From 09fe5828660af2713c699ff2b4718fe91e8aa328 Mon Sep 17 00:00:00 2001
From: vermeul <swen@ethz.ch>
Date: Mon, 29 Jan 2018 15:06:19 +0100
Subject: [PATCH] startet working on persons and authorization groups
---
src/python/PyBis/pybis/pybis.py | 558 +++++++++++++++++++++++-----
src/python/PyBis/pybis/utils.py | 2 +-
src/vagrant/jupyter-bis/Vagrantfile | 2 +-
3 files changed, 468 insertions(+), 94 deletions(-)
diff --git a/src/python/PyBis/pybis/pybis.py b/src/python/PyBis/pybis/pybis.py
index a14dc1bba33..31dd60f53e3 100644
--- a/src/python/PyBis/pybis/pybis.py
+++ b/src/python/PyBis/pybis/pybis.py
@@ -81,6 +81,22 @@ def _definitions(entity):
"cre_type": "as.dto.sample.create.SampleCreation",
"multi": "parents children components tags attachments".split(),
},
+ "SemanticAnnotation": {
+ "attrs_new": "permId entityType propertyType predicateOntologyId predicateOntologyVersion predicateAccessionId descriptorOntologyId descriptorOntologyVersion descriptorAccessionId".split(),
+ "attrs_up": "entityType propertyType predicateOntologyId predicateOntologyVersion predicateAccessionId descriptorOntologyId descriptorOntologyVersion descriptorAccessionId ".split(),
+ "attrs": "permId entityType propertyType predicateOntologyId predicateOntologyVersion predicateAccessionId descriptorOntologyId descriptorOntologyVersion descriptorAccessionId creationDate".split(),
+ "ids2type": {
+ "propertyTypeId": {
+ "permId": "as.dto.property.id.PropertyTypePermId"
+ },
+ "entityTypeId": {
+ "permId": "as.dto.entity.id.EntityTypePermId"
+ },
+ },
+ "identifier": "permId",
+ "cre_type": "as.dto.sample.create.SampleCreation",
+ "multi": "parents children components tags attachments".split(),
+ },
"DataSet": {
"attrs_new": "type experiment sample parents children components tags".split(),
"attrs_up": "parents children experiment sample components tags".split(),
@@ -103,6 +119,19 @@ def _definitions(entity):
"attrs_new": "code description experiments samples dataSets materials".split(),
"attrs": "code description experiments samples dataSets materials registrationDate".split(),
},
+ "Person": {
+ "attrs_new": "userId space".split(),
+ "attrs_up": "space".split(),
+ "attrs": "permId userId firstName lastName email roleAssignments space registrationDate ".split(),
+ "multi": "".split(),
+ "identifier": "userId",
+ },
+ "AuthorizationGroup" : {
+ "attrs": "code description users roleAssignments registrator registrationDate modificationDate".split(),
+ "attrs_new": "code description userIds".split(),
+ "multi": "users".split()
+
+ },
"attr2ids": {
"space": "spaceId",
"project": "projectId",
@@ -120,6 +149,8 @@ def _definitions(entity):
"parents": "parentIds",
"children": "childIds",
"tags": "tagIds",
+ "userId": "userId",
+ "users": "userIds",
},
"ids2type": {
'spaceId': {'permId': {'@type': 'as.dto.space.id.SpacePermId'}},
@@ -130,20 +161,48 @@ def _definitions(entity):
}
return entities[entity]
-
-search_criteria = {
- "space": "as.dto.space.search.SpaceSearchCriteria",
- "project": "as.dto.project.search.ProjectSearchCriteria",
- "experiment": "as.dto.experiment.search.ExperimentSearchCriteria",
- "sample": "as.dto.sample.search.SampleSearchCriteria",
- "dataset": "as.dto.dataset.search.DataSetSearchCriteria",
- "code": "as.dto.common.search.CodeSearchCriteria",
- "sample_type": "as.dto.sample.search.SampleTypeSearchCriteria",
-}
+def get_search_criteria_for_entity(entity):
+ """ Creates a basic search object for a given entity. Returns a dictionary.
