monitor containers for modified entities

synapsemonitor/__main__.py

@@ -20,13 +20,13 @@ def monitor_cli(syn, args):
 
     email_action = actions.EmailAction(
         syn=syn,
-        syn_id=args.view_id,
+        syn_id=args.synapse_id,
         email_subject=args.email_subject,
         users=args.users,
         days=args.days,
     )
     action_results = actions.synapse_action(action_cls=email_action)
-    filesdf = pd.DataFrame({"syn_id": action_results})
+    ids = pd.DataFrame({"syn_id": action_results})
     if args.output:
         pd.DataFrame(ids).to_csv(args.output, index=False, header=False)
     else:
@@ -48,11 +48,12 @@ def create_file_view_cli(syn, args):
 def build_parser():
     """Set up argument parser and returns"""
     parser = argparse.ArgumentParser(
-        description="Checks for new/modified entities in a Fileview. A Synapse "
-        "Fileview can be created to allow users to track entities in a Project "
-        "or Folder.  For more information, head to "
+        description="Checks for new/modified Synapse entities. "
+        "If a Project or Folder entity is specified, that entity and all its contents will be monitored. "
+        "A Synapse File View can be created to allow users to track the contents of Projects "
+        "or Folders with many entities more efficiently. For more information, head to "
         "https://docs.synapse.org/articles/views.html. You can use the "
-        "`create-file-view` function provided in this package to create a File View."
+        "`create` function provided in this package to create a File View."
     )
     parser.add_argument(
         "-c",
@@ -75,7 +76,7 @@ def build_parser():
         "synapse_id",
         metavar="synapse_id",
         type=str,
-        help="Synapse ID of fileview to be monitored.",
+        help="Synapse ID of entity to be monitored.",
     )
     parser_monitor.add_argument(
         "--users",
@@ -107,7 +108,6 @@ def build_parser():
     parser_monitor.add_argument(
         "--log",
         "-l",
-        metavar="level",
         type=str,
         choices=["debug", "info", "warning", "error"],
         default="error",

synapsemonitor/monitor.py

@@ -113,6 +113,47 @@ def _find_modified_entities_file(syn: Synapse, syn_id: str, days: int = 1) -> li
     return []
 
 
+def _traverse(
+    syn: Synapse,
+    synid_root: str,
+    include_types: typing.List = ["folder", "file", "project"],
+) -> list:
+    """Traverse Synapse entity hierarchy to gather all descendant
+    entities of a root entity.
+    Args:
+        syn: Synapse connection
+        synid_root: Synapse ID of root entity.
+        include_types: Must be a list of entity types (ie. [“folder”,”file”])
+            which can be found here:
+            http://docs.synapse.org/rest/org/sagebionetworks/repo/model/EntityType.html
+    Returns:
+        List of descendant Synapse IDs and root Synapse ID
+    """
+
+    synid_desc = []
+
+    # full traverse depends on examining folder entities, even if not requested
+    include_types_mod = set(include_types)
+    include_types_mod.add("folder")
+    include_types_mod = list(include_types_mod)
+
+    synid_children = syn.getChildren(parent=synid_root, includeTypes=include_types_mod)
+    for synid_child in synid_children:
+        synid_desc.extend(
+            _traverse(
+                syn=syn, synid_root=synid_child["id"], include_types=include_types
+            )
+        )
+
+    # only requested entity types
+    entity = syn.get(synid_root, downloadFile=False)
+    entity_type = entity["concreteType"].split(".")[-1].lower().replace("entity", "")
+    if entity_type in include_types:
+        synid_desc.append(synid_root)
+
+    return synid_desc
+
+
 def _find_modified_entities_container(syn: Synapse, syn_id: str, days: int = 1) -> list:
     """Finds entities in a folder or project modified in the past N number of days
 
@@ -124,7 +165,15 @@ def _find_modified_entities_container(syn: Synapse, syn_id: str, days: int = 1)
     Returns:
         List of synapse ids
     """
-    raise NotImplementedError("Projects and folders not supported yet")
+    syn_id_mod = []
+    syn_id_children = _traverse(syn, syn_id)
+
+    for syn_id_child in syn_id_children:
+        syn_id_res = _find_modified_entities_file(syn, syn_id_child, days)
+        if syn_id_res:
+            syn_id_mod.extend(syn_id_res)
+
+    return syn_id_mod
 
 
 def _force_update_view(syn: Synapse, view_id: str):