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Merge pull request #455 from VariantEffect/release-2025.2.0
Release 2025.2.0
2 parents cbacd63 + d8f3b37 commit 0c1b391

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Lines changed: 11530 additions & 5082 deletions

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

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

‎Dockerfile‎

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

‎alembic/versions/34026092c7f8_clinvar_variant_table.py‎

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"""clinvar variant table
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Revision ID: 34026092c7f8
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Revises: e8a3b5d8f885
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Create Date: 2025-01-28 21:48:42.532346
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"""
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from alembic import op
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import sqlalchemy as sa
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# revision identifiers, used by Alembic.
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revision = "34026092c7f8"
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down_revision = "e8a3b5d8f885"
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branch_labels = None
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depends_on = None
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def upgrade():
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# ### commands auto generated by Alembic - please adjust! ###
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op.create_table(
23+
"clinvar_variants",
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sa.Column("id", sa.Integer(), nullable=False),
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sa.Column("allele_id", sa.Integer(), nullable=False),
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sa.Column("gene_symbol", sa.String(), nullable=False),
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sa.Column("clinical_significance", sa.String(), nullable=False),
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sa.Column("clinical_review_status", sa.String(), nullable=False),
29+
sa.Column("clinvar_db_version", sa.String(), nullable=False),
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sa.Column("creation_date", sa.Date(), nullable=False),
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sa.Column("modification_date", sa.Date(), nullable=False),
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sa.PrimaryKeyConstraint("id"),
33+
)
34+
op.create_index(op.f("ix_clinvar_variants_allele_id"), "clinvar_variants", ["allele_id"], unique=False)
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op.add_column("mapped_variants", sa.Column("clinvar_variant_id", sa.Integer(), nullable=True))
36+
op.create_index(
37+
op.f("ix_mapped_variants_clinvar_variant_id"), "mapped_variants", ["clinvar_variant_id"], unique=False
38+
)
39+
op.create_foreign_key(
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"mapped_variant_clinvar_variant_id_foreign_key_constraint",
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"mapped_variants",
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"clinvar_variants",
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["clinvar_variant_id"],
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["id"],
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)
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# ### end Alembic commands ###
47+
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49+
def downgrade():
50+
# ### commands auto generated by Alembic - please adjust! ###
51+
op.drop_constraint(
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"mapped_variant_clinvar_variant_id_foreign_key_constraint", "mapped_variants", type_="foreignkey"
53+
)
54+
op.drop_index(op.f("ix_mapped_variants_clinvar_variant_id"), table_name="mapped_variants")
55+
op.drop_column("mapped_variants", "clinvar_variant_id")
56+
op.drop_index(op.f("ix_clinvar_variants_allele_id"), table_name="clinvar_variants")
57+
op.drop_table("clinvar_variants")
58+
# ### end Alembic commands ###

‎alembic/versions/695b73abe581_genericize_clinvar_variants_table.py‎

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"""genericize clinvar variants table
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Revision ID: 695b73abe581
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Revises: 34026092c7f8
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Create Date: 2025-02-18 11:54:15.243078
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"""
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9+
from alembic import op
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import sqlalchemy as sa
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12+
13+
# revision identifiers, used by Alembic.
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revision = "695b73abe581"
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down_revision = "34026092c7f8"
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branch_labels = None
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depends_on = None
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def upgrade():
21+
op.rename_table("clinvar_variants", "clinical_controls")
22+
op.execute("ALTER SEQUENCE clinvar_variants_id_seq RENAME TO clinical_controls_id_seq")
23+
op.execute("ALTER INDEX clinvar_variants_pkey RENAME TO clinical_controls_pkey")
24+
25+
op.alter_column("clinical_controls", "clinvar_db_version", nullable=False, new_column_name="db_version")
26+
op.alter_column("clinical_controls", "allele_id", nullable=False, new_column_name="db_identifier")
27+
op.add_column("clinical_controls", sa.Column("db_name", sa.String(), nullable=True))
28+
29+
op.create_index("ix_clinical_controls_gene_symbol", "clinical_controls", ["gene_symbol"])
30+
op.create_index("ix_clinical_controls_db_name", "clinical_controls", ["db_name"])
31+
op.create_index("ix_clinical_controls_db_identifier", "clinical_controls", ["db_identifier"])
32+
op.create_index("ix_clinical_controls_db_version", "clinical_controls", ["db_version"])
33+
34+
op.create_table(
35+
"mapped_variants_clinical_controls",
36+
sa.Column("mapped_variant_id", sa.Integer(), nullable=False),
37+
sa.Column("clinical_control_id", sa.Integer(), nullable=False),
38+
sa.ForeignKeyConstraint(
39+
["mapped_variant_id"],
40+
["mapped_variants.id"],
41+
),
42+
sa.ForeignKeyConstraint(
43+
["clinical_control_id"],
44+
["clinical_controls.id"],
45+
),
46+
sa.PrimaryKeyConstraint("mapped_variant_id", "clinical_control_id"),
47+
)
48+
49+
# Convert any existing ClinVar variants into clinical control variants. Since
50+
# this table is being update from a clinvar specific table, we assume all existing
51+
# controls are from ClinVar.
52+
op.execute(
53+
"""
54+
INSERT INTO mapped_variants_clinical_controls (
55+
mapped_variant_id,
56+
clinical_control_id
57+
)
58+
SELECT id, clinvar_variant_id
59+
FROM mapped_variants
60+
WHERE clinvar_variant_id IS NOT NULL
61+
"""
62+
)
63+
64+
op.execute("UPDATE clinical_controls SET db_name='ClinVar'")
65+
op.alter_column("clinical_controls", "db_name", nullable=False)
66+
67+
op.drop_index("ix_mapped_variants_clinvar_variant_id", "mapped_variants")
68+
op.drop_column("mapped_variants", "clinvar_variant_id")
69+
70+
71+
def downgrade():
72+
op.rename_table("clinical_controls", "clinvar_variants")
73+
op.execute("ALTER SEQUENCE clinical_controls_id_seq RENAME TO clinvar_variants_id_seq")
74+
op.execute("ALTER INDEX clinical_controls_pkey RENAME TO clinvar_variants_pkey")
75+
76+
op.drop_index("ix_clinical_controls_gene_symbol", "clinical_controls")
77+
op.drop_index("ix_clinical_controls_db_name", "clinical_controls")
78+
op.drop_index("ix_clinical_controls_db_identifier", "clinical_controls")
79+
op.drop_index("ix_clinical_controls_db_version", "clinical_controls")
80+
81+
op.alter_column("clinvar_variants", "db_version", nullable=False, new_column_name="clinvar_db_version")
82+
op.alter_column("clinvar_variants", "db_identifier", nullable=False, new_column_name="allele_id")
83+
op.drop_column("clinvar_variants", "db_name")
84+
85+
op.add_column(
86+
"mapped_variants",
87+
sa.Column("clinvar_variant_id", sa.Integer(), sa.ForeignKey("clinvar_variants.id"), nullable=True),
88+
)
89+
90+
# Downgrades a many-to-many relationship to a one to many. This will result in data loss.
91+
op.execute(
92+
"""
93+
UPDATE mapped_variants
94+
SET clinvar_variant_id=mapped_variants_clinical_controls.clinical_control_id
95+
FROM mapped_variants_clinical_controls
96+
WHERE mapped_variants_clinical_controls.mapped_variant_id=mapped_variants.id
97+
"""
98+
)
99+
100+
op.create_index("ix_mapped_variants_clinvar_variant_id", "mapped_variants", ["clinvar_variant_id"])
101+
op.drop_table("mapped_variants_clinical_controls")

