From 074408daecb0c253d516256fc9f69934f07b55b0 Mon Sep 17 00:00:00 2001
From: vermeul <swen@ethz.ch>
Date: Wed, 31 Jan 2018 11:29:24 +0100
Subject: [PATCH] get_group implemented, _repr_html_ for groups
---
src/python/PyBis/pybis/pybis.py | 246 +++++++++++++++++++++++++-------
1 file changed, 195 insertions(+), 51 deletions(-)
diff --git a/src/python/PyBis/pybis/pybis.py b/src/python/PyBis/pybis/pybis.py
index 31dd60f53e3..99f8ac05c27 100644
--- a/src/python/PyBis/pybis/pybis.py
+++ b/src/python/PyBis/pybis/pybis.py
@@ -161,10 +161,14 @@ def _definitions(entity):
}
return entities[entity]
-def get_search_criteria_for_entity(entity):
- """ Creates a basic search object for a given entity. Returns a dictionary.
+
+def get_search_type_for_entity(entity):
+ """ Returns a dictionary containing the correct search criteria type
+ for a given entity.
+
Example::
- get_search_criteria_for_entity('space')
+ get_search_type_for_entity('space')
+ # returns:
{'@type': 'as.dto.space.search.SpaceSearchCriteria'}
"""
search_criteria = {
@@ -185,24 +189,33 @@ def get_search_criteria_for_entity(entity):
"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",
+ "authorizationGroup": "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 {}
+ return {
+ "@type": search_criteria[entity]
+ }
+
+def get_attrs_for_entity(entity):
+ """ For a given entity this method returns an iterator for all searchable
+ attributes.
+ """
+ search_args = {
+ "person": ['firstName','lastName','email','userId']
+ }
+ for search_arg in search_args[entity]:
+ yield search_arg
+
fetch_option = {
"space": {"@type": "as.dto.space.fetchoptions.SpaceFetchOptions"},
"project": {"@type": "as.dto.project.fetchoptions.ProjectFetchOptions"},
"person": {"@type": "as.dto.person.fetchoptions.PersonFetchOptions"},
+ "users": {"@type": "as.dto.person.fetchoptions.PersonFetchOptions" },
"experiment": {
"@type": "as.dto.experiment.fetchoptions.ExperimentFetchOptions",
"type": {"@type": "as.dto.experiment.fetchoptions.ExperimentTypeFetchOptions"}
@@ -272,6 +285,21 @@ def search_request_for_identifier(ident, entity):
}
return search_request
+def get_search_criteria(entity, **search_args):
+ search_criteria = get_search_type_for_entity(entity)
+
+ criteria = []
+ for attr in get_attrs_for_entity(entity):
+ if attr in search_args:
+ sub_crit = get_search_type_for_entity(attr)
+ sub_crit['fieldValue'] = get_field_value_search(attr, search_args[attr])
+ criteria.append(sub_crit)
+
+ search_criteria['criteria'] = criteria
+ search_criteria['operator'] = "AND"
+
+ return search_criteria
+
def extract_code(obj):
if not isinstance(obj, dict):
@@ -341,6 +369,11 @@ def extract_person(person):
return person['userId']
+def extract_users(users):
+ if not isinstance(users, dict):
+ return str(users)
+
+
def crc32(fileName):
"""since Python3 the zlib module returns unsigned integers (2.7: signed int)
"""
@@ -655,7 +688,7 @@ def _subcriteria_for_code(code, object_type):
fieldtype = "as.dto.common.search.CodeSearchCriteria"
- search_criteria = get_search_criteria_for_entity(object_type.lower())
+ search_criteria = get_search_type_for_entity(object_type.lower())
search_criteria['criteria'] = [{
"fieldName": fieldname,
"fieldType": "ATTRIBUTE",
@@ -669,7 +702,7 @@ def _subcriteria_for_code(code, object_type):
search_criteria["operator"] = "AND"
return search_criteria
else:
