def connect_to_remote(password, username):
c = omero.client(host=OMERO_SERVER, port=OMERO_PORT,
args=["--Ice.Config=/dev/null", "--omero.debug=1"])
c.createSession(username, password)
remote_conn = BlitzGateway(client_obj=c)
cli = omero.cli.CLI()
cli.loadplugins()
cli.set_client(c)
# del os.environ["ICE_CONFIG"]
return c, cli, remote_conn
def cliImport(client,
ipath,
destID,
skip,
depth,
namespace,
dataset=None,
conn=None):
# create import call string
args = createArgumentList(ipath, destID, skip, depth)
images_skipped = None
images_imported = None
try:
with tempfile.NamedTemporaryFile(suffix=".stdout") as stdout:
with tempfile.NamedTemporaryFile(suffix=".stderr") as stderr:
cli = omero.cli.CLI()
cli.loadplugins()
#cli.set_client(client)
cli.set_client(client.createClient(secure=True))
args.extend(["--file", stdout.name])
args.extend(["--errs", stderr.name])
cli.invoke(args)
images_skipped, images_imported = parseLogFile(stderr)
print("Images imported: ", len(images_imported))
print("Images skipped: ", len(images_skipped))
if dataset:
#append log file
#link reportFile to object
ann = conn.createFileAnnfromLocalFile(stderr.name,
mimetype="text/csv",
ns=namespace +
"_log")
dataset.linkAnnotation(ann)
return images_skipped, images_imported, stderr
except Exception as e:
exc_type, exc_obj, exc_tb = sys.exc_info()
print('ERROR at cli import: %s\n %s %s' %
(str(e), exc_type, exc_tb.tb_lineno))
return None, None, None
finally:
return images_skipped, images_imported, None
# Connect to remote omero
c = omero.client(host=host,
port=port,
args=["--Ice.Config=/dev/null", "--omero.debug=1"])
c.joinSession(sessionUuid)
try:
# Just to test connection, print the projects.
remote_conn = BlitzGateway(client_obj=c)
for p in remote_conn.getObjects("Project"):
print p.id, p.name
print "Connected to ", REMOTE_HOST, ", now to transfer image"
cli = omero.cli.CLI()
cli.loadplugins()
cli.set_client(c)
del os.environ["ICE_CONFIG"]
# Find image files
uploaded_image_ids = []
for image_id in ids:
image = local_conn.getObject("Image", image_id)
print image.getName()
temp_file = NamedTemporaryFile().name
try:
# TODO haven't tested an image with multiple files.
for f in image.getImportedImageFiles():
file_loc = os.path.join(managed_dir, f.path, f.name)
print "file location is: ", file_loc
with open(temp_file, 'wr') as f, stdout_redirected(f):