Release 2025.2.0

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

@@ -6,9 +6,23 @@ env:
   LOG_CONFIG: test
 
 jobs:
+  run-tests-3_9-core-dependencies:
+    runs-on: ubuntu-latest
+    name: Pytest on Core Dependencies-- Python 3.9
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: "3.9"
+        cache: 'pip'
+    - run: pip install --upgrade pip
+    - run: pip install poetry
+    - run: poetry install --with dev
+    - run: poetry run pytest tests/
+
   run-tests-3_9:
-    runs-on: ubuntu-20.04
-    name: Pytest on Python 3.9 / Ubuntu 20.04
+    runs-on: ubuntu-latest
+    name: Pytest on Optional Dependencies-- Python 3.9
     steps:
     - uses: actions/checkout@v4
     - uses: actions/setup-python@v5
@@ -20,9 +34,23 @@ jobs:
     - run: poetry install --with dev --extras server
     - run: poetry run pytest tests/ --show-capture=stdout --cov=src
 
+  run-tests-3_10-core-dependencies:
+    runs-on: ubuntu-latest
+    name: Pytest on Core Dependencies-- 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
+    - run: poetry run pytest tests/
+
   run-tests-3_10:
     runs-on: ubuntu-latest
-    name: Pytest on Python 3.10
+    name: Pytest on Optional Dependencies-- Python 3.10
     steps:
     - uses: actions/checkout@v4
     - uses: actions/setup-python@v5
@@ -34,9 +62,23 @@ jobs:
     - run: poetry install --with dev --extras server
     - run: poetry run pytest tests/ --show-capture=stdout --cov=src
 
+  run-tests-3_11-core-dependencies:
+    runs-on: ubuntu-latest
+    name: Pytest on Core Dependencies-- Python 3.11
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: "3.11"
+        cache: 'pip'
+    - run: pip install --upgrade pip
+    - run: pip install poetry
+    - run: poetry install --with dev
+    - run: poetry run pytest tests/
+
   run-tests-3_11:
     runs-on: ubuntu-latest
-    name: Pytest on Python 3.11
+    name: Pytest on Optional Dependencies-- Python 3.11
     steps:
     - uses: actions/checkout@v4
     - uses: actions/setup-python@v5
@@ -50,7 +92,7 @@ jobs:
 
   run-mypy-3_10:
     runs-on: ubuntu-latest
-    name: MyPy checks on Python 3.10
+    name: MyPy on Full Codebase-- Python 3.10
     steps:
     - uses: actions/checkout@v4
     - uses: actions/setup-python@v5
@@ -64,7 +106,7 @@ jobs:
 
   run-ruff-lint:
     runs-on: ubuntu-latest
-    name: Ruff linting on Python 3.10
+    name: Ruff on Full Codebase-- Python 3.10
     steps:
     - uses: actions/checkout@v4
     - uses: actions/setup-python@v5

Dockerfile

@@ -2,7 +2,7 @@
 # python-base
 # Set up shared environment variables
 ################################
-FROM python:3.9 as python-base
+FROM python:3.9 AS python-base
 
     # Poetry
     # https://python-poetry.org/docs/configuration/#using-environment-variables
@@ -69,7 +69,7 @@ RUN samtools faidx GCF_000001405.39_GRCh38.p13_genomic.fna.gz
 # builder
 # Builds application dependencies and creates venv
 ################################
-FROM python-base as builder
+FROM python-base AS builder
 
 WORKDIR /code
 
@@ -90,7 +90,7 @@ COPY src/mavedb/server_main.py /code/main.py
 # worker
 # Worker image
 ################################
-FROM builder as worker
+FROM builder AS worker
 COPY --from=downloader /data /data
 
 # copy pre-built poetry + venv
@@ -103,7 +103,7 @@ CMD ["arq", "mavedb.worker.WorkerSettings"]
 # application
 # Application image
 ################################
-FROM builder as application
+FROM builder AS application
 COPY --from=downloader /data /data
 
