networkAcess, envDef, and initialWorkDir tests

tests/dir5_noiwdr.cwl

@@ -0,0 +1,18 @@
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+requirements:
+  - class: ShellCommandRequirement
+initialWorkDir: $(inputs.indir.listing)
+inputs:
+  indir:
+    type: Directory
+    loadListing: shallow_listing
+outputs:
+  outlist:
+    type: File
+    outputBinding:
+      glob: output.txt
+arguments: ["find", "-L", ".", "!", "-path", "*.txt",
+  {shellQuote: false, valueFrom: "|"},
+  "sort"]
+stdout: output.txt

tests/env-tool1_noreq.cwl

@@ -0,0 +1,16 @@
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+inputs:
+  in: string
+outputs:
+  out:
+    type: File
+    outputBinding:
+      glob: out
+
+envDef:
+  TEST_ENV: $(inputs.in)
+
+baseCommand: ["/bin/sh", "-c", "echo $TEST_ENV"]
+
+stdout: out

tests/env-tool4_noreq.cwl

@@ -0,0 +1,16 @@
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+inputs:
+  in: string
+outputs:
+  out:
+    type: File
+    outputBinding:
+      glob: out
+
+envDef:
+  TEST_ENV: conflict_original
+
+baseCommand: ["/bin/bash", "-c", "echo $TEST_ENV"]
+
+stdout: out

tests/env-wf1_noreq.cwl

@@ -0,0 +1,23 @@
+#!/usr/bin/env cwl-runner
+class: Workflow
+cwlVersion: v1.3.0-dev1
+
+inputs:
+    in: string
+
+outputs:
+    out:
+      type: File
+      outputSource: step1/out
+
+requirements:
+  EnvVarRequirement:
+    envDef:
+      TEST_ENV: override
+
+steps:
+  step1:
+    run: env-tool1_noreq.cwl
+    in:
+      in: in
+    out: [out]

tests/initialwork-path_noiwdr.cwl

@@ -0,0 +1,14 @@
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+requirements:
+  ShellCommandRequirement: {}
+initialWorkDir:
+  - entry: $(inputs.file1)
+    entryname: bob.txt
+inputs:
+  file1: File
+outputs: []
+arguments:
+  - shellQuote: false
+    valueFrom: |
+      test "$(inputs.file1.path)" = "$(runtime.outdir)/bob.txt"

tests/initialworkdir-glob-fullpath_noiwdr.cwl

@@ -0,0 +1,26 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.3.0-dev1
+
+initialWorkDir:
+  - $(inputs.INPUT)
+
+class: CommandLineTool
+
+inputs:
+  - id: INPUT
+    type: File
+
+outputs:
+  - id: OUTPUT
+    type: File
+    outputBinding:
+      glob: $(runtime.outdir)/$(inputs.INPUT.basename)
+    secondaryFiles:
+      - .fai
+
+arguments:
+  - valueFrom: $(inputs.INPUT.basename).fai
+    position: 0
+
+baseCommand: [touch]

tests/initialworkdirrequirement-docker-out_noiwdr.cwl

@@ -0,0 +1,30 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.3.0-dev1
+
+requirements:
+  - class: DockerRequirement
+    dockerPull: docker.io/debian:stable-slim
+
+initialWorkDir:    
+  - $(inputs.INPUT)
+
+class: CommandLineTool
+
+inputs:
+  - id: INPUT
+    type: File
+
+outputs:
+  - id: OUTPUT
+    type: File
+    outputBinding:
+      glob: $(inputs.INPUT.basename)
+    secondaryFiles:
+      - .fai
+
+arguments:
+  - valueFrom: $(inputs.INPUT.basename).fai
+    position: 0
+
+baseCommand: [touch]

tests/inp_update_wf_noiwdr.cwl

@@ -0,0 +1,33 @@
+#!/usr/bin/env cwl-runner
+class: Workflow
+cwlVersion: v1.3.0-dev1
+inputs: []
+outputs:
+  a:
+    type: int
+    outputSource: step3/output
+  b:
+    type: int
+    outputSource: step4/output
+steps:
+  step1:
+    in:
+      in: {default: "3"}
+    out: [out]
+    run: echo-file-tool.cwl
+  step2:
+    in:
+      r: step1/out
+    out: [out]
+    run: updateval_inplace_noiwdr.cwl
+  step3:
+    in:
+      file1: step1/out
+      wait: step2/out
+    out: [output]
+    run: parseInt-tool.cwl
+  step4:
+    in:
+      file1: step2/out
+    out: [output]
+    run: parseInt-tool.cwl

tests/inpdir_update_wf_noiwdr.cwl

@@ -0,0 +1,42 @@
+#!/usr/bin/env cwl-runner
+class: Workflow
+cwlVersion: v1.3.0-dev1
+inputs: []
+requirements:
+  InlineJavascriptRequirement: {}
+outputs:
+  a:
+    type: File[]
+    outputSource: step3/d1out
+  b:
+    type: File[]
+    outputSource: step3/d2out
+steps:
+  step1:
+    in:
+      dirname: {default: step1dir}
+    out: [out]
+    run: mkdir.cwl
+  step2:
+    in:
+      r: step1/out
+    out: [out]
+    run: updatedir_inplace_noiwdr.cwl
+  step3:
+    in:
+      d1: step1/out
+      d2: step2/out
+    out: [d1out, d2out]
+    run:
+      class: ExpressionTool
+      inputs:
+        d1:
+          type: Directory
+          loadListing: shallow_listing
+        d2:
+          type: Directory
+          loadListing: shallow_listing
+      outputs:
+        d1out: File[]
+        d2out: File[]
+      expression: "$({d1out: inputs.d1.listing, d2out: inputs.d2.listing})"

