Pattern 12 - one input, three outputs of different kind¶

The CWL includes:

one input parameter type Directory;
output parameters:
- two of type Directory;
- one of type Directory[].

This scenario takes as input an array of acquisition, applies an algorithm to each of them.

This scenario shows the need to flatten the output of the subworkflow, which is an array of arrays, into a single array of directories.

Building the Worflow¶

In [1]:

Copied!





from eoap_cwlwrap import wrap
from eoap_cwlwrap.loader import ( load_workflow, dump_workflow )
import sys

base_url = 'https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/main'
workflow_id = 'pattern-12'

directory_stage_in = load_workflow(path=f"{base_url}/templates/stage-in.cwl")
file_stage_in = load_workflow(path=f"{base_url}/templates/stage-in-file.cwl")
workflows_cwl = load_workflow(path=f"{base_url}/cwl-workflow/{workflow_id}.cwl")
stage_out_cwl = load_workflow(path=f"{base_url}/templates/stage-out.cwl")

main_workflow = wrap(
    directory_stage_in=directory_stage_in,
    file_stage_in=file_stage_in,
    workflows=workflows_cwl,
    workflow_id=workflow_id,
    stage_out=stage_out_cwl
)

print('------------------------------------------------------------------------')
print('BUILD SUCCESS')
print('------------------------------------------------------------------------')

dump_workflow(main_workflow, sys.stdout)
from eoap_cwlwrap import wrap
from eoap_cwlwrap.loader import ( load_workflow, dump_workflow )
import sys

base_url = 'https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/main'
workflow_id = 'pattern-12'

directory_stage_in = load_workflow(path=f"{base_url}/templates/stage-in.cwl")
file_stage_in = load_workflow(path=f"{base_url}/templates/stage-in-file.cwl")
workflows_cwl = load_workflow(path=f"{base_url}/cwl-workflow/{workflow_id}.cwl")
stage_out_cwl = load_workflow(path=f"{base_url}/templates/stage-out.cwl")

main_workflow = wrap(
    directory_stage_in=directory_stage_in,
    file_stage_in=file_stage_in,
    workflows=workflows_cwl,
    workflow_id=workflow_id,
    stage_out=stage_out_cwl
)

print('------------------------------------------------------------------------')
print('BUILD SUCCESS')
print('------------------------------------------------------------------------')

dump_workflow(main_workflow, sys.stdout)

Loading CWL document from https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/main/templates/stage-in.cwl...
Raw CWL document successfully loaded from https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/main/templates/stage-in.cwl! Now updating the model to v1.2...
Raw CWL document successfully updated! Now converting to the CWL model...

Raw CWL document successfully updated! Now dereferencing the FQNs...
  Cleaning CommandLineTool my-asthonishing-stage-in-directory...
CWL document successfully dereferenced!
Loading CWL document from https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/main/templates/stage-in-file.cwl...
Raw CWL document successfully loaded from https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/main/templates/stage-in-file.cwl! Now updating the model to v1.2...
Raw CWL document successfully updated! Now converting to the CWL model...

Raw CWL document successfully updated! Now dereferencing the FQNs...
  Cleaning CommandLineTool my-asthonishing-stage-in-file...
CWL document successfully dereferenced!
Loading CWL document from https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/main/cwl-workflow/pattern-12.cwl...
Raw CWL document successfully loaded from https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/main/cwl-workflow/pattern-12.cwl! Now updating the model to v1.2...
Raw CWL document successfully updated! Now converting to the CWL model...

Raw CWL document successfully updated! Now dereferencing the FQNs...
  Cleaning Workflow pattern-12...
  Cleaning CommandLineTool crop...
  Cleaning CommandLineTool norm_diff...
  Cleaning CommandLineTool otsu...
CWL document successfully dereferenced!
Loading CWL document from https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/main/templates/stage-out.cwl...
Raw CWL document successfully loaded from https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/main/templates/stage-out.cwl! Now updating the model to v1.2...
Raw CWL document successfully updated! Now converting to the CWL model...

