diff --git a/api-openbis-python3-pybis/src/python/pybis/dataset.py b/api-openbis-python3-pybis/src/python/pybis/dataset.py
index 8222f8de6e855d1bac388367193a1add526664e2..9ba2f319b59b4f2e3776b74d40d077571bd6157f 100644
--- a/api-openbis-python3-pybis/src/python/pybis/dataset.py
+++ b/api-openbis-python3-pybis/src/python/pybis/dataset.py
@@ -814,7 +814,7 @@ class DataSet(
parentIds = []
dataset_type = self.type.code
- properties = self.props.all_nonempty()
+ properties = self.formatter.format(self.props.all_nonempty())
request = {
"method": "createReportFromAggregationService",
@@ -882,7 +882,7 @@ class DataSet(
else:
request["params"][1][0]["autoGeneratedCode"] = False
- props = self.p._all_props()
+ props = self.formatter.format(self.p._all_props())
DSpermId = data_stores["code"][0]
request["params"][1][0]["properties"] = props
request["params"][1][0]["dataStoreId"] = {
@@ -902,7 +902,7 @@ class DataSet(
# updating the DataSET
else:
request = self._up_attrs()
- props = self.p._all_props()
+ props = self.formatter.format(self.p._all_props())
request["params"][1][0]["properties"] = props
self.openbis._post_request(self.openbis.as_v3, request)
@@ -960,6 +960,7 @@ class DataSet(
wait_until_finished=True,
)
+ props = self.formatter.format(self.props.all_nonempty())
param = {
"@type": "dss.dto.dataset.create.UploadedDataSetCreation",
"@id": "1",
@@ -969,7 +970,7 @@ class DataSet(
"permId": self.type.code,
"entityKind": "DATA_SET"},
- "properties": self.props.all_nonempty(),
+ "properties": props,
"parentIds": [],
"uploadId": upload_id
}
diff --git a/api-openbis-python3-pybis/src/python/pybis/material.py b/api-openbis-python3-pybis/src/python/pybis/material.py
index 74b8e3b6040edba8df5cd80aecb4cf9613195506..f5ed4c6a54df290c5ba8bfcff24fd95705c5b849 100644
--- a/api-openbis-python3-pybis/src/python/pybis/material.py
+++ b/api-openbis-python3-pybis/src/python/pybis/material.py
@@ -15,6 +15,7 @@
from .attribute import AttrHolder
from .openbis_object import OpenBisObject
from .property import PropertyHolder
+from .property_reformatter import PropertyReformatter
from .utils import VERBOSE
@@ -25,8 +26,11 @@ class Material(OpenBisObject):
self.__dict__["entity"] = "material"
self.__dict__["openbis"] = openbis_obj
self.__dict__["type"] = type
- self.__dict__["p"] = PropertyHolder(openbis_obj, type)
+ ph = PropertyHolder(openbis_obj, type)
+ self.__dict__["p"] = ph
+ self.__dict__["props"] = ph
self.__dict__["a"] = AttrHolder(openbis_obj, "material", type)
+ self.__dict__["formatter"] = PropertyReformatter(openbis_obj)
if data is not None:
self._set_data(data)
@@ -53,7 +57,7 @@ class Material(OpenBisObject):
f"Property '{prop_name}' is mandatory and must not be None"
)
- props = self.p._all_props()
+ props = self.formatter.format(self.p._all_props())
if self.is_new:
request = self._new_attrs()
diff --git a/api-openbis-python3-pybis/src/python/pybis/openbis_object.py b/api-openbis-python3-pybis/src/python/pybis/openbis_object.py
index 812f6afe8f10745cac1ddb4d6d2458e0b84e0458..5afb398015beec585ff177b47a25ea1a3af9b000 100644
