Merge pull request #508 from VariantEffect/release-2025.3.1

Release 2025.3.1

Author: jstone-dev

Dockerfile

@@ -2,7 +2,7 @@
 # python-base
 # Set up shared environment variables
 ################################
-FROM python:3.11 AS python-base
+FROM --platform=amd64 python:3.11 AS python-base
 
     # Poetry
     # https://python-poetry.org/docs/configuration/#using-environment-variables

alembic/versions/019eb75ad9ae_rename_tax_id_to_code.py

@@ -0,0 +1,28 @@
+"""rename_tax_id_to_code
+
+Revision ID: 019eb75ad9ae
+Revises: b29bbfb2a13a
+Create Date: 2025-08-20 16:21:15.872816
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '019eb75ad9ae'
+down_revision = '0b29eefbe1dd'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.alter_column('taxonomies', 'tax_id', new_column_name='code', existing_type=sa.Integer(), existing_nullable=False)
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.alter_column('taxonomies', 'code', new_column_name='tax_id', existing_type=sa.Integer(), existing_nullable=False)
+    # ### end Alembic commands ###

alembic/versions/0b29eefbe1dd_controlled_keyword_modification.py

@@ -0,0 +1,46 @@
+"""controlled keyword modification
+
+Revision ID: 0b29eefbe1dd
+Revises: 2b7a977e7e98
+Create Date: 2025-08-07 15:45:43.241567
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '0b29eefbe1dd'
+down_revision = '2b7a977e7e98'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    # Rename existing columns
+    op.alter_column('controlled_keywords', 'value', new_column_name='label', existing_type=sa.String(), existing_nullable=False)
+    op.alter_column('controlled_keywords', 'vocabulary', new_column_name='system', existing_type=sa.String(), existing_nullable=True)
+    # Add new columns
+    op.add_column('controlled_keywords', sa.Column('code', sa.String(), nullable=True))
+    op.add_column('controlled_keywords', sa.Column('version', sa.String(), nullable=True))
+    # Drop and recreate the correct unique constraint
+    op.drop_constraint('ix_controlled_keywords_key_value', 'controlled_keywords', type_='unique')
+    op.create_unique_constraint('ix_controlled_keywords_key_label', 'controlled_keywords', ['key', 'label'])
+    # ### end Alembic commands ###
+
+    # TODO: Will modify this part when we get the final GO terms.
+    op.execute(
+        """INSERT INTO controlled_keywords (key, label, system, code, version, special, description, creation_date, modification_date) VALUES ('Phenotypic Assay Mechanism', 'Other', NULL, NULL, NULL, False, 'The Gene Ontology (GO) is a structured, standardized representation of biological knowledge.', NOW(), NOW())"""
+    )
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.alter_column('controlled_keywords', 'label', new_column_name='value', existing_type=sa.String(), existing_nullable=False)
+    op.alter_column('controlled_keywords', 'system', new_column_name='vocabulary', existing_type=sa.String(), existing_nullable=True)
+    op.drop_constraint('ix_controlled_keywords_key_label', 'controlled_keywords', type_='unique')
+    op.create_unique_constraint('ix_controlled_keywords_key_value', 'controlled_keywords', ['key', 'value'])
+    op.drop_column('controlled_keywords', 'version')
+    op.drop_column('controlled_keywords', 'code')
+    # ### end Alembic commands ###

src/mavedb/lib/experiments.py

@@ -100,7 +100,7 @@ def search_experiments(
         query = query.filter(
             Experiment.keyword_objs.any(
                 ExperimentControlledKeywordAssociation.controlled_keyword.has(
-                    ControlledKeyword.value.in_(search.keywords)
+                    ControlledKeyword.label.in_(search.keywords)
                 )
             )
         )

src/mavedb/lib/keywords.py

@@ -6,16 +6,16 @@
 from mavedb.models.controlled_keyword import ControlledKeyword
 
