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Kaushik Ghose
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Add tests for staging File[]
1. Add three conformance tests to check staging of an array of Files to initial Directory 2. Tests check that entryname and basename work by themselves and if both are supplied, entryname overrides basename Fixes: common-workflow-language/common-workflow-language#777
1 parent dab1b18 commit 15b64b7

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‎conformance_tests.yaml

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class: "Directory"
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listing: []
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tags: [ required, command_line_tool ]
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- doc: Test that array of input files can be staged to directory with entryname
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label: stage_file_array
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tool: tests/stage_file_array.cwl
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job: tests/stage_file_array.job.json
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output:
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output:
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[
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{
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"basename": "sfa-1.txt",
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"checksum": "sha1$4c1cd0638ab3580310823fd1556d27ecb4816df6",
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"class": "File",
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"size": 49
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},
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{
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"basename": "sfa-1.txt.sec",
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"checksum": "sha1$40f4ee1bcd1a9466fcd2e48cf7fc3798025d2f9a",
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"class": "File",
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"size": 59
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},
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{
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"basename": "sfa-2.txt",
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"checksum": "sha1$4c1cd0638ab3580310823fd1556d27ecb4816df6",
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"class": "File",
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"size": 49
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},
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{
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"basename": "sfa-2.txt.sec",
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"checksum": "sha1$40f4ee1bcd1a9466fcd2e48cf7fc3798025d2f9a",
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"class": "File",
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"size": 59
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}
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]
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tags: [ required, command_line_tool ]
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- doc: Test that array of input files can be staged to directory with basename
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label: stage_file_array
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tool: tests/stage_file_array_basename.cwl
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job: tests/stage_file_array.job.json
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output:
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output:
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[
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{
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"basename": "sfa-1.txt",
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"checksum": "sha1$4c1cd0638ab3580310823fd1556d27ecb4816df6",
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"class": "File",
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"size": 49
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},
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{
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"basename": "sfa-1.txt.sec",
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"checksum": "sha1$40f4ee1bcd1a9466fcd2e48cf7fc3798025d2f9a",
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"class": "File",
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"size": 59
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},
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{
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"basename": "sfa-2.txt",
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"checksum": "sha1$4c1cd0638ab3580310823fd1556d27ecb4816df6",
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"class": "File",
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"size": 49
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},
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{
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"basename": "sfa-2.txt.sec",
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"checksum": "sha1$40f4ee1bcd1a9466fcd2e48cf7fc3798025d2f9a",
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"class": "File",
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"size": 59
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}
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]
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tags: [ required, command_line_tool ]
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- doc: Test that if array of input files are staged to directory with basename and entryname, entryname overrides
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label: stage_file_array
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tool: tests/stage_file_array_basename_and_entryname.cwl
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job: tests/stage_file_array.job.json
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output:
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output:
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[
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{
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"basename": "sfa-1.txt",
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"checksum": "sha1$4c1cd0638ab3580310823fd1556d27ecb4816df6",
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"class": "File",
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"size": 49
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},
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{
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"basename": "sfa-1.txt.sec",
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"checksum": "sha1$40f4ee1bcd1a9466fcd2e48cf7fc3798025d2f9a",
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"class": "File",
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"size": 59
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},
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{
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"basename": "sfa-2.txt",
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"checksum": "sha1$4c1cd0638ab3580310823fd1556d27ecb4816df6",
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"class": "File",
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"size": 49
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},
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{
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"basename": "sfa-2.txt.sec",
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"checksum": "sha1$40f4ee1bcd1a9466fcd2e48cf7fc3798025d2f9a",
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"class": "File",
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"size": 59
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}
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]
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tags: [ required, command_line_tool ]

‎tests/sfa-1.txt

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Test file for staging array of files to Directory

‎tests/sfa-1.txt.sec

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Secondary test file for staging array of files to Directory

‎tests/sfa-2.txt

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Test file for staging array of files to Directory

‎tests/sfa-2.txt.sec

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Secondary test file for staging array of files to Directory

‎tests/stage_file_array.cwl

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#!/usr/bin/env cwl-runner
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class: CommandLineTool
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cwlVersion: v1.1.0-dev1
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id: stage_file_array
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label: Stage File Array
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arguments: [ls]
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inputs:
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- id: input_list
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type: 'File[]'
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secondaryFiles:
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- .sec
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outputs:
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- id: output
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type: File[]
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outputBinding:
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glob: input_dir/*
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requirements:
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- class: InlineJavascriptRequirement
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- class: InitialWorkDirRequirement
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listing:
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- entryname: input_dir
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entry: "${ return {class: 'Directory', listing: inputs.input_list} }"
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writable: true

‎tests/stage_file_array.job.json

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{
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"input_list": [
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{
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"class": "File",
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"location": "sfa-1.txt"
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},
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{
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"class": "File",
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"location": "sfa-2.txt"
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}
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]
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}

‎tests/stage_file_array_basename.cwl

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#!/usr/bin/env cwl-runner
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class: CommandLineTool
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cwlVersion: v1.1.0-dev1
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id: stage_file_array_basename
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label: Stage File Array (with Directory Basename)
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arguments: [ls]
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inputs:
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- id: input_list
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type: 'File[]'
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secondaryFiles:
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- .sec
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outputs:
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- id: output
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type: File[]
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outputBinding:
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glob: input_dir/*
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requirements:
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- class: InlineJavascriptRequirement
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- class: InitialWorkDirRequirement
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listing:
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- entry: "${ return {class: 'Directory', basename: 'input_dir', listing: inputs.input_list} }"
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writable: true

‎tests/stage_file_array_basename_and_entryname.cwl

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#!/usr/bin/env cwl-runner
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class: CommandLineTool
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cwlVersion: v1.1.0-dev1
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id: stage_file_array_basename_and_entryname
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label: Stage File Array (with Directory Basename AND entryname)
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arguments: [ls]
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inputs:
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- id: input_list
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type: 'File[]'
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secondaryFiles:
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- .sec
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outputs:
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- id: output
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type: File[]
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outputBinding:
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glob: input_dir/*
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requirements:
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- class: InlineJavascriptRequirement
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- class: InitialWorkDirRequirement
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listing:
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- entryname: input_dir
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entry: "${ return {class: 'Directory', basename: 'not_input_dir', listing: inputs.input_list} }"
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writable: true

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