CSIRO

CSIRO Specimen Images API

The Specimen_Images API from CSIRO — 6 operation(s) for specimen_images.

Documentation GitHub OpenAPI

Operations 9

GET /ws/v2/domains/specimenImages/validateTerms Given a comma-separated list of terms, returns those that do not match any… #

POST /ws/v2/domains/specimenImages/validateTerms POST variant of the validateTerms endpoint. #

GET /ws/v2/domains/specimenImages/search This function allows a client to search for specimen images by accession number… #

POST /ws/v2/domains/specimenImages/search POST variant of the specimen images search endpoint. #

GET /ws/v2/domains/specimenImages/search/export Export specimen image search results #

POST /ws/v2/domains/specimenImages/search/export Post export specimen image search results #

POST /ws/v2/domains/specimenImages/metadata.csv Get metadata #

POST /ws/v2/domains/specimenImages/metadata Get metadata 1 #

POST /ws/v2/domains/specimenImages/download This function allows a client to retrieve a ZIP of a subset of files across… #

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OpenAPI Specification

openapi: 3.2.0
info:
  title: Csiro Specimen Images API
  version: v2
  description: 'Operations tagged Specimen_Images across 2 of this provider''s published API definitions: csiro-dap-ws-v2-openapi.json, csiro-dap-ws-v2-openapi.yml. Each path carries the servers of the definition it was published in.'
servers:
- url: https://data.csiro.au/dap
  description: Generated server url
security:
- basicAuth: []
- bearerAuth: []
- oauth2: []
tags:
- name: Specimen_Images
paths:
  /ws/v2/domains/specimenImages/validateTerms:
    get:
      tags:
      - Specimen_Images
      summary: Given a comma-separated list of terms, returns those that do not match any…
      operationId: validateTerms
      parameters:
      - name: any
        in: query
        required: true
        schema:
          type: string
      - name: nationalSpecimenCollection
        in: query
        required: false
        schema:
          type: string
      - name: fieldType
        in: query
        required: false
        schema:
          type: string
      responses:
        '200':
          description: OK
          content:
            application/json:
              schema:
                type: object
                additionalProperties: {}
    post:
      tags:
      - Specimen_Images
      summary: POST variant of the validateTerms endpoint.
      operationId: postValidateTerms
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/SpecimenImageValidateTermsRequestDto'
        required: true
      responses:
        '200':
          description: OK
          content:
            application/json:
              schema:
                type: object
                additionalProperties: {}
    servers:
    - url: https://data.csiro.au/dap
      description: Generated server url
  /ws/v2/domains/specimenImages/search:
    get:
      tags:
      - Specimen_Images
      summary: This function allows a client to search for specimen images by accession number…
      operationId: getSpecimenImageResults
      parameters:
      - name: nationalSpecimenCollection
        in: query
        required: false
        schema:
          type: string
      - name: any
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
      - name: taxonomy
        in: query
        description: '<b>Taxonomy</b> (optional) returns specimen images which include the either the kingdom, phylum, class, order,family, subfamily, genus, subgenus, species, subspecies or scientific name as the taxonomy. Value can be a Plantae, Commelinaceae, Commelina, tricarinata etc '
        required: false
        schema:
          type: array
          items:
            type: string
      - name: specimenId
        in: query
        description: <b>SpecimenId</b> (optional) returns specimen images which include the either the accession number or the catalog number as the specimenId.
        required: false
        schema:
          type: array
          items:
            type: string
      - name: dataCollectionId
        in: query
        required: false
        schema:
          type: string
      - name: fieldNumber
        in: query
        description: '<b>FieldNumber</b> (optional) returns specimen images which include field number '
        required: false
        schema:
          type: array
          items:
            type: string
      - name: dataAccessLevel
        in: query
        required: false
        schema:
          type: string
      - name: q
        in: query
        description: <b>General Search</b> (optional) performs a general search across taxonomy (kingdom, phylum, class, order, family, subfamily, genus, subgenus, species, subspecies, scientific names), catalog number, accession number, and field number. This parameter searches across multiple fields simultaneously.
