com.imsweb.algorithms.multipleprimary.MPGroup Maven / Gradle / Ivy
/*
* Copyright (C) 2013 Information Management Services, Inc.
*/
package com.imsweb.algorithms.multipleprimary;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.apache.commons.lang3.Range;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.math.NumberUtils;
import org.joda.time.Days;
import org.joda.time.LocalDate;
import org.joda.time.Years;
import com.imsweb.algorithms.multipleprimary.MPUtils.MPResult;
import com.imsweb.algorithms.multipleprimary.MPUtils.RuleResult;
public abstract class MPGroup {
// List of specific histologies for a given NOS, this list is used in few of the groups
private static final Map _NOS_VS_SPECIFIC_MAP = new HashMap<>();
static {
_NOS_VS_SPECIFIC_MAP.put("8000", "8001, 8002, 8003, 8004, 8005"); //Cancer/malignant neoplasm, NOS
_NOS_VS_SPECIFIC_MAP.put("8010", "8011, 8012, 8013, 8014, 8015"); //Carcinoma, NOS
_NOS_VS_SPECIFIC_MAP.put("8140", "8141, 8142, 8143, 8144, 8145, 8147, 8148"); //Adenocarcinoma, NOS
_NOS_VS_SPECIFIC_MAP.put("8070", "8071, 8072, 8073, 8074, 8075, 8076, 8077, 8078, 8080, 8081, 8082, 8083, 8084, 8094, 8323"); //Squamous cell carcinoma, NOS
_NOS_VS_SPECIFIC_MAP.put("8720", "8721, 8722, 8723, 8726, 8728, 8730, 8740, 8741, 8742, 8743, 8744, 9745, 8746, 8761, 8770, 8771, 8772, 8773, 8774, 8780"); //Melanoma, NOS
_NOS_VS_SPECIFIC_MAP.put("8800", "8801. 8802, 8803, 8804, 8805, 8806"); //Sarcoma, NOS
_NOS_VS_SPECIFIC_MAP.put("8312", "8313, 8314, 8315, 8316, 8317, 8318, 8319, 8320"); //Renal cell carcinoma, NOS
}
protected String _id;
protected String _name;
protected String _siteInclusions;
protected String _siteExclusions;
protected String _histInclusions;
protected String _histExclusions;
protected List _behavInclusions;
protected List _rules;
private List> _siteIncRanges;
private List> _siteExcRanges;
private List> _histIncRanges;
private List> _histExcRanges;
public MPGroup(String id, String name, String siteInclusions, String siteExclusions, String histInclusions, String histExclusions, List behavInclusions) {
_id = id;
_name = name;
_siteInclusions = siteInclusions;
_siteExclusions = siteExclusions;
_histInclusions = histInclusions;
_histExclusions = histExclusions;
_behavInclusions = behavInclusions;
_rules = new ArrayList<>();
// compute the raw inclusions/exclusions into ranges
_siteIncRanges = computeRange(siteInclusions, true);
_siteExcRanges = computeRange(siteExclusions, true);
_histIncRanges = computeRange(histInclusions, false);
_histExcRanges = computeRange(histExclusions, false);
}
public String getId() {
return _id;
}
public String getName() {
return _name;
}
public String getSiteInclusions() {
return _siteInclusions;
}
public String getSiteExclusions() {
return _siteExclusions;
}
public String getHistInclusions() {
return _histInclusions;
}
public String getHistExclusions() {
return _histExclusions;
}
public List getBehavInclusions() {
return _behavInclusions;
}
public List getRules() {
return _rules;
}
public boolean isApplicable(String primarySite, String histology, String behavior) {
if (!MPUtils.validateProperties(primarySite, histology, behavior) || !_behavInclusions.contains(behavior))
return false;
boolean siteOk, histOk = false;
Integer site = Integer.parseInt(primarySite.substring(1)), hist = Integer.parseInt(histology);
// check site
if (_siteIncRanges != null)
siteOk = isContained(_siteIncRanges, site);
else
siteOk = _siteExcRanges == null || !isContained(_siteExcRanges, site);
// check histology (only if site matched)
if (siteOk) {
if (_histIncRanges != null)
histOk = isContained(_histIncRanges, hist);
else
histOk = _histExcRanges == null || !isContained(_histExcRanges, hist);
}
return siteOk && histOk;
}
protected boolean isContained(List> list, Integer value) {
for (Range range : list)
if (range.contains(value))
return true;
return false;
}
protected List> computeRange(String rawValue, boolean isSite) {
if (rawValue == null)
return null;
List> result = new ArrayList<>();
for (String item : StringUtils.split(rawValue, ',')) {
String[] parts = StringUtils.split(item.trim(), '-');
if (parts.length == 1) {
if (isSite)
result.add(Range.is(Integer.parseInt(parts[0].substring(1))));
else
result.add(Range.is(Integer.parseInt(parts[0])));
}
else {
if (isSite)
result.add(Range.between(Integer.parseInt(parts[0].substring(1)), Integer.parseInt(parts[1].substring(1))));
else
result.add(Range.between(Integer.parseInt(parts[0]), Integer.parseInt(parts[1])));
}
}
return result;
}
//This method is to expand lists with range. Invalid ranges will cause exception
public static List expandList(List list) {
List result = new ArrayList<>();
if (list == null || list.isEmpty())
return null;
for (String item : list) {
String [] ranges = StringUtils.split(item.trim(), ',');
for (String range : ranges) {
String[] parts = StringUtils.split(range.trim(), '-');
if (parts.length <= 1)
result.add(range);
else {
Integer start = Integer.valueOf(parts[0]);
Integer end = Integer.valueOf(parts[1]);
while (start <= end) {
result.add(String.valueOf(start++));
}
}
}
}
return result;
}
protected Map getNosVsSpecificMap() {
return Collections.unmodifiableMap(_NOS_VS_SPECIFIC_MAP);
}
@Override
public boolean equals(Object o) {
if (this == o) {
return true;
}
if (o == null || getClass() != o.getClass()) {
return false;
}
MPGroup mpGroup = (MPGroup)o;
return _id.equals(mpGroup._id);
}
@Override
public int hashCode() {
return _id.hashCode();
}
/* *********************************************************************************************************************
* *************************** COMMON RULES USED IN MOST OF THE GROUPS ****************************************
* *********************************************************************************************************************/
public static class MPRuleHistologyCode extends MPRule {
public MPRuleHistologyCode(String groupId, String step) {
super(groupId, step, MPResult.MULTIPLE_PRIMARIES);
setQuestion("Do the tumors haveICD-O-3 histology codes that are different at the first (?xxx), second (x?xx) or third (xx?x) number?");
setReason("Tumors with ICD-O-3 histology codes that are different at the first (?xxx), second (x?xx) or third (xx?x) number are multiple primaries.");
}
@Override
public MPRuleResult apply(MPInput i1, MPInput i2) {
MPRuleResult result = new MPRuleResult();
String hist1 = i1.getHistologyIcdO3(), hist2 = i2.getHistologyIcdO3();
result.setResult((!hist1.substring(0, 3).equals(hist2.substring(0, 3))) ? RuleResult.TRUE : RuleResult.FALSE);
return result;
}
}
public static class MPRulePrimarySiteCode extends MPRule {
public MPRulePrimarySiteCode(String groupId, String step) {
super(groupId, step, MPResult.MULTIPLE_PRIMARIES);
setQuestion("Are there tumors in sites with ICD-O-3 topography codes that are different at the second (C?xx) and/or third character (Cx?x)?");
setReason("Tumors in sites with ICD-O-3 topography codes that are different at the second (C?xx) and/or third (Cx?x) character are multiple primaries.");
}
@Override
public MPRuleResult apply(MPInput i1, MPInput i2) {
MPRuleResult result = new MPRuleResult();
result.setResult((!i1.getPrimarySite().substring(1, 3).equals(i2.getPrimarySite().substring(1, 3))) ? RuleResult.TRUE : RuleResult.FALSE);
return result;
}
}
public static class MPRuleBehavior extends MPRule {
public MPRuleBehavior(String groupId, String step) {
super(groupId, step, MPResult.MULTIPLE_PRIMARIES);
setQuestion("Is there an invasive tumor following an in situ tumor more than 60 days after diagnosis?");
setReason("An invasive tumor following an in situ tumor more than 60 days after diagnosis are multiple primaries.");
getNotes().add("The purpose of this rule is to ensure that the case is counted as an incident (invasive) case when incidence data are analyzed.");
getNotes().add("Abstract as multiple primaries even if the medical record/physician states it is recurrence or progression of disease.");
}
@Override
public MPRuleResult apply(MPInput i1, MPInput i2) {
MPRuleResult result = new MPRuleResult();
String beh1 = i1.getBehaviorIcdO3(), beh2 = i2.getBehaviorIcdO3();
if (!differentCategory(beh1, beh2, Collections.singletonList("2"), Collections.singletonList("3"))) {
result.setResult(RuleResult.FALSE);
return result;
}
int diff = verify60DaysApart(i1, i2, true);
if (-1 == diff) {
result.setResult(RuleResult.UNKNOWN);
result.setMessage("Unable to apply Rule " + this.getStep() + " of " + this.getGroupId() + ". There is no enough diagnosis date information.");
}
else if ((1 == diff && "3".equals(beh1) && "2".equals(beh2)) || (2 == diff && "3".equals(beh2) && "2".equals(beh1)))
result.setResult(RuleResult.TRUE);
else
result.setResult(RuleResult.FALSE);
return result;
}
}
public static class MPRuleDiagnosisDate extends MPRule {
public MPRuleDiagnosisDate(String groupId, String step) {
super(groupId, step, MPResult.MULTIPLE_PRIMARIES);
setQuestion("Are there tumors diagnosed more than five (5) years apart?");
setReason("Tumors diagnosed more than five (5) years apart are multiple primaries.");
}
@Override
public MPRuleResult apply(MPInput i1, MPInput i2) {
MPRuleResult result = new MPRuleResult();
int diff = verifyYearsApart(i1, i2, 5);
if (-1 == diff) {
result.setResult(RuleResult.UNKNOWN);
result.setMessage("Unable to apply Rule " + this.getStep() + " of " + this.getGroupId() + ". There is no enough diagnosis date information.");
}
else
result.setResult(1 == diff ? RuleResult.TRUE : RuleResult.FALSE);
return result;
}
}
public static class MPRuleNoCriteriaSatisfied extends MPRule {
public MPRuleNoCriteriaSatisfied(String groupId, String step) {
super(groupId, step, MPResult.SINGLE_PRIMARY);
setQuestion("Does not meet any of the criteria?");
setReason("Tumors that do not meet any of the criteria are abstracted as a single primary.");
}
@Override
public MPRuleResult apply(MPInput i1, MPInput i2) {
MPRuleResult result = new MPRuleResult();
result.setResult(RuleResult.TRUE);
return result;
}
}
/* *********************************************************************************************************************
* *************************** HELPER METHODS USED IN MOST OF THE GROUPS ****************************************
* *********************************************************************************************************************/
//helper method, checks if one property belongs to some category and the other to different category
public static boolean differentCategory(String prop1, String prop2, List cat1, List cat2) {
return !(cat1 == null || cat2 == null || cat1.isEmpty() || cat2.isEmpty()) && ((cat1.contains(prop1) && cat2.contains(prop2)) || (cat1.contains(prop2) && cat2.contains(prop1)));
}
//checks if the two tumors are diagnosed "x" years apart. It returns Yes (1), No (0) or Unknown (-1) (If there is no enough information)
public static int verifyYearsApart(MPInput input1, MPInput input2, int yearsApart) {
int yes = 1, no = 0, unknown = -1;
int year1 = NumberUtils.isDigits(input1.getDateOfDiagnosisYear()) ? Integer.parseInt(input1.getDateOfDiagnosisYear()) : 9999;
int year2 = NumberUtils.isDigits(input2.getDateOfDiagnosisYear()) ? Integer.parseInt(input2.getDateOfDiagnosisYear()) : 9999;
int month1 = NumberUtils.isDigits(input1.getDateOfDiagnosisMonth()) ? Integer.parseInt(input1.getDateOfDiagnosisMonth()) : 99;
int month2 = NumberUtils.isDigits(input2.getDateOfDiagnosisMonth()) ? Integer.parseInt(input2.getDateOfDiagnosisMonth()) : 99;
int day1 = NumberUtils.isDigits(input1.getDateOfDiagnosisDay()) ? Integer.parseInt(input1.getDateOfDiagnosisDay()) : 99;
int day2 = NumberUtils.isDigits(input2.getDateOfDiagnosisDay()) ? Integer.parseInt(input2.getDateOfDiagnosisDay()) : 99;
//If year is missing or in the future, return unknown
int currYear = LocalDate.now().getYear();
if (year1 == 9999 || year2 == 9999 || year1 > currYear || year2 > currYear)
return unknown;
else if (Math.abs(year1 - year2) > yearsApart)
return yes;
else if (Math.abs(year1 - year2) < yearsApart)
return no;
else {
//if month is missing, set day to 99
if (month1 == 99)
day1 = 99;
if (month2 == 99)
day2 = 99;
//if month and day are invalid set them to 99 (Example: if month is 13 or day is 35)
try {
new LocalDate(year1, month1 == 99 ? 1 : month1, day1 == 99 ? 1 : day1);
}
catch (Exception e) {
day1 = 99;
if (month1 < 1 || month1 > 12)
month1 = 99;
}
try {
new LocalDate(year2, month2 == 99 ? 1 : month2, day2 == 99 ? 1 : day2);
}
catch (Exception e) {
day2 = 99;
if (month2 < 1 || month2 > 12)
month2 = 99;
}
if (month1 == 99 || month2 == 99)
return unknown;
else if ((year1 > year2 && month1 > month2) || (year2 > year1 && month2 > month1))
return yes;
else if ((year1 > year2 && month1 < month2) || (year2 > year1 && month2 < month1))
return no;
else if (day1 == 99 || day2 == 99)
return unknown;
else
return Math.abs(Years.yearsBetween(new LocalDate(year1, month1, day1), new LocalDate(year2, month2, day2)).getYears()) >= yearsApart ? yes : no;
}
}
//helper method, checks whether there are 60 *days* between diagnosis date of the two tumors. It returns 1 (if tumor 1 is diagnosed after 60 days of tumor 2),
//2 (if tumor 2 is diagnosed 60 days after tumor 1), 0 (if the days between two diagnosis is less than 60 days) or -1 (if there is insufficient information);
// If checkBehavior is true, it also checks if invasive is after in situ tumor
public static int verify60DaysApart(MPInput input1, MPInput input2, boolean checkBehavior) {
int yes1 = 1, yes2 = 2, no = 0, unknown = -1;
int year1 = NumberUtils.isDigits(input1.getDateOfDiagnosisYear()) ? Integer.parseInt(input1.getDateOfDiagnosisYear()) : 9999;
int year2 = NumberUtils.isDigits(input2.getDateOfDiagnosisYear()) ? Integer.parseInt(input2.getDateOfDiagnosisYear()) : 9999;
int month1 = NumberUtils.isDigits(input1.getDateOfDiagnosisMonth()) ? Integer.parseInt(input1.getDateOfDiagnosisMonth()) : 99;
int month2 = NumberUtils.isDigits(input2.getDateOfDiagnosisMonth()) ? Integer.parseInt(input2.getDateOfDiagnosisMonth()) : 99;
int day1 = NumberUtils.isDigits(input1.getDateOfDiagnosisDay()) ? Integer.parseInt(input1.getDateOfDiagnosisDay()) : 99;
int day2 = NumberUtils.isDigits(input2.getDateOfDiagnosisDay()) ? Integer.parseInt(input2.getDateOfDiagnosisDay()) : 99;
//If year is missing or in the future, return unknown
int currYear = LocalDate.now().getYear();
if (year1 == 9999 || year2 == 9999 || year1 > currYear || year2 > currYear)
return unknown;
//if month is missing, set day to 99
if (month1 == 99)
day1 = 99;
if (month2 == 99)
day2 = 99;
//if month and day are invalid set them to 99 (Example: if month is 13 or day is 35)
try {
new LocalDate(year1, month1 == 99 ? 1 : month1, day1 == 99 ? 1 : day1);
}
catch (Exception e) {
day1 = 99;
if (month1 < 1 || month1 > 12)
month1 = 99;
}
try {
new LocalDate(year2, month2 == 99 ? 1 : month2, day2 == 99 ? 1 : day2);
}
catch (Exception e) {
day2 = 99;
if (month2 < 1 || month2 > 12)
month2 = 99;
}
if (month1 != 99 && month2 != 99 && day1 != 99 && day2 != 99) {
if (Days.daysBetween(new LocalDate(year2, month2, day2), new LocalDate(year1, month1, day1)).getDays() > 60)
return yes1;
else if (Days.daysBetween(new LocalDate(year1, month1, day1), new LocalDate(year2, month2, day2)).getDays() > 60)
return yes2;
else
return no;
}
else if (year1 - year2 >= 2)
return yes1;
else if (year2 - year1 >= 2)
return yes2;
else if (year1 > year2) {
// If invasive is diagnosed before in situ
if (checkBehavior && "2".equals(input1.getBehaviorIcdO3()) && "3".equals(input2.getBehaviorIcdO3()))
return no;
return verify60DaysApart(year2, month2, day2, year1, month1, day1);
}
else if (year2 > year1) {
// If invasive is diagnosed before in situ
if (checkBehavior && "3".equals(input1.getBehaviorIcdO3()) && "2".equals(input2.getBehaviorIcdO3()))
return no;
return 1 == verify60DaysApart(year1, month1, day1, year2, month2, day2) ? yes2 : verify60DaysApart(year1, month1, day1, year2, month2, day2);
}
else {
if (month1 == 99 || month2 == 99)
return unknown;
else if (month1 > month2) {
// If invasive is diagnosed before in situ
if (checkBehavior && "2".equals(input1.getBehaviorIcdO3()) && "3".equals(input2.getBehaviorIcdO3()))
return no;
return verify60DaysApart(year2, month2, day2, year1, month1, day1);
}
else if (month2 > month1) {
// If invasive is diagnosed before in situ
if (checkBehavior && "3".equals(input1.getBehaviorIcdO3()) && "2".equals(input2.getBehaviorIcdO3()))
return no;
return 1 == verify60DaysApart(year1, month1, day1, year2, month2, day2) ? yes2 : verify60DaysApart(year1, month1, day1, year2, month2, day2);
}
else
return no;
}
}
//This method is called with valid years
private static int verify60DaysApart(int startYr, int startMon, int startDay, int endYr, int endMon, int endDay) {
LocalDate startDateMin, startDateMax, endDateMin, endDateMax;
if (startMon == 99 && endMon == 99)
return -1;
else if (startMon != 99 && endMon != 99) {
startDateMin = new LocalDate(startYr, startMon, 1);
startDateMax = startDateMin.dayOfMonth().withMaximumValue();
endDateMin = new LocalDate(endYr, endMon, 1);
endDateMax = endDateMin.dayOfMonth().withMaximumValue();
if (startDay != 99)
startDateMin = startDateMax = new LocalDate(startYr, startMon, startDay);
if (endDay != 99)
endDateMin = endDateMax = new LocalDate(endYr, endMon, endDay);
}
else if (endMon == 99) {
endDateMin = new LocalDate(endYr, 1, 1);
endDateMax = new LocalDate(endYr, 12, 31);
if (startDay != 99)
startDateMin = startDateMax = new LocalDate(startYr, startMon, startDay);
else {
startDateMin = new LocalDate(startYr, startMon, 1);
startDateMax = startDateMin.dayOfMonth().withMaximumValue();
}
}
else {
startDateMin = new LocalDate(startYr, 1, 1);
startDateMax = new LocalDate(startYr, 12, 31);
if (endDay != 99)
endDateMin = endDateMax = new LocalDate(endYr, endMon, endDay);
else {
endDateMin = new LocalDate(endYr, endMon, 1);
endDateMax = endDateMin.dayOfMonth().withMaximumValue();
}
}
int minDaysBetween = Days.daysBetween(startDateMax, endDateMin).getDays();
int maxDaysBetween = Days.daysBetween(startDateMin, endDateMax).getDays();
if (minDaysBetween > 60)
return 1;
else if (maxDaysBetween <= 60)
return 0;
else
return -1;
}
//helper method, checks which tumor is diagnosed later. It returns 1 (if tumor 1 is diagnosed after tumor 2),
//2 (if tumor 2 is diagnosed after tumor 1), 0 (if the diagnosis takes at the same day) or -1 (if there is insufficient information e.g if both year is 2007, but month and day is unknown);
public static int compareDxDate(MPInput input1, MPInput input2) {
int tumor1 = 1, tumor2 = 2, sameDay = 0, unknown = -1;
int year1 = NumberUtils.isDigits(input1.getDateOfDiagnosisYear()) ? Integer.parseInt(input1.getDateOfDiagnosisYear()) : 9999;
int year2 = NumberUtils.isDigits(input2.getDateOfDiagnosisYear()) ? Integer.parseInt(input2.getDateOfDiagnosisYear()) : 9999;
int month1 = NumberUtils.isDigits(input1.getDateOfDiagnosisMonth()) ? Integer.parseInt(input1.getDateOfDiagnosisMonth()) : 99;
int month2 = NumberUtils.isDigits(input2.getDateOfDiagnosisMonth()) ? Integer.parseInt(input2.getDateOfDiagnosisMonth()) : 99;
int day1 = NumberUtils.isDigits(input1.getDateOfDiagnosisDay()) ? Integer.parseInt(input1.getDateOfDiagnosisDay()) : 99;
int day2 = NumberUtils.isDigits(input2.getDateOfDiagnosisDay()) ? Integer.parseInt(input2.getDateOfDiagnosisDay()) : 99;
//If year is missing or in the future, return unknown
int currYear = LocalDate.now().getYear();
if (year1 == 9999 || year2 == 9999 || year1 > currYear || year2 > currYear)
return unknown;
else if (year1 > year2)
return tumor1;
else if (year2 > year1)
return tumor2;
if (month1 == 99)
day1 = 99;
if (month2 == 99)
day2 = 99;
//if month and day are invalid set them to 99 (Example: if month is 13 or day is 35)
try {
new LocalDate(year1, month1 == 99 ? 1 : month1, day1 == 99 ? 1 : day1);
}
catch (Exception e) {
day1 = 99;
if (month1 < 1 || month1 > 12)
month1 = 99;
}
try {
new LocalDate(year2, month2 == 99 ? 1 : month2, day2 == 99 ? 1 : day2);
}
catch (Exception e) {
day2 = 99;
if (month2 < 1 || month2 > 12)
month2 = 99;
}
if (month1 == 99 || month2 == 99)
return unknown;
else if (month1 > month2)
return tumor1;
else if (month2 > month1)
return tumor2;
else if (day1 == 99 || day2 == 99)
return unknown;
else if (day1 > day2)
return tumor1;
else if (day2 > day1)
return tumor2;
else
return sameDay;
}
}
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