integrationUser.yaml

openapi: 3.1.0
info:
  description: |-
    This swagger page describes the integrationUser APIs for ODM. These are typically used to find and retrieve study, sample and processed (signal) data and metadata for a given query.

    Before carrying out any API calls you will need an API token. API tokens can be obtained under your profile within the Genestack software.

    To try out calls in this swagger page:

    1.  Click the 'Authorize' button below to enter your API token
    2.  Scroll to the 'Parameters' section for the method you wish to try out and click the 'Try it out' button
    3.  Enter parameter values that you wish to try
    4.  Scroll to the bottom of the Parameters section and click the 'Execute' bar that appears


     The server response will be in the section that follows.
  title: ODM Integration API
  version: default-released
tags:
- name: Expression integration as User
- name: Files integration as User
- name: Flow Cytometry (FACS) integration as User
- name: Library integration as User
- name: Linkage as User
- name: Omics queries as User
- name: Preparation integration as User
- name: Sample integration as User
- name: Study integration as User
- name: Variant integration as User
paths:
  /api/v1/as-user/data-types:
    get:
      description: This endpoint is for instructional uses and can be used to get
        the latest list of Data Types.
      operationId: getDataTypesAsUser
      responses:
        "200":
          content:
            application/json:
              schema:
                items:
                  type: string
                type: array
                uniqueItems: true
          description: The request was successful. The returned value is a list of
            objects.
        "400":
          content: {}
          description: Entities cannot be retrieved.
        "401":
          content: {}
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "500":
          content: {}
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
      - Access-token: []
      - Genestack-API-Token: []
      summary: Lists all available data types.
      tags:
      - Linkage as User
  /api/v1/as-user/data-types/links:
    get:
      description: "This endpoint should be used for instructional needs, and can\
        \ be used in order to get the links between the Data Types."
      operationId: getDataTypesLinksAsUser
      parameters:
      - description: Return only links with the specified data type.
        in: query
        name: type
        schema:
          type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                items:
                  $ref: "#/components/schemas/SourceTypePair"
                type: array
                uniqueItems: true
          description: The request was successful. The returned value is a list of
            objects.
        "400":
          content: {}
          description: Entities cannot be retrieved.
        "401":
          content: {}
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "500":
          content: {}
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
      - Access-token: []
      - Genestack-API-Token: []
      summary: List all possible links between data types that match the specified
        criteria.
      tags:
      - Linkage as User
  /api/v1/as-user/integration/link/expression/by/library/{id}:
    get:
      description: |+
        ## Versioning
        Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.

        Example usage:
        useVersions=* (query all versions, including those without CHAIN_IDs)
        useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
        useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
        useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
        useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)

        Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.

        ## Paging
        For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.

      operationId: getExpressionByLibraryAsUser
      parameters:
      - description: Supply this parameter with the value `term_id` as part of the
          query to return extended information including IDs for values and dictionaries.
        in: query
        name: responseFormat
        schema:
          $ref: "#/components/schemas/ResponseFormat"
      - description: Unique identifier (accession) of the object.
        in: path
        name: id
        required: true
        schema:
          type: string
      - description: Maximum number of results to return. This value must be between
          0 and 2000 (inclusive).
        in: query
        name: pageLimit
        schema:
          format: int32
          type: integer
      - description: "Show the page {pageOffset+1} results from the start of the results.\
          \ E.g. 100 will show a page of results  starting from the 101st result.\
          \ The default value is 0."
        in: query
        name: pageOffset
        schema:
          format: int32
          type: integer
      - description: |-
          Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:

          \* or `v<version number>` or `<CHAIN_ID>`:`v<version number>` or `<CHAIN_ID>`:`<accession1,accession2,..>`
        in: query
        name: useVersions
        schema:
          type: string
      - description: |-
          The parameter defines amount of metadata attributes to return:

          1. `minimal_data` - return metadata attributes according to the default template.
          2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
          3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
        in: query
        name: returnedMetadataFields
        schema:
          enum:
          - minimal_data
          - extended_data_included
          - original_data_included
          type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/ListResponse"
            text/tab-separated-values:
              schema:
                $ref: "#/components/schemas/ListResponse"
          description: The request was successful. The returned value is a list of
            objects.
        "400":
          content: {}
          description: Entities cannot be retrieved.
        "401":
          content: {}
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "500":
          content: {}
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
      - Access-token: []
      - Genestack-API-Token: []
      summary: Retrieve expression run-level data by querying related library ID (accession)
      tags:
      - Expression integration as User
  /api/v1/as-user/integration/link/expression/by/preparation/{id}:
    get:
      description: |+
        ## Versioning
        Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.

        Example usage:
        useVersions=* (query all versions, including those without CHAIN_IDs)
        useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
        useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
        useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
        useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)

        Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.

        ## Paging
        For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.

      operationId: getExpressionByPreparationAsUser
      parameters:
      - description: Supply this parameter with the value `term_id` as part of the
          query to return extended information including IDs for values and dictionaries.
        in: query
        name: responseFormat
        schema:
          $ref: "#/components/schemas/ResponseFormat"
      - description: Unique identifier (accession) of the object.
        in: path
        name: id
        required: true
        schema:
          type: string
      - description: Maximum number of results to return. This value must be between
          0 and 2000 (inclusive).
        in: query
        name: pageLimit
        schema:
          format: int32
          type: integer
      - description: "Show the page {pageOffset+1} results from the start of the results.\
          \ E.g. 100 will show a page of results  starting from the 101st result.\
          \ The default value is 0."
        in: query
        name: pageOffset
        schema:
          format: int32
          type: integer
      - description: |-
          Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:

          \* or `v<version number>` or `<CHAIN_ID>`:`v<version number>` or `<CHAIN_ID>`:`<accession1,accession2,..>`
        in: query
        name: useVersions
        schema:
          type: string
      - description: |-
          The parameter defines amount of metadata attributes to return:

          1. `minimal_data` - return metadata attributes according to the default template.
          2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
          3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
        in: query
        name: returnedMetadataFields
        schema:
          enum:
          - minimal_data
          - extended_data_included
          - original_data_included
          type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/ListResponse"
            text/tab-separated-values:
              schema:
                $ref: "#/components/schemas/ListResponse"
          description: The request was successful. The returned value is a list of
            objects.
        "400":
          content: {}
          description: Entities cannot be retrieved.
        "401":
          content: {}
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "500":
          content: {}
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
      - Access-token: []
      - Genestack-API-Token: []
      summary: Retrieve expression run-level data by querying related preparation
        ID (accession)
      tags:
      - Expression integration as User
  /api/v1/as-user/integration/link/expression/by/sample/{id}:
    get:
      description: |+
        ## Versioning
        Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.

        Example usage:
        useVersions=* (query all versions, including those without CHAIN_IDs)
        useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
        useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
        useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
        useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)

        Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.

        ## Paging
        For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.

      operationId: getExpressionBySampleAsUser
      parameters:
      - description: Supply this parameter with the value `term_id` as part of the
          query to return extended information including IDs for values and dictionaries.
        in: query
        name: responseFormat
        schema:
          $ref: "#/components/schemas/ResponseFormat"
      - description: Unique identifier (accession) of the object.
        in: path
        name: id
        required: true
        schema:
          type: string
      - description: Maximum number of results to return. This value must be between
          0 and 2000 (inclusive).
        in: query
        name: pageLimit
        schema:
          format: int32
          type: integer
      - description: "Show the page {pageOffset+1} results from the start of the results.\
          \ E.g. 100 will show a page of results  starting from the 101st result.\
          \ The default value is 0."
        in: query
        name: pageOffset
        schema:
          format: int32
          type: integer
      - description: |-
          Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:

          \* or `v<version number>` or `<CHAIN_ID>`:`v<version number>` or `<CHAIN_ID>`:`<accession1,accession2,..>`
        in: query
        name: useVersions
        schema:
          type: string
      - description: |-
          The parameter defines amount of metadata attributes to return:

          1. `minimal_data` - return metadata attributes according to the default template.
          2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
          3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
        in: query
        name: returnedMetadataFields
        schema:
          enum:
          - minimal_data
          - extended_data_included
          - original_data_included
          type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/ListResponse"
            text/tab-separated-values:
              schema:
                $ref: "#/components/schemas/ListResponse"
          description: The request was successful. The returned value is a list of
            objects.
        "400":
          content: {}
          description: Entities cannot be retrieved.
        "401":
          content: {}
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "500":
          content: {}
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
      - Access-token: []
      - Genestack-API-Token: []
      summary: Retrieve expression run-level data by querying related sample ID (accession)
      tags:
      - Expression integration as User
  /api/v1/as-user/integration/link/expression/group/by/study/{id}:
    get:
      description: |+
        ## Versioning
        Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.

        Example usage:
        useVersions=* (query all versions, including those without CHAIN_IDs)
        useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
        useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
        useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
        useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)

        Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.

      operationId: getExpressionGroupsByStudyAsUser
      parameters:
      - description: Supply this parameter with the value `term_id` as part of the
          query to return extended information including IDs for values and dictionaries.
        in: query
        name: responseFormat
        schema:
          $ref: "#/components/schemas/ResponseFormat"
      - description: Unique identifier (accession) of the object.
        in: path
        name: id
        required: true
        schema:
          type: string
      - description: |-
          Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:

          \* or `v<version number>` or `<CHAIN_ID>`:`v<version number>` or `<CHAIN_ID>`:`<accession1,accession2,..>`
        in: query
        name: useVersions
        schema:
          type: string
      - description: |-
          The parameter defines amount of metadata attributes to return:

          1. `minimal_data` - return metadata attributes according to the default template.
          2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
          3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
        in: query
        name: returnedMetadataFields
        schema:
          enum:
          - minimal_data
          - extended_data_included
          - original_data_included
          type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                items:
                  $ref: "#/components/schemas/MetadataWithId"
                type: array
          description: The request was successful. The returned value is the object.
        "400":
          content: {}
          description: The supplied object ID is invalid.
        "401":
          content: {}
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "500":
          content: {}
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
      - Access-token: []
      - Genestack-API-Token: []
      summary: Retrieve group metadata by querying study ID (accession)
      tags:
      - Expression integration as User
  /api/v1/as-user/integration/link/expression/run-to-libraries/by/group/{id}:
    get:
      description: |+
        ## Paging
        For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.

      operationId: getExpressionRunToLibraryPairsAsUser
      parameters:
      - description: Unique identifier (accession) of the object.
        in: path
        name: id
        required: true
        schema:
          type: string
      - description: Maximum number of results to return. This value must be between
          0 and 2000 (inclusive).
        in: query
        name: pageLimit
        schema:
          format: int32
          type: integer
      - description: "Show the page {pageOffset+1} results from the start of the results.\
          \ E.g. 100 will show a page of results  starting from the 101st result.\
          \ The default value is 0."
        in: query
        name: pageOffset
        schema:
          format: int32
          type: integer
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/ListResponse"
          description: The request was successful. The returned value is a list of
            objects.
        "400":
          content: {}
          description: Entities cannot be retrieved.
        "401":
          content: {}
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "404":
          content: {}
          description: No object exists with the given ID.
        "500":
          content: {}
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
      - Access-token: []
      - Genestack-API-Token: []
      summary: "Retrieve run-library pairs by group id. Pagination is based on unique\
        \ runs, not unique pairs."
      tags:
      - Expression integration as User
  /api/v1/as-user/integration/link/expression/run-to-preparations/by/group/{id}:
    get:
      description: |+
        ## Paging
        For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.

      operationId: getExpressionRunToPreparationPairsAsUser
      parameters:
      - description: Unique identifier (accession) of the object.
        in: path
        name: id
        required: true
        schema:
          type: string
      - description: Maximum number of results to return. This value must be between
          0 and 2000 (inclusive).
        in: query
        name: pageLimit
        schema:
          format: int32
          type: integer
      - description: "Show the page {pageOffset+1} results from the start of the results.\
          \ E.g. 100 will show a page of results  starting from the 101st result.\
          \ The default value is 0."
        in: query
        name: pageOffset
        schema:
          format: int32
          type: integer
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/ListResponse"
          description: The request was successful. The returned value is a list of
            objects.
        "400":
          content: {}
          description: Entities cannot be retrieved.
        "401":
          content: {}
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "404":
          content: {}
          description: No object exists with the given ID.
        "500":
          content: {}
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
      - Access-token: []
      - Genestack-API-Token: []
      summary: "Retrieve run-preparation pairs by group id. Pagination is based on\
        \ unique runs, not unique pairs."
      tags:
      - Expression integration as User
  /api/v1/as-user/integration/link/expression/run-to-samples/by/group/{id}:
    get:
      description: |+
        ## Paging
        For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.

      operationId: getExpressionRunToSamplePairsAsUser
      parameters:
      - description: Unique identifier (accession) of the object.
        in: path
        name: id
        required: true
        schema:
          type: string
      - description: Maximum number of results to return. This value must be between
          0 and 2000 (inclusive).
        in: query
        name: pageLimit
        schema:
          format: int32
          type: integer
      - description: "Show the page {pageOffset+1} results from the start of the results.\
          \ E.g. 100 will show a page of results  starting from the 101st result.\
          \ The default value is 0."
        in: query
        name: pageOffset
        schema:
          format: int32
          type: integer
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/ListResponse"
          description: The request was successful. The returned value is a list of
            objects.
        "400":
          content: {}
          description: Entities cannot be retrieved.
        "401":
          content: {}
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "404":
          content: {}
          description: No object exists with the given ID.
        "500":
          content: {}
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
      - Access-token: []
      - Genestack-API-Token: []
      summary: "Retrieve run-sample pairs by group id. Pagination is based on unique\
        \ runs, not unique pairs."
      tags:
      - Expression integration as User
  /api/v1/as-user/integration/link/flow-cytometry/by/sample/{id}:
    get:
      description: |+
        ## Versioning
        Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.

        Example usage:
        useVersions=* (query all versions, including those without CHAIN_IDs)
        useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
        useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
        useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
        useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)

        Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.

        ## Paging
        For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.

      operationId: getFlowCytometryBySampleAsUser
      parameters:
      - description: Supply this parameter with the value `term_id` as part of the
          query to return extended information including IDs for values and dictionaries.
        in: query
        name: responseFormat
        schema:
          $ref: "#/components/schemas/ResponseFormat"
      - description: Unique identifier (accession) of the object.
        in: path
        name: id
        required: true
        schema:
          type: string
      - description: Maximum number of results to return. This value must be between
          0 and 2000 (inclusive).
        in: query
        name: pageLimit
        schema:
          format: int32
          type: integer
      - description: "Show the page {pageOffset+1} results from the start of the results.\
          \ E.g. 100 will show a page of results  starting from the 101st result.\
          \ The default value is 0."
        in: query
        name: pageOffset
        schema:
          format: int32
          type: integer
      - description: |-
          Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:

          \* or `v<version number>` or `<CHAIN_ID>`:`v<version number>` or `<CHAIN_ID>`:`<accession1,accession2,..>`
        in: query
        name: useVersions
        schema:
          type: string
      - description: |-
          The parameter defines amount of metadata attributes to return:

          1. `minimal_data` - return metadata attributes according to the default template.
          2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
          3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
        in: query
        name: returnedMetadataFields
        schema:
          enum:
          - minimal_data
          - extended_data_included
          - original_data_included
          type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/ListResponse"
            text/tab-separated-values:
              schema:
                $ref: "#/components/schemas/ListResponse"
          description: The request was successful. The returned value is a list of
            objects.
        "400":
          content: {}
          description: Entities cannot be retrieved.
        "401":
          content: {}
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "500":
          content: {}
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
      - Access-token: []
      - Genestack-API-Token: []
      summary: Retrieve flow cytometry run-level data by querying related sample ID
        (accession)
      tags:
      - Flow Cytometry (FACS) integration as User
  /api/v1/as-user/integration/link/flow-cytometry/group/by/study/{id}:
    get:
      description: |+
        ## Versioning
        Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.

        Example usage:
        useVersions=* (query all versions, including those without CHAIN_IDs)
        useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
        useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
        useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
        useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)

        Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.

      operationId: getFlowCytometryGroupsByStudyAsUser
      parameters:
      - description: Supply this parameter with the value `term_id` as part of the
          query to return extended information including IDs for values and dictionaries.
        in: query
        name: responseFormat
        schema:
          $ref: "#/components/schemas/ResponseFormat"
      - description: Unique identifier (accession) of the object.
        in: path
        name: id
        required: true
        schema:
          type: string
      - description: |-
          Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:

          \* or `v<version number>` or `<CHAIN_ID>`:`v<version number>` or `<CHAIN_ID>`:`<accession1,accession2,..>`
        in: query
        name: useVersions
        schema:
          type: string
      - description: |-
          The parameter defines amount of metadata attributes to return:

          1. `minimal_data` - return metadata attributes according to the default template.
          2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
          3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
        in: query
        name: returnedMetadataFields
        schema:
          enum:
          - minimal_data
          - extended_data_included
          - original_data_included
          type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                items:
                  $ref: "#/components/schemas/MetadataWithId"
                type: array
          description: The request was successful. The returned value is the object.
        "400":
          content: {}
          description: The supplied object ID is invalid.
        "401":
          content: {}
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "500":
          content: {}
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
      - Access-token: []
      - Genestack-API-Token: []
      summary: Retrieve group metadata by querying study ID (accession)
      tags:
      - Flow Cytometry (FACS) integration as User
  /api/v1/as-user/integration/link/flow-cytometry/run-to-samples/by/group/{id}:
    get:
      description: |+
        ## Paging
        For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.

      operationId: getFlowCytometryRunToSamplePairsAsUser
      parameters:
      - description: Unique identifier (accession) of the object.
        in: path
        name: id
        required: true
        schema:
          type: string
      - description: Maximum number of results to return. This value must be between
          0 and 2000 (inclusive).
        in: query
        name: pageLimit
        schema:
          format: int32
          type: integer
      - description: "Show the page {pageOffset+1} results from the start of the results.\
          \ E.g. 100 will show a page of results  starting from the 101st result.\
          \ The default value is 0."
        in: query
        name: pageOffset
        schema:
          format: int32
          type: integer
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/ListResponse"
          description: The request was successful. The returned value is a list of
            objects.
        "400":
          content: {}
          description: Entities cannot be retrieved.
        "401":
          content: {}
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "404":
          content: {}
          description: No object exists with the given ID.
        "500":
          content: {}
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
      - Access-token: []
      - Genestack-API-Token: []
      summary: "Retrieve run-sample pairs by group id. Pagination is based on unique\
        \ runs, not unique pairs."
      tags:
      - Flow Cytometry (FACS) integration as User
  /api/v1/as-user/integration/link/libraries/by/samples:
    get:
      description: |+
        Retrieve library metadata objects whose linked sample metadata matches all supplied conditions.

        ## Conditions
        It is possible to supply conditions for:

        1. Samples (full-text or metadata key-value pair)
        2. Parent studies (full-text or metadata key-value pair)
        3. Linked variant objects (list of data key-value pairs)
        4. Linked flow cytometry objects (list of data key-value pairs)
        5. Linked any data (except variant and flow cytometry) objects (list of data key-value pairs)

        ## Metadata full-text queries
        Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).

        ## Metadata filters
        Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).

        ## Data queries
        Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values.

        ## Combinations
        Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.

        ## Versioning
        Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.

        Example usage:
        useVersions=* (query all versions, including those without CHAIN_IDs)
        useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
        useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
        useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
        useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)

        Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.

        ## Paging
        For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.

      operationId: getLibrariesBySamplesAsUser
      parameters:
      - description: Supply this parameter with the value `term_id` as part of the
          query to return extended information including IDs for values and dictionaries.
        in: query
        name: responseFormat
        schema:
          $ref: "#/components/schemas/ResponseFormat"
      - description: |
          Filter by sample metadata (key-value metadata pair(s)). E.g. `"Species or strain"="Homo sapiens"`
        in: query
        name: filter
        schema:
          type: string
      - description: Search for objects via a full-text query over all sample metadata
          fields. E.g. `Clozapine`. Queries matching dictionary terms are automatically
          expanded to include synonyms.
        in: query
        name: query
        schema:
          type: string
      - description: |-
          If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.

          For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of  "Body fluid") so files containing either "Body fluid" or  "Blood"  in their metadata will be returned in the search results.

          The parent-child relationship is defined by the key "broaders" or "subClassOf"  in the dictionary.

