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ome / omero-downloader

An OMERO client for downloading data in bulk from the server.
https://www.openmicroscopy.org/omero/apps/
GNU General Public License v2.0
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Image does not download #36

Closed pwalczysko closed 4 years ago

pwalczysko commented 4 years ago

The image https://nightshade.openmicroscopy.org/webclient/?show=image-4330619 does not download when downloader is deployed on it.

Strangely, also OMERO.web UI original file download fails.

See the original (different topic) issue reported in https://github.com/ome/omero-iviewer/issues/304

cc @mtbc

pwalczysko commented 4 years ago

Interestingly, it also does not export as ome-tiff

(base) pwalczysko@ls31618~/Montpellier/OMERO.downloader-0.2.1$ sh download.sh -b /Users/pwalczysko/Montpellier/fresh -s ni......copy.org -u p...ko -w xxxx  -f ome-tiff Image:4330619
finding target images... done
mapping filesets of images... done
(1/1) commencingcaught unexpected exception: java.lang.NoSuchMethodError: java.nio.ByteBuffer.position(I)Ljava/nio/ByteBuffer;
(base) pwalczysko@ls31618~/Montpellier/OMERO.downloader-0.2.1$
mtbc commented 4 years ago

That looks like a different issue related to the artifact packaging. From the source checkout the export runs fine for me.

pwalczysko commented 4 years ago

The image has 29 G.

Not sure what to make out of the export failure then ?

mtbc commented 4 years ago

Nor I so far. I wonder if it's related to change in dependencies for gateway or something. :man_shrugging: Released artifacts might also be otherwise problematic.

mtbc commented 4 years ago

I am afraid that you must download with -f binary,companion to work around a bug in Bio-Formats that is confusing about which files are companion files. Be especially suspicious of the formats I list in https://trello.com/c/lJtRpXGZ/515-bug-used-files-getters#comment-5af1adc9a3ad6613ca89bbdf.

I tried the OMERO.downloader-0.2.1 release artifact with both Java 8 and 11 and it seems to be running fine for me today!

mtbc commented 4 years ago

(I tried using that same image, also ome-tiff export.)