Fixes to seqr sync (#772)

* Fixes to seqr sync

* Add backoff to server requirements

db/python/layers/participant.py

@@ -765,13 +765,14 @@ async def get_seqr_individual_template(
             set_headers.update(set(row.keys()))
 
         rows = [{h: r.get(h) for h in set_headers if h in r} for r in rows]
+        headers = []  # get ordered headers if we have data for it
+        for h in SeqrMetadataKeys.get_ordered_headers():
+            if header := lheader_to_json.get(h.value.lower()) in set_headers:
+                headers.append(header)
 
         return {
             'rows': rows,
-            # get ordered headers if we have data for it
-            'headers': [
-                h for h in SeqrMetadataKeys.get_ordered_headers() if h in set_headers
-            ],
+            'headers': headers,
             'header_map': json_header_map,
         }
 

db/python/layers/seqr.py

@@ -11,6 +11,7 @@
 import aiohttp
 import slack_sdk
 import slack_sdk.errors
+from backoff import expo, on_exception
 from cloudpathlib import AnyPath
 
 from cpg_utils.cloud import get_google_identity_token
@@ -498,6 +499,7 @@ async def update_es_index(
         messages.extend(await asyncio.gather(*requests))
         return messages
 
+    @on_exception(expo, aiohttp.ClientResponseError, max_tries=3)
     async def update_saved_variants(
         self,
         session: aiohttp.ClientSession,

requirements.txt

@@ -1,5 +1,6 @@
 # requirements are for running the server
 # fix boto3/core version to prevent pip downloading all the versions caused by cloudpathlib
+backoff>=2.2.1
 boto3==1.28.56
 botocore==1.31.56
 cpg-utils>=5.0.5