+ Example::
+ get_search_criteria_for_entity('space')
+ {'@type': 'as.dto.space.search.SpaceSearchCriteria'}
+ """
+ search_criteria = {
+ "space": "as.dto.space.search.SpaceSearchCriteria",
+ "userId": "as.dto.person.search.UserIdSearchCriteria",
+ "email": "as.dto.person.search.EmailSearchCriteria",
+ "firstName": "as.dto.person.search.FirstNameSearchCriteria",
+ "lastName": "as.dto.person.search.LastNameSearchCriteria",
+ "project": "as.dto.project.search.ProjectSearchCriteria",
+ "experiment": "as.dto.experiment.search.ExperimentSearchCriteria",
+ "experiment_type": "as.dto.experiment.search.ExperimentTypeSearchCriteria",
+ "sample": "as.dto.sample.search.SampleSearchCriteria",
+ "sample_type": "as.dto.sample.search.SampleTypeSearchCriteria",
+ "dataset": "as.dto.dataset.search.DataSetSearchCriteria",
+ "dataset_type": "as.dto.dataset.search.DataSetTypeSearchCriteria",
+ "external_dms": "as.dto.externaldms.search.ExternalDmsSearchCriteria",
+ "material": "as.dto.material.search.MaterialSearchCriteria",
+ "material_type": "as.dto.material.search.MaterialTypeSearchCriteria",
+ "vocabulary_term": "as.dto.vocabulary.search.VocabularyTermSearchCriteria",
+ "tag": "as.dto.tag.search.TagSearchCriteria",
+ "authorization_group": "as.dto.authorizationgroup.search.AuthorizationGroupSearchCriteria",
+ "role_assignment": "as.dto.roleassignment.search.RoleAssignmentSearchCriteria",
+ "person": "as.dto.person.search.PersonSearchCriteria",
+ "code": "as.dto.common.search.CodeSearchCriteria",
+ "sample_type": "as.dto.sample.search.SampleTypeSearchCriteria",
+ "global": "as.dto.global.GlobalSearchObject",
+ }
+ if entity in search_criteria:
+ return {
+ "@type": search_criteria[entity]
+ }
+ else:
+ return {}
fetch_option = {
"space": {"@type": "as.dto.space.fetchoptions.SpaceFetchOptions"},
"project": {"@type": "as.dto.project.fetchoptions.ProjectFetchOptions"},
+ "person": {"@type": "as.dto.person.fetchoptions.PersonFetchOptions"},
"experiment": {
"@type": "as.dto.experiment.fetchoptions.ExperimentFetchOptions",
"type": {"@type": "as.dto.experiment.fetchoptions.ExperimentTypeFetchOptions"}
@@ -163,7 +222,12 @@ fetch_option = {
"externalDms": {"@type": "as.dto.externaldms.fetchoptions.ExternalDmsFetchOptions"},
"@type": "as.dto.dataset.fetchoptions.LinkedDataFetchOptions"
},
-
+ "roleAssignments": {
+ "@type": "as.dto.roleassignment.fetchoptions.RoleAssignmentFetchOptions",
+ "space": {
+ "@type": "as.dto.space.fetchoptions.SpaceFetchOptions"
+ }
+ },
"properties": {"@type": "as.dto.property.fetchoptions.PropertyFetchOptions"},
"propertyAssignments": {
"@type": "as.dto.property.fetchoptions.PropertyAssignmentFetchOptions",
@@ -189,6 +253,7 @@ fetch_option = {
},
"history": {"@type": "as.dto.history.fetchoptions.HistoryEntryFetchOptions"},
"dataStore": {"@type": "as.dto.datastore.fetchoptions.DataStoreFetchOptions"},
+ "authorizationGroup": {"@type": "as.dto.authorizationgroup.fetchoptions.AuthorizationGroupFetchOptions"},
}
@@ -259,6 +324,17 @@ def extract_property_assignments(pas):
return pa_strings
+def extract_role_assignments(ras):
+ ra_strings = []
+ for ra in ras:
+ ra_strings.append({
+ "role": ra['role'],
+ "roleLevel": ra['roleLevel'],
+ "space": ra['space']['code'] if ra['space'] else None
+ })
+ return ra_strings
+
+
def extract_person(person):
if not isinstance(person, dict):
return str(person)
@@ -367,6 +443,11 @@ def _create_experimentId(ident):
"@type": "as.dto.experiment.id.ExperimentIdentifier"
}
+def get_field_value_search(field, value, comparison="StringEqualToValue"):
+ return {
+ "value": value,
+ "@type": "as.dto.common.search.{}".format(comparison)
+ }
def _common_search(search_type, value, comparison="StringEqualToValue"):
sreq = {
@@ -544,6 +625,27 @@ def _subcriteria_for_permid(permids, entity, parents_or_children=''):
def _subcriteria_for_code(code, object_type):
+ """ Creates the often used search criteria for code values. Returns a dictionary.
