Adding changes for set and get

Author: BryanFauble

synapseclient/__main__.py

@@ -379,8 +379,8 @@ def onweb(args, syn):
     syn.onweb(args.id)
 
 
-def setProvenance(args, syn):
-    """Set provenance information on a synapse entity."""
+def set_activity(args, syn: synapseclient.Synapse):
+    """Set activity information on a synapse entity."""
 
     activity = Activity(name=args.name, description=args.description)
 
@@ -390,7 +390,7 @@ def setProvenance(args, syn):
     if args.executed:
         for item in syn._convertProvenanceList(args.executed, args.limitSearch):
             activity.used(item, wasExecuted=True)
-    activity = syn.setProvenance(args.id, activity)
+    activity = syn.set_activity(args.id, activity)
 
     # Display the activity record, if -o or -output specified
     if args.output:
@@ -403,10 +403,22 @@ def setProvenance(args, syn):
                 f.write("\n")
     else:
         syn.logger.info(
-            "Set provenance record %s on entity %s\n", str(activity["id"]), str(args.id)
+            "Set activity record %s on entity %s\n", str(activity["id"]), str(args.id)
         )
 
 
+@deprecated.sphinx.deprecated(
+    version="3.1.0",
+    reason="deprecated and replaced with :py:meth:`set_activity`",
+)
+def setProvenance(args, syn):
+    """Set provenance information on a synapse entity."""
+    syn.logger.warn(
+        "deprecated and replaced with `set_activity` -- Deprecated since version 3.1.0"
+    )
+    set_activity(args, syn)
+
+
 def get_activity(args, syn: synapseclient.Synapse):
     activity = syn.get_activity(args.id, args.version)
 
@@ -423,6 +435,9 @@ def get_activity(args, syn: synapseclient.Synapse):
     reason="deprecated and replaced with :py:meth:`get_activity`",
 )
 def getProvenance(args, syn: synapseclient.Synapse):
+    syn.logger.warn(
+        "deprecated and replaced with `get_activity` -- Deprecated since version 3.1.0"
+    )
     get_activity(args, syn)
 
 
@@ -1417,7 +1432,8 @@ def build_parser():
     parser_config.set_defaults(func=config)
 
     parser_set_provenance = subparsers.add_parser(
-        "set-provenance", help="create provenance records"
+        "set-provenance",
+        help="create provenance records. This is *deprecated* - Swap to using `set-activity` instead.",
     )
     parser_set_provenance.add_argument(
         "--id",
@@ -1465,8 +1481,58 @@ def build_parser():
     )
     parser_set_provenance.set_defaults(func=setProvenance)
 
+    parser_set_activity = subparsers.add_parser(
+        "set-activity", help="create activity records"
+    )
+    parser_set_activity.add_argument(
+        "--id",
+        metavar="syn123",
+        type=str,
+        required=True,
+        help="Synapse ID of entity whose activity we are accessing.",
+    )
+    parser_set_activity.add_argument(
+        "--name",
+        metavar="NAME",
+        type=str,
+        required=False,
+        help="Name of the activity that generated the entity",
+    )
+    parser_set_activity.add_argument(
+        "--description",
+        metavar="DESCRIPTION",
+        type=str,
+        required=False,
+        help="Description of the activity that generated the entity",
+    )
+    parser_set_activity.add_argument(
+        "-o",
+        "--output",
+        metavar="OUTPUT_FILE",
+        dest="output",
+        const="STDOUT",
+        nargs="?",
+        type=str,
+        help="Output the activity record in JSON format",
+    )
+    parser_set_activity.add_argument(
+        "--used", metavar="target", type=str, nargs="*", help=USED_HELP
+    )
+    parser_set_activity.add_argument(
+        "--executed", metavar="target", type=str, nargs="*", help=EXECUTED_HELP
+    )
+    parser_set_activity.add_argument(
+        "--limitSearch",
+        metavar="projId",
+        type=str,
+        help="Synapse ID of a container such as project or folder to limit search for "
+        "activity files.",
+    )
+    parser_set_activity.set_defaults(func=set_activity)
+
     parser_get_provenance = subparsers.add_parser(
-        "get-provenance", help="show provenance records"
+        "get-provenance",
+        help="show provenance records. This is *deprecated* - Swap to using `get-activity` instead.",
     )
     parser_get_provenance.add_argument(
         "--id",
@@ -1493,7 +1559,37 @@ def build_parser():
         type=str,
         help="Output the provenance record in JSON format",
     )
-    parser_get_provenance.set_defaults(func=get_activity)
+    parser_get_provenance.set_defaults(func=getProvenance)
+
+    parser_get_activity = subparsers.add_parser(
+        "get-activity", help="show activity records."
+    )
+    parser_get_activity.add_argument(
+        "--id",
+        metavar="syn123",
+        type=str,
+        required=True,
+        help="Synapse ID of entity whose activity we are accessing.",
+    )
+    parser_get_activity.add_argument(
+        "--version",
+        metavar="version",
+        type=int,
+        required=False,
+        help="version of Synapse entity whose activity we are accessing.",
+    )
+
+    parser_get_activity.add_argument(
+        "-o",
+        "--output",
+        metavar="OUTPUT_FILE",
+        dest="output",
+        const="STDOUT",
+        nargs="?",
+        type=str,
+        help="Output the activity record in JSON format",
+    )
+    parser_get_activity.set_defaults(func=get_activity)
 
     parser_set_annotations = subparsers.add_parser(
         "set-annotations", help="create annotations records"

synapseclient/client.py

@@ -1460,7 +1460,7 @@ def store(
 
         # If we have an Activity, set it as the Entity's provenance record
         if activity:
-            self.setProvenance(properties, activity)
+            self.set_activity(properties, activity)
 
