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OMERO 2.7 install - BUILD FAILED

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Re: OMERO 2.7 install - BUILD FAILED

Postby MarkUNSW » Tue Feb 28, 2017 5:12 am

OK we are finally up and running with manual install of all components.

http://149.171.80.223:8080/webclient/public/

Following OMERO.insight log in, I have now tried to upload some test JPEGXR format images created using photoshop from original uncompressed tiff file and have the error screen "unknown format".

Screen Shot 2017-02-28 at 3.58.35 pm.png
JXR fail upload screen
Screen Shot 2017-02-28 at 3.58.35 pm.png (85.47 KiB) Viewed 2867 times


Screen Shot 2017-02-28 at 4.05.06 pm.png
OMERO.insight version screen
Screen Shot 2017-02-28 at 4.05.06 pm.png (53.43 KiB) Viewed 2867 times
MarkUNSW
 
Posts: 13
Joined: Wed Oct 29, 2014 2:10 am

Re: OMERO 2.7 install - BUILD FAILED

Postby MarkUNSW » Tue Feb 28, 2017 5:20 am

OMERO.insight log file.

2017-02-28 15:56:31,365 INFO [ o.o.shoola.env.data.DataServicesFactory] (nitializer) Server version: 5.2.7
Client version: 5.2.7-ice35-b40
os_version: 10.12.3
java_version: 1.8.0_121
os_arch: x86_64
os_name: Mac OS X

2017-02-28 15:56:31,471 INFO [ o.o.s.env.data.login.LoginServiceImpl] (nitializer) Logged onto OMERO at: 149.171.80.223
User Name: MarkUNSW -- Password: ********

