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

README.md

@@ -453,6 +453,18 @@ ensure the lifetime of the updatable instance extends beyond the time needed for
 
 See `irods/test/data_obj_test.py` for examples of these and other subtleties of progress bar usage.
 
+Replica access and sorting
+--------------------------
+
+The `replicas` member of an instance of `iRODSDataObject` allows a view into the various replicas that exist under a
+given logical path.  For an example of this, jump forward to [working with data objects](#working-with-data-objects-files).
+
+Note that a `replica_sort_function` option exists in the `iRODSDataObject` constructor and in
+`<session_object>.data_objects.get`. If `replica_sort_function` is not specified, the replicas
+list contained in the returned object will be sorted according to replica number
+(REPLICA_NUMBER_SORT_KEY_FN) in PRC < v4 or by general fitness to be considered a
+good representation of that object (REPLICA_FITNESS_SORT_KEY_FN) in PRC >= v4.  For those definitions, see `irods/data_object.py`.
+
 Working with collections (directories)
 --------------------------------------
 

irods/data_object.py

@@ -1,14 +1,24 @@
+"""
+Interface for iRODS data objects.
+
+Provides high level abstraction and POSIX-like facilities (create, open,
+read/write) allowing clients to manipulate data objects very much as if they
+were local files.
+"""
+
+import ast
+import enum
 import io
-import sys
 import logging
 import os
-import ast
+import sys
+from datetime import datetime, timezone
 
-from irods.models import DataObject
-from irods.meta import iRODSMetaCollection
 import irods.keywords as kw
 from irods.api_number import api_number
 from irods.message import JSON_Message, iRODSMessage
+from irods.meta import iRODSMetaCollection
+from irods.models import DataObject
 
 logger = logging.getLogger(__name__)
 
@@ -41,11 +51,57 @@ def __repr__(self):
         return "<{}.{} {}>".format(self.__class__.__module__, self.__class__.__name__, self.resource_name)
 
 
+class _repl_status(enum.Enum):  # noqa: N801
+    STALE_REPLICA, GOOD_REPLICA, INTERMEDIATE_REPLICA, READ_LOCKED, WRITE_LOCKED = range(5)
+
+
+# An ordering of the various replica status values, by descending fitness for use/interface
+_REPL_STATUSES = tuple(
+    getattr(_repl_status, ident).value
+    for ident in (
+        "GOOD_REPLICA",
+        "STALE_REPLICA",
+        "INTERMEDIATE_REPLICA",
+        "READ_LOCKED",
+        "WRITE_LOCKED",
+    )
+)
+
+# An appropriate reference datetime value for gauging replica age as part of
+# the default sort key in PRC4 and onward.
+_REFERENCE_DATETIME = datetime.fromtimestamp(0, timezone.utc)
+
+# ruff: noqa: D103 off
+
+# Key functions to dictate how replica row results will be sorted within an iRODSDataObject.
+
+
+def REPLICA_NUMBER_SORT_KEY_FN(row):  # noqa: N802
+    return row[DataObject.replica_number]
+
+
+def REPLICA_FITNESS_SORT_KEY_FN(row):  # noqa: N802
+    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])
+
+
+# ruff: noqa: D103 on
+
+_DEFAULT_SORT_KEY_FN = REPLICA_NUMBER_SORT_KEY_FN
+
+
 class iRODSDataObject:
-    def __init__(self, manager, parent=None, results=None):
+    # iRODSDataObject's constructor is not usually directly accessed by iRODS client applications.  See the main README.
+    # ruff: noqa: D107 off
+
+    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 +110,8 @@ def __init__(self, manager, parent=None, results=None):
                         # 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 = [
                 (
@@ -75,18 +130,20 @@ def __init__(self, manager, parent=None, results=None):
                         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]
 
         self._meta = None
 
+    # ruff: noqa: D107 off
+
     def __repr__(self):
         return f"<iRODSDataObject {self.id} {self.name}>"
 

