Cannot get it to run, maybe "ReferenceError: SharedArrayBuffer is not defined"

[JensWendt]

Hi Will,

I finally got around to testing this. I followed everything for installation, including omero web restart I did not Update MDV, but I hope I do not need this (I am unsure though)?

I open a Project with MDV, select the attached table with ~30k rows of ROI specific measurements on 48 images, and the MDV window opens up as expected (https:///omero_mdv/?dir=config/2664/). But it stays empty. Nothing in omero-web logs. Upon further inspection in the browser (Firefox and Chrome) with F12 it gives me an Error message:

Upon further inspection it seems that MDV recognizes almost all column types of the table as text, although they are supposed to be int or double. Withouth seeing the final result, is this okay?

[xinaesthete]

Hi Jens, SharedArrayBuffer is not defined indicates that it's not running in a secure context which is necessary for MDV. We should really present that information more usefully to the user when it fails.

I should do some testing of Omero-MDV again at some point - probably when my work laptop is finally fixed. I'd encourage you to update MDV as well if you can (I've put quite a bit of work into it in the last few months, especially related to spatial image views as well as some robustness and quality of life - although I don't expect it would fix this issue). Documentation could probably do with some more attention.

Anyway, hope you manage to get it working, and I may try to look into this soon-ish.

Best, Peter

[will-moore]

Hi @JensWendt The part of the install steps required to enable SharedArrayBuffer is:

    $ omero config append omero.web.nginx_server_extra_config '"add_header Cross-Origin-Opener-Policy same-origin;"'
    $ omero config append omero.web.nginx_server_extra_config '"add_header Cross-Origin-Embedder-Policy require-corp;"'

To check if that is working (after web restart), when you open the MDV page itself the initial html page should have those headers and so should the other static js responses:

I'm just running it from the web dev server here using --no-static but the result should be the same.

The Data-types of each column coming from an OMERO.table are derived from the column types in the original table. File ID 12743 in your case. See https://github.com/will-moore/omero-mdv/blob/dbf603440300678919ca85a57a3c1ed723bec167/omero_mdv/utils.py#L224 If you open the table by clicking on it in the webcient right panel under Annotations, or go to /webclient/omero_table/12743/ and you mouse over the column headers, it should say whether they are StringColumn or LongColumn etc.

The omero metadata populate command should now auto-detect column types to set them correctly - see https://github.com/ome/omero-metadata/?tab=readme-ov-file#populate

I assume you used my branch of MDV to build as described?

@xinaesthete unfortunately I never managed to update to a more recent version of MDV and to get it working with omero-mdv. I forget where I had notes on that... So you need to use https://github.com/will-moore/MDV/tree/omero-mdv-build.

[will-moore]

The branch where I was looking to update MDV is at https://github.com/will-moore/omero-mdv/pull/9, but I didn't make any notes there of the issues I was having

[JensWendt]

got it working by adding

# add headers for MDV plugin
add_header 'Cross-Origin-Opener-Policy' 'same-origin';
add_header 'Cross-Origin-Embedder-Policy' 'require-corp';

to /etc/nginx/conf.d/omeroweb.conf There is maybe a typo or the correct version how to add it via the omero web config but I did not have the patience to test that ^^

[will-moore]

@JensWendt - glad you fixed it. Are you sure you regenerated the nginx config after running omero config append omero.web.nginx_server_extra_config... etc? with omero web config nginx etc?

[JensWendt]

@will-moore , eerrrmmm.... if I understand this correctly the omero web config nginx gives me a config snippet that I can copy&paste into the actual omeroweb.conf I did not do this, as I was under the impressions that it will be added automatically into the nginx conf when I add it to the omero conf with the omero.web.nginx_server_extra_config key. Instead I typed it "manually" to the omeroweb.conf, which had the desired effect. Please correct me if I understood this wrong.

[will-moore]

The config commands omero config append omero.web.nginx_server_extra_config... will simply result in a different output from omero web config nginx. omero web config nginx should give you a complete nginx.conf output, but omero-web doesn't know where your config file is, so you need to pipe it to the file yourself. E.g. see https://omero.readthedocs.io/en/stable/sysadmins/unix/install-web/walkthrough/omeroweb-install-rockylinux9-ice3.6.html#configuring-omero-web