Merge pull request #16 from TheJacksonLaboratory/G3-232-create-post-v…

…ersions-of-the-aon-mapping-endpoints

G3 232 create post versions of the aon mapping endpoints

.gitignore

@@ -11,9 +11,15 @@ ORTHOLOGY-ALLIANCE_COMBINED.tsv
 fix.py
 map.py
 test.py
-env.py
+#env.py
 .gitignore
 __pycache__
 flask/src/config.py
-flask/alembic.ini
-alembic.ini
+#flask/alembic.ini
+#alembic.ini
+*.tsv
+*.tsv.gz
+.python-version
+.coverage
+.idea
+*.pdf

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "geneweaver-aon"
-version = "0.2.4"
+version = "0.3.0"
 description = "A service to do Homology and Orthology mapping."
 authors = ["Sophie Kearney <[email protected]>", "Alexander Berger <[email protected]>"]
 readme = "README.md"

src/geneweaver/aon/alembic/env.py

@@ -1,10 +1,11 @@
-from logging.config import fileConfig
+"""The script that Alembic uses to run migrations."""
 
-from sqlalchemy import engine_from_config, text
-from sqlalchemy import pool
+# ruff: noqa: ERA001, ANN201
 
-from alembic import context
+from logging.config import fileConfig
 
+from alembic import context
+from sqlalchemy import engine_from_config, pool, text
 from sqlalchemy.ext.declarative import declarative_base
 
 Base = declarative_base()
@@ -64,9 +65,9 @@ def run_migrations_online():
     x_arguments = context.get_x_argument(as_dictionary=True)
 
     current_tenant = x_arguments.get("tenant")
-    dburi = x_arguments.get('dburi')
+    dburi = x_arguments.get("dburi")
     if dburi:
-        _config_section['sqlalchemy.url'] = dburi
+        _config_section["sqlalchemy.url"] = dburi
 
     connectable = engine_from_config(
         _config_section,
@@ -75,7 +76,7 @@ def run_migrations_online():
     )
 
     with connectable.connect() as connection:
-        connection.execute(text('CREATE SCHEMA IF NOT EXISTS "%s"' % 'versions'))
+        connection.execute(text('CREATE SCHEMA IF NOT EXISTS "%s"' % "versions"))
         connection.execute(text('CREATE SCHEMA IF NOT EXISTS "%s"' % current_tenant))
         connection.execute(text('set search_path to "%s"' % current_tenant))
         connection.commit()

src/geneweaver/aon/controller/genes.py

@@ -30,6 +30,37 @@ def get_gene_prefixes(db: deps.Session = Depends(deps.session)):
     return genes_service.gene_prefixes(db)
 
 
+@router.post("/ortholog/mapping")
+def map_gene_orthologs(
+    db: deps.Session = Depends(deps.session),
+    gene_ref_ids: list[str] = None,
+    to_species: Optional[int] = None,
+    algorithm_id: Optional[int] = None,
+    paging_params: dict = Depends(deps.paging_parameters),
+) -> list:
+    """Map gene orthologs."""
+    return genes_service.map_gene_orthologs(
+        db,
+        gene_ref_ids,
+        to_species=to_species,
+        algorithm_id=algorithm_id,
+        **paging_params
+    )
+
+
+@router.post("/homolog/mapping")
+def map_gene_homologs(
+    db: deps.Session = Depends(deps.session),
+    gene_ref_ids: list[str] = None,
+    to_species: Optional[int] = None,
+    paging_params: dict = Depends(deps.paging_parameters),
+) -> list:
+    """Map gene orthologs."""
+    return genes_service.map_gene_homologs(
+        db, gene_ref_ids, to_species=to_species, **paging_params
+    )
+
+
 @router.get("/{gene_id}")
 def get_gene(gene_id: int, db: deps.Session = Depends(deps.session)):
     """Get gene by id."""

src/geneweaver/aon/controller/orthologs.py

@@ -15,7 +15,7 @@ def get_orthologs(
     to_species: Optional[int] = None,
     from_gene_id: Optional[int] = None,
     to_gene_id: Optional[int] = None,
-    algorithm_id: Optional[int] = deps.DEFAULT_ALGORITHM_ID,
+    algorithm_id: Optional[int] = None,
     best: Optional[bool] = None,
     revised: Optional[bool] = None,
     paging_params: dict = Depends(deps.paging_parameters),

src/geneweaver/aon/dependencies.py

@@ -28,6 +28,8 @@ async def lifespan(app: FastAPI) -> None:
 
