Merge branch 'rc4.2.0' into feat-pubmlst-util-retry

Author: karlnyr

.github/workflows/run_tests.yml

@@ -9,16 +9,13 @@ env:
 
 jobs:
   build-linux:
-    runs-on: ubuntu-20.04
-    strategy:
-      max-parallel: 5
-
+    runs-on: ubuntu-latest
+    container:
+      image: python:3.6-slim
+  
     steps:
     - uses: actions/checkout@v4
-    - name: Set up Python 3.6
-      uses: actions/setup-python@v3
-      with:
-        python-version: '3.6.15'
+
     - name: Create conda/mamba environment using micromamba
       uses: mamba-org/setup-micromamba@v1
       with:

configExample.json

@@ -33,8 +33,8 @@
     "resistances": "/tmp/MLST/references/resistances",
     "_comment": "Download path for NCBI genomes, for alignment usage",
     "genomes": "/tmp/MLST/references/genomes",
-    "_comment": "PubMLST credentials",
-    "pubmlst_credentials": "/tmp/MLST/credentials"
+    "_comment": "Credentials",
+    "credentials": "/tmp/MLST/credentials"
   },
   "_comment": "Database/Flask configuration",
   "database": {
@@ -75,9 +75,13 @@
     "username": "limsuser",
     "password": "mypassword"
   },
-  "_comment": "PubMLST credentials",
+  "_comment": "Credentials",
   "pubmlst": {
     "client_id": "",
     "client_secret": ""
+  },
+  "pasteur": {
+    "client_id": "",
+    "client_secret": ""
   }
 }

microSALT/__init__.py

@@ -52,13 +52,9 @@
 
         # Ensure PubMLST configuration is included
 
-        app.config["pubmlst"] = preset_config.get("pubmlst", {
-            "client_id": "",
-            "client_secret": ""        
-            })
-
         app.config["pubmlst"] = preset_config.get("pubmlst", {"client_id": "", "client_secret": ""})
 
+        app.config["pasteur"] = preset_config.get("pasteur", {"client_id": "", "client_secret": ""})
 
         # Add extrapaths to config
         preset_config["folders"]["expec"] = os.path.abspath(

microSALT/utils/pubmlst/authentication.py

@@ -5,116 +5,142 @@
 from dateutil import parser
 from rauth import OAuth1Session
 
-from microSALT import logger
+from microSALT import app, logger
 from microSALT.utils.pubmlst.exceptions import (
-    PUBMLSTError,
+    PubMLSTError,
     SessionTokenRequestError,
     SessionTokenResponseError,
 )
 from microSALT.utils.pubmlst.helpers import (
-    BASE_API,
-    credentials_path_key,
     folders_config,
     get_path,
+    get_service_config,
     load_auth_credentials,
-    pubmlst_session_credentials_file_name,
     save_session_token,
 )
+from microSALT.utils.pubmlst.constants import CREDENTIALS_KEY
 
 session_token_validity = 12  # 12-hour validity
 session_expiration_buffer = 60  # 60-second buffer
 
 
-def get_new_session_token(db: str):
-    """Request a new session token using all credentials for a specific database."""
-    logger.debug(f"Fetching a new session token for database '{db}'...")
+class ClientAuthentication:
 
-    try:
-        consumer_key, consumer_secret, access_token, access_secret = load_auth_credentials()
+    def __init__(self, service: str):
+        """Initialize the client with the specified service."""
+        self.service: str = service
+        self.service_config: dict = get_service_config(service)
+        self.base_api: str = self.service_config["base_api"]
 
-        url = f"{BASE_API}/db/{db}/oauth/get_session_token"
+    def get_new_session_token(self, db: str):
+        """Request a new session token using all credentials for a specific database."""
 
-        session = OAuth1Session(
-            consumer_key=consumer_key,
-            consumer_secret=consumer_secret,
-            access_token=access_token,
-            access_token_secret=access_secret,
-        )
+        try:
+            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"
 
-        response = session.get(url, headers={"User-Agent": "BIGSdb API downloader"})
-        logger.debug(f"Response Status Code: {response.status_code}")
+            logger.debug(f"Requesting session token from URL: {url}")
 
-        if response.ok:
-            try:
-                token_data = response.json()
-                session_token = token_data.get("oauth_token")
-                session_secret = token_data.get("oauth_token_secret")
+            session = OAuth1Session(
+                consumer_key=consumer_key,
+                consumer_secret=consumer_secret,
+                access_token=access_token,
+                access_token_secret=access_secret,
+            )
 