--- a/api-openbis-python3-pybis/src/python/pybis/openbis_object.py
+++ b/api-openbis-python3-pybis/src/python/pybis/openbis_object.py
@@ -12,15 +12,17 @@
# See the License for the specific language governing permissions and
# limitations under the License.
#
-from .property import PropertyHolder
+from collections import defaultdict
+
from .attribute import AttrHolder
-from .utils import VERBOSE
from .definitions import (
get_definition_for_entity,
get_type_for_entity,
get_method_for_entity,
)
-from collections import defaultdict
+from .property import PropertyHolder
+from .property_reformatter import PropertyReformatter
+from .utils import VERBOSE
class OpenBisObject:
@@ -39,6 +41,7 @@ class OpenBisObject:
self.__dict__["type"] = type
self.__dict__["p"] = PropertyHolder(openbis_obj, type)
self.__dict__["a"] = AttrHolder(openbis_obj, self._entity, type)
+ self.__dict__["formatter"] = PropertyReformatter(openbis_obj)
# existing OpenBIS object
if data is not None:
@@ -196,7 +199,7 @@ class OpenBisObject:
f"Property '{prop_name}' is mandatory and must not be None"
)
- props = self.p._all_props()
+ props = self.formatter.format(self.p._all_props())
# NEW
if self.is_new:
diff --git a/api-openbis-python3-pybis/src/python/pybis/property_reformatter.py b/api-openbis-python3-pybis/src/python/pybis/property_reformatter.py
new file mode 100644
index 0000000000000000000000000000000000000000..ff9acad285bc78ec43796fd59d01a6cfc3e9b018
--- /dev/null
+++ b/api-openbis-python3-pybis/src/python/pybis/property_reformatter.py
@@ -0,0 +1,63 @@
+# 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.
+#
+from datetime import datetime
+
+import pandas as pd
+
+
+def is_of_openbis_supported_date_format(value):
+ is_supported = False
+ for date_format in PropertyReformatter.SUPPORTED_DATETIME_FORMATS:
+ try:
+ datetime.strptime(value, date_format)
+ is_supported = True
+ except ValueError:
+ pass
+ return is_supported
+
+
+class PropertyReformatter:
+ """Helper class for reformatting of properties, is needed"""
+ LONG_DATETIME_FORMAT = "%Y-%m-%d %H:%M:%S"
+
+ SUPPORTED_DATETIME_FORMATS = ["%Y-%m-%d", "%y-%m-%d", # ShortDateFormat
+ "%Y-%m-%d %H:%M", "%y-%m-%d %H:%M", # NormalDateFormat
+ "%Y-%m-%d %H:%M:%S", "%y-%m-%d %H:%M:%S"] # LongDateFormat
+
+ def __init__(self, openbis_obj):
+ self.openbis = openbis_obj
+
+ def format(self, properties):
+ if properties is None:
+ raise ValueError('properties can not be None!')
+
+ for key, value in properties.items():
+ property_type = self.openbis.get_property_type(key)
+ match property_type.dataType:
+ case 'TIMESTAMP':
+ properties[key] = self._format_timestamp(value)
+ case _:
+ pass
+
+ return properties
+
+ def _format_timestamp(self, value):
+ if is_of_openbis_supported_date_format(value):
+ return value
+ timestamp = pd.to_datetime(value)
+ result = timestamp.strftime(PropertyReformatter.LONG_DATETIME_FORMAT)
+ print(
+ f'WARNING: "{value}" is not of any OpenBis supported datetime formats. Reformatting to "{result}"')
+ return result
diff --git a/api-openbis-python3-pybis/src/python/pybis/sample.py b/api-openbis-python3-pybis/src/python/pybis/sample.py
index f60147c1b67bea18345cb168b925c577094788a2..5514a7f6821d71de91e62fd10c0cc3426c62a991 100644
