diff --git a/api-openbis-python3-pybis/src/python/CHANGELOG.md b/api-openbis-python3-pybis/src/python/CHANGELOG.md
index 192d809f9d59101d66966dd467a0d368fe5e6d41..d35eade24a93da1e76e6b3ab1624daa28dcb7842 100644
--- a/api-openbis-python3-pybis/src/python/CHANGELOG.md
+++ b/api-openbis-python3-pybis/src/python/CHANGELOG.md
@@ -1,3 +1,10 @@
+## Changes with pybis-1.36.3
+
+- Refactored metaData and multiValue properties to be backwards-compatible.
+- Refactored get_children/get_parents methods
+- Refactored property formatting functionality
+
+
## Changes with pybis-1.36.2
- Refactoring of the set_token method.
diff --git a/api-openbis-python3-pybis/src/python/pybis/attribute.py b/api-openbis-python3-pybis/src/python/pybis/attribute.py
index 7ca192e5c12328e1996204cb74c57a4790463ef1..a5e9a8fa0b268a012ab75e5fc1ab5c95e0b6c924 100644
--- a/api-openbis-python3-pybis/src/python/pybis/attribute.py
+++ b/api-openbis-python3-pybis/src/python/pybis/attribute.py
@@ -745,6 +745,8 @@ class AttrHolder:
"""get the current parents and return them as a list (Things/DataFrame)
or return empty list
"""
+ if self.parents is None or self.parents == []:
+ return self.parents
return getattr(self._openbis, "get_" + self._entity.lower())(
self.parents, **kwargs
)
@@ -791,6 +793,8 @@ class AttrHolder:
"""get the current children and return them as a list (Things/DataFrame)
or return empty list
"""
+ if self.children is None or self.children == []:
+ return self.children
return getattr(self._openbis, "get_" + self._entity.lower())(
self.children, **kwargs
)
diff --git a/api-openbis-python3-pybis/src/python/pybis/experiment.py b/api-openbis-python3-pybis/src/python/pybis/experiment.py
index 7e9f0bfd9f345c39e53c89f518eca1d6d9be65de..dd23a54ae0d3b40db2431a8f134a3c6af2aa2573 100644
--- a/api-openbis-python3-pybis/src/python/pybis/experiment.py
+++ b/api-openbis-python3-pybis/src/python/pybis/experiment.py
@@ -30,15 +30,26 @@ class Experiment(
for key, value in data["properties"].items():
property_type = self.p._property_names[key.lower()]
data_type = property_type['dataType']
- if data_type in ("ARRAY_INTEGER", "ARRAY_REAL", "ARRAY_STRING", "ARRAY_TIMESTAMP"):
- value = self.formatter.to_array(data_type, value)
- elif "multiValue" in property_type:
+ if "multiValue" in property_type:
if property_type['multiValue'] is True:
if type(value) is not list:
value = [value]
+ if data_type in (
+ "ARRAY_INTEGER", "ARRAY_REAL", "ARRAY_STRING", "ARRAY_TIMESTAMP"):
+ value = [self.formatter.to_array(data_type, x) for x in value]
+ else:
+ value = self.formatter.to_array(data_type, value)
else:
- if type(value) is list:
- raise ValueError(f'Property type {property_type["code"]} is not a multi-value property!')
+ if type(value) is list and data_type not in (
+ "ARRAY_INTEGER", "ARRAY_REAL", "ARRAY_STRING", "ARRAY_TIMESTAMP"):
+ raise ValueError(
+ f'Property type {property_type} is not a multi-value property!')
+ if data_type in (
+ "ARRAY_INTEGER", "ARRAY_REAL", "ARRAY_STRING", "ARRAY_TIMESTAMP"):
+ value = self.formatter.to_array(data_type, value)
+ else:
+ if data_type in ("ARRAY_INTEGER", "ARRAY_REAL", "ARRAY_STRING", "ARRAY_TIMESTAMP"):
+ value = self.formatter.to_array(data_type, value)
self.p.__dict__[key.lower()] = value
def __str__(self):
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 d19d90b8663914cd324e08e4130962df82702553..b6203079c3e952fdfc9389191adf0347554000dd 100644
--- a/api-openbis-python3-pybis/src/python/pybis/openbis_object.py
+++ b/api-openbis-python3-pybis/src/python/pybis/openbis_object.py
@@ -71,8 +71,26 @@ class OpenBisObject:
# put the properties in the self.p namespace (without checking them)
if "properties" in data:
for key, value in data["properties"].items():
- if self.p.type:
- data_type = self.p._property_names[key.lower()]['dataType']
+ property_type = self.p._property_names[key.lower()]
+ data_type = property_type['dataType']
+ if "multiValue" in property_type:
+ if property_type['multiValue'] is True:
+ if type(value) is not list:
+ value = [value]
+ if data_type in (
+ "ARRAY_INTEGER", "ARRAY_REAL", "ARRAY_STRING", "ARRAY_TIMESTAMP"):
+ value = [self.formatter.to_array(data_type, x) for x in value]
+ else:
+ value = self.formatter.to_array(data_type, value)
+ else:
+ if type(value) is list and data_type not in (
+ "ARRAY_INTEGER", "ARRAY_REAL", "ARRAY_STRING", "ARRAY_TIMESTAMP"):
+ raise ValueError(
+ f'Property type {property_type} is not a multi-value property!')
