diff --git a/src/python/PyBis/pybis/pybis.py b/src/python/PyBis/pybis/pybis.py
index b245e48a911991447e4b5f30348c2fa8ee5e2ebf..c38f1e236745367d4b5b81e2c15449d4e7ce3140 100644
--- a/src/python/PyBis/pybis/pybis.py
+++ b/src/python/PyBis/pybis/pybis.py
@@ -52,6 +52,17 @@ except Exception:
else:
VERBOSE = True
+LOG_NONE = 0
+LOG_SEVERE = 1
+LOG_ERROR = 2
+LOG_WARNING = 3
+LOG_INFO = 4
+LOG_ENTRY = 5
+LOG_PARM = 6
+LOG_DEBUG = 7
+
+DEBUG_LEVEL = LOG_NONE
+
def _definitions(entity):
@@ -136,10 +147,11 @@ def _definitions(entity):
"identifier": "userId",
},
"AuthorizationGroup" : {
- "attrs": "permId code description users registrator registrationDate modificationDate".split(),
"attrs_new": "code description userIds".split(),
- "multi": "users".split()
-
+ "attrs_up": "code description userIds".split(),
+ "attrs": "permId code description registrator registrationDate modificationDate users".split(),
+ "multi": "users".split(),
+ "identifier": "groupId",
},
"RoleAssignment" : {
"attrs": "id user authorizationGroup role roleLevel space project registrator registrationDate".split(),
@@ -320,8 +332,8 @@ def get_search_criteria(entity, **search_args):
def extract_code(obj):
if not isinstance(obj, dict):
- return str(obj)
- return obj['code']
+ return '' if obj is None else str(obj)
+ return '' if obj['code'] is None else obj['code']
def extract_deletion(obj):
@@ -355,8 +367,8 @@ def extract_permid(permid):
def extract_nested_permid(permid):
if not isinstance(permid, dict):
- return str(permid)
- return permid['permId']['permId']
+ return '' if permid is None else str(permid)
+ return '' if permid['permId']['permId'] is None else permid['permId']['permId']
def extract_property_assignments(pas):
@@ -434,19 +446,6 @@ def _create_tagIds(tags=None):
})
return tagIds
-def _create_userIds(users=None):
- if users is None:
- return None
- if not isinstance(users, list):
- users = [users]
- userIds = []
- for user in users:
- userIds.append({
- "permId": user,
- "@type": "as.dto.person.id.PersonPermId"
- })
- return userIds
-
def _tagIds_for_tags(tags=None, action='Add'):
"""creates an action item to add or remove tags.
@@ -782,10 +781,18 @@ class Openbis:
For creation of datasets, dataset-uploader-api needs to be installed.
"""
- def __init__(self, url, verify_certificates=True, token=None):
+ def __init__(self, url=None, verify_certificates=True, token=None):
"""Initialize a new connection to an openBIS server.
:param host:
"""
+
+ if url is None:
+ try:
+ url = os.environ["OPENBIS_URL"]
+ token = os.environ["OPENBIS_TOKEN"] if "OPENBIS_TOKEN" in os.environ else None
+ except KeyError:
+ raise ValueError("please provide a URL you want to connect to.")
+
url_obj = urlparse(url)
if url_obj.netloc is None:
raise ValueError("please provide the url in this format: https://openbis.host.ch:8443")
@@ -810,6 +817,11 @@ class Openbis:
# use an existing token, if available
if self.token is None:
self.token = self._get_cached_token()
+ elif self.is_token_valid(token):
+ pass
+ else:
+ print("Session is no longer valid. Please log in again.")
