diff --git a/pybis/src/python/CHANGELOG.md b/pybis/src/python/CHANGELOG.md
index d857b94747a9d903a952b99e87055c622ce17623..a2aeb52b069e3917bb34c1af40fc675b8086b17b 100644
--- a/pybis/src/python/CHANGELOG.md
+++ b/pybis/src/python/CHANGELOG.md
@@ -2,6 +2,7 @@
- throw error when invalid token is assigned
- to not show an error message if stored token is invalid (just do not use it)
+- fixed a bug which led to missing parents and children
## Changes with pybis-1.31.6
diff --git a/pybis/src/python/pybis/__init__.py b/pybis/src/python/pybis/__init__.py
index 48ae574245e1fe9f7cb6f6ec59641d68af47529c..b1ad2c1edf6ceb4ced5016633528bf43ca3ee5e6 100644
--- a/pybis/src/python/pybis/__init__.py
+++ b/pybis/src/python/pybis/__init__.py
@@ -1,7 +1,7 @@
name = "pybis"
__author__ = "Swen Vermeul"
__email__ = "swen@ethz.ch"
-__version__ = "1.31.6"
+__version__ = "1.32.0"
from . import pybis
from .pybis import DataSet
diff --git a/pybis/src/python/pybis/pybis.py b/pybis/src/python/pybis/pybis.py
index 3e78318f20e0dfd6474123301f0aaad13b12060e..6106a95ad9fd3b9c0e00b6313d00708419046196 100644
--- a/pybis/src/python/pybis/pybis.py
+++ b/pybis/src/python/pybis/pybis.py
@@ -35,7 +35,6 @@ from texttable import Texttable
from . import data_set as pbds
from .dataset import DataSet
from .definitions import (
- fetch_option,
get_definition_for_entity,
get_fetchoption_for_entity,
get_fetchoptions,
@@ -1617,9 +1616,9 @@ class Openbis:
"@type": "as.dto.authorizationgroup.fetchoptions.AuthorizationGroupFetchOptions"
}
for option in ["roleAssignments", "users", "registrator"]:
- fetchopts[option] = fetch_option[option]
+ fetchopts[option] = get_fetchoption_for_entity(option)
- fetchopts["users"]["space"] = fetch_option["space"]
+ fetchopts["users"]["space"] = get_fetchoption_for_entity("space")
request = {
"method": "getAuthorizationGroups",
@@ -1680,11 +1679,11 @@ class Openbis:
search_criteria["criteria"] = sub_crit
method_name = get_method_for_entity(entity, "search")
- fetchopts = fetch_option[entity]
+ fetchopts = get_fetchoption_for_entity(entity)
fetchopts["from"] = start_with
fetchopts["count"] = count
for option in ["space", "project", "user", "authorizationGroup", "registrator"]:
- fetchopts[option] = fetch_option[option]
+ fetchopts[option] = get_fetchoption_for_entity(option)
request = {
"method": method_name,
@@ -1722,9 +1721,9 @@ class Openbis:
def get_role_assignment(self, techId, only_data=False):
"""Fetches one assigned role by its techId."""
