CSIRO

CSIRO Api-V2 DNA Sequence Collections API

The Api-V2 DNA Sequence Collections API from CSIRO — 6 operation(s) for api-v2 dna sequence collections.

GitHub OpenAPI

Operations 6

POST /api/v2/domains/publishedDnaSequence/searchByUids Retrieve published Sequence collection IDs by specified unique IDs #
GET /api/v2/domains/publishedDnaSequenceByCollectionId/{dapCollectionId} Get a published sequence collection by DAP collection ID #
GET /api/v2/domains/publishedDnaSequenceByCollectionId/{dapCollectionId}/data Get a list of a collection's data files #
GET /api/v2/domains/publishedDnaSequenceByCollectionId/{dapCollectionId}/data/{fileId} Get one of a collection's data files #
GET /api/v2/domains/publishedDnaSequence/{uid} Retrieve a published Sequence collection by unique id #
GET /api/v2/domains/dnaSequence/{uid} Retrieve a Sequence collection (can be any deposit status) by unique id #

Documentation

📖
Documentation
https://research.csiro.au/dap/developer-tools/

Specifications

⚙
OpenAPI
https://artifacts.apis.io/csiro/openapi/csiro-api-v2-dna-sequence-collections-api-openapi.yml

Schemas & Data

📊
JSONSchema
https://artifacts.apis.io/csiro/json-schema/csiro-data-collection-dto-v2-schema.json
📊
JSONSchema
https://artifacts.apis.io/csiro/json-schema/csiro-casda-metadata-dto-schema.json
📊
JSONSchema
https://artifacts.apis.io/csiro/json-schema/csiro-casda-observation-search-dto-schema.json
📊
JSONSchema
https://artifacts.apis.io/csiro/json-schema/csiro-data-collections-result-dto-schema.json
📊
JSONSchema
https://artifacts.apis.io/csiro/json-schema/csiro-specimen-image-result-dto-schema.json
📊
JSONSchema
https://artifacts.apis.io/csiro/json-schema/csiro-specimen-image-search-request-dto-schema.json
📊
JSONSchema
https://artifacts.apis.io/csiro/json-schema/csiro-data-collection-dto-schema.json
📊
JSONSchema
https://artifacts.apis.io/csiro/json-schema/csiro-my-collection-schema.json
📊
JSONSchema
https://artifacts.apis.io/csiro/json-schema/csiro-casda-observation-validation-dto-schema.json
📊
JSONSchema
https://artifacts.apis.io/csiro/json-schema/csiro-doi-files-dataset-dto-schema.json
📊
JSONSchema
https://artifacts.apis.io/csiro/json-schema/csiro-globus-collection-dto-schema.json
📊
JSONSchema
https://artifacts.apis.io/csiro/json-schema/csiro-orcid-results-dto-schema.json
📊
JSONSchema
https://artifacts.apis.io/csiro/json-schema/csiro-orcid-work-dto-schema.json
📊
JSONSchema
https://artifacts.apis.io/csiro/json-schema/csiro-orcid-user-dto-schema.json