+
def __dir__(self):
return [
@@ -851,7 +863,7 @@ class Openbis:
"get_group(code)",
"get_role_assignments()",
"get_role_assignment(techId)",
- "new_group(code, description, users)",
+ "new_group(code, description, userIds)",
'new_space(name, description)',
'new_project(space, code, description, attachments)',
'new_experiment(type, code, project, props={})',
@@ -946,17 +958,18 @@ class Openbis:
request["jsonrpc"] = "2.0"
if request["params"][0] is None:
raise ValueError("Your session expired, please log in again")
+
+ if DEBUG_LEVEL >=LOG_DEBUG: print(json.dumps(request))
resp = requests.post(
full_url,
json.dumps(request),
verify=self.verify_certificates
)
-
if resp.ok:
resp = resp.json()
if 'error' in resp:
- if VERBOSE: print(json.dumps(request))
+ if DEBUG_LEVEL >= LOG_ERROR: print(json.dumps(request))
raise ValueError(resp['error']['message'])
elif 'result' in resp:
return resp['result']
@@ -1048,10 +1061,10 @@ class Openbis:
)
- def new_group(self, code, description=None, users=None):
+ def new_group(self, code, description=None, userIds=None):
""" creates an openBIS person
"""
- return Group(self, code=code, description=description, users=users)
+ return Group(self, code=code, description=description, userIds=userIds)
def get_group(self, groupId, only_data=False):
@@ -1353,6 +1366,9 @@ class Openbis:
)
return p
+ get_users = get_persons # Alias
+
+
def get_person(self, userId, only_data=False):
""" Get a person (user)
"""
@@ -1389,6 +1405,8 @@ class Openbis:
else:
return Person(self, data=person)
+ get_user = get_person # Alias
+
def get_spaces(self, code=None):
""" Get a list of all available spaces (DataFrame object). To create a sample or a
@@ -1873,7 +1891,7 @@ class Openbis:
update_object = update_sample # Alias
- def delete_entity(self, entity, id, reason, id_name='PermId'):
+ def delete_entity(self, entity, id, reason, id_name='permId'):
"""Deletes Spaces, Projects, Experiments, Samples and DataSets
"""
@@ -2809,6 +2827,9 @@ class OpenBisObject():
if 'properties' in data:
for key, value in data['properties'].items():
self.p.__dict__[key.lower()] = value
+
+ # object is already saved to openBIS, so it is not new anymore
+ self.a.__dict__['_is_new'] = False
@property
def attrs(self):
@@ -3233,8 +3254,6 @@ class DataSet(OpenBisObject):
else:
raise ValueError('Error while creating the DataSet: ' + resp['rows'][0][1]['value'])
- self.__dict__['_is_new'] = False
-
else:
request = self._up_attrs()
@@ -3279,18 +3298,24 @@ class AttrHolder():
Since the data comes from openBIS, we do not have to check it (hence the
self.__dict__ statements to prevent invoking the __setattr__ method)
Internally data is stored with an underscore, e.g.
- sample._space --> { '@id': 4,
- '@type': 'as.dto.space.id.SpacePermId',
- 'permId': 'MATERIALS' }
+ sample._space = {
+ '@type': 'as.dto.space.id.SpacePermId',
+ 'permId': 'MATERIALS'
+ }
but when fetching the attribute without the underscore, we only return
the relevant data for the user:
- sample.space --> 'MATERIALS'
+ sample.space  # MATERIALS
"""
+ # entity is read from openBIS, so it is not new anymore
self.__dict__['_is_new'] = False
+
for attr in self._allowed_attrs:
if attr in ["code", "permId", "identifier",
"type", "container", "components"]:
self.__dict__['_' + attr] = data.get(attr, None)
+ # remove the @id attribute
+ if isinstance(self.__dict__['_' + attr], dict):
+ self.__dict__['_' + attr].pop('@id')
elif attr in ["space"]:
d = data.get(attr, None)
@@ -3354,19 +3379,35 @@ class AttrHolder():
items = getattr(self, '_' + attr)
if items is None:
items = []
+
+ elif attr == 'userIds':
+ if '_changed_users' not in self.__dict__:
+ continue
+
+ new_obj[attr]=[]
+ for userId in self.__dict__['_changed_users']:
+ if self.__dict__['_changed_users'][userId]['action'] == 'Add':
+ new_obj[attr].append({
+ "permId": userId,
+ "@type": "as.dto.person.id.PersonPermId"
+ })
+
+ elif attr == 'description':
+ new_obj[attr] = self.__dict__['_description'].get('value')
+
else:
items = getattr(self, '_' + attr)
- key = None
- if attr in attr2ids:
- # translate parents into parentIds, children into childIds etc.
- key = attr2ids[attr]
- else:
- key = attr
+ key = None
+ if attr in attr2ids:
+ # translate parents into parentIds, children into childIds etc.
