From 66079b4b2e5edfe78277a5129bd9cd54e514de50 Mon Sep 17 00:00:00 2001
From: alaskowski <alaskowski@ethz.ch>
Date: Mon, 27 Feb 2023 13:19:45 +0100
Subject: [PATCH] SSDM-13330: Added collection set/get commands flow for
physical data management, refactored code
---
.../src/python/obis/dm/commands/collection.py | 96 +++++++++++++++++++
.../src/python/obis/dm/commands/object.py | 1 -
.../src/python/obis/dm/data_mgmt.py | 5 +-
3 files changed, 99 insertions(+), 3 deletions(-)
create mode 100644 app-openbis-command-line/src/python/obis/dm/commands/collection.py
diff --git a/app-openbis-command-line/src/python/obis/dm/commands/collection.py b/app-openbis-command-line/src/python/obis/dm/commands/collection.py
new file mode 100644
index 00000000000..3a82e8a8e14
--- /dev/null
+++ b/app-openbis-command-line/src/python/obis/dm/commands/collection.py
@@ -0,0 +1,96 @@
+# 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
diff --git a/app-openbis-command-line/src/python/obis/dm/commands/object.py b/app-openbis-command-line/src/python/obis/dm/commands/object.py
index 6d9785a3212..1e6517330b4 100644
--- a/app-openbis-command-line/src/python/obis/dm/commands/object.py
+++ b/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):
diff --git a/app-openbis-command-line/src/python/obis/dm/data_mgmt.py b/app-openbis-command-line/src/python/obis/dm/data_mgmt.py
index ee0d19bf848..589fd5a5edb 100644
--- a/app-openbis-command-line/src/python/obis/dm/data_mgmt.py
+++ b/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)
--
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