          If the full query term is not present in a dictionary then this parameter has no effect.
        in: query
        name: searchSpecificTerms
        schema:
          type: boolean
      - description: Maximum number of results to return. This value must be between
          0 and 2000 (inclusive).
        in: query
        name: pageLimit
        schema:
          format: int32
          type: integer
      - description: "Show the page {pageOffset+1} results from the start of the results.\
          \ E.g. 100 will show a page of results  starting from the 101st result.\
          \ The default value is 0."
        in: query
        name: pageOffset
        schema:
          format: int32
          type: integer
      - description: |-
          The parameter defines amount of metadata attributes to return:

          1. `minimal_data` - return metadata attributes according to the default template.
          2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
          3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
        in: query
        name: returnedMetadataFields
        schema:
          enum:
          - minimal_data
          - extended_data_included
          - original_data_included
          type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/ListResponse"
            text/tab-separated-values:
              schema:
                $ref: "#/components/schemas/ListResponse"
          description: The request was successful. The returned value is a list of
            objects.
        "401":
          content: {}
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "500":
          content: {}
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
      - Access-token: []
      - Genestack-API-Token: []
      summary: Retrieve library metadata by querying related samples
      tags:
      - Library integration as User
  /api/v1/as-user/integration/link/library/by/sample/{id}:
    get:
      operationId: getLibraryBySampleAsUser
      parameters:
      - description: Supply this parameter with the value `term_id` as part of the
          query to return extended information including IDs for values and dictionaries.
        in: query
        name: responseFormat
        schema:
          $ref: "#/components/schemas/ResponseFormat"
      - description: Unique identifier (accession) of the object.
        in: path
        name: id
        required: true
        schema:
          type: string
      - description: |-
          The parameter defines amount of metadata attributes to return:

          1. `minimal_data` - return metadata attributes according to the default template.
          2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
          3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
        in: query
        name: returnedMetadataFields
        schema:
          enum:
          - minimal_data
          - extended_data_included
          - original_data_included
          type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                items:
                  $ref: "#/components/schemas/Library"
                type: array
            text/tab-separated-values:
              schema:
                items:
                  $ref: "#/components/schemas/Library"
                type: array
          description: The request was successful. The returned value is a list of
            objects.
        "400":
          content: {}
          description: Entities cannot be retrieved.
        "401":
          content: {}
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "500":
          content: {}
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
      - Access-token: []
      - Genestack-API-Token: []
      summary: Retrieve library metadata by querying related sample ID (accession)
      tags:
      - Library integration as User
  /api/v1/as-user/integration/link/library/group/by/study/{id}:
    get:
      operationId: getLibraryGroupsByStudyAsUser
      parameters:
      - description: Supply this parameter with the value `term_id` as part of the
          query to return extended information including IDs for values and dictionaries.
        in: query
        name: responseFormat
        schema:
          $ref: "#/components/schemas/ResponseFormat"
      - description: Unique identifier (accession) of the object.
        in: path
        name: id
        required: true
        schema:
          type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                items:
                  $ref: "#/components/schemas/MetadataWithId"
                type: array
          description: The request was successful. The returned value is the object.
        "400":
          content: {}
          description: The supplied object ID is invalid.
        "401":
          content: {}
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "500":
          content: {}
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
      - Access-token: []
      - Genestack-API-Token: []
      summary: Retrieve group metadata by querying study ID (accession)
      tags:
      - Library integration as User
  /api/v1/as-user/integration/link/library/libraries-to-samples/by/group/{id}:
    get:
      description: |+
        ## Paging
        For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.

      operationId: getLibraryLinksToSamplesAsUser
      parameters:
      - description: Unique identifier (accession) of the object.
        in: path
        name: id
        required: true
        schema:
          type: string
      - description: Maximum number of results to return. This value must be between
          0 and 2000 (inclusive).
        in: query
        name: pageLimit
        schema:
          format: int32
          type: integer
      - description: "Show the page {pageOffset+1} results from the start of the results.\
          \ E.g. 100 will show a page of results  starting from the 101st result.\
          \ The default value is 0."
        in: query
        name: pageOffset
        schema:
          format: int32
          type: integer
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/ListResponse"
          description: The request was successful. The returned value is a list of
            objects.
        "400":
          content: {}
          description: Entities cannot be retrieved.
        "401":
          content: {}
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "404":
          content: {}
          description: No object exists with the given ID.
        "500":
          content: {}
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
      - Access-token: []
      - Genestack-API-Token: []
      summary: "Retrieve library-samples pairs by group id. Pagination is based on\
        \ unique libraries, not unique pairs."
      tags:
      - Library integration as User
  /api/v1/as-user/integration/link/preparation/by/sample/{id}:
    get:
      operationId: getPreparationBySampleAsUser
      parameters:
      - description: Supply this parameter with the value `term_id` as part of the
          query to return extended information including IDs for values and dictionaries.
        in: query
        name: responseFormat
        schema:
          $ref: "#/components/schemas/ResponseFormat"
      - description: Unique identifier (accession) of the object.
        in: path
        name: id
        required: true
        schema:
          type: string
      - description: |-
          The parameter defines amount of metadata attributes to return:

          1. `minimal_data` - return metadata attributes according to the default template.
          2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
          3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
        in: query
        name: returnedMetadataFields
        schema:
          enum:
          - minimal_data
          - extended_data_included
          - original_data_included
          type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                items:
                  $ref: "#/components/schemas/Preparation"
                type: array
            text/tab-separated-values:
              schema:
                items:
                  $ref: "#/components/schemas/Preparation"
                type: array
          description: The request was successful. The returned value is a list of
            objects.
        "400":
          content: {}
          description: Entities cannot be retrieved.
        "401":
          content: {}
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "500":
          content: {}
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
      - Access-token: []
      - Genestack-API-Token: []
      summary: Retrieve preparation metadata by querying related sample ID (accession)
      tags:
      - Preparation integration as User
  /api/v1/as-user/integration/link/preparation/group/by/study/{id}:
    get:
      operationId: getPreparationGroupsByStudyAsUser
      parameters:
      - description: Supply this parameter with the value `term_id` as part of the
          query to return extended information including IDs for values and dictionaries.
        in: query
        name: responseFormat
        schema:
          $ref: "#/components/schemas/ResponseFormat"
      - description: Unique identifier (accession) of the object.
        in: path
        name: id
        required: true
        schema:
          type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                items:
                  $ref: "#/components/schemas/MetadataWithId"
                type: array
          description: The request was successful. The returned value is the object.
        "400":
          content: {}
          description: The supplied object ID is invalid.
        "401":
          content: {}
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "500":
          content: {}
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
      - Access-token: []
      - Genestack-API-Token: []
      summary: Retrieve group metadata by querying study ID (accession)
      tags:
      - Preparation integration as User
  /api/v1/as-user/integration/link/preparation/preparations-to-samples/by/group/{id}:
    get:
      description: |+
        ## Paging
        For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.

      operationId: getPreparationLinksToSamplesAsUser
      parameters:
      - description: Unique identifier (accession) of the object.
        in: path
        name: id
        required: true
        schema:
          type: string
      - description: Maximum number of results to return. This value must be between
          0 and 2000 (inclusive).
        in: query
        name: pageLimit
        schema:
          format: int32
          type: integer
      - description: "Show the page {pageOffset+1} results from the start of the results.\
          \ E.g. 100 will show a page of results  starting from the 101st result.\
          \ The default value is 0."
        in: query
        name: pageOffset
        schema:
          format: int32
          type: integer
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/ListResponse"
          description: The request was successful. The returned value is a list of
            objects.
        "400":
          content: {}
          description: Entities cannot be retrieved.
        "401":
          content: {}
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "404":
          content: {}
          description: No object exists with the given ID.
        "500":
          content: {}
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
      - Access-token: []
      - Genestack-API-Token: []
      summary: "Retrieve run-sample pairs by group id. Pagination is based on unique\
        \ preparations, not unique pairs."
      tags:
      - Preparation integration as User
  /api/v1/as-user/integration/link/preparations/by/samples:
    get:
      description: |+
        Retrieve preparation metadata objects whose linked sample metadata matches all supplied conditions.

        ## Conditions
        It is possible to supply conditions for:

        1. Samples (full-text or metadata key-value pair)
        2. Parent studies (full-text or metadata key-value pair)
        3. Linked variant objects (list of data key-value pairs)
        4. Linked flow cytometry objects (list of data key-value pairs)
        5. Linked any data (except variant and flow cytometry) objects (list of data key-value pairs)

        ## Metadata full-text queries
        Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).

        ## Metadata filters
        Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).

        ## Data queries
        Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values.

        ## Combinations
        Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.

        ## Versioning
        Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.

        Example usage:
        useVersions=* (query all versions, including those without CHAIN_IDs)
        useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
        useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
        useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
        useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)

        Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.

        ## Paging
        For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.

      operationId: getPreparationsBySamplesAsUser
      parameters:
      - description: Supply this parameter with the value `term_id` as part of the
          query to return extended information including IDs for values and dictionaries.
        in: query
        name: responseFormat
        schema:
          $ref: "#/components/schemas/ResponseFormat"
      - description: |
          Filter by sample metadata (key-value metadata pair(s)). E.g. `"Species or strain"="Homo sapiens"`
        in: query
        name: filter
        schema:
          type: string
      - description: Search for objects via a full-text query over all sample metadata
          fields. E.g. `Clozapine`. Queries matching dictionary terms are automatically
          expanded to include synonyms.
        in: query
        name: query
        schema:
          type: string
      - description: |-
          If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.

          For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of  "Body fluid") so files containing either "Body fluid" or  "Blood"  in their metadata will be returned in the search results.

          The parent-child relationship is defined by the key "broaders" or "subClassOf"  in the dictionary.

          If the full query term is not present in a dictionary then this parameter has no effect.
        in: query
        name: searchSpecificTerms
        schema:
          type: boolean
      - description: Maximum number of results to return. This value must be between
          0 and 2000 (inclusive).
        in: query
        name: pageLimit
        schema:
          format: int32
          type: integer
      - description: "Show the page {pageOffset+1} results from the start of the results.\
          \ E.g. 100 will show a page of results  starting from the 101st result.\
          \ The default value is 0."
        in: query
        name: pageOffset
        schema:
          format: int32
          type: integer
      - description: |-
          The parameter defines amount of metadata attributes to return:

          1. `minimal_data` - return metadata attributes according to the default template.
          2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
          3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
        in: query
        name: returnedMetadataFields
        schema:
          enum:
          - minimal_data
          - extended_data_included
          - original_data_included
          type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/ListResponse"
            text/tab-separated-values:
              schema:
                $ref: "#/components/schemas/ListResponse"
          description: The request was successful. The returned value is a list of
            objects.
        "401":
          content: {}
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "500":
          content: {}
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
      - Access-token: []
      - Genestack-API-Token: []
      summary: Retrieve preparation metadata by querying related samples
      tags:
      - Preparation integration as User
  /api/v1/as-user/integration/link/samples/by/libraries:
    get:
      description: |+
        Retrieve sample metadata objects whose linked library metadata matches all supplied conditions.

        ## Conditions
        It is possible to supply conditions for:

        1. Samples (full-text or metadata key-value pair)
        2. Parent studies (full-text or metadata key-value pair)
        3. Linked variant objects (list of data key-value pairs)
        4. Linked flow cytometry objects (list of data key-value pairs)
        5. Linked any data (except variant and flow cytometry) objects (list of data key-value pairs)

        ## Metadata full-text queries
        Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).

        ## Metadata filters
        Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).

        ## Data queries
        Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values.

        ## Combinations
        Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.

        ## Versioning
        Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.

        Example usage:
        useVersions=* (query all versions, including those without CHAIN_IDs)
        useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
        useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
        useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
        useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)

        Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.

        ## Paging
        For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.

      operationId: getSamplesByLibrariesAsUser
      parameters:
      - description: Supply this parameter with the value `term_id` as part of the
          query to return extended information including IDs for values and dictionaries.
        in: query
        name: responseFormat
        schema:
          $ref: "#/components/schemas/ResponseFormat"
      - description: Filter by library metadata (key-value metadata pair(s)). E.g.
          `"Library Type"=RNA-Seq-1`
        in: query
        name: filter
        schema:
          type: string
      - description: Search for library objects via a full-text query over all library
          metadata fields. E.g. `"illumina HiSeq500"`. Queries matching dictionary
          terms are automatically expanded to include synonyms.
        in: query
        name: query
        schema:
          type: string
      - description: |-
          If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.

          For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of  "Body fluid") so files containing either "Body fluid" or  "Blood"  in their metadata will be returned in the search results.

          The parent-child relationship is defined by the key "broaders" or "subClassOf"  in the dictionary.

          If the full query term is not present in a dictionary then this parameter has no effect.
        in: query
        name: searchSpecificTerms
        schema:
          type: boolean
      - description: Maximum number of results to return. This value must be between
          0 and 2000 (inclusive).
        in: query
        name: pageLimit
        schema:
          format: int32
          type: integer
      - description: "Show the page {pageOffset+1} results from the start of the results.\
          \ E.g. 100 will show a page of results  starting from the 101st result.\
          \ The default value is 0."
        in: query
        name: pageOffset
        schema:
          format: int32
          type: integer
      - description: |-
          The parameter defines amount of metadata attributes to return:

          1. `minimal_data` - return metadata attributes according to the default template.
          2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
          3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
        in: query
        name: returnedMetadataFields
        schema:
          enum:
          - minimal_data
          - extended_data_included
          - original_data_included
          type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/ListResponse"
            text/tab-separated-values:
              schema:
                $ref: "#/components/schemas/ListResponse"
          description: The request was successful. The returned value is a list of
            objects.
        "401":
          content: {}
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "500":
          content: {}
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
      - Access-token: []
      - Genestack-API-Token: []
      summary: Retrieve sample metadata by querying related libraries
      tags:
      - Sample integration as User
  /api/v1/as-user/integration/link/samples/by/preparations:
    get:
      description: |+
        Retrieve sample metadata objects whose linked preparation metadata matches all supplied conditions.

        ## Conditions
        It is possible to supply conditions for:

        1. Samples (full-text or metadata key-value pair)
        2. Parent studies (full-text or metadata key-value pair)
        3. Linked variant objects (list of data key-value pairs)
        4. Linked flow cytometry objects (list of data key-value pairs)
        5. Linked any data (except variant and flow cytometry) objects (list of data key-value pairs)

        ## Metadata full-text queries
        Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).

        ## Metadata filters
        Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).

        ## Data queries
        Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values.

        ## Combinations
        Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.

        ## Versioning
        Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.

        Example usage:
        useVersions=* (query all versions, including those without CHAIN_IDs)
        useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
        useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
        useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
        useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)

        Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.

        ## Paging
        For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.

      operationId: getSamplesByPreparationsAsUser
      parameters:
      - description: Supply this parameter with the value `term_id` as part of the
          query to return extended information including IDs for values and dictionaries.
        in: query
        name: responseFormat
        schema:
          $ref: "#/components/schemas/ResponseFormat"
      - description: Filter by preparation metadata (key-value metadata pair(s)).
          E.g. `Digestion=Trypsin`
        in: query
        name: filter
        schema:
          type: string
      - description: Search for preparation objects via a full-text query over all
          preparation metadata fields. E.g. `"reversed-phase liquid chromatography"`.
          Queries matching dictionary terms are automatically expanded to include
          synonyms.
        in: query
        name: query
        schema:
          type: string
      - description: |-
          If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.

          For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of  "Body fluid") so files containing either "Body fluid" or  "Blood"  in their metadata will be returned in the search results.

          The parent-child relationship is defined by the key "broaders" or "subClassOf"  in the dictionary.

          If the full query term is not present in a dictionary then this parameter has no effect.
        in: query
        name: searchSpecificTerms
        schema:
          type: boolean
      - description: Maximum number of results to return. This value must be between
          0 and 2000 (inclusive).
        in: query
        name: pageLimit
        schema:
          format: int32
          type: integer
      - description: "Show the page {pageOffset+1} results from the start of the results.\
          \ E.g. 100 will show a page of results  starting from the 101st result.\
          \ The default value is 0."
        in: query
        name: pageOffset
        schema:
          format: int32
          type: integer
      - description: |-
          The parameter defines amount of metadata attributes to return:

          1. `minimal_data` - return metadata attributes according to the default template.
          2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
          3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
        in: query
        name: returnedMetadataFields
        schema:
          enum:
          - minimal_data
          - extended_data_included
          - original_data_included
          type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/ListResponse"
            text/tab-separated-values:
              schema:
                $ref: "#/components/schemas/ListResponse"
          description: The request was successful. The returned value is a list of
            objects.
        "401":
          content: {}
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "500":
          content: {}
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
      - Access-token: []
      - Genestack-API-Token: []
      summary: Retrieve sample metadata by querying related preparations
      tags:
      - Sample integration as User
  /api/v1/as-user/integration/link/samples/by/study/{id}:
    get:
      description: |+
        ## Paging
        For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.

      operationId: getSamplesByStudyAsUser
      parameters:
      - description: Supply this parameter with the value `term_id` as part of the
          query to return extended information including IDs for values and dictionaries.
        in: query
        name: responseFormat
        schema:
          $ref: "#/components/schemas/ResponseFormat"
      - description: Unique identifier (accession) of the object.
        in: path
        name: id
        required: true
        schema:
          type: string
      - description: Maximum number of results to return. This value must be between
          0 and 2000 (inclusive).
        in: query
        name: pageLimit
        schema:
          format: int32
          type: integer
      - description: "Show the page {pageOffset+1} results from the start of the results.\
          \ E.g. 100 will show a page of results  starting from the 101st result.\
          \ The default value is 0."
        in: query
        name: pageOffset
        schema:
          format: int32
          type: integer
      - description: |-
          The parameter defines amount of metadata attributes to return:

          1. `minimal_data` - return metadata attributes according to the default template.
          2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
          3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
        in: query
        name: returnedMetadataFields
        schema:
          enum:
          - minimal_data
          - extended_data_included
          - original_data_included
          type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/ListResponse"
            text/tab-separated-values:
              schema:
                $ref: "#/components/schemas/ListResponse"
          description: The request was successful. The returned value is a list of
            objects.
        "400":
          content: {}
          description: Entities cannot be retrieved.
        "401":
          content: {}
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "500":
          content: {}
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
      - Access-token: []
      - Genestack-API-Token: []
      summary: Retrieve sample metadata by querying related study ID (accession)
      tags:
      - Sample integration as User
  /api/v1/as-user/integration/link/studies/by/libraries:
    get:
      description: |+
        Retrieve study metadata objects whose linked library metadata matches all supplied conditions.

        ## Conditions
        It is possible to supply conditions for:

        1. Samples (full-text or metadata key-value pair)
        2. Parent studies (full-text or metadata key-value pair)
        3. Linked variant objects (list of data key-value pairs)
        4. Linked flow cytometry objects (list of data key-value pairs)
        5. Linked any data (except variant and flow cytometry) objects (list of data key-value pairs)

        ## Metadata full-text queries
        Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).

        ## Metadata filters
        Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).

        ## Data queries
        Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values.

        ## Combinations
        Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.

        ## Versioning
        Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.

        Example usage:
        useVersions=* (query all versions, including those without CHAIN_IDs)
        useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
        useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
        useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
        useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)

        Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.

        ## Paging
        For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.

      operationId: getStudiesByLibrariesAsUser
      parameters:
      - description: Supply this parameter with the value `term_id` as part of the
          query to return extended information including IDs for values and dictionaries.
        in: query
        name: responseFormat
        schema:
          $ref: "#/components/schemas/ResponseFormat"
      - description: Filter by library metadata (key-value metadata pair(s)). E.g.
          `"Library Type"=RNA-Seq-1`
        in: query
        name: filter
        schema:
          type: string
      - description: Search for library objects via a full-text query over all library
          metadata fields. E.g. `"illumina HiSeq500"`. Queries matching dictionary
          terms are automatically expanded to include synonyms.
        in: query
        name: query
        schema:
          type: string
      - description: |-
          If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.

          For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of  "Body fluid") so files containing either "Body fluid" or  "Blood"  in their metadata will be returned in the search results.

          The parent-child relationship is defined by the key "broaders" or "subClassOf"  in the dictionary.

          If the full query term is not present in a dictionary then this parameter has no effect.
        in: query
        name: searchSpecificTerms
        schema:
          type: boolean
      - description: Maximum number of results to return. This value must be between
          0 and 2000 (inclusive).
        in: query
        name: pageLimit
        schema:
          format: int32
          type: integer
      - description: "Show the page {pageOffset+1} results from the start of the results.\
          \ E.g. 100 will show a page of results  starting from the 101st result.\
          \ The default value is 0."
        in: query
        name: pageOffset
        schema:
          format: int32
          type: integer
      - description: |-
          The parameter defines amount of metadata attributes to return:

          1. `minimal_data` - return metadata attributes according to the default template.
          2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
          3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
        in: query
        name: returnedMetadataFields
        schema:
          enum:
          - minimal_data
          - extended_data_included
          - original_data_included
          type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/ListResponse"
            text/tab-separated-values:
              schema:
                $ref: "#/components/schemas/ListResponse"
          description: The request was successful. The returned value is a list of
            objects.
        "401":
          content: {}
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "500":
          content: {}
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
      - Access-token: []
      - Genestack-API-Token: []
      summary: Retrieve study metadata objects by querying related libraries
      tags:
      - Study integration as User
  /api/v1/as-user/integration/link/studies/by/preparations:
    get:
      description: |+
        Retrieve study metadata objects whose linked preparation metadata matches all supplied conditions.

        ## Conditions
        It is possible to supply conditions for:

        1. Samples (full-text or metadata key-value pair)
        2. Parent studies (full-text or metadata key-value pair)
        3. Linked variant objects (list of data key-value pairs)
        4. Linked flow cytometry objects (list of data key-value pairs)
        5. Linked any data (except variant and flow cytometry) objects (list of data key-value pairs)

        ## Metadata full-text queries
        Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).

        ## Metadata filters
        Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).

        ## Data queries
        Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values.

        ## Combinations
        Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.

        ## Versioning
        Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.

        Example usage:
        useVersions=* (query all versions, including those without CHAIN_IDs)
        useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
        useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
        useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
        useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)

        Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.

        ## Paging
        For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.

      operationId: getStudiesByPreparationsAsUser
      parameters:
      - description: Supply this parameter with the value `term_id` as part of the
          query to return extended information including IDs for values and dictionaries.
        in: query
        name: responseFormat
        schema:
          $ref: "#/components/schemas/ResponseFormat"
      - description: Filter by preparation metadata (key-value metadata pair(s)).
          E.g. `Digestion=Trypsin`
        in: query
        name: filter
        schema:
          type: string
      - description: Search for preparation objects via a full-text query over all
          preparation metadata fields. E.g. `"reversed-phase liquid chromatography"`.
          Queries matching dictionary terms are automatically expanded to include
          synonyms.
        in: query
        name: query
        schema:
          type: string
      - description: |-
          If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.

          For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of  "Body fluid") so files containing either "Body fluid" or  "Blood"  in their metadata will be returned in the search results.

          The parent-child relationship is defined by the key "broaders" or "subClassOf"  in the dictionary.

          If the full query term is not present in a dictionary then this parameter has no effect.
        in: query
        name: searchSpecificTerms
        schema:
          type: boolean
      - description: Maximum number of results to return. This value must be between
          0 and 2000 (inclusive).
        in: query
        name: pageLimit
        schema:
          format: int32
          type: integer
      - description: "Show the page {pageOffset+1} results from the start of the results.\
          \ E.g. 100 will show a page of results  starting from the 101st result.\
          \ The default value is 0."
        in: query
        name: pageOffset
        schema:
          format: int32
          type: integer
      - description: |-
          The parameter defines amount of metadata attributes to return:

          1. `minimal_data` - return metadata attributes according to the default template.
          2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
          3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
        in: query
        name: returnedMetadataFields
        schema:
          enum:
          - minimal_data
          - extended_data_included
          - original_data_included
          type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/ListResponse"
            text/tab-separated-values:
              schema:
                $ref: "#/components/schemas/ListResponse"
          description: The request was successful. The returned value is a list of
            objects.
        "401":
          content: {}
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "500":
          content: {}
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
      - Access-token: []
      - Genestack-API-Token: []
      summary: Retrieve study metadata objects by querying related preparations
      tags:
      - Study integration as User
  /api/v1/as-user/integration/link/studies/by/samples:
    get:
      description: |+
        Retrieve study metadata objects whose linked sample metadata matches all supplied conditions.

        ## Conditions
        It is possible to supply conditions for:

        1. Samples (full-text or metadata key-value pair)
        2. Parent studies (full-text or metadata key-value pair)
        3. Linked variant objects (list of data key-value pairs)
        4. Linked flow cytometry objects (list of data key-value pairs)
        5. Linked any data (except variant and flow cytometry) objects (list of data key-value pairs)

        ## Metadata full-text queries
        Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).

        ## Metadata filters
        Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).

        ## Data queries
        Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values.

        ## Combinations
        Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.

        ## Versioning
        Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.

        Example usage:
        useVersions=* (query all versions, including those without CHAIN_IDs)
        useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
        useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
        useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
        useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)

        Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.

        ## Paging
        For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.

      operationId: getStudiesBySamplesAsUser
      parameters:
      - description: Supply this parameter with the value `term_id` as part of the
          query to return extended information including IDs for values and dictionaries.
        in: query
        name: responseFormat
        schema:
          $ref: "#/components/schemas/ResponseFormat"
      - description: Filter by sample metadata (key-value metadata pair(s)). E.g.
          "Species or strain"="Homo sapiens"
        in: query
        name: filter
        schema:
          type: string
      - description: Search for study metadata objects via a full-text query over
          all sample metadata fields. E.g. "RNA-Seq of human dendritic cells". Queries
          matching dictionary terms are automatically expanded to include synonyms.
        in: query
        name: query
        schema:
          type: string
      - description: |-
          If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.

          For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of  "Body fluid") so files containing either "Body fluid" or  "Blood"  in their metadata will be returned in the search results.

          The parent-child relationship is defined by the key "broaders" or "subClassOf"  in the dictionary.