+ key = attr2ids[attr]
+ else:
+ key = attr
- new_obj[key] = items
+ new_obj[key] = items
- # create a new entity
+ # guess the method name for creating a new entity and build the request
if method_name is None:
method_name = "create{}s".format(self.entity)
request = {
@@ -3411,9 +3452,8 @@ class AttrHolder():
"@type": "as.dto.attachment.update.AttachmentListUpdateValue"
}
- elif attr in ['tags','users']:
+ elif attr == 'tags':
# look which tags/users have been added or removed and update them
- id_name = _definitions(attr)['attr2ids'] # tagIds, userIds
if getattr(self, '_prev_'+attr) is None:
self.__dict__['_prev_'+attr] = []
@@ -3432,11 +3472,33 @@ class AttrHolder():
"@type": "as.dto.common.update.ListUpdateActionAdd"
})
- up_obj[id_name] = {
+ up_obj['tagIds'] = {
"@type": "as.dto.common.update.IdListUpdateValue",
"actions": actions
}
+ elif attr == 'userIds':
+ actions = []
+ if '_changed_users' not in self.__dict__:
+ continue
+ for userId in self.__dict__['_changed_users']:
+ actions.append({
+ "items": [
+ {
+ "permId": userId,
+ "@type": "as.dto.person.id.PersonPermId"
+ }
+ ],
+ "@type": "as.dto.common.update.ListUpdateAction{}".format(
+ self.__dict__['_changed_users'][userId]['action']
+ )
+ })
+
+ up_obj['userIds'] = {
+ "actions": actions,
+ "@type": "as.dto.common.update.IdListUpdateValue"
+ }
+
elif '_' + attr in self.__dict__:
# handle multivalue attributes (parents, children, tags etc.)
# we only cover the Set mechanism, which means we always update
@@ -3471,6 +3533,8 @@ class AttrHolder():
for x in ['identifier','permId','@type']:
if x in value:
val[x] = value[x]
+ if attr in ['description']:
+ val = value['value']
up_obj[attr2ids[attr]] = {
"@type": "as.dto.common.update.FieldUpdateValue",
@@ -3587,6 +3651,15 @@ class AttrHolder():
new_sample.space = 'MATERIALS'
new_sample.parents = ['/MATERIALS/YEAST747']
"""
+ #allowed_attrs = []
+ #if self.is_new:
+ # allowed_attrs = _definitions(self.entity)['attrs_new']
+ #else:
+ # allowed_attrs = _definitions(self.entity)['attrs_up']
+
+ #if name not in allowed_attrs:
+ # raise ValueError("{} is not in the list of changeable attributes ({})".format(name, ", ".join(allowed_attrs) ) )
+
if name in ["parents", "parent", "children", "child", "components"]:
if name == "parent":
name = "parents"
@@ -3612,10 +3685,6 @@ class AttrHolder():
if '@id' in permid: permid.pop('@id')
permids.append(permid)
- # setting self._parents = [{
- # '@type': 'as.dto.sample.id.SampleIdentifier',
- # 'identifier': '/SPACE_NAME/SAMPLE_NAME'
- # }]
self.__dict__['_' + name] = permids
elif name in ["tags"]:
self.set_tags(value)
@@ -3686,8 +3755,20 @@ class AttrHolder():
self.__dict__['_code'] = value
- elif name in [ "description", "userId" ]:
- self.__dict__['_'+name] = value
+ elif name in [ "description" ]:
+ self.__dict__['_'+name] = {
+ "value": value,
+ }
+ if not self.is_new:
+ self.__dict__['_' + name]['isModified'] = True
+
+ elif name in ["userId"]:
+ # values that are directly assigned
+ self.__dict__['_' + name] = value
+
+ elif name in ["userIds"]:
+ self.add_users(value)
+
else:
raise KeyError("no such attribute: {}".format(name))
@@ -3797,38 +3878,46 @@ class AttrHolder():
if tagId not in self.__dict__['_tags']:
self.__dict__['_tags'].append(tagId)
- def set_users(self, users):
- if getattr(self, '_users') is None:
- self.__dict__['_users'] = []
- if not isinstance(users, list):
- users = [users]
- for user in users:
- # TODO
+ def set_users(self, userIds):
+ if userIds is None:
+ return
+ if getattr(self, '_userIds') is None:
+ self.__dict__['_userIds'] = []
+ if not isinstance(userIds, list):
+ userIds = [userIds]
+ for userId in userIds:
person = self.openbis.get_person(userId=user, only_data=True)
-
+ self.__dict__['_userIds'].append({
