Import image

[jburel]

This PR adds a method to import images into OMERO

cc @dominikl
background https://github.com/ome/training-scripts/blob/master/practical/groovy/crop_rectangle_from_image.groovy

Corresponding tests added to ome/openmicroscopy#6212

[joshmoore]

From my experiences with ImportLibrary, I'm going to guess that we will eventually need other signatures for upload methods. Something to be aware of if we will need to deprecate methods in the *Helper class.

There might also be an issue with the Ice communicator and thread pool in the Library which will need cleaning up.

[jburel]

It will be fine to deprecate method when we start working on new methods in the import library
The problem is that all the code is in the clients/scripts and people start to copy/paste such code

[dominikl]

Why is the Connector needed in that case, just to check if the user is logged in?

[jburel]

just to check if we have a connection

[dominikl]

Thanks for adding this method 👍
Generally looks alright and works as expected. The only problem I noticed is that you have to force quit the java process when importing an image. For some reason the import process seems to create a thread which isn't cleaned up by the Gateway.disconnect() method. To test just run it in simple main() method:

public static void main(String[] args) throws Exception {
        LoginCredentials lc = new LoginCredentials("user", "pass", "merge-ci-devspace.openmicroscopy.org");
        Gateway gw = new Gateway(new SimpleLogger());
        ExperimenterData user = gw.connect(lc);
        System.out.println(user.getUserName());
        
        SecurityContext ctx = new SecurityContext(user.getGroupId());
        List<String> paths = Collections.singletonList("cats.jpg");
        boolean result = gw.getFacility(TransferFacility.class).uploadImagesDirect(ctx, paths, null);
        System.out.println(result);

        gw.disconnect();

        System.out.println("Disconnected");
    }

It'll print "Disconnected" but the Java process won't exit. I'll have a look why this happens.

[joshmoore]

Discussed today a holding pattern on this PR to work on the issues above.

[imagesc-bot]

This pull request has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/how-to-eliminate-verbose-messages-on-the-console/37956/4

[sbesson]

Two inline suggestions to use DynamicMetadataOptionsrather than DefaultMetadataOptions as the latter class is completely removed in the IDR fork and this is the source of the failure observed in https://idr-ci.openmicroscopy.org/jenkins/job/OMERO-build-build/250/.

More generally, this makes me wonder whether we should deprecate the DefaultMetadataOptions implementation in Bio-Formats 6.6 @dgault

[jburel]

The import tests associated this PR have failed for the past 3 runs

[jburel]

--exclude

[imagesc-bot]

This pull request has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/api-for-in-place-omero-imports/108420/13