          If the full query term is not present in a dictionary then this parameter has no effect.
        in: query
        name: searchSpecificTerms
        schema:
          type: boolean
      - description: Maximum number of results to return. This value must be between
          0 and 2000 (inclusive).
        in: query
        name: pageLimit
        schema:
          format: int32
          type: integer
      - description: "Show the page {pageOffset+1} results from the start of the results.\
          \ E.g. 100 will show a page of results  starting from the 101st result.\
          \ The default value is 0."
        in: query
        name: pageOffset
        schema:
          format: int32
          type: integer
      - description: |-
          The parameter defines amount of metadata attributes to return:

          1. `minimal_data` - return metadata attributes according to the default template.
          2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
          3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
        in: query
        name: returnedMetadataFields
        schema:
          enum:
          - minimal_data
          - extended_data_included
          - original_data_included
          type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/ListResponse"
            text/tab-separated-values:
              schema:
                $ref: "#/components/schemas/ListResponse"
          description: The request was successful. The returned value is a list of
            objects.
        "401":
          content: {}
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "500":
          content: {}
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
      - Access-token: []
      - Genestack-API-Token: []
      summary: Retrieve study metadata objects by querying related samples
      tags:
      - Study integration as User
  /api/v1/as-user/integration/link/study/by/sample/{id}:
    get:
      operationId: getStudyBySampleAsUser
      parameters:
      - description: Supply this parameter with the value `term_id` as part of the
          query to return extended information including IDs for values and dictionaries.
        in: query
        name: responseFormat
        schema:
          $ref: "#/components/schemas/ResponseFormat"
      - description: Unique identifier (accession) of the object.
        in: path
        name: id
        required: true
        schema:
          type: string
      - description: |-
          The parameter defines amount of metadata attributes to return:

          1. `minimal_data` - return metadata attributes according to the default template.
          2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
          3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
        in: query
        name: returnedMetadataFields
        schema:
          enum:
          - minimal_data
          - extended_data_included
          - original_data_included
          type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/Study"
          description: The request was successful. The returned value is the object.
        "400":
          content: {}
          description: The supplied object ID is invalid.
        "401":
          content: {}
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "500":
          content: {}
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
      - Access-token: []
      - Genestack-API-Token: []
      summary: Retrieve study metadata by querying sample ID (accession)
      tags:
      - Study integration as User
  /api/v1/as-user/integration/link/studies/by/files:
    get:
      description: |+
        Retrieve study metadata objects whose linked attached files metadata matches all supplied conditions.

        ## Conditions
        It is possible to supply conditions for:

        1. Attachment files (full-text or metadata key-value pair)
        2. Parent studies (full-text or metadata key-value pair)

        ## Metadata full-text queries
        Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).

        ## Metadata filters
        Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).

        ## Combinations
        Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.

        ## Paging
        For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.

      operationId: getStudiesByFilesAsUser
      parameters:
      - description: Supply this parameter with the value `term_id` as part of the
          query to return extended information including IDs for values and dictionaries.
        in: query
        name: responseFormat
        schema:
          $ref: "#/components/schemas/ResponseFormat"
      - description: Filter by attachment file metadata (key-value metadata pair(s)). E.g.
          "Species or strain"="Homo sapiens"
        in: query
        name: filter
        schema:
          type: string
      - description: Search for study metadata objects via a full-text query over
          all attached files metadata fields. E.g. "RNA-Seq of human dendritic cells". Queries
          matching dictionary terms are automatically expanded to include synonyms.
        in: query
        name: query
        schema:
          type: string
      - description: Maximum number of results to return. This value must be between
          0 and 2000 (inclusive).
        in: query
        name: pageLimit
        schema:
          format: int32
          type: integer
      - description: "Show the page {pageOffset+1} results from the start of the results.\
          \ E.g. 100 will show a page of results  starting from the 101st result.\
          \ The default value is 0."
        in: query
        name: pageOffset
        schema:
          format: int32
          type: integer
      - description: |-
          The parameter defines amount of metadata attributes to return:

          1. `minimal_data` - return metadata attributes according to the default template.
          2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
          3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
        in: query
        name: returnedMetadataFields
        schema:
          enum:
          - minimal_data
          - extended_data_included
          - original_data_included
          type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/ListResponse"
            text/tab-separated-values:
              schema:
                $ref: "#/components/schemas/ListResponse"
          description: The request was successful. The returned value is a list of
            objects.
        "401":
          content: {}
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "500":
          content: {}
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
      - Access-token: []
      - Genestack-API-Token: []
      summary: Retrieve study metadata objects by querying related attachment files
      tags:
      - Study integration as User
  /api/v1/as-user/integration/link/study/by/file/{id}:
    get:
      operationId: getStudyByFileAsUser
      parameters:
      - description: Supply this parameter with the value `term_id` as part of the
          query to return extended information including IDs for values and dictionaries.
        in: query
        name: responseFormat
        schema:
          $ref: "#/components/schemas/ResponseFormat"
      - description: Unique identifier (accession) of the object.
        in: path
        name: id
        required: true
        schema:
          type: string
      - description: |-
          The parameter defines amount of metadata attributes to return:

          1. `minimal_data` - return metadata attributes according to the default template.
          2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
          3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
        in: query
        name: returnedMetadataFields
        schema:
          enum:
          - minimal_data
          - extended_data_included
          - original_data_included
          type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/Study"
          description: The request was successful. The returned value is the object.
        "400":
          content: {}
          description: The supplied object ID is invalid.
        "401":
          content: {}
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "500":
          content: {}
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
      - Access-token: []
      - Genestack-API-Token: []
      summary: Retrieve study metadata by querying attachment file ID (accession)
      tags:
      - Study integration as User
  /api/v1/as-user/integration/fulltext/search/studies:
    post:
      description: |-
        Find studies and retrieve their data using full-text search or facet search by metadata of study itself or child object (samples, libraries, preparations, signal groups). Only studies available to that users are returned.

        The endpoint returns:
        - a list of studies with their metadata summary;
        - a list of filter objects with counts; filter list is the same for all users in an and can be configured in “Study Browser” application via "Configure facets" (by a user with corresponding permission); for each filter object, only the first 5 most popular facets are returned, the facts are sorted by the count value in descending order; only studies available to user are counted.

        Filter attributes for fulltext search:
        - `"type": "FULL_TEXT"`
        - `"match"`
        - `"mode"`

        For details on two latter ones, see the request body model. Only one filter with `"type=": "FULL_TEXT"` can be passed in the request body.

        To filter studies via facets, the filter attributes are necessary: type = SELECT, filterOptionId. For details, use the request body model. filterOptionId can be obtained from the response body when the endpoint is first called without filters. Multiple filters with type = SELECT can be passed in the request body. Filters within the same attribute are automatically used with the OR operator. Filters of different attributes are automatically used with the AND operator. This behaviour can not be changed.

        It is possible to call the endpoint without any filters, then all the studies available to the user are returned.
      operationId: searchStudiesByFilterAsUser
      requestBody:
        content:
          application/json:
            schema:
              $ref: "#/components/schemas/SearchStudyRequest"
        required: true
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/FindObjectsResponse"
          description: The request was successful. Retrieved studies and filters.
        "400":
          content: {}
          description: Invalid request body
        "401":
          content: {}
          description: User is not authenticated. Please supply a valid Genestack
            API token in the `Genestack-API-Token` HTTP header (this token may be
            obtained from the Genestack UI _Profile_ page).
        "500":
          content: {}
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
      - Genestack-API-Token: []
      summary: Find and retrieve studies by full-text or facet query
      tags:
      - Study integration as User
      x-codegen-request-body-name: request
  /api/v1/as-user/integration/link/variant/by/sample/{id}:
    get:
      description: |+
        ## Versioning
        Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.

        Example usage:
        useVersions=* (query all versions, including those without CHAIN_IDs)
        useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
        useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
        useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
        useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)

        Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.

        ## Paging
        For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.

      operationId: getVariantBySampleAsUser
      parameters:
      - description: Supply this parameter with the value `term_id` as part of the
          query to return extended information including IDs for values and dictionaries.
        in: query
        name: responseFormat
        schema:
          $ref: "#/components/schemas/ResponseFormat"
      - description: Unique identifier (accession) of the object.
        in: path
        name: id
        required: true
        schema:
          type: string
      - description: Maximum number of results to return. This value must be between
          0 and 2000 (inclusive).
        in: query
        name: pageLimit
        schema:
          format: int32
          type: integer
      - description: "Show the page {pageOffset+1} results from the start of the results.\
          \ E.g. 100 will show a page of results  starting from the 101st result.\
          \ The default value is 0."
        in: query
        name: pageOffset
        schema:
          format: int32
          type: integer
      - description: |-
          Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:

          \* or `v<version number>` or `<CHAIN_ID>`:`v<version number>` or `<CHAIN_ID>`:`<accession1,accession2,..>`
        in: query
        name: useVersions
        schema:
          type: string
      - description: |-
          The parameter defines amount of metadata attributes to return:

          1. `minimal_data` - return metadata attributes according to the default template.
          2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
          3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
        in: query
        name: returnedMetadataFields
        schema:
          enum:
          - minimal_data
          - extended_data_included
          - original_data_included
          type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/ListResponse"
            text/tab-separated-values:
              schema:
                $ref: "#/components/schemas/ListResponse"
          description: The request was successful. The returned value is a list of
            objects.
        "400":
          content: {}
          description: Entities cannot be retrieved.
        "401":
          content: {}
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "500":
          content: {}
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
      - Access-token: []
      - Genestack-API-Token: []
      summary: Retrieve variant run-level data by querying related sample ID (accession)
      tags:
      - Variant integration as User
  /api/v1/as-user/integration/link/variant/group/by/study/{id}:
    get:
      description: |+
        ## Versioning
        Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.

        Example usage:
        useVersions=* (query all versions, including those without CHAIN_IDs)
        useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
        useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
        useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
        useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)

        Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.

      operationId: getVariantGroupsByStudyAsUser
      parameters:
      - description: Supply this parameter with the value `term_id` as part of the
          query to return extended information including IDs for values and dictionaries.
        in: query
        name: responseFormat
        schema:
          $ref: "#/components/schemas/ResponseFormat"
      - description: Unique identifier (accession) of the object.
        in: path
        name: id
        required: true
        schema:
          type: string
      - description: |-
          Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:

          \* or `v<version number>` or `<CHAIN_ID>`:`v<version number>` or `<CHAIN_ID>`:`<accession1,accession2,..>`
        in: query
        name: useVersions
        schema:
          type: string
      - description: |-
          The parameter defines amount of metadata attributes to return:

          1. `minimal_data` - return metadata attributes according to the default template.
          2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
          3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
        in: query
        name: returnedMetadataFields
        schema:
          enum:
          - minimal_data
          - extended_data_included
          - original_data_included
          type: string
      responses:
        "200":
          content:
            application/json:
              schema:
                items:
                  $ref: "#/components/schemas/MetadataWithId"
                type: array
          description: The request was successful. The returned value is the object.
        "400":
          content: {}
          description: The supplied object ID is invalid.
        "401":
          content: {}
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "500":
          content: {}
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
      - Access-token: []
      - Genestack-API-Token: []
      summary: Retrieve group metadata by querying study ID (accession)
      tags:
      - Variant integration as User
  /api/v1/as-user/integration/link/variant/run-to-samples/by/group/{id}:
    get:
      description: |+
        ## Paging
        For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.

      operationId: getVariantRunToSamplePairsAsUser
      parameters:
      - description: Unique identifier (accession) of the object.
        in: path
        name: id
        required: true
        schema:
          type: string
      - description: Maximum number of results to return. This value must be between
          0 and 2000 (inclusive).
        in: query
        name: pageLimit
        schema:
          format: int32
          type: integer
      - description: "Show the page {pageOffset+1} results from the start of the results.\
          \ E.g. 100 will show a page of results  starting from the 101st result.\
          \ The default value is 0."
        in: query
        name: pageOffset
        schema:
          format: int32
          type: integer
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/ListResponse"
          description: The request was successful. The returned value is a list of
            objects.
        "400":
          content: {}
          description: Entities cannot be retrieved.
        "401":
          content: {}
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "404":
          content: {}
          description: No object exists with the given ID.
        "500":
          content: {}
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
      - Access-token: []
      - Genestack-API-Token: []
      summary: "Retrieve run-sample pairs by group id. Pagination is based on unique\
        \ runs, not unique pairs."
      tags:
      - Variant integration as User
  /api/v1/as-user/links:
    get:
      description: Please make sure that this endpoint should be used only for getting
        all links to a specific object. In case you specify both firstId and secondId
        an expected answer would be true for existing links and false for no link
        between the objects.
      operationId: getLinksByParamsAsUser
      parameters:
      - description: Object ID (accession) (e.g. accession of study)
        in: query
        name: firstId
        required: true
        schema:
          type: string
      - description: Type of the object (e.g. study)
        in: query
        name: firstType
        schema:
          type: string
      - description: Object ID (accession) (e.g. accession of study)
        in: query
        name: secondId
        schema:
          type: string
      - description: Type of the object (e.g. study)
        in: query
        name: secondType
        schema:
          type: string
      - description: Param says to skip that many links before beginning to return
          links.
        in: query
        name: offset
        schema:
          default: 0
          format: int32
          type: integer
      - description: Param says to limit the count of returned links.
        in: query
        name: limit
        schema:
          default: 1000
          format: int32
          type: integer
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/ListResponse"
          description: The request was successful. The returned value is a list of
            objects.
        "400":
          content: {}
          description: Entities cannot be retrieved.
        "401":
          content: {}
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "500":
          content: {}
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
      - Access-token: []
      - Genestack-API-Token: []
      summary: Finds existing links matching the specified criteria.
      tags:
      - Linkage as User
  /api/v1/as-user/links/get-batch:
    post:
      description: Please make sure to use that endpoint for batch calls only. You
        are not allowed to pass 'mixed' objects. e.g. Studies and Samples at the same
        time. Please always specify firstType.
      operationId: getLinksByIdsAsUser
      requestBody:
        content:
          application/json:
            schema:
              $ref: "#/components/schemas/BatchOfIds"
        required: false
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/ListResponse"
          description: The request was successful. The returned value is a list of
            objects.
        "400":
          content: {}
          description: Entities cannot be retrieved.
        "401":
          content: {}
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "500":
          content: {}
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
      - Access-token: []
      - Genestack-API-Token: []
      summary: "Finds existing links by passing many IDs. \nPagination goes through\
        \ all links matched the criteria."
      tags:
      - Linkage as User
      x-codegen-request-body-name: request
  /api/v1/as-user/omics/cells:
    get:
      description: |-
        Retrieve cell objects whose linked data matches all supplied conditions.

        ## Conditions
        It is possible to supply conditions for:
        1. Parent studies (full-text or metadata key-value pair)
        2. Samples (full-text or metadata key-value pair)
        3. Libraries (full-text or metadata key-value pair)
        4. Preparations (full-text or metadata key-value pair)

        ## Metadata full-text queries
        Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).

        ## Metadata filters
        Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).

        ## Data queries
        Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values.

        ## Combinations
        Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.

        ## Paging
        For performance reasons this endpoint returns results in "pages" of limited size together with a `cursor` tag. To retrieve the next page of results please supply this `cursor` tag to resume the query from your previous result and get the next page. If there are no more results you will just retrieve an empty result.
      operationId: omicsSearchCellsAsUser
      parameters:
        - description: |
            Filter by study metadata (key-value metadata pair(s)). E.g. `"Study Source"=ArrayExpress`
          in: query
          name: studyFilter
          schema:
            type: string
        - description: |
            Search for objects via a full-text query over all study metadata fields. E.g. `RNA-Seq of human dendritic cells`. Queries matching dictionary terms are automatically expanded to include synonyms.
          in: query
          name: studyQuery
          schema:
            type: string
        - description: |
            Filter by sample metadata (key-value metadata pair(s)). E.g. `"Species or strain"="Homo sapiens"`
          in: query
          name: sampleFilter
          schema:
            type: string
        - description: |
            Search for objects via a full-text query over all sample metadata fields. E.g. `Clozapine`. Queries matching dictionary terms are automatically expanded to include synonyms.
          in: query
          name: sampleQuery
          schema:
            type: string
        - description: |
            Filter by library metadata (key-value metadata pair(s)). E.g. `"Library Type"=RNA-Seq-1`
          in: query
          name: libraryFilter
          schema:
            type: string
        - description: |
            Search for library objects via a full-text query over all library metadata fields. E.g. `illumina HiSeq500`. Queries matching dictionary terms are automatically expanded to include synonyms.
          in: query
          name: libraryQuery
          schema:
            type: string
        - description: |
            Filter by preparation metadata (key-value metadata pair(s)). E.g. `Digestion=Trypsin`
          in: query
          name: preparationFilter
          schema:
            type: string
        - description: |
            Search for preparation objects via a full-text query over all preparation metadata fields. E.g. `reversed-phase liquid chromatography`. Queries matching dictionary terms are automatically expanded to include synonyms.
          in: query
          name: preparationQuery
          schema:
            type: string
        - description: |-
            If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.

            For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of  "Body fluid") so files containing either "Body fluid" or  "Blood"  in their metadata will be returned in the search results.

            The parent-child relationship is defined by the key "broaders" or "subClassOf"  in the dictionary.

            If the full query term is not present in a dictionary then this parameter has no effect.
          in: query
          name: searchSpecificTerms
          schema:
            type: boolean
        - description: |-
            Search for cells by their metadata attributes. The following attributes are supported:
            1. Strings: `barcode`, `batch`, `cellType`, `cluster`, and all custom attributes.
            2. Integers: `nCounts`
            3. Floats: `percentMito`
            4. Float coordinates: `UMAP`, `PCA`, `TSNE`.
            5. All other attributes are considered to be custom and stored as string data type.

            To use filters for cell metadata objects use the following query types:
            1. By key=value pair for attributes. Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace: `cellType=T_cell`, `batch="PBMC batch 01"` - quote values that include spaces, `nCounts=3000`, `custom_attribute="disease"` - custom attribute with string data type.
            2. It is possible to specify a set of possible values, separated by comma: `cellType=Macrophage,Monocyte`.
            3. Utilize range filters to search numeric attributes. Apply `<` (less than), `>` (greater than), and `=` (equal to) symbols to specify the desired ranges as follows: `nCounts > 2000`, `-3 < percentMito < 10`. To retrieve UMAP, PCA or TSNE values use `umap.1`, `umap.2`, `pca.1`, `pca.2`, `tsne.1`, `tsne.2`, e.g. `umap.1 > 0.5`.
            4. Use substring search to get the records where the attribute field contains the provided substring: `cellType =~ "B cell"`.
            5. Combine multiple filters for different feature attributes and measurements using `AND` (`&&`), `OR` (`||`), `NOT` (`!`) logical operators and parentheses:
            * `NOT cellType=Erythrocyte` or `cellType!=B_cell,T_cell`: exclude objects with defined values from search.
            * `batch=BatchA && percentMito<0.8` or `batch=BatchA AND percentMito<8`: select all objects with BatchA and percentMito less than 0.8.
            * `cluster=1 || cluster=2` or `cluster=1 OR cluster=2`: select all objects where cluster 1 or 2.
            * `percentMito>0.2 && nCounts>=1000`: select all objects where percentMito is greater than 0.2 and nCounts is more or equal to 1000.
            * `batch=BatchA && (cluster=3 || -3 < percentMito < 8)`: combine logical operators in one query.

          in: query
          name: cellQuery
          schema:
            type: string
        - description: "Search for objects linked to cell expression data and originally\
            \ uploaded in TSV format via data query, e.g., `feature=ENSG00000230368,ENSG00000188976\
            \ value>=1.50`\n For the case when the original data is represented by multiple\
            \ attributes per feature scenarios, extended filtering syntax is as follows:\
            \ \n1. By feature attribute value for numeric and string attributes: `feature.NAME=1007_s_at`\
            \ or `feature.\"Average Mz\"=2.218`. As in the case of sample metadata queries,\
            \ single words can be supplied as is; otherwise, use speech marks (`\"`)\
            \ to quote queries that include whitespace. \n2. It is possible to specify\
            \ a set of possible values, separated by comma: `feature.NAME=1007_s_at,121_at`.\
            \ \n3. Utilize range filters to search numeric attributes. Apply `<` (less\
            \ than), `>` (greater than), and `=` (equal to) symbols to specify the desired\
            \ ranges as follows: \n`feature.Name_1 > 3`: Select all rows where the feature\
            \ attribute Name_1 values are greater than 3. \n`feature.Name_2 >= 6`: Select\
            \ all rows where the feature attribute Name_2 values are greater than or\
            \ equal to 6. \n`-3 < feature.Name_3 < 3`: Select all rows where the feature\
            \ attribute Name_3 values lie within the interval between -3 and 3. \n4.\
            \ Use substring search to get the records where the attribute field contains\
            \ the provided substring: `feature.attribute1 =~ \"some text\"`. \n5. The\
            \ first column for each original data file is identified as feature accession\
            \ (typically, it contains gene or protein names, accession IDs, etc.). Searching\
            \ by such feature accession would significantly outperform more complex\
            \ queries by combining the other feature attributes. To enable such a search,\
            \ use `feature` without any attribute extension, e.g., `feature=ENSG00000230368,ENSG00000188976`.\n\
            \ \nThe `value` keyword can be used to select rows where the cell
            \ measurements has values from a certain range. Examples:\
            \ `value = 3`, `value > 3`, `-3 < value < 3`.\n
            \ \nCombine multiple filters for different feature attributes and measurements\
            \ using `AND` (`&&`), `OR` (`||`), `NOT` (`!`) logical operators and parentheses: \n\
            * `NOT feature.Name_1=A`: Select all rows where Name_1 is not A. \n* `feature.Name_1!=A,B,C`:\
            \ Select all rows where Name_1 is not A, B, or C. \n* `feature.Name_1=A\
            \ AND feature.Name_2=B`: Select all rows where Name_1 is A and Name_2 is\
            \ B. \n* `feature.Name_1=A && feature.Name_2=B`: Equivalent to the example\
            \ above. \n* `feature.Name_1=A OR feature.Name_2=B`: Select all rows where\
            \ Name_1 is A or Name_2 is B. \n* `feature.Name_1=A || feature.Name_2=B`:\
            \ Equivalent to the example above. \n* `feature.Name_1=A AND (feature.Name_2=B\
            \ OR value>=1.0)`: Select all rows where Name_1 is A and either Name_2 is\
            \ B or minimal possible measurement value is 1.0."
          in: query
          name: exQuery
          schema:
            type: string
        - description: "Filter by expression metadata (key-value metadata pair(s)).\
            \ E.g. `\"Genome Version\"=hg19-BROAD`."
          in: query
          name: exFilter
          schema:
            type: string
        - description: The page tag to resume results from (see paging above).
          in: query
          name: cursor
          schema:
            type: string
        - description: This parameter determines the number of results to retrieve per page, with the default set at 2000.
          in: query
          name: pageLimit
          schema:
            format: int32
            type: integer
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/OmicsResponse"
          description: Omics query result.
        "400":
          content: { }
          description: Invalid data in request. See error message for details.
        "401":
          content: { }
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "500":
          content: { }
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
        - Access-token: [ ]
        - Genestack-API-Token: [ ]
      summary: Retrieve Cell objects by searching across multiple data types
      tags:
        - Omics queries as User
  /api/v1/as-user/omics/cells/expression/data:
    get:
      description: |-
        Retrieve cell expression objects by searching across multiple metadata types.