        required: false
        schema:
          type: string
          default: ''
      - name: p
        in: query
        required: false
        schema:
          type: integer
          format: int32
          default: 1
      - name: rpp
        in: query
        required: false
        schema:
          type: integer
          format: int32
          default: 25
      - name: sb
        in: query
        required: false
        schema:
          type: string
          default: catalogNumber
      - name: so
        in: query
        required: false
        schema:
          type: string
          default: asc
          enum:
          - asc
          - desc
      - name: showFacets
        in: query
        required: false
        schema:
          type: boolean
          default: false
      - name: fSize
        in: query
        required: false
        schema:
          type: integer
          format: int32
          default: 10
      - name: collector
        in: query
        description: <b>Collector</b> (optional) returns specimen images which include collector name.
      responses:
        '200':
          description: OK
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/SpecimenImageResultDto'
            application/xml:
              schema:
                $ref: '#/components/schemas/SpecimenImageResultDto'
            text/xml:
              schema:
                $ref: '#/components/schemas/SpecimenImageResultDto'
            application/vnd.openxmlformats-officedocument.spreadsheetml.sheet:
              schema:
                $ref: '#/components/schemas/SpecimenImageResultDto'
    post:
      tags:
      - Specimen_Images
      summary: POST variant of the specimen images search endpoint.
      operationId: postSpecimenImageResults
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/SpecimenImageSearchRequestDto'
        required: true
      responses:
        '200':
          description: OK
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/SpecimenImageResultDto'
            application/xml:
              schema:
                $ref: '#/components/schemas/SpecimenImageResultDto'
            text/xml:
              schema:
                $ref: '#/components/schemas/SpecimenImageResultDto'
            application/vnd.openxmlformats-officedocument.spreadsheetml.sheet:
              schema:
                $ref: '#/components/schemas/SpecimenImageResultDto'
    servers:
    - url: https://data.csiro.au/dap
      description: Generated server url
  /ws/v2/domains/specimenImages/search/export:
    get:
      tags:
      - Specimen_Images
      operationId: exportSpecimenImageSearchResults
      parameters:
      - name: nationalSpecimenCollection
        in: query
        required: false
        schema:
          type: string
      - name: any
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
      - name: taxonomy
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
      - name: specimenId
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
      - name: dataCollectionId
        in: query
        required: false
        schema:
          type: string
      - name: fieldNumber
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
      - name: dataAccessLevel
        in: query
        required: false
        schema:
          type: string
      - name: q
        in: query
        required: false
        schema:
          type: string
          default: ''
      - name: p
        in: query
        required: false
        schema:
          type: integer
          format: int32
          default: 1
      - name: rpp
        in: query
        required: false
        schema:
          type: integer
          format: int32
          default: 25
      - name: sb
        in: query
        required: false
        schema:
          type: string
          default: catalogNumber
      - name: so
        in: query
        required: false
        schema:
          type: string
          default: asc
          enum:
          - asc
          - desc
      - name: showFacets
        in: query
        required: false
        schema:
          type: boolean
          default: false
      - name: fSize
        in: query
        required: false
        schema:
          type: integer
          format: int32
          default: 10
      responses:
        '200':
          description: OK
      summary: Export specimen image search results
      x-summary-source: derived
    post:
      tags:
      - Specimen_Images
      operationId: postExportSpecimenImageSearchResults
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/SpecimenImageSearchRequestDto'
        required: true
      responses:
        '200':
          description: OK
      summary: Post export specimen image search results
