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GlassOfWhiskeyGlassOfWhiskey
committedDec 9, 2024·
Added extension tests
1 parent fb2e645 commit 5cb0a70

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‎MANIFEST.in

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@@ -21,6 +21,7 @@ include testdata/workflows/*.cwl
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include testdata/workflows/*.yaml
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include testdata/types/*.yml
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include testdata/checker_wf/*.cwl
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include testdata/extensions/*.cwl
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include cwl_utils/py.typed
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include docs/conf.py docs/Makefile docs/_static/favicon.ico docs/requirements.txt
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include docs/*.rst

‎Makefile

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@@ -191,19 +191,19 @@ flake8: $(PYSOURCES)
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cwl_utils/parser/cwl_v1_0.py: FORCE
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schema-salad-tool --codegen python \
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--codegen-parser-info "org.w3id.cwl.v1_0" \
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https://github.com/common-workflow-language/common-workflow-language/raw/codegen/v1.0/CommonWorkflowLanguage.yml \
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https://github.com/common-workflow-language/common-workflow-language/raw/codegen/v1.0/extensions.yml \
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> $@
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cwl_utils/parser/cwl_v1_1.py: FORCE
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schema-salad-tool --codegen python \
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--codegen-parser-info "org.w3id.cwl.v1_1" \
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https://github.com/common-workflow-language/cwl-v1.1/raw/codegen/CommonWorkflowLanguage.yml \
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https://github.com/common-workflow-language/cwl-v1.1/raw/codegen/extensions.yml \
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> $@
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cwl_utils/parser/cwl_v1_2.py: FORCE
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schema-salad-tool --codegen python \
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--codegen-parser-info "org.w3id.cwl.v1_2" \
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https://github.com/common-workflow-language/cwl-v1.2/raw/codegen/CommonWorkflowLanguage.yml \
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https://github.com/common-workflow-language/cwl-v1.2/raw/codegen/extensions.yml \
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> $@
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regen_parsers: cwl_utils/parser/cwl_v1_*.py

‎pyproject.toml

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@@ -67,6 +67,7 @@ packages = [
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"cwl_utils.tests",
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"cwl_utils.testdata",
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"cwl_utils.testdata.checker_wf",
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"cwl_utils.testdata.extensions",
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"cwl_utils.testdata.types",
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"cwl_utils.testdata.workflows",
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]
@@ -77,6 +78,7 @@ include-package-data = true
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"cwl_utils.tests" = "tests"
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"cwl_utils.testdata" = "testdata"
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"cwl_utils.testdata.checker_wf" = "testdata/checker_wf"
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"cwl_utils.testdata.extensions" = "testdata/extensions"
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"cwl_utils.testdata.types" = "testdata/types"
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"cwl_utils.testdata.workflows" = "testdata/workflows"
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‎requirements.txt

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@@ -2,5 +2,5 @@ cwl-upgrader >= 1.2.3
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packaging
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rdflib
44
requests
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schema-salad @ git+https://github.com/common-workflow-language/schema_salad.git
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schema-salad >= 8.8.20241206093842, < 9
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ruamel.yaml >= 0.17.6, < 0.19

‎testdata/extensions/all-output-loop_v1_2.cwl

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@@ -0,0 +1,32 @@
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#!/usr/bin/env cwl-runner
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cwlVersion: v1.2
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class: Workflow
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$namespaces:
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cwltool: "http://commonwl.org/cwltool#"
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requirements:
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InlineJavascriptRequirement: {}
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inputs:
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i1: int
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outputs:
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o1:
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type: int[]
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outputSource: subworkflow/o1
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steps:
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subworkflow:
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run:
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class: ExpressionTool
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inputs:
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i1: int
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outputs:
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o1: int
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expression: >
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${return {'o1': inputs.i1 + 1};}
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in:
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i1: i1
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out: [o1]
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requirements:
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cwltool:Loop:
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loopWhen: $(inputs.i1 < 10)
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loop:
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i1: o1
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outputMethod: all