+
+ Example::
+ _subcriteria_for_code("username", "space")
+
+ {
+ "criteria": [
+ {
+ "fieldType": "ATTRIBUTE",
+ "@type": "as.dto.common.search.CodeSearchCriteria",
+ "fieldName": "code",
+ "fieldValue": {
+ "@type": "as.dto.common.search.StringEqualToValue",
+ "value": "USERNAME"
+ }
+ }
+ ],
+ "operator": "AND",
+ "@type": "as.dto.space.search.SpaceSearchCriteria"
+ }
+ """
if code is not None:
if is_permid(code):
fieldname = "permId"
@@ -552,25 +654,22 @@ def _subcriteria_for_code(code, object_type):
fieldname = "code"
fieldtype = "as.dto.common.search.CodeSearchCriteria"
- criteria = {
- "criteria": [
- {
- "fieldName": fieldname,
- "fieldType": "ATTRIBUTE",
- "fieldValue": {
- "value": code.upper(),
- "@type": "as.dto.common.search.StringEqualToValue"
- },
- "@type": fieldtype
- }
- ],
- "@type": search_criteria[object_type.lower()],
- "operator": "AND"
- }
- return criteria
+
+ search_criteria = get_search_criteria_for_entity(object_type.lower())
+ search_criteria['criteria'] = [{
+ "fieldName": fieldname,
+ "fieldType": "ATTRIBUTE",
+ "fieldValue": {
+ "value": code.upper(),
+ "@type": "as.dto.common.search.StringEqualToValue"
+ },
+ "@type": fieldtype
+ }]
+
+ search_criteria["operator"] = "AND"
+ return search_criteria
else:
- criteria = {"@type": search_criteria[object_type.lower()]}
- return criteria
+ return get_search_criteria_for_entity(object_type.lower())
class Openbis:
@@ -640,6 +739,10 @@ class Openbis:
"get_spaces()",
"get_tags()",
"get_terms()",
+ "get_persons()",
+ "get_person(userId=None)",
+ "new_person(userId, firstName, lastName, email)",
+ "new_group(code, description, userIds)",
'new_space(name, description)',
'new_project(space, code, description, attachments)',
'new_experiment(type, code, project, props={})',
@@ -739,6 +842,7 @@ class Openbis:
json.dumps(request),
verify=self.verify_certificates
)
+ #print(json.dumps(request))
if resp.ok:
resp = resp.json()
@@ -821,18 +925,156 @@ class Openbis:
else:
raise ValueError("No datastore found!")