             # 'etag' has changed, so get the new Entity
             properties = self._getEntity(properties)
@@ -2231,7 +2231,7 @@ def setPermissions(
     ############################################################
     def get_activity(
         self, entity: typing.Union[Entity, str, numbers.Number], version: str = None
-    ) -> any:
+    ) -> Activity:
         """
         Retrieve provenance information for a Synapse Entity.
 
@@ -2259,7 +2259,7 @@ def get_activity(
     )
     def getProvenance(
         self, entity: typing.Union[Entity, str, numbers.Number], version: str = None
-    ):
+    ) -> Activity:
         """
         Deprecated and replaced with :py:meth:`get_activity`.
 
@@ -2274,7 +2274,26 @@ def getProvenance(
         """
         return self.get_activity(entity, version)
 
-    def setProvenance(self, entity, activity):
+    @deprecated.sphinx.deprecated(
+        version="3.1.0",
+        reason="deprecated and replaced with :py:meth:`set_activity`",
+    )
+    def setProvenance(
+        self, entity: typing.Union[Entity, str, numbers.Number], activity: Activity
+    ):
+        """
+        Stores a record of the code and data used to derive a Synapse entity.
+
+        :param entity:   An Entity or Synapse ID to modify
+        :param activity: a :py:class:`synapseclient.activity.Activity`
+
+        :returns: An updated :py:class:`synapseclient.activity.Activity` object
+        """
+        return self.set_activity(entity, activity)
+
+    def set_activity(
+        self, entity: typing.Union[Entity, str, numbers.Number], activity: Activity
+    ):
         """
         Stores a record of the code and data used to derive a Synapse entity.
 
@@ -2293,10 +2312,26 @@ def setProvenance(self, entity, activity):
 
         return activity
 
-    def deleteProvenance(self, entity):
+    @deprecated.sphinx.deprecated(
+        version="3.1.0",
+        reason="deprecated and replaced with :py:meth:`delete_activity`",
+    )
+    def deleteProvenance(
+        self, entity: typing.Union[Entity, str, numbers.Number]
+    ) -> None:
         """
         Removes provenance information from an Entity and deletes the associated Activity.
 
+        :param entity: An Entity or Synapse ID to modify
+        """
+        self.delete_activity(entity)
+
+    def delete_activity(
+        self, entity: typing.Union[Entity, str, numbers.Number]
+    ) -> None:
+        """
+        Removes activity information from an Entity and deletes the associated Activity.
+
         :param entity: An Entity or Synapse ID to modify
         """
 

synapseutils/sync.py

@@ -2,14 +2,17 @@
 import concurrent.futures
 from contextlib import contextmanager
 import io
+import numbers
 import os
 import re
 import sys
 import threading
 import typing
 
+import synapseclient
+
 from .monitor import notifyMe
-from synapseclient.entity import is_container
+from synapseclient.entity import Entity, is_container
 from synapseclient.core import config
 from synapseclient.core.utils import id_of, is_url, is_synapse_id_str
 from synapseclient import File, table
@@ -764,18 +767,20 @@ def _extract_file_entity_metadata(syn, allFiles, *, provenance_cache=None):
     return keys, data
 
 
-def _get_file_entity_provenance_dict(syn, entity):
+def _get_file_entity_provenance_dict(
+    syn: synapseclient.Synapse, entity: typing.Union[Entity, str, numbers.Number]
+) -> dict:
     """
     Returns a dict with a subset of the provenance metadata for the entity.
     An empty dict is returned if the metadata does not have a provenance record.
     """
     try:
-        prov = syn.getProvenance(entity)
+        activity = syn.get_activity(entity)
         return {
-            "used": ";".join(prov._getUsedStringList()),
-            "executed": ";".join(prov._getExecutedStringList()),
-            "activityName": prov.get("name", ""),
-            "activityDescription": prov.get("description", ""),
+            "used": ";".join(activity._getUsedStringList()),
+            "executed": ";".join(activity._getExecutedStringList()),
+            "activityName": activity.get("name", ""),
+            "activityDescription": activity.get("description", ""),
         }
     except SynapseHTTPError as e:
         if e.response.status_code == 404:

tests/integration/synapseclient/integration_test.py

@@ -350,10 +350,10 @@ def test_provenance(syn, project, schedule_for_cleanup):
         {"name": "Superhack", "url": "https://github.com/joe_coder/Superhack"},
         wasExecuted=True,
     )
-    activity = syn.setProvenance(data_entity, activity)
+    activity = syn.set_activity(data_entity, activity)
 
