Merge pull request #334 from VariantEffect/release-2024.4.1

Release 2024.4.1

Author: bencap

.flake8

@@ -18,7 +18,7 @@ jobs:
     - run: pip install --upgrade pip
     - run: pip install poetry
     - run: poetry install --with dev --extras server
-    - run: poetry run pytest tests/ --show-capture=stdout
+    - run: poetry run pytest tests/ --show-capture=stdout --cov=src
 
   run-tests-3_10:
     runs-on: ubuntu-latest
@@ -32,7 +32,7 @@ jobs:
     - run: pip install --upgrade pip
     - run: pip install poetry
     - run: poetry install --with dev --extras server
-    - run: poetry run pytest tests/ --show-capture=stdout
+    - run: poetry run pytest tests/ --show-capture=stdout --cov=src
 
   run-tests-3_11:
     runs-on: ubuntu-latest
@@ -46,7 +46,7 @@ jobs:
     - run: pip install --upgrade pip
     - run: pip install poetry
     - run: poetry install --with dev --extras server
-    - run: poetry run pytest tests/ --show-capture=stdout
+    - run: poetry run pytest tests/ --show-capture=stdout --cov=src
 
   run-mypy-3_10:
     runs-on: ubuntu-latest
@@ -61,3 +61,17 @@ jobs:
     - run: pip install poetry
     - run: poetry install --with dev --extras server
     - run: poetry run mypy src/
+
+  run-ruff-lint:
+    runs-on: ubuntu-latest
+    name: Ruff linting on Python 3.10
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: "3.10"
+        cache: 'pip'
+    - run: pip install --upgrade pip
+    - run: pip install poetry
+    - run: poetry install --with dev --extras server
+    - run: poetry run ruff check

.github/workflows/run-tests-on-push.yml

@@ -1,8 +1,9 @@
 repos:
-  - repo: https://github.com/psf/black
-    rev: 23.3.0
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.6.8
     hooks:
-      - id: black
-        # Latest version of Python supported by the project
-        # See https://pre-commit.com/#top_level-default_language_version
-        language_version: python3.9
+      # Run the linter.
+      - id: ruff
+      # Run the formatter.
+      - id: ruff-format

.pre-commit-config.yaml

@@ -1,10 +1,11 @@
 # From https://improveandrepeat.com/2021/09/python-friday-87-handling-pre-existing-tables-with-alembic-and-sqlalchemy/
 # Based on https://github.com/talkpython/data-driven-web-apps-with-flask
 
-from alembic import op
 from sqlalchemy import engine_from_config
 from sqlalchemy.engine import reflection
 
+from alembic import op
+
 
 def table_does_not_exist(table, schema=None):
     config = op.get_context().config

alembic/alembic_helpers.py

@@ -1,8 +1,7 @@
-from logging.config import fileConfig
 import os
+from logging.config import fileConfig
 
-from sqlalchemy import engine_from_config
-from sqlalchemy import pool
+from sqlalchemy import engine_from_config, pool
 
