[#746] establish default order for replicas listed by an iRODSDataObject

irods/data_object.py

@@ -1,8 +1,9 @@
+import ast
+import datetime
 import io
-import sys
 import logging
 import os
-import ast
+import sys
 
 from irods.models import DataObject
 from irods.meta import iRODSMetaCollection
@@ -41,11 +42,30 @@
         return "<{}.{} {}>".format(self.__class__.__module__, self.__class__.__name__, self.resource_name)
 
 
+_REPL_STATUSES = (1, 0, 2, 3, 4)
+_REFERENCE_DATETIME = datetime.datetime(1970, 1, 1, 0, 0, 0, tzinfo=datetime.timezone.utc)
+
+
+def _REPLICA_NUMBER_SORT_KEY_FN(row):
+    return row[DataObject.replica_number]
+
+def _REPLICA_FITNESS_SORT_KEY_FN(row):
+    repl_status = int(row[DataObject.replica_status])
+
+    repl_status_rank = _REPL_STATUSES.index(repl_status) if _REPL_STATUSES.count(repl_status) else sys.maxsize
+
+    return (repl_status_rank, _REFERENCE_DATETIME - row[DataObject.modify_time])
+
+
+_DEFAULT_SORT_KEY_FN = _REPLICA_NUMBER_SORT_KEY_FN
+
+
 class iRODSDataObject:
-    def __init__(self, manager, parent=None, results=None):
+    def __init__(self, manager, parent=None, results=None, replica_sort_function=None):
         self.manager = manager
         if parent and results:
             self.collection = parent
+            results = sorted(results, key=(replica_sort_function or _DEFAULT_SORT_KEY_FN))
             for attr, value in DataObject.__dict__.items():
                 if not attr.startswith("_"):
                     try:
@@ -54,9 +74,8 @@
                         # backward compatibility with older schema versions
                         pass
             self.path = self.collection.path + "/" + self.name
-            replicas = sorted(results, key=lambda r: r[DataObject.replica_number])
 
-            # The status quo before iRODS 5
+            # Copy pre-iRODS 5 fields
 
             replica_args = [
                 (
@@ -75,13 +94,13 @@
                         modify_time=r[DataObject.modify_time],
                     ),
                 )
-                for r in replicas
+                for r in results
             ]
 
             # Adjust for adding access_time in the iRODS 5 case.
 
             if self.manager.sess.server_version >= (5,):
-                for n, r in enumerate(replicas):
+                for n, r in enumerate(results):
                     replica_args[n][1]['access_time'] = r[DataObject.access_time]
             self.replicas = [iRODSReplica(*a, **k) for a, k in replica_args]
 

irods/manager/data_object_manager.py

@@ -218,13 +218,13 @@
             if size is not None and isinstance(open_options, dict):
                 open_options[kw.DATA_SIZE_KW] = size
 
-    def _download(self, obj, local_path, num_threads, updatables=(), **options):
+    def _download(self, obj_path, local_path, num_threads, updatables=(), **options):
         """Transfer the contents of a data object to a local file.
 
         Called from get() when a local path is named.
         """
         if os.path.isdir(local_path):
-            local_file = os.path.join(local_path, irods_basename(obj))
+            local_file = os.path.join(local_path, irods_basename(obj_path))
         else:
             local_file = local_path
 
@@ -233,12 +233,12 @@
             raise ex.OVERWRITE_WITHOUT_FORCE_FLAG
 
         data_open_returned_values_ = {}
-        with self.open(obj, "r", returned_values=data_open_returned_values_, **options) as o:
+        with self.open(obj_path, "r", returned_values=data_open_returned_values_, **options) as o:
             if self.should_parallelize_transfer(num_threads, o, open_options=options.items()):
                 error = RuntimeError("parallel get failed")
                 try:
                     if not self.parallel_get(
-                        (obj, o),
+                        (obj_path, o),
                         local_file,
                         num_threads=num_threads,
                         target_resource_name=options.get(kw.RESC_NAME_KW, ""),
@@ -265,6 +265,8 @@
         """
         parent = self.sess.collections.get(irods_dirname(path))
 
+        replica_sort_function = options.pop('replica_sort_function', None)
+
         # TODO: optimize
         if local_path:
             self._download(path, local_path, num_threads=num_threads, updatables=updatables, **options)
@@ -284,7 +286,7 @@
         results = query.all()  # get up to max_rows replicas
         if len(results) <= 0:
             raise ex.DataObjectDoesNotExist()
-        return iRODSDataObject(self, parent, results)
+        return iRODSDataObject(self, parent, results, replica_sort_function=replica_sort_function)
 
