openapi: 3.0.0
info:
  contact:
    email: cdis@uchicago.edu
  description: A data submission API for CDIS Gen 3 data commons. Code is available
    on [GitHub](https://github.com/uc-cdis/sheepdog).
  license:
    name: Apache 2.0
    url: http://www.apache.org/licenses/LICENSE-2.0.html
  termsOfService: http://cdis.uchicago.edu/terms/
  title: Sheepdog OpenAPI Specification
  version: '1.0'
servers:
- url: /
paths:
  /_status:
    get:
      responses:
        '200':
          description: Healthy
        default:
          description: Unhealthy
      summary: Health check endpoint
      tags:
      - system
  /_version:
    get:
      responses:
        '200':
          description: successful operation
      summary: Returns the version of Sheepdog
      tags:
      - system
  /v0/submission/:
    get:
      description: Return the available resources at the top level above programs
        i.e. registered programs.
      responses:
        '200':
          description: Success
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/schema_links'
        '403':
          description: Unauthorized request.
      summary: Get the programs
      tags:
      - program
    patch:
      description: Register a program. The content of the request is a JSON containing
        the information describing a program.  Authorization for registering programs
        is limited to administrative users.
      responses:
        '200':
          description: Registered successfully.
        '403':
          description: Unauthorized request.
      summary: Create a program
      tags:
      - program
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/schema_program'
        description: input body
    post:
      description: Register a program. The content of the request is a JSON containing
        the information describing a program.  Authorization for registering programs
        is limited to administrative users.
      responses:
        '200':
          description: Registered successfully.
        '403':
          description: Unauthorized request.
      summary: Create a program
      tags:
      - program
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/schema_program'
        description: input body
    put:
      description: Register a program. The content of the request is a JSON containing
        the information describing a program.  Authorization for registering programs
        is limited to administrative users.
      responses:
        '200':
          description: Registered successfully.
        '403':
          description: Unauthorized request.
      summary: Create a program
      tags:
      - program
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/schema_program'
        description: input body
  /v0/submission/<program>:
    delete:
      description: Delete a program given program name. If the program is not empty
        raise an appropriate exception
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      responses:
        '204':
          description: Success.
        '400':
          description: User error.
        '403':
          description: Unauthorized request.
        '404':
          description: Program not found.
      summary: Delete a program
      tags:
      - program
    get:
      description: Return the available resources at the top level of program ``program``,
        i.e. registered projects.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      responses:
        '200':
          description: Success
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/schema_links'
        '403':
          description: Unauthorized request.
        '404':
          description: Program not found.
      summary: Get the projects
      tags:
      - project
    patch:
      description: Register a project. The content of the request is a JSON containing
        the information describing a project. Authorization for registering projects
        is limited to administrative users.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      responses:
        '200':
          description: Registered successfully.
        '400':
          description: User error.
        '403':
          description: Unauthorized request.
        '404':
          description: Program not found.
      summary: Create a project
      tags:
      - project
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/schema_project'
        description: input body
    post:
      description: Register a project. The content of the request is a JSON containing
        the information describing a project. Authorization for registering projects
        is limited to administrative users.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      responses:
        '200':
          description: Registered successfully.
        '400':
          description: User error.
        '403':
          description: Unauthorized request.
        '404':
          description: Program not found.
      summary: Create a project
      tags:
      - project
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/schema_project'
        description: input body
    put:
      description: Register a project. The content of the request is a JSON containing
        the information describing a project. Authorization for registering projects
        is limited to administrative users.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      responses:
        '200':
          description: Registered successfully.
        '400':
          description: User error.
        '403':
          description: Unauthorized request.
        '404':
          description: Program not found.
      summary: Create a project
      tags:
      - project
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/schema_project'
        description: input body
  /v0/submission/<program>/<project>:
    delete:
      description: Delete project under a specific program
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      responses:
        '204':
          description: Success.
        '400':
          description: User error.
        '403':
          description: Unauthorized request.
        '404':
          description: Resource not found.
      summary: Delete a project
      tags:
      - project
    post:
      description: Create or update any valid entities specified in the request body.
        To associate an entity with an existing, already indexed data file, specify
        the `object_id` in the body of the entity.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      - description: application/json (default), text/tab-separated-values, text/tsv
          or text/csv
        in: header
        name: Content-Type
        schema:
          type: string
      responses:
        '201':
          description: Entities created successfully
        '400':
          description: At least one entity was invalid.
