3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/7f783a4889f7/ changeset: 7f783a4889f7 user: natefoo date: 2011-12-08 23:34:19 summary: Object store bug fix (direct filesystem access in the default tool action) affected #: 1 file diff -r 8d668e1d51520f7663915ff5535852e47a7dd235 -r 7f783a4889f74bacf61a97a8e8d39ebda1cc9b9d lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -291,14 +291,11 @@ trans.sa_session.flush() trans.app.security_agent.set_all_dataset_permissions( data.dataset, output_permissions ) # Create an empty file immediately - # open( data.file_name, "w" ).close() trans.app.object_store.create( data.id, store_name=store_name ) if not store_name_set: # Ensure all other datasets in this job are created in the same store store_name = trans.app.object_store.store_name( data.id ) store_name_set = True - # Fix permissions - util.umask_fix_perms( data.file_name, trans.app.config.umask, 0666 ) # This may not be neccesary with the new parent/child associations data.designation = name # Copy metadata from one of the inputs if requested. https://bitbucket.org/galaxy/galaxy-central/changeset/95529ba09179/ changeset: 95529ba09179 user: natefoo date: 2011-12-08 23:45:48 summary: Missing part of the last commit. affected #: 1 file diff -r 7f783a4889f74bacf61a97a8e8d39ebda1cc9b9d -r 95529ba09179dcd08da79f1c67151a138284e8b1 lib/galaxy/objectstore/__init__.py --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -204,6 +204,7 @@ def __init__(self, config, file_path=None, extra_dirs=None): super(DiskObjectStore, self).__init__() self.file_path = file_path or config.file_path + self.config = config if extra_dirs is not None: self.extra_dirs = extra_dirs @@ -300,6 +301,7 @@ if not dir_only: path = os.path.join(path, alt_name if alt_name else "dataset_%s.dat" % dataset_id) open(path, 'w').close() + util.umask_fix_perms( path, self.config.umask, 0666 ) def empty(self, dataset_id, **kwargs): return os.path.getsize(self.get_filename(dataset_id, **kwargs)) > 0 https://bitbucket.org/galaxy/galaxy-central/changeset/c6735493b09f/ changeset: c6735493b09f user: natefoo date: 2011-12-08 23:46:05 summary: Merge. affected #: 1 file diff -r 95529ba09179dcd08da79f1c67151a138284e8b1 -r c6735493b09f507e02564e6c79f9fef39d7bf7fa lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -224,7 +224,7 @@ int( self.value ) except: raise ValueError( "An integer is required" ) - elif self.value is None: + elif self.value is None and not self.optional: raise ValueError( "The settings for the field named '%s' require a 'value' setting and optionally a default value which must be an integer" % self.name ) self.min = elem.get( 'min' ) self.max = elem.get( 'max' ) @@ -296,7 +296,7 @@ float( self.value ) except: raise ValueError( "A real number is required" ) - elif self.value is None: + elif self.value is None and not self.optional: raise ValueError( "The settings for this field require a 'value' setting and optionally a default value which must be a real number" ) if self.min: try: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.