openapi: 3.0.3
info:
  title: Girder REST API (Emory Digital Slide Archive) annotation tcga API
  version: 3.2.14
  description: OpenAPI 3.0 conversion of the Girder REST API powering the Emory Digital Slide Archive (computablebrain). Converted faithfully from the live Swagger 2.0 document at https://computablebrain.emory.edu/api/v1/describe.
  license:
    name: Apache-2.0
    url: https://www.apache.org/licenses/LICENSE-2.0.txt
servers:
- url: https://computablebrain.emory.edu/api/v1
tags:
- description: tcga resource
  name: tcga
paths:
  /tcga:
    delete:
      operationId: tcga_deleteCollection_delete_tcga
      responses:
        '200':
          description: Success
        '400':
          description: A parameter was invalid.
      summary: Remove the TCGA collection
      tags:
      - tcga
      parameters: []
    get:
      operationId: tcga_getCollection_tcga
      responses:
        '200':
          description: Success
        '400':
          description: A parameter was invalid.
      summary: Get the TCGA collection
      tags:
      - tcga
      parameters: []
    post:
      operationId: tcga_setCollection_post_tcga
      parameters:
      - name: collectionId
        in: query
        required: true
        description: The id of the collection
        schema:
          type: string
      responses:
        '200':
          description: Success
        '400':
          description: A parameter was invalid.
      summary: Set the TCGA collection
      tags:
      - tcga
  /tcga/aperio:
    post:
      operationId: tcga_importTCGADocument_post_aperio
      parameters:
      - name: id
        in: query
        required: true
        description: The id of the item or root to import
        schema:
          type: string
      - name: tag
        in: query
        required: false
        description: Import annotations with this tag
        schema:
          type: string
      - name: recursive
        in: query
        required: false
        description: Perform a recursive search for annotations
        schema:
          type: boolean
      responses:
        '200':
          description: Success
        '400':
          description: A parameter was invalid.
      summary: Import an item as an Aperio annotation
      tags:
      - tcga
  /tcga/case:
    get:
      operationId: tcga_findCase_case
      parameters:
      - name: cohort
        in: query
        required: true
        description: The id of the cohort document
        schema:
          type: string
      - name: limit
        in: query
        required: false
        description: Result set size limit.
        schema:
          type: integer
          format: int32
          default: 50
      - name: offset
        in: query
        required: false
        description: Offset into result set.
        schema:
          type: integer
          format: int32
          default: 0
      - name: sort
        in: query
        required: false
        description: Field to sort the result set by.
        schema:
          type: string
          default: name
      - name: sortdir
        in: query
        required: false
        description: 'Sort order: 1 for ascending, -1 for descending.'
        schema:
          type: integer
          format: int32
          enum:
          - 1
          - -1
          default: 1
      responses:
        '200':
          description: Success
        '400':
          description: A parameter was invalid.
      summary: List cases in the TCGA dataset
      tags:
      - tcga
    post:
      operationId: tcga_importCase_post_case
      parameters:
      - name: folderId
        in: query
        required: true
        description: The id of the folder to import
        schema:
          type: string
      responses:
        '200':
          description: Success
        '400':
          description: A parameter was invalid.
      summary: Import a folder as a TCGA case
      tags:
      - tcga
  /tcga/case/label/{label}:
    get:
      operationId: tcga_getCaseByLabel_case_label_label
      parameters:
      - name: label
        in: path
        required: true
        description: The label of the case
        schema:
          type: string
      responses:
        '200':
          description: Success
        '400':
          description: Label was invalid
      summary: Get a case document from a label
      tags:
      - tcga
  /tcga/case/search:
    get:
      description: Only one of "value" or "substring" may be provided.
      operationId: tcga_searchCase_case_search
      parameters:
      - name: table
        in: query
        required: true
        description: A table to search
        schema:
          type: string
      - name: key
        in: query
        required: false
        description: A key that should be present
        schema:
          type: string
      - name: value
        in: query
        required: false
        description: The value associated with the given key
        schema:
          type: string
      - name: substring
        in: query
        required: false
        description: Find values containing this substring
        schema:
          type: string
      - name: limit
        in: query
        required: false
        description: Result set size limit.
        schema:
          type: integer
          format: int32
          default: 50
      - name: offset
        in: query
        required: false
        description: Offset into result set.
        schema:
          type: integer
          format: int32
          default: 0
      - name: sort
        in: query
        required: false
        description: Field to sort the result set by.
        schema:
          type: string
          default: name
      - name: sortdir
        in: query
        required: false
        description: 'Sort order: 1 for ascending, -1 for descending.'
        schema:
          type: integer
          format: int32
          enum:
          - 1
          - -1
          default: 1
      responses:
        '200':
          description: Success
        '400':
          description: A parameter was invalid.
