failing gracefully for failed sapbert or name res calls

parsers/LitCoin/src/NER/nameres.py

@@ -47,7 +47,8 @@ def annotate(self, text, props, limit=1):
         response = self.requests_session.get(NAMERES_ENDPOINT, params=nameres_options, timeout=timeout)
         logging.debug(f"Response from NameRes: {response.content}")
         if not response.ok:
-            raise RuntimeError(f"Could not contact NameRes: {response}")
+            logging.debug(f"Could not contact NameRes: {response}")
+            response.raise_for_status()
 
         results = response.json()
         annotations = []

parsers/LitCoin/src/NER/sapbert.py

@@ -41,7 +41,8 @@ def annotate(self, text, props, limit=1):
         response = self.requests_session.post(SAPBERT_ANNOTATE_ENDPOINT, json=request)
         logging.debug(f"Response from {SAPBERT_MODEL_NAME}: {response.content}")
         if not response.ok:
-            raise RuntimeError(f"Server error from SAPBERT for text '{text}': {response}")
+            logging.debug(f"Server error from SAPBERT for text '{text}': {response}")
+            response.raise_for_status()
 
         results = response.json()
         annotations = []

parsers/LitCoin/src/bagel/bagel.py

@@ -25,8 +25,15 @@
 def get_orion_bagel_results(text, term, abstract_id):
     # print(f'bagelizing term {term}.')
     taxon_id_to_name = {}
-    nr_results = nameres.annotate(term, props={}, limit=10)
-    sb_results = sapbert.annotate(term, props={}, limit=10)
+    try:
+        nr_results = nameres.annotate(term, props={}, limit=10)
+    except requests.exceptions.HTTPError:
+        nr_results = []
+    try:
+        sb_results = sapbert.annotate(term, props={}, limit=10)
+    except requests.exceptions.HTTPError:
+        sb_results = []
+
     # We have results from both nr and sb. But we want to fill those out with consistent information that may
     # or may not be returned from each source
     # First merge the results by identifier (not label) and store in terms dict