Add two overrides for cwltool --pack bug

mvdbeek · Nov 6, 2023 · b8a3a5c · b8a3a5c
1 parent 557e64c
commit b8a3a5c
Showing 1 changed file with 88 additions and 1 deletion.
diff --git a/lib/galaxy_test/base/cwl_location_rewriter.py b/lib/galaxy_test/base/cwl_location_rewriter.py
@@ -10,6 +10,89 @@
 
 log = logging.getLogger(__name__)
 
+# https://github.com/common-workflow-language/cwltool/issues/1937
+PACKED_WORKFLOWS_CWL_BUG = {
+    "conflict-wf.cwl": """
+$graph:
+- baseCommand: echo
+  class: CommandLineTool
+  id: echo
+  inputs:
+    text:
+      inputBinding: {}
+      type: string
+  outputs:
+    fileout:
+      outputBinding: {glob: out.txt}
+      type: File
+  stdout: out.txt
+- baseCommand: cat
+  class: CommandLineTool
+  id: cat
+  inputs:
+    file1:
+      inputBinding: {position: 1}
+      type: File
+    file2:
+      inputBinding: {position: 2}
+      type: File
+  outputs:
+    fileout:
+      outputBinding: {glob: out.txt}
+      type: File
+  stdout: out.txt
+- class: Workflow
+  id: collision
+  inputs: {input_1: string, input_2: string}
+  outputs:
+    fileout: {outputSource: cat_step/fileout, type: File}
+  steps:
+    cat_step:
+      in:
+        file1: {source: echo_1/fileout}
+        file2: {source: echo_2/fileout}
+      out: [fileout]
+      run: '#cat'
+    echo_1:
+      in: {text: input_1}
+      out: [fileout]
+      run: '#echo'
+    echo_2:
+      in: {text: input_2}
+      out: [fileout]
+      run: '#echo'
+cwlVersion: v1.1
+""",
+    "js-expr-req-wf.cwl": """
+$graph:
+- arguments: [echo, $(foo())]
+  class: CommandLineTool
+  hints:
+    ResourceRequirement: {ramMin: 8}
+  id: tool
+  inputs: []
+  outputs: {out: stdout}
+  requirements:
+    InlineJavascriptRequirement:
+      expressionLib: ['function foo() { return 2; }']
+  stdout: whatever.txt
+- class: Workflow
+  id: wf
+  inputs: []
+  outputs:
+    out: {outputSource: tool/out, type: File}
+  requirements:
+    InlineJavascriptRequirement:
+      expressionLib: ['function bar() { return 1; }']
+  steps:
+    tool:
+      in: {}
+      out: [out]
+      run: '#tool'
+cwlVersion: v1.0
+""",
+}
+
 
 def get_cwl_test_url(cwl_version):
     branch = "main"
@@ -42,6 +125,11 @@ def get_url(item, cwl_version, base_dir):
 
 
 def rewrite_locations(workflow_path: str, output_path: str):
+    workflow_path_basename = os.path.basename(workflow_path)
+    if workflow_path_basename in PACKED_WORKFLOWS_CWL_BUG:
+        with open(output_path, "w") as output:
+            output.write(PACKED_WORKFLOWS_CWL_BUG[workflow_path_basename])
+            return
     loading_context, workflow_obj, _uri = fetch_document(workflow_path)
     workflow_obj = pack(loading_context, workflow_path)
     cwl_version = workflow_path.split("test/functional/tools/cwl_tools/v")[1].split("/")[0]
@@ -54,4 +142,3 @@ def rewrite_locations(workflow_path: str, output_path: str):
     )
     with open(output_path, "w") as output:
         json.dump(workflow_obj, output)
-    return workflow_obj