cwlVersion: v1.2
$namespaces:
  s: https://schema.org/
  cwltool: http://commonwl.org/cwltool#
  edam: http://edamontology.org/
$graph:
  - class: Workflow
    id: booms_visualization_pipeline
    doc: >-
      This pipeline runs an oil spill simulation pipeline with openoil, and
      creates visualizations of the simulation results.
    inputs:
      latitude:
        type: double
        doc: Spill center latitude (WGS-84)
      longitude:
        type: double
        doc: Spill center longitude (WGS-84)
      radius:
        type: int
        doc: Initial radius of the oil spill on the sea surface
      start_time:
        type: string
        doc: Calendar date and time when the spill begins (UTC)
      duration:
        type: int
        doc: Total number of hours to simulate
      particles:
        type: int?
        doc: >-
          Number of particles used to represent the oil slick. More particles
          provide higher detail, require more computation time
      mass:
        type: int?
        doc: Total mass of oil spilled in kilograms
      reader_ocean:
        type: string?
        doc: THREDDS or OPeNDAP URL for ocean currents data
      reader_wave:
        type: string?
        doc: THREDDS or OPeNDAP URL for wave data
      reader_wind:
        type: string?
        doc: THREDDS or OPeNDAP URL for wind data
      time_step:
        type: int?
        doc: Model's internal calculation interval
      time_step_output:
        type: int?
        doc: Result interval. Must be greater than time_step
      oil_type:
        type: string?
        doc: >-
          Type of oil spilled. This determines its physical and chemical
          properties
      booms:
        type: string
        doc: List of containment booms
      density:
        type: double?
        doc: Oil density values
      viscosity:
        type: double?
        doc: Oil viscosity values
    steps:
      step_simulation:
        run: '#openoil_booms'
        in:
          latitude: latitude
          longitude: longitude
          radius: radius
          start_time: start_time
          duration: duration
          particles: particles
          mass: mass
          reader_ocean: reader_ocean
          reader_wave: reader_wave
          reader_wind: reader_wind
          time_step: time_step
          time_step_output: time_step_output
          oil_type: oil_type
          booms: booms
          density: density
          viscosity: viscosity
        out:
          - map
          - result
          - simulation
          - simulation_currents
      step_netcdf_metadata:
        run: '#netcdf_metadata'
        in:
          netcdf_file: step_simulation/result
        out:
          - metadata
      step_2stac2:
        run: '#2stac2_openoil_pipeline'
        in:
          simulation: step_simulation/result
          metadata: step_netcdf_metadata/metadata
        out:
          - stac_result
    outputs:
      - id: wf_outputs
        outputSource:
          - step_2stac2/stac_result
        type: Directory
    hints:
      cwltool:Secrets:
        secrets:
          - access_key
          - secret_key
          - session_token
          - password
    requirements:
      InlineJavascriptRequirement: {}
      SubworkflowFeatureRequirement: {}
    s:name: booms_visualization_pipeline
    s:description: >
      This pipeline runs an oil spill pipeline with openoil and creates
      visualizations of the simulation results.
    s:keywords:
      - oil spill
      - openoil
      - opendrift
      - visualization
    s:softwareVersion: 0.1.0
    s:producer:
      class: s:Organization
      s:name: INESCTEC
      s:url: https://inesctec.pt
      s:address:
        class: s:PostalAddress
        s:addressCountry: PT
    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:dateCreated: '2025-12-04T10:49:31Z'
  - class: CommandLineTool
    id: openoil_booms
    baseCommand:
      - python
      - /opt/headless.py
    inputs:
      latitude:
        type: double
        doc: Spill center latitude (WGS-84)
        inputBinding:
          prefix: '--lat'
      longitude:
        type: double
        doc: Spill center longitude (WGS-84)
        inputBinding:
          prefix: '--lon'
      radius:
        type: int
        doc: Initial radius of the oil spill on the sea surface
        inputBinding:
          prefix: '--radius'
      start_time:
        type: string
        doc: Calendar date and time when the spill begins (UTC)
        inputBinding:
          prefix: '--start_time'
      duration:
        type: int
        doc: Total number of hours to simulate
        inputBinding:
          prefix: '--duration_hours'
      particles:
        type: int?
        doc: >-
          Number of particles used to represent the oil slick. More particles
          provide higher detail, require more computation time
        inputBinding:
          prefix: '--number'
      mass:
        type: int?
        doc: Total mass of oil spilled in kilograms
        inputBinding:
          prefix: '--total_mass_kg'
      reader_ocean:
        type: string?
        doc: THREDDS or OPeNDAP URL for ocean currents data
        inputBinding:
          prefix: '--reader_ocean'
      reader_wave:
        type: string?
        doc: THREDDS or OPeNDAP URL for wave data
        inputBinding:
          prefix: '--reader_wave'
      reader_wind:
        type: string?
        doc: THREDDS or OPeNDAP URL for wind data
        inputBinding:
          prefix: '--reader_wind'
      time_step:
        type: int?
        doc: Model's internal calculation interval
        inputBinding:
          prefix: '--time_step'
      time_step_output:
        type: int?
