Merge branch 'release-2024.4.2' into maintenance/bencap/74/update-permitted-licenses

Author: bencap

alembic/manual_migrations/migrate_non_api_like_constants.py

@@ -0,0 +1,40 @@
+import sqlalchemy as sa
+from sqlalchemy.orm import Session, configure_mappers
+
+from mavedb.models import *
+from mavedb.models.enums.target_category import TargetCategory
+from mavedb.models.target_gene import TargetGene
+
+from mavedb.db.session import SessionLocal
+
+configure_mappers()
+
+def api_like_target_gene_category(category: str):
+    if category == "Protein coding":
+        return TargetCategory.protein_coding
+    elif category == "Other noncoding":
+        return TargetCategory.other_noncoding
+    elif category == "Regulatory":
+        return TargetCategory.regulatory
+    else:
+        raise ValueError()
+
+
+def do_migration(db: Session):
+    target_genes = db.scalars(sa.select(TargetGene)).all()
+
+    for target in target_genes:
+        target.category = api_like_target_gene_category(target.category)
+        db.add(target)
+
+    db.commit()
+
+
+if __name__ == "__main__":
+    db = SessionLocal()
+    db.current_user = None  # type: ignore
+
+    do_migration(db)
+
+    db.commit()
+    db.close()

alembic/manual_migrations/refresh_published_tmp_urns.py

@@ -0,0 +1,33 @@
+import sqlalchemy as sa
+from sqlalchemy.orm import Session, configure_mappers
+
+from mavedb.models import *
+
+from mavedb.lib.score_sets import refresh_variant_urns
+
+from mavedb.models.score_set import ScoreSet
+from mavedb.models.variant import Variant
+
+from mavedb.db.session import SessionLocal
+
+configure_mappers()
+
+
+def do_migration(db: Session):
+    published_score_sets_with_associated_tmp_variants: sa.ScalarResult[str]
+    published_score_sets_with_associated_tmp_variants = db.execute(
+        sa.select(sa.distinct(ScoreSet.urn)).join(Variant).where(ScoreSet.published_date.is_not(None), Variant.urn.like("%tmp:%"))
+    ).scalars()
+
+    for score_set_urn in published_score_sets_with_associated_tmp_variants:
+        refresh_variant_urns(db, db.execute(sa.select(ScoreSet).where(ScoreSet.urn == score_set_urn)).scalar_one())
+
+
+if __name__ == "__main__":
+    db = SessionLocal()
+    db.current_user = None  # type: ignore
+
+    do_migration(db)
+
+    db.commit()
+    db.close()

alembic/versions/03c7124c33e1_target_category_enum.py

@@ -0,0 +1,54 @@
+"""Target category enum
+
+Revision ID: 03c7124c33e1
+Revises: 2b6f40ea2fb6
+Create Date: 2024-11-01 11:27:03.609116
+
+"""
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = "03c7124c33e1"
+down_revision = "2b6f40ea2fb6"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.alter_column(
+        "target_genes",
+        "category",
+        type_=sa.Enum(
+            "protein_coding",
+            "other_noncoding",
+            "regulatory",
+            name="targetcategory",
+            native_enum=False,
+            create_constraint=True,
+            length=32,
+        ),
+    )
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.alter_column(
+        "target_genes",
+        "category",
+        type_=sa.String(),
+        existing_type=sa.Enum(
+            "protein_coding",
+            "other_noncoding",
+            "regulatory",
+            name="targetcategory",
+            native_enum=False,
+            create_constraint=True,
+            length=32,
+        ),
+    )
+    # ### end Alembic commands ###

poetry.lock

@@ -26,7 +26,7 @@ python = "^3.9"
 
 fqfa = "~1.3.0"
 pyhumps = "~3.8.0"
-pyyaml = "~5.1"
+pyyaml = "~6.0.1"
 IDUtils = "~1.2.0"
 mavehgvs = "~0.6.0"
 eutils = "~0.6.0"
@@ -99,6 +99,7 @@ mypy_path = "mypy_stubs"
 addopts = "-v -rP --import-mode=importlib --disable-socket --allow-hosts localhost,::1,127.0.0.1"
 asyncio_mode = 'strict'
 testpaths = "tests/"
+pythonpath = "."
 norecursedirs = "tests/helpers/"
 # Uncomment the following lines to include application log output in Pytest logs.
 # log_cli = true

pyproject.toml

@@ -99,7 +99,7 @@ def search_experiments(
             )
         )
 
-    items: list[Experiment] = query.order_by(Experiment.title).all()
+    items: list[Experiment] = query.order_by(Experiment.urn, Experiment.title).all()
     if not items:
         items = []
 

src/mavedb/lib/experiments.py

@@ -617,6 +617,21 @@ def create_variants(db, score_set: ScoreSet, variants_data: list[VariantData], b
     return len(score_set.variants)
 
 
+def refresh_variant_urns(db: Session, score_set: ScoreSet):
+    variants = db.execute(select(Variant).where(Variant.score_set_id == score_set.id)).scalars()
+
+    for variant in variants:
+        if not variant.urn:
+            raise ValueError("All variants should have an associated URN.")
+
+        variant_number = variant.urn.split("#")[1]
+        refreshed_urn = f"{score_set.urn}#{variant_number}"
+        variant.urn = refreshed_urn
+        db.add(variant)
+
+    db.commit()
+
+
 def bulk_create_urns(n, score_set, reset_counter=False) -> list[str]:
     start_value = 0 if reset_counter else score_set.num_variants
     parent_urn = score_set.urn

src/mavedb/lib/score_sets.py

@@ -1,2 +1 @@
-valid_categories = ["Protein coding", "Regulatory", "Other noncoding"]
 valid_sequence_types = ["infer", "dna", "protein"]

src/mavedb/lib/validation/constants/target.py

@@ -1,31 +1,10 @@
 from fqfa import infer_sequence_type
 from fqfa.validator import amino_acids_validator, dna_bases_validator
 
-from mavedb.lib.validation.constants.target import valid_categories, valid_sequence_types
+from mavedb.lib.validation.constants.target import valid_sequence_types
 from mavedb.lib.validation.exceptions import ValidationError
 
 
-def validate_target_category(category: str):
-    """
-    If the target category provided does not fall within a pre-defined list of valid categories.
-
-    Parameters
-    __________
-    category: str
-        The target category to be validated.
-
-    Raises
-    ______
-    ValidationError
-        If the target category provided is not valid.
-    """
-    if category not in valid_categories:
-        raise ValidationError(
-            "{} is not a valid target category. Valid categories are "
-            "Protein coding, Regulatory, and Other noncoding".format(category)
-        )
-
-
 def validate_sequence_category(sequence_type: str):
     """
     If the sequence type provided does not fall within a pre-defined list of valid sequence types.

src/mavedb/lib/validation/target.py

@@ -0,0 +1,7 @@
+from enum import Enum
+
+
+class TargetCategory(str, Enum):
+    protein_coding = "protein_coding"
+    regulatory = "regulatory"
+    other_noncoding = "other_noncoding"