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]:

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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')

cwl_document = load_cwl_from_location('/home/stripodi/Downloads/hotspot.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')

cwl_document = load_cwl_from_location('/home/stripodi/Downloads/hotspot.cwl')

2025-12-01 09:33:51.287 | DEBUG    | cwl_loader:load_cwl_from_location:228 - Loading CWL document from /home/stripodi/Downloads/hotspot.cwl...

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[1], line 5
      1 from cwl_loader import load_cwl_from_location
      3 # 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')
----> 5 cwl_document = load_cwl_from_location('/home/stripodi/Downloads/hotspot.cwl')

File /opt/hostedtoolcache/Python/3.14.0/x64/lib/python3.14/site-packages/cwl_loader/__init__.py:263, in load_cwl_from_location(path, cwl_version, sort)
    261         return _load_cwl_from_stream(f)
    262 else:
--> 263     raise ValueError(f"Invalid source {path}: not a URL or existing file path")

ValueError: Invalid source /home/stripodi/Downloads/hotspot.cwl: not a URL or existing file path

1.2 Serializing¶

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

In [2]:

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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)

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
Cell In[2], line 4
      1 from cwl_loader import dump_cwl
      2 import sys
----> 4 dump_cwl(process=cwl_document, stream=sys.stderr)

NameError: name 'cwl_document' is not defined

2.1 Parsing a CommandLineTool¶

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

In [3]:

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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')

2025-12-01 09:33:51.462 | DEBUG    | cwl_loader:load_cwl_from_location:228 - Loading CWL document from https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/main/templates/stage-in-file.cwl...

2025-12-01 09:33:51.609 | DEBUG    | cwl_loader:_load_cwl_from_stream:231 - Reading stream from https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/main/templates/stage-in-file.cwl...

2025-12-01 09:33:51.616 | DEBUG    | cwl_loader:load_cwl_from_stream:203 - CWL data of type <class 'ruamel.yaml.comments.CommentedMap'> successfully loaded from stream

2025-12-01 09:33:51.616 | DEBUG    | cwl_loader:load_cwl_from_yaml:130 - Updating the model from version 'v1.0' to version 'v1.2'...

2025-12-01 09:33:51.617 | DEBUG    | cwl_loader:load_cwl_from_yaml:141 - Raw CWL document successfully updated to v1.2!

2025-12-01 09:33:51.617 | DEBUG    | cwl_loader:load_cwl_from_yaml:145 - Parsing the raw CWL document to the CWL Utils DOM...

2025-12-01 09:33:52.534 | DEBUG    | cwl_loader:load_cwl_from_yaml:158 - Raw CWL document successfully parsed to the CWL Utils DOM!

2025-12-01 09:33:52.535 | DEBUG    | cwl_loader:load_cwl_from_yaml:160 - Dereferencing the steps[].run...

2025-12-01 09:33:52.535 | DEBUG    | cwl_loader:load_cwl_from_yaml:167 - steps[].run successfully dereferenced! Dereferencing the FQNs...

2025-12-01 09:33:52.535 | DEBUG    | cwl_loader:load_cwl_from_yaml:171 - CWL document successfully dereferenced! Now verifying steps[].run integrity...

2025-12-01 09:33:52.536 | DEBUG    | cwl_loader:load_cwl_from_yaml:175 - All steps[].run link are resolvable!

2025-12-01 09:33:52.536 | DEBUG    | cwl_loader:load_cwl_from_yaml:178 - Sorting Process instances by dependencies....

2025-12-01 09:33:52.537 | DEBUG    | cwl_loader:load_cwl_from_yaml:180 - Sorting process is over.

2025-12-01 09:33:52.538 | DEBUG    | cwl_loader:_load_cwl_from_stream:240 - 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 [4]:

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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 [5]:

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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)

2025-12-01 09:33:52.566 | DEBUG    | cwl_loader:load_cwl_from_yaml:143 - No needs to update the Raw CWL document since it targets already the v1.2

2025-12-01 09:33:52.567 | DEBUG    | cwl_loader:load_cwl_from_yaml:145 - Parsing the raw CWL document to the CWL Utils DOM...

2025-12-01 09:33:55.344 | DEBUG    | cwl_loader:load_cwl_from_yaml:158 - Raw CWL document successfully parsed to the CWL Utils DOM!

2025-12-01 09:33:55.345 | DEBUG    | cwl_loader:load_cwl_from_yaml:160 - Dereferencing the steps[].run...

2025-12-01 09:33:55.345 | DEBUG    | cwl_loader:load_cwl_from_yaml:167 - steps[].run successfully dereferenced! Dereferencing the FQNs...

2025-12-01 09:33:55.346 | DEBUG    | cwl_loader:load_cwl_from_yaml:171 - CWL document successfully dereferenced! Now verifying steps[].run integrity...

