def testChgrpDatasetToTargetProject(self, credentials):
"""
Tests that an Admin can move a user's Dataset to a private
group and link it to an existing user's Project there.
Also tests that the user can do the same chgrp themselves.
"""
# One user in two groups
client, user = self.new_client_and_user(perms=PRIVATE)
target_grp = self.new_group([user], perms=PRIVATE)
eCtx = client.sf.getAdminService().getEventContext() # Reset session
userId = eCtx.userId
target_gid = target_grp.id.val
# User creates Dataset in current group...
update = client.sf.getUpdateService()
ds = self.make_dataset(client=client)
# ...and Project in target group
ctx = {'omero.group': str(target_gid)}
pr = self.new_project()
pr = update.saveAndReturnObject(pr, ctx)
requests = []
saves = []
chgrp = Chgrp2(
targetObjects={"Dataset": [ds.id.val]}, groupId=target_gid)
requests.append(chgrp)
link = ProjectDatasetLinkI()
link.details.owner = ExperimenterI(userId, False)
link.child = DatasetI(ds.id.val, False)
link.parent = ProjectI(pr.id.val, False)
save = Save()
save.obj = link
saves.append(save)
requests.extend(saves)
if credentials == "user":
c = client
else:
c = self.root
self.doSubmit(requests, c, omero_group=target_gid)
queryService = client.sf.getQueryService()
ctx = {'omero.group': '-1'} # query across groups
dataset = queryService.get('Dataset', ds.id.val, ctx)
ds_gid = dataset.details.group.id.val
assert target_gid == ds_gid,\
"Dataset should be in group: %s, NOT %s" % (target_gid, ds_gid)
def testChgrpDatasetToTargetProject(self, credentials):
"""
Tests that an Admin can move a user's Dataset to a private
group and link it to an existing user's Project there.
Also tests that the user can do the same chgrp themselves.
"""
# One user in two groups
client, user = self.new_client_and_user(perms=PRIVATE)
target_grp = self.new_group([user], perms=PRIVATE)
eCtx = client.sf.getAdminService().getEventContext() # Reset session
userId = eCtx.userId
target_gid = target_grp.id.val
# User creates Dataset in current group...
update = client.sf.getUpdateService()
ds = self.make_dataset(client=client)
# ...and Project in target group
ctx = {'omero.group': str(target_gid)}
pr = self.new_project()
pr = update.saveAndReturnObject(pr, ctx)
requests = []
saves = []
chgrp = Chgrp2(targetObjects={"Dataset": [ds.id.val]},
groupId=target_gid)
requests.append(chgrp)
link = ProjectDatasetLinkI()
link.details.owner = ExperimenterI(userId, False)
link.child = DatasetI(ds.id.val, False)
link.parent = ProjectI(pr.id.val, False)
save = Save()
save.obj = link
saves.append(save)
requests.extend(saves)
if credentials == "user":
c = client
else:
c = self.root
self.doSubmit(requests, c, omero_group=target_gid)
queryService = client.sf.getQueryService()
ctx = {'omero.group': '-1'} # query across groups
dataset = queryService.get('Dataset', ds.id.val, ctx)
ds_gid = dataset.details.group.id.val
assert target_gid == ds_gid,\
"Dataset should be in group: %s, NOT %s" % (target_gid, ds_gid)
def run(password, project_name, dataset_name, host, port):
for user_number in range(1, 41):
username = "******" % user_number
print(username)
conn = BlitzGateway(username, password, host=host, port=port)
try:
conn.connect()
project = ProjectI()
project.setName(rstring(project_name))
update_service = conn.getUpdateService()
project = update_service.saveAndReturnObject(project)
ds = conn.getObject("Dataset",
attributes={'name': dataset_name},
opts={'owner': conn.getUserId()})
if ds is None:
print("No dataset with name %s found" % dataset_name)
continue
dataset_id = ds.getId()
print(username, dataset_id)
link = ProjectDatasetLinkI()
link.setParent(ProjectI(project.getId().getValue(), False))
link.setChild(DatasetI(dataset_id, False))
conn.getUpdateService().saveObject(link)
except Exception as exc:
print("Error while creating project: %s" % str(exc))
finally:
conn.close()
def post_dataset(conn, dataset_name, project_id=None, description=None):
"""Create a new dataset.
Parameters
----------
conn : ``omero.gateway.BlitzGateway`` object
OMERO connection.
dataset_name : str
Name of the Dataset being created.
project_id : int, optional
Id of Project in which to create the Dataset. If no Project is
specified, the Dataset will be orphaned.
description : str
Description for the new Dataset.
Returns
-------
dataset_id : int
Id of the dataset that has been created.
