Examples¶

The following examples show how to use the loader APIs:

1.1 Parsing a Workflow¶

This sample shows how to read a CWL document from a remote public URL:

In [1]:

Copied!

from cwl_loader import load_cwl_from_location

cwl_document = load_cwl_from_location('https://github.com/eoap/zarr-cloud-native-format/releases/download/0.3.0/app-water-bodies.0.3.0.cwl')
from cwl_loader import load_cwl_from_location

cwl_document = load_cwl_from_location('https://github.com/eoap/zarr-cloud-native-format/releases/download/0.3.0/app-water-bodies.0.3.0.cwl')

2025-09-24 07:17:28.337 | DEBUG    | cwl_loader:load_cwl_from_location:231 - Loading CWL document from https://github.com/eoap/zarr-cloud-native-format/releases/download/0.3.0/app-water-bodies.0.3.0.cwl...

2025-09-24 07:17:28.565 | DEBUG    | cwl_loader:_load_cwl_from_stream:234 - Reading stream from https://github.com/eoap/zarr-cloud-native-format/releases/download/0.3.0/app-water-bodies.0.3.0.cwl...

2025-09-24 07:17:28.615 | DEBUG    | cwl_loader:load_cwl_from_stream:206 - CWL data of type <class 'ruamel.yaml.comments.CommentedMap'> successfully loaded from stream

2025-09-24 07:17:28.615 | DEBUG    | cwl_loader:load_cwl_from_yaml:133 - Updating the model from version 'v1.0' to version 'v1.2'...

2025-09-24 07:17:28.616 | DEBUG    | cwl_loader:load_cwl_from_yaml:144 - Raw CWL document successfully updated to v1.2!

2025-09-24 07:17:28.617 | DEBUG    | cwl_loader:load_cwl_from_yaml:148 - Parsing the raw CWL document to the CWL Utils DOM...

2025-09-24 07:17:31.078 | DEBUG    | cwl_loader:load_cwl_from_yaml:161 - Raw CWL document successfully parsed to the CWL Utils DOM!

2025-09-24 07:17:31.079 | DEBUG    | cwl_loader:load_cwl_from_yaml:163 - Dereferencing the steps[].run...

2025-09-24 07:17:31.079 | DEBUG    | cwl_loader:_on_process:81 - Checking if https://github.com/eoap/schemas/releases/download/0.2.0/stac-api-client.0.2.0.cwl must be externally imported...

2025-09-24 07:17:31.080 | DEBUG    | cwl_loader:_on_process:85 - run_url: https://github.com/eoap/schemas/releases/download/0.2.0/stac-api-client.0.2.0.cwl - uri: https://github.com/eoap/zarr-cloud-native-format/releases/download/0.3.0/app-water-bodies.0.3.0.cwl

2025-09-24 07:17:31.080 | DEBUG    | cwl_loader:load_cwl_from_location:231 - Loading CWL document from https://github.com/eoap/schemas/releases/download/0.2.0/stac-api-client.0.2.0.cwl...

2025-09-24 07:17:31.194 | DEBUG    | cwl_loader:_load_cwl_from_stream:234 - Reading stream from https://github.com/eoap/schemas/releases/download/0.2.0/stac-api-client.0.2.0.cwl...

2025-09-24 07:17:31.202 | DEBUG    | cwl_loader:load_cwl_from_stream:206 - CWL data of type <class 'ruamel.yaml.comments.CommentedMap'> successfully loaded from stream

2025-09-24 07:17:31.203 | DEBUG    | cwl_loader:load_cwl_from_yaml:146 - No needs to update the Raw CWL document since it targets already the v1.2

2025-09-24 07:17:31.204 | DEBUG    | cwl_loader:load_cwl_from_yaml:148 - Parsing the raw CWL document to the CWL Utils DOM...

2025-09-24 07:17:31.950 | DEBUG    | cwl_loader:load_cwl_from_yaml:161 - Raw CWL document successfully parsed to the CWL Utils DOM!

2025-09-24 07:17:31.951 | DEBUG    | cwl_loader:load_cwl_from_yaml:163 - Dereferencing the steps[].run...

2025-09-24 07:17:31.952 | DEBUG    | cwl_loader:load_cwl_from_yaml:170 - steps[].run successfully dereferenced! Dereferencing the FQNs...

2025-09-24 07:17:31.953 | DEBUG    | cwl_loader:load_cwl_from_yaml:174 - CWL document successfully dereferenced! Now verifying steps[].run integrity...

2025-09-24 07:17:31.953 | DEBUG    | cwl_loader:load_cwl_from_yaml:178 - All steps[].run link are resolvable!

2025-09-24 07:17:31.954 | DEBUG    | cwl_loader:load_cwl_from_yaml:181 - Sorting Process instances by dependencies....

2025-09-24 07:17:31.954 | DEBUG    | cwl_loader:load_cwl_from_yaml:183 - Sorting process is over.

2025-09-24 07:17:31.955 | DEBUG    | cwl_loader:_load_cwl_from_stream:243 - Stream from https://github.com/eoap/schemas/releases/download/0.2.0/stac-api-client.0.2.0.cwl successfully load!

2025-09-24 07:17:31.956 | DEBUG    | cwl_loader:_on_process:81 - Checking if https://github.com/eoap/zarr-cloud-native-format/releases/download/0.3.0/app-water-bodies.0.3.0.cwl#convert-search must be externally imported...

2025-09-24 07:17:31.957 | DEBUG    | cwl_loader:_on_process:85 - run_url: https://github.com/eoap/zarr-cloud-native-format/releases/download/0.3.0/app-water-bodies.0.3.0.cwl - uri: https://github.com/eoap/zarr-cloud-native-format/releases/download/0.3.0/app-water-bodies.0.3.0.cwl

2025-09-24 07:17:31.957 | DEBUG    | cwl_loader:_on_process:81 - Checking if https://github.com/eoap/zarr-cloud-native-format/releases/download/0.3.0/app-water-bodies.0.3.0.cwl#detect_water_body must be externally imported...

2025-09-24 07:17:31.958 | DEBUG    | cwl_loader:_on_process:85 - run_url: https://github.com/eoap/zarr-cloud-native-format/releases/download/0.3.0/app-water-bodies.0.3.0.cwl - uri: https://github.com/eoap/zarr-cloud-native-format/releases/download/0.3.0/app-water-bodies.0.3.0.cwl

2025-09-24 07:17:31.958 | DEBUG    | cwl_loader:_on_process:81 - Checking if https://github.com/eoap/zarr-cloud-native-format/releases/download/0.3.0/app-water-bodies.0.3.0.cwl#stac must be externally imported...

2025-09-24 07:17:31.959 | DEBUG    | cwl_loader:_on_process:85 - run_url: https://github.com/eoap/zarr-cloud-native-format/releases/download/0.3.0/app-water-bodies.0.3.0.cwl - uri: https://github.com/eoap/zarr-cloud-native-format/releases/download/0.3.0/app-water-bodies.0.3.0.cwl

2025-09-24 07:17:31.959 | DEBUG    | cwl_loader:_on_process:81 - Checking if https://github.com/eoap/zarr-cloud-native-format/releases/download/0.3.0/app-water-bodies.0.3.0.cwl#stac-zarr must be externally imported...

2025-09-24 07:17:31.960 | DEBUG    | cwl_loader:_on_process:85 - run_url: https://github.com/eoap/zarr-cloud-native-format/releases/download/0.3.0/app-water-bodies.0.3.0.cwl - uri: https://github.com/eoap/zarr-cloud-native-format/releases/download/0.3.0/app-water-bodies.0.3.0.cwl

2025-09-24 07:17:31.960 | DEBUG    | cwl_loader:_on_process:81 - Checking if https://github.com/eoap/zarr-cloud-native-format/releases/download/0.3.0/app-water-bodies.0.3.0.cwl#crop must be externally imported...

2025-09-24 07:17:31.961 | DEBUG    | cwl_loader:_on_process:85 - run_url: https://github.com/eoap/zarr-cloud-native-format/releases/download/0.3.0/app-water-bodies.0.3.0.cwl - uri: https://github.com/eoap/zarr-cloud-native-format/releases/download/0.3.0/app-water-bodies.0.3.0.cwl

2025-09-24 07:17:31.961 | DEBUG    | cwl_loader:_on_process:81 - Checking if https://github.com/eoap/zarr-cloud-native-format/releases/download/0.3.0/app-water-bodies.0.3.0.cwl#norm_diff must be externally imported...