 
-def search_keyword(db: Session, key: str, value: Optional[str]):
+def search_keyword(db: Session, key: str, label: Optional[str]):
     lower_key = key.lower().strip()
-    lower_value = value.lower().strip() if value is not None else None
+    lower_label = label.lower().strip() if label is not None else None
     query = db.query(ControlledKeyword)
     if lower_key:
         query = query.filter(func.lower(ControlledKeyword.key) == lower_key)
-    if lower_value:
-        query = query.filter(func.lower(ControlledKeyword.value) == lower_value)
+    if lower_label:
+        query = query.filter(func.lower(ControlledKeyword.label) == lower_label)
 
     controlled_keyword = query.one_or_none()
     if controlled_keyword is None:
-        raise ValueError(f"Invalid keyword {key} or {value}")
+        raise ValueError(f"Invalid keyword {key} or {label}")
     return controlled_keyword

src/mavedb/lib/score_sets.py

@@ -114,7 +114,7 @@ def search_score_sets(db: Session, owner_or_contributor: Optional[User], search:
                 ScoreSet.target_genes.any(
                     TargetGene.target_accession.has(func.lower(TargetAccession.assembly).icontains(lower_search_text))
                 ),
-                # TODO(#94): add LICENSE, plus TAX_ID if numeric
+                # TODO(#94): add LICENSE, plus TAXONOMY CODE if numeric
                 ScoreSet.publication_identifiers.any(
                     func.lower(PublicationIdentifier.identifier).icontains(lower_search_text)
                 ),
@@ -208,7 +208,7 @@ def search_score_sets(db: Session, owner_or_contributor: Optional[User], search:
             ScoreSet.experiment.has(
                 Experiment.keyword_objs.any(
                     ExperimentControlledKeywordAssociation.controlled_keyword.has(
-                        ControlledKeyword.value.in_(search.keywords)
+                        ControlledKeyword.label.in_(search.keywords)
                     )
                 )
             )

src/mavedb/lib/taxonomies.py

@@ -10,16 +10,16 @@
 
 async def find_or_create_taxonomy(db: Session, taxonomy: TaxonomyCreate):
     """
-    Find an existing taxonomy ID record with the specified tax_id int, or create a new one.
+    Find an existing taxonomy ID record with the specified code, or create a new one.
 
     :param db: An active database session
     :param taxonomy: A TaxonomyCreate object containing the taxonomy details to search for or create.
     :return: An existing Taxonomy containing the specified taxonomy ID, or a new, unsaved Taxonomy
-    tax_id: A valid taxonomy ID from NCBI
+    code: A valid taxonomy ID from NCBI
     """
-    taxonomy_record = db.query(Taxonomy).filter(Taxonomy.tax_id == taxonomy.tax_id).one_or_none()
+    taxonomy_record = db.query(Taxonomy).filter(Taxonomy.code == taxonomy.code).one_or_none()
     if not taxonomy_record:
-        taxonomy_record = await search_NCBI_taxonomy(db, str(taxonomy.tax_id))
+        taxonomy_record = await search_NCBI_taxonomy(db, str(taxonomy.code))
     return taxonomy_record
 
 
@@ -51,14 +51,14 @@ async def search_NCBI_taxonomy(db: Session, search: str) -> Any:
                 ncbi_taxonomy.setdefault("rank", "NULL")
                 ncbi_taxonomy.setdefault("has_described_species_name", False)
                 taxonomy_record = Taxonomy(
-                    tax_id=ncbi_taxonomy["tax_id"],
+                    code=ncbi_taxonomy["code"],
                     organism_name=ncbi_taxonomy["organism_name"],
                     common_name=ncbi_taxonomy["common_name"],
                     rank=ncbi_taxonomy["rank"],
                     has_described_species_name=ncbi_taxonomy["has_described_species_name"],
                     url="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=info&id="
-                    + str(ncbi_taxonomy["tax_id"]),
-                    article_reference="NCBI:txid" + str(ncbi_taxonomy["tax_id"]),
+                    + str(ncbi_taxonomy["code"]),
+                    article_reference="NCBI:txid" + str(ncbi_taxonomy["code"]),
                 )
                 db.add(taxonomy_record)
                 db.commit()

src/mavedb/lib/validation/keywords.py

@@ -1,32 +1,41 @@
+import re
 from typing import Optional
 
 from mavedb.lib.validation.exceptions import ValidationError
 from mavedb.lib.validation.utilities import is_null
 
 
-# TODO: value will not be Optional when we confirm the final controlled keyword list.
-def validate_description(value: str, key: str, description: Optional[str]):
-    if value.lower() == "other" and (description is None or description.strip() == ""):
+def validate_code(key: str, label: str, code: Optional[str]):
+    if key.lower() == "phenotypic assay mechanism" and label.lower() != "other":
+        # The Gene Ontology accession is a unique seven digit identifier prefixed by GO:.
+        # e.g. GO:0005739, GO:1904659, or GO:0016597.
+        if code is None or not re.match(r"^GO:\d{7}$", code):
+            raise ValidationError("Invalid Gene Ontology accession.")
+
+
+# TODO: label will not be Optional when we confirm the final controlled keyword list.
+def validate_description(label: str, key: str, description: Optional[str]):
+    if label.lower() == "other" and (description is None or description.strip() == ""):
         raise ValidationError(
             "Other option does not allow empty description.", custom_loc=["body", "keywordDescriptions", key]
         )
 
