Add shared module for handling obsolescence chains / revisions

Author: rogerdahl

lib_common/src/d1_common/revision.py

@@ -0,0 +1,95 @@
+# -*- coding: utf-8 -*-
+
+# This work was created by participants in the DataONE project, and is
+# jointly copyrighted by participating institutions in DataONE. For
+# more information on DataONE, see our web site at http://dataone.org.
+#
+#   Copyright 2009-2016 DataONE
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""Utilities for working with revision / obsolescence chains
+"""
+from __future__ import absolute_import
+
+import d1_common.util
+import d1_common.xml
+
+
+def get_identifiers(sysmeta_pyxb):
+  """Return: (pid, sid, obsoletes_pid, obsoleted_by_pid)
+  """
+  pid = d1_common.xml.get_opt_val(sysmeta_pyxb, 'identifier')
+  sid = d1_common.xml.get_opt_val(sysmeta_pyxb, 'seriesId')
+  obsoletes_pid = d1_common.xml.get_opt_val(sysmeta_pyxb, 'obsoletes')
+  obsoleted_by_pid = d1_common.xml.get_opt_val(sysmeta_pyxb, 'obsoletedBy')
+  return pid, sid, obsoletes_pid, obsoleted_by_pid
+
+
+def topological_sort(unsorted_dict):
+  """Sort objects by dependency
+
+  {unconnected_dict} is a dict of PID to obsoleted PID.
+
+  Return:
+    sorted_list: A list of PIDs ordered so that all PIDs that obsolete an object
+    are listed after the object they obsolete.
+    unconnected_dict: A dict of PID to obsoleted PID of any objects that could not
+    be added to a revision chain.
+
+  {obsoletes_dict} is modified by the sort and on return holds any items that
+  could not be sorted. These items will have obsoletes PIDs that directly or
+  indirectly reference a PID that could not be sorted.
+
+  The sort works by repeatedly iterating over an unsorted list of PIDs and
+  moving PIDs to the sorted list as they become available. A PID is available to
+  be moved to the sorted list if it does not obsolete a PID or if the PID it
+  obsoletes is already in the sorted list.
+  """
+  sorted_list = []
+  sorted_set = set()
+  found = True
+  unconnected_dict = unsorted_dict.copy()
+  while found:
+    found = False
+    for pid, obsoletes_pid in unconnected_dict.items():
+      if obsoletes_pid is None or obsoletes_pid in sorted_set:
+        found = True
+        sorted_list.append(pid)
+        sorted_set.add(pid)
+        del unconnected_dict[pid]
+  return sorted_list, unconnected_dict
+
+
+def get_pids_in_revision_chain(client, did):
+  """Given a SID or a PID of any object in a chain, return a list of all PIDs in
+  the chain. The returned list is in the same order as the chain. The initial
+  PID is typically obtained by resolving a SID. If the given PID is not in a
+  chain, a list containing the single object is returned.
+  """
+
+  def req(p):
+    return d1_common.xml.get_req_val(p)
+
+  def opt(p, a):
+    return d1_common.xml.get_opt_val(p, a)
+
+  sysmeta_pyxb = client.getSystemMetadata(did)
+  # Walk to tail
+  while opt(sysmeta_pyxb, 'obsoletes'):
+    sysmeta_pyxb = client.getSystemMetadata(opt(sysmeta_pyxb, 'obsoletes'))
+  chain_pid_list = [req(sysmeta_pyxb.identifier)]
+  # Walk from tail to head, recording traversed PIDs
+  while opt(sysmeta_pyxb, 'obsoletedBy'):
+    sysmeta_pyxb = client.getSystemMetadata(opt(sysmeta_pyxb, 'obsoletedBy'))
+    chain_pid_list.append(req(sysmeta_pyxb.identifier))
+  return chain_pid_list

lib_common/src/d1_common/util.py

@@ -143,11 +143,11 @@ def count(self, event_str, inc_int=1):
     self._event_dict.setdefault(event_str, 0)
     self._event_dict[event_str] += inc_int
 
-  def log_and_count(self, event_str, log_str=None, inc_int=1):
+  def log_and_count(self, event_str, msg_str=None, inc_int=1):
     """{event_str} is both a key for the count and part of the log message.
     {log_str} is a message with details that may change for each call
     """
-    logging.info(event_str + ('. ' + log_str if log_str else ''))
+    logging.info(u'{} - {}: {}'.format(event_str, msg_str, inc_int))
     self.count(event_str, inc_int)
 
   def dump_to_log(self):