------------------------------------------------------------------------
BUILD SUCCESS
------------------------------------------------------------------------
cwlVersion: v1.2
$graph:
- id: main
  class: Workflow
  label: Workflow pattern-12 orchestrator
  doc: This Workflow is used to orchestrate the Workflow pattern-12
  inputs:
  - id: aoi
    label: area of interest - pattern-12/aoi
    doc: area of interest as a bounding box - This parameter is derived from 
      pattern-12/aoi
    type: https://raw.githubusercontent.com/eoap/schemas/main/ogc.yaml#BBox
  - id: bands
    label: bands used for the NDWI - pattern-12/bands
    doc: bands used for the NDWI - This parameter is derived from 
      pattern-12/bands
    default:
    - green
    - nir
    type:
      name: _:b7fa8882-6bd2-464b-9990-e97ec8a2f7cf
      items: string
      type: array
  - id: another_input
    label: Another Input - my-asthonishing-stage-in-directory/another_input
    doc: An additional input for demonstration purposes - This parameter is 
      derived from my-asthonishing-stage-in-directory/another_input
    type: string
  - id: item
    label: Landsat-8/9 acquisition reference - pattern-12/item
    doc: Landsat-8/9 acquisition reference - This parameter is derived from 
      pattern-12/item
    type: 
      https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI
  - id: cropped-collection
    label: cropped reflectances STAC Collection - pattern-12/cropped-collection
    doc: STAC Collection URL for the cropped reflectances - This parameter is 
      derived from pattern-12/cropped-collection
    type: 
      https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI
  - id: ndwi-collection
    label: NDWI STAC Collection - pattern-12/ndwi-collection
    doc: STAC Collection URL for the NDWI - This parameter is derived from 
      pattern-12/ndwi-collection
    type: 
      https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI
  - id: water-bodies-collection
    label: Water bodies STAC Collection - pattern-12/water-bodies-collection
    doc: STAC Collection URL for the water bodies - This parameter is derived 
      from pattern-12/water-bodies-collection
    type: 
      https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI
  - id: s3_bucket
    label: my-super-stage-out/s3_bucket
    doc: 'This parameter is derived from: my-super-stage-out/s3_bucket'
    type: string
  - id: sub_path
    label: my-super-stage-out/sub_path
    doc: 'This parameter is derived from: my-super-stage-out/sub_path'
    type: string
  - id: aws_access_key_id
    label: my-super-stage-out/aws_access_key_id
    doc: 'This parameter is derived from: my-super-stage-out/aws_access_key_id'
    type: string
  - id: aws_secret_access_key
    label: my-super-stage-out/aws_secret_access_key
    doc: 'This parameter is derived from: my-super-stage-out/aws_secret_access_key'
    type: string
  - id: region_name
    label: my-super-stage-out/region_name
    doc: 'This parameter is derived from: my-super-stage-out/region_name'
    type: string
  - id: endpoint_url
    label: my-super-stage-out/endpoint_url
    doc: 'This parameter is derived from: my-super-stage-out/endpoint_url'
    type: string
  outputs:
  - id: cropped
    label: Cropped reflectances
    doc: Cropped reflectances
    outputSource:
    - stage_out_0/s3_catalog_output
    type:
      name: _:9dc94164-5b17-4c19-8fa6-aeae5cd507a8
      items: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI
      type: array
  - id: ndwi
    label: Normalized Difference Water Index
    doc: Normalized Difference Water Index calculated from the input bands
    outputSource:
    - stage_out_1/s3_catalog_output
    type: 
      https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI
  - id: water_bodies
    label: Water bodies detected
    doc: Water bodies detected based on the NDWI and otsu threshold
    outputSource:
    - stage_out_2/s3_catalog_output
    type: 
      https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI
  requirements:
  - class: SubworkflowFeatureRequirement
  - class: ScatterFeatureRequirement
  - class: SchemaDefRequirement
    types:
    - $import: https://raw.githubusercontent.com/eoap/schemas/main/ogc.yaml
    - $import: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml
  steps:
  - id: directory_stage_in_0
    in:
    - id: reference
      source: item
    - id: another_input
      source: another_input
    out:
    - staged
    run: '#my-asthonishing-stage-in-directory'
  - id: app
    in:
    - id: aoi
      source: aoi
    - id: bands
      source: bands
    - id: item
      source: directory_stage_in_0/staged
    - id: cropped-collection
      source: cropped-collection
    - id: ndwi-collection