        '404':
          description: Resource not found.
      summary: Create entities
      tags:
      - entity
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/schema_entity'
        description: input body
    put:
      description: Create or update any valid entities specified in the request body.
        To associate an entity with an existing, already indexed data file, specify
        the `object_id` in the body of the entity.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      - description: application/json (default), text/tab-separated-values, text/tsv
          or text/csv
        in: header
        name: Content-Type
        schema:
          type: string
      responses:
        '201':
          description: Entities created successfully
        '400':
          description: At least one entity was invalid.
        '404':
          description: Resource not found.
      summary: Update entities
      tags:
      - entity
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/schema_entity'
        description: input body
  /v0/submission/<program>/<project>/_dictionary:
    get:
      description: Return links to the project level JSON schema definitions.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      responses:
        '200':
          description: Success
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/schema_links'
        '403':
          description: Unauthorized request.
      summary: Get the dictionary schema for entities of a project
      tags:
      - dictionary
  /v0/submission/<program>/<project>/_dictionary/<entry>:
    get:
      description: Get the dictionary entry for a specific project.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      - description: entity type to retrieve the schema for (e.g. ``aliquot``)
        in: path
        name: entry
        required: true
        schema:
          type: string
      responses:
        '200':
          description: Success
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/schema_entity'
        '403':
          description: Unauthorized request.
        '404':
          description: Resource not found.
      summary: Get the dictionary schema for an entity of a project
      tags:
      - dictionary
  /v0/submission/<program>/<project>/_dry_run:
    post:
      description: Create or update any valid entities specified in the request body.
        To associate an entity with an existing, already indexed data file, specify
        the `object_id` in the body of the entity.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      - description: application/json (default), text/tab-separated-values, text/tsv
          or text/csv
        in: header
        name: Content-Type
        schema:
          type: string
      responses:
        '201':
          description: Entities created successfully
        '400':
          description: At least one entity was invalid.
        '404':
          description: Resource not found.
      summary: Create entities
      tags:
      - dry run
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/schema_entity'
        description: input body
    put:
      description: Create or update any valid entities specified in the request body.
        To associate an entity with an existing, already indexed data file, specify
        the `object_id` in the body of the entity.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      - description: application/json (default), text/tab-separated-values, text/tsv
          or text/csv
        in: header
        name: Content-Type
        schema:
          type: string
      responses:
        '201':
          description: Entities created successfully
        '400':
          description: At least one entity was invalid.
        '404':
          description: Resource not found.
      summary: Update entities
      tags:
      - dry run
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/schema_entity'
        description: input body
  /v0/submission/<program>/<project>/bulk:
    post:
      description: Handle bulk transaction instead of single transaction.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      responses:
        '201':
          description: Entities created successfully
        '400':
          description: At least one entity was invalid.
        '404':
          description: Resource not found.
      summary: Create entities in bulk
      tags:
      - entity
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/schema_entity_bulk'
        description: input body
    put:
      description: Handle bulk transaction instead of single transaction.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      responses:
        '201':
          description: Entities created successfully
        '400':
          description: At least one entity was invalid.
        '404':
          description: Resource not found.
      summary: Update entities in bulk
      tags:
      - entity
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/schema_entity_bulk'
        description: input body
  /v0/submission/<program>/<project>/bulk/_dry_run:
    post:
      description: Handle bulk transaction instead of single transaction.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      responses:
        '201':
          description: Entities created successfully
        '400':
          description: At least one entity was invalid.
        '404':
          description: Resource not found.
      summary: Create entities in bulk
      tags:
      - dry run
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/schema_entity_bulk'
        description: input body
    put:
      description: Handle bulk transaction instead of single transaction.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      responses:
        '201':
          description: Entities created successfully
        '400':
          description: At least one entity was invalid.
        '404':
          description: Resource not found.
      summary: Update entities in bulk
      tags:
      - dry run
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/schema_entity_bulk'
        description: input body
  /v0/submission/<program>/<project>/entities/<entity_id_string>:
    get:
      description: Retrieve existing entities by ID. The return type of a HTTP `get`
        on this endpoint is a JSON array containing JSON object elements, each corresponding
        to a provided ID. Return results are unordered. If any ID is not found in
        the database, a status code of 404 is returned with the missing IDs.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      - description: A comma-separated list of ids specifying the entities to retrieve.
        in: path
        name: entity_id_string
        required: true
        schema:
          type: string
      responses:
        '200':
          description: Success.
