Metadata is now correctly wired up to the database and Datasets. Please review this as I got stuck on a bug for a few hours and may have something blatantly stupid going on. Next step is to add the metadata to all of the datatypes and do the edit.tml

lib/galaxy/datatypes/data.py

@@ -27,8 +27,8 @@ class Data( object ):
     'test'
     >>> DataTest.get_metadata_spec()['test'].desc
     >>> DataTest.get_metadata_spec()['test'].attributes
-    >>> DataTest.get_metadata_spec()['test'].wrapper
-    <class 'galaxy.datatypes.metadata.MetadataWrapper'>
+    >>> DataTest.get_metadata_spec()['test'].param
+    <class 'galaxy.datatypes.metadata.MetadataParameter'>
     
     """
     __metaclass__ = DataMeta

lib/galaxy/datatypes/metadata.py

@@ -1,4 +1,5 @@
 import sys
+from cookbook.patterns import Bunch
 
 # Taken in part from Elixir and how they do it: http://elixir.ematia.de
 
@@ -22,16 +23,7 @@ class MetadataSpecCollection( dict ):
     def iter( self ):
         return self.itervalues()
 
-class MetadataWrapper( object ):
-    def __init__( self, metadata ):
-        self.set_value( metadata )
-    def get_value( self ):
-        return self.value
-    def set_value( self, value ):
-        value = self.marshal(value)
-        self.validate(value)
-        self.value = value
-        
+class MetadataParameter( object ):
     def marshal( self, value ):
         '''
         This method should/can be overridden to convert the incomming
@@ -47,36 +39,56 @@ class MetadataWrapper( object ):
 
 class MetadataElementSpec( object ):
     READONLY = 1
-    def __init__( self, datatype, name=None, desc=None, wrapper=MetadataWrapper, attributes=None, default=None ):
+    def __init__( self, datatype, name=None, desc=None, param=MetadataParameter, attributes=None, default=None ):
         self.name = name
         self.desc = desc
-        self.wrapper = wrapper
+        self.param = param
         self.attributes = attributes
         self.default = default
         datatype._metadataspec.append( self )
     def hasAttribute( self, attribute ):
         return ((self.permission & attribute) == attribute)
     def wrap( self, metadata ):
-        return self.wrapper(metadata)
+        return self.param(metadata)
 
-class MetadataCollection( dict ):
-    def __init__( self, spec=None, *args ):
-        dict.__init__( self )
-        self.spec = spec
-    def __setitem__( self, key, value ):
-        if spec:
-            wrapper = spec[key].wrap( value )
-            dict.__setitem__( self, key, wrapper )
-        else:
-            dict.__setitem__( self, key, value )
-    def __getitem__( self, key ):
-        if spec:
-            if key not in self:
-                return self.spec[key].default
+class MetadataCollection:
+    """
+    MetadataCollection is not a collection at all, but rather a proxy
+    to the real metadata which is stored as a Bunch.  This class
+    handles updating the reference to the Bunch when it is changed (so
+    that SQLAlchemy knows to update it) as well as returning default
+    values in cases when metadata is not set.
+    """
+    def __init__(self, parent, spec):
+        self.parent = parent
+        self.bunch = parent._metadata or Bunch()
+        self.spec = spec or dict()
+    def __iter__(self):
+        return self.bunch.__iter__()
+    def get( self, key, default=None ):
+        if self.spec:
+            if self.spec.get(name, None):
+                default = default or self.spec[name].default
+        return self.bunch.get( key, default )
+    def items(self):
+        return self.bunch.items()
+    def __str__(self):
+        return self.bunch.__str__()
+    def __nonzero__(self):
+        return self.bunch.__nonzero__()
+    def __getattr__(self, name):
+        try:
+            return self.bunch.get( name )
+        except AttributeError, e:
+            if self.spec.get(name, None):
+                return self.spec[name].default
             else:
-                return dict.__getitem__(self, key).get_value()
+                return None
+    def __setattr__(self, name, value):
+        if name in ["parent","bunch","spec"]:
+            self.__dict__[name] = value
         else:
-            return dict.__getitem__(self, key)
+            setattr(self.__dict__["bunch"], name, value)
+            self.bunch = self.parent._metadata = Bunch( **self.bunch.__dict__ )
 