+ if data_type in (
+ "ARRAY_INTEGER", "ARRAY_REAL", "ARRAY_STRING", "ARRAY_TIMESTAMP"):
+ value = self.formatter.to_array(data_type, value)
+ else:
if data_type in ("ARRAY_INTEGER", "ARRAY_REAL", "ARRAY_STRING", "ARRAY_TIMESTAMP"):
value = self.formatter.to_array(data_type, value)
self.p.__dict__[key.lower()] = value
@@ -208,6 +226,16 @@ class OpenBisObject:
# NEW
if self.is_new:
request = self._new_attrs()
+
+ version = self.openbis.get_server_information().openbis_version
+ if version is not None:
+ if 'SNAPSHOT' not in version and not version.startswith('7') and 'UNKNOWN' not in version:
+ if request['method'] == 'createPropertyTypes' and 'multiValue' in request['params'][1][0]:
+ del request['params'][1][0]['multiValue']
+ if (request['method'] in ('createSampleTypes', 'createExperimentTypes', 'createDataSetTypes')
+ and 'metaData' in request['params'][1][0]):
+ del request['params'][1][0]['metaData']
+
if props:
request["params"][1][0]["properties"] = props
@@ -223,6 +251,13 @@ class OpenBisObject:
else:
request = self._up_attrs(method_name=None, permId=self._permId)
+ version = self.openbis.get_server_information().openbis_version
+ if version is not None:
+ if 'SNAPSHOT' not in version and not version.startswith('7') and 'UNKNOWN' not in version:
+ if (request['method'] in ('updateSampleTypes', 'updateExperimentTypes', 'updateDataSetTypes')
+ and 'metaData' in request['params'][1][0]):
+ del request['params'][1][0]['metaData']
+
if props:
request["params"][1][0]["properties"] = props
diff --git a/api-openbis-python3-pybis/src/python/pybis/property.py b/api-openbis-python3-pybis/src/python/pybis/property.py
index e6fe02d6bfc02c98b012bc26ed253abd2247d181..d070345abca27ed5b650d06ed0b688460a06b24f 100644
--- a/api-openbis-python3-pybis/src/python/pybis/property.py
+++ b/api-openbis-python3-pybis/src/python/pybis/property.py
@@ -14,10 +14,6 @@
#
from tabulate import tabulate
-from pybis.utils import (
- check_datatype,
-)
-
class PropertyHolder:
def __init__(self, openbis_obj, type=None):
@@ -163,8 +159,9 @@ class PropertyHolder:
elif data_type in (
"INTEGER", "BOOLEAN", "VARCHAR", "ARRAY_INTEGER", "ARRAY_REAL", "ARRAY_STRING",
"ARRAY_TIMESTAMP"):
- if not check_datatype(data_type, value):
- raise ValueError(f"Value must be of type {data_type}")
+ pass
+ # if not check_datatype(data_type, value):
+ # raise ValueError(f"Value must be of type {data_type}")
self.__dict__[name] = value
def __setitem__(self, key, value):
diff --git a/api-openbis-python3-pybis/src/python/pybis/property_reformatter.py b/api-openbis-python3-pybis/src/python/pybis/property_reformatter.py
index 5257595ca8ddcdc129821f284f645104795a044a..2a038909b13c19765eeeae70dd1db5860236acad 100644
