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

Kai Schleicher kai.schleicher at unibas.ch
Thu Mar 8 12:29:18 GMT 2018 

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> 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> 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> 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> 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> 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)<<
>>>>>>>>>>>> Kai Schleicher, PhD | Research Associate in Advanced 
>>>>>>>>>>>> Light Microscopy | Biozentrum, University of Basel 
>>>>>>>>>>>> | Klingelbergstrasse 50/70 | CH-4056 Basel |
>>>>>>>>>>>> Phone: +41 61 207 57 31 (direct) +41 61 207 22 50 (central) 
>>>>>>>>>>>> | kai.schleicher at unibas.ch | www.biozentrum.unibas.ch | 
>>>>>>>>>>>> www.microscopynetwork.unibas.ch
>>>>>>>>>>>>
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>> ome-users mailing list
>>>>>>>>>>>> ome-users at lists.openmicroscopy.org.uk
>>>>>>>>>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> The University of Dundee is a registered Scottish 
>>>>>>>>>>> Charity, No: SC015096
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> ome-users mailing list
>>>>>>>>>>>
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>>>>>>>>>>
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>>>>>>>>>> ome-users mailing list
>>>>>>>>>> ome-users at lists.openmicroscopy.org.uk
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>>>>>>>>>
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>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> ome-users mailing list
>>>>>>>>>
>>>>>>>>> ome-users at lists.openmicroscopy.org.uk
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>>>>>>>>
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>>>>>>
>>>>>
>>>>>
>>>>> The University of Dundee is a registered Scottish Charity, No: 
>>>>> SC015096
>>>>> _______________________________________________
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>>>
>>> <Screenshot from 2018-02-13 14-09-55.png>
>>
>>
>> The University of Dundee is a registered Scottish Charity, No: SC015096
>
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