com.imsweb.algorithms.iarc.IarcUtils Maven / Gradle / Ivy
/*
* Copyright (C) 2018 Information Management Services, Inc.
*/
package com.imsweb.algorithms.iarc;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
import org.apache.commons.lang3.math.NumberUtils;
import com.imsweb.algorithms.internal.Utils;
/**
* This class is used to calculate the International Primary indicator variable.
*
* See http://www.iacr.com.fr/images/doc/MPrules_july2004.pdf/.
*/
public class IarcUtils {
public static final String ALG_NAME = "IARC Multiple Primary Indicator";
public static final String VERSION = "ICD-O Third Edition";
public static final String ALG_INFO = "International rules for multiple primary cancers released in 2004";
public static final Integer DUPLICATE = 0;
public static final Integer PRIMARY = 1;
public static final Integer INSITU = 9;
public static List calculateIarcMp(List records) {
//No records
if (records == null || records.isEmpty())
return null;
//If there is only one tumor
if (records.size() == 1) {
if (isInsitu(records.get(0)))
records.get(0).setInternationalPrimaryIndicator(INSITU);
else
records.get(0).setInternationalPrimaryIndicator(PRIMARY);
return records;
}
//Calculate the site group and hist group
//let's also use a different list so we don't change the order of the original records
List internalRecords = new ArrayList<>();
for (IarcMpInputRecordDto record : records) {
//Set iarc as primary by default
record.setInternationalPrimaryIndicator(PRIMARY);
record.setSiteGroup(calculateSiteGroup(record.getSite()));
record.setHistGroup(calculateHistGroup(record.getHistology()));
internalRecords.add(new InternalRecDto(record));
}
Collections.sort(internalRecords);
//Calculate IARC MP variable
for (int i = 0; i < internalRecords.size(); i++) {
IarcMpInputRecordDto r1 = internalRecords.get(i).getOriginalRecord();
if (DUPLICATE.equals(r1.getInternationalPrimaryIndicator()) || INSITU.equals(r1.getInternationalPrimaryIndicator()))
continue;
//Insitu cases are ignored except bladder
if (isInsitu(r1)) {
r1.setInternationalPrimaryIndicator(INSITU);
continue;
}
for (int j = i + 1; j < internalRecords.size(); j++) {
IarcMpInputRecordDto r2 = internalRecords.get(j).getOriginalRecord();
//Insitu cases are ignored except bladder
if (isInsitu(r2)) {
r2.setInternationalPrimaryIndicator(INSITU);
continue;
}
if (r1.getHistGroup() != null && r2.getHistGroup() != null && r1.getSiteGroup() != null && r2.getSiteGroup() != null) {
//Kaposi sarcoma or Hemato, no need to check the site
if (isKaposiSarcoma(r1, r2) || isHemato(r1, r2) || (isSameSiteGroup(r1, r2) && (isSameHistGroup(r1, r2) || isNosVsSpecific(r1, r2)))) {
r2.setInternationalPrimaryIndicator(DUPLICATE);
if (needToUpdateHistology(r1, r2)) {
r1.setHistology(r2.getHistology());
r1.setHistGroup(calculateHistGroup(r1.getHistology()));
}
}
}
}
}
return records;
}
private static String calculateSiteGroup(String site) {
String siteGroup = site != null && site.length() >= 3 ? site.toUpperCase().substring(0, 3) : null;
if (siteGroup != null) {
if (Arrays.asList("C01", "C02").contains(siteGroup))
siteGroup = "C02";
else if (Arrays.asList("C00", "C03", "C04", "C05", "C06").contains(siteGroup))
siteGroup = "C06";
else if (Arrays.asList("C09", "C10", "C12", "C13", "C14").contains(siteGroup))
siteGroup = "C14";
else if (Arrays.asList("C19", "C20").contains(siteGroup))
siteGroup = "C20";
else if (Arrays.asList("C23", "C24").contains(siteGroup))
siteGroup = "C24";
else if (Arrays.asList("C33", "C34").contains(siteGroup))