2025-09-24 07:17:31.961 | DEBUG    | cwl_loader:_on_process:85 - run_url: https://github.com/eoap/zarr-cloud-native-format/releases/download/0.3.0/app-water-bodies.0.3.0.cwl - uri: https://github.com/eoap/zarr-cloud-native-format/releases/download/0.3.0/app-water-bodies.0.3.0.cwl

2025-09-24 07:17:31.962 | DEBUG    | cwl_loader:_on_process:81 - Checking if https://github.com/eoap/zarr-cloud-native-format/releases/download/0.3.0/app-water-bodies.0.3.0.cwl#otsu must be externally imported...

2025-09-24 07:17:31.962 | DEBUG    | cwl_loader:_on_process:85 - run_url: https://github.com/eoap/zarr-cloud-native-format/releases/download/0.3.0/app-water-bodies.0.3.0.cwl - uri: https://github.com/eoap/zarr-cloud-native-format/releases/download/0.3.0/app-water-bodies.0.3.0.cwl

2025-09-24 07:17:31.963 | DEBUG    | cwl_loader:load_cwl_from_yaml:170 - steps[].run successfully dereferenced! Dereferencing the FQNs...

2025-09-24 07:17:31.963 | DEBUG    | cwl_loader:load_cwl_from_yaml:174 - CWL document successfully dereferenced! Now verifying steps[].run integrity...

2025-09-24 07:17:31.964 | DEBUG    | cwl_loader:load_cwl_from_yaml:178 - All steps[].run link are resolvable!

2025-09-24 07:17:31.964 | DEBUG    | cwl_loader:load_cwl_from_yaml:181 - Sorting Process instances by dependencies....

2025-09-24 07:17:31.965 | DEBUG    | cwl_loader:load_cwl_from_yaml:183 - Sorting process is over.

2025-09-24 07:17:31.965 | DEBUG    | cwl_loader:_load_cwl_from_stream:243 - Stream from https://github.com/eoap/zarr-cloud-native-format/releases/download/0.3.0/app-water-bodies.0.3.0.cwl successfully load!

1.2 Serializing¶

This sample shows how to write a CWL document to a stream (string, file, ...):

In [2]:

Copied!

from cwl_loader import dump_cwl
import sys

dump_cwl(process=cwl_document, stream=sys.stderr)
from cwl_loader import dump_cwl
import sys

dump_cwl(process=cwl_document, stream=sys.stderr)