Examples
--------
Create a new orphaned Dataset:
>>> did = post_dataset(conn, "New Dataset")
>>> did
234
Create a new Dataset in Project:120:
>>> did = post_dataset(conn, "Child of 120", project_id=120)
>>> did
"""
if type(dataset_name) is not str:
raise TypeError('Dataset name must be a string')
if type(description) is not str and description is not None:
raise TypeError('Dataset description must be a string')
dataset = DatasetWrapper(conn, DatasetI())
dataset.setName(dataset_name)
if description is not None:
dataset.setDescription(description)
dataset.save()
if project_id is not None:
if type(project_id) is not int:
raise TypeError('Project ID must be integer')
link = ProjectDatasetLinkI()
link.setParent(ProjectI(project_id, False))
link.setChild(DatasetI(dataset.getId(), False))
conn.getUpdateService().saveObject(link)
return dataset.getId()
def create_new_dataset(ctx, project_id, ds_name, ):
dataset_obj = omero.model.DatasetI()
dataset_obj.setName(rstring(ds_name))
dataset_obj = gateway.getUpdateService(ctx).saveAndReturnObject(dataset_obj)
dataset_id = dataset_obj.getId().getValue()
dm = gateway.getFacility(DataManagerFacility)
link = ProjectDatasetLinkI();
link.setChild(dataset_obj);
link.setParent(ProjectI(project_id, False));
r = dm.saveAndReturnObject(ctx, link);
return dataset_id
def run(password, project_name, dataset_name, host, port):
for user_number in range(1, 51):
username = "******" % user_number
print(username)
conn = BlitzGateway(username, password, host=host, port=port)
try:
conn.connect()
params = omero.sys.ParametersI()
params.addString('username', username)
# make sure only one result is returned by query
params.page(0, 1)
query = "from Project where name='%s' \
AND details.owner.omeName=:username \
ORDER BY id DESC" % project_name
service = conn.getQueryService()
pr_list = service.findAllByQuery(query, params, conn.SERVICE_OPTS)
if pr_list is None:
print("No project with name %s found" % project_name)
continue
project_id = pr_list[0].getId().getValue()
print(username, project_id)
params = omero.sys.ParametersI()
params.addString('username', username)
# make sure only one result is returned by query
params.page(0, 1)
query = "from Dataset where name='%s' \
AND details.owner.omeName=:username \
ORDER BY id DESC" % dataset_name
service = conn.getQueryService()
ds_list = service.findAllByQuery(query, params, conn.SERVICE_OPTS)
if ds_list is None:
print("No dataset with name %s found" % dataset_name)
continue
dataset_id = ds_list[0].getId().getValue()
print(username, dataset_id)
link = ProjectDatasetLinkI()
link.setParent(ProjectI(project_id, False))
link.setChild(DatasetI(dataset_id, False))
conn.getUpdateService().saveObject(link)
except Exception as exc:
print("Error while linking to project: %s" % str(exc))
finally:
conn.close()
def link(self, obj1, obj2, client=None):
"""
Links two linkable model entities together by creating an instance of
the correct link entity (e.g. ProjectDatasetLinkI) and persisting it
in the DB. Accepts client instance to allow calls to happen in correct
user contexts. Currently support links are:
* project/dataset
* dataset/image
* image/annotation
:param obj1: parent object
:param obj2: child object
:param client: The client to use to create the link
"""
if client is None:
client = self.client
if isinstance(obj1, ProjectI):
if isinstance(obj2, DatasetI):
link = ProjectDatasetLinkI()
elif isinstance(obj1, DatasetI):
if isinstance(obj2, ImageI):
link = DatasetImageLinkI()
elif isinstance(obj1, ImageI):
if isinstance(obj2, Annotation):
link = ImageAnnotationLinkI()
else:
assert False, "Object type not supported."
"""check if object exist or not"""
if obj1.id is None:
link.setParent(obj1)
else:
link.setParent(obj1.proxy())
if obj2.id is None:
link.setChild(obj2)
else:
link.setChild(obj2.proxy())
return client.sf.getUpdateService().saveAndReturnObject(link)
def link(self, obj1, obj2, client=None):
"""
Links two linkable model entities together by creating an instance of
the correct link entity (e.g. ProjectDatasetLinkI) and persisting it
in the DB. Accepts client instance to allow calls to happen in correct
user contexts. Currently support links are:
* project/dataset
* dataset/image
* image/annotation
:param obj1: parent object
:param obj2: child object
:param client: The client to use to create the link
"""
if client is None:
client = self.client
if isinstance(obj1, ProjectI):
if isinstance(obj2, DatasetI):
link = ProjectDatasetLinkI()
elif isinstance(obj1, DatasetI):
if isinstance(obj2, ImageI):
link = DatasetImageLinkI()
elif isinstance(obj1, ImageI):
if isinstance(obj2, Annotation):
link = ImageAnnotationLinkI()
else:
assert False, "Object type not supported."
"""check if object exist or not"""
if obj1.id is None:
link.setParent(obj1)
else:
link.setParent(obj1.proxy())
if obj2.id is None:
link.setChild(obj2)
else:
link.setChild(obj2.proxy())
return client.sf.getUpdateService().saveAndReturnObject(link)