      summary: Search for cases by clinical data
      tags:
      - tcga
  /tcga/case/{id}:
    delete:
      operationId: tcga_deleteCase_delete_case_id
      parameters:
      - name: id
        in: path
        required: true
        description: The id of the case
        schema:
          type: string
      responses:
        '200':
          description: Success
        '400':
          description: A parameter was invalid.
      summary: Remove a case document
      tags:
      - tcga
    get:
      operationId: tcga_getCase_case_id
      parameters:
      - name: id
        in: path
        required: true
        description: The id of the case
        schema:
          type: string
      responses:
        '200':
          description: Success
        '400':
          description: A parameter was invalid.
      summary: Get a case document from an id
      tags:
      - tcga
  /tcga/case/{id}/images:
    get:
      operationId: tcga_listCaseImages_case_id_images
      parameters:
      - name: id
        in: path
        required: true
        description: The id of the case
        schema:
          type: string
      - name: limit
        in: query
        required: false
        description: Result set size limit.
        schema:
          type: integer
          format: int32
          default: 50
      - name: offset
        in: query
        required: false
        description: Offset into result set.
        schema:
          type: integer
          format: int32
          default: 0
      - name: sort
        in: query
        required: false
        description: Field to sort the result set by.
        schema:
          type: string
          default: name
      - name: sortdir
        in: query
        required: false
        description: 'Sort order: 1 for ascending, -1 for descending.'
        schema:
          type: integer
          format: int32
          enum:
          - 1
          - -1
          default: 1
      responses:
        '200':
          description: Success
        '400':
          description: A parameter was invalid.
      summary: List images under a case
      tags:
      - tcga
  /tcga/case/{id}/metadata/tables:
    get:
      operationId: tcga_listCaseTables_case_id_metadata_tables
      parameters:
      - name: id
        in: path
        required: true
        description: The id of the case
        schema:
          type: string
      responses:
        '200':
          description: Success
        '400':
          description: A parameter was invalid.
      summary: List tables present inside case metadata
      tags:
      - tcga
  /tcga/case/{id}/metadata/{table}:
    delete:
      operationId: tcga_deleteCaseMetadata_delete_case_id_metadata_table
      parameters:
      - name: id
        in: path
        required: true
        description: The id of the case
        schema:
          type: string
      - name: table
        in: path
        required: true
        description: The table to remove
        schema:
          type: string
      responses:
        '200':
          description: Success
        '400':
          description: A parameter was invalid.
      summary: Delete case metadata
      tags:
      - tcga
    get:
      operationId: tcga_getCaseMetadata_case_id_metadata_table
      parameters:
      - name: id
        in: path
        required: true
        description: The id of the case
        schema:
          type: string
      - name: table
        in: path
        required: true
        description: The table name to get
        schema:
          type: string
      responses:
        '200':
          description: Success
        '400':
          description: A parameter was invalid.
      summary: Get case metadata
      tags:
      - tcga
    post:
      operationId: tcga_setCaseMetadata_post_case_id_metadata_table
      parameters:
      - name: id
        in: path
        required: true
        description: The id of the case
        schema:
          type: string
      - name: table
        in: path
        required: true
        description: The table to update
        schema:
          type: string
      responses:
        '200':
          description: Success
        '400':
          description: A parameter was invalid.
      summary: Create or replace case metadata
      tags:
      - tcga
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/string'
        required: true
        description: A JSON object containing the metadata to create
    put:
      description: Set metadata fields to null to delete them.
      operationId: tcga_updateCaseMetadata_put_case_id_metadata_table
      parameters:
      - name: id
        in: path
        required: true
        description: The id of the case
        schema:
          type: string
      - name: table
        in: path
        required: true
        description: The table to update
        schema:
          type: string
      responses:
        '200':
          description: Success
        '400':
          description: A parameter was invalid.
      summary: Update case metadata
      tags:
      - tcga
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/string'
        required: true
        description: A JSON object containing the metadata to update
  /tcga/cohort:
    get:
      operationId: tcga_findCohort_cohort
      parameters:
      - name: limit
        in: query
        required: false
        description: Result set size limit.
        schema:
          type: integer
          format: int32
          default: 50
      - name: offset
        in: query
        required: false
        description: Offset into result set.
        schema:
          type: integer
          format: int32
          default: 0
      - name: sort
        in: query
        required: false
        description: Field to sort the result set by.
        schema:
          type: string
          default: name
      - name: sortdir
        in: query
        required: false
        description: 'Sort order: 1 for ascending, -1 for descending.'
        schema:
          type: integer
          format: int32
          enum:
          - 1
          - -1
          default: 1
      responses:
        '200':
          description: Success
        '400':
          description: A parameter was invalid.
