@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 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 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 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 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())); }
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 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 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 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 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 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())); } }
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())); }
@Override public Show handleRequest(Database db, Tuple request, OutputStream out) { ServiceLocator.instance() .getContext() .getAutowireCapableBeanFactory() .initializeBean(db, "org.molgenis.framework.db.Database"); try { if (StringUtils.isEmpty(request.getAction())) this.getModel().setAction("init"); else this.getModel().setAction(request.getAction()); if ("1".equals(request.getString("expertSearch"))) this.getModel().getQueryParametersVO().setExpertSearch(true); else this.getModel().getQueryParametersVO().setExpertSearch(false); if (this.getModel().getAction().equals("findMutationsByTerm")) { this.handleFindMutationsByTerm(request); } else if (this.getModel().getAction().equals("findMutations")) { this.handleFindMutations(request); } else if (this.getModel().getAction().equals("findPatients")) { this.handleFindPatients(request); } else if (this.getModel().getAction().equals("listAllMutations")) { this.listAllMutations(request); } else if (this.getModel().getAction().equals("listAllPatients")) { this.listAllPatients(request); } else if (this.getModel().getAction().equals("showProteinDomain")) { this.handleShowProteinDomain(request); } else if (this.getModel().getAction().equals("showExon")) { this.handleShowExon(request); } else if (this.getModel().getAction().equals("showFirstExon")) { this.handleShowFirstExon(request); } else if (this.getModel().getAction().equals("showPrevExon")) { this.handleShowPrevExon(request); } else if (this.getModel().getAction().equals("showNextExon")) { this.handleShowNextExon(request); } else if (this.getModel().getAction().equals("showLastExon")) { this.handleShowLastExon(request); } else if (this.getModel().getAction().equals("showMutation")) { this.handleShowMutation(request); } else if (this.getModel().getAction().equals("showFirstMutation")) { this.handleShowFirstMutation(request); } else if (this.getModel().getAction().equals("showPrevMutation")) { this.handleShowPrevMutation(request); } else if (this.getModel().getAction().equals("showNextMutation")) { this.handleShowNextMutation(request); } else if (this.getModel().getAction().equals("showLastMutation")) { this.handleShowLastMutation(request); } else if (this.getModel().getAction().equals("showPatient")) { this.handleShowPatient(request); } else if (this.getModel().getAction().equals("showPhenotypeDetails")) { this.handleShowPhenotypeDetails(request); } else if (this.getModel().getAction().startsWith("mutationsFirstPage")) { this.getModel().getPager().first(); } else if (this.getModel().getAction().startsWith("mutationsPrevPage")) { this.getModel().getPager().prev(); } else if (this.getModel().getAction().startsWith("mutationsNextPage")) { this.getModel().getPager().next(); } else if (this.getModel().getAction().startsWith("mutationsLastPage")) { this.getModel().getPager().last(); } else { this.setView(new FreemarkerView("init.ftl", this.getModel())); } this.populateDisplayOptionsForm(); // for (ScreenController<?> child : this.getChildren()) // { // child.handleRequest(db, request, out); // } } 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&__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()); // this.getMessages().add(new ScreenMessage(el.toString(), false)); } return Show.SHOW_MAIN; }
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); }