commit/galaxy-central: 2 new changesets

28 Jan 2013

2 new commits in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/5315471299a9/
changeset:   5315471299a9
user:        kellrott
date:        2013-01-10 20:46:20
summary:     Adding UUIDType to data model and uuid column to dataset table.
affected #:  4 files

diff -r c015b82b3944f967e2c859d5552c00e3e38a2da0 -r 5315471299a992d4fd243fbb681e5caf65ff2092 lib/galaxy/model/__init__.py

--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -895,6 +895,7 @@
         self.external_filename = external_filename
         self._extra_files_path = extra_files_path
         self.file_size = file_size
+        self.uuid = None
 
     def get_file_name( self ):
         if not self.external_filename:

diff -r c015b82b3944f967e2c859d5552c00e3e38a2da0 -r 5315471299a992d4fd243fbb681e5caf65ff2092 lib/galaxy/model/custom_types.py
--- a/lib/galaxy/model/custom_types.py
+++ b/lib/galaxy/model/custom_types.py
@@ -1,9 +1,11 @@
 from sqlalchemy.types import *
+
 import pkg_resources
 pkg_resources.require("simplejson")
 import simplejson
 import pickle
 import copy
+import uuid
 import binascii
 from galaxy.util.bunch import Bunch
 from galaxy.util.aliaspickler import AliasPickleModule
@@ -84,6 +86,39 @@
                 ret = None
         return ret
 
+
+
+class UUIDType(TypeDecorator):
+    """
+    Platform-independent UUID type.
+    
+    Based on http://docs.sqlalchemy.org/en/rel_0_8/core/types.html#backend-agnostic-guid-...
+    Changed to remove sqlalchemy 0.8 specific code
+
+    CHAR(32), storing as stringified hex values.
+    """
+    impl = CHAR
+
+    def load_dialect_impl(self, dialect):
+        return dialect.type_descriptor(CHAR(32))
+
+    def process_bind_param(self, value, dialect):
+        if value is None:
+            return value
+        else:
+            if not isinstance(value, uuid.UUID):
+                return "%.32x" % uuid.UUID(value)
+            else:
+                # hexstring
+                return "%.32x" % value
+
+    def process_result_value(self, value, dialect):
+        if value is None:
+            return value
+        else:
+            return uuid.UUID(value)
+
+
 class TrimmedString( TypeDecorator ):
     impl = String
     def process_bind_param( self, value, dialect ):

diff -r c015b82b3944f967e2c859d5552c00e3e38a2da0 -r 5315471299a992d4fd243fbb681e5caf65ff2092 lib/galaxy/model/mapping.py
--- a/lib/galaxy/model/mapping.py
+++ b/lib/galaxy/model/mapping.py
@@ -135,7 +135,8 @@
     Column( "external_filename" , TEXT ),
     Column( "_extra_files_path", TEXT ),
     Column( 'file_size', Numeric( 15, 0 ) ),
-    Column( 'total_size', Numeric( 15, 0 ) ) )
+    Column( 'total_size', Numeric( 15, 0 ) ),
+    Column( 'uuid', UUIDType() ) )
 
 HistoryDatasetAssociationDisplayAtAuthorization.table = Table( "history_dataset_association_display_at_authorization", metadata,
     Column( "id", Integer, primary_key=True ),

diff -r c015b82b3944f967e2c859d5552c00e3e38a2da0 -r 5315471299a992d4fd243fbb681e5caf65ff2092 lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py
--- /dev/null
+++ b/lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py
@@ -0,0 +1,50 @@
+"""
+Add UUID column to dataset table
+"""
+
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from migrate import *
+from migrate.changeset import *
+from galaxy.model.custom_types import UUIDType
+
+import logging
+log = logging.getLogger( __name__ )
+
+metadata = MetaData( migrate_engine )
+#db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) )
+
+dataset_uuid_column = Column( "uuid", UUIDType, nullable=True )
+
+
+def display_migration_details():
+    print ""
+    print "This migration adds uuid column to dataset table"
+
+def upgrade():
+    print __doc__
+    metadata.reflect()
+    
+    # Add the uuid colum to the dataset table
+    try:
+        dataset_table = Table( "dataset", metadata, autoload=True )
+        dataset_uuid_column.create( dataset_table )
+        assert dataset_uuid_column is dataset_table.c.uuid
+    except Exception, e:
+        print str(e)
+        log.error( "Adding column 'uuid' to dataset table failed: %s" % str( e ) )
+        return 
+
+
+def downgrade():
+    metadata.reflect()
+    
+    # Drop the Job table's exit_code column. 
+    try:
+        dataset_table = Table( "dataset", metadata, autoload=True )
+        dataset_uuid = dataset_table.c.uuid
+        dataset_uuid.drop()
+    except Exception, e:
+        log.debug( "Dropping 'uuid' column from dataset table failed: %s" % ( str( e ) ) )
+
+


https://bitbucket.org/galaxy/galaxy-central/commits/d4d5588574cc/
changeset:   d4d5588574cc
user:        dannon
date:        2013-01-28 19:56:01
summary:     Merged in kellrott/galaxy-central (pull request #105)