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/schema_entity_list'
        '400':
          description: User error.
        '403':
          description: Unauthorized request.
        '404':
          description: Entity not found.
      summary: Get entities by ID
      tags:
      - entity
  /v0/submission/<program>/<project>/entities/<ids>:
    delete:
      description: Delete existing entities. Using the :http:method:`delete` on a
        project's endpoint will *completely delete* an entity. The Gen3 commons does
        not allow deletions or creations that would leave nodes without parents, i.e.
        nodes that do not have an entity from which they were derived. To prevent
        catastrophic mistakes, the current philosophy is to disallow automatic cascading
        of deletes. However, to inform a user which entities must be deleted for the
        target entity to be deleted, the API will respond with at least one entity
        that must be deleted prior to deleting the target entity.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      - description: A comma separated list of ids specifying the entities to delete.
          These ids must be official ids.
        in: path
        name: ids
        required: true
        schema:
          type: string
      - description: Set the to_delete sysan as true or false. If none, then don't
          try to set the sysan, and instead delete the node.
        in: query
        name: to_delete
        schema:
          type: boolean
      responses:
        '200':
          description: Entities deleted successfully
        '400':
          description: User error.
        '403':
          description: Unauthorized request.
        '404':
          description: Entity not found.
      summary: Delete entities
      tags:
      - entity
  /v0/submission/<program>/<project>/entities/_dry_run/<ids>:
    delete:
      description: Delete existing entities. Using the :http:method:`delete` on a
        project's endpoint will *completely delete* an entity. The Gen3 commons does
        not allow deletions or creations that would leave nodes without parents, i.e.
        nodes that do not have an entity from which they were derived. To prevent
        catastrophic mistakes, the current philosophy is to disallow automatic cascading
        of deletes. However, to inform a user which entities must be deleted for the
        target entity to be deleted, the API will respond with at least one entity
        that must be deleted prior to deleting the target entity.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      - description: A comma separated list of ids specifying the entities to delete.
          These ids must be official ids.
        in: path
        name: ids
        required: true
        schema:
          type: string
      - description: Set the to_delete sysan as true or false. If none, then don't
          try to set the sysan, and instead delete the node.
        in: query
        name: to_delete
        schema:
          type: boolean
      responses:
        '200':
          description: Entities deleted successfully
        '400':
          description: User error.
        '403':
          description: Unauthorized request.
        '404':
          description: Entity not found.
      summary: Delete entities
      tags:
      - dry run
  /v0/submission/<program>/<project>/export:
    get:
      description: 'Return a file with the requested entities as an attachment. Either
        ``ids`` or ``node_label`` must be provided in the parameters. When both are
        provided, ``node_label`` is ignored and ``ids`` is used. If ``ids`` is provided,
        all entities matching given ``ids`` will be exported. If there is only one
        entity type in the output, it will return a ``{node_type}.tsv`` or ``{node_type}.json``
        file, e.g.: ``aliquot.tsv``. If there are multiple entity types, it returns
        ``gdc_export_{one_time_sha}.tar.gz`` for TSV format, or ``gdc_export_{one_time_sha}.json``
        for JSON format. CSV is similar to TSV. If ``node_label`` is provided, it
        will export all entities of type with name ``node_label`` to a TSV file or
        JSON file. CSV is not supported yet in this case.'
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      - description: one or a list of node IDs seperated by commas.
        in: query
        name: ids
        schema:
          type: string
      - description: type of nodes to look up, for example ``'case'``
        in: query
        name: node_label
        schema:
          type: string
      - description: output format, ``json`` or ``tsv`` or ``csv``; default is ``tsv``
        in: query
        name: format
        schema:
          type: string
      - description: whether to recursively find children or not; default is False
        in: query
        name: with_children
        schema:
          type: string
      - description: 'category of node to filter on children. Example: ``clinical``'
        in: query
        name: category
        schema:
          type: string
      - description: whether to include the ids in the export file; default is False
        in: query
        name: without_id
        schema:
          type: boolean
      responses:
        '200':
          description: Success
        '400':
          description: Bad Request
        '403':
          description: Unauthorized request.
