com.imsweb.algorithms.iccc.IcccRecodeUtils Maven / Gradle / Ivy
package com.imsweb.algorithms.iccc;
import java.io.IOException;
import java.io.InputStreamReader;
import java.net.URL;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.regex.Pattern;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.math.NumberUtils;
import com.opencsv.CSVReader;
import com.opencsv.exceptions.CsvException;
import com.imsweb.algorithms.internal.Utils;
/**
* This class can be used to calculate the ICCC Recode variable.
* User: depryf
* Date: 8/22/12
*/
public final class IcccRecodeUtils {
// algorithm name
public static final String ALG_NAME = "International Classification of Childhood Cancer";
// version for the 2010+ data (http://seer.cancer.gov/iccc/iccc3.html)
public static final String VERSION_THIRD_EDITION = "Third Edition";
public static final String VERSION_THIRD_EDITION_INFO = "International Classification of Childhood Cancer, Third edition (ICCC-3) based on ICD-O-3";
// version based on the WHO 2008 classification (http://seer.cancer.gov/iccc/iccc-who2008.html)
public static final String VERSION_WHO_2008 = "ICD-O-3/WHO 2008";
public static final String VERSION_WHO_2008_INFO = "International Classification of Childhood Cancer based on ICD-O-3/WHO 2008";
// version for the 2010+ data/IARC 2017 (https://seer.cancer.gov/iccc/iccc-iarc-2017.html)
public static final String VERSION_THIRD_EDITION_IARC_2017 = "Third Edition/IARC 2017";
public static final String VERSION_THIRD_EDITION_IARC_2017_INFO = "International Classification of Childhood Cancer, Third edition based on ICD-O-3/IARC 2017";
// cached versions
private static final Map _VERSIONS = new HashMap<>();
// default version
public static final String VERSION_DEFAULT = VERSION_THIRD_EDITION_IARC_2017;
static {
_VERSIONS.put(VERSION_THIRD_EDITION, VERSION_THIRD_EDITION_INFO);
_VERSIONS.put(VERSION_WHO_2008, VERSION_WHO_2008_INFO);
_VERSIONS.put(VERSION_THIRD_EDITION_IARC_2017, VERSION_THIRD_EDITION_IARC_2017_INFO);
}
// unknown value
public static final String ICCC_UNKNOWN_RECODE = "999";
public static final String ICCC_UNKNOWN_MAJOR_CATEGORY = "99";
// cached formatted data
private static final Map> _DATA = new HashMap<>();
// cached runtime data
private static final Map> _INTERNAL_DATA = new HashMap<>();
// cached regexes
private static final Pattern _SITE_REGEX = Pattern.compile("C\\d+");
/**
* Private constructor, no instanciation of this class!
*/
private IcccRecodeUtils() {}
public static String calculateIcccMajorCategory(String icccSiteRecode) {
int iICCC = Integer.parseInt(icccSiteRecode);
String icccMajorCategory = ICCC_UNKNOWN_MAJOR_CATEGORY;
int major = -1;
if (11 <= iICCC && iICCC <= 15) major = 1; // I. Lymphoid leukemias
else if (21 <= iICCC && iICCC <= 25) major = 2; // II. Lymphomas and reticuloendothelial neoplasms
else if (31 <= iICCC && iICCC <= 36) major = 3; // III. CNS and miscellaneous intracranial and intraspinal neoplasms
else if (41 <= iICCC && iICCC <= 42) major = 4; // IV. Neuroblastoma and other peripheral nervous cell tumors
else if (50 == iICCC) major = 5; // V. Retinoblastoma
else if (61 <= iICCC && iICCC <= 63) major = 6; // VI. Renal tumors
else if (71 <= iICCC && iICCC <= 73) major = 7; // VII. Hepatic tumors
else if (81 <= iICCC && iICCC <= 85) major = 8; // VIII. Malignant bone tumors
else if (91 <= iICCC && iICCC <= 95) major = 9; // IX. Soft tissue and other extraosseous sarcomas
else if (101 <= iICCC && iICCC <= 105) major = 10; // X. Germ cell tumors, trophoblastic tumors, and neoplasms of gonads
else if (112 == iICCC) major = 11; // XI. Other malignant epithelial neoplasms and malignant melanomas (Thyroid carcinomas)
else if (114 == iICCC) major = 12; // XI. Other malignant epithelial neoplasms and malignant melanomas (Malignant melanomas)
else if (115 == iICCC) major = 13; // XI. Other malignant epithelial neoplasms and malignant melanomas (Skin carcinomas)
else if (111 == iICCC || 113 == iICCC || 116 == iICCC) major = 14; // XI. Other malignant epithelial neoplasms and malignant melanomas
else if (121 <= iICCC && iICCC <= 122) major = 15; // XII. Other and unspecified malignant neoplasms
if (major != -1)
icccMajorCategory = StringUtils.leftPad(String.valueOf(major), 2, "0");
return icccMajorCategory;
}
/**
* Returns the available versions, ID is the version key, value is the version description.
* @return the available versions
*/
public static Map getAvailableVersions() {
return Collections.unmodifiableMap(_VERSIONS);
}
/**
* Returns the calculated site recode for the provided parameters, unknown if it can't be calculated.
