From 2445e2dcc25306cd0643e5367a48d34be1737e32 Mon Sep 17 00:00:00 2001
From: alaskowski <alaskowski@ethz.ch>
Date: Fri, 19 May 2023 11:41:10 +0200
Subject: [PATCH] SSDM-13524: Added handling of array-type properties to pybis.
Minor code refactor.
---
.../src/python/pybis/definitions.py | 5 ++++
.../src/python/pybis/entity_type.py | 29 +++++++------------
.../src/python/pybis/experiment.py | 9 +++---
.../src/python/pybis/openbis_object.py | 3 ++
.../src/python/pybis/property.py | 9 ++----
.../src/python/pybis/property_reformatter.py | 21 ++++++++++++++
.../src/python/pybis/pybis.py | 4 +--
.../src/python/pybis/sample.py | 5 +++-
.../src/python/pybis/utils.py | 5 ++--
9 files changed, 55 insertions(+), 35 deletions(-)
diff --git a/api-openbis-python3-pybis/src/python/pybis/definitions.py b/api-openbis-python3-pybis/src/python/pybis/definitions.py
index 25c31e6656e..035130bb4d9 100644
--- a/api-openbis-python3-pybis/src/python/pybis/definitions.py
+++ b/api-openbis-python3-pybis/src/python/pybis/definitions.py
@@ -167,6 +167,11 @@ def openbis_definitions(entity):
"MATERIAL",
"HYPERLINK",
"XML",
+ "ARRAY_INTEGER",
+ "ARRAY_REAL",
+ "ARRAY_STRING",
+ "ARRAY_TIMESTAMP",
+ "JSON"
],
"identifier": "typeId",
},
diff --git a/api-openbis-python3-pybis/src/python/pybis/entity_type.py b/api-openbis-python3-pybis/src/python/pybis/entity_type.py
index 139d3a9d0cf..a17be6eb6b3 100644
--- a/api-openbis-python3-pybis/src/python/pybis/entity_type.py
+++ b/api-openbis-python3-pybis/src/python/pybis/entity_type.py
@@ -12,29 +12,22 @@
# See the License for the specific language governing permissions and
# limitations under the License.
#
-from tabulate import tabulate
-from texttable import Texttable
from pandas import DataFrame
+
+from .definitions import (
+ get_method_for_entity,
+ get_type_for_entity,
+ get_definition_for_entity,
+)
from .openbis_object import OpenBisObject
+from .semantic_annotation import SemanticAnnotation
from .things import Things
from .utils import (
- check_datatype,
- split_identifier,
format_timestamp,
- is_identifier,
- is_permid,
- nvl,
- extract_permid,
extract_code,
extract_name,
VERBOSE,
)
-from .definitions import (
- get_method_for_entity,
- get_type_for_entity,
- get_definition_for_entity,
-)
-from .semantic_annotation import SemanticAnnotation
class EntityType:
@@ -193,7 +186,7 @@ class EntityType:
# assign plugin
if plugin is not None:
plugin_obj = self.openbis.get_plugin(plugin)
- new_assignment["plugin"] = plugin_obj.name
+ new_assignment["plugin"] = plugin_obj.permId
request = self._get_request_for_pa(new_assignment, "Add")
try:
@@ -229,11 +222,11 @@ class EntityType:
}
request = self._get_request_for_pa(items, "Remove", force)
resp = self.openbis._post_request(self.openbis.as_v3, request)
- if not resp and VERBOSE:
+ if not resp:
new_data = self._get_method(self.permId, only_data=True)
self._set_entity_data(new_data)
-
- print(f"Property {property_type} revoked from {self.permId}")
+ if VERBOSE:
+ print(f"Property {property_type} revoked from {self.permId}")
def _get_request_for_pa(self, items, item_action, force=False):
diff --git a/api-openbis-python3-pybis/src/python/pybis/experiment.py b/api-openbis-python3-pybis/src/python/pybis/experiment.py