     :param app: The FastAPI application (dependency injection).
     """
+    logger.level = logging.getLevelName(config.LOG_LEVEL)
+
     logger.info("Setting up DB connection pools.")
     schema_versions = get_schema_versions()
     app.session_managers, app.engines = set_up_sessionmanager_by_schema(schema_versions)
@@ -38,7 +40,7 @@ async def lifespan(app: FastAPI) -> None:
             None if default_schema_version is None else default_schema_version.id
         )
         logger.info(
-            f"Using latest schema version as default: {default_schema_version}."
+            f"Using latest schema version as default: {default_schema_version.id}."
         )
     else:
         default_version_id = next(
@@ -69,6 +71,8 @@ def session(request: Request) -> sessionmaker:
     """Get a session from the connection pool."""
     try:
         schema_version = request.state.schema_version_id
+        logger.info(f"Using schema version {schema_version.id}.")
+
         try:
             _session = request.app.session_managers[schema_version]()
         except KeyError as e:
@@ -84,6 +88,7 @@ def session(request: Request) -> sessionmaker:
                     status_code=404, detail="Schema version not found."
                 ) from e
     except AttributeError:
+        logger.info("Using default schema version.")
         _session = request.app.session()
 
     yield _session

src/geneweaver/aon/service/genes.py

@@ -2,9 +2,9 @@
 
 from typing import List, Optional, Type
 
-from geneweaver.aon.models import Gene
+from geneweaver.aon.models import Gene, Homology, Ortholog, OrthologAlgorithms
 from geneweaver.aon.service.utils import apply_paging
-from sqlalchemy.orm import Session
+from sqlalchemy.orm import Session, aliased
 
 
 def get_genes(
@@ -62,6 +62,93 @@ def genes_by_prefix(db: Session, prefix: str) -> List[Type[Gene]]:
     return db.query(Gene).filter(Gene.gn_prefix == prefix).all()
 
 
+def map_gene_orthologs(
+    db: Session,
+    gene_ref_ids: List[str],
+    to_species: Optional[int] = None,
+    algorithm_id: Optional[int] = None,
+    start: Optional[int] = None,
+    limit: Optional[int] = 1000,
+) -> list:
+    """Map gene orthologs.
+
+    :param db: The database session.
+    :param gene_ref_ids: The gene reference ids to map.
+    :return: The mapped gene orthologs.
+    """
+    from_gene = aliased(Gene)
+    to_gene = aliased(Gene)
+    query = (
+        db.query(from_gene, to_gene, Ortholog, OrthologAlgorithms)
+        .join(Ortholog, Ortholog.from_gene == from_gene.gn_id)
+        .join(to_gene, Ortholog.to_gene == to_gene.gn_id)
+        .join(OrthologAlgorithms, Ortholog.ort_id == OrthologAlgorithms.ort_id)
+        .filter(from_gene.gn_ref_id.in_(gene_ref_ids))
+    )
+
+    if to_species is not None:
+        query = query.filter(to_gene.sp_id == to_species)
+
+    if algorithm_id is not None:
+        query = query.filter(OrthologAlgorithms.alg_id == algorithm_id)
+
+    query = apply_paging(query, start, limit)
+
+    results = query.all()
+
+    return [
+        {
+            "from_gene": r[0].gn_ref_id,
+            "to_gene": r[1].gn_ref_id,
+            "ortholog_id": r[2].ort_id,
+            "algorithm_id": r[3].alg_id,
+        }
+        for r in results
+    ]
+
+
+def map_gene_homologs(
+    db: Session,
+    gene_ref_ids: List[str],
+    to_species: Optional[int] = None,
+    start: Optional[int] = None,
+    limit: Optional[int] = 1000,
+) -> list:
+    """Map gene homologs.
+
+    :param db: The database session.
+    :param gene_ref_ids: The gene reference ids to map.
+    :return: The mapped gene homologs.
+    """
+    from_hom = aliased(Homology)
+    to_hom = aliased(Homology)
+    from_gene = aliased(Gene)
+    to_gene = aliased(Gene)
+    query = (
+        db.query(from_gene, from_hom, to_hom, to_gene)
+        .join(from_hom, from_gene.gn_id == from_hom.gn_id)
+        .join(to_hom, from_hom.hom_id == to_hom.hom_id)
+        .join(to_gene, to_hom.gn_id == to_gene.gn_id)
+        .filter(from_gene.gn_ref_id.in_(gene_ref_ids))
+    )
+
+    if to_species is not None:
+        query = query.filter(to_gene.sp_id == to_species)
+
+    query = apply_paging(query, start, limit)
+
+    results = query.all()
+
+    return [
+        {
+            "from_gene": r[0].gn_ref_id,
+            "to_gene": r[3].gn_ref_id,
+            "homolog_id": r[1].hom_id,
+        }
+        for r in results
+    ]
+
+
 def gene_prefixes(db: Session) -> List[str]:
     """Get all gene prefixes.
 