- fetchopts = fetch_option["roleAssignment"]
+ fetchopts = get_fetchoption_for_entity("roleAssignment")
for option in ["space", "project", "user", "authorizationGroup", "registrator"]:
- fetchopts[option] = fetch_option[option]
+ fetchopts[option] = get_fetchoption_for_entity(option)
request = {
"method": "getRoleAssignments",
@@ -1837,11 +1836,11 @@ class Openbis:
search_criteria["criteria"] = criteria
search_criteria["operator"] = "AND"
- fetchopts = fetch_option["authorizationGroup"]
+ fetchopts = get_fetchoption_for_entity("authorizationGroup")
fetchopts["from"] = start_with
fetchopts["count"] = count
for option in ["roleAssignments", "registrator", "users"]:
- fetchopts[option] = fetch_option[option]
+ fetchopts[option] = get_fetchoption_for_entity(option)
request = {
"method": "searchAuthorizationGroups",
"params": [self.token, search_criteria, fetchopts],
@@ -1891,11 +1890,11 @@ class Openbis:
"""Get openBIS users"""
search_criteria = get_search_criteria("person", **search_args)
- fetchopts = fetch_option["person"]
+ fetchopts = get_fetchoption_for_entity("person")
fetchopts["from"] = start_with
fetchopts["count"] = count
for option in ["space"]:
- fetchopts[option] = fetch_option[option]
+ fetchopts[option] = get_fetchoption_for_entity(option)
request = {
"method": "searchPersons",
"params": [self.token, search_criteria, fetchopts],
@@ -1947,7 +1946,7 @@ class Openbis:
fetchopts = {"@type": "as.dto.person.fetchoptions.PersonFetchOptions"}
for option in ["roleAssignments", "space"]:
- fetchopts[option] = fetch_option[option]
+ fetchopts[option] = get_fetchoption_for_entity(option)
request = {
"method": "getPersons",
@@ -1980,7 +1979,7 @@ class Openbis:
method = get_method_for_entity("space", "search")
search_criteria = _subcriteria_for_code(code, "space")
- fetchopts = fetch_option["space"]
+ fetchopts = get_fetchoption_for_entity("space")
fetchopts["from"] = start_with
fetchopts["count"] = count
request = {
@@ -2031,7 +2030,7 @@ class Openbis:
fetchopts = {"@type": "as.dto.space.fetchoptions.SpaceFetchOptions"}
for option in ["registrator"]:
- fetchopts[option] = fetch_option[option]
+ fetchopts[option] = get_fetchoption_for_entity(option)
method = get_method_for_entity("space", "get")
@@ -2167,7 +2166,7 @@ class Openbis:
}
# build the various fetch options
- fetchopts = copy.deepcopy(fetch_option["sample"])
+ fetchopts = get_fetchoption_for_entity("sample")
fetchopts["from"] = start_with
fetchopts["count"] = count
@@ -2184,13 +2183,13 @@ class Openbis:
if self.get_server_information().project_samples_enabled:
options.append("project")
for option in options:
- fetchopts[option] = fetch_option[option]
+ fetchopts[option] = get_fetchoption_for_entity(option)
for relation in ["parents", "children", "components", "container"]:
if relation in attrs:
- fetchopts[relation] = fetch_option["sample"]
+ fetchopts[relation] = get_fetchoption_for_entity("sample")
if props is not None:
- fetchopts["properties"] = fetch_option["properties"]
+ fetchopts["properties"] = get_fetchoption_for_entity("properties")
request = {
"method": "searchSamples",
@@ -2352,7 +2351,7 @@ class Openbis:
search_criteria["criteria"] = sub_criteria
search_criteria["operator"] = "AND"
- fetchopts = fetch_option["experiment"]
+ fetchopts = get_fetchoption_for_entity("experiment")
fetchopts["from"] = start_with
fetchopts["count"] = count
@@ -2360,7 +2359,7 @@ class Openbis:
attrs = []
options = self._get_fetchopts_for_attrs(attrs)
for option in ["tags", "properties", "registrator", "modifier"] + options:
- fetchopts[option] = fetch_option[option]
+ fetchopts[option] = get_fetchoption_for_entity(option)
request = {
"method": "searchExperiments",
@@ -2593,7 +2592,7 @@ class Openbis:
fetchopts["count"] = count
for relation in ["parents", "children", "components", "containers"]:
if relation in attrs:
- fetchopts[relation] = fetch_option["dataSet"]
+ fetchopts[relation] = get_fetchoption_for_entity("dataSet")
for option in [
"tags",
