def create_tag(self, name, description, text="tag"):
"""
Creates a new tag object. Returns the new tag object.
If either the name or description parameters are None, the user will be
prompted to input them.
The "text" parameter should be the text description to use upon user
input. For example, if we were creating a tag, this would be "tag"
(the default). If we were creating a tagset, this could be "tag set".
"""
if name is None:
name = raw_input("Please enter a name for this %s: " % text)
if description is None:
description = raw_input("Please enter a description for this %s: "
% text)
if name is not None and description is not None and name != '':
tag = TagAnnotationI()
tag.textValue = rstring(name)
if description is not None and len(description) > 0:
tag.description = rstring(description)
return tag
else:
self.ctx.err("Tag/tagset name cannot be 'None' or empty.")
sys.exit(1)
def test_container_tags_update(self, user1, dtype):
"""
Test updating a Object without losing linked Tags.
If we load a Object without loading Annotations, then update
and save the Object, we don't want to lose Annotation links
"""
conn = get_connection(user1)
user_name = conn.getUser().getName()
django_client = self.new_django_client(user_name, user_name)
container = dtype[1]()
container.name = rstring('test_container_tags_update')
tag = TagAnnotationI()
tag.textValue = rstring('tag')
container.linkAnnotation(tag)
container = get_update_service(user1).saveAndReturnObject(container)
version = api_settings.API_VERSIONS[-1]
object_url = reverse('api_%s' % dtype[0],
kwargs={
'api_version': version,
'object_id': container.id.val
})
save_url = reverse('api_save', kwargs={'api_version': version})
# Get container, update and save back
rsp = get_json(django_client, object_url)
object_json = rsp['data']
object_json['Name'] = 'renamed container'
put_json(django_client, save_url, object_json)
# Check container has been updated and still has annotation links
proj = conn.getObject(dtype[0], container.id.val)
assert proj.getName() == 'renamed container'
assert len(list(proj.listAnnotations())) == 1
def createTag(name, description=None):
print "Create Tag:", name
tag = TagAnnotationI()
tag.textValue = rstring(name)
if description is not None:
tag.description = rstring(description)
return tag
def test_validation_exception(self, user_A):
"""Test handling when we try to save something invalid."""
conn = get_connection(user_A)
group = conn.getEventContext().groupId
userName = conn.getUser().getName()
django_client = self.new_django_client(userName, userName)
version = api_settings.API_VERSIONS[-1]
save_url = reverse('api_save', kwargs={'api_version': version})
save_url += '?group=' + native_str(group)
# Create Tag
tag = TagAnnotationI()
tag.textValue = rstring('test_tag')
tag = conn.getUpdateService().saveAndReturnObject(tag)
tag_json = {'Value': 'test_tag',
'@id': tag.id.val,
'@type': OME_SCHEMA_URL + '#TagAnnotation'}
# Add Tag twice to Project to get Validation Exception
payload = {'Name': 'test_validation',
'@type': OME_SCHEMA_URL + '#Project',
'Annotations': [tag_json, tag_json]}
rsp = post_json(django_client, save_url, payload, status_code=400)
# NB: message contains whole stack trace
assert "ValidationException" in rsp['message']
assert rsp['stacktrace'].startswith(
'Traceback (most recent call last):')
def create_tag(self, name, description, text="tag"):
"""
Creates a new tag object. Returns the new tag object.
If either the name or description parameters are None, the user will be
prompted to input them.
The "text" parameter should be the text description to use upon user
input. For example, if we were creating a tag, this would be "tag"
(the default). If we were creating a tagset, this could be "tag set".
"""
if name is None:
name = raw_input("Please enter a name for this %s: " % text)
if description is None:
description = raw_input(
"Please enter a description for this %s: " % text)
if name is not None and description is not None and name != '':
tag = TagAnnotationI()
tag.textValue = rstring(name)
if description is not None and len(description) > 0:
tag.description = rstring(description)
return tag
else:
self.ctx.err("Tag/tagset name cannot be 'None' or empty.")
sys.exit(1)
def tag(self, request):
"""Returns a new OMERO TagAnnotation with required fields set."""
name = rstring(self.uuid())
for index in range(request.param):
tag = TagAnnotationI()
tag.textValue = name
tag = self.update.saveAndReturnObject(tag)
return tag
def tag(request, itest, update_service):
"""Returns a new OMERO TagAnnotation with required fields set."""
