How to make Mapr show all by default

Usage & Issues
, ,
#1

I’m trying to setup Omero-Mapr to search strain, organism type, etc., following the guide here. On IDR, it seems as though you’re able to browse all mapped annotations without entering a search term, but when I set it up, the Mapr searches are blank by default. Is there a way to show all by default?

Here is how I’ve configured it with Ansible:

      omero_web_apps_config_set:
        omero.web.mapr.config:
          - menu: organism
            config:
              default:
                - Organism
              all: ["Organism"]
              ns:
                - openmicroscopy.org/omero/client/mapAnnotation
              label: Organism
      omero_web_apps_top_links:
        - label: Organisms
          link:
            viewname: maprindex_organism
          attrs:
            title: Find organisms

A follow up question I have is whether the mapped annotations only create a clickable link in the image view if the annotation was added by an administrator. This seems to be how it’s working for me so far, but I’d like the links to be added for any user.

#2

@jsakkos

I believe the answer to your first question is that you need to enable wildcard in the mapr configuration - see e.g. the configuration for the Organism, Cell Line or Phenotype categories in IDR

For the second point, we probably need to test further and get back to you. The development of mapr was driven by the IDR use case which is a read-only public instance with a single data owner so it is possible there are some limitations in the multi-user case.

#3

Thanks @s.besson! That did the trick.

I think it would be quite useful to be able to more easily browse key:value links, in addition to the Mapr interface, but I understand that it might create some problems with a multi-user setup.

#4

@jsakkos

I think it would be quite useful to be able to more easily browse key:value links

Thank you for this. Could you please expand on your suggestion ? Do you maybe imagine something like Tags tab in the OMERO.web ? Or something else ? Any feedback welcome.

Thank you
Petr

OME Team

#5

@pwalczysko

I was thinking something like the Tags tab, but I suppose it’s more complicated with key-value pairs. One way it could be incorporated would be to make both keys and values clickable from the image General tab. Clicking on the link for either a key or a value would then open a Mapr view of that search. It would compliment the current implementation of Mapr, which allows dedicated links for a small subset of important keys (e.g. Organisms), by allowing the user to quickly browse related images from an image of interest.

#6

Hi,
So this behaviour (clicking on Values to link to other Images with the same Key-Value pair) does exist when specifically configured, for example in IDR, clicking the PRM2 link in:

Screenshot 2021-02-17 at 23.06.56
Screenshot 2021-02-17 at 23.06.56682×636 63.5 KB

Will take you to
http://idr.openmicroscopy.org/mapr/gene/?value=PRM2
which allows you to browse a hierarchy down to find images with Gene: PRM2

But it may be more useful to make this the default behaviour without requiring specific configuration. However I’m not sure what this would look like for clicking on the key, eg. Gene. I guess that could take you to the top-level search page for that key, e.g. Webclient

I’ve created an issue for this feedback at All Key-Values browsable · Issue #66 · ome/omero-mapr · GitHub

Many thanks,
Will