@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 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()));
}
}
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");
}