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Pattern 1

2025-09-08 10:55:07.058 | DEBUG    | cwl_loader:load_cwl_from_location:196 - Loading CWL document from ../cwl-workflow/pattern-1.cwl...

2025-09-08 10:55:07.059 | DEBUG    | cwl_loader:_load_cwl_from_stream:199 - Reading stream from ../cwl-workflow/pattern-1.cwl...

2025-09-08 10:55:07.078 | DEBUG    | cwl_loader:load_cwl_from_stream:173 - CWL data of type <class 'ruamel.yaml.comments.CommentedMap'> successfully loaded from stream

2025-09-08 10:55:07.079 | DEBUG    | cwl_loader:load_cwl_from_yaml:124 - Updating the model of type 'CommentedMap' to version 'v1.2'...

2025-09-08 10:55:07.083 | DEBUG    | cwl_loader:load_cwl_from_yaml:135 - Raw CWL document successfully updated to v1.2! Now converting to the CWL model...

2025-09-08 10:55:07.090 | DEBUG    | cwl_loader:load_cwl_from_yaml:143 - Raw CWL document successfully updated to v1.2! Now dereferencing the FQNs...

2025-09-08 10:55:07.091 | DEBUG    | cwl_loader:_clean_process:66 -   Cleaning Workflow pattern-1...

2025-09-08 10:55:07.092 | DEBUG    | cwl_loader:_clean_process:66 -   Cleaning CommandLineTool clt...

2025-09-08 10:55:07.092 | DEBUG    | cwl_loader:load_cwl_from_yaml:151 - CWL document successfully dereferenced!

2025-09-08 10:55:07.093 | DEBUG    | cwl_loader:_load_cwl_from_stream:207 - 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¶

2025-09-08 10:55:08.083 | DEBUG    | cwl_loader:load_cwl_from_location:196 - Loading CWL document from https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/develop/templates/stage-in.cwl...

2025-09-08 10:55:08.273 | DEBUG    | cwl_loader:_load_cwl_from_stream:199 - Reading stream from https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/develop/templates/stage-in.cwl...

2025-09-08 10:55:08.279 | DEBUG    | cwl_loader:load_cwl_from_stream:173 - CWL data of type <class 'ruamel.yaml.comments.CommentedMap'> successfully loaded from stream

2025-09-08 10:55:08.280 | DEBUG    | cwl_loader:load_cwl_from_yaml:124 - Updating the model of type 'CommentedMap' to version 'v1.2'...

2025-09-08 10:55:08.281 | DEBUG    | cwl_loader:load_cwl_from_yaml:135 - Raw CWL document successfully updated to v1.2! Now converting to the CWL model...

2025-09-08 10:55:08.558 | DEBUG    | cwl_loader:load_cwl_from_yaml:143 - Raw CWL document successfully updated to v1.2! Now dereferencing the FQNs...

2025-09-08 10:55:08.559 | DEBUG    | cwl_loader:_clean_process:66 -   Cleaning CommandLineTool my-asthonishing-stage-in-directory...

2025-09-08 10:55:08.559 | DEBUG    | cwl_loader:load_cwl_from_yaml:151 - CWL document successfully dereferenced!

2025-09-08 10:55:08.560 | DEBUG    | cwl_loader:_load_cwl_from_stream:207 - Stream from https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/develop/templates/stage-in.cwl successfully load!

2025-09-08 10:55:08.560 | DEBUG    | cwl_loader:load_cwl_from_location:196 - Loading CWL document from https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/develop/templates/stage-in-file.cwl...

2025-09-08 10:55:08.711 | DEBUG    | cwl_loader:_load_cwl_from_stream:199 - Reading stream from https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/develop/templates/stage-in-file.cwl...

2025-09-08 10:55:08.716 | DEBUG    | cwl_loader:load_cwl_from_stream:173 - CWL data of type <class 'ruamel.yaml.comments.CommentedMap'> successfully loaded from stream

2025-09-08 10:55:08.717 | DEBUG    | cwl_loader:load_cwl_from_yaml:124 - Updating the model of type 'CommentedMap' to version 'v1.2'...

2025-09-08 10:55:08.717 | DEBUG    | cwl_loader:load_cwl_from_yaml:135 - Raw CWL document successfully updated to v1.2! Now converting to the CWL model...

2025-09-08 10:55:08.966 | DEBUG    | cwl_loader:load_cwl_from_yaml:143 - Raw CWL document successfully updated to v1.2! Now dereferencing the FQNs...

2025-09-08 10:55:08.967 | DEBUG    | cwl_loader:_clean_process:66 -   Cleaning CommandLineTool my-asthonishing-stage-in-file...