src/geneweaver/aon/service/orthologs.py

@@ -1,11 +1,14 @@
 """Module with functions for querying orthologs from the database."""
 
+import logging
 from typing import List, Optional, Type
 
 from geneweaver.aon.models import Algorithm, Gene, Ortholog, OrthologAlgorithms
 from geneweaver.aon.service.utils import apply_paging
 from sqlalchemy.orm import Session, aliased
 
+logger = logging.getLogger("uvicorn.error")
+
 
 def get_ortholog_from_gene(db: Session, ortholog_id: int) -> Optional[Type[Gene]]:
     """Get ortholog by id.
@@ -59,46 +62,62 @@ def get_orthologs(
     :param limit: The limit for paging.
     :return: The orthologs for the provided query.
     """
+    logger.debug("Constructing get_orthologs query")
+
     query = db.query(Ortholog)
 
     if algorithm_id is not None:
+        logger.debug(f"Filtering get_orthologs by algorithm id: {algorithm_id}")
         query = (
             query.join(OrthologAlgorithms)
             .join(Algorithm)
             .filter(Algorithm.alg_id == algorithm_id)
         )
 
     if from_species is not None:
+        logger.debug(f"Filtering get_orthologs by from species: {from_species}")
         from_gene = aliased(Gene)
         query = query.join(from_gene, Ortholog.from_gene == from_gene.gn_id).filter(
             from_gene.sp_id == from_species
         )
 
     if to_species is not None:
+        logger.debug(f"Filtering get_orthologs by to species: {to_species}")
         to_gene = aliased(Gene)
         query = query.join(to_gene, Ortholog.to_gene == to_gene.gn_id).filter(
             to_gene.sp_id == to_species
         )
 
     if from_gene_id:
+        logger.debug(f"Filtering get_orthologs by from gene id: {from_gene_id}")
         query = query.filter(Ortholog.from_gene == from_gene_id)
 
     if to_gene_id:
+        logger.debug(f"Filtering get_orthologs by to gene id: {to_gene_id}")
         query = query.filter(Ortholog.to_gene.id == to_gene_id)
 
     if best is not None:
+        logger.debug(f"Filtering get_orthologs by best: {best}")
         query = query.filter(Ortholog.ort_is_best == best)
 
     if revised is not None:
+        logger.debug(f"Filtering get_orthologs by revised: {revised}")
         query = query.filter(Ortholog.ort_is_best_revised == revised)
 
     if possible_match_algorithms is not None:
+        logger.debug(
+            "Filtering get_orthologs by possible match algorithms: "
+            f"{possible_match_algorithms}"
+        )
         query = query.filter(
             Ortholog.ort_num_possible_match_algorithms == possible_match_algorithms
         )
 
+    logger.debug(f"Using limit={limit} and start={start} for get_orthologs.")
     query = apply_paging(query, start, limit)
 
+    logger.debug(f"Running get_orthologs with query: `{str(query)}`")
+
     return query.all()
 
 

src/geneweaver/aon/service/species.py

@@ -1,10 +1,13 @@
 """Species database queries."""
 
+import logging
 from typing import List, Optional, Type
 
 from geneweaver.aon.models import GeneweaverSpecies, Species
 from sqlalchemy.orm import Session
 
+logger = logging.getLogger("uvicorn.error")
+
 
 def get_species(db: Session, name: Optional[str] = None) -> List[Type[Species]]:
     """Get species.
@@ -16,7 +19,7 @@ def get_species(db: Session, name: Optional[str] = None) -> List[Type[Species]]:
     base_query = db.query(Species)
     if name is not None:
         base_query = base_query.filter(Species.sp_name == name)
-    print(str(base_query))
+    logger.debug(f"Running get_species with query: `{str(base_query)}`")
     return base_query.all()