Genialis

Genialis Expressions API

The REST API behind the Genialis Expressions platform, built on the open-source Resolwe dataflow engine and Django REST Framework. Covers data objects, samples, collections, relations, processes, descriptor schemas, annotations, prediction fields and values, variants and variant calls, permissions, users and groups, plus session/SAML authentication and platform version endpoints. The live OpenAPI 3.0.3 document is served by drf-spectacular at https://app.genialis.com/api/schema and describes 254 operations across 169 paths.

GitHub OpenAPI

Documentation

📖
Documentation
https://docs.genialis.com/resdk/
📖
APIReference
https://app.genialis.com/api/schema

Specifications

⚙
OpenAPI
https://raw.githubusercontent.com/api-evangelist/genialis/refs/heads/main/openapi/genialis-base-openapi.yaml

Other Resources

🔗
Overlay
https://raw.githubusercontent.com/api-evangelist/genialis/refs/heads/main/overlays/genialis-base-overlay.yaml
🔗
APIsJSON
https://raw.githubusercontent.com/api-evangelist/genialis/refs/heads/main/apis.yml

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OpenAPI Specification

genialis-base-openapi.yaml Raw ↑ 
openapi: 3.0.3
info:
  title: Genialis base
  version: 0.0.0
  description: Backend of the Genialis platform.
paths:
  /about/process_resources:
    get:
      operationId: about_process_resources_retrieve
      description: Return the resources of the installed platform.
      tags:
      - about
      security:
      - cookieAuth: []
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Resources'
          description: ''
  /about/resdk_minimal_supported_version:
    get:
      operationId: about_resdk_minimal_supported_version_retrieve
      description: Return the minimal supported resdk version.
      tags:
      - about
      security:
      - cookieAuth: []
      - {}
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ReSDKMinimalSupportedVersion'
          description: ''
  /about/versions:
    get:
      operationId: about_versions_retrieve
      description: Return the versions of the installed Genialis packages.
      tags:
      - about
      security:
      - cookieAuth: []
      - {}
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Versions'
          description: ''
  /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 <pagination/#limitoffsetpagination>`
        * 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
          nullable: true
          minLength: 1
      - in: query
        name: species
        schema:
          type: string
          nullable: true
          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:
      - api
      security:
      - cookieAuth: []
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/PaginatedGenesetSearchSerializerWithPermissionsList'
          description: ''
    post:
      operationId: api__modules_differential_expression_geneset_search_create
      description: Get list by POST request.
      tags:
      - api
      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: ''
  /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:
      - api
      security:
      - cookieAuth: []
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/PaginatedDifferentialExpressionsSerializerWithPermissionsList'
          description: ''
    post:
      operationId: api__modules_differential_expression_list_create
      description: Get list by POST request.
      tags:
      - api
      requestBody:
        content:
   

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# Full source: https://raw.githubusercontent.com/api-evangelist/genialis/refs/heads/main/openapi/genialis-base-openapi.yaml