 # copy pre-built poetry + venv

alembic/versions/34026092c7f8_clinvar_variant_table.py

@@ -0,0 +1,58 @@
+"""clinvar variant table
+
+Revision ID: 34026092c7f8
+Revises: e8a3b5d8f885
+Create Date: 2025-01-28 21:48:42.532346
+
+"""
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = "34026092c7f8"
+down_revision = "e8a3b5d8f885"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_table(
+        "clinvar_variants",
+        sa.Column("id", sa.Integer(), nullable=False),
+        sa.Column("allele_id", sa.Integer(), nullable=False),
+        sa.Column("gene_symbol", sa.String(), nullable=False),
+        sa.Column("clinical_significance", sa.String(), nullable=False),
+        sa.Column("clinical_review_status", sa.String(), nullable=False),
+        sa.Column("clinvar_db_version", sa.String(), nullable=False),
+        sa.Column("creation_date", sa.Date(), nullable=False),
+        sa.Column("modification_date", sa.Date(), nullable=False),
+        sa.PrimaryKeyConstraint("id"),
+    )
+    op.create_index(op.f("ix_clinvar_variants_allele_id"), "clinvar_variants", ["allele_id"], unique=False)
+    op.add_column("mapped_variants", sa.Column("clinvar_variant_id", sa.Integer(), nullable=True))
+    op.create_index(
+        op.f("ix_mapped_variants_clinvar_variant_id"), "mapped_variants", ["clinvar_variant_id"], unique=False
+    )
+    op.create_foreign_key(
+        "mapped_variant_clinvar_variant_id_foreign_key_constraint",
+        "mapped_variants",
+        "clinvar_variants",
+        ["clinvar_variant_id"],
+        ["id"],
+    )
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_constraint(
+        "mapped_variant_clinvar_variant_id_foreign_key_constraint", "mapped_variants", type_="foreignkey"
+    )
+    op.drop_index(op.f("ix_mapped_variants_clinvar_variant_id"), table_name="mapped_variants")
+    op.drop_column("mapped_variants", "clinvar_variant_id")
+    op.drop_index(op.f("ix_clinvar_variants_allele_id"), table_name="clinvar_variants")
+    op.drop_table("clinvar_variants")
+    # ### end Alembic commands ###

alembic/versions/695b73abe581_genericize_clinvar_variants_table.py

@@ -0,0 +1,101 @@
+"""genericize clinvar variants table
+
+Revision ID: 695b73abe581
+Revises: 34026092c7f8
+Create Date: 2025-02-18 11:54:15.243078
+
+"""
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = "695b73abe581"
+down_revision = "34026092c7f8"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    op.rename_table("clinvar_variants", "clinical_controls")
+    op.execute("ALTER SEQUENCE clinvar_variants_id_seq RENAME TO clinical_controls_id_seq")
+    op.execute("ALTER INDEX clinvar_variants_pkey RENAME TO clinical_controls_pkey")
+
+    op.alter_column("clinical_controls", "clinvar_db_version", nullable=False, new_column_name="db_version")
+    op.alter_column("clinical_controls", "allele_id", nullable=False, new_column_name="db_identifier")
+    op.add_column("clinical_controls", sa.Column("db_name", sa.String(), nullable=True))
+
+    op.create_index("ix_clinical_controls_gene_symbol", "clinical_controls", ["gene_symbol"])
+    op.create_index("ix_clinical_controls_db_name", "clinical_controls", ["db_name"])
+    op.create_index("ix_clinical_controls_db_identifier", "clinical_controls", ["db_identifier"])
+    op.create_index("ix_clinical_controls_db_version", "clinical_controls", ["db_version"])
+
+    op.create_table(
+        "mapped_variants_clinical_controls",
+        sa.Column("mapped_variant_id", sa.Integer(), nullable=False),
+        sa.Column("clinical_control_id", sa.Integer(), nullable=False),
+        sa.ForeignKeyConstraint(
+            ["mapped_variant_id"],
+            ["mapped_variants.id"],
+        ),
+        sa.ForeignKeyConstraint(
+            ["clinical_control_id"],
+            ["clinical_controls.id"],
+        ),
+        sa.PrimaryKeyConstraint("mapped_variant_id", "clinical_control_id"),
+    )
+
+    # Convert any existing ClinVar variants into clinical control variants. Since
+    # this table is being update from a clinvar specific table, we assume all existing
+    # controls are from ClinVar.
+    op.execute(
+        """
+        INSERT INTO mapped_variants_clinical_controls (
+            mapped_variant_id,
+            clinical_control_id
+        )
+        SELECT id, clinvar_variant_id
+        FROM mapped_variants
+        WHERE clinvar_variant_id IS NOT NULL
+        """
+    )
+
+    op.execute("UPDATE clinical_controls SET db_name='ClinVar'")
+    op.alter_column("clinical_controls", "db_name", nullable=False)
+
+    op.drop_index("ix_mapped_variants_clinvar_variant_id", "mapped_variants")
+    op.drop_column("mapped_variants", "clinvar_variant_id")
+
+
+def downgrade():
+    op.rename_table("clinical_controls", "clinvar_variants")
+    op.execute("ALTER SEQUENCE clinical_controls_id_seq RENAME TO clinvar_variants_id_seq")
+    op.execute("ALTER INDEX clinical_controls_pkey RENAME TO clinvar_variants_pkey")
+
+    op.drop_index("ix_clinical_controls_gene_symbol", "clinical_controls")
+    op.drop_index("ix_clinical_controls_db_name", "clinical_controls")
+    op.drop_index("ix_clinical_controls_db_identifier", "clinical_controls")
+    op.drop_index("ix_clinical_controls_db_version", "clinical_controls")
+
+    op.alter_column("clinvar_variants", "db_version", nullable=False, new_column_name="clinvar_db_version")
+    op.alter_column("clinvar_variants", "db_identifier", nullable=False, new_column_name="allele_id")
+    op.drop_column("clinvar_variants", "db_name")
+
+    op.add_column(
+        "mapped_variants",
+        sa.Column("clinvar_variant_id", sa.Integer(), sa.ForeignKey("clinvar_variants.id"), nullable=True),
+    )
+
+    # Downgrades a many-to-many relationship to a one to many. This will result in data loss.
+    op.execute(
+        """
+        UPDATE mapped_variants
+        SET clinvar_variant_id=mapped_variants_clinical_controls.clinical_control_id
+        FROM mapped_variants_clinical_controls
+        WHERE mapped_variants_clinical_controls.mapped_variant_id=mapped_variants.id
+        """
+    )
+
+    op.create_index("ix_mapped_variants_clinvar_variant_id", "mapped_variants", ["clinvar_variant_id"])
+    op.drop_table("mapped_variants_clinical_controls")