        '404':
          description: No id is found
      summary: Export entities
      tags:
      - export
    post:
      description: 'Return a file with the requested entities as an attachment. Either
        ``ids`` or ``node_label`` must be provided in the parameters. When both are
        provided, ``node_label`` is ignored and ``ids`` is used. If ``ids`` is provided,
        all entities matching given ``ids`` will be exported. If there is only one
        entity type in the output, it will return a ``{node_type}.tsv`` or ``{node_type}.json``
        file, e.g.: ``aliquot.tsv``. If there are multiple entity types, it returns
        ``gdc_export_{one_time_sha}.tar.gz`` for TSV format, or ``gdc_export_{one_time_sha}.json``
        for JSON format. CSV is similar to TSV. If ``node_label`` is provided, it
        will export all entities of type with name ``node_label`` to a TSV file or
        JSON file. CSV is not supported yet in this case.'
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      - description: one or a list of node IDs seperated by commas.
        in: query
        name: ids
        schema:
          type: string
      - description: type of nodes to look up, for example ``'case'``
        in: query
        name: node_label
        schema:
          type: string
      - description: output format, ``json`` or ``tsv`` or ``csv``; default is ``tsv``
        in: query
        name: format
        schema:
          type: string
      - description: whether to recursively find children or not; default is False
        in: query
        name: with_children
        schema:
          type: string
      - description: 'category of node to filter on children. Example: ``clinical``'
        in: query
        name: category
        schema:
          type: string
      - description: whether to include the ids in the export file; default is False
        in: query
        name: without_id
        schema:
          type: boolean
      responses:
        '200':
          description: Success
        '400':
          description: Bad Request
        '403':
          description: Unauthorized request.
        '404':
          description: No id is found
      summary: Export entities
      tags:
      - export
  /v0/submission/<program>/<project>/files/<file_uuid>:
    delete:
      description: Delete molecular data from object storage.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      - description: The id of the file to upload.
        in: path
        name: uuid
        required: true
        schema:
          type: string
      - description: to abort a multipart upload
        in: query
        name: uploadId
        schema:
          type: string
      responses:
        '200':
          description: Success.
        '400':
          description: Bad Request
        '403':
          description: Unauthorized request.
        '404':
          description: File not found.
        '405':
          description: Method Not Allowed.
      summary: Delete a data file
      tags:
      - file
    get:
      description: Get a data file from object storage
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      - description: The id of the file to upload.
        in: path
        name: uuid
        required: true
        schema:
          type: string
      - description: to list parts
        in: query
        name: uploadId
        schema:
          type: string
      responses:
        '200':
          description: Success.
        '400':
          description: Bad Request
        '403':
          description: Unauthorized request.
        '404':
          description: File not found.
        '405':
          description: Method Not Allowed.
      summary: Get a data file
      tags:
      - file
    post:
      description: Upload data by multipart upload
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      - description: The id of the file to upload.
        in: path
        name: uuid
        required: true
        schema:
          type: string
      - description: to initiate multipart upload
        in: query
        name: uploads
        schema:
          type: string
      - description: to complete multipart upload
        in: query
        name: uploadId
        schema:
          type: string
      responses:
        '200':
          description: Success.
        '400':
          description: Bad Request
        '403':
          description: Unauthorized request.
        '404':
          description: File not found.
        '405':
          description: Method Not Allowed.
      summary: Upload data by multipart upload
      tags:
      - file
    put:
      description: Upload data using single PUT. The request body should contain binary
        data of the file.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      - description: The id of the file to upload.
        in: path
        name: uuid
        required: true
        schema:
          type: string
      - description: to upload part (use with uploadId)
        in: query
        name: partNumber
        schema:
          type: string
      - description: to upload part (use with partNumber)
        in: query
        name: uploadId
        schema:
          type: string
      responses:
        '200':
          description: Success.
        '400':
          description: Bad Request
        '403':
          description: Unauthorized request.
        '404':
          description: File not found.
        '405':
          description: Method Not Allowed.
      summary: Upload a data file
      tags:
      - file
  /v0/submission/<program>/<project>/files/<file_uuid>/_dry_run:
    delete:
      description: Delete molecular data from object storage.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      - description: The id of the file to upload.
        in: path
        name: uuid
        required: true
        schema:
          type: string
      - description: to abort a multipart upload
        in: query
        name: uploadId
        schema:
          type: string
      responses:
        '200':
          description: Success.