name = rstring(itest.uuid())
for index in range(request.param):
tag = TagAnnotationI()
tag.textValue = name
tag = update_service.saveAndReturnObject(tag)
return tag
def tags_userA_userB(request, userA, userB, groupA):
"""
Returns new OMERO Tags
"""
tags = []
ctx = {'omero.group': str(groupA.id.val)}
for name, user in zip(["userAtag", "userBtag"], [userA, userB]):
tag = TagAnnotationI()
tag.textValue = rstring(name)
tag = get_update_service(user).saveAndReturnObject(tag, ctx)
tags.append(tag)
tags.sort(cmp_id)
return tags
def test_tag_annotation(self):
"""Tests AnnotationWrapper methods return strings"""
ns = u'πλζ.test.ζ'
text_value = u'Tαg - ℗'
obj = TagAnnotationI()
obj.textValue = rstring(text_value)
obj.ns = rstring(ns)
tag = MockConnection(obj).getObject("Annotation", 1)
assert tag.getValue() == text_value.encode('utf8')
assert tag.textValue == text_value
assert tag.getNs() == ns.encode('utf8')
assert tag.ns == ns
def tags_userA_userB(request, userA, userB, groupA):
"""
Returns new OMERO Tags
"""
tags = []
ctx = {'omero.group': str(groupA.id.val)}
for name, user in zip(["userAtag", "userBtag"], [userA, userB]):
tag = TagAnnotationI()
tag.textValue = rstring(name)
tag = get_update_service(user).saveAndReturnObject(tag, ctx)
tags.append(tag)
tags.sort(cmp_id)
return tags
def tagset_tag(request, itest, update_service):
"""
Returns a new OMERO TagAnnotation, with the OMERO.insight tagset
namespace set, and linked TagAnnotation with required fields set.
"""
tagset = TagAnnotationI()
tagset.ns = rstring(omero.constants.metadata.NSINSIGHTTAGSET)
tagset.textValue = rstring(itest.uuid())
tag = TagAnnotationI()
tag.textValue = rstring(itest.uuid())
tagset.linkAnnotation(tag)
return update_service.saveAndReturnObject(tagset)
def tags_userA_userB(request, userA, userB, groupA):
"""
Returns new OMERO Tags with descriptions
"""
tags = []
ctx = {'omero.group': native_str(groupA.id.val)}
for name, user in zip(["userAtag", "userBtag"], [userA, userB]):
tag = TagAnnotationI()
tag.textValue = rstring(name)
# Only add description to first tag
if name == "userAtag":
tag.description = rstring('tag description')
tag = get_update_service(user).saveAndReturnObject(tag, ctx)
tags.append(tag)
tags.sort(key=lambda x: unwrap(x.id))
return tags
def createset(self, args):
"""
Create a tag set command.
"""
tags = []
if args.tag:
if type(args.tag) is list:
tags = args.tag
else:
tags = [args.tag]
else:
# Should not happen
self.ctx.err("Missing tag parameter")
sys.exit(1)
tag = self.create_tag(args.name, args.desc, text="tag set")
tag.ns = rstring(omero.constants.metadata.NSINSIGHTTAGSET)
links = []
for t in tags:
link = AnnotationAnnotationLinkI()
link.parent = tag
link.child = TagAnnotationI(rlong(int(t)), False)
links.append(link)
client = self.ctx.conn(args)
session = client.getSession()
update_service = session.getUpdateService()
try:
links = update_service.saveAndReturnArray(links)
self.ctx.out("TagAnnotation:%s" % links[0].parent.id.val)
except omero.ValidationException as e:
self.ctx.err(e.message)
self.ctx.err("Check that tag '%s' exists." % t)
sys.exit(1)
def run(password, admin_name, target, tag, host, port):
for i in range(1, 51):
username = "******" % i
print(username)
conn = BlitzGateway(username, password, host=host, port=port)
try:
conn.connect()
updateService = conn.getUpdateService()
ds = conn.getObject("Dataset",
attributes={'name': target},
opts={'owner': conn.getUserId()})
if ds is None:
print("No dataset with name %s found" % target)
continue
params = omero.sys.ParametersI()
params.addString('username', admin_name)
query = "from TagAnnotation where textvalue='%s' \
AND details.owner.omeName=:username" % tag
query_service = conn.getQueryService()
tags = query_service.findAllByQuery(query, params,
conn.SERVICE_OPTS)
if len(tags) == 0:
print("No tag with name %s found" % tag)
continue
tag_id = tags[0].id.getValue()
print(tag_id)
links = []
for image in ds.listChildren():
name = image.getName()
if name in images_to_tag:
# Check first that the image is not tagged
params = omero.sys.ParametersI()
params.addLong('parent', image.id)
params.addLong('child', tag_id)
query = "select link from ImageAnnotationLink as link \
where link.parent.id=:parent \
AND link.child.id=:child"
values = query_service.findAllByQuery(
query, params, conn.SERVICE_OPTS)
if len(values) == 0:
link = ImageAnnotationLinkI()
link.parent = ImageI(image.id, False)
link.child = TagAnnotationI(tag_id, False)
links.append(link)
else:
print("Tag %s already linked to %s" % (tag, name))
if len(links) > 0:
updateService.saveArray(links)
except Exception as exc:
print("Error when tagging the images: %s" % str(exc))
finally:
conn.close()
def projects_dataset_image_tag(self):
"""
Returns 2 new OMERO Projects, linked Dataset and linked Image populated
by an L{test.integration.library.ITest} instance with required fields
set. Also a Tag linked to both Projects.