tests/iwd/iwd-container-entryname1_noiwdr.cwl

@@ -0,0 +1,27 @@
+cwlVersion: v1.3.0-dev1
+class: CommandLineTool
+doc: |
+  When executing in a container, entryname can have an absolute path
+  to a mount location inside the container.
+
+inputs:
+  filelist: File
+
+outputs:
+  head:
+    type: File
+    outputBinding:
+      glob: head.txt
+
+requirements:
+  DockerRequirement:
+    dockerPull: docker.io/debian:stable-slim
+    dockerOutputDirectory: /output
+  ShellCommandRequirement: {}
+
+initialWorkDir:
+  - entryname: /tmp2j3y7rpb/input/stuff.txt  # Give it a weird prefix to minimize chance of conflict with a real file
+    entry: $(inputs.filelist)
+
+arguments:
+  - {shellQuote: false, valueFrom: "head -n10 /tmp2j3y7rpb/input/stuff.txt > /output/head.txt"}

tests/iwd/iwd-container-entryname2_noiwdr.cwl

@@ -0,0 +1,21 @@
+cwlVersion: v1.3.0-dev1
+class: CommandLineTool
+doc: |
+  Must fail if entryname is an absolute path and DockerRequirement is
+  not in the 'requirements' section.
+inputs:
+  filelist: File
+outputs:
+  head:
+    type: File
+    outputBinding:
+      glob: head.txt
+requirements:
+  ShellCommandRequirement: {}
+
+initialWorkDir:
+  - entryname: /tmp2j3y7rpb/input/stuff.txt  # Give it a weird prefix to minimize chance of conflict with a real file
+    entry: $(inputs.filelist)
+
+arguments:
+  - {shellQuote: false, valueFrom: "head -n10 /tmp2j3y7rpb/input/stuff.txt > /output/head.txt"}

tests/iwd/iwd-container-entryname3_noiwdr.cwl

@@ -0,0 +1,24 @@
+cwlVersion: v1.3.0-dev1
+class: CommandLineTool
+doc: |
+  Must fail if entryname is an absolute path and DockerRequirement is
+  not in the 'requirements' section.
+inputs:
+  filelist: File
+outputs:
+  head:
+    type: File
+    outputBinding:
+      glob: head.txt
+hints:
+  DockerRequirement:
+    dockerPull: docker.io/debian:stable-slim
+    dockerOutputDirectory: /output
+requirements:
+  ShellCommandRequirement: {}
+
+initialWorkDir:
+  - entryname: /tmp2j3y7rpb/input/stuff.txt  # Give it a weird prefix to minimize chance of conflict with a real file
+    entry: $(inputs.filelist)
+arguments:
+  - {shellQuote: false, valueFrom: "head -n10 /tmp2j3y7rpb/input/stuff.txt > /output/head.txt"}

tests/iwd/iwd-container-entryname4_noiwdr.cwl

@@ -0,0 +1,21 @@
+cwlVersion: v1.3.0-dev1
+class: CommandLineTool
+doc: |
+  Must fail if entryname starts with ../
+inputs:
+  filelist: File
+outputs:
+  head:
+    type: File
+    outputBinding:
+      glob: head.txt
+
+initialWorkDir:
+  - entryname: ../input/stuff.txt  # Illegal
+    entry: $(inputs.filelist)
+
+requirements:
+  ShellCommandRequirement: {}
+
+arguments:
+  - {shellQuote: false, valueFrom: "head -n10 ../input/stuff.txt > head.txt"}

tests/iwd/iwd-fileobjs1_noiwdr.cwl

@@ -0,0 +1,20 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+doc: Can have a file declared directly in an initialWorkDir
+initialWorkDir:
+  - class: File
+    location: ../loadContents/inp-filelist.txt
+  - class: Directory
+    location: ../testdir
+inputs: []
+outputs:
+  filelist:
+    type: File
+    outputBinding:
+      glob: inp-filelist.txt
+  testdir:
+    type: Directory
+    outputBinding:
+      glob: testdir
+baseCommand: "true"

tests/iwd/iwd-fileobjs2_noiwdr.cwl

@@ -0,0 +1,18 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+doc: Can have a file declared directly in initialWorkDir
+initialWorkDir:
+  - [{class: File, location: ../loadContents/inp-filelist.txt},
+     {class: Directory, location: ../testdir}]
+inputs: []
+outputs:
+  filelist:
+    type: File
+    outputBinding:
+      glob: inp-filelist.txt
+  testdir:
+    type: Directory
+    outputBinding:
+      glob: testdir
+baseCommand: "true"

tests/iwd/iwd-jsondump1-nl_noiwdr.cwl

@@ -0,0 +1,22 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+initialWorkDir:
+  - entryname: "out-filelist.json"
+    entry: |
+      ${
+        var ls = [];
+        for (var i = 1; i < 10000; i++) {
+          ls.push("example_input_file"+i+".txt");
+        }
+        return ls;
+      }
+requirements:
+  InlineJavascriptRequirement: {}
+inputs: []
+outputs:
+  filelist:
+    type: File
+    outputBinding:
+      glob: out-filelist.json
+arguments: ["true"]