Merge pull request #280 from galaxyproject/drop_metadata_hacks

Drop metadata directory hacks for pre-16.04 Galaxies.

pulsar/client/client.py

@@ -649,6 +649,8 @@ def _setup_params_from_job_config(job_config):
     tool_id = job_config.get("tool_id", None)
     tool_version = job_config.get("tool_version", None)
     preserve_galaxy_python_environment = job_config.get("preserve_galaxy_python_environment", None)
+    # use_metadata ignored post Pulsar 0.14.12+ but keep setting it for older Pulsar's that
+    # had hacks for pre-2017 Galaxies.
     return dict(
         job_id=job_id,
         tool_id=tool_id,

pulsar/manager_endpoint_util.py

@@ -80,13 +80,11 @@ def submit_job(manager, job_config):
             input_job_id = setup_params.get("job_id", job_id)
             tool_id = setup_params.get("tool_id", None)
             tool_version = setup_params.get("tool_version", None)
-            use_metadata = setup_params.get("use_metadata", False)
             job_config = setup_job(
                 manager,
                 input_job_id,
                 tool_id,
                 tool_version,
-                use_metadata,
             )
 
         if job_config is not None:
@@ -111,13 +109,11 @@ def submit_job(manager, job_config):
         raise
 
 
-def setup_job(manager, job_id, tool_id, tool_version, use_metadata=False):
+def setup_job(manager, job_id, tool_id, tool_version):
     """ Setup new job from these inputs and return dict summarizing state
     (used to configure command line).
     """
     job_id = manager.setup_job(job_id, tool_id, tool_version)
-    if use_metadata:
-        manager.enable_metadata_directory(job_id)
     return build_job_config(
         job_id=job_id,
         job_directory=manager.job_directory(job_id),

pulsar/managers/__init__.py

@@ -107,9 +107,6 @@ def stderr_contents(self, *args, **kwargs):
     def kill(self, *args, **kwargs):
         return self._proxied_manager.kill(*args, **kwargs)
 
-    def enable_metadata_directory(self, *args, **kwargs):
-        return self._proxied_manager.enable_metadata_directory(*args, **kwargs)
-
     def shutdown(self, timeout=None):
         """ Optional. """
         try:

pulsar/managers/base/__init__.py

@@ -228,13 +228,6 @@ def __init__(
         # Assert this job id isn't hacking path somehow.
         assert job_id == basename(job_id)
 
-    def enable_metadata_directory(self):
-        self.store_metadata("use_metadata_directory", True)
-
-    @property
-    def use_metadata_directory(self):
-        return self.has_metadata("use_metadata_directory")
-
     def _job_file(self, name):
         return os.path.join(self.job_directory, name)
 
@@ -329,12 +322,6 @@ def job_directory_contents(self):
         # Set recursive to False to just get the top-level artifacts
         return self.__directory_contents(self.job_directory, recursive=False)
 
-    def metadata_directory(self):
-        if self.use_metadata_directory:
-            return super(JobDirectory, self).metadata_directory()
-        else:
-            return self.working_directory()
-
     def __directory_contents(self, directory, recursive=True):
         contents = []
         if recursive:

pulsar/managers/base/directory.py

@@ -84,9 +84,6 @@ def _write_tool_info(self, job_id, tool_id, tool_version):
     def _write_command_line(self, job_id, command_line):
         self._write_job_file(job_id, JOB_FILE_COMMAND_LINE, command_line)
 
-    def enable_metadata_directory(self, job_id):
-        self._job_directory(job_id).enable_metadata_directory()
-
     def _record_cancel(self, job_id):
         try:
             self._job_directory(job_id).store_metadata(JOB_FILE_CANCELLED, True)

pulsar/web/routes.py

@@ -45,13 +45,12 @@ def _app_args(self, args, req):
 
 
 @PulsarController(path="/jobs", method="POST", response_type='json')
-def setup(manager, job_id, tool_id=None, tool_version=None, use_metadata='false'):
-    return __setup(manager, job_id, tool_id=tool_id, tool_version=tool_version, use_metadata=use_metadata)
+def setup(manager, job_id, tool_id=None, tool_version=None, use_metadata='true'):
+    return __setup(manager, job_id, tool_id=tool_id, tool_version=tool_version)
 
 
-def __setup(manager, job_id, tool_id, tool_version, use_metadata):
-    use_metadata = loads(use_metadata)
-    response = setup_job(manager, job_id, tool_id, tool_version, use_metadata)
+def __setup(manager, job_id, tool_id, tool_version):
+    response = setup_job(manager, job_id, tool_id, tool_version)
     log.debug("Setup job with configuration: %s" % response)
     return response