@@ -2606,9 +2605,9 @@ class Openbis:
"registrator",
"modifier",
]:
- fetchopts[option] = fetch_option[option]
+ fetchopts[option] = get_fetchoption_for_entity(option)
- fetchopts["experiment"]["project"] = fetch_option["project"]
+ fetchopts["experiment"]["project"] = get_fetchoption_for_entity("project")
if kind:
kind = kind.upper()
@@ -2664,7 +2663,7 @@ class Openbis:
if experiment:
return experiment
- fetchopts = fetch_option["experiment"]
+ fetchopts = get_fetchoption_for_entity("experiment")
search_request = _type_for_id(code, "experiment")
for option in [
@@ -2676,10 +2675,12 @@ class Openbis:
"registrator",
"modifier",
]:
- fetchopts[option] = fetch_option[option]
+ fetchopts[option] = get_fetchoption_for_entity(option)
if withAttachments:
- fetchopts["attachments"] = fetch_option["attachmentsWithContent"]
+ fetchopts["attachments"] = get_fetchoption_for_entity(
+ "attachmentsWithContent"
+ )
request = {
"method": "getExperiments",
@@ -2774,8 +2775,8 @@ class Openbis:
def get_deletions(self, start_with=None, count=None):
search_criteria = {"@type": "as.dto.deletion.search.DeletionSearchCriteria"}
- fetchopts = fetch_option["deletion"]
- fetchoptsDeleted = fetch_option["deletedObjects"]
+ fetchopts = get_fetchoption_for_entity("deletion")
+ fetchoptsDeleted = get_fetchoption_for_entity("deletedObjects")
fetchoptsDeleted["from"] = start_with
fetchoptsDeleted["count"] = count
fetchopts["deletedObjects"] = fetchoptsDeleted
@@ -2808,7 +2809,7 @@ class Openbis:
def _gen_fetchoptions(self, options, foType):
fo = {"@type": foType}
for option in options:
- fo[option] = fetch_option[option]
+ fo[option] = get_fetchoption_for_entity(option)
return fo
def get_project(self, projectId, only_data=False, use_cache=True):
@@ -2887,7 +2888,7 @@ class Openbis:
fetchopts["from"] = start_with
fetchopts["count"] = count
for option in ["registrator", "modifier", "leader"]:
- fetchopts[option] = fetch_option[option]
+ fetchopts[option] = get_fetchoption_for_entity(option)
request = {
"method": "searchProjects",
@@ -2960,7 +2961,7 @@ class Openbis:
fo = {"@type": foType}
for option in options:
- fo[option] = fetch_option[option]
+ fo[option] = get_fetchoption_for_entity(option)
request = {
"method": method_name,
@@ -3019,7 +3020,7 @@ class Openbis:
"@type"
] = "as.dto.vocabulary.search.VocabularyTermSearchCriteria"
- fetchopts = fetch_option["vocabularyTerm"]
+ fetchopts = get_fetchoption_for_entity("vocabularyTerm")
fetchopts["from"] = start_with
fetchopts["count"] = count
@@ -3122,11 +3123,11 @@ class Openbis:
"operator": "AND",
}
- fetchopts = fetch_option["vocabulary"]
+ fetchopts = get_fetchoption_for_entity("vocabulary")
fetchopts["from"] = start_with
fetchopts["count"] = count
for option in ["registrator"]:
- fetchopts[option] = fetch_option[option]
+ fetchopts[option] = get_fetchoption_for_entity(option)
request = {
"method": "searchVocabularies",
@@ -3178,7 +3179,7 @@ class Openbis:
entity = "vocabulary"
method_name = get_method_for_entity(entity, "get")
objectIds = _type_for_id(code.upper(), entity)
- fetchopts = fetch_option[entity]
+ fetchopts = get_fetchoption_for_entity(entity)
request = {
"method": method_name,
@@ -3209,11 +3210,11 @@ class Openbis:
search_criteria = get_search_type_for_entity("tag", "AND")
criteria = []
- fetchopts = fetch_option["tag"]
+ fetchopts = get_fetchoption_for_entity("tag")
fetchopts["from"] = start_with
fetchopts["count"] = count
for option in ["owner"]:
- fetchopts[option] = fetch_option[option]
+ fetchopts[option] = get_fetchoption_for_entity(option)
if code:
criteria.append(_criteria_for_code(code))
search_criteria["criteria"] = criteria
@@ -3246,9 +3247,9 @@ class Openbis:
return tag
identifiers.append(_type_for_id(permId, "tag"))
- fetchopts = fetch_option["tag"]
+ fetchopts = get_fetchoption_for_entity("tag")
for option in ["owner"]:
- fetchopts[option] = fetch_option[option]
+ fetchopts[option] = get_fetchoption_for_entity(option)
request = {
"method": "getTags",
