diff --git a/src/python/PyBis/pybis/pybis.py b/src/python/PyBis/pybis/pybis.py
index 99f8ac05c2778c0239b5e60e0ba98758ab12153c..a963cc0a02c449d468ebc33cb543821015daa48a 100644
--- a/src/python/PyBis/pybis/pybis.py
+++ b/src/python/PyBis/pybis/pybis.py
@@ -44,6 +44,15 @@ from datetime import datetime
PYBIS_PLUGIN = "dataset-uploader-api"
+# display messages when in a interactive context (IPython or Jupyter)
+try:
+ get_ipython()
+except Exception:
+ VERBOSE = False
+else:
+ VERBOSE = True
+
+
def _definitions(entity):
entities = {
@@ -162,7 +171,7 @@ def _definitions(entity):
return entities[entity]
-def get_search_type_for_entity(entity):
+def get_search_type_for_entity(entity, operator=None):
""" Returns a dictionary containing the correct search criteria type
for a given entity.
@@ -190,15 +199,18 @@ def get_search_type_for_entity(entity):
"vocabulary_term": "as.dto.vocabulary.search.VocabularyTermSearchCriteria",
"tag": "as.dto.tag.search.TagSearchCriteria",
"authorizationGroup": "as.dto.authorizationgroup.search.AuthorizationGroupSearchCriteria",
- "role_assignment": "as.dto.roleassignment.search.RoleAssignmentSearchCriteria",
+ "roleAssignment": "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",
}
- return {
- "@type": search_criteria[entity]
- }
+
+ sc = { "@type": search_criteria[entity] }
+ if operator is not None:
+ sc["operator"] = operator
+
+ return sc
def get_attrs_for_entity(entity):
""" For a given entity this method returns an iterator for all searchable
@@ -216,6 +228,8 @@ fetch_option = {
"project": {"@type": "as.dto.project.fetchoptions.ProjectFetchOptions"},
"person": {"@type": "as.dto.person.fetchoptions.PersonFetchOptions"},
"users": {"@type": "as.dto.person.fetchoptions.PersonFetchOptions" },
+ "user": {"@type": "as.dto.person.fetchoptions.PersonFetchOptions" },
+ "authorizationGroup": {"@type": "as.dto.authorizationgroup.fetchoptions.AuthorizationGroupFetchOptions"},
"experiment": {
"@type": "as.dto.experiment.fetchoptions.ExperimentFetchOptions",
"type": {"@type": "as.dto.experiment.fetchoptions.ExperimentTypeFetchOptions"}
@@ -266,7 +280,6 @@ fetch_option = {
},
"history": {"@type": "as.dto.history.fetchoptions.HistoryEntryFetchOptions"},
"dataStore": {"@type": "as.dto.datastore.fetchoptions.DataStoreFetchOptions"},
- "authorizationGroup": {"@type": "as.dto.authorizationgroup.fetchoptions.AuthorizationGroupFetchOptions"},
}
@@ -368,10 +381,30 @@ def extract_person(person):
return str(person)
return person['userId']
-
-def extract_users(users):
- if not isinstance(users, dict):
- return str(users)
+def extract_person_details(person):
+ if not isinstance(person, dict):
+ return str(person)
+ return "{} {} <{}>".format(
+ person['firstName'],
+ person['lastName'],
+ person['email']
+ )
+
+def extract_id(id):
+ if not isinstance(id, dict):
+ return str(id)
+ else:
+ return id['techId']
+
+def extract_userId(user):
+ if isinstance(user, list):
+ return ", ".join([
+ u['userId'] for u in user
+ ])
+ elif isinstance(user, dict):
+ return user['userId']
+ else:
+ return str(user)
def crc32(fileName):
@@ -502,6 +535,23 @@ def _criteria_for_code(code):
"@type": "as.dto.common.search.CodeSearchCriteria"
}
+def _subcriteria_for_userId(userId):
+ return {
+ "criteria": [
+ {
+ "fieldName": "userId",
+ "fieldType": "ATTRIBUTE",
+ "fieldValue": {
+ "value": userId,
+ "@type": "as.dto.common.search.StringEqualToValue"
+ },
+ "@type": "as.dto.person.search.UserIdSearchCriteria"
