Enhance authentication and client setup to support dynamic database configuration and improve logging for session token requests

Author: karlnyr

microSALT/utils/pubmlst/authentication.py

@@ -39,9 +39,15 @@ def get_new_session_token(self, db: str):
             consumer_key, consumer_secret, access_token, access_secret = load_auth_credentials(
                 self.service
             )
+            logger.debug(f"Consumer Key: {consumer_key}")
+            logger.debug(f"Consumer Secret: {consumer_secret}")
+            logger.debug(f"Access Token: {access_token}")
+            logger.debug(f"Access Secret: {access_secret}")
 
             url = f"{self.base_api}/db/{db}/oauth/get_session_token"
 
+            logger.debug(f"Requesting session token from URL: {url}")
+
             session = OAuth1Session(
                 consumer_key=consumer_key,
                 consumer_secret=consumer_secret,
@@ -50,6 +56,7 @@ def get_new_session_token(self, db: str):
             )
 
             response = session.get(url, headers={"User-Agent": "BIGSdb API downloader"})
+            logger.debug(f"Response Content: {response.content}")
             logger.debug(f"Response Status Code: {response.status_code}")
 
             if response.ok:

microSALT/utils/pubmlst/client.py

@@ -17,7 +17,7 @@
 class BaseClient:
     """Base client for interacting with authenticated APIs."""
 
-    def __init__(self, service: str):
+    def __init__(self, service: str, database: str = None):
         """Initialize the client with the specified service."""
         try:
             self.service = service
@@ -27,7 +27,7 @@ def __init__(self, service: str):
             self.client_auth = ClientAuthentication(service)
             service_config = get_service_config(service)
             self.base_api = service_config["base_api"]
-            self.database = service_config["database"]
+            self.database = database or service_config["database"]
             self.base_api_host = service_config["base_api_host"]
             self.session_token, self.session_secret = self.client_auth.load_session_credentials(
                 self.database
@@ -171,16 +171,16 @@ def __init__(self):
 class PasteurClient(BaseClient):
     """Client for interacting with the Pasteur authenticated API."""
 
-    def __init__(self):
+    def __init__(self, database: str):
         """Initialize the Pasteur client."""
-        super().__init__(service="pasteur")
+        super().__init__(service="pasteur", database=database)
 
 
-def get_client(service: str):
+def get_client(service: str, database: str = None):
     """Get the appropriate client for the specified service."""
     if service == "pubmlst":
         return PubMLSTClient()
     elif service == "pasteur":
-        return PasteurClient()
+        return PasteurClient(database=database)
     else:
         raise ValueError(f"Unknown service: {service}")

microSALT/utils/pubmlst/helpers.py

@@ -55,7 +55,6 @@ def get_service_config(service: str):
             "base_web": "https://bigsdb.pasteur.fr/cgi-bin/bigsdb/bigsdb.pl",
             "base_api": "https://bigsdb.pasteur.fr/api",
             "base_api_host": "bigsdb.pasteur.fr",
-            "database": "pasteur_test_seqdef",
             "auth_credentials_file_name": "pasteur_credentials.env",
             "session_credentials_file_name": "pasteur_session_credentials.json",
             "config": app.config["pasteur"],

microSALT/utils/referencer.py

@@ -48,9 +48,9 @@ def __init__(self, config, log, sampleinfo={}, force=False):
             self.sample = self.sampleinfo
         self.client = None
 
-    def set_client(self, service: str):
+    def set_client(self, service: str, database: str = None):
         """Set the client for PubMLST API interactions."""
-        self.client: BaseClient = get_client(service)
+        self.client: BaseClient = get_client(service, database)
 
     def identify_new(self, cg_id="", project=False):
         """Automatically downloads pubMLST & NCBI organisms not already downloaded"""
@@ -152,7 +152,7 @@ def fetch_external(self, force=False):
                         currver = self.db_access.get_version("profile_{}".format(organ))
                         st_link = entry.find("./mlst/database/profiles/url").text
                         service: str = get_service_by_url(st_link)
-                        self.set_client(service)
+                        self.set_client(service, database=organ)
                         # Parse the database name and scheme ID
                         try:
                             parsed_data = self.client.parse_url(url=st_link)