--- a/api-openbis-python3-pybis/src/python/pybis/sample.py
+++ b/api-openbis-python3-pybis/src/python/pybis/sample.py
@@ -13,9 +13,9 @@
# limitations under the License.
#
from .attribute import AttrHolder
-from .definitions import openbis_definitions
from .openbis_object import OpenBisObject
from .property import PropertyHolder
+from .property_reformatter import PropertyReformatter
from .utils import VERBOSE
@@ -23,7 +23,7 @@ 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, attrs=None, **kwargs
+ self, openbis_obj, type, project=None, data=None, props=None, attrs=None, **kwargs
):
self.__dict__["openbis"] = openbis_obj
self.__dict__["type"] = type
@@ -31,6 +31,7 @@ class Sample(OpenBisObject, entity="sample", single_item_method_name="get_sample
self.__dict__["p"] = ph
self.__dict__["props"] = ph
self.__dict__["a"] = AttrHolder(openbis_obj, "sample", type)
+ self.__dict__["formatter"] = PropertyReformatter(openbis_obj)
if data is not None:
self._set_data(data)
@@ -227,8 +228,8 @@ class Sample(OpenBisObject, entity="sample", single_item_method_name="get_sample
for prop_name, prop in self.props._property_names.items():
if prop["mandatory"]:
if (
- getattr(self.props, prop_name) is None
- or getattr(self.props, prop_name) == ""
+ getattr(self.props, prop_name) is None
+ or getattr(self.props, prop_name) == ""
):
raise ValueError(
f"Property '{prop_name}' is mandatory and must not be None"
@@ -236,6 +237,7 @@ class Sample(OpenBisObject, entity="sample", single_item_method_name="get_sample
sampleProject = self.project.code if self.project else None
sampleExperiment = self.experiment.code if self.experiment else None
+ properties = PropertyReformatter(self.openbis).format(self.props())
request = {
"method": "createReportFromAggregationService",
@@ -250,7 +252,7 @@ class Sample(OpenBisObject, entity="sample", single_item_method_name="get_sample
"sampleExperiment": sampleExperiment,
"sampleCode": self.code,
"sampleType": self.type.code,
- "sampleProperties": self.props(),
+ "sampleProperties": properties,
"sampleParents": self.parents,
"sampleParentsNew": None,
"sampleChildrenNew": self.children,
diff --git a/api-openbis-python3-pybis/src/python/tests/test_dataset.py b/api-openbis-python3-pybis/src/python/tests/test_dataset.py
index 616833729b97569d1e6f0d562b14761415d10e9e..9df35c4a92bd8fbe54867274b99e503a6ed8b279 100644
--- a/api-openbis-python3-pybis/src/python/tests/test_dataset.py
+++ b/api-openbis-python3-pybis/src/python/tests/test_dataset.py
@@ -12,9 +12,11 @@
# See the License for the specific language governing permissions and
# limitations under the License.
#
+import datetime
import os
import re
import time
+import uuid
import pytest
from pybis.things import Things
@@ -209,3 +211,49 @@ def test_create_new_dataset_v3_directory(space):
assert dataset.permId is not None
assert dataset.file_list == ["testdir/testfile"]
+
+def test_dataset_property_in_isoformat_date(space):
+ o = space.openbis
+
+ timestamp = time.strftime("%a_%y%m%d_%H%M%S").lower()
+
+ # Create custom TIMESTAMP property type
+ property_type_code = "test_property_type_" + timestamp + "_" + str(uuid.uuid4())
+ pt_date = o.new_property_type(
+ code=property_type_code,
+ label='custom property of data type timestamp',
+ description='custom property created in unit test',
+ dataType='TIMESTAMP',
+ )
+ pt_date.save()
+
+ # Create new dataset type
+ type_code = "test_dataset_type_" + timestamp + "_" + str(uuid.uuid4())
+ dataset_type = o.new_dataset_type(code=type_code)
+ dataset_type.save()
+
+ # Assign created property to new dataset type
+ dataset_type.assign_property(property_type_code)
+
+ # Create new dataset with timestamp property in non-supported format
+ timestamp_property = datetime.datetime.now().isoformat()
+ testfile_path = os.path.join(os.path.dirname(__file__), "testdir/testfile")
+
+ dataset = o.new_dataset(
+ type=type_code,
+ experiment="/DEFAULT/DEFAULT/DEFAULT",
+ files=[testfile_path],
+ props={property_type_code: timestamp_property},
+ )
+ dataset.save()
+
+ # New dataset case
+ assert len(dataset.p()) == 1
+ assert dataset.p[property_type_code] is not None
+
+ # Update dataset case
+ dataset.p[property_type_code] = timestamp_property
+ dataset.save()
+
+ assert len(dataset.p()) == 1
+ assert dataset.p[property_type_code] is not None
diff --git a/api-openbis-python3-pybis/src/python/tests/test_experiment.py b/api-openbis-python3-pybis/src/python/tests/test_experiment.py
index 557b0c6eb12d4c3060e7e98b0f13ade6092bca69..68a0c6ec0ed7b9c8c741912fbd0f522a1944a93e 100644