+
+ def new_person(self, userId, space=None):
+ """ creates an openBIS person
+ """
+ return Person(self, userId=userId, space=space)
+
+
+ def new_group(self, code, description=None, users=None):
+ """ creates an openBIS person
+ """
+ return Group(self, code=code, description=description, users=users)
+
+ def get_groups(self, code=None):
+ """ Get openBIS AuthorizationGroups
+ """
+
+ criterias = []
+ if code:
+ criterias.append(_subcriteria_for_code(code))
+ criteria = get_search_criteria_for_entity('authorizationGroup')
+ criteria['criteria'] = criterias
+
+ fetchopts = fetch_option['authorizationGroup']
+ for option in ['roleAssignments']:
+ fetchopts[option] = fetch_option[option]
+ request = {
+ "method": "searchAuthorizationGroups",
+ "params": [
+ self.token,
+ criteria,
+ fetchopts
+ ],
+ }
+ resp = self._post_request(self.as_v3, request)
+ if len(resp['objects']) == 0:
+ raise ValueError("No persons found!")
+
+ objects = resp['objects']
+ parse_jackson(objects)
+
+ persons = DataFrame(resp['objects'])
+ persons['permId'] = persons['permId'].map(extract_permid)
+ persons['registrationDate'] = persons['registrationDate'].map(format_timestamp)
+ persons['space'] = persons['space'].map(extract_nested_permid)
+ p = Things(
+ self, entity='person',
+ df=persons[['permId', 'userId', 'firstName', 'lastName', 'email', 'space', 'registrationDate', 'active']],
+ identifier_name='permId'
+ )
+ return p
+
+
+ def get_persons(self, **search_args):
+ """ Get openBIS users
+ """
+
+ criteria = []
+ for search_arg in ['userId','firstName','lastName','email']:
+ if search_arg in search_args:
+ sub_crit = get_search_criteria_for_entity(search_arg)
+ sub_crit['fieldValue'] = get_field_value_search(search_arg, search_args[search_arg])
+ #sub_crit['fieldValue'] = {
+ # "value": search_args[search_arg],
+ # "@type": "as.dto.common.search.StringEqualToValue"
+ #}
+ criteria.append(sub_crit)
+
+ search_criteria = get_search_criteria_for_entity('person')
+ search_criteria['criteria'] = criteria
+ search_criteria['operator'] = "AND"
+
+ fetchopts = {}
+ for option in ['space']:
+ fetchopts[option] = fetch_option[option]
+ request = {
+ "method": "searchPersons",
+ "params": [
+ self.token,
+ search_criteria,
+ fetchopts
+ ],
+ }
+ resp = self._post_request(self.as_v3, request)
+ if len(resp['objects']) == 0:
+ raise ValueError("No persons found!")
+
+ objects = resp['objects']
+ parse_jackson(objects)
+
+ persons = DataFrame(resp['objects'])
+ persons['permId'] = persons['permId'].map(extract_permid)
+ persons['registrationDate'] = persons['registrationDate'].map(format_timestamp)
+ persons['space'] = persons['space'].map(extract_nested_permid)
+ p = Things(
+ self, entity='person',
+ df=persons[['permId', 'userId', 'firstName', 'lastName', 'email', 'space', 'registrationDate', 'active']],
+ identifier_name='permId'
+ )
+ return p
+
+ def get_person(self, userId, only_data=False):
+ """ Get a person (user)
+ """
+
+ ids = [{
+ "@type": "as.dto.person.id.PersonPermId",
+ "permId": userId
+ }]
+
+ fetchopts = {}
+ for option in ['space', 'roleAssignments', 'project']:
+ fetchopts[option] = fetch_option[option]
+
+ request = {
+ "method": "getPersons",
+ "params": [
+ self.token,
+ ids,
+ fetchopts,
+ ],
+ }
+
+ resp = self._post_request(self.as_v3, request)
+ if len(resp) == 0:
+ raise ValueError("No person found!")
+
+
+ #persons['roleAssignments'] = persons['roleAssignments'].map(extract_role_assignments)
+ for permid in resp:
+ person = resp[permid]
+ parse_jackson(person)
+
+ if only_data:
+ return person
+ else:
+ return Person(self, data=person)
+
+
def get_spaces(self, code=None):
""" Get a list of all available spaces (DataFrame object). To create a sample or a
dataset, you need to specify in which space it should live.
