fix cwl:requirement, add test for it (#979)

Author: mr-c

cwltool/executors.py

@@ -77,11 +77,12 @@ def execute(self,
         runtime_context.workflow_eval_lock = threading.Condition(threading.RLock())
 
         job_reqs = None
-        if "cwl:requirements" in job_order_object:
-            job_reqs = job_order_object["cwl:requirements"]
+        if "https://w3id.org/cwl/cwl#requirements" in job_order_object:
+            job_reqs = job_order_object["https://w3id.org/cwl/cwl#requirements"]
         elif ("cwl:defaults" in process.metadata
-              and "cwl:requirements" in process.metadata["cwl:defaults"]):
-            job_reqs = process.metadata["cwl:defaults"]["cwl:requirements"]
+              and "https://w3id.org/cwl/cwl#requirements"
+              in process.metadata["cwl:defaults"]):
+            job_reqs = process.metadata["cwl:defaults"]["https://w3id.org/cwl/cwl#requirements"]
         if job_reqs is not None:
             for req in job_reqs:
                 process.requirements.append(req)

tests/override/env-tool.cwl

@@ -0,0 +1,10 @@
+class: CommandLineTool
+cwlVersion: v1.0
+inputs:
+  in: string
+outputs:
+  value: string
+
+baseCommand: ["/bin/bash", "-c", 'echo {\"value\": \"$TEST_ENV\"}']
+
+stdout: cwl.output.json

tests/override/env-tool_requirement_override.yaml

@@ -0,0 +1,6 @@
+in: "hello test env"
+cwl:requirements:
+ - class: EnvVarRequirement
+   envDef:
+     - envName: TEST_ENV
+       envValue: $(inputs.in)

tests/override/env-tool_requirement_override_default.yaml

@@ -0,0 +1,7 @@
+in: "hello test env"
+cwl:tool: env-tool.cwl
+cwl:requirements:
+ - class: EnvVarRequirement
+   envDef:
+     - envName: TEST_ENV
+       envValue: $(inputs.in)

tests/test_override.py

@@ -44,6 +44,13 @@
       get_data('tests/override/echo-job.yml')],
      {"out": "zing hello6\n"}
      ),
+    ([get_data('tests/override/env-tool.cwl'),
+      get_data('tests/override/env-tool_requirement_override.yaml')],
+     {"value": "hello test env"}
+     ),
+    ([get_data('tests/override/env-tool_requirement_override_default.yaml')],
+     {"value": "hello test env"}
+     ),
 ]
 
 @needs_docker