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Apply transaction context manager to select revisions

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Wrap multiple sql statements in a transaction to ensure per-revision
transactional control.
This commit is contained in:
John Davis
2023-04-26 08:53:35 -04:00
parent bec3b1f5c8
commit c2ed5685c1
5 changed files with 53 additions and 40 deletions
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lib/galaxy/model/migrations/alembic/versions_gxy/6a67bf27e6a6_deferred_data_tables.py
+7 -4
View File
@@ -13,6 +13,7 @@ from sqlalchemy import (
from galaxy.model.migrations.util import (
add_column,
drop_column,
transaction,
)
# revision identifiers, used by Alembic.
@@ -23,10 +24,12 @@ depends_on = None
def upgrade():
add_column("history_dataset_association", Column("metadata_deferred", Boolean(), default=False))
add_column("library_dataset_dataset_association", Column("metadata_deferred", Boolean(), default=False))
with transaction():
add_column("history_dataset_association", Column("metadata_deferred", Boolean(), default=False))
add_column("library_dataset_dataset_association", Column("metadata_deferred", Boolean(), default=False))
def downgrade():
drop_column("history_dataset_association", "metadata_deferred")
drop_column("library_dataset_dataset_association", "metadata_deferred")
with transaction():
drop_column("history_dataset_association", "metadata_deferred")
drop_column("library_dataset_dataset_association", "metadata_deferred")
lib/galaxy/model/migrations/alembic/versions_gxy/9540a051226e_preferred_object_store_ids.py
+12 -9
View File
@@ -14,6 +14,7 @@ from galaxy.model.custom_types import JSONType
from galaxy.model.migrations.util import (
add_column,
drop_column,
transaction,
)
# revision identifiers, used by Alembic.
@@ -24,15 +25,17 @@ depends_on = None
def upgrade():
preferred_object_store_type = String(255)
add_column("galaxy_user", Column("preferred_object_store_id", preferred_object_store_type, default=None))
add_column("history", Column("preferred_object_store_id", preferred_object_store_type, default=None))
add_column("job", Column("preferred_object_store_id", preferred_object_store_type, default=None))
add_column("job", Column("object_store_id_overrides", JSONType))
with transaction():
preferred_object_store_type = String(255)
add_column("galaxy_user", Column("preferred_object_store_id", preferred_object_store_type, default=None))
add_column("history", Column("preferred_object_store_id", preferred_object_store_type, default=None))
add_column("job", Column("preferred_object_store_id", preferred_object_store_type, default=None))
add_column("job", Column("object_store_id_overrides", JSONType))
def downgrade():
drop_column("galaxy_user", "preferred_object_store_id")
drop_column("history", "preferred_object_store_id")
drop_column("job", "preferred_object_store_id")
drop_column("job", "object_store_id_overrides")
with transaction():
drop_column("galaxy_user", "preferred_object_store_id")
drop_column("history", "preferred_object_store_id")
drop_column("job", "preferred_object_store_id")
drop_column("job", "object_store_id_overrides")
lib/galaxy/model/migrations/alembic/versions_gxy/c39f1de47a04_add_skipped_state_to_collection_job_.py
+8 -8
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@@ -7,6 +7,8 @@ Create Date: 2023-01-16 11:53:59.783836
"""
from alembic import op
from galaxy.model.migrations.util import transaction
# revision identifiers, used by Alembic.
revision = "c39f1de47a04"
down_revision = "3100452fa030"
@@ -88,14 +90,12 @@ GROUP BY jobstates.hdca_id
def upgrade():
op.execute("BEGIN")
op.execute(f"DROP VIEW IF EXISTS {view_name}")
op.execute(f"CREATE VIEW {view_name} AS {new_aggregate_query}")
op.execute("END")
with transaction():
op.execute(f"DROP VIEW IF EXISTS {view_name}")
op.execute(f"CREATE VIEW {view_name} AS {new_aggregate_query}")
def downgrade():
op.execute("BEGIN")
op.execute(f"DROP VIEW IF EXISTS {view_name}")
op.execute(f"CREATE VIEW {view_name} AS {previous_aggregate_query}")
op.execute("END")
with transaction():
op.execute(f"DROP VIEW IF EXISTS {view_name}")
op.execute(f"CREATE VIEW {view_name} AS {previous_aggregate_query}")
lib/galaxy/model/migrations/alembic/versions_gxy/d0583094c8cd_add_quota_source_labels.py
+22 -17
View File
@@ -22,6 +22,7 @@ from galaxy.model.migrations.util import (
drop_index,
drop_table,
drop_unique_constraint,
transaction,
)
# revision identifiers, used by Alembic.
@@ -32,23 +33,27 @@ depends_on = None
def upgrade():
add_column("quota", Column("quota_source_label", String(32), default=None))
create_table(
"user_quota_source_usage",
Column("id", Integer, primary_key=True),
Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
Column("quota_source_label", String(32), index=True),
# user had an index on disk_usage - does that make any sense? -John
Column("disk_usage", Numeric(15, 0)),
)
add_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"])
with transaction():
add_column("quota", Column("quota_source_label", String(32), default=None))
create_table(
"user_quota_source_usage",
Column("id", Integer, primary_key=True),
Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
Column("quota_source_label", String(32), index=True),
# user had an index on disk_usage - does that make any sense? -John
Column("disk_usage", Numeric(15, 0)),
)
add_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"])
def downgrade():
drop_index("ix_quota_quota_source_label", "quota")
create_index("ix_default_quota_association_type", "default_quota_association", ["type"], unique=True)
drop_unique_constraint("uqsu_unique_label_per_user", "user_quota_source_usage")
drop_table("user_quota_source_usage")
drop_column("quota", "quota_source_label")
with transaction():
drop_index("ix_quota_quota_source_label", "quota")
create_index("ix_default_quota_association_type", "default_quota_association", ["type"], unique=True)
drop_unique_constraint("uqsu_unique_label_per_user", "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
+4 -2
View File
@@ -14,6 +14,7 @@ from galaxy.model.migrations.util import (
add_column,
drop_column,
drop_index,
transaction,
)
# revision identifiers, used by Alembic.
@@ -33,5 +34,6 @@ def upgrade():
def downgrade():
drop_index("ix_api_keys_deleted", table_name)
drop_column(table_name, column_name)
with transaction():
drop_index("ix_api_keys_deleted", table_name)
drop_column(table_name, column_name)