      source: ndwi-collection
    - id: water-bodies-collection
      source: water-bodies-collection
    out:
    - cropped
    - ndwi
    - water_bodies
    run: '#pattern-12'
  - id: stage_out_0
    in:
    - id: s3_bucket
      source: s3_bucket
    - id: sub_path
      source: sub_path
    - id: aws_access_key_id
      source: aws_access_key_id
    - id: aws_secret_access_key
      source: aws_secret_access_key
    - id: region_name
      source: region_name
    - id: endpoint_url
      source: endpoint_url
    - id: stac_catalog
      source: app/cropped
    out:
    - s3_catalog_output
    run: '#my-super-stage-out'
    scatter: stac_catalog
    scatterMethod: dotproduct
  - id: stage_out_1
    in:
    - id: s3_bucket
      source: s3_bucket
    - id: sub_path
      source: sub_path
    - id: aws_access_key_id
      source: aws_access_key_id
    - id: aws_secret_access_key
      source: aws_secret_access_key
    - id: region_name
      source: region_name
    - id: endpoint_url
      source: endpoint_url
    - id: stac_catalog
      source: app/ndwi
    out:
    - s3_catalog_output
    run: '#my-super-stage-out'
  - id: stage_out_2
    in:
    - id: s3_bucket
      source: s3_bucket
    - id: sub_path
      source: sub_path
    - id: aws_access_key_id
      source: aws_access_key_id
    - id: aws_secret_access_key
      source: aws_secret_access_key
    - id: region_name
      source: region_name
    - id: endpoint_url
      source: endpoint_url
    - id: stac_catalog
      source: app/water_bodies
    out:
    - s3_catalog_output
    run: '#my-super-stage-out'
- http://commonwl.org/cwltool#original_cwlVersion: v1.2
  id: my-asthonishing-stage-in-directory
  class: CommandLineTool
  inputs:
  - id: reference
    label: STAC Item URL
    doc: A STAC Item to stage
    type: 
      https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI
  - id: another_input
    label: Another Input
    doc: An additional input for demonstration purposes
    type: string
  outputs:
  - id: staged
    type: Directory
    outputBinding:
      glob: .
  requirements:
  - class: SchemaDefRequirement
    types:
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Date
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Date/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#DateTime
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#DateTime/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Duration
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Duration/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Email
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Email/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Hostname
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Hostname/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IDNEmail
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IDNEmail/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IDNHostname
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IDNHostname/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IPv4
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IPv4/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IPv6
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IPv6/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IRI
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IRI/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IRIReference
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IRIReference/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#JsonPointer
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#JsonPointer/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Password
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Password/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#RelativeJsonPointer
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#RelativeJsonPointer/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#UUID
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#UUID/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URIReference
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URIReference/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URITemplate
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URITemplate/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Time
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Time/value
        type: string
      type: record
  - class: DockerRequirement
    dockerPull: ghcr.io/eoap/mastering-app-package/stage:1.0.0
  - class: InlineJavascriptRequirement
  - class: InitialWorkDirRequirement
    listing:
    - entryname: stage.py
      entry: |-
        import pystac
        import stac_asset
        import asyncio
        import os
        import sys

