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Pattern 2

2025-09-08 10:58:01.508 | DEBUG    | cwl_loader:load_cwl_from_location:196 - Loading CWL document from ../cwl-workflow/pattern-2.cwl...

2025-09-08 10:58:01.509 | DEBUG    | cwl_loader:_load_cwl_from_stream:199 - Reading stream from ../cwl-workflow/pattern-2.cwl...

2025-09-08 10:58:01.526 | DEBUG    | cwl_loader:load_cwl_from_stream:173 - CWL data of type <class 'ruamel.yaml.comments.CommentedMap'> successfully loaded from stream

2025-09-08 10:58:01.526 | DEBUG    | cwl_loader:load_cwl_from_yaml:124 - Updating the model of type 'CommentedMap' to version 'v1.2'...

2025-09-08 10:58:01.531 | 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 10:58:01.538 | DEBUG    | cwl_loader:load_cwl_from_yaml:143 - Raw CWL document successfully updated to v1.2! Now dereferencing the FQNs...

2025-09-08 10:58:01.539 | DEBUG    | cwl_loader:_clean_process:66 -   Cleaning Workflow pattern-2...

2025-09-08 10:58:01.539 | DEBUG    | cwl_loader:_clean_process:66 -   Cleaning CommandLineTool clt...

2025-09-08 10:58:01.540 | DEBUG    | cwl_loader:load_cwl_from_yaml:151 - CWL document successfully dereferenced!

2025-09-08 10:58:01.540 | DEBUG    | cwl_loader:_load_cwl_from_stream:207 - Stream from ../cwl-workflow/pattern-2.cwl successfully load!

Application Package Pattern 2¶

The CWL includes:

two input parameters of type Directory
one output parameter of type Directory

This scenario typically takes as input one pre-event acquisition, one post-even acquisition, applies an algorithm and produces a result

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

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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`	Landsat-8/9 acquisition reference	Landsat-8/9 acquisition reference
`item_2`	`Directory`	Landsat-8/9 acquisition reference	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 10:58:02.235 | 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 10:58:02.269 | 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 10:58:02.276 | DEBUG    | cwl_loader:load_cwl_from_stream:173 - CWL data of type <class 'ruamel.yaml.comments.CommentedMap'> successfully loaded from stream

2025-09-08 10:58:02.276 | DEBUG    | cwl_loader:load_cwl_from_yaml:124 - Updating the model of type 'CommentedMap' to version 'v1.2'...

2025-09-08 10:58:02.277 | 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 10:58:02.417 | DEBUG    | cwl_loader:load_cwl_from_yaml:143 - Raw CWL document successfully updated to v1.2! Now dereferencing the FQNs...

2025-09-08 10:58:02.418 | DEBUG    | cwl_loader:_clean_process:66 -   Cleaning CommandLineTool my-asthonishing-stage-in-directory...

2025-09-08 10:58:02.418 | DEBUG    | cwl_loader:load_cwl_from_yaml:151 - CWL document successfully dereferenced!

2025-09-08 10:58:02.419 | 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 10:58:02.419 | 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 10:58:02.452 | 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 10:58:02.458 | DEBUG    | cwl_loader:load_cwl_from_stream:173 - CWL data of type <class 'ruamel.yaml.comments.CommentedMap'> successfully loaded from stream

2025-09-08 10:58:02.458 | DEBUG    | cwl_loader:load_cwl_from_yaml:124 - Updating the model of type 'CommentedMap' to version 'v1.2'...

2025-09-08 10:58:02.459 | 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 10:58:02.605 | DEBUG    | cwl_loader:load_cwl_from_yaml:143 - Raw CWL document successfully updated to v1.2! Now dereferencing the FQNs...

2025-09-08 10:58:02.606 | DEBUG    | cwl_loader:_clean_process:66 -   Cleaning CommandLineTool my-asthonishing-stage-in-file...

2025-09-08 10:58:02.607 | DEBUG    | cwl_loader:load_cwl_from_yaml:151 - CWL document successfully dereferenced!

2025-09-08 10:58:02.607 | 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 10:58:02.609 | 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 10:58:02.639 | 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 10:58:02.648 | DEBUG    | cwl_loader:load_cwl_from_stream:173 - CWL data of type <class 'ruamel.yaml.comments.CommentedMap'> successfully loaded from stream

2025-09-08 10:58:02.649 | DEBUG    | cwl_loader:load_cwl_from_yaml:124 - Updating the model of type 'CommentedMap' to version 'v1.2'...

