Development

app/core/scalar_docs.py

@@ -9,8 +9,7 @@ def _remove_doc_routes(fastapi_app: FastAPI) -> None:
         route
         for route in fastapi_app.router.routes
         if not (
-            isinstance(route, APIRoute)
-            and route.path in ("/docs", "/redoc")
+            getattr(route, "path", None) in ("/docs", "/redoc")
         )
     ]
     fastapi_app.docs_url = None

app/routers/chem.py

@@ -38,7 +38,6 @@ def get_health() -> HealthCheck:
 
 @router.get(
     "/hosecode",
-    tags=["chem"],
     summary="Generate HOSE codes for a molecule",
     description=(
         "Generate **Hierarchically Ordered Spherical Environment (HOSE)** codes "

app/routers/converter.py

@@ -35,7 +35,6 @@ def get_health() -> HealthCheck:
 
 @router.get(
     "/spectra",
-    tags=["converter"],
     summary="Convert NMR raw data to NMRium JSON",
     description=(
         "Fetch NMR raw data from a remote URL and convert it into "

app/routers/predict.py

@@ -472,7 +472,6 @@ def get_health() -> HealthCheck:
 
 @router.post(
     "/",
-    tags=["predict"],
     summary="Predict NMR spectra from a MOL string",
     description=(
         "Submit a molecular structure as a MOL block string and predict NMR spectra "
@@ -553,7 +552,6 @@ async def predict_from_structure(request: PredictRequest):
 
 @router.post(
     "/file",
-    tags=["predict"],
     summary="Predict NMR spectra from an uploaded MOL file",
     description=(
         "Upload a MOL file and predict NMR spectra using one of the supported engines. "

app/routers/registration.py

@@ -48,7 +48,6 @@ def get_health() -> HealthCheck:
 
 @router.post(
     "/init",
-    tags=["registration"],
     summary="Initialize the registration database",
     description=(
         "Initialize (or re-initialize) the molecule registration database. "
@@ -91,7 +90,6 @@ async def initialise_database(
 
 @router.post(
     "/register",
-    tags=["registration"],
     summary="Register new molecules",
     description=(
         "Register one or more molecules in the database. Accepts SMILES strings "
@@ -199,7 +197,6 @@ async def register_compounds(
 
 @router.get(
     "/query",
-    tags=["registration"],
     summary="Query if a molecule is already registered",
     description=(
         "Check whether a molecule (given as a SMILES string) has already been "
@@ -249,7 +246,6 @@ async def query_compounds(
 
 @router.post(
     "/retrieve",
-    tags=["registration"],
     summary="Retrieve registered molecules by ID",
     description=(
         "Retrieve one or more registered molecules by their registry IDs (molregnos). "

app/routers/spectra.py

@@ -118,7 +118,7 @@ def run_command(
         result = subprocess.run(
             ["docker", "exec", NMR_CLI_CONTAINER] + cmd,
             capture_output=True,
-            timeout=120,
+            timeout=600,
         )
     except subprocess.TimeoutExpired:
         raise HTTPException(
@@ -329,7 +329,6 @@ def run_peaks_to_nmrium_command(payload: dict) -> str:
 
 @router.post(
     "/parse/file",
-    tags=["spectra"],
     summary="Parse spectra from an uploaded file",
     description=(
         "Upload an NMR spectra file (JCAMP-DX, Bruker, etc.) and parse it into "
@@ -425,7 +424,6 @@ async def parse_spectra_from_file(
 
 @router.post(
     "/parse/url",
-    tags=["spectra"],
     summary="Parse spectra from a remote URL",
     description=(
         "Provide a URL pointing to an NMR spectra file and parse it into structured "
@@ -478,7 +476,6 @@ async def parse_spectra_from_url(request: UrlParseRequest):
 
 @router.post(
     "/parse/publication-string",
-    tags=["spectra"],
     summary="Resurrect NMR spectrum from an ACS publication string",
     description=(
         "Parse an ACS-style NMR publication string and resurrect it into a full "
@@ -558,7 +555,6 @@ async def parse_publication_string(
 
 @router.post(
     "/parse/peaks",
-    tags=["spectra"],
     summary="Convert a peak list to an NMRium-compatible spectrum",
     description=(
         "Convert a list of NMR peaks (chemical shifts with optional intensity and "