     @staticmethod
     def _resolve_force_put_option(options, default_setting=None, true_value=""):
@@ -304,36 +306,38 @@
         else:
             del options[kw.FORCE_FLAG_KW]
 
     def put(
         self,
         local_path,
         irods_path,
         return_data_object=False,
         num_threads=DEFAULT_NUMBER_OF_THREADS,
         updatables=(),
         **options,
     ):
         # Decide if a put option should be used and modify options accordingly.
         self._resolve_force_put_option(options, default_setting=client_config.data_objects.force_put_by_default)
 
         if self.sess.collections.exists(irods_path):
-            obj = iRODSCollection.normalize_path(irods_path, os.path.basename(local_path))
+            obj_path = iRODSCollection.normalize_path(irods_path, os.path.basename(local_path))
         else:
-            obj = irods_path
-            if kw.FORCE_FLAG_KW not in options and self.exists(obj):
+            obj_path = irods_path
+            if kw.FORCE_FLAG_KW not in options and self.exists(obj_path):
                 raise ex.OVERWRITE_WITHOUT_FORCE_FLAG
         options.pop(kw.FORCE_FLAG_KW, None)
 
+        replica_sort_function = options.pop('replica_sort_function', None)
+
         with open(local_path, "rb") as f:
             sizelist = []
             if self.should_parallelize_transfer(num_threads, f, measured_obj_size=sizelist, open_options=options):
-                o = deferred_call(self.open, (obj, "w"), options)
+                o = deferred_call(self.open, (obj_path, "w"), options)
                 f.close()
                 error = RuntimeError("parallel put failed")
                 try:
                     if not self.parallel_put(
                         local_path,
-                        (obj, o),
+                        (obj_path, o),
                         total_bytes=sizelist[0],
                         num_threads=num_threads,
                         target_resource_name=options.get(kw.RESC_NAME_KW, "") or options.get(kw.DEST_RESC_NAME_KW, ""),
@@ -346,7 +350,7 @@
                 except BaseException as e:
                     raise error from e
             else:
-                with self.open(obj, "w", **options) as o:
+                with self.open(obj_path, "w", **options) as o:
                     # Set operation type to trigger acPostProcForPut
                     if kw.OPR_TYPE_KW not in options:
                         options[kw.OPR_TYPE_KW] = 1  # PUT_OPR
@@ -360,10 +364,10 @@
             # Requested to register checksum without verifying, but source replica has a checksum. This can result
             # in multiple replicas being marked good with different checksums, which is an inconsistency.
             del repl_options[kw.REG_CHKSUM_KW]
-            self.replicate(obj, **repl_options)
+            self.replicate(obj_path, **repl_options)
 
         if return_data_object:
-            return self.get(obj)
+            return self.get(obj_path, replica_sort_function=replica_sort_function)
 
     def chksum(self, path, **options):
         """
@@ -480,6 +484,7 @@
             raise ex.DataObjectExistsAtLogicalPath
 
         options = {**options, kw.DATA_TYPE_KW: "generic"}
+        replica_sort_function = options.pop('replica_sort_function', None)
 
         if resource:
             options[kw.DEST_RESC_NAME_KW] = resource
@@ -508,7 +513,7 @@
             desc = response.int_info
             conn.close_file(desc)
 
-        return self.get(path)
+        return self.get(path, replica_sort_function=replica_sort_function)
 
     def open_with_FileRaw(self, *arg, **kw_options):
         holder = []

irods/test/data_obj_test.py

@@ -49,26 +49,26 @@
     return localhost_with_optional_domain_pattern.match(name.lower()) or is_localhost_ip(name)
 
 
 from irods.access import iRODSAccess
 from irods.models import Collection, DataObject
 from irods.path import iRODSPath
 from irods.test.helpers import iRODSUserLogins
 import irods.exception as ex
 from irods.column import Criterion
-from irods.data_object import chunks, irods_dirname
+from irods.data_object import chunks, irods_dirname, _REPLICA_FITNESS_SORT_KEY_FN
 import irods.test.helpers as helpers
 import irods.test.modules as test_modules
 import irods.keywords as kw
 import irods.client_configuration as config
 from irods.manager import data_object_manager
 from irods.message import RErrorStack
 from irods.message import ET, XML_Parser_Type, default_XML_parser, current_XML_parser
 from datetime import datetime, timezone, timedelta
 from tempfile import NamedTemporaryFile, gettempdir, mktemp
 from irods.test.helpers import unique_name, my_function_name
 from irods.ticket import Ticket
 import irods.parallel
 from irods.manager.data_object_manager import Server_Checksum_Warning
 
