OMERO Reader crashes KNIME

Hi,

when I click "start OMERO insight" in the OMERO Reader node, KNIME crashes entirely (see below whats printed into the terminal).

I am running Knime 3.1.2 on linux mint 17.3.

If it helps I'd glady provide the error report file that is mentioned below.

Thanks for your help!

-----------------------------------

# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00007fbaab201eaf, pid=2663, tid=140439585056512
#
# JRE version: Java(TM) SE Runtime Environment (8.0_60-b27) (build 1.8.0_60-b27)
# Java VM: Java HotSpot(TM) 64-Bit Server VM (25.60-b23 mixed mode linux-amd64 compressed oops)
# Problematic frame:
# C  [libgdk-x11-2.0.so.0+0x4ceaf]  gdk_display_open+0x3f
#
# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
# An error report file with more information is saved as:
hs_err_pid2663.log
#
# If you would like to submit a bug report, please visit:
#   http://bugreport.java.com/bugreport/crash.jsp
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.

Dear Kai,

sorry for the trouble and thanks for letting us know. We will try to reproduce the problem and come back with a solution asap.

Best,

Christian

PS: Which OMERO Version are you using on the Server side? Just out of curiosity and to make sure that KNIME can connect.
PPS: We are working on a more flexible solution (based on imagej) to read/write images from and to OMERO.

Dear Christian,

thanks for the quick reply!

we are currently using OMERO 5.1.2 but are also in the process of upgrading to a more recent version.

Thanks for your help and cheers,

Kai

Hi Kai,

I was able to reproduce the problem. No I will work on a fix. ;-)

Thanks again for reporting,

Christian

Hi Kai,

I opened an issue in our GitHub Repo. We will tackle the problem next week.

https://github.com/knime-ip/knip-omero/issues/3

Christian

HI Christian,

 

thanks for the update! I'll stay tuned for next week then :)

 

Cheers,

Kai

Dear Christian,

many thanks for the feedback and the issue tracker link!

 

Cheers

Niko

Hi Niko & Kai,

we fixed the Client for OMERO 5.2.x (available via our nightly build). We will also provide a version for OMERO 5.1.x (probably only via nightly build, hopefully next week).

However, as mentoined above, we want to redesign our OMERO integration and offer a new Reader/Writer based on imagej-omero / scifio. It would be great, as we don't have too much experience with OMERO, if you could provide us some feedback what are "must haves" and/or "nice-to-haves" of such new nodes (e.g. you want to read a complete dataset and then write back the results, or ...).  We opened a GitHub issue for further discussion:

https://github.com/knime-ip/knip-omero/issues/5

I hope this helps,

Christian