 
 def validate_duplicates(keywords: list):
     keys = []
-    values = []
+    labels = []
     for k in keywords:
         keys.append(k.keyword.key.lower())  # k: ExperimentControlledKeywordCreate object
-        if k.keyword.value.lower() != "other":
-            values.append(k.keyword.value.lower())
+        if k.keyword.label.lower() != "other":
+            labels.append(k.keyword.label.lower())
 
     keys_set = set(keys)
-    values_set = set(values)
+    labels_set = set(labels)
 
     if len(keys) != len(keys_set):
         raise ValidationError("Duplicate keys found in keywords.")
-    if len(values) != len(values_set):
-        raise ValidationError("Duplicate values found in keywords.")
+    if len(labels) != len(labels_set):
+        raise ValidationError("Duplicate labels found in keywords.")
 
 
 def validate_keyword(keyword: str):
@@ -47,7 +56,7 @@ def validate_keyword(keyword: str):
 
 
 def validate_keyword_keys(keywords: list):
-    keyword_dict = {k.keyword.key.lower(): k.keyword.value.lower() for k in keywords}
+    keyword_dict = {k.keyword.key.lower(): k.keyword.label.lower() for k in keywords}
     variant_library_method = keyword_dict.get("variant library creation method", "")
 
     if variant_library_method == "endogenous locus library method":

src/mavedb/models/controlled_keyword.py

@@ -10,10 +10,12 @@ class ControlledKeyword(Base):
 
     id = Column(Integer, primary_key=True, index=True)
     key = Column(String, nullable=False)
-    value = Column(String, nullable=False)
-    vocabulary = Column(String, nullable=True)
+    label = Column(String, nullable=False)
+    system = Column(String, nullable=True)
+    code = Column(String, nullable=True)
+    version = Column(String, nullable=True)
     special = Column(Boolean, nullable=True)
     description = Column(String, nullable=True)
     creation_date = Column(Date, nullable=False, default=date.today)
     modification_date = Column(Date, nullable=False, default=date.today, onupdate=date.today)
-    __table_args__ = (UniqueConstraint("key", "value", name="ix_controlled_keywords_key_value"),)
+    __table_args__ = (UniqueConstraint("key", "label", name="ix_controlled_keywords_key_label"),)

src/mavedb/models/experiment.py

@@ -161,8 +161,10 @@ def keywords(self) -> list[dict]:
                 {
                     "keyword": {
                         "key": controlled_keyword.key,
-                        "value": controlled_keyword.value,
-                        "vocabulary": controlled_keyword.vocabulary,
+                        "label": controlled_keyword.label,
+                        "system": controlled_keyword.system,
+                        "code": controlled_keyword.code,
+                        "version": controlled_keyword.version,
                         "special": controlled_keyword.special,
                         "description": controlled_keyword.description,
                     },
@@ -190,8 +192,8 @@ async def set_keywords(self, db, keywords: list):
                     controlled_keyword=await self._find_keyword(
                         db,
                         keyword_obj.keyword.key,
-                        keyword_obj.keyword.value,
-                        keyword_obj.keyword.vocabulary,
+                        keyword_obj.keyword.label,
+                        keyword_obj.keyword.code,
                     ),
                     description=keyword_obj.description,
                 )
@@ -211,15 +213,15 @@ async def _find_or_create_legacy_keyword(self, db, keyword_text):
             keyword_obj = LegacyKeyword(text=keyword_text)
         return keyword_obj
 
-    async def _find_keyword(self, db, key: str, value: str, vocabulary: Optional[str]):
+    async def _find_keyword(self, db, key: str, label: str, code: Optional[str]):
         query = (
-            db.query(ControlledKeyword).filter(ControlledKeyword.key == key).filter(ControlledKeyword.value == value)
+            db.query(ControlledKeyword).filter(ControlledKeyword.key == key).filter(ControlledKeyword.label == label)
         )
-        if vocabulary:
-            query = query.filter(ControlledKeyword.vocabulary == vocabulary)
+        if code:
+            query = query.filter(ControlledKeyword.code == code)
         controlled_keyword_obj = query.one_or_none()
         if controlled_keyword_obj is None:
-            raise ValueError(f"Unknown keyword {key}:{value}")
+            raise ValueError(f"Unknown keyword {key}:{label}")
         return controlled_keyword_obj