OMERO.web openwith URL

An OMERO.web plugin for opening images via configured URLs:

$ omero config append omero.web.apps '"omero_openwith_url"'

$ omero config append omero.web.open_with '["openwith_url", "https://hms-dbmi.github.io/vizarr?source=https%3A%2F%2Fs3.embassy.ebi.ac.uk%2Fidr%2Fzarr%2Fv0.1%2F$ID.zarr", {"script_url": "omero_openwith_url/openwith.js", "label":"vizarr"}]'

Dev install:

$ cd omero_openwith_url
$ pip install -e .

Or install from master branch on github:

pip install git+https://github.com/ome/omero-openwith-url.git@master#egg=omero-openwith-url

How it works

The open_with config above adds an vizarr option to the Open-with menu of webclient. It also loads the static/omero_openwith_url/openwith.js script into the webclient.

When the open-with contextmenu is opened, we use the Image ID to ping https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.1/IMAGE_ID.zarr/.zgroup. If we get any error, the Open-with > vizarr menu item is disabled.

If the menu item it clicked, we Open the url configured above, replacing the $ID with the ID of the chosen Image.

NB: to enable testing this when the actual ID of the Image doesn't match the IDR ID.zarr (when we're not running this on IDR itself), if the Image name starts with a number, so that parseInt(name) gives us a number, that will be used instead of the image ID e.g. Name an Image like 6001240_B1_C1.tif to Open 6001240.zarr.