1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/7ac62afbcdf2/ changeset: 7ac62afbcdf2 user: jgoecks date: 2012-08-10 15:58:59 summary: Make from_work_dir attribute work when outputs_to_working_directory is True. affected #: 1 file

diff -r 18462a6cbf46566307eaa4fd33c8891b5979d699 -r 7ac62afbcdf2b983e002b79e52753f9cf142db60 lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -40,7 +40,18 @@ 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 @@ # 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 ) )

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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