Dryad datasets API

openapi: 3.1.0
info:
  title: Dryad datasets API
  description: "Dryad's REST API allows detailed interaction and programmatic interfacing with Dryad contents. The most common case is to use GET requests to retrieve information about datasets, versions, and files.\n\nWhen using the API, any DOI included must be <a href=\"https://www.w3schools.com/tags/ref_urlencode.ASP\" target=\"blank\">URL-encoded<i class=\"fas fa-arrow-up-right-from-square exit-icon\" aria-label=\" (opens in new window)\" role=\"img\"></i></a> to ensure correct processing. Anonymous users of the API are limited to 30 requests per minute, and are not allowed to download data files. \n\nExamples:\n\n- [List datasets](https://datadryad.org/api/v2/datasets)\n- [Search for datasets](https://datadryad.org/api/v2/search?q=carbon)\n- [Get information about a dataset](https://datadryad.org/api/v2/datasets/doi%3A10.5061%2Fdryad.j1fd7)\n- [List versions of a dataset](https://datadryad.org/api/v2/datasets/doi%3A10.5061%2Fdryad.j1fd7/versions)\n- [List files in a version](https://datadryad.org/api/v2/versions/26724/files)\n\nDetailed documentation:\n\n- For details on all of our REST API operations, click the links in the menu on this page.\n- [Search API](https://github.com/datadryad/dryad-app/blob/main/documentation/apis/search.md)\n- [Submission API](https://github.com/datadryad/dryad-app/blob/main/documentation/apis/submission.md)\n\n## API accounts \n\nTo access more powerful features, an API account is required. API accounts allow users to:\n\n- Access the API at higher rates (authenticated users may make up to 240 requests per minute)\n- Download data files\n- Access datasets that are not yet public, but are associated with the account's community (institution, journal, etc.)\n- Update datasets associated with the account's community\n\nSee the <a href=\"https://github.com/datadryad/dryad-app/blob/main/documentation/apis/api_accounts.md\" target=\"blank\">API accounts document<i class=\"fas fa-arrow-up-right-from-square exit-icon\" aria-label=\" (opens in new window)\" role=\"img\"></i></a> for more information on requesting an API account and using it to access datasets.\n\n\n## Submission\n\nThe Submission API is used by organizations that partner closely with Dryad, and use systems to create dataset submissions directly. Please contact us if you are [interested in partnering with Dryad](/contact#get-involved), and setting up an API account for submission.\n\nThe <a href=\"https://github.com/datadryad/dryad-app/blob/main/documentation/apis/submission.md\" target=\"blank\">API submission examples document<i class=\"fas fa-arrow-up-right-from-square exit-icon\" aria-label=\" (opens in new window)\" role=\"img\"></i></a> gives concrete examples of submission through the Dryad API.\n\n\n### Dryad sandbox\n\n<a href=\"https://sandbox.datadryad.org/\" target=\"blank\">Dryad's sandbox server<i class=\"fas fa-arrow-up-right-from-square exit-icon\" aria-label=\" (opens in new window)\" role=\"img\"></i></a> allows users to experiment with data submission and the Dryad API, without worrying about the effects on \"real\" data. Anyone may create an account on the sandbox server for testing purposes. When creating an account, keep in mind that Dryad's sandbox relies on the <a href=\"https://sandbox.orcid.org/\" target=\"_blank\">sandbox version of ORCID<i class=\"fas fa-arrow-up-right-from-square exit-icon\" aria-label=\" (opens in new window)\" role=\"img\"></i></a>, which allows you to make test ORCID accounts. Sandbox ORCID IDs should be used in the Dryad sandbox, while use of Dryad's production system requires a real ORCID ID.\n"
  version: 2.1.0
servers:
- url: https://datadryad.org/api/v2
  description: Main Dryad server
- url: https://sandbox.datadryad.org/api/v2
  description: Sandbox server, for testing new features.
tags:
- name: datasets
  description: Dataset operations
paths:
  /datasets:
    get:
      summary: Get a list of all datasets
      tags:
      - datasets
      description: The items returned may depend on user permissions, and are paged.
      parameters:
      - $ref: '#/components/parameters/page'
      - $ref: '#/components/parameters/per_page'
      - $ref: '#/components/parameters/publicationISSN'
      - $ref: '#/components/parameters/publicationName'
      - $ref: '#/components/parameters/manuscriptNumber'
      - $ref: '#/components/parameters/curationStatus'
      responses:
        '200':
          description: A list of datasets.
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/datasets'
              examples:
                success:
                  $ref: api/v2/docs/examples/datasets.json
        '406':
          $ref: '#/components/responses/Unacceptable'
    post:
      summary: Create a new dataset with an automatically-generated DOI
      tags:
      - datasets
      description: 'You must be <a href="https://github.com/datadryad/dryad-app/blob/main/documentation/apis/api_accounts.md">logged in</a>. Use a JSON structure as shown below.


        If no funders are declared, users will be asked to list them later; to declare no funding submit a funder with <code>identifier&#x0003A; ''0''</code> (see the "Set no funding" example). If human subject information is in the dataset, include a statement explaining how the data was de-identified (see the ''Include HSI statement'' example).


        For a more full list of properties that can be sent, check the Model below and the <a href="https://github.com/datadryad/dryad-app/blob/main/documentation/apis/sample_dataset.json" target="_blank">sample dataset object</a>.'
      security:
      - bearerAuth: []
      requestBody:
        required: true
        content:
          application/json:
            schema:
              allOf:
              - $ref: '#/components/schemas/dc_metadata'
              - $ref: '#/components/schemas/admin_values'
            examples:
              Post:
                $ref: api/v2/docs/examples/dataset_post_request.json
              Include journal information:
                $ref: api/v2/docs/examples/dataset_post_request_jr.json
              Set no funding:
                $ref: api/v2/docs/examples/dataset_post_request_nf.json
              Include HSI statement:
                $ref: api/v2/docs/examples/dataset_post_request_hsi.json
      responses:
        '201':
          description: Show the dataset information that has been saved.
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/datasets'
              examples:
                Success:
                  $ref: api/v2/docs/examples/dataset_post_response.json
                With journal:
                  $ref: api/v2/docs/examples/dataset_post_response_jr.json
                Without funding:
                  $ref: api/v2/docs/examples/dataset_post_response_nf.json
                With HSI statement:
                  $ref: api/v2/docs/examples/dataset_post_response_hsi.json
        '406':
          $ref: '#/components/responses/Unacceptable'
        '401':
          $ref: '#/components/responses/Unauthorized'
        '422':
          $ref: '#/components/responses/UnprocessableEntity'
        '400':
          $ref: '#/components/responses/BadRequest'
  /datasets/{doi}:
    get:
      summary: Get a dataset record by its DOI
      tags:
      - datasets
      description: Be sure to URL encode the DOI (see example below). Datasets that are not yet published are only retrievable by users with permission to access them.
      parameters:
      - $ref: '#/components/parameters/doi'
      responses:
        '200':
          description: Dataset information retrieved.
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/dataset'
              examples:
                success:
                  $ref: api/v2/docs/examples/dataset.json
        '406':
          $ref: '#/components/responses/Unacceptable'
        '401':
          $ref: '#/components/responses/Unauthorized'
        '404':
          $ref: '#/components/responses/NotFound'
    put:
      summary: Update (overwrite) dataset metadata for DOI
      tags:
      - datasets
      description: This will overwrite writeable metadata for an in-progress dataset.  This is an insert or update action (upsert). Be sure to URL encode the DOI (see example below). You must be <a href="https://github.com/datadryad/dryad-app/blob/main/documentation/apis/api_accounts.md">logged in</a>. Use a JSON structure as shown below. For a more full list of properties that can be sent, check the Schema below and the <a href="https://github.com/datadryad/dryad-app/blob/main/documentation/apis/sample_dataset.json" target="_blank">sample dataset object</a>.
      parameters:
      - $ref: '#/components/parameters/doi'
      security:
      - bearerAuth: []
      requestBody:
        required: true
        content:
          application/json:
            schema:
              allOf:
              - $ref: '#/components/schemas/dc_metadata'
              - properties:
                  identifier:
                    type: string
                    description: The Dryad dataset DOI
              - $ref: '#/components/schemas/admin_values'
            examples:
              success:
                $ref: api/v2/docs/examples/dataset_post_request.json
      responses:
        '200':
          description: Show the dataset information that has been saved.
