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Fix Pulsar remote metadata temp files for https://github.com/galaxyproject/galaxy/pull/1688/commits/a2e31403753c407e7f6966b69b157e32f5f3ef8a

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xref #1688 and https://github.com/galaxyproject/galaxy/commit/2a90811ea37e1361d58538f11500643ff1f537e5
This commit is contained in:
John Chilton
2016-05-20 10:22:41 -04:00
committed by Dannon Baker
parent e194c64e26
commit 8d0e1c51df
2 changed files with 19 additions and 5 deletions
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lib/galaxy/jobs/__init__.py
+16 -4
View File
@@ -1125,12 +1125,21 @@ class JobWrapper( object ):
self.app.config, key, default
)
def finish( self, stdout, stderr, tool_exit_code=None, remote_working_directory=None ):
def finish(
self,
stdout,
stderr,
tool_exit_code=None,
remote_working_directory=None,
remote_metadata_directory=None,
):
"""
Called to indicate that the associated command has been run. Updates
the output datasets based on stderr and stdout from the command, and
the contents of the output files.
"""
# remote_working_directory not used with updated (7.0+ pulsar and 16.04+
# originated Galaxy job - keep for a few releases for older jobs)
finish_timer = util.ExecutionTimer()
# default post job setup
@@ -1258,12 +1267,15 @@ class JobWrapper( object ):
output_filename = self.external_output_metadata.get_output_filenames_by_dataset( dataset, self.sa_session ).filename_out
def path_rewriter( path ):
if not remote_working_directory or not path:
if not path:
return path
normalized_remote_working_directory = os.path.normpath( remote_working_directory )
normalized_remote_working_directory = remote_working_directory and os.path.normpath( remote_working_directory )
normalized_remote_metadata_directory = remote_metadata_directory and os.path.normpath( remote_metadata_directory )
normalized_path = os.path.normpath( path )
if normalized_path.startswith( normalized_remote_working_directory ):
if remote_working_directory and normalized_path.startswith( normalized_remote_working_directory ):
return normalized_path.replace( normalized_remote_working_directory, self.working_directory, 1 )
if remote_metadata_directory and normalized_path.startswith( normalized_remote_metadata_directory ):
return normalized_path.replace( normalized_remote_metadata_directory, self.working_directory, 1 )
return path
dataset.metadata.from_JSON_dict( output_filename, path_rewriter=path_rewriter )
lib/galaxy/jobs/runners/pulsar.py
+3 -1
View File
@@ -451,6 +451,7 @@ class PulsarJobRunner( AsynchronousJobRunner ):
client = self.get_client_from_state(job_state)
run_results = client.full_status()
remote_working_directory = run_results.get("working_directory", None)
remote_metadata_directory = run_results.get("metadata_directory", None)
stdout = run_results.get('stdout', '')
stderr = run_results.get('stderr', '')
exit_code = run_results.get('returncode', None)
@@ -482,7 +483,8 @@ class PulsarJobRunner( AsynchronousJobRunner ):
stdout,
stderr,
exit_code,
remote_working_directory=remote_working_directory
remote_working_directory=remote_working_directory,
remote_metadata_directory=remote_metadata_directory,
)
except Exception:
log.exception("Job wrapper finish method failed")