cwlVersion: v1.2
$graph:
- id: stac-zarr
  class: CommandLineTool
  inputs:
  - id: stac_catalog
    type: Directory
    inputBinding:
      prefix: --stac-catalog
  outputs:
  - id: zarr_stac_catalog
    type: Directory
    outputBinding:
      glob: .
  requirements:
  - class: InlineJavascriptRequirement
  - class: EnvVarRequirement
    envDef:
    - envName: PATH
      envValue: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
    - envName: PYTHONPATH
      envValue: /app
  - class: ResourceRequirement
    coresMax: 1
    ramMax: 512
  hints:
  - class: DockerRequirement
    dockerPull: 
      ghcr.io/eoap/zarr-cloud-native-format/stac-zarr@sha256:5d3522f67b6ee73276563e01b436772161fd8e1658149e38e64615d296170692
  cwlVersion: v1.2
  baseCommand:
  - python
  - -m
  - app
  arguments: []
  $namespaces: &id001
    s: https://schema.org/
- id: water-bodies
  class: Workflow
  label: Water bodies detection based on NDWI and otsu threshold
  doc: Water bodies detection based on NDWI and otsu threshold applied to 
    Sentinel-2 COG STAC items
  inputs:
  - id: stac_api_endpoint
    label: STAC API endpoint
    doc: STAC API endpoint
    type: |-
      https://raw.githubusercontent.com/eoap/schemas/main/experimental/api-endpoint.yaml#APIEndpoint
  - id: search_request
    label: STAC search request
    doc: STAC search request
    type: |-
      https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACSearchSettings
  - id: bands
    label: bands used for the NDWI
    doc: bands used for the NDWI
    default:
    - green
    - nir
    type:
      name: _:40c762a6-1b82-4e59-9699-b2a3673d2d29
      items: string
      type: array
  outputs:
  - id: zarr_stac_catalog
    outputSource:
    - stac_zarr/zarr_stac_catalog
    type: Directory
  - id: stac_catalog
    outputSource:
    - stac/temp_stac_catalog
    type: Directory
  requirements:
  - class: ScatterFeatureRequirement
  - class: SubworkflowFeatureRequirement
  - class: SchemaDefRequirement
    types:
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#Date
      fields:
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          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:
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          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:
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          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
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#PointType
      symbols:
      - https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#PointType/Point
      type: enum
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#Point
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#Point/type
        type: 
          https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#PointType
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#Point/coordinates
        type:
          name: _:179e9d0e-decb-4c50-90e3-0ee9b8def22c
          items: double
          type: array
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#Point/bbox
        type:
          name: _:71756cc4-7db0-487b-abfe-a6c44a6435bf
          items: double
          type: array
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#LineStringType
      symbols:
      - https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#LineStringType/LineString
      type: enum
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#LineString
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#LineString/type
        type: 
          https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#LineStringType
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#LineString/coordinates
        type:
          name: _:0d6b107b-5c2b-4d10-be53-d090a32315c8
          items: double
          type: array
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#LineString/bbox
        type:
          name: _:29cb1814-baee-45ef-8e6d-3755f44e4e8a
          items: double
          type: array
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#PolygonType
      symbols:
      - https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#PolygonType/Polygon
      type: enum
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#Polygon
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#Polygon/type
        type: 
          https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#PolygonType
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#Polygon/coordinates
        type:
          name: _:645e4c7d-0411-49dc-9e50-d6491e9fac8e
          items:
            name: _:bf742d25-3ecd-4c42-8157-3a0ea3597a22
            items: double
            type: array
          type: array
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#Polygon/bbox
        type:
          name: _:5e23a304-1faa-4b56-b9f6-e5330a338576
          items: double
          type: array
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiPointType
      symbols:
      - https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiPointType/MultiPoint
      type: enum
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiPoint
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiPoint/type
        type: 
          https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiPointType
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiPoint/coordinates
        type:
          name: _:a2688e1a-a234-42e6-b6ec-9a9bce39aa81
          items:
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            items: double
            type: array
          type: array
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiPoint/bbox
        type:
          name: _:edcfa610-5388-48c7-9dab-ea3e1370e39e
          items: double
          type: array
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiLineStringType
      symbols:
      - https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiLineStringType/MultiLineString
      type: enum
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiLineString
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiLineString/type
        type: 
          https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiLineStringType
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiLineString/coordinates
        type:
          name: _:31c75abe-0581-49f8-801e-4982e0a6c82c
          items:
            name: _:d99b06e1-0860-41b9-9eba-afa70c97a699
            items:
              name: _:ef3a735f-5956-4f81-b056-587e2a561099
              items: double
              type: array
            type: array
          type: array
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiLineString/bbox
        type:
          name: _:1a502b75-1e2d-431d-859d-6dcdd97f3fc4
          items: double
          type: array
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiPolygonType
      symbols:
      - https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiPolygonType/MultiPolygon
      type: enum
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiPolygon
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiPolygon/type
        type: 
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  cwlVersion: v1.2
  steps:
  - id: discovery
    label: STAC API discovery
    doc: Discover STAC items from a STAC API endpoint based on a search request
    in:
    - id: api_endpoint
      source: stac_api_endpoint
    - id: search_request
      source: search_request
    out:
    - search_output
    run: '#stac-client'
  - id: convert_search
    label: Convert Search
    doc: Convert Search results to get the item self hrefs and the area of 
      interest
    in:
    - id: search_results
      source: discovery/search_output
    - id: search_request
      source: search_request
    out:
    - items
    - aoi
    run: '#convert-search'
  - id: water_bodies
    label: Water bodies detection
    doc: Water bodies detection based on NDWI and otsu threshold applied to each
      STAC item (sub-workflow)
    in:
    - id: item
      source: convert_search/items
    - id: aoi
      source: convert_search/aoi
    - id: bands
      source: bands
    out:
    - detected_water_body
    run: '#detect_water_body'
    scatter: water_bodies/item
    scatterMethod: dotproduct
  - id: stac
    label: Create a STAC catalog with COG outputs
    doc: Create a STAC catalog with the detected water bodies COG outputs
    in:
    - id: item
      source: convert_search/items
    - id: rasters
      source: water_bodies/detected_water_body
    out:
    - temp_stac_catalog
    run: '#stac'
  - id: stac_zarr
    label: Create a STAC Catalog for the Zarr store
    doc: Create a STAC Catalog for the Zarr store from the STAC catalog with COG
      outputs
    in:
    - id: stac_catalog
      source: stac/temp_stac_catalog
    out:
    - zarr_stac_catalog
    run: '#stac-zarr'
  $namespaces: *id001
- id: otsu
  class: CommandLineTool
  inputs:
  - id: raster
    type: File
    inputBinding:
      position: 1
  outputs:
  - id: binary_mask_item
    type: File
    outputBinding:
      glob: '*.tif'
  requirements:
  - class: InlineJavascriptRequirement
  - class: EnvVarRequirement
    envDef:
    - envName: PATH
      envValue: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
    - envName: PYTHONPATH
      envValue: /app
  - class: ResourceRequirement
    coresMax: 1
    ramMax: 512
  hints:
  - class: DockerRequirement
    dockerPull: 
      ghcr.io/eoap/mastering-app-package/otsu@sha256:45866d928037c38c1c0d90678bfeda885991e85dbc6edb2ecaba5873bf4a8d83
  cwlVersion: v1.2
  baseCommand:
  - python
  - -m
  - app
  arguments: []
  $namespaces: *id001
- id: stac-client
  class: CommandLineTool
  label: STAC Client Tool
  doc: |
    This tool uses the STAC Client to search for STAC items
  inputs:
  - id: api_endpoint
    label: STAC API endpoint
    doc: STAC API endpoint for Landsat-9 data
    type: |-
      https://raw.githubusercontent.com/eoap/schemas/main/experimental/api-endpoint.yaml#APIEndpoint
  - id: search_request
    label: STAC API settings
    doc: STAC API settings for Landsat-9 data
    type: |-
      https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACSearchSettings
  outputs:
  - id: search_output
    type: File
    outputBinding:
      glob: discovery-output.json
  requirements:
  - class: InlineJavascriptRequirement
  - class: NetworkAccess
    networkAccess: true
  - class: SchemaDefRequirement
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        type: string
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        type:
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        - https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#LineString
        - https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#Polygon
        - https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiPoint
        - https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiLineString
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    - name: 
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      type: enum
    - name: 
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      fields:
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        type: 
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        type:
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          items:
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          type: array
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        type:
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          items: double
          type: array
      type: record
    - name: 
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      fields:
      - name: 
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        doc: "i.e. http://data.example.com/buildings/123"
        type: string
      - name: 
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        doc: "i.e. alternate"
        type: string
      - name: 
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        doc: "i.e. application/geo+json"
        type: string
      - name: 
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        doc: "i.e. en"
        type: string
      - name: 
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        doc: "i.e. Trierer Strasse 70, 53115 Bonn"
        type: string
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#Link/length
        type: int
      type: record
    - name: 
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      symbols:
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      type: enum
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      fields:
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        type: 
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        type:
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      - name: 
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        type:
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          items: 
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        type: string
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        type: int
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        type: int
      type: record
    - name: 
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      fields:
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        type: string
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        type: string
      type: record
    - name: 
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      fields:
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        type: 
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        - name: _:2f7bdb57-770b-418c-ab98-a1fb42923d0f
          items: 
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      type: record
    - name: 
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      fields:
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        type: 
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      - name: 
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        type: 
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      type: record
    - name: 
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          items: string
          type: array
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        type:
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          items: string
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      type: record
    - name: 
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      symbols:
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      - https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#FilterLang/cql2-json
      type: enum
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      symbols:
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      type: enum
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      fields:
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        type: string
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      type: record
    - name: 
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      fields:
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        type:
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        - name: _:768a1d59-85d8-4a77-9346-940abeb0fd42
          items: double
          type: array
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        type:
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        - https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#DateTime
      - name: 
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        type:
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      - name: 
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        type:
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      - name: 
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        type:
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        - name: _:ed1979ef-63c7-4183-a74e-32456c0b2ec6
          items: string
          type: array
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        type:
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        - name: _:520624fd-84d7-4014-aaf8-695c8a738d19
          items: string
          type: array
      - name: 
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        type:
        - 'null'
        - int
      - name: 
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        type:
        - 'null'
        - int
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACSearchSettings/fields
        type:
        - 'null'
        - https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#Fields
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACSearchSettings/filter
        type:
        - 'null'
        - Any
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACSearchSettings/filter-lang
        type:
        - 'null'
        - https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#FilterLang
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACSearchSettings/filter-crs
        type:
        - 'null'
        - name: _:03cdc224-3b36-49ab-ba54-c587e4ba8be2
          items: 
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          type: array
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACSearchSettings/sortby
        type:
        - 'null'
        - name: _:cdd97e7a-bd0c-4d4e-a452-5e9342972ff3
          items: 
            https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#SortBy
          type: array
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACAPI
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACAPI/api_endpoint
        type: 
          https://raw.githubusercontent.com/eoap/schemas/main/experimental/api-endpoint.yaml#APIEndpoint
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACAPI/search_request
        type: 
          https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACSearchSettings
      type: record
  hints:
  - class: DockerRequirement
    dockerPull: 
      ghcr.io/eoap/schemas/stac-api-client@sha256:a7e346f704836d07f5dabc6b29ee3359e7253f4a294d74f3899973b8920da6f7
  cwlVersion: v1.2
  baseCommand:
  - stac-client
  arguments:
  - search
  - $(inputs.api_endpoint.url.value)
  - ${ const args = []; const collections = inputs.search_request.collections; 
    args.push('--collections', collections.join(",")); return args; }
  - ${ const args = []; const bbox = inputs.search_request?.bbox; if 
    (Array.isArray(bbox) && bbox.length >= 4) { args.push('--bbox', 
    ...bbox.map(String)); } return args; }
  - ${ const args = []; const limit = inputs.search_request?.limit; 
    args.push("--limit", (limit ?? 10).toString()); return args; }
  - ${ const maxItems = inputs.search_request?.['max-items']; return 
    ['--max-items', (maxItems ?? 20).toString()]; }
  - ${ const args = []; const filter = inputs.search_request?.filter; const 
    filterLang = inputs.search_request?.['filter-lang']; if (filterLang) { 
    args.push('--filter-lang', filterLang); } if (filter) { 
    args.push('--filter', JSON.stringify(filter)); } return args; }
  - ${ const datetime = inputs.search_request?.datetime; const datetimeInterval 
    = inputs.search_request?.datetime_interval; if (datetime) { return 
    ['--datetime', datetime]; } else if (datetimeInterval) { const start = 
    datetimeInterval.start?.value || '..'; const end = 
    datetimeInterval.end?.value || '..'; return ['--datetime', 
    `${start}/${end}`]; } return []; }
  - ${ const ids = inputs.search_request?.ids; const args = []; if 
    (Array.isArray(ids) && ids.length > 0) { args.push('--ids', 
    ...ids.map(String)); } return args; }
  - ${ const intersects = inputs.search_request?.intersects; if (intersects) { 
    return ['--intersects', JSON.stringify(intersects)]; } return []; }
  - --save
  - discovery-output.json
- id: stac
  class: CommandLineTool
  inputs:
  - id: item
    type:
      name: _:7a9cacf0-3fd8-4552-9f4f-8cf6943176cc
      items: string
      type: array
      inputBinding:
        prefix: --input-item
  - id: rasters
    type:
      name: _:6af3cdba-0aa8-49a1-abec-14bdab0cd222
      items: File
      type: array
      inputBinding:
        prefix: --water-body
  outputs:
  - id: temp_stac_catalog
    label: temporary STAC catalog with COG outputs
    type: Directory
    outputBinding:
      glob: .
  requirements:
  - class: InlineJavascriptRequirement
  - class: EnvVarRequirement
    envDef:
    - envName: PATH
      envValue: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
    - envName: PYTHONPATH
      envValue: /app
  - class: ResourceRequirement
    coresMax: 1
    ramMax: 512
  hints:
  - class: DockerRequirement
    dockerPull: 
      ghcr.io/eoap/mastering-app-package/stac@sha256:cb54ab738a7d6544f2037368604c1c40e3f5af3eac1250ed14d365e5acb0c6b5
  cwlVersion: v1.2
  baseCommand:
  - python
  - -m
  - app
  arguments: []
  $namespaces: *id001
- id: detect_water_body
  class: Workflow
  label: Water body detection based on NDWI and otsu threshold
  doc: Water body detection based on NDWI and otsu threshold
  inputs:
  - id: aoi
    doc: area of interest as a bounding box
    type: string
  - id: epsg
    doc: EPSG code
    default: EPSG:4326
    type: string
  - id: bands
    doc: bands used for the NDWI
    type:
      name: _:af637533-1416-44c8-9ac1-b48b73e446ef
      items: string
      type: array
  - id: item
    doc: STAC item
    type: string
  outputs:
  - id: detected_water_body
    outputSource:
    - otsu/binary_mask_item
    type: File
  requirements:
  - class: ScatterFeatureRequirement
  cwlVersion: v1.2
  steps:
  - id: crop
    in:
    - id: item
      source: item
    - id: aoi
      source: aoi
    - id: epsg
      source: epsg
    - id: band
      source: bands
    out:
    - cropped
    run: '#crop'
    scatter: crop/band
    scatterMethod: dotproduct
  - id: normalized_difference
    in:
    - id: rasters
      source: crop/cropped
    out:
    - ndwi
    run: '#norm_diff'
  - id: otsu
    in:
    - id: raster
      source: normalized_difference/ndwi
    out:
    - binary_mask_item
    run: '#otsu'
  $namespaces: *id001
- id: norm_diff
  class: CommandLineTool
  inputs:
  - id: rasters
    type:
      name: _:2bdd4b9d-5269-48d4-b287-8f638462c6b7
      items: File
      type: array
    inputBinding:
      position: 1
  outputs:
  - id: ndwi
    type: File
    outputBinding:
      glob: '*.tif'
  requirements:
  - class: InlineJavascriptRequirement
  - class: EnvVarRequirement
    envDef:
    - envName: PATH
      envValue: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
    - envName: PYTHONPATH
      envValue: /app
  - class: ResourceRequirement
    coresMax: 1
    ramMax: 512
  hints:
  - class: DockerRequirement
    dockerPull: 
      ghcr.io/eoap/mastering-app-package/norm_diff@sha256:9332428544aec5d694c4834fcd286d60c5bd973aa96313998f5f5a8dd181ed56
  cwlVersion: v1.2
  baseCommand:
  - python
  - -m
  - app
  arguments: []
  $namespaces: *id001
- id: crop
  class: CommandLineTool
  inputs:
  - id: item
    type: string
    inputBinding:
      prefix: --input-item
  - id: aoi
    type: string
    inputBinding:
      prefix: --aoi
  - id: epsg
    type: string
    inputBinding:
      prefix: --epsg
  - id: band
    type: string
    inputBinding:
      prefix: --band
  outputs:
  - id: cropped
    type: File
    outputBinding:
      glob: '*.tif'
  requirements:
  - class: InlineJavascriptRequirement
  - class: EnvVarRequirement
    envDef:
    - envName: PATH
      envValue: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
    - envName: PYTHONPATH
      envValue: /app
  - class: ResourceRequirement
    coresMax: 1
    ramMax: 512
  hints:
  - class: DockerRequirement
    dockerPull: 
      ghcr.io/eoap/mastering-app-package/crop@sha256:25985f43b299e12b8c476746c4b5edf328f4d0b0fea9d017c3dafd2f4f5116ba
  cwlVersion: v1.2
  baseCommand:
  - python
  - -m
  - app
  arguments: []
  $namespaces: *id001
- id: convert-search
  class: CommandLineTool
  label: Gets the item self hrefs
  doc: Gets the item self hrefs from a STAC search result
  inputs:
  - id: search_request
    label: Search Request
    doc: Search request from the discovery step
    type: 
      https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACSearchSettings
  - id: search_results
    label: Search Results
    doc: Search results from the discovery step
    type: File
  outputs:
  - id: items
    type: Any
    outputBinding:
      loadContents: true
      glob: items.json
      outputEval: ${ return JSON.parse(self[0].contents); }
  - id: aoi
    type: string
    outputBinding:
      loadContents: true
      glob: aoi.txt
      outputEval: ${ return self[0].contents.trim(); }
  requirements:
  - class: InlineJavascriptRequirement
  - class: SchemaDefRequirement
    types:
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      fields:
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        type: string
      type: record
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      fields:
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      type: record
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      fields:
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        type: string
      type: record
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      fields:
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        type: string
      type: record
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      fields:
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        type: string
      type: record
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      fields:
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        type: string
      type: record
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      fields:
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        type: string
      type: record
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      fields:
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        type: string
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      fields:
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        type: string
      type: record
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      fields:
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        type: string
      type: record
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      fields:
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        type: string
      type: record
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      fields:
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        type: string
      type: record
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      fields:
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        type: string
      type: record
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      fields:
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        type: string
      type: record
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      fields:
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        type: string
      type: record
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      fields:
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        type: string
      type: record
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      fields:
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        type: string
      type: record
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      fields:
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type: string
      type: record
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      symbols:
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      type: enum
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      fields:
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        type: 
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      type: record
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      type: enum
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      fields:
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        type: 
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        type:
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          type: array
      type: record
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      symbols:
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      type: enum
    - name: 
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      fields:

