omero_update_bf.py

#! /usr/bin/env python
# Script to update Bio-Formats server-side

import urllib2
import os
import shutil

DONWLOADS_URL = "http://downloads.openmicroscopy.org/bio-formats"
RELEASE = "5.1.4"
JARS = [
    "formats-api.jar",
    "formats-bsd.jar",
    "formats-common.jar",
    "formats-gpl.jar",
    "jai_imageio.jar",
    "lwf-stubs.jar",
    "mdbtools-java.jar",
    "metakit.jar",
    "ome-poi.jar",
    "ome-xml.jar",
    "specification.jar",
    "turbojpeg.jar"]


artifact_url = DONWLOADS_URL + '/' + RELEASE + '/artifacts/'
server_dir = os.path.realpath("lib/server")
client_dir = os.path.realpath("lib/client")
backup_dir = os.path.realpath("lib/backup")

if not os.path.exists(backup_dir):
    os.makedirs(backup_dir)

for jar in JARS:
    
    # Backing up
    server_jar = os.path.join(server_dir, jar)
    client_jar = os.path.join(client_dir, jar)
    backup_jar = os.path.join(backup_dir, jar)
    print 'backing up %s to %s' % (server_jar, backup_jar)    
    shutil.copyfile(server_jar, backup_jar)

    jar_url = artifact_url + jar
    print "Downloading %s" % jar_url
    f = urllib2.urlopen(jar_url)
    data = f.read()
    with open(server_jar, "wb") as f:
        print "Copying to %s" % server_jar
        f.write(data)
    with open(client_jar, "wb") as f:
        print "Copying to %s" % client_jar
        f.write(data)

Things to consider before using this:

• Can it be used multiple times? (Does an existing backup/ cause an exception? idempotency)
• How does one know if the number of jars has changed? (catalog)
• What happens if there's a network issue while downloading? (checksum)

Coming back to this a year later. See https://github.com/sbesson/bio-formats-omero for an experimental solution (inspired by https://github.com/openmicroscopy/bio-formats-fiji).

The advantage of using Maven is the dependency management i.e. partly addressing/delegating the idempotency, catalog and checksum questions above.

Main drawbacks as mentioned in the README is this approach is currently based on the Bio-Formats POM rather than the OMERO POM. Thus:

• conflict/exclusions managed at the OMERO level are not handled (dependencies defined in BF trump)
• since only a subset of the dependencies are copied, the target is additive only and does not handle deletion/renaming etc

If this turns out to be useful, a way to resolve the above might be to base the pom.xml on https://github.com/ome/pom-omero-client, clean lib/server and lib/client in the clean phase and copy blitz and the overriden Bio-Formats dependencies in the package phase.