      x-summary-source: derived
    servers:
    - url: https://data.csiro.au/dap
      description: Generated server url
  /ws/v2/domains/specimenImages/metadata.csv:
    post:
      tags:
      - Specimen_Images
      operationId: getMetadata
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/DataObjectsDto'
        required: true
      responses:
        '200':
          description: OK
      summary: Get metadata
      x-summary-source: derived
    servers:
    - url: https://data.csiro.au/dap
      description: Generated server url
  /ws/v2/domains/specimenImages/metadata:
    post:
      tags:
      - Specimen_Images
      operationId: getMetadata_1
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/DataObjectsDto'
        required: true
      responses:
        '200':
          description: OK
      summary: Get metadata 1
      x-summary-source: derived
    servers:
    - url: https://data.csiro.au/dap
      description: Generated server url
  /ws/v2/domains/specimenImages/download:
    post:
      tags:
      - Specimen_Images
      summary: This function allows a client to retrieve a ZIP of a subset of files across…
      operationId: getDownloadZip
      parameters:
      - name: dataObjectId
        in: query
        required: true
        schema:
          type: array
          items:
            type: integer
            format: int64
      responses:
        '200':
          description: OK
    servers:
    - url: https://data.csiro.au/dap
      description: Generated server url
components:
  schemas:
    SpecimenImageFileDetailsDto:
      type: object
      properties:
        id:
          type: integer
          format: int64
        fileFormat:
          type: string
        fileSize:
          type: integer
          format: int64
        resolution:
          type: string
        fileName:
          type: string
        filePath:
          type: string
        downloadUrl:
          type: string
          format: uri
      xml:
        name: specimen_image_file
        namespace: urn:au:csiro:rds:dap:1.0
    SpecimenImageSearchRequestDto:
      type: object
      properties:
        nationalSpecimenCollection:
          type: string
        filters:
          type: object
          additionalProperties:
            type: array
            items:
              type: string
        any:
          type: array
          items:
            type: string
        taxonomy:
          type: array
          items:
            type: string
        specimenId:
          type: array
          items:
            type: string
        dataCollectionId:
          type: string
        fieldNumber:
          type: array
          items:
            type: string
        dataAccessLevel:
          type: string
        searchQuery:
          type: string
        pageNumber:
          type: integer
          format: int32
        resultsPerPage:
          type: integer
          format: int32
        sortBy:
          type: string
        sortOrder:
          type: string
          enum:
          - asc
          - desc
        showFacets:
          type: boolean
        facetsSize:
          type: integer
          format: int32
    FacetDto:
      type: object
      properties:
        field:
          type: string
        values:
          type: array
          items:
            $ref: '#/components/schemas/FacetValueDto'
          xml:
            wrapped: true
      required:
      - field
      xml:
        name: facet
        namespace: urn:au:csiro:rds:dap:1.0
    SpecimenImageResultDto:
      type: object
      properties:
        elapsedTime:
          type: integer
          format: int64
        totalResults:
          type: string
        page:
          type: integer
          format: int32
        resultsPerPage:
          type: integer
          format: int32
        next:
          $ref: '#/components/schemas/LinkDto'
        previous:
          $ref: '#/components/schemas/LinkDto'
        first:
          $ref: '#/components/schemas/LinkDto'
        last:
          $ref: '#/components/schemas/LinkDto'
        facets:
          type: array
          items:
            $ref: '#/components/schemas/FacetDto'
          xml:
            wrapped: true
        specimens:
          type: array
          items:
            $ref: '#/components/schemas/SpecimenImageDto'
          xml:
            wrapped: true
      required:
      - elapsedTime
      - first
      - last
      - page
      - resultsPerPage
      - totalResults
      xml:
        name: specimenImageResult
        namespace: urn:au:csiro:rds:dap:1.0
    LinkDto:
      type: object
      properties:
        relationship:
          type: string
          xml:
            name: rel
            attribute: true
        mediaType:
          type: string
          xml:
            name: type