        config = stac_asset.Config(warn=True)

        async def main(href: str):
            
            item = pystac.read_file(href)
            
            os.makedirs(item.id, exist_ok=True)
            cwd = os.getcwd()
            
            os.chdir(item.id)
            item = await stac_asset.download_item(item=item, directory=".", config=config)
            os.chdir(cwd)
            
            cat = pystac.Catalog(
                id="catalog",
                description=f"catalog with staged {item.id}",
                title=f"catalog with staged {item.id}",
            )
            cat.add_item(item)
            
            cat.normalize_hrefs("./")
            cat.save(catalog_type=pystac.CatalogType.SELF_CONTAINED)

            return cat

        href = sys.argv[1]
        empty_arg = sys.argv[2]

        cat = asyncio.run(main(href))
  cwlVersion: v1.2
  baseCommand:
  - python
  - stage.py
  arguments:
  - $( inputs.reference.value )
  - $( inputs.another_input )
- id: pattern-12
  class: Workflow
  label: Water body detection based on NDWI and the otsu threshold
  doc: Water bodies detection based on NDWI and otsu threshold applied to 
    Sentinel-2 or Landsat-9 staged acquisitions
  inputs:
  - id: aoi
    label: area of interest
    doc: area of interest as a bounding box
    type: https://raw.githubusercontent.com/eoap/schemas/main/ogc.yaml#BBox
  - id: bands
    label: bands used for the NDWI
    doc: bands used for the NDWI
    default:
    - green
    - nir
    type:
      name: _:b7fa8882-6bd2-464b-9990-e97ec8a2f7cf
      items: string
      type: array
  - id: item
    label: Landsat-8/9 acquisition reference
    doc: Landsat-8/9 acquisition reference
    type: Directory
  - id: cropped-collection
    label: cropped reflectances STAC Collection
    doc: STAC Collection URL for the cropped reflectances
    type: 
      https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI
  - id: ndwi-collection
    label: NDWI STAC Collection
    doc: STAC Collection URL for the NDWI
    type: 
      https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI
  - id: water-bodies-collection
    label: Water bodies STAC Collection
    doc: STAC Collection URL for the water bodies
    type: 
      https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI
  outputs:
  - id: cropped
    label: Cropped reflectances
    doc: Cropped reflectances
    outputSource:
    - node_crop/cropped
    type:
      name: _:adcb6c13-4094-494f-9c8c-a18d7c7c6a09
      items: Directory
      type: array
  - id: ndwi
    label: Normalized Difference Water Index
    doc: Normalized Difference Water Index calculated from the input bands
    outputSource:
    - node_normalized_difference/ndwi
    type: Directory
  - id: water_bodies
    label: Water bodies detected
    doc: Water bodies detected based on the NDWI and otsu threshold
    outputSource:
    - node_otsu/water_bodies
    type: Directory
  requirements:
  - class: ScatterFeatureRequirement
  - class: SchemaDefRequirement
    types:
    - name: https://raw.githubusercontent.com/eoap/schemas/main/ogc.yaml#CRS
      symbols:
      - https://raw.githubusercontent.com/eoap/schemas/main/ogc.yaml#CRS/CRS84
      - https://raw.githubusercontent.com/eoap/schemas/main/ogc.yaml#CRS/CRS84h
      type: enum
    - name: https://raw.githubusercontent.com/eoap/schemas/main/ogc.yaml#BBox
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/ogc.yaml#BBox/bbox
        type:
          name: _:5f695a5a-372e-4cde-8309-a383aa119349
          items: double
          type: array
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/ogc.yaml#BBox/crs
        type: https://raw.githubusercontent.com/eoap/schemas/main/ogc.yaml#CRS
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Date
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Date/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#DateTime
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#DateTime/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Duration
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Duration/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Email
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Email/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Hostname
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Hostname/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IDNEmail
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IDNEmail/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IDNHostname
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IDNHostname/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IPv4
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IPv4/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IPv6
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IPv6/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IRI
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IRI/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IRIReference
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IRIReference/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#JsonPointer
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#JsonPointer/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Password
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Password/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#RelativeJsonPointer
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#RelativeJsonPointer/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#UUID
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#UUID/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URIReference
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URIReference/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URITemplate
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URITemplate/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Time
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Time/value
        type: string
      type: record
  cwlVersion: v1.2
  steps:
  - id: node_crop
    in:
    - id: item
      source: item
    - id: aoi
      source: aoi
    - id: epsg
      source: aoi
    - id: band
      source: bands
    - id: collection
      source: cropped-collection
    out:
    - cropped
    run: '#crop'
    scatter: node_crop/band
    scatterMethod: dotproduct
  - id: node_normalized_difference
    in:
    - id: rasters
      source: node_crop/cropped
    - id: item
      source: item
    - id: collection
      source: ndwi-collection
    out:
    - ndwi
    run: '#norm_diff'
  - id: node_otsu
    in:
    - id: raster
      source: node_normalized_difference/ndwi
    - id: item
      source: item
    - id: collection
      source: water-bodies-collection
    out:
    - water_bodies
    run: '#otsu'
  $namespaces: &id001
    s: https://schema.org/
- http://commonwl.org/cwltool#original_cwlVersion: v1.2
  id: my-super-stage-out
  class: CommandLineTool
  doc: Stage-out the results to S3
  inputs:
  - id: s3_bucket
    type: string
  - id: sub_path
    type: string
  - id: aws_access_key_id
    type: string
  - id: aws_secret_access_key
    type: string
  - id: region_name
    type: string
  - id: endpoint_url
    type: string
  - id: stac_catalog
    label: STAC Catalog folder
    doc: The folder containing the STAC catalog to stage out
    type: Directory
  outputs:
  - id: s3_catalog_output
    type: 
      https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI
    outputBinding:
      loadContents: true
      glob: catalog-uri.txt
      outputEval: |
        ${ 
          return { "value": self[0].contents, "type": "https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI" };
        }
  requirements:
  - class: SchemaDefRequirement
    types:
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Date
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Date/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#DateTime
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#DateTime/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Duration
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Duration/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Email
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Email/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Hostname
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Hostname/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IDNEmail
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IDNEmail/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IDNHostname
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IDNHostname/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IPv4
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IPv4/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IPv6
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IPv6/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IRI
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IRI/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IRIReference
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IRIReference/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#JsonPointer
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#JsonPointer/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Password
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Password/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#RelativeJsonPointer
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#RelativeJsonPointer/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#UUID
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#UUID/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URIReference
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URIReference/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URITemplate
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URITemplate/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Time
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Time/value
        type: string
      type: record
  - class: DockerRequirement
    dockerPull: ghcr.io/eoap/mastering-app-package/stage:1.0.0
  - class: InlineJavascriptRequirement
  - class: EnvVarRequirement
    envDef:
    - envName: aws_access_key_id
      envValue: $( inputs.aws_access_key_id )
    - envName: aws_secret_access_key
      envValue: $( inputs.aws_secret_access_key )
    - envName: aws_region_name
      envValue: $( inputs.region_name )
    - envName: aws_endpoint_url
      envValue: $( inputs.endpoint_url )
  - class: ResourceRequirement
  - class: InitialWorkDirRequirement
    listing:
    - entryname: stage.py
      entry: |-
        import os
        import sys
        import pystac
        import botocore
        import boto3
        import shutil
        from pystac.stac_io import DefaultStacIO, StacIO
        from urllib.parse import urlparse

