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Adjust stderr collection to (Legacy-)ToolProvidedMetadata

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mvdbeek
2017-12-15 11:23:38 +01:00
parent 62a3ff3562
commit 9ee2a7d457
1 changed files with 15 additions and 8 deletions
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lib/galaxy/jobs/__init__.py
+15 -8
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@@ -27,7 +27,10 @@ from galaxy.exceptions import ObjectInvalid, ObjectNotFound
from galaxy.jobs.actions.post import ActionBox
from galaxy.jobs.mapper import JobRunnerMapper
from galaxy.jobs.runners import BaseJobRunner, JobState
from galaxy.tools.parameters.output_collect import NullToolProvidedMetadata
from galaxy.tools.parameters.output_collect import (
LegacyToolProvidedMetadata,
ToolProvidedMetadata
)
from galaxy.util import safe_makedirs, unicodify
from galaxy.util.bunch import Bunch
from galaxy.util.expressions import ExpressionContext
@@ -1181,13 +1184,17 @@ class JobWrapper(object, HasResourceParameters):
# We collect the stderr from tools that write their stderr to galaxy.json
tool_provided_metadata = self.get_tool_provided_job_metadata()
if not isinstance(tool_provided_metadata, NullToolProvidedMetadata):
extra_stderr = "\n".join([item.get('stderr') for item in tool_provided_metadata.tool_provided_job_metadata if item.get('stderr')])
if extra_stderr:
if stderr:
stderr = "%s\n%s" % (stderr, extra_stderr)
else:
stderr = extra_stderr
extra_stderr = ''
if isinstance(tool_provided_metadata, LegacyToolProvidedMetadata):
extra_stderr = [item.get('stderr') for item in tool_provided_metadata.tool_provided_job_metadata if item.get('stderr')]
elif isinstance(tool_provided_metadata, ToolProvidedMetadata):
extra_stderr = [item.get('stderr') for item in tool_provided_metadata.tool_provided_job_metadata.values() if item.get('stderr')]
if extra_stderr:
extra_stderr = "\n".join(extra_stderr)
if stderr:
stderr = "%s\n%s" % (stderr, extra_stderr)
else:
stderr = extra_stderr
# Check the tool's stdout, stderr, and exit code for errors, but only
# if the job has not already been marked as having an error.