            attribute: true
        href:
          type: string
          format: uri
          xml:
            attribute: true
        fileUpload:
          type: boolean
        fileId:
          type: integer
          format: int32
    SpecimenImageDto:
      type: object
      properties:
        id:
          type: string
        dataCollectionId:
          type: integer
          format: int32
        dataCollectionVers:
          type: integer
          format: int32
        licenceId:
          type: integer
          format: int32
        projectName:
          type: string
        nationalSpecimenCollection:
          type: string
        externalInstitutionCode:
          type: string
        externalContact:
          type: string
        externalInstitutionName:
          type: string
        dateTimeDigitised:
          type: string
        specimenPreparationView:
          type: string
        specimenCollectionLatitude:
          type: number
          format: double
        specimenCollectionLongitude:
          type: number
          format: double
        taxonRank:
          type: string
        scientificName:
          type: string
        identificationQualifier:
          type: string
        kingdom:
          type: string
        phylum:
          type: string
        specimenClass:
          type: string
        order:
          type: string
        family:
          type: string
        subfamily:
          type: string
        genus:
          type: string
        subgenus:
          type: string
        species:
          type: string
        subspecies:
          type: string
        scientificNameAuthorship:
          type: string
        acceptedScientificName:
          type: string
        acceptedCanonicalScientificName:
          type: string
        acceptedScientificNameId:
          type: string
        taxonomicStatus:
          type: string
        scientificNameId:
          type: string
        collector:
          type: string
        fieldNumber:
          type: string
        locality:
          type: string
        user:
          type: string
        contact:
          type: string
        accessionNo:
          type: string
        typeStatus:
          type: string
        collectionDate:
          type: string
        country:
          type: string
        stateProvince:
          type: string
        catalogNumber:
          type: string
        dataAccessLevel:
          type: string
        thumbnails:
          $ref: '#/components/schemas/ThumbnailDto'
        imageOnly:
          type: boolean
        files:
          type: array
          items:
            $ref: '#/components/schemas/SpecimenImageFileDetailsDto'
        resolutions:
          type: array
          items:
            type: string
        formats:
          type: array
          items:
            type: string
        dataRestricted:
          type: boolean
        specimenImageIdentifier:
          type: string
        view:
          type: string
      xml:
        name: specimen_image
        namespace: urn:au:csiro:rds:dap:1.0
    FacetValueDto:
      type: object
      properties:
        value:
          type: string
        count:
          type: integer
          format: int64
      xml:
        name: facetValue
        namespace: urn:au:csiro:rds:dap:1.0
    ThumbnailDto:
      type: object
      properties:
        smallThumbnail:
          $ref: '#/components/schemas/LinkDto'
        mediumThumbnail:
          $ref: '#/components/schemas/LinkDto'
        largeThumbnail:
          $ref: '#/components/schemas/LinkDto'
        fullThumbnail:
          $ref: '#/components/schemas/LinkDto'
      xml:
        name: thumbnail
        namespace: urn:au:csiro:rds:dap:1.0
    SpecimenImageValidateTermsRequestDto:
      type: object
      properties:
        any:
          type: string
        nationalSpecimenCollection:
          type: string
        fieldType:
          type: string
    DataObjectsDto:
      type: object
      properties:
        dataObjectIds:
          type: array
          items:
            type: integer
            format: int64
  securitySchemes:
    basicAuth:
      type: http
      scheme: basic
    bearerAuth:
      type: http
      scheme: bearer
      bearerFormat: opaque
    oauth2:
      type: oauth2
      flows:
        authorizationCode:
          authorizationUrl: https://login.microsoftonline.com/0fe05593-19ac-4f98-adbf-0375fce7f160/oauth2/v2.0/authorize
          tokenUrl: /dap/auth/csiro/token
          scopes:
            openid: OpenID Connect
x-refined-from:
- csiro-dap-ws-v2-openapi.json
- csiro-dap-ws-v2-openapi.yml

CSIRO Specimen Images API

Operations 9

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Schemas & Data

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