        '400':
          description: Bad Request
        '403':
          description: Unauthorized request.
        '404':
          description: File not found.
        '405':
          description: Method Not Allowed.
      summary: Delete a data file
      tags:
      - dry run
    get:
      description: Get a data file from object storage
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      - description: The id of the file to upload.
        in: path
        name: uuid
        required: true
        schema:
          type: string
      - description: to list parts
        in: query
        name: uploadId
        schema:
          type: string
      responses:
        '200':
          description: Success.
        '400':
          description: Bad Request
        '403':
          description: Unauthorized request.
        '404':
          description: File not found.
        '405':
          description: Method Not Allowed.
      summary: Get a data file
      tags:
      - dry run
    post:
      description: Upload data by multipart upload
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      - description: The id of the file to upload.
        in: path
        name: uuid
        required: true
        schema:
          type: string
      - description: to initiate multipart upload
        in: query
        name: uploads
        schema:
          type: string
      - description: to complete multipart upload
        in: query
        name: uploadId
        schema:
          type: string
      responses:
        '200':
          description: Success.
        '400':
          description: Bad Request
        '403':
          description: Unauthorized request.
        '404':
          description: File not found.
        '405':
          description: Method Not Allowed.
      summary: Upload data by multipart upload
      tags:
      - dry run
    put:
      description: Upload data using single PUT. The request body should contain binary
        data of the file.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      - description: The id of the file to upload.
        in: path
        name: uuid
        required: true
        schema:
          type: string
      - description: to upload part (use with uploadId)
        in: query
        name: partNumber
        schema:
          type: string
      - description: to upload part (use with partNumber)
        in: query
        name: uploadId
        schema:
          type: string
      responses:
        '200':
          description: Success.
        '400':
          description: Bad Request
        '403':
          description: Unauthorized request.
        '404':
          description: File not found.
        '405':
          description: Method Not Allowed.
      summary: Upload a data file
      tags:
      - dry run
  /v0/submission/<program>/<project>/manifest:
    get:
      description: Create a json manifest of the files.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      responses:
        '200':
          description: Success
        '400':
          description: User error.
        '403':
          description: Unauthorized request.
        '404':
          description: Resource not found.
      summary: Get a manifest of data files
      tags:
      - file
  /v0/submission/<program>/<project>/open:
    post:
      description: Mark a project ``open``. Opening a project means uploads, deletions,
        etc. are allowed.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      responses:
        '200':
          description: Success
        '403':
          description: Unauthorized request.
        '404':
          description: Resource not found.
      summary: Open a project
      tags:
      - project
    put:
      description: Mark a project ``open``. Opening a project means uploads, deletions,
        etc. are allowed.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      responses:
        '200':
          description: Success
        '403':
          description: Unauthorized request.
        '404':
          description: Resource not found.
      summary: Open a project
      tags:
      - project
  /v0/submission/<program>/<project>/open/_dry_run:
    post:
      description: Mark a project ``open``. Opening a project means uploads, deletions,
        etc. are allowed.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      responses:
        '200':
          description: Success
        '403':
          description: Unauthorized request.
        '404':
          description: Resource not found.
      summary: Open a project
      tags:
      - dry run
    put:
      description: Mark a project ``open``. Opening a project means uploads, deletions,
        etc. are allowed.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      responses:
        '200':
          description: Success
        '403':
          description: Unauthorized request.
        '404':
          description: Resource not found.
      summary: Open a project
      tags:
      - dry run
  /v0/submission/<program>/<project>/release:
    post:
      description: Release a project.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      responses:
        '200':
          description: Success
        '403':
          description: Unauthorized request.
        '404':
          description: Resource not found.
      summary: Release a project
      tags:
      - project
    put:
      description: Release a project.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      responses:
        '200':
          description: Success
        '403':
          description: Unauthorized request.
        '404':
          description: Resource not found.
      summary: Release a project
      tags:
      - project
  /v0/submission/<program>/<project>/release/_dry_run:
    post:
      description: Release a project.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      responses:
        '200':
          description: Success
        '403':
          description: Unauthorized request.
        '404':
          description: Resource not found.
      summary: Release a project
      tags:
      - dry run
    put:
      description: Release a project.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      responses:
        '200':
          description: Success
        '403':
          description: Unauthorized request.
