Merge pull request #489 from VariantEffect/release-2025.3.0

Release 2025.3.0

Author: bencap

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

@@ -6,61 +6,37 @@ env:
   LOG_CONFIG: test
 
 jobs:
-  run-tests-3_9-core-dependencies:
+  run-mypy-3_11:
     runs-on: ubuntu-latest
-    name: Pytest on Core Dependencies-- Python 3.9
+    name: MyPy checks on Python 3.11
     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-latest
-    name: Pytest on Optional Dependencies-- Python 3.9
-    steps:
-    - uses: actions/checkout@v4
-    - uses: actions/setup-python@v5
-      with:
-        python-version: "3.9"
+        python-version: "3.11"
         cache: 'pip'
+    - run: sudo apt-get update
+    - run: sudo apt-get install -y tabix
     - run: pip install --upgrade pip
     - run: pip install poetry
     - 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: poetry run mypy src/
 
-  run-tests-3_10:
+  run-ruff-lint:
     runs-on: ubuntu-latest
-    name: Pytest on Optional Dependencies-- Python 3.10
+    name: Ruff linting on Python 3.11
     steps:
     - uses: actions/checkout@v4
     - uses: actions/setup-python@v5
       with:
-        python-version: "3.10"
+        python-version: "3.11"
         cache: 'pip'
+    - run: sudo apt-get update
+    - run: sudo apt-get install -y tabix
     - run: pip install --upgrade pip
     - run: pip install poetry
     - run: poetry install --with dev --extras server
-    - run: poetry run pytest tests/ --show-capture=stdout --cov=src
+    - run: poetry run ruff check
 
   run-tests-3_11-core-dependencies:
     runs-on: ubuntu-latest
@@ -85,35 +61,39 @@ jobs:
       with:
         python-version: "3.11"
         cache: 'pip'
+    - run: sudo apt-get update
+    - run: sudo apt-get install -y tabix
     - run: pip install --upgrade pip
     - run: pip install poetry
     - run: poetry install --with dev --extras server
     - run: poetry run pytest tests/ --show-capture=stdout --cov=src
 
-  run-mypy-3_10:
+  run-tests-3_12-core-dependencies:
     runs-on: ubuntu-latest
-    name: MyPy on Full Codebase-- Python 3.10
+    name: Pytest on Core Dependencies-- Python 3.12
     steps:
     - uses: actions/checkout@v4
     - uses: actions/setup-python@v5
       with:
-        python-version: "3.10"
+        python-version: "3.12"
         cache: 'pip'
     - run: pip install --upgrade pip
     - run: pip install poetry
-    - run: poetry install --with dev --extras server
-    - run: poetry run mypy src/
+    - run: poetry install --with dev
+    - run: poetry run pytest tests/
 
-  run-ruff-lint:
+  run-tests-3_12:
     runs-on: ubuntu-latest
-    name: Ruff on Full Codebase-- Python 3.10
+    name: Pytest on Optional Dependencies-- Python 3.12
     steps:
     - uses: actions/checkout@v4
     - uses: actions/setup-python@v5
       with:
-        python-version: "3.10"
+        python-version: "3.12"
         cache: 'pip'
+    - run: sudo apt-get update
+    - run: sudo apt-get install -y tabix
     - run: pip install --upgrade pip
     - run: pip install poetry
     - run: poetry install --with dev --extras server
-    - run: poetry run ruff check
+    - run: poetry run pytest tests/ --show-capture=stdout --cov=src

Dockerfile

@@ -2,7 +2,7 @@
 # python-base
 # Set up shared environment variables
 ################################
-FROM python:3.9 AS python-base
+FROM python:3.11 AS python-base
 
     # Poetry
     # https://python-poetry.org/docs/configuration/#using-environment-variables

README.md

@@ -24,7 +24,7 @@ Or add `mavedb` to your Python project's dependencies.
 
