chore(refactor): clarify cfg comments, consolidate logic for getting …

…all projects

fence/config-default.yaml

@@ -408,7 +408,7 @@ dbGaP:
     # 'studyZ': 'test_common_exchange_area'
   # A mapping from the dbgap study / Fence project to which authorization namespaces the
   # actual data lives in. For example, `studyX` data may exist in multiple organizations, so
-  # we need to know to map authorization to all orgs resources
+  # we need to know how to map authorization to all orgs resources
   study_to_resource_namespaces:
     '_default': ['/']
     'test_common_exchange_area': ['/dbgap/']

fence/sync/sync_users.py

@@ -465,8 +465,8 @@ def _parse_csv(self, file_dict, sess, encrypted=True):
 
                         # c999 indicates full access to all consents and access
                         # to a study-specific exchange area
-                        # access to at least one study-specific exchange implies access
-                        # to the common exchange area
+                        # access to at least one study-specific exchange area implies access
+                        # to the parent study's common exchange area
                         #
                         # NOTE: Handling giving access to all consents is done at
                         #       a later time, when we have full information about possible
@@ -1083,10 +1083,8 @@ def _grant_all_consents_to_c999_users(
         access_number_matcher = re.compile(config["DBGAP_ACCESSION_WITH_CONSENT_REGEX"])
         # combine dbgap/user.yaml projects into one big list (in case not all consents
         # are in either)
-        all_projects = []
-        all_projects.extend([project for project, _ in self._projects.items()])
-        all_projects.extend(
-            [project for project, _ in user_yaml_project_to_resources.items()]
+        all_projects = set(
+            list(self._projects.keys()) + list(user_yaml_project_to_resources.keys())
         )
 
         self.logger.debug(f"all projects: {all_projects}")