 MetadataElement = Statement(MetadataElementSpec)
-

lib/galaxy/model/__init__.py

@@ -12,6 +12,7 @@ from cookbook.patterns import Bunch
 from galaxy import util
 import tempfile
 import galaxy.datatypes.registry
+from galaxy.datatypes.metadata import MetadataCollection
 
 datatypes_registry = galaxy.datatypes.registry.Registry() #Default Value Required for unit tests
 
@@ -152,7 +153,7 @@ class Dataset( object ):
         self.extension = extension
         self.dbkey = dbkey
         self.state = state
-        self.metadata = metadata or Bunch()
+        self._metadata = metadata or Bunch()
         self.parent_id = parent_id
         self.designation = designation
         self.deleted = False
@@ -160,6 +161,9 @@ class Dataset( object ):
         # Relationships
         self.history = history
         self.validation_errors = validation_errors
+
+    # Deprecated: the metadatacollection now updates the object
+    # reference whenever any metadata is changed
     def mark_metadata_changed( self ):
         """
         Register changes to metadata with the history
@@ -167,8 +171,10 @@ class Dataset( object ):
         FIXME: This is just temporary, I'd like to implement some kind of 
                object proxy mapper property for SQLAlchemy that handles 
                this magically.
+
+               Fixed.  INS, 7/5/2007  Waiting to remove...
         """
-        self.metadata = Bunch( **self.metadata.__dict__ )
+        self._metadata = Bunch( **self._metadata.__dict__ )
         
     @property
     def ext( self ):
@@ -180,6 +186,15 @@ class Dataset( object ):
     @property
     def datatype( self ):
         return datatypes_registry.get_datatype_by_extension( self.extension )
+
+    def get_metadata( self ):
+        if not self._metadata: self._metadata = Bunch()
+        return MetadataCollection( self, self.datatype.get_metadata_spec() )
+    def set_metadata( self, bunch ):
+        # Needs to accept a MetadataCollection, a bunch, or a dict
+        self._metadata = Bunch( **dict( bunch.items() ) )
+    metadata = property( get_metadata, set_metadata )
+    
     def change_datatype( self, new_ext ):
         datatypes_registry.change_datatype( self, new_ext )
     def get_size( self ):
@@ -286,19 +301,6 @@ class Dataset( object ):
         except OSError, e:
             log.critical('%s delete error %s' % (self.__class__.__name__, e))
             
-    # change datatype
-    def set_datatype( self, ext ):
-        current = datatypes_registry.get_datatype_by_extension( self.extension )
-        new = datatypes_registry.get_datatype_by_extension( ext )
-
-        # Copy over metadata that applies...according to spec (?)
-        new_meta = new.get_metadata_spec()
-        new_meta_bunch = Bunch()
-        for item in new_meta:
-            if item.name in self.metadata:
-                new_meta_bunch[item.name] = self.metadata[item.name]
-        self.metadata = new_meta_bunch
-        
 class ValidationError( object ):
     def __init__( self, message=None, err_type=None, attributes=None ):
         self.message = message

lib/galaxy/model/mapping.py

@@ -65,7 +65,7 @@ Dataset.table = Table( "dataset", metadata,
     Column( "extension", TrimmedString( 64 ) ),
     Column( "dbkey", TrimmedString( 64 ) ),
     Column( "state", TrimmedString( 64 ) ),
-    Column( "metadata", PickleType() ),
+    Column( "metadata", PickleType(), key="_metadata" ),
     Column( "parent_id", Integer, nullable=True ),
     Column( "designation", TrimmedString( 255 ) ),
     Column( "deleted", Boolean ),

lib/galaxy/model/mapping_tests.py

@@ -31,7 +31,7 @@ class MappingTests( unittest.TestCase ):
         assert hists[1].name == ( "H" * 255 )
         assert hists[0].user == users[0]
         assert hists[1].user is None
-        assert hists[1].datasets[0].metadata['chromCol'] == 1
+        assert hists[1].datasets[0].metadata.chromCol == 1
         assert hists[1].datasets[0].file_name == "/tmp/dataset_%d.dat" % hists[1].datasets[0].id
         # Do an update and check
         hists[1].name = "History 2b"

lib/galaxy/tools/actions/__init__.py

@@ -117,7 +117,7 @@ class DefaultToolAction( object ):
             # FIXME: init_meta should take a dataset to copy from as an 
             # argument
             if metadata_source:
-                data.metadata = Bunch( ** inp_data[metadata_source].metadata.__dict__ )
+                data.metadata = inp_data[metadata_source].metadata
             else:
                 data.init_meta()
             # Take dbkey from LAST input