"""
project1 = ProjectI()
project1.name = rstring(self.uuid())
project2 = ProjectI()
project2.name = rstring(self.uuid())
dataset = DatasetI()
dataset.name = rstring(self.uuid())
image = self.new_image(name=self.uuid())
dataset.linkImage(image)
project1.linkDataset(dataset)
project2.linkDataset(dataset)
tag = TagAnnotationI()
tag.textValue = rstring("ChgrpTag")
project1.linkAnnotation(tag)
project2.linkAnnotation(tag)
return self.update.saveAndReturnArray([project1, project2])
def projects_dataset_image_tag(self):
"""
Returns 2 new OMERO Projects, linked Dataset and linked Image populated
by an L{test.integration.library.ITest} instance with required fields
set. Also a Tag linked to both Projects.
"""
project1 = ProjectI()
project1.name = rstring(f'P1_{self.uuid()}')
project2 = ProjectI()
project2.name = rstring(f'P2_{self.uuid()}')
dataset = DatasetI()
dataset.name = rstring(f'D{self.uuid()}')
image = self.new_image(f'I{self.uuid()}')
dataset.linkImage(image)
project1.linkDataset(dataset)
project2.linkDataset(dataset)
tag = TagAnnotationI()
tag.textValue = rstring("ChgrpTag")
project1.linkAnnotation(tag)
project2.linkAnnotation(tag)
return self.update.saveAndReturnArray([project1, project2])
def tagset_tag(self):
"""
Returns a new OMERO TagAnnotation, with the OMERO.insight tagset
namespace set, and linked TagAnnotation with required fields set.
"""
tagset = TagAnnotationI()
tagset.ns = rstring(omero.constants.metadata.NSINSIGHTTAGSET)
tagset.textValue = rstring(self.uuid())
tag = TagAnnotationI()
tag.textValue = rstring(self.uuid())
tagset.linkAnnotation(tag)
return self.update.saveAndReturnObject(tagset)
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 add_annotations(o):
'''
Annotation
BasicAnnotation
BooleanAnnotation
BooleanAnnotationI
NumericAnnotation
DoubleAnnotation
DoubleAnnotationI
LongAnnotation
LongAnnotationI
TermAnnotation
TermAnnotationI
TimestampAnnotation
TimestampAnnotationI
ListAnnotation
ListAnnotationI
MapAnnotation
MapAnnotationI
TextAnnotation
CommentAnnotation
CommentAnnotationI
TagAnnotation
TagAnnotationI
XmlAnnotation
XmlAnnotationI
TypeAnnotation
FileAnnotation
FileAnnotationI
'''
annotation = BooleanAnnotationI()
annotation.description = rstring('the_description')
annotation.ns = rstring('boolean_annotation')
annotation.boolValue = rbool(True)
o.linkAnnotation(annotation)
annotation = CommentAnnotationI()
annotation.description = rstring('the_description')
annotation.ns = rstring('comment_annotation')
annotation.textValue = rstring('text_value')
o.linkAnnotation(annotation)
annotation = DoubleAnnotationI()
annotation.description = rstring('the_description')
annotation.ns = rstring('double_annotation')
annotation.doubleValue = rdouble(1.0)
o.linkAnnotation(annotation)
annotation = LongAnnotationI()
annotation.description = rstring('the_description')
annotation.ns = rstring('long_annotation')
annotation.longValue = rlong(1L)
o.linkAnnotation(annotation)
annotation = MapAnnotationI()
annotation.description = rstring('the_description')
annotation.ns = rstring('map_annotation')
annotation.setMapValue([NamedValue('a', '1'), NamedValue('b', '2')])
o.linkAnnotation(annotation)
annotation = TagAnnotationI()
annotation.description = rstring('the_description')
annotation.ns = rstring('tag_annotation')
annotation.textValue = rstring('tag_value')
o.linkAnnotation(annotation)
annotation = TermAnnotationI()
annotation.description = rstring('the_description')