--- a/api-openbis-python3-pybis/src/python/tests/test_experiment.py
+++ b/api-openbis-python3-pybis/src/python/tests/test_experiment.py
@@ -12,20 +12,18 @@
# See the License for the specific language governing permissions and
# limitations under the License.
#
-import json
-import random
-import re
-import pytest
+import datetime
import time
-from pybis import DataSet
-from pybis import Openbis
+import uuid
+
+import pytest
def test_create_delete_experiment(space):
- o=space.openbis
+ o = space.openbis
timestamp = time.strftime('%a_%y%m%d_%H%M%S').upper()
- new_code='test_experiment_'+timestamp
+ new_code = 'test_experiment_' + timestamp
with pytest.raises(TypeError):
# experiments must be assigned to a project
@@ -52,7 +50,7 @@ def test_create_delete_experiment(space):
e_exists = o.get_experiment(e_new.permId)
assert e_exists is not None
- e_new.delete('delete test experiment '+new_code.upper())
+ e_new.delete('delete test experiment ' + new_code.upper())
with pytest.raises(ValueError):
e_no_longer_exists = o.get_experiment(e_exists.permId)
@@ -60,9 +58,53 @@ def test_create_delete_experiment(space):
def test_get_experiments(space):
# test paging
- o=space.openbis
+ o = space.openbis
current_datasets = o.get_experiments(start_with=1, count=1)
assert current_datasets is not None
# we cannot assert == 1, because search is delayed due to lucene search...
assert len(current_datasets) <= 1
+
+def test_experiment_property_in_isoformat_date(space):
+ o = space.openbis
+
+ timestamp = time.strftime("%a_%y%m%d_%H%M%S").lower()
+
+ # Create custom TIMESTAMP property type
+ property_type_code = "test_property_type_" + timestamp + "_" + str(uuid.uuid4())
+ pt_date = o.new_property_type(
+ code=property_type_code,
+ label='custom property of data type timestamp for experiment',
+ description='custom property created in unit test',
+ dataType='TIMESTAMP',
+ )
+ pt_date.save()
+
+ type_code = "test_experiment_type_" + timestamp + "_" + str(uuid.uuid4())
+ experiment_type = o.new_experiment_type(
+ type_code,
+ description=None,
+ validationPlugin=None,
+ )
+ experiment_type.save()
+ experiment_type.assign_property(property_type_code)
+
+ project = o.get_projects()[0]
+ code = "my_experiment_{}".format(timestamp)
+ timestamp_property = datetime.datetime.now().isoformat()
+ props = {property_type_code: timestamp_property}
+
+ exp = o.new_experiment(code=code, project=project, type=type_code, props=props)
+ exp.save()
+
+ # New experiment case
+ assert len(exp.p()) == 1
+ assert exp.p[property_type_code] is not None
+
+ # Update experiment case
+ exp.p[property_type_code] = timestamp_property
+ exp.save()
+
+ assert len(exp.p()) == 1
+ assert exp.p[property_type_code] is not None
+
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 b6600b2951370d1c17d672a93fa5fbf668e979d8..595e6fb097414cd162ad3253bf4658f9dab914ab 100644