        ## Conditions
        It is possible to supply conditions for:
        1. Parent studies (full-text or metadata key-value pair)
        2. Samples (full-text or metadata key-value pair)
        3. Libraries (full-text or metadata key-value pair)
        4. Preparations (full-text or metadata key-value pair)

        ## Metadata full-text queries
        Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).

        ## Metadata filters
        Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).

        ## Data queries
        Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values.

        ## Combinations
        Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.

        ## Paging
        For performance reasons this endpoint returns results in "pages" of limited size together with a `cursor` tag. To retrieve the next page of results please supply this `cursor` tag to resume the query from your previous result and get the next page. If there are no more results you will just retrieve an empty result.
      operationId: omicsSearchCellsExpressionDataAsUser
      parameters:
        - description: |
            Filter by study metadata (key-value metadata pair(s)). E.g. `"Study Source"=ArrayExpress`
          in: query
          name: studyFilter
          schema:
            type: string
        - description: Search for objects via a full-text query over all study metadata
            fields. E.g. `"RNA-Seq of human dendritic cells"`. Queries matching dictionary
            terms are automatically expanded to include synonyms.
          in: query
          name: studyQuery
          schema:
            type: string
        - description: |
            Filter by sample metadata (key-value metadata pair(s)). E.g. `"Species or strain"="Homo sapiens"`
          in: query
          name: sampleFilter
          schema:
            type: string
        - description: Search for objects via a full-text query over all sample metadata
            fields. E.g. `Clozapine`. Queries matching dictionary terms are automatically
            expanded to include synonyms.
          in: query
          name: sampleQuery
          schema:
            type: string
        - description: Filter by library metadata (key-value metadata pair(s)). E.g.
            `"Library Type"=RNA-Seq-1`
          in: query
          name: libraryFilter
          schema:
            type: string
        - description: Search for library objects via a full-text query over all library
            metadata fields. E.g. `"illumina HiSeq500"`. Queries matching dictionary
            terms are automatically expanded to include synonyms.
          in: query
          name: libraryQuery
          schema:
            type: string
        - description: Filter by preparation metadata (key-value metadata pair(s)).
            E.g. `Digestion=Trypsin`
          in: query
          name: preparationFilter
          schema:
            type: string
        - description: Search for preparation objects via a full-text query over all
            preparation metadata fields. E.g. `"reversed-phase liquid chromatography"`.
            Queries matching dictionary terms are automatically expanded to include
            synonyms.
          in: query
          name: preparationQuery
          schema:
            type: string
        - description: |-
            Search for cells by their metadata attributes. The following attributes are supported:
            1. Strings: `barcode`, `batch`, `cellType`, `cluster`, and all custom attributes.
            2. Integers: `nCounts`
            3. Floats: `percentMito`
            4. Float coordinates: `UMAP`, `PCA`, `TSNE`.
            5. All other attributes are considered to be custom and stored as string data type.

            To use filters for cell metadata objects use the following query types:
            1. By key=value pair for attributes. Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace: `cellType=T_cell`, `batch="PBMC batch 01"` - quote values that include spaces, `nCounts=3000`, `custom_attribute="disease"` - custom attribute with string data type.
            2. It is possible to specify a set of possible values, separated by comma: `cellType=Macrophage,Monocyte`.
            3. Utilize range filters to search numeric attributes. Apply `<` (less than), `>` (greater than), and `=` (equal to) symbols to specify the desired ranges as follows: `nCounts > 2000`, `-3 < percentMito < 10`. To retrieve UMAP, PCA or `TSNE` values use `umap.1`, `umap.2`, `pca.1`, `pca.2`, `tsne.1`, `tsne.2`, e.g. `umap.1 > 0.5`.
            4. Use substring search to get the records where the attribute field contains the provided substring: `cellType =~ "B cell"`.
            5. Combine multiple filters for different feature attributes and measurements using `AND` (`&&`), `OR` (`||`), `NOT` (`!`) logical operators and parentheses:
            * `NOT cellType=Erythrocyte` or `cellType!=B_cell,T_cell`: exclude objects with defined values from search.
            * `batch=BatchA && percentMito<0.8` or `batch=BatchA AND percentMito<8`: select all objects with BatchA and percentMito less than 0.8.
            * `cluster=1 || cluster=2` or `cluster=1 OR cluster=2`: select all objects where cluster 1 or 2.
            * `percentMito>0.2 && nCounts>=1000`: select all objects where percentMito is greater than 0.2 and nCounts is more or equal to 1000.
            * `batch=BatchA && (cluster=3 || -3 < percentMito < 8)`: combine logical operators in one query.
          in: query
          name: cellQuery
          schema:
            type: string
        - description: "Search for objects linked to expression data and originally\
          \ uploaded in TSV or GCT format via data query, e.g., `feature=ENSG00000230368,ENSG00000188976\
          \ value>=1.50`\n For the case when the original data is represented by multiple\
          \ attributes per feature scenarios, extended filtering syntax is as follows:\
          \ \n1. By feature attribute value for numeric and string attributes: `feature.NAME=1007_s_at`\
          \ or `feature.\"Average Mz\"=2.218`. As in the case of sample metadata queries,\
          \ single words can be supplied as is; otherwise, use speech marks (`\"`)\
          \ to quote queries that include whitespace. \n2. It is possible to specify\
          \ a set of possible values, separated by comma: `feature.NAME=1007_s_at,121_at`.\
          \ \n3. Utilize range filters to search numeric attributes. Apply `<` (less\
          \ than), `>` (greater than), and `=` (equal to) symbols to specify the desired\
          \ ranges as follows: \n`feature.Name_1 > 3`: Select all rows where the feature\
          \ attribute Name_1 values are greater than 3. \n`feature.Name_2 >= 6`: Select\
          \ all rows where the feature attribute Name_2 values are greater than or\
          \ equal to 6. \n`-3 < feature.Name_3 < 3`: Select all rows where the feature\
          \ attribute Name_3 values lie within the interval between -3 and 3. \n4.\
          \ Use substring search to get the records where the attribute field contains\
          \ the provided substring: `feature.attribute1 =~ \"some text\"`. \n5. The\
          \ first column for each original data file is identified as feature accession\
          \ (typically, it contains gene or protein names, accession IDs, etc.). Searching\
          \ by such feature accession would significantly outperform more complex\
          \ queries by combining the other feature attributes. To enable such a search,\
          \ use `feature` without any attribute extension, e.g., `feature=ENSG00000230368,ENSG00000188976`.\n\
          \ \nThe `value` keyword can be used to select rows where the sample (library\
          \ or preparation) measurements has values from a certain range. Examples:\
          \ `value = 3`, `value > 3`, `-3 < value < 3`. When the original data contains\
          \ multiple measurements for a single item, such as a sample (library or\
          \ preparation), use the measurement name to specify the exact column type,\
          \ e.g.: \n1. `value.intensity = 3`: Selects all rows where the measurement\
          \ attribute intensity equals 3. \n `value.intensity != 2,null`: Select all\
          \ rows where the measurement attribute intensity is not equal 2 and is not\
          \ an empty value. \n`value.p_value > 3`: Selects all rows where the measurement\
          \ attribute 'p_value' values are greater than 3. \n`-3 < value.FC < 3`:\
          \ Selects all rows where the measurement attribute 'FC' values lie within\
          \ the interval between -3 and 3.\n \n2. Note: The `MinValue` keyword has\
          \ been deprecated and should be replaced with the aforementioned comparisons.\n\
          \ \nCombine multiple filters for different feature attributes and measurements\
          \ using `AND` (`&&`), `OR` (`||`), `NOT` (`!`) logical operators and parentheses: \n\
          * `NOT feature.Name_1=A`: Select all rows where Name_1 is not A. \n* `feature.Name_1!=A,B,C`:\
          \ Select all rows where Name_1 is not A, B, or C. \n* `feature.Name_1=A\
          \ AND feature.Name_2=B`: Select all rows where Name_1 is A and Name_2 is\
          \ B. \n* `feature.Name_1=A && feature.Name_2=B`: Equivalent to the example\
          \ above. \n* `feature.Name_1=A OR feature.Name_2=B`: Select all rows where\
          \ Name_1 is A or Name_2 is B. \n* `feature.Name_1=A || feature.Name_2=B`:\
          \ Equivalent to the example above. \n* `feature.Name_1=A AND (feature.Name_2=B\
          \ OR value>=1.0)`: Select all rows where Name_1 is A and either Name_2 is\
          \ B or minimal possible measurement value is 1.0."
          in: query
          name: exQuery
          schema:
            type: string
        - description: "Filter by expression metadata (key-value metadata pair(s)).\
          \ E.g. `\"Genome Version\"=hg19-BROAD`."
          in: query
          name: exFilter
          schema:
            type: string
        - description: |-
            If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.

            For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of  "Body fluid") so files containing either "Body fluid" or  "Blood"  in their metadata will be returned in the search results.

            The parent-child relationship is defined by the key "broaders" or "subClassOf"  in the dictionary.

            If the full query term is not present in a dictionary then this parameter has no effect.
          in: query
          name: searchSpecificTerms
          schema:
            type: boolean
        - description: The page tag to resume results from (see paging above).
          in: query
          name: cursor
          schema:
            type: string
        - description: "This parameter determines the number of results to retrieve\
          \ per page, with the default set at 2000."
          in: query
          name: pageLimit
          schema:
            format: int32
            type: integer
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/OmicsResponse"
          description: Omics query result.
        "400":
          content: { }
          description: Invalid data in request. See error message for details.
        "401":
          content: { }
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "500":
          content: { }
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
        - Access-token: [ ]
        - Genestack-API-Token: [ ]
      summary: Retrieve cell expression objects by searching across multiple metadata types
      tags:
        - Omics queries as User
  /api/v1/as-user/omics/expression/data:
    get:
      description: "Retrieve any data objects whose linked data matches all supplied\
        \ conditions.This endpoint does not support search by expression linked to Cell\
        \ group. Use /omics/cells/expression/data endpoint for search by Cell expression.\
        \n\nNote: An expression data query must be supplied.\n\n## Conditions\n\
        It is possible to supply conditions for:\n\n1. Samples (full-text or metadata\
        \ key-value pair)\n2. Parent studies (full-text or metadata key-value pair)\n\
        3. Linked variant objects (list of data key-value pairs)\n4. Linked flow cytometry\
        \ objects (list of data key-value pairs)\n5. Linked any data (except variant\
        \ and flow cytometry) objects (list of data key-value pairs)\n\n## Metadata\
        \ full-text queries\nSingle words can be supplied as is; otherwise, use speech\
        \ marks (`\"`) to quote queries that include whitespace. Speech marks and\
        \ backslash characters in the query need to be escaped with a backslash (`\\\
        `).\n\n## Metadata filters\nMetadata filters are key-value pairs joined by\
        \ an operator. The `=` operator matches literal values/string. The `!=` operator\
        \ matches anything except the literal value/string. The `<` or `>` operators\
        \ match numerical results that are less or greater than the supplied value.\
        \ Strings containing whitespace need to be quoted with (`\"`).\n\n## Data\
        \ queries\nData queries must be a list of key-value pairs, separated by whitespace.\
        \ The set of valid keys depends on the specific query type, and is documented\
        \ in the query parameter summary. The values can be simple non-whitespace\
        \ strings, or strings enclosed by speech marks (`\"`). Depending on the key,\
        \ the value may be be a comma-delimited list of string values. Others require\
        \ numerical values.\n\n## Combinations\nMetadata queries/filters for the same parameter\
        \ can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space\
        \ to separate out the terms and operators. Parentheses `( )` can be used for\
        \ complex expressions.\n\n## Versioning\nSpecific versions of omics data files\
        \ (eg. GCT) can be queried via the useVersions parameter. Different versions\
        \ of an omics data file are associated via their CHAIN_ID metadata value.\
        \ This CHAIN_ID can be supplied to the useVersions parameter along with the\
        \ version number or specific omics data file accessions to include them in\
        \ the query. If nothing is supplied to the useVersions parameter then only\
        \ the active version (which is usually the last one imported) is queried.\
        \ This acts as a filter before the rest of the query is carried out.\n\nExample\
        \ usage:\nuseVersions=* (query all versions, including those without CHAIN_IDs)\n\
        useVersions=v2 (query the second version. If there is no second version then\
        \ the data file is not queried)\nuseVersions=v1,v0 (query the first version\
        \ and any data files without CHAIN_IDs(v0) )\nuseVersions=GSVC002:v3 (for\
        \ omics data files with a CHAIN_ID of GSCV002 query the third version)\nuseVersions=GSVC002:GSF00494,GSF000496\
        \ (for omics data files with a CHAIN_ID of GSCV002 query only the specific\
        \ accessions GSF00494 and GSF000496)\n\nRules for multiple CHAIN_IDs can be\
        \ supplied to the parameter using the ; separator.\n\n## Paging\nFor performance\
        \ reasons this endpoint returns results in \"pages\" of limited size together\
        \ with a `cursor` tag. To retrieve the next page of results please supply\
        \ this `cursor` tag to resume the query from your previous result and get\
        \ the next page. To return all results iterate through pages using cursor \
        \ values until the `resultsExhausted` response field is true.\n\n"
      operationId: omicsSearchExpressionDataAsUser
      parameters:
      - description: Supply this parameter with the value `term_id` as part of the
          query to return extended information including IDs for values and dictionaries.
        in: query
        name: responseFormat
        schema:
          $ref: "#/components/schemas/ResponseFormat"
      - description: |
          Filter by study metadata (key-value metadata pair(s)). E.g. `"Study Source"=ArrayExpress`
        in: query
        name: studyFilter
        schema:
          type: string
      - description: Search for objects via a full-text query over all study metadata
          fields. E.g. `"RNA-Seq of human dendritic cells"`. Queries matching dictionary
          terms are automatically expanded to include synonyms.
        in: query
        name: studyQuery
        schema:
          type: string
      - description: |
          Filter by sample metadata (key-value metadata pair(s)). E.g. `"Species or strain"="Homo sapiens"`
        in: query
        name: sampleFilter
        schema:
          type: string
      - description: Search for objects via a full-text query over all sample metadata
          fields. E.g. `Clozapine`. Queries matching dictionary terms are automatically
          expanded to include synonyms.
        in: query
        name: sampleQuery
        schema:
          type: string
      - description: Filter by library metadata (key-value metadata pair(s)). E.g.
          `"Library Type"=RNA-Seq-1`
        in: query
        name: libraryFilter
        schema:
          type: string
      - description: Search for library objects via a full-text query over all library
          metadata fields. E.g. `"illumina HiSeq500"`. Queries matching dictionary
          terms are automatically expanded to include synonyms.
        in: query
        name: libraryQuery
        schema:
          type: string
      - description: Filter by preparation metadata (key-value metadata pair(s)).
          E.g. `Digestion=Trypsin`
        in: query
        name: preparationFilter
        schema:
          type: string
      - description: Search for preparation objects via a full-text query over all
          preparation metadata fields. E.g. `"reversed-phase liquid chromatography"`.
          Queries matching dictionary terms are automatically expanded to include
          synonyms.
        in: query
        name: preparationQuery
        schema:
          type: string
      - description: |-
          If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.

          For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of  "Body fluid") so files containing either "Body fluid" or  "Blood"  in their metadata will be returned in the search results.

          The parent-child relationship is defined by the key "broaders" or "subClassOf"  in the dictionary.

          If the full query term is not present in a dictionary then this parameter has no effect.
        in: query
        name: searchSpecificTerms
        schema:
          type: boolean
      - description: "Search for objects linked to variant data by SNPs properties. Filtering is currently supported by `filter`, `id`, `region` and `info` keywords,
          as well as `exists` keyword for `INFO` field and their logical combinations by means of `not` (`!`), `and` (`&&`), and `or` (`||`) operators with standard boolean precedence. Keyword case is ignored.\n
          * `filter` corresponds to the `FILTER` column in the original vcf file. Could be either equals or not equals to `PASS` : `filter = PASS`
              or `filter != pass`.\n
          * `id` is a string value that corresponds to the `ID` column. Multiple values could be added via a comma. Expression `id = rs3214,rg1234` is equivalent
              to `id = rs3214 or id = rg1234`.\n
          * `region` corresponds to CHROM and POS columns. Supports querying by the whole chromosome `region = chr1` , by interval within a chromosome
              `region = chr1:4567-9876543` by exact position `region = chr1:456789` or by indefinite ranges like `region = x:3456789-*` . Multiple regions could be
              separated via comma, e.g. `region = chr1:34567-98767,chr3` is equivalent to  `region = chr1:34567-98767 or region = chr3`.\n
          * `feature` is the name of the reference gene associated with a specific location in the reference genome which corresponds to the VCF file (variant group) from which the variant information is derived.
              By providing the gene name(s), such as `feature=TP53` or `feature=TP53,TGFB`, variants located within the same genomic region as the specified gene(s) will be retrieved.\n
          * Filter by vcf `INFO` fields. E.g. to filter all variants annotated in dbSNP add `exists(INFO.KEY)`. Use `!exists(INFO.KEY)` to exclude variants having the key from the search results.
              Provide `info.key=value` pair to search for an exact match or `info.key!=value` to exclude it from the search. Due to the limits of precision in floating point numbers,
              we use a small range of 0.0000001 to identify close matches. This means any differences smaller than that won't be detected. For more precise results, please use range queries."
        in: query
        name: vxQuery
        schema:
          type: string
      - description: "Filter by variant metadata (key-value metadata pair(s)). E.g.\
          \ `\"Variant Source\"=dbSNP`."
        in: query
        name: vxFilter
        schema:
          type: string
      - description: "Search for objects linked to expression data and originally\
          \ uploaded in TSV or GCT format via data query, e.g., `feature=ENSG00000230368,ENSG00000188976\
          \ value>=1.50`\n For the case when the original data is represented by multiple\
          \ attributes per feature scenarios, extended filtering syntax is as follows:\
          \ \n1. By feature attribute value for numeric and string attributes: `feature.NAME=1007_s_at`\
          \ or `feature.\"Average Mz\"=2.218`. As in the case of sample metadata queries,\
          \ single words can be supplied as is; otherwise, use speech marks (`\"`)\
          \ to quote queries that include whitespace. \n2. It is possible to specify\
          \ a set of possible values, separated by comma: `feature.NAME=1007_s_at,121_at`.\
          \ \n3. Utilize range filters to search numeric attributes. Apply `<` (less\
          \ than), `>` (greater than), and `=` (equal to) symbols to specify the desired\
          \ ranges as follows: \n`feature.Name_1 > 3`: Select all rows where the feature\
          \ attribute Name_1 values are greater than 3. \n`feature.Name_2 >= 6`: Select\
          \ all rows where the feature attribute Name_2 values are greater than or\
          \ equal to 6. \n`-3 < feature.Name_3 < 3`: Select all rows where the feature\
          \ attribute Name_3 values lie within the interval between -3 and 3. \n4.\
          \ Use substring search to get the records where the attribute field contains\
          \ the provided substring: `feature.attribute1 =~ \"some text\"`. \n5. The\
          \ first column for each original data file is identified as feature accession\
          \ (typically, it contains gene or protein names, accession IDs, etc.). Searching\
          \ by such feature accession would significantly outperform more complex\
          \ queries by combining the other feature attributes. To enable such a search,\
          \ use `feature` without any attribute extension, e.g., `feature=ENSG00000230368,ENSG00000188976`.\n\
          \ \nThe `value` keyword can be used to select rows where the sample (library\
          \ or preparation) measurements has values from a certain range. Examples:\
          \ `value = 3`, `value > 3`, `-3 < value < 3`. When the original data contains\
          \ multiple measurements for a single item, such as a sample (library or\
          \ preparation), use the measurement name to specify the exact column type,\
          \ e.g.: \n1. `value.intensity = 3`: Selects all rows where the measurement\
          \ attribute intensity equals 3. \n `value.intensity != 2,null`: Select all\
          \ rows where the measurement attribute intensity is not equal 2 and is not\
          \ an empty value. \n`value.p_value > 3`: Selects all rows where the measurement\
          \ attribute 'p_value' values are greater than 3. \n`-3 < value.FC < 3`:\
          \ Selects all rows where the measurement attribute 'FC' values lie within\
          \ the interval between -3 and 3.\n \n2. Note: The `MinValue` keyword has\
          \ been deprecated and should be replaced with the aforementioned comparisons.\n\
          \ \nCombine multiple filters for different feature attributes and measurements\
          \ using `AND` (`&&`), `OR` (`||`), `NOT` (`!`) logical operators and parentheses: \n\
          * `NOT feature.Name_1=A`: Select all rows where Name_1 is not A. \n* `feature.Name_1!=A,B,C`:\
          \ Select all rows where Name_1 is not A, B, or C. \n* `feature.Name_1=A\
          \ AND feature.Name_2=B`: Select all rows where Name_1 is A and Name_2 is\
          \ B. \n* `feature.Name_1=A && feature.Name_2=B`: Equivalent to the example\
          \ above. \n* `feature.Name_1=A OR feature.Name_2=B`: Select all rows where\
          \ Name_1 is A or Name_2 is B. \n* `feature.Name_1=A || feature.Name_2=B`:\
          \ Equivalent to the example above. \n* `feature.Name_1=A AND (feature.Name_2=B\
          \ OR value>=1.0)`: Select all rows where Name_1 is A and either Name_2 is\
          \ B or minimal possible measurement value is 1.0."
        in: query
        name: exQuery
        schema:
          type: string
      - description: "Filter by expression metadata (key-value metadata pair(s)).\
          \ E.g. `\"Genome Version\"=hg19-BROAD`."
        in: query
        name: exFilter
        schema:
          type: string
      - description: "Search for objects linked to flow cytometry data via data query\
          \ (key-value pair(s)). E.g. `ReadoutType=Median|Count` `CellPopulation=\"\
          CD45+, live\"` `MinValue=3.5`"
        in: query
        name: fxQuery
        schema:
          type: string
      - description: "Filter by flow cytometry metadata (key-value metadata pair(s)).\
          \ E.g. `Organ=blood`."
        in: query
        name: fxFilter
        schema:
          type: string
      - description: |-
          Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:

          \* or `v<version number>` or `<CHAIN_ID>`:`v<version number>` or `<CHAIN_ID>`:`<accession1,accession2,..>`
        in: query
        name: useVersions
        schema:
          type: string
      - description: |-
          The parameter defines amount of metadata attributes to return:

          1. `minimal_data` - return metadata attributes according to the default template.
          2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
          3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
        in: query
        name: returnedMetadataFields
        schema:
          enum:
          - minimal_data
          - extended_data_included
          - original_data_included
          type: string
      - description: The page tag to resume results from (see paging above).
        in: query
        name: cursor
        schema:
          type: string
      - description: "This parameter determines the number of results to retrieve\
          \ per page, with the default set at 2000."
        in: query
        name: pageLimit
        schema:
          format: int32
          type: integer
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/OmicsResponse"
          description: Omics query result.
        "400":
          content: {}
          description: Invalid data in request. See error message for details.
        "401":
          content: {}
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "500":
          content: {}
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
      - Access-token: []
      - Genestack-API-Token: []
      summary: Retrieve data objects by searching across multiple data types
      tags:
      - Omics queries as User
  /api/v1/as-user/omics/expression/group:
    get:
      description: |+
        Retrieve group objects whose linked data matches all supplied conditions.