      summary: List cohorts in the TCGA dataset
      tags:
      - tcga
    post:
      operationId: tcga_importCohort_post_cohort
      parameters:
      - name: folderId
        in: query
        required: true
        description: The id of the folder to import
        schema:
          type: string
      responses:
        '200':
          description: Success
        '400':
          description: A parameter was invalid.
      summary: Import a folder as a TCGA cohort type
      tags:
      - tcga
  /tcga/cohort/{id}:
    delete:
      operationId: tcga_deleteCohort_delete_cohort_id
      parameters:
      - name: id
        in: path
        required: true
        description: The id of the cohort
        schema:
          type: string
      responses:
        '200':
          description: Success
        '400':
          description: A parameter was invalid.
      summary: Remove a cohort type
      tags:
      - tcga
    get:
      operationId: tcga_getCohort_cohort_id
      parameters:
      - name: id
        in: path
        required: true
        description: The id of the cohort
        schema:
          type: string
      responses:
        '200':
          description: Success
        '400':
          description: A parameter was invalid.
      summary: Get a cohort document from an id
      tags:
      - tcga
  /tcga/cohort/{id}/images:
    get:
      operationId: tcga_cohortListImages_cohort_id_images
      parameters:
      - name: id
        in: path
        required: true
        description: The id of the cohort
        schema:
          type: string
      - name: limit
        in: query
        required: false
        description: Result set size limit.
        schema:
          type: integer
          format: int32
          default: 50
      - name: offset
        in: query
        required: false
        description: Offset into result set.
        schema:
          type: integer
          format: int32
          default: 0
      - name: sort
        in: query
        required: false
        description: Field to sort the result set by.
        schema:
          type: string
          default: name
      - name: sortdir
        in: query
        required: false
        description: 'Sort order: 1 for ascending, -1 for descending.'
        schema:
          type: integer
          format: int32
          enum:
          - 1
          - -1
          default: 1
      responses:
        '200':
          description: Success
        '400':
          description: A parameter was invalid.
      summary: List slide images in a cohort
      tags:
      - tcga
  /tcga/cohort/{id}/slides:
    get:
      operationId: tcga_cohortListSlides_cohort_id_slides
      parameters:
      - name: id
        in: path
        required: true
        description: The id of the cohort
        schema:
          type: string
      - name: limit
        in: query
        required: false
        description: Result set size limit.
        schema:
          type: integer
          format: int32
          default: 50
      - name: offset
        in: query
        required: false
        description: Offset into result set.
        schema:
          type: integer
          format: int32
          default: 0
      - name: sort
        in: query
        required: false
        description: Field to sort the result set by.
        schema:
          type: string
          default: name
      - name: sortdir
        in: query
        required: false
        description: 'Sort order: 1 for ascending, -1 for descending.'
        schema:
          type: integer
          format: int32
          enum:
          - 1
          - -1
          default: 1
      responses:
        '200':
          description: Success
        '400':
          description: A parameter was invalid.
      summary: List slides in a cohort
      tags:
      - tcga
  /tcga/image:
    get:
      operationId: tcga_findImage_image
      parameters:
      - name: slide
        in: query
        required: false
        description: The id of slide document
        schema:
          type: string
      - name: caseName
        in: query
        required: false
        description: The name of the case
        schema:
          type: string
      - name: limit
        in: query
        required: false
        description: Result set size limit.
        schema:
          type: integer
          format: int32
          default: 50
      - name: offset
        in: query
        required: false
        description: Offset into result set.
        schema:
          type: integer
          format: int32
          default: 0
      - name: sort
        in: query
        required: false
        description: Field to sort the result set by.
        schema:
          type: string
          default: name
      - name: sortdir
        in: query
        required: false
        description: 'Sort order: 1 for ascending, -1 for descending.'
        schema:
          type: integer
          format: int32
          enum:
          - 1
          - -1
          default: 1
      responses:
        '200':
          description: Success
        '400':
          description: A parameter was invalid.
      summary: Find images
      tags:
      - tcga
    post:
      operationId: tcga_importImage_post_image
      parameters:
      - name: itemId
        in: query
        required: true
        description: The id of the item to import
        schema:
          type: string
      responses:
        '200':
          description: Success
        '400':
          description: A parameter was invalid.
      summary: Import an item as a TCGA slide image
      tags:
      - tcga
  /tcga/image/{id}:
    delete:
      operationId: tcga_deleteImage_delete_image_id
      parameters:
      - name: id
        in: path
        required: true
        description: The id of the image
        schema:
          type: string
      responses:
        '200':
          description: Success
        '400':
          description: A parameter was invalid.