2025-12-01 09:33:55.346 | DEBUG    | cwl_loader:load_cwl_from_yaml:175 - All steps[].run link are resolvable!

2025-12-01 09:33:55.346 | DEBUG    | cwl_loader:load_cwl_from_yaml:178 - Sorting Process instances by dependencies....

2025-12-01 09:33:55.347 | DEBUG    | cwl_loader:load_cwl_from_yaml:180 - 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
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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 [6]:

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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)

2025-12-01 09:33:55.409 | DEBUG    | cwl_loader:load_cwl_from_location:228 - Loading CWL document from https://raw.githubusercontent.com/eoap/how-to/refs/heads/main/cwl-workflows/conditional-workflows.cwl...

2025-12-01 09:33:55.541 | DEBUG    | cwl_loader:_load_cwl_from_stream:231 - Reading stream from https://raw.githubusercontent.com/eoap/how-to/refs/heads/main/cwl-workflows/conditional-workflows.cwl...

2025-12-01 09:33:55.565 | DEBUG    | cwl_loader:load_cwl_from_stream:203 - CWL data of type <class 'ruamel.yaml.comments.CommentedMap'> successfully loaded from stream

2025-12-01 09:33:55.566 | DEBUG    | cwl_loader:load_cwl_from_yaml:143 - No needs to update the Raw CWL document since it targets already the v1.2

2025-12-01 09:33:55.567 | DEBUG    | cwl_loader:load_cwl_from_yaml:145 - Parsing the raw CWL document to the CWL Utils DOM...

2025-12-01 09:33:56.243 | DEBUG    | cwl_loader:load_cwl_from_yaml:158 - Raw CWL document successfully parsed to the CWL Utils DOM!

2025-12-01 09:33:56.244 | DEBUG    | cwl_loader:load_cwl_from_yaml:160 - Dereferencing the steps[].run...

2025-12-01 09:33:56.245 | DEBUG    | cwl_loader:_on_process:78 - Checking if https://raw.githubusercontent.com/eoap/how-to/refs/heads/main/cwl-workflows/conditional-workflows.cwl#stac must be externally imported...

2025-12-01 09:33:56.245 | DEBUG    | cwl_loader:_on_process:82 - 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

2025-12-01 09:33:56.245 | DEBUG    | cwl_loader:_on_process:78 - Checking if https://raw.githubusercontent.com/eoap/how-to/refs/heads/main/cwl-workflows/conditional-workflows.cwl#rio_stack must be externally imported...

2025-12-01 09:33:56.246 | DEBUG    | cwl_loader:_on_process:82 - 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

2025-12-01 09:33:56.246 | DEBUG    | cwl_loader:_on_process:78 - Checking if https://raw.githubusercontent.com/eoap/how-to/refs/heads/main/cwl-workflows/conditional-workflows.cwl#rio_warp_stack must be externally imported...

2025-12-01 09:33:56.247 | DEBUG    | cwl_loader:_on_process:82 - 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

2025-12-01 09:33:56.247 | DEBUG    | cwl_loader:_on_process:78 - Checking if https://raw.githubusercontent.com/eoap/how-to/refs/heads/main/cwl-workflows/conditional-workflows.cwl#rio_color must be externally imported...

2025-12-01 09:33:56.248 | DEBUG    | cwl_loader:_on_process:82 - 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

2025-12-01 09:33:56.248 | DEBUG    | cwl_loader:load_cwl_from_yaml:167 - steps[].run successfully dereferenced! Dereferencing the FQNs...

2025-12-01 09:33:56.248 | DEBUG    | cwl_loader:load_cwl_from_yaml:171 - CWL document successfully dereferenced! Now verifying steps[].run integrity...

2025-12-01 09:33:56.249 | DEBUG    | cwl_loader:load_cwl_from_yaml:175 - All steps[].run link are resolvable!

2025-12-01 09:33:56.249 | DEBUG    | cwl_loader:load_cwl_from_yaml:178 - Sorting Process instances by dependencies....

2025-12-01 09:33:56.251 | DEBUG    | cwl_loader:load_cwl_from_yaml:180 - Sorting process is over.

2025-12-01 09:33:56.251 | DEBUG    | cwl_loader:_load_cwl_from_stream:240 - Stream from https://raw.githubusercontent.com/eoap/how-to/refs/heads/main/cwl-workflows/conditional-workflows.cwl successfully load!

cwlVersion: v1.2
$graph:
- id: rio_warp_stack
  class: CommandLineTool
  inputs:
  - id: tiffs
    type:
      name: _:26b0721c-703f-4953-8ad6-23ced85ebf6b
      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: 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: main
  class: Workflow
  inputs:
  - id: stac-item
    type: string
  - id: epsg_code
    default: native
    type: string
  - id: bands
    type:
      name: _:bba7f928-bd75-4479-b485-44bf980d8521
      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: _:dc15de89-07f1-4a81-b80a-2fc09e82d0a4
      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
- 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 )