siteGroup = "C34";
else if (Arrays.asList("C40", "C41").contains(siteGroup))
siteGroup = "C41";
else if (Arrays.asList("C65", "C66", "C67", "C68").contains(siteGroup))
siteGroup = "C68";
}
return siteGroup;
}
private static Integer calculateHistGroup(String histology) {
Integer histologyGroup = null;
if (NumberUtils.isDigits(histology)) {
int hist = NumberUtils.toInt(histology);
if (Utils.isHistologyContained("8051-8084,8120-8131", hist))
histologyGroup = 1;
else if (Utils.isHistologyContained("8090-8110", hist))
histologyGroup = 2;
else if (Utils.isHistologyContained("8140-8149,8160-8162,8190-8221,8260-8337,8350-8551,8570-8576,8940-8941", hist))
histologyGroup = 3;
else if (Utils.isHistologyContained("8030-8046,8150-8157,8170-8180,8230-8255,8340-8347,8560-8562,8580-8671", hist))
histologyGroup = 4;
else if (Utils.isHistologyContained("8010-8015,8020-8022,8050", hist))
histologyGroup = 5;
else if (Utils.isHistologyContained("8680-8713,8800-8921,8990-8991,9040-9044,9120-9125,9130-9136,9141-9252,9370-9373,9540-9582", hist))
histologyGroup = 6;
else if (Utils.isHistologyContained("9050-9055", hist))
histologyGroup = 7;
else if (Utils.isHistologyContained("9840,9861-9931,9945-9946,9950,9961-9964,9980-9987,9991-9992", hist))
histologyGroup = 8;
else if (Utils.isHistologyContained("9597,9670-9699,9712,9728,9731-9738,9761-9767,9769,9811-9818,9823-9826,9833,9836,9940", hist))
histologyGroup = 9;
else if (Utils.isHistologyContained("9700-9726,9729,9768,9827-9831,9834,9837,9948", hist))
histologyGroup = 10;
else if (Utils.isHistologyContained("9650-9667", hist))
histologyGroup = 11;
else if (Utils.isHistologyContained("9740-9742", hist))
histologyGroup = 12;
else if (Utils.isHistologyContained("9750-9759", hist))
histologyGroup = 13;
else if (Utils.isHistologyContained("9590-9591,9596,9727,9760,9800-9809,9820,9832,9835,9860,9960,9965-9975,9989", hist))
histologyGroup = 14;
else if (hist == 9140)
histologyGroup = 15;
else if (Utils.isHistologyContained("8720-8790,8930-8936,8950-8983,9000-9030,9060-9110,9260-9365,9380-9539", hist))
histologyGroup = 16;
else if (Utils.isHistologyContained("8000-8005", hist))
histologyGroup = 17;
}
return histologyGroup;
}
private static boolean isInsitu(IarcMpInputRecordDto record) {
return !"3".equals(record.getBehavior()) && !(record.getSite() != null && record.getSite().toUpperCase().startsWith("C67"));
}
private static boolean isKaposiSarcoma(IarcMpInputRecordDto rec1, IarcMpInputRecordDto rec2) {
return rec1.getHistGroup() == 15 && rec2.getHistGroup() == 15;
}
private static boolean isHemato(IarcMpInputRecordDto rec1, IarcMpInputRecordDto rec2) {
return rec1.getHistGroup() >= 8 && rec1.getHistGroup() <= 14 && rec2.getHistGroup() >= 8 && rec2.getHistGroup() <= 14 && (rec1.getHistGroup() == 14 || rec2.getHistGroup() == 14 || rec1
.getHistGroup().equals(rec2.getHistGroup()));
}
private static boolean isSameSiteGroup(IarcMpInputRecordDto rec1, IarcMpInputRecordDto rec2) {
return rec1.getSiteGroup().equals(rec2.getSiteGroup());
}
private static boolean isSameHistGroup(IarcMpInputRecordDto rec1, IarcMpInputRecordDto rec2) {
return rec1.getHistGroup().equals(rec2.getHistGroup());
}
private static boolean isNosVsSpecific(IarcMpInputRecordDto rec1, IarcMpInputRecordDto rec2) {
//17 is NOS for 1-7, 15 and 16
//14 is NOS for 8-13
//5 is NOS for 1-4
return (rec1.getHistGroup() == 17 && ((rec2.getHistGroup() >= 1 && rec2.getHistGroup() <= 7) || rec2.getHistGroup() == 15 || rec2.getHistGroup() == 16)) ||
(rec2.getHistGroup() == 17 && ((rec1.getHistGroup() >= 1 && rec1.getHistGroup() <= 7) || rec1.getHistGroup() == 15 || rec1.getHistGroup() == 16)) ||
(rec1.getHistGroup() == 14 && rec2.getHistGroup() >= 8 && rec2.getHistGroup() <= 13) ||
(rec2.getHistGroup() == 14 && rec1.getHistGroup() >= 8 && rec1.getHistGroup() <= 13) ||
(rec1.getHistGroup() == 5 && rec2.getHistGroup() >= 1 && rec2.getHistGroup() <= 4) ||
(rec2.getHistGroup() == 5 && rec1.getHistGroup() >= 1 && rec1.getHistGroup() <= 4);
}
private static boolean needToUpdateHistology(IarcMpInputRecordDto primaryRec, IarcMpInputRecordDto dupRecord) {
return (primaryRec.getHistGroup() == 17 && ((dupRecord.getHistGroup() >= 1 && dupRecord.getHistGroup() <= 7) || dupRecord.getHistGroup() == 15 || dupRecord.getHistGroup() == 16)) ||
(primaryRec.getHistGroup() == 14 && dupRecord.getHistGroup() >= 8 && dupRecord.getHistGroup() <= 13) ||
(primaryRec.getHistGroup() == 5 && dupRecord.getHistGroup() >= 1 && dupRecord.getHistGroup() <= 4) ||
(primaryRec.getHistGroup().equals(dupRecord.getHistGroup()) && NumberUtils.toInt(primaryRec.getHistology()) < NumberUtils.toInt(dupRecord.getHistology()));
}
private static class InternalRecDto implements Comparable {
IarcMpInputRecordDto _originalRecord;
int _year, _month, _day, _seqNum;
public InternalRecDto(IarcMpInputRecordDto record) {
_originalRecord = record;
String yearStr = record.getDateOfDiagnosisYear();
String monthStr = record.getDateOfDiagnosisMonth();
String dayStr = record.getDateOfDiagnosisDay();
_year = NumberUtils.isDigits(yearStr) ? Integer.parseInt(yearStr) : 9999;
_month = NumberUtils.isDigits(monthStr) ? Integer.parseInt(monthStr) : 99;
_day = NumberUtils.isDigits(dayStr) ? Integer.parseInt(dayStr) : 99;
if (_month == 99)
_day = 99;
_seqNum = record.getSequenceNumber() == null ? -1 : record.getSequenceNumber();
// the sequence numbers might be used to determine the order; there are two families of sequences: federal (00-59, 98, 99) and non-federal (60-97);
// sine the non-federal need to always be after the federal, let's add 100 to all the non-federal (making them 160-197)
if (_seqNum >= 60 && _seqNum <= 97)
_seqNum += 100;
}
public IarcMpInputRecordDto getOriginalRecord() {
return _originalRecord;
}
@Override
public int compareTo(InternalRecDto other) {
if (_year == 9999 || other._year == 9999)
return _seqNum - other._seqNum;
else if (_year != other._year)
return _year - other._year;
else {
if (_month == 99 || other._month == 99)
return _seqNum - other._seqNum;
else if (_month != other._month)
return _month - other._month;
else {
if (_day == 99 || other._day == 99 || this._day == other._day)
return _seqNum - other._seqNum;
else
return _day - other._day;
}
}
}
@Override
@SuppressWarnings("SimplifiableIfStatement")
public boolean equals(Object o) {
if (this == o)
return true;
if (o == null || getClass() != o.getClass())
return false;
InternalRecDto other = (InternalRecDto)o;
if (_year == 9999 || other._year == 9999)
return _seqNum == other._seqNum;
else if (_year != other._year)
return false;
else {
if (_month == 99 || other._month == 99)
return _seqNum == other._seqNum;
else if (_month != other._month)
return false;
else {
if (_day == 99 || other._day == 99 || this._day == other._day)
return _seqNum == other._seqNum;
else
return false;
}
}
}
@Override
public int hashCode() {
int result = _year;
result = 31 * result + _month;
result = 31 * result + _day;
result = 31 * result + _seqNum;
return result;
}
}
}
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