index f078aef9b9b..14eba9723d4 100644
--- a/api-openbis-python3-pybis/src/python/pybis/experiment.py
+++ b/api-openbis-python3-pybis/src/python/pybis/experiment.py
@@ -12,11 +12,7 @@
# See the License for the specific language governing permissions and
# limitations under the License.
#
-from .property import PropertyHolder
-from .attribute import AttrHolder
from .openbis_object import OpenBisObject
-from .definitions import openbis_definitions
-from .utils import VERBOSE
class Experiment(
@@ -30,8 +26,11 @@ class Experiment(
self.a(data)
self.__dict__["data"] = data
- # put the properties in the self.p namespace (without checking them)
+ # put the properties in the self.p namespace
for key, value in data["properties"].items():
+ data_type = self.p._property_names[key.lower()]['dataType']
+ 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 5afb398015b..d351da74857 100644
--- a/api-openbis-python3-pybis/src/python/pybis/openbis_object.py
+++ b/api-openbis-python3-pybis/src/python/pybis/openbis_object.py
@@ -71,6 +71,9 @@ class OpenBisObject:
# put the properties in the self.p namespace (without checking them)
if "properties" in data:
for key, value in data["properties"].items():
+ data_type = self.p._property_names[key.lower()]['dataType']
+ 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
# object is already saved to openBIS, so it is not new anymore
diff --git a/api-openbis-python3-pybis/src/python/pybis/property.py b/api-openbis-python3-pybis/src/python/pybis/property.py
index c792454a77b..54b8577de72 100644
--- a/api-openbis-python3-pybis/src/python/pybis/property.py
+++ b/api-openbis-python3-pybis/src/python/pybis/property.py
@@ -13,14 +13,9 @@
# limitations under the License.
#
from tabulate import tabulate
-from texttable import Texttable
+
from pybis.utils import (
check_datatype,
- split_identifier,
- format_timestamp,
- is_identifier,
- is_permid,
- nvl,
)
@@ -147,7 +142,7 @@ class PropertyHolder:
raise ValueError(
f"Value for attribute «{name}» must be one of these terms: {', '.join(terms.df['code'].values)}"
)
- elif data_type in ("INTEGER", "BOOLEAN", "VARCHAR"):
+ 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}")
self.__dict__[name] = 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 59739cd644f..5257595ca8d 100644
--- a/api-openbis-python3-pybis/src/python/pybis/property_reformatter.py
+++ b/api-openbis-python3-pybis/src/python/pybis/property_reformatter.py
@@ -12,6 +12,7 @@
# See the License for the specific language governing permissions and
# limitations under the License.
#
+import re
from datetime import datetime
import pandas as pd
@@ -44,9 +45,15 @@ class PropertyReformatter:
raise ValueError('properties can not be None!')
for key, value in properties.items():
+ if value is None:
+ continue
property_type = self.openbis.get_property_type(key)
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])
+ elif property_type.dataType.startswith('ARRAY'):
+ properties[key] = ",".join(map(str, value))
return properties
@@ -60,3 +67,17 @@ class PropertyReformatter:
print(
f'WARNING: "{value}" is not of any OpenBis supported datetime formats. Reformatting to "{result}"')
return result
+
+ def to_array(self, data_type, prop_value):
+ 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(',')]
+ 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 a48ba586b9a..3cb5587b4de 100644
--- a/api-openbis-python3-pybis/src/python/pybis/pybis.py
+++ b/api-openbis-python3-pybis/src/python/pybis/pybis.py
@@ -1292,7 +1292,6 @@ class Openbis:
if resp.ok:
resp = resp.json()
if "error" in resp:
- # print(full_url)
print(json.dumps(request))
raise ValueError(resp["error"]["message"])
elif "result" in resp:
@@ -1300,7 +1299,8 @@ class Openbis:
else:
raise ValueError("request did not return either result nor error")
else:
- raise ValueError("general error while performing post request")
+ raise ValueError(
+ f"general error while performing post request. {resp.status_code}:{resp.reason}")
def logout(self):
"""Log out of openBIS. After logout, the session token is no longer valid."""
diff --git a/api-openbis-python3-pybis/src/python/pybis/sample.py b/api-openbis-python3-pybis/src/python/pybis/sample.py
index 5514a7f6821..be92088af1c 100644
--- a/api-openbis-python3-pybis/src/python/pybis/sample.py
+++ b/api-openbis-python3-pybis/src/python/pybis/sample.py
@@ -90,8 +90,11 @@ class Sample(OpenBisObject, entity="sample", single_item_method_name="get_sample
self.a(data)
self.__dict__["data"] = data
- # put the properties in the self.p namespace (without checking them)
+ # put the properties in the self.p namespace
for key, value in data["properties"].items():
+ data_type = self.p._property_names[key.lower()]['dataType']
+ 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):
diff --git a/api-openbis-python3-pybis/src/python/pybis/utils.py b/api-openbis-python3-pybis/src/python/pybis/utils.py
index 9dff312fda7..11bfb5d8742 100644
--- a/api-openbis-python3-pybis/src/python/pybis/utils.py
+++ b/api-openbis-python3-pybis/src/python/pybis/utils.py
@@ -12,9 +12,8 @@
# See the License for the specific language governing permissions and
# limitations under the License.
#
-from datetime import datetime
-from pathlib import Path
import re
+from datetime import datetime
# display messages when in a interactive context (IPython or Jupyter)
try:
@@ -128,6 +127,8 @@ def check_datatype(type_name, value):
return isinstance(value, bool)
if type_name == "VARCHAR":
return isinstance(value, str)
+ if type_name is not None and type_name.startswith("ARRAY"):
+ return isinstance(value, list)
return True
--
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