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| FROM docker.io/eoepca/cwl-wrapper@sha256:066566ab6dcee685bb95d4eeab20ef07eefc5aaaf320857a251a3a608c81e694 | ||
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| COPY cwl-wrapper/templates /templates | ||
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| COPY cwl-wrapper/default.conf /home/jovyan/.cwlwrapper/default.conf | ||
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| ENTRYPOINT [ "cwl-wrapper" ] |
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| @@ -0,0 +1,4 @@ | ||
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| docker run --rm -i cwl-wrapper:latest $PWD:/app-package eoepca/ | ||
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| docker run --rm -i -v $PWD:/app cwl-wrapper:latest --stagein /app/stage/stage-in.yaml --stageout /app/stage/stage-out.yaml app/app-water-bodies.1.3.1.cwl |
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| maincwl="/templates/main.yaml" | ||
| rulez="/templates/rules.yaml" |
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| class: Workflow | ||
| doc: Main stage manager | ||
| id: main | ||
| label: macro-cwl | ||
| inputs: {} | ||
| outputs: {} | ||
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| requirements: | ||
| SubworkflowFeatureRequirement: {} | ||
| ScatterFeatureRequirement: {} | ||
| InlineJavascriptRequirement: {} |
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| rulez: | ||
| version: 1 | ||
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| parser: | ||
| type: $graph | ||
| driver: cwl | ||
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| onstage: | ||
| driver: cwl | ||
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| stage_in: | ||
| connection_node: node_stage_in | ||
| if_scatter: | ||
| scatterMethod: dotproduct | ||
| input: | ||
| template: | ||
| overwrite: True | ||
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| on_stage: | ||
| connection_node: on_stage | ||
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| stage_out: | ||
| connection_node: node_stage_out | ||
| scatter: False | ||
| if_scatter: | ||
| scatterMethod: dotproduct | ||
| follow_node: node_metrics_out | ||
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| output: | ||
| driver: cwl | ||
| name: '-' | ||
| type: $graph | ||
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| cwl: | ||
| GlobalInput: | ||
| Directory: string | ||
| Directory[]: string[] | ||
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| OptionalInput: | ||
| Directory: string? | ||
| Directory[]: string[]? | ||
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| stage_in: | ||
| Directory?: | ||
| type: string? | ||
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| Directory: | ||
| type: string? | ||
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| Directory[]: | ||
| type: string[] | ||
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| stage_out: | ||
| Directory: | ||
| type: Directory | ||
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| Directory[]: | ||
| type: Directory[] | ||
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| outputBindingResult: | ||
| command: | ||
| Directory: | ||
| outputBinding: | ||
| glob: . | ||
| type: Directory | ||
| Directory[]: | ||
| outputBinding: | ||
| glob: . | ||
| type: Directory[] | ||
| Directory?: | ||
| outputBinding: | ||
| glob: ${ if (inputs.input == null) {return null } else {return ".";} } | ||
| type: Directory? | ||
| stepOut: | ||
| type: | ||
| items: Directory | ||
| type: array |
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| cwlVersion: v1.0 | ||
| doc: "Run Stars for staging input data" | ||
| class: CommandLineTool | ||
| hints: | ||
| DockerRequirement: | ||
| dockerPull: ghcr.io/terradue/stars:2.14.5 | ||
| "cwltool:Secrets": | ||
| secrets: [] | ||
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| id: stars | ||
| requirements: | ||
| EnvVarRequirement: | ||
| envDef: | ||
| PATH: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin | ||
| ResourceRequirement: {} | ||
| InlineJavascriptRequirement: {} | ||
| InitialWorkDirRequirement: | ||
| listing: | ||
| - entryname: stagein.sh | ||
| entry: |- | ||
| #!/bin/bash | ||
| set -x | ||
| res=0 | ||
| input='$( inputs.input )' | ||
| usersettings='$( inputs.usersettings.path )' | ||
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| [ "\${input}" != "null" ] && { | ||
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| IFS='#' read -r -a reference <<< '$( inputs.input )' | ||
| input_len=\${#reference[@]} | ||
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| [[ \${input_len} == 2 ]] && { | ||
| IFS=',' read -r -a assets <<< \${reference[1]} | ||
| af=" " | ||
| for asset in \${assets[@]} | ||
| do | ||
| af="\${af} -af \${asset}" | ||
| done | ||
| } || { | ||
| af="--empty" | ||
| } | ||
| Stars copy -conf \${usersettings} -v -rel -r '4' \${af} -o ./ \${reference[0]} | ||
| res=$? | ||
| } | ||
| rm -fr stagein.sh | ||
| exit 0 | ||
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| baseCommand: ['/bin/bash', 'stagein.sh'] | ||
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| inputs: {} | ||
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| outputs: {} |
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| FROM docker.io/python:3.9.18-slim-bullseye | ||
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| RUN pip install --no-cache-dir --upgrade pip stac-asset boto3 |
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| #!/usr/bin/env cwl-runner | ||
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| cwlVersion: v1.0 | ||
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| class: CommandLineTool | ||
| id: stage | ||
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| inputs: {} | ||
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| outputs: {} | ||
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| baseCommand: | ||
| - python | ||
| - stage.py | ||
| arguments: | ||
| - $( inputs.input ) | ||
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| requirements: | ||
| DockerRequirement: | ||
| dockerPull: stac-asset:latest | ||
| EnvVarRequirement: | ||
| envDef: | ||
| A: "2" | ||
| InlineJavascriptRequirement: {} | ||
| InitialWorkDirRequirement: | ||
| listing: | ||
| - entryname: stage.py | ||
| entry: |- | ||
| import pystac | ||
| import stac_asset | ||
| import asyncio | ||
| import os | ||
| import sys | ||
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| config = stac_asset.Config(warn=True) | ||
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| async def main(href: str): | ||
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| item = pystac.read_file(href) | ||
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| os.makedirs(item.id, exist_ok=True) | ||
| cwd = os.getcwd() | ||
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| os.chdir(item.id) | ||
| item = await stac_asset.download_item(item=item, directory=".", config=config) | ||
| os.chdir(cwd) | ||
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| cat = pystac.Catalog( | ||
| id="catalog", | ||
| description=f"catalog with staged {item.id}", | ||
| title=f"catalog with staged {item.id}", | ||
| ) | ||
| cat.add_item(item) | ||
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| cat.normalize_hrefs("./") | ||
| cat.save(catalog_type=pystac.CatalogType.SELF_CONTAINED) | ||
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| return cat | ||
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| href = sys.argv[1] | ||
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| cat = asyncio.run(main(href)) | ||
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