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Pattern 7

2025-09-08 11:01:04.043 | DEBUG    | cwl_loader:load_cwl_from_location:196 - Loading CWL document from ../cwl-workflow/pattern-7.cwl...

2025-09-08 11:01:04.044 | DEBUG    | cwl_loader:_load_cwl_from_stream:199 - Reading stream from ../cwl-workflow/pattern-7.cwl...

2025-09-08 11:01:04.060 | DEBUG    | cwl_loader:load_cwl_from_stream:173 - CWL data of type <class 'ruamel.yaml.comments.CommentedMap'> successfully loaded from stream

2025-09-08 11:01:04.061 | DEBUG    | cwl_loader:load_cwl_from_yaml:124 - Updating the model of type 'CommentedMap' to version 'v1.2'...

2025-09-08 11:01:04.066 | 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 11:01:04.075 | DEBUG    | cwl_loader:load_cwl_from_yaml:143 - Raw CWL document successfully updated to v1.2! Now dereferencing the FQNs...

2025-09-08 11:01:04.075 | DEBUG    | cwl_loader:_clean_process:66 -   Cleaning Workflow pattern-7...

2025-09-08 11:01:04.076 | DEBUG    | cwl_loader:_clean_process:66 -   Cleaning CommandLineTool clt...

2025-09-08 11:01:04.076 | DEBUG    | cwl_loader:load_cwl_from_yaml:151 - CWL document successfully dereferenced!

2025-09-08 11:01:04.077 | DEBUG    | cwl_loader:_load_cwl_from_stream:207 - Stream from ../cwl-workflow/pattern-7.cwl successfully load!

Application Package Pattern 7¶

The CWL includes:

one optional input parameter of type Directory?
one output parameter of type Directory

This scenario may take as input an acquisition, an optional input, applies an algorithm and generates an output

Implementation: detects water bodies using the Normalized Difference Water Index (NDWI) and Otsu thresholding.

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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_1`	`Directory`	Mandatory Landsat-8/9 acquisition reference	Landsat-8/9 acquisition reference
`item_2`	`[ null, Directory ]`	Optional Landsat-8/9 acquisition reference	Optional Landsat-8/9 acquisition reference

Steps¶

Id	Runs	Label	Doc
`step`	`#clt`	None	None

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 11:01:04.797 | 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 11:01:04.836 | 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 11:01:04.843 | DEBUG    | cwl_loader:load_cwl_from_stream:173 - CWL data of type <class 'ruamel.yaml.comments.CommentedMap'> successfully loaded from stream

2025-09-08 11:01:04.844 | DEBUG    | cwl_loader:load_cwl_from_yaml:124 - Updating the model of type 'CommentedMap' to version 'v1.2'...

2025-09-08 11:01:04.845 | 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 11:01:04.999 | DEBUG    | cwl_loader:load_cwl_from_yaml:143 - Raw CWL document successfully updated to v1.2! Now dereferencing the FQNs...

2025-09-08 11:01:05.000 | DEBUG    | cwl_loader:_clean_process:66 -   Cleaning CommandLineTool my-asthonishing-stage-in-directory...

2025-09-08 11:01:05.000 | DEBUG    | cwl_loader:load_cwl_from_yaml:151 - CWL document successfully dereferenced!

2025-09-08 11:01:05.001 | 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 11:01:05.001 | 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 11:01:05.034 | 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 11:01:05.040 | DEBUG    | cwl_loader:load_cwl_from_stream:173 - CWL data of type <class 'ruamel.yaml.comments.CommentedMap'> successfully loaded from stream

2025-09-08 11:01:05.041 | DEBUG    | cwl_loader:load_cwl_from_yaml:124 - Updating the model of type 'CommentedMap' to version 'v1.2'...

2025-09-08 11:01:05.041 | 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 11:01:05.186 | DEBUG    | cwl_loader:load_cwl_from_yaml:143 - Raw CWL document successfully updated to v1.2! Now dereferencing the FQNs...

2025-09-08 11:01:05.186 | DEBUG    | cwl_loader:_clean_process:66 -   Cleaning CommandLineTool my-asthonishing-stage-in-file...

2025-09-08 11:01:05.188 | DEBUG    | cwl_loader:load_cwl_from_yaml:151 - CWL document successfully dereferenced!

2025-09-08 11:01:05.188 | 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 11:01:05.189 | 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 11:01:05.332 | 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 11:01:05.341 | DEBUG    | cwl_loader:load_cwl_from_stream:173 - CWL data of type <class 'ruamel.yaml.comments.CommentedMap'> successfully loaded from stream

2025-09-08 11:01:05.342 | DEBUG    | cwl_loader:load_cwl_from_yaml:124 - Updating the model of type 'CommentedMap' to version 'v1.2'...

2025-09-08 11:01:05.343 | 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 11:01:05.517 | DEBUG    | cwl_loader:load_cwl_from_yaml:143 - Raw CWL document successfully updated to v1.2! Now dereferencing the FQNs...

2025-09-08 11:01:05.518 | DEBUG    | cwl_loader:_clean_process:66 -   Cleaning CommandLineTool my-super-stage-out...

