Rev cwltool for a Python 3 fix.

There was a Python 3 problem with the dependency resolver stuff in the version previously targetted, reving this and praying. Had to replace some CWL draft 3 testing artifacts with version 1.0 since the former is not longer compatible with latest versions of CWL.

Author: jmchilton

project_templates/cwl_draft3_spec/cat1-tool.cwl

@@ -1,7 +1,7 @@
 #!/usr/bin/env cwl-runner
-cwlVersion: cwl:draft-3
+cwlVersion: 'v1.0'
 class: CommandLineTool
-description: "Print the contents of a file to stdout using 'cat' running in a docker container."
+doc: "Print the contents of a file to stdout using 'cat' running in a docker container."
 hints:
   - class: DockerRequirement
     dockerPull: debian:wheezy
@@ -15,4 +15,5 @@ inputs:
       position: 0
       prefix: -n
 outputs: []
-baseCommand: cat
+baseCommand:
+  - cat

requirements.txt

@@ -15,4 +15,4 @@ gxformat2>=0.2.0
 ephemeris>=0.8
 galaxy-lib>=18.5.11
 html5lib>=0.9999999,!=0.99999999,!=0.999999999,!=1.0b10,!=1.0b09
-cwltool==1.0.20170828135420
+cwltool==1.0.20180508202931

tests/data/count-lines2-wf.cwl

@@ -0,0 +1,50 @@
+#!/usr/bin/env cwl-runner
+class: Workflow
+cwlVersion: v1.0
+requirements:
+  InlineJavascriptRequirement: {}
+
+inputs:
+    file1:
+      type: File
+
+outputs:
+    count_output:
+      type: int
+      outputSource: step2/parseInt_output
+
+steps:
+  step1:
+    in:
+      wc_file1: file1
+    out: [wc_output]
+    run:
+      id: wc
+      class: CommandLineTool
+      inputs:
+        wc_file1:
+          type: File
+          inputBinding: {}
+      outputs:
+        wc_output:
+          type: File
+          outputBinding:
+            glob: output.txt
+      stdout: output.txt
+      baseCommand: wc
+
+  step2:
+    in:
+      parseInt_file1: step1/wc_output
+    out: [parseInt_output]
+    run:
+      class: ExpressionTool
+      inputs:
+        parseInt_file1:
+          type: File
+          inputBinding: { loadContents: true }
+      outputs:
+        parseInt_output:
+          type: int
+      expression: >
+        ${return {'parseInt_output': parseInt(inputs.parseInt_file1.contents)};}

tests/data/int_tool.cwl

@@ -2,7 +2,7 @@
 class: ExpressionTool
 requirements:
   - class: InlineJavascriptRequirement
-cwlVersion: cwl:draft-3
+cwlVersion: 'v1.0'
 inputs: []
 outputs:
   - { id: output, type: int }

tests/data/output_tests_tool.cwl

@@ -1,19 +1,20 @@
 #!/usr/bin/env cwl-runner
 class: CommandLineTool
-cwlVersion: cwl:draft-3
-description: "Print the contents of a file to stdout using 'cat' running in a docker container."
+cwlVersion: 'v1.0'
+doc: "Print the contents of a file to stdout using 'cat' running in a docker container."
 hints:
   - class: DockerRequirement
     dockerPull: debian:wheezy
 inputs:
-  - id: file1
+  file1:
     type: File
     label: Input File
-    description: "The file that will be copied using 'cat'"
+    doc: "The file that will be copied using 'cat'"
     inputBinding: {position: 1}
 outputs:
-  - id: output_file
+  output_file:
     type: File
     outputBinding: {glob: output.txt}
-baseCommand: cat
+baseCommand:
+  - cat
 stdout: output.txt

tests/test_engines.py

@@ -5,10 +5,10 @@
 from planemo.engine import engine_context
 from planemo.runnable import for_path
 from planemo.runnable import get_outputs
-from .test_utils import CWL_DRAFT3_DIR, test_context, TEST_DATA_DIR
+from .test_utils import test_context, TEST_DATA_DIR
 
-A_CWL_TOOL = os.path.join(CWL_DRAFT3_DIR, "cat3-tool.cwl")
-A_CWL_WORKFLOW = os.path.join(CWL_DRAFT3_DIR, "count-lines1-wf.cwl")
+A_CWL_TOOL = os.path.join(TEST_DATA_DIR, "tools", "ok-cat1-tool.cwl")
+A_CWL_WORKFLOW = os.path.join(TEST_DATA_DIR, "count-lines2-wf.cwl")
 
 A_GALAXY_TOOL = os.path.join(TEST_DATA_DIR, "tools", "ok_select_param.xml")
 A_GALAXY_GA_WORKFLOW = os.path.join(TEST_DATA_DIR, "test_workflow_1.ga")
@@ -41,7 +41,7 @@ def test_can_handle():
 
 
 def test_outputs():
-    outputs = get_outputs(for_path(A_CWL_TOOL))
+    outputs = get_outputs(for_path(A_CWL_WORKFLOW))
     assert len(outputs) == 1
     output_id = outputs[0].get_id()
-    assert output_id == "output_file"
+    assert output_id == "count_output"