def experimenter():
o = ExperimenterI()
o.id = rlong(1L)
o.email = rstring('the_email')
o.firstName = rstring('the_firstName')
o.institution = rstring('the_institution')
o.lastName = rstring('the_lastName')
o.middleName = rstring('the_middleName')
o.omeName = rstring('the_omeName')
return o
def wrapped_image():
experimenter = ExperimenterI()
experimenter.firstName = rstring('first_name')
experimenter.lastName = rstring('last_name')
image = ImageI()
image.id = rlong(1L)
image.description = rstring('description')
image.name = rstring('name')
image.acquisitionDate = rtime(1000) # In milliseconds
image.details.owner = ExperimenterI(1L, False)
creation_event = EventI()
creation_event.time = rtime(2000) # In milliseconds
image.details.creationEvent = creation_event
return ImageWrapper(conn=MockConnection(experimenter), obj=image)
def test_experimenter(self):
"""
Tests methods handled by BlitzObjectWrapper.__getattr__
These will return unicode strings
"""
first_name = u'fîrst_nąmę'
last_name = u'làst_NÅMÉ'
experimenter = ExperimenterI()
experimenter.firstName = rstring(first_name)
experimenter.lastName = rstring(last_name)
exp = MockConnection(experimenter).getObject("Experimenter", 1)
assert exp.getFirstName() == first_name
assert exp.getLastName() == last_name
assert exp.getFullName() == "%s %s" % (first_name, last_name)
def experimenter():
o = ExperimenterI()
o.id = rlong(1L)
o.email = rstring("the_email")
o.firstName = rstring("the_firstName")
o.institution = rstring("the_institution")
o.lastName = rstring("the_lastName")
o.middleName = rstring("the_middleName")
o.omeName = rstring("the_omeName")
return o
def link_tags(conn, datasetname, image_tag_links, image_ratings):
for i in range(1, 51):
username = "******" % i
print(username)
exp = conn.getAdminService().lookupExperimenter(username)
exp_id = exp.id.val
dataset = conn.getObject("Dataset",
attributes={'name': datasetname},
opts={'owner': exp_id})
if dataset is None:
print("Dataset not found")
continue
links = []
for image in dataset.listChildren():
name = image.name
if name in image_tag_links:
for tag_id in image_tag_links[name]:
link = ImageAnnotationLinkI()
link.parent = ImageI(image.id, False)
link.child = TagAnnotationI(tag_id, False)
link.details.owner = ExperimenterI(exp_id, False)
links.append(link)
if name in image_ratings:
link = ImageAnnotationLinkI()
link.parent = ImageI(image.id, False)
r = LongAnnotationI()
r.ns = rstring(RATING_NS)
r.longValue = rlong(image_ratings[name])
link.child = r
link.details.owner = ExperimenterI(exp_id, False)
links.append(link)
print('links', len(links))
group_id = dataset.getDetails().getGroup().id
conn.SERVICE_OPTS.setOmeroGroup(group_id)
try:
conn.getUpdateService().saveArray(links, conn.SERVICE_OPTS)
except ValidationException:
print("Failed to link for %s" % username)
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 new_user(self,
group=None,
perms=None,
owner=False,
system=False,
uname=None,
email=None):
"""
:owner: If user is to be an owner of the created group
:system: If user is to be a system admin
"""
if not self.root:
raise Exception("No root client. Cannot create user")
adminService = self.root.getSession().getAdminService()
if uname is None:
uname = self.uuid()
# Create group if necessary
if not group:
g = self.new_group(perms=perms)
group = g.name.val
else:
g, group = self.group_and_name(group)
# Create user
e = ExperimenterI()
e.omeName = rstring(uname)
e.firstName = rstring(uname)
e.lastName = rstring(uname)
e.ldap = rbool(False)
e.email = rstring(email)
listOfGroups = list()
listOfGroups.append(adminService.lookupGroup('user'))
uid = adminService.createExperimenterWithPassword(
e, rstring(uname), g, listOfGroups)
e = adminService.lookupExperimenter(uname)
if owner:
adminService.setGroupOwner(g, e)
if system:
adminService.addGroups(e, [ExperimenterGroupI(0, False)])
return adminService.getExperimenter(uid)
def createExperimenter(self, omeName, firstName, lastName, email, admin, active, dGroup, otherGroups, password, middleName=None, institution=None):
new_exp = ExperimenterI()
new_exp.omeName = rstring(str(omeName))
new_exp.firstName = rstring(str(firstName))
new_exp.middleName = middleName is not None and rstring(str(middleName)) or None
new_exp.lastName = rstring(str(lastName))
new_exp.email = rstring(str(email))
new_exp.institution = (institution!="" and institution is not None) and rstring(str(institution)) or None
listOfGroups = set()
# default group
for g in self.groups:
if long(dGroup) == g.id:
defaultGroup = g._obj
break
# system group
if admin:
for g in self.groups:
if g.name == "system":
sysGroup = g._obj
break
listOfGroups.add(sysGroup)