annotation.ns = rstring('term_annotation')
annotation.termValue = rstring('term_value')
o.linkAnnotation(annotation)
annotation = TimestampAnnotationI()
annotation.description = rstring('the_description')
annotation.ns = rstring('timestamp_annotation')
annotation.timeValue = rtime(1)
o.linkAnnotation(annotation)
annotation = XmlAnnotationI()
annotation.description = rstring('the_description')
annotation.ns = rstring('xml_annotation')
annotation.textValue = rstring('<xml_value></xml_value>')
o.linkAnnotation(annotation)
for exp in allUsers:
username = exp.getOmeName()
print username
userConn = BlitzGateway(username, "ome")
userConn.connect()
for g in userConn.getGroupsMemberOf():
if g.getName() == "user":
continue
print " ", g.getName()
userConn.SERVICE_OPTS.setOmeroGroup(g.getId())
params = omero.sys.Parameters()
params.theFilter = omero.sys.Filter()
params.theFilter.ownerId = rlong(exp.getId())
tags = list(userConn.getObjects("TagAnnotation", params=params))
for i in range(TAG_COUNT - len(tags)):
t = TagAnnotationI()
newTagVal = "%s_%s_TEST" % (username, g.getName())
print "creating TAG:", newTagVal
t.textValue = wrap(str(newTagVal))
userConn.getUpdateService().saveObject(t, userConn.SERVICE_OPTS)
# for t in tags:
# print " TAG", t.getId(), t.getTextValue()
userConn.c.closeSession()
print "\n---- DOING ANNOTATING... ----\n"
# We want to Tag loads of stuff with OUR tags and Others' tags
for exp in allUsers:
username = exp.getOmeName()
if username not in USER_NAMES:
continue
print "\n\n------------ USER:"******"------------"
def testQueryTaggedUnique(self):
# get group we're working on...
ctx = self.client.sf.getAdminService().getEventContext()
groupId = ctx.groupId
print 'groupId', groupId
# Admin sets permissions to read-ann
admin = self.root.sf.getAdminService()
rootUpdate = self.root.sf.getUpdateService()
gr = admin.getGroup(groupId)
p = PermissionsI()
p.setUserRead(True)
p.setUserWrite(True)
p.setGroupRead(True)
p.setGroupAnnotate(True)
p.setGroupWrite(False)
p.setWorldRead(False)
p.setWorldAnnotate(False)
p.setWorldWrite(False)
gr.details.permissions = p
admin.updateGroup(gr)
# Update context for user
ctx = self.client.sf.getAdminService().getEventContext()
update = self.client.sf.getUpdateService()
queryService = self.client.sf.getQueryService()
tagCount = 5
# User creates tag linked to images
tag = TagAnnotationI()
tag.textValue = wrap("test_iQuerySpeed")
links = []
for i in range(tagCount):
iid = createImageWithPixels(self.client, self.uuid())
link = ImageAnnotationLinkI()
link.parent = ImageI(iid, False)
link.child = tag
links.append(link)
links = update.saveAndReturnArray(links)
tag = links[0].child
# check permissions
p = tag.getDetails().getPermissions()
assert p.isGroupRead()
assert p.isGroupAnnotate()
# Root also links user's tag to images
rootLinks = []
for l in links:
link = ImageAnnotationLinkI()
link.parent = ImageI(l.parent.id, False)
link.child = TagAnnotationI(l.child.id, False)
rootLinks.append(link)
rootUpdate.saveAndReturnArray(rootLinks, {'omero.group': str(groupId)})
q = """select distinct new map(obj.id as id,
obj.name as name,
obj.details.owner.id as ownerId,
obj as image_details_permissions,
obj.fileset.id as filesetId,
lower(obj.name) as n
,
pix.sizeX as sizeX,
pix.sizeY as sizeY,
pix.sizeZ as sizeZ
)
from Image obj left outer join obj.pixels pix
join obj.annotationLinks alink
where %s
order by lower(obj.name), obj.id """
params = ParametersI()
params.add('tid', tag.id)
