Ensure directories exist

microSALT/utils/referencer.py

@@ -35,9 +35,40 @@ def resolve_path(path):
         path = os.path.abspath(path)
     return path
 
+def resolve_config_paths(self, config):
+    # Ensure all paths in 'folders' are resolved
+    if 'folders' in config:
+        for key, value in config['folders'].items():
+            if isinstance(value, str) and '/' in value:
+                config['folders'][key] = resolve_path(value)
+
+    # Resolve pubmlst credentials_files_path if present
+    if 'pubmlst' in config and 'credentials_files_path' in config['pubmlst']:
+        config['pubmlst']['credentials_files_path'] = resolve_path(config['pubmlst']['credentials_files_path'])
+
+    return config
+
+def ensure_directories(self):
+    """Ensure all required directories are created."""
+    required_dirs = [
+        self.config["folders"].get("results"),
+        self.config["folders"].get("reports"),
+        self.config["folders"].get("profiles"),
+        self.config["folders"].get("references"),
+        self.config["folders"].get("resistances"),
+        self.config["folders"].get("genomes"),
+    ]
+    for dir_path in required_dirs:
+        if dir_path:
+            resolved_path = resolve_path(dir_path)
+            os.makedirs(resolved_path, exist_ok=True)
+            self.logger.info(f"Ensured directory exists: {resolved_path}")
+
+
 class Referencer:
     def __init__(self, config, log, sampleinfo={}, force=False):
         self.config = self.resolve_config_paths(config)
+        self.ensure_directories() 
         self.logger = log
         self.db_access = DB_Manipulator(config, log)
         self.updated = list()
@@ -70,7 +101,7 @@ def __init__(self, config, log, sampleinfo={}, force=False):
             self.token, self.secret = get_new_session_token(default_db)
 
     def resolve_config_paths(self, config):
-        # Resolve all folder paths
+        # Ensure all paths in 'folders' are resolved
         if 'folders' in config:
             for key, value in config['folders'].items():
                 if isinstance(value, str) and '/' in value:
@@ -125,6 +156,7 @@ def update_refs(self):
     def index_db(self, full_dir, suffix):
         """Check for indexation, makeblastdb job if not enough of them."""
         reindexation = False
+        full_dir = resolve_path(full_dir)
         files = os.listdir(full_dir)
         sufx_files = glob.glob("{}/*{}".format(full_dir, suffix))  # List of source files
         for file in sufx_files: