Update v1_to_v2 migration for changes in dependencies

Author: rogerdahl

gmn/src/d1_gmn/app/event_log.py

@@ -36,7 +36,6 @@ def _log(pid, request, event, timestamp=None):
   """
   ip_address = request.META['REMOTE_ADDR']
   user_agent = request.META['HTTP_USER_AGENT']
-  subject = d1_gmn.app.auth.format_active_subjects()
 
   # Support logging events that are not associated with an object.
   object_model = None
@@ -51,7 +50,7 @@ def _log(pid, request, event, timestamp=None):
       raise d1_common.types.exceptions.ServiceFailure(0, err_msg)
 
   event_log_model = create_log_entry(
-    object_model, event, ip_address, user_agent, subject
+    object_model, event, ip_address, user_agent, request.primary_subject_str
   )
 
   # The datetime is an optional parameter. If it is not provided, a

gmn/src/d1_gmn/app/management/commands/import.py

@@ -275,7 +275,9 @@ def _handle(self):
       inc_int=len(revision_list)
     )
 
-    obsoletes_dict = self._revision_list_to_obsoletes_dict(revision_list)
+    obsoletes_dict = d1_common.revision.revision_list_to_obsoletes_dict(
+      revision_list
+    )
     topo_list, unconnected_dict = d1_common.revision.topological_sort(
       obsoletes_dict
     )
@@ -411,9 +413,3 @@ def _create_source_client(self):
     return d1_client.util.get_client_class_by_version_tag(self._api_major)(
       self._opt['baseurl'], **self._get_client_args_dict()
     )
-
-  def _revision_list_to_obsoletes_dict(self, revision_list):
-    return {
-      pid: obsoletes_pid
-      for pid, sid, obsoletes_pid, obsoleted_by_pid in revision_list
-    }

gmn/src/d1_gmn/app/management/commands/migrate_v1_to_v2.py

@@ -170,16 +170,26 @@ def _migrate_sciobj(self):
     revision_list = self._get_revision_list()
     # revision_list = self._load_json(UNSORTED_CHAINS_PATH)
     # self._dump_json(revision_list, UNSORTED_CHAINS_PATH)
-    obsoletes_pid_list = []
-    obsoleted_by_pid_list = []
-    for pid, sid, obsoletes_pid, obsoleted_by_pid in revision_list:
-      obsoletes_pid_list.append((pid, obsoletes_pid))
-      obsoleted_by_pid_list.append((pid, obsoleted_by_pid))
-    topo_revision_list = d1_common.revision.topological_sort(
-      obsoletes_pid_list, self._events, UNCONNECTED_CHAINS_PATH
+    obsoletes_dict = d1_common.revision.revision_list_to_obsoletes_dict(
+      revision_list
     )
-    self._create_sciobj(topo_revision_list)
-    self._update_obsoleted_by(obsoleted_by_pid_list)
+    topo_list, unconnected_dict = d1_common.revision.topological_sort(
+      obsoletes_dict
+    )
+    #
+    # obsoletes_pid_list = []
+    # obsoleted_by_pid_list = []
+    # for pid, sid, obsoletes_pid, obsoleted_by_pid in revision_list:
+    #   obsoletes_pid_list.append((pid, obsoletes_pid))
+    #   obsoleted_by_pid_list.append((pid, obsoleted_by_pid))
+    # topo_list = d1_common.revision.topological_sort(
+    #   obsoletes_pid_list
+    # )
+    self._create_sciobj(topo_list)
+    obsoleted_by_dict = d1_common.revision.revision_list_to_obsoleted_by_dict(
+      revision_list
+    )
+    self._update_obsoleted_by(obsoleted_by_dict)
 
   def _get_revision_list(self):
     revision_list = []
@@ -202,9 +212,9 @@ def _get_revision_list(self):
       revision_list.append(d1_common.revision.get_identifiers(sysmeta_pyxb))
     return revision_list
 
