Merge pull request #107 from geneontology/exception_handler

no data found exception handler

Makefile

@@ -23,13 +23,14 @@ integration-tests:
 	poetry run pytest tests/integration/step_defs/*.py
 
 lint:
+	poetry run tox -e flake8
 	poetry run tox -e lint-fix
 
 spell:
 	poetry run tox -e codespell
 
 unit-tests:
-	poetry run pytest tests/unit/*.py
+	poetry run pytest -v tests/unit/*.py
 
 export-requirements:
 	poetry export -f requirements.txt --output requirements.txt
@@ -38,12 +39,14 @@ install:
 	poetry install
 
 help:
-	@echo ""
+	@echo "##################################################################################################"
 	@echo "make all -- installs requirements, deploys and starts the site locally"
 	@echo "make install -- install dependencies"
 	@echo "make start -- start the API locally"
 	@echo "make test -- runs tests, linter in fix mode, and spell checker"
 	@echo "make lint -- runs linter in fix mode"
 	@echo "make spell -- runs spell checker"
 	@echo "make help -- show this help"
-	@echo ""
+	@echo "make start -- start the API locally at localhost:8080/docs (takes about 10 seconds to start)"
+	@echo "make start-dev -- start the API locally at localhost:8081/docs (takes about 10 seconds to start)"
+	@echo "##################################################################################################"

app/exceptions/global_exceptions.py

@@ -0,0 +1,45 @@
+"""Global exception handlers for API endpoints."""
+
+from fastapi import HTTPException
+
+
+class DataNotFoundException(HTTPException):
+    """
+    Exception for when data is not found.
+
+    :param detail: The detail message for the exception.
+    :type detail: str, optional
+    :returns: A DataNotFoundException object.
+
+    """
+
+    def __init__(self, detail: str = "Data not found"):
+        """
+        Initialize the DataNotFoundException object.
+
+        :param detail:
+        :type detail:
+        :returns:
+        """
+        super().__init__(status_code=404, detail=detail)
+
+
+class InvalidIdentifier(HTTPException):
+    """
+    Exception for when data is not found.
+
+    :param detail: The detail message for the exception.
+    :type detail: str, optional
+    :returns: A DataNotFoundException object.
+
+    """
+
+    def __init__(self, detail: str = "Data not found"):
+        """
+        Initialize the DataNotFoundException object.
+
+        :param detail:
+        :type detail:
+        :returns:
+        """
+        super().__init__(status_code=400, detail=detail)

app/main.py

@@ -7,6 +7,7 @@
 from fastapi.middleware.cors import CORSMiddleware
 from fastapi.responses import JSONResponse
 
+from app.exceptions.global_exceptions import DataNotFoundException
 from app.middleware.logging_middleware import LoggingMiddleware
 from app.routers import (
     bioentity,
@@ -15,7 +16,6 @@
     ontology,
     pathway_widget,
     prefixes,
-    publications,
     ribbon,
     search,
     slimmer,
@@ -24,6 +24,7 @@
 
 logger = logging.getLogger("uvicorn.error")
 
+
 app = FastAPI(
     title="GO API",
     description="The Gene Ontology API.\n\n __Source:__ 'https://github.com/geneontology/go-fastapi'",
@@ -44,7 +45,6 @@
 app.include_router(prefixes.router)
 app.include_router(labeler.router)
 app.include_router(search.router)
-app.include_router(publications.router)
 app.include_router(users_and_groups.router)
 
 # Logging
@@ -82,5 +82,17 @@ async def general_exception_handler(request: Request, exc: Exception):
     )
 
 
+@app.exception_handler(DataNotFoundException)
+async def data_not_found_exception_handler(request: Request, exc: DataNotFoundException):
+    """
+    Global exception handler for DataNotFoundException.
+
+    :param request:
+    :param exc:
+    :return:
+    """
+    return JSONResponse(status_code=exc.status_code, content={"detail": exc.detail})
+
+
 if __name__ == "__main__":
     uvicorn.run("main:app", host="127.0.0.1", port=8080, log_level="info", reload=True)

app/routers/bioentity.py

@@ -8,9 +8,11 @@
 from ontobio.config import get_config
 from ontobio.golr.golr_associations import search_associations
 
-from app.utils.golr_utils import gu_run_solr_text_on
+from app.exceptions.global_exceptions import DataNotFoundException, InvalidIdentifier
+from app.utils.golr_utils import gu_run_solr_text_on, is_valid_bioentity
 from app.utils.settings import ESOLR, ESOLRDoc, get_user_agent
 
+from ..utils.ontology_utils import is_valid_goid
 from .slimmer import gene_to_uniprot_from_mygene
 
 INVOLVED_IN = "involved_in"
@@ -78,6 +80,13 @@ async def get_bioentity_by_id(
           'start' determines the starting index for fetching results, and 'rows' specifies
           the number of results to be retrieved per page.
     """
+    try:
+        is_valid_bioentity(id)
+    except DataNotFoundException as e:
+        raise DataNotFoundException(detail=str(e)) from e
+    except ValueError as e:
+        raise InvalidIdentifier(detail=str(e)) from e
+
     if rows is None:
         rows = 100000
     # special case MGI, sigh
@@ -91,11 +100,12 @@ async def get_bioentity_by_id(
     # query_filters is translated to the qf solr parameter
     # boost fields %5E2 -> ^2, %5E1 -> ^1
     query_filters = "bioentity%5E2"
-    logger.info(id)
 
     optionals = "&defType=edismax&start=" + str(start) + "&rows=" + str(rows)
     # id here is passed to solr q parameter, query_filters go to the boost, fields are what's returned
     bioentity = gu_run_solr_text_on(ESOLR.GOLR, ESOLRDoc.BIOENTITY, id, query_filters, fields, optionals, False)
+    if not bioentity:
+        raise DataNotFoundException(detail=f"Item with ID {id} not found")
     return bioentity
 
