From 5b3c722c2606ffbaa573c766c9075edda8a5f4fe Mon Sep 17 00:00:00 2001
From: alaskowski <alaskowski@ethz.ch>
Date: Thu, 15 Jun 2023 10:47:38 +0200
Subject: [PATCH] SSDM-13623: Fixing property assignment flow to newly created
sample type; Updating docs. PyBIS-1.35.6rc2
---
.../src/python/CHANGELOG.md | 2 +
.../src/python/README.md | 4 +-
.../src/python/pybis/__init__.py | 2 +-
.../src/python/pybis/pybis.py | 18 ++++++--
.../src/python/setup.cfg | 2 +-
api-openbis-python3-pybis/src/python/setup.py | 2 +-
.../src/python/tests/test_sample.py | 42 +++++++++++++++++++
7 files changed, 63 insertions(+), 9 deletions(-)
diff --git a/api-openbis-python3-pybis/src/python/CHANGELOG.md b/api-openbis-python3-pybis/src/python/CHANGELOG.md
index 1d609f04893..9ea53b8d317 100644
--- a/api-openbis-python3-pybis/src/python/CHANGELOG.md
+++ b/api-openbis-python3-pybis/src/python/CHANGELOG.md
@@ -1,6 +1,8 @@
## Changes with pybis-1.35.6
- Added metaData attribute handling for sample, sampleType, experiment, experimentType, dataset, datasetType
+- Fixed property assignment to a newly created sample type
+- Updated docs
## Changes with pybis-1.35.5
diff --git a/api-openbis-python3-pybis/src/python/README.md b/api-openbis-python3-pybis/src/python/README.md
index 739421c0092..20ba1f6a2f7 100644
--- a/api-openbis-python3-pybis/src/python/README.md
+++ b/api-openbis-python3-pybis/src/python/README.md
@@ -563,7 +563,7 @@ o.get_projects(
o.get_projects(space='MY_SPACE')
space.get_projects()
-project.get_experiments()
+project.get_experiments() # see details and limitations in Section 'search for experiments'
project.get_attachments() # deprecated, as attachments are not compatible with ELN-LIMS.
# Attachments are an old concept and should not be used anymore.
@@ -745,7 +745,7 @@ sample.save()
sample = o.get_sample('/MY_SPACE/MY_SAMPLE_CODE')
sample = o.get_sample('20170518112808649-52')
-samples= o.get_samples(type='UNKNOWN') # search for samples, see below
+samples= o.get_samples(type='UNKNOWN') # see details and limitations in Section 'search for samples / objects'
# get individual attributes
sample.space
diff --git a/api-openbis-python3-pybis/src/python/pybis/__init__.py b/api-openbis-python3-pybis/src/python/pybis/__init__.py
index b065fb1d23c..ed69f7363be 100644
--- a/api-openbis-python3-pybis/src/python/pybis/__init__.py
+++ b/api-openbis-python3-pybis/src/python/pybis/__init__.py
@@ -15,7 +15,7 @@
name = "pybis"
__author__ = "ID SIS • ETH Zürich"
__email__ = "openbis-support@id.ethz.ch"
-__version__ = "1.35.6rc1"
+__version__ = "1.35.6rc2"
from . import pybis
from .pybis import DataSet
diff --git a/api-openbis-python3-pybis/src/python/pybis/pybis.py b/api-openbis-python3-pybis/src/python/pybis/pybis.py
index 3cb5587b4de..c37bcd9f607 100644
--- a/api-openbis-python3-pybis/src/python/pybis/pybis.py
+++ b/api-openbis-python3-pybis/src/python/pybis/pybis.py
@@ -2382,7 +2382,10 @@ class Openbis:
where=None,
**properties,
):
- """Returns a DataFrame of all samples for a given space/project/experiment (or any combination)
+ """Returns a DataFrame of all samples for a given space/project/experiment (or any combination).
+ The default result contains only basic attributes, i.e identifier, permId, type, registrator,
+ registrationDate, modifier, modificationDate. Additional attributes may be downloaded by specifying
+ 'attrs' list.
Filters
-------
@@ -2560,7 +2563,10 @@ class Openbis:
where=None,
**properties,
):
- """Returns a DataFrame of all samples for a given space/project (or any combination)
+ """Returns a DataFrame of all samples for a given space/project (or any combination).
+ The default result contains only basic attributes, i.e identifier, permId, type, registrator,
+ registrationDate, modifier, modificationDate. Additional attributes may be downloaded by specifying
+ 'attrs' list.
