1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/483cbfc5341a/ changeset: 483cbfc5341a user: natefoo date: 2012-08-28 19:50:54 summary: Don't attempt to run util.umask_fix_perms() on data that is being linked to. Fixes #801. affected #: 1 file

diff -r d8bff94d8aac276ff77b65104c958ab5cc9ee243 -r 483cbfc5341a0331cc86185f8821cdecec52a0b4 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -471,7 +471,7 @@ job.user.total_disk_usage += bytes

# fix permissions - for path in [ dp.real_path for dp in self.get_output_fnames() ]: + for path in [ dp.real_path for dp in self.get_mutable_output_fnames() ]: util.umask_fix_perms( path, self.app.config.umask, 0666, self.app.config.gid ) self.sa_session.flush() log.debug( 'job %d ended' % self.job_id ) @@ -679,6 +679,11 @@ self.compute_outputs() return self.output_paths

+ def get_mutable_output_fnames( self ): + if self.output_paths is None: + self.compute_outputs() + return filter( lambda dsp: dsp.mutable, self.output_paths ) + def get_output_hdas_and_fnames( self ): if self.output_hdas_and_paths is None: self.compute_outputs() @@ -686,10 +691,11 @@

def compute_outputs( self ) : class DatasetPath( object ): - def __init__( self, dataset_id, real_path, false_path = None ): + def __init__( self, dataset_id, real_path, false_path = None, mutable = True ): self.dataset_id = dataset_id self.real_path = real_path self.false_path = false_path + self.mutable = mutable def __str__( self ): if self.false_path is None: return self.real_path @@ -706,13 +712,13 @@ self.output_hdas_and_paths = {} for name, hda in [ ( da.name, da.dataset ) for da in job.output_datasets + job.output_library_datasets ]: false_path = os.path.abspath( os.path.join( self.working_directory, "galaxy_dataset_%d.dat" % hda.dataset.id ) ) - dsp = DatasetPath( hda.dataset.id, hda.dataset.file_name, false_path ) + dsp = DatasetPath( hda.dataset.id, hda.dataset.file_name, false_path, mutable = hda.dataset.external_filename is None ) self.output_paths.append( dsp ) self.output_hdas_and_paths[name] = hda, dsp if special: false_path = os.path.abspath( os.path.join( self.working_directory, "galaxy_dataset_%d.dat" % special.dataset.id ) ) else: - results = [ ( da.name, da.dataset, DatasetPath( da.dataset.dataset.id, da.dataset.file_name ) ) for da in job.output_datasets + job.output_library_datasets ] + results = [ ( da.name, da.dataset, DatasetPath( da.dataset.dataset.id, da.dataset.file_name, mutable = da.dataset.dataset.external_filename is None ) ) for da in job.output_datasets + job.output_library_datasets ] self.output_paths = [t[2] for t in results] self.output_hdas_and_paths = dict([(t[0], t[1:]) for t in results]) if special:

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

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