irods/manager/data_object_manager.py

@@ -6,37 +6,36 @@
 import os
 import weakref
 from typing import Any, List, Type
-from irods.models import DataObject, Collection
-from irods.manager import Manager
-from irods.manager._internal import _api_impl, _logical_path
-from irods.message import (
-    iRODSMessage,
-    FileOpenRequest,
-    ObjCopyRequest,
-    StringStringMap,
-    DataObjInfo_for_session,
-    ModDataObjMeta_for_session,
-    DataObjChksumRequest,
-    DataObjChksumResponse,
-    RErrorStack,
-    STR_PI,
-)
+
+import irods.client_configuration as client_config
 import irods.exception as ex
+import irods.keywords as kw
+from irods import parallel
 from irods.api_number import api_number
 from irods.collection import iRODSCollection
 from irods.data_object import (
-    iRODSDataObject,
-    iRODSDataObjectFileRaw,
     chunks,
-    irods_dirname,
     irods_basename,
+    irods_dirname,
+    iRODSDataObject,
+    iRODSDataObjectFileRaw,
 )
-import irods.client_configuration as client_config
-import irods.keywords as kw
-import irods.parallel as parallel
+from irods.manager import Manager
+from irods.manager._internal import _api_impl, _logical_path
+from irods.message import (
+    STR_PI,
+    DataObjChksumRequest,
+    DataObjChksumResponse,
+    DataObjInfo_for_session,
+    FileOpenRequest,
+    ModDataObjMeta_for_session,
+    ObjCopyRequest,
+    StringStringMap,
+    iRODSMessage,
+)
+from irods.models import Collection, DataObject
 from irods.parallel import deferred_call
 
-
 logger = logging.getLogger(__name__)
 
 _update_types: List[Type] = []
@@ -218,27 +217,29 @@ def should_parallelize_transfer(
             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))
-        else:
-            local_file = local_path
+
+        local_file = (
+            os.path.join(local_path, irods_basename(obj_path))  # noqa: PTH118
+            if os.path.isdir(local_path)  # noqa: PTH112
+            else local_path
+        )
 
         # Check for force flag if local_file exists
         if os.path.exists(local_file) and kw.FORCE_FLAG_KW not in options:
             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, ""),
@@ -256,12 +257,46 @@ def _download(self, obj, local_path, num_threads, updatables=(), **options):
                         f.write(chunk)
                         do_progress_updates(updatables, len(chunk))
 
-    def get(self, path, local_path=None, num_threads=DEFAULT_NUMBER_OF_THREADS, updatables=(), **options):
+    def get(
+        self,
+        path,
+        local_path=None,
+        num_threads=DEFAULT_NUMBER_OF_THREADS,
+        updatables=(),
+        replica_sort_function=None,
+        **options,
+    ):
         """
-        Get a reference to the data object at the specified `path'.
-
-        Only download the object if the local_path is a string (specifying
-        a path in the local filesystem to use as a destination file).
+        Create an iRODSDataObject instance representing the data object at the specified path.
+
+        If local_path is not None, it names a local file to which the content of the
+        data object will be downloaded.
+
+        Args:
+            path: an absolute logical path where the data object may be found.
+            local_path: a filename within the local filesystem, the target for download ("GET") of the data
+                object if one is requested.  Directory components in the path must already exist.
+            num_threads: in the case of a parallel data transfer (for large files), specifies the number of
+                transfer control threads to be spawned. If not specified, this number will be DEFAULT_NUMBER_OF_THREADS,
+                i.e. a reasonable small integer value.
+            updatables: a tuple or list in which each element is a tqdm-like progress bar object, or the equivalent:
+                an instance on which func.update(n) can be called with n being the number of bytes successfully
+                copied in the data transfer increment just completed.  If not a tuple or list, this argument
+                is interpreted as a single updatable.  The parameter defaults to (), meaning no such objects will be
+                slated for update.
+            replica_sort_function: a sort key function dictating the order of replica query results in 'self.replicas'.
+                If not specified, a default value of None will cause irods.data_objects._DEFAULT_SORT_KEY_FN to be
+                selected to determine the sort order.
+            **options: a combination of possible iRODS keyword options to be relayed to the data object open() call.
+                For a download request, FORCE_FLAG_KW may be used to ensure any pre-existing file at the 'local_path'
+                will be overwritten.
+
+        Returns:
+            an iRODSDataObject representing the object at the given path.
+
+        Raises:
+            DataObjectDoesNotExist: if the specified path does not exist, or exists as a collection rather than a data
+                object.
         """
         parent = self.sess.collections.get(irods_dirname(path))
 
@@ -284,7 +319,7 @@ def get(self, path, local_path=None, num_threads=DEFAULT_NUMBER_OF_THREADS, upda
         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=""):
@@ -317,23 +352,25 @@ def put(
         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))  # noqa: PTH119
         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 +383,7 @@ def put(
                 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 +397,11 @@ def put(
             # 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)
+        return None
 
     def chksum(self, path, **options):
         """
@@ -480,6 +518,7 @@ def create(
             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 +547,7 @@ def create(
             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 = []