Post refactor release

.vscode/settings.json

@@ -16,7 +16,7 @@
     "statusBarItem.hoverBackground": "#5ce637",
     "statusBar.foreground": "#15202b"
   },
-  "python.pythonPath": ".venv/bin/python",
+  "python.pythonPath": ".venv/bin/python3",
   "python.analysis.openFilesOnly": false,
   "python.analysis.memory.keepLibraryLocalVariables": true,
   "python.autoComplete.addBrackets": true,

api/app/core/middleware.py

@@ -3,7 +3,6 @@
 import time
 
 # Third Party
-# Local Imports
 from loguru import logger
 from starlette.middleware.base import BaseHTTPMiddleware
 

api/app/main.py

@@ -7,9 +7,9 @@
 import time
 
 # Third Party
-# Third Party Imports
 from fastapi import FastAPI
 from fastapi import __version__ as fastapi_version
+from fastapi.responses import JSONResponse
 from loguru import logger
 from starlette.middleware.cors import CORSMiddleware
 from starlette.middleware.gzip import GZipMiddleware
@@ -19,17 +19,16 @@
 from starlette_prometheus import PrometheusMiddleware, metrics
 
 # Local
-# Local Imports
 import bel.core.settings as settings
 from bel.__version__ import __version__ as version
+from bel.api.core.middleware import StatsMiddleware
 from bel.api.endpoints.bel import router as bel_router
 from bel.api.endpoints.belspec import router as belspec_router
 from bel.api.endpoints.info import router as info_router
 from bel.api.endpoints.nanopubs import router as nanopubs_router
 from bel.api.endpoints.orthology import router as orthology_router
 from bel.api.endpoints.pubmed import router as pubmed_router
 from bel.api.endpoints.terms import router as terms_router
-from core.middleware import StatsMiddleware
 
 logger.remove()
 
@@ -58,6 +57,22 @@
     version=version,
 )
 
+# Added user_flag to HTTPException
+@app.exception_handler(HTTPException)
+async def http_exception_handler(request: Request, exc: HTTPException) -> JSONResponse:
+    headers = getattr(exc, "headers", None)
+    if headers:
+        return JSONResponse(
+            {"detail": exc.detail, "user_flag": exc.user_flag},
+            status_code=exc.status_code,
+            headers=headers,
+        )
+    else:
+        return JSONResponse(
+            {"detail": exc.detail, "user_flag": exc.user_flag}, status_code=exc.status_code
+        )
+
+
 logger.info("Starting BEL API")
 logger.info(f"Fast API Version: {fastapi_version}")
 

bel/api/core/exceptions.py

@@ -0,0 +1,17 @@
+# Standard Library
+from typing import Any, Dict, Optional
+
+# Third Party
+from fastapi.exceptions import HTTPException as FastAPIHTTPException
+
+
+class HTTPException(FastAPIHTTPException):
+    def __init__(
+        self,
+        status_code: int,
+        detail: Any = None,
+        user_flag: bool = False,
+        headers: Optional[Dict[str, Any]] = None,
+    ) -> None:
+        super().__init__(status_code=status_code, detail=detail, headers=headers)
+        self.user_flag = user_flag

bel/api/core/jwt.py

@@ -0,0 +1,69 @@
+# Standard Library
+from datetime import datetime, timedelta
+
+# Third Party
+import jwt
+from loguru import logger
+
+# Local
+from bel.Config import config
+
+jwt_algorithm = "HS256"
+
+
+def jwt_create(userid, payload, expiration=None):
+    """Create a JSON Web Token
+    payload: dictionary to be added to JWT
+    expiration:  number of seconds from now to expire token -- defaults to 3600 seconds
+
+    """
+
+    if expiration:
+        exp = datetime.utcnow() + timedelta(seconds=expiration)
+    else:
+        exp = datetime.utcnow() + timedelta(seconds=3600)
+
+    additional_payload = {
+        "sub": userid,
+        "exp": exp,
+        "iat": datetime.utcnow(),
+    }
+
+    logger.debug("UserId: ", userid, " Payload: ", payload)
+
+    payload.update(additional_payload)
+    token = jwt.encode(
+        payload, config["secrets"]["bel_api"]["shared_secret"], algorithm=jwt_algorithm
+    )
+
+    return token.decode("utf-8")
+
+
+def jwt_validate(token):
+    """Validates JSON Web Token
+    Returns:
+        valid:          boolean - true if valid token
+        token_payload:  dict of token payload
+    """
+    try:
+        jwt.decode(token, config["secrets"]["bel_api"]["shared_secret"], algorithm=jwt_algorithm)
+        return True
+    except Exception as e:
+        return False
+
+
+def jwt_extract(token):
+    logger.debug("In JWT Extract")
+    try:
+        return (
+            jwt.decode(
+                token, config["secrets"]["bel_api"]["shared_secret"], algorithm=jwt_algorithm
+            ),
+            "",
+        )
+    except jwt.ExpiredSignatureError:
+        logger.debug("JWT expired")
+        return None, "JWT expired"
+    except Exception as e:
+        logger.debug("JWT extraction error ", e)
+        return None, e

