Clean Up CWL Conformance Test Execution.

Makefile

@@ -161,7 +161,7 @@ push-release: ## Push a tagged release to github
 	git push $(UPSTREAM) master
 	git push --tags $(UPSTREAM)
 
-release: release-local push-release release-brew ## package, review, and upload a release
+release: release-local push-release ## package, review, and upload a release
 
 add-history: ## Reformat HISTORY.rst with data from Github's API
 	$(IN_VENV) python $(BUILD_SCRIPTS_DIR)/bootstrap_history.py $(ITEM)

cwl-runner/cwl-runner

@@ -41,9 +41,11 @@ done
 # TODO: Do something with USE_CONTAINER
 if [ -n USE_CONTAINER ];
 then
-    PLANEMO_ARGS="$PLANEMO_ARGS --docker --cwl"
+    PLANEMO_ARGS="$PLANEMO_ARGS --docker --cwl --output_json outputs.json"
 fi
 
-echo "$PLANEMO_ARGS"
+# echo "$PLANEMO_ARGS"
 
-"$PLANEMO_BIN" --verbose run $PLANEMO_ARGS
+"$PLANEMO_BIN" $VERBOSE_ARG run $PLANEMO_ARGS >planemo_run.log 2>&1
+
+cat outputs.json

planemo/commands/cmd_shed_serve.py

@@ -14,7 +14,6 @@
 @options.shed_read_options()
 @options.galaxy_run_options()
 @options.galaxy_config_options()
-@options.pid_file_option()
 @click.option(
     "--skip_dependencies",
     is_flag=True,

planemo/galaxy/activity.py

@@ -360,18 +360,16 @@ def get_dataset(dataset_details, filename=None):
         ctx.vlog("collecting outputs to directory %s" % output_directory)
         for runnable_output in get_outputs(self._runnable):
             output_id = runnable_output.get_id()
-
             output_dict_value = None
             if self._runnable.type in [RunnableType.cwl_workflow, RunnableType.cwl_tool]:
                 galaxy_output = self.to_galaxy_output(runnable_output)
-
                 cwl_output = output_to_cwl_json(
                     galaxy_output,
                     self._get_metadata,
                     get_dataset,
                     self._get_extra_files,
+                    pseduo_location=True,
                 )
-
                 output_dict_value = cwl_output
             else:
                 # TODO: deprecate this route for finding workflow outputs,
@@ -389,8 +387,8 @@ def get_dataset(dataset_details, filename=None):
 
             outputs_dict[output_id] = output_dict_value
 
-        ctx.vlog("collected outputs [%s]" % self._outputs_dict)
         self._outputs_dict = outputs_dict
+        ctx.vlog("collected outputs [%s]" % self._outputs_dict)
 
     @property
     def log(self):

planemo/galaxy/config.py

@@ -514,8 +514,6 @@ def config_join(*args):
 
         write_file(shed_data_manager_config_file, SHED_DATA_MANAGER_CONF_TEMPLATE)
 
-        pid_file = kwds.get("pid_file") or config_join("galaxy.pid")
-
         yield LocalGalaxyConfig(
             config_directory,
             env,
@@ -525,7 +523,6 @@ def config_join(*args):
             master_api_key,
             runnables,
             galaxy_root,
-            pid_file,
         )
 
 
@@ -827,7 +824,6 @@ def __init__(
         master_api_key,
         runnables,
         galaxy_root,
-        pid_file,
     ):
         super(LocalGalaxyConfig, self).__init__(
             config_directory,
@@ -839,10 +835,9 @@ def __init__(
             runnables,
         )
         self.galaxy_root = galaxy_root
-        self._pid_file = pid_file
 
     def kill(self):
-        kill_pid_file(self._pid_file)
+        kill_pid_file(self.pid_file)
 
     def startup_command(self, ctx, **kwds):
         """Return a shell command used to startup this instance.
@@ -851,13 +846,12 @@ def startup_command(self, ctx, **kwds):
         ``daemon`` keyword.
         """
         daemon = kwds.get("daemon", False)
-        pid_file = self._pid_file
         # TODO: Allow running dockerized Galaxy here instead.
         setup_venv_command = setup_venv(ctx, kwds)
         run_script = os.path.join(self.galaxy_root, "run.sh")
         run_script += " $COMMON_STARTUP_ARGS"
         if daemon:
-            run_script += " --pid-file '%s' --daemon" % pid_file
+            run_script += "--daemon"
             self.env["GALAXY_RUN_ALL"] = "1"
         else:
             run_script += " --server-name '%s' --reload" % self.server_name
@@ -876,6 +870,11 @@ def log_file(self):
         file_name = "%s.log" % self.server_name
         return os.path.join(self.galaxy_root, file_name)
 
+    @property
+    def pid_file(self):
+        pid_file_name = "%s.pid" % self.server_name
+        return os.path.join(self.galaxy_root, pid_file_name)
+
     @property
     def log_contents(self):
         if not os.path.exists(self.log_file):

planemo/io.py

@@ -174,10 +174,12 @@ def ps1_for_path(path, base="PS1"):
 
 def kill_pid_file(pid_file):
     if not os.path.exists(pid_file):
+        print("No pid file...")
         return
 
     pid = int(open(pid_file, "r").read())
-    kill_posix(pid)
+    killed = kill_posix(pid)
+    print("killed? s" % killed)
 
 
 def kill_posix(pid):

planemo/options.py

@@ -969,14 +969,6 @@ def galaxy_target_options():
     )
 
 
-def pid_file_option():
-    return planemo_option(
-        "--pid_file",
-        default=None,
-        help="Location of pid file is executed with --daemon."
-    )
-
-
 def daemon_option():
     return planemo_option(
         "--daemon",
@@ -1002,7 +994,6 @@ def galaxy_serve_options():
         docker_galaxy_image_option(),
         galaxy_config_options(),
         daemon_option(),
-        pid_file_option(),
     )
 
 

planemo/runnable.py

@@ -296,7 +296,8 @@ def get_outputs(runnable):
         tool_source = get_tool_source(runnable.path)
         # TODO: do something with collections at some point
         output_datasets, _ = tool_source.parse_outputs(None)
-        return [ToolOutput(o) for o in output_datasets.values()]
+        outputs = [ToolOutput(o) for o in output_datasets.values()]
+        return outputs
     elif runnable.type == RunnableType.galaxy_workflow:
         workflow_outputs = describe_outputs(runnable.path)
         return [GalaxyWorkflowOutput(o) for o in workflow_outputs]

scripts/test_conformance_cwl.bash

@@ -5,13 +5,6 @@
 #  Run all conformance tests:
 #    bash scripts/test_conformance_cwl.bash
 #
-# This script installs planemo and a Galaxy/planemo cwl-runner implementation
-# in the current virtualenv, clones down CWL spec, and runs a configuration test.
-# Very few tests will pass - tests which don't have actual data (specify fake jobs)
-# will not work, nor will tests which depend on the cwl-runner preserving filenames
-# instead of output IDs (this isn't implemented in Galaxy/planemo and I'm not convinced
-# it should be), finally any tests of workflows at all or tools using features not
-# yet implemented in the CWL will not pass.
 
 set -e
 # Ensure working directory is planemo project.