+ }
+ ],
+ "@type": "as.dto.person.search.PersonSearchCriteria",
+ "operator": "AND"
+ }
+
def _subcriteria_for_type(code, entity):
return {
@@ -631,7 +681,7 @@ def _subcriteria_for_properties(prop, val):
}
-def _subcriteria_for_permid(permids, entity, parents_or_children=''):
+def _subcriteria_for_permid(permids, entity, parents_or_children='', operator='AND'):
if not isinstance(permids, list):
permids = [permids]
@@ -652,7 +702,7 @@ def _subcriteria_for_permid(permids, entity, parents_or_children=''):
"@type": "as.dto.{}.search.{}{}SearchCriteria".format(
entity.lower(), entity, parents_or_children
),
- "operator": "OR"
+ "operator": operator
}
return criteria
@@ -721,6 +771,7 @@ class Openbis:
if url_obj.hostname is None:
raise ValueError("hostname is missing")
+
self.url = url_obj.geturl()
self.port = url_obj.port
self.hostname = url_obj.hostname
@@ -777,6 +828,7 @@ class Openbis:
"get_person(userId)",
"get_groups()",
"get_group(code)",
+ "get_assigned_roles()",
"new_group(code, description, userIds)",
'new_space(name, description)',
'new_project(space, code, description, attachments)',
@@ -882,7 +934,7 @@ class Openbis:
if resp.ok:
resp = resp.json()
if 'error' in resp:
- print(json.dumps(request))
+ if VERBOSE: print(json.dumps(request))
raise ValueError(resp['error']['message'])
elif 'result' in resp:
return resp['result']
@@ -1013,8 +1065,79 @@ class Openbis:
return group
else:
return Group(self, data=group)
-
+ def get_assigned_roles(self, **search_args):
+ """ Get the assigned roles for a given group, person or space
+ """
+ search_criteria = get_search_type_for_entity('roleAssignment', 'AND')
+ allowed_search_attrs = ['role', 'roleLevel', 'user', 'group', 'space']
+
+ sub_crit = []
+ for attr in search_args:
+ if attr in allowed_search_attrs:
+ if attr == 'space':
+ sub_crit.append(
+ _subcriteria_for_code(search_args[attr], 'space')
+ )
+ elif attr == 'user':
+ userId = ''
+ if isinstance(search_args[attr], str):
+ userId = search_args[attr]
+ else:
+ userId = search_args[attr].userId
+
+ sub_crit.append(
+ _subcriteria_for_userId(userId)
+ )
+ elif attr == 'group':
+ sub_crit.append(
+ _subcriteria_for_permid(search_args[attr], 'AuthorizationGroup')
+ )
+ elif attr == 'role':
+ # TODO
+ raise ValueError("not yet implemented")
+ elif attr == 'roleLevel':
+ # TODO
+ raise ValueError("not yet implemented")
+ else:
+ pass
+ else:
+ raise ValueError("unknown search argument {}".format(search_arg))
+
+ search_criteria['criteria'] = sub_crit
+
+ fetchopts = {}
+ for option in ['roleAssignments', 'space', 'user', 'authorizationGroup','registrator']:
+ fetchopts[option] = fetch_option[option]
+
+ request = {
+ "method": "searchRoleAssignments",
+ "params": [
+ self.token,
+ search_criteria,
+ fetchopts
+ ]
+ }
+
+ resp = self._post_request(self.as_v3, request)
+ if len(resp['objects']) == 0:
+ raise ValueError("No assigned roles found!")
+
+ objects = resp['objects']
+ parse_jackson(objects)
+ roles = DataFrame(objects)
+
+ roles['id'] = roles['id'].map(extract_id)
+ roles['user'] = roles['user'].map(extract_userId)
+ roles['group'] = roles['authorizationGroup'].map(extract_code)
+ roles['space'] = roles['space'].map(extract_code)
+ p = Things(
+ self, entity='role',
+ df=roles[['id', 'role', 'roleLevel', 'user', 'group', 'space']],
+ identifier_name='permId'
+ )
+ return p
+
def get_groups(self, **search_args):
""" Get openBIS AuthorizationGroups. Returns a «Things» object.