bel/api/core/middleware.py

@@ -0,0 +1,43 @@
+# Standard Library
+import re
+import time
+
+# Third Party
+from loguru import logger
+from starlette.middleware.base import BaseHTTPMiddleware
+
+
+@logger.catch
+class StatsMiddleware(BaseHTTPMiddleware):
+    """Get duration of request"""
+
+    async def dispatch(self, request, call_next):
+
+        url = str(request.url)
+        method = str(request.method)
+        t0 = time.time()
+
+        response = await call_next(request)
+
+        url = url.rstrip("/")
+        route_name = url.split("/")[-1]
+
+        # logger.info("Skipping status/metrics", url=url, route_name=route_name)
+
+        if method == "OPTIONS" or route_name in ["status", "metrics", "ping"]:
+            return response
+        else:
+            t1 = time.time()
+
+            duration = f"{(t1 - t0) * 1000:.0f}"
+
+            logger.opt(exception=True).info(
+                "Request Metrics {duration_ms} ms, status_code: {status_code}  {method} {url}",
+                # "Request Metrics {duration_ms} ms, status_code: {status_code}",
+                duration_ms=duration,
+                status_code=response.status_code,
+                method=method,
+                url=url,
+            )
+
+            return response

bel/api/endpoints/bel.py

@@ -4,11 +4,8 @@
 from typing import List, Optional
 
 # Third Party
-# Third Party Imports
 import fastapi
 from fastapi import APIRouter, Depends, Query
-
-# Local Imports
 from loguru import logger
 
 # Local

bel/api/endpoints/belspec.py

@@ -1,15 +1,15 @@
 """belspec endpoints"""
 
-# Third Party Imports
+
 # Third Party
 import fastapi
-from fastapi import APIRouter, Depends, HTTPException, Query
+from fastapi import APIRouter, Depends, Query
 from fastapi.responses import PlainTextResponse
 from loguru import logger
 
 # Local
-# Local Imports
 import bel.belspec.crud
+from bel.api.core.exceptions import HTTPException
 from bel.schemas.belspec import BelSpec, BelSpecVersions, EnhancedBelSpec
 
 router = APIRouter()
@@ -40,7 +40,9 @@ def get_belspec_version(
 
     belspec = bel.belspec.crud.get_enhanced_belspec(version)
     if not belspec:
-        raise HTTPException(status_code=404, detail=f"No BEL specification for version {version}")
+        raise HTTPException(
+            status_code=404, detail=f"No BEL specification for version {version}", user_flag=True
+        )
 
     return belspec
 
@@ -61,7 +63,9 @@ def get_enhanced_belspec(
 
     if not enhanced_belspec:
         raise HTTPException(
-            status_code=404, detail=f"No enhanced BEL specification for version {version}"
+            status_code=404,
+            detail=f"No enhanced BEL specification for version {version}",
+            user_flag=True,
         )
 
     return enhanced_belspec

bel/api/endpoints/info.py

@@ -6,13 +6,11 @@
 import re
 
 # Third Party
-# Third Party Imports
 import fastapi
 from fastapi import APIRouter, Depends
 from loguru import logger
 
 # Local
-# Local Imports
 import bel.core.settings as settings
 import bel.terms.terms
 from bel.__version__ import __version__ as bel_lib_version

bel/api/endpoints/nanopubs.py

@@ -3,14 +3,13 @@
 from typing import List
 
 # Third Party
-# Third Party Imports
 import fastapi
-from fastapi import APIRouter, Depends, HTTPException
+from fastapi import APIRouter, Depends
 from loguru import logger
 