--- a/api-openbis-python3-pybis/src/python/pybis/property_reformatter.py
+++ b/api-openbis-python3-pybis/src/python/pybis/property_reformatter.py
@@ -12,7 +12,6 @@
# See the License for the specific language governing permissions and
# limitations under the License.
#
-import re
from datetime import datetime
import pandas as pd
@@ -51,10 +50,14 @@ class PropertyReformatter:
if property_type.dataType == 'TIMESTAMP':
properties[key] = self._format_timestamp(value)
elif property_type.dataType == 'ARRAY_TIMESTAMP':
- properties[key] = ",".join([self._format_timestamp(x) for x in value])
+ if property_type.multiValue:
+ properties[key] = ["[" + ",".join(map(str, [self._format_timestamp(x) for x in arr])) + "]" for arr in value]
+ else:
+ properties[key] = [self._format_timestamp(x) for x in value]
elif property_type.dataType.startswith('ARRAY'):
- properties[key] = ",".join(map(str, value))
-
+ if property_type.multiValue:
+ properties[key] = ["[" + ",".join(map(str, x)) + "]" for x in value]
+
return properties
def _format_timestamp(self, value):
@@ -72,12 +75,14 @@ class PropertyReformatter:
if prop_value is None or prop_value == "":
return []
result = []
- if data_type == "ARRAY_INTEGER":
- result = [int(x.strip()) for x in prop_value.split(',')]
- elif data_type == "ARRAY_REAL":
- result = [float(x.strip()) for x in prop_value.split(',')]
- elif data_type == "ARRAY_STRING":
- result = [x.strip() for x in re.split(r"(?<!\\),", prop_value)]
- elif data_type == "ARRAY_TIMESTAMP":
- result = [x.strip() for x in prop_value.split(',')]
+ if data_type in ("ARRAY_INTEGER", "INTEGER"):
+ result = [int(x.strip()) for x in prop_value]
+ elif data_type in ("ARRAY_REAL", "REAL"):
+ result = [float(x.strip()) for x in prop_value]
+ elif data_type == "BOOLEAN":
+ result = [x.strip().lower() == "true" for x in prop_value]
+ elif data_type in ("ARRAY_TIMESTAMP", "TIMESTAMP", "DATE"):
+ result = [x.strip() for x in prop_value]
+ else:
+ result = prop_value
return result
diff --git a/api-openbis-python3-pybis/src/python/pybis/pybis.py b/api-openbis-python3-pybis/src/python/pybis/pybis.py
index 1bf4019b30f090a429ebb574fdecd9dacad8b5f6..bd29d9171a85b47dfae7c69ec9aa7accefd74ed5 100644
--- a/api-openbis-python3-pybis/src/python/pybis/pybis.py
+++ b/api-openbis-python3-pybis/src/python/pybis/pybis.py
@@ -4112,7 +4112,7 @@ class Openbis:
get_collection_types = get_experiment_types # Alias
- def get_experiment_type(self, type, only_data=False):
+ def get_experiment_type(self, type, only_data=False, **kwargs):
return self.get_entity_type(
entity="experimentType",
cls=ExperimentType,
@@ -4133,7 +4133,7 @@ class Openbis:
count=count,
)
- def get_dataset_type(self, type, only_data=False):
+ def get_dataset_type(self, type, only_data=False, **kwargs):
return self.get_entity_type(
entity="dataSetType",
identifier=type,
diff --git a/api-openbis-python3-pybis/src/python/pybis/sample.py b/api-openbis-python3-pybis/src/python/pybis/sample.py
index 717355be8b71991f3b34e304936490374afefa58..edddcdcedb848339d9abc097fd77a18c6083d599 100644
--- a/api-openbis-python3-pybis/src/python/pybis/sample.py
+++ b/api-openbis-python3-pybis/src/python/pybis/sample.py
@@ -94,15 +94,22 @@ class Sample(OpenBisObject, entity="sample", single_item_method_name="get_sample
for key, value in data["properties"].items():
property_type = self.p._property_names[key.lower()]
data_type = property_type['dataType']
- if data_type in ("ARRAY_INTEGER", "ARRAY_REAL", "ARRAY_STRING", "ARRAY_TIMESTAMP"):
- value = self.formatter.to_array(data_type, value)
- elif "multiValue" in property_type:
+ if "multiValue" in property_type:
if property_type['multiValue'] is True:
if type(value) is not list:
value = [value]
+ if data_type in ("ARRAY_INTEGER", "ARRAY_REAL", "ARRAY_STRING", "ARRAY_TIMESTAMP"):
+ value = [self.formatter.to_array(data_type, x) for x in value]
+ else:
+ value = self.formatter.to_array(data_type, value)
else:
- if type(value) is list:
+ if type(value) is list and data_type not in ("ARRAY_INTEGER", "ARRAY_REAL", "ARRAY_STRING", "ARRAY_TIMESTAMP"):
raise ValueError(f'Property type {property_type} is not a multi-value property!')
+ if data_type in ("ARRAY_INTEGER", "ARRAY_REAL", "ARRAY_STRING", "ARRAY_TIMESTAMP"):
+ value = self.formatter.to_array(data_type, value)
+ else:
+ if data_type in ("ARRAY_INTEGER", "ARRAY_REAL", "ARRAY_STRING", "ARRAY_TIMESTAMP"):
+ value = self.formatter.to_array(data_type, value)
self.p.__dict__[key.lower()] = value
def __dir__(self):