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Pattern 1

2025-12-02 12:42:19.117 | DEBUG    | cwl_loader:load_cwl_from_location:228 - Loading CWL document from ../cwl-workflow/pattern-1.cwl...

2025-12-02 12:42:19.118 | DEBUG    | cwl_loader:_load_cwl_from_stream:231 - Reading stream from ../cwl-workflow/pattern-1.cwl...

2025-12-02 12:42:19.140 | DEBUG    | cwl_loader:load_cwl_from_stream:203 - CWL data of type <class 'ruamel.yaml.comments.CommentedMap'> successfully loaded from stream

2025-12-02 12:42:19.140 | DEBUG    | cwl_loader:load_cwl_from_yaml:130 - Updating the model from version 'v1.0' to version 'v1.2'...

2025-12-02 12:42:19.141 | DEBUG    | cwl_loader:load_cwl_from_yaml:141 - Raw CWL document successfully updated to v1.2!

2025-12-02 12:42:19.141 | DEBUG    | cwl_loader:load_cwl_from_yaml:145 - Parsing the raw CWL document to the CWL Utils DOM...

2025-12-02 12:42:19.288 | DEBUG    | cwl_loader:load_cwl_from_yaml:158 - Raw CWL document successfully parsed to the CWL Utils DOM!

2025-12-02 12:42:19.288 | DEBUG    | cwl_loader:load_cwl_from_yaml:160 - Dereferencing the steps[].run...

2025-12-02 12:42:19.289 | DEBUG    | cwl_loader:_on_process:78 - Checking if ../cwl-workflow/pattern-1.cwl#clt must be externally imported...

2025-12-02 12:42:19.289 | DEBUG    | cwl_loader:_on_process:82 - run_url: ../cwl-workflow/pattern-1.cwl - uri: ../cwl-workflow/pattern-1.cwl

2025-12-02 12:42:19.290 | DEBUG    | cwl_loader:load_cwl_from_yaml:167 - steps[].run successfully dereferenced! Dereferencing the FQNs...

2025-12-02 12:42:19.290 | DEBUG    | cwl_loader:load_cwl_from_yaml:171 - CWL document successfully dereferenced! Now verifying steps[].run integrity...

2025-12-02 12:42:19.291 | DEBUG    | cwl_loader:load_cwl_from_yaml:175 - All steps[].run link are resolvable!

2025-12-02 12:42:19.291 | DEBUG    | cwl_loader:load_cwl_from_yaml:178 - Sorting Process instances by dependencies....

2025-12-02 12:42:19.291 | DEBUG    | cwl_loader:load_cwl_from_yaml:180 - Sorting process is over.

2025-12-02 12:42:19.292 | DEBUG    | cwl_loader:_load_cwl_from_stream:240 - Stream from ../cwl-workflow/pattern-1.cwl successfully load!

Application Package Pattern¶

The CWL includes:

one input parameter of type Directory
one output parameter of type Directory

This scenario typically takes one input, applies an algorithm and produces a result

Implementation: delineate water bodies using NDWI and Otsu automatic threshold taking as input a Landsat-8/9 acquisition

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Inputs¶

Id	Type	Label	Doc
`aoi`	`string`	area of interest	area of interest as a bounding box
`epsg`	`string`	EPSG code	EPSG code
`bands`	`string[]`	bands used for the NDWI	bands used for the NDWI
`item`	`Directory`	Landsat-8/9 acquisition reference	Landsat-8/9 acquisition reference

Steps¶

Id	Runs	Label	Doc
`step`	`#clt`	Water bodies detection	Water bodies detection based on NDWI and otsu threshold applied to a single Landsat-8/9 acquisition

Outputs¶

Id	Type	Label	Doc
`water_bodies`	`Directory`	Water bodies detected	Water bodies detected based on the NDWI and otsu threshold

Data flow management¶

2025-12-02 12:42:20.204 | DEBUG    | cwl_loader:load_cwl_from_location:228 - Loading CWL document from https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/develop/templates/stage-in.cwl...

2025-12-02 12:42:20.307 | DEBUG    | cwl_loader:_load_cwl_from_stream:231 - Reading stream from https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/develop/templates/stage-in.cwl...