"""
- criteria = {}
- options = {}
+ search_criteria = _subcriteria_for_code(code, 'space')
+ fetchopts = {}
request = {
"method": "searchSpaces",
"params": [self.token,
- criteria,
- options,
+ search_criteria,
+ fetchopts,
],
}
resp = self._post_request(self.as_v3, request)
@@ -981,9 +1223,19 @@ class Openbis:
get_objects = get_samples # Alias
- def get_experiments(self, code=None, type=None, space=None, project=None, tags=None, is_finished=None, props=None,
- **properties):
- """ Get a list of all experiment for a given space or project (or any combination)
+ def get_experiments(self, code=None, type=None, space=None, project=None, tags=None, is_finished=None, props=None, **properties):
+ """ Searches for all experiment which match the search criteria. Returns a
+ «Things» object which can be used in many different situations.
+
+ Usage::
+ experiments = get_experiments(project='PROJECT_NAME', props=['NAME','FINISHED_FLAG'])
+ experiments[0] # returns first experiment
+ experiments['/MATERIALS/REAGENTS/ANTIBODY_COLLECTION']
+ for experiment in experiment:
+ # handle every experiment
+ ...
+ experiments.df # returns DataFrame object of the experiment list
+ print(experiments) # prints a nice ASCII table
"""
sub_criteria = []
@@ -1003,21 +1255,21 @@ class Openbis:
for prop in properties:
sub_criteria.append(_subcriteria_for_properties(prop, properties[prop]))
- criteria = {
- "criteria": sub_criteria,
- "@type": "as.dto.experiment.search.ExperimentSearchCriteria",
- "operator": "AND"
- }
+ search_criteria = get_search_criteria_for_entity('experiment')
+ search_criteria['criteria'] = sub_criteria
+ search_criteria['operator'] = 'AND'
+
fetchopts = fetch_option['experiment']
for option in ['tags', 'properties', 'registrator', 'modifier', 'project']:
fetchopts[option] = fetch_option[option]
request = {
"method": "searchExperiments",
- "params": [self.token,
- criteria,
- fetchopts,
- ],
+ "params": [
+ self.token,
+ search_criteria,
+ fetchopts,
+ ],
}
resp = self._post_request(self.as_v3, request)
if len(resp['objects']) == 0:
@@ -1081,11 +1333,9 @@ class Openbis:
for prop in properties:
sub_criteria.append(_subcriteria_for_properties(prop, properties[prop]))
- criteria = {
- "criteria": sub_criteria,
- "@type": "as.dto.dataset.search.DataSetSearchCriteria",
- "operator": "AND"
- }
+ search_criteria = get_search_criteria_for_entity('dataset')
+ search_criteria['criteria'] = sub_criteria
+ search_criteria['operator'] = 'AND'
fetchopts = {
"containers": {"@type": "as.dto.dataset.fetchoptions.DataSetFetchOptions"},
@@ -1098,7 +1348,7 @@ class Openbis:
request = {
"method": "searchDataSets",
"params": [self.token,
- criteria,
+ search_criteria,
fetchopts,
],
}
@@ -1417,28 +1667,28 @@ class Openbis:
}
resp = self._post_request(self.as_v3, request)
- if resp is not None:
- objects = resp['objects']
- parse_jackson(objects)
+ objects = resp['objects']
+ if len(objects) == 0:
+ raise ValueError("No projects found!")
+
+ parse_jackson(objects)
- projects = DataFrame(objects)
- if len(projects) is 0:
- raise ValueError("No projects found!")
-
- projects['registrationDate'] = projects['registrationDate'].map(format_timestamp)
- projects['modificationDate'] = projects['modificationDate'].map(format_timestamp)
- projects['leader'] = projects['leader'].map(extract_person)
- projects['registrator'] = projects['registrator'].map(extract_person)
- projects['modifier'] = projects['modifier'].map(extract_person)
- projects['permId'] = projects['permId'].map(extract_permid)
- projects['identifier'] = projects['identifier'].map(extract_identifier)
-
- pros = projects[['identifier', 'permId', 'leader', 'registrator', 'registrationDate',
- 'modifier', 'modificationDate']]
- return Things(self, 'project', pros, 'identifier')
- else:
+ projects = DataFrame(objects)
+ if len(projects) is 0:
raise ValueError("No projects found!")
