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Make from_work_dir attribute work when outputs_to_working_directory is True.

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This commit is contained in:
Jeremy Goecks
2012-08-10 09:58:59 -04:00
parent 5bdef6884b
commit 2a1bbec58f
1 changed files with 16 additions and 4 deletions
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lib/galaxy/jobs/runners/__init__.py
+16 -4
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@@ -40,7 +40,18 @@ class BaseJobRunner( object ):
if job_wrapper.dependency_shell_commands:
commands = "; ".join( job_wrapper.dependency_shell_commands + [ commands ] )
# Append commands to copy job outputs based on from_work_dir attribute.
# -- Append commands to copy job outputs based on from_work_dir attribute. --
# Set up dict of dataset id --> output path; output path can be real or
# false depending on outputs_to_working_directory
output_paths = {}
for dataset_path in job_wrapper.get_output_fnames():
path = dataset_path.real_path
if self.app.config.outputs_to_working_directory:
path = dataset_path.false_path
output_paths[ dataset_path.dataset_id ] = path
# Walk job's output associations to find and use from_work_dir attributes.
job = job_wrapper.get_job()
job_tool = self.app.toolbox.tools_by_id.get( job.tool_id, None )
for dataset_assoc in job.output_datasets + job.output_library_datasets:
@@ -53,12 +64,13 @@ class BaseJobRunner( object ):
# Copy from working dir to HDA.
# TODO: move instead of copy to save time?
source_file = os.path.join( os.path.abspath( job_wrapper.working_directory ), hda_tool_output.from_work_dir )
destination = output_paths[ dataset.dataset_id ]
if in_directory( source_file, job_wrapper.working_directory ):
try:
commands += "; cp %s %s" % ( source_file, dataset.file_name )
log.debug( "Copying %s to %s as directed by from_work_dir" % ( source_file, dataset.file_name ) )
commands += "; cp %s %s" % ( source_file, destination )
log.debug( "Copying %s to %s as directed by from_work_dir" % ( source_file, destination ) )
except ( IOError, OSError ):
log.debug( "Could not copy %s to %s as directed by from_work_dir" % ( source_file, dataset.file_name ) )
log.debug( "Could not copy %s to %s as directed by from_work_dir" % ( source_file, destination ) )
else:
# Security violation.
log.exception( "from_work_dir specified a location not in the working directory: %s, %s" % ( source_file, job_wrapper.working_directory ) )