2025-12-02 12:42:20.313 | DEBUG    | cwl_loader:load_cwl_from_stream:203 - CWL data of type <class 'ruamel.yaml.comments.CommentedMap'> successfully loaded from stream

2025-12-02 12:42:20.313 | DEBUG    | cwl_loader:load_cwl_from_yaml:130 - Updating the model from version 'v1.0' to version 'v1.2'...

2025-12-02 12:42:20.314 | DEBUG    | cwl_loader:load_cwl_from_yaml:141 - Raw CWL document successfully updated to v1.2!

2025-12-02 12:42:20.314 | DEBUG    | cwl_loader:load_cwl_from_yaml:145 - Parsing the raw CWL document to the CWL Utils DOM...

2025-12-02 12:42:20.527 | DEBUG    | cwl_loader:load_cwl_from_yaml:158 - Raw CWL document successfully parsed to the CWL Utils DOM!

2025-12-02 12:42:20.528 | DEBUG    | cwl_loader:load_cwl_from_yaml:160 - Dereferencing the steps[].run...

2025-12-02 12:42:20.529 | DEBUG    | cwl_loader:load_cwl_from_yaml:167 - steps[].run successfully dereferenced! Dereferencing the FQNs...

2025-12-02 12:42:20.529 | DEBUG    | cwl_loader:load_cwl_from_yaml:171 - CWL document successfully dereferenced! Now verifying steps[].run integrity...

2025-12-02 12:42:20.531 | DEBUG    | cwl_loader:load_cwl_from_yaml:175 - All steps[].run link are resolvable!

2025-12-02 12:42:20.531 | DEBUG    | cwl_loader:load_cwl_from_yaml:178 - Sorting Process instances by dependencies....

2025-12-02 12:42:20.532 | DEBUG    | cwl_loader:load_cwl_from_yaml:180 - Sorting process is over.

2025-12-02 12:42:20.532 | DEBUG    | cwl_loader:_load_cwl_from_stream:240 - Stream from https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/develop/templates/stage-in.cwl successfully load!

2025-12-02 12:42:20.532 | DEBUG    | cwl_loader:load_cwl_from_location:228 - Loading CWL document from https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/develop/templates/stage-in-file.cwl...

2025-12-02 12:42:20.633 | DEBUG    | cwl_loader:_load_cwl_from_stream:231 - Reading stream from https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/develop/templates/stage-in-file.cwl...

2025-12-02 12:42:20.639 | DEBUG    | cwl_loader:load_cwl_from_stream:203 - CWL data of type <class 'ruamel.yaml.comments.CommentedMap'> successfully loaded from stream

2025-12-02 12:42:20.639 | DEBUG    | cwl_loader:load_cwl_from_yaml:130 - Updating the model from version 'v1.0' to version 'v1.2'...

2025-12-02 12:42:20.640 | DEBUG    | cwl_loader:load_cwl_from_yaml:141 - Raw CWL document successfully updated to v1.2!

2025-12-02 12:42:20.640 | DEBUG    | cwl_loader:load_cwl_from_yaml:145 - Parsing the raw CWL document to the CWL Utils DOM...

2025-12-02 12:42:20.800 | DEBUG    | cwl_loader:load_cwl_from_yaml:158 - Raw CWL document successfully parsed to the CWL Utils DOM!

2025-12-02 12:42:20.800 | DEBUG    | cwl_loader:load_cwl_from_yaml:160 - Dereferencing the steps[].run...

2025-12-02 12:42:20.801 | DEBUG    | cwl_loader:load_cwl_from_yaml:167 - steps[].run successfully dereferenced! Dereferencing the FQNs...

2025-12-02 12:42:20.801 | DEBUG    | cwl_loader:load_cwl_from_yaml:171 - CWL document successfully dereferenced! Now verifying steps[].run integrity...

2025-12-02 12:42:20.803 | DEBUG    | cwl_loader:load_cwl_from_yaml:175 - All steps[].run link are resolvable!