Other Resources

🔗
APIExplorer
https://data.csiro.au/dap/swagger-ui.html

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OpenAPI Specification

csiro-api-v2-dna-sequence-collections-api-openapi.yml Raw ↑ 
openapi: 3.2.0
info:
  title: Csiro Api-V2 DNA Sequence Collections API
  version: v2
  description: 'Operations tagged Api-V2 DNA Sequence Collections across 2 of this provider''s published API definitions: csiro-dap-api-v2-openapi.json, csiro-dap-api-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: Api-V2 DNA Sequence Collections
paths:
  /api/v2/domains/publishedDnaSequence/searchByUids:
    post:
      tags:
      - Api-V2 DNA Sequence Collections
      summary: Retrieve published Sequence collection IDs by specified unique IDs
      operationId: getAllCollectionIds
      requestBody:
        content:
          application/json:
            schema:
              type: array
              items:
                type: string
        required: true
      responses:
        '200':
          description: OK
          content:
            '*/*':
              schema:
                $ref: '#/components/schemas/SequenceCollectionsDTO'
    servers:
    - url: https://data.csiro.au/dap
      description: Generated server url
  /api/v2/domains/publishedDnaSequenceByCollectionId/{dapCollectionId}:
    get:
      tags:
      - Api-V2 DNA Sequence Collections
      summary: Get a published sequence collection by DAP collection ID
      operationId: getCollectionByCollectionId
      parameters:
      - name: dapCollectionId
        in: path
        required: true
        schema:
          type: string
      responses:
        '200':
          description: OK
          content:
            '*/*':
              schema:
                $ref: '#/components/schemas/DataCollectionDtoV2'
    servers:
    - url: https://data.csiro.au/dap
      description: Generated server url
  /api/v2/domains/publishedDnaSequenceByCollectionId/{dapCollectionId}/data:
    get:
      tags:
      - Api-V2 DNA Sequence Collections
      summary: Get a list of a collection's data files
      operationId: getCollectionDataFileList
      parameters:
      - name: dapCollectionId
        in: path
        required: true
        schema:
          type: string
      responses:
        '200':
          description: OK
          content:
            '*/*':
              schema:
                $ref: '#/components/schemas/DataFilesDto'
      deprecated: true
    servers:
    - url: https://data.csiro.au/dap
      description: Generated server url
  /api/v2/domains/publishedDnaSequenceByCollectionId/{dapCollectionId}/data/{fileId}:
    get:
      tags:
      - Api-V2 DNA Sequence Collections
      summary: Get one of a collection's data files
      operationId: getCollectionDataFile
      parameters:
      - name: dapCollectionId
        in: path
        required: true
        schema:
          type: string
      - name: fileId
        in: path
        required: true
        schema:
          type: integer
          format: int64
      responses:
        '200':
          description: OK
      deprecated: true
    servers:
    - url: https://data.csiro.au/dap
      description: Generated server url
  /api/v2/domains/publishedDnaSequence/{uid}:
    get:
      tags:
      - Api-V2 DNA Sequence Collections
      summary: Retrieve a published Sequence collection by unique id
      operationId: getCollectionByUid
      parameters:
      - name: uid
        in: path
        required: true
        schema:
          type: string
      responses:
        '200':
          description: OK
          content:
            '*/*':
              schema:
                $ref: '#/components/schemas/DataCollectionDtoV2'
    servers:
    - url: https://data.csiro.au/dap
      description: Generated server url
  /api/v2/domains/dnaSequence/{uid}:
    get:
      tags:
      - Api-V2 DNA Sequence Collections
      summary: Retrieve a Sequence collection (can be any deposit status) by unique id
      operationId: getDNASequenceCollectionByUid
      parameters:
      - name: uid
        in: path
        required: true
        schema:
          type: string
      responses:
        '200':
          description: OK
          content:
            '*/*':
              schema:
                $ref: '#/components/schemas/DataCollectionDtoV2'
    servers:
    - url: https://data.csiro.au/dap
      description: Generated server url
components:
  schemas:
    ProjectDto:
      type: object
      properties:
        irpHierarchy:
          type: boolean
          xml:
            attribute: true
        wbs:
          type: string
        businessUnit:
          type: string
        program:
          type: string
        group:
          type: string
        portfolio:
          type: string
        theme:
          type: string
        stream:
          type: string
        projectDescription:
          type: string
        projectLeader:
          type: string
        projectTitle:
          type: string
      xml:
        name: project
        namespace: urn:au:csiro:rds:dap:1.0
    ProgressDoiDto:
      type: object
      properties:
        andsDoi:
          type: string
        issueDate:
          type: string
          format: date-time
