Note

This documentation is for the new OMERO 5.2 version. See the latest OMERO 5.1.x version or the previous versions page to find documentation for the OMERO version you are using if you have not upgraded yet.

Search bridges

A “bridge” is the mapping between your metadata and how it is stored in the  Lucene index. OMERO search uses one internal bridge to parse all of your metadata for later searching. If, however, there is more metadata that you would like to add to the index, you can implement the org.hibernate.search.bridge.FieldBridge interface yourself, or subclass the helper class components/server/src/ome/services/fulltext/BridgeHelper.java

Example

Assume you wanted to be able to search for a project based on the name of all images contained in that project. In the set method,

public void set(final String name, final Object value,
        final Document document, final Field.Store store,
        final Field.Index index, final Float boost) {

you would need to add a field to the Document for each Image.

Project p = (Project) value;
List<Image> images = getImages(p);
for (Image image : images) {
        add(document, "image_name", image.getName(), store, index, boost);

 }

Configuration

Custom bridges are configured in Search but can be overridden via the standard configuration mechanisms. The omero.search.bridges property defines a comma-separated list of bridge classes which will be passed to components/server/src/ome/services/fulltext/FullTextBridge.java.

See Java deployment for how to have your bridge classes included on the server’s classpath if it doesn’t get built by the Build System.

Available bridges

See components/server/src/ome/services/fulltext/bridges for a list of provided (example) bridges.

Re-indexing

BridgeHelper provides two methods – reindex(IObject) and reindexAll(List<IObject>) – for keeping the indexes for objects in sync.

For example, if the image.name above were to be changed, the index for the Project would be stale until the Project itself were re-indexed. Custom bridges can call reindex(Project) while indexing the image to have the Project re-indexed from the backlog. Before any new changes are processed, the backlog is always first cleared. One caveat: while processing the backlog, no new objects can be added to it.

For bridge writers, this means concretely that implementations should check for all related types and index them in groups, rather than relying on transitivity. For example,

       if (value instanceof Project) {
            final Project p = (Project) value;
            handleProject(p, document, store, index, boost);

            for (final ProjectDatasetLink pdl : p.unmodifiableDatasetLinks()) {
                final Dataset d = pdl.child();
                reindex.add(d);
                handleDataset(d, document, store, index, boost);

                for (final DatasetImageLink dil : d.unmodifiableImageLinks()) {
                    final Image i = dil.child();
                    reindex.add(i);
                    handleImage(document, store, index, two_step_boost, i);
                }
            }
        } else if (value instanceof Dataset) {
            final Dataset d = (Dataset) value;
            handleDataset(d, document, store, index, boost);

            for (final ProjectDatasetLink pdl : d.unmodifiableProjectLinks()) {
                final Project p = pdl.parent();
                reindex.add(p);
                handleProject(p, document, store, index, two_step_boost);
            }

            for (final DatasetImageLink dil : d.unmodifiableImageLinks()) {
                final Image i = dil.child();
                reindex.add(i);
                handleImage(document, store, index, two_step_boost, i);
            }

        } else if (value instanceof Image) {

            final Image i = (Image) value;
            handleImage(document, store, index, two_step_boost, i);


            for (final DatasetImageLink dil : i.unmodifiableDatasetLinks()) {
                final Dataset d = dil.parent();
                reindex.add(d);
                handleDataset(d, document, store, index, boost);
                for (final ProjectDatasetLink pdl : d
                        .unmodifiableProjectLinks()) {
                    final Project p = pdl.parent();
                    reindex.add(p);
                    handleProject(p, document, store, index, boost);
                }
            }
        }

        //
        // Handle re-indexing
        //
        if (reindex.size() > 0) {
            reindexAll(reindex);
        }

}

In which case, regardless of whether an Image, Dataset, or Project is indexed, all related objects are simultaneously added to the backlog, which will be processed in the next cycle, but their indexing will not add any new values to the backlog.

See #955 and #1102

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See also

OMERO search