        cat_url = sys.argv[1]
        bucket = sys.argv[2]
        subfolder = sys.argv[3]

        aws_access_key_id = os.environ["aws_access_key_id"]
        aws_secret_access_key = os.environ["aws_secret_access_key"]
        region_name = os.environ["aws_region_name"]
        endpoint_url = os.environ["aws_endpoint_url"]

        shutil.copytree(cat_url, "/tmp/catalog")
        cat = pystac.read_file(os.path.join("/tmp/catalog", "catalog.json"))

        class CustomStacIO(DefaultStacIO):
            """Custom STAC IO class that uses boto3 to read from S3."""

            def __init__(self):
                self.session = botocore.session.Session()
                self.s3_client = self.session.create_client(
                    service_name="s3",
                    use_ssl=True,
                    aws_access_key_id=aws_access_key_id,
                    aws_secret_access_key=aws_secret_access_key,
                    endpoint_url=endpoint_url,
                    region_name=region_name,
                )

            def write_text(self, dest, txt, *args, **kwargs):
                parsed = urlparse(dest)
                if parsed.scheme == "s3":
                    self.s3_client.put_object(
                        Body=txt.encode("UTF-8"),
                        Bucket=parsed.netloc,
                        Key=parsed.path[1:],
                        ContentType="application/geo+json",
                    )
                else:
                    super().write_text(dest, txt, *args, **kwargs)


        client = boto3.client(
            "s3",
            aws_access_key_id=aws_access_key_id,
            aws_secret_access_key=aws_secret_access_key,
            endpoint_url=endpoint_url,
            region_name=region_name,
        )

