Merge pull request #196 from mgcam/drop_json_props_column

Dropped column 'properties' from sub_product db table.

CHANGELOG.md

@@ -7,9 +7,11 @@ and this project adheres to [Semantic Versioning](http://semver.org/).
 
 ### Changed
 
-* The properties column of the LangQC sub_product database table
-  is made nullable. The correctness of data in this column is no
-  longer guaranteed, the column will be dropped in future.
+* The correctness of data in the 'properties' column of the
+  LangQC 'sub_product' database table is no longer guaranteed
+  because of the changes introduced in v. 5.0.0 of https://github.com/wtsi-npg/npg_id_generation
+  The column is made nullable and then dropped. The ORM for
+  the LangQC database is updated accordingly.
 
 * The production code no longer depends on the npg_id_generation
   package, therefore this dependency was moved to the dev section

alembic/README.md

@@ -19,13 +19,27 @@ Set `ALEMBIC_DB_URL` env. variable to the SQLAlchemy URL for the database you
 want to operate on. The format is `driver://user:pass@host:port/dbname`, where
 for MySQL and our software stack the driver is `mysql+pymysql`.
 
-Ensure `alembic` in on your PATH. Create a revision:
+Ensure `alembic` is on your PATH. Run all commands from the root of the
+repository, where the configuration for alembic `alembic.ini` resides.
 
-```alembic revision -m 'This is a revision description'```
+Create a revision:
 
-Define explicitly SQL statements that have to be executed both for the
-`upgrade` and `downgrade` function definitions in the generated script.
-Call execution of these statements, one at a time. Executing multiple
+```
+ # This example command generates alembic/versions/2.0.0_drop_json_properties_column.py
+ # python script, which contains an empty template for defining the migration.
+ alembic revision -m 'drop_json_properties_column' --rev-id 2.0.0 --head 3814003a709a
+```
+
+If `--rev_id` is not specified, `alembic` generates a random id for the migration,
+which does not present the problem immideately, but makes it difficult long term to
+understand the order of migrations and identify the latest migration. Set `--rev_id`
+to the next release version.
+
+The value of the `--head` argument is the version of the previous migration.
+
+Edit the newly generated script. Define explicitly SQL statements that have to be
+executed both for the `upgrade` and `downgrade` function definitions in the
+script. Call execution of these statements, one at a time. Executing multiple
 statements in one go does not work. See examples in the [versions](./versions)
 directory.
 

alembic/versions/2.0.0_drop_json_properties_column.py

@@ -0,0 +1,29 @@
+"""drop_json_properties_column
+
+Revision ID: 2.0.0
+Revises: 3814003a709a
+Create Date: 2024-02-20 10:51:40.326882
+
+"""
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = "2.0.0"
+down_revision = "3814003a709a"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    sql = """
+    ALTER TABLE sub_product DROP COLUMN properties
+    """
+    op.execute(sql)
+
+
+def downgrade() -> None:
+    sql = """
+    ALTER TABLE sub_product ADD COLUMN properties JSON DEFAULT NULL AFTER value_attr_three
+    """
+    op.execute(sql)
+    pass

lang_qc/db/qc_schema.py

@@ -180,7 +180,6 @@ class SubProduct(Base):
     value_attr_two = Column(String(20), nullable=False, index=True)
     id_attr_three = Column(INTEGER, nullable=True, index=True)
     value_attr_three = Column(String(20), nullable=True, index=True)
-    properties = Column(JSON, nullable=True)
     properties_digest = Column(CHAR(64), nullable=False, unique=True)
     tags = Column(String(255), index=True)