2017-02-28 15:56:32,307 WARN [ o.o.s.a.m.editor.AnnotationTaskPane] (nitializer) UI for displaying ROIS annotations not implemented yet!
2017-02-28 15:56:32,932 DEBUG [ omero.gateway.facility.Facility$1] ( Thread-16) Created new BrowseFacility
2017-02-28 15:58:22,568 INFO [ ome.formats.importer.ImportConfig] ( Thread-22) OMERO Version: 5.2.7-ice35-b40
2017-02-28 15:58:22,569 INFO [ ome.formats.importer.ImportConfig] ( Thread-22) Bioformats version: 5.1.10 revision: 3125500841deff07687b25eb3f430dca62dee648 date: 6 May 2016
2017-02-28 15:58:22,591 INFO [ ome.formats.importer.ImportCandidates] ( Thread-22) Depth: 4 Metadata Level: MINIMUM
2017-02-28 15:58:22,649 INFO [ ome.formats.importer.ImportCandidates] ( Thread-22) 1 file(s) parsed into 0 group(s) with 1 call(s) to setId in 54ms. (58ms total) [1 unknowns]
2017-02-28 15:58:22,651 INFO [ ome.formats.importer.ImportConfig] ( Thread-22) OMERO Version: 5.2.7-ice35-b40
2017-02-28 15:58:22,651 INFO [ ome.formats.importer.ImportConfig] ( Thread-22) Bioformats version: 5.1.10 revision: 3125500841deff07687b25eb3f430dca62dee648 date: 6 May 2016
2017-02-28 15:58:22,653 INFO [ ome.formats.importer.ImportCandidates] ( Thread-22) Depth: 4 Metadata Level: MINIMUM
2017-02-28 15:58:22,733 INFO [ ome.formats.importer.ImportCandidates] ( Thread-22) 1 file(s) parsed into 0 group(s) with 1 call(s) to setId in 76ms. (80ms total) [1 unknowns]
2017-02-28 15:58:22,734 INFO [ ome.formats.importer.ImportConfig] ( Thread-22) OMERO Version: 5.2.7-ice35-b40
2017-02-28 15:58:22,734 INFO [ ome.formats.importer.ImportConfig] ( Thread-22) Bioformats version: 5.1.10 revision: 3125500841deff07687b25eb3f430dca62dee648 date: 6 May 2016
2017-02-28 15:58:22,736 INFO [ ome.formats.importer.ImportCandidates] ( Thread-22) Depth: 4 Metadata Level: MINIMUM
2017-02-28 15:58:22,790 INFO [ ome.formats.importer.ImportCandidates] ( Thread-22) 1 file(s) parsed into 0 group(s) with 1 call(s) to setId in 52ms. (54ms total) [1 unknowns]
2017-02-28 15:59:38,301 INFO [ ome.formats.importer.ImportConfig] ( Thread-23) OMERO Version: 5.2.7-ice35-b40
2017-02-28 15:59:38,301 INFO [ ome.formats.importer.ImportConfig] ( Thread-23) Bioformats version: 5.1.10 revision: 3125500841deff07687b25eb3f430dca62dee648 date: 6 May 2016
2017-02-28 15:59:38,303 INFO [ ome.formats.importer.ImportCandidates] ( Thread-23) Depth: 4 Metadata Level: MINIMUM
2017-02-28 15:59:38,351 INFO [ ome.formats.importer.ImportCandidates] ( Thread-23) 1 file(s) parsed into 0 group(s) with 1 call(s) to setId in 44ms. (48ms total) [1 unknowns]
2017-02-28 15:59:38,352 INFO [ ome.formats.importer.ImportConfig] ( Thread-23) OMERO Version: 5.2.7-ice35-b40
2017-02-28 15:59:38,353 INFO [ ome.formats.importer.ImportConfig] ( Thread-23) Bioformats version: 5.1.10 revision: 3125500841deff07687b25eb3f430dca62dee648 date: 6 May 2016
2017-02-28 15:59:38,354 INFO [ ome.formats.importer.ImportCandidates] ( Thread-23) Depth: 4 Metadata Level: MINIMUM
2017-02-28 15:59:38,432 INFO [ ome.formats.importer.ImportCandidates] ( Thread-23) 1 file(s) parsed into 0 group(s) with 1 call(s) to setId in 76ms. (78ms total) [1 unknowns]
2017-02-28 15:59:38,433 INFO [ ome.formats.importer.ImportConfig] ( Thread-23) OMERO Version: 5.2.7-ice35-b40
2017-02-28 15:59:38,433 INFO [ ome.formats.importer.ImportConfig] ( Thread-23) Bioformats version: 5.1.10 revision: 3125500841deff07687b25eb3f430dca62dee648 date: 6 May 2016
2017-02-28 15:59:38,462 INFO [ ome.formats.importer.ImportCandidates] ( Thread-23) Depth: 4 Metadata Level: MINIMUM
2017-02-28 15:59:38,524 INFO [ ome.formats.importer.ImportCandidates] ( Thread-23) 1 file(s) parsed into 0 group(s) with 1 call(s) to setId in 61ms. (62ms total) [1 unknowns]
2017-02-28 16:15:29,486 INFO [ ome.formats.importer.ImportConfig] ( Thread-34) OMERO Version: 5.2.7-ice35-b40
2017-02-28 16:15:29,487 INFO [ ome.formats.importer.ImportConfig] ( Thread-34) Bioformats version: 5.1.10 revision: 3125500841deff07687b25eb3f430dca62dee648 date: 6 May 2016
2017-02-28 16:15:29,497 INFO [ ome.formats.importer.ImportCandidates] ( Thread-34) Depth: 4 Metadata Level: MINIMUM
2017-02-28 16:15:29,554 INFO [ ome.formats.importer.ImportCandidates] ( Thread-34) 1 file(s) parsed into 0 group(s) with 1 call(s) to setId in 55ms. (58ms total) [1 unknowns]
2017-02-28 16:15:29,555 INFO [ ome.formats.importer.ImportConfig] ( Thread-34) OMERO Version: 5.2.7-ice35-b40
2017-02-28 16:15:29,555 INFO [ ome.formats.importer.ImportConfig] ( Thread-34) Bioformats version: 5.1.10 revision: 3125500841deff07687b25eb3f430dca62dee648 date: 6 May 2016
2017-02-28 16:15:29,557 INFO [ ome.formats.importer.ImportCandidates] ( Thread-34) Depth: 4 Metadata Level: MINIMUM
2017-02-28 16:15:29,674 INFO [ ome.formats.importer.ImportCandidates] ( Thread-34) 1 file(s) parsed into 0 group(s) with 1 call(s) to setId in 115ms. (117ms total) [1 unknowns]
2017-02-28 16:15:29,675 INFO [ ome.formats.importer.ImportConfig] ( Thread-34) OMERO Version: 5.2.7-ice35-b40
2017-02-28 16:15:29,676 INFO [ ome.formats.importer.ImportConfig] ( Thread-34) Bioformats version: 5.1.10 revision: 3125500841deff07687b25eb3f430dca62dee648 date: 6 May 2016
2017-02-28 16:15:29,679 INFO [ ome.formats.importer.ImportCandidates] ( Thread-34) Depth: 4 Metadata Level: MINIMUM
2017-02-28 16:15:29,782 INFO [ ome.formats.importer.ImportCandidates] ( Thread-34) 1 file(s) parsed into 0 group(s) with 1 call(s) to setId in 101ms. (104ms total) [1 unknowns]
MarkUNSW
 
Posts: 13
Joined: Wed Oct 29, 2014 2:10 am

Re: OMERO 2.7 install - BUILD FAILED

Postby MarkUNSW » Tue Feb 28, 2017 5:25 am

Uploads original tiff file OK. M

Screen Shot 2017-02-28 at 4.23.30 pm.png
original tiff
Screen Shot 2017-02-28 at 4.23.30 pm.png (78.09 KiB) Viewed 2865 times
MarkUNSW
 
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Re: OMERO 2.7 install - BUILD FAILED

Postby sbesson » Tue Feb 28, 2017 10:30 am

Hi Mark,

glad to hear your server is up and running. OMERO 5.2 has generally no support for JPEG-XR compressed images so the import errors you are receiving are completely expected. Is there a particular reason for using these types of images in addition to your plain TIFF which imported correctly?

OMERO 5.3.0 will include some support for JPEG-XR compression initially in the context of Zeiss CZI files only. However the jxr files you tried to upload remain unsupported by Bio-Formats and hence OMERO.

Best,
Sebastien
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Re: OMERO 2.7 install - BUILD FAILED

Postby MarkUNSW » Sun Mar 05, 2017 4:00 am

Thanks Sebastian,

Yes I do have CZI files from a Zeiss Axioscanner. The images are being converted into JPGXR as we do not have the server space to store the uncompressed images. I thought the December updated software would support JPGXR images, hence I wanted to test their import with Omero.insight. I guess I still have to wait for 5.3. M
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Posts: 13
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