Adding UUIDType to data model and uuid column to dataset table.
affected #:  4 files

diff -r b1a778e027ff330f044d44ca0ba1a07992d376b4 -r d4d5588574ccb7faea8abfb0f0ca9fe9b48e701e lib/galaxy/model/__init__.py
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -895,6 +895,7 @@
         self.external_filename = external_filename
         self._extra_files_path = extra_files_path
         self.file_size = file_size
+        self.uuid = None
 
     def get_file_name( self ):
         if not self.external_filename:

diff -r b1a778e027ff330f044d44ca0ba1a07992d376b4 -r d4d5588574ccb7faea8abfb0f0ca9fe9b48e701e lib/galaxy/model/custom_types.py
--- a/lib/galaxy/model/custom_types.py
+++ b/lib/galaxy/model/custom_types.py
@@ -1,9 +1,11 @@
 from sqlalchemy.types import *
+
 import pkg_resources
 pkg_resources.require("simplejson")
 import simplejson
 import pickle
 import copy
+import uuid
 import binascii
 from galaxy.util.bunch import Bunch
 from galaxy.util.aliaspickler import AliasPickleModule
@@ -84,6 +86,39 @@
                 ret = None
         return ret
 
+
+
+class UUIDType(TypeDecorator):
+    """
+    Platform-independent UUID type.
+    
+    Based on http://docs.sqlalchemy.org/en/rel_0_8/core/types.html#backend-agnostic-guid-...
+    Changed to remove sqlalchemy 0.8 specific code
+
+    CHAR(32), storing as stringified hex values.
+    """
+    impl = CHAR
+
+    def load_dialect_impl(self, dialect):
+        return dialect.type_descriptor(CHAR(32))
+
+    def process_bind_param(self, value, dialect):
+        if value is None:
+            return value
+        else:
+            if not isinstance(value, uuid.UUID):
+                return "%.32x" % uuid.UUID(value)
+            else:
+                # hexstring
+                return "%.32x" % value
+
+    def process_result_value(self, value, dialect):
+        if value is None:
+            return value
+        else:
+            return uuid.UUID(value)
+
+
 class TrimmedString( TypeDecorator ):
     impl = String
     def process_bind_param( self, value, dialect ):

diff -r b1a778e027ff330f044d44ca0ba1a07992d376b4 -r d4d5588574ccb7faea8abfb0f0ca9fe9b48e701e lib/galaxy/model/mapping.py
--- a/lib/galaxy/model/mapping.py
+++ b/lib/galaxy/model/mapping.py
@@ -135,7 +135,8 @@
     Column( "external_filename" , TEXT ),
     Column( "_extra_files_path", TEXT ),
     Column( 'file_size', Numeric( 15, 0 ) ),
-    Column( 'total_size', Numeric( 15, 0 ) ) )
+    Column( 'total_size', Numeric( 15, 0 ) ),
+    Column( 'uuid', UUIDType() ) )
 
 HistoryDatasetAssociationDisplayAtAuthorization.table = Table( "history_dataset_association_display_at_authorization", metadata,
     Column( "id", Integer, primary_key=True ),

diff -r b1a778e027ff330f044d44ca0ba1a07992d376b4 -r d4d5588574ccb7faea8abfb0f0ca9fe9b48e701e lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py
--- /dev/null
+++ b/lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py
@@ -0,0 +1,50 @@
+"""
+Add UUID column to dataset table
+"""
+
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from migrate import *
+from migrate.changeset import *
+from galaxy.model.custom_types import UUIDType
+
+import logging
+log = logging.getLogger( __name__ )
+
+metadata = MetaData( migrate_engine )
+#db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) )
+
+dataset_uuid_column = Column( "uuid", UUIDType, nullable=True )
+
+
+def display_migration_details():
+    print ""
+    print "This migration adds uuid column to dataset table"
+
+def upgrade():
+    print __doc__
+    metadata.reflect()
+    
+    # Add the uuid colum to the dataset table
+    try:
+        dataset_table = Table( "dataset", metadata, autoload=True )
+        dataset_uuid_column.create( dataset_table )
+        assert dataset_uuid_column is dataset_table.c.uuid
+    except Exception, e:
+        print str(e)
+        log.error( "Adding column 'uuid' to dataset table failed: %s" % str( e ) )
+        return 
+
+
+def downgrade():
+    metadata.reflect()
+    
+    # Drop the Job table's exit_code column. 
+    try:
+        dataset_table = Table( "dataset", metadata, autoload=True )
+        dataset_uuid = dataset_table.c.uuid
+        dataset_uuid.drop()
+    except Exception, e:
+        log.debug( "Dropping 'uuid' column from dataset table failed: %s" % ( str( e ) ) )
+
+

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

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