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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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Exception: no repository known with hash #45

Open joshmoore opened 3 years ago

joshmoore commented 3 years ago

I tried the latest version but I can’t get past the error below. I don’t know what ‘repository’ is in this context so I don’t know if I’m missing something, and I can’t see it in the guide (https://omero-guides.readthedocs.io/en/latest/download/docs/download.html). Is it a bug or am I just not holding it right?

Thanks,

Michael.

C:\Users\mporter\Downloads\OMERO.downloader-0.2.2-release\OMERO.downloader-0.2.2
>download.bat -b .\tmp\repo -s nightshade.openmicroscopy.org -u mike -w ***** -f
binary Image:4329667
cannot retrieve repositories
finding target images... done
mapping filesets of images...caught unexpected exception: java.lang.IllegalState
Exception: no repository known with hash 065ab24b-3979-46db-8853-dd8dfc9235f9

From: Josh Moore [mailto:notifications@github.com] Sent: 11 November 2020 08:13 To: ome/omero-web omero-web@noreply.github.com Cc: Michael Porter (Staff) m.porter@dundee.ac.uk; Mention mention@noreply.github.com Subject: Re: [ome/omero-web] Improve user experience with large image downloads (#241)

see also: https://trello.com/c/HXHVwDXg/140-omeroweb-download-issue

@mporter-grehttps://github.com/mporter-gre, you might also try https://github.com/ome/omero-downloader in the mean time.

Originally posted by @mporter-gre in https://github.com/ome/omero-web/issues/241#issuecomment-725314445

dominikl commented 3 years ago

Unfortunately I can't replicate the problem. Tested latest version against nightshade and merge-ci. Or could it be a file size problem? Tested only with a ~500mb czi file.

joshmoore commented 3 years ago

I wonder if this comes down to @mporter-gre's special status as user:1 on nightshade...

mporter-gre commented 3 years ago

Hi Dominik

The problem was happening over the 500 MB mark. I can supply a file if needed?

Michael.

From: Dominik Lindner notifications@github.com Sent: 12 November 2020 1:19 PM To: ome/omero-downloader omero-downloader@noreply.github.com Cc: Michael Porter (Staff) m.porter@dundee.ac.uk; Mention mention@noreply.github.com Subject: Re: [ome/omero-downloader] Exception: no repository known with hash (#45)

Unfortunately I can't replicate the problem. Tested latest version against nightshade and merge-ci. Or could it be a file size problem? Tested only with a ~500mb czi file.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/ome/omero-downloader/issues/45#issuecomment-726072092, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABCH44EQYCIITCUQFEUYDW3SPPOFBANCNFSM4TR2E35A.

The University of Dundee is a registered Scottish Charity, No: SC015096

joshmoore commented 3 years ago

I can supply a file if needed?

Definitely can't hurt to retry the exact file.

mporter-gre commented 3 years ago

Happy to! What’s the preferred method these days?

From: Josh Moore notifications@github.com Sent: 12 November 2020 3:09 PM To: ome/omero-downloader omero-downloader@noreply.github.com Cc: Michael Porter (Staff) m.porter@dundee.ac.uk; Mention mention@noreply.github.com Subject: Re: [ome/omero-downloader] Exception: no repository known with hash (#45)

I can supply a file if needed?

Definitely can't hurt to retry the exact file.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/ome/omero-downloader/issues/45#issuecomment-726136540, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABCH44C2NZVJFK5OE2EECKTSPP3BJANCNFSM4TR2E35A.

The University of Dundee is a registered Scottish Charity, No: SC015096

joshmoore commented 3 years ago

Happy to! What’s the preferred method these days?

Perhaps just the ID on nightshade?

Edit: Doh. I have that above. I'll give it a try.

joshmoore commented 3 years ago

Ha. As root or myself (an admin), I see:

finding target images... done
mapping filesets of images... done
(1/1) determining files used by image 4329667... done
(1/1, 0/0) no files to download for image 4329667

As mike (group member) or jason (group owner), I see the error above.

mporter-gre commented 3 years ago

Absolutely. The id of the first image of the set is 4392224. The dataset is 79727.

From: Josh Moore notifications@github.com Sent: 12 November 2020 3:11 PM To: ome/omero-downloader omero-downloader@noreply.github.com Cc: Michael Porter (Staff) m.porter@dundee.ac.uk; Mention mention@noreply.github.com Subject: Re: [ome/omero-downloader] Exception: no repository known with hash (#45)

Happy to! What’s the preferred method these days?

Perhaps just the ID on nightshade?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/ome/omero-downloader/issues/45#issuecomment-726137989, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABCH44DPP5GPKTSTCZ2JKF3SPP3JPANCNFSM4TR2E35A.

The University of Dundee is a registered Scottish Charity, No: SC015096

joshmoore commented 2 years ago

I see the same thing as myself.

pwalczysko commented 2 years ago

@joshmoore not sure if this is very valuable, but might exclude the "special user owning the image" suspicion. I have downloaded the image using OMERO.web and re-imported it into ns server as myself. Then went on to attempt to download it (now the image is owned by me and I am the downloading agent too).

Result is

./download.sh -b /tmp/repo -s nightshade.openmicroscopy.org -u pxxx -w xxx  -f binary Image:4471884
finding target images.... done
mapping filesets of images... done
(1/1) determining files used by image 4471884... done
(1/1, 0/0) no files to download for image 4471884