# We can get all the tagged images like this.
# We use an additional select statement to give 'unique' results
uniqueClause = """alink.id = (select max(alink.id)
from ImageAnnotationLink alink
where alink.child.id=:tid and alink.parent.id=obj.id)"""
query = q % uniqueClause
result1 = queryService.projection(query, params,
{'omero.group': str(groupId)})
assert len(result1) == tagCount
# Without the select statement, we get the same image returned
# multiple times if there is no 'distinct'
clause = "alink.child.id=:tid"
query = q % clause
result2 = queryService.projection(query, params,
{'omero.group': str(groupId)})
assert len(result2) == tagCount
for idx in range(len(result1)-1):
# Omit final since == isn't defined for Ice objects.
assert result1[idx] == result2[idx]
for exp in allUsers:
username = exp.getOmeName()
print username
userConn = BlitzGateway(username, "ome")
userConn.connect()
for g in userConn.getGroupsMemberOf():
if g.getName() == "user":
continue
print " ", g.getName()
userConn.SERVICE_OPTS.setOmeroGroup(g.getId())
params = omero.sys.Parameters()
params.theFilter = omero.sys.Filter()
params.theFilter.ownerId = rlong(exp.getId())
tags = list( userConn.getObjects("TagAnnotation", params=params) )
for i in range( TAG_COUNT-len(tags) ):
t = TagAnnotationI()
newTagVal = "%s_%s_TEST" % (username, g.getName())
print "creating TAG:", newTagVal
t.textValue = wrap(str(newTagVal))
userConn.getUpdateService().saveObject(t, userConn.SERVICE_OPTS)
# for t in tags:
# print " TAG", t.getId(), t.getTextValue()
userConn.c.closeSession()
print "\n---- DOING ANNOTATING... ----\n"
# We want to Tag loads of stuff with OUR tags and Others' tags
for exp in allUsers:
username = exp.getOmeName()
if username not in USER_NAMES:
def testQueryTaggedUnique(self):
# get group we're working on...
ctx = self.client.sf.getAdminService().getEventContext()
groupId = ctx.groupId
print 'groupId', groupId
# Admin sets permissions to read-ann
admin = self.root.sf.getAdminService()
rootUpdate = self.root.sf.getUpdateService()
gr = admin.getGroup(groupId)
p = PermissionsI()
p.setUserRead(True)
p.setUserWrite(True)
p.setGroupRead(True)
p.setGroupAnnotate(True)
p.setGroupWrite(False)
p.setWorldRead(False)
p.setWorldAnnotate(False)
p.setWorldWrite(False)
gr.details.permissions = p
admin.updateGroup(gr)
# Update context for user
ctx = self.client.sf.getAdminService().getEventContext()
update = self.client.sf.getUpdateService()
queryService = self.client.sf.getQueryService()
tagCount = 5
# User creates tag linked to images
tag = TagAnnotationI()
tag.textValue = wrap("test_iQuerySpeed")
links = []
for i in range(tagCount):
iid = createImageWithPixels(self.client, self.uuid())
link = ImageAnnotationLinkI()
link.parent = ImageI(iid, False)
link.child = tag
links.append(link)
links = update.saveAndReturnArray(links)
tag = links[0].child
# check permissions
p = tag.getDetails().getPermissions()
assert p.isGroupRead()
assert p.isGroupAnnotate()
# Root also links user's tag to images
rootLinks = []
for l in links:
link = ImageAnnotationLinkI()
link.parent = ImageI(l.parent.id, False)
link.child = TagAnnotationI(l.child.id, False)
rootLinks.append(link)
rootUpdate.saveAndReturnArray(rootLinks, {'omero.group': str(groupId)})
q = """select distinct new map(obj.id as id,
obj.name as name,
obj.details.owner.id as ownerId,
obj as image_details_permissions,
obj.fileset.id as filesetId,
lower(obj.name) as n
,
pix.sizeX as sizeX,
pix.sizeY as sizeY,
pix.sizeZ as sizeZ
)
from Image obj left outer join obj.pixels pix
join obj.annotationLinks alink
where %s
order by lower(obj.name), obj.id """
params = ParametersI()
params.add('tid', tag.id)
# We can get all the tagged images like this.
# We use an additional select statement to give 'unique' results
uniqueClause = """alink.id = (select max(alink.id)
from ImageAnnotationLink alink
where alink.child.id=:tid and alink.parent.id=obj.id)"""
query = q % uniqueClause
result1 = queryService.projection(query, params,
{'omero.group': str(groupId)})
assert len(result1) == tagCount
# Without the select statement, we get the same image returned
# multiple times if there is no 'distinct'
clause = "alink.child.id=:tid"
query = q % clause
result2 = queryService.projection(query, params,
{'omero.group': str(groupId)})
assert len(result2) == tagCount
for idx in range(len(result1)-1):
# Omit final since == isn't defined for Ice objects.
assert result1[idx] == result2[idx]