      summary: Remove an image
      tags:
      - tcga
    get:
      operationId: tcga_getImage_image_id
      parameters:
      - name: id
        in: path
        required: true
        description: The id of the image
        schema:
          type: string
      responses:
        '200':
          description: Success
        '400':
          description: A parameter was invalid.
      summary: Get an image document by id
      tags:
      - tcga
  /tcga/import:
    post:
      description: This will run as a local job that will execute asynchronously.
      operationId: tcga_importCollection_post_import
      responses:
        '200':
          description: Success
        '400':
          description: A parameter was invalid.
      summary: Recursively import the TCGA collection
      tags:
      - tcga
      parameters: []
  /tcga/pathology:
    get:
      operationId: tcga_findPathology_pathology
      parameters:
      - name: case
        in: query
        required: true
        description: The id of a case document
        schema:
          type: string
      - name: limit
        in: query
        required: false
        description: Result set size limit.
        schema:
          type: integer
          format: int32
          default: 50
      - name: offset
        in: query
        required: false
        description: Offset into result set.
        schema:
          type: integer
          format: int32
          default: 0
      - name: sort
        in: query
        required: false
        description: Field to sort the result set by.
        schema:
          type: string
          default: name
      - name: sortdir
        in: query
        required: false
        description: 'Sort order: 1 for ascending, -1 for descending.'
        schema:
          type: integer
          format: int32
          enum:
          - 1
          - -1
          default: 1
      responses:
        '200':
          description: Success
        '400':
          description: A parameter was invalid.
      summary: Find pathologies for a case
      tags:
      - tcga
    post:
      operationId: tcga_importPathology_post_pathology
      parameters:
      - name: id
        in: query
        required: true
        description: The id of the item to import
        schema:
          type: string
      - name: recursive
        in: query
        required: false
        description: Perform a recursive search for pathologies
        schema:
          type: boolean
      responses:
        '200':
          description: Success
        '400':
          description: A parameter was invalid.
      summary: Import an item as a TCGA pathology
      tags:
      - tcga
  /tcga/pathology/{id}:
    delete:
      operationId: tcga_deletePathology_delete_pathology_id
      parameters:
      - name: id
        in: path
        required: true
        description: The id of the pathology
        schema:
          type: string
      responses:
        '200':
          description: Success
        '400':
          description: A parameter was invalid.
      summary: Remove a pathology
      tags:
      - tcga
    get:
      operationId: tcga_getPathology_pathology_id
      parameters:
      - name: id
        in: path
        required: true
        description: The id of the pathology
        schema:
          type: string
      responses:
        '200':
          description: Success
        '400':
          description: A parameter was invalid.
      summary: Get a pathology document by id
      tags:
      - tcga
  /tcga/slide:
    get:
      operationId: tcga_findSlide_slide
      parameters:
      - name: case
        in: query
        required: true
        description: The id of case document
        schema:
          type: string
      - name: limit
        in: query
        required: false
        description: Result set size limit.
        schema:
          type: integer
          format: int32
          default: 50
      - name: offset
        in: query
        required: false
        description: Offset into result set.
        schema:
          type: integer
          format: int32
          default: 0
      - name: sort
        in: query
        required: false
        description: Field to sort the result set by.
        schema:
          type: string
          default: name
      - name: sortdir
        in: query
        required: false
        description: 'Sort order: 1 for ascending, -1 for descending.'
        schema:
          type: integer
          format: int32
          enum:
          - 1
          - -1
          default: 1
      responses:
        '200':
          description: Success
        '400':
          description: A parameter was invalid.
      summary: Find slides for a case
      tags:
      - tcga
    post:
      operationId: tcga_importSlide_post_slide
      parameters:
      - name: folderId
        in: query
        required: true
        description: The id of the folder to import
        schema:
          type: string
      responses:
        '200':
          description: Success
        '400':
          description: A parameter was invalid.
      summary: Import a folder as a TCGA slide
      tags:
      - tcga
  /tcga/slide/{id}:
    delete:
      operationId: tcga_deleteSlide_delete_slide_id
      parameters:
      - name: id
        in: path
        required: true
        description: The id of the slide
        schema:
          type: string
      responses:
        '200':
          description: Success
        '400':
          description: A parameter was invalid.
      summary: Remove a slide
      tags:
      - tcga
    get:
      operationId: tcga_getSlide_slide_id
      parameters:
      - name: id
        in: path
        required: true
        description: The id of the slide
        schema:
          type: string
      responses:
        '200':
          description: Success
        '400':
          description: A parameter was invalid.
      summary: Get a slide document by id
      tags:
      - tcga
components:
  schemas:
    string:
      type: string
  securitySchemes:
    Girder-Token:
      in: header
      name: Girder-Token
      type: apiKey