diff --git a/src/idpyoidc/configure.py b/src/idpyoidc/configure.py
index 222146d6..62500826 100644
--- a/src/idpyoidc/configure.py
+++ b/src/idpyoidc/configure.py
@@ -3,6 +3,7 @@
 from typing import Dict
 from typing import List
 from typing import Optional
+from typing import Union
 
 from idpyoidc.logging import configure_logging
 from idpyoidc.util import load_config_file
@@ -38,6 +39,9 @@ def add_path_to_directory_name(directory_name, base_path):
 
 def add_base_path(conf: dict, base_path: str, attributes: List[str], attribute_type: str = "file"):
     for key, val in conf.items():
+        if not val:
+            continue
+
         if key in attributes:
             if attribute_type == "file":
                 conf[key] = add_path_to_filename(val, base_path)
@@ -168,7 +172,7 @@ def complete_paths(self, conf: Dict, keys: List[str], default_config: Dict, base
 
     def format(self, conf, base_path: str, domain: str, port: int,
                file_attributes: Optional[List[str]] = None,
-               dir_attributes: Optional[List[str]] = None) -> None:
+               dir_attributes: Optional[List[str]] = None) -> Union[Dict, str]:
         """
         Formats parts of the configuration. That includes replacing the strings {domain} and {port}
         with the used domain and port and making references to files and directories absolute
@@ -183,11 +187,17 @@ def format(self, conf, base_path: str, domain: str, port: int,
         """
         if isinstance(conf, dict):
             if file_attributes:
-                add_base_path(conf, base_path, file_attributes, attribute_type="file")
+                conf = add_base_path(conf, base_path, file_attributes, attribute_type="file")
             if dir_attributes:
-                add_base_path(conf, base_path, dir_attributes, attribute_type="dir")
+                conf = add_base_path(conf, base_path, dir_attributes, attribute_type="dir")
             if isinstance(conf, dict):
-                set_domain_and_port(conf, domain=domain, port=port)
+                conf = set_domain_and_port(conf, domain=domain, port=port)
+        elif isinstance(conf, list):
+            conf = [_conv(v, domain=domain, port=port) for v in conf]
+        elif isinstance(conf, str):
+            conf = _conv(conf, domain, port)
+
+        return conf
 
 
 class Configuration(Base):
@@ -215,10 +225,20 @@ def __init__(self,
         self.web_conf = lower_or_upper(self.conf, "webserver")
 
         if entity_conf:
+            skip = [ec["path"] for ec in entity_conf]
+
             self.extend(conf=self.conf, base_path=base_path,
                         domain=self.domain, port=self.port, entity_conf=entity_conf,
                         file_attributes=self._file_attributes,
                         dir_attributes=self._dir_attributes)
+            for key, val in conf.items():
+                for path in skip:
+                    if key == path[0]:
+                        continue
+                setattr(self, key, val)
+        else:
+            for key, val in conf.items():
+                setattr(self, key, val)
 
 
 def create_from_config_file(cls,
diff --git a/src/idpyoidc/server/configure.py b/src/idpyoidc/server/configure.py
index d3cfbace..3dfb1928 100755
--- a/src/idpyoidc/server/configure.py
+++ b/src/idpyoidc/server/configure.py
@@ -168,7 +168,8 @@ def __init__(
     ):
 
         conf = copy.deepcopy(conf)
-        Base.__init__(self, conf, base_path, file_attributes, dir_attributes=dir_attributes)
+        Base.__init__(self, conf, base_path, file_attributes=file_attributes,
+                      dir_attributes=dir_attributes, domain=domain, port=port)
 
         self.key_conf = conf.get('key_conf')
 
@@ -176,9 +177,8 @@ def __init__(
             _val = conf.get(key)
             if not _val:
                 if key in self.default_config:
-                    _val = copy.deepcopy(self.default_config[key])
-                    self.format(
-                        _val,
+                    _val = self.format(
+                        copy.deepcopy(self.default_config[key]),
                         base_path=base_path,
                         file_attributes=file_attributes,
                         domain=domain,
@@ -466,7 +466,9 @@ def __init__(
         "jwks_def": {
             "private_path": "private/token_jwks.json",
             "read_only": False,
-            "key_defs": [{"type": "oct", "bytes": "24", "use": ["enc"], "kid": "code"}],
+            "key_defs": [
+                {"type": "oct", "bytes": "24", "use": ["enc"], "kid": "code"}
+            ],
         },
         "code": {"kwargs": {"lifetime": 600}},
         "token": {