Fixes and changes for Bagel

Author: Hina Shah

Common/config.py

@@ -23,7 +23,7 @@ class Config:
     # Base parent directory for all storage paths (relative to ORION root)
     storage_base_path: str = "Storage"
     base_path: str = ""
-    
+
     # Subdirectories under storage_base_path
     orion_storage_dir_name: str = "ORION_STORAGE"
     orion_graphs_dir_name: str = "ORION_KG"
@@ -47,6 +47,10 @@ class Config:
     name_resolver_url: str = "https://name-resolution-sri.renci.org/"
     litcoin_pred_mapping_url: str = "https://pred-mapping.apps.renci.org/"
     sapbert_url: str = "https://babel-sapbert.apps.renci.org/"
+    bagel_url: str = "https://bagel.apps.renci.org/"
+
+    bagel_service_username : str = "default_bagel_username"
+    bagel_service_password: str = "default_bagel_password"
 
     env_vars = {
             "storage_base_path": "STORAGE_BASE_PATH",
@@ -62,7 +66,8 @@ class Config:
             "edge_normalization_url": "EDGE_NORMALIZATION_ENDPOINT",
             "name_resolver_url": "NAMERES_URL",
             "litcoin_pred_mapping_url": "LITCOIN_PRED_MAPPING_URL",
-            "sapbert_url": "SAPBERT_URL"
+            "sapbert_url": "SAPBERT_URL",
+            "bagel_url": "BAGEL_ENDPOINT"
         }
 
     def __post_init__(self):
@@ -85,35 +90,35 @@ def create_path(self, env_var:str):
             if not Path(self.orion_storage_path).exists():
                 logger.info(f"--- Creating ORION Storage Path: {self.orion_storage_path}")
                 Path(self.orion_storage_path).mkdir(exist_ok=True, parents=True)
-                return self.orion_storage_path
+            return self.orion_storage_path
         elif env_var == "ORION_LOGS_DIR_NAME" and len(self.orion_logs_path) > 0:
             logger.info(f"Checking for existence of ORION Logs Path: {self.orion_logs_path}")
             if not Path(self.orion_logs_path).exists():
                 logger.info(f"--- Creating ORION Logs Path: {self.orion_logs_path}")
                 Path(self.orion_logs_path).mkdir(exist_ok=True, parents=True)
-                return self.orion_logs_path
+            return self.orion_logs_path
         elif env_var == "ORION_GRAPHS_DIR_NAME" and len(self.orion_graphs_path) > 0:
             logger.info(f"Checking for existence of ORION Knowledge Graph Path: {self.orion_graphs_path}")
             if not Path(self.orion_graphs_path).exists():
                 logger.info(f"--- Creating ORION Knowledge Graph Path: {self.orion_graphs_path}")
                 Path(self.orion_graphs_path).mkdir(exist_ok=True, parents=True)
-                return self.orion_graphs_path
+            return self.orion_graphs_path
         elif env_var == "SHARED_SOURCE_DIR_NAME" and len(self.shared_source_data_path) > 0:
             logger.info(f"Checking for existence of ORION Shared Source Path: {self.shared_source_data_path}")
             if not Path(self.shared_source_data_path).exists():
                 logger.info(f"--- Creating ORION Shared Source Path: {self.shared_source_data_path}")
                 Path(self.shared_source_data_path).mkdir(exist_ok=True, parents=True)
-                return self.shared_source_data_path
+            return self.shared_source_data_path
         return None
 
     def getenv(self, env_name:str):
-        if env_name in self. env_vars.values():
+        if env_name in self.env_vars.values():
             if 'DIR_NAME' in env_name.upper():
                 ## This is a directory variable, create the path if needed.
                 value = self.create_path(env_name)
             else:
                 attr_name = [k for k in self.env_vars if self.env_vars[k] == env_name.upper()]
-                value = getattr(self, attr_name) if attr_name is not None else None
+                value = getattr(self, attr_name[0]) if len(attr_name) == 1 else None
             return value
         else:
             return os.environ.get(env_name) 

parsers/LitCoin/src/bagel/bagel_gpt.py

@@ -1,21 +1,23 @@
 import requests
 from requests.auth import HTTPBasicAuth
-from Common.config import CONFIG
+from Common.config import Config
 
-BAGEL_ENDPOINT = 'https://bagel.apps.renci.org/'
+config = Config.from_env()
+
+BAGEL_ENDPOINT = config.getenv("BAGEL_ENDPOINT")
 BAGEL_ENDPOINT += 'find_curies_openai'
 
-bagel_nameres_url = CONFIG.get('NAMERES_ENDPOINT', 'https://name-resolution-sri.renci.org/')
+bagel_nameres_url = config.getenv("NAMERES_URL")
 bagel_nameres_url += 'lookup?autocomplete=false&offset=0&limit=10&string="'
 
-bagel_sapbert_url = CONFIG.get('SAPBERT_URL', 'https://sap-qdrant.apps.renci.org/')
+bagel_sapbert_url = config.getenv("SAPBERT_URL") # This default is different: 'https://sap-qdrant.apps.renci.org/'
 bagel_sapbert_url += "annotate/"
 
-bagel_nodenorm_url = CONFIG.get('NODE_NORMALIZATION_ENDPOINT', 'https://nodenormalization-sri.renci.org/')
+bagel_nodenorm_url = config.getenv("NODE_NORMALIZATION_ENDPOINT")
 bagel_nodenorm_url += 'get_normalized_nodes'
 
-BAGEL_SERVICE_USERNAME = CONFIG.get("BAGEL_SERVICE_USERNAME", 'default_bagel_username')
-BAGEL_SERVICE_PASSWORD = CONFIG.get("BAGEL_SERVICE_PASSWORD", 'default_bagel_password')
+BAGEL_SERVICE_USERNAME = config.getenv("BAGEL_SERVICE_USERNAME")
+BAGEL_SERVICE_PASSWORD = config.getenv("BAGEL_SERVICE_PASSWORD")
 
 
 def call_bagel_service(text, entity, entity_type=''):

parsers/LitCoin/src/bagel/bagel_service.py

@@ -5,7 +5,6 @@
 
 @mock.patch.dict(os.environ, {
     "STORAGE_BASE_PATH":"tmp",
-    "ORION_STORAGE_DIR_NAME": "custom_orion_storage",
     "ORION_GRAPHS_DIR_NAME": "custom_orion_graphs"
 })
 def test_config_created_from_env_vars():
@@ -28,4 +27,9 @@ def test_config_created_from_env_vars():
 
     orion_graphs_path = cfg.getenv("ORION_GRAPHS_DIR_NAME")
     assert (Path(orion_graphs_path).exists())
-    assert (cfg.orion_logs_path == '')
+    assert (cfg.orion_logs_path == '')
+    storage_path = cfg.getenv("ORION_STORAGE_DIR_NAME")
+    print(storage_path)
+    assert(Path(storage_path).exists())
+
+    assert(cfg.getenv("ORION_GRAPH_SPEC") == "example-graph-spec.yaml" )