add timeout to plannotate (#225)

dna_functions.py

@@ -319,14 +319,14 @@ async def get_sequence_from_euroscarf_url(plasmid_id: str) -> Dseqrecord:
 
 
 async def annotate_with_plannotate(
-    file_content: str, file_name: str, url: str
+    file_content: str, file_name: str, url: str, timeout: int = 20
 ) -> tuple[Dseqrecord, PlannotateAnnotationReport, str]:
     async with httpx.AsyncClient() as client:
         try:
             response = await client.post(
                 url,
                 files={'file': (file_name, file_content, 'text/plain')},
-                timeout=20,
+                timeout=timeout,
             )
             if response.status_code != 200:
                 detail = response.json().get('detail', 'plannotate server error')

main.py

@@ -85,6 +85,7 @@
 RECORD_STUBS = os.environ['RECORD_STUBS'] == '1' if 'RECORD_STUBS' in os.environ else False
 SERVE_FRONTEND = os.environ['SERVE_FRONTEND'] == '1' if 'SERVE_FRONTEND' in os.environ else False
 PLANNOTATE_URL = os.environ['PLANNOTATE_URL'] if 'PLANNOTATE_URL' in os.environ else None
+PLANNOTATE_TIMEOUT = int(os.environ['PLANNOTATE_TIMEOUT']) if 'PLANNOTATE_TIMEOUT' in os.environ else 20
 
 # Handle trailing slash:
 if PLANNOTATE_URL is not None and not PLANNOTATE_URL.endswith('/'):
@@ -1360,7 +1361,7 @@ async def annotate_with_plannotate(
         # Make a request submitting sequence as a file:
         try:
             seqr, annotations, version = await _annotate_with_plannotate(
-                sequence.file_content, f'{sequence.id}.gb', PLANNOTATE_URL + 'annotate'
+                sequence.file_content, f'{sequence.id}.gb', PLANNOTATE_URL + 'annotate', PLANNOTATE_TIMEOUT
             )
         except HTTPError as e:
             raise HTTPException(e.code, e.msg) from e