--- a/api-openbis-python3-pybis/src/python/tests/test_sample.py
+++ b/api-openbis-python3-pybis/src/python/tests/test_sample.py
@@ -12,12 +12,14 @@
# See the License for the specific language governing permissions and
# limitations under the License.
#
+import datetime
import random
import re
-import uuid
-import pytest
import time
+import uuid
+
import pandas as pd
+import pytest
def test_create_delete_sample(space):
@@ -54,11 +56,11 @@ def test_create_delete_sample(space):
assert sample_by_permId.registrationDate is not None
# check date format: 2019-03-22 11:36:40
assert (
- re.search(
- r"^\d{4}\-\d{2}\-\d{2} \d{2}\:\d{2}\:\d{2}$",
- sample_by_permId.registrationDate,
- )
- is not None
+ re.search(
+ r"^\d{4}\-\d{2}\-\d{2} \d{2}\:\d{2}\:\d{2}$",
+ sample_by_permId.registrationDate,
+ )
+ is not None
)
# get sample by identifier
@@ -91,7 +93,7 @@ def test_parent_child(space):
sample_type = "UNKNOWN"
timestamp = time.strftime("%a_%y%m%d_%H%M%S").upper()
parent_code = (
- "parent_sample_{}".format(timestamp) + "_" + str(random.randint(0, 1000))
+ "parent_sample_{}".format(timestamp) + "_" + str(random.randint(0, 1000))
)
sample_parent = o.new_sample(code=parent_code, type=sample_type, space=space)
sample_parent.save()
@@ -106,7 +108,7 @@ def test_parent_child(space):
ex_sample_parents = sample_child.get_parents()
ex_sample_parent = ex_sample_parents[0]
assert (
- ex_sample_parent.identifier == "/{}/{}".format(space.code, parent_code).upper()
+ ex_sample_parent.identifier == "/{}/{}".format(space.code, parent_code).upper()
)
ex_sample_children = ex_sample_parent.get_children()
@@ -137,3 +139,62 @@ def test_empty_data_frame(openbis_instance):
pa = s.get_property_assignments()
pd.testing.assert_frame_equal(pa.df, pd.DataFrame())
+
+
+def test_sample_property_in_isoformat_date(space):
+ o = space.openbis
+
+ timestamp = time.strftime("%a_%y%m%d_%H%M%S").lower()
+
+ # Create custom TIMESTAMP property type
+ property_type_code = "test_property_type_" + timestamp + "_" + str(uuid.uuid4())
+ pt_date = o.new_property_type(
+ code=property_type_code,
+ label='custom property of data type timestamp',
+ description='custom property created in unit test',
+ dataType='TIMESTAMP',
+ )
+ pt_date.save()
+
+ # Create custom sample type
+ sample_type_code = "test_sample_type_" + timestamp + "_" + str(uuid.uuid4())
+ sample_type = o.new_sample_type(
+ code=sample_type_code,
+ generatedCodePrefix="S",
+ autoGeneratedCode=True,
+ listable=True,
+ )
+ sample_type.save()
+
+ # Assign created property to new sample type
+ sample_type.assign_property(
+ prop=property_type_code,
+ section='',
+ ordinal=5,
+ mandatory=False,
+ showInEditView=True,
+ showRawValueInForms=True
+ )
+
+ sample_code = "my_sample_{}".format(timestamp)
+ # Create new sample with timestamp property in non-supported format
+ timestamp_property = datetime.datetime.now().isoformat()
+ sample = o.new_sample(code=sample_code,
+ type=sample_type_code,
+ space=space,
+ props={
+ property_type_code: timestamp_property})
+ sample.save()
+
+ # New item case
+ assert len(sample.props()) == 1
+ key, val = sample.props().popitem()
+ assert key == property_type_code
+
+ # Update item case
+ sample.props = {property_type_code: timestamp_property}
+ sample.save()
+
+ assert len(sample.props()) == 1
+ key, val = sample.props().popitem()
+ assert key == property_type_code