# user group
if active:
for g in self.groups:
if g.name == "user":
userGroup = g._obj
break
listOfGroups.add(userGroup)
# rest of groups
for g in self.groups:
for og in otherGroups:
# remove defaultGroup from otherGroups if contains
if long(og) == long(defaultGroup.id.val):
pass
elif long(og) == g.id:
listOfGroups.add(g._obj)
return self.conn.createExperimenter(new_exp, defaultGroup, list(listOfGroups), password)
def new_user(self, group=None, perms=None,
owner=False, system=False, uname=None,
email=None):
"""
:owner: If user is to be an owner of the created group
:system: If user is to be a system admin
"""
if not self.root:
raise Exception("No root client. Cannot create user")
adminService = self.root.getSession().getAdminService()
if uname is None:
uname = self.uuid()
# Create group if necessary
if not group:
g = self.new_group(perms=perms)
group = g.name.val
else:
g, group = self.group_and_name(group)
# Create user
e = ExperimenterI()
e.omeName = rstring(uname)
e.firstName = rstring(uname)
e.lastName = rstring(uname)
e.ldap = rbool(False)
e.email = rstring(email)
listOfGroups = list()
listOfGroups.append(adminService.lookupGroup('user'))
uid = adminService.createExperimenterWithPassword(
e, rstring(uname), g, listOfGroups)
e = adminService.lookupExperimenter(uname)
if owner:
adminService.setGroupOwner(g, e)
if system:
adminService.addGroups(e, [ExperimenterGroupI(0, False)])
return adminService.getExperimenter(uid)
def findByQuery(self, query, params, _ctx=None):
experimenter = ExperimenterI()
experimenter.firstName = rstring('first_name')
experimenter.lastName = rstring('last_name')
return experimenter
# list users with the 'IDs' parameter
#exp_id = script_params["Experimenter"]
experimenters = conn.getObjects("Experimenter")
exp_ids = []
for e in experimenters:
print e.id, e.firstName, e.lastName
if e.id > 1:
exp_ids.append(e.id)
print "list ids", exp_ids
# move users to a single object, in this case public domain
public_group_id = 5
adminService = conn.getAdminService()
for eid in exp_ids:
adminService.addGroups(ExperimenterI(eid, False),
[ExperimenterGroupI(public_group_id, False)])
# Return some value(s).
# Here, we return anything useful the script has produced.
# NB: The Insight and web clients will display the "Message" output.
msg = "Script ran OK"
client.setOutput("Message", rstring(msg))
client.closeSession()
def findByQuery(self, query, params, _ctx=None):
experimenter = ExperimenterI()
experimenter.firstName = rstring('first_name')
experimenter.lastName = rstring('last_name')
return experimenter
def move_well_annotations(conn, well, ann_type, remove_anns, ns):
"""Move annotations from Images in this Well onto the Well itself."""
log("Processing Well: %s %s" % (well.id, well.getWellPos()))
iids = [wellSample.getImage().id for wellSample in well.listChildren()]
log(" Image IDs: %s" % iids)
if len(iids) == 0:
return 0
# Params to query links. If not Admin, only work with our own links
params = ParametersI()
if not conn.isAdmin():
params.theFilter = Filter()
params.theFilter.ownerId = rlong(conn.getUserId())
old_links = list(conn.getAnnotationLinks('Image', iids,
ns=ns, params=params))
# Filter by type
old_links = [l for l in old_links
if (ann_type is None
or (l.child.__class__.__name__ == ann_type))]
link_ids = [l.id for l in old_links]
def get_key(ann_link, with_owner=False):
# We use ann's 'key' to avoid adding duplicate annotations
# Key includes link owner (allows multiple links with different owners)
ann = ann_link.child
return "%s_%s" % (ann_link.details.owner.id.val, ann.id.val)
links_dict = {}
# Remove duplicate annotations according to get_key(l)
for l in old_links:
links_dict[get_key(l, conn.isAdmin())] = l
old_links = links_dict.values()
# Find existing links on Well so we don't try to duplicate them
existing_well_links = list(conn.getAnnotationLinks('Well', [well.id],
ns=ns, params=params))
existing_well_keys = [get_key(l) for l in existing_well_links]
new_links = []
for l in old_links:
if get_key(l) in existing_well_keys:
continue
log(" Annotation: %s %s" % (l.child.id.val,
l.child.__class__.__name__))
link = WellAnnotationLinkI()
link.parent = WellI(well.id, False)
link.child = l.child
# If Admin, the new link Owner is same as old link Owner
if conn.isAdmin():
owner_id = l.details.owner.id.val
link.details.owner = ExperimenterI(owner_id, False)
new_links.append(link)
try:
conn.getUpdateService().saveArray(new_links)
except Exception, ex:
log("Failed to create links: %s" % ex.message)
return 0
def roi_with_unloaded_details_children(roi):
roi.details.owner = ExperimenterI(1, False)
roi.details.group = ExperimenterGroupI(1, False)
return roi