public Set<TaxonLabelSet> createTaxonLabelSets(Study s, boolean justTrees, boolean justMatrices) {
bindSession();
Set<TaxonLabelSet> newSets = new HashSet<TaxonLabelSet>();
Set<TaxonLabelSet> oldSets = s.getTaxonLabelSets();
Hibernate.initialize(oldSets);
for (Analysis an : s.getAnalyses()) {
TaxonLabelSet theSet = new TaxonLabelSet();
theSet.setStudy(s);
theSet.setTitle(an.getName());
Collection<TreeBlock> treeBlocks = new LinkedList<TreeBlock>();
for (AnalysisStep as : an.getAnalysisStepsReadOnly()) {
for (AnalyzedData ad : as.getDataSetReadOnly()) {
Matrix m = ad.getMatrixData();
PhyloTree t = ad.getTreeData();
if (m != null && !justTrees) {
addToSetIfNecessary(theSet, m.getAllTaxonLabels());
m.setTaxa(theSet);
// tlService.updateStudyForAllLabels(m, s);
}
if (t != null && !justMatrices) {
addToSetIfNecessary(theSet, t.getAllTaxonLabels());
// tlService.updateStudyForAllLabels(t, s);
treeBlocks.add(t.getTreeBlock());
}
}
}
ContextManager.getTaxonLabelService().save(theSet);
for (TreeBlock tb : treeBlocks) {
tb.setTaxonLabelSet(theSet);
ContextManager.getTaxonLabelService().save(tb); // XXX Should be treeBlockService
}
newSets.add(theSet);
}
s.setTaxonLabelSets(newSets);
unbindSession();
return newSets;
}
public static void main(String[] args) {
setupContext();
RegenerateTaxonLabelSetsInterface rt =
(RegenerateTaxonLabelSetsInterface) ContextManager.getBean("regenerateTaxonLabelSets");
GetOpts<UnixOptions> go = new GetOpts<UnixOptions>(new UnixOptions("tm"));
UnixOptions opts = go.getOpts(args);
// Kind of silly to convert the IDs to strings just to convert them back to numbers again...
if (args.length == 0) {
Collection<Study> allStudies = rt.getStudyHome().findAll(Study.class);
List<String> newArgs = new LinkedList<String>();
for (Study s : allStudies) newArgs.add(s.getId().toString());
args = newArgs.toArray(args);
}
for (String arg : args) {
Long id = Long.parseLong(arg);
System.err.println("Processing study " + id);
Set<TaxonLabelSet> newSets =
rt.createTaxonLabelSets(id, opts.getBoolOpt("t"), opts.getBoolOpt("m"));
rt.getTlHome().flush();
/*
* Do this another time, just destroy all sets that should be garbage-collected
for (TaxonLabelSet tlSet : oldSets) {
tlHome.deletePersist(tlSet); // XXX Should be taxonLabelSetHome
}
// tlHome.flush(); // XXX Should be taxonLabelSetHome
*/
String sets = newSets.size() == 1 ? "set" : "sets";
System.err.println(
" Rebuilt " + newSets.size() + " taxon label " + sets + " for study " + id);
}
}