Refactor migrations adding indexes

lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py

@@ -3,9 +3,15 @@
 import logging
 import sys
 
-from sqlalchemy import Index, MetaData, Table
+from sqlalchemy import (
+    MetaData,
+    Table
+)
 
-from galaxy.model.migrate.versions.util import engine_false
+from galaxy.model.migrate.versions.util import (
+    add_index,
+    engine_false
+)
 
 log = logging.getLogger(__name__)
 log.setLevel(logging.DEBUG)
@@ -23,18 +29,8 @@ def upgrade(migrate_engine):
     metadata.reflect()
 
     User_table = Table("galaxy_user", metadata, autoload=True)
-    HistoryDatasetAssociation_table = Table("history_dataset_association", metadata, autoload=True)
-    # Add 2 indexes to the galaxy_user table
-    i = Index('ix_galaxy_user_deleted', User_table.c.deleted)
-    try:
-        i.create()
-    except Exception:
-        log.exception("Adding index 'ix_galaxy_user_deleted' to galaxy_user table failed.")
-    i = Index('ix_galaxy_user_purged', User_table.c.purged)
-    try:
-        i.create()
-    except Exception:
-        log.exception("Adding index 'ix_galaxy_user_purged' to galaxy_user table failed.")
+    add_index('ix_galaxy_user_deleted', User_table, 'deleted')
+    add_index('ix_galaxy_user_purged', User_table, 'purged')
     # Set the default data in the galaxy_user table, but only for null values
     cmd = "UPDATE galaxy_user SET deleted = %s WHERE deleted is null" % engine_false(migrate_engine)
     try:
@@ -46,12 +42,9 @@ def upgrade(migrate_engine):
         migrate_engine.execute(cmd)
     except Exception:
         log.exception("Setting default data for galaxy_user.purged column failed.")
-    # Add 1 index to the history_dataset_association table
-    i = Index('ix_hda_copied_from_library_dataset_dataset_association_id', HistoryDatasetAssociation_table.c.copied_from_library_dataset_dataset_association_id)
-    try:
-        i.create()
-    except Exception:
-        log.exception("Adding index 'ix_hda_copied_from_library_dataset_dataset_association_id' to history_dataset_association table failed.")
+    add_index('ix_hda_copied_from_library_dataset_dataset_association_id',
+        'history_dataset_association',
+        'copied_from_library_dataset_dataset_association_id', metadata)
 
 
 def downgrade(migrate_engine):

lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py

@@ -6,7 +6,8 @@ from __future__ import print_function
 import logging
 
 from sqlalchemy import Index, MetaData, Table
-from sqlalchemy.engine import reflection
+
+from galaxy.model.migrate.versions.util import add_index
 
 log = logging.getLogger(__name__)
 log.setLevel(logging.DEBUG)
@@ -54,18 +55,9 @@ def upgrade(migrate_engine):
     print(__doc__)
     metadata.bind = migrate_engine
     metadata.reflect()
-    insp = reflection.Inspector.from_engine(migrate_engine)
-    # Create missing indexes
+
     for ix, table, col in indexes:
-        try:
-            log.debug("Creating index '%s' on column '%s' in table '%s'" % (ix, col, table))
-            t = Table(table, metadata, autoload=True)
-            if ix not in [ins_ix.get('name', None) for ins_ix in insp.get_indexes(table)]:
-                Index(ix, t.c[col]).create()
-            else:
-                pass  # Index already exists, don't recreate.
-        except Exception:
-            log.exception("Unable to create index '%s'.", ix)
+        add_index(ix, table, col, metadata)
 
 
 def downgrade(migrate_engine):

lib/galaxy/model/migrate/versions/util.py

@@ -1,6 +1,9 @@
 import logging
 
-from sqlalchemy import Table
+from sqlalchemy import (
+    Index,
+    Table
+)
 
 log = logging.getLogger(__name__)
 
@@ -68,7 +71,7 @@ def add_column(column, table, metadata=None, **kwds):
             assert metadata is not None
             table = Table(table, metadata, autoload=True)
         column.create(table, **kwds)
-        assert column is getattr(table.c, column.name)
+        assert column is table.c[column.name]
     except Exception:
         log.exception("Adding column '%s' to table '%s' failed.", column, table)
 
@@ -85,7 +88,7 @@ def alter_column(column_name, table, metadata=None, **kwds):
         if not isinstance(table, Table):
             assert metadata is not None
             table = Table(table, metadata, autoload=True)
-        column = getattr(table.c, column_name)
+        column = table.c[column_name]
         column.alter(**kwds)
     except Exception:
         log.exception("Modifying column '%s' of table '%s' failed.", column_name, table)
@@ -103,7 +106,28 @@ def drop_column(column_name, table, metadata=None):
         if not isinstance(table, Table):
             assert metadata is not None
             table = Table(table, metadata, autoload=True)
-        column = getattr(table.c, column_name)
+        column = table.c[column_name]
         column.drop()
     except Exception:
         log.exception("Dropping column '%s' from table '%s' failed.", column_name, table)
+
+
+def add_index(index_name, table, column_name, metadata=None):
+    """
+    :param table: Table to drop the column from
+    :type table: :class:`Table` or str
+
+    :param metadata: Needed only if ``table`` is a table name
+    :type metadata: :class:`Metadata`
+    """
+    try:
+        if not isinstance(table, Table):
+            assert metadata is not None
+            table = Table(table, metadata, autoload=True)
+        if index_name not in [ix.name for ix in table.indexes]:
+            index = Index(index_name, table.c[column_name])
+            index.create()
+        else:
+            log.debug("Index '%s' on column '%s' in table '%s' already exists.", index_name, column_name, table)
+    except Exception:
+        log.exception("Adding index '%s' on column '%s' to table '%s' failed.", index_name, column_name, table)