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/datasets'
              examples:
                success:
                  $ref: api/v2/docs/examples/dataset.json
        '406':
          $ref: '#/components/responses/Unacceptable'
        '401':
          $ref: '#/components/responses/Unauthorized'
        '400':
          $ref: '#/components/responses/BadRequest'
    patch:
      parameters:
      - $ref: '#/components/parameters/doi'
      security:
      - bearerAuth: []
      summary: Update the state of an in-progress dataset
      tags:
      - datasets
      description: 'Sending a JSON patch request whose JSON body looks like **[ { ''op'': ''replace'', ''path'': ''/versionStatus'', ''value'': ''submitted'' } ]**. (This is the most common command, attempting to change the versionStatus to ''submitted''.) Other options are available that are useful for integration with manuscript processing systems. See the [embedded Dryad documentation](https://github.com/datadryad/dryad-app/blob/main/documentation/apis/embedded_submission.md) for details. Set http header **''Content-Type: application/json-patch+json''** when making the request instead of a standard json content-type.'
      requestBody:
        description: JSON Patch object
        required: true
        content:
          application/json:
            schema:
              type: array
              items:
                $ref: '#/components/schemas/dataset_submission'
      responses:
        '202':
          description: Submission taking place, watch the dataset versionStatus for changes.
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/dataset'
              examples:
                success:
                  $ref: api/v2/docs/examples/dataset.json
        '406':
          $ref: '#/components/responses/Unacceptable'
        '401':
          $ref: '#/components/responses/Unauthorized'
        '403':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Error'
              example:
                error: Your dataset cannot be updated now
        '400':
          $ref: '#/components/responses/BadRequest'
  /datasets/{doi}/download:
    get:
      summary: Get a download package for a dataset
      tags:
      - datasets
      description: This downloads the zip package of the latest submitted version of the dataset that is visible to the user (or public).
      security:
      - bearerAuth: []
      parameters:
      - $ref: '#/components/parameters/doi'
      responses:
        '200':
          description: The binary content for a compressed archive.
          content:
            application/zip:
              schema:
                type: string
                format: binary
        '401':
          $ref: '#/components/responses/Unauthorized'
        '404':
          $ref: '#/components/responses/NotFound'
  /datasets/{doi}/versions:
    get:
      summary: Show all versions of a dataset
      tags:
      - datasets
      description: The <code>/versions</code> endpoint lists all versions visible to the user (or public). This is in contrast to GETting the datasets endpoint for a DOI, since it only embeds metadata for the latest visible version.
      parameters:
      - $ref: '#/components/parameters/doi'
      - $ref: '#/components/parameters/page'
      - $ref: '#/components/parameters/per_page'
      responses:
        '200':
          description: A list of a dataset's versions.
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/versions'
              examples:
                success:
                  $ref: api/v2/docs/examples/versions.json
        '406':
          $ref: '#/components/responses/Unacceptable'
        '401':
          $ref: '#/components/responses/Unauthorized'
        '404':
          $ref: '#/components/responses/NotFound'
components:
  parameters:
    per_page:
      in: query
      name: per_page
      schema:
        type: integer
      description: Number of results to return on each page. Defaults to 20. Maximum allowed is 100.
    curationStatus:
      in: query
      name: curationStatus
      schema:
        type: string
      description: Curation Status
    page:
      in: query
      name: page
      schema:
        type: integer
      description: Which page of results to view. Defaults to page 1.
    publicationName:
      in: query
      name: publicationName
      schema:
        type: string
      description: ISSN of a journal associated with the datasets.
    doi:
      in: path
      name: doi
      schema:
        type: string
      required: true
      description: 'DOI like doi:10.1000/18238577 that should be URL encoded (example: <code>doi%3A10.1000%2F18238577</code>)'
    manuscriptNumber:
      in: query
      name: manuscriptNumber
      schema:
        type: string
      description: Manuscript number associated with the dataset.
    publicationISSN:
      in: query
      name: publicationISSN
      schema:
        type: string
      description: ISSN of a journal associated with the datasets.
  schemas:
    embedded_datasets:
      type: object
      properties:
        _embedded:
          type: object
          properties:
            stash:datasets:
              type: array
              items:
                $ref: '#/components/schemas/dataset'
    dataset_submission:
      properties:
        op:
          type: string
          enum:
          - replace
          example: replace
        path:
          type: string
          enum:
          - /versionStatus
          - /curationStatus
          - publicationISSN
          example: /versionStatus
        value:
          type: string
          oneOf:
          - title: /versionStatus
            enum:
            - in_progress
            - processing
            - submitted
          - title: /curationStatus
            enum:
            - queued
            - submitted
            - peer_review
            - curation
            - action_required
            - withdrawn
          - title: /publicationISSN
          example: queued
    geolocationBox:
      properties:
        swLongitude:
          description: The longitude of the southwest corner of the box.
