Merge pull request #656 from uc-cdis/fix/dbgap-combination

Fix/dbgap combination

fence/sync/sync_users.py

@@ -460,6 +460,13 @@ def _parse_csv(self, file_dict, sess, encrypted=True):
 
                     if dbgap_project not in self.project_mapping:
                         if dbgap_project not in self._projects:
+
+                            self.logger.debug(
+                                "creating Project in fence from dbGaP study: {}".format(
+                                    dbgap_project
+                                )
+                            )
+
                             project = self._get_or_create(
                                 sess, Project, auth_id=dbgap_project
                             )
@@ -858,6 +865,9 @@ def _init_projects(self, user_project, sess):
         if self.project_mapping:
             for projects in self.project_mapping.values():
                 for p in projects:
+                    self.logger.debug(
+                        "creating Project with info from project_mapping: {}".format(p)
+                    )
                     project = self._get_or_create(sess, Project, **p)
                     self._projects[p["auth_id"]] = project
         for _, projects in user_project.iteritems():
@@ -1028,6 +1038,9 @@ def _update_arborist(self, session, user_yaml):
         for path_list in self._dbgap_study_to_resources.values():
             dbgap_resource_paths.extend(path_list)
 
+        self.logger.debug("user_yaml resources: {}".format(resources))
+        self.logger.debug("dbgap resource paths: {}".format(dbgap_resource_paths))
+
         combined_resources = utils.combine_provided_and_dbgap_resources(
             resources, dbgap_resource_paths
         )

fence/sync/utils.py

@@ -139,6 +139,10 @@ def insert_segment(current, segment):
                 # In [3]: list(map(lambda x: x["name"] == "b", xs)).index(True)
                 # Out[3]: 1
                 i = list(map(lambda c: c["name"] == segment, current)).index(True)
+
+            if "subresources" not in current[i]:
+                current[i]["subresources"] = []
+
             return current[i]["subresources"]
 
         reduce(insert_segment, segments, start)

tests/dbgap_sync/test_utils.py

@@ -11,6 +11,7 @@ def test_combine_arborist_resources():
     yaml_string = """
     rbac:
       resources:
+        - name: 'root_no_subresources'
         - name: 'gen3'
           subresources:
             - name: 'programs'
@@ -36,6 +37,7 @@ def test_combine_arborist_resources():
     useryaml_resources = useryaml.get("rbac", {}).get("resources")
 
     test_paths = [
+        "/root_no_subresources",
         "/programs/phs000172",
         "/orgA/programs/phs000175",
         "/orgC/programs/phs000175",
@@ -48,7 +50,14 @@ def test_combine_arborist_resources():
         useryaml_resources, test_paths
     )
 
-    expected_roots = ["orgA", "orgB", "orgC", "programs", "gen3"]
+    expected_roots = [
+        "root_no_subresources",
+        "orgA",
+        "orgB",
+        "orgC",
+        "programs",
+        "gen3",
+    ]
     for item in combined:
         # ensure one of each of the items in expected roots
         assert item.get("name") in expected_roots
@@ -57,7 +66,9 @@ def test_combine_arborist_resources():
         subresources = _get_subresources(item)
 
         # ensure result has correct subresources
-        if item.get("name") == "orgA":
+        if item.get("name") == "root_no_subresources":
+            assert not subresources
+        elif item.get("name") == "orgA":
             program_subresources = _get_subresources(subresources["programs"])
             assert "phs000179" in program_subresources
             assert "phs000175" in program_subresources
@@ -97,4 +108,4 @@ def test_combine_arborist_resources():
 
 
 def _get_subresources(item):
-    return {subr.get("name"): subr for subr in item.get("subresources")}
+    return {subr.get("name"): subr for subr in item.get("subresources", [])}