name

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        type: 
          https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#PolygonType
      - name: 
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        type:
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            items: double
            type: array
          type: array
      - name: 
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        type:
          name: _:5e23a304-1faa-4b56-b9f6-e5330a338576
          items: double
          type: array
      type: record
    - name: 
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      symbols:
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      type: enum
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiPoint
      fields:
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          https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiPoint/type
        type: 
          https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiPointType
      - name: 
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        type:
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          type: array
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          type: array
      type: record
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      symbols:
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      type: enum
    - name: 
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      fields:
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        type: 
          https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiLineStringType
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      type: enum
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      fields:
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        type: 
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        type: string
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        type:
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        type: string
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        type: string
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      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#DatetimeInterval
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#DatetimeInterval/start
        type: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#DateTime
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#DatetimeInterval/end
        type: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#DateTime
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#Fields
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#Fields/include
        type:
        - 'null'
        - name: _:fcebe76f-ee86-4bb5-ba00-3a1042e63c8c
          items: string
          type: array
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#Fields/exclude
        type:
        - 'null'
        - name: _:05559eee-b434-456f-9ca1-aea29078b9be
          items: string
          type: array
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#FilterLang
      symbols:
      - https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#FilterLang/cql2-text
      - https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#FilterLang/cql2-json
      type: enum
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#Direction
      symbols:
      - https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#Direction/asc
      - https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#Direction/desc
      type: enum
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#SortBy
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#SortBy/field
        type: string
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#SortBy/direction
        type: 
          https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#Direction
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACSearchSettings
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACSearchSettings/bbox
        type:
        - 'null'
        - name: _:9bd9a3d2-fdc3-4a3b-bd9c-677af132cdce
          items: double
          type: array
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACSearchSettings/datetime
        type:
        - 'null'
        - https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#DateTime
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACSearchSettings/datetime-interval
        type:
        - 'null'
        - https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#DatetimeInterval
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACSearchSettings/intersects
        type:
        - 'null'
        - https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#Point
        - https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiPoint
        - https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#LineString
        - https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiLineString
        - https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#Polygon
        - https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiPolygon
        - https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#GeometryCollection
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACSearchSettings/collections
        type:
        - 'null'
        - name: _:fc084504-ff41-4e65-b123-92844784d813
          items: string
          type: array
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACSearchSettings/ids
        type:
        - 'null'
        - name: _:4c3ed8a1-960f-4f14-87d3-b8877d9d2712
          items: string
          type: array
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACSearchSettings/limit
        type:
        - 'null'
        - int
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACSearchSettings/max-items
        type:
        - 'null'
        - int
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACSearchSettings/fields
        type:
        - 'null'
        - https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#Fields
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACSearchSettings/filter
        type:
        - 'null'
        - Any
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACSearchSettings/filter-lang
        type:
        - 'null'
        - https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#FilterLang
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACSearchSettings/filter-crs
        type:
        - 'null'
        - name: _:53e26aee-e233-482e-a1a8-d962f429dadc
          items: 
            https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI
          type: array
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACSearchSettings/sortby
        type:
        - 'null'
        - name: _:42f5f7d1-c15b-4351-828f-f46cb418aeba
          items: 
            https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#SortBy
          type: array
      type: record
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACAPI
      fields:
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACAPI/api_endpoint
        type: 
          https://raw.githubusercontent.com/eoap/schemas/main/experimental/api-endpoint.yaml#APIEndpoint
      - name: 
          https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACAPI/search_request
        type: 
          https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACSearchSettings
      type: record
  - class: InitialWorkDirRequirement
    listing:
    - entryname: run.sh
      entry: |-
        #!/usr/bin/env sh
        set -x
        set -euo pipefail

        yq '[.features[].links[] | select(.rel=="self") | .href]' "$(inputs.search_results.path)" > items.json

        echo "$(inputs.search_request)" | yq '.bbox | @csv' - > aoi.txt
  hints:
  - class: DockerRequirement
    dockerPull: 
      ghcr.io/eoap/zarr-cloud-native-format/yq@sha256:401655f3f4041bf3d03b05f3b24ad4b9d18cfcf908c3b44f5901383621d0688a
  cwlVersion: v1.2
  baseCommand:
  - /bin/sh
  - run.sh
  arguments: []
  $namespaces: *id001