-                if not session_token or not session_secret:
-                    raise SessionTokenResponseError(
-                        db, "Missing 'oauth_token' or 'oauth_token_secret' in response."
+            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:
+                try:
+                    token_data = response.json()
+                    session_token = token_data.get("oauth_token")
+                    session_secret = token_data.get("oauth_token_secret")
+
+                    if not session_token or not session_secret:
+                        raise SessionTokenResponseError(
+                            db, "Missing 'oauth_token' or 'oauth_token_secret' in response."
+                        )
+
+                    expiration_time = datetime.now() + timedelta(hours=session_token_validity)
+
+                    save_session_token(
+                        service=self.service,
+                        db=db,
+                        token=session_token,
+                        secret=session_secret,
+                        expiration_date=expiration_time,
                     )
+                    return session_token, session_secret
+
+                except (ValueError, KeyError) as e:
+                    raise SessionTokenResponseError(db, f"Invalid response format: {str(e)}")
+            else:
+                raise SessionTokenRequestError(db, response.status_code, response.text)
+
+        except PubMLSTError as e:
+            logger.error(f"Error during token fetching: {e}")
+            raise
+        except Exception as e:
+            logger.error(f"Unexpected error: {e}")
+            raise PubMLSTError(
+                f"Unexpected error while fetching session token for database '{db}': {e}"
+            )
 
-                expiration_time = datetime.now() + timedelta(hours=session_token_validity)
+    def load_session_credentials(
+        self,
+        db: str,
+    ):
+        """Load session token from file for a specific database."""
+        try:
+            credentials_file = os.path.join(
+                get_path(folders_config, CREDENTIALS_KEY),
+                self.service_config["session_credentials_file_name"],
+            )
+
+            if not os.path.exists(credentials_file):
+                logger.debug("Session file does not exist. Fetching a new session token.")
+                return self.get_new_session_token(db)
+
+            with open(credentials_file, "r") as f:
+                try:
+                    all_sessions = json.load(f)
+                except json.JSONDecodeError as e:
+                    raise SessionTokenResponseError(db, f"Failed to parse session file: {str(e)}")
+
+            db_session_data = all_sessions.get("databases", {}).get(db)
+            if not db_session_data:
+                logger.debug(
+                    f"No session token found for database '{db}'. Fetching a new session token."
+                )
+                return self.get_new_session_token(db)
+
+            expiration = parser.parse(db_session_data.get("expiration", ""))
+            if datetime.now() < expiration - timedelta(seconds=session_expiration_buffer):
+                logger.debug(f"Using existing session token for database '{db}'.")
+                session_token = db_session_data.get("token")
+                session_secret = db_session_data.get("secret")
 
-                save_session_token(db, session_token, session_secret, expiration_time)
                 return session_token, session_secret
 
-            except (ValueError, KeyError) as e:
-                raise SessionTokenResponseError(db, f"Invalid response format: {str(e)}")
-        else:
-            raise SessionTokenRequestError(db, response.status_code, response.text)
-
-    except PUBMLSTError as e:
-        logger.error(f"Error during token fetching: {e}")
-        raise
-    except Exception as e:
-        logger.error(f"Unexpected error: {e}")
-        raise PUBMLSTError(
-            f"Unexpected error while fetching session token for database '{db}': {e}"
-        )
-
-
-def load_session_credentials(db: str):
-    """Load session token from file for a specific database."""
-    try:
-        credentials_file = os.path.join(
-            get_path(folders_config, credentials_path_key), pubmlst_session_credentials_file_name
-        )
-
-        if not os.path.exists(credentials_file):
-            logger.debug("Session file does not exist. Fetching a new session token.")
-            return get_new_session_token(db)
-
-        with open(credentials_file, "r") as f:
-            try:
-                all_sessions = json.load(f)
-            except json.JSONDecodeError as e:
-                raise SessionTokenResponseError(db, f"Failed to parse session file: {str(e)}")
-
-        db_session_data = all_sessions.get("databases", {}).get(db)
-        if not db_session_data:
             logger.debug(
-                f"No session token found for database '{db}'. Fetching a new session token."
+                f"Session token for database '{db}' has expired. Fetching a new session token."
+            )
+            return self.get_new_session_token(db)
+
+        except PubMLSTError as e:
+            logger.error(f"PuBMLST-specific error occurred: {e}")
+            raise
+        except Exception as e:
+            logger.error(f"Unexpected error: {e}")
+            raise PubMLSTError(
+                f"Unexpected error while loading session token for database '{db}': {e}"
             )
-            return get_new_session_token(db)
-
-        expiration = parser.parse(db_session_data.get("expiration", ""))
-        if datetime.now() < expiration - timedelta(seconds=session_expiration_buffer):
-            logger.debug(f"Using existing session token for database '{db}'.")
-            session_token = db_session_data.get("token")
-            session_secret = db_session_data.get("secret")
-
-            return session_token, session_secret
-
-        logger.debug(
-            f"Session token for database '{db}' has expired. Fetching a new session token."
-        )
-        return get_new_session_token(db)
-
-    except PUBMLSTError as e:
-        logger.error(f"PUBMLST-specific error occurred: {e}")
-        raise
-    except Exception as e:
-        logger.error(f"Unexpected error: {e}")
-        raise PUBMLSTError(f"Unexpected error while loading session token for database '{db}': {e}")