        doc: Result interval. Must be greater than time_step
        inputBinding:
          prefix: '--time_step_output'
      oil_type:
        type: string?
        doc: >-
          Type of oil spilled. This determines its physical and chemical
          properties
        inputBinding:
          prefix: '--oil_type'
      density:
        type: double?
        doc: Mass per unit volume of the oil
        inputBinding:
          prefix: '--density'
      viscosity:
        type: double?
        doc: Oil's resistance to flow
        inputBinding:
          prefix: '--viscosity'
      booms:
        type: string?
        doc: List of containment booms
        inputBinding:
          prefix: '--boom'
          position: 1
    outputs:
      map:
        type: File
        format: edam:format_3603
        doc: Map of particles
        outputBinding:
          glob: map.png
      result:
        type: File
        format: edam:format_3650
        doc: Result NetCDF file
        outputBinding:
          glob: results.nc
      simulation:
        type: File
        format: edam:format_3997
        doc: Video of particle simulation
        outputBinding:
          glob: simulation.mp4
      simulation_currents:
        type: File?
        format: edam:format_3997
        doc: Video of particle simulation with currents data
        outputBinding:
          glob: initial_simulation_with_currents.mp4
      statistics:
        type: File
        format: edam:format_3464
        doc: Extra process data
        outputBinding:
          glob: statistics.json
    requirements:
      NetworkAccess:
        networkAccess: true
      ResourceRequirement: {}
      InlineJavascriptRequirement: {}
      DockerRequirement:
        dockerPull: iliad-repository.inesctec.pt/openoil-booms:0.4.0
    s:name: openoil_booms
    s:description: OpenOil with Booms
    s:keywords:
      - opendrift
      - openoil
      - booms
    s:programmingLanguage: python
    s:softwareVersion: 0.4.0
    s:producer:
      class: s:Organization
      s:name: INESCTEC
      s:url: https://inesctec.pt
      s:address:
        class: s:PostalAddress
        s:addressCountry: PT
    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: Joao Campos
        s:email: joao.campos@inesctec.pt
    s:dateCreated: '2025-12-04T09:02:27Z'
  - class: CommandLineTool
    id: netcdf_metadata
    baseCommand: python
    arguments:
      - /opt/parse.py
      - '--netcdf_file'
      - valueFrom: $(inputs.netcdf_file)
      - valueFrom: $(inputs.extra_props ? ['--extra_props', inputs.extra_props] :[])
    inputs:
      netcdf_file:
        type: File
      extra_props:
        type: File?
    outputs:
      metadata:
        outputBinding:
          glob: ./metadata.json
        type: File
        format: edam:format_3464
    requirements:
      MultipleInputFeatureRequirement: {}
      ResourceRequirement: {}
      InlineJavascriptRequirement: {}
      DockerRequirement:
        dockerPull: iliad-repository.inesctec.pt/netcdf-metadata:0.1.0
    s:name: netcdf_metadata
    s:softwareVersion: 0.1.0
    s:description: Extract metadata from NetCDF file
    s:keywords:
      - netcdf
      - metadata
    s:programmingLanguage: python
    s:producer:
      class: s:Organization
      s:name: INESCTEC
      s:url: https://inesctec.pt
      s:address:
        class: s:PostalAddress
        s:addressCountry: PT
    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:dateCreated: '2025-11-13T17:39:29Z'
  - class: CommandLineTool
    id: 2stac2_openoil_pipeline
    baseCommand: python
    arguments:
      - /opt/2stac2.py
    inputs:
      simulation:
        format: edam:format_3650
        doc: simulation NetCDF file
        type: File
        inputBinding:
          prefix: '--file'
      animation:
        format: edam:format_3467
        doc: animation Gif file
        type: File?
        inputBinding:
          prefix: '--file'
      metadata:
        format: edam:format_3464
        doc: metadata file description
        type: File
        loadContents: true
        inputBinding:
          prefix: '--metadata'
          valueFrom: $(runtime.outdir + '/multiple_metadata.json')
    outputs:
      stac_result:
        outputBinding:
          glob: stac_result
        type: Directory
        doc: STAC output
    requirements:
      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/2stac2:0.3.1
      InplaceUpdateRequirement:
        inplaceUpdate: true
      InitialWorkDirRequirement:
        listing: |
          ${
            const content = JSON.parse(inputs.metadata.contents);
            const metadata = [];
            metadata.push({...content, filename:inputs["simulation"].basename});
            if(inputs["animation"] != null) {
              metadata.push({...content, filename:inputs["animation"].basename , media_type:"image/gif" });
            }
            return [{"class": "File", "basename": "multiple_metadata.json", "contents": JSON.stringify(metadata) }];
          }
    s:name: 2stac2_openoil_pipeline
    s:softwareVersion: 0.3.1
    s:description: >-
      2stac2 tool to transform OpenOil simulation and animation files into a
      STAC
    s:keywords:
      - stac
      - metadata
    s:programmingLanguage: python
    s:producer:
      class: s:Organization
      s:name: INESCTEC
      s:url: https://inesctec.pt
      s:address:
        class: s:PostalAddress
        s:addressCountry: PT
    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:dateCreated: '2025-11-17T16:08:31Z'