/** Gets all Genomic Data. */
private ProfileDataSummary getGenomicData(
String cancerStudyId,
HashMap<String, GeneticProfile> defaultGeneticProfileSet,
SampleList defaultSampleSet,
String geneListStr,
ArrayList<SampleList> sampleList,
HttpServletRequest request,
HttpServletResponse response)
throws IOException, ServletException, DaoException {
// parse geneList, written in the OncoPrintSpec language (except for changes by XSS clean)
double zScore =
ZScoreUtil.getZScore(
new HashSet<String>(defaultGeneticProfileSet.keySet()),
new ArrayList<GeneticProfile>(defaultGeneticProfileSet.values()),
request);
double rppaScore = ZScoreUtil.getRPPAScore(request);
ParserOutput theOncoPrintSpecParserOutput =
OncoPrintSpecificationDriver.callOncoPrintSpecParserDriver(
geneListStr,
new HashSet<String>(defaultGeneticProfileSet.keySet()),
new ArrayList<GeneticProfile>(defaultGeneticProfileSet.values()),
zScore,
rppaScore);
ArrayList<String> geneList = new ArrayList<String>();
geneList.addAll(theOncoPrintSpecParserOutput.getTheOncoPrintSpecification().listOfGenes());
ArrayList<ProfileData> profileDataList = new ArrayList<ProfileData>();
Set<String> warningUnion = new HashSet<String>();
for (GeneticProfile profile : defaultGeneticProfileSet.values()) {
try {
GetProfileData remoteCall =
new GetProfileData(
profile, geneList, StringUtils.join(defaultSampleSet.getSampleList(), " "));
ProfileData pData = remoteCall.getProfileData();
warningUnion.addAll(remoteCall.getWarnings());
profileDataList.add(pData);
} catch (IllegalArgumentException e) {
e.getStackTrace();
}
}
ProfileMerger merger = new ProfileMerger(profileDataList);
ProfileData mergedProfile = merger.getMergedProfile();
ProfileDataSummary dataSummary =
new ProfileDataSummary(
mergedProfile,
theOncoPrintSpecParserOutput.getTheOncoPrintSpecification(),
zScore,
rppaScore);
return dataSummary;
}
protected Person recalculatePersonBiodemInfo(
final Person person,
final SorPerson sorPerson,
final RecalculationType recalculationType,
boolean mistake) {
final List<SorPerson> sorPersons = this.personRepository.getSoRRecordsForPerson(person);
logger.info("recalculatePersonBiodemInfo: start");
if (recalculationType == RecalculationType.ADD
|| (recalculationType == RecalculationType.DELETE && !mistake)) {
sorPersons.add(sorPerson);
}
copySorNamesToPerson(person, sorPersons);
final Date birthDate =
this.birthDateFieldElector.elect(
sorPerson, sorPersons, recalculationType == RecalculationType.DELETE);
final String gender =
this.genderFieldElector.elect(
sorPerson, sorPersons, recalculationType == RecalculationType.DELETE);
final SorName preferredName =
this.preferredNameFieldElector.elect(
sorPerson, sorPersons, recalculationType == RecalculationType.DELETE);
final SorName officialName =
this.officialNameFieldElector.elect(
sorPerson, sorPersons, recalculationType == RecalculationType.DELETE);
final EmailAddress emailAddress =
this.preferredContactEmailAddressFieldElector.elect(
sorPerson, sorPersons, recalculationType == RecalculationType.DELETE);
final Phone phone =
this.preferredContactPhoneNumberFieldElector.elect(
sorPerson, sorPersons, recalculationType == RecalculationType.DELETE);
final Map<String, String> attributes =
this.attributesElector.elect(
sorPerson, sorPersons, recalculationType == RecalculationType.DELETE);
final SorDisclosureSettings disclosure =
this.disclosureFieldElector.elect(
sorPerson, sorPersons, recalculationType == RecalculationType.DELETE);
final String ssn =
this.ssnFieldElector.elect(
sorPerson, sorPersons, recalculationType == RecalculationType.DELETE);
Identifier primarySSN = person.getPrimaryIdentifiersByType().get("SSN");
// check if the elector elcted some ssn and person does have previous ssn assigned to it
if (!org.apache.commons.lang.StringUtils.isEmpty(ssn) && primarySSN != null) {
try {
this.identifierChangeService.change(person.getPrimaryIdentifiersByType().get("SSN"), ssn);
} catch (IllegalArgumentException e) {
logger.debug(e.getStackTrace().toString());
} // all other exception should be propogated
}
person.setDateOfBirth(birthDate);
person.setGender(gender);
person.getPreferredContactEmailAddress().update(emailAddress);
person.getPreferredContactPhoneNumber().update(phone);
person.calculateDisclosureSettings(disclosure);
person.setAttributes(attributes);
String affiliation = "";
Type affiliationType = null;
if (disclosure != null) {
logger.info(
"after person.calculateDisclosureSettings, disclosure code : "
+ disclosure.getDisclosureCode());
} else {
logger.info("Disclosure is null");
}
List<SorRole> sorroles = sorPerson.getRoles();
for (SorRole role : sorroles) {
if (role != null) {
logger.info("Role = " + role.getTitle());
if (role.getAffiliationType() != null) {
logger.info("Role desc= " + role.getAffiliationType().getDescription());
affiliation = role.getAffiliationType().getDescription();
if (person.getDisclosureSettings() != null) {
logger.info("recalculating disclosure setting 1...");
// person.getDisclosureSettings().recalculate(this.strategyRepository.getDisclosureRecalculationStrategy());
person
.getDisclosureSettings()
.recalculate(
this.strategyRepository.getDisclosureRecalculationStrategy(),
affiliation,
referenceRepository);
}
}
}
}
// SSN election is happening in the ssn identifier assigner.
boolean preferred = false;
boolean official = false;
for (final Name name : person.getNames()) {
if (!preferred && name.sameAs(preferredName)) {
name.setPreferredName(true);
preferred = true;
}
if (!official && name.sameAs(officialName)) {
name.setOfficialName(true);
official = true;
}
if (official && preferred) {
break;
}
}
logger.info("recalculatePersonBiodemInfo: end");
// return this.personRepository.savePerson(person);
return person;
}