    SensorDto:
      type: object
      properties:
        network:
          type: string
        platform:
          type: string
        sensor:
          type: string
        featureOfInterest:
          type: string
        verticalExtent:
          type: string
        sensorSerialNumber:
          type: string
        phenomena:
          type: string
        latestDeploymentStartDate:
          type: string
          format: date-time
        latestDeploymentEndDate:
          type: string
          format: date-time
        deployer:
          type: string
        latestDeploymentOrganisation:
          type: string
        latestDeploymentContact:
          type: string
        latestDeploymentOffsetX:
          type: string
        latestDeploymentOffsetY:
          type: string
        latestDeploymentOffsetZ:
          type: string
        latestCalibrationDate:
          type: string
          format: date-time
        latestCalibrationOrganisation:
          type: string
        latestCalibrationGroup:
          type: string
        latestConformanceDate:
          type: string
          format: date-time
        latestConformanceOrganisation:
          type: string
        latestConformanceGroup:
          type: string
        latestConformanceRequirement:
          type: string
        latestConformancePassed:
          type: boolean
        latestConformanceReason:
          type: string
        unitOfMeasure:
          type: string
        method:
          type: string
        observedProperty:
          type: string
      xml:
        name: Sensor
        namespace: urn:au:csiro:rds:dap:1.0
    DataFilesDto:
      type: object
      properties:
        id:
          type: string
        self:
          type: string
          format: uri
        licence:
          type: string
        licenceLink:
          $ref: '#/components/schemas/LinkDto'
          xml:
            name: link
        rights:
          type: string
        access:
          type: string
        file:
          type: array
          items:
            $ref: '#/components/schemas/FileDto'
          xml:
            name: files
            wrapped: true
        filesInFolder:
          type: integer
          format: int64
      required:
      - access
      - id
      - licence
      - licenceLink
      - rights
      - self
      xml:
        name: dataFiles
        namespace: urn:au:csiro:rds:dap:1.0
    SpecimenTaxonomyDto:
      type: object
      properties:
        family:
          type: string
        genus:
          type: string
        kingdom:
          type: string
        order:
          type: string
        phylum:
          type: string
        scientificName:
          type: string
        species:
          type: string
        subfamily:
          type: string
        taxonomyClass:
          type: string
        subPhylum:
          type: string
        infraPhylum:
          type: string
        parvPhylum:
          type: string
        gigaClass:
          type: string
        megaClass:
          type: string
        superClass:
          type: string
        subClass:
          type: string
        infraClass:
          type: string
        subterClass:
          type: string
        superOrder:
          type: string
        subOrder:
          type: string
        infraOrder:
          type: string
        parvOrder:
          type: string
        nanoOrder:
          type: string
        sectionZoology:
          type: string
        superFamily:
          type: string
        epiFamily:
          type: string
        superTribe:
          type: string
        tribe:
          type: string
        subTribe:
          type: string
        subGenus:
          type: string
        infragenericName:
          type: string
        section:
          type: string
        subSection:
          type: string
        subSpecies:
          type: string
    FileMetadataDto:
      type: object
      properties:
        name:
          type: string
        dateValue:
          type: string
          format: date-time
        dateValueString:
          type: string
        numericValue:
          type: number
          format: double
        stringValue:
          type: string
    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
    SequenceCollectionsDTO:
      type: object
      properties:
        idPairs:
          type: array
          items:
            $ref: '#/components/schemas/SequenceCollectionDTO'
    SequenceCollectionDTO:
      type: object
      properties:
        uniqueSequenceId:
          type: string
        dataCollectionId:
          type: integer
          format: int32
    DistributionDto:
      type: object
      properties:
        id:
          type: integer
          format: int32
        title:
          type: string
        version:
          type: string
    ActivityDto:
      type: object
      properties:
        activityId:
          type: integer
          format: int32
        activityTitle:
          type: string
        activityType:
          type: string
        activityDescription:
          type: string
        activityInstrument:
          type: string
      xml:
        name: activity