 ### Prerequisites
 
-- Python 3.9 or later
+- Python 3.11 or later
 - PIP
 - [Poetry](https://python-poetry.org/) for building and publishing distributions. For details on installing poetry, consult its [documentation](https://python-poetry.org/docs/#installation).
 

alembic/manual_migrations/migrate_consolidated_score_ranges_and_calibrations.py

@@ -0,0 +1,125 @@
+"""
+To be run as part of revision af87c9953d2d
+"""
+
+import sqlalchemy as sa
+from sqlalchemy.orm import Session, configure_mappers
+
+from mavedb.models import *
+from sqlalchemy.orm import Session
+
+from mavedb.models.score_set import ScoreSet
+from mavedb.view_models.score_range import ScoreSetRangesCreate, InvestigatorScoreRangesCreate, PillarProjectScoreRangesCreate, PillarProjectScoreRangeCreate
+
+
+from mavedb.db.session import SessionLocal
+
+configure_mappers()
+
+
+evidence_strength_to_label = {
+    -8: "BS3_VERY_STRONG",
+    -4: "BS3_STRONG",
+    -3: "BS3_MODERATE+",
+    -2: "BS3_MODERATE",
+    -1: "BS3_SUPPORTING",
+    1: "PS3_SUPPORTING",
+    2: "PS3_MODERATE",
+    3: "PS3_MODERATE+",
+    4: "PS3_STRONG",
+    8: "PS3_VERY_STRONG",
+}
+
+
+def do_migration(db: Session):
+    score_sets_with_ranges_or_calibrations = db.scalars(sa.select(ScoreSet).where(ScoreSet.score_ranges.isnot(None) | ScoreSet.score_calibrations.isnot(None))).all()
+
+    for score_set in score_sets_with_ranges_or_calibrations:
+        if score_set.score_ranges is not None:
+            investigator_ranges = InvestigatorScoreRangesCreate(
+                **score_set.score_ranges
+            )
+            for score_range in investigator_ranges.ranges:
+                score_range.inclusive_lower_bound = False if score_range.range[0] is None else True
+                score_range.inclusive_upper_bound = False
+
+        else:
+            investigator_ranges = None
+
+        if score_set.score_calibrations is not None:
+            thresholds = score_set.score_calibrations.get("pillar_project", {}).get("thresholds", [])
+            evidence_strengths = score_set.score_calibrations.get("pillar_project", {}).get("evidence_strengths", [])
+            positive_likelihood_ratios = score_set.score_calibrations.get("pillar_project", {}).get("positive_likelihood_ratios", [])
+            prior_probability_pathogenicity = score_set.score_calibrations.get("pillar_project", {}).get("prior_probability_pathogenicity", None)
+            parameter_sets = score_set.score_calibrations.get("pillar_project", {}).get("parameter_sets", [])
+
+            ranges = []
+            boundary_direction = -1  # Start with a negative sign to indicate the first range has the lower boundary appearing prior to the threshold
+            for idx, vals in enumerate(zip(thresholds, evidence_strengths, positive_likelihood_ratios)):
+                threshold, evidence_strength, positive_likelihood_ratio = vals
+
+                if idx == 0:
+                    calculated_range = (None, threshold)
+                    ranges.append(PillarProjectScoreRangeCreate(
+                        range=(None, threshold),
+                        classification="normal" if evidence_strength < 0 else "abnormal",
+                        label=str(evidence_strength),
+                        evidence_strength=evidence_strength,
+                        positive_likelihood_ratio=positive_likelihood_ratio,
+                        inclusive_lower_bound=False,
+                        inclusive_upper_bound=False,
+                    ))
+                elif idx == len(thresholds) - 1:
+                    calculated_range = (threshold, None)
+                    ranges.append(PillarProjectScoreRangeCreate(
+                        range=(threshold, None),
+                        classification="normal" if evidence_strength < 0 else "abnormal",
+                        evidence_strength=evidence_strength,
+                        label=str(evidence_strength),
+                        positive_likelihood_ratio=positive_likelihood_ratio,
+                        inclusive_lower_bound=True,
+                        inclusive_upper_bound=False,
+                    ))
+                else:
+                    if boundary_direction < 0:
+                        calculated_range = (thresholds[idx - 1], threshold)
+                    else:
+                        calculated_range = (threshold, thresholds[idx + 1])
+
+                    ranges.append(PillarProjectScoreRangeCreate(
+                        range=calculated_range,
+                        classification="normal" if evidence_strength < 0 else "abnormal",
+                        label=str(evidence_strength),
+                        evidence_strength=evidence_strength,
+                        positive_likelihood_ratio=positive_likelihood_ratio,
+                        inclusive_lower_bound=True,
+                        inclusive_upper_bound=False,
+                    ))
+
+                # Set boundary_direction if the sign of evidence_strength flips compared to the next one
+                if idx != len(evidence_strengths) - 1 and (evidence_strengths[idx + 1] * evidence_strength < 0):
+                    boundary_direction = -boundary_direction
+
+                pillar_project_ranges = PillarProjectScoreRangesCreate(
+                    prior_probability_pathogenicity=prior_probability_pathogenicity,
+                    parameter_sets=parameter_sets,
+                    ranges=ranges,
+                )
+        else:
+            pillar_project_ranges = None
+
+        score_set.score_ranges = ScoreSetRangesCreate(
+            investigator_provided=investigator_ranges if investigator_ranges else None,
+            pillar_project=pillar_project_ranges if pillar_project_ranges else None,
+        ).model_dump()
+        db.add(score_set)
+
+
+if __name__ == "__main__":
+    db = SessionLocal()
+    db.current_user = None  # type: ignore
+
+    do_migration(db)
+
+    db.commit()
+    db.close()

