remove cwltool:requirements

Author: mr-c

cwltool/executors.py

@@ -51,7 +51,6 @@ def run_jobs(self,
                  runtime_context     # type: RuntimeContext
                 ):  # type: (...) -> None
         """ Execute the jobs for the given Process. """
-        pass
 
     def execute(self,
                 process,           # type: Process
@@ -81,26 +80,20 @@ def execute(self,
             if process.metadata["cwlVersion"] == 'v1.0':
                 raise WorkflowException(
                     "`cwl:requirements` in the input object is not part of CWL "
-                    "v1.0. You can use `cwltool:requirements` instead; or you "
+                    "v1.0. You can adjust to use `cwltool:overrides` instead; or you "
                     "can set the cwlVersion to v1.1.0-dev1 or greater and re-run with "
                     "--enable-dev.")
             job_reqs = job_order_object["https://w3id.org/cwl/cwl#requirements"]
-        elif "http://commonwl.org/cwltool#requirements" in job_order_object:
-            job_reqs = job_order_object["http://commonwl.org/cwltool#requirements"]
         elif ("cwl:defaults" in process.metadata
               and "https://w3id.org/cwl/cwl#requirements"
               in process.metadata["cwl:defaults"]):
             if process.metadata["cwlVersion"] == 'v1.0':
                 raise WorkflowException(
                     "`cwl:requirements` in the input object is not part of CWL "
-                    "v1.0. You can use `cwltool:requirements` instead; or you "
+                    "v1.0. You can adjust to use `cwltool:overrides` instead; or you "
                     "can set the cwlVersion to v1.1.0-dev1 or greater and re-run with "
                     "--enable-dev.")
             job_reqs = process.metadata["cwl:defaults"]["https://w3id.org/cwl/cwl#requirements"]
-        elif ("cwl:defaults" in process.metadata
-              and "http://commonwl.org/cwltool#requirements"
-              in process.metadata["cwl:defaults"]):
-            job_reqs = process.metadata["cwl:defaults"]["http://commonwl.org/cwltool#requirements"]
         if job_reqs is not None:
             for req in job_reqs:
                 process.requirements.append(req)
@@ -251,10 +244,11 @@ def run_job(self,
         while self.pending_jobs:
             with self.pending_jobs_lock:
                 job = self.pending_jobs[0]
-                if isinstance(job, JobBase) and \
+                if isinstance(job, JobBase) \
+                        and \
                         ((self.allocated_ram + job.builder.resources["ram"])
-                         > self.max_ram or
-                         (self.allocated_cores + job.builder.resources["cores"])
+                         > self.max_ram
+                         or (self.allocated_cores + job.builder.resources["cores"])
                          > self.max_cores):
                     _logger.warning(
                         'Job "%s" requested more resources (%s) than are '

tests/override/env-tool_cwltool-requirement_override.yaml

@@ -44,17 +44,10 @@
       get_data('tests/override/echo-job.yml')],
      {"out": "zing hello6\n"}
      ),
-    ([get_data('tests/override/env-tool.cwl'),
-      get_data('tests/override/env-tool_cwltool-requirement_override.yaml')],
-     {"value": "hello test env"}
-     ),
     (["--enable-dev", get_data('tests/override/env-tool_v1.1.0-dev1.cwl'),
       get_data('tests/override/env-tool_cwl-requirement_override.yaml')],
      {"value": "hello test env"}
      ),
-    ([get_data('tests/override/env-tool_cwltool-requirement_override_default.yaml')],
-     {"value": "hello test env"}
-     ),
     (["--enable-dev",
       get_data('tests/override/env-tool_cwl-requirement_override_default.yaml')],
      {"value": "hello test env"}
@@ -70,11 +63,12 @@ def test_overrides(parameters, result):
     assert main(parameters, stdout=sio) == 0
     assert json.loads(sio.getvalue()) == result
 
+
 failing_override_parameters = [
     ([get_data('tests/override/env-tool.cwl'),
       get_data('tests/override/env-tool_cwl-requirement_override.yaml')],
      "`cwl:requirements` in the input object is not part of CWL v1.0. You can "
-     "use `cwltool:requirements` instead; or you can set the cwlVersion to "
+     "adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to "
      "v1.1.0-dev1 or greater and re-run with --enable-dev."
      ),
     ([get_data('tests/override/env-tool_v1.1.0-dev1.cwl'),
@@ -85,7 +79,7 @@ def test_overrides(parameters, result):
      ),
     ([get_data('tests/override/env-tool_cwl-requirement_override_default_wrongver.yaml')],
      "`cwl:requirements` in the input object is not part of CWL v1.0. You can "
-     "use `cwltool:requirements` instead; or you can set the cwlVersion to "
+     "adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to "
      "v1.1.0-dev1 or greater and re-run with --enable-dev."
      ),
     ([get_data('tests/override/env-tool_cwl-requirement_override_default.yaml')],