"params": [self.token, identifiers, fetchopts],
@@ -3496,9 +3497,9 @@ class Openbis:
search_criteria = get_search_type_for_entity("plugin", "AND")
search_criteria["criteria"] = criteria
- fetchopts = fetch_option["plugin"]
+ fetchopts = get_fetchoption_for_entity("plugin")
for option in ["registrator"]:
- fetchopts[option] = fetch_option[option]
+ fetchopts[option] = get_fetchoption_for_entity(option)
fetchopts["from"] = start_with
fetchopts["count"] = count
@@ -3557,13 +3558,13 @@ class Openbis:
def get_plugin(self, permId, only_data=False, with_script=True):
search_request = _type_for_id(permId, "plugin")
- fetchopts = fetch_option["plugin"]
+ fetchopts = get_fetchoption_for_entity("plugin")
options = ["registrator"]
if with_script:
options.append("script")
for option in options:
- fetchopts[option] = fetch_option[option]
+ fetchopts[option] = get_fetchoption_for_entity(option)
request = {
"method": "getPlugins",
@@ -3676,10 +3677,10 @@ class Openbis:
{"permId": c.upper(), "@type": "as.dto.property.id.PropertyTypePermId"}
)
- fetchopts = fetch_option["propertyType"]
+ fetchopts = get_fetchoption_for_entity("propertyType")
options = ["vocabulary", "materialType", "semanticAnnotations", "registrator"]
for option in options:
- fetchopts[option] = fetch_option[option]
+ fetchopts[option] = get_fetchoption_for_entity(option)
request = {
"method": "getPropertyTypes",
@@ -3713,7 +3714,7 @@ class Openbis:
)
def get_property_types(self, code=None, start_with=None, count=None):
- fetchopts = fetch_option["propertyType"]
+ fetchopts = get_fetchoption_for_entity("propertyType")
fetchopts["from"] = start_with
fetchopts["count"] = count
search_criteria = get_search_criteria("propertyType", code=code)
@@ -4002,9 +4003,11 @@ class Openbis:
search_request = _gen_search_criteria(
{entity.lower(): entity + "Type", "operator": "AND", "code": type_name}
)
- fetch_options["propertyAssignments"] = fetch_option["propertyAssignments"]
+ fetch_options["propertyAssignments"] = get_fetchoption_for_entity(
+ "propertyAssignments"
+ )
if self.get_server_information().api_version > "3.3":
- fetch_options["validationPlugin"] = fetch_option["plugin"]
+ fetch_options["validationPlugin"] = get_fetchoption_for_entity("plugin")
request = {
"method": method_name,
@@ -4125,7 +4128,7 @@ class Openbis:
else:
identifiers.append(_type_for_id(permIds, "dataset"))
- fetchopts = fetch_option["dataSet"]
+ fetchopts = get_fetchoption_for_entity("dataSet")
for option in [
"tags",
@@ -4138,7 +4141,7 @@ class Openbis:
"registrator",
"modifier",
]:
- fetchopts[option] = fetch_option[option]
+ fetchopts[option] = get_fetchoption_for_entity(option)
request = {
"method": "getDataSets",
@@ -4357,7 +4360,7 @@ class Openbis:
else:
identifiers.append(_type_for_id(sample_ident, "sample"))
- fetchopts = fetch_option["sample"]
+ fetchopts = get_fetchoption_for_entity("sample")
options = [
"tags",
"properties",
@@ -4371,10 +4374,12 @@ class Openbis:
if self.get_server_information().project_samples_enabled:
options.append("project")
for option in options:
- fetchopts[option] = fetch_option[option]
+ fetchopts[option] = get_fetchoption_for_entity(option)
if withAttachments:
- fetchopts["attachments"] = fetch_option["attachmentsWithContent"]
+ fetchopts["attachments"] = get_fetchoption_for_entity(
+ "attachmentsWithContent"
+ )
for key in ["parents", "children", "container", "components"]:
fetchopts[key] = {"@type": "as.dto.sample.fetchoptions.SampleFetchOptions"}
diff --git a/pybis/src/python/setup.py b/pybis/src/python/setup.py
index 77513791c50d2e6f790c6daf2a5fd48fcd237844..8248b021bd413ccc0be6c35e0453f5b8420fa413 100644
--- a/pybis/src/python/setup.py
+++ b/pybis/src/python/setup.py
@@ -13,7 +13,7 @@ with open("README.md", "r", encoding="utf-8") as fh:
setup(
name="PyBIS",
- version="1.31.6",
+ version="1.32.0rc2",
author="Swen Vermeul • ID SIS • ETH Zürich",
author_email="swen@ethz.ch",
description="openBIS connection and interaction, optimized for using with Jupyter",