects. properties: checksum: type: string readOnly: true created: type: string format: date-time readOnly: true descriptor_dirty: type: boolean readOnly: true duplicated: type: - string - 'null' format: date-time readOnly: true finished: type: - string - 'null' format: date-time readOnly: true id: type: integer readOnly: true modified: type: string format: date-time readOnly: true process_cores: type: integer readOnly: true process_error: type: array items: type: string maxLength: 255 readOnly: true process_info: type: array items: type: string maxLength: 255 readOnly: true process_memory: type: integer readOnly: true process_progress: type: integer readOnly: true process_rc: type: - integer - 'null' readOnly: true process_warning: type: array items: type: string maxLength: 255 readOnly: true output: {} scheduled: type: - string - 'null' format: date-time readOnly: true size: type: integer readOnly: true started: type: - string - 'null' format: date-time readOnly: true status: allOf: - $ref: '#/components/schemas/DataStatus' readOnly: true contributor: $ref: '#/components/schemas/Contributor' input: {} process: $ref: '#/components/schemas/RelationshipDict' collection: allOf: - $ref: '#/components/schemas/RelationshipDict' descriptor: {} descriptor_schema: allOf: - $ref: '#/components/schemas/RelationshipDict' entity: allOf: - $ref: '#/components/schemas/RelationshipDict' name: type: string slug: type: - string - 'null' tags: type: array items: type: string maxLength: 255 process_resources: {} required: - checksum - contributor - created - descriptor_dirty - duplicated - finished - id - modified - process - process_cores - process_error - process_info - process_memory - process_progress - process_rc - process_warning - scheduled - size - started - status GeneIds: type: object description: 'Serializer for gene_ids query parameter. Enforce that if gene_ids are specified, source and species are also.' properties: gene_ids: type: array items: type: string source: type: - string - 'null' species: type: - string - 'null' CurrentUserPermissions: type: object description: Current user permissions serializer. properties: id: type: integer type: $ref: '#/components/schemas/CurrentUserPermissionsTypeEnum' name: type: string maxLength: 100 username: type: string maxLength: 150 permissions: type: array items: $ref: '#/components/schemas/PermissionsEnum' required: - permissions - type Expression: type: object description: Expression serializer. properties: sample: type: string expression: type: number format: double gene: type: string type: type: string exp_type: type: string required: - exp_type - expression - gene - sample - type CaseControlExpressions: type: object description: CaseControlExpressions serializer. properties: expressions: type: array items: $ref: '#/components/schemas/Expression' stats: type: array items: $ref: '#/components/schemas/Statistics' exceptions: type: array items: {} required: - exceptions - expressions - stats BasketExpressions: type: object description: Basket expressions serializer. properties: id: type: integer exp_type: type: string description: Return expression type. readOnly: true required: - exp_type - id AttributifyDeserializer: type: object description: Serializer for parsing attributify endpoint input. properties: attribute: {} annotation_version: allOf: - $ref: '#/components/schemas/AnnotationVersionEnum' default: v2 sample_ids: type: array items: type: integer basket: type: string format: uuid required: - attribute RelationshipDict: type: object description: Serializer for the DictRelatedField relation. properties: id: type: integer slug: type: - string - 'null' CaseControlExpressionsDeserializer: type: object description: Serializer for parsing case and control expressions endpoint input. properties: diff_expr_id: type: integer selected_genes: type: array items: type: string highlighted_genes: type: array items: type: string log2: type: boolean default: false required: - diff_expr_id - selected_genes PaginatedRose2List: type: object required: - count - results properties: count: type: integer example: 123 next: type: - string - 'null' format: uri example: http://api.example.org/accounts/?offset=400&limit=100 previous: type: - string - 'null' format: uri example: http://api.example.org/accounts/?offset=200&limit=100 results: type: array items: $ref: '#/components/schemas/Rose2' PaginatedCollectionSpeciesList: type: object required: - count - results properties: count: type: integer example: 123 next: type: - string - 'null' format: uri example: http://api.example.org/accounts/?offset=400&limit=100 previous: type: - string - 'null' format: uri example: http://api.example.org/accounts/?offset=200&limit=100 results: type: array items: $ref: '#/components/schemas/CollectionSpecies' ExpressionBoxPlot: type: object description: ExpressionBoxPlot serializer. properties: attribute: type: string gene: type: string exp_types: type: array items: {} min: type: number format: double max: type: number format: double median: type: number format: double q1: type: number format: double q3: type: number format: double lowerwhisker: type: number format: double upperwhisker: type: number format: double required: - attribute - exp_types - gene - lowerwhisker - max - median - min - q1 - q3 - upperwhisker RelationAttribute: type: object description: Relation attribute serializer. properties: attribute_type: type: string label: type: string relation_type: type: string relation_category: type: string required: - attribute_type - label - relation_category - relation_type securitySchemes: cookieAuth: type: apiKey in: cookie name: sessionid