BUG: loadTagSets return AnnotationAnnotationLinkI

[atarkowska]

loadTagSet return AnnotationAnnotationLinkI rather then AnnotationI. It complicate to build hierarchy because everything is returned separately. Currently omero.gateway lazy loading approch does not allow to use wrap the implementation. It should return hierarchy of:

• TagAnnotationI (tagset)
  • TagAnnotationI (tag1)
  • TagAnnotationI (tag2)
• TagAnnotationI (tag3)

...

[jmoore]

Methods were added by J-M:

commit 9c6b400d64e6c7686df46b37702a5393a5e27895
Author: jburel <jburel@05709c45-44f0-0310-885b-81a1db45b4a6>
Date:   Tue Feb 17 09:46:33 2009 +0000

    Added new methods
    
    git-svn-id: file:///home/svn/omero/trunk@3622 05709c45-44f0-0310-885b-81a1db45b4a6

git blame components/server/src/ome/logic/MetadataImpl.java
...
0770b041 (jburel     2009-02-17 09:43:30 +0000  718)     /**
839fdf3c (jburel     2009-07-04 15:45:36 +0000  719)      * Implemented as specified by the {@link IMetadata} I/F
009cbb7d (jmoore     2009-03-10 08:54:25 +0000  720)      * @see IMetadata#loadTagSets(Parameters)
0770b041 (jburel     2009-02-17 09:43:30 +0000  721)      */
0770b041 (jburel     2009-02-17 09:43:30 +0000  722)     @RolesAllowed("user")
0770b041 (jburel     2009-02-17 09:43:30 +0000  723)     @Transactional(readOnly = true)
009cbb7d (jmoore     2009-03-10 08:54:25 +0000  724)     public Set<IObject> loadTagSets(Parameters options)
0770b041 (jburel     2009-02-17 09:43:30 +0000  725)    {
0770b041 (jburel     2009-02-17 09:43:30 +0000  726)        Set result = new HashSet();
d0092b19 (jmoore     2009-03-11 15:06:04 +0000  727)        Parameters po = new Parameters(options);
0770b041 (jburel     2009-02-17 09:43:30 +0000  728)        Parameters param = new Parameters();
0770b041 (jburel     2009-02-17 09:43:30 +0000  729)        StringBuilder sb = new StringBuilder();
bb787da7 (jburel     2010-03-25 16:52:57 +0000  730)        sb.append("select link from AnnotationAnnotationLink as link ");
bb787da7 (jburel     2010-03-25 16:52:57 +0000  731)        sb.append("left outer join fetch link.child child ");
bb787da7 (jburel     2010-03-25 16:52:57 +0000  732)        sb.append("left outer join fetch link.parent parent ");
bb787da7 (jburel     2010-03-25 16:52:57 +0000  733)        sb.append("left outer join fetch child.details.owner ownerChild ");
bb787da7 (jburel     2010-03-25 16:52:57 +0000  734)        sb.append("left outer join fetch parent.details.owner ownerParent ");
bb787da7 (jburel     2010-03-25 16:52:57 +0000  735)        sb.append("where child member of "+TAG_TYPE);
0770b041 (jburel     2009-02-17 09:43:30 +0000  736)        sb.append(" and parent member of "+TAG_TYPE);
7964c034 (jburel     2010-03-22 08:39:24 +0000  737)        if (po.isExperimenter()) {
7964c034 (jburel     2010-03-22 08:39:24 +0000  738)            sb.append(" and parent.details.owner.id = :userID");
7964c034 (jburel     2010-03-22 08:39:24 +0000  739)            param.addLong("userID", po.getExperimenter());

Passing to him to see what he thinks about the change.

[jburel]

Looking closely at the code we have 2 possibilities:

• actual implementation:A collection of objects (tag annotation or link) is returned
  • tag if orphaned
  • AnnotationAnnotationLink object so we can extract the tag set linked to the tags i.e. displaying a hierarchical structure from a flat structure

    link = (AnnotationAnnotationLink) object;
    parent = link.getParent();
    child = link.getChild();
    id = parent.getId().getValue();
    if (sets.get(id) == null) {
      tagSet = new TagAnnotationData((TagAnnotation) parent);
      sets.put(id, tagSet);
      result.add(tagSet);
      tagSet.setTags(new HashSet<TagAnnotationData>());
    } else 
     tagSet = sets.get(parent.getId().getValue());
    

• Change the method and return a map
  • key are tag or tag Set
  • If it is a tag Set, the value is a list containing tag object.

The first option was chosen to mimic the returned value of loadContainerHierarchy method in ContainerService

[atarkowska]

I do not see any problems with returning TagAnnotationI and AnnotationAnnotationLinkI list but the problem is that List should contain single AnnotationAnnotationLinkI where Parent is TagSet? and children are tags. Having structure in graph will help a lot.

Currently is see:

<class 'omero.model.AnnotationAnnotationLinkI'>
parent 8902 child 6591
<class 'omero.model.AnnotationAnnotationLinkI'>
parent 8902 child 8905

[jburel]

we will use linkedAnnotationList()

[atarkowska]

We could change the query to:

sql = "select roottag from TagAnnotation as roottag "\
            "left outer join fetch roottag.annotationLinks tal "\
            "left outer join fetch tal.child tag "\
            "left outer join fetch roottag.details.owner ownerroottag "\
            "left outer join fetch tag.details.owner ownerTag "
        if eid is not None:
            params.map = {}
            params.map["eid"] = rlong(long(eid))
            sql+=" where roottag.details.owner.id = :eid and tag.details.owner.id = :eid"

[jburel]

Query will be a bit more complicated than that, I will review that later on.

[jburel]

TODO:

• Change method
• Check tests
• modify insight

[jburel <j.burel@…>]

(In [24c693aee63b618267f38a3c3f92faa340c27c55/ome.git] on branch develop) Modify the implementation of the loadTagSets mehtod in medataservice.
Now only returned tagAnnotation objects. (close #5785)