2025-09-08 11:01:05.518 | DEBUG    | cwl_loader:load_cwl_from_yaml:151 - CWL document successfully dereferenced!

2025-09-08 11:01:05.519 | 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 11:01:05.519 | INFO     | eoap_cwlwrap.types:_validate_stage_in:273 - Validating stage-in 'my-asthonishing-stage-in-directory'...

2025-09-08 11:01:05.520 | INFO     | eoap_cwlwrap.types:_validate_stage_in:295 - stage-in 'my-asthonishing-stage-in-directory' is valid

2025-09-08 11:01:05.520 | INFO     | eoap_cwlwrap.types:_validate_stage_in:273 - Validating stage-in 'my-asthonishing-stage-in-file'...

2025-09-08 11:01:05.521 | INFO     | eoap_cwlwrap.types:_validate_stage_in:295 - stage-in 'my-asthonishing-stage-in-file' is valid

2025-09-08 11:01:05.521 | INFO     | eoap_cwlwrap.types:validate_stage_out:331 - Validating stage-out 'my-super-stage-out'...

2025-09-08 11:01:05.521 | INFO     | eoap_cwlwrap.types:validate_stage_out:353 - stage-out 'my-super-stage-out' is valid

2025-09-08 11:01:05.522 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:90 - Building the CWL Orchestrator Workflow...

2025-09-08 11:01:05.523 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:119 - Analyzing pattern-7 inputs...

2025-09-08 11:01:05.525 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:135 - * pattern-7/aoi: string

2025-09-08 11:01:05.525 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:135 - * pattern-7/epsg: string

2025-09-08 11:01:05.526 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:135 - * pattern-7/bands: string[]

2025-09-08 11:01:05.527 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:135 - * pattern-7/item_1: Directory

2025-09-08 11:01:05.527 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:148 -   Directory type detected, creating a related 'directory_stage_in_0'...

2025-09-08 11:01:05.527 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:150 -   Converting Directory to URL-compatible type...

2025-09-08 11:01:05.528 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:154 -   Directory converted to https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI

2025-09-08 11:01:05.529 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:195 -   Connecting 'app/item_1' to 'directory_stage_in_0' output...

2025-09-08 11:01:05.529 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:135 - * pattern-7/item_2: [ null, Directory ]

2025-09-08 11:01:05.530 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:148 -   Directory type detected, creating a related 'directory_stage_in_1'...

2025-09-08 11:01:05.530 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:150 -   Converting [ null, Directory ] to URL-compatible type...

2025-09-08 11:01:05.531 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:154 -   [ null, Directory ] converted to [ null, https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI ]

2025-09-08 11:01:05.532 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:186 -   Nullable detected, 'when' required for reference:item_2

2025-09-08 11:01:05.532 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:195 -   Connecting 'app/item_2' to 'directory_stage_in_1' output...

2025-09-08 11:01:05.533 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:246 - Analyzing pattern-7 outputs...

2025-09-08 11:01:05.533 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:252 - * pattern-7/water_bodies: Directory

2025-09-08 11:01:05.534 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:257 -   Directory type detected, creating a related 'stage_out_0'...

2025-09-08 11:01:05.534 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:259 -   Converting Directory to URL-compatible type...

2025-09-08 11:01:05.535 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:263 -   Directory converted to https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI

2025-09-08 11:01:05.536 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:304 -   Connecting 'app/water_bodies' to 'stage_out_0' output...

2025-09-08 11:01:05.537 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:379 - Orchestrator Workflow built in 0.0146 seconds

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Workflow components diagram¶

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Inputs¶

Id	Type	Label	Doc
`aoi`	`string`	area of interest - pattern-7/aoi	area of interest as a bounding box - This parameter is derived from pattern-7/aoi
`epsg`	`string`	EPSG code - pattern-7/epsg	EPSG code - This parameter is derived from pattern-7/epsg
`bands`	`string[]`	bands used for the NDWI - pattern-7/bands	bands used for the NDWI - This parameter is derived from pattern-7/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_1`	`https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI`	Mandatory Landsat-8/9 acquisition reference - pattern-7/item_1	Landsat-8/9 acquisition reference - This parameter is derived from pattern-7/item_1
`item_2`	`[ null, https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI ]`	Optional Landsat-8/9 acquisition reference - pattern-7/item_2	Optional Landsat-8/9 acquisition reference - This parameter is derived from pattern-7/item_2
`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
`directory_stage_in_1`	`#my-asthonishing-stage-in-directory`	None	None
`app`	`#pattern-7`	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_1": {
    "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"
  },
  "item_2": {
    "class": "https://raw.githubusercontent.com/eoap/schemas/main/url.yaml#URL",
    "value": "https://planetarycomputer.microsoft.com/api/stac/v1/collections/landsat-c2-l2/items/LC09_L2SP_042033_20231015_02_T1"
  }
}

Outputs¶

{
    "water_bodies": {
        "value": "s3://my-bucket/my/sub/path-s0xh67/catalog.json",
        "type": "https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI"
    }
}