1.3 Obtaining a dictionary¶

Probably users need a plain dictionary to add it inside another document, just invoke:

In [3]:

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document_dict = dump_cwl(process=cwl_document)

import yaml
yaml.dump(
    document_dict,
    stream=sys.stdout,
    sort_keys=False
)
document_dict = dump_cwl(process=cwl_document)

import yaml
yaml.dump(
    document_dict,
    stream=sys.stdout,
    sort_keys=False
)

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[3], line 1
----> 1 document_dict = dump_cwl(process=cwl_document)
      3 import yaml
      4 yaml.dump(
      5     document_dict,
      6     stream=sys.stdout,
      7     sort_keys=False
      8 )

TypeError: dump_cwl() missing 1 required positional argument: 'stream'

2.1 Parsing a CommandLineTool¶

This sample shows how to read a CWL document from a remote public URL:

In [4]:

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cwl_document = load_cwl_from_location('https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/main/templates/stage-in-file.cwl')
cwl_document = load_cwl_from_location('https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/main/templates/stage-in-file.cwl')

2025-09-24 07:17:32.383 | DEBUG    | cwl_loader:load_cwl_from_location:231 - Loading CWL document from https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/main/templates/stage-in-file.cwl...

2025-09-24 07:17:32.465 | DEBUG    | cwl_loader:_load_cwl_from_stream:234 - Reading stream from https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/main/templates/stage-in-file.cwl...

2025-09-24 07:17:32.471 | DEBUG    | cwl_loader:load_cwl_from_stream:206 - CWL data of type <class 'ruamel.yaml.comments.CommentedMap'> successfully loaded from stream

2025-09-24 07:17:32.472 | DEBUG    | cwl_loader:load_cwl_from_yaml:133 - Updating the model from version 'v1.0' to version 'v1.2'...

2025-09-24 07:17:32.472 | DEBUG    | cwl_loader:load_cwl_from_yaml:144 - Raw CWL document successfully updated to v1.2!

2025-09-24 07:17:32.473 | DEBUG    | cwl_loader:load_cwl_from_yaml:148 - Parsing the raw CWL document to the CWL Utils DOM...

2025-09-24 07:17:32.629 | DEBUG    | cwl_loader:load_cwl_from_yaml:161 - Raw CWL document successfully parsed to the CWL Utils DOM!

2025-09-24 07:17:32.629 | DEBUG    | cwl_loader:load_cwl_from_yaml:163 - Dereferencing the steps[].run...

2025-09-24 07:17:32.630 | DEBUG    | cwl_loader:load_cwl_from_yaml:170 - steps[].run successfully dereferenced! Dereferencing the FQNs...

2025-09-24 07:17:32.631 | DEBUG    | cwl_loader:load_cwl_from_yaml:174 - CWL document successfully dereferenced! Now verifying steps[].run integrity...

2025-09-24 07:17:32.632 | DEBUG    | cwl_loader:load_cwl_from_yaml:178 - All steps[].run link are resolvable!

2025-09-24 07:17:32.632 | DEBUG    | cwl_loader:load_cwl_from_yaml:181 - Sorting Process instances by dependencies....

2025-09-24 07:17:32.633 | DEBUG    | cwl_loader:load_cwl_from_yaml:183 - Sorting process is over.

2025-09-24 07:17:32.633 | DEBUG    | cwl_loader:_load_cwl_from_stream:243 - Stream from https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/main/templates/stage-in-file.cwl successfully load!

2.2 Serializing¶

This sample shows how to write a CWL document to a stream (string, file, ...):

In [5]:

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dump_cwl(process=cwl_document, stream=sys.stderr)
dump_cwl(process=cwl_document, stream=sys.stderr)

id: my-asthonishing-stage-in-file
class: CommandLineTool
inputs:
- id: reference
  label: Reference URL
  doc: An URL 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: File
  outputBinding:
    glob: staged
requirements:
- class: NetworkAccess
  networkAccess: true
- 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/application-package-patterns/vegetation-indexes:0.1.1
- class: InlineJavascriptRequirement
- class: InitialWorkDirRequirement
  listing:
  - entryname: stage.py
    entry: |-
      import sys
      import requests
      import planetary_computer

      href = sys.argv[1]

      signed_url = planetary_computer.sign(href)
      output_path = "staged"

      response = requests.get(signed_url, stream=True)
      response.raise_for_status()  # Raise an error for bad status codes

      with open(output_path, "wb") as f:
          for chunk in response.iter_content(chunk_size=8192):
              f.write(chunk)

      print(f"Downloaded to {output_path}")

      empty_arg = sys.argv[2]
cwlVersion: v1.2
baseCommand:
- python
- stage.py
arguments:
- $( inputs.reference.value )
- $( inputs.another_input )

3. Parsing existing data structures¶

Users can load CWL Worflow(s) even from existing dictionaries:

In [6]:

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from cwl_loader import load_cwl_from_yaml

cwl_document = load_cwl_from_yaml(raw_process={
  "cwlVersion": "v1.2", 
  "inputs": {
    "api_endpoint": {
      "doc": "STAC API endpoint for Landsat-9 data", 
      "type": "https://raw.githubusercontent.com/eoap/schemas/main/experimental/api-endpoint.yaml#APIEndpoint", 
      "label": "STAC API endpoint"
    }, 
    "search_request": {
      "doc": "STAC API settings for Landsat-9 data", 
      "type": "https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACSearchSettings", 
      "label": "STAC API settings"
    }
  }, 
  "requirements": [
    {
      "class": "InlineJavascriptRequirement"
    }, 
    {
      "class": "NetworkAccess", 
      "networkAccess": True
    }, 
    {
      "class": "SchemaDefRequirement", 
      "types": [
        {
          "$import": "https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml"
        }, 
        {
          "$import": "https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml"
        }, 
        {
          "$import": "https://raw.githubusercontent.com/eoap/schemas/main/experimental/api-endpoint.yaml"
        }, 
        {
          "$import": "https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml"
        }
      ]
    }
  ], 
  "doc": "This tool uses the STAC Client to search for STAC items\n", 
  "class": "CommandLineTool", 
  "baseCommand": [
    "stac-client"
  ], 
  "label": "STAC Client Tool", 
  "arguments": [
    "search", 
    "$(inputs.api_endpoint.url.value)", 
    "${ const args = []; const collections = inputs.search_request.collections; args.push('--collections', collections.join(\",\")); return args; }", 
    "${ const args = []; const bbox = inputs.search_request?.bbox; if (Array.isArray(bbox) && bbox.length >= 4) { args.push('--bbox', ...bbox.map(String)); } return args; }", 
    "${ const args = []; const limit = inputs.search_request?.limit; args.push(\"--limit\", (limit ?? 10).toString()); return args; }", 
    "${ const maxItems = 5; return ['--max-items', maxItems.toString()]; }", 
    "${ const args = []; const filter = inputs.search_request?.filter; const filterLang = inputs.search_request?.['filter-lang']; if (filterLang) { args.push('--filter-lang', filterLang); } if (filter) { args.push('--filter', JSON.stringify(filter)); } return args; }", 
    "${ const datetime = inputs.search_request?.datetime; const datetimeInterval = inputs.search_request?.datetime_interval; if (datetime) { return ['--datetime', datetime]; } else if (datetimeInterval) { const start = datetimeInterval.start?.value || '..'; const end = datetimeInterval.end?.value || '..'; return ['--datetime', `${start}/${end}`]; } return []; }", 
    "${ const ids = inputs.search_request?.ids; const args = []; if (Array.isArray(ids) && ids.length > 0) { args.push('--ids', ...ids.map(String)); } return args; }", 
    "${ const intersects = inputs.search_request?.intersects; if (intersects) { return ['--intersects', JSON.stringify(intersects)]; } return []; }", 
    "--save", 
    "discovery-output.json"
  ], 
  "outputs": {
    "search_output": {
      "outputBinding": {
        "glob": "discovery-output.json"
      }, 
      "type": "File"
    }
  }, 
  "id": "stac-client", 
  "hints": [
    {
      "dockerPull": "docker.io/library/stac-client", 
      "class": "DockerRequirement"
    }
  ]
})

