1:14 a.m.
details: http://www.bx.psu.edu/hg/galaxy/rev/b6420d2f247c
changeset: 1527:b6420d2f247c
user: Dan Blankenberg <dan(a)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 ):