Remove CWL conformance test code.

The conformance tests no longer need to be flagged in a special way and cwltool no longer implements this either.

planemo/commands/cmd_run.py

@@ -8,7 +8,7 @@
 from planemo import options
 from planemo.cli import command_function
 from planemo.engine import engine_context
-from planemo.io import conditionally_captured_io, warn
+from planemo.io import warn
 from planemo.tools import uri_to_path
 
 
@@ -18,7 +18,6 @@
 @options.galaxy_run_options()
 @options.galaxy_config_options()
 @options.galaxy_cwl_root_option()
-@options.cwl_conformance_test()
 @options.run_output_directory_option()
 @options.run_output_json_option()
 @options.engine_options()
@@ -29,32 +28,21 @@ def cli(ctx, uri, job_path, **kwds):
     \b
         % planemo run cat1-tool.cwl cat-job.json
     """
-    path = DEFAULT_TOOL_LOCATION_FETCHER.to_tool_path(uri)
+    path = uri_to_path(ctx, uri)
     kwds["cwl"] = path.endswith(".cwl")
-    conformance_test = kwds.get("conformance_test", False)
 
-    with conditionally_captured_io(conformance_test):
-        with engine_context(ctx, **kwds) as engine:
-            run_result = engine.run(path, job_path)
+    with engine_context(ctx, **kwds) as engine:
+        run_result = engine.run(path, job_path)
 
     if not run_result.was_successful:
         warn("Run failed [%s]" % str(run_result))
         ctx.exit(1)
 
-    if conformance_test:
-        if hasattr(run_result, "cwl_command_state"):
-            command_state = run_result.cwl_command_state
-            dumped_json = json.dumps(command_state)
-            if hasattr(run_result, "galaxy_paths"):
-                for (local_path, galaxy_path) in run_result.galaxy_paths:
-                    dumped_json = dumped_json.replace(galaxy_path, local_path)
-            print(dumped_json)
-    else:
-        outputs_dict = run_result.outputs_dict
-        print(outputs_dict)
-        output_json = kwds.get("output_json", None)
-        if output_json:
-            with open(output_json, "w") as f:
-                json.dump(outputs_dict, f)
+    outputs_dict = run_result.outputs_dict
+    print(outputs_dict)
+    output_json = kwds.get("output_json", None)
+    if output_json:
+        with open(output_json, "w") as f:
+            json.dump(outputs_dict, f)
 
     return 0

planemo/cwl/run.py

@@ -25,9 +25,8 @@
 class CwlToolRunResponse(SuccessfulRunResponse):
     """Describe the resut of a cwltool invocation."""
 
-    def __init__(self, log, cwl_command_state=None, outputs=None):
+    def __init__(self, log, outputs=None):
         self._log = log
-        self._cwl_command_state = cwl_command_state
         self._outputs = outputs
 
     @property
@@ -38,19 +37,8 @@ def log(self):
     def job_info(self):
         return None
 
-    @property
-    def cwl_command_state(self):
-        if self._cwl_command_state is None:
-            message = "Can only call cwl_command_state if running conformance_test."
-            raise NotImplementedError(message)
-
-        return self._cwl_command_state
-
     @property
     def outputs_dict(self):
-        if self._outputs is None:
-            message = "Can not call outputs if running conformance_test."
-            raise NotImplementedError(message)
         return self._outputs
 
 
@@ -59,9 +47,6 @@ def run_cwltool(ctx, path, job_path, **kwds):
     ensure_cwltool_available()
 
     args = []
-    conformance_test = kwds.get("conformance_test", False)
-    if conformance_test:
-        args.append("--conformance-test")
     if ctx.verbose:
         args.append("--verbose")
     output_directory = kwds.get("output_directory", None)
@@ -105,15 +90,9 @@ def run_cwltool(ctx, path, job_path, **kwds):
 
         if ret_code != 0:
             return ErrorRunResponse("Error running cwltool", log=log)
-        if conformance_test:
-            cwl_command_state = result
-            outputs = None
-        else:
-            cwl_command_state = None
-            outputs = result
+        outputs = result
     return CwlToolRunResponse(
         log,
-        cwl_command_state=cwl_command_state,
         outputs=outputs,
     )
 

planemo/galaxy/activity.py

@@ -215,13 +215,6 @@ def job_info(self):
             )
         return None
 
-    @property
-    def cwl_command_state(self):
-        cwl_command_state = None
-        if self._job_info is not None:
-            cwl_command_state = self._job_info["cwl_command_state"]
-        return cwl_command_state
-
     @property
     def outputs_dict(self):
         return self._outputs_dict

planemo/options.py

@@ -234,17 +234,6 @@ def run_output_json_option():
     )
 
 
-def cwl_conformance_test():
-    return planemo_option(
-        "--conformance_test",
-        "--conformance-test",
-        is_flag=True,
-        help=("Generate CWL conformance test object describing job. "
-              "Required by CWL conformance test suite and implemented "
-              "by cwltool reference implementation."),
-    )
-
-
 def no_dependency_resolution():
     return planemo_option(
         "--no_dependency_resolution",

planemo/runnable.py

@@ -385,10 +385,6 @@ def was_successful(self):
         """Return `True` to indicate this run was successful."""
         return True
 
-    @abc.abstractproperty
-    def cwl_command_state(self):
-        """JSON result of command state for an execution."""
-
     @abc.abstractproperty
     def outputs_dict(self):
         """Return a dict of output descriptions."""

tests/test_run.py

@@ -45,7 +45,6 @@ def test_run_cat_cwltool_more_options(self):
                 "run",
                 "--engine", "cwltool",
                 "--no_container",
-                "--conformance-test",
                 tool_path,
                 job_path,
             ]
@@ -78,21 +77,6 @@ def test_run_cat(self):
             ]
             self._check_exit_code(test_cmd)
 
-    # Conformance test option is deprecated in CWL land and obsecures errors.
-    # @skip_unless_python_2_7()
-    # @skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
-    # def test_run_cat_conformance(self):
-    #     with self._isolate():
-    #         tool_path = _cwl_file("cat1-tool.cwl")
-    #         job_path = _cwl_file("cat-job.json")
-    #         test_cmd = [
-    #             "run",
-    #             "--conformance-test",
-    #             tool_path,
-    #             job_path,
-    #        ]
-    #        self._check_exit_code(test_cmd)
-
     @skip_unless_python_2_7()
     @skip_if_environ("PLANEMO_SKIP_CWLTOOL_TESTS")
     @skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")