private void handleShowNextMutation(Tuple request) {
SearchService searchService = ServiceLocator.instance().getSearchService();
MutationSummaryDTO mutationSummaryDTO =
searchService.findNextMutation(request.getString("mid"));
request.set("mid", mutationSummaryDTO.getIdentifier());
this.handleShowMutation(request);
}
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()));
}
private void handleShowPrevExon(Tuple request) {
SearchService searchService = ServiceLocator.instance().getSearchService();
ExonDTO exonDTO = searchService.findPrevExon(request.getInt("exon_id"));
request.set("__action", "showExon");
request.set("exon_id", exonDTO.getId());
this.handleShowExon(request);
}
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()));
}
@SuppressWarnings("unchecked")
@Override
protected void populateExpertSearchForm() {
PhenoService phenoService = ServiceLocator.instance().getPhenoService();
SearchService searchService = ServiceLocator.instance().getSearchService();
Container expertSearchForm = this.getModel().getExpertSearchFormWrapper().getForm();
((HiddenInput) expertSearchForm.get("__target")).setValue(this.getName());
((HiddenInput) expertSearchForm.get("select")).setValue(this.getName());
if (this.getModel().getMutationSearchCriteriaVO().getVariation() != null)
((TextLineInput<String>) expertSearchForm.get("variation"))
.setValue(this.getModel().getMutationSearchCriteriaVO().getVariation());
if (this.getModel().getMutationSearchCriteriaVO().getCdnaPosition() != null)
((IntInput) expertSearchForm.get("nuclno"))
.setValue(this.getModel().getMutationSearchCriteriaVO().getCdnaPosition());
if (this.getModel().getMutationSearchCriteriaVO().getCodonNumber() != null)
((IntInput) expertSearchForm.get("aano"))
.setValue(this.getModel().getMutationSearchCriteriaVO().getCodonNumber());
List<ValueLabel> exonIdOptions = new ArrayList<ValueLabel>();
exonIdOptions.add(new ValueLabel("", "Select"));
for (ExonDTO exonSummaryVO : searchService.findAllExons())
exonIdOptions.add(new ValueLabel(exonSummaryVO.getId(), exonSummaryVO.getName()));
((SelectInput) expertSearchForm.get("exon_id")).setOptions(exonIdOptions);
if (this.getModel().getMutationSearchCriteriaVO().getExonId() != null)
((SelectInput) expertSearchForm.get("exon_id"))
.setValue(this.getModel().getMutationSearchCriteriaVO().getExonId());
else ((SelectInput) expertSearchForm.get("exon_id")).setValue("Select");
List<ValueLabel> typeOptions = new ArrayList<ValueLabel>();
typeOptions.add(0, new ValueLabel("", "Select"));
for (String mutationType : phenoService.findObservedValues("Type of mutation"))
typeOptions.add(new ValueLabel(mutationType, mutationType));
((SelectInput) expertSearchForm.get("type")).setOptions(typeOptions);
if (this.getModel().getMutationSearchCriteriaVO().getType() != null)
((SelectInput) expertSearchForm.get("type"))
.setValue(this.getModel().getMutationSearchCriteriaVO().getType());
else ((SelectInput) expertSearchForm.get("type")).setValue("Select");
List<ValueLabel> phenotypeOptions = new ArrayList<ValueLabel>();
phenotypeOptions.add(new ValueLabel("", "Select"));
for (String phenotypeName : phenoService.findObservedValues("Onset"))
phenotypeOptions.add(new ValueLabel(phenotypeName, phenotypeName));
((SelectInput) expertSearchForm.get("phenotype")).setOptions(phenotypeOptions);
if (this.getModel().getMutationSearchCriteriaVO().getPhenotypeId() != null)
((SelectInput) expertSearchForm.get("phenotype"))
.setValue(this.getModel().getMutationSearchCriteriaVO().getPhenotypeId());
else ((SelectInput) expertSearchForm.get("phenotype")).setValue("Select");
}
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 populateShowMutationForm() {
SearchService searchService = ServiceLocator.instance().getSearchService();
this.getModel().getShowMutationForm().get("__target").setValue(this.getName());
this.getModel().getListAllMutationsForm().get("select").setValue(this.getName());
List<ValueLabel> mutationIdOptions = new ArrayList<ValueLabel>();
mutationIdOptions.add(new ValueLabel("", "Select mutation"));
for (VariantDTO variantDTO : searchService.getAllVariants())
mutationIdOptions.add(
new ValueLabel(
variantDTO.getIdentifier(),
variantDTO.getCdnaNotation() + " (" + variantDTO.getAaNotation() + ")"));
((SelectInput) this.getModel().getShowMutationForm().get("mid")).setOptions(mutationIdOptions);
((SelectInput) this.getModel().getShowMutationForm().get("mid")).setValue("Select mutation");
}
private void handleShowPatient(Tuple request) {
if (StringUtils.isNotEmpty(request.getString("pid"))) {
String patientIdentifier = request.getString("pid");