+ projects['registrationDate'] = projects['registrationDate'].map(format_timestamp)
+ projects['modificationDate'] = projects['modificationDate'].map(format_timestamp)
+ projects['leader'] = projects['leader'].map(extract_person)
+ projects['registrator'] = projects['registrator'].map(extract_person)
+ projects['modifier'] = projects['modifier'].map(extract_person)
+ projects['permId'] = projects['permId'].map(extract_permid)
+ projects['identifier'] = projects['identifier'].map(extract_identifier)
+
+ pros = projects[['identifier', 'permId', 'leader', 'registrator', 'registrationDate',
+ 'modifier', 'modificationDate']]
+ return Things(self, 'project', pros, 'identifier')
+
def _create_get_request(self, method_name, entity, permids, options):
if not isinstance(permids, list):
@@ -1758,10 +2008,11 @@ class Openbis:
request = {
"method": "getDataSets",
- "params": [self.token,
- criteria,
- fetchopts,
- ],
+ "params": [
+ self.token,
+ criteria,
+ fetchopts,
+ ],
}
resp = self._post_request(self.as_v3, request)
@@ -2053,7 +2304,10 @@ class Openbis:
return DataSet(self, type=type_obj, files=files, folder=folder, props=props, **kwargs)
def new_semantic_annotation(self, entityType=None, propertyType=None, **kwargs):
- return SemanticAnnotation(openbis_obj=self, isNew=True, entityType=entityType, propertyType=propertyType, **kwargs)
+ return SemanticAnnotation(
+ openbis_obj=self, isNew=True,
+ entityType=entityType, propertyType=propertyType, **kwargs
+ )
def _get_dss_url(self, dss_code=None):
""" internal method to get the downloadURL of a datastore.
@@ -2268,7 +2522,6 @@ class OpenBisObject():
def __setattr__(self, name, value):
if name in ['set_properties', 'set_tags', 'add_tags']:
raise ValueError("These are methods which should not be overwritten")
-
setattr(self.__dict__['a'], name, value)
def _repr_html_(self):
@@ -2743,7 +2996,7 @@ class AttrHolder():
else:
self.__dict__['_' + attr] = data.get(attr, None)
- def _new_attrs(self):
+ def _new_attrs(self, method_name=None):
"""Returns the Python-equivalent JSON request when a new object is created.
It is used internally by the save() method of a newly created object.
"""
@@ -2786,8 +3039,10 @@ class AttrHolder():
new_obj[key] = items
# create a new entity
+ if method_name is None:
+ method_name = "create{}s".format(self.entity)
request = {
- "method": "create{}s".format(self.entity),
+ "method": method_name,
"params": [
self.openbis.token,
[new_obj]
@@ -2796,7 +3051,7 @@ class AttrHolder():
return request
- def _up_attrs(self):
+ def _up_attrs(self, method_name=None):
"""Returns the Python-equivalent JSON request when a new object is updated.
It is used internally by the save() method of an object to be updated.
