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genopri-shcs/project/PPPClient/src/framework/ClinicalAnalyzer.java
9270d993aa95ms_access_migration

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ClinicalAnalyzer.java
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package framework;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.logging.Level;
import java.util.logging.Logger;
import database.DBconnectorClient;
import framework.test.TestName;
import framework.test.TestResult;
import framework.test.TestResultRaw;
public class ClinicalAnalyzer {
private static final Logger LOGGER = Logger.getLogger(ClinicalAnalyzer.class.getName());
DBconnectorClient connDBMU = null;
HashMap<Integer, ArrayList<WeightedMarker>> weightedMarkers;
HashMap<Integer, ArrayList<ClinicalFactor>> clinicalFactors;
public ClinicalAnalyzer(DBconnectorClient connDBMU) {
this.connDBMU = connDBMU;
this.weightedMarkers = new HashMap<>();
this.clinicalFactors = new HashMap<>();
}
/**
* Get set of markers needed to compute a range of tests
* @param tests
* @return
* @throws SQLException
*/
public HashSet<Marker> getMarkerSet(Collection<Integer> testIds) throws SQLException {
HashSet<Marker> markers = new HashSet<>();
connDBMU.openConnection();
for (Integer testId : testIds) {
ArrayList<WeightedMarker> currentWgtMkrs = connDBMU.getMarkers(testId);
// put if absent
if (weightedMarkers.get(testId) == null) {
weightedMarkers.put(testId, currentWgtMkrs);
}
else {
LOGGER.log(Level.WARNING, "Markers entry already found! Ignore new entry");
}
for (WeightedMarker wgtMkr : currentWgtMkrs) {
markers.add(wgtMkr.getMarker());
}
}
connDBMU.closeConnection();
return markers;
}
public HashSet<Integer> getClinicalFactorSet(Collection<Integer> testIds) {
HashSet<Integer> markers = new HashSet<>();
connDBMU.openConnection();
for (Integer testId : testIds) {
ArrayList<ClinicalFactor> currentCFs = connDBMU.getCFs(testId);
// put if absent
if (clinicalFactors.get(testId) == null) {
clinicalFactors.put(testId, currentCFs);
}
else {
LOGGER.log(Level.WARNING, "Markers entry already found! Ignore new entry");
}
for (ClinicalFactor cf : currentCFs) {
markers.add(cf.getClinicalFactorId());
}
}
connDBMU.closeConnection();
return markers;
}
public HashSet<Integer> getRequiredTests(Collection<TestName> tests) {
HashSet<Integer> testIds = new HashSet<>();
for (TestName testName : tests) {
int testId = testName.getId();
testIds.add(testId);
if (testId == 2) { // HIV Progression test
// add markers of test id 1
testIds.add(1);
// add markers of test id 201
testIds.add(201);
}
else if (testId == 8) { // EFV PHARMACOKINETICS_CYP2B6
// add markers of test 801
testIds.add(801);
}
}
return testIds;
}
public HashMap<Integer, ArrayList<WeightedMarker>> getWeightedMarkers() {
return weightedMarkers;
}
public HashMap<Integer, ArrayList<ClinicalFactor>> getClinicalFactors() {
return clinicalFactors;
}
public TestResultRaw getIfExistsAndNonNull(HashMap<Integer, TestResultRaw> rawResults, Integer id, int parentId) throws MissingMaterialException {
TestResultRaw raw = rawResults.get(id);
if (raw == null) {
throw new MissingMaterialException(parentId);
}
return raw;
}
public Diagnostic analyze(int patientId, DiagnosticRaw diagRaw) {
String[] hlaA = diagRaw.getHlaA();
String[] hlaB = diagRaw.getHlaB();
String[] hlaC = diagRaw.getHlaC();
Diagnostic diag = new Diagnostic(hlaA, hlaB, hlaC);
// analyze test results
HashMap<Integer, TestResultRaw> rawResults = diagRaw.getTestResults();
for (Integer testId : rawResults.keySet()) {
TestResult result = new TestResult(testId);
try {
switch (testId) {
case 2: // handle HIV test
// analyze results of testId=1
// FIXME was this a mistake?
// TestResultRaw resultRaw1 = getIfExists(rawResults, Integer.valueOf(2));
TestResultRaw resultRaw1 = getIfExistsAndNonNull(rawResults, 1, 2);
if (resultRaw1.getGenomic() == 2.0) {
result.setResultStd(0.0);
}
else { // analyze results of testId=201
TestResultRaw resultRaw201 = getIfExistsAndNonNull(rawResults, 201, 2);
if (resultRaw201.getGenomic() >= 1.0) {
result.setResultStd(2.0);
}
else { // analyze results of initial testId=2
TestResultRaw resultRawDefault = getIfExistsAndNonNull(rawResults, testId, 2);
result.setResultStd(resultRawDefault.getGenomic());
}
}
break;
case 8: // handle EFV PHARMACOKINETICS_CYP2B6
// analyze results of inial testId=8
TestResultRaw resultRawDefault = getIfExistsAndNonNull(rawResults, testId, 8);
if (resultRawDefault.getGenomic() < 2.0) {
result.setResultStd(resultRawDefault.getGenomic());
}
else { // run EFV PHARMACOKINETICS_CYP2A6 (801)
// FIXME: was this a mistake?
// TestResultRaw resultRaw801 = getIfExists(rawResults, Integer.valueOf(201));
TestResultRaw resultRaw801 = getIfExistsAndNonNull(rawResults, 801, 8);
if (resultRaw801.getGenomic() >= 1.0) {
result.setResultStd(21.0);
}
else {
result.setResultStd(resultRawDefault.getClinical());
}
}
break;
// Do not process result directly
case 1:
case 201:
case 801:
// do not process result directly
result = null;
break;
default:
// insert test in database
TestResultRaw resultRaw = getIfExistsAndNonNull(rawResults, testId, testId);
result.setResultStd(resultRaw.getGenomic());
if (resultRaw.isClinical()) {
result.setResultCAD(resultRaw.getClinical());
diag.setResultCAD(result.getResultCAD());
connDBMU.insertResult(patientId, testId, result.getResultCAD());
}
else {
connDBMU.insertResult(patientId, testId, result.getResultStd());
}
break;
}
if (result != null) {
diag.addResult(result);
}
} catch (MissingMaterialException e) {
// could not complete the test
diag.addInvalidTest(e.getParentTestId());
}
}
return diag;
}
}
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