SearchService searchService = ServiceLocator.instance().getSearchService();
PatientSummaryDTO patientSummaryVO =
searchService.findPatientByPatientIdentifier(patientIdentifier);
this.getModel().setPatientSummaryVO(patientSummaryVO);
this.getModel().setHeader("Details for patient " + patientIdentifier);
this.setView(new FreemarkerView(this.getModel().getPatientViewer(), getModel()));
}
}
private void handleShowPhenotypeDetails(Tuple request) throws Exception {
if (StringUtils.isNotEmpty(request.getString("pid"))) {
String patientIdentifier = request.getString("pid");
PhenoService phenoService = ServiceLocator.instance().getPhenoService();
SearchService searchService = ServiceLocator.instance().getSearchService();
PatientSummaryDTO patientSummaryVO =
searchService.findPatientByPatientIdentifier(patientIdentifier);
this.getModel()
.setIndividualDTO(phenoService.findPhenotypeDetails(patientSummaryVO.getPatientId()));
this.getModel().setHeader("Phenotypic details for Patient " + patientIdentifier);
this.setView(new FreemarkerView("phenotypedetails.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()));
}
private void handleShowMutation(Tuple request) {
if (StringUtils.isNotEmpty(request.getString("mid"))) {
String mutationIdentifier = request.getString("mid");
// if (StringUtils.isNotEmpty(request.getString("snpbool")))
// if (request.getString("snpbool").equals("hide"))
// this.getModel().getMutationSearchCriteriaVO().setReportedAsSNP(false);
SearchService searchService = ServiceLocator.instance().getSearchService();
MutationSummaryDTO mutationSummaryDTO =
searchService.findMutationByIdentifier(mutationIdentifier);
this.getModel().setMutationSummaryVO(mutationSummaryDTO);
this.getModel().setPositionMutations(searchService.findPositionMutations(mutationSummaryDTO));
this.getModel().setCodonMutations(searchService.findCodonMutations(mutationSummaryDTO));
this.getModel().setHeader("Details for mutation " + mutationIdentifier);
this.setView(new FreemarkerView("mutation.ftl", getModel()));
}
}
protected void populateExpertSearchForm() {
PhenoService phenoService = ServiceLocator.instance().getPhenoService();
SearchService searchService = ServiceLocator.instance().getSearchService();
Container expertSearchForm = this.getModel().getExpertSearchFormWrapper().getForm();
expertSearchForm.get("__target").setValue(this.getName());
expertSearchForm.get("select").setValue(this.getName());
if (this.getModel().getMutationSearchCriteriaVO().getVariation() != null)
((TextLineInput) expertSearchForm.get("variation"))
.setValue(this.getModel().getMutationSearchCriteriaVO().getVariation());
if (this.getModel().getMutationSearchCriteriaVO().getCdnaPosition() != null)
((IntInput) expertSearchForm.get("nuclno"))
.setValue(this.getModel().getMutationSearchCriteriaVO().getCdnaPosition());
if (this.getModel().getMutationSearchCriteriaVO().getCodonNumber() != null)
((IntInput) expertSearchForm.get("aano"))
.setValue(this.getModel().getMutationSearchCriteriaVO().getCodonNumber());
List<ValueLabel> exonIdOptions = new ArrayList<ValueLabel>();
exonIdOptions.add(new ValueLabel("", "Select"));
for (ExonDTO exonSummaryVO : searchService.findAllExons())
exonIdOptions.add(new ValueLabel(exonSummaryVO.getId(), exonSummaryVO.getName()));
((SelectInput) expertSearchForm.get("exon_id")).setOptions(exonIdOptions);
if (this.getModel().getMutationSearchCriteriaVO().getExonId() != null)
((SelectInput) expertSearchForm.get("exon_id"))
.setValue(this.getModel().getMutationSearchCriteriaVO().getExonId());
else ((SelectInput) expertSearchForm.get("exon_id")).setValue("Select");
List<ValueLabel> typeOptions = new ArrayList<ValueLabel>();
typeOptions.add(0, new ValueLabel("", "Select"));
for (String mutationType : phenoService.findObservedValues("Type of mutation"))
typeOptions.add(new ValueLabel(mutationType, mutationType));
((SelectInput) expertSearchForm.get("type")).setOptions(typeOptions);
if (this.getModel().getMutationSearchCriteriaVO().getType() != null)
((SelectInput) expertSearchForm.get("type"))
.setValue(this.getModel().getMutationSearchCriteriaVO().getType());
else ((SelectInput) expertSearchForm.get("type")).setValue("Select");
List<ValueLabel> consequenceOptions = new ArrayList<ValueLabel>();
consequenceOptions.add(0, new ValueLabel("", "Select"));
for (String consequence : phenoService.findObservedValues("consequence"))
consequenceOptions.add(new ValueLabel(consequence, consequence));
((SelectInput) expertSearchForm.get("consequence")).setOptions(consequenceOptions);
if (this.getModel().getMutationSearchCriteriaVO().getConsequence() != null)
((SelectInput) expertSearchForm.get("consequence"))
