cwlVersion: v1.2
$namespaces:
  s: https://schema.org/
  cwltool: http://commonwl.org/cwltool#
  edam: http://edamontology.org/
$graph:
  - class: Workflow
    id: bathymetry_pipeline
    inputs:
      lon_min:
        type: float
        label: Minimum Longitude
        doc: The minimum longitude of the study area
      lon_max:
        type: float
        label: Maximum Longitude
        doc: The maximum longitude of the study area
      lat_min:
        type: float
        label: Minimum Latitude
        doc: The minimum latitude of the study area
      lat_max:
        type: float
        label: Maximum Latitude
        doc: The maximum latitude of the study area
      endpoint:
        type: string?
        doc: S3 storage endpoint
      region:
        type: string?
        doc: S3 storage region
      access_key:
        type: string?
        doc: S3 storage access_key
      secret_key:
        type: string?
        doc: S3 storage secret_key
      session_token:
        type: string?
        doc: S3 storage region
      bucket:
        type: string?
        doc: S3 storage bucket
      base_path:
        type: string?
        doc: S3 storage final directory name
        default: bathymetry_pipeline
    steps:
      step_bathymetry:
        run: '#bathymetry'
        in:
          lon_min: lon_min
          lon_max: lon_max
          lat_min: lat_min
          lat_max: lat_max
        out:
          - result
          - metadata
      step_2stac:
        run: '#2stac'
        in:
          result: step_bathymetry/result
          metadata: step_bathymetry/metadata
        out:
          - results
      step_2s3:
        run: '#2s3'
        when: $(inputs.endpoint != null && inputs.endpoint != "")
        in:
          region: region
          endpoint: endpoint
          access_key: access_key
          secret_key: secret_key
          session_token: session_token
          bucket: bucket
          directory: step_2stac/results
          base_path: base_path
        out:
          - base_path
    outputs:
      - id: wf_outputs
        outputSource:
          - step_2stac/results
        type: Directory
    hints:
      cwltool:Secrets:
        secrets:
          - access_key
          - secret_key
          - session_token
    requirements:
      InlineJavascriptRequirement: {}
    s:name: bathymetry_pipeline
    s:description: >
      This pipeline crops the bathymetry for a given area, transforms the result
      to STAC format and stores the results in a S3 bucket.


      The step of saving the results to S3 is optional: if the input endpoint is
      not set, the S3 step is skipped.
    s:keywords:
      - bathymetry
      - stac
    s:softwareVersion: 10.3.0
    s:sourceOrganization:
      class: s:Organization
      s:name: INESCTEC
      s:url: https://inesctec.pt
      s:address:
        class: s:PostalAddress
        s:addressCountry: PT
    s:author:
      class: s:Person
      s:name: Miguel Correia
      s:email: miguel.r.correia@inesctec.pt
    s:codeRepository: >-
      https://pipe-drive.inesctec.pt/application-packages/workflows/bathymetry-pipeline/bathymetry_pipeline_10_3_0.cwl
    s:dateCreated: '2025-02-13T10:49:29Z'
  - class: CommandLineTool
    id: bathymetry
    baseCommand: python
    arguments:
      - /opt/bathymetry.py
      - '--lon_min'
      - valueFrom: $( inputs.lon_min )
      - '--lon_max'
      - valueFrom: $( inputs.lon_max )
      - '--lat_min'
      - valueFrom: $( inputs.lat_min )
      - '--lat_max'
      - valueFrom: $( inputs.lat_max )
    inputs:
      lon_min:
        type: float
        doc: The minimum longitude of the study area.
      lon_max:
        type: float
        doc: The maximum longitude of the study area.
      lat_min:
        type: float
        doc: The minimum latitude of the study area.
      lat_max:
        type: float
        doc: The maximum latitude of the study area.
    outputs:
      result:
        format: edam:format_3650
        type: File
        outputBinding:
          glob: result/out.nc
        doc: |
          The output NetCDF file generated by the bathymetry model.
          The file is in the OGC NetCDF media type.
      metadata:
        format: edam:format_3464
        type: File
        outputBinding:
          glob: result/metadata.json
        doc: metadata description
    requirements:
      NetworkAccess:
        networkAccess: true
      EnvVarRequirement:
        envDef:
          PATH: >-
            /opt/conda/envs/application/bin:/opt/conda/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
      ResourceRequirement: {}
      InlineJavascriptRequirement: {}
      DockerRequirement:
        dockerPull: iliad-repository.inesctec.pt/bathymetry-forth:0.2.0
    s:name: bathymetry
    s:description: Get bathymetry to a given bounding box. You can define an outside source.
    s:keywords:
      - bathymetry
      - bounding box
    s:softwareVersion: 0.2.0
    s:programmingLanguage: python
    s:sourceOrganization:
      class: s:Organization
      s:name: FORTH
      s:url: https://forth.gr
      s:address:
        class: s:PostalAddress
        s:addressCountry: GR
    s:author:
      class: s:Person
      s:email: kspanoudaki@gmail.com
      s:name: Katerina Spanoudaki
    s:contributor:
      class: s:Person
      s:email: miguel.r.correia@inesctec.pt
      s:name: Miguel Correia
    s:codeRepository: >-
      https://pipe-drive.inesctec.pt/application-packages/tools/bathymetry-forth/bathymetry_forth_0_2_0.cwl
    s:dateCreated: '2025-02-07T17:02:04Z'
  - class: CommandLineTool
    id: 2stac
    baseCommand: python
    arguments:
      - /opt/2stac.py
      - '--result'
      - valueFrom: $( inputs.result )
      - '--metadata'
      - valueFrom: $( inputs.metadata )
    inputs:
      result:
        type: File
        doc: The resulting file of the previous model to insert in STAC
      metadata:
        format: edam:format_3464
        type: File
        doc: The resulting metadata of the previous model to insert in STAC
    outputs:
      results:
        outputBinding:
          glob: .
        type: Directory
        doc: STAC output
    requirements:
      ResourceRequirement: {}
      InlineJavascriptRequirement: {}
      DockerRequirement:
        dockerPull: iliad-repository.inesctec.pt/2stac:0.2.0
    s:name: 2stac
    s:softwareVersion: 0.2.0
    s:description: Transform the result into a STAC
    s:keywords:
      - stac
      - metadata
    s:programmingLanguage: python
    s:sourceOrganization:
      class: s:Organization
      s:name: INESCTEC
      s:url: https://inesctec.pt
      s:address:
        class: s:PostalAddress
        s:addressCountry: PT
    s:author:
      class: s:Person
      s:name: Miguel Correia
      s:email: miguel.r.correia@inesctec.pt
    s:codeRepository: >-
      https://pipe-drive.inesctec.pt/application-packages/tools/2stac/2stac_0_2_0.cwl
    s:dateCreated: '2025-02-07T16:53:16Z'
  - class: CommandLineTool
    id: 2s3
    baseCommand: python
    arguments:
      - /opt/2s3.py
      - '--endpoint'
      - valueFrom: $( inputs.endpoint )
      - '--access_key'
      - valueFrom: $( inputs.access_key )
      - '--secret_key'
      - valueFrom: $( inputs.secret_key )
      - '--bucket'
      - valueFrom: $( inputs.bucket )
      - '--endpoint'
      - valueFrom: $( inputs.endpoint )
      - valueFrom: >-
          $( function () { if (inputs.region) { return ["--region",
          inputs.region]; } else { return []; } }())
      - valueFrom: >-
          $( function () { if (inputs.base_path) { return ["--base_path",
          `${inputs.base_path}_${new Date().toISOString().replace(/:/g,
          '').replace(/\-/g, '').split('.')[0]}`]; } else { return []; } }())
      - valueFrom: >-
          $( function () { if (inputs.session_token) { return
          ["--session_token", inputs.session_token]; } else { return []; } }())
      - valueFrom: >-
          $( function () { if(inputs.files) { var files_array = [];