dump_cwl(process=cwl_document, stream=sys.stderr)
from cwl_loader import load_cwl_from_yaml

cwl_document = load_cwl_from_yaml(raw_process={
  "cwlVersion": "v1.2", 
  "inputs": {
    "api_endpoint": {
      "doc": "STAC API endpoint for Landsat-9 data", 
      "type": "https://raw.githubusercontent.com/eoap/schemas/main/experimental/api-endpoint.yaml#APIEndpoint", 
      "label": "STAC API endpoint"
    }, 
    "search_request": {
      "doc": "STAC API settings for Landsat-9 data", 
      "type": "https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACSearchSettings", 
      "label": "STAC API settings"
    }
  }, 
  "requirements": [
    {
      "class": "InlineJavascriptRequirement"
    }, 
    {
      "class": "NetworkAccess", 
      "networkAccess": True
    }, 
    {
      "class": "SchemaDefRequirement", 
      "types": [
        {
          "$import": "https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml"
        }, 
        {
          "$import": "https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml"
        }, 
        {
          "$import": "https://raw.githubusercontent.com/eoap/schemas/main/experimental/api-endpoint.yaml"
        }, 
        {
          "$import": "https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml"
        }
      ]
    }
  ], 
  "doc": "This tool uses the STAC Client to search for STAC items\n", 
  "class": "CommandLineTool", 
  "baseCommand": [
    "stac-client"
  ], 
  "label": "STAC Client Tool", 
  "arguments": [
    "search", 
    "$(inputs.api_endpoint.url.value)", 
    "${ const args = []; const collections = inputs.search_request.collections; args.push('--collections', collections.join(\",\")); return args; }", 
    "${ const args = []; const bbox = inputs.search_request?.bbox; if (Array.isArray(bbox) && bbox.length >= 4) { args.push('--bbox', ...bbox.map(String)); } return args; }", 
    "${ const args = []; const limit = inputs.search_request?.limit; args.push(\"--limit\", (limit ?? 10).toString()); return args; }", 
    "${ const maxItems = 5; return ['--max-items', maxItems.toString()]; }", 
    "${ const args = []; const filter = inputs.search_request?.filter; const filterLang = inputs.search_request?.['filter-lang']; if (filterLang) { args.push('--filter-lang', filterLang); } if (filter) { args.push('--filter', JSON.stringify(filter)); } return args; }", 
    "${ const datetime = inputs.search_request?.datetime; const datetimeInterval = inputs.search_request?.datetime_interval; if (datetime) { return ['--datetime', datetime]; } else if (datetimeInterval) { const start = datetimeInterval.start?.value || '..'; const end = datetimeInterval.end?.value || '..'; return ['--datetime', `${start}/${end}`]; } return []; }", 
    "${ const ids = inputs.search_request?.ids; const args = []; if (Array.isArray(ids) && ids.length > 0) { args.push('--ids', ...ids.map(String)); } return args; }", 
    "${ const intersects = inputs.search_request?.intersects; if (intersects) { return ['--intersects', JSON.stringify(intersects)]; } return []; }", 
    "--save", 
    "discovery-output.json"
  ], 
  "outputs": {
    "search_output": {
      "outputBinding": {
        "glob": "discovery-output.json"
      }, 
      "type": "File"
    }
  }, 
  "id": "stac-client", 
  "hints": [
    {
      "dockerPull": "docker.io/library/stac-client", 
      "class": "DockerRequirement"
    }
  ]
})

dump_cwl(process=cwl_document, stream=sys.stderr)

2025-09-24 07:17:32.665 | DEBUG    | cwl_loader:load_cwl_from_yaml:146 - No needs to update the Raw CWL document since it targets already the v1.2

2025-09-24 07:17:32.666 | DEBUG    | cwl_loader:load_cwl_from_yaml:148 - Parsing the raw CWL document to the CWL Utils DOM...

2025-09-24 07:17:33.134 | DEBUG    | cwl_loader:load_cwl_from_yaml:161 - Raw CWL document successfully parsed to the CWL Utils DOM!

2025-09-24 07:17:33.135 | DEBUG    | cwl_loader:load_cwl_from_yaml:163 - Dereferencing the steps[].run...

2025-09-24 07:17:33.135 | DEBUG    | cwl_loader:load_cwl_from_yaml:170 - steps[].run successfully dereferenced! Dereferencing the FQNs...

2025-09-24 07:17:33.136 | DEBUG    | cwl_loader:load_cwl_from_yaml:174 - CWL document successfully dereferenced! Now verifying steps[].run integrity...

2025-09-24 07:17:33.137 | DEBUG    | cwl_loader:load_cwl_from_yaml:178 - All steps[].run link are resolvable!

2025-09-24 07:17:33.137 | DEBUG    | cwl_loader:load_cwl_from_yaml:181 - Sorting Process instances by dependencies....

2025-09-24 07:17:33.138 | DEBUG    | cwl_loader:load_cwl_from_yaml:183 - Sorting process is over.