        '404':
          description: Resource not found.
      summary: Release a project
      tags:
      - dry run
  /v0/submission/<program>/<project>/review:
    post:
      description: Mark a project project for review. Reviewing a project means uploads
        are locked. An ``open`` or ``submit`` action must be taken after ``review``.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      responses:
        '200':
          description: Success
        '403':
          description: Unauthorized request.
        '404':
          description: Resource not found.
      summary: Review a project
      tags:
      - project
    put:
      description: Mark a project project for review. Reviewing a project means uploads
        are locked. An ``open`` or ``submit`` action must be taken after ``review``.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      responses:
        '200':
          description: Success
        '403':
          description: Unauthorized request.
        '404':
          description: Resource not found.
      summary: Review a project
      tags:
      - project
  /v0/submission/<program>/<project>/review/_dry_run:
    post:
      description: Mark a project project for review. Reviewing a project means uploads
        are locked. An ``open`` or ``submit`` action must be taken after ``review``.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      responses:
        '200':
          description: Success
        '403':
          description: Unauthorized request.
        '404':
          description: Resource not found.
      summary: Review a project
      tags:
      - dry run
    put:
      description: Mark a project project for review. Reviewing a project means uploads
        are locked. An ``open`` or ``submit`` action must be taken after ``review``.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      responses:
        '200':
          description: Success
        '403':
          description: Unauthorized request.
        '404':
          description: Resource not found.
      summary: Review a project
      tags:
      - dry run
  /v0/submission/<program>/<project>/submit:
    post:
      description: Submit a project.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      responses:
        '200':
          description: Project submitted successfully
        '403':
          description: Unauthorized request.
        '404':
          description: Resource not found.
      summary: Submit a project
      tags:
      - project
    put:
      description: Submit a project.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      responses:
        '200':
          description: Project submitted successfully
        '403':
          description: Unauthorized request.
        '404':
          description: Resource not found.
      summary: Submit a project
      tags:
      - project
  /v0/submission/<program>/<project>/submit/_dry_run:
    post:
      description: Submit a project.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      responses:
        '200':
          description: Project submitted successfully
        '403':
          description: Unauthorized request.
        '404':
          description: Resource not found.
      summary: Submit a project
      tags:
      - dry run
    put:
      description: Submit a project.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      responses:
        '200':
          description: Project submitted successfully
        '403':
          description: Unauthorized request.
        '404':
          description: Resource not found.
      summary: Submit a project
      tags:
      - dry run
  /v0/submission/<program>/<project>/template:
    get:
      description: Get templates for all entity types. In the template, Links are
        represented as {link_type}.{link_unique_key} for one_to_one  and many_to_one
        relationships. For many_to_many relationships, they are represented as {link_type}.{link_unique_key}#1
        to infer user the multiplicity
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      - description: output format, ``csv`` or ``tsv``, default is tsv
        in: query
        name: format
        schema:
          type: string
      - description: list of entities' categories to include in the template
        in: query
        name: categories
        schema:
          type: string
      - description: list of entities' categories to exclude from the template
        in: query
        name: exclude
        schema:
          type: string
      responses:
        '200':
          description: Success
        '404':
          description: Resource not found.
      summary: Get templates for all entity types of a project
      tags:
      - dictionary
  /v0/submission/<program>/<project>/template/<entity>:
    get:
      description: Return TSV template of an entity type. In the template, links are
        represented as {link_type}.{link_unique_key} for one_to_one and many_to_one
        relationships. For many_to_many relationships, they are represented as {link_type}.{link_unique_key}#1
        to infer user the multiplicity.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      - description: type of the entity
        in: path
        name: entity
        required: true
        schema:
          type: string
      - description: output format, ``csv`` or ``tsv``, default is tsv
        in: query
        name: format
        schema:
          type: string
      responses:
        '200':
          description: Success
        '404':
          description: Entity type is not found
      summary: Get a template for an entity type of a project
      tags:
      - dictionary
  /v0/submission/<program>/<project>/transactions/<int:transaction_id>/close:
    post:
      description: Close a transaction. The transaction is prevented from being committed
        in the future.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      - description: transaction_id
        in: path
        name: transaction_id
        required: true
        schema:
          type: integer
      responses:
        '200':
          description: Success
        '403':
          description: Unauthorized request.