        ## Conditions
        It is possible to supply conditions for:

        1. Samples (full-text or metadata key-value pair)
        2. Parent studies (full-text or metadata key-value pair)
        3. Linked variant objects (list of data key-value pairs)
        4. Linked flow cytometry objects (list of data key-value pairs)
        5. Linked any data (except variant and flow cytometry) objects (list of data key-value pairs)

        ## Metadata full-text queries
        Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).

        ## Metadata filters
        Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).

        ## Data queries
        Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values.

        ## Combinations
        Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.

        ## Versioning
        Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.

        Example usage:
        useVersions=* (query all versions, including those without CHAIN_IDs)
        useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
        useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
        useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
        useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)

        Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.

        ## Paging
        For performance reasons this endpoint returns results in "pages" of limited size together with a cursor tag. To retrieve the next page of results please supply this cursor tag to resume the query from your previous result and get the next page. If there are no more results you will just retrieve an empty result. To return all results iterate through pages using cursor values until the `resultsExhausted` response field is true.

      operationId: omicsSearchExpressionGroupsAsUser
      parameters:
      - description: Supply this parameter with the value `term_id` as part of the
          query to return extended information including IDs for values and dictionaries.
        in: query
        name: responseFormat
        schema:
          $ref: "#/components/schemas/ResponseFormat"
      - description: |
          Filter by study metadata (key-value metadata pair(s)). E.g. `"Study Source"=ArrayExpress`
        in: query
        name: studyFilter
        schema:
          type: string
      - description: Search for objects via a full-text query over all study metadata
          fields. E.g. `"RNA-Seq of human dendritic cells"`. Queries matching dictionary
          terms are automatically expanded to include synonyms.
        in: query
        name: studyQuery
        schema:
          type: string
      - description: |
          Filter by sample metadata (key-value metadata pair(s)). E.g. `"Species or strain"="Homo sapiens"`
        in: query
        name: sampleFilter
        schema:
          type: string
      - description: Search for objects via a full-text query over all sample metadata
          fields. E.g. `Clozapine`. Queries matching dictionary terms are automatically
          expanded to include synonyms.
        in: query
        name: sampleQuery
        schema:
          type: string
      - description: Filter by library metadata (key-value metadata pair(s)). E.g.
          `"Library Type"=RNA-Seq-1`
        in: query
        name: libraryFilter
        schema:
          type: string
      - description: Search for library objects via a full-text query over all library
          metadata fields. E.g. `"illumina HiSeq500"`. Queries matching dictionary
          terms are automatically expanded to include synonyms.
        in: query
        name: libraryQuery
        schema:
          type: string
      - description: Filter by preparation metadata (key-value metadata pair(s)).
          E.g. `Digestion=Trypsin`
        in: query
        name: preparationFilter
        schema:
          type: string
      - description: Search for preparation objects via a full-text query over all
          preparation metadata fields. E.g. `"reversed-phase liquid chromatography"`.
          Queries matching dictionary terms are automatically expanded to include
          synonyms.
        in: query
        name: preparationQuery
        schema:
          type: string
      - description: |-
          If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.

          For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of  "Body fluid") so files containing either "Body fluid" or  "Blood"  in their metadata will be returned in the search results.

          The parent-child relationship is defined by the key "broaders" or "subClassOf"  in the dictionary.

          If the full query term is not present in a dictionary then this parameter has no effect.
        in: query
        name: searchSpecificTerms
        schema:
          type: boolean
      - description: "Search for objects linked to variant data by SNPs properties. Filtering is currently supported by `filter`, `id`, `region` and `info` keywords,
          as well as `exists` keyword for `INFO` field and their logical combinations by means of `not` (`!`), `and` (`&&`), and `or` (`||`) operators with standard boolean precedence. Keyword case is ignored.\n
          * `filter` corresponds to the `FILTER` column in the original vcf file. Could be either equals or not equals to `PASS` : `filter = PASS`
              or `filter != pass`.\n
          * `id` is a string value that corresponds to the `ID` column. Multiple values could be added via a comma. Expression `id = rs3214,rg1234` is equivalent
              to `id = rs3214 or id = rg1234`.\n
          * `region` corresponds to CHROM and POS columns. Supports querying by the whole chromosome `region = chr1` , by interval within a chromosome
              `region = chr1:4567-9876543` by exact position `region = chr1:456789` or by indefinite ranges like `region = x:3456789-*` . Multiple regions could be
              separated via comma, e.g. `region = chr1:34567-98767,chr3` is equivalent to  `region = chr1:34567-98767 or region = chr3`.\n
          * `feature` is the name of the reference gene associated with a specific location in the reference genome which corresponds to the VCF file (variant group) from which the variant information is derived.
              By providing the gene name(s), such as `feature=TP53` or `feature=TP53,TGFB`, variants located within the same genomic region as the specified gene(s) will be retrieved.\n
          * Filter by vcf `INFO` fields. E.g. to filter all variants annotated in dbSNP add `exists(INFO.KEY)`. Use `!exists(INFO.KEY)` to exclude variants having the key from the search results.
              Provide `info.key=value` pair to search for an exact match or `info.key!=value` to exclude it from the search. Due to the limits of precision in floating point numbers,
              we use a small range of 0.0000001 to identify close matches. This means any differences smaller than that won't be detected. For more precise results, please use range queries."
        in: query
        name: vxQuery
        schema:
          type: string
      - description: "Filter by variant metadata (key-value metadata pair(s)). E.g.\
          \ `\"Variant Source\"=dbSNP`."
        in: query
        name: vxFilter
        schema:
          type: string
      - description: "Search for objects linked to expression data and originally\
          \ uploaded in TSV or GCT format via data query, e.g., `feature=ENSG00000230368,ENSG00000188976\
          \ value>=1.50`\n For the case when the original data is represented by multiple\
          \ attributes per feature scenarios, extended filtering syntax is as follows:\
          \ \n1. By feature attribute value for numeric and string attributes: `feature.NAME=1007_s_at`\
          \ or `feature.\"Average Mz\"=2.218`. As in the case of sample metadata queries,\
          \ single words can be supplied as is; otherwise, use speech marks (`\"`)\
          \ to quote queries that include whitespace. \n2. It is possible to specify\
          \ a set of possible values, separated by comma: `feature.NAME=1007_s_at,121_at`.\
          \ \n3. Utilize range filters to search numeric attributes. Apply `<` (less\
          \ than), `>` (greater than), and `=` (equal to) symbols to specify the desired\
          \ ranges as follows: \n`feature.Name_1 > 3`: Select all rows where the feature\
          \ attribute Name_1 values are greater than 3. \n`feature.Name_2 >= 6`: Select\
          \ all rows where the feature attribute Name_2 values are greater than or\
          \ equal to 6. \n`-3 < feature.Name_3 < 3`: Select all rows where the feature\
          \ attribute Name_3 values lie within the interval between -3 and 3. \n4.\
          \ Use substring search to get the records where the attribute field contains\
          \ the provided substring: `feature.attribute1 =~ \"some text\"`. \n5. The\
          \ first column for each original data file is identified as feature accession\
          \ (typically, it contains gene or protein names, accession IDs, etc.). Searching\
          \ by such feature accession would significantly outperform more complex\
          \ queries by combining the other feature attributes. To enable such a search,\
          \ use `feature` without any attribute extension, e.g., `feature=ENSG00000230368,ENSG00000188976`.\n\
          \ \nThe `value` keyword can be used to select rows where the sample (library\
          \ or preparation) measurements has values from a certain range. Examples:\
          \ `value = 3`, `value > 3`, `-3 < value < 3`. When the original data contains\
          \ multiple measurements for a single item, such as a sample (library or\
          \ preparation), use the measurement name to specify the exact column type,\
          \ e.g.: \n1. `value.intensity = 3`: Selects all rows where the measurement\
          \ attribute intensity equals 3. \n `value.intensity != 2,null`: Select all\
          \ rows where the measurement attribute intensity is not equal 2 and is not\
          \ an empty value. \n`value.p_value > 3`: Selects all rows where the measurement\
          \ attribute 'p_value' values are greater than 3. \n`-3 < value.FC < 3`:\
          \ Selects all rows where the measurement attribute 'FC' values lie within\
          \ the interval between -3 and 3.\n \n2. Note: The `MinValue` keyword has\
          \ been deprecated and should be replaced with the aforementioned comparisons.\n\
          \ \nCombine multiple filters for different feature attributes and measurements\
          \ using `AND` (`&&`), `OR` (`||`), `NOT` (`!`) logical operators and parentheses: \n\
          * `NOT feature.Name_1=A`: Select all rows where Name_1 is not A. \n* `feature.Name_1!=A,B,C`:\
          \ Select all rows where Name_1 is not A, B, or C. \n* `feature.Name_1=A\
          \ AND feature.Name_2=B`: Select all rows where Name_1 is A and Name_2 is\
          \ B. \n* `feature.Name_1=A && feature.Name_2=B`: Equivalent to the example\
          \ above. \n* `feature.Name_1=A OR feature.Name_2=B`: Select all rows where\
          \ Name_1 is A or Name_2 is B. \n* `feature.Name_1=A || feature.Name_2=B`:\
          \ Equivalent to the example above. \n* `feature.Name_1=A AND (feature.Name_2=B\
          \ OR value>=1.0)`: Select all rows where Name_1 is A and either Name_2 is\
          \ B or minimal possible measurement value is 1.0."
        in: query
        name: exQuery
        schema:
          type: string
      - description: "Filter by expression metadata (key-value metadata pair(s)).\
          \ E.g. `\"Genome Version\"=hg19-BROAD`."
        in: query
        name: exFilter
        schema:
          type: string
      - description: "Search for objects linked to flow cytometry data via data query\
          \ (key-value pair(s)). E.g. `ReadoutType=Median|Count` `CellPopulation=\"\
          CD45+, live\"` `MinValue=3.5`"
        in: query
        name: fxQuery
        schema:
          type: string
      - description: "Filter by flow cytometry metadata (key-value metadata pair(s)).\
          \ E.g. `Organ=blood`."
        in: query
        name: fxFilter
        schema:
          type: string
      - description: |-
          Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:

          \* or `v<version number>` or `<CHAIN_ID>`:`v<version number>` or `<CHAIN_ID>`:`<accession1,accession2,..>`
        in: query
        name: useVersions
        schema:
          type: string
      - description: |-
          The parameter defines amount of metadata attributes to return:

          1. `minimal_data` - return metadata attributes according to the default template.
          2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
          3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
        in: query
        name: returnedMetadataFields
        schema:
          enum:
          - minimal_data
          - extended_data_included
          - original_data_included
          type: string
      - description: The page tag to resume results from (see paging above).
        in: query
        name: cursor
        schema:
          type: string
      - description: "This parameter determines the number of results to retrieve\
          \ per page, with the default set at 2000."
        in: query
        name: pageLimit
        schema:
          format: int32
          type: integer
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/OmicsResponse"
          description: Omics query result.
        "400":
          content: {}
          description: Invalid data in request. See error message for details.
        "401":
          content: {}
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "500":
          content: {}
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
      - Access-token: []
      - Genestack-API-Token: []
      summary: Retrieve group objects by searching across multiple data types
      tags:
      - Omics queries as User
  /api/v1/as-user/omics/expression/streamed-data:
    get:
      description: "Stream data from a given group for a tabular file that matches\
        \ a sample/library/preparations query/filter. If no query/filters are supplied\
        \ all expression data is returned. If a metadata filter is specified, this\
        \ endpoint will only return expression data that is associated with a sample\
        \ via the Sample Source ID attribute.\n## Conditions\nIt is possible to supply\
        \ conditions for:\n\n1. Samples (full-text or metadata key-value pair)\n2.\
        \ Libraries (full-text or metadata key-value pair)\n3. Preparations (full-text\
        \ or metadata key-value pair)\n## Metadata full-text queries\nSingle words\
        \ can be supplied as is; otherwise, use speech marks (`\"`) to quote queries\
        \ that include whitespace. Speech marks and backslash characters in the query\
        \ need to be escaped with a backslash (`\\`).\n\n## Metadata filters\nMetadata\
        \ filters are key-value pairs joined by an operator. The `=` operator matches\
        \ literal values/string. The `!=` operator matches anything except the literal\
        \ value/string. The `<` or `>` operators match numerical results that are\
        \ less or greater than the supplied value. Strings containing whitespace need\
        \ to be quoted with (`\"`).\n\n## Combinations\nMetadata queries/filters for\
        \ the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators,\
        \ using white-space to separate out the terms and operators. Parentheses `(\
        \ )` can be used for complex expressions.\n  \n\n## Error Handling\n  In case\
        \ of unexpected internal error during data retrieval, the last line of the\
        \ body will contain an error message, prefixed by the `#` character \n\n"
      operationId: omicsSearchStreamedExpressionDataAsUser
      parameters:
      - description: |
          Filter by sample metadata (key-value metadata pair(s)). E.g.`"Species or strain"="Homo sapiens"`
        in: query
        name: sampleFilter
        schema:
          type: string
      - description: Search for objects via a full-text query over all sample metadata
          fields. E.g. `Clozapine`. Queries matching dictionary terms are automatically
          expanded to include synonyms.
        in: query
        name: sampleQuery
        schema:
          type: string
      - description: Filter by library metadata (key-value metadata pair(s)). E.g.
          `"Library Type"=RNA-Seq-1`
        in: query
        name: libraryFilter
        schema:
          type: string
      - description: Search for library objects via a full-text query over all library
          metadata fields. E.g. `"illumina HiSeq500"`. Queries matching dictionary
          terms are automatically expanded to include synonyms.
        in: query
        name: libraryQuery
        schema:
          type: string
      - description: Filter by preparation metadata (key-value metadata pair(s)).
          E.g. `Digestion=Trypsin`
        in: query
        name: preparationFilter
        schema:
          type: string
      - description: Search for preparation objects via a full-text query over all
          preparation metadata fields. E.g. `"reversed-phase liquid chromatography"`.
          Queries matching dictionary terms are automatically expanded to include
          synonyms.
        in: query
        name: preparationQuery
        schema:
          type: string
      - description: |-
          If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.

          For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of  "Body fluid") so files containing either "Body fluid" or  "Blood"  in their metadata will be returned in the search results.

          The parent-child relationship is defined by the key "broaders" or "subClassOf"  in the dictionary.

          If the full query term is not present in a dictionary then this parameter has no effect.
        in: query
        name: searchSpecificTerms
        schema:
          type: boolean
      - description: "Search for objects linked to expression data and originally\
          \ uploaded in TSV or GCT format via data query, e.g., `feature=ENSG00000230368,ENSG00000188976\
          \ value>=1.50`\n For the case when the original data is represented by multiple\
          \ attributes per feature scenarios, extended filtering syntax is as follows:\
          \ \n1. By feature attribute value for numeric and string attributes: `features.NAME=1007_s_at`\
          \ or `features.\"Average Mz\"=2.218`. As in the case of sample metadata\
          \ queries, single words can be supplied as is; otherwise, use speech marks\
          \ (`\"`) to quote queries that include whitespace. \n2. It is possible to\
          \ specify a set of possible values, separated by comma: `features.NAME=1007_s_at,121_at`.\
          \ \n3. Utilize range filters to search numeric attributes. Apply `<` (less\
          \ than), `>` (greater than), and `=` (equal to) symbols to specify the desired\
          \ ranges as follows: \n`features.Name_1 > 3`: Select all rows where the\
          \ feature attribute Name_1 values are greater than 3. \n`features.Name_2\
          \ >= 6`: Select all rows where the feature attribute Name_2 values are greater\
          \ than or equal to 6. \n`-3 < features.Name_3 < 3`: Select all rows where\
          \ the feature attribute Name_3 values lie within the interval between -3\
          \ and 3. \n4. Use substring search to get the records where the attribute\
          \ field contains the provided substring: `features.attribute1 =~ \"some\
          \ text\"`. \n5. The first column for each original data file is identified\
          \ as feature accession (typically, it contains gene or protein names, accession\
          \ IDs, etc.). Searching by such feature accession would significantly outperform\
          \ more complex queries by combining the other feature attributes. To enable\
          \ such a search, use `feature` without any attribute extension, e.g., `feature=ENSG00000230368,ENSG00000188976`.\n\
          \ \nThe `value` keyword can be used to select rows where the sample (library\
          \ or preparation) measurements has values from a certain range. Examples:\
          \ `value = 3`, `value > 3`, `-3 < value < 3`. When the original data contains\
          \ multiple measurements for a single item, such as a sample (library or\
          \ preparation), use the measurement name to specify the exact column type,\
          \ e.g.: \n1. `value.intensity = 3`: Selects all rows where the measurement\
          \ attribute intensity equals 3. \n `value.intensity != 2,null`: Select all\
          \ rows where the measurement attribute intensity is not equal 2 and is not\
          \ an empty value. \n`values.p_value > 3`: Selects all rows where the measurement\
          \ attribute 'p_value' values are greater than 3. \n`-3 < values.FC < 3`:\
          \ Selects all rows where the measurement attribute 'FC' values lie within\
          \ the interval between -3 and 3.\n \n2. Note: The `MinValue` keyword has\
          \ been deprecated and should be replaced with the aforementioned comparisons.\n\
          \ \nCombine multiple filters for different feature attributes and measurements\
          \ using `AND` (`&&`), `OR` (`||`) logical operators and parentheses: \n\
          * `features.Name_1!=A`: Select all rows where Name_1 is not A. \n* `features.Name_1!=A,B,C`:\
          \ Select all rows where Name_1 is not A, B, or C. \n* `features.Name_1=A\
          \ AND features.Name_2=B`: Select all rows where Name_1 is A and Name_2 is\
          \ B. \n* `features.Name_1=A && features.Name_2=B`: Equivalent to the example\
          \ above. \n* `features.Name_1=A OR features.Name_2=B`: Select all rows where\
          \ Name_1 is A or Name_2 is B. \n* `features.Name_1=A || features.Name_2=B`:\
          \ Equivalent to the example above. \n* `features.Name_1=A AND (features.Name_2=B\
          \ OR value>=1.0)`: Select all rows where Name_1 is A and either Name_2 is\
          \ B or minimal possible measurement value is 1.0."
        in: query
        name: exQuery
        schema:
          type: string
      - description: "Deprecated; use `exQuery` parameter instead. Filters results\
          \ by the feature column (e.g., Gene ID). The feature parameter value must\
          \ match the name of the identifier in the GCT file (under the NAME column).\
          \ Example: `ENSG00000077044`"
        explode: true
        in: query
        name: featureList
        schema:
          items:
            type: string
            example: KRAS
          type: array
        style: form
      - description: Accession of the expression group object (GCT)
        in: query
        name: groupAccession
        required: true
        schema:
          type: string
      - description: The number of digits after the decimal point for floating-point
          values. The final value is rounded up. Must be non-negative. The default
          is 4.
        in: query
        name: roundDigits
        schema:
          default: 4
          format: int32
          type: integer
      responses:
        "200":
          content:
            text/csv:
              schema:
                $ref: "#/components/schemas/StreamingOutput"
          description: Stream of retrieved Expression data.
        "400":
          content: {}
          description: Invalid data in request. See error message for details.
        "401":
          content: {}
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "500":
          content: {}
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
      - Access-token: []
      - Genestack-API-Token: []
      summary: Stream data from a given tabular file
      tags:
      - Omics queries as User
  /api/v1/as-user/omics/flow-cytometry/data:
    get:
      description: |+
        Retrieve flow cytometry data objects whose linked data matches all supplied conditions.

        Note: A flow cytometry data query must be supplied.

        ## Conditions
        It is possible to supply conditions for:

        1. Samples (full-text or metadata key-value pair)
        2. Parent studies (full-text or metadata key-value pair)
        3. Linked variant objects (list of data key-value pairs)
        4. Linked flow cytometry objects (list of data key-value pairs)
        5. Linked any data (except variant and flow cytometry) objects (list of data key-value pairs)

        ## Metadata full-text queries
        Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).

        ## Metadata filters
        Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).

        ## Data queries
        Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values.

        ## Combinations
        Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.

        ## Versioning
        Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.

        Example usage:
        useVersions=* (query all versions, including those without CHAIN_IDs)
        useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
        useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
        useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
        useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)

        Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.

        ## Paging
        For performance reasons this endpoint returns results in "pages" of limited size together with a cursor tag. To retrieve the next page of results please supply this cursor tag to resume the query from your previous result and get the next page. If there are no more results you will just retrieve an empty result. To return all results iterate through pages using cursor values until the `resultsExhausted` response field is true.

      operationId: omicsSearchFlowCytometryDataAsUser
      parameters:
      - description: Supply this parameter with the value `term_id` as part of the
          query to return extended information including IDs for values and dictionaries.
        in: query
        name: responseFormat
        schema:
          $ref: "#/components/schemas/ResponseFormat"
      - description: |
          Filter by study metadata (key-value metadata pair(s)). E.g. `"Study Source"=ArrayExpress`
        in: query
        name: studyFilter
        schema:
          type: string
      - description: Search for objects via a full-text query over all study metadata
          fields. E.g. `"RNA-Seq of human dendritic cells"`. Queries matching dictionary
          terms are automatically expanded to include synonyms.
        in: query
        name: studyQuery
        schema:
          type: string
      - description: |
          Filter by sample metadata (key-value metadata pair(s)). E.g. `"Species or strain"="Homo sapiens"`
        in: query
        name: sampleFilter
        schema:
          type: string
      - description: Search for objects via a full-text query over all sample metadata
          fields. E.g. `Clozapine`. Queries matching dictionary terms are automatically
          expanded to include synonyms.
        in: query
        name: sampleQuery
        schema:
          type: string
      - description: Filter by library metadata (key-value metadata pair(s)). E.g.
          `"Library Type"=RNA-Seq-1`
        in: query
        name: libraryFilter
        schema:
          type: string
      - description: Search for library objects via a full-text query over all library
          metadata fields. E.g. `"illumina HiSeq500"`. Queries matching dictionary
          terms are automatically expanded to include synonyms.
        in: query
        name: libraryQuery
        schema:
          type: string
      - description: Filter by preparation metadata (key-value metadata pair(s)).
          E.g. `Digestion=Trypsin`
        in: query
        name: preparationFilter
        schema:
          type: string
      - description: Search for preparation objects via a full-text query over all
          preparation metadata fields. E.g. `"reversed-phase liquid chromatography"`.
          Queries matching dictionary terms are automatically expanded to include
          synonyms.
        in: query
        name: preparationQuery
        schema:
          type: string
      - description: |-
          If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.

          For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of  "Body fluid") so files containing either "Body fluid" or  "Blood"  in their metadata will be returned in the search results.

          The parent-child relationship is defined by the key "broaders" or "subClassOf"  in the dictionary.

