From 8c1d750bcc3b592e62764f3e7bcdef6cbb6ab30b Mon Sep 17 00:00:00 2001
From: alaskowski <alaskowski@ethz.ch>
Date: Tue, 7 Feb 2023 14:25:46 +0100
Subject: [PATCH] SSDM-13417: Changed update in transaction mechanism so None
list attributes are not counted as updated. Created a test that verifies that
update based on get_samples method is not overriding parents/children
---
pybis/src/python/pybis/attribute.py | 13 ++-
pybis/src/python/pybis/pybis.py | 1 +
pybis/src/python/pybis/sample.py | 12 +-
pybis/src/python/tests/test_openbis.py | 155 +++++++++++++++++++++++++
4 files changed, 176 insertions(+), 5 deletions(-)
diff --git a/pybis/src/python/pybis/attribute.py b/pybis/src/python/pybis/attribute.py
index bf767fc3626..a9fa8589e70 100644
--- a/pybis/src/python/pybis/attribute.py
+++ b/pybis/src/python/pybis/attribute.py
@@ -284,8 +284,9 @@ class AttrHolder:
# all items in a list
if "multi" in self._defs and attr in self._defs["multi"]:
items = self.__dict__.get("_" + attr, [])
- if items == None:
- items = []
+ if items is None:
+ # 'None' multivalue attributes should be omitted during update
+ continue
up_obj[attr2ids[attr]] = {
"actions": [
{
@@ -745,6 +746,8 @@ class AttrHolder:
"""add parent to _parents list"""
if not isinstance(parents_to_add, list):
parents_to_add = [parents_to_add]
+ if self.__dict__["_parents"] is None:
+ self.__dict__["_parents"] = []
for parent in parents_to_add:
ident = self._ident_for_whatever(parent)
if ident not in self.__dict__["_parents"]:
@@ -754,6 +757,8 @@ class AttrHolder:
"""remove parent from _parents list"""
if not isinstance(parents_to_remove, list):
parents_to_remove = [parents_to_remove]
+ if self.__dict__["_parents"] is None:
+ self.__dict__["_parents"] = []
for parent in parents_to_remove:
ident = self._ident_for_whatever(parent)
for i, item in enumerate(self.__dict__["_parents"]):
@@ -787,6 +792,8 @@ class AttrHolder:
"""add children to _children list"""
if getattr(self, "_children") is None:
self.__dict__["_children"] = []
+ if self.__dict__["_children"] is None:
+ self.__dict__["_children"] = []
if not isinstance(children, list):
children = [children]
for child in children:
@@ -798,6 +805,8 @@ class AttrHolder:
return
if not isinstance(children, list):
children = [children]
+ if self.__dict__["_children"] is None:
+ self.__dict__["_children"] = []
for child in children:
ident = self._ident_for_whatever(child)
for i, item in enumerate(self.__dict__["_children"]):
diff --git a/pybis/src/python/pybis/pybis.py b/pybis/src/python/pybis/pybis.py
index 07e3567e2cf..f8e118db98c 100644
--- a/pybis/src/python/pybis/pybis.py
+++ b/pybis/src/python/pybis/pybis.py
@@ -4811,6 +4811,7 @@ class Openbis:
openbis_obj=self,
type=self.get_sample_type(obj["type"]["code"]),
data=obj,
+ attrs=attrs
),
response,
)
diff --git a/pybis/src/python/pybis/sample.py b/pybis/src/python/pybis/sample.py
index 790e9681c4b..9311815a333 100644
--- a/pybis/src/python/pybis/sample.py
+++ b/pybis/src/python/pybis/sample.py
@@ -9,7 +9,7 @@ class Sample(OpenBisObject, entity="sample", single_item_method_name="get_sample
"""A Sample (new: Object) is one of the most commonly used entities in openBIS."""