@@ -1040,6 +1163,7 @@ class Openbis:
search_criteria = get_search_type_for_entity('authorizationGroup')
search_criteria['criteria'] = criteria
+ search_criteria['operator'] = 'AND'
fetchopts = fetch_option['authorizationGroup']
for option in ['roleAssignments', 'registrator', 'users']:
@@ -1059,11 +1183,11 @@ class Openbis:
objects = resp['objects']
parse_jackson(objects)
- groups = DataFrame(resp['objects'])
+ groups = DataFrame(objects)
groups['permId'] = groups['permId'].map(extract_permid)
groups['registrator'] = groups['registrator'].map(extract_person)
- groups['users'] = groups['users'].map(extract_users)
+ groups['users'] = groups['users'].map(extract_userId)
groups['registrationDate'] = groups['registrationDate'].map(format_timestamp)
groups['modificationDate'] = groups['modificationDate'].map(format_timestamp)
p = Things(
@@ -2772,14 +2896,14 @@ class DataSet(OpenBisObject):
"@type": "as.dto.dataset.archive.DataSetArchiveOptions"
}
self.archive_unarchive('archiveDataSets', fetchopts)
- print("DataSet {} archived".format(self.permId))
+ if VERBOSE: print("DataSet {} archived".format(self.permId))
def unarchive(self):
fetchopts = {
"@type": "as.dto.dataset.unarchive.DataSetUnarchiveOptions"
}
self.archive_unarchive('unarchiveDataSets', fetchopts)
- print("DataSet {} unarchived".format(self.permId))
+ if VERBOSE: print("DataSet {} unarchived".format(self.permId))
def archive_unarchive(self, method, fetchopts):
dss = self.get_datastore
@@ -2835,7 +2959,7 @@ class DataSet(OpenBisObject):
if wait_until_finished:
queue.join()
- print("Files downloaded to: %s" % os.path.join(destination, self.permId))
+ if VERBOSE: print("Files downloaded to: %s" % os.path.join(destination, self.permId))
@property
def folder(self):
@@ -2980,11 +3104,11 @@ class DataSet(OpenBisObject):
permId = resp['rows'][0][2]['value']
if permId is None or permId == '':
self.__dict__['is_new'] = False
- print("DataSet successfully created. Because you connected to an openBIS version older than 16.05.04, you cannot update the object.")
+ if VERBOSE: print("DataSet successfully created. Because you connected to an openBIS version older than 16.05.04, you cannot update the object.")
else:
new_dataset_data = self.openbis.get_dataset(permId, only_data=True)
self._set_data(new_dataset_data)
- print("DataSet successfully created.")
+ if VERBOSE: print("DataSet successfully created.")
else:
raise ValueError('Error while creating the DataSet: ' + resp['rows'][0][1]['value'])
@@ -2999,7 +3123,7 @@ class DataSet(OpenBisObject):
request["params"][1][0].pop('childIds')
self.openbis._post_request(self.openbis.as_v3, request)
- print("DataSet successfully updated.")
+ if VERBOSE: print("DataSet successfully updated.")
class AttrHolder():
@@ -3245,25 +3369,54 @@ class AttrHolder():
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
- as an array of values.
+ """ handles all attribute requests dynamically.
+ Values are returned in a sensible way, for example:
+ the identifiers of parents, children and components are returned as an
+ array of values, whereas attachments, users (of groups) and
+ roleAssignments are returned as an array of dictionaries.
"""
int_name = '_' + name
if int_name in self.__dict__:
- if int_name in ['_attachments']:
- return [
- {
- "fileName": x['fileName'],
- "title": x['title'],
- "description": x['description']
- } for x in self._attachments
- ]
- if int_name in ['_registrator', '_modifier', '_dataProducer']:
+ if int_name == '_attachments':
+ attachments = []
+ for att in self._attachments:
+ attachments.append({
+ "fileName": att.get('fileName'),
+ "title": att.get('title'),
+ "description": att.get('description'),
+ "version": att.get('version'),
+ })
+ return attachments
+
+ elif int_name == '_users':
+ users = []
+ for user in self._users:
+ users.append({
+ "firstName": user.get('firstName'),
+ "lastName" : user.get('lastName'),
+ "email" : user.get('email'),
+ "userId" : user.get('userId'),
+ })
+ return users
+
+ elif int_name == '_roleAssignments':
+ ras = []
+ for ra in self._roleAssignments:
+ ras.append({
+ "role": ra.get('role'),
+ "roleLevel": ra.get('roleLevel'),
+ "space": ra.get('space').get('code'),
+ "project": ra.get('role'),
+ })
+ return ras
+
+ elif int_name in ['_registrator', '_modifier', '_dataProducer']:
return self.__dict__[int_name].get('userId', None)
+
elif int_name in ['_registrationDate', '_modificationDate', '_accessDate', '_dataProductionDate']:
return format_timestamp(self.__dict__[int_name])
+
# if the attribute contains a list,
# return a list of either identifiers, codes or
# permIds (whatever is available first)
@@ -3279,6 +3432,7 @@ class AttrHolder():
else:
pass
return values
+
# attribute contains a dictionary: same procedure as above.
elif isinstance(self.__dict__[int_name], dict):
if "identifier" in self.__dict__[int_name]:
@@ -3287,6 +3441,7 @@ class AttrHolder():
return self.__dict__[int_name]['code']
elif "permId" in self.__dict__[int_name]:
return self.__dict__[int_name]['permId']
+
else:
return self.__dict__[int_name]
else:
@@ -3608,16 +3763,41 @@ class AttrHolder():
return html
def __repr__(self):
+ """ When using iPython, this method displays a nice table
+ of all attributes and their values when the object is printed.