          If the full query term is not present in a dictionary then this parameter has no effect.
        in: query
        name: searchSpecificTerms
        schema:
          type: boolean
      - description: "Search for objects linked to variant data by SNPs properties. Filtering is currently supported by `filter`, `id`, `region` and `info` keywords,
          as well as `exists` keyword for `INFO` field and their logical combinations by means of `not` (`!`), `and` (`&&`), and `or` (`||`) operators with standard boolean precedence. Keyword case is ignored.\n
          * `filter` corresponds to the `FILTER` column in the original vcf file. Could be either equals or not equals to `PASS` : `filter = PASS`
              or `filter != pass`.\n
          * `id` is a string value that corresponds to the `ID` column. Multiple values could be added via a comma. Expression `id = rs3214,rg1234` is equivalent
              to `id = rs3214 or id = rg1234`.\n
          * `region` corresponds to CHROM and POS columns. Supports querying by the whole chromosome `region = chr1` , by interval within a chromosome
              `region = chr1:4567-9876543` by exact position `region = chr1:456789` or by indefinite ranges like `region = x:3456789-*` . Multiple regions could be
              separated via comma, e.g. `region = chr1:34567-98767,chr3` is equivalent to  `region = chr1:34567-98767 or region = chr3`.\n
          * `feature` is the name of the reference gene associated with a specific location in the reference genome which corresponds to the VCF file (variant group) from which the variant information is derived.
              By providing the gene name(s), such as `feature=TP53` or `feature=TP53,TGFB`, variants located within the same genomic region as the specified gene(s) will be retrieved.\n
          * Filter by vcf `INFO` fields. E.g. to filter all variants annotated in dbSNP add `exists(INFO.KEY)`. Use `!exists(INFO.KEY)` to exclude variants having the key from the search results.
              Provide `info.key=value` pair to search for an exact match or `info.key!=value` to exclude it from the search. Due to the limits of precision in floating point numbers,
              we use a small range of 0.0000001 to identify close matches. This means any differences smaller than that won't be detected. For more precise results, please use range queries."
        in: query
        name: vxQuery
        schema:
          type: string
      - description: "Filter by variant metadata (key-value metadata pair(s)). E.g.\
          \ `\"Variant Source\"=dbSNP`."
        in: query
        name: vxFilter
        schema:
          type: string
      - description: "Search for objects linked to expression data and originally\
          \ uploaded in TSV or GCT format via data query, e.g., `feature=ENSG00000230368,ENSG00000188976\
          \ value>=1.50`\n For the case when the original data is represented by multiple\
          \ attributes per feature scenarios, extended filtering syntax is as follows:\
          \ \n1. By feature attribute value for numeric and string attributes: `feature.NAME=1007_s_at`\
          \ or `feature.\"Average Mz\"=2.218`. As in the case of sample metadata queries,\
          \ single words can be supplied as is; otherwise, use speech marks (`\"`)\
          \ to quote queries that include whitespace. \n2. It is possible to specify\
          \ a set of possible values, separated by comma: `feature.NAME=1007_s_at,121_at`.\
          \ \n3. Utilize range filters to search numeric attributes. Apply `<` (less\
          \ than), `>` (greater than), and `=` (equal to) symbols to specify the desired\
          \ ranges as follows: \n`feature.Name_1 > 3`: Select all rows where the feature\
          \ attribute Name_1 values are greater than 3. \n`feature.Name_2 >= 6`: Select\
          \ all rows where the feature attribute Name_2 values are greater than or\
          \ equal to 6. \n`-3 < feature.Name_3 < 3`: Select all rows where the feature\
          \ attribute Name_3 values lie within the interval between -3 and 3. \n4.\
          \ Use substring search to get the records where the attribute field contains\
          \ the provided substring: `feature.attribute1 =~ \"some text\"`. \n5. The\
          \ first column for each original data file is identified as feature accession\
          \ (typically, it contains gene or protein names, accession IDs, etc.). Searching\
          \ by such feature accession would significantly outperform more complex\
          \ queries by combining the other feature attributes. To enable such a search,\
          \ use `feature` without any attribute extension, e.g., `feature=ENSG00000230368,ENSG00000188976`.\n\
          \ \nThe `value` keyword can be used to select rows where the sample (library\
          \ or preparation) measurements has values from a certain range. Examples:\
          \ `value = 3`, `value > 3`, `-3 < value < 3`. When the original data contains\
          \ multiple measurements for a single item, such as a sample (library or\
          \ preparation), use the measurement name to specify the exact column type,\
          \ e.g.: \n1. `value.intensity = 3`: Selects all rows where the measurement\
          \ attribute intensity equals 3. \n `value.intensity != 2,null`: Select all\
          \ rows where the measurement attribute intensity is not equal 2 and is not\
          \ an empty value. \n`value.p_value > 3`: Selects all rows where the measurement\
          \ attribute 'p_value' values are greater than 3. \n`-3 < value.FC < 3`:\
          \ Selects all rows where the measurement attribute 'FC' values lie within\
          \ the interval between -3 and 3.\n \n2. Note: The `MinValue` keyword has\
          \ been deprecated and should be replaced with the aforementioned comparisons.\n\
          \ \nCombine multiple filters for different feature attributes and measurements\
          \ using `AND` (`&&`), `OR` (`||`), `NOT` (`!`) logical operators and parentheses: \n\
          * `NOT feature.Name_1=A`: Select all rows where Name_1 is not A. \n* `feature.Name_1!=A,B,C`:\
          \ Select all rows where Name_1 is not A, B, or C. \n* `feature.Name_1=A\
          \ AND feature.Name_2=B`: Select all rows where Name_1 is A and Name_2 is\
          \ B. \n* `feature.Name_1=A && feature.Name_2=B`: Equivalent to the example\
          \ above. \n* `feature.Name_1=A OR feature.Name_2=B`: Select all rows where\
          \ Name_1 is A or Name_2 is B. \n* `feature.Name_1=A || feature.Name_2=B`:\
          \ Equivalent to the example above. \n* `feature.Name_1=A AND (feature.Name_2=B\
          \ OR value>=1.0)`: Select all rows where Name_1 is A and either Name_2 is\
          \ B or minimal possible measurement value is 1.0."
        in: query
        name: exQuery
        schema:
          type: string
      - description: "Filter by expression metadata (key-value metadata pair(s)).\
          \ E.g. `\"Genome Version\"=hg19-BROAD`."
        in: query
        name: exFilter
        schema:
          type: string
      - description: "Search for objects linked to flow cytometry data via data query\
          \ (key-value pair(s)). E.g. `ReadoutType=Median|Count` `CellPopulation=\"\
          CD45+, live\"` `MinValue=3.5`"
        in: query
        name: fxQuery
        schema:
          type: string
      - description: "Filter by flow cytometry metadata (key-value metadata pair(s)).\
          \ E.g. `Organ=blood`."
        in: query
        name: fxFilter
        schema:
          type: string
      - description: |-
          Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:

          \* or `v<version number>` or `<CHAIN_ID>`:`v<version number>` or `<CHAIN_ID>`:`<accession1,accession2,..>`
        in: query
        name: useVersions
        schema:
          type: string
      - description: |-
          The parameter defines amount of metadata attributes to return:

          1. `minimal_data` - return metadata attributes according to the default template.
          2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
          3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
        in: query
        name: returnedMetadataFields
        schema:
          enum:
          - minimal_data
          - extended_data_included
          - original_data_included
          type: string
      - description: The page tag to resume results from (see paging above).
        in: query
        name: cursor
        schema:
          type: string
      - description: "This parameter determines the number of results to retrieve\
          \ per page, with the default set at 2000."
        in: query
        name: pageLimit
        schema:
          format: int32
          type: integer
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/OmicsResponse"
          description: Omics query result.
        "400":
          content: {}
          description: Invalid data in request. See error message for details.
        "401":
          content: {}
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "500":
          content: {}
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
      - Access-token: []
      - Genestack-API-Token: []
      summary: Retrieve flow cytometry data objects by searching across multiple data
        types
      tags:
      - Omics queries as User
  /api/v1/as-user/omics/flow-cytometry/group:
    get:
      description: |+
        Retrieve group objects whose linked data matches all supplied conditions.

        ## Conditions
        It is possible to supply conditions for:

        1. Samples (full-text or metadata key-value pair)
        2. Parent studies (full-text or metadata key-value pair)
        3. Linked variant objects (list of data key-value pairs)
        4. Linked flow cytometry objects (list of data key-value pairs)
        5. Linked any data (except variant and flow cytometry) objects (list of data key-value pairs)

        ## Metadata full-text queries
        Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).

        ## Metadata filters
        Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).

        ## Data queries
        Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values.

        ## Combinations
        Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.

        ## Versioning
        Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.

        Example usage:
        useVersions=* (query all versions, including those without CHAIN_IDs)
        useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
        useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
        useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
        useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)

        Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.

        ## Paging
        For performance reasons this endpoint returns results in "pages" of limited size together with a cursor tag. To retrieve the next page of results please supply this cursor tag to resume the query from your previous result and get the next page. If there are no more results you will just retrieve an empty result. To return all results iterate through pages using cursor values until the `resultsExhausted` response field is true.

      operationId: omicsSearchFlowCytometryGroupsAsUser
      parameters:
      - description: Supply this parameter with the value `term_id` as part of the
          query to return extended information including IDs for values and dictionaries.
        in: query
        name: responseFormat
        schema:
          $ref: "#/components/schemas/ResponseFormat"
      - description: |
          Filter by study metadata (key-value metadata pair(s)). E.g. `"Study Source"=ArrayExpress`
        in: query
        name: studyFilter
        schema:
          type: string
      - description: Search for objects via a full-text query over all study metadata
          fields. E.g. `"RNA-Seq of human dendritic cells"`. Queries matching dictionary
          terms are automatically expanded to include synonyms.
        in: query
        name: studyQuery
        schema:
          type: string
      - description: |
          Filter by sample metadata (key-value metadata pair(s)). E.g. `"Species or strain"="Homo sapiens"`
        in: query
        name: sampleFilter
        schema:
          type: string
      - description: Search for objects via a full-text query over all sample metadata
          fields. E.g. `Clozapine`. Queries matching dictionary terms are automatically
          expanded to include synonyms.
        in: query
        name: sampleQuery
        schema:
          type: string
      - description: Filter by library metadata (key-value metadata pair(s)). E.g.
          `"Library Type"=RNA-Seq-1`
        in: query
        name: libraryFilter
        schema:
          type: string
      - description: Search for library objects via a full-text query over all library
          metadata fields. E.g. `"illumina HiSeq500"`. Queries matching dictionary
          terms are automatically expanded to include synonyms.
        in: query
        name: libraryQuery
        schema:
          type: string
      - description: Filter by preparation metadata (key-value metadata pair(s)).
          E.g. `Digestion=Trypsin`
        in: query
        name: preparationFilter
        schema:
          type: string
      - description: Search for preparation objects via a full-text query over all
          preparation metadata fields. E.g. `"reversed-phase liquid chromatography"`.
          Queries matching dictionary terms are automatically expanded to include
          synonyms.
        in: query
        name: preparationQuery
        schema:
          type: string
      - description: |-
          If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.

          For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of  "Body fluid") so files containing either "Body fluid" or  "Blood"  in their metadata will be returned in the search results.

          The parent-child relationship is defined by the key "broaders" or "subClassOf"  in the dictionary.

          If the full query term is not present in a dictionary then this parameter has no effect.
        in: query
        name: searchSpecificTerms
        schema:
          type: boolean
      - description: "Search for objects linked to variant data by SNPs properties. Filtering is currently supported by `filter`, `id`, `region` and `info` keywords,
          as well as `exists` keyword for `INFO` field and their logical combinations by means of `not` (`!`), `and` (`&&`), and `or` (`||`) operators with standard boolean precedence. Keyword case is ignored.\n
          * `filter` corresponds to the `FILTER` column in the original vcf file. Could be either equals or not equals to `PASS` : `filter = PASS`
              or `filter != pass`.\n
          * `id` is a string value that corresponds to the `ID` column. Multiple values could be added via a comma. Expression `id = rs3214,rg1234` is equivalent
              to `id = rs3214 or id = rg1234`.\n
          * `region` corresponds to CHROM and POS columns. Supports querying by the whole chromosome `region = chr1` , by interval within a chromosome
              `region = chr1:4567-9876543` by exact position `region = chr1:456789` or by indefinite ranges like `region = x:3456789-*` . Multiple regions could be
              separated via comma, e.g. `region = chr1:34567-98767,chr3` is equivalent to  `region = chr1:34567-98767 or region = chr3`.\n
          * `feature` is the name of the reference gene associated with a specific location in the reference genome which corresponds to the VCF file (variant group) from which the variant information is derived.
              By providing the gene name(s), such as `feature=TP53` or `feature=TP53,TGFB`, variants located within the same genomic region as the specified gene(s) will be retrieved.\n
          * Filter by vcf `INFO` fields. E.g. to filter all variants annotated in dbSNP add `exists(INFO.KEY)`. Use `!exists(INFO.KEY)` to exclude variants having the key from the search results.
              Provide `info.key=value` pair to search for an exact match or `info.key!=value` to exclude it from the search. Due to the limits of precision in floating point numbers,
              we use a small range of 0.0000001 to identify close matches. This means any differences smaller than that won't be detected. For more precise results, please use range queries."
        in: query
        name: vxQuery
        schema:
          type: string
      - description: "Filter by variant metadata (key-value metadata pair(s)). E.g.\
          \ `\"Variant Source\"=dbSNP`."
        in: query
        name: vxFilter
        schema:
          type: string
      - description: "Search for objects linked to expression data and originally\
          \ uploaded in TSV or GCT format via data query, e.g., `feature=ENSG00000230368,ENSG00000188976\
          \ value>=1.50`\n For the case when the original data is represented by multiple\
          \ attributes per feature scenarios, extended filtering syntax is as follows:\
          \ \n1. By feature attribute value for numeric and string attributes: `feature.NAME=1007_s_at`\
          \ or `feature.\"Average Mz\"=2.218`. As in the case of sample metadata queries,\
          \ single words can be supplied as is; otherwise, use speech marks (`\"`)\
          \ to quote queries that include whitespace. \n2. It is possible to specify\
          \ a set of possible values, separated by comma: `feature.NAME=1007_s_at,121_at`.\
          \ \n3. Utilize range filters to search numeric attributes. Apply `<` (less\
          \ than), `>` (greater than), and `=` (equal to) symbols to specify the desired\
          \ ranges as follows: \n`feature.Name_1 > 3`: Select all rows where the feature\
          \ attribute Name_1 values are greater than 3. \n`feature.Name_2 >= 6`: Select\
          \ all rows where the feature attribute Name_2 values are greater than or\
          \ equal to 6. \n`-3 < feature.Name_3 < 3`: Select all rows where the feature\
          \ attribute Name_3 values lie within the interval between -3 and 3. \n4.\
          \ Use substring search to get the records where the attribute field contains\
          \ the provided substring: `feature.attribute1 =~ \"some text\"`. \n5. The\
          \ first column for each original data file is identified as feature accession\
          \ (typically, it contains gene or protein names, accession IDs, etc.). Searching\
          \ by such feature accession would significantly outperform more complex\
          \ queries by combining the other feature attributes. To enable such a search,\
          \ use `feature` without any attribute extension, e.g., `feature=ENSG00000230368,ENSG00000188976`.\n\
          \ \nThe `value` keyword can be used to select rows where the sample (library\
          \ or preparation) measurements has values from a certain range. Examples:\
          \ `value = 3`, `value > 3`, `-3 < value < 3`. When the original data contains\
          \ multiple measurements for a single item, such as a sample (library or\
          \ preparation), use the measurement name to specify the exact column type,\
          \ e.g.: \n1. `value.intensity = 3`: Selects all rows where the measurement\
          \ attribute intensity equals 3. \n `value.intensity != 2,null`: Select all\
          \ rows where the measurement attribute intensity is not equal 2 and is not\
          \ an empty value. \n`value.p_value > 3`: Selects all rows where the measurement\
          \ attribute 'p_value' values are greater than 3. \n`-3 < value.FC < 3`:\
          \ Selects all rows where the measurement attribute 'FC' values lie within\
          \ the interval between -3 and 3.\n \n2. Note: The `MinValue` keyword has\
          \ been deprecated and should be replaced with the aforementioned comparisons.\n\
          \ \nCombine multiple filters for different feature attributes and measurements\
          \ using `AND` (`&&`), `OR` (`||`), `NOT` (`!`) logical operators and parentheses: \n\
          * `NOT feature.Name_1=A`: Select all rows where Name_1 is not A. \n* `feature.Name_1!=A,B,C`:\
          \ Select all rows where Name_1 is not A, B, or C. \n* `feature.Name_1=A\
          \ AND feature.Name_2=B`: Select all rows where Name_1 is A and Name_2 is\
          \ B. \n* `feature.Name_1=A && feature.Name_2=B`: Equivalent to the example\
          \ above. \n* `feature.Name_1=A OR feature.Name_2=B`: Select all rows where\
          \ Name_1 is A or Name_2 is B. \n* `feature.Name_1=A || feature.Name_2=B`:\
          \ Equivalent to the example above. \n* `feature.Name_1=A AND (feature.Name_2=B\
          \ OR value>=1.0)`: Select all rows where Name_1 is A and either Name_2 is\
          \ B or minimal possible measurement value is 1.0."
        in: query
        name: exQuery
        schema:
          type: string
      - description: "Filter by expression metadata (key-value metadata pair(s)).\
          \ E.g. `\"Genome Version\"=hg19-BROAD`."
        in: query
        name: exFilter
        schema:
          type: string
      - description: "Search for objects linked to flow cytometry data via data query\
          \ (key-value pair(s)). E.g. `ReadoutType=Median|Count` `CellPopulation=\"\
          CD45+, live\"` `MinValue=3.5`"
        in: query
        name: fxQuery
        schema:
          type: string
      - description: "Filter by flow cytometry metadata (key-value metadata pair(s)).\
          \ E.g. `Organ=blood`."
        in: query
        name: fxFilter
        schema:
          type: string
      - description: |-
          Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:

          \* or `v<version number>` or `<CHAIN_ID>`:`v<version number>` or `<CHAIN_ID>`:`<accession1,accession2,..>`
        in: query
        name: useVersions
        schema:
          type: string
      - description: |-
          The parameter defines amount of metadata attributes to return:

          1. `minimal_data` - return metadata attributes according to the default template.
          2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
          3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
        in: query
        name: returnedMetadataFields
        schema:
          enum:
          - minimal_data
          - extended_data_included
          - original_data_included
          type: string
      - description: The page tag to resume results from (see paging above).
        in: query
        name: cursor
        schema:
          type: string
      - description: "This parameter determines the number of results to retrieve\
          \ per page, with the default set at 2000."
        in: query
        name: pageLimit
        schema:
          format: int32
          type: integer
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/OmicsResponse"
          description: Omics query result.
        "400":
          content: {}
          description: Invalid data in request. See error message for details.
        "401":
          content: {}
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "500":
          content: {}
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
      - Access-token: []
      - Genestack-API-Token: []
      summary: Retrieve group objects by searching across multiple data types
      tags:
      - Omics queries as User
  /api/v1/as-user/omics/samples:
    get:
      description: |+
        Retrieve sample metadata objects whose linked data matches all supplied conditions.

        ## Conditions
        It is possible to supply conditions for:

        1. Samples (full-text or metadata key-value pair)
        2. Parent studies (full-text or metadata key-value pair)
        3. Linked variant objects (list of data key-value pairs)
        4. Linked flow cytometry objects (list of data key-value pairs)
        5. Linked any data (except variant and flow cytometry) objects (list of data key-value pairs)

        ## Metadata full-text queries
        Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).

        ## Metadata filters
        Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).

        ## Data queries
        Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values.

        ## Combinations
        Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.

        ## Versioning
        Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.

        Example usage:
        useVersions=* (query all versions, including those without CHAIN_IDs)
        useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
        useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
        useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
        useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)

        Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.

        ## Paging
        For performance reasons this endpoint returns results in "pages" of limited size together with a cursor tag. To retrieve the next page of results please supply this cursor tag to resume the query from your previous result and get the next page. If there are no more results you will just retrieve an empty result. To return all results iterate through pages using cursor values until the `resultsExhausted` response field is true.

      operationId: omicsSearchSamplesAsUser
      parameters:
      - description: Supply this parameter with the value `term_id` as part of the
          query to return extended information including IDs for values and dictionaries.
        in: query
        name: responseFormat
        schema:
          $ref: "#/components/schemas/ResponseFormat"
      - description: |
          Filter by study metadata (key-value metadata pair(s)). E.g. `"Study Source"=ArrayExpress`
        in: query
        name: studyFilter
        schema:
          type: string
      - description: Search for objects via a full-text query over all study metadata
          fields. E.g. `"RNA-Seq of human dendritic cells"`. Queries matching dictionary
          terms are automatically expanded to include synonyms.
        in: query
        name: studyQuery
        schema:
          type: string
      - description: |
          Filter by sample metadata (key-value metadata pair(s)). E.g. `"Species or strain"="Homo sapiens"`
        in: query
        name: sampleFilter
        schema:
          type: string
      - description: Search for objects via a full-text query over all sample metadata
          fields. E.g. `Clozapine`. Queries matching dictionary terms are automatically
          expanded to include synonyms.
        in: query
        name: sampleQuery
        schema:
          type: string
      - description: Filter by library metadata (key-value metadata pair(s)). E.g.
          `"Library Type"=RNA-Seq-1`
        in: query
        name: libraryFilter
        schema:
          type: string
      - description: Search for library objects via a full-text query over all library
          metadata fields. E.g. `"illumina HiSeq500"`. Queries matching dictionary
          terms are automatically expanded to include synonyms.
        in: query
        name: libraryQuery
        schema:
          type: string
      - description: Filter by preparation metadata (key-value metadata pair(s)).
          E.g. `Digestion=Trypsin`
        in: query
        name: preparationFilter
        schema:
          type: string
      - description: Search for preparation objects via a full-text query over all
          preparation metadata fields. E.g. `"reversed-phase liquid chromatography"`.
          Queries matching dictionary terms are automatically expanded to include
          synonyms.
        in: query
        name: preparationQuery
        schema:
          type: string
      - description: |-
          If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.

          For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of  "Body fluid") so files containing either "Body fluid" or  "Blood"  in their metadata will be returned in the search results.

          The parent-child relationship is defined by the key "broaders" or "subClassOf"  in the dictionary.