+ "permId": userId,
+ "@type": "as.dto.person.id.PersonPermId"
+ })
- def add_users(self, users):
- if getattr(self, '_users') is None:
- self.__dict__['_users'] = []
+
+ def add_users(self, userIds):
+ if userIds is None:
+ return
+ if getattr(self, '_changed_users') is None:
+ self.__dict__['_changed_users'] = {}
- # add the new users to the _users and _new_users list,
- # if not listed yet
- userIds = _create_userIds(users)
+ if not isinstance(userIds, list):
+ userIds = [userIds]
for userId in userIds:
- if not userId in self.__dict__['_users']:
- self.__dict__['_users'].append(userId)
+ self.__dict__['_changed_users'][userId] = {
+ "action": "Add"
+ }
- def del_users(self, users):
- if getattr(self, '_users') is None:
- self.__dict__['_users'] = []
+ def del_users(self, userIds):
+ if userIds is None:
+ return
+ if getattr(self, '_changed_users') is None:
+ self.__dict__['_changed_users'] = {}
- # remove the users from the _users and _del_users list,
- # if listed there
- userIds = _create_userIds(users)
+ if not isinstance(userIds, list):
+ userIds = [userIds]
for userId in userIds:
- if userId in self.__dict__['_users']:
- self.__dict__['_users'].remove(userId)
-
+ self.__dict__['_changed_users'][userId] = {
+ "action": "Remove"
+ }
def add_tags(self, tags):
if getattr(self, '_tags') is None:
@@ -3942,12 +4031,12 @@ class AttrHolder():
for attr in self._allowed_attrs:
if attr == 'attachments':
continue
- elif attr == 'users':
+ elif attr == 'users' and '_users' in self.__dict__:
lines.append([
attr,
", ".join(att['userId'] for att in self._users)
])
- elif attr == 'roleAssignments':
+ elif attr == 'roleAssignments' and '_roleAssignments' in self.__dict__:
roles = []
for role in self._roleAssignments:
if role.get('space') is not None:
@@ -4002,6 +4091,7 @@ class Sample():
for key, value in data['properties'].items():
self.p.__dict__[key.lower()] = value
+
def __dir__(self):
return [
'props', 'get_parents()', 'get_children()',
@@ -4068,7 +4158,7 @@ class Sample():
def delete(self, reason):
self.openbis.delete_entity(entity='Sample',id=self.permId, reason=reason)
- if VERBOSE: print("Sample {} has been sucessfully deleted.".format(self.permId))
+ if VERBOSE: print("Sample {} successfully deleted.".format(self.permId))
def get_datasets(self, **kwargs):
return self.openbis.get_datasets(sample=self.permId, **kwargs)
@@ -4123,7 +4213,7 @@ class RoleAssignment(OpenBisObject):
entity='RoleAssignment', id=self.id,
reason=reason, id_name='techId'
)
- if VERBOSE: print("RoleAssignment has been sucessfully deleted.".format(self.permId))
+ if VERBOSE: print("RoleAssignment successfully deleted.".format(self.permId))
class Person(OpenBisObject):
@@ -4150,7 +4240,7 @@ class Person(OpenBisObject):
return [
'permId', 'userId', 'firstName', 'lastName', 'email',
'registrator', 'registrationDate','space',
- 'get_roles()', 'assign_role()', 'revoke_role(techId)',
+ 'get_roles()', 'assign_role(role, space)', 'revoke_role(techId)',
]
@@ -4166,25 +4256,57 @@ class Person(OpenBisObject):
def assign_role(self, role, **kwargs):
- self.openbis.assign_role(role=role, person=self, **kwargs)
- if VERBOSE:
- print(
- "Role {} successfully assigned to person {}".format(role, self.userId)
- )
+ try:
+ self.openbis.assign_role(role=role, person=self, **kwargs)
+ if VERBOSE:
+ print(
+ "Role {} successfully assigned to person {}".format(role, self.userId)
+ )
+ except ValueError as e:
+ if 'exists' in str(e):
+ if VERBOSE:
+ print(
+ "Role {} already assigned to person {}".format(role, self.userId)
+ )
+ else:
+ raise ValueError(str(e))
- def revoke_role(self, role, reason='no specific reason'):
+
+ def revoke_role(self, role, space=None, project=None, reason='no specific reason'):
""" Revoke a role from this person.