"""
@@ -2893,9 +3148,11 @@ class AttrHolder():
"value": val
}
- # update a new entity
+ # update an existing entity
+ if method_name is None:
+ method_name = "update{}s".format(self.entity)
request = {
- "method": "update{}s".format(self.entity),
+ "method": method_name,
"params": [
self.openbis.token,
[up_obj]
@@ -2903,6 +3160,7 @@ class AttrHolder():
}
return request
+
def __getattr__(self, name):
""" handles all attribute requests dynamically. Values are returned in a sensible way,
for example the identifiers of parents, children and components are returned
@@ -3003,6 +3261,10 @@ class AttrHolder():
elif name in ["space"]:
obj = None
+ if value is None:
+ self.__dict__['_'+name] = None
+ return
+
if isinstance(value, str):
# fetch object in openBIS, make sure it actually exists
obj = getattr(self._openbis, "get_" + name)(value)
@@ -3050,8 +3312,8 @@ class AttrHolder():
self.__dict__['_code'] = value
- elif name == "description":
- self.__dict__['_description'] = value
+ elif name in [ "description", "userId" ]:
+ self.__dict__['-'+name] = value
else:
raise KeyError("no such attribute: {}".format(name))
@@ -3204,13 +3466,14 @@ class AttrHolder():
entity = self.entity.lower()
request = {
"method": method,
- "params": [self._openbis.token,
- [self._permId],
- dict(
- attachments=fetch_option['attachmentsWithContent'],
- **fetch_option[entity]
- )
- ]
+ "params": [
+ self._openbis.token,
+ [self._permId],
+ dict(
+ attachments=fetch_option['attachmentsWithContent'],
+ **fetch_option[entity]
+ )
+ ]
}
resp = self._openbis._post_request(self._openbis.as_v3, request)
attachments = resp[self.permId]['attachments']
@@ -3365,6 +3628,7 @@ class Sample():
else:
request = self._up_attrs()
+ request["params"][1][0]["properties"] = props
self.openbis._post_request(self.openbis.as_v3, request)
print("Sample successfully updated.")
new_sample_data = self.openbis.get_sample(self.permId, only_data=True)
@@ -3393,6 +3657,109 @@ class Sample():
pass
+class Person(OpenBisObject):
+ """ managing openBIS persons
+ """
+
+ def __init__(self, openbis_obj, data=None, **kwargs):
+ self.__dict__['openbis'] = openbis_obj
+ self.__dict__['a'] = AttrHolder(openbis_obj, 'Person' )
+
+ if data is not None:
+ self.a(data)
+ self.__dict__['data'] = data
+
+ if kwargs is not None:
+ for key in kwargs:
+ setattr(self, key, kwargs[key])
+
+
+ def __dir__(self):
+ """all the available methods and attributes that should be displayed
+ when using the autocompletion feature (TAB) in Jupyter
+ """
+ return [
+ 'permId', 'userId', 'firstName', 'lastName', 'email',
+ 'registrator', 'registrationDate','roleAssignments','space'
+ ]
+
+ def __str__(self):
+ return "{} {}".format(self.get('firstName'), self.get('lastName'))
+
+ def delete(self, reason):
+ raise ValueError("Persons cannot be deleted")
+
+ def save(self):
+ if self.is_new:
+ request = self._new_attrs()
+ # for new and updated objects, the parameter is
+ # unfortunately called homeSpaceId, spaceId throws no error
+ # but makes no change either
+ if "spaceId" in request['params'][1][0]:
+ request['params'][1][0]['homeSpaceId'] = request['params'][1][0]['spaceId']
+ del(request['params'][1][0]['spaceId'])
+ resp = self.openbis._post_request(self.openbis.as_v3, request)
+ print("Person successfully created.")
+ new_person_data = self.openbis.get_person(resp[0]['permId'], only_data=True)
+ self._set_data(new_person_data)
+ return self
+
+ else:
+ request = self._up_attrs()
+ # for new and updated objects, the parameter is
+ # unfortunately called homeSpaceId, spaceId throws no error
+ # but makes no change either
+ if "spaceId" in request['params'][1][0]:
+ request['params'][1][0]['homeSpaceId'] = request['params'][1][0]['spaceId']
+ del(request['params'][1][0]['spaceId'])
+
+ self.openbis._post_request(self.openbis.as_v3, request)
+ print("Person successfully updated.")
