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(long(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 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 createAndSaveTags(names, descriptions, tagGroup=None):
tags = []
for name, desc in zip(names, descriptions):
tags.append(createTag(name, desc))
if tagGroup is not None:
links = []
for t in tags:
link = AnnotationAnnotationLinkI()
link.parent = tagGroup
link.child = t
links.append(link)
updateService.saveArray(links)
else:
updateService.saveArray(tags)
print " Saving a list of %s tags \n" % len(tags)
def load(self, args):
"""
Import new tag(s) from json.
"""
if args.filename:
fobj = open(args.filename)
else:
fobj = sys.stdin
p = json.load(fobj)
if fobj is not sys.stdin:
fobj.close()
to_add = []
for element in p:
if 'set' in element:
tag = self.create_tag(str(element['name']),
str(element['desc']))
tag.ns = rstring(omero.constants.metadata.NSINSIGHTTAGSET)
links = []
for e in element['set']:
t = self.create_tag(str(e['name']), str(e['desc']))
link = AnnotationAnnotationLinkI()
link.parent = tag
link.child = t
links.append(link)
to_add.extend(links)
else:
to_add.append(
self.create_tag(str(element['name']),
str(element['desc'])))
client = self.ctx.conn(args)
session = client.getSession()
update_service = session.getUpdateService()
to_add = update_service.saveAndReturnArray(to_add)
ids = []
for element in to_add:
if isinstance(element, TagAnnotationI):
self.ctx.out("TagAnnotation:%s" % element.id.val)
ids.append(element.id.val)
else:
tag_id = element.parent.id.val
if tag_id not in ids:
self.ctx.out("TagAnnotation:%s" % tag_id)
ids.append(tag_id)
def load(self, args):
"""
Import new tag(s) from json.
"""
if args.filename:
fobj = open(args.filename)
else:
fobj = sys.stdin
p = json.load(fobj)
if fobj is not sys.stdin:
fobj.close()
to_add = []
for element in p:
if 'set' in element:
tag = self.create_tag(str(element['name']),
str(element['desc']))
tag.ns = rstring(omero.constants.metadata.NSINSIGHTTAGSET)
links = []
for e in element['set']:
t = self.create_tag(str(e['name']), str(e['desc']))
link = AnnotationAnnotationLinkI()
link.parent = tag
link.child = t
links.append(link)
to_add.extend(links)
else:
to_add.append(self.create_tag(str(element['name']),
str(element['desc'])))
client = self.ctx.conn(args)
session = client.getSession()
update_service = session.getUpdateService()
to_add = update_service.saveAndReturnArray(to_add)
ids = []
for element in to_add:
if isinstance(element, TagAnnotationI):
self.ctx.out("TagAnnotation:%s" % element.id.val)
ids.append(element.id.val)
else:
tag_id = element.parent.id.val
if tag_id not in ids:
self.ctx.out("TagAnnotation:%s" % tag_id)
ids.append(tag_id)
