OMERO 2.7 install - BUILD FAILED

[MarkUNSW]

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".

JXR fail upload screen

Screen Shot 2017-02-28 at 3.58.35 pm.png (85.47 KiB) Viewed 2869 times

OMERO.insight version screen

Screen Shot 2017-02-28 at 4.05.06 pm.png (53.43 KiB) Viewed 2869 times

[MarkUNSW]

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]

Uploads original tiff file OK. M

original tiff

Screen Shot 2017-02-28 at 4.23.30 pm.png (78.09 KiB) Viewed 2867 times

[sbesson]

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

[MarkUNSW]

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