2025-09-08 10:58:02.649 | 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 10:58:02.823 | DEBUG    | cwl_loader:load_cwl_from_yaml:143 - Raw CWL document successfully updated to v1.2! Now dereferencing the FQNs...

2025-09-08 10:58:02.823 | DEBUG    | cwl_loader:_clean_process:66 -   Cleaning CommandLineTool my-super-stage-out...

2025-09-08 10:58:02.824 | DEBUG    | cwl_loader:load_cwl_from_yaml:151 - CWL document successfully dereferenced!

2025-09-08 10:58:02.824 | 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 10:58:02.825 | INFO     | eoap_cwlwrap.types:_validate_stage_in:273 - Validating stage-in 'my-asthonishing-stage-in-directory'...

2025-09-08 10:58:02.825 | INFO     | eoap_cwlwrap.types:_validate_stage_in:295 - stage-in 'my-asthonishing-stage-in-directory' is valid

2025-09-08 10:58:02.825 | INFO     | eoap_cwlwrap.types:_validate_stage_in:273 - Validating stage-in 'my-asthonishing-stage-in-file'...

2025-09-08 10:58:02.826 | INFO     | eoap_cwlwrap.types:_validate_stage_in:295 - stage-in 'my-asthonishing-stage-in-file' is valid

2025-09-08 10:58:02.826 | INFO     | eoap_cwlwrap.types:validate_stage_out:331 - Validating stage-out 'my-super-stage-out'...

2025-09-08 10:58:02.827 | INFO     | eoap_cwlwrap.types:validate_stage_out:353 - stage-out 'my-super-stage-out' is valid

2025-09-08 10:58:02.827 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:90 - Building the CWL Orchestrator Workflow...

2025-09-08 10:58:02.828 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:119 - Analyzing pattern-2 inputs...

2025-09-08 10:58:02.828 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:135 - * pattern-2/aoi: string

2025-09-08 10:58:02.829 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:135 - * pattern-2/epsg: string

2025-09-08 10:58:02.830 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:135 - * pattern-2/bands: string[]

2025-09-08 10:58:02.830 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:135 - * pattern-2/item_1: Directory

2025-09-08 10:58:02.831 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:148 -   Directory type detected, creating a related 'directory_stage_in_0'...

2025-09-08 10:58:02.833 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:150 -   Converting Directory to URL-compatible type...

2025-09-08 10:58:02.833 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:154 -   Directory converted to https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI

2025-09-08 10:58:02.834 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:195 -   Connecting 'app/item_1' to 'directory_stage_in_0' output...

2025-09-08 10:58:02.835 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:135 - * pattern-2/item_2: Directory

2025-09-08 10:58:02.835 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:148 -   Directory type detected, creating a related 'directory_stage_in_1'...

2025-09-08 10:58:02.836 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:150 -   Converting Directory to URL-compatible type...

2025-09-08 10:58:02.836 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:154 -   Directory converted to https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI

2025-09-08 10:58:02.837 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:195 -   Connecting 'app/item_2' to 'directory_stage_in_1' output...

2025-09-08 10:58:02.839 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:246 - Analyzing pattern-2 outputs...

2025-09-08 10:58:02.839 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:252 - * pattern-2/water_bodies: Directory

2025-09-08 10:58:02.840 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:257 -   Directory type detected, creating a related 'stage_out_0'...

2025-09-08 10:58:02.840 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:259 -   Converting Directory to URL-compatible type...

2025-09-08 10:58:02.841 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:263 -   Directory converted to https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI

2025-09-08 10:58:02.842 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:304 -   Connecting 'app/water_bodies' to 'stage_out_0' output...

2025-09-08 10:58:02.843 | INFO     | eoap_cwlwrap:_build_orchestrator_workflow:379 - Orchestrator Workflow built in 0.0156 seconds

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Workflow components diagram¶

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Inputs¶

Id	Type	Label	Doc
`aoi`	`string`	area of interest - pattern-2/aoi	area of interest as a bounding box - This parameter is derived from pattern-2/aoi
`epsg`	`string`	EPSG code - pattern-2/epsg	EPSG code - This parameter is derived from pattern-2/epsg
`bands`	`string[]`	bands used for the NDWI - pattern-2/bands	bands used for the NDWI - This parameter is derived from pattern-2/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`	Landsat-8/9 acquisition reference - pattern-2/item_1	Landsat-8/9 acquisition reference - This parameter is derived from pattern-2/item_1
`item_2`	`https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI`	Landsat-8/9 acquisition reference - pattern-2/item_2	Landsat-8/9 acquisition reference - This parameter is derived from pattern-2/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-2`	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-uqj0mq/catalog.json",
        "type": "https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI"
    }
}