        '404':
          description: Resource not found.
      summary: Close a transaction
      tags:
      - dry run
    put:
      description: Close a transaction. The transaction is prevented from being committed
        in the future.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      - description: transaction_id
        in: path
        name: transaction_id
        required: true
        schema:
          type: integer
      responses:
        '200':
          description: Success
        '403':
          description: Unauthorized request.
        '404':
          description: Resource not found.
      summary: Close a transaction
      tags:
      - dry run
  /v0/submission/<program>/<project>/transactions/<int:transaction_id>/commit:
    post:
      description: 'Commit a dry run transaction. This call should only succeed if:
        1. transaction_id points to a dry_run transaction; 2. transaction_id points
        to a transaction that hasn''t been committed already; 3. transaction_id points
        to a successful transaction.'
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      - description: transaction_id
        in: path
        name: transaction_id
        required: true
        schema:
          type: integer
      responses:
        '200':
          description: Success.
        '403':
          description: Unauthorized request.
        '404':
          description: Resource not found.
      summary: Commit a dry run transaction
      tags:
      - dry run
    put:
      description: 'Commit a dry run transaction. This call should only succeed if:
        1. transaction_id points to a dry_run transaction; 2. transaction_id points
        to a transaction that hasn''t been committed already; 3. transaction_id points
        to a successful transaction.'
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      - description: transaction_id
        in: path
        name: transaction_id
        required: true
        schema:
          type: integer
      responses:
        '200':
          description: Success.
        '403':
          description: Unauthorized request.
        '404':
          description: Resource not found.
      summary: Commit a dry run transaction
      tags:
      - dry run
  /v0/submission/<program>/<project>/upload_manifest:
    get:
      description: Create a json manifest of the files.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      responses:
        '200':
          description: Success
        '400':
          description: User error.
        '403':
          description: Unauthorized request.
        '404':
          description: Resource not found.
      summary: Get a manifest of data files
      tags:
      - file
  /v0/submission/<program>/<project>/xml/biospecimen/bcr:
    put:
      description: The entities stored in BRC XML are converted to JSON before being
        updated.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      responses:
        '200':
          description: Success.
        '403':
          description: Unauthorized request.
        '404':
          description: Resource not found.
      summary: Update Biospecimen Supplement entities
      tags:
      - entity
      requestBody:
        content:
          multipart/form-data:
            schema:
              type: object
              properties:
                file:
                  type: string
                  format: binary
              required:
              - file
  /v0/submission/<program>/<project>/xml/biospecimen/bcr/_dry_run:
    put:
      description: The entities stored in BRC XML are converted to JSON before being
        updated.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      responses:
        '200':
          description: Success.
        '403':
          description: Unauthorized request.
        '404':
          description: Resource not found.
      summary: Update Biospecimen Supplement entities
      tags:
      - dry run
      requestBody:
        content:
          multipart/form-data:
            schema:
              type: object
              properties:
                file:
                  type: string
                  format: binary
              required:
              - file
  /v0/submission/<program>/<project>/xml/clinical/bcr:
    put:
      description: The entities stored in BRC XML are converted to JSON before being
        updated.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      responses:
        '200':
          description: Success.
        '403':
          description: Unauthorized request.
        '404':
          description: Resource not found.
      summary: Update Clinical Supplement entities
      tags:
      - entity
      requestBody:
        content:
          multipart/form-data:
            schema:
              type: object
              properties:
                file:
                  type: string
                  format: binary
              required:
              - file
  /v0/submission/<program>/<project>/xml/clinical/bcr/_dry_run:
    put:
      description: The entities stored in BRC XML are converted to JSON before being
        updated.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      responses:
        '200':
          description: Success.
        '403':
          description: Unauthorized request.
        '404':
          description: Resource not found.
      summary: Update Clinical Supplement entities
      tags:
      - dry run
      requestBody:
        content:
          multipart/form-data:
            schema:
              type: object
              properties:
                file:
                  type: string
                  format: binary
              required:
              - file
  /v0/submission/_dictionary:
    get:
      description: Return links to the JSON schema definitions.
      responses:
        '200':
          description: Success
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/schema_links'
        '403':
          description: Unauthorized request.
      summary: Get the dictionary schema
      tags:
      - dictionary
  /v0/submission/_dictionary/<entry>:
    get:
      description: Return the project level JSON schema definition for a given entity
        type.
      parameters:
      - description: entity type to retrieve the schema for (e.g. ``aliquot``)
        in: path
        name: entry
        required: true
        schema:
          type: string
      responses:
        '200':
          description: Success
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/schema_entity'
        '403':
          description: Unauthorized request.
