com.imsweb.algorithms.seersiterecode.SeerSiteRecodeUtils Maven / Gradle / Ivy
package com.imsweb.algorithms.seersiterecode;
import java.io.IOException;
import java.io.InputStreamReader;
import java.net.URL;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.regex.Pattern;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.math.NumberUtils;
import com.opencsv.CSVReader;
import com.imsweb.algorithms.AlgorithmsUtils;
/**
* This class can be used to calculate the SEER Site Recode variable.
* User: depryf
* Date: 8/22/12
*/
public final class SeerSiteRecodeUtils {
/**
* Properties used to calculate Site Recode **
*/
public static final String PROP_PRIMARY_SITE = "primarySite";
public static final String PROP_HISTOLOGY_3 = "histologyIcdO3";
/**
* Version for the 2010+ data (http://seer.cancer.gov/siterecode/icdo3_dwhoheme/index.html)
*/
public static final String VERSION_2010 = "2010+";
/**
* Version for the 2003 data (http://seer.cancer.gov/siterecode/icdo3_d01272003/)
*/
public static final String VERSION_2003 = "2003-27-01";
/**
* Version for the 2003 data without Mesothelioma (9050-9055) and Kaposi Sarcoma (9140) as separate groupings
*/
public static final String VERSION_2003_WITHOUT_KSM = "2003-27-01 (no Meso and Kapo)";
/**
* Default version
*/
public static final String VERSION_DEFAULT = VERSION_2010;
/**
* Unknown label
*/
public static final String UNKNOWN_LABEL = "Unknown";
/**
* Map of available versions along with a description
*/
private static final Map _VERSIONS = new HashMap<>();
static {
_VERSIONS.put(VERSION_2010, "SEER Site Recode ICD-O-3 2010+ Cases WHO Heme Definition");
_VERSIONS.put(VERSION_2003, "SEER Site Recode ICD-O-3 (1/27/2003) Definition");
_VERSIONS.put(VERSION_2003_WITHOUT_KSM, "SEER Site Recode ICD-O-3 (1/27/2003) Definition without Mesothelioma (9050-9055) and Kaposi Sarcoma (9140) as separate groupings");
}
// nice data for the different versions, this is what is exposed to the outside world (lazy)
private static final Map> _DATA = new HashMap<>();
// optimized data for the different versions, this is what is used for the calculation (lazy)
private static final Map> _INTERNAL_DATA = new HashMap<>();
// cached site regex
private static Pattern _SITE_PATTERN = Pattern.compile("C\\d+");
/**
* Private constructor, no instantiation of this class!
*/
private SeerSiteRecodeUtils() {}
/**
* 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 record, unknown if it can't be calculated.
* @param record record
* @return the calculated site recode for the provided record, unknown if it can't be calculated
*/
public static String calculateSiteRecode(Map record) {
return calculateSiteRecode(VERSION_DEFAULT, record.get(PROP_PRIMARY_SITE), record.get(PROP_HISTOLOGY_3));
}
/**
* Returns the calculated site recode for the provided version and record, unknown if it can't be calculated.
* @param version data version
* @param record record
* @return the calculated site recode for the provided version and record, unknown if it can't be calculated
*/
public static String calculateSiteRecode(String version, Map record) {
return calculateSiteRecode(version, record.get(PROP_PRIMARY_SITE), record.get(PROP_HISTOLOGY_3));
}
/**
* Returns the calculated site recode for the provided parameters, unknown if it can't be calculated.
* @param site site
* @param histology histology
* @return the calculated site recode for the provided parameters, unknown if it can't be calculated
*/
public static String calculateSiteRecode(String site, String histology) {
return calculateSiteRecode(VERSION_DEFAULT, site, histology);
}
/**
* 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
* @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 result = "99999";
if (StringUtils.isBlank(site) || !_SITE_PATTERN.matcher(site).matches() || StringUtils.isBlank(histology) || !NumberUtils.isDigits(histology))
return result;
ensureVersion(version);
Integer s = Integer.valueOf(site.substring(1)), h = Integer.valueOf(histology);
for (SeerExecutableSiteGroupDto dto : _INTERNAL_DATA.get(version)) {
if (dto.matches(s, h)) {
result = dto.getRecode();
break;
}
}
return result;
}
/**
* Returns the recode name for the provided recode and the default version of the data.
* @param recode recode
* @return the corresponding recode name, UNKNOWN_LABEL if it can't be found.
*/
public static String getRecodeName(String recode) {
return getRecodeName(recode, VERSION_DEFAULT);
}
/**
* Returns the recode name for the provided recode and data version.
* @param recode recode
* @param version data version
* @return the corresponding recode name, UNKNOWN_LABEL if it can't be found.
*/
public static String getRecodeName(String recode, String version) {
String result = UNKNOWN_LABEL;
if (StringUtils.isBlank(recode) || !NumberUtils.isDigits(recode))
return result;
ensureVersion(version);
for (SeerExecutableSiteGroupDto dto : _INTERNAL_DATA.get(version)) {
if (recode.equals(dto.getRecode())) {
result = dto.getName();
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_2010.equals(version))
url = Thread.currentThread().getContextClassLoader().getResource("seersiterecode/site-recode-data-2010.csv");
else if (VERSION_2003.equals(version))
url = Thread.currentThread().getContextClassLoader().getResource("seersiterecode/site-recode-data-2003.csv");
else if (VERSION_2003_WITHOUT_KSM.equals(version))
url = Thread.currentThread().getContextClassLoader().getResource("seersiterecode/site-recode-data-2003-without-kms.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);
try {
Set names = new HashSet<>();
List allData = new CSVReader(new InputStreamReader(url.openStream(), "US-ASCII")).readAll();
for (int i = 1; i < allData.size(); i++) {
String[] data = allData.get(i);
String id = data[0].isEmpty() ? null : data[0];
String name = data[1].isEmpty() ? null : data[1];
String level = data[2].isEmpty() ? null : data[2];
String siteIn = data[3].isEmpty() ? null : data[3];
String siteOut = data[4].isEmpty() ? null : data[4];
String histIn = data[5].isEmpty() ? null : data[5];
String histOut = data[6].isEmpty() ? null : data[6];
String recode = data[7].isEmpty() ? null : data[7];
String children = data[8].isEmpty() ? null : data[8];
if (!names.contains(name)) {
SeerSiteGroupDto group = new SeerSiteGroupDto();
group.setId(id);
group.setName(name);
group.setLevel(Integer.valueOf(level));
group.setSiteInclusions(siteIn);
group.setSiteExclusions(siteOut);
group.setHistologyInclusions(histIn);
group.setHistologyExclusions(histOut);
group.setRecode(recode);
if (children != null)
group.setChildrenRecodes(Arrays.asList(children.split(",")));
groups.add(group);
names.add(name);
}
if (recode != null) {
SeerExecutableSiteGroupDto executable = new SeerExecutableSiteGroupDto();
executable.setId(id);
executable.setName(name);
executable.setSiteInclusions(AlgorithmsUtils.expandSitesAsIntegers(siteIn));
executable.setSiteExclusions(AlgorithmsUtils.expandSitesAsIntegers(siteOut));
executable.setHistologyInclusions(AlgorithmsUtils.expandHistologiesAsIntegers(histIn));
executable.setHistologyExclusions(AlgorithmsUtils.expandHistologiesAsIntegers(histOut));
executable.setRecode(recode);
executables.add(executable);
}
}
}
catch (IOException e) {
throw new RuntimeException(e);
}
}
}
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