1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/d781366bc120/ Changeset: d781366bc120 User: jmchilton Date: 2014-06-20 06:07:21 Summary: Improved (different at least) extra_files_path handling for dataset outputs. $output.extra_files_path will now mimic $output.files_path behavior - writing these files to the working directory to have them copied over later. This is more correct when using outputs_to_working_directory, running jobs as the real user, running jobs through LWR/Pulsar, or when using the NestedObjectStore. This is less efficient the 90% of the time when none of these conditions hold.
There is still an open issue that for inputs - $input.extra_files_path returns a non-exist path for DiskObjectStores but throws an error for NestedObjectStores. This behavior could be synchronized by this patch (https://gist.github.com/jmchilton/d05bcf02874762cdb829) - though I do not know if this is the intended behavior of NestedObjectStores. Affected #: 1 file
diff -r 4eba60282f9d06ce6123478ea1bfa1f9ec741f45 -r d781366bc120787e201b73a4dd99b56282169d86 lib/galaxy/tools/wrappers.py --- a/lib/galaxy/tools/wrappers.py +++ b/lib/galaxy/tools/wrappers.py @@ -1,4 +1,5 @@ import pipes +from galaxy import exceptions from galaxy.util.none_like import NoneDataset from galaxy.util import odict
@@ -211,6 +212,17 @@ return self.false_path elif self.false_extra_files_path is not None and key == 'extra_files_path': return self.false_extra_files_path + elif key == 'extra_files_path': + try: + return self.files_path + except AttributeError: + try: + return self.dataset.extra_files_path + except exceptions.ObjectNotFound: + # NestedObjectstore raises an error here + # instead of just returning a non-existent + # path like DiskObjectStore. + raise else: return getattr( self.dataset, key )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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