        '404':
          description: Resource not found.
      summary: Get the dictionary schema for an entity
      tags:
      - dictionary
  /v0/submission/admin/<program>/<project>/entities/<ids>/to_delete/<to_delete>:
    delete:
      description: Delete existing entities. Using the :http:method:`delete` on a
        project's endpoint will *completely delete* an entity. The Gen3 commons does
        not allow deletions or creations that would leave nodes without parents, i.e.
        nodes that do not have an entity from which they were derived. To prevent
        catastrophic mistakes, the current philosophy is to disallow automatic cascading
        of deletes. However, to inform a user which entities must be deleted for the
        target entity to be deleted, the API will respond with at least one entity
        that must be deleted prior to deleting the target entity.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      - description: A comma separated list of ids specifying the entities to delete.
          These ids must be official ids.
        in: path
        name: ids
        required: true
        schema:
          type: string
      - description: Set the to_delete sysan as true or false. If none, then don't
          try to set the sysan, and instead delete the node.
        in: query
        name: to_delete
        schema:
          type: boolean
      responses:
        '200':
          description: Entities deleted successfully
        '400':
          description: User error.
        '403':
          description: Unauthorized request.
        '404':
          description: Entity not found.
      summary: Delete entities
      tags:
      - entity
  /v0/submission/admin/<program>/<project>/files/<file_uuid>/reassign:
    put:
      description: Manually (re)assign the S3 url for a given node.
      parameters:
      - description: The program to which the submitter belongs and in which the entities
          will be created. The `program` is the human-readable name, e.g. TCGA.
        in: path
        name: program
        required: true
        schema:
          type: string
      - description: The project to which the submitter belongs and in which the entities
          will be created. The `project` is the human-readable code, e.g. BRCA.
        in: path
        name: project
        required: true
        schema:
          type: string
      - description: The id of the file to upload.
        in: path
        name: uuid
        required: true
        schema:
          type: string
      responses:
        '200':
          description: Success.
        '400':
          description: Bad Request
        '403':
          description: Unauthorized request.
        '404':
          description: File not found.
        '405':
          description: Method Not Allowed.
      summary: Reassign the S3 URL of a data file
      tags:
      - file
  /v0/submission/template:
    get:
      description: Get templates for all entity types.
      parameters:
      - description: output format, ``csv`` or ``tsv``, default is tsv
        in: query
        name: format
        schema:
          type: string
      - description: list of entities' categories to include in the template
        in: query
        name: categories
        schema:
          type: string
      - description: list of entities' categories to exclude from the template
        in: query
        name: exclude
        schema:
          type: string
      responses:
        '200':
          description: Success.
      summary: Get templates for all entity types
      tags:
      - dictionary
  /v0/submission/template/<entity>:
    get:
      description: Get a template for an entity type.
      parameters:
      - description: entity
        in: path
        name: entity
        required: true
        schema:
          type: string
      responses:
        '200':
          description: Success.
      summary: Get a template for an entity type
      tags:
      - dictionary
  /v0/submission/validation/upload_manifest:
    post:
      description: Generate a list of errors found in JSON Schema validation.
      responses:
        '200':
          description: Success.
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/schema_error_list'
      summary: Validate a manifest of data files
      tags:
      - file
components:
  schemas:
    schema_entity:
      properties:
        '...fields specific to this entity':
          type: string
        type:
          type: string
      type: object
    schema_entity_bulk:
      properties:
        doc:
          type: string
        doc_format:
          type: string
        name:
          type: string
      required:
      - name
      - doc_format
      - doc
      type: object
    schema_entity_list:
      items:
        $ref: '#/components/schemas/schema_entity'
      type: array
    schema_error_list:
      items:
        type: string
      type: array
    schema_links:
      properties:
        links:
          items:
            type: string
          type: array
      required:
      - links
      type: object
    schema_program:
      properties:
        dbgap_accession_number:
          type: string
        name:
          type: string
        type:
          type: string
      required:
      - name
      - dbgap_accession_number
      type: object
    schema_project:
      properties:
        code:
          type: string
        dbgap_accession_number:
          type: string
        investigator_name:
          type: string
        name:
          type: string
        type:
          type: string
      required:
      - name
      - code
      type: object