id: stac-client
class: CommandLineTool
label: STAC Client Tool
doc: "This tool uses the STAC Client to search for STAC items\n"
inputs:
- id: api_endpoint
  label: STAC API endpoint
  doc: STAC API endpoint for Landsat-9 data
  type: 
    https://raw.githubusercontent.com/eoap/schemas/main/experimental/api-endpoint.yaml#APIEndpoint
- id: search_request
  label: STAC API settings
  doc: STAC API settings for Landsat-9 data
  type: 
    https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACSearchSettings
outputs:
- id: search_output
  type: File
  outputBinding:
    glob: discovery-output.json
requirements:
- class: InlineJavascriptRequirement
- class: NetworkAccess
  networkAccess: true
- 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: 
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    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:
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        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
  - name: 
      https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#PointType
    symbols:
    - https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#PointType/Point
    type: enum
  - name: https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#Point
    fields:
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#Point/type
      type: 
        https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#PointType
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#Point/coordinates
      type:
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        items: double
        type: array
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#Point/bbox
      type:
        name: _:9c3414cb-764b-4e0b-8532-557b9cfc5a87
        items: double
        type: array
    type: record
  - name: 
      https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#LineStringType
    symbols:
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    type: enum
  - name: 
      https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#LineString
    fields:
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#LineString/type
      type: 
        https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#LineStringType
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#LineString/coordinates
      type:
        name: _:e3039424-88fe-4d1e-aefa-06ccbffd9427
        items: double
        type: array
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#LineString/bbox
      type:
        name: _:a6e7709d-8c67-4f0e-b778-34c40578895f
        items: double
        type: array
    type: record
  - name: 
      https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#PolygonType
    symbols:
    - https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#PolygonType/Polygon
    type: enum
  - name: 
      https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#Polygon
    fields:
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#Polygon/type
      type: 
        https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#PolygonType
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#Polygon/coordinates
      type:
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        items:
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          items: double
          type: array
        type: array
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#Polygon/bbox
      type:
        name: _:b672d1f9-a548-4268-8a86-74b1dd6fd6cf
        items: double
        type: array
    type: record
  - name: 
      https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiPointType
    symbols:
    - https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiPointType/MultiPoint
    type: enum
  - name: 
      https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiPoint
    fields:
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiPoint/type
      type: 
        https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiPointType
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiPoint/coordinates
      type:
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        items:
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          items: double
          type: array
        type: array
    - name: 
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      type:
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        items: double
        type: array
    type: record
  - name: 
      https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiLineStringType
    symbols:
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    type: enum
  - name: 
      https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiLineString
    fields:
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        https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiLineString/type
      type: 
        https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiLineStringType
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiLineString/coordinates
      type:
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        items:
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          items:
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            items: double
            type: array
          type: array
        type: array
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiLineString/bbox
      type:
        name: _:eb0c1093-f7a6-44c8-9073-211a3556b308
        items: double
        type: array
    type: record
  - name: 
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    symbols:
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    type: enum
  - name: 
      https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiPolygon
    fields:
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        https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiPolygon/type
      type: 
        https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiPolygonType
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiPolygon/coordinates
      type:
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              items: double
              type: array
            type: array
          type: array
        type: array
    - name: 
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      type:
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    type: enum
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    fields:
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      type: 
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      doc: "Identifier"
      type: string
    - name: 
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      type:
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      - https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#LineString
      - https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#Polygon
      - https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiPoint
      - https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiLineString
      - https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiPolygon
    - name: 
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      type:
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        type: array
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      type: string
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      type: string
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      type: string
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    type: record
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      type: 
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      type: int
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      type: int
    type: record
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      type: string
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      - name: _:f7c6d3eb-312c-409f-82a5-5cd27fa98d58
        items: 
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    type: record
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    fields:
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      type: 
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    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#DatetimeInterval/end
      type: 
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    type: record
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    fields:
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        items: string
        type: array
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      https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#FilterLang
    symbols:
    - https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#FilterLang/cql2-text
    - https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#FilterLang/cql2-json
    type: enum
  - name: 
      https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#Direction
    symbols:
    - https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#Direction/asc
    - https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#Direction/desc
    type: enum
  - name: 
      https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#SortBy
    fields:
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#SortBy/field
      type: string
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#SortBy/direction
      type: 
        https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#Direction
    type: record
  - name: 
      https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACSearchSettings
    fields:
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACSearchSettings/bbox
      type:
      - 'null'
      - name: _:bdbd98bc-6713-41e6-8f25-952f465b23d9
        items: double
        type: array
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACSearchSettings/datetime
      type:
      - 'null'
      - https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#DateTime
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACSearchSettings/datetime-interval
      type:
      - 'null'
      - https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#DatetimeInterval
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACSearchSettings/intersects
      type:
      - 'null'
      - https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#Point
      - https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiPoint
      - https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#LineString
      - https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiLineString
      - https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#Polygon
      - https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#MultiPolygon
      - https://raw.githubusercontent.com/eoap/schemas/main/geojson.yaml#GeometryCollection
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACSearchSettings/collections
      type:
      - 'null'
      - name: _:4ad8825d-9ab2-4cab-afb1-290ac511cab5
        items: string
        type: array
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACSearchSettings/ids
      type:
      - 'null'
      - name: _:650c0ad4-cd00-4e78-926b-9e58fca441ef
        items: string
        type: array
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACSearchSettings/limit
      type:
      - 'null'
      - int
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACSearchSettings/max-items
      type:
      - 'null'
      - int
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACSearchSettings/fields
      type:
      - 'null'
      - https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#Fields
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACSearchSettings/filter
      type:
      - 'null'
      - Any
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACSearchSettings/filter-lang
      type:
      - 'null'
      - https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#FilterLang
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACSearchSettings/filter-crs
      type:
      - 'null'
      - name: _:6a9d3418-5c3f-4fc1-bfc7-74d1f5f8dc53
        items: 
          https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI
        type: array
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACSearchSettings/sortby
      type:
      - 'null'
      - name: _:aa580c41-9bba-4eb9-b94f-6be9b279eb86
        items: 
          https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#SortBy
        type: array
    type: record
  - name: 
      https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACAPI
    fields:
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACAPI/api_endpoint
      type: 
        https://raw.githubusercontent.com/eoap/schemas/main/experimental/api-endpoint.yaml#APIEndpoint
    - name: 
        https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACAPI/search_request
      type: 
        https://raw.githubusercontent.com/eoap/schemas/main/experimental/discovery.yaml#STACSearchSettings
    type: record
hints:
- class: DockerRequirement
  dockerPull: docker.io/library/stac-client
cwlVersion: v1.2
baseCommand:
- stac-client
arguments:
- search
- $(inputs.api_endpoint.url.value)
- ${ const args = []; const collections = inputs.search_request.collections; 
  args.push('--collections', collections.join(",")); return args; }
- ${ const args = []; const bbox = inputs.search_request?.bbox; if 
  (Array.isArray(bbox) && bbox.length >= 4) { args.push('--bbox', 
  ...bbox.map(String)); } return args; }
- ${ const args = []; const limit = inputs.search_request?.limit; 
  args.push("--limit", (limit ?? 10).toString()); return args; }
- ${ const maxItems = 5; return ['--max-items', maxItems.toString()]; }
- ${ const args = []; const filter = inputs.search_request?.filter; const 
  filterLang = inputs.search_request?.['filter-lang']; if (filterLang) { 
  args.push('--filter-lang', filterLang); } if (filter) { args.push('--filter', 
  JSON.stringify(filter)); } return args; }
- ${ const datetime = inputs.search_request?.datetime; const datetimeInterval = 
  inputs.search_request?.datetime_interval; if (datetime) { return 
  ['--datetime', datetime]; } else if (datetimeInterval) { const start = 
  datetimeInterval.start?.value || '..'; const end = datetimeInterval.end?.value
  || '..'; return ['--datetime', `${start}/${end}`]; } return []; }
- ${ const ids = inputs.search_request?.ids; const args = []; if 
  (Array.isArray(ids) && ids.length > 0) { args.push('--ids', 
  ...ids.map(String)); } return args; }
- ${ const intersects = inputs.search_request?.intersects; if (intersects) { 
  return ['--intersects', JSON.stringify(intersects)]; } return []; }
- --save
- discovery-output.json

4. Parsing conditional Workflow¶

In [7]:

Copied!

cwl_document = load_cwl_from_location('https://raw.githubusercontent.com/eoap/how-to/refs/heads/main/cwl-workflows/conditional-workflows.cwl')
dump_cwl(process=cwl_document, stream=sys.stderr)
cwl_document = load_cwl_from_location('https://raw.githubusercontent.com/eoap/how-to/refs/heads/main/cwl-workflows/conditional-workflows.cwl')
dump_cwl(process=cwl_document, stream=sys.stderr)

2025-09-24 07:17:33.208 | DEBUG    | cwl_loader:load_cwl_from_location:231 - Loading CWL document from https://raw.githubusercontent.com/eoap/how-to/refs/heads/main/cwl-workflows/conditional-workflows.cwl...

2025-09-24 07:17:33.304 | DEBUG    | cwl_loader:_load_cwl_from_stream:234 - Reading stream from https://raw.githubusercontent.com/eoap/how-to/refs/heads/main/cwl-workflows/conditional-workflows.cwl...

2025-09-24 07:17:33.326 | DEBUG    | cwl_loader:load_cwl_from_stream:206 - CWL data of type <class 'ruamel.yaml.comments.CommentedMap'> successfully loaded from stream

2025-09-24 07:17:33.327 | DEBUG    | cwl_loader:load_cwl_from_yaml:146 - No needs to update the Raw CWL document since it targets already the v1.2

2025-09-24 07:17:33.327 | DEBUG    | cwl_loader:load_cwl_from_yaml:148 - Parsing the raw CWL document to the CWL Utils DOM...

2025-09-24 07:17:33.457 | DEBUG    | cwl_loader:load_cwl_from_yaml:161 - Raw CWL document successfully parsed to the CWL Utils DOM!

2025-09-24 07:17:33.458 | DEBUG    | cwl_loader:load_cwl_from_yaml:163 - Dereferencing the steps[].run...

2025-09-24 07:17:33.458 | DEBUG    | cwl_loader:_on_process:81 - Checking if https://raw.githubusercontent.com/eoap/how-to/refs/heads/main/cwl-workflows/conditional-workflows.cwl#stac must be externally imported...

2025-09-24 07:17:33.459 | DEBUG    | cwl_loader:_on_process:85 - run_url: https://raw.githubusercontent.com/eoap/how-to/refs/heads/main/cwl-workflows/conditional-workflows.cwl - uri: https://raw.githubusercontent.com/eoap/how-to/refs/heads/main/cwl-workflows/conditional-workflows.cwl

2025-09-24 07:17:33.460 | DEBUG    | cwl_loader:_on_process:81 - Checking if https://raw.githubusercontent.com/eoap/how-to/refs/heads/main/cwl-workflows/conditional-workflows.cwl#rio_stack must be externally imported...