def __init__(
- self, openbis_obj, type, project=None, data=None, props=None, **kwargs
+ self, openbis_obj, type, project=None, data=None, props=None, attrs=None, **kwargs
):
self.__dict__["openbis"] = openbis_obj
self.__dict__["type"] = type
@@ -49,13 +49,19 @@ class Sample(OpenBisObject, entity="sample", single_item_method_name="get_sample
self.a.__dict__["_parents"] = []
else:
if not self.is_new:
- self.a.__dict__["_parents_orig"] = self.a.__dict__["_parents"]
+ if attrs is not None and "parents" not in attrs:
+ self.a.__dict__["_parents"] = None
+ else:
+ self.a.__dict__["_parents_orig"] = self.a.__dict__["_parents"]
if getattr(self, "children") is None:
self.a.__dict__["_children"] = []
else:
if not self.is_new:
- self.a.__dict__["_children_orig"] = self.a.__dict__["_children"]
+ if attrs is not None and "children" not in attrs:
+ self.a.__dict__["_children"] = None
+ else:
+ self.a.__dict__["_children_orig"] = self.a.__dict__["_children"]
if getattr(self, "components") is None:
self.a.__dict__["_components"] = []
diff --git a/pybis/src/python/tests/test_openbis.py b/pybis/src/python/tests/test_openbis.py
index 4215263aef6..8db5be30fbb 100644
--- a/pybis/src/python/tests/test_openbis.py
+++ b/pybis/src/python/tests/test_openbis.py
@@ -41,3 +41,158 @@ def test_create_permId(openbis_instance):
assert ts is not None
count = m.group(1)
assert count is not None
+
+
+def test_get_samples_update_in_transaction(openbis_instance):
+ '''
+ Update samples in transaction without overriding parents/children
+ '''
+ name_suffix = str(time.time())
+ # Create new space
+ space = openbis_instance.new_space(code='space_name' + name_suffix, description='')
+ space.save()
+
+ # Create new project
+ project = space.new_project(code='project_code' + name_suffix)
+ project.save()
+
+ # Create new experiment
+ experiment = openbis_instance.new_experiment(
+ code='MY_NEW_EXPERIMENT',
+ type='DEFAULT_EXPERIMENT',
+ project=project.code
+ )
+ experiment.save()
+
+ # Create parent sample
+ sample1 = openbis_instance.new_sample(
+ type='YEAST',
+ space=space.code,
+ experiment=experiment.identifier,
+ parents=[],
+ children=[],
+ props={"$name": "sample1"}
+ )
+ sample1.save()
+
+ # Create child sample
+ sample2 = openbis_instance.new_sample(
+ type='YEAST',
+ space=space.code,
+ experiment=experiment.identifier,
+ parents=[sample1],
+ children=[],
+ props={"$name": "sample2"}
+ )
+ sample2.save()
+
+ # Verify samples parent/child relationship
+ sample1 = openbis_instance.get_sample(
+ sample_ident=sample1.identifier,
+ space=space.code,
+ props="*"
+ )
+ sample2 = openbis_instance.get_sample(
+ sample_ident=sample2.identifier,
+ space=space.code,
+ props="*"
+ )
+ assert sample1.children == [sample2.identifier]
+ assert sample2.parents == [sample1.identifier]
+
+ trans = openbis_instance.new_transaction()
+ # get samples that have parents and update name
+ samples = openbis_instance.get_samples(space=space.code, props="*", withParents="*")
+ for sample in samples:
+ sample.props["$name"] = 'new name for sample2'
+ trans.add(sample)
+ # get samples that have children and update name
+ samples = openbis_instance.get_samples(space=space.code, props="*", withChildren="*")
+ for sample in samples:
+ sample.props["$name"] = 'new name for sample1'
+ trans.add(sample)
+ trans.commit()
+
+ # Verify that name has been changed and parent/child relationship remains
+ sample1 = openbis_instance.get_sample(
+ sample_ident=sample1.identifier,
+ space=space.code,
+ props="*"
+ )
+ sample2 = openbis_instance.get_sample(
+ sample_ident=sample2.identifier,
+ space=space.code,
+ props="*"
+ )
+ assert sample1.props["$name"] == 'new name for sample1'
+ assert sample1.children == [sample2.identifier]
+ assert sample2.props["$name"] == 'new name for sample2'
+ assert sample2.parents == [sample1.identifier]
+
+ trans = openbis_instance.new_transaction()
+ # get samples with attributes and change name
+ samples = openbis_instance.get_samples(space=space.code, attrs=["parents", "children"])
+ for sample in samples:
+ sample.props["$name"] = "default name"
+ trans.add(sample)
+ trans.commit()
+
+ # Verify that name has been changed and parent/child relationship remains
+ sample1 = openbis_instance.get_sample(
+ sample_ident=sample1.identifier,
+ space=space.code,
+ props="*"
+ )
+ sample2 = openbis_instance.get_sample(
+ sample_ident=sample2.identifier,
+ space=space.code,
+ props="*"
+ )
+ assert sample1.props["$name"] == 'default name'
+ assert sample1.children == [sample2.identifier]
+ assert sample2.props["$name"] == 'default name'
+ assert sample2.parents == [sample1.identifier]
+
+ sample3 = openbis_instance.new_sample(
+ type='YEAST',
+ space=space.code,
+ experiment=experiment.identifier,
+ parents=[],
+ children=[],
+ props={"$name": "sample3"}
+ )
+ sample3.save()
+
+ trans = openbis_instance.new_transaction()
+ # get sample1 without attributes and add sample3 as a parent
+ samples = openbis_instance.get_samples(space=space.code, identifier=sample1.identifier)
+ for sample in samples:
+ sample.add_parents([sample3.identifier])
+ trans.add(sample)
+ # get sample2 without attributes and remove sample1 as a parent
+ samples = openbis_instance.get_samples(space=space.code, identifier=sample2.identifier)
+ for sample in samples:
+ sample.del_parents([sample1.identifier])
+ trans.add(sample)
+ trans.commit()
+
+ # Verify changes
+ sample1 = openbis_instance.get_sample(
+ sample_ident=sample1.identifier,
+ space=space.code,
+ props="*"
+ )
+ sample2 = openbis_instance.get_sample(
+ sample_ident=sample2.identifier,
+ space=space.code,
+ props="*"
+ )
+ sample3 = openbis_instance.get_sample(
+ sample_ident=sample3.identifier,
+ space=space.code,
+ props="*"
+ )
+ assert sample1.children == []
+ assert sample1.parents == [sample3.identifier]
+ assert sample2.parents == []
+ assert sample3.children == [sample1.identifier]
--
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