‎alembic/versions/d6e5a9fde3c9_move_clingen_allele_id_to_mapped_.py‎

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"""move clingen allele id to mapped variants table
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Revision ID: d6e5a9fde3c9
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Revises: 695b73abe581
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Create Date: 2025-02-19 10:51:07.319962
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"""
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from alembic import op
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import sqlalchemy as sa
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12+
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# revision identifiers, used by Alembic.
14+
revision = "d6e5a9fde3c9"
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down_revision = "695b73abe581"
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branch_labels = None
17+
depends_on = None
18+
19+
20+
def upgrade():
21+
# ### commands auto generated by Alembic - please adjust! ###
22+
op.drop_index("ix_variants_clingen_allele_id", table_name="variants")
23+
op.add_column("mapped_variants", sa.Column("clingen_allele_id", sa.String(), nullable=True))
24+
op.execute(
25+
"""
26+
UPDATE mapped_variants
27+
SET clingen_allele_id=variants.clingen_allele_id
28+
FROM variants
29+
WHERE variants.id=mapped_variants.variant_id
30+
"""
31+
)
32+
op.drop_column("variants", "clingen_allele_id")
33+
op.create_index(
34+
op.f("ix_mapped_variants_clingen_allele_id"), "mapped_variants", ["clingen_allele_id"], unique=False
35+
)
36+
# ### end Alembic commands ###
37+
38+
39+
def downgrade():
40+
# ### commands auto generated by Alembic - please adjust! ###
41+
op.drop_index(op.f("ix_mapped_variants_clingen_allele_id"), table_name="mapped_variants")
42+
op.add_column("variants", sa.Column("clingen_allele_id", sa.String(), nullable=True))
43+
op.execute(
44+
"""
45+
UPDATE variants
46+
SET clingen_allele_id=mapped_variants.clingen_allele_id
47+
FROM mapped_variants
48+
WHERE variants.id=mapped_variants.variant_id
49+
"""
50+
)
51+
op.drop_column("mapped_variants", "clingen_allele_id")
52+
op.create_index("ix_variants_clingen_allele_id", "variants", ["clingen_allele_id"], unique=False)
53+
# ### end Alembic commands ###

‎alembic/versions/e8a3b5d8f885_add_clingen_allele_ids.py‎

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"""Add ClinGen allele IDs
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Revision ID: e8a3b5d8f885
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Revises: 4726e4dddde8
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Create Date: 2025-01-27 18:55:09.283855
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"""
8+
9+
from alembic import op
10+
import sqlalchemy as sa
11+
12+
13+
# revision identifiers, used by Alembic.
14+
revision = "e8a3b5d8f885"
15+
down_revision = "4726e4dddde8"
16+
branch_labels = None
17+
depends_on = None
18+
19+
20+
def upgrade():
21+
op.add_column("variants", sa.Column("clingen_allele_id", sa.String(), nullable=True))
22+
op.create_index(op.f("ix_variants_clingen_allele_id"), "variants", ["clingen_allele_id"], unique=False)
23+
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25+
def downgrade():
26+
op.drop_index(op.f("ix_variants_clingen_allele_id"), table_name="variants")
27+
op.drop_column("variants", "clingen_allele_id")

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