+ """
headers = ['attribute', 'value']
lines = []
for attr in self._allowed_attrs:
if attr == 'attachments':
continue
- lines.append([
- attr,
- nvl(getattr(self, attr, ''))
- ])
+ elif attr == 'users':
+ lines.append([
+ attr,
+ ", ".join(att['userId'] for att in self._users)
+ ])
+ elif attr == 'roleAssignments':
+ roles = []
+ for role in self._roleAssignments:
+ if role.get('space') is not None:
+ roles.append("{} ({})".format(
+ role.get('role'),
+ role.get('space').get('code')
+ ))
+ else:
+ roles.append(role.get('role'))
+
+ lines.append([
+ attr,
+ ", ".join(roles)
+ ])
+
+ else:
+ lines.append([
+ attr,
+ nvl(getattr(self, attr, ''))
+ ])
return tabulate(lines, headers=headers)
@@ -3703,7 +3883,7 @@ class Sample():
request["params"][1][0]["properties"] = props
resp = self.openbis._post_request(self.openbis.as_v3, request)
- print("Sample successfully created.")
+ if VERBOSE: print("Sample successfully created.")
new_sample_data = self.openbis.get_sample(resp[0]['permId'], only_data=True)
self._set_data(new_sample_data)
return self
@@ -3712,7 +3892,7 @@ class Sample():
request = self._up_attrs()
request["params"][1][0]["properties"] = props
self.openbis._post_request(self.openbis.as_v3, request)
- print("Sample successfully updated.")
+ if VERBOSE: print("Sample successfully updated.")
new_sample_data = self.openbis.get_sample(self.permId, only_data=True)
self._set_data(new_sample_data)
@@ -3762,9 +3942,27 @@ class Person(OpenBisObject):
"""
return [
'permId', 'userId', 'firstName', 'lastName', 'email',
- 'registrator', 'registrationDate','roleAssignments','space'
+ 'registrator', 'registrationDate','roleAssignments','space',
+ 'get_roles()', 'assign_role()', 'revoke_role()',
]
+ def get_roles(self):
+ return self.openbis.get_roles(person=self)
+
+ def assign_role(self, role):
+ self.openbis.assign_role(person=self, role=role)
+ if VERBOSE:
+ print(
+ "Role {} successfully assigned to person {}".format(role, self.userId)
+ )
+
+ def revoke_role(self, role):
+ self.openbis.revoke_role(person=self, role=role)
+ if VERBOSE:
+ print(
+ "Role {} successfully revoked from person {}".format(role, self.userId)
+ )
+
def __str__(self):
return "{} {}".format(self.get('firstName'), self.get('lastName'))
@@ -3781,7 +3979,7 @@ class Person(OpenBisObject):
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.")
+ if VERBOSE: 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
@@ -3797,7 +3995,7 @@ class Person(OpenBisObject):
return json.dumps(request)
self.openbis._post_request(self.openbis.as_v3, request)
- print("Person successfully updated.")
+ if VERBOSE: print("Person successfully updated.")
new_person_data = self.openbis.get_person(self.permId, only_data=True)
self._set_data(new_person_data)
@@ -3820,11 +4018,31 @@ class Group(OpenBisObject):
def __dir__(self):
return [
- 'get_users()', 'add_users()', 'del_users()',
- 'get_roles()', 'add_roles()', 'del_roles()'
+ 'code','description','users','roleAssignments',
+ 'get_users()', 'set_users()', 'add_users()', 'del_users()',
+ 'get_roles()', 'assgin_role()', 'revoke_role()'
]
+ def get_roles(self):
+ return self.openbis.get_roles(group=self)
+
+ def assign_role(self, role):
+ self.openbis.assign_role(group=self, role=role)
+ if VERBOSE:
+ print(
+ "Role {} successfully assigned to group {}".format(role, self.code)
+ )
+
+ def revoke_role(self, role):
+ self.openbis.revoke_role(group=self, role=role)
+ if VERBOSE:
+ print(
+ "Role {} successfully revoked from group {}".format(role, self.code)
+ )
+
def _repr_html_(self):
+ """ creates a nice table in Jupyter notebooks when the object itself displayed
+ """
def nvl(val, string=''):
if val is None:
return string
@@ -3889,7 +4107,7 @@ class Group(OpenBisObject):
if self.is_new:
request = self._new_attrs()
resp = self.openbis._post_request(self.openbis.as_v3, request)
- print("Group successfully created.")