2025-12-02 12:42:20.803 | DEBUG    | cwl_loader:load_cwl_from_yaml:178 - Sorting Process instances by dependencies....

2025-12-02 12:42:20.804 | DEBUG    | cwl_loader:load_cwl_from_yaml:180 - Sorting process is over.

2025-12-02 12:42:20.804 | DEBUG    | cwl_loader:_load_cwl_from_stream:240 - Stream from https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/develop/templates/stage-in-file.cwl successfully load!

2025-12-02 12:42:20.805 | DEBUG    | cwl_loader:load_cwl_from_location:228 - Loading CWL document from https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/develop/templates/stage-out.cwl...

2025-12-02 12:42:20.910 | DEBUG    | cwl_loader:_load_cwl_from_stream:231 - Reading stream from https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/develop/templates/stage-out.cwl...

2025-12-02 12:42:20.919 | DEBUG    | cwl_loader:load_cwl_from_stream:203 - CWL data of type <class 'ruamel.yaml.comments.CommentedMap'> successfully loaded from stream

2025-12-02 12:42:20.919 | DEBUG    | cwl_loader:load_cwl_from_yaml:130 - Updating the model from version 'v1.0' to version 'v1.2'...

2025-12-02 12:42:20.920 | DEBUG    | cwl_loader:load_cwl_from_yaml:141 - Raw CWL document successfully updated to v1.2!

2025-12-02 12:42:20.921 | DEBUG    | cwl_loader:load_cwl_from_yaml:145 - Parsing the raw CWL document to the CWL Utils DOM...

2025-12-02 12:42:21.099 | DEBUG    | cwl_loader:load_cwl_from_yaml:158 - Raw CWL document successfully parsed to the CWL Utils DOM!

2025-12-02 12:42:21.099 | DEBUG    | cwl_loader:load_cwl_from_yaml:160 - Dereferencing the steps[].run...

2025-12-02 12:42:21.100 | DEBUG    | cwl_loader:load_cwl_from_yaml:167 - steps[].run successfully dereferenced! Dereferencing the FQNs...

2025-12-02 12:42:21.100 | DEBUG    | cwl_loader:load_cwl_from_yaml:171 - CWL document successfully dereferenced! Now verifying steps[].run integrity...

2025-12-02 12:42:21.100 | DEBUG    | cwl_loader:load_cwl_from_yaml:175 - All steps[].run link are resolvable!

2025-12-02 12:42:21.101 | DEBUG    | cwl_loader:load_cwl_from_yaml:178 - Sorting Process instances by dependencies....

2025-12-02 12:42:21.101 | DEBUG    | cwl_loader:load_cwl_from_yaml:180 - Sorting process is over.

2025-12-02 12:42:21.102 | DEBUG    | cwl_loader:_load_cwl_from_stream:240 - Stream from https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/develop/templates/stage-out.cwl successfully load!

2025-12-02 12:42:21.102 | INFO     | eoap_cwlwrap.types:_validate_stage_in:281 - Validating stage-in 'my-asthonishing-stage-in-directory'...

2025-12-02 12:42:21.103 | INFO     | eoap_cwlwrap.types:_validate_stage_in:303 - stage-in 'my-asthonishing-stage-in-directory' is valid

2025-12-02 12:42:21.103 | INFO     | eoap_cwlwrap.types:_validate_stage_in:281 - Validating stage-in 'my-asthonishing-stage-in-file'...

2025-12-02 12:42:21.103 | INFO     | eoap_cwlwrap.types:_validate_stage_in:303 - stage-in 'my-asthonishing-stage-in-file' is valid

2025-12-02 12:42:21.104 | INFO     | eoap_cwlwrap.types:validate_stage_out:339 - Validating stage-out 'my-super-stage-out'...

2025-12-02 12:42:21.104 | INFO     | eoap_cwlwrap.types:validate_stage_out:361 - stage-out 'my-super-stage-out' is valid

2025-12-02 12:42:21.105 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:101 - Building the CWL Orchestrator Workflow...

2025-12-02 12:42:21.105 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:130 - Analyzing pattern-1 inputs...

