Merge pull request #334 from VariantEffect/release-2024.4.1

Release 2024.4.1

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

@@ -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

.pre-commit-config.yaml

@@ -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

alembic/alembic_helpers.py

@@ -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/env.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/manual_migrations/migrate_single_target_endogenous_edit_transcripts_to_be_fully_qualified.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/versions/194cfebabe32_rename_wild_type_sequence.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/1cee01c42909_make_index_on_contributors_unique.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/1d4933b4b6f7_merge_76e1e55bc5c1_and_d7e6f8c3b9dc.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/22e2d92d602e_add_publication_identifier_metadata_.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.

alembic/versions/2b6f40ea2fb6_add_score_range_column.py

@@ -0,0 +1,30 @@
+"""Add score range column
+
+Revision ID: 2b6f40ea2fb6
+Revises: 1d4933b4b6f7
+Create Date: 2024-09-09 12:25:33.180077
+
+"""
+
+import sqlalchemy as sa
+from sqlalchemy.dialects import postgresql
+
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = "2b6f40ea2fb6"
+down_revision = "1cee01c42909"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.add_column("scoresets", sa.Column("score_ranges", postgresql.JSONB(astext_type=sa.Text()), nullable=True))
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_column("scoresets", "score_ranges")
+    # ### end Alembic commands ###

alembic/versions/2c8d7e2bf2fe_consolidate_publication_identifier_dois.py

@@ -5,9 +5,10 @@
 Create Date: 2024-05-16 13:06:05.561411
 
 """
-from alembic import op
+
 import sqlalchemy as sa
 
+from alembic import op
 
 # revision identifiers, used by Alembic.
 revision = "2c8d7e2bf2fe"

alembic/versions/33e99d4b90cc_add_mapped_variants_table.py

@@ -5,33 +5,39 @@
 Create Date: 2023-05-15 17:24:07.847206
 
 """
-from alembic import op
+
 import sqlalchemy as sa
 from sqlalchemy.dialects import postgresql
 
+from alembic import op
+
 # revision identifiers, used by Alembic.
-revision = '33e99d4b90cc'
-down_revision = 'da9ba478647d'
+revision = "33e99d4b90cc"
+down_revision = "da9ba478647d"
 branch_labels = None
 depends_on = None
 
 
 def upgrade():
     # ### commands auto generated by Alembic - please adjust! ###
-    op.create_table('mapped_variants',
-    sa.Column('id', sa.Integer(), nullable=False),
-    sa.Column('pre_mapped', postgresql.JSONB(astext_type=sa.Text()), nullable=False),
-    sa.Column('post_mapped', postgresql.JSONB(astext_type=sa.Text()), nullable=False),
-    sa.Column('variant_id', sa.Integer(), nullable=False),
-    sa.ForeignKeyConstraint(['variant_id'], ['variants.id'], ),
-    sa.PrimaryKeyConstraint('id')
+    op.create_table(
+        "mapped_variants",
+        sa.Column("id", sa.Integer(), nullable=False),
+        sa.Column("pre_mapped", postgresql.JSONB(astext_type=sa.Text()), nullable=False),
+        sa.Column("post_mapped", postgresql.JSONB(astext_type=sa.Text()), nullable=False),
+        sa.Column("variant_id", sa.Integer(), nullable=False),
+        sa.ForeignKeyConstraint(
+            ["variant_id"],
+            ["variants.id"],
+        ),
+        sa.PrimaryKeyConstraint("id"),
     )
-    op.create_index(op.f('ix_mapped_variants_id'), 'mapped_variants', ['id'], unique=False)
+    op.create_index(op.f("ix_mapped_variants_id"), "mapped_variants", ["id"], unique=False)
     # ### end Alembic commands ###
 
 
 def downgrade():
     # ### commands auto generated by Alembic - please adjust! ###
-    op.drop_index(op.f('ix_mapped_variants_id'), table_name='mapped_variants')
-    op.drop_table('mapped_variants')
+    op.drop_index(op.f("ix_mapped_variants_id"), table_name="mapped_variants")
+    op.drop_table("mapped_variants")
     # ### end Alembic commands ###

alembic/versions/377bb8c30bde_roles_as_enums_access_keys_can_have_.py

@@ -5,9 +5,10 @@
 Create Date: 2024-04-18 09:19:04.008237
 
 """
-from alembic import op
+
 import sqlalchemy as sa
 
+from alembic import op
 
 # revision identifiers, used by Alembic.
 revision = "377bb8c30bde"

alembic/versions/44a45d616036_make_index_on_users_unique.py

@@ -5,8 +5,8 @@
 Create Date: 2024-08-16 13:25:14.980820
 
 """
+
 from alembic import op
-import sqlalchemy as sa
 
 # revision identifiers, used by Alembic.
 revision = "44a45d616036"

alembic/versions/44d5c568f64b_simplify_reference_genome_target_.py

@@ -5,9 +5,10 @@
 Create Date: 2023-08-24 15:20:01.208691
 
 """
-from alembic import op
+
 import sqlalchemy as sa
 
+from alembic import op
 
 # revision identifiers, used by Alembic.
 revision = "44d5c568f64b"

alembic/versions/5cad62af3705_rename_pubmed_identifiers_table_to_publication_identifiers.py

@@ -5,9 +5,8 @@
 Create Date: 2023-05-09 16:18:41.360541
 
 """
-from alembic import op
-import sqlalchemy as sa
 
+from alembic import op
 
 # revision identifiers, used by Alembic.
 revision = "5cad62af3705"

alembic/versions/60103ad1cb5b_add_target_sequence_label.py

@@ -5,9 +5,10 @@
 Create Date: 2023-08-29 16:04:44.620385
 
 """
-from alembic import op
+
 import sqlalchemy as sa
 
+from alembic import op
 
 # revision identifiers, used by Alembic.
 revision = "60103ad1cb5b"