Merge release-2025.3.1

Author: EstelleDa

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

@@ -6,65 +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
@@ -96,30 +68,32 @@ jobs:
     - 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

@@ -36,7 +36,13 @@ def do_migration(db: Session):
 
     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)
+            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
 
@@ -60,6 +66,8 @@ def do_migration(db: Session):
                         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)
@@ -69,6 +77,8 @@ def do_migration(db: Session):
                         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:
@@ -82,6 +92,8 @@ def do_migration(db: Session):
                         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
@@ -99,7 +111,7 @@ def do_migration(db: Session):
         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,
-        ).dict()
+        ).model_dump()
         db.add(score_set)
 
 

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 ###

alembic/versions/986b635a697f_variant_translations_data_model.py

@@ -0,0 +1,36 @@
+"""Variant translations data model
+
+Revision ID: 986b635a697f
+Revises: af87c9953d2d
+Create Date: 2025-03-24 14:00:18.063245
+
+"""
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = "986b635a697f"
+down_revision = "af87c9953d2d"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_table(
+        "variant_translations",
+        sa.Column("aa_clingen_id", sa.String(), nullable=False),
+        sa.Column("nt_clingen_id", sa.String(), nullable=False),
+        sa.Column("creation_date", sa.Date(), nullable=False),
+        sa.Column("modification_date", sa.Date(), nullable=False),
+        sa.PrimaryKeyConstraint("aa_clingen_id", "nt_clingen_id"),
+    )
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_table("variant_translations")
+    # ### end Alembic commands ###

alembic/versions/a8e345cca190_cast_db_identifier_in_clinical_controls_.py

@@ -0,0 +1,59 @@
+"""cast db_identifier in clinical controls table to a string
+
+Revision ID: a8e345cca190
+Revises: 986b635a697f
+Create Date: 2025-08-20 12:30:05.388503
+
+"""
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = "a8e345cca190"
+down_revision = "986b635a697f"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.alter_column(
+        "clinical_controls", "db_identifier", existing_type=sa.INTEGER(), type_=sa.String(), existing_nullable=False
+    )
+    op.alter_column(
+        "publication_identifiers", "title", existing_type=sa.TEXT(), type_=sa.String(), existing_nullable=False
+    )
+    op.alter_column(
+        "publication_identifiers", "abstract", existing_type=sa.TEXT(), type_=sa.String(), existing_nullable=True
+    )
+    op.alter_column(
+        "publication_identifiers",
+        "publication_journal",
+        existing_type=sa.TEXT(),
+        type_=sa.String(),
+        existing_nullable=True,
+    )
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.alter_column(
+        "publication_identifiers",
+        "publication_journal",
+        existing_type=sa.String(),
+        type_=sa.TEXT(),
+        existing_nullable=True,
+    )
+    op.alter_column(
+        "publication_identifiers", "abstract", existing_type=sa.String(), type_=sa.TEXT(), existing_nullable=True
+    )
+    op.alter_column(
+        "publication_identifiers", "title", existing_type=sa.String(), type_=sa.TEXT(), existing_nullable=False
+    )
+    op.alter_column(
+        "clinical_controls", "db_identifier", existing_type=sa.String(), type_=sa.INTEGER(), existing_nullable=False
+    )
+    # ### end Alembic commands ###