* @param version data version
* @param site site
* @param histology histology
* @param behavior behavior
* @return the calculated site recode for the provided parameters, unknown if it can't be calculated
*/
public static String calculateSiteRecode(String version, String site, String histology, String behavior) {
return calculateSiteRecode(version, site, histology, behavior, false);
}
/**
* Returns the calculated site recode for the provided parameters, unknown if it can't be calculated.
* @param version data version
* @param site site
* @param histology histology
* @param behavior behavior
* @param recodeExtended if true, extended recode value otherwise main recode classification will be calculated
* @return the calculated site recode/ recode extended for the provided parameters, unknown if it can't be calculated
*/
public static String calculateSiteRecode(String version, String site, String histology, String behavior, boolean recodeExtended) {
String result = ICCC_UNKNOWN_RECODE;
if (StringUtils.isBlank(site) || !_SITE_REGEX.matcher(site).matches() || StringUtils.isBlank(histology) || !NumberUtils.isDigits(histology))
return result;
// behavior is not required for all versions...
if (!VERSION_THIRD_EDITION.equals(version) && (StringUtils.isBlank(behavior) || !NumberUtils.isDigits(behavior)))
return result;
ensureVersion(version);
Integer s = Integer.valueOf(site.substring(1)), h = Integer.valueOf(histology), b = -1;
if (!StringUtils.isBlank(behavior))
b = Integer.valueOf(behavior);
for (IcccExecutableSiteGroupDto dto : _INTERNAL_DATA.get(version)) {
if (dto.matches(s, h, b)) {
result = recodeExtended ? (StringUtils.isEmpty(dto.getRecodeExtended()) ? ICCC_UNKNOWN_RECODE : dto.getRecodeExtended()) : dto.getRecode();
break;
}
}
return result;
}
public static List getRawData(String version) {
ensureVersion(version);
return _DATA.get(version);
}
private static synchronized void ensureVersion(String version) {
if (_DATA.containsKey(version))
return;
URL url;
if (VERSION_THIRD_EDITION.equals(version))
url = Thread.currentThread().getContextClassLoader().getResource("iccc/iccc-data-third-edition.csv");
else if (VERSION_WHO_2008.equals(version))
url = Thread.currentThread().getContextClassLoader().getResource("iccc/iccc-data-who-2008.csv");
else if (VERSION_THIRD_EDITION_IARC_2017.equals(version))
url = Thread.currentThread().getContextClassLoader().getResource("iccc/iccc-data-third-edition-iarc-2017.csv");
else
throw new RuntimeException("Unsupported version: " + version);
if (url == null)
throw new RuntimeException("Unable to find internal data file for version " + version);
List groups = new ArrayList<>();
_DATA.put(version, groups);
List executables = new ArrayList<>();
_INTERNAL_DATA.put(version, executables);
Pattern codePattern = Pattern.compile("\\d{3}");
try {
List allData = new CSVReader(new InputStreamReader(url.openStream(), StandardCharsets.US_ASCII)).readAll();
for (int i = 1; i < allData.size(); i++) {
String[] data = allData.get(i);
String id = data[0];
String name = data[1];
String level = data[2];
String siteIn = data[3];
String siteOut = data[4];
String histIn = data[5];
String histOut = data[6];
String recode = data[7];
String children = data[8];
String recodeExtended = "";
String behaviorInclusions = "";
if (!VERSION_THIRD_EDITION.equals(version)) {
recodeExtended = data[9];
behaviorInclusions = data[10];
}
IcccSiteGroupDto group = new IcccSiteGroupDto();
group.setId(id);
group.setName(name);
group.setLevel(Integer.valueOf(level));
group.setSiteInclusions(siteIn);
group.setSiteExclusions(siteOut);
group.setHistologyInclusions(histIn);
group.setHistologyExclusions(histOut);
group.setBehaviorInclusions(behaviorInclusions);
group.setRecode(recode);
group.setRecodeExtended(recodeExtended);
if (!StringUtils.isBlank(children)) {
group.setChildrenRecodes(Arrays.asList(children.split(",")));
for (String s : group.getChildrenRecodes())
if (!codePattern.matcher(s).matches())
throw new RuntimeException("Invalid recode reference for " + group.getName() + ": " + s);
}
if (!groups.contains(group))
groups.add(group);
if (!StringUtils.isBlank(recode)) {
if (!codePattern.matcher(recode).matches())
throw new RuntimeException("Invalid recode: " + recode + " for id " + id);
if (!VERSION_THIRD_EDITION.equals(version) && !codePattern.matcher(recodeExtended).matches())
throw new RuntimeException("Invalid recode extended: " + recodeExtended + " for id " + id);
IcccExecutableSiteGroupDto executable = new IcccExecutableSiteGroupDto();
executable.setId(id);
executable.setSiteInclusions(Utils.expandSitesAsIntegers(siteIn));
executable.setSiteExclusions(Utils.expandSitesAsIntegers(siteOut));
executable.setHistologyInclusions(Utils.expandHistologiesAsIntegers(histIn));
executable.setHistologyExclusions(Utils.expandHistologiesAsIntegers(histOut));
executable.setBehaviorInclusions(Utils.expandBehaviorsAsIntegers(behaviorInclusions));
executable.setRecode(recode);
executable.setRecodeExtended(recodeExtended);
executables.add(executable);
}
}
}
catch (CsvException | IOException e) {
throw new RuntimeException(e);
}
}
}
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