def create_project(connection, name, description=None):
new_project = gw.ProjectWrapper(connection, model.ProjectI())
new_project.setName(name)
if description:
new_project.setDescription(description)
new_project.save()
return new_project
def create_project(connection, project_name, project_description=None):
new_project = model.ProjectI()
new_project.setName(rtypes.rstring(project_name))
if project_description is not None:
new_project.setDescription(rtypes.rstring(project_description))
new_project = connection.getUpdateService().saveAndReturnObject(new_project)
return new_project
def link_dataset_to_project(connection, dataset, project):
link = model.ProjectDatasetLinkI()
link.setParent(model.ProjectI(
project.getId(),
False)) # linking to a loaded project might raise exception
link.setChild(model.DatasetI(dataset.getId(), False))
connection.getUpdateService().saveObject(link)
return
def create_dataset(connection, dataset_name, dataset_description=None, parent_project=None):
new_dataset = model.DatasetI()
new_dataset.setName(rtypes.rstring(dataset_name))
if dataset_description:
new_dataset.setDescription(rtypes.rstring(dataset_description))
new_dataset = connection.getUpdateService().saveAndReturnObject(new_dataset)
if parent_project:
link = model.ProjectDatasetLinkI()
link.setChild(model.DatasetI(new_dataset.getId(), False))
link.setParent(model.ProjectI(parent_project.getId(), False))
connection.getUpdateService().saveObject(link)
return new_dataset
def add_tags(self, tag_values, object_type, object_id):
update_service = self.SESSION.getUpdateService()
for tag_value in tag_values:
# tags shouldn't contain commas?
split_tag_values = [x.strip() for x in tag_value.split(',')]
# ignore empty tag strings
for split_tag_value in split_tag_values:
if len(split_tag_value.strip()) < 1:
continue
# TODO: add check here to see if tag with specific value already exists and link it if so
# use stateless update service instead of blitz
new_tag_anno = model.TagAnnotationI()
# TODO: determine what description the tag annotation should have; e.g. date, strain
# Use 'client' namespace to allow editing in Insight & web
new_tag_anno.setTextValue(rtypes.rstring(split_tag_value))
tag_anno = update_service.saveAndReturnObject(new_tag_anno)
# do link with parent object
om_object = self.retrieve_objects(object_type,
[int(object_id)])
link = None
if object_type == str(OMERODataType.project):
link = model.ProjectAnnotationLinkI()
link.parent = model.ProjectI(object_id, False)
elif object_type == str(OMERODataType.dataset):
link = model.DatasetAnnotationLinkI()
link.parent = model.DatasetI(object_id, False)
elif object_type == str(OMERODataType.image):
link = model.ImageAnnotationLinkI()
link.parent = model.ImageI(object_id, False)
link.child = model.TagAnnotationI(tag_anno.id, False)
update_service.saveAndReturnObject(link)
def add_kvps(self, key_value_data, object_type, object_id):
# use stateless update service instead of blitz
new_map_anno = model.MapAnnotationI()
# Use 'client' namespace to allow editing in Insight & web
namespace = constants.metadata.NSCLIENTMAPANNOTATION
new_map_anno.setNs(rtypes.rstring(namespace))
# key_value_data = [{i[0]: i[1:]} for i in key_value_data]
key_value_data = [
model.NamedValue(i[0], str(i[1:])) for i in key_value_data
]
# key_value_data = [model.NamedValue(i[0], i[1:]) for i in key_value_data]
new_map_anno.setMapValue(key_value_data)
update_service = self.SESSION.getUpdateService()
map_anno = update_service.saveAndReturnObject(new_map_anno)
# do link with parent object
om_object = self.retrieve_objects(object_type, [int(object_id)])
link = None
if object_type == str(OMERODataType.project):
link = model.ProjectAnnotationLinkI()
link.parent = model.ProjectI(object_id, False)
elif object_type == str(OMERODataType.dataset):
link = model.DatasetAnnotationLinkI()
link.parent = model.DatasetI(object_id, False)
elif object_type == str(OMERODataType.image):
link = model.ImageAnnotationLinkI()
link.parent = model.ImageI(object_id, False)
link.child = model.MapAnnotationI(map_anno.id, False)
update_service.saveAndReturnObject(link)