        namespace: urn:au:csiro:rds:dap:1.0
    RelatedLinkDTO:
      type: object
      properties:
        id:
          type: integer
          format: int32
        address:
          type: string
        displayText:
          type: string
        toolTip:
          type: string
        type:
          type: string
        attributionStatement:
          type: string
    NameDto:
      type: object
      properties:
        name:
          type: string
        display:
          type: string
        orcidId:
          type: string
        type:
          type: string
        orgInfo:
          type: string
      xml:
        name: name
    VoResourceDto:
      type: object
      properties:
        id:
          type: integer
          format: int32
        ivoIdentifier:
          type: string
      xml:
        name: VoResource
    AnzlicDto:
      type: object
      properties:
        id:
          type: integer
          format: int32
        spatialId:
          type: integer
          format: int32
        altCollectionTitle:
          type: string
        individualName:
          type: string
        position:
          type: string
        verticalExtentMin:
          type: number
          format: double
        verticalExtentMax:
          type: number
          format: double
        spatialRepresentationType:
          type: string
        spatialResolution:
          type: string
        metadataLanguage:
          type: string
        metadataCharacterSet:
          type: string
        anzlicTopicCategoryCode:
          type: string
    IdentifierDto:
      type: object
      properties:
        identifierType:
          type: string
          xml:
            attribute: true
        identifier:
          type: string
    SpecimenDto:
      type: object
      properties:
        uniqueSequenceId:
          type: string
        accessionNo:
          type: string
        campaignId:
          type: string
        campaignName:
          type: string
        institutionName:
          type: string
        scientificNameAuthorship:
          type: string
        campaignFunder:
          type: string
        campaignCollaborators:
          type: string
        campaignDataRelease:
          type: string
        contractNumber:
          type: string
        collectionId:
          type: string
        institutionId:
          type: string
        mtaNumber:
          type: string
        collectionName:
          type: string
        projectName:
          type: string
        contact:
          type: string
        speciesNameSupplied:
          type: string
        higherTaxonomySupplied:
          type: string
        biome:
          type: string
        marineEcoRegions:
          type: array
          items:
            type: string
        terrestrialEcoRegions:
          type: array
          items:
            type: string
        taxonomicGroup:
          type: string
        taxonomicStatus:
          type: string
        taxonRemarks:
          type: string
        vernacularName:
          type: string
        nuclearGeneticCode:
          type: string
        mitochondrialGeneticCode:
          type: string
        plastidGeneticCode:
          type: string
        nameAccordingTo:
          type: string
        taxonRank:
          type: string
        specimen:
          type: string
        preservedSpecimen:
          type: string
        preparations:
          type: string
        specimenNotes:
          type: string
        materialCollectionId:
          type: string
        recordNumber:
          type: string
        tissueSampleId:
          type: string
        otherIdentifiers:
          type: string
        releaseDate:
          type: string
        dataGeneralizations:
          type: string
        licence:
          type: string
        acknowledgement:
          type: string
        collector:
          type: string
        collectionPermits:
          type: string
        identifiedBy:
          type: string
        privateLatitude:
          type: string
        privateLongitude:
          type: string
        verbatimLocality:
          type: string
        verbatimLatitude:
          type: string
        verbatimLongitude:
          type: string
        decimalEndLat:
          type: string
        decimalEndLong:
          type: string
        occurrenceRemarks:
          type: string
        lifeStage:
          type: string
        typeStatus:
          type: string
        specimenPreservation:
          type: string
        dateIdentified:
          type: string
        sex:
          type: string
        collectionDate:
          type: string
        fieldNumber:
          type: string
        eventRemarks:
          type: string
        country:
          type: string
        stateProvince:
          type: string
        locality:
          type: string
        station:
          type: string
        specimenCollectionLatitude:
          type: number
          format: double
        specimenCollectionLongitude:
          type: number
          format: double
        geodeticDatum:
          type: string
        depth:
          type: string
        depthStart:
          type: string
        depthEnd:
          type: string
