[ome-users] install Slidebook file format extension for OMERO

Sebastien Besson (Staff) s.besson at dundee.ac.uk
Thu Mar 8 13:16:00 GMT 2018 

Hi Kai,

thanks for uploading all the log files. After looking at it, we identified in the
master.err the following error which seems to be the main issue happening
prior to the server restart:

*** Error in `java': double free or corruption (out): 0x00007fabb83fa030 ***
======= Backtrace: =========
/usr/lib64/libc.so.6(+0x7c503)[0x7fc50b217503]
/tmp/libSlideBook6Reader5668132563358476192.so(_ZN9__gnu_cxx13new_allocatorISt10shared_ptrI10CImageDataEE10deallocateEPS3_m+0x20)[0x7fab18eb72e6]

From this stack trace, the problem happens within the native library invoked by the
3i Slidebook reader. Unfortunately this is where we cannot provide further help as we
have no visibility over this source code. I recommend you contact 3i support [1] directly
to report this issue.

Best,
Sebastien

[1] https://www.intelligent-imaging.com/support

On 8 Mar 2018, at 12:29, Kai Schleicher <kai.schleicher at unibas.ch<mailto:kai.schleicher at unibas.ch>>
wrote:


Hi Kenny,

thank you very much for have a look at the logs!

We took now some more log files from before the crash<https://filesender.switch.ch/filesender/?vid=3de95035-be53-1e09-e2ae-00007137f95f> - they are a bit heavier, but I hope you can find something there.

Thanks again for your help and cheers from Basel,
Kai

On 03/07/2018 05:49 PM, Kenneth Gillen (Staff) wrote:
Hi Kai,

It might be useful to see more Blitz log files -  from before a crash, too – the log there is only from a server-start onwards. What happens before the server startup could be useful.

All the best,

Kenny

--

Kenneth Gillen
OME System Administrator

Wellcome Trust Centre for Gene Regulation & Expression
School of Life Sciences
CTIR 2
University of Dundee
Dow Street
Dundee  DD1 5EH
United Kingdom

Tel: +44 (0) 1382 388797

http://www.twitter.com/openmicroscopy

From: ome-users <ome-users-bounces at lists.openmicroscopy.org.uk<mailto:ome-users-bounces at lists.openmicroscopy.org.uk>> on behalf of Kai Schleicher <kai.schleicher at unibas.ch<mailto:kai.schleicher at unibas.ch>>
Reply-To: OME User Support List <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Date: Wednesday, 7 March 2018 16:37
To: "Sebastien Besson (Staff)" <s.besson at dundee.ac.uk<mailto:s.besson at dundee.ac.uk>>
Cc: users OME <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Subject: Re: [ome-users] install Slidebook file format extension for OMERO


Hi Sebastien,

we have tested the upload of slidebook files now a little bit more extensively and realised that when uploading several files (with OMERO.insight) the server crashes and reboots.

We are not sure what happened there, but I have uploaded the relevant log files for you to download<https://filesender.switch.ch/filesender/?vid=731f7cfc-c738-85e9-120b-000071d43069>.

From going through the logs its unfortunately not clear to me what happened. If you have a free moment, could you have a look and maybe point us in the right direction?

Thank you and cheers,
Kai

On 02/13/2018 04:06 PM, Sebastien Besson (Staff) wrote:
Hi Kai,

On 13 Feb 2018, at 13:41, Kai Schleicher <kai.schleicher at unibas.ch<mailto:kai.schleicher at unibas.ch>> wrote:


Hi Sebastien,

This is brilliant! thanks so much!

It does now work on windows (which is the most prominent usecase anyway). We added the jar file also to our server and indeed the upload as well as reading metadadata and generating thumbnails succeeded :)

Great. Very glad to hear it. And really interesting example of workflow integrating
third-party libraries developed by the constructors.

Except for one file<x-msg://42/,,https://filesender.switch.ch/filesender/?vid=469ebaef-1b1d-5349-f357-00001c21ea73>, which opend fine in Fiji or the native slidebook reader. I am not so sure what the difference is to the ones that work<https://filesender.switch.ch/filesender/?vid=2be15da3-c0a1-8e28-0b76-000023dfc166> (see screenshot).

To know more we would probably need to see what failed in the server-side import log.
If the failure happens when SlideBook6Reader tries to read the data, this is something
worth reporting to them.

While it works on windows, it still fails on my linux (on which I tried it in the beginning). Is there maybe a cache somewhere that needs to be delete first?