          If the full query term is not present in a dictionary then this parameter has no effect.
        in: query
        name: searchSpecificTerms
        schema:
          type: boolean
      - description: "Search for objects linked to variant data by SNPs properties. Filtering is currently supported by `filter`, `id`, `region` and `info` keywords,
          as well as `exists` keyword for `INFO` field and their logical combinations by means of `not` (`!`), `and` (`&&`), and `or` (`||`) operators with standard boolean precedence. Keyword case is ignored.\n
          * `filter` corresponds to the `FILTER` column in the original vcf file. Could be either equals or not equals to `PASS` : `filter = PASS`
              or `filter != pass`.\n
          * `id` is a string value that corresponds to the `ID` column. Multiple values could be added via a comma. Expression `id = rs3214,rg1234` is equivalent
              to `id = rs3214 or id = rg1234`.\n
          * `region` corresponds to CHROM and POS columns. Supports querying by the whole chromosome `region = chr1` , by interval within a chromosome
              `region = chr1:4567-9876543` by exact position `region = chr1:456789` or by indefinite ranges like `region = x:3456789-*` . Multiple regions could be
              separated via comma, e.g. `region = chr1:34567-98767,chr3` is equivalent to  `region = chr1:34567-98767 or region = chr3`.\n
          * `feature` is the name of the reference gene associated with a specific location in the reference genome which corresponds to the VCF file (variant group) from which the variant information is derived.
              By providing the gene name(s), such as `feature=TP53` or `feature=TP53,TGFB`, variants located within the same genomic region as the specified gene(s) will be retrieved.\n
          * Filter by vcf `INFO` fields. E.g. to filter all variants annotated in dbSNP add `exists(INFO.KEY)`. Use `!exists(INFO.KEY)` to exclude variants having the key from the search results.
              Provide `info.key=value` pair to search for an exact match or `info.key!=value` to exclude it from the search. Due to the limits of precision in floating point numbers,
              we use a small range of 0.0000001 to identify close matches. This means any differences smaller than that won't be detected. For more precise results, please use range queries."
        in: query
        name: vxQuery
        schema:
          type: string
      - description: "Filter by variant metadata (key-value metadata pair(s)). E.g.\
          \ `\"Variant Source\"=dbSNP`."
        in: query
        name: vxFilter
        schema:
          type: string
      - description: "Search for objects linked to expression data and originally\
          \ uploaded in TSV or GCT format via data query, e.g., `feature=ENSG00000230368,ENSG00000188976\
          \ value>=1.50`\n For the case when the original data is represented by multiple\
          \ attributes per feature scenarios, extended filtering syntax is as follows:\
          \ \n1. By feature attribute value for numeric and string attributes: `feature.NAME=1007_s_at`\
          \ or `feature.\"Average Mz\"=2.218`. As in the case of sample metadata queries,\
          \ single words can be supplied as is; otherwise, use speech marks (`\"`)\
          \ to quote queries that include whitespace. \n2. It is possible to specify\
          \ a set of possible values, separated by comma: `feature.NAME=1007_s_at,121_at`.\
          \ \n3. Utilize range filters to search numeric attributes. Apply `<` (less\
          \ than), `>` (greater than), and `=` (equal to) symbols to specify the desired\
          \ ranges as follows: \n`feature.Name_1 > 3`: Select all rows where the feature\
          \ attribute Name_1 values are greater than 3. \n`feature.Name_2 >= 6`: Select\
          \ all rows where the feature attribute Name_2 values are greater than or\
          \ equal to 6. \n`-3 < feature.Name_3 < 3`: Select all rows where the feature\
          \ attribute Name_3 values lie within the interval between -3 and 3. \n4.\
          \ Use substring search to get the records where the attribute field contains\
          \ the provided substring: `feature.attribute1 =~ \"some text\"`. \n5. The\
          \ first column for each original data file is identified as feature accession\
          \ (typically, it contains gene or protein names, accession IDs, etc.). Searching\
          \ by such feature accession would significantly outperform more complex\
          \ queries by combining the other feature attributes. To enable such a search,\
          \ use `feature` without any attribute extension, e.g., `feature=ENSG00000230368,ENSG00000188976`.\n\
          \ \nThe `value` keyword can be used to select rows where the sample (library\
          \ or preparation) measurements has values from a certain range. Examples:\
          \ `value = 3`, `value > 3`, `-3 < value < 3`. When the original data contains\
          \ multiple measurements for a single item, such as a sample (library or\
          \ preparation), use the measurement name to specify the exact column type,\
          \ e.g.: \n1. `value.intensity = 3`: Selects all rows where the measurement\
          \ attribute intensity equals 3. \n `value.intensity != 2,null`: Select all\
          \ rows where the measurement attribute intensity is not equal 2 and is not\
          \ an empty value. \n`value.p_value > 3`: Selects all rows where the measurement\
          \ attribute 'p_value' values are greater than 3. \n`-3 < value.FC < 3`:\
          \ Selects all rows where the measurement attribute 'FC' values lie within\
          \ the interval between -3 and 3.\n \n2. Note: The `MinValue` keyword has\
          \ been deprecated and should be replaced with the aforementioned comparisons.\n\
          \ \nCombine multiple filters for different feature attributes and measurements\
          \ using `AND` (`&&`), `OR` (`||`), `NOT` (`!`) logical operators and parentheses: \n\
          * `NOT feature.Name_1=A`: Select all rows where Name_1 is not A. \n* `feature.Name_1!=A,B,C`:\
          \ Select all rows where Name_1 is not A, B, or C. \n* `feature.Name_1=A\
          \ AND feature.Name_2=B`: Select all rows where Name_1 is A and Name_2 is\
          \ B. \n* `feature.Name_1=A && feature.Name_2=B`: Equivalent to the example\
          \ above. \n* `feature.Name_1=A OR feature.Name_2=B`: Select all rows where\
          \ Name_1 is A or Name_2 is B. \n* `feature.Name_1=A || feature.Name_2=B`:\
          \ Equivalent to the example above. \n* `feature.Name_1=A AND (feature.Name_2=B\
          \ OR value>=1.0)`: Select all rows where Name_1 is A and either Name_2 is\
          \ B or minimal possible measurement value is 1.0."
        in: query
        name: exQuery
        schema:
          type: string
      - description: "Filter by expression metadata (key-value metadata pair(s)).\
          \ E.g. `\"Genome Version\"=hg19-BROAD`."
        in: query
        name: exFilter
        schema:
          type: string
      - description: "Search for objects linked to flow cytometry data via data query\
          \ (key-value pair(s)). E.g. `ReadoutType=Median|Count` `CellPopulation=\"\
          CD45+, live\"` `MinValue=3.5`"
        in: query
        name: fxQuery
        schema:
          type: string
      - description: "Filter by flow cytometry metadata (key-value metadata pair(s)).\
          \ E.g. `Organ=blood`."
        in: query
        name: fxFilter
        schema:
          type: string
      - description: |-
          Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:

          \* or `v<version number>` or `<CHAIN_ID>`:`v<version number>` or `<CHAIN_ID>`:`<accession1,accession2,..>`
        in: query
        name: useVersions
        schema:
          type: string
      - description: |-
          The parameter defines amount of metadata attributes to return:

          1. `minimal_data` - return metadata attributes according to the default template.
          2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
          3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
        in: query
        name: returnedMetadataFields
        schema:
          enum:
          - minimal_data
          - extended_data_included
          - original_data_included
          type: string
      - description: The page tag to resume results from (see paging above).
        in: query
        name: cursor
        schema:
          type: string
      - description: "This parameter determines the number of results to retrieve\
          \ per page, with the default set at 2000."
        in: query
        name: pageLimit
        schema:
          format: int32
          type: integer
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/OmicsResponse"
          description: Omics query result.
        "400":
          content: {}
          description: Invalid data in request. See error message for details.
        "401":
          content: {}
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "500":
          content: {}
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
      - Access-token: []
      - Genestack-API-Token: []
      summary: Retrieve sample metadata objects by searching across multiple data
        types
      tags:
      - Omics queries as User
  /api/v1/as-user/omics/variant/data:
    get:
      description: |+
        Retrieve variant data objects whose linked data matches all supplied conditions.

        Note: A variant data query must be supplied.

        ## Conditions
        It is possible to supply conditions for:

        1. Samples (full-text or metadata key-value pair)
        2. Parent studies (full-text or metadata key-value pair)
        3. Linked variant objects (list of data key-value pairs)
        4. Linked expression objects (list of data key-value pairs)
        5. Linked any data (except variant and flow cytometry) objects (list of data key-value pairs)

        ## Metadata full-text queries
        Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).

        ## Metadata filters
        Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).

        ## Data queries
        Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values.

        ## Combinations
        Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.

        ## Versioning
        Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.

        Example usage:
        useVersions=* (query all versions, including those without CHAIN_IDs)
        useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
        useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
        useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
        useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)

        Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.

        ## Paging
        For performance reasons this endpoint returns results in "pages" of limited size together with a cursor tag. To retrieve the next page of results please supply this cursor tag to resume the query from your previous result and get the next page. If there are no more results you will just retrieve an empty result. To return all results iterate through pages using cursor values until the `resultsExhausted` response field is true.

      operationId: omicsSearchVariantDataAsUser
      parameters:
      - description: Supply this parameter with the value `term_id` as part of the
          query to return extended information including IDs for values and dictionaries.
        in: query
        name: responseFormat
        schema:
          $ref: "#/components/schemas/ResponseFormat"
      - description: |
          Filter by study metadata (key-value metadata pair(s)). E.g. `"Study Source"=ArrayExpress`
        in: query
        name: studyFilter
        schema:
          type: string
      - description: Search for objects via a full-text query over all study metadata
          fields. E.g. `"RNA-Seq of human dendritic cells"`. Queries matching dictionary
          terms are automatically expanded to include synonyms.
        in: query
        name: studyQuery
        schema:
          type: string
      - description: |
          Filter by sample metadata (key-value metadata pair(s)). E.g. `"Species or strain"="Homo sapiens"`
        in: query
        name: sampleFilter
        schema:
          type: string
      - description: Search for objects via a full-text query over all sample metadata
          fields. E.g. `Clozapine`. Queries matching dictionary terms are automatically
          expanded to include synonyms.
        in: query
        name: sampleQuery
        schema:
          type: string
      - description: Filter by library metadata (key-value metadata pair(s)). E.g.
          `"Library Type"=RNA-Seq-1`
        in: query
        name: libraryFilter
        schema:
          type: string
      - description: Search for library objects via a full-text query over all library
          metadata fields. E.g. `"illumina HiSeq500"`. Queries matching dictionary
          terms are automatically expanded to include synonyms.
        in: query
        name: libraryQuery
        schema:
          type: string
      - description: Filter by preparation metadata (key-value metadata pair(s)).
          E.g. `Digestion=Trypsin`
        in: query
        name: preparationFilter
        schema:
          type: string
      - description: Search for preparation objects via a full-text query over all
          preparation metadata fields. E.g. `"reversed-phase liquid chromatography"`.
          Queries matching dictionary terms are automatically expanded to include
          synonyms.
        in: query
        name: preparationQuery
        schema:
          type: string
      - description: |-
          If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.

          For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of  "Body fluid") so files containing either "Body fluid" or  "Blood"  in their metadata will be returned in the search results.

          The parent-child relationship is defined by the key "broaders" or "subClassOf"  in the dictionary.

          If the full query term is not present in a dictionary then this parameter has no effect.
        in: query
        name: searchSpecificTerms
        schema:
          type: boolean
      - description: "Search for objects linked to variant data by SNPs properties. Filtering is currently supported by `filter`, `id`, `region` and `info` keywords,
          as well as `exists` keyword for `INFO` field and their logical combinations by means of `not` (`!`), `and` (`&&`), and `or` (`||`) operators with standard boolean precedence. Keyword case is ignored.\n
          * `filter` corresponds to the `FILTER` column in the original vcf file. Could be either equals or not equals to `PASS` : `filter = PASS`
              or `filter != pass`.\n
          * `id` is a string value that corresponds to the `ID` column. Multiple values could be added via a comma. Expression `id = rs3214,rg1234` is equivalent
              to `id = rs3214 or id = rg1234`.\n
          * `region` corresponds to CHROM and POS columns. Supports querying by the whole chromosome `region = chr1` , by interval within a chromosome
              `region = chr1:4567-9876543` by exact position `region = chr1:456789` or by indefinite ranges like `region = x:3456789-*` . Multiple regions could be
              separated via comma, e.g. `region = chr1:34567-98767,chr3` is equivalent to  `region = chr1:34567-98767 or region = chr3`.\n
          * `feature` is the name of the reference gene associated with a specific location in the reference genome which corresponds to the VCF file (variant group) from which the variant information is derived.
              By providing the gene name(s), such as `feature=TP53` or `feature=TP53,TGFB`, variants located within the same genomic region as the specified gene(s) will be retrieved.\n
          * Filter by vcf `INFO` fields. E.g. to filter all variants annotated in dbSNP add `exists(INFO.KEY)`. Use `!exists(INFO.KEY)` to exclude variants having the key from the search results.
              Provide `info.key=value` pair to search for an exact match or `info.key!=value` to exclude it from the search. Due to the limits of precision in floating point numbers,
              we use a small range of 0.0000001 to identify close matches. This means any differences smaller than that won't be detected. For more precise results, please use range queries."
        in: query
        name: vxQuery
        schema:
          type: string
      - description: "Filter by variant metadata (key-value metadata pair(s)). E.g.\
          \ `\"Variant Source\"=dbSNP`."
        in: query
        name: vxFilter
        schema:
          type: string
      - description: "Search for objects linked to expression data and originally\
          \ uploaded in TSV or GCT format via data query, e.g., `feature=ENSG00000230368,ENSG00000188976\
          \ value>=1.50`\n For the case when the original data is represented by multiple\
          \ attributes per feature scenarios, extended filtering syntax is as follows:\
          \ \n1. By feature attribute value for numeric and string attributes: `feature.NAME=1007_s_at`\
          \ or `feature.\"Average Mz\"=2.218`. As in the case of sample metadata queries,\
          \ single words can be supplied as is; otherwise, use speech marks (`\"`)\
          \ to quote queries that include whitespace. \n2. It is possible to specify\
          \ a set of possible values, separated by comma: `feature.NAME=1007_s_at,121_at`.\
          \ \n3. Utilize range filters to search numeric attributes. Apply `<` (less\
          \ than), `>` (greater than), and `=` (equal to) symbols to specify the desired\
          \ ranges as follows: \n`feature.Name_1 > 3`: Select all rows where the feature\
          \ attribute Name_1 values are greater than 3. \n`feature.Name_2 >= 6`: Select\
          \ all rows where the feature attribute Name_2 values are greater than or\
          \ equal to 6. \n`-3 < feature.Name_3 < 3`: Select all rows where the feature\
          \ attribute Name_3 values lie within the interval between -3 and 3. \n4.\
          \ Use substring search to get the records where the attribute field contains\
          \ the provided substring: `feature.attribute1 =~ \"some text\"`. \n5. The\
          \ first column for each original data file is identified as feature accession\
          \ (typically, it contains gene or protein names, accession IDs, etc.). Searching\
          \ by such feature accession would significantly outperform more complex\
          \ queries by combining the other feature attributes. To enable such a search,\
          \ use `feature` without any attribute extension, e.g., `feature=ENSG00000230368,ENSG00000188976`.\n\
          \ \nThe `value` keyword can be used to select rows where the sample (library\
          \ or preparation) measurements has values from a certain range. Examples:\
          \ `value = 3`, `value > 3`, `-3 < value < 3`. When the original data contains\
          \ multiple measurements for a single item, such as a sample (library or\
          \ preparation), use the measurement name to specify the exact column type,\
          \ e.g.: \n1. `value.intensity = 3`: Selects all rows where the measurement\
          \ attribute intensity equals 3. \n `value.intensity != 2,null`: Select all\
          \ rows where the measurement attribute intensity is not equal 2 and is not\
          \ an empty value. \n`value.p_value > 3`: Selects all rows where the measurement\
          \ attribute 'p_value' values are greater than 3. \n`-3 < value.FC < 3`:\
          \ Selects all rows where the measurement attribute 'FC' values lie within\
          \ the interval between -3 and 3.\n \n2. Note: The `MinValue` keyword has\
          \ been deprecated and should be replaced with the aforementioned comparisons.\n\
          \ \nCombine multiple filters for different feature attributes and measurements\
          \ using `AND` (`&&`), `OR` (`||`), `NOT` (`!`) logical operators and parentheses: \n\
          * `NOT feature.Name_1=A`: Select all rows where Name_1 is not A. \n* `feature.Name_1!=A,B,C`:\
          \ Select all rows where Name_1 is not A, B, or C. \n* `feature.Name_1=A\
          \ AND feature.Name_2=B`: Select all rows where Name_1 is A and Name_2 is\
          \ B. \n* `feature.Name_1=A && feature.Name_2=B`: Equivalent to the example\
          \ above. \n* `feature.Name_1=A OR feature.Name_2=B`: Select all rows where\
          \ Name_1 is A or Name_2 is B. \n* `feature.Name_1=A || feature.Name_2=B`:\
          \ Equivalent to the example above. \n* `feature.Name_1=A AND (feature.Name_2=B\
          \ OR value>=1.0)`: Select all rows where Name_1 is A and either Name_2 is\
          \ B or minimal possible measurement value is 1.0."
        in: query
        name: exQuery
        schema:
          type: string
      - description: "Filter by expression metadata (key-value metadata pair(s)).\
          \ E.g. `\"Genome Version\"=hg19-BROAD`."
        in: query
        name: exFilter
        schema:
          type: string
      - description: "Search for objects linked to flow cytometry data via data query\
          \ (key-value pair(s)). E.g. `ReadoutType=Median|Count` `CellPopulation=\"\
          CD45+, live\"` `MinValue=3.5`"
        in: query
        name: fxQuery
        schema:
          type: string
      - description: "Filter by flow cytometry metadata (key-value metadata pair(s)).\
          \ E.g. `Organ=blood`."
        in: query
        name: fxFilter
        schema:
          type: string
      - description: |-
          Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:

          \* or `v<version number>` or `<CHAIN_ID>`:`v<version number>` or `<CHAIN_ID>`:`<accession1,accession2,..>`
        in: query
        name: useVersions
        schema:
          type: string
      - description: |-
          The parameter defines amount of metadata attributes to return:

          1. `minimal_data` - return metadata attributes according to the default template.
          2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
          3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
        in: query
        name: returnedMetadataFields
        schema:
          enum:
          - minimal_data
          - extended_data_included
          - original_data_included
          type: string
      - description: The page tag to resume results from (see paging above).
        in: query
        name: cursor
        schema:
          type: string
      - description: "This parameter determines the number of results to retrieve\
          \ per page, with the default set at 2000."
        in: query
        name: pageLimit
        schema:
          format: int32
          type: integer
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/OmicsResponse"
          description: Omics query result.
        "400":
          content: {}
          description: Invalid data in request. See error message for details.
        "401":
          content: {}
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "500":
          content: {}
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
      - Access-token: []
      - Genestack-API-Token: []
      summary: Retrieve variant data objects by searching across multiple data types
      tags:
      - Omics queries as User
  /api/v1/as-user/omics/variant/group:
    get:
      description: |+
        Retrieve group objects whose linked data matches all supplied conditions.

        ## Conditions
        It is possible to supply conditions for:

        1. Samples (full-text or metadata key-value pair)
        2. Parent studies (full-text or metadata key-value pair)
        3. Linked variant objects (list of data key-value pairs)
        4. Linked flow cytometry objects (list of data key-value pairs)
        5. Linked any data (except variant and flow cytometry) objects (list of data key-value pairs)

        ## Metadata full-text queries
        Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).

        ## Metadata filters
        Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).

        ## Data queries
        Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values.

        ## Combinations
        Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.

        ## Versioning
        Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.

        Example usage:
        useVersions=* (query all versions, including those without CHAIN_IDs)
        useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
        useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
        useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
        useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)

        Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.

        ## Paging
        For performance reasons this endpoint returns results in "pages" of limited size together with a cursor tag. To retrieve the next page of results please supply this cursor tag to resume the query from your previous result and get the next page. If there are no more results you will just retrieve an empty result. To return all results iterate through pages using cursor values until the `resultsExhausted` response field is true.

      operationId: omicsSearchVariantGroupsAsUser
      parameters:
      - description: Supply this parameter with the value `term_id` as part of the
          query to return extended information including IDs for values and dictionaries.
        in: query
        name: responseFormat
        schema:
          $ref: "#/components/schemas/ResponseFormat"
      - description: |
          Filter by study metadata (key-value metadata pair(s)). E.g. `"Study Source"=ArrayExpress`
        in: query
        name: studyFilter
        schema:
          type: string
      - description: Search for objects via a full-text query over all study metadata
          fields. E.g. `"RNA-Seq of human dendritic cells"`. Queries matching dictionary
          terms are automatically expanded to include synonyms.
        in: query
        name: studyQuery
        schema:
          type: string
      - description: |
          Filter by sample metadata (key-value metadata pair(s)). E.g. `"Species or strain"="Homo sapiens"`
        in: query
        name: sampleFilter
        schema:
          type: string
      - description: Search for objects via a full-text query over all sample metadata
          fields. E.g. `Clozapine`. Queries matching dictionary terms are automatically
          expanded to include synonyms.
        in: query
        name: sampleQuery
        schema:
          type: string
      - description: Filter by library metadata (key-value metadata pair(s)). E.g.
          `"Library Type"=RNA-Seq-1`
        in: query
        name: libraryFilter
        schema:
          type: string
      - description: Search for library objects via a full-text query over all library
          metadata fields. E.g. `"illumina HiSeq500"`. Queries matching dictionary
          terms are automatically expanded to include synonyms.
        in: query
        name: libraryQuery
        schema:
          type: string
      - description: Filter by preparation metadata (key-value metadata pair(s)).
          E.g. `Digestion=Trypsin`
        in: query
        name: preparationFilter
        schema:
          type: string
      - description: Search for preparation objects via a full-text query over all
          preparation metadata fields. E.g. `"reversed-phase liquid chromatography"`.
          Queries matching dictionary terms are automatically expanded to include
          synonyms.
        in: query
        name: preparationQuery
        schema:
          type: string
      - description: |-
          If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.

          For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of  "Body fluid") so files containing either "Body fluid" or  "Blood"  in their metadata will be returned in the search results.

          The parent-child relationship is defined by the key "broaders" or "subClassOf"  in the dictionary.

