Merge pull request #198 from wtsi-npg/devel

pull from devel to master to create release 2.0.0

CHANGELOG.md

@@ -5,6 +5,24 @@ and this project adheres to [Semantic Versioning](http://semver.org/).
 
 ## [Unreleased]
 
+### Changed
+
+* 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
+  of pyproject.toml. The package is still used by tests and test
+  fixtures.
+
+* Upgraded some of dev dependencies: npg_id_generation to 5.0.1,
+  alembic to 1.13.0 or later.
+
+* Regenerated poetry.lock file.
+
 ## [1.5.1] - 2024-01-25
 
 ### Changed

alembic/README.md

@@ -5,7 +5,7 @@
 Planned changes should be applied in [lang_qc/db/qc_schema.py](../lang_qc/db/qc_schema.py).
 We recommend doing this manually.
 
-Changes to unit test,test fixtures and the source code should be applied as
+Changes to unit tests, test fixtures and the source code should be applied as
 appropriate. 
 
 ## Creating migrations for the QC database schema
@@ -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

alembic/versions/3814003a709a_make_column_properties_nullable.py

@@ -0,0 +1,28 @@
+"""Make column properties nullable
+
+Revision ID: 3814003a709a
+Revises: 36952df5b8ba
+Create Date: 2024-02-02 14:30:20.079955
+
+"""
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = "3814003a709a"
+down_revision = "36952df5b8ba"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    sql = """
+    ALTER TABLE sub_product MODIFY properties JSON DEFAULT NULL
+    """
+    op.execute(sql)
+
+
+def downgrade() -> None:
+    sql = """
+    ALTER TABLE sub_product MODIFY properties JSON NOT NULL
+    """
+    op.execute(sql)

frontend/package.json

@@ -1,6 +1,6 @@
 {
   "name": "npg-longue-vue",
-  "version": "1.5.1",
+  "version": "2.0.0",
   "description": "UI for LangQC",
   "author": "Kieron Taylor <[email protected]>",
   "license": "GPL-3.0-or-later",

lang_qc/__init__.py

@@ -1 +1 @@
-__version__ = "1.5.1"
+__version__ = "2.0.0"

lang_qc/db/helper/well.py

@@ -24,7 +24,6 @@
 for interaction with the LangQC database.
 """
 
-from npg_id_generation.pac_bio import PacBioEntity
 from sqlalchemy import select
 from sqlalchemy.orm import Session
 
@@ -84,9 +83,6 @@ def _create_well(
     product_attr_pn = session.execute(
         select(SubProductAttr).where(SubProductAttr.attr_name == "plate_number")
     ).scalar_one()
-    product_json = PacBioEntity(
-        run_name=run_name, well_label=well_label, plate_number=plate_number
-    ).model_dump_json()
 
     # TODO: in future for composite products we have to check whether any of
     # the `sub_product` table entries we are linking to already exist.
@@ -103,7 +99,6 @@ def _create_well(
                 value_attr_three=str(plate_number)
                 if plate_number is not None
                 else None,
-                properties=product_json,
                 properties_digest=id_product,
             )
         ],

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=False)
     properties_digest = Column(CHAR(64), nullable=False, unique=True)
     tags = Column(String(255), index=True)