Filters:
--------
@@ -2783,7 +2789,10 @@ class Openbis:
where=None,
**properties,
):
- """Returns a DataFrame of all dataSets for a given project/experiment/sample (or any combination)
+ """Returns a DataFrame of all dataSets for a given project/experiment/sample (or any combination).
+ The default result contains only basic attributes, i.e permId, type, experiment, sample, registrationDate,
+ modificationDate, location, status, presentInArchive, size.
+ Additional attributes may be downloaded by specifying 'attrs' list.
Filters
-------
@@ -4140,7 +4149,7 @@ class Openbis:
get_object_types = get_sample_types # Alias
- def get_sample_type(self, type, only_data=False, with_vocabulary=False):
+ def get_sample_type(self, type, only_data=False, with_vocabulary=False, use_cache=True):
return self.get_entity_type(
entity="sampleType",
identifier=type,
@@ -4148,6 +4157,7 @@ class Openbis:
with_vocabulary=with_vocabulary,
method=self.get_sample_type,
only_data=only_data,
+ use_cache=use_cache
)
get_object_type = get_sample_type # Alias
diff --git a/api-openbis-python3-pybis/src/python/setup.cfg b/api-openbis-python3-pybis/src/python/setup.cfg
index ca77a8a16e7..59c9b3405cd 100644
--- a/api-openbis-python3-pybis/src/python/setup.cfg
+++ b/api-openbis-python3-pybis/src/python/setup.cfg
@@ -1,6 +1,6 @@
[metadata]
name = PyBIS
-version = 1.35.6rc1
+version = 1.35.6rc2
author = ID SIS • ETH Zürich
author_email = openbis-support@id.ethz.ch
license = Apache Software License Version 2.0
diff --git a/api-openbis-python3-pybis/src/python/setup.py b/api-openbis-python3-pybis/src/python/setup.py
index fb31b656c0a..0a56f53fe16 100644
--- a/api-openbis-python3-pybis/src/python/setup.py
+++ b/api-openbis-python3-pybis/src/python/setup.py
@@ -26,7 +26,7 @@ with open("README.md", "r", encoding="utf-8") as fh:
setup(
name="PyBIS",
- version="1.35.6rc1",
+ version="1.35.6rc2",
author="ID SIS • ETH Zürich",
author_email="openbis-support@id.ethz.ch",
description="openBIS connection and interaction, optimized for using with Jupyter",
diff --git a/api-openbis-python3-pybis/src/python/tests/test_sample.py b/api-openbis-python3-pybis/src/python/tests/test_sample.py
index eb7e326e489..50420c887c3 100644
--- a/api-openbis-python3-pybis/src/python/tests/test_sample.py
+++ b/api-openbis-python3-pybis/src/python/tests/test_sample.py
@@ -278,3 +278,45 @@ def test_sample_array_properties(space):
sample.save()
assert sample.props['sample_array_integer'] == [3, 2, 1]
+
+
+def test_create_sample_type_assign_property(space):
+ name_suffix = str(time.time())
+ sc = "TEST_" + name_suffix
+ pc = "ESFA_" + name_suffix
+ ptc1 = "START_DATE_" + name_suffix
+ ptc2 = "EXP_DESCRIPTION_" + name_suffix
+ stc = "EXPERIMENTAL_STEP_MILAR_" + name_suffix
+
+ # Create the new space and project
+ sp = space.openbis.new_space(code=sc, description="Test space")
+ sp.save()
+ pr = space.openbis.new_project(code=pc, space=sc, description="ESFA experiments")
+ pr.save()
+
+ # Create the experiment
+ exp = space.openbis.new_collection(code=pc, project="/" + sc + "/" + pc, type="COLLECTION")
+ exp.save()
+
+ # Create the sample type
+ date_prop = space.openbis.new_property_type(code=ptc1, dataType="TIMESTAMP",
+ label="Start date",
+ description="Date of the measurement")
+ date_prop.save()
+ date_prop = space.openbis.new_property_type(code=ptc2, dataType="MULTILINE_VARCHAR",
+ label="Experimental description",
+ description="Experimental description")
+ date_prop.save()
+ st = space.openbis.new_sample_type(code=stc, generatedCodePrefix="EXSTEPMILAR")
+ st.save()
+
+ if st is None:
+ print(space.openbis.get_sample_types())
+ st = space.openbis.get_sample_type(stc)
+ st.save()
+
+ st.assign_property(ptc1)
+ st.assign_property(ptc2)
+ st.assign_property("$NAME")
+ st.save()
+
--
GitLab