private void handleFindMutationsByTerm(Tuple request) {
// if (StringUtils.isNotEmpty(request.getString("term")) && request.getString("term").length()
// < 3)
// throw new SearchException("Search term is too general. Please use a more specific one.");
if (StringUtils.isNotEmpty(request.getString("result")))
this.getModel().setResult(request.getString("result"));
else this.getModel().setResult("mutations"); // Default: Show mutations
this.getModel().setMutationSummaryVOHash(new HashMap<String, String>());
this.getModel().setPatientSummaryVOHash(new HashMap<String, String>());
SearchService searchService = ServiceLocator.instance().getSearchService();
if (this.getModel().getResult().equals("patients")) {
HashMap<String, List<PatientSummaryDTO>> result =
searchService.findPatientsByTerm(request.getString("term"));
int numPatients = 0;
for (String key : result.keySet()) {
if (CollectionUtils.isNotEmpty(result.get(key))) {
((HttpServletRequestTuple) request)
.getRequest()
.setAttribute("patientSummaryVOs", result.get(key));
this.getModel()
.getPatientSummaryVOHash()
.put(" " + key + " ", this.include(request, this.getModel().getPatientPager()));
numPatients += result.get(key).size();
}
}
this.getModel().setHeader(numPatients + " patients found.");
} else if (this.getModel().getResult().equals("mutations")) {
HashMap<String, List<MutationSummaryDTO>> result =
searchService.findMutationsByTerm(request.getString("term"));
int numMutations = 0;
for (String key : result.keySet()) {
if (CollectionUtils.isNotEmpty(result.get(key))) {
((HttpServletRequestTuple) request)
.getRequest()
.setAttribute("mutationSummaryDTOList", result.get(key));
this.getModel()
.getMutationSummaryVOHash()
.put(" " + key + " ", this.include(request, this.getModel().getMutationPager()));
numMutations += result.get(key).size();
}
}
this.getModel().setHeader(numMutations + " mutations found.");
}
this.setView(new FreemarkerView("freetext.ftl", this.getModel()));
}
private void handleShowProteinDomain(Tuple request) throws Exception {
if (StringUtils.isNotEmpty(request.getString("domain_id")))
this.getModel().getMutationSearchCriteriaVO().setProteinDomainId(request.getInt("domain_id"));
if (StringUtils.isNotEmpty(request.getString("snpbool")))
if (request.getString("snpbool").equals("hide"))
this.getModel().getMutationSearchCriteriaVO().setReportedAsSNP(false);
SearchService searchService = ServiceLocator.instance().getSearchService();
this.getModel()
.setProteinDomainDTO(searchService.findProteinDomain(request.getInt("domain_id"), false));
this.getModel()
.setMutationSummaryDTOList(
searchService.findMutationsByDomainId(request.getInt("domain_id")));
((HttpServletRequestTuple) request)
.getRequest()
.setAttribute("mutationSummaryVOList", this.getModel().getMutationSummaryDTOList());
this.getModel().setRawOutput(this.include(request, this.getModel().getMutationPager()));
this.getModel().setHeader((this.getModel().getProteinDomainDTO() == null) ? "Unknown id." : "");
this.getModel().getMbrowse().setProteinDomainDTO(this.getModel().getProteinDomainDTO());
if (this.getModel().getMbrowse().getExonDTOList() == null)
this.getModel().getMbrowse().setExonDTOList(searchService.findAllExons());
this.setView(new FreemarkerView("proteindomain.ftl", getModel()));
}
public void show(Database db, Tuple request) {
try {
PublicationService publicationService = ServiceLocator.instance().getPublicationService();
this.getModel().setPublicationDTOList(publicationService.getAll());
((HttpServletRequestTuple) request)
.getRequest()
.setAttribute("publicationDTOList", this.getModel().getPublicationDTOList());
this.getModel().setRawOutput(this.include(request, this.getModel().getPublicationPager()));
} catch (Exception e) {
e.printStackTrace();
}
}
private void handleFindMutations(Tuple request) {
this.getModel().setMutationSearchCriteriaVO(new MutationSearchCriteriaDTO());
if (StringUtils.isNotEmpty(request.getString("variation")))
this.getModel().getMutationSearchCriteriaVO().setVariation(request.getString("variation"));
if (StringUtils.isNotEmpty(request.getString("consequence")))
this.getModel()
.getMutationSearchCriteriaVO()
.setConsequence(request.getString("consequence"));
if (StringUtils.isNotEmpty(request.getString("mutation_id")))
this.getModel().getMutationSearchCriteriaVO().setMutationId(request.getInt("mutation_id"));
if (StringUtils.isNotEmpty(request.getString("mid")))
this.getModel().getMutationSearchCriteriaVO().setMid(request.getString("mid"));
if (StringUtils.isNotEmpty(request.getString("nuclno")))
this.getModel().getMutationSearchCriteriaVO().setCdnaPosition(request.getInt("nuclno"));
if (StringUtils.isNotEmpty(request.getString("aano")))
this.getModel().getMutationSearchCriteriaVO().setCodonChangeNumber(request.getInt("aano"));