        StacIO.set_default(CustomStacIO)

        for item in cat.get_items():
            for key, asset in item.get_assets().items():
                s3_path = os.path.normpath(
                    os.path.join(os.path.join(subfolder, item.id, asset.href))
                )
                print(f"upload {asset.href} to s3://{bucket}/{s3_path}",file=sys.stderr)
                client.upload_file(
                    asset.get_absolute_href(),
                    bucket,
                    s3_path,
                )
                asset.href = f"s3://{bucket}/{s3_path}"
                item.add_asset(key, asset)

        cat.normalize_hrefs(f"s3://{bucket}/{subfolder}")

        for item in cat.get_items():
            # upload item to S3
            print(f"upload {item.id} to s3://{bucket}/{subfolder}", file=sys.stderr)
            pystac.write_file(item, item.get_self_href())

        # upload catalog to S3
        print(f"upload catalog.json to s3://{bucket}/{subfolder}", file=sys.stderr)
        pystac.write_file(cat, cat.get_self_href())

        print(f"s3://{bucket}/{subfolder}/catalog.json", end="", file=sys.stdout)
  cwlVersion: v1.2
  baseCommand:
  - python
  - stage.py
  arguments:
  - $( inputs.stac_catalog.path )
  - $( inputs.s3_bucket )
  - ${ var firstPart = (Math.random() * 46656) | 0; var secondPart = 
    (Math.random() * 46656) | 0; firstPart = ("000" + 
    firstPart.toString(36)).slice(-3); secondPart = ("000" + 
    secondPart.toString(36)).slice(-3); return inputs.sub_path + "-" + firstPart
    + secondPart; }
  stdout: catalog-uri.txt
- id: crop
  class: CommandLineTool
  inputs:
  - id: item
    type: Directory
    inputBinding:
      prefix: --input-item
  - id: aoi
    label: Area of interest
    doc: Area of interest defined as a bounding box
    type: https://raw.githubusercontent.com/eoap/schemas/main/ogc.yaml#BBox
    inputBinding:
      valueFrom: |
        ${
          // Validate the length of bbox to be either 4 or 6
          var bboxLength = inputs.aoi.bbox.length;
          if (bboxLength !== 4 && bboxLength !== 6) {
            throw "Invalid bbox length: bbox must have either 4 or 6 elements.";
          }
          // Convert bbox array to a space-separated string for echo
          return ["--aoi", inputs.aoi.bbox.join(",")];
        }
  - id: epsg
    type: https://raw.githubusercontent.com/eoap/schemas/main/ogc.yaml#BBox
    inputBinding:
      valueFrom: |
        ${
          const crs = inputs.epsg.crs;
          if (typeof crs !== "string") {
            throw "Invalid CRS: must be a string.";
          }
          if (["CRS84"].includes(crs)) {
            return ["--epsg", "EPSG:4326"];
          } else {
            throw "Unsupported CRS: only CRS84 is currently supported.";
          }
        }
  - id: band
    type: string
    inputBinding:
      prefix: --band
  - id: collection
    type: 
      https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI
    inputBinding:
      valueFrom: |
        ${
          // parse the URI provided in the input
          var product_uri = inputs.collection.value;
          // Validate the URI format
          var uriPattern = /^(https?|ftp):\/\/[^\s/$.?#].[^\s]*$/i;
          if (!uriPattern.test(product_uri)) {
            throw "Invalid URI format: " + product_uri;
          }
          // Return the URI as a string
          return ["--collection", product_uri];
        }
  outputs:
  - id: cropped
    type: Directory
    outputBinding:
      glob: .
  requirements:
  - class: InlineJavascriptRequirement
  - class: EnvVarRequirement
    envDef:
    - envName: PATH
      envValue: /app/envs/runner/bin
  - class: ResourceRequirement
    coresMax: 1
    ramMax: 512
  - class: SchemaDefRequirement
    types:
    - name: https://raw.githubusercontent.com/eoap/schemas/main/ogc.yaml#CRS
      symbols:
      - https://raw.githubusercontent.com/eoap/schemas/main/ogc.yaml#CRS/CRS84
      - https://raw.githubusercontent.com/eoap/schemas/main/ogc.yaml#CRS/CRS84h
      type: enum
    - name: https://raw.githubusercontent.com/eoap/schemas/main/ogc.yaml#BBox
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/ogc.yaml#BBox/bbox
        type:
          name: _:5f695a5a-372e-4cde-8309-a383aa119349
          items: double
          type: array
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/ogc.yaml#BBox/crs
        type: https://raw.githubusercontent.com/eoap/schemas/main/ogc.yaml#CRS
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Date
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Date/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#DateTime
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#DateTime/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Duration
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Duration/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Email
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Email/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Hostname
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Hostname/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IDNEmail
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IDNEmail/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IDNHostname
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IDNHostname/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IPv4
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IPv4/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IPv6
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IPv6/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IRI
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IRI/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IRIReference
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IRIReference/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#JsonPointer
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#JsonPointer/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Password
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Password/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#RelativeJsonPointer
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#RelativeJsonPointer/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#UUID
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#UUID/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URIReference
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URIReference/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URITemplate
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URITemplate/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Time
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Time/value
        type: string
      type: record
  - class: NetworkAccess
    networkAccess: true
  hints:
  - class: DockerRequirement
    dockerPull: ghcr.io/eoap/application-package-patterns/runner:0.2.0
  cwlVersion: v1.2
  baseCommand:
  - runner
  arguments:
  - crop-cli
  $namespaces: *id001
- id: norm_diff
  class: CommandLineTool
  inputs:
  - id: rasters
    type:
      name: _:8321b636-f22a-4917-b557-72c8dd7b7b63
      items: Directory
      type: array
    inputBinding:
      valueFrom: |
        ${
          var args = [];
          for (var i = 0; i < inputs.rasters.length; i++) {