        altitude:
          type: string
        maximumElevationInMeters:
          type: number
          format: double
        minimumElevationInMeters:
          type: number
          format: double
        specimenTaxonomyAtSequencing:
          $ref: '#/components/schemas/SpecimenTaxonomyDto'
        currentSpecimenTaxonomy:
          $ref: '#/components/schemas/SpecimenTaxonomyDto'
      xml:
        name: Specimen
        namespace: urn:au:csiro:rds:dap:1.0
    FileDto:
      type: object
      properties:
        id:
          type: integer
          format: int64
        filename:
          type: string
        path:
          type: string
        lastUpdated:
          type: string
        fileSize:
          type: integer
          format: int64
        parameters:
          type: array
          items:
            $ref: '#/components/schemas/FileMetadataDto'
        downloadUrl:
          type: string
          format: url
        smallThumbnail:
          type: string
        mediumThumbnail:
          type: string
        largeThumbnail:
          type: string
        fullThumbnail:
          type: string
    DataCollectionDtoV2:
      type: object
      properties:
        dataCollectionTypeCode:
          type: string
        id:
          $ref: '#/components/schemas/IdentifierDto'
        dataCollectionId:
          type: integer
          format: int32
        dataCollectionCommonId:
          type: integer
          format: int32
        versionNumber:
          type: integer
          format: int32
        dataVersionNumber:
          type: integer
          format: int32
        self:
          type: string
          format: uri
        landingPage:
          $ref: '#/components/schemas/LinkDto'
        title:
          type: string
        description:
          type: string
        legacyId:
          type: string
        fieldsOfResearch:
          type: array
          items:
            type: string
            xml:
              name: fieldOfResearch
          xml:
            wrapped: true
        contact:
          $ref: '#/components/schemas/ContactDto'
        dataStartDate:
          type: string
        dataEndDate:
          type: string
        keywords:
          type: string
        relatedLinks:
          type: array
          items:
            $ref: '#/components/schemas/RelatedLinkDTO'
          xml:
            wrapped: true
        lineage:
          type: string
        credit:
          type: string
        licence:
          type: string
        licenceLink:
          $ref: '#/components/schemas/LinkDto'
          xml:
            name: link
        organisations:
          type: array
          items:
            type: string
            xml:
              name: organisation
          xml:
            wrapped: true
        attributionStatement:
          type: string
        rights:
          type: string
        access:
          type: string
        size:
          type: string
        dataCollectionVersionId:
          type: integer
          format: int32
        published:
          type: string
        leadResearcher:
          type: string
        versions:
          type: string
          format: uri
        metadata:
          type: string
          format: uri
        data:
          type: string
          format: uri
        serviceCount:
          type: integer
          format: int32
        supportingFiles:
          type: string
          format: uri
        spatialParameters:
          $ref: '#/components/schemas/SpatialParametersDto'
        contributors:
          type: array
          items:
            type: string
            xml:
              name: contributor
          xml:
            wrapped: true
        allNames:
          type: array
          items:
            $ref: '#/components/schemas/NameDto'
        activity:
          $ref: '#/components/schemas/ActivityDto'
        fundingSources:
          type: array
          items:
            type: string
            xml:
              name: fundingSource
          xml:
            wrapped: true
        domainType:
          type: string
        collectionContentType:
          type: string
        andsPid:
          type: string
        doi:
          type: string
        project:
          $ref: '#/components/schemas/ProjectDto'
        nationalFacility:
          type: string
        nationalCollection:
          type: string
        organisationalLevels:
          $ref: '#/components/schemas/OrganisationalLevelsDto'
        accessLevel:
          type: string
        dataRestricted:
          type: string
        voResource:
          $ref: '#/components/schemas/VoResourceDto'
        software:
          $ref: '#/components/schemas/SoftwareDto'
        specimen:
          $ref: '#/components/schemas/SpecimenDto'
        sensor:
          $ref: '#/components/schemas/SensorDto'
        darwinCore:
          $ref: '#/components/schemas/DarwinCoreDto'
        marineCommunityProfile:
          $ref: '#/components/schemas/MarineCommunityProfileDto'
        anzlic:
          $ref: '#/components/schemas/AnzlicDto'
        latestVersion:
          type: integer
          format: int32
        progressDois:
          type: object
