Use automated naming convention to generate indexes and constraints in database

lib/galaxy/model/__init__.py

@@ -69,6 +69,7 @@
     inspect,
     Integer,
     join,
+    MetaData,
     not_,
     Numeric,
     or_,
@@ -215,6 +216,20 @@ class _HasTable:
     _HasTable = object
 
 
+# Naming convention applied to database constraints and indexes.
+# All except "ix" are conventions used by PostgreSQL by default.
+# We keep the "ix" template consistent with historical Galaxy usage.
+#
+# NOTE: If editing, also update model.migrations.utils.DbObjectNames.
+NAMING_CONVENTION = {
+    "pk": "%(table_name)s_pkey",
+    "fk": "%(table_name)s_%(column_0_name)s_fkey",
+    "uq": "%(table_name)s_%(column_0_name)s_key",
+    "ck": "%(table_name)s_%(column_0_name)s_check",
+    "ix": "ix_%(table_name)s_%(column_0_name)s",
+}
+
+
 def get_uuid(uuid: Optional[Union[UUID, str]] = None) -> UUID:
     if isinstance(uuid, UUID):
         return uuid
@@ -225,8 +240,9 @@ def get_uuid(uuid: Optional[Union[UUID, str]] = None) -> UUID:
 
 class Base(_HasTable, metaclass=DeclarativeMeta):
     __abstract__ = True
+    metadata = MetaData(naming_convention=NAMING_CONVENTION)
+    mapper_registry.metadata = metadata
     registry = mapper_registry
-    metadata = mapper_registry.metadata
     __init__ = mapper_registry.constructor
 
     @classmethod

lib/galaxy/model/migrations/alembic/env.py

@@ -11,14 +11,15 @@
 from alembic.script.base import Script
 from sqlalchemy import create_engine
 
+from galaxy.model import Base
 from galaxy.model.migrations import (
     GXY,
     ModelId,
     TSI,
 )
 
 config = context.config
-target_metadata = None  # Not implemented: used for autogenerate, which we don't use here.
+target_metadata = Base.metadata
 log = logging.getLogger(__name__)
 
 

lib/galaxy/model/migrations/alembic/versions_gxy/3a2914d703ca_add_index_wf_r_s_s__workflow_invocation_.py

@@ -7,6 +7,7 @@
 """
 from galaxy.model.migrations.util import (
     create_index,
+    DbObjectNames,
     drop_index,
 )
 
@@ -17,12 +18,12 @@
 depends_on = None
 
 table_name = "workflow_request_step_states"
-columns = ["workflow_invocation_id"]
-index_name = "ix_workflow_request_step_states_workflow_invocation_id"
+column_name = "workflow_invocation_id"
+index_name = DbObjectNames.index(table_name, column_name)
 
 
 def upgrade():
-    create_index(index_name, table_name, columns)
+    create_index(index_name, table_name, [column_name])
 
 
 def downgrade():

lib/galaxy/model/migrations/alembic/versions_gxy/caa7742f7bca_add_index_wf_r_i_p__workflow_invocation_.py

@@ -7,6 +7,7 @@
 """
 from galaxy.model.migrations.util import (
     create_index,
+    DbObjectNames,
     drop_index,
 )
 
@@ -18,12 +19,12 @@
 
 
 table_name = "workflow_request_input_parameters"
-columns = ["workflow_invocation_id"]
-index_name = "ix_workflow_request_input_parameters_workflow_invocation_id"
+column_name = "workflow_invocation_id"
+index_name = DbObjectNames.index(table_name, column_name)
 
 
 def upgrade():
-    create_index(index_name, table_name, columns)
+    create_index(index_name, table_name, [column_name])
 
 
 def downgrade():

lib/galaxy/model/migrations/alembic/versions_gxy/d0583094c8cd_add_quota_source_labels.py

@@ -18,6 +18,7 @@
     create_index,
     create_table,
     create_unique_constraint,
+    DbObjectNames,
     drop_column,
     drop_constraint,
     drop_index,
@@ -31,6 +32,10 @@
 branch_labels = None
 depends_on = None
 
+old_index_name = DbObjectNames.index("default_quota_association", "type")
+new_index_name = DbObjectNames.index("quota", "quota_source_label")
+unique_constraint_name = "uqsu_unique_label_per_user"  # leave unchanged
+
 
 def upgrade():
     with transaction():
@@ -43,17 +48,15 @@ def upgrade():
             # user had an index on disk_usage - does that make any sense? -John
             Column("disk_usage", Numeric(15, 0)),
         )
-        create_unique_constraint(
-            "uqsu_unique_label_per_user", "user_quota_source_usage", ["user_id", "quota_source_label"]
-        )
-        drop_index("ix_default_quota_association_type", "default_quota_association")
-        create_index("ix_quota_quota_source_label", "quota", ["quota_source_label"])
+        create_unique_constraint(unique_constraint_name, "user_quota_source_usage", ["user_id", "quota_source_label"])
+        drop_index(old_index_name, "default_quota_association")
+        create_index(new_index_name, "quota", ["quota_source_label"])
 
 
 def downgrade():
     with transaction():
-        drop_index("ix_quota_quota_source_label", "quota")
-        create_index("ix_default_quota_association_type", "default_quota_association", ["type"], unique=True)
-        drop_constraint("uqsu_unique_label_per_user", "user_quota_source_usage")
+        drop_index(new_index_name, "quota")
+        create_index(old_index_name, "default_quota_association", ["type"], unique=True)
+        drop_constraint(unique_constraint_name, "user_quota_source_usage")
         drop_table("user_quota_source_usage")
         drop_column("quota", "quota_source_label")

lib/galaxy/model/migrations/alembic/versions_gxy/e0e3bb173ee6_add_column_deleted_to_api_keys.py

@@ -12,6 +12,7 @@
 
 from galaxy.model.migrations.util import (
     add_column,
+    DbObjectNames,
     drop_column,
     drop_index,
     transaction,
@@ -27,6 +28,7 @@
 # database object names used in this revision
 table_name = "api_keys"
 column_name = "deleted"
+index_name = DbObjectNames.index(table_name, column_name)
 
 
 def upgrade():
@@ -35,5 +37,5 @@ def upgrade():
 
 def downgrade():
     with transaction():
-        drop_index("ix_api_keys_deleted", table_name)
+        drop_index(index_name, table_name)
         drop_column(table_name, column_name)

lib/galaxy/model/migrations/util.py

@@ -450,3 +450,26 @@ def transaction():
         except OperationalError:
             op.execute("ROLLBACK")
             raise
+
+
+class DbObjectNames:
+    """
+    Helper methods for generating names for database constraints and indexes.
+    This format is based on the naming convention specified in the galaxy.model module.
+    """
+
+    @staticmethod
+    def foreign_key(table_name, column_name):
+        return f"{table_name}_{column_name}_fkey"
+
+    @staticmethod
+    def unique_constraint(table_name, column_name):
+        return f"{table_name}_{column_name}_key"
+
+    @staticmethod
+    def check_constraint(table_name, column_name):
+        return f"{table_name}_{column_name}_check"
+
+    @staticmethod
+    def index(table_name, column_name):
+        return f"ix_{table_name}_{column_name}"