            args.push(`--item-${i + 1}`);
            args.push(inputs.rasters[i].path);
          }
          return args;
        }
  - id: item
    type: Directory
    inputBinding:
      prefix: --item
  - id: collection
    type: 
      https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI
    inputBinding:
      valueFrom: |
        ${
          // parse the URI provided in the input
          var product_uri = inputs.collection.value;
          // Validate the URI format
          var uriPattern = /^(https?|ftp):\/\/[^\s/$.?#].[^\s]*$/i;
          if (!uriPattern.test(product_uri)) {
            throw "Invalid URI format: " + product_uri;
          }
          // Return the URI as a string
          return ["--collection", product_uri];
        }
  outputs:
  - id: ndwi
    type: Directory
    outputBinding:
      glob: .
  requirements:
  - class: InlineJavascriptRequirement
  - class: EnvVarRequirement
    envDef:
    - envName: PATH
      envValue: /app/envs/runner/bin
  - class: ResourceRequirement
    coresMax: 1
    ramMax: 512
  - class: SchemaDefRequirement
    types:
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Date
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Date/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#DateTime
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#DateTime/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Duration
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Duration/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Email
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Email/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Hostname
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Hostname/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IDNEmail
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IDNEmail/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IDNHostname
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IDNHostname/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IPv4
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IPv4/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IPv6
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IPv6/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IRI
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IRI/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IRIReference
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IRIReference/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#JsonPointer
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#JsonPointer/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Password
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Password/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#RelativeJsonPointer
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#RelativeJsonPointer/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#UUID
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#UUID/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URIReference
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URIReference/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URITemplate
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URITemplate/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Time
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Time/value
        type: string
      type: record
  - class: NetworkAccess
    networkAccess: true
  hints:
  - class: DockerRequirement
    dockerPull: ghcr.io/eoap/application-package-patterns/runner:0.2.0
  cwlVersion: v1.2
  baseCommand:
  - runner
  arguments:
  - ndi-cli
  $namespaces: *id001
- id: otsu
  class: CommandLineTool
  inputs:
  - id: raster
    type: Directory
    inputBinding:
      prefix: --input-ndi
  - id: item
    type: Directory
    inputBinding:
      prefix: --item
  - id: collection
    type: 
      https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI
    inputBinding:
      valueFrom: |
        ${
          // parse the URI provided in the input
          var product_uri = inputs.collection.value;
          // Validate the URI format
          var uriPattern = /^(https?|ftp):\/\/[^\s/$.?#].[^\s]*$/i;
          if (!uriPattern.test(product_uri)) {
            throw "Invalid URI format: " + product_uri;
          }
          // Return the URI as a string
          return ["--collection", product_uri];
        }
  outputs:
  - id: water_bodies
    type: Directory
    outputBinding:
      glob: .
  requirements:
  - class: InlineJavascriptRequirement
  - class: EnvVarRequirement
    envDef:
    - envName: PATH
      envValue: /app/envs/runner/bin
  - class: ResourceRequirement
    coresMax: 1
    ramMax: 512
  - class: SchemaDefRequirement
    types:
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Date
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Date/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#DateTime
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#DateTime/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Duration
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Duration/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Email
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Email/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Hostname
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Hostname/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IDNEmail
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IDNEmail/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IDNHostname
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IDNHostname/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IPv4
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IPv4/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IPv6
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IPv6/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IRI
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IRI/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IRIReference
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#IRIReference/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#JsonPointer
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#JsonPointer/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Password
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Password/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#RelativeJsonPointer
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#RelativeJsonPointer/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#UUID
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#UUID/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URIReference
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URIReference/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URITemplate
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URITemplate/value
        type: string
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Time
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Time/value
        type: string
      type: record
  - class: NetworkAccess
    networkAccess: true
  hints:
  - class: DockerRequirement
    dockerPull: ghcr.io/eoap/application-package-patterns/runner:0.2.0
  cwlVersion: v1.2
  baseCommand:
  - runner
  arguments:
  - otsu-cli
  $namespaces: *id001