          additionalProperties:
            type: string
        progressDoisVerbose:
          type: array
          items:
            $ref: '#/components/schemas/ProgressDoiDto'
        coveragePreviewLink:
          type: string
        depositStatus:
          type: string
        accessViewable:
          type: boolean
        withdrawn:
          type: boolean
        blocked:
          type: boolean
        askapLevel7:
          type: boolean
        fileCount:
          type: integer
          format: int64
        imageCount:
          type: integer
          format: int64
        collectionSize:
          type: integer
          format: int64
        permaLink:
          type: string
        selfLink:
          type: string
        templateCollection:
          type: boolean
      required:
      - dataCollectionCommonId
      - dataCollectionId
      - dataCollectionTypeCode
      - dataVersionNumber
      - id
      - self
      - title
      - versionNumber
      xml:
        name: dataCollection
    ContactDto:
      type: object
      properties:
        contactName:
          type: string
        contactDetails:
          type: string
      xml:
        name: contact
        namespace: urn:au:csiro:rds:dap:1.0
    SpatialParametersDto:
      type: object
      properties:
        id:
          type: integer
          format: int32
        projection:
          type: string
        northLatitude:
          type: string
        southLatitude:
          type: string
        westLongitude:
          type: string
        eastLongitude:
          type: string
    DarwinCoreDto:
      type: object
      properties:
        scientificName:
          type: string
        commonName:
          type: string
        kingdom:
          type: string
        phylum:
          type: string
        class:
          type: string
        order:
          type: string
        family:
          type: string
        genus:
          type: string
        species:
          type: string
        comments:
          type: string
      xml:
        name: DarwinCore
        namespace: urn:au:csiro:rds:dap:1.0
    SoftwareDto:
      type: object
      properties:
        environmentRequirements:
          type: string
        programmingLanguage:
          type: string
        operatingSystem:
          type: string
        version:
          type: string
      xml:
        name: Software
        namespace: urn:au:csiro:rds:dap:1.0
    MarineCommunityProfileDto:
      type: object
      properties:
        voyageId:
          type: string
        alternateTitle:
          type: string
        supplementalInformation:
          type: string
        isoTopicCategories:
          type: array
          items:
            type: string
            xml:
              name: isoTopicCategory
          xml:
            wrapped: true
        gcmdKeywords:
          type: string
        mcpCollectionMethods:
          type: string
        mcpGeographicExtentNames:
          type: string
        csiroAreasOfInterest:
          type: string
        csiroGlobalProjectList:
          type: string
        csiroSourceList:
          type: string
        csiroSurveyList:
          type: string
        csiroStandardDataTypes:
          type: string
        region:
          type: string
        australianNationalSpeciesList:
          type: string
        worldRegisterOfMarineSpeciesAlgae:
          type: string
        verticalCoordinateSystem:
          type: string
        verticalExtentMin:
          type: string
        verticalExtentMax:
          type: string
        spatialRepresentationType:
          type: string
        spatialResolution:
          type: string
        completenessOmission:
          type: string
        distributions:
          type: array
          items:
            $ref: '#/components/schemas/DistributionDto'
          xml:
            wrapped: true
        metadataContacts:
          type: array
          items:
            $ref: '#/components/schemas/MetadataContactDto'
          xml:
            wrapped: true
        metadataLanguage:
          type: string
        metadataCharacterSet:
          type: string
        metadataDateStamp:
          type: string
        revisionDate:
          type: string
      xml:
        name: MarineCommunityProfile
        namespace: urn:au:csiro:rds:dap:1.0
    MetadataContactDto:
      type: object
      properties:
        id:
          type: integer
          format: int32
        organisation:
          type: string
        individualName:
          type: string
        position:
          type: string
        role:
          type: string
        contactInformation:
          type: string
    OrganisationalLevelsDto:
      type: object
      properties:
        irpHierarchy:
          type: boolean
          xml:
            attribute: true
        businessUnit:
          type: string
        team:
          type: string
        program:
          type: string
        group:
          type: string
        costCentre:
          type: string
        researchProgram:
          type: string
        researchGroup:
          type: string
  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-api-v2-openapi.json
- csiro-dap-api-v2-openapi.yml