alembic/versions/d6e5a9fde3c9_move_clingen_allele_id_to_mapped_.py

@@ -0,0 +1,53 @@
+"""move clingen allele id to mapped variants table
+
+Revision ID: d6e5a9fde3c9
+Revises: 695b73abe581
+Create Date: 2025-02-19 10:51:07.319962
+
+"""
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = "d6e5a9fde3c9"
+down_revision = "695b73abe581"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_index("ix_variants_clingen_allele_id", table_name="variants")
+    op.add_column("mapped_variants", sa.Column("clingen_allele_id", sa.String(), nullable=True))
+    op.execute(
+        """
+        UPDATE mapped_variants
+        SET clingen_allele_id=variants.clingen_allele_id
+        FROM variants
+        WHERE variants.id=mapped_variants.variant_id
+        """
+    )
+    op.drop_column("variants", "clingen_allele_id")
+    op.create_index(
+        op.f("ix_mapped_variants_clingen_allele_id"), "mapped_variants", ["clingen_allele_id"], unique=False
+    )
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_index(op.f("ix_mapped_variants_clingen_allele_id"), table_name="mapped_variants")
+    op.add_column("variants", sa.Column("clingen_allele_id", sa.String(), nullable=True))
+    op.execute(
+        """
+        UPDATE variants
+        SET clingen_allele_id=mapped_variants.clingen_allele_id
+        FROM mapped_variants
+        WHERE variants.id=mapped_variants.variant_id
+        """
+    )
+    op.drop_column("mapped_variants", "clingen_allele_id")
+    op.create_index("ix_variants_clingen_allele_id", "variants", ["clingen_allele_id"], unique=False)
+    # ### end Alembic commands ###

alembic/versions/e8a3b5d8f885_add_clingen_allele_ids.py

@@ -0,0 +1,27 @@
+"""Add ClinGen allele IDs
+
+Revision ID: e8a3b5d8f885
+Revises: 4726e4dddde8
+Create Date: 2025-01-27 18:55:09.283855
+
+"""
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = "e8a3b5d8f885"
+down_revision = "4726e4dddde8"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    op.add_column("variants", sa.Column("clingen_allele_id", sa.String(), nullable=True))
+    op.create_index(op.f("ix_variants_clingen_allele_id"), "variants", ["clingen_allele_id"], unique=False)
+
+
+def downgrade():
+    op.drop_index(op.f("ix_variants_clingen_allele_id"), table_name="variants")
+    op.drop_column("variants", "clingen_allele_id")