alembic/versions/2b7a977e7e98_make_faf95_max_and_ancestry_possibly_.py

@@ -0,0 +1,31 @@
+"""Make faf95_max and ancestry possibly nullable
+
+Revision ID: 2b7a977e7e98
+Revises: a8e345cca190
+Create Date: 2025-08-21 10:08:58.565416
+
+"""
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = "2b7a977e7e98"
+down_revision = "a8e345cca190"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.alter_column("gnomad_variants", "faf95_max", existing_type=sa.DOUBLE_PRECISION(precision=53), nullable=True)
+    op.alter_column("gnomad_variants", "faf95_max_ancestry", existing_type=sa.VARCHAR(), nullable=True)
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.alter_column("gnomad_variants", "faf95_max_ancestry", existing_type=sa.VARCHAR(), nullable=False)
+    op.alter_column("gnomad_variants", "faf95_max", existing_type=sa.DOUBLE_PRECISION(precision=53), nullable=False)
+    # ### end Alembic commands ###

alembic/versions/4b9fb51a460d_add_uniprot_id_field_for_mapped_metadata.py

@@ -0,0 +1,29 @@
+"""add uniprot id field for mapped metadata
+
+Revision ID: 4b9fb51a460d
+Revises: aa3933cf0cb3
+Create Date: 2025-07-24 16:07:51.548202
+
+"""
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = "4b9fb51a460d"
+down_revision = "aa3933cf0cb3"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.add_column("target_genes", sa.Column("uniprot_id_from_mapped_metadata", sa.String(), nullable=True))
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_column("target_genes", "uniprot_id_from_mapped_metadata")
+    # ### end Alembic commands ###

alembic/versions/79b28316dd0c_add_gnomad_variants_table.py

@@ -0,0 +1,45 @@
+"""add gnomad variants table
+
+Revision ID: 79b28316dd0c
+Revises: 4b9fb51a460d
+Create Date: 2025-06-17 08:38:51.954238
+
+"""
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = "79b28316dd0c"
+down_revision = "4b9fb51a460d"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_table(
+        "gnomad_variants",
+        sa.Column("id", sa.Integer(), nullable=False),
+        sa.Column("db_name", sa.String(), nullable=False),
+        sa.Column("db_identifier", sa.String(), nullable=False),
+        sa.Column("db_version", sa.String(), nullable=False),
+        sa.Column("allele_count", sa.Integer(), nullable=False),
+        sa.Column("allele_number", sa.Integer(), nullable=False),
+        sa.Column("allele_frequency", sa.Float(), nullable=False),
+        sa.Column("faf95_max", sa.Float(), nullable=False),
+        sa.Column("faf95_max_ancestry", 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_gnomad_variants_db_identifier"), "gnomad_variants", ["db_identifier"], unique=False)
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_index(op.f("ix_gnomad_variants_db_identifier"), table_name="gnomad_variants")
+    op.drop_table("gnomad_variants")
+    # ### end Alembic commands ###