cwlVersion: v1.2

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

$graph:

- class: Workflow
  id: pipeline-fisheries
  doc: Pipeline to ILVO fisheries
  inputs:
    username:
      type: string
      doc: CMEMS username
      s:name: CMEMS username
      s:description: CMEMS username to download datasets
      s:keywords:
        - username
        - CMEMS
    password:
      type: string
      doc: CMEMS password
      s:name: CMEMS password
      s:description: CMEMS password to download datasets
      s:keywords:
        - password
        - CMEMS
  steps:
    step_1:
      run: '#fisheries'
      in:
        username: username
        password: password
      out:
      - output1
      - output2
      - metadata
    step_2:
      run: '#2stac2'
      in:
        file1: step_1/output1
        file2: step_1/output2
        metadata: step_1/metadata
      out:
      - results
    
  outputs:
  - id: wf_outputs
    outputSource:
    - step_2/results
    type:
      Directory

- class: CommandLineTool
  baseCommand: fisheries
  id: fisheries

  arguments:
  - --username
  - valueFrom: $( inputs.username )
  - --password
  - valueFrom: $( inputs.password )

  inputs:
    username:
      type: string
      doc: CMEMS username
      s:name: CMEMS username
      s:description: CMEMS username to download datasets
      s:keywords:
        - username
        - CMEMS
    password:
      type: string
      doc: CMEMS password
      s:name: CMEMS password
      s:description: CMEMS password to download datasets
      s:keywords:
        - password
        - CMEMS

  outputs:
    output1:
      type: File
      outputBinding:
        glob: "Output/PLE*.tiff"
    output2:
      type: File
      outputBinding:
        glob: "Output/SOL*.tiff"

    metadata:
      type: File
      outputBinding:
        glob: "Output/metadata.json"
      doc: metadata description
      s:fileFormat: "application/json"

  requirements:
    NetworkAccess:
      networkAccess: true

    ResourceRequirement: {}
    InlineJavascriptRequirement: {}
  
  hints:
    "cwltool:Secrets":
      secrets: [username,password]
    DockerRequirement:
      dockerPull: iliad-repository.inesctec.pt/fisheries:1.0.0


- class: CommandLineTool
  baseCommand: 2stac
  id: 2stac2

  arguments:
  - valueFrom: $(
      function () {
        var files_array = [];

        Object.keys(inputs).forEach(element => {
          if(element != 'metadata') {
            files_array.push('--files');
            files_array.push(inputs[element]);
          } else {
            files_array.push('--metadata');
            files_array.push(inputs[element]);
          }
        });

        return files_array;
      }())
  
  inputs:
    file1:
      type: File
      doc: The resulting file of the previous model to insert in STAC 
      s:name: Input result file
      s:description: The resulting file of the previous model to insert in STAC 
      s:keywords:
        - result
        - File
      s:fileFormat: "image/tiff"
    file2:
      type: File
      doc: The resulting file of the previous model to insert in STAC 
      s:name: Input result file
      s:description: The resulting file of the previous model to insert in STAC 
      s:keywords:
        - result
        - File
      s:fileFormat: "image/tiff"
    metadata:
      type: File
      doc: The resulting metadata of the previous model to insert in STAC 
      s:name: Input metadata file
      s:description: The resulting metadata of the previous model to insert in STAC 
      s:keywords:
        - metadata
        - File
      s:fileFormat: "application/json"

  outputs:
    results:
      outputBinding:
        glob: .
      type: Directory
      doc: STAC output

  requirements:
    EnvVarRequirement:
      envDef:
        PATH: /srv/conda/envs/model-env/bin:/srv/conda/bin:/srv/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
    ResourceRequirement: {}
    InlineJavascriptRequirement: {}
    DockerRequirement:
      dockerPull: iliad-repository.inesctec.pt/2stac2:1.0.0


s:softwareVersion: 1.0.0
s:name: fisheries
s:dateCreated: "2023-10-09"