Deprecate getProvenance and create get_activity

Author: BryanFauble

synapseclient/__main__.py

@@ -16,6 +16,8 @@
 import re
 import shutil
 
+import deprecated
+
 import synapseclient
 import synapseutils
 
@@ -341,7 +343,7 @@ def show(args, syn):
     syn.printEntity(ent)
     sys.stdout.write("Provenance:\n")
     try:
-        prov = syn.getProvenance(ent)
+        prov = syn.get_activity(ent)
         syn.logger.info(prov)
     except SynapseHTTPError:
         syn.logger.error("  No Activity specified.\n")
@@ -405,8 +407,8 @@ def setProvenance(args, syn):
         )
 
 
-def getProvenance(args, syn):
-    activity = syn.getProvenance(args.id, args.version)
+def get_activity(args, syn: synapseclient.Synapse):
+    activity = syn.get_activity(args.id, args.version)
 
     if args.output is None or args.output == "STDOUT":
         syn.logger.info(json.dumps(activity, sort_keys=True, indent=2))
@@ -416,6 +418,14 @@ def getProvenance(args, syn):
             f.write("\n")
 
 
+@deprecated.sphinx.deprecated(
+    version="3.1.0",
+    reason="deprecated and replaced with :py:meth:`get_activity`",
+)
+def getProvenance(args, syn: synapseclient.Synapse):
+    get_activity(args, syn)
+
+
 def setAnnotations(args, syn):
     """Method to set annotations on an entity.
 
@@ -1483,7 +1493,7 @@ def build_parser():
         type=str,
         help="Output the provenance record in JSON format",
     )
-    parser_get_provenance.set_defaults(func=getProvenance)
+    parser_get_provenance.set_defaults(func=get_activity)
 
     parser_set_annotations = subparsers.add_parser(
         "set-annotations", help="create annotations records"

synapseclient/client.py

@@ -6,6 +6,7 @@
 import collections.abc
 import configparser
 import csv
+import numbers
 import deprecated
 import errno
 import functools
@@ -846,7 +847,7 @@ def get(self, entity, **kwargs):
 
            # Determine the provenance of a locally stored file as indicated in Synapse
            entity = syn.get('/path/to/file.txt', limitSearch='syn12312')
-           print(syn.getProvenance(entity))
+           print(syn.get_activity(entity))
 
         """
         # If entity is a local file determine the corresponding synapse entity
@@ -2187,9 +2188,9 @@ def setPermissions(
     ############################################################
     #                        Provenance                        #
     ############################################################
-
-    # TODO: rename these to Activity
-    def getProvenance(self, entity, version=None):
+    def get_activity(
+        self, entity: typing.Union[Entity, str, numbers.Number], version: str = None
+    ) -> any:
         """
         Retrieve provenance information for a Synapse Entity.
 
@@ -2211,6 +2212,27 @@ def getProvenance(self, entity, version=None):
             uri = "/entity/%s/generatedBy" % id_of(entity)
         return Activity(data=self.restGET(uri))
 
+    @deprecated.sphinx.deprecated(
+        version="3.1.0",
+        reason="deprecated and replaced with :py:meth:`get_activity`",
+    )
+    def getProvenance(
+        self, entity: typing.Union[Entity, str, numbers.Number], version: str = None
+    ):
+        """
+        Deprecated and replaced with :py:meth:`get_activity`.
+
+        Retrieve provenance information for a Synapse Entity.
+
+        :param entity:  An Entity or Synapse ID to lookup
+        :param version: The version of the Entity to retrieve.
+                        Gets the most recent version if omitted
+
+        :returns: An Activity object or
+                  raises exception if no provenance record exists
+        """
+        return self.get_activity(entity, version)
+
     def setProvenance(self, entity, activity):
         """
         Stores a record of the code and data used to derive a Synapse entity.
@@ -2237,7 +2259,7 @@ def deleteProvenance(self, entity):
         :param entity: An Entity or Synapse ID to modify
         """
 
-        activity = self.getProvenance(entity)
+        activity = self.get_activity(entity)
         if not activity:
             return
 

synapseutils/copy_functions.py

@@ -564,7 +564,7 @@ def _copyFile(
     # if existing, check if provenance exists
     elif setProvenance == "existing":
         try:
-            act = syn.getProvenance(ent.id)
+            act = syn.get_activity(ent.id)
         except SynapseHTTPError as e:
             if e.response.status_code == 404:
                 act = None