     # Retrieve and verify the saved Provenance record
-    retrieved_activity = syn.getProvenance(data_entity)
+    retrieved_activity = syn.get_activity(data_entity)
     assert retrieved_activity == activity
 
     # Test Activity update
@@ -365,7 +365,7 @@ def test_provenance(syn, project, schedule_for_cleanup):
 
     # Test delete
     syn.deleteProvenance(data_entity)
-    pytest.raises(SynapseHTTPError, syn.getProvenance, data_entity["id"])
+    pytest.raises(SynapseHTTPError, syn.get_activity, data_entity["id"])
 
 
 def test_annotations(syn, project, schedule_for_cleanup):

tests/integration/synapseclient/integration_test_Entity.py

@@ -355,7 +355,7 @@ def test_store_activity(syn, project, schedule_for_cleanup):
     entity = syn.store(entity, activity=honking)
 
     # But this does
-    honking = syn.getProvenance(entity.id)
+    honking = syn.get_activity(entity.id)
 
     # Verify the Activity
     assert honking["name"] == "Hinkle horn honking"
@@ -384,7 +384,7 @@ def test_store_activity(syn, project, schedule_for_cleanup):
     entity = syn.store(entity, activity=honking)
 
     # The Activities should match
-    honking2 = syn.getProvenance(entity)
+    honking2 = syn.get_activity(entity)
     assert honking["id"] == honking2["id"]
 
 

tests/integration/synapseclient/test_command_line_client.py

@@ -701,10 +701,10 @@ def test_command_copy(test_state):
     copied_ent_annot = test_state.syn.get_annotations(copied_id)
     copied_url_annot = test_state.syn.get_annotations(copied_URL_id)
 
-    copied_prov = test_state.syn.getProvenance(copied_id)["used"][0]["reference"][
+    copied_prov = test_state.syn.get_activity(copied_id)["used"][0]["reference"][
         "targetId"
     ]
-    copied_url_prov = test_state.syn.getProvenance(copied_URL_id)["used"][0][
+    copied_url_prov = test_state.syn.get_activity(copied_URL_id)["used"][0][
         "reference"
     ]["targetId"]
 

tests/integration/synapseutils/test_synapseutils_copy.py

@@ -51,7 +51,7 @@ def test_copy(syn, schedule_for_cleanup):
     )
     syn.set_annotations(Annotations(file_entity, file_entity.etag, annos))
     syn.set_annotations(Annotations(externalURL_entity, externalURL_entity.etag, annos))
-    syn.setProvenance(externalURL_entity.id, prov)
+    syn.set_activity(externalURL_entity.id, prov)
     schedule_for_cleanup(file_entity.id)
     schedule_for_cleanup(externalURL_entity.id)
     # ------------------------------------
@@ -71,8 +71,8 @@ def test_copy(syn, schedule_for_cleanup):
 
     copied_ent_annot = syn.get_annotations(copied_ent)
     copied_url_annot = syn.get_annotations(copied_URL_ent)
-    copied_prov = syn.getProvenance(copied_ent)
-    copied_url_prov = syn.getProvenance(copied_URL_ent)
+    copied_prov = syn.get_activity(copied_ent)
+    copied_url_prov = syn.get_activity(copied_URL_ent)
     schedule_for_cleanup(copied_ent.id)
     schedule_for_cleanup(copied_URL_ent.id)
 
@@ -111,27 +111,27 @@ def test_copy(syn, schedule_for_cleanup):
         syn,
         file_entity.id,
         destinationId=third_folder.id,
-        setProvenance="gib",
+        set_activity="gib",
     )
     pytest.raises(
         ValueError, synapseutils.copy, syn, file_entity.id, destinationId=file_entity.id
     )
 
-    # Test: setProvenance = None
+    # Test: set_activity = None
     output = synapseutils.copy(
-        syn, file_entity.id, destinationId=second_folder.id, setProvenance=None
+        syn, file_entity.id, destinationId=second_folder.id, set_activity=None
     )
-    pytest.raises(SynapseHTTPError, syn.getProvenance, output[file_entity.id])
+    pytest.raises(SynapseHTTPError, syn.get_activity, output[file_entity.id])
     schedule_for_cleanup(output[file_entity.id])
 
-    # Test: setProvenance = Existing
+    # Test: set_activity = Existing
     output_URL = synapseutils.copy(
         syn,
         externalURL_entity.id,
         destinationId=second_folder.id,
-        setProvenance="existing",
+        set_activity="existing",
     )
-    output_prov = syn.getProvenance(output_URL[externalURL_entity.id])
+    output_prov = syn.get_activity(output_URL[externalURL_entity.id])
     schedule_for_cleanup(output_URL[externalURL_entity.id])
     assert output_prov["name"] == prov["name"]
     assert output_prov["used"] == prov["used"]