 
@@ -141,6 +151,13 @@ async def get_annotations_by_goterm_id(
           'start' determines the starting index for fetching results, and 'rows' specifies
           the number of results to be retrieved per page.
     """
+    try:
+        is_valid_goid(id)
+    except DataNotFoundException as e:
+        raise DataNotFoundException(detail=str(e)) from e
+    except ValueError as e:
+        raise InvalidIdentifier(detail=str(e)) from e
+
     if rows is None:
         rows = 100000
     # dictates the fields to return, annotation_class,aspect
@@ -170,7 +187,8 @@ async def get_annotations_by_goterm_id(
 
     optionals = "&defType=edismax&start=" + str(start) + "&rows=" + str(rows) + evidence
     data = gu_run_solr_text_on(ESOLR.GOLR, ESOLRDoc.ANNOTATION, id, query_filters, fields, optionals, False)
-
+    if not data:
+        raise DataNotFoundException(detail=f"Item with ID {id} not found")
     return data
 
 
@@ -224,9 +242,16 @@ async def get_genes_by_goterm_id(
              and 'annotation_extension_class_label' associated with the provided GO term.
 
     """
+    try:
+        is_valid_goid(id)
+    except DataNotFoundException as e:
+        raise DataNotFoundException(detail=str(e)) from e
+    except ValueError as e:
+        raise InvalidIdentifier(detail=str(e)) from e
+
     if rows is None:
         rows = 100000
-    association_return = {}
+
     if relationship_type == ACTS_UPSTREAM_OF_OR_WITHIN:
         association_return = search_associations(
             subject_category="gene",
@@ -273,6 +298,7 @@ async def get_genes_by_goterm_id(
             url=ESOLR.GOLR,
             rows=rows,
         )
+
     return {"associations": association_return.get("associations")}
 
 
@@ -310,6 +336,13 @@ async def get_taxon_by_goterm_id(
     :return: A dictionary containing the taxon information for genes annotated to the provided GO term.
              The dictionary will contain fields such as 'taxon' and 'taxon_label' associated with the genes.
     """
+    try:
+        is_valid_goid(id)
+    except DataNotFoundException as e:
+        raise DataNotFoundException(detail=str(e)) from e
+    except ValueError as e:
+        raise InvalidIdentifier(detail=str(e)) from e
+
     if rows is None:
         rows = 100000
     fields = "taxon,taxon_label"
@@ -342,7 +375,8 @@ async def get_taxon_by_goterm_id(
 
     optionals = "&defType=edismax&start=" + str(start) + "&rows=" + str(rows) + evidence + taxon_restrictions
     data = gu_run_solr_text_on(ESOLR.GOLR, ESOLRDoc.ANNOTATION, id, query_filters, fields, optionals, False)
-
+    if not data:
+        raise DataNotFoundException(detail=f"Item with ID {id} not found")
     return data
 
 
@@ -394,6 +428,13 @@ async def get_annotations_by_gene_id(
     scenes for querying.
 
     """
+    try:
+        is_valid_bioentity(id)
+    except DataNotFoundException as e:
+        raise DataNotFoundException(detail=str(e)) from e
+    except ValueError as e:
+        raise InvalidIdentifier(detail=str(e)) from e
+
     if rows is None:
         rows = 100000
 
@@ -410,8 +451,6 @@ async def get_annotations_by_gene_id(
         rows=rows,
         slim=slim,
     )
-    logger.info("should be null assocs")
-    logger.info(assocs)
     # If there are no associations for the given ID, try other IDs.
     # Note the AmiGO instance does *not* support equivalent IDs
     if len(assocs["associations"]) == 0:
@@ -435,6 +474,7 @@ async def get_annotations_by_gene_id(
                 num_found = num_found + pr_assocs.get("numFound")
             assocs["numFound"] = num_found
             for asc in pr_assocs["associations"]:
-                logger.info(asc)
                 assocs["associations"].append(asc)
+    if not assocs or assocs["associations"] == 0:
+        raise DataNotFoundException(detail=f"Item with ID {id} not found")
     return {"associations": assocs.get("associations")}

app/routers/labeler.py

@@ -5,6 +5,7 @@
 
 from fastapi import APIRouter, Query
 
+from app.exceptions.global_exceptions import DataNotFoundException
 from app.utils.ontology_utils import batch_fetch_labels
 from app.utils.settings import get_user_agent
 
@@ -22,4 +23,7 @@ async def expand_curie(
 ):
     """Fetches a map from IDs to labels e.g. GO:0003677."""
     logger.info("fetching labels for IDs")
-    return batch_fetch_labels(id)
+    labels = batch_fetch_labels(id)
+    if not labels:
+        raise DataNotFoundException(detail=f"Item with ID {id} not found")
+    return labels