cwlVersion: v1.2

$namespaces:
  s: https://schema.org/
  cwltool: http://commonwl.org/cwltool#

$graph:

- class: Workflow
  id: bathymetry_pipeline_2s3
  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
    region:
      type: string?
      doc: region
    endpoint:
      type: string
      doc: endpoint
    access_key:
      type: string
      doc: access_key
    secret_key:
      type: string
      doc: secret_key
    session_token:
      type: string?
      doc: region
    bucket:
      type: string
      doc: bucket
  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'
      in:
        region: region
        endpoint: endpoint
        access_key: access_key
        secret_key: secret_key
        session_token: session_token
        bucket: bucket
        stac_result: step_2stac/results
      out:
        - base_path

  outputs:
  - id: wf_outputs
    outputSource:
    - step_2stac/results
    type:
      Directory
  hints:
    "cwltool:Secrets":
      secrets: [access_key,secret_key,session_token]

  s:name: Bathymetry for a given area to STAC
  s:description: Bathymetry for a given area to STAC
  s:keywords:
    - bathymetry
    - stac
  s:programmingLanguage: python
  s:sourceOrganization:
    - class: s:Organization
      s:name: INESCTEC
      s:url: https://inesctec.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/others/bathymetry_pipeline_2s3.cwl
  s:dateCreated: "2024-04-01T13:00:00Z"


# tools

- 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: ogc:netcdf
      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:
      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
        # GEBCO_URL: https://pipe-drive.inesctec.pt/inputs/GEBCO_2014_1D.nc
    ResourceRequirement: {}
    InlineJavascriptRequirement: {}
    DockerRequirement:
      dockerPull: iliad-repository.inesctec.pt/bathymetry-forth:0.1.0

  s:name: Bathymetry for given bounding box
  s:description: Get bathymetry to a given bounding box. You can define an outside source.
  s:keywords:
    - bathymetry
    - bounding box
  s:softwareVersion: 0.1.0
  s:programmingLanguage: python
  s:sourceOrganization:
    - class: s:Organization
      s:name: INESCTEC
      s:url: https://inesctec.pt
    - class: s:Organization
      s:name: FORTH
      s:url: https://forth.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_1_0.cwl
  s:dateCreated: "2024-04-01T13:00:00Z"

- 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:
      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:0.1.0

  s:name: 2Stac
  s:softwareVersion: 0.1.0
  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: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_1_0.cwl
  s:dateCreated: "2024-04-01T13:00:00Z"

- 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 [];
        }
      }())
  - --base_path
  - valueFrom: $(
      function () {
        return "bathymetry_pipeline_2s3_result_" + new Date().toISOString().replace(/:/g, '').replace(/\-/g, '').split('.')[0];
      }())
  - valueFrom: $(
      function () {
        if (inputs.session_token) {
          return ["--session_token", inputs.session_token];
        } else {
          return [];
        }
      }())
  - --directory
  - valueFrom: $( inputs.stac_result )

  inputs:
    region:
      type: string?
      doc: region
    endpoint:
      type: string
      doc: endpoint
    access_key:
      type: string
      doc: access_key
    secret_key:
      type: string
      doc: secret_key
    session_token:
      type: string?
      doc: session_token
    bucket:
      type: string
      doc: bucket
    stac_result:
      type: Directory
      doc: stac result folder

  outputs:
    base_path:
      type: string

  requirements:
    NetworkAccess:
      networkAccess: true
    ResourceRequirement: {}
    InlineJavascriptRequirement: {}
    DockerRequirement:
      dockerPull: iliad-repository.inesctec.pt/2s3:0.1.0
  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: 0.1.0
  s:sourceOrganization:
    - class: s:Organization
      s:name: INESCTEC
      s:url: https://inesctec.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_1_0.cwl
  s:dateCreated: "2024-04-01T13:00:00Z"