-  def _create_sciobj(self, topo_revision_list):
-    n = len(topo_revision_list)
-    for i, pid in enumerate(topo_revision_list):
+  def _create_sciobj(self, topo_list):
+    n = len(topo_list)
+    for i, pid in enumerate(topo_list):
       # noinspection SqlResolve
       sciobj_row = self._db.run(
         'select * from mn_scienceobject where pid = %s;',
@@ -222,9 +232,9 @@ def _create_sciobj(self, topo_revision_list):
       )
       d1_gmn.app.sysmeta.create_or_update(sysmeta_pyxb, sciobj_row['url'])
 
-  def _update_obsoleted_by(self, obsoleted_by_pid_list):
-    n = len(obsoleted_by_pid_list)
-    for i, pid_tup in enumerate(obsoleted_by_pid_list):
+  def _update_obsoleted_by(self, obsoleted_by_dict):
+    n = len(obsoleted_by_dict)
+    for i, pid_tup in enumerate(obsoleted_by_dict.items()):
       pid, obsoleted_by_pid = pid_tup
       if obsoleted_by_pid is not None:
         if d1_gmn.app.sysmeta.is_did(pid) and d1_gmn.app.sysmeta.is_did(

gmn/src/d1_gmn/app/views/external.py

@@ -604,13 +604,17 @@ def put_object(request, old_pid):
   )
   new_pid = request.POST['newPid']
   sysmeta_pyxb.obsoletes = old_pid
+
+  # SID
+  sid = d1_gmn.app.revision.get_sid(sysmeta_pyxb)
+  d1_gmn.app.views.asserts.is_valid_sid_for_chain(old_pid, sid)
+
   _create(request, sysmeta_pyxb, new_pid)
+
   # The create event for the new object is added in _create(). The update event
   # on the old object is added here.
   d1_gmn.app.revision.set_revision(old_pid, obsoleted_by_pid=new_pid)
-  # SID
-  sid = d1_gmn.app.revision.get_sid(sysmeta_pyxb)
-  d1_gmn.app.views.asserts.is_valid_sid_for_chain(old_pid, sid)
+
   # d1_gmn.app.revision.add_pid_to_chain(sid, old_pid, new_pid)
   # if d1_gmn.app.sysmeta_revision.has_sid(sysmeta_pyxb):
   #   sid = d1_gmn.app.sysmeta_revision.get_sid(sysmeta_pyxb)

gmn/src/d1_gmn/tests/test_update_with_sid.py

@@ -88,7 +88,7 @@ def test_1030(self, mn_client_v2):
       mn_client_v2, sid=None
     )
     with pytest.raises(d1_common.types.exceptions.IdentifierNotUnique):
-      self.update_obj(mn_client_v2, old_pid, sid=other_pid)
+      self.update_obj(mn_client_v2, old_pid, sid=other_sid)
 
   @responses.activate
   def test_1040(self, mn_client_v2):

lib_common/src/d1_common/revision.py

@@ -93,3 +93,17 @@ def opt(p, a):
     sysmeta_pyxb = client.getSystemMetadata(opt(sysmeta_pyxb, 'obsoletedBy'))
     chain_pid_list.append(req(sysmeta_pyxb.identifier))
   return chain_pid_list
+
+
+def revision_list_to_obsoletes_dict(revision_list):
+  return {
+    pid: obsoletes_pid
+    for pid, sid, obsoletes_pid, obsoleted_by_pid in revision_list
+  }
+
+
+def revision_list_to_obsoleted_by_dict(revision_list):
+  return {
+    pid: obsoleted_by_pid
+    for pid, sid, obsoletes_pid, obsoleted_by_pid in revision_list
+  }

test_utilities/src/d1_test/test_docs/test_cmd_migrate_v1_to_v2_migrate_v1_to_v2.sample

@@ -2,6 +2,5 @@ Events:
   Creating SciObj DB representation: 200
   Retrieving revision chains: 200
   Skipped Node registry update on CN because this MN does not appear to be registered in a DataONE environment yet.: 1
-  Sorting revision chains: 200
   Updating obsoletedBy: 42
   Whitelisted subject: 2