+ new_person_data = self.openbis.get_person(self.permId, only_data=True)
+ self._set_data(new_person_data)
+
+
+class Group(OpenBisObject):
+ """ Managing openBIS authorization groups
+ """
+
+ def __init__(self, openbis_obj, data=None, **kwargs):
+ self.__dict__['openbis'] = openbis_obj
+ self.__dict__['a'] = AttrHolder(openbis_obj, 'AuthorizationGroup')
+
+ if data is not None:
+ self.a(data)
+ self.__dict__['data'] = data
+
+ if kwargs is not None:
+ for key in kwargs:
+ setattr(self, key, kwargs[key])
+
+ def __dir__(self):
+ return [
+ 'get_users()', 'add_users()', 'del_users()',
+ 'get_roles()', 'add_roles()', 'del_roles()'
+ ]
+
+ def save(self):
+ if self.is_new:
+ request = self._new_attrs()
+ resp = self.openbis._post_request(self.openbis.as_v3, request)
+ print("Group successfully created.")
+ # re-fetch group from openBIS
+ new_data = self.openbis.get_person(resp[0]['permId'], only_data=True)
+ self._set_data(new_data)
+ return self
+
+ else:
+ request = self._up_attrs()
+ self.openbis._post_request(self.openbis.as_v3, request)
+ print("Group successfully updated.")
+ # re-fetch group from openBIS
+ new_data = self.openbis.get_group(self.permId, only_data=True)
+ self._set_data(new_data)
+
+
class Space(OpenBisObject):
""" managing openBIS spaces
"""
@@ -3608,7 +3975,7 @@ class Things():
row = self.df[self.df[self.identifier_name] == key.upper()]
if row is not None:
- # invoke the openbis.get_entity() method
+ # invoke the openbis.get_<entity>() method
return getattr(self.openbis, 'get_' + self.entity)(row[self.identifier_name].values[0])
def __iter__(self):
@@ -3901,7 +4268,14 @@ class SemanticAnnotation():
self.creationDate = kwargs.get('creationDate')
def __dir__(self):
- return ['permId', 'entityType', 'propertyType', 'predicateOntologyId', 'predicateOntologyVersion', 'predicateAccessionId', 'descriptorOntologyId', 'descriptorOntologyVersion', 'descriptorAccessionId', 'creationDate', 'save()', 'delete()' ]
+ return [
+ 'permId', 'entityType', 'propertyType',
+ 'predicateOntologyId', 'predicateOntologyVersion',
+ 'predicateAccessionId', 'descriptorOntologyId',
+ 'descriptorOntologyVersion', 'descriptorAccessionId',
+ 'creationDate',
+ 'save()', 'delete()'
+ ]
def save(self):
if self._isNew:
diff --git a/src/python/PyBis/pybis/utils.py b/src/python/PyBis/pybis/utils.py
index a16f6ac7dda..e992594c9e2 100644
--- a/src/python/PyBis/pybis/utils.py
+++ b/src/python/PyBis/pybis/utils.py
@@ -10,7 +10,7 @@ def parse_jackson(input_json):
interesting=['tags', 'registrator', 'modifier', 'type', 'parents',
'children', 'containers', 'properties', 'experiment', 'sample',
'project', 'space', 'propertyType', 'entityType', 'propertyType', 'propertyAssignment',
- 'externalDms'
+ 'externalDms', 'roleAssignments'
]
found = {}
def build_cache(graph):
diff --git a/src/vagrant/jupyter-bis/Vagrantfile b/src/vagrant/jupyter-bis/Vagrantfile
index f474ba79633..0d95784a045 100644
--- a/src/vagrant/jupyter-bis/Vagrantfile
+++ b/src/vagrant/jupyter-bis/Vagrantfile
@@ -18,7 +18,7 @@ Vagrant.configure(2) do |config|
# Create a forwarded port mapping which allows access to a specific port
# within the machine from a port on the host machine. In the example below,
# accessing "localhost:8080" will access port 80 on the guest machine.
- config.vm.network "forwarded_port", guest: 8888, host: 8888
+ config.vm.network "forwarded_port", guest: 8888, host: 8887
config.vm.network "forwarded_port", guest: 8000, host: 8000
config.vm.network "forwarded_port", guest: 8443, host: 8443
config.vm.network "forwarded_port", guest: 8444, host: 8444
--
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