          If the full query term is not present in a dictionary then this parameter has no effect.
        in: query
        name: searchSpecificTerms
        schema:
          type: boolean
      - description: "Search for objects linked to variant data by SNPs properties. Filtering is currently supported by `filter`, `id`, `region` and `info` keywords,
          as well as `exists` keyword for `INFO` field and their logical combinations by means of `not` (`!`), `and` (`&&`), and `or` (`||`) operators with standard boolean precedence. Keyword case is ignored.\n
          * `filter` corresponds to the `FILTER` column in the original vcf file. Could be either equals or not equals to `PASS` : `filter = PASS`
              or `filter != pass`.\n
          * `id` is a string value that corresponds to the `ID` column. Multiple values could be added via a comma. Expression `id = rs3214,rg1234` is equivalent
              to `id = rs3214 or id = rg1234`.\n
          * `region` corresponds to CHROM and POS columns. Supports querying by the whole chromosome `region = chr1` , by interval within a chromosome
              `region = chr1:4567-9876543` by exact position `region = chr1:456789` or by indefinite ranges like `region = x:3456789-*` . Multiple regions could be
              separated via comma, e.g. `region = chr1:34567-98767,chr3` is equivalent to  `region = chr1:34567-98767 or region = chr3`.\n
          * `feature` is the name of the reference gene associated with a specific location in the reference genome which corresponds to the VCF file (variant group) from which the variant information is derived.
              By providing the gene name(s), such as `feature=TP53` or `feature=TP53,TGFB`, variants located within the same genomic region as the specified gene(s) will be retrieved.\n
          * Filter by vcf `INFO` fields. E.g. to filter all variants annotated in dbSNP add `exists(INFO.KEY)`. Use `!exists(INFO.KEY)` to exclude variants having the key from the search results.
              Provide `info.key=value` pair to search for an exact match or `info.key!=value` to exclude it from the search. Due to the limits of precision in floating point numbers,
              we use a small range of 0.0000001 to identify close matches. This means any differences smaller than that won't be detected. For more precise results, please use range queries."
        in: query
        name: vxQuery
        schema:
          type: string
      - description: "Filter by variant metadata (key-value metadata pair(s)). E.g.\
          \ `\"Variant Source\"=dbSNP`."
        in: query
        name: vxFilter
        schema:
          type: string
      - description: "Search for objects linked to expression data and originally\
          \ uploaded in TSV or GCT format via data query, e.g., `feature=ENSG00000230368,ENSG00000188976\
          \ value>=1.50`\n For the case when the original data is represented by multiple\
          \ attributes per feature scenarios, extended filtering syntax is as follows:\
          \ \n1. By feature attribute value for numeric and string attributes: `feature.NAME=1007_s_at`\
          \ or `feature.\"Average Mz\"=2.218`. As in the case of sample metadata queries,\
          \ single words can be supplied as is; otherwise, use speech marks (`\"`)\
          \ to quote queries that include whitespace. \n2. It is possible to specify\
          \ a set of possible values, separated by comma: `feature.NAME=1007_s_at,121_at`.\
          \ \n3. Utilize range filters to search numeric attributes. Apply `<` (less\
          \ than), `>` (greater than), and `=` (equal to) symbols to specify the desired\
          \ ranges as follows: \n`feature.Name_1 > 3`: Select all rows where the feature\
          \ attribute Name_1 values are greater than 3. \n`feature.Name_2 >= 6`: Select\
          \ all rows where the feature attribute Name_2 values are greater than or\
          \ equal to 6. \n`-3 < feature.Name_3 < 3`: Select all rows where the feature\
          \ attribute Name_3 values lie within the interval between -3 and 3. \n4.\
          \ Use substring search to get the records where the attribute field contains\
          \ the provided substring: `feature.attribute1 =~ \"some text\"`. \n5. The\
          \ first column for each original data file is identified as feature accession\
          \ (typically, it contains gene or protein names, accession IDs, etc.). Searching\
          \ by such feature accession would significantly outperform more complex\
          \ queries by combining the other feature attributes. To enable such a search,\
          \ use `feature` without any attribute extension, e.g., `feature=ENSG00000230368,ENSG00000188976`.\n\
          \ \nThe `value` keyword can be used to select rows where the sample (library\
          \ or preparation) measurements has values from a certain range. Examples:\
          \ `value = 3`, `value > 3`, `-3 < value < 3`. When the original data contains\
          \ multiple measurements for a single item, such as a sample (library or\
          \ preparation), use the measurement name to specify the exact column type,\
          \ e.g.: \n1. `value.intensity = 3`: Selects all rows where the measurement\
          \ attribute intensity equals 3. \n `value.intensity != 2,null`: Select all\
          \ rows where the measurement attribute intensity is not equal 2 and is not\
          \ an empty value. \n`value.p_value > 3`: Selects all rows where the measurement\
          \ attribute 'p_value' values are greater than 3. \n`-3 < value.FC < 3`:\
          \ Selects all rows where the measurement attribute 'FC' values lie within\
          \ the interval between -3 and 3.\n \n2. Note: The `MinValue` keyword has\
          \ been deprecated and should be replaced with the aforementioned comparisons.\n\
          \ \nCombine multiple filters for different feature attributes and measurements\
          \ using `AND` (`&&`), `OR` (`||`), `NOT` (`!`) logical operators and parentheses: \n\
          * `NOT feature.Name_1=A`: Select all rows where Name_1 is not A. \n* `feature.Name_1!=A,B,C`:\
          \ Select all rows where Name_1 is not A, B, or C. \n* `feature.Name_1=A\
          \ AND feature.Name_2=B`: Select all rows where Name_1 is A and Name_2 is\
          \ B. \n* `feature.Name_1=A && feature.Name_2=B`: Equivalent to the example\
          \ above. \n* `feature.Name_1=A OR feature.Name_2=B`: Select all rows where\
          \ Name_1 is A or Name_2 is B. \n* `feature.Name_1=A || feature.Name_2=B`:\
          \ Equivalent to the example above. \n* `feature.Name_1=A AND (feature.Name_2=B\
          \ OR value>=1.0)`: Select all rows where Name_1 is A and either Name_2 is\
          \ B or minimal possible measurement value is 1.0."
        in: query
        name: exQuery
        schema:
          type: string
      - description: "Filter by expression metadata (key-value metadata pair(s)).\
          \ E.g. `\"Genome Version\"=hg19-BROAD`."
        in: query
        name: exFilter
        schema:
          type: string
      - description: "Search for objects linked to flow cytometry data via data query\
          \ (key-value pair(s)). E.g. `ReadoutType=Median|Count` `CellPopulation=\"\
          CD45+, live\"` `MinValue=3.5`"
        in: query
        name: fxQuery
        schema:
          type: string
      - description: "Filter by flow cytometry metadata (key-value metadata pair(s)).\
          \ E.g. `Organ=blood`."
        in: query
        name: fxFilter
        schema:
          type: string
      - description: "Unique identifier (accession) of Reference Genome object."
        in: query
        name: referenceGenomeId
        schema:
          type: string
      - description: |-
          Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:

          \* or `v<version number>` or `<CHAIN_ID>`:`v<version number>` or `<CHAIN_ID>`:`<accession1,accession2,..>`
        in: query
        name: useVersions
        schema:
          type: string
      - description: |-
          The parameter defines amount of metadata attributes to return:

          1. `minimal_data` - return metadata attributes according to the default template.
          2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
          3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
        in: query
        name: returnedMetadataFields
        schema:
          enum:
          - minimal_data
          - extended_data_included
          - original_data_included
          type: string
      - description: The page tag to resume results from (see paging above).
        in: query
        name: cursor
        schema:
          type: string
      - description: "This parameter determines the number of results to retrieve\
          \ per page, with the default set at 2000."
        in: query
        name: pageLimit
        schema:
          format: int32
          type: integer
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/OmicsResponse"
          description: Omics query result.
        "400":
          content: {}
          description: Invalid data in request. See error message for details.
        "401":
          content: {}
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "500":
          content: {}
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
      - Access-token: []
      - Genestack-API-Token: []
      summary: Retrieve group objects by searching across multiple data types
      tags:
      - Omics queries as User
  /api/v1/as-user/omics/variant/streamed-data:
    get:
      description: |+
        Stream data from a given group for a VCF file that matches a sample query/filter. If no query/filters are supplied all variant data is returned. If a metadata filter is specified, this endpoint will only return variant data that is associated with a sample via metadata attribute.

        ## Conditions
        It is possible to supply conditions for Samples (full-text or metadata key-value pair)

        ## Metadata full-text queries
        Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).

        ## Metadata filters
        Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).

        ## Combinations
        Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.

      operationId: omicsSearchStreamedVariantDataAsUser
      parameters:
        - description: |
            Filter by sample metadata (key-value metadata pair(s)). E.g. `"Species or strain"="Homo sapiens"`
          in: query
          name: sampleFilter
          schema:
            type: string
        - description: Search for objects via a full-text query over all sample metadata
            fields. E.g. `Clozapine`. Queries matching dictionary terms are automatically
            expanded to include synonyms.
          in: query
          name: sampleQuery
          schema:
            type: string
        - description: |-
            If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.

            For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of  "Body fluid") so files containing either "Body fluid" or  "Blood"  in their metadata will be returned in the search results.

            The parent-child relationship is defined by the key "broaders" or "subClassOf"  in the dictionary.

            If the full query term is not present in a dictionary then this parameter has no effect.
          in: query
          name: searchSpecificTerms
          schema:
            type: boolean
        - description: "Search for objects linked to expression data and originally\
            \ uploaded in TSV or GCT format via data query, e.g., `feature=ENSG00000230368,ENSG00000188976\
            \ value>=1.50`\n For the case when the original data is represented by multiple\
            \ attributes per feature scenarios, extended filtering syntax is as follows:\
            \ \n1. By feature attribute value for numeric and string attributes: `features.NAME=1007_s_at`\
            \ or `features.\"Average Mz\"=2.218`. As in the case of sample metadata\
            \ queries, single words can be supplied as is; otherwise, use speech marks\
            \ (`\"`) to quote queries that include whitespace. \n2. It is possible to\
            \ specify a set of possible values, separated by comma: `features.NAME=1007_s_at,121_at`.\
            \ \n3. Utilize range filters to search numeric attributes. Apply `<` (less\
            \ than), `>` (greater than), and `=` (equal to) symbols to specify the desired\
            \ ranges as follows: \n`features.Name_1 > 3`: Select all rows where the\
            \ feature attribute Name_1 values are greater than 3. \n`features.Name_2\
            \ >= 6`: Select all rows where the feature attribute Name_2 values are greater\
            \ than or equal to 6. \n`-3 < features.Name_3 < 3`: Select all rows where\
            \ the feature attribute Name_3 values lie within the interval between -3\
            \ and 3. \n4. Use substring search to get the records where the attribute\
            \ field contains the provided substring: `features.attribute1 =~ \"some\
            \ text\"`. \n5. The first column for each original data file is identified\
            \ as feature accession (typically, it contains gene or protein names, accession\
            \ IDs, etc.). Searching by such feature accession would significantly outperform\
            \ more complex queries by combining the other feature attributes. To enable\
            \ such a search, use `feature` without any attribute extension, e.g., `feature=ENSG00000230368,ENSG00000188976`.\n\
            \ \nThe `value` keyword can be used to select rows where the sample (library\
            \ or preparation) measurements has values from a certain range. Examples:\
            \ `value = 3`, `value > 3`, `-3 < value < 3`. When the original data contains\
            \ multiple measurements for a single item, such as a sample (library or\
            \ preparation), use the measurement name to specify the exact column type,\
            \ e.g.: \n1. `value.intensity = 3`: Selects all rows where the measurement\
            \ attribute intensity equals 3. \n `value.intensity != 2,null`: Select all\
            \ rows where the measurement attribute intensity is not equal 2 and is not\
            \ an empty value. \n`values.p_value > 3`: Selects all rows where the measurement\
            \ attribute 'p_value' values are greater than 3. \n`-3 < values.FC < 3`:\
            \ Selects all rows where the measurement attribute 'FC' values lie within\
            \ the interval between -3 and 3.\n \n2. Note: The `MinValue` keyword has\
            \ been deprecated and should be replaced with the aforementioned comparisons.\n\
            \ \nCombine multiple filters for different feature attributes and measurements\
            \ using `AND` (`&&`), `OR` (`||`) logical operators and parentheses: \n\
            * `features.Name_1!=A`: Select all rows where Name_1 is not A. \n* `features.Name_1!=A,B,C`:\
            \ Select all rows where Name_1 is not A, B, or C. \n* `features.Name_1=A\
            \ AND features.Name_2=B`: Select all rows where Name_1 is A and Name_2 is\
            \ B. \n* `features.Name_1=A && features.Name_2=B`: Equivalent to the example\
            \ above. \n* `features.Name_1=A OR features.Name_2=B`: Select all rows where\
            \ Name_1 is A or Name_2 is B. \n* `features.Name_1=A || features.Name_2=B`:\
            \ Equivalent to the example above. \n* `features.Name_1=A AND (features.Name_2=B\
            \ OR value>=1.0)`: Select all rows where Name_1 is A and either Name_2 is\
            \ B or minimal possible measurement value is 1.0."
          in: query
          name: exQuery
          schema:
            type: string
        - description: "Search for objects linked to variant data by SNPs properties. Filtering is currently supported by `filter`, `id`, `region` and `info` keywords,
          as well as `exists` keyword for `INFO` field and their logical combinations by means of `not` (`!`), `and` (`&&`), and `or` (`||`) operators with standard boolean precedence. Keyword case is ignored.\n
          * `filter` corresponds to the `FILTER` column in the original vcf file. Could be either equals or not equals to `PASS` : `filter = PASS`
              or `filter != pass`.\n
          * `id` is a string value that corresponds to the `ID` column. Multiple values could be added via a comma. Expression `id = rs3214,rg1234` is equivalent
              to `id = rs3214 or id = rg1234`.\n
          * `region` corresponds to CHROM and POS columns. Supports querying by the whole chromosome `region = chr1` , by interval within a chromosome
              `region = chr1:4567-9876543` by exact position `region = chr1:456789` or by indefinite ranges like `region = x:3456789-*` . Multiple regions could be
              separated via comma, e.g. `region = chr1:34567-98767,chr3` is equivalent to  `region = chr1:34567-98767 or region = chr3`.\n
          * `feature` is the name of the reference gene associated with a specific location in the reference genome which corresponds to the VCF file (variant group) from which the variant information is derived.
              By providing the gene name(s), such as `feature=TP53` or `feature=TP53,TGFB`, variants located within the same genomic region as the specified gene(s) will be retrieved.\n
          * Filter by vcf `INFO` fields. E.g. to filter all variants annotated in dbSNP add `exists(INFO.KEY)`. Use `!exists(INFO.KEY)` to exclude variants having the key from the search results.
              Provide `info.key=value` pair to search for an exact match or `info.key!=value` to exclude it from the search. Due to the limits of precision in floating point numbers,
              we use a small range of 0.0000001 to identify close matches. This means any differences smaller than that won't be detected. For more precise results, please use range queries."
          in: query
          name: vxQuery
          schema:
            type: string
        - description: Accession of the variant group object (VCF)
          in: query
          name: groupAccession
          required: true
          schema:
            type: string
      responses:
        "200":
          content:
            text/tab-separated-values:
              schema:
                $ref: "#/components/schemas/StreamingOutput"
          description: Stream of retrieved Variant data.
        "400":
          content: { }
          description: Invalid data in request. See error message for details.
        "401":
          content: { }
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "500":
          content: { }
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
        - Access-token: [ ]
        - Genestack-API-Token: [ ]
      summary: Stream data from a given VCF file
      tags:
        - Omics queries as User
  /api/v1/as-user/omics/cells/analytics/cell-ratio:
    post:
      operationId: cellRatioAsUser
      summary: "[BETA] Compute cell ratio statistics across groups or metadata attributes in single-cell data."
      tags:
        - "[BETA] Analytics omics queries as User"
      description: |+
        This endpoint calculates cell ratio statistics based on single-cell metadata.

        It allows quantifying the proportion of cells that meet specific criteria (`countSelected`, e.g. expression threshold, cell type, or cluster)
        relative to a defined reference group or the total cell population (`countAvailable`) defined by study, samples, library, or preparation metadata.

        `countAvailable` parameter returns all cells specified in study, sample, library, or preparation queries and filters.
        In case `exQuery` is selected, only cells linked to cell expression will be counted in `countSelected` parameter.

        The endpoint supports filtering by study, sample, library, or preparation metadata and filtering by cell expression or cell metadata fields.

        Request and response parameters are subject to change as this feature is in BETA.
      requestBody:
        content:
          application/json:
            schema:
              $ref: "#/components/schemas/CRRequest"
        required: true
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/CRResponse"
          description: Cell ratio result
        "400":
          content: { }
          description: Entities cannot be retrieved.
        "401":
          content: { }
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "500":
          content: { }
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
        - Access-token: [ ]
        - Genestack-API-Token: [ ]
  /api/v1/as-user/omics/cells/analytics/differential-expression:
    post:
      operationId: differentialExpressionAsUser
      summary: "[BETA] Perform differential gene expression analytics between case and control cell groups"
      tags:
        - "[BETA] Analytics omics queries as User"
      # The descriptions below are also duplicated in the schema description, make sure to keep them in sync.
      description: |+
        This endpoint computes differential gene expression between two specified cell groups (case vs control) within single-cell data.

        Consult `/omics` search endpoints to find description of parameters within the cell groups.
        The response includes per-gene metrics that characterize expression differences between the two groups:
        - `Gene name` - gene identifier.
        - `Case cell count` - number of cells expressing the gene in the case group.
        - `Control cell count` - number of cells expressing the gene in the control group.
        - `Average expression (case)` - mean expression level across case cells.
        - `Average expression (control)` - mean expression level across control cells.
        - `Expression difference` - numerical difference between average expressions.
        - `Fold change` - ratio of average expressions between case and control groups.
        - `U statistic` - Mann–Whitney U test statistic that measures the difference between Case and Control groups.
        - `p-value` - the probability of observing results as extreme as (or more extreme than) those obtained, assuming that the null hypothesis is true.

        Results are sorted by absolute value of fold change in descending order, allowing easy identification of the most differentially expressed genes.

        Request and response parameters are subject to change as this feature is in BETA.
      requestBody:
        content:
          application/json:
            schema:
              $ref: "#/components/schemas/DERequest"
        required: true
      responses:
        "200":
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/DEResponse"
          description: Differential expression result
        "400":
          content: { }
          description: Entities cannot be retrieved.
        "401":
          content: { }
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "500":
          content: { }
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
        - Access-token: [ ]
        - Genestack-API-Token: [ ]
  /api/v1/as-user/omics/cells/analytics/gene-summary:
    post:
      operationId: geneSummaryAsUser
      summary: "[BETA] Compute and retrieve descriptive statistics and visual summaries for single-cell data."
      tags:
        - "[BETA] Analytics omics queries as User"
      description: |+
        This endpoint provides descriptive statistical metrics for gene expression across single-cell datasets.
        It aggregates and summarizes expression data for each gene to help assess variability, distribution,
        and intensity of expression within the population of cells.

        The computed metrics include:
          - `Gene name` - gene identifier.
          - `Cell count` - number of cells with measurable expression for each gene.
          - `Mean expression value`
          - `Median expression value`
          - `Quantiles` - configurable expression percentiles.
          - `Histogram (density)` - binned distribution of expression levels for visualization.
          - `Standard deviation` - dispersion of expression values.
          - `Minimum and maximum values` - range of expression across cells.

        Results are sorted by gene name.

        Request and response parameters are subject to change as this feature is in BETA.
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: "#/components/schemas/GSRequest"
      responses:
        "200":
          description: Gene summary result
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/GSResponse"
        "400":
          content: { }
          description: Invalid data in the request. See the error message for details.
        "401":
          content: { }
          description: |+
            User is not authenticated. Please supply a valid Access Token in the `Authorization`
            HTTP header (e.g. Authorization: bearer [token]) or  Genestack API token in the `Genestack-API-Token`
            header (this token may be obtained from the Genestack UI _Profile_ page).
        "500":
          content: { }
          description: |+
            An internal server error occurred. This indicates an unexpected
            failure in the Genestack system, please file a bug report to support@genestack.com,
            including the error details."
      security:
        - Access-token: [ ]
        - Genestack-API-Token: [ ]
  /api/v1/as-user/integration/link/files/by/study/{id}:
    get:
      operationId: getFilesByStudyAsUser
      parameters:
        - description: Unique identifier (accession) of the object.
          in: path
          name: id
          required: true
          schema:
            type: string
        - description: Select `true` in order to include file structure (contents) for .h5, .h5ad, .zip, .gz to the response.
          in: query
          name: includeContents
          required: false
          schema:
            default: false
            type: boolean
      responses:
        "200":
          content:
            application/json:
              schema:
                items:
                  $ref: "#/components/schemas/AFile"
                type: array
            text/tab-separated-values:
              schema:
                items:
                  $ref: "#/components/schemas/AFile"
                type: array
          description: The request was successful. The returned value is a list of objects.
        "400":
          content: { }
          description: Invalid data in the request. See the error message for details.
        "401":
          content: { }
          description: |-
            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
        "404":
          content: { }
          description: Object with provided accession could not be found in ODM.
        "500":
          content: { }
          description: "An internal server error occurred. This indicates an unexpected\
            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
            \ including the error details."
      security:
        - Access-token: [ ]
        - Genestack-API-Token: [ ]
      summary: Retrieve file's metadata by study ID
      tags:
        - Files integration as User
components:
  schemas:
    BatchOfIds:
      $ref: "./schemas/integration/BatchOfIds.yaml"
    DataItem:
      $ref: "./schemas/integration/DataItem.yaml"
    DataPresentation:
      $ref: "./schemas/integration/DataPresentation.yaml"
    IMetadata:
      $ref: "./schemas/integration/IMetadata.yaml"
    IntegrationHelper:
      $ref: "./schemas/common/IntegrationHelper.yaml"
    Library:
      $ref: "./schemas/library/Library.yaml"
    ListResponse:
      $ref: "./schemas/common/ListResponse.yaml"
    MetaResponse:
      $ref: "./schemas/common/MetaResponse.yaml"
    MetadataContent:
      $ref: "./schemas/common/MetadataContent.yaml"
    MetadataPresentation:
      $ref: "./schemas/integration/MetadataPresentation.yaml"
    MetadataWithId:
      $ref: "./schemas/common/MetadataWithId.yaml"
    OmicsResponse:
      $ref: "./schemas/integration/OmicsResponse.yaml"
    OmicsResponseDataPresentation:
      $ref: "./schemas/integration/OmicsResponseDataPresentation.yaml"
    OmicsResponseMetadataPresentation:
      $ref: "./schemas/integration/OmicsResponseMetadataPresentation.yaml"
    OmicsResponseMetadataWithId:
      $ref: "./schemas/integration/OmicsResponseMetadataWithId.yaml"
    PaginationInfo:
      $ref: "./schemas/common/PaginationInfo.yaml"
    Preparation:
      $ref: "./schemas/preparation/Preparation.yaml"
    Relationships:
      $ref: "./schemas/integration/Relationships.yaml"
    SourceTypePair:
      $ref: "./schemas/integration/SourceTypePair.yaml"
    StreamingOutput:
      $ref: "./schemas/integration/StreamingOutput.yaml"
    Study:
      $ref: "./schemas/study/Study.yaml"
    SearchStudyRequest:
      $ref: "./schemas/integration/SearchStudyRequest.yaml"
    AppliedFilter:
      $ref: "./schemas/integration/AppliedFilter.yaml"
    PageRequest:
      $ref: "./schemas/integration/PageRequest.yaml"
    FindObjectsResponse:
      $ref: "./schemas/integration/FindObjectsResponse.yaml"
    ObjectsPage:
      $ref: "./schemas/integration/ObjectsPage.yaml"
    StudySearchInfo:
      $ref: "./schemas/integration/StudySearchInfo.yaml"
    ResponseFormat:
      $ref: "./schemas/common/ResponseFormat.yaml"
    MetainfoKeyForSummary:
      $ref: "./schemas/integration/MetainfoKeyForSummary.yaml"
    FilterOptionGroup:
      $ref: "./schemas/integration/FilterOptionGroup.yaml"
    FilterOption:
      $ref: "./schemas/integration/FilterOption.yaml"
    AFile:
      $ref: "./schemas/afile/AFile.yaml"
    DERequest:
      $ref: "./schemas/cell/DERequest.yaml"
    DEResponse:
      $ref: "./schemas/cell/DEResponse.yaml"
    GSRequest:
      $ref: "./schemas/cell/GSRequest.yaml"
    GSResponse:
      $ref: "./schemas/cell/GSResponse.yaml"
    CRRequest:
      $ref: "./schemas/cell/CRRequest.yaml"
    CRResponse:
      $ref: "./schemas/cell/CRResponse.yaml"
  securitySchemes:
    Access-token:
      in: header
      name: Authorization
      type: apiKey
    Genestack-API-Token:
      in: header
      name: Genestack-API-Token
      type: apiKey