          type: number
        swLatitude:
          description: The latitude of the southwest corner of the box.
          type: number
        neLongitude:
          description: The longitude of the northeast corner of the box.
          type: number
        neLatitude:
          description: The latitude of the northeast corner of the box.
          type: number
    hal_page_links:
      properties:
        first:
          $ref: '#/components/schemas/hal_link'
        last:
          $ref: '#/components/schemas/hal_link'
        prev:
          $ref: '#/components/schemas/hal_link'
        next:
          $ref: '#/components/schemas/hal_link'
    embedded_versions:
      type: object
      properties:
        _embedded:
          type: object
          properties:
            stash:versions:
              type: array
              items:
                $ref: '#/components/schemas/version'
    relatedWork:
      properties:
        relationship:
          format: string
          enum:
          - article
          - dataset
          - preprint
          - software
          - supplemental_information
          - primary_article
          - data_management_plan
        identifierType:
          type: string
        identifier:
          type: string
    hal_paged_response:
      allOf:
      - properties:
          _links:
            allOf:
            - $ref: '#/components/schemas/hal_self_link'
            - $ref: '#/components/schemas/hal_page_links'
      - $ref: '#/components/schemas/paging_counts'
    admin_values:
      properties:
        userId:
          type: string
          description: The Dryad user ID, or ORCID iD, of the user who will submit the dataset. If this is unknown, the userId must be set to `0` to allow for an invitation link.
        publicationISSN:
          type: string
          description: An ISSN for the associated journal
        publicationName:
          type: string
          description: The title of the associated journal
        manuscriptNumber:
          type: string
          description: The internal manuscript number assigned to an associated article before publication
        skipEmails:
          type: boolean
          default: false
          description: Administrator value. Prevents emails being sent automatically.
        triggerSubmitInvitation:
          type: boolean
          default: false
          description: Administrator value. Sends an editing invitation email to the first author.
        preserveCurationStatus:
          type: boolean
          default: false
          description: Administrator value. Prevents automatic curation status changes.
        holdForPeerReview:
          type: boolean
          default: false
          description: Administrator value. Sets whether the submission will be sent to curation or a peer review hold status.
        loosenValidation:
          type: boolean
          default: false
          description: For superusers only.
        skipDataciteUpdate:
          type: boolean
          default: false
          description: For superusers only.
        invoiceId:
          type: string
          description: For superusers only.
    paging_counts:
      properties:
        count:
          type: integer
        total:
          type: integer
    dataset_links:
      properties:
        _links:
          allOf:
          - $ref: '#/components/schemas/hal_self_link'
          - $ref: '#/components/schemas/hal_dataset_links'
    versions:
      allOf:
      - $ref: '#/components/schemas/hal_paged_response'
      - $ref: '#/components/schemas/embedded_versions'
    hal_version_links:
      properties:
        stash:dataset:
          $ref: '#/components/schemas/hal_link'
        stash:files:
          $ref: '#/components/schemas/hal_link'
        stash:download:
          $ref: '#/components/schemas/hal_link'
        curies:
          type: array
          items:
            $ref: '#/components/schemas/hal_curie'
    funder:
      properties:
        organization:
          type: string
        identifier:
          type: string
          description: The organization identifier, for example a ROR ID.
          example: https://ror.org/00x6h5n95
        identifierType:
          description: Type of identifier — ror, isni, grid, crossref_funder_id or other.
          type: string
          example: ror
        awardNumber:
          type: string
        awardDescription:
          description: Usually used for the program or the division of the award.
          type: string
        order:
          type: integer
    hal_link:
      type: object
      properties:
        href:
          type: string
          format: uri
      required:
      - href
    Error:
      type: object
      properties:
        error:
          type: string
    geolocationPoint:
      type: object
      properties:
        latitude:
          description: The latitude of the point.
          type: number
        longitude:
          description: The longitude of the point.
          type: number
    dataset:
      allOf:
      - properties:
          identifier:
            type: string
          id:
            type: integer
          storageSize:
            type: integer
          relatedPublicationISSN:
            type: string
      - $ref: '#/components/schemas/version'
      - $ref: '#/components/schemas/dataset_links'
      - properties:
          metrics:
            type: object
            properties:
              views:
                type: integer
              downloads:
                type: integer
              citations:
                type: integer
          license:
            type: string
            description: The license of the dataset
    dc_metadata:
      type: object
      properties:
        title:
          type: string
        authors:
          type: array
          items:
            $ref: '#/components/schemas/author'
        abstract:
          type: string
          description: An abstract introducing the dataset.