 RODSUSER = "nonadmin"
 
@@ -1253,8 +1253,7 @@
 
         # assertions on replicas
         self.assertEqual(len(obj.replicas), number_of_replicas)
-        for i, replica in enumerate(obj.replicas):
-            self.assertEqual(replica.number, i)
+        self.assertEqual({repl.number for repl in obj.replicas}, {*range(len(obj.replicas))})
 
         # now trim odd-numbered replicas
         # note (see irods/irods#4861): COPIES_KW might disappear in the future
@@ -1267,10 +1266,7 @@
         obj = session.data_objects.get(obj_path)
 
         # check remaining replica numbers
-        replica_numbers = []
-        for replica in obj.replicas:
-            replica_numbers.append(replica.number)
-        self.assertEqual(replica_numbers, [0, 2, 4, 6])
+        self.assertEqual({r.number for r in obj.replicas}, {0, 2, 4, 6})
 
         # remove object
         obj.unlink(force=True)
@@ -1728,11 +1724,12 @@
             self.assertIsNotNone(obj.replicas[1].__getattribute__(i))
 
         # ensure replica info is sensible
+        replicas = sorted(obj.replicas, key=lambda repl: repl.number)
         for i in range(2):
-            self.assertEqual(obj.replicas[i].number, i)
-            self.assertEqual(obj.replicas[i].status, "1")
-            self.assertEqual(obj.replicas[i].path.split("/")[-1], filename)
-            self.assertEqual(obj.replicas[i].resc_hier.split(";")[-1], ufs_resources[i].name)
+            self.assertEqual(replicas[i].number, i)
+            self.assertEqual(replicas[i].status, "1")
+            self.assertEqual(replicas[i].path.split("/")[-1], filename)
+            self.assertEqual(replicas[i].resc_hier.split(";")[-1], ufs_resources[i].name)
 
         self.assertEqual(obj.replicas[0].resource_name, ufs_resources[0].name)
         if self.sess.server_version < (4, 2, 0):
@@ -2992,6 +2989,49 @@
 
         test_put__issue_722(self)
 
+    def test_modified_sorting_of_replicas__issue_746(self):
+        basename = unique_name(my_function_name(), datetime.now()) + '_dataobj_647'
+        with self.create_simple_resc() as newResc1, self.create_simple_resc() as newResc2:
+            data = helpers.make_object(self.sess, f'{helpers.home_collection(self.sess)}/{basename}')
+
+            # Precondition for an eventual total of 3 replicas: initial data replica is not on either of the new resources.
+            self.assertFalse({repl.resource_name for repl in data.replicas} & {newResc1, newResc2})
+            try:
+                data.replicate(resource=newResc1)
+
+                # Ensure that one of the replicas is stale, to test proper sorting.
+                with data.open('a', **{kw.RESC_NAME_KW: newResc1}) as f:
+                    f.write(b'.')
+                time.sleep(2)
+
+                data.replicate(resource=newResc2)
+
+                # At this point, there should ensure exactly two good replicas of the three.
+                # Assert exactly one replica is stale, to corroborate 
+                data = self.sess.data_objects.get(
+                    data.path, 
+                    replica_sort_function=lambda row: int(row[DataObject.replica_status])
+                )
+                self.assertEqual(
+                    [repl.status for repl in data.replicas],
+                    ['0', '1', '1']
+                )
+
+                options = {}
+                if irods.version.version_as_tuple() < (4,):
+                    options['replica_sort_function'] = _REPLICA_FITNESS_SORT_KEY_FN
+
+                # Get a data object with the PRC3-alternative/PRC4-default sort order.
+                data = self.sess.data_objects.get(data.path, **options)
+
+                # Test default replica sorting.
+                self.assertEqual(data.replicas[0].status, '1')
+                self.assertEqual(data.replicas[0].modify_time, data.modify_time)
+                self.assertGreater(data.replicas[0].modify_time, data.replicas[1].modify_time)
+            finally:
+                if data:
+                    data.unlink(force=True)
+
 
 if __name__ == "__main__":
     # let the tests find the parent irods lib