          Object.keys(inputs.files).forEach(function (element) {
          files_array.push('--file'); files_array.push(inputs.files[element]);
          });

          return files_array; } else { return []; } }())
      - valueFrom: >-
          $( function () { if(inputs.directories) { var directories_array = [];

          Object.keys(inputs.directories).forEach(function (element) {
          directories_array.push('--directory');
          directories_array.push(inputs.directories[element]); });

          return directories_array; } else { return []; } }())
      - valueFrom: >-
          $( function () { if(inputs.file) { return ['--file', inputs.file]; }
          else { return []; } }())
      - valueFrom: >-
          $( function () { if(inputs.directory) { return ['--directory',
          inputs.directory]; } else { return []; } }())
    inputs:
      endpoint:
        type: string?
        doc: S3 storage endpoint
      region:
        type: string?
        doc: S3 storage region
      access_key:
        type: string?
        doc: S3 storage access_key
      secret_key:
        type: string?
        doc: S3 storage secret_key
      session_token:
        type: string?
        doc: S3 storage region
      bucket:
        type: string?
        doc: S3 storage bucket
      base_path:
        type: string?
        doc: S3 storage final directory name
      files:
        type: File[]?
        doc: Multiple files to upload
      directories:
        type: Directory[]?
        doc: Multiple directories to upload
      directory:
        type: Directory?
        doc: Single directory to upload
      file:
        type: File?
        doc: Single file to upload
    outputs:
      base_path:
        type: string
    requirements:
      NetworkAccess:
        networkAccess: true
      ResourceRequirement: {}
      InlineJavascriptRequirement: {}
      DockerRequirement:
        dockerPull: iliad-repository.inesctec.pt/2s3:0.2.0
    hints:
      cwltool:Secrets:
        secrets:
          - access_key
          - secret_key
          - session_token
    s:name: 2s3
    s:description: Uploads files and/or folders to a S3 bucket storage.
    s:keywords:
      - s3
      - storage
    s:programmingLanguage: python
    s:softwareVersion: 0.2.0
    s:sourceOrganization:
      class: s:Organization
      s:name: INESCTEC
      s:url: https://inesctec.pt
      s:address:
        class: s:PostalAddress
        s:addressCountry: PT
    s:author:
      class: s:Person
      s:name: Miguel Correia
      s:email: miguel.r.correia@inesctec.pt
    s:codeRepository: >-
      https://pipe-drive.inesctec.pt/application-packages/tools/2s3/2s3_0_2_0.cwl
    s:dateCreated: '2025-02-07T16:52:37Z'