From dbf5aae883d7dd48fb6cc32aa25e429bb3d09721 Mon Sep 17 00:00:00 2001
From: alaskowski <alaskowski@ethz.ch>
Date: Wed, 2 Aug 2023 12:52:53 +0200
Subject: [PATCH] SSDM-13689: fixes to object-search, performance improvements,
OBIS 0.4.2rc7
---
.../src/python/obis/__init__.py | 2 +-
.../src/python/obis/dm/commands/search.py | 15 +++++++--------
app-openbis-command-line/src/python/setup.py | 2 +-
3 files changed, 9 insertions(+), 10 deletions(-)
diff --git a/app-openbis-command-line/src/python/obis/__init__.py b/app-openbis-command-line/src/python/obis/__init__.py
index 6d545ea634c..abd8a4890fa 100644
--- a/app-openbis-command-line/src/python/obis/__init__.py
+++ b/app-openbis-command-line/src/python/obis/__init__.py
@@ -14,6 +14,6 @@
#
__author__ = "ID SIS • ETH Zürich"
__email__ = "openbis-support@id.ethz.ch"
-__version__ = "0.4.2rc7"
+__version__ = "0.4.2"
from .dm import *
diff --git a/app-openbis-command-line/src/python/obis/dm/commands/search.py b/app-openbis-command-line/src/python/obis/dm/commands/search.py
index 3198164bd16..5f525bb8146 100644
--- a/app-openbis-command-line/src/python/obis/dm/commands/search.py
+++ b/app-openbis-command-line/src/python/obis/dm/commands/search.py
@@ -30,7 +30,8 @@ def _dfs(objects, prop, func, func_specific):
with concurrent.futures.ThreadPoolExecutor(
max_workers=5) as pool_simple, concurrent.futures.ThreadPoolExecutor(
max_workers=20) as pool_full:
- stack = [openbis_obj[prop] for openbis_obj in objects] # datasets and samples provide children in different formats
+ stack = [openbis_obj[prop] for openbis_obj in
+ objects] # datasets and samples provide children in different formats
visited = set()
stack.reverse()
output = []
@@ -180,10 +181,8 @@ class Search(OpenbisCommand):
return self.openbis.get_samples(identifier, attrs=["children", "dataSets"])
def _get_sample_with_datasets(self, identifier):
- return self.openbis.get_sample(identifier, withDataSetIds=True)
-
- def _get_sample_with_datasets2(self, identifier):
- return self.openbis.get_sample(identifier, withDataSetIds=True, raw_response=True)
+ return self.openbis.get_sample(identifier, withDataSetIds=True, raw_response=True,
+ props=self.props)
def _search_samples(self, raw_response=False):
"""Helper method to search samples"""
@@ -202,8 +201,8 @@ class Search(OpenbisCommand):
results = self.openbis.get_samples(**args)
if self.recursive:
- click_echo(f"Recursive search enabled. It may take time to produce results.")
- output2 = _dfs_samples(results['objects'], 'identifier', self._get_sample_with_datasets2)
+ click_echo("Recursive search enabled. It may take time to produce results.")
+ output2 = _dfs_samples(results['objects'], 'identifier', self._get_sample_with_datasets)
search_results = output2
else:
@@ -237,7 +236,7 @@ class Search(OpenbisCommand):
datasets = [x["dataSets"] for x in search_results]
datasets = flatten(datasets)
datasets = [x['permId']['permId'] for x in datasets]
- datasets = self.openbis.get_dataset(permIds=datasets)
+ datasets = self.openbis.get_dataset(permIds=datasets, props=self.props)
filtered_datasets = []
for dataset in datasets:
diff --git a/app-openbis-command-line/src/python/setup.py b/app-openbis-command-line/src/python/setup.py
index 993559aaf63..e6b3c06626f 100644
--- a/app-openbis-command-line/src/python/setup.py
+++ b/app-openbis-command-line/src/python/setup.py
@@ -31,7 +31,7 @@ data_files = [
setup(
name="obis",
- version="0.4.2rc7",
+ version="0.4.2",
description="Local data management with assistance from OpenBIS.",
long_description=long_description,
long_description_content_type="text/markdown",
--
GitLab