"""
+
+ techId = None
if isinstance(role, int):
- ra = self.openbis.get_role_assignment(role)
- ra.delete(reason)
- if VERBOSE:
- print(
- "Role {} successfully revoked from person {}".format(role, self.code)
+ techId = role
+ else:
+ query = { "role": role }
+ if space is None:
+ query['space'] = ''
+ else:
+ query['space'] = space.upper()
+
+ if project is None:
+ query['project'] = ''
+ else:
+ query['project'] = project.upper()
+
+ querystr = " & ".join(
+ '{} == "{}"'.format(key, value) for key, value in query.items()
+ )
+ return querystr
+
+ roles = self.get_roles().df
+ techId = roles.query(querystr)['techId'].values[0]
+
+ # finally delete the role assignment
+ ra = self.openbis.get_role_assignment(techId)
+ ra.delete(reason)
+ if VERBOSE:
+ print(
+ "Role {} successfully revoked from person {}".format(role, self.code)
)
return
- else:
- raise ValueError("Please provide the techId of the role assignment you want to revoke")
def __str__(self):
return "{} {}".format(self.get('firstName'), self.get('lastName'))
@@ -4215,8 +4337,6 @@ class Person(OpenBisObject):
if "spaceId" in request['params'][1][0]:
request['params'][1][0]['homeSpaceId'] = request['params'][1][0]['spaceId']
del(request['params'][1][0]['spaceId'])
-
- return json.dumps(request)
self.openbis._post_request(self.openbis.as_v3, request)
if VERBOSE: print("Person successfully updated.")
new_person_data = self.openbis.get_person(self.permId, only_data=True)
@@ -4250,6 +4370,7 @@ class Group(OpenBisObject):
""" Returns a Things object wich contains all Persons (Users)
that belong to this group.
"""
+
persons = DataFrame(self._users)
persons['permId'] = persons['permId'].map(extract_permid)
persons['registrationDate'] = persons['registrationDate'].map(format_timestamp)
@@ -4370,6 +4491,16 @@ class Group(OpenBisObject):
"""
return html
+ def delete(self, reason='unknown'):
+ self.openbis.delete_entity(
+ entity = "AuthorizationGroup",
+ id = self.permId,
+ reason = reason
+ )
+ if VERBOSE:
+ print("Authorization group {} successfully deleted".format(
+ self.permId
+ ))
def save(self):
if self.is_new:
@@ -4445,7 +4576,7 @@ class Space(OpenBisObject):
def delete(self, reason):
self.openbis.delete_entity('Space', self.permId, reason)
- if VERBOSE: print("Space {} has been sucessfully deleted.".format(self.permId))
+ if VERBOSE: print("Space {} has been sucsessfully deleted.".format(self.permId))
def save(self):
if self.is_new:
@@ -4728,7 +4859,7 @@ class Experiment(OpenBisObject):
if self.permId is None:
return None
self.openbis.delete_entity(entity='Experiment', id=self.permId, reason=reason)
- if VERBOSE: print("Experiment {} has been sucessfully deleted.".format(self.permId))
+ if VERBOSE: print("Experiment {} successfully deleted.".format(self.permId))
def get_datasets(self, **kwargs):
if self.permId is None:
@@ -4866,13 +4997,12 @@ class Project(OpenBisObject):
def delete(self, reason):
self.openbis.delete_entity(entity='Project', id=self.permId, reason=reason)
- if VERBOSE: print("Project {} has been sucessfully deleted.".format(self.permId))
+ if VERBOSE: print("Project {} successfully 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)
- self.a.__dict__['_is_new'] = False
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)