- return get_search_criteria_for_entity(object_type.lower())
+ return get_search_type_for_entity(object_type.lower())
class Openbis:
@@ -739,9 +772,11 @@ class Openbis:
"get_spaces()",
"get_tags()",
"get_terms()",
+ "new_person(userId, space)",
"get_persons()",
- "get_person(userId=None)",
- "new_person(userId, firstName, lastName, email)",
+ "get_person(userId)",
+ "get_groups()",
+ "get_group(code)",
"new_group(code, description, userIds)",
'new_space(name, description)',
'new_project(space, code, description, attachments)',
@@ -832,7 +867,7 @@ class Openbis:
data
"""
if "id" not in request:
- request["id"] = "1"
+ request["id"] = "2"
if "jsonrpc" not in request:
request["jsonrpc"] = "2.0"
if request["params"][0] is None:
@@ -929,7 +964,14 @@ class Openbis:
def new_person(self, userId, space=None):
""" creates an openBIS person
"""
- return Person(self, userId=userId, space=space)
+ try:
+ person = self.get_person(userId=userId)
+ except Exception:
+ return Person(self, userId=userId, space=space)
+
+ raise ValueError(
+ "There already exists a user with userId={}".format(userId)
+ )
def new_group(self, code, description=None, users=None):
@@ -937,41 +979,96 @@ class Openbis:
"""
return Group(self, code=code, description=description, users=users)
- def get_groups(self, code=None):
- """ Get openBIS AuthorizationGroups
+
+ def get_group(self, groupId, only_data=False):
+ """ Get an openBIS AuthorizationGroup. Returns a Group object.
"""
- criterias = []
- if code:
- criterias.append(_subcriteria_for_code(code))
- criteria = get_search_criteria_for_entity('authorizationGroup')
- criteria['criteria'] = criterias
+ ids = [{
+ "@type": "as.dto.authorizationgroup.id.AuthorizationGroupPermId",
+ "permId": groupId
+ }]
+
+ fetchopts = {}
+ for option in ['roleAssignments', 'users', 'registrator']:
+ fetchopts[option] = fetch_option[option]
+
+ request = {
+ "method": "getAuthorizationGroups",
+ "params": [
+ self.token,
+ ids,
+ fetchopts
+ ]
+ }
+ resp = self._post_request(self.as_v3, request)
+ if len(resp) == 0:
+ raise ValueError("No group found!")
+
+ for permid in resp:
+ group = resp[permid]
+ parse_jackson(group)
+
+ if only_data:
+ return group
+ else:
+ return Group(self, data=group)
+
+
+
+ def get_groups(self, **search_args):
+ """ Get openBIS AuthorizationGroups. Returns a «Things» object.
+
+ Usage::
+ groups = e.get.groups()
+ groups[0] # select first group
+ groups['GROUP_NAME'] # select group with this code
+ for group in groups:
+ ... # a Group object
+ groups.df # get a DataFrame object of the group list
+ print(groups) # print a nice ASCII table (eg. in IPython)
+ groups # HTML table (in a Jupyter notebook)
+
+ """
+
+ criteria = []
+ for search_arg in ['code', 'description', 'registrator']:
+ if search_arg in search_args:
+ pass
+ #sub_crit = get_search_type_for_entity(search_arg)
+ #criteria.append(sub_crit)
+
+ search_criteria = get_search_type_for_entity('authorizationGroup')
+ search_criteria['criteria'] = criteria
fetchopts = fetch_option['authorizationGroup']
- for option in ['roleAssignments']:
+ for option in ['roleAssignments', 'registrator', 'users']:
fetchopts[option] = fetch_option[option]
request = {
"method": "searchAuthorizationGroups",
"params": [
self.token,
- criteria,
+ search_criteria,
fetchopts
],
}
resp = self._post_request(self.as_v3, request)
if len(resp['objects']) == 0:
- raise ValueError("No persons found!")