Raw CWL document successfully updated! Now dereferencing the FQNs...
  Cleaning CommandLineTool my-super-stage-out...
CWL document successfully dereferenced!
Validating stage-in 'my-asthonishing-stage-in-directory'...
stage-in 'my-asthonishing-stage-in-directory' is valid
Validating stage-in 'my-asthonishing-stage-in-file'...
stage-in 'my-asthonishing-stage-in-file' is valid
Validating stage-out 'my-super-stage-out'...
stage-out 'my-super-stage-out' is valid
Building the CWL Orchestrator Workflow...
Analyzing pattern-12 inputs...
* pattern-12/aoi: https://raw.githubusercontent.com/eoap/schemas/main/ogc.yaml#BBox
* pattern-12/bands: string[]
* pattern-12/item: Directory
  Directory type detected, creating a related 'directory_stage_in_0'...
  Converting Directory to URL-compatible type...
  Directory converted to https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI
  Connecting 'app/item' to 'directory_stage_in_0' output...
* pattern-12/cropped-collection: https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI
* pattern-12/ndwi-collection: https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI
* pattern-12/water-bodies-collection: https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI
Analyzing pattern-12 outputs...
* pattern-12/cropped: Directory[]
  Directory type detected, creating a related 'stage_out_0'...
  Converting Directory[] to URL-compatible type...
  Directory[] converted to https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI[]
  Array detected, scatter required for stac_catalog:app/cropped
  Connecting 'app/cropped' to 'stage_out_0' output...
* pattern-12/ndwi: Directory
  Directory type detected, creating a related 'stage_out_1'...
  Converting Directory to URL-compatible type...
  Directory converted to https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI
  Connecting 'app/ndwi' to 'stage_out_1' output...
* pattern-12/water_bodies: Directory
  Directory type detected, creating a related 'stage_out_2'...
  Converting Directory to URL-compatible type...
  Directory converted to https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI
  Connecting 'app/water_bodies' to 'stage_out_2' output...
Orchestrator Workflow built in 0.0035 seconds

Workflow Diagram¶

file

Components Diagram¶

file

Class Diagram¶

file