SSDM-13330: Added collection set/get commands flow for physical data management, refactored code

app-openbis-command-line/src/python/obis/dm/commands/collection.py

+#   Copyright ETH 2023 Zürich, Scientific IT Services
+#
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+#
+#        http://www.apache.org/licenses/LICENSE-2.0
+#
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+#
+
+import os
+
+from .openbis_command import OpenbisCommand
+from ..utils import is_valid_perm_id, OperationType
+from ...scripts.click_util import click_echo
+
+
+class Collection(OpenbisCommand):
+    """
+    Command to operate on parent collection of downloaded physical datasets.
+    """
+
+    def __init__(self, dm, operation_type, prop, value):
+        """
+        :param dm: data management
+        :param operation_type: type of operation to perform: get/set
+        :param prop: property to operate on
+        :param value: value to set for property prop
+        """
+        self.operation_type = operation_type
+        self.prop = prop
+        self.value = value
+        self.load_global_config(dm)
+        super(Collection, self).__init__(dm)
+
+    def run(self):
+        if self.operation_type is OperationType.GET:
+            return self.get()
+        if self.operation_type is OperationType.SET:
+            return self.set()
+        else:
+            click_echo(f"Operation {self.operation_type} is not supported!")
+            return -1
+
+    def get(self):
+        dataset_perm_ids = self.get_downloaded_datasets()
+        datasets = []
+        for perm_id in dataset_perm_ids:
+            ds = self.get_dataset(perm_id)
+            datasets += [ds] if ds is not None and ds.sample is None else []
+        datasets = set(datasets)
+        for dataset in datasets:
+            experiment = dataset.experiment
+            click_echo(
+                f"Collection: {experiment.permId} '{self.prop}' = {experiment.props[self.prop]}")
+        return 0
+
+    def set(self):
+        dataset_perm_ids = self.get_downloaded_datasets()
+        datasets = []
+        for perm_id in dataset_perm_ids:
+            ds = self.get_dataset(perm_id)
+            datasets += [ds] if ds is not None and ds.sample is None else []
+        datasets = set(datasets)
+        for dataset in datasets:
+            experiment = dataset.experiment
+            experiment.props[self.prop] = self.value
+            click_echo(
+                f"Setting collection: {experiment.permId} property '{self.prop}' to '{experiment.props[self.prop]}'")
+            experiment.save()
+        return 0
+
+    def empty_or_split(self):
+        if self.value == "":
+            return []
+        return self.value.split(',')
+
+    def get_downloaded_datasets(self):
+        result = set()
+        for root, dirs, files in os.walk(self.data_mgmt.invocation_path):
+            for dir_name in dirs:
+                if is_valid_perm_id(dir_name) is True:
+                    result.add(dir_name)
+        return result
+
+    def get_dataset(self, perm_id):
+        try:
+            return self.openbis.get_dataset(perm_id, props="*")
+        except ValueError as e:
+            click_echo(f"Could not get dataset! {e}")
+            return None

app-openbis-command-line/src/python/obis/dm/commands/object.py

@@ -36,7 +36,6 @@ class Object(OpenbisCommand):
         self.prop = prop
         self.value = value
         self.load_global_config(dm)
-        self.PERM_ID_DATE_FORMAT_PATTERN = "%Y%m%d%H%M%S%f"
         super(Object, self).__init__(dm)
 
     def run(self):

app-openbis-command-line/src/python/obis/dm/data_mgmt.py

@@ -29,6 +29,7 @@ from . import config as dm_config
 from .command_result import CommandResult
 from .commands.addref import Addref
 from .commands.clone import Clone
+from .commands.collection import Collection
 from .commands.download_physical import DownloadPhysical
 from .commands.move import Move
 from .commands.object import Object
@@ -688,8 +689,8 @@ class PhysicalDataMgmt(AbstractDataMgmt):
             cmd = Object(self, operation_type, prop, value)
             return cmd.run()
         elif category == "collection":
-            click_echo("Not yet implemented.")
-            return 0
+            cmd = Collection(self, operation_type, prop, value)
+            return cmd.run()
         else:
             return update_config(resolver, self.debug, is_global, is_data_set_property,
                                  operation_type, prop, value)