2025-09-24 07:17:33.460 | DEBUG    | cwl_loader:_on_process:85 - run_url: https://raw.githubusercontent.com/eoap/how-to/refs/heads/main/cwl-workflows/conditional-workflows.cwl - uri: https://raw.githubusercontent.com/eoap/how-to/refs/heads/main/cwl-workflows/conditional-workflows.cwl

2025-09-24 07:17:33.461 | DEBUG    | cwl_loader:_on_process:81 - Checking if https://raw.githubusercontent.com/eoap/how-to/refs/heads/main/cwl-workflows/conditional-workflows.cwl#rio_warp_stack must be externally imported...

2025-09-24 07:17:33.462 | DEBUG    | cwl_loader:_on_process:85 - run_url: https://raw.githubusercontent.com/eoap/how-to/refs/heads/main/cwl-workflows/conditional-workflows.cwl - uri: https://raw.githubusercontent.com/eoap/how-to/refs/heads/main/cwl-workflows/conditional-workflows.cwl

2025-09-24 07:17:33.463 | DEBUG    | cwl_loader:_on_process:81 - Checking if https://raw.githubusercontent.com/eoap/how-to/refs/heads/main/cwl-workflows/conditional-workflows.cwl#rio_color must be externally imported...

2025-09-24 07:17:33.463 | DEBUG    | cwl_loader:_on_process:85 - run_url: https://raw.githubusercontent.com/eoap/how-to/refs/heads/main/cwl-workflows/conditional-workflows.cwl - uri: https://raw.githubusercontent.com/eoap/how-to/refs/heads/main/cwl-workflows/conditional-workflows.cwl

2025-09-24 07:17:33.464 | DEBUG    | cwl_loader:load_cwl_from_yaml:170 - steps[].run successfully dereferenced! Dereferencing the FQNs...

2025-09-24 07:17:33.465 | DEBUG    | cwl_loader:load_cwl_from_yaml:174 - CWL document successfully dereferenced! Now verifying steps[].run integrity...

2025-09-24 07:17:33.465 | DEBUG    | cwl_loader:load_cwl_from_yaml:178 - All steps[].run link are resolvable!

2025-09-24 07:17:33.466 | DEBUG    | cwl_loader:load_cwl_from_yaml:181 - Sorting Process instances by dependencies....

2025-09-24 07:17:33.467 | DEBUG    | cwl_loader:load_cwl_from_yaml:183 - Sorting process is over.

2025-09-24 07:17:33.468 | DEBUG    | cwl_loader:_load_cwl_from_stream:243 - Stream from https://raw.githubusercontent.com/eoap/how-to/refs/heads/main/cwl-workflows/conditional-workflows.cwl successfully load!

cwlVersion: v1.2
$graph:
- id: stac
  class: CommandLineTool
  inputs:
  - id: stac_item
    type: string
  - id: common_band_name
    type: string
  outputs:
  - id: hrefs
    type: string
    outputBinding:
      loadContents: true
      glob: message
      outputEval: |
        ${
          const assets = JSON.parse(self[0].contents).assets;
          const bandKey = Object.keys(assets).find(key =>
            assets[key]['eo:bands'] &&
            assets[key]['eo:bands'].length === 1 &&
            assets[key]['eo:bands'].some(band => band.common_name === inputs.common_band_name)
          );
          if (!bandKey) {
            throw new Error(`No valid asset found for band: ${inputs.common_band_name}`);
          }
          return assets[bandKey].href;
        }
  requirements:
  - class: DockerRequirement
    dockerPull: docker.io/curlimages/curl:latest
  cwlVersion: v1.2
  baseCommand: curl
  arguments:
  - $( inputs.stac_item )
  stdout: message
- id: rio_color
  class: CommandLineTool
  inputs:
  - id: stacked
    type: File
  outputs:
  - id: rgb
    type: File
    outputBinding:
      glob: rgb.tif
  requirements:
  - class: DockerRequirement
    dockerPull: ghcr.io/eoap/how-to/rio:1.0.0
  - class: InitialWorkDirRequirement
    listing:
    - entryname: run.sh
      entry: |-
        #!/bin/bash
        rio color -j -1 --out-dtype uint8 $1 rgb.tif "gamma 3 0.95, sigmoidal rgb 35 0.13"
  cwlVersion: v1.2
  baseCommand:
  - /bin/bash
  - run.sh
  arguments:
  - $( inputs.stacked.path )
- id: rio_warp_stack
  class: CommandLineTool
  inputs:
  - id: tiffs
    type:
      name: _:3d5c3b2c-bddf-4801-8c99-a7a47c9c898b
      items: string
      type: array
  - id: epsg_code
    type: string
  outputs:
  - id: stacked
    type: File
    outputBinding:
      glob: warped.tif
  requirements:
  - class: DockerRequirement
    dockerPull: ghcr.io/eoap/how-to/rio:1.0.0
  - class: EnvVarRequirement
    envDef:
    - envName: GDAL_TIFF_INTERNAL_MASK
      envValue: YES
    - envName: GDAL_HTTP_MERGE_CONSECUTIVE_RANGES
      envValue: YES
    - envName: CPL_VSIL_CURL_ALLOWED_EXTENSIONS
      envValue: .tif
  - class: InitialWorkDirRequirement
    listing:
    - entryname: run.sh
      entry: |-
        #!/bin/bash
        rio stack $@

        rio warp --dst-crs $(inputs.epsg_code) stacked.tif warped.tif
  cwlVersion: v1.2
  baseCommand:
  - /bin/bash
  - run.sh
  arguments:
  - valueFrom: |
      ${  
        var arr = [];
        for(var i=0; i<inputs.tiffs.length; i++) {
            arr.push(inputs.tiffs[i]); 
        }
        return arr; 
        }
  - stacked.tif
- id: main
  class: Workflow
  inputs:
  - id: stac-item
    type: string
  - id: epsg_code
    default: native
    type: string
  - id: bands
    type:
      name: _:65301f32-d8f6-4a66-8006-fc9140eb476a
      items: string
      type: array
  outputs:
  - id: rgb-tif
    outputSource: step_color/rgb
    type: File
  - id: stack
    outputSource:
    - step_stack/stacked
    - step_warp_stack/stacked
    pickValue: the_only_non_null
    type: File
  requirements:
  - class: InlineJavascriptRequirement
  - class: NetworkAccess
    networkAccess: true
  - class: ScatterFeatureRequirement
  - class: MultipleInputFeatureRequirement
  cwlVersion: v1.2
  steps:
  - id: step_curl
    in:
    - id: stac_item
      source: stac-item
    - id: common_band_name
      source: bands
    out:
    - hrefs
    run: '#stac'
    scatter: step_curl/common_band_name
    scatterMethod: dotproduct
  - id: step_warp_stack
    in:
    - id: tiffs
      source: step_curl/hrefs
    - id: epsg_code
      source: epsg_code
    out:
    - stacked
    run: '#rio_warp_stack'
    when: $( inputs.epsg_code != "native")
  - id: step_stack
    in:
    - id: tiffs
      source: step_curl/hrefs
    - id: epsg_code
      source: epsg_code
    out:
    - stacked
    run: '#rio_stack'
    when: $( inputs.epsg_code == "native")
  - id: step_color
    in:
    - id: stacked
      source:
      - step_stack/stacked
      - step_warp_stack/stacked
      pickValue: the_only_non_null
    out:
    - rgb
    run: '#rio_color'
- id: rio_stack
  class: CommandLineTool
  inputs:
  - id: tiffs
    type:
      name: _:1798ef1a-bfe1-4cf4-bd5c-c0ad4c2f355e
      items: string
      type: array
  outputs:
  - id: stacked
    type: File
    outputBinding:
      glob: stacked.tif
  requirements:
  - class: DockerRequirement
    dockerPull: ghcr.io/eoap/how-to/rio:1.0.0
  - class: EnvVarRequirement
    envDef:
    - envName: GDAL_TIFF_INTERNAL_MASK
      envValue: YES
    - envName: GDAL_HTTP_MERGE_CONSECUTIVE_RANGES
      envValue: YES
    - envName: CPL_VSIL_CURL_ALLOWED_EXTENSIONS
      envValue: .tif
  - class: InitialWorkDirRequirement
    listing:
    - entryname: run.sh
      entry: |-
        #!/bin/bash
        rio stack $@
  cwlVersion: v1.2
  baseCommand:
  - /bin/bash
  - run.sh
  arguments:
  - valueFrom: |
      ${  
        var arr = [];
        for(var i=0; i<inputs.tiffs.length; i++) {
            arr.push(inputs.tiffs[i]); 
        }
        return arr; 
        }
  - stacked.tif