Update how database env variables are consumed

macrostrat_db_insertion/server.py

@@ -23,20 +23,13 @@ def load_config():
         if env_variable_value is None:
             raise Exception("Environment variable " + env_variable_name + " is not set")
         config_values[required_name] = env_variable_value
-    
+
     return config_values
 
 def load_flask_app(config):
-    # Create the app 
+    # Create the app
     app = Flask(__name__)
-    app.config["SQLALCHEMY_DATABASE_URI"] = sqlalchemy.URL.create(
-        "postgresql",
-        username = config["username"],
-        password = config["password"],  
-        host = config["host"],
-        port = config["port"],
-        database = config["database"],
-    )
+    app.config["SQLALCHEMY_DATABASE_URI"] = os.environ['uri']
 
     # Create the db
     Base = declarative_base(metadata = sqlalchemy.MetaData(schema = config["schema"]))
@@ -86,7 +79,7 @@ def get_db_entity_id(run_id, entity_name, entity_type, source_id):
     except:
         error_msg =  "Failed to insert entity " + entity_name +  " for run " + str(run_id) + " due to error: " + traceback.format_exc()
         return False, error_msg
-    
+
     # Get this entity id
     entity_id = ""
     try:
@@ -100,7 +93,7 @@ def get_db_entity_id(run_id, entity_name, entity_type, source_id):
         # Ensure we got a result
         if len(entities_result) == 0:
             raise Exception("Got zero rows matching query " + str(entities_select_statement))
-        
+
         # Extract the sources id
         first_row = entities_result[0]._mapping
         entity_id = str(first_row["entity_id"])
@@ -131,16 +124,16 @@ def record_relationship(run_id, source_id, relationship):
         if provided_relationship_type.startswith(key_name):
             db_relationship_type, src_entity_type, dst_entity_type = RELATIONSHIP_DETAILS[key_name]
             break
-    
+
     # Ignore this type
     if len(db_relationship_type) == 0 or len(src_entity_type) == 0 or len(dst_entity_type) == 0:
         return True, ""
-    
+
     # Get the entity ids
     sucessful, src_entity_id = get_db_entity_id(run_id, relationship_values["src"], src_entity_type, source_id)
     if not sucessful:
         return sucessful, src_entity_id
-    
+
     sucessful, dst_entity_id = get_db_entity_id(run_id, relationship_values["dst"], dst_entity_type, source_id)
     if not sucessful:
         return sucessful, dst_entity_id
@@ -164,22 +157,22 @@ def record_relationship(run_id, source_id, relationship):
         error_msg = "Failed to insert relationship type " + str(provided_relationship_type) + " for source " + str(source_id)
         error_msg += " for run " + str(run_id) + " due to error: " + traceback.format_exc()
         return False, error_msg
-    
+
     return True, ""
 
 def record_for_result(run_id, request):
     # Ensure txt exists
     if "text" not in request:
         return False, "result is missing text field"
-    
+
     source_fields = ["preprocessor_id", "paper_id", "hashed_text", "weaviate_id", "paragraph_text"]
     source_values = {"run_id" : run_id}
     text_data = request["text"]
     for field_name in source_fields:
         if field_name not in text_data:
             return False, "Request text is missing field " + str(field_name)
         source_values[field_name] = text_data[field_name]
-    
+
     # Remove non ascii data from text
     paragraph_txt = source_values["paragraph_text"]
     source_values["paragraph_text"] = paragraph_txt.encode("ascii", errors="ignore").decode()
@@ -195,11 +188,11 @@ def record_for_result(run_id, request):
         error_msg =  "Failed to insert paragraph " + str(source_values["weaviate_id"])
         error_msg += " for run " + str(source_values["run_id"]) + " due to error: " + traceback.format_exc()
         return False, error_msg
-        
+
     # Deal with case if we have no relationships
     if "relationships" not in request:
         return True, ""
-    
+
     # Get the sources id
     source_id = ""
     try:
@@ -212,15 +205,15 @@ def record_for_result(run_id, request):
         # Ensure we got a result
         if len(sources_result) == 0:
             raise Exception("Got zero rows matching query " + str(sources_select_statement))
-        
+
         # Extract the sources id
         first_row = sources_result[0]._mapping
         source_id = str(first_row["source_id"])
     except:
         error_msg =  "Failed to get sources id for paragraph " + str(source_values["weaviate_id"])
         error_msg += " for run " + str(source_values["run_id"]) + " due to error: " + traceback.format_exc()
         return False, error_msg
-    
+
     # Record the relationships
     if "relationships" in request:
         for relationship in request["relationships"]:
@@ -235,13 +228,13 @@ def record_for_result(run_id, request):
             # Ensure that it has all the required keys
             for key in required_entity_keys:
                 if key not in entity_data:
-                    return False, "Provided just entities missing key " + str(key) 
+                    return False, "Provided just entities missing key " + str(key)
 
             # Only record strats
             entity_type = entity_data["entity_type"]
             if not entity_type.startswith("strat"):
                 continue
-            
+
             # Record the entity
             sucessful, entity_id = get_db_entity_id(run_id, entity_data["entity"], "strat_name", source_id)
             if not sucessful:
@@ -265,7 +258,7 @@ def get_user_id(user_name):
     except:
         error_msg =  "Failed to insert user " + user_name + " due to error: " + traceback.format_exc()
         return False, error_msg
-    
+
     # Get this entity id
     user_id = ""
     try:
@@ -277,7 +270,7 @@ def get_user_id(user_name):
         # Ensure we got a result
         if len(users_result) == 0:
             raise Exception("Got zero rows matching query " + str(users_select_statement))
-        
+
         # Extract the sources id
         first_row = users_result[0]._mapping
         user_id = str(first_row["user_id"])
@@ -295,7 +288,7 @@ def get_model_internal_details(request):
         if field not in request:
             return False, "Request missing field " + field
         model_values[field] = str(request[field])
-    
+
     # Try to insert the model
     model_name = model_values["model_name"]
     models_tables = db.metadata.tables['macrostrat_kg_new.models']
@@ -322,14 +315,14 @@ def get_model_internal_details(request):
         # Ensure we got a result
         if len(models_result) == 0:
             raise Exception("Got zero rows matching query " + str(models_select_statement))
-        
+
         # Extract the sources id
         first_row = models_result[0]._mapping
         data_to_return["internal_model_id"] = str(first_row["model_id"])
     except:
         error_msg =  "Failed to get id for model " + model_name + " due to error: " + traceback.format_exc()
         return False, error_msg
-    
+
     # Try to insert the model version
     model_version = model_values["model_version"]
     versions_table = db.metadata.tables['macrostrat_kg_new.model_versions']
@@ -357,7 +350,7 @@ def get_model_internal_details(request):
         # Ensure we got a result
         if len(version_result) == 0:
             raise Exception("Got zero rows matching query " + str(version_select_statement))
-        
+
         # Extract the sources id
         first_row = version_result[0]._mapping
         data_to_return["internal_version_id"] = str(first_row["version_id"])
@@ -422,8 +415,8 @@ def record_run():
     if not sucessful:
         print("Returning error of", error_msg)
         return jsonify({"error" : error_msg}), 400
-    
-    return jsonify({"sucess" : "Sucessfully processed the run"}), 200 
+
+    return jsonify({"sucess" : "Sucessfully processed the run"}), 200
 
 if __name__ == "__main__":
    app.run(host = "0.0.0.0", port = 9543, debug = True)