        funders:
          type: array
          items:
            $ref: '#/components/schemas/funder'
        keywords:
          type: array
          items:
            type: string
        fieldOfScience:
          type: string
          description: A term from the FOS (Fields of Science and Technology) controlled vocabulary. The main category of the dataset.
        hsiStatement:
          type: string
          description: A statement explaining the de-identification of any human subject data in the dataset.
        methods:
          type: string
          description: The methods by which the data was produced. Not required for publication.
        usageNotes:
          type: string
          description: Usage notes for the dataset (Deprecated; It is preferred for this content to appear in the README file for the dataset). If the dataset has been retracted, the retraction statement will appear here.
        locations:
          type: array
          items:
            $ref: '#/components/schemas/geolocation'
        relatedWorks:
          type: array
          items:
            $ref: '#/components/schemas/relatedWork'
      required:
      - title
      - authors
      - abstract
    version:
      allOf:
      - $ref: '#/components/schemas/version_links'
      - $ref: '#/components/schemas/dc_metadata'
      - properties:
          versionNumber:
            type: integer
          versionStatus:
            type: string
            enum:
            - in_progress
            - processing
            - submitted
            description: Internal processing status of files.
          curationStatus:
            type: string
            enum:
            - In progress
            - Processing
            - Queued for curation
            - Private for Peer Review
            - Awaiting payment
            - Curation
            - Action required
            - Withdrawn
            - Embargoed
            - Published
            description: Status of the submission in the curation workflow.
          versionChanges:
            type: string
            enum:
            - files_changed
            - metadata_changed
          publicationDate:
            type: string
          lastModificationDate:
            type: string
          visibility:
            type: string
            description: Whether or not this version is publicly visible.
    geolocation:
      properties:
        place:
          description: A place name.
          type: string
        box:
          $ref: '#/components/schemas/geolocationBox'
          description: A bounding box.
        point:
          $ref: '#/components/schemas/geolocationPoint'
          description: A coordinate point.
    hal_self_link:
      type: object
      properties:
        self:
          $ref: '#/components/schemas/hal_link'
    hal_curie:
      type: object
      properties:
        name:
          type: string
        href:
          type: string
          format: uri
        templated:
          type: boolean
      required:
      - name
      - href
      - templated
    hal_dataset_links:
      properties:
        stash:versions:
          $ref: '#/components/schemas/hal_link'
        stash:version:
          $ref: '#/components/schemas/hal_link'
        stash:download:
          $ref: '#/components/schemas/hal_link'
        curies:
          type: array
          items:
            $ref: '#/components/schemas/hal_curie'
    version_links:
      properties:
        _links:
          allOf:
          - $ref: '#/components/schemas/hal_self_link'
          - $ref: '#/components/schemas/hal_version_links'
    author:
      properties:
        firstName:
          type: string
        lastName:
          type: string
        email:
          type: string
        affiliation:
          type: string
        affiliationROR:
          type: string
          description: Preferred identifier for the author affiliation.
        affiliations:
          type: array
          items:
            name: string
            ror_id: string
        affiliationISNI:
          type: string
        orcid:
          type: string
        order:
          type: integer
    datasets:
      allOf:
      - $ref: '#/components/schemas/hal_paged_response'
      - $ref: '#/components/schemas/embedded_datasets'
  responses:
    BadRequest:
      content:
        application/json:
          schema:
            $ref: '#/components/schemas/Error'
          example:
            error: 400 - Bad Request
    NotFound:
      content:
        application/json:
          schema:
            $ref: '#/components/schemas/Error'
          example:
            error: Not Found
    Unauthorized:
      content:
        application/json:
          schema:
            $ref: '#/components/schemas/Error'
          example:
            error: Unauthorized, must have current bearer token.
    Unacceptable:
      content:
        application/json:
          schema:
            $ref: '#/components/schemas/Error'
          example:
            error: '406 - unacceptable: please set your `Content-Type` or `Accept` headers for application/json. `Accept` header is optional if you are using `Content-Type: application/json`.'
    UnprocessableEntity:
      content:
        application/json:
          schema:
            $ref: '#/components/schemas/Error'
          example:
            error: '422 - Unprocessable Content: the server understood the content type of the request, and the syntax of the request content was correct, but it was unable to process the contained instructions.


              Example: _A dataset with same information already exists._'
  securitySchemes:
    bearerAuth:
      type: http
      scheme: bearer
      bearerFormat: JWT