I do not think there should be any caching involved. Using the linux client, after downloading
and moving SlideBook6Reader.jar under the libs/ folder, I have

[sbesson at ome-c6100-1 OMERO.importer-5.3.5-ice36-b73-linux]$ ./importer-cli --debug ERROR -f /ome/data_repo/curated/slidebook/alexia/utrophinGFP_sih_e1_time1.sld
Starting OMERO.importer...
…
#======================================
# Group: /ome/data_repo/curated/slidebook/alexia/utrophinGFP_sih_e1_time1.sld SPW: false Reader: loci.formats.in.SlideBook6Reader
/ome/data_repo/curated/slidebook/alexia/utrophinGFP_sih_e1_time1.sld

Is your import failing client-side or server-side? Also is your Linux architecture 32bit or 64bit?

Best,
Sebastien

Thanks so much for you help and cheers,
Kai

On 02/13/2018 01:37 PM, Sebastien Besson (Staff) wrote:
Hi Kai,

Follow-up of my answer from yesterday, I performed additional testing using OMERO.insight 5.3.5
against an OMERO 5.3. server (as an aside, very easily created using docker-compose [1]).

Using the vanilla Insight 5.3.5 client, the import of an unsupported Slidebook file, gives a File Not Valid
exception:
<Screen Shot 2018-02-13 at 11.50.08.png>
After putting SlideBook6Reader.jar under the Java folder, the same file uploads correctly to the server
and fails at the metadata processing step server-side since the JAR has not been added there.
<Screen Shot 2018-02-13 at 11.51.54.png>
In summary, this workflow should work on OMERO 5.3.x as well as OMERO 5.4.x. As an indication
that the 3i JAR is properly recognized by Insight, the Format Type dropdown menu in the Importer
window should include an entry called “SlideBook 6 SLD (native)”.

Best,
Sebastien


[1] https://github.com/openmicroscopy/omero-test-infra/blob/v0.2.1/docker-compose.yml

On 12 Feb 2018, at 17:25, Sebastien Besson (Staff) <s.besson at dundee.ac.uk><mailto:s.besson at dundee.ac.uk> wrote:

Hi Kai,

great. From your original exception the following line

java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
    at java.util.ArrayList.rangeCheck(ArrayList.java:653)
    at java.util.ArrayList.get(ArrayList.java:429)
    at loci.formats.in.SlidebookReader.initFile(SlidebookReader.java:654)

indicates that the old Slidebook reader is still used to detect the import candidate rather than
the 3i SlideBook6Reader.

I have tested this workflow: download OMERO.insight, rename the 3i slidebook jar, add it to
the Java folder, start OMERO.Insight, try to import a new Slidebook file and it worked on
OMERO 5.4 (at least it was uploaded to the server which did not know how to read it because
I hadn’t added the JAR there).

I have not tested on OMERO 5.3 but will do tomorrow although i would expect it to work under this
series. Also which operating system are you using for the import?

Best,
Sebastien

On 9 Feb 2018, at 16:21, Kai Schleicher <kai.schleicher at unibas.ch><mailto:kai.schleicher at unibas.ch> wrote:

Hi Sebastian,


Did you rename the file as xxx.jar before putting them under your Java
folder?
yes I did, I renamed it to "SlideBook6Reader.jar". Sorry, I should have written that in my previous mail.

cheers,
Kai

On 02/09/2018 04:21 PM, Sebastien Besson (Staff) wrote:
Hi Kai,


On 9 Feb 2018, at 13:43, Kai Schleicher <kai.schleicher at unibas.ch><mailto:kai.schleicher at unibas.ch> wrote:

Hi Sebastien,

thanks for the update!
We have added the JAR [1] to the insight client as described. Do you think that this one file was is all thats needed or should there be some more JARs?

No the 3i Slidebook JAR should be the only requirement.
Upload unfortunately still fails with "file format not valid", but this time we also receive an exception which might contain some further hints (see below). It seems like it actually tried to read my file but found some issues with it - the file itself is fine, at least it opens with the latest bioformats.

The file format not valid error indicates an error client-side i.e. during the
detection of the file as a format support by Bio-Formats.
I can see you downloaded the file straight away from the 3i Fiji update site.
Did you rename the file as xxx.jar before putting them under your Java
folder?

Sebastien
We are still on OMERO5.3.3, could that be the reason?

Thanks for your help and cheers,
Kai

java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
    at java.util.ArrayList.rangeCheck(ArrayList.java:653)
    at java.util.ArrayList.get(ArrayList.java:429)
    at loci.formats.in.SlidebookReader.initFile(SlidebookReader.java:654)
    at loci.formats.FormatReader.setId(FormatReader.java:1397)
    at loci.formats.ImageReader.setId(ImageReader.java:839)
    at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
    at loci.formats.ChannelFiller.setId(ChannelFiller.java:223)
    at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
    at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:291)
    at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
    at loci.formats.Memoizer.setId(Memoizer.java:649)
    at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
    at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:427)
    at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:576)
    at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:384)
    at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:222)
    at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:174)
    at org.openmicroscopy.shoola.env.data.OMEROGateway.getImportCandidates(OMEROGateway.java:5945)
    at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1068)
    at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:73)
    at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:48)
    at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:97)
    at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
    at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
    at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
    at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
    at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
    at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
    at java.lang.Thread.run(Thread.java:748)

    at org.openmicroscopy.shoola.env.data.util.StatusLabel.update(StatusLabel.java:671)
    at ome.formats.importer.ImportCandidates.safeUpdate(ImportCandidates.java:536)
    at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:471)
    at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:576)
    at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:384)
    at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:222)
    at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:174)
    at org.openmicroscopy.shoola.env.data.OMEROGateway.getImportCandidates(OMEROGateway.java:5945)
    at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1068)
    at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:73)
    at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:48)
    at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:97)
    at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
    at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
    at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
    at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
    at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
    at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
    at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
    at java.util.ArrayList.rangeCheck(ArrayList.java:653)
    at java.util.ArrayList.get(ArrayList.java:429)
    at loci.formats.in.SlidebookReader.initFile(SlidebookReader.java:654)
    at loci.formats.FormatReader.setId(FormatReader.java:1397)
    at loci.formats.ImageReader.setId(ImageReader.java:839)
    at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
    at loci.formats.ChannelFiller.setId(ChannelFiller.java:223)
    at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
    at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:291)
    at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
    at loci.formats.Memoizer.setId(Memoizer.java:649)
    at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
    at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:427)
    ... 16 more



[1] http://sites.imagej.net/SlideBook/jars/bio-formats/SlideBook6Reader.jar-20161214162742

On 02/09/2018 09:21 AM, Sebastien Besson (Staff) wrote:
Hi Kai,

thanks for getting back to us. I realise my initial answer was incomplete to test the
full workflow. In addition to the server addition, you will also need to add the third-party
JARs to the client you will use for the import.

See [1] for adding JARs to OMERO.insight. If you are using the CLI, you need to
add your third-party JARs under lib/client

Best,
Sebastien

[1] http://help.openmicroscopy.org/configure-client.html#jar



On 8 Feb 2018, at 13:56, Kai Schleicher <kai.schleicher at unibas.ch><mailto:kai.schleicher at unibas.ch> wrote:

Hi Sebastien,

thanks for your help!

We have tried and put the jar file under lib/server and restarted the server. However, that seems to not have been enough - upload of *.sld files still fails.

Probably we missed additional steps, but unfortunately it is not too clear to us right now what else needs to happen. Are there additional files that need to be placed at other locations?
Sorry for the vague question...

If you have some more details on that would be greatly appreciated :)

Thanks and cheers,
Kai

On 02/06/2018 06:01 PM, Sebastien Besson (Staff) wrote:
Hi Kai,

Since Bio-Formats 5.2.0, the native support for 3i Slidebook
 files is indeed provided via a external third-party JAR developed and maintained by Intelligent Imaging [1]. In Fiji, the installation of this JAR is managed via the Slidebook update site maintained by 3i.


Adding support for this reader in OMERO should work
 the same way as other server extensions [2]. The critical part is to have the Slidebook classes available to the server, typically by putting the appropriate JAR under lib/server and restarting the latter.


It would be really interesting to hear from the 3i developer
 or support team whether they have tested this workflow or if they have plans to support it in the future.

Best,
Sebastien

[1]

http://blog.openmicroscopy.org/file-formats/community/2016/08/31/bf-partnerships/
[2]

https://docs.openmicroscopy.org/omero/5.4.3/developers/Server/ExtendingOmero.html


On 5 Feb 2018, at 12:26, Kai Schleicher <kai.schleicher at unibas.ch><mailto:kai.schleicher at unibas.ch> wrote:

Dear OME team,

I'd like to import slidebook *.sld files in OMERO.

Since Bio-Formats relies on a plugin from an external update site [1] to enable import of SlideBook SLD files, I was wondering if there is a way to integrate this plugin into our OMERO as well?

Thanks and cheers,
Kai

[1]: http://sites.imagej.net/SlideBook/

--
Please note my NEW PHONE NUMBERS: +41 61 207 57 31 (direct) +41 61 207 22 50 (central)<<
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Phone: +41 61 207 57 31 (direct) +41 61 207 22 50 (central) | kai.schleicher at unibas.ch<mailto:kai.schleicher at unibas.ch> | www.biozentrum.unibas.ch<http://www.biozentrum.unibas.ch/> | www.microscopynetwork.unibas.ch<http://www.microscopynetwork.unibas.ch/>

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