From 327adb62d60c496f148ccbfdca12f67d81ae33f7 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Wed, 7 Oct 2020 11:53:33 -0400
Subject: [PATCH] Add more missing indexes

---
 lib/galaxy/model/mapping.py                   | 10 ++--
 .../versions/0170_add_more_missing_indexes.py | 60 +++++++++++++++++++
 2 files changed, 65 insertions(+), 5 deletions(-)
 create mode 100644 lib/galaxy/model/migrate/versions/0170_add_more_missing_indexes.py

diff --git a/lib/galaxy/model/mapping.py b/lib/galaxy/model/mapping.py
index 11e84951eca..7d68dd3a8d4 100644
--- a/lib/galaxy/model/mapping.py
+++ b/lib/galaxy/model/mapping.py
@@ -1125,18 +1125,18 @@ model.WorkflowInvocationOutputDatasetAssociation.table = Table(
     "workflow_invocation_output_dataset_association", metadata,
     Column("id", Integer, primary_key=True),
     Column("workflow_invocation_id", Integer, ForeignKey("workflow_invocation.id"), index=True),
-    Column("workflow_step_id", Integer, ForeignKey("workflow_step.id")),
+    Column("workflow_step_id", Integer, ForeignKey("workflow_step.id"), index=True),
     Column("dataset_id", Integer, ForeignKey("history_dataset_association.id"), index=True),
-    Column("workflow_output_id", Integer, ForeignKey("workflow_output.id")),
+    Column("workflow_output_id", Integer, ForeignKey("workflow_output.id"), index=True),
 )
 
 model.WorkflowInvocationOutputDatasetCollectionAssociation.table = Table(
     "workflow_invocation_output_dataset_collection_association", metadata,
     Column("id", Integer, primary_key=True),
     Column("workflow_invocation_id", Integer, ForeignKey("workflow_invocation.id", name='fk_wiodca_wii'), index=True),
-    Column("workflow_step_id", Integer, ForeignKey("workflow_step.id", name='fk_wiodca_wsi')),
+    Column("workflow_step_id", Integer, ForeignKey("workflow_step.id", name='fk_wiodca_wsi'), index=True),
     Column("dataset_collection_id", Integer, ForeignKey("history_dataset_collection_association.id", name='fk_wiodca_dci'), index=True),
-    Column("workflow_output_id", Integer, ForeignKey("workflow_output.id", name='fk_wiodca_woi')),
+    Column("workflow_output_id", Integer, ForeignKey("workflow_output.id", name='fk_wiodca_woi'), index=True),
 )
 
 model.WorkflowInvocationOutputValue.table = Table(
@@ -1160,7 +1160,7 @@ model.WorkflowInvocationStepOutputDatasetCollectionAssociation.table = Table(
     "workflow_invocation_step_output_dataset_collection_association", metadata,
     Column("id", Integer, primary_key=True),
     Column("workflow_invocation_step_id", Integer, ForeignKey("workflow_invocation_step.id", name='fk_wisodca_wisi'), index=True),
-    Column("workflow_step_id", Integer, ForeignKey("workflow_step.id", name='fk_wisodca_wsi')),
+    Column("workflow_step_id", Integer, ForeignKey("workflow_step.id", name='fk_wisodca_wsi'), index=True),
     Column("dataset_collection_id", Integer, ForeignKey("history_dataset_collection_association.id", name='fk_wisodca_dci'), index=True),
     Column("output_name", String(255), nullable=True),
 )
diff --git a/lib/galaxy/model/migrate/versions/0170_add_more_missing_indexes.py b/lib/galaxy/model/migrate/versions/0170_add_more_missing_indexes.py
new file mode 100644
index 00000000000..d5f5fa54703
--- /dev/null
+++ b/lib/galaxy/model/migrate/versions/0170_add_more_missing_indexes.py
@@ -0,0 +1,60 @@
+"""
+Migration script to create missing indexes.  Adding new columns to existing tables via SQLAlchemy does not create the index, even if the column definition includes index=True.
+"""
+
+import logging
+
+from sqlalchemy import MetaData
+
+from galaxy.model.migrate.versions.util import (
+    add_index,
+    drop_index
+)
+
+log = logging.getLogger(__name__)
+metadata = MetaData()
+
+indexes = [
+    [
+        "ix_workflow_invocation_output_dataset_association_workflow_output_id",
+        "workflow_invocation_output_dataset_association",
+        "workflow_output_id"
+    ],
+    [
+        "ix_workflow_invocation_output_dataset_association_workflow_step_id",
+        "workflow_invocation_output_dataset_association",
+        "workflow_step_id"
+    ],
+    [
+        "ix_workflow_invocation_output_dataset_collection_association_workflow_output_id",
+        "workflow_invocation_output_dataset_collection_association",
+        "workflow_output_id"
+    ],
+    [
+        "ix_workflow_invocation_output_dataset_collection_association_workflow_step_id",
+        "workflow_invocation_output_dataset_collection_association",
+        "workflow_step_id"
+    ],
+    [
+        "ix_workflow_invocation_step_output_dataset_collection_association_workflow_step_id",
+        "workflow_invocation_step_output_dataset_collection_association",
+        "workflow_step_id"
+    ],
+]
+
+
+def upgrade(migrate_engine):
+    print(__doc__)
+    metadata.bind = migrate_engine
+    metadata.reflect()
+
+    for ix, table, col in indexes:
+        add_index(ix, table, col, metadata)
+
+
+def downgrade(migrate_engine):
+    metadata.bind = migrate_engine
+    metadata.reflect()
+
+    for ix, table, col in indexes:
+        drop_index(ix, table, col, metadata)