details: http://www.bx.psu.edu/hg/galaxy/rev/b6420d2f247c changeset: 1527:b6420d2f247c user: Dan Blankenberg dan@bx.psu.edu date: Wed Sep 24 13:52:01 2008 -0400 description: Some metadata updates.
3 file(s) affected in this change:
lib/galaxy/datatypes/metadata.py lib/galaxy/model/__init__.py lib/galaxy/tools/__init__.py
diffs (84 lines):
diff -r 38e533287df4 -r b6420d2f247c lib/galaxy/datatypes/metadata.py --- a/lib/galaxy/datatypes/metadata.py Wed Sep 24 11:14:44 2008 -0400 +++ b/lib/galaxy/datatypes/metadata.py Wed Sep 24 13:52:01 2008 -0400 @@ -155,11 +155,8 @@ else: self.spec = spec
#set default metadata values - if not self.parent._metadata: + if self.parent._metadata is None: self.parent._metadata = {} - for name, value in self.spec.items(): - if name not in self.bunch: - self.bunch[name] = value.default
def __iter__(self): return self.bunch.__iter__() @@ -177,12 +174,10 @@ def __getattr__(self, name): if name == "bunch": return self.parent._metadata - rval = self.bunch.get( name ) - if rval is None: - rval = self.spec.get( name, None ) - if rval: - rval = rval.no_value - return rval + if name in self.bunch: + return self.bunch[name] + if name in self.spec: + return self.spec[name].default def __setattr__(self, name, value): if name in ["parent","spec"]: self.__dict__[name] = value diff -r 38e533287df4 -r b6420d2f247c lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Wed Sep 24 11:14:44 2008 -0400 +++ b/lib/galaxy/model/__init__.py Wed Sep 24 13:52:01 2008 -0400 @@ -5,7 +5,7 @@ the relationship cardinalities are obvious (e.g. prefer Dataset to Data) """
-import os.path, os, errno +import os.path, os, errno, copy import sha import galaxy.datatypes from galaxy.util.bunch import Bunch @@ -114,7 +114,8 @@ self.extension = extension self.designation = designation self.metadata = metadata or dict() - self.dbkey = dbkey + if dbkey: #dbkey is stored in metadata, only set if non-zero, or else we could clobber one supplied by input 'metadata' + self.dbkey = dbkey self.deleted = deleted self.visible = visible # Relationships @@ -164,7 +165,7 @@ return self._metadata_collection def set_metadata( self, bunch ): # Needs to accept a MetadataCollection, a bunch, or a dict - self._metadata = dict( bunch.items() ) + self._metadata = dict( [ ( key, copy.deepcopy( value ) ) for key, value in bunch.items() ] ) metadata = property( get_metadata, set_metadata )
""" diff -r 38e533287df4 -r b6420d2f247c lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Wed Sep 24 11:14:44 2008 -0400 +++ b/lib/galaxy/tools/__init__.py Wed Sep 24 13:52:01 2008 -0400 @@ -1185,6 +1185,7 @@ primary_data.info = dataset.info primary_data.state = primary_data.states.OK primary_data.init_meta( copy_from=dataset ) + primary_data.set_meta() primary_data.set_peek() primary_data.set_size() primary_data.flush() @@ -1245,6 +1246,8 @@ def __getattr__( self, name ): rval = self.metadata.get( name, None ) if name in self.metadata.spec: + if rval is None: + rval = self.metadata.spec[name].no_value rval = self.metadata.spec[name].wrap( rval, self.metadata.parent ) return rval def __nonzero__( self ):