Move configurable retry_on_conflict setting from app.cfg.example to s…

…earch-config.yaml.example.

src/hubmap_translator.py

@@ -66,8 +66,7 @@ class Translator(TranslatorInterface):
     failed_entity_api_calls = []
     failed_entity_ids = []
 
-    def __init__(self, indices, app_client_id, app_client_secret, token, ontology_api_base_url:str=None
-                 , es_retry_on_conflict_freq:int=0):
+    def __init__(self, indices, app_client_id, app_client_secret, token, ontology_api_base_url:str=None):
         try:
             self.ingest_api_soft_assay_url = indices['ingest_api_soft_assay_url'].strip('/')
             self.indices: dict = {}
@@ -82,7 +81,7 @@ def __init__(self, indices, app_client_id, app_client_secret, token, ontology_ap
             self.INDICES: dict = {'default_index': self.DEFAULT_INDEX_WITHOUT_PREFIX, 'indices': self.indices}
             self.DEFAULT_ENTITY_API_URL = self.INDICES['indices'][self.DEFAULT_INDEX_WITHOUT_PREFIX]['document_source_endpoint'].strip('/')
             self._ontology_api_base_url = ontology_api_base_url
-            self.es_retry_on_conflict_freq = es_retry_on_conflict_freq
+            self.es_retry_on_conflict_param_value = indices['es_retry_on_conflict_param_value']
 
             self.indexer = Indexer(self.indices, self.DEFAULT_INDEX_WITHOUT_PREFIX)
 
@@ -376,7 +375,7 @@ def _directly_modify_related_entities(  self, es_url:str, es_index:str, entity_i
             f'  \"lang\": \"painless\",' \
             f'  \"source\": \"{painless_query}\",' \
             f'  \"params\": {{' \
-            f'   \"retry_on_conflict\": {self.es_retry_on_conflict_freq},' \
+            f'   \"retry_on_conflict\": {self.es_retry_on_conflict_param_value},' \
             f'   \"modified_entity_uuid\": \"<TARGET_MODIFIED_ENTITY_UUID>\",' \
             f'   \"revised_related_entity\": <THIS_REVISED_ENTITY>' \
             f'  }}' \

src/instance/app.cfg.example

@@ -14,9 +14,6 @@ AWS_OBJECT_URL_EXPIRATION_IN_SECS = 60*60 # 1 hour
 # returned in the response to avoid the AWS Gateway 10Mb constraint
 LARGE_RESPONSE_THRESHOLD = 9*(2**20) + 900*(2**10) #9.9Mb
 
-# ElasticSearch retry_on_conflict value. Positive integer or zero.
-ES_RETRY_ON_CONFLICT_FREQ = 5
-
 # Base URL for the Ontology API
 ONTOLOGY_API_BASE_URL = 'https://ontology-api.dev.hubmapconsortium.org'
 

src/instance/search-config.yaml.example

@@ -6,6 +6,8 @@
 ingest_api_soft_assay_url: https://ingest-api.dev.hubmapconsortium.org/assaytype/ 
 # default index name for endpoints that don't specify an index
 default_index: entities
+# ElasticSearch retry_on_conflict value. Positive integer or zero.
+es_retry_on_conflict_param_value: 5
 
 # specify multiple indices
 indices:

src/main.py

@@ -28,7 +28,6 @@
 config['AWS_S3_BUCKET_NAME'] = app.config['AWS_S3_BUCKET_NAME']
 config['AWS_S3_OBJECT_PREFIX'] = app.config['AWS_S3_OBJECT_PREFIX']
 config['AWS_OBJECT_URL_EXPIRATION_IN_SECS'] = app.config['AWS_OBJECT_URL_EXPIRATION_IN_SECS']
-config['ES_RETRY_ON_CONFLICT_FREQ'] = app.config['ES_RETRY_ON_CONFLICT_FREQ']
 config['LARGE_RESPONSE_THRESHOLD'] = app.config['LARGE_RESPONSE_THRESHOLD']
 config['PARAM_SEARCH_RECOGNIZED_ENTITIES_BY_INDEX'] = app.config['PARAM_SEARCH_RECOGNIZED_ENTITIES_BY_INDEX']
 config['ONTOLOGY_API_BASE_URL'] = app.config['ONTOLOGY_API_BASE_URL'].strip('/')