/**
* Insert patient and set primary key
*
* @param patient
* @return number of patients inserted
* @throws Exception
*/
public void insert(PatientSummaryVO patientSummaryVO) throws Exception {
if (patientSummaryVO == null) return;
Patient patient = this.toPatient(patientSummaryVO);
// submissions are never inserted via patients, just select newest
// by date
// TODO: Do we still need that???
// List<Submission> submissions =
// this.db.query(Submission.class).equals(Submission.DATE_,
// patientSummaryVO.getSubmissionDate()).sortDESC("id").find();
//
// if (submissions.size() > 0)
// {
// patientSummaryVO.getPatient().setSubmission(submissions.get(0));
// }
// mutations are never inserted via patients, just select
for (MutationSummaryVO mutationSummaryVO : patientSummaryVO.getVariantSummaryVOList()) {
List<Mutation> mutations =
this.db
.query(Mutation.class)
.equals(Mutation.CDNA_NOTATION, mutationSummaryVO.getCdnaNotation())
.find();
// System.out.println(">>> Queried: " +
// mutationSummaryVO.getCdnaNotation() + ", found: " +
// mutations.size());
if (mutations.size() != 1)
throw new Exception("ERROR: No mutation found for " + mutationSummaryVO.getCdnaNotation());
patient.getMutations_Id().add(mutations.get(0).getId());
}
// phenotypes are never inserted via patients, just select
// if (patientSummaryVO.getPhenotypeId() == null)
// {
// // System.out.println(">>> Query: majortype==" +
// patientSummaryVO.getPhenotypeMajor() + ", subtype==" +
// patientSummaryVO.getPhenotypeSub());
// List<MutationPhenotype> phenotypes =
// this.db.query(MutationPhenotype.class).equals(MutationPhenotype.MAJORTYPE,
// patientSummaryVO.getPhenotypeMajor()).equals(MutationPhenotype.SUBTYPE,
// patientSummaryVO.getPhenotypeSub()).find();
//
// if (phenotypes.size() != 1)
// throw new Exception("No phenotype found for " +
// patientSummaryVO.getPhenotypeMajor() + ", " +
// patientSummaryVO.getPhenotypeSub());
//
// patientSummaryVO.setPhenotypeId(phenotypes.get(0).getId());
// }
// patient.setPhenotype_Id(patientSummaryVO.getPhenotypeId());
// Publications are never inserted via patients, just select
if (CollectionUtils.isNotEmpty(patientSummaryVO.getPublicationVOList())) {
List<Integer> publicationIds = new ArrayList<Integer>();
for (PublicationVO publicationVO : patientSummaryVO.getPublicationVOList()) {
if (publicationVO.getPubmedId() == null) continue;
List<OntologyTerm> pubmedTerms =
this.db
.query(OntologyTerm.class)
.equals(OntologyTerm.NAME, publicationVO.getPubmedId())
.find();
if (pubmedTerms.size() != 1) continue;
List<Publication> publications =
this.db
.query(Publication.class)
.equals(Publication.PUBMEDID, pubmedTerms.get(0).getId())
.find();
if (publications.size() != 1)
throw new Exception("No publication found for Pubmed ID " + publicationVO.getPubmedId());
publicationIds.add(publications.get(0).getId());
}
patient.setPatientreferences_Id(publicationIds);
}
patient.setSubmission_Id(1);
// Insert patient
this.db.add(patient);
// Insert ObservedValues
for (ObservedValueVO observedValueVO : patientSummaryVO.getObservedValueVOList()) {
if (observedValueVO == null) return;
List<ObservableFeature> features =
this.db
.query(ObservableFeature.class)
.equals(ObservableFeature.NAME, observedValueVO.getFeatureName())
.find();
if (features.size() != 1) return;
List<Patient> patients =
this.db
.query(Patient.class)
.equals(Patient.IDENTIFIER, observedValueVO.getTargetName())
.find();
if (patients.size() != 1) return;
ObservedValue observedValue = new ObservedValue();
observedValue.setFeature(features.get(0));
observedValue.setInvestigation(1);
observedValue.setTarget(patient.getId());
observedValue.setValue(observedValueVO.getValue());
this.db.add(observedValue);
}
}
private Patient toPatient(PatientSummaryVO patientSummaryVO) {
Patient patient = new Patient();
patient.setIdentifier(patientSummaryVO.getPatientIdentifier());
patient.setName(patientSummaryVO.getPatientName());
patient.setNumber(patientSummaryVO.getPatientNumber());
patient.setConsent(patientSummaryVO.getPatientConsent());
patient.setAge(patientSummaryVO.getPatientAge());
patient.setGender(patientSummaryVO.getPatientGender());
patient.setEthnicity(patientSummaryVO.getPatientEthnicity());
patient.setDeceased(patientSummaryVO.getPatientDeceased());
patient.setDeath_Cause(patientSummaryVO.getPatientDeathCause());
patient.setMmp1_Allele1(patientSummaryVO.getPatientMmp1Allele1());
patient.setMmp1_Allele2(patientSummaryVO.getPatientMmp1Allele2());
if (StringUtils.isNotEmpty(patientSummaryVO.getVariantComment()))
patient.setMutation2remark(patientSummaryVO.getVariantComment());
// patientSummaryVO.setPatientMaterialList(patient.getMaterial_Name());
//
// Submission submission = this.db.findById(Submission.class,
// patient.getSubmission_Id());
// MolgenisUser submitter = this.db.findById(MolgenisUser.class,
// submission.getSubmitters_Id().get(0));
// patientSummaryVO.setSubmitterDepartment(submitter.getDepartment());
// patientSummaryVO.setSubmitterInstitute(submitter.getInstitute());
// patientSummaryVO.setSubmitterCity(submitter.getCity());
// patientSummaryVO.setSubmitterCountry(submitter.getCountry());
return patient;
}