2025-12-02 12:42:21.106 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:146 - * pattern-1/aoi: string

2025-12-02 12:42:21.107 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:146 - * pattern-1/epsg: string

2025-12-02 12:42:21.107 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:146 - * pattern-1/bands: string[]

2025-12-02 12:42:21.108 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:146 - * pattern-1/item: Directory

2025-12-02 12:42:21.108 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:159 -   Directory type detected, creating a related 'directory_stage_in_0'...

2025-12-02 12:42:21.109 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:161 -   Converting Directory to URL-compatible type...

2025-12-02 12:42:21.110 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:165 -   Directory converted to https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI

2025-12-02 12:42:21.110 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:206 -   Connecting 'app/item' to 'directory_stage_in_0' output...

2025-12-02 12:42:21.111 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:257 - Analyzing pattern-1 outputs...

2025-12-02 12:42:21.114 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:263 - * pattern-1/water_bodies: Directory

2025-12-02 12:42:21.115 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:268 -   Directory type detected, creating a related 'stage_out_0'...

2025-12-02 12:42:21.115 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:270 -   Converting Directory to URL-compatible type...

2025-12-02 12:42:21.116 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:274 -   Directory converted to https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI

2025-12-02 12:42:21.117 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:315 -   Connecting 'app/water_bodies' to 'stage_out_0' output...

2025-12-02 12:42:21.117 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:390 - Orchestrator Workflow built in 0.0126 seconds

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Workflow components diagram¶

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Inputs¶

Id	Type	Label	Doc
`aoi`	`string`	area of interest - pattern-1/aoi	area of interest as a bounding box - This parameter is derived from pattern-1/aoi
`epsg`	`string`	EPSG code - pattern-1/epsg	EPSG code - This parameter is derived from pattern-1/epsg
`bands`	`string[]`	bands used for the NDWI - pattern-1/bands	bands used for the NDWI - This parameter is derived from pattern-1/bands
`another_input`	`string`	Another Input - my-asthonishing-stage-in-directory/another_input	An additional input for demonstration purposes - This parameter is derived from my-asthonishing-stage-in-directory/another_input
`item`	`https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI`	Landsat-8/9 acquisition reference - pattern-1/item	Landsat-8/9 acquisition reference - This parameter is derived from pattern-1/item
`s3_bucket`	`string`	my-super-stage-out/s3_bucket	This parameter is derived from: my-super-stage-out/s3_bucket
`sub_path`	`string`	my-super-stage-out/sub_path	This parameter is derived from: my-super-stage-out/sub_path
`aws_access_key_id`	`string`	my-super-stage-out/aws_access_key_id	This parameter is derived from: my-super-stage-out/aws_access_key_id
`aws_secret_access_key`	`string`	my-super-stage-out/aws_secret_access_key	This parameter is derived from: my-super-stage-out/aws_secret_access_key
`region_name`	`string`	my-super-stage-out/region_name	This parameter is derived from: my-super-stage-out/region_name
`endpoint_url`	`string`	my-super-stage-out/endpoint_url	This parameter is derived from: my-super-stage-out/endpoint_url

Steps¶

Id	Runs	Label	Doc
`directory_stage_in_0`	`#my-asthonishing-stage-in-directory`	None	None
`app`	`#pattern-1`	None	None
`stage_out_0`	`#my-super-stage-out`	None	None

Outputs¶

Id	Type	Label	Doc
`water_bodies`	`https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI`	Water bodies detected	Water bodies detected based on the NDWI and otsu threshold

Execution¶

Inputs¶

{
  "aoi": "-118.985,38.432,-118.183,38.938",
  "epsg": "EPSG:4326",
  "bands": [
    "green",
    "nir08"
  ],
  "item": {
    "class": "https://raw.githubusercontent.com/eoap/schemas/main/url.yaml#URL",
    "value": "https://planetarycomputer.microsoft.com/api/stac/v1/collections/landsat-c2-l2/items/LC08_L2SP_042033_20231007_02_T1"
  }
}

Outputs¶

{
    "water_bodies": {
        "value": "s3://my-bucket/my/sub/path-kzzeab/catalog.json",
        "type": "https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI"
    }
}