Smuggler 5.6 - Githubissues

jburel commented 6 years ago

This brings smuggler to 5.6 gateway

To build and deploy http://c0c0n3.github.io/ome-smuggler/docs/content/examples/whirlwind-tour.html

cc @c0c0n3

To test:

open a terminal and checkout this PR
docker build -t smuggler .
docker run -it -p 8000:8000 smuggler
Make sure the user has an email address set up or use the daily build of OMERO.insight
in insight/config/container.xml Edit <entry name="omero.client.import.offline.enabled" type="boolean">true</entry>
Import an image using insight. Check the output in smuggler. Ignore failure when sending email. This is not set up.

c0c0n3 commented 6 years ago

Looks good to me. Just a couple of questions tough.

Should we do some kind of versioning? For example, this is what I had in Smuggler. BTW files & version numbers are still there, but I don't know how meaningful they will be now in the context of OMERA?
How should we release it? This was our release & deployment procedure at IGH back in the day. Not sure what you guys would like to do going forward...

This PR resolves #12, so I'm going to ditch my OMERO upgrade branch.

cc @jburel @juliomateoslangerak

jburel commented 5 years ago

@c0c0n3 I have modified the gradle file in order to work with 5.5 I have so far not been able to import "sessionKey:•9-30d6-44a4-90b2-8b8c083631de" always seems to be truncated when they are used in smuggler.

jburel commented 5 years ago

error so it seems to come from

Exception in thread "main" java.lang.reflect.InvocationTargetException
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.springframework.boot.loader.MainMethodRunner.run(MainMethodRunner.java:48)
    at org.springframework.boot.loader.Launcher.launch(Launcher.java:87)
    at org.springframework.boot.loader.Launcher.launch(Launcher.java:50)
    at org.springframework.boot.loader.JarLauncher.main(JarLauncher.java:51)
Caused by: java.lang.NoClassDefFoundError: gnu/getopt/LongOpt
    at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:556)
    at ome.cli.omero.imports.ImportAdapter.main(ImportAdapter.java:14)
    at ome.cli.Main.main(Main.java:36)
    ... 8 more
Caused by: java.lang.ClassNotFoundException: gnu.getopt.LongOpt
    at java.net.URLClassLoader.findClass(URLClassLoader.java:382)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
    at org.springframework.boot.loader.LaunchedURLClassLoader.loadClass(LaunchedURLClassLoader.java:94)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:357)

jburel commented 5 years ago

Now I can import from script but not insight yet!!

jburel commented 5 years ago

I can now import from insight

jburel commented 4 years ago

I have tested against a 5.6.dev server and outreach (5.5)

joshmoore commented 4 years ago

LGTM. (I assume along with ome/openmicroscopy's Dockerfile we could simplify this one when the time comes).

ome / omero-ms-queue

Smuggler 5.6 #18