Files upload but don't deploy - maximum file size limit / ndpi file reading issue?

[AndyBlake]

I'm adding ndpi images to the docker setup and whenever I try with a file larger than 5gb they upload but fail to deploy. Nothing is shouting out in the logs but maybe you can help?

I'm emailing the reporting tar to [email protected] with a link to this issue - thanks in advance for your help

[geektortoise]

Hello,

Regarding your logs, the uploads reached the server but Cytomine was not able to identify the format.

I assume that it is related to this OpenSlide limitation
openslide/openslide#174

[AndyBlake]

You are right, thanks so much for the link - looks like it's fixed in that openslide pull - any idea how I can get that into cytomine?

…

On Wed, 1 Apr 2020, 17:48 geektortoise, ***@***.***> wrote: Hello, Regarding your logs, the uploads reached the server but Cytomine was not able to identify the format. I assume that it is related to this OpenSlide limitation openslide/openslide#174 <openslide/openslide#174> — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#1180 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AALBROQYLW6ITRSMTZVF7ITRKNV6PANCNFSM4LYVC7MA> .

[geektortoise]

Hello,

A first test could be to compile custom Docker images to integrate this OpenSlide version.

OpenSlide is active in two components :

• ims for the image metadata fetching
• iipCyto for the tiling.

The Dockerfile for the iipCyto is here :
https://github.com/cytomine/Dockerfiles/blob/master/iipCyto/Dockerfile#L26
You can change the line by
RUN cd /tmp && git clone https://github.com/ntrahearn/openslide && cd /tmp/openslide && autoreconf -i && ./configure && make && make install

And the same modification for ims
https://github.com/cytomine/Dockerfiles/blob/master/ims/Dockerfile#L41

recompile your Docker images with the docker build -t command (as shown in the Dockerfiles README), restart your Cytomine and it would be ready for a test.

I'm not able to currently make the tests because I don't have one of the concerned image in my test set.

Have a nice day

[geektortoise]

Hello, @AndyBlake

Did you succeed with this operation ?

Have a nice day

[AndyBlake]

Hiya
Sorry for the delay in replying - Even though the hotfix looked like it should have worked when I tried it with some recompiled binaries it still doesn't seem to handle the larger files. When I have fixed this I'll be sure to update this with how I managed to integrate this into the system - thanks for your help and guidance.
Kind regards
Andy