2025-09-08 10:55:08.967 | DEBUG    | cwl_loader:load_cwl_from_yaml:151 - CWL document successfully dereferenced!

2025-09-08 10:55:08.968 | DEBUG    | cwl_loader:_load_cwl_from_stream:207 - Stream from https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/develop/templates/stage-in-file.cwl successfully load!

2025-09-08 10:55:08.968 | DEBUG    | cwl_loader:load_cwl_from_location:196 - Loading CWL document from https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/develop/templates/stage-out.cwl...

2025-09-08 10:55:09.127 | DEBUG    | cwl_loader:_load_cwl_from_stream:199 - Reading stream from https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/develop/templates/stage-out.cwl...

2025-09-08 10:55:09.137 | DEBUG    | cwl_loader:load_cwl_from_stream:173 - CWL data of type <class 'ruamel.yaml.comments.CommentedMap'> successfully loaded from stream

2025-09-08 10:55:09.137 | DEBUG    | cwl_loader:load_cwl_from_yaml:124 - Updating the model of type 'CommentedMap' to version 'v1.2'...

2025-09-08 10:55:09.138 | DEBUG    | cwl_loader:load_cwl_from_yaml:135 - Raw CWL document successfully updated to v1.2! Now converting to the CWL model...

2025-09-08 10:55:09.434 | DEBUG    | cwl_loader:load_cwl_from_yaml:143 - Raw CWL document successfully updated to v1.2! Now dereferencing the FQNs...

2025-09-08 10:55:09.435 | DEBUG    | cwl_loader:_clean_process:66 -   Cleaning CommandLineTool my-super-stage-out...

2025-09-08 10:55:09.435 | DEBUG    | cwl_loader:load_cwl_from_yaml:151 - CWL document successfully dereferenced!

2025-09-08 10:55:09.436 | DEBUG    | cwl_loader:_load_cwl_from_stream:207 - Stream from https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/develop/templates/stage-out.cwl successfully load!

2025-09-08 10:55:09.436 | INFO     | eoap_cwlwrap.types:_validate_stage_in:273 - Validating stage-in 'my-asthonishing-stage-in-directory'...

2025-09-08 10:55:09.436 | INFO     | eoap_cwlwrap.types:_validate_stage_in:295 - stage-in 'my-asthonishing-stage-in-directory' is valid

2025-09-08 10:55:09.437 | INFO     | eoap_cwlwrap.types:_validate_stage_in:273 - Validating stage-in 'my-asthonishing-stage-in-file'...

2025-09-08 10:55:09.438 | INFO     | eoap_cwlwrap.types:_validate_stage_in:295 - stage-in 'my-asthonishing-stage-in-file' is valid

2025-09-08 10:55:09.438 | INFO     | eoap_cwlwrap.types:validate_stage_out:331 - Validating stage-out 'my-super-stage-out'...

2025-09-08 10:55:09.438 | INFO     | eoap_cwlwrap.types:validate_stage_out:353 - stage-out 'my-super-stage-out' is valid

2025-09-08 10:55:09.439 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:90 - Building the CWL Orchestrator Workflow...

2025-09-08 10:55:09.440 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:119 - Analyzing pattern-1 inputs...

2025-09-08 10:55:09.440 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:135 - * pattern-1/aoi: string

2025-09-08 10:55:09.441 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:135 - * pattern-1/epsg: string

2025-09-08 10:55:09.441 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:135 - * pattern-1/bands: string[]

2025-09-08 10:55:09.442 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:135 - * pattern-1/item: Directory

2025-09-08 10:55:09.442 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:148 -   Directory type detected, creating a related 'directory_stage_in_0'...

2025-09-08 10:55:09.443 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:150 -   Converting Directory to URL-compatible type...

2025-09-08 10:55:09.443 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:154 -   Directory converted to https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI

2025-09-08 10:55:09.444 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:195 -   Connecting 'app/item' to 'directory_stage_in_0' output...

2025-09-08 10:55:09.444 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:246 - Analyzing pattern-1 outputs...

2025-09-08 10:55:09.445 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:252 - * pattern-1/water_bodies: Directory

2025-09-08 10:55:09.445 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:257 -   Directory type detected, creating a related 'stage_out_0'...

2025-09-08 10:55:09.446 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:259 -   Converting Directory to URL-compatible type...

2025-09-08 10:55:09.446 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:263 -   Directory converted to https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI

2025-09-08 10:55:09.448 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:304 -   Connecting 'app/water_bodies' to 'stage_out_0' output...

2025-09-08 10:55:09.448 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:379 - Orchestrator Workflow built in 0.0095 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-291dfi/catalog.json",
        "type": "https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI"
    }
}