+ if VERBOSE: 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)
@@ -3898,7 +4116,7 @@ class Group(OpenBisObject):
else:
request = self._up_attrs()
self.openbis._post_request(self.openbis.as_v3, request)
- print("Group successfully updated.")
+ if VERBOSE: 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)
@@ -3959,13 +4177,13 @@ class Space(OpenBisObject):
def delete(self, reason):
self.openbis.delete_entity('Space', self.permId, reason)
- print("Space {} has been sucessfully deleted.".format(self.permId))
+ if VERBOSE: print("Space {} has been sucessfully deleted.".format(self.permId))
def save(self):
if self.is_new:
request = self._new_attrs()
resp = self.openbis._post_request(self.openbis.as_v3, request)
- print("Space successfully created.")
+ if VERBOSE: print("Space successfully created.")
new_space_data = self.openbis.get_space(resp[0]['permId'], only_data=True)
self._set_data(new_space_data)
return self
@@ -3973,7 +4191,7 @@ class Space(OpenBisObject):
else:
request = self._up_attrs()
self.openbis._post_request(self.openbis.as_v3, request)
- print("Space successfully updated.")
+ if VERBOSE: print("Space successfully updated.")
new_space_data = self.openbis.get_space(self.permId, only_data=True)
self._set_data(new_space_data)
@@ -4225,7 +4443,7 @@ class Experiment(OpenBisObject):
request["params"][1][0]["properties"] = props
resp = self.openbis._post_request(self.openbis.as_v3, request)
- print("Experiment successfully created.")
+ if VERBOSE: print("Experiment successfully created.")
new_exp_data = self.openbis.get_experiment(resp[0]['permId'], only_data=True)
self._set_data(new_exp_data)
return self
@@ -4234,7 +4452,7 @@ class Experiment(OpenBisObject):
props = self.p._all_props()
request["params"][1][0]["properties"] = props
self.openbis._post_request(self.openbis.as_v3, request)
- print("Experiment successfully updated.")
+ if VERBOSE: print("Experiment successfully updated.")
new_exp_data = self.openbis.get_experiment(resp[0]['permId'], only_data=True)
self._set_data(new_exp_data)
@@ -4385,14 +4603,14 @@ class Project(OpenBisObject):
request = self._new_attrs()
resp = self.openbis._post_request(self.openbis.as_v3, request)
self.a.__dict__['_is_new'] = False
- print("Project successfully created.")
+ if VERBOSE: print("Project successfully created.")
new_project_data = self.openbis.get_project(resp[0]['permId'], only_data=True)
self._set_data(new_project_data)
return self
else:
request = self._up_attrs()
self.openbis._post_request(self.openbis.as_v3, request)
- print("Project successfully updated.")
+ if VERBOSE: print("Project successfully updated.")
class SemanticAnnotation():
@@ -4472,7 +4690,7 @@ class SemanticAnnotation():
self._openbis._post_request(self._openbis.as_v3, request)
self._isNew = False
- print("Semantic annotation successfully created.")
+ if VERBOSE: print("Semantic annotation successfully created.")
def _update(self):
@@ -4500,8 +4718,8 @@ class SemanticAnnotation():
}
self._openbis._post_request(self._openbis.as_v3, request)
- print("Semantic annotation successfully updated.")
+ if VERBOSE: print("Semantic annotation successfully updated.")
def delete(self, reason):
self._openbis.delete_entity('SemanticAnnotation', self.permId, reason, False)
- print("Semantic annotation successfully deleted.")
+ if VERBOSE: print("Semantic annotation successfully deleted.")
diff --git a/src/python/PyBis/pybis/utils.py b/src/python/PyBis/pybis/utils.py
index e992594c9e2a855ae78bb6777755ae4018e8871a..31cdfd7e12fbc79cfe2b7b6c39f57a7e2939e5eb 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', 'roleAssignments'
+ 'externalDms', 'roleAssignments', 'user', 'authorizationGroup'
]
found = {}
def build_cache(graph):