com.imsweb.algorithms.surgery.SiteSpecificSurgeryUtils Maven / Gradle / Ivy
/*
* Copyright (C) 2012 Information Management Services, Inc.
*/
package com.imsweb.algorithms.surgery;
import com.imsweb.algorithms.surgery.xml.SurgeryTablesXmlDto;
import com.thoughtworks.xstream.XStream;
import com.thoughtworks.xstream.converters.basic.BooleanConverter;
import com.thoughtworks.xstream.converters.basic.ByteConverter;
import com.thoughtworks.xstream.converters.basic.DateConverter;
import com.thoughtworks.xstream.converters.basic.DoubleConverter;
import com.thoughtworks.xstream.converters.basic.FloatConverter;
import com.thoughtworks.xstream.converters.basic.IntConverter;
import com.thoughtworks.xstream.converters.basic.LongConverter;
import com.thoughtworks.xstream.converters.basic.NullConverter;
import com.thoughtworks.xstream.converters.basic.ShortConverter;
import com.thoughtworks.xstream.converters.basic.StringConverter;
import com.thoughtworks.xstream.converters.collections.CollectionConverter;
import com.thoughtworks.xstream.converters.reflection.ReflectionConverter;
import com.thoughtworks.xstream.io.xml.XppDriver;
import com.thoughtworks.xstream.security.NoTypePermission;
import com.thoughtworks.xstream.security.WildcardTypePermission;
import org.apache.commons.lang3.StringUtils;
import java.net.URL;
import java.time.LocalDate;
import java.util.HashMap;
import java.util.Map;
import java.util.concurrent.locks.ReentrantReadWriteLock;
import java.util.regex.Pattern;
/**
* Utility class to return site-specific surgery information that can be used to build application-specific lookups.
*/
public final class SiteSpecificSurgeryUtils {
/**
* Unique instance of this class
*/
private static final SiteSpecificSurgeryUtils _INSTANCE = new SiteSpecificSurgeryUtils();
/**
* Returns the unique instance of the site-specific surgery tables utility class.
*
* Created on Jul 18, 2012 by depryf
* @return the unique instance of the site-specific surgery tables utility class
*/
public static SiteSpecificSurgeryUtils getInstance() {
return _INSTANCE;
}
/**
* Reads the site-specific surgery data from the provided URL, expects XML format.
*
* The provided stream will be closed when this method returns
*
* Created on Jul 18, 2012 by depryf
* @param url URL to the data file, cannot be null
* @return a SurgeryTablesXmlDto, never null
*/
public static SurgeryTablesXmlDto readTables(URL url) {
XStream xStream = new XStream(new XppDriver()) {
// only register the converters we need; other converters generate a private access warning in the console on Java9+...
@Override
protected void setupConverters() {
registerConverter(new NullConverter(), PRIORITY_VERY_HIGH);
registerConverter(new IntConverter(), PRIORITY_NORMAL);
registerConverter(new FloatConverter(), PRIORITY_NORMAL);
registerConverter(new DoubleConverter(), PRIORITY_NORMAL);
registerConverter(new LongConverter(), PRIORITY_NORMAL);
registerConverter(new ShortConverter(), PRIORITY_NORMAL);
registerConverter(new BooleanConverter(), PRIORITY_NORMAL);
registerConverter(new ByteConverter(), PRIORITY_NORMAL);
registerConverter(new StringConverter(), PRIORITY_NORMAL);
registerConverter(new DateConverter(), PRIORITY_NORMAL);
registerConverter(new CollectionConverter(getMapper()), PRIORITY_NORMAL);
registerConverter(new ReflectionConverter(getMapper(), getReflectionProvider()), PRIORITY_VERY_LOW);
}
};
xStream.autodetectAnnotations(true);
xStream.alias("surgery-tables", SurgeryTablesXmlDto.class);
// setup proper security by limiting what classes can be loaded by XStream (#79515)
xStream.addPermission(NoTypePermission.NONE);
xStream.addPermission(new WildcardTypePermission(new String[] {"com.imsweb.algorithms.surgery.xml.**"}));
return (SurgeryTablesXmlDto)xStream.fromXML(url);
}
// cached data
private Map _data = new HashMap<>();
// cached regex
private Pattern _sitePattern = Pattern.compile("C\\d\\d\\d?"), _histPattern = Pattern.compile("\\d\\d\\d\\d");
// internal lock to control concurrency (this is needed because we lazily initialize the data)
private ReentrantReadWriteLock _lock = new ReentrantReadWriteLock();
/**
* No public constructor, use the instance.