 from alembic import context
 

alembic/env.py

@@ -0,0 +1,56 @@
+import sqlalchemy as sa
+from sqlalchemy.orm import Session, configure_mappers
+
+from mavedb.models import *
+
+from mavedb.models.score_set import ScoreSet
+from mavedb.models.variant import Variant
+from mavedb.models.target_gene import TargetGene
+from mavedb.models.target_accession import TargetAccession
+
+from mavedb.db.session import SessionLocal
+
+configure_mappers()
+
+
+def do_migration(db: Session):
+    accession_based_score_sets = db.execute(
+        sa.select(ScoreSet).join(TargetGene).where(TargetGene.accession_id.isnot(None))
+    ).scalars()
+
+    for score_set in accession_based_score_sets:
+        total_targets = len(
+            list(db.execute(sa.select(TargetGene).where(TargetGene.score_set_id == score_set.id)).scalars())
+        )
+
+        # Variants from score sets with multiple targets are already in the desired format.
+        if total_targets > 1:
+            continue
+
+        target_accession = db.execute(
+            sa.select(TargetAccession.accession).join(TargetGene).where(TargetGene.score_set_id == score_set.id)
+        ).scalar()
+        variants = db.execute(sa.select(Variant).where(Variant.score_set_id == score_set.id)).scalars()
+
+        if target_accession is None:
+            raise ValueError("target accession should never be None.")
+
+        for variant in variants:
+            if variant.hgvs_nt:
+                variant.hgvs_nt = f"{target_accession}:{variant.hgvs_nt}"
+            if variant.hgvs_pro:
+                variant.hgvs_pro = f"{target_accession}:{variant.hgvs_pro}"
+            if variant.hgvs_splice:
+                variant.hgvs_splice = f"{target_accession}:{variant.hgvs_splice}"
+
+            db.add(variant)
+
+
+if __name__ == "__main__":
+    db = SessionLocal()
+    db.current_user = None  # type: ignore
+
+    do_migration(db)
+
+    db.commit()
+    db.close()

alembic/manual_migrations/migrate_single_target_endogenous_edit_transcripts_to_be_fully_qualified.py

@@ -5,9 +5,8 @@
 Create Date: 2023-08-29 12:48:18.390567
 
 """
-from alembic import op
-import sqlalchemy as sa
 
+from alembic import op
 
 # revision identifiers, used by Alembic.
 revision = "194cfebabe32"

alembic/versions/194cfebabe32_rename_wild_type_sequence.py

@@ -0,0 +1,29 @@
+"""make index on contributors unique
+
+Revision ID: 1cee01c42909
+Revises: 76e1e55bc5c1
+Create Date: 2024-09-03 09:53:21.635751
+
+"""
+
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = "1cee01c42909"
+down_revision = "1d4933b4b6f7"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_index("ix_contributors_orcid_id", table_name="contributors")
+    op.create_index(op.f("ix_contributors_orcid_id"), "contributors", ["orcid_id"], unique=True)
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_index(op.f("ix_contributors_orcid_id"), table_name="contributors")
+    op.create_index("ix_contributors_orcid_id", "contributors", ["orcid_id"], unique=False)
+    # ### end Alembic commands ###

alembic/versions/1cee01c42909_make_index_on_contributors_unique.py

@@ -5,13 +5,10 @@
 Create Date: 2024-09-04 16:17:20.875937
 
 """
-from alembic import op
-import sqlalchemy as sa
-
 
 # revision identifiers, used by Alembic.
-revision = '1d4933b4b6f7'
-down_revision = ('76e1e55bc5c1', 'd7e6f8c3b9dc')
+revision = "1d4933b4b6f7"
+down_revision = ("76e1e55bc5c1", "d7e6f8c3b9dc")
 branch_labels = None
 depends_on = None
 

alembic/versions/1d4933b4b6f7_merge_76e1e55bc5c1_and_d7e6f8c3b9dc.py

@@ -5,20 +5,21 @@
 Create Date: 2023-06-01 14:51:04.700969
 
 """
-from typing import Optional
+
 import os
+from typing import Optional
 
 import eutils
-from eutils._internal.xmlfacades.pubmedarticleset import PubmedArticleSet
 import sqlalchemy as sa
 from eutils import EutilsNCBIError
-from mavedb.lib.exceptions import AmbiguousIdentifierError
+from eutils._internal.xmlfacades.pubmedarticleset import PubmedArticleSet
 from sqlalchemy.dialects.postgresql import JSONB
 from sqlalchemy.orm import Session
 
 from alembic import op
-from mavedb.lib.identifiers import ExternalPublication
+from mavedb.lib.exceptions import AmbiguousIdentifierError
 from mavedb.lib.external_publications import Rxiv
+from mavedb.lib.identifiers import ExternalPublication
 from mavedb.models.publication_identifier import PublicationIdentifier
 
 # revision identifiers, used by Alembic.