.setValue(this.getModel().getMutationSearchCriteriaVO().getConsequence());
else ((SelectInput) expertSearchForm.get("consequence")).setValue("Select");
List<ValueLabel> domainOptions = new ArrayList<ValueLabel>();
domainOptions.add(new ValueLabel("", "Select"));
for (ProteinDomainDTO domainVO : searchService.findAllProteinDomains())
domainOptions.add(new ValueLabel(domainVO.getDomainId(), domainVO.getDomainName()));
((SelectInput) expertSearchForm.get("domain_id")).setOptions(domainOptions);
if (this.getModel().getMutationSearchCriteriaVO().getProteinDomainId() != null)
((SelectInput) expertSearchForm.get("domain_id"))
.setValue(this.getModel().getMutationSearchCriteriaVO().getProteinDomainId());
else ((SelectInput) expertSearchForm.get("domain_id")).setValue("Select");
List<ValueLabel> phenotypeOptions = new ArrayList<ValueLabel>();
phenotypeOptions.add(new ValueLabel("", "Select"));
for (String phenotypeName : phenoService.findObservedValues("Phenotype"))
phenotypeOptions.add(new ValueLabel(phenotypeName, phenotypeName));
((SelectInput) expertSearchForm.get("phenotype")).setOptions(phenotypeOptions);
if (this.getModel().getMutationSearchCriteriaVO().getPhenotypeId() != null)
((SelectInput) expertSearchForm.get("phenotype"))
.setValue(this.getModel().getMutationSearchCriteriaVO().getPhenotypeId());
else ((SelectInput) expertSearchForm.get("phenotype")).setValue("Select");
List<ValueLabel> inheritanceOptions = new ArrayList<ValueLabel>();
inheritanceOptions.add(0, new ValueLabel("", "Select"));
for (String inheritance : phenoService.findObservedValues("Inheritance"))
inheritanceOptions.add(new ValueLabel(inheritance, inheritance));
((SelectInput) expertSearchForm.get("inheritance")).setOptions(inheritanceOptions);
if (this.getModel().getMutationSearchCriteriaVO().getInheritance() != null)
((SelectInput) expertSearchForm.get("inheritance"))
.setValue(this.getModel().getMutationSearchCriteriaVO().getInheritance());
else ((SelectInput) expertSearchForm.get("inheritance")).setValue("Select");
}
@Override
public void reload(Database db) {
ServiceLocator.instance()
.getContext()
.getAutowireCapableBeanFactory()
.initializeBean(db, "org.molgenis.framework.db.Database");
try {
SearchService searchService = ServiceLocator.instance().getSearchService();
this.getModel().setGeneDTO(searchService.findGene());
if (this.getModel().getMbrowse().getIsVisible()) {
if (this.getModel().getMbrowse().getGeneDTO() == null)
this.getModel().getMbrowse().setGeneDTO(this.getModel().getGeneDTO());
if (this.getModel().getMbrowse().getProteinDomainDTOList() == null)
this.getModel()
.getMbrowse()
.setProteinDomainDTOList(searchService.findAllProteinDomains());
}
CmsService cmsService = ServiceLocator.instance().getCmsService();
this.getModel().setTextRemarks(cmsService.findContentByName("remarks"));
this.getModel().setTextCollaborations(cmsService.findContentByName("collaborators"));
if (this.getModel().getQueryParametersVO().getExpertSearch()) {
this.populateExpertSearchForm();
this.populateShowMutationForm();
this.populateToSimpleSearchForm();
} else {
this.getModel().setTextWelcome(cmsService.findContentByName("welcome"));
this.getModel().setTextSearch(cmsService.findContentByName("search"));
StatisticsService statisticsService = ServiceLocator.instance().getStatisticsService();
this.getModel().setNumMutations(statisticsService.getNumMutations());
this.getModel().setNumPatients(statisticsService.getNumPatients());
this.getModel().setNumUnpublished(statisticsService.getNumUnpublishedPatients());
this.getModel()
.setNumMutationsByPathogenicity(statisticsService.getNumMutationsByPathogenicity());
this.getModel()
.setNumPatientsByPathogenicity(statisticsService.getNumPatientsByPathogenicity());
this.populateSimpleSearchForm();
this.populateListAllMutationsForm();
this.populateListAllPatientsForm();
this.populateToExpertSearchForm();
}
} catch (Exception e) {
String message =
"Oops, an error occurred. We apologize and will work on fixing it as soon as possible. <a href=\"molgenis.do?__target=SearchPlugin&select=SearchPlugin&__action=init&expertSearch=0\">Return to home page</a>";
this.getModel().getMessages().add(new ScreenMessage(message, false));
for (StackTraceElement el : e.getStackTrace()) logger.error(el.toString());
}
for (ScreenController<?> child : this.getChildren())
try {
child.reload(db);
} catch (Exception e) {
e.printStackTrace();
}
}
private void handleShowFirstExon(Tuple request) {
SearchService searchService = ServiceLocator.instance().getSearchService();
ExonDTO exonDTO = searchService.findFirstExon();
request.set("exon_id", exonDTO.getId());
this.handleShowExon(request);
}