Python script for downloading and re-importing an image into OMERO

reimport.py

import subprocess

from omero.gateway import BlitzGateway
conn = BlitzGateway("username", "passwork", port=4064, host="localhost")
conn.connect()


image = conn.getObject("Image", 54973)
dataset = image.getParent()

filename = None
for f in image.getImportedImageFiles():
    filename = f.getName()
    t = open(f.getName(), 'wb')
    try:
        for chunk in f.getFileInChunks():
            t.write(chunk)
    finally:
        t.close()

client = conn.c
server = client.getProperty("omero.host")
port = client.getProperty("omero.port")
key = client.getSessionId()


args = []
# Assume we have 'omero' on PATH
args.append("omero")
args.extend(["-s", server, "-k", key, "-p", port, "import"])
# re-import into same Dataset
if dataset is not None:
    args.extend(["-d", str(dataset.getId())])
args.append(filename)

popen = subprocess.Popen(args,
                         stdout=subprocess.PIPE,
                         stderr=subprocess.PIPE)
out, err = popen.communicate()
rc = popen.wait()
if rc != 0:
    raise Exception("import failed: [%r] %s\n%s" % (args, rc, err))
pix_ids = []
for x in out.split("\n"):
    try:    # if the line has pixels ID...
        pixId = str(long(x.strip()))
        # Occasionally during tests an id is duplicated on stdout
        if pixId not in pix_ids:
            pix_ids.append(pixId)
    except:
        pass

print pix_ids

# Get Image ID from Pixels ID
pix = conn.getQueryService().get("Pixels", long(pix_ids[0]))
print pix.image.id.val