+ raise ValueError("No groups 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)
+ groups = DataFrame(resp['objects'])
+
+ groups['permId'] = groups['permId'].map(extract_permid)
+ groups['registrator'] = groups['registrator'].map(extract_person)
+ groups['users'] = groups['users'].map(extract_users)
+ groups['registrationDate'] = groups['registrationDate'].map(format_timestamp)
+ groups['modificationDate'] = groups['modificationDate'].map(format_timestamp)
p = Things(
- self, entity='person',
- df=persons[['permId', 'userId', 'firstName', 'lastName', 'email', 'space', 'registrationDate', 'active']],
+ self, entity='group',
+ df=groups[['permId', 'code', 'description', 'users', 'registrator', 'registrationDate', 'modificationDate']],
identifier_name='permId'
)
return p
@@ -981,21 +1078,7 @@ class Openbis:
""" 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"
-
+ search_criteria = get_search_criteria('person', **search_args)
fetchopts = {}
for option in ['space']:
fetchopts[option] = fetch_option[option]
@@ -1255,7 +1338,7 @@ class Openbis:
for prop in properties:
sub_criteria.append(_subcriteria_for_properties(prop, properties[prop]))
- search_criteria = get_search_criteria_for_entity('experiment')
+ search_criteria = get_search_type_for_entity('experiment')
search_criteria['criteria'] = sub_criteria
search_criteria['operator'] = 'AND'
@@ -1333,7 +1416,7 @@ class Openbis:
for prop in properties:
sub_criteria.append(_subcriteria_for_properties(prop, properties[prop]))
- search_criteria = get_search_criteria_for_entity('dataset')
+ search_criteria = get_search_type_for_entity('dataset')
search_criteria['criteria'] = sub_criteria
search_criteria['operator'] = 'AND'
@@ -3298,7 +3381,6 @@ class AttrHolder():
else:
self.__dict__['_' + name]['isModified'] = True
-
elif name in ["identifier"]:
raise KeyError("you can not modify the {}".format(name))
elif name == "code":
@@ -3313,7 +3395,7 @@ class AttrHolder():
self.__dict__['_code'] = value
elif name in [ "description", "userId" ]:
- self.__dict__['-'+name] = value
+ self.__dict__['_'+name] = value
else:
raise KeyError("no such attribute: {}".format(name))
@@ -3713,6 +3795,7 @@ class Person(OpenBisObject):
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)
print("Person successfully updated.")
new_person_data = self.openbis.get_person(self.permId, only_data=True)
@@ -3741,6 +3824,67 @@ class Group(OpenBisObject):
'get_roles()', 'add_roles()', 'del_roles()'
]
+ def _repr_html_(self):
+ def nvl(val, string=''):
+ if val is None:
+ return string
+ return val
+
+ html = """
+ <table border="1" class="dataframe">
+ <thead>
+ <tr style="text-align: right;">
+ <th>attribute</th>
+ <th>value</th>
+ </tr>
+ </thead>
+ <tbody>
+ """
+
+ for attr in self._allowed_attrs:
+ if attr in ['users','roleAssignments']:
+ continue
+ html += "<tr> <td>{}</td> <td>{}</td> </tr>".format(
+ attr, nvl(getattr(self, attr, ''), '')
+ )
+
+ if getattr(self, '_users') is not None:
+ html += "<tr><td>Users</td><td>"
+ html += ", ".join(att['userId'] for att in self._users)
+ html += "</td></tr>"
+
+ html += """
+ </tbody>
+ </table>
+ """
+
+ if getattr(self, '_roleAssignments') is not None:
+ html += """
+ <br/>
+ <b>Role Assignments</b>
+ <table border="1" class="dataframe">
+ <thead>
+ <tr style="text-align: right;">
+ <th>Role</th>
+ <th>Role Level</th>
+ <th>Space</th>
+ </tr>
+ </thead>
+ <tbody>
+ """
+ for roleAssignment in self._roleAssignments:
+ html += "<tr><td>{}</td><td>{}</td><td>{}</td></tr>".format(
+ roleAssignment.get('role'),
+ roleAssignment.get('roleLevel'),
+ roleAssignment.get('space').get('code'),
+ )
+ html += """
+ </tbody>
+ </table>
+ """
+ return html
+
+
def save(self):
if self.is_new:
request = self._new_attrs()
--
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