*/
private SiteSpecificSurgeryUtils() {
}
/**
* Returns the data for the requested DX year.
*
* Created on Jul 18, 2012 by depryf
* @param dxYear requested DX year, cannot be null
* @return available data, null if no data correspond to the requested year
*/
public SurgeryTablesDto getTables(int dxYear) {
if (dxYear < 2010 || dxYear > LocalDate.now().getYear())
return null;
// optimization: some years share the same data, so let's adjust the DX year so its XML data actually exists
int year = dxYear == 2011 || dxYear == 2017 || dxYear == 2019 ? dxYear - 1 : dxYear;
_lock.readLock().lock();
if (!_data.containsKey(year)) {
_lock.readLock().unlock();
_lock.writeLock().lock();
try {
URL url = Thread.currentThread().getContextClassLoader().getResource("surgery/site-specific-surgery-tables-" + year + ".xml");
_data.put(year, new SurgeryTablesDto(readTables(url)));
_lock.readLock().lock();
}
finally {
_lock.writeLock().unlock();
}
}
try {
return _data.get(year);
}
finally {
_lock.readLock().unlock();
}
}
/**
* Returns the site-specific surgery table corresponding to the requested year and title, null if not found.
*
* Created on Jul 18, 2012 by depryf
* @param dxYear requested DX year, cannot be null
* @param title requested table title
* @return site-specific surgery table, maybe null
*/
public SurgeryTableDto getTable(int dxYear, String title) {
SurgeryTablesDto tables = getTables(dxYear);
if (tables == null)
return null;
for (SurgeryTableDto table : tables.getTables())
if (table.getTitle().equals(title))
return table;
return null;
}
/**
* Returns the site-specific surgery table corresponding to the requested year and site/histology, null if not found.
*
* Created on Jul 18, 2012 by depryf
* @param dxYear requested DX year, cannot be null
* @param site primary site, cannot be null, format must be Cnnn or Cnn (in which case a trailing 9 is assumed)
* @param histology histology, cannot be null, format must be nnnn
* @return site-specific surgery table, maybe null
*/
public SurgeryTableDto getTable(int dxYear, String site, String histology) {
if (site == null || !_sitePattern.matcher(site).matches())
return null;
if (histology == null || !_histPattern.matcher(histology).matches())
return null;
SurgeryTablesDto tables = getTables(dxYear);
if (tables == null)
return null;
// for site, assume trailing 9 if not provided
if (site.length() == 3)
site = site + "9";
SurgeryTableDto result = null;
for (SurgeryTableDto table : tables.getTables()) {
// if the table has an histology inclusion, check it first
boolean includeHist = false;
String histInc = table.getHistInclusion();
if (histInc != null) {
for (String s : StringUtils.split(histInc, ',')) {
s = s.trim();
if (s.contains("-")) {
String[] parts = StringUtils.split(s, '-');
if (parts[0].compareTo(histology) <= 0 && parts[1].compareTo(histology) >= 0) {
includeHist = true;
break;
}
}
else {
if (s.equals(histology)) {
includeHist = true;
break;
}
}
}
}
if (includeHist) {
result = table;
break;
}
// check the site inclusion
boolean includeSite = false;
if (table.getSiteInclusion() != null) {
for (String s : StringUtils.split(table.getSiteInclusion(), ',')) {
s = s.trim();
if (s.contains("-")) {
String[] parts = StringUtils.split(s, '-');
if (parts[0].compareTo(site) <= 0 && parts[1].compareTo(site) >= 0) {
includeSite = true;
break;
}
}
else {
if (s.equals(site)) {
includeSite = true;
break;
}
}
}
}
if (includeSite) {
// check the histology exclusion
boolean excludeHist = false;
String histExc = table.getHistExclusion();
if (histExc != null) {
for (String s : StringUtils.split(histExc, ',')) {
s = s.trim();
if (s.contains("-")) {
String[] parts = StringUtils.split(s, '-');
if (parts[0].compareTo(histology) <= 0 && parts[1].compareTo(histology) >= 0) {
excludeHist = true;
break;
}
}
else {
if (s.equals(histology)) {
excludeHist = true;
break;
}
}
}
}
if (!excludeHist) {
result = table;
break;
}
}
}
return result;
}
}
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