if (StringUtils.isNotEmpty(request.getString("exon_id")))
this.getModel().getMutationSearchCriteriaVO().setExonId(request.getInt("exon_id"));
if (StringUtils.isNotEmpty(request.getString("exon")))
this.getModel().getMutationSearchCriteriaVO().setExonName(request.getString("exon"));
if (StringUtils.isNotEmpty(request.getString("type")))
this.getModel().getMutationSearchCriteriaVO().setType(request.getString("type"));
if (StringUtils.isNotEmpty(request.getString("domain_id")))
this.getModel().getMutationSearchCriteriaVO().setProteinDomainId(request.getInt("domain_id"));
if (StringUtils.isNotEmpty(request.getString("phenotype")))
this.getModel()
.getMutationSearchCriteriaVO()
.setPhenotypeName(request.getString("phenotype"));
if (StringUtils.isNotEmpty(request.getString("inheritance")))
this.getModel()
.getMutationSearchCriteriaVO()
.setInheritance(request.getString("inheritance"));
if (StringUtils.isNotEmpty(request.getString("snpbool")))
if (request.getString("snpbool").equals("hide"))
this.getModel().getMutationSearchCriteriaVO().setReportedAsSNP(false);
SearchService searchService = ServiceLocator.instance().getSearchService();
this.getModel()
.setMutationSummaryDTOList(
searchService.findMutations(this.getModel().getMutationSearchCriteriaVO()));
((HttpServletRequestTuple) request)
.getRequest()
.setAttribute("mutationSummaryDTOList", this.getModel().getMutationSummaryDTOList());
this.getModel().setRawOutput(this.include(request, this.getModel().getMutationPager()));
this.getModel().setHeader(this.getModel().getMutationSummaryDTOList().size() + " results.");
this.setView(new FreemarkerView("included.ftl", this.getModel()));
}
private void listAllMutations(Tuple request) {
SearchService searchService = ServiceLocator.instance().getSearchService();
this.getModel().setMutationSummaryDTOList(searchService.findAllMutationSummaries());
((HttpServletRequestTuple) request)
.getRequest()
.setAttribute("mutationSummaryDTOList", this.getModel().getMutationSummaryDTOList());
this.getModel().setRawOutput(this.include(request, this.getModel().getMutationPager()));
this.getModel()
.setHeader(
this.getModel().getMutationSummaryDTOList().size()
+ " results for \"Display all mutations\".");
this.setView(new FreemarkerView("included.ftl", getModel()));
}
private void handleFindPatients(Tuple request) {
if (StringUtils.isNotEmpty(request.getString("mid"))) {
String mutationIdentifier = request.getString("mid");
SearchService searchService = ServiceLocator.instance().getSearchService();
List<PatientSummaryDTO> patientSummaryVOList =
searchService.findPatientsByMutationIdentifier(mutationIdentifier);
((HttpServletRequestTuple) request)
.getRequest()
.setAttribute("patientSummaryVOs", patientSummaryVOList);
this.getModel().setRawOutput(this.include(request, this.getModel().getPatientPager()));
this.getModel().setHeader(patientSummaryVOList.size() + " results for " + mutationIdentifier);
this.setView(new FreemarkerView("included.ftl", this.getModel()));
}
}
private void listAllPatients(Tuple request) {
// MolgenisUser user = new MolgenisUser();
// user.setId(this.getLogin().getUserId());
// this.getModel().setPatientSummaryVOs(this.patientService.find(user));
SearchService searchService = ServiceLocator.instance().getSearchService();
List<PatientSummaryDTO> patientSummaryVOs = searchService.findAllPatientSummaries();
this.getModel().setPatientSummaryVOs(patientSummaryVOs);
((HttpServletRequestTuple) request)
.getRequest()
.setAttribute("patientSummaryVOs", this.getModel().getPatientSummaryVOs());
this.getModel().setRawOutput(this.include(request, this.getModel().getPatientPager()));
this.getModel()
.setHeader(
this.getModel().getPatientSummaryVOs().size()
+ " results for \"Display all patients\".");
this.setView(new FreemarkerView("included.ftl", this.getModel()));
}
private void handleShowExon(Tuple request) {
SearchService searchService = ServiceLocator.instance().getSearchService();
Integer exonId = request.getInt("exon_id");
this.getModel().setExonDTO(searchService.findExonById(exonId));
if (this.getModel().getQueryParametersVO().getShowMutations()) {
this.getModel().setMutationSummaryDTOList(searchService.findMutationsByExonId(exonId));
((HttpServletRequestTuple) request)
.getRequest()
.setAttribute("mutationSummaryDTOList", this.getModel().getMutationSummaryDTOList());
this.getModel().setRawOutput(this.include(request, this.getModel().getMutationPager()));
}
this.getModel().setHeader("");
this.getModel().getMbrowse().setExonDTO(this.getModel().getExonDTO());
this.getModel()
.getMbrowse()
.setMutationSummaryDTOList(this.getModel().getMutationSummaryDTOList());
this.setView(new FreemarkerView("exon.ftl", getModel()));
}