‎testdata/extensions/cuda-requirement_v1_0.cwl

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@@ -0,0 +1,16 @@
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#!/usr/bin/env cwl-runner
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cwlVersion: v1.0
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class: CommandLineTool
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$namespaces:
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cwltool: "http://commonwl.org/cwltool#"
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requirements:
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cwltool:CUDARequirement:
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cudaVersionMin: "1.0"
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cudaComputeCapability: "1.0"
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cudaDeviceCountMin: $(inputs.gpus)
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inputs:
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gpus:
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type: int
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default: 1
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outputs: []
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baseCommand: "nvidia-smi"

‎testdata/extensions/cuda-requirement_v1_1.cwl

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@@ -0,0 +1,16 @@
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#!/usr/bin/env cwl-runner
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cwlVersion: v1.1
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class: CommandLineTool
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$namespaces:
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cwltool: "http://commonwl.org/cwltool#"
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requirements:
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cwltool:CUDARequirement:
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cudaVersionMin: "1.0"
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cudaComputeCapability: "1.0"
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cudaDeviceCountMin: $(inputs.gpus)
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inputs:
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gpus:
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type: int
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default: 1
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outputs: []
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baseCommand: "nvidia-smi"

‎testdata/extensions/cuda-requirement_v1_2.cwl

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@@ -0,0 +1,16 @@
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#!/usr/bin/env cwl-runner
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cwlVersion: v1.2
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class: CommandLineTool
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$namespaces:
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cwltool: "http://commonwl.org/cwltool#"
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requirements:
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cwltool:CUDARequirement:
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cudaVersionMin: "1.0"
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cudaComputeCapability: "1.0"
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cudaDeviceCountMin: $(inputs.gpus)
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inputs:
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gpus:
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type: int
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default: 1
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outputs: []
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baseCommand: "nvidia-smi"

‎testdata/extensions/inplace-update-requirement_v1_0.cwl

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@@ -0,0 +1,21 @@
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#!/usr/bin/env cwl-runner
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class: CommandLineTool
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cwlVersion: v1.0
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$namespaces:
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cwltool: "http://commonwl.org/cwltool#"
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requirements:
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cwltool:InplaceUpdateRequirement:
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inplaceUpdate: true
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inputs:
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r: File
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script:
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type: File
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default:
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class: File
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location: updateval.py
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outputs:
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out:
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type: File
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outputBinding:
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glob: $(inputs.r.basename)
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arguments: [python, $(inputs.script), $(inputs.r.basename)]

‎testdata/extensions/load-listing-requirement_v1_0.cwl

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#!/usr/bin/env cwl-runner
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class: CommandLineTool
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cwlVersion: v1.0
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$namespaces:
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cwltool: http://commonwl.org/cwltool#
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requirements:
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cwltool:LoadListingRequirement:
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loadListing: shallow_listing
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inputs:
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d: Directory
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outputs: []
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arguments:
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[echo, "$(inputs.d.listing[0].listing[0])"]

‎testdata/extensions/mpi-requirement_v1_0.cwl

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#!/usr/bin/env cwl-runner
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class: CommandLineTool
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cwlVersion: v1.0
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$namespaces:
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cwltool: "http://commonwl.org/cwltool#"
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baseCommand: env
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requirements:
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cwltool:MPIRequirement:
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processes: 1
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inputs: {}
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outputs:
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environment:
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type: stdout

‎testdata/extensions/mpi-requirement_v1_1.cwl

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#!/usr/bin/env cwl-runner
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class: CommandLineTool
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cwlVersion: v1.1
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$namespaces:
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cwltool: "http://commonwl.org/cwltool#"
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baseCommand: env
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requirements:
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cwltool:MPIRequirement:
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processes: 1
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inputs: {}
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outputs:
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environment:
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type: stdout

‎testdata/extensions/mpi-requirement_v1_2.cwl

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#!/usr/bin/env cwl-runner
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class: CommandLineTool
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cwlVersion: v1.2
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$namespaces:
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cwltool: "http://commonwl.org/cwltool#"
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baseCommand: env
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requirements:
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cwltool:MPIRequirement:
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processes: 1
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inputs: {}
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outputs:
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environment:
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type: stdout

‎testdata/extensions/network-access_v1_0.cwl

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#!/usr/bin/env cwl-runner
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class: CommandLineTool
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cwlVersion: v1.0
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$namespaces:
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cwltool: "http://commonwl.org/cwltool#"
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requirements:
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cwltool:NetworkAccess:
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networkAccess: true
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inputs: []
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outputs: []
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baseCommand: python
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arguments:
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- "-c"
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- valueFrom: |
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import urllib.request
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assert(urllib.request.urlopen("http://commonwl.org").code == 200)

‎testdata/extensions/process-generator_v1_0.cwl

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#!/usr/bin/env cwl-runner
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cwlVersion: v1.0
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$namespaces:
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cwltool: "http://commonwl.org/cwltool#"
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class: cwltool:ProcessGenerator
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inputs:
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script: string
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dir: Directory
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outputs: {}
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run:
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class: CommandLineTool
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inputs:
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script: string
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dir: Directory
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outputs:
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runProcess:
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type: File
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outputBinding:
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glob: main.cwl
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requirements:
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InlineJavascriptRequirement: {}
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LoadListingRequirement:
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loadListing: shallow_listing
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InitialWorkDirRequirement:
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listing: |
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${
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var v = inputs.dir.listing;
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v.push({entryname: "inp.py", entry: inputs.script});
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return v;
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}
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arguments: [python3, inp.py]
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stdout: main.cwl

‎testdata/extensions/process-generator_v1_1.cwl

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#!/usr/bin/env cwl-runner
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cwlVersion: v1.1
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$namespaces:
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cwltool: "http://commonwl.org/cwltool#"
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class: cwltool:ProcessGenerator
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inputs:
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script: string
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dir: Directory
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outputs: {}
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run:
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class: CommandLineTool
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inputs:
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script: string
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dir: Directory
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outputs:
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runProcess:
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type: File
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outputBinding:
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glob: main.cwl
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requirements:
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InlineJavascriptRequirement: {}
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LoadListingRequirement:
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loadListing: shallow_listing
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InitialWorkDirRequirement:
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listing: |
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${
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var v = inputs.dir.listing;
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v.push({entryname: "inp.py", entry: inputs.script});
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return v;
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}
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arguments: [python3, inp.py]
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stdout: main.cwl

‎testdata/extensions/process-generator_v1_2.cwl

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#!/usr/bin/env cwl-runner
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cwlVersion: v1.2
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$namespaces:
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cwltool: "http://commonwl.org/cwltool#"
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class: cwltool:ProcessGenerator
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inputs:
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script: string
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dir: Directory
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outputs: {}
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run:
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class: CommandLineTool
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inputs:
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script: string
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dir: Directory
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outputs:
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runProcess:
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type: File
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outputBinding:
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glob: main.cwl
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requirements:
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InlineJavascriptRequirement: {}
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LoadListingRequirement:
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loadListing: shallow_listing
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InitialWorkDirRequirement:
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listing: |
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${
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var v = inputs.dir.listing;
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v.push({entryname: "inp.py", entry: inputs.script});
29+
return v;
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}
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arguments: [python3, inp.py]
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stdout: main.cwl

‎testdata/extensions/secrets_v1_0.cwl

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#!/usr/bin/env cwl-runner
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cwlVersion: v1.0
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class: CommandLineTool
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$namespaces:
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cwltool: http://commonwl.org/cwltool#
6+
requirements:
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cwltool:Secrets:
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secrets: [pw]
9+
inputs:
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pw: string
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outputs:
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out: stdout
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arguments: [cat, example.conf]

‎testdata/extensions/secrets_v1_1.cwl

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#!/usr/bin/env cwl-runner
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cwlVersion: v1.1
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class: CommandLineTool
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$namespaces:
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cwltool: http://commonwl.org/cwltool#
6+
requirements:
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cwltool:Secrets:
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secrets: [pw]
9+
inputs:
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pw: string
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outputs:
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out: stdout
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arguments: [cat, example.conf]

‎testdata/extensions/secrets_v1_2.cwl

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#!/usr/bin/env cwl-runner
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cwlVersion: v1.2
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class: CommandLineTool
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$namespaces:
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cwltool: http://commonwl.org/cwltool#
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requirements:
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cwltool:Secrets:
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secrets: [pw]
9+
inputs:
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pw: string
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outputs:
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out: stdout
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arguments: [cat, example.conf]
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