def main(import_md):
# Load metadata to orchestrate import
with open(import_md, 'r') as fp:
batch_md = json.load(fp)
import_user = batch_md['user']
import_group = batch_md['group']
file_metadata = batch_md['import_targets']
data_dir = Path(batch_md['server_path'])
# Create user connection
suconn = BlitzGateway(OMERO_USER,
OMERO_PASS,
host=OMERO_HOST,
port=OMERO_PORT,
secure=True)
suconn.connect()
conn = suconn.suConn(import_user, import_group, 2160000000)
suconn.close()
# Import targets from import.json
for md in file_metadata:
filename = md['filename']
file_path = data_dir / filename
print(f'Preparing to import {str(file_path)}')
imp_ctl = Importer(conn, file_path, md)
imp_ctl.import_ln_s(OMERO_HOST, OMERO_PORT)
print("import done")
if imp_ctl.screen:
print("it's a screen")
imp_ctl.get_plate_ids()
print(f"plate ids get! {str(imp_ctl.plate_ids[0])}")
imp_ctl.organize_plates()
print("plate organized")
imp_ctl.annotate_plates()
print("plate annotated")
else:
imp_ctl.get_image_ids()
imp_ctl.organize_images()
imp_ctl.annotate_images()
conn.close()
return
def connect_as_user(username):
"""Establish a connection to OMERO with a given user context.
To establish a connection as a specific user without knowing their
credential, a two-stage process is required: first the bsae connection is
created with an admin user, then this existing connection is switched over
to a (non-privileged) user account.
Returns the connection in the user's context.
"""
# establish the base connection with an admin account
su_conn = BlitzGateway(SU_USER, SU_PASS, host=HOST, port=PORT)
if su_conn.connect() is False:
raise RuntimeError('Connection to OMERO failed, check settings!')
# now switch to the requested user
conn = su_conn.suConn(username)
if conn.connect() is False:
raise RuntimeError('User switching in OMERO failed, check settings!')
log.debug("Successfully connected to OMERO.")
return conn
print kv
if len(kv) == 2:
data.append(kv)
elif len(kv) == 1:
data.append([kv[0], ""])
print "list data", data
to_delete = []
for ann in obj.listAnnotations(ns=namespace):
kv = ann.getValue()
to_delete.append(ann.id)
#for dataset in conn.getObjects("Dataset", ids):
suconn = conn.suConn(
owner
) #this line has been introduced to allow sysadmin to copy kvpairs on behalf of the owner's image
map_ann = omero.gateway.MapAnnotationWrapper(
suconn
) #this line tells that the connection to the Map annotation is done by sysadmin but with the name of the owner of the data
map_ann.setNs(namespace)
map_ann.setValue(data)
map_ann.save()
obj.linkAnnotation(map_ann)
suconn.close(
) #this line is necessary to "close" also the connection as "other user" as the sysadmin is now concluding to operate on behalf of the owner of the image
if len(to_delete) > 0:
conn.deleteObjects('Annotation', to_delete)
# Return some value(s).
def main(md_filepath, user_name, group, admin_user, server, port):
# create connection and establish context
password = getpass(f'Enter password for {admin_user}: ')
su_conn = BlitzGateway(admin_user, password, host=server, port=port)
su_conn.connect()
conn = su_conn.suConn(user_name, group, 600000)
su_conn.close()
orphan_ids = get_image_ids(conn)
# load and prepare metadata
md = load_md(md_filepath)
if 'filename' not in md.columns:
logging.error('Metadata file missing filename column')
return
if 'dataset' not in md.columns:
logging.error('Metadata file missing dataset column')
return
if 'project' not in md.columns:
logging.error('Metadata file missing project column')
return
md_json = json.loads(md.to_json(orient='table', index=False))
# loop over metadata, move and annotate matching images
processed_filenames = []
for row in md_json['data']:
row.pop('OMERO_group', None) # No longer using this field
project_name = str(row.pop('project'))
dataset_name = str(row.pop('dataset'))
filename = row.pop('filename')
if filename not in processed_filenames:
image_ids = filter_by_filename(conn, orphan_ids, filename)
if len(image_ids) > 0:
# move image into place, create projects/datasets as necessary
project_id = set_or_create_project(conn, project_name)
dataset_id = set_or_create_dataset(conn,
project_id,
dataset_name)
link_images_to_dataset(conn, image_ids, dataset_id)
print(f'Moved images:{image_ids} to dataset:{dataset_id}')
# map annotations
ns = CURRENT_MD_NS
map_ann_id = multi_post_map_annotation(conn,
"Image",
image_ids,
row,
ns)
print(f'Created annotation:{map_ann_id}'
f' and linked to images:{image_ids}')
processed_filenames.append(filename)
else:
print(f'Image with filename:{filename} not found in orphans')
else:
print(f'Already processed images with filename:{filename}')
conn.close()
print('Complete!')
# PASS = '******'
# PASS = '******'
SU_USER = "******"
SU_PASS = "******"
try:
from localconfig import USER, SU_USER, SU_PASS, MANAGED_REPO
except ImportError:
print "Using hard-coded configuration values!"
su_conn = BlitzGateway(SU_USER, SU_PASS, host=HOST, port=PORT)
if su_conn.connect() is False:
raise RuntimeError("Connection to OMERO failed, check settings!")
conn = su_conn.suConn(USER)
if conn.connect() is False:
raise RuntimeError("User switching in OMERO failed, check settings!")
su_conn = BlitzGateway(SU_USER, SU_PASS, host=HOST, port=PORT)
su_conn.connect()
conn = su_conn.suConn(USER)
conn.connect()
# projs = [ x for x in conn.listProjects() ]
projs = [x for x in conn.listProjects(eid=conn.getUserId())]
for proj in projs:
print proj.getName()
proj = projs[0]