YDA-5698: add size option group lifecycle report

For optionally showing the size of the research and vault collection
in the report.

README.md

@@ -365,17 +365,19 @@ optional arguments:
 ### yreport\_grouplifecycle
 
 ```
-usage: yreport_grouplifecycle [-h] [-q] [-y {1.7,1.8,1.9,1.10}]
+usage: yreport_grouplifecycle [-h] [-q] [-s] [-y {1.7,1.8,1.9,1.10}]
 
 Generates a list of research groups, along with their creation date,
 expiration date (if available), lists of group managers, regular members, and
 readonly members. The report also shows whether each research compartment
 contains data, as well as whether its vault compartment contains data.
 
-options:
+optional arguments:
   -h, --help            show this help message and exit
   -q, --quasi-xml       Enable Quasi-XML parser in order to be able to parse
                         characters not supported by regular XML parser
+  -s, --size            Include size of research collection and vault
+                        collection in output
   -y {1.7,1.8,1.9,1.10}, --yoda-version {1.7,1.8,1.9,1.10}
                         Override Yoda version on the server
 ```

yclienttools/common_queries.py

@@ -1,10 +1,12 @@
 from itertools import chain
 import os
+from typing import Dict
 
 from irods.column import Like
 from irods.models import Collection, DataObject, Resource, User, UserGroup
-from yclienttools.options import GroupByOption
+from irods.session import iRODSSession
 from yclienttools import exceptions
+from yclienttools.options import GroupByOption
 
 
 def get_collections_in_root(session, root):
@@ -26,8 +28,11 @@ def get_collections_in_root(session, root):
     return chain(generator_collection, generator_subcollections)
 
 
-def get_collection_size(session, collection_name,
-                        count_all_replicas, group_by, include_revisions):
+def get_collection_size(session: iRODSSession,
+                        collection_name: str,
+                        count_all_replicas: bool,
+                        group_by: GroupByOption,
+                        include_revisions: bool) -> Dict[str, int]:
     '''Get total size of all data objects in collection (including its subcollections).
        Options:
        - count_all_replicas (boolean): specifies whether to count the size of each data
@@ -39,7 +44,7 @@ def get_collection_size(session, collection_name,
          collection in the collection size.
     '''
 
-    result = {}
+    result: Dict[str, int] = {}
 
     collections = get_collections_in_root(
         session, collection_name)

yclienttools/reportgrouplifecycle.py

@@ -9,12 +9,14 @@
 import sys
 from typing import Dict, List, Union
 
+import humanize
 from irods.column import Like
 from irods.message import (ET, XML_Parser_Type)
 from irods.models import Collection, DataObject, User
 from irods.session import iRODSSession
-from yclienttools import common_args, common_config
-from yclienttools import session as s
+from yclienttools import common_args, common_config, session as s
+from yclienttools.common_queries import collection_exists, get_collection_size
+from yclienttools.options import GroupByOption
 
 
 def entry():
@@ -37,6 +39,8 @@ def _get_args() -> argparse.Namespace:
     parser = argparse.ArgumentParser(description=__doc__)
     parser.add_argument("-q", "--quasi-xml", default=False, action='store_true',
                         help='Enable Quasi-XML parser in order to be able to parse characters not supported by regular XML parser')
+    parser.add_argument("-s", "--size", default=False, action='store_true',
+                        help='Include size of research collection and vault collection in output')
     common_args.add_default_args(parser)
     return parser.parse_args()
 
@@ -82,8 +86,7 @@ def _group_research_has_data(session: iRODSSession, group_name: str) -> int:
 
        :returns: number of data objects in research group
     """
-    research_collection = f"/{session.zone}/home/{group_name}"
-    return _collection_has_data(session, research_collection)
+    return _collection_has_data(session, _get_research_group_collection(session, group_name))
 
 
 def _group_vault_has_data(session: iRODSSession, group_name: str) -> int:
@@ -97,9 +100,36 @@ def _group_vault_has_data(session: iRODSSession, group_name: str) -> int:
        :returns: number of data objects in vault group
 
     """
-    vault_collection = f"/{session.zone}/home/{group_name}".replace(
+    return _collection_has_data(session, _get_vault_group_collection(session, group_name))
+
+
+def _get_vault_group_collection(session: iRODSSession, group_name: str) -> str:
+    return f"/{session.zone}/home/{group_name}".replace(
         "research-", "vault-", 1)
-    return _collection_has_data(session, vault_collection)
+
+
+def _get_research_group_collection(session: iRODSSession, group_name: str) -> str:
+    return f"/{session.zone}/home/{group_name}"
+
+
+def _get_research_size(session: iRODSSession, group_name: str) -> Union[int, None]:
+    collection = _get_research_group_collection(session, group_name)
+    if collection_exists(session, collection):
+        return _get_collection_size_for_glr(session, collection)
+    else:
+        return None
+
+
+def _get_vault_size(session: iRODSSession, group_name: str) -> Union[int, None]:
+    collection = _get_vault_group_collection(session, group_name)
+    if collection_exists(session, collection):
+        return _get_collection_size_for_glr(session, collection)
+    else:
+        return None
+
+
+def _get_collection_size_for_glr(session: iRODSSession, collection_name: str) -> int:
+    return get_collection_size(session, collection_name, True, GroupByOption.none, True)['all']
 
 
 def _collection_has_data(session: iRODSSession, coll_name: str) -> int:
@@ -142,18 +172,38 @@ def _get_group_managers(session: iRODSSession, group_name: str, attributes: Dict
     return [manager.split("#")[0] for manager in attributes["manager"]]
 
 
+def _get_columns(args: argparse.Namespace) -> List[str]:
+    base_cols = ["Group name", "Category", "Subcategory",
+                 "Group managers", "Regular members", "Read-only members",
+                 "Creation date", "Expiration date", "Has research data", "Has vault data"]
+
+    if args.size:
+        extra_cols = ["Research collection size", "Vault collection size"]
+    else:
+        extra_cols = []
+
+    result = base_cols
+    result.extend(extra_cols)
+    return result
+
+
 def _list_or_str_to_str(value: Union[str, List[str]]) -> str:
     if type(value) is str:
         return value
     else:
         return ";".join(value)
 
 
+def _size_to_str(value: Union[int, None]) -> str:
+    if value is None:
+        return "N/A"
+    else:
+        return humanize.naturalsize(value)
+
+
 def report_groups_lifecycle(args: argparse.Namespace, session: iRODSSession):
     output = csv.writer(sys.stdout, delimiter=',')
-    output.writerow(["Group name", "Category", "Subcategory",
-                     "Group managers", "Regular members", "Read-only members",
-                     "Creation date", "Expiration date", "Has research data", "Has vault data"])
+    output.writerow(_get_columns(args))
 
     def _has_data_to_string(value):
         if value is None:
@@ -176,6 +226,12 @@ def _has_data_to_string(value):
             _group_research_has_data(session, group))
         vault_has_data = _has_data_to_string(
             _group_vault_has_data(session, group))
-        output.writerow([group, category, subcategory,
-                         group_managers, regular_members, readonly_members,
-                         creation_date_str, expiration_date, research_has_data, vault_has_data])
+        rowdata = [group, category, subcategory,
+                   group_managers, regular_members, readonly_members,
+                   creation_date_str, expiration_date, research_has_data, vault_has_data]
+
+        if args.size:
+            rowdata.append(_size_to_str(_get_research_size(session, group)))
+            rowdata.append(_size_to_str(_get_vault_size(session, group)))
+
+        output.writerow(rowdata)