com.imsweb.algorithms.surgery.SiteSpecificSurgeryUtils Maven / Gradle / Ivy
/*
* Copyright (C) 2012 Information Management Services, Inc.
*/
package com.imsweb.algorithms.surgery;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.net.URL;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.List;
import com.thoughtworks.xstream.XStream;
import com.thoughtworks.xstream.io.xml.XppDriver;
import com.imsweb.algorithms.surgery.xml.SurgeryRowXmlDto;
import com.imsweb.algorithms.surgery.xml.SurgeryTableXmlDto;
import com.imsweb.algorithms.surgery.xml.SurgeryTablesXmlDto;
/**
* 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 SiteSpecificSurgeryUtils _INSTANCE;
/**
* Version for the surgery tables
*/
private String _version;
/**
* Version name for the surgery tables
*/
private String _versionName;
/**
* Cached surgery tables
*/
private List _tables;
/**
* 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 synchronized SiteSpecificSurgeryUtils getInstance() {
try {
if (_INSTANCE == null)
_INSTANCE = new SiteSpecificSurgeryUtils(readSiteSpecificSurgeryData(getInternalSiteSpecificSurgeryDataUrl().openStream()));
return _INSTANCE;
}
catch (IOException e) {
throw new RuntimeException("Unable to read internal data", e);
}
}
/**
* Registers an instance of the data.
*
* Created on Jul 18, 2012 by depryf
* @param data the data to initialize from
*/
public static void registerInstance(SurgeryTablesXmlDto data) {
_INSTANCE = new SiteSpecificSurgeryUtils(data);
}
/**
* Returns the URL to the internal site-specific surgery tables XML file.
*
* Created on Jul 18, 2012 by depryf
* @return the URL to the internal site-specific surgery tables XML file
*/
public static URL getInternalSiteSpecificSurgeryDataUrl() {
return Thread.currentThread().getContextClassLoader().getResource("surgery/site-specific-surgery-tables.xml");
}
/**
* 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 stream InputStream to the data file, cannot be null
* @return a SurgeryTablesXmlDto, never null
* @throws IOException
*/
@SuppressWarnings("unchecked")
public static SurgeryTablesXmlDto readSiteSpecificSurgeryData(InputStream stream) throws IOException {
try {
return (SurgeryTablesXmlDto)createSiteSpecificSurgeryDataXstream().fromXML(stream);
}
finally {
stream.close();
}
}
/**
* Writes the site-specific surgery data to the provided URL, using XML format.
*
* Created on Jul 18, 2012 by depryf
* @param stream OutputStream to the data file, cannot be null
* @param data the SurgeryTablesXmlDto to write, cannot be null
* @throws IOException
*/
public static void writeSiteSpecificSurgeryData(OutputStream stream, SurgeryTablesXmlDto data) throws IOException {
try {
createSiteSpecificSurgeryDataXstream().toXML(data, stream);
}
finally {
stream.close();
}
}
private static XStream createