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Hi Kai,
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<blockquote type="cite" class="">
<div class="">On 9 Feb 2018, at 13:43, Kai Schleicher <<a href="mailto:kai.schleicher@unibas.ch" class="">kai.schleicher@unibas.ch</a>> wrote:</div>
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<p class="">Hi Sebastien,</p>
<p class="">thanks for the update!<br class="">
</p>
<p class="">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?
</p>
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No the 3i Slidebook JAR should be the only requirement.<br class="">
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<p class="">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 -
<a moz-do-not-send="true" href="https://filesender.switch.ch/filesender/?vid=20c7b50f-f673-e329-1276-00007a6287f3" class="">
the file itself</a> is fine, at least it opens with the latest bioformats.</p>
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<div>The file format not valid error indicates an error client-side i.e. during the</div>
<div>detection of the file as a format support by Bio-Formats.</div>
I can see you downloaded the file straight away from the 3i Fiji update site.</div>
<div>Did you rename the file as xxx.jar before putting them under your Java</div>
<div>folder?</div>
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</div>
<div>Sebastien<br class="">
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<p class="">We are still on OMERO5.3.3, could that be the reason?</p>
<p class="">Thanks for your help and cheers,<br class="">
Kai<br class="">
</p>
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</p>
<blockquote type="cite" class="">java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
<br class="">
at java.util.ArrayList.rangeCheck(ArrayList.java:653) <br class="">
at java.util.ArrayList.get(ArrayList.java:429) <br class="">
at loci.formats.in.SlidebookReader.initFile(SlidebookReader.java:654) <br class="">
at loci.formats.FormatReader.setId(FormatReader.java:1397) <br class="">
at loci.formats.ImageReader.setId(ImageReader.java:839) <br class="">
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650) <br class="">
at loci.formats.ChannelFiller.setId(ChannelFiller.java:223) <br class="">
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650) <br class="">
at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:291) <br class="">
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650) <br class="">
at loci.formats.Memoizer.setId(Memoizer.java:649) <br class="">
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650) <br class="">
at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:427)<br class="">
at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:576)<br class="">
at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:384) <br class="">
at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:222)<br class="">
at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:174)<br class="">
at org.openmicroscopy.shoola.env.data.OMEROGateway.getImportCandidates(OMEROGateway.java:5945)<br class="">
at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1068)<br class="">
at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:73)<br class="">
at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:48)<br class="">
at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:97)<br class="">
at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)<br class="">
at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)<br class="">
at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)<br class="">
at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)<br class="">
at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)<br class="">
at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)<br class="">
at java.lang.Thread.run(Thread.java:748) <br class="">
<br class="">
at org.openmicroscopy.shoola.env.data.util.StatusLabel.update(StatusLabel.java:671)<br class="">
at ome.formats.importer.ImportCandidates.safeUpdate(ImportCandidates.java:536)<br class="">
at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:471)<br class="">
at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:576)<br class="">
at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:384) <br class="">
at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:222)<br class="">
at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:174)<br class="">
at org.openmicroscopy.shoola.env.data.OMEROGateway.getImportCandidates(OMEROGateway.java:5945)<br class="">
at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1068)<br class="">
at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:73)<br class="">
at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:48)<br class="">
at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:97)<br class="">
at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)<br class="">
at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)<br class="">
at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)<br class="">
at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)<br class="">
at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)<br class="">
at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)<br class="">
at java.lang.Thread.run(Thread.java:748) <br class="">
Caused by: java.lang.IndexOutOfBoundsException: Index: 0, Size: 0 <br class="">
at java.util.ArrayList.rangeCheck(ArrayList.java:653) <br class="">
at java.util.ArrayList.get(ArrayList.java:429) <br class="">
at loci.formats.in.SlidebookReader.initFile(SlidebookReader.java:654) <br class="">
at loci.formats.FormatReader.setId(FormatReader.java:1397) <br class="">
at loci.formats.ImageReader.setId(ImageReader.java:839) <br class="">
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650) <br class="">
at loci.formats.ChannelFiller.setId(ChannelFiller.java:223) <br class="">
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650) <br class="">
at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:291) <br class="">
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650) <br class="">
at loci.formats.Memoizer.setId(Memoizer.java:649) <br class="">
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650) <br class="">
at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:427)<br class="">
... 16 more </blockquote>
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<p class="">[1] <a class="moz-txt-link-freetext" href="http://sites.imagej.net/SlideBook/jars/bio-formats/SlideBook6Reader.jar-20161214162742">
http://sites.imagej.net/SlideBook/jars/bio-formats/SlideBook6Reader.jar-20161214162742</a>
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<div class="moz-cite-prefix">On 02/09/2018 09:21 AM, Sebastien Besson (Staff) wrote:<br class="">
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<blockquote type="cite" cite="mid:628D5921-7BE8-4FEC-9B0C-6A07DFC959BA@dundee.ac.uk" class="">
Hi Kai,
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</div>
<div class="">thanks for getting back to us. I realise my initial answer was incomplete to test the</div>
<div class="">full workflow. In addition to the server addition, you will also need to add the third-party</div>
<div class="">JARs to the client you will use for the import. </div>
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</div>
<div class="">See [1] for adding JARs to OMERO.insight. If you are using the CLI, you need to</div>
<div class="">add your third-party JARs under lib/client</div>
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</div>
<div class="">Best,</div>
<div class="">Sebastien</div>
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</div>
<div class="">[1] <a href="http://help.openmicroscopy.org/configure-client.html#jar" class="" moz-do-not-send="true">http://help.openmicroscopy.org/configure-client.html#jar</a></div>
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</div>
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<blockquote type="cite" class="">
<div class="">On 8 Feb 2018, at 13:56, Kai Schleicher <<a href="mailto:kai.schleicher@unibas.ch" class="" moz-do-not-send="true">kai.schleicher@unibas.ch</a>> wrote:</div>
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<p class="">Hi Sebastien,</p>
<p class="">thanks for your help!</p>
<p class="">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.</p>
<p class="">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?
<br class="">
</p>
<p class="">Sorry for the vague question...</p>
<p class="">If you have some more details on that would be greatly appreciated :)</p>
<p class="">Thanks and cheers,<br class="">
Kai<br class="">
</p>
<br class="">
<div class="moz-cite-prefix">On 02/06/2018 06:01 PM, Sebastien Besson (Staff) wrote:<br class="">
</div>
<blockquote type="cite" cite="mid:6F15D1CF-4BC8-4AE1-AC2D-721D729E3D16@dundee.ac.uk" class="">
<div style="line-height: 1.38; margin-top: 0pt;
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<span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Hi Kai,</span></div>
<br class="">
<div style="line-height: 1.38; margin-top: 0pt;
margin-bottom: 0pt;" class="">
<span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">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.</span></div>
<br class="">
<div style="line-height: 1.38; margin-top: 0pt;
margin-bottom: 0pt;" class="">
<span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">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.</span></div>
<br class="">
<div style="line-height: 1.38; margin-top: 0pt;
margin-bottom: 0pt;" class="">
<span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">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.</span></div>
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margin-bottom: 0pt;" class="">
<span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class=""></span><span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Best,</span></div>
<div style="line-height: 1.38; margin-top: 0pt;
margin-bottom: 0pt;" class="">
<span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Sebastien</span></div>
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<span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">[1]
</span><a href="http://blog.openmicroscopy.org/file-formats/community/2016/08/31/bf-partnerships/" style="text-decoration:none;" class="" moz-do-not-send="true"><span style="font-size: 11pt; font-family: Arial; color: rgb(17, 85, 204); font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; text-decoration: underline; -webkit-text-decoration-skip: none; vertical-align: baseline; white-space: pre-wrap;" class="">http://blog.openmicroscopy.org/file-formats/community/2016/08/31/bf-partnerships/</span></a><span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">
</span></div>
<div style="line-height: 1.38; margin-top: 0pt;
margin-bottom: 0pt;" class="">
<span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">[2]
</span><a href="https://docs.openmicroscopy.org/omero/5.4.3/developers/Server/ExtendingOmero.html" style="text-decoration:none;" class="" moz-do-not-send="true"><span style="font-size: 11pt; font-family: Arial; color: rgb(17, 85, 204); font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; text-decoration: underline; -webkit-text-decoration-skip: none; vertical-align: baseline; white-space: pre-wrap;" class="">https://docs.openmicroscopy.org/omero/5.4.3/developers/Server/ExtendingOmero.html</span></a></div>
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<blockquote type="cite" class="">
<div class="">On 5 Feb 2018, at 12:26, Kai Schleicher <<a href="mailto:kai.schleicher@unibas.ch" class="" moz-do-not-send="true">kai.schleicher@unibas.ch</a>> wrote:</div>
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<div class="">Dear OME team,<br class="">
<br class="">
I'd like to import slidebook *.sld files in OMERO.<br class="">
<br class="">
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?<br class="">
<br class="">
Thanks and cheers,<br class="">
Kai<br class="">
<br class="">
[1]: <a href="http://sites.imagej.net/SlideBook/" class="" moz-do-not-send="true">
http://sites.imagej.net/SlideBook/</a><br class="">
<br class="">
-- <br class="">
<blockquote type="cite" class="">
<blockquote type="cite" class="">Please note my NEW PHONE NUMBERS: +41 61 207 57 31 (direct) +41 61 207 22 50 (central)<<<br class="">
</blockquote>
</blockquote>
Kai Schleicher, PhD | Research Associate in Advanced Light Microscopy | Biozentrum, University of Basel | Klingelbergstrasse 50/70 | CH-4056 Basel |<br class="">
Phone: +41 61 207 57 31 (direct) +41 61 207 22 50 (central) | <a href="mailto:kai.schleicher@unibas.ch" class="" moz-do-not-send="true">
kai.schleicher@unibas.ch</a> | <a href="http://www.biozentrum.unibas.ch/" class="" moz-do-not-send="true">
www.biozentrum.unibas.ch</a> | <a href="http://www.microscopynetwork.unibas.ch/" class="" moz-do-not-send="true">
www.microscopynetwork.unibas.ch</a><br class="">
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