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

Kai Schleicher kai.schleicher at unibas.ch
Wed Mar 7 16:37:01 GMT 2018 

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
>>>>>>>>>>
>>>>>>>>>> ome-users at lists.openmicroscopy.org.uk
>>>>>>>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>>>>>>>
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>>>>>>>>> ome-users mailing list
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>>>>>>>>
>>>>>>>>
>>>>>>>> The University of Dundee is a registered Scottish Charity, No: 
>>>>>>>> SC015096
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> 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
>>>>>
>>>>
>>>>
>>>> The University of Dundee is a registered Scottish Charity, No: SC015096
>>>> _______________________________________________
>>>> ome-users mailing list
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>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>
>>>
>>> The University of Dundee is a registered Scottish Charity, No: SC015096
>>
>> <Screenshot from 2018-02-13 14-09-55.png>
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096 

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