}
flush();
}
for (PhyloTree t : trees.values()) {
// Detach this tree from the pseudosubmission it was temporarily attached to
TreeBlock tb = t.getTreeBlock();
if (tb != null) {
warn(" Removing tree " + t.getId());
tb.removePhyloTree(t);
ContextManager.getPhyloTreeService().save(tb);
}
flush();
}
// t2.commit();
}
// Transaction t = getSession().beginTransaction();
Study theStudy = aux.study(ContextManager.getStudyService());
if (theStudy == null) {
theStudy = new Study();
ContextManager.getSubmissionService().createSubmission(null, theStudy);
}
theStudy.setTB1StudyID(study_id);
theStudy.setAccessionNumber(study_id);
theStudy.setStudyStatus(ContextManager.getStudyStatusHome().findStatusPublished());
ContextManager.getStudyService().save(theStudy);
Submission theSubmission = theStudy.getSubmission();
ContextManager.getSubmissionService().save(theSubmission);
Citation theCitation = theStudy.getCitation();
if (theCitation == null) {
theCitation = ContextManager.getCitationService().createCitation("TB1");
theCitation.setStudy(theStudy);
theStudy.setCitation(theCitation);
ContextManager.getStudyService().save(theStudy);
}
{ // Truncate extremely long abstracts
String theAbstract = aux.getString(null, "abstract");
if (theAbstract.length() > citationMaxLength - 4) {
theAbstract = theAbstract.substring(0, citationMaxLength - 4) + "...";
}
theCitation.setAbstract(theAbstract);
}
// this next isn't quite right, because TB1 "citation" contains title, author, publisher, etc.
// nothing to be done here, I think. 20080229 MJD
// We can postprocess the citation data with Perl or something
// to break it up into its component parts. 20080605 MJD
// Piel says that Rod Page already did this. 20080702 MJD
// Rutger has a program in util.CitationDataImporter that should do it 20090220 MJD
{
String citation = aux.getString(null, "citation");
if (citation.length() > 250) {
// It won't all fit into the "title" field of the database
citation = citation.substring(0, 250); // XXX
}
theCitation.setTitle(citation); // XXX
}
ContextManager.getCitationService().save(theCitation);
// Create or link authors
for (ValueSection a : aux.getSections("AUTHOR")) {
Person theAuthor = new Person();
theAuthor.setFirstName(a.getsval("first_name"));
theAuthor.setLastName(a.getsval("last_name"));
theAuthor.setMiddleName("");
// ContextManager.getPersonService().save(theAuthor);
// TB1 "author_id" ??
Person oldAuthor = ContextManager.getPersonService().findByExactMatch(theAuthor);
if (oldAuthor != null) {
theAuthor = oldAuthor;
} else {
ContextManager.getPersonService().createPerson(theAuthor);
theAuthor = ContextManager.getPersonService().findByExactMatch(theAuthor);
}
String oldEmail = theAuthor.getEmailAddressString();
if (oldEmail == null || oldEmail.equals("")) {
theAuthor.setEmailAddressString(a.getsval("email"));
}
ContextManager.getPersonService().save(theAuthor);
theCitation.addAuthor(theAuthor);
}
ContextManager.getCitationHome().flush();
ContextManager.getCitationService().save(theCitation);
// TODO: submission.setSubmitter
theSubmission.setTest(isForTesting() ? 0 : 1);
{
Date creationDate = aux.getCreationDate();
if (creationDate != null) {
theSubmission.setCreateDate(creationDate);
} else {
warn(" Couldn't find creation date");
}
}
for (ValueAnalysisSection an : aux.getAnalysisSections()) {
Analysis theAnalysis = new Analysis();
theAnalysis.setStudy(theStudy);
theAnalysis.setName(an.getString("analysis_name"));
// TODO: TB_ANALYSISID
AnalysisStep theAnalysisStep = new AnalysisStep();
theAnalysisStep.setAnalysis(theAnalysis);
theAnalysis.addAnalysisStep(theAnalysisStep);
ContextManager.getAnalysisService().save(theAnalysis);
ContextManager.getAnalysisStepService().save(theAnalysisStep);
Algorithm theAlgorithm;
String tb1Algorithm = an.getString("algorithm");
if (tb1Algorithm.equalsIgnoreCase("parsimony")) {
theAlgorithm = new ParsimonyAlgorithm();
} else if (tb1Algorithm.equalsIgnoreCase("bayesian")) {
theAlgorithm = new BayesianAlgorithm();
} else if (tb1Algorithm.equalsIgnoreCase("evolution")) {
theAlgorithm = new EvolutionAlgorithm();
} else if (tb1Algorithm.equalsIgnoreCase("joining")) {
theAlgorithm = new JoiningAlgorithm();
} else if (tb1Algorithm.equalsIgnoreCase("UPGMA")) {
theAlgorithm = new UPGMAAlgorithm();
} else if (tb1Algorithm.equalsIgnoreCase("likelihood")) {
theAlgorithm = new LikelihoodAlgorithm();
} else {
theAlgorithm = new OtherAlgorithm();
}
theAlgorithm.setDescription(tb1Algorithm);
ContextManager.getAlgorithmHome().save(theAlgorithm);
theAnalysisStep.setAlgorithmInfo(theAlgorithm);
{ // handle INPUT_MATRIX and OUTPUT_TREE in each ANALYSIS section
TreeBlock theTreeBlock = null;
for (ValueSection ioSection : an.getIOSections()) {
AnalyzedData theData;
if (ioSection.label.equals("INPUT_MATRIX")) {
AnalyzedMatrix theMatrix = new AnalyzedMatrix();
theMatrix.setInput(true);
String matrixID = ioSection.getsval("matrix_id");
Matrix matrixData = matrices.get(matrixID);
if (matrixData == null) {
warn("Matrix " + matrixID + "is used in analysis " + an.getString("analysis_id") + " but is not listed in any MATRIX section for its study");
return new ValueNone();
}
matrixData.setStudy(theStudy);
ContextManager.getTaxonLabelService().updateStudyForAllLabels(matrixData, theStudy);
matrixData.setTB1MatrixID(matrixID);
ContextManager.getMatrixService().save(matrixData);
theSubmission.addMatrixIfNecessary(matrixData);
ContextManager.getSubmissionService().save(theSubmission);
theMatrix.setMatrix(matrixData);
theData = theMatrix;
} else if (ioSection.label.equals("OUTPUT_TREE")) {
if (theTreeBlock == null) {
theTreeBlock = new TreeBlock();
ContextManager.getStudyService().save(theTreeBlock); // XXX should be some treeblock-specific service
theSubmission.addPhyloTreeBlock(theTreeBlock);
ContextManager.getSubmissionService().save(theSubmission);
}
AnalyzedTree theTree = new AnalyzedTree();
theTree.setInput(false);
String treeID = ioSection.getsval("tree_id");
PhyloTree treeData = trees.get(treeID);
treeData.setStudy(theStudy);
ContextManager.getTaxonLabelService().updateStudyForAllLabels(treeData, theStudy);
treeData.setTB1TreeID(treeID);
ContextManager.getPhyloTreeService().save(treeData);
theTreeBlock.addPhyloTree(treeData);
theSubmission.addPhyloTreeBlockIfNecessary(theTreeBlock);
ContextManager.getSubmissionService().save(theSubmission);
theTree.setTree(treeData);
theData = theTree;
} else {