High level scripting API to run UI commands ?

[Rdornier]

Hi @Rylern

I'm working on a script to delete ROIs from specific owners on OMERO (the script is not doing only that ; doing analysis and send ROIs as well).

Currently, I've found that I can use:

omeroImageServer.getClient().getApisHandler().deleteShapes(
                omeroImageServer.getId(),
                ownerIdsToDelete
        ).get()

However, this requires a list of owner IDs rather than usernames. Since users typically work with usernames (which are more accessible than IDs ; IDs are only accessible by admins and users cannot find them), I was wondering if there's a way to retrieve user information from usernames using the current API. The ICE API allows that with gateway.getFacility(AdminFacility.class).lookupExperimenter(ctx, username).getId().

Additionally, I would like to know how I can run menu commands via scripting. For example, if I want to send annotations & measurements to OMERO while deleting existing ones owned by the current user, I'd like to keep the same logic implemented in the menu commands but I couldn't find any accessible methods reflecting that. I noticed there are individual methods like deleteShapes(), deleteAttachments(), and addShapes(), which are the ones used in the sample scripts, but I'm wondering if there are higher-level methods similar to these examples. which are way more convenient to run and which keep all the logic/checks that are made in the code, to not re-implement them each time in a new script.

Let me know if I'm missing something in the current API.

Best,

Rémy.

ping @romainGuiet

[Rylern]

I added a function to easily convert an experimenter name to an experimenter ID. I also updated the sample scripts to use this function, as well as other improvements to replicate what's happening when a menu command is run. Everything is available on v0.2.3.

Does that solve the issue?

[Rdornier]

Hi @Rylern

Thanks for the updated plugin. It's a indeed better now, but writing the full name is to get ids is not ideal.
For me, for example, I have to write Rémy Jean Daniel Dornier, with accents, etc, whereas if you can get the username (i.e. getOmeName()), it will be shorter and more convenient (also for people with rather long names).

Moreover, I think usernames should be unique in the database (this is true when OMERO is linked to LDAP), whereas the full name, not, if there are homonyms.

[Rylern]

That's true, but my concern was that the usernames are not easy to find on OMERO (except your own one), whereas the full names are displayed everywhere. Don't you think that's an issue? Do you know an easy way for a regular user to get the usernames of other users? For example when several users annotated the same image.

[Rdornier]

There are ways here and here, but it's all using the Java API.

Actually, I filtered owners in this method. Basically,

• get the owner ID of the ROIs (or other objects)
• retrieve the Experimenter object from the owner id
• compare the current owner username with the one given by the user
• keep only ROIs with matching owner

That's true, but my concern was that the usernames are not easy to find on OMERO (except your own one), whereas the full names are displayed everywhere. Don't you think that's an issue?

When you get an experimenter from the JSON API, the username should come with the object, right ? If this is not the case, then, yes, it's an issue. On my side, I managed to get it with https://host/api/v0/m/experimenters/id/

[Rylern]

That's not exactly what I meant. It is easy for me to get the usernames of experimenters, there will be a new method getUsername() in the Experimenter class as soon as #125 is merged.

My concern was about using usernames in the sample scripts. If a regular user wants to create a script that deletes annotations of specific users and there was a function like deleteAnnotations(imageId, usernames), then the user would have to define the usernames, which are not easily findable (as far as I know). When you browse an OMERO server, you often see the names of users, but not their usernames. What do you think?

[Rdornier]

Ah, I see now... Sorry for the confusion ; I didn't think about that, and it's indeed a good point.

Then, I would do the following

• keeping the function deleteAnnotations(imageId, usernames)
• introducing another function getUsernameFromFullName(fullName) to get the username

Doing like this, there is the possibility to use the short and unique user identifier directly, or to get it via the full name (which can be identical for both users => we have the case for one user). In such case, maybe checking the group of both users can help discriminating the right one ? If they are in the same group, then, we cannot do more.

[Rylern]

I added the possibility to use usernames in v0.2.4. Does that solve this issue?

[Rdornier]

That's good, yes, thanks ! Maybe one last point: I think it is missing a way to delete all annotations, whatever the owner, without having to manually enter the fullname/username of all of them. I've seen that providing a user Id of -1 is doing the job. So, maybe adding in the template scripts a way to handle this case will be the last feature I see to provide a full convenient pipeline.

It can simply be adding in the annotationOwner list allOwners, and this will create a list of owner ids with -1.

if(annotationOwners.contains('allOwners')){
      userIds = [-1]
}else{
      userIds = ....
}

[Rylern]

I added the possilbity to delete annotations and attachments of all users in the last commit. I'll wait a bit before making a new release since #24 may be fixed soon (see ome/omero-gateway-java#110)

[Rdornier]

Sounds good !
Thanks a lot !