 # Local
-# Local Imports
 import bel.nanopub.validate
+from bel.api.core.exceptions import HTTPException
 from bel.schemas.nanopubs import NanopubR
 
 router = APIRouter()
@@ -33,7 +32,7 @@ def nanopub_validation(nanopub: NanopubR, validation_level: str = "complete"):
     # data = json.loads(data)
 
     if not nanopub:
-        raise HTTPException(400, detail=f"No nanopub provided")
+        raise HTTPException(400, detail=f"No nanopub provided", user_flag=True)
 
     nanopub = bel.nanopub.validate.validate(nanopub, validation_level=validation_level)
 

bel/api/endpoints/orthology.py

@@ -4,13 +4,11 @@
 from typing import List
 
 # Third Party
-# Third Party Imports
 import fastapi
 from fastapi import APIRouter, Depends, File, Query, UploadFile
 from loguru import logger
 
 # Local
-# Local Imports
 import bel.terms.orthologs
 
 router = APIRouter()

bel/api/endpoints/pubmed.py

@@ -1,14 +1,14 @@
 """pubmed endpoints"""
 
-# Third Party Imports
+
 # Third Party
 import fastapi
-from fastapi import APIRouter, Depends, HTTPException, Query
+from fastapi import APIRouter, Depends, Query
 from loguru import logger
 
 # Local
-# Local Imports
 import bel.nanopub.pubmed
+from bel.api.core.exceptions import HTTPException
 
 router = APIRouter()
 
@@ -25,6 +25,8 @@ def get_pubmed_info(
     pubmed = bel.nanopub.pubmed.get_pubmed_for_beleditor(pmid, pubmed_only=pubmed_only)
 
     if pubmed is None:
-        raise HTTPException(status_code=404, detail=f"No Pubmed response for {pmid}")
+        raise HTTPException(
+            status_code=404, detail=f"No Pubmed response for {pmid}", user_flag=True
+        )
 
     return pubmed

bel/api/endpoints/resources.py

@@ -4,16 +4,14 @@
 from typing import List, Optional
 
 # Third Party
-# Third Party Imports
 import fastapi
-from fastapi import APIRouter, Body, Depends, File, HTTPException, Query, UploadFile
+from fastapi import APIRouter, Body, Depends, File, Query, UploadFile
 from loguru import logger
 
 # Local
 import bel.resources.manage
-
-# Local Imports
 import bel.terms.terms
+from bel.api.core.exceptions import HTTPException
 from bel.schemas.terms import Term, TermCompletionResponse
 
 router = APIRouter()

bel/api/endpoints/terms.py

@@ -4,14 +4,13 @@
 from typing import List
 
 # Third Party
-# Third Party Imports
 import fastapi
-from fastapi import APIRouter, Depends, File, HTTPException, Query, UploadFile
+from fastapi import APIRouter, Depends, File, Query, UploadFile
 from loguru import logger
 
 # Local
-# Local Imports
 import bel.terms.terms
+from bel.api.core.exceptions import HTTPException
 from bel.schemas.terms import Term, TermCompletionResponse
 
 router = APIRouter()
@@ -67,7 +66,7 @@ def get_terms(term_id: str):
     terms = bel.terms.terms.get_terms(term_id)
 
     if not terms:
-        raise HTTPException(status_code=404, detail=f"Term {term_id} not found")
+        raise HTTPException(status_code=404, detail=f"Term {term_id} not found", user_flag=True)
 
     return terms
 
@@ -79,7 +78,7 @@ def get_term_equivalents(term_id: str):
     equivalents = bel.terms.terms.get_equivalents(term_id)
 
     if not equivalents:
-        raise HTTPException(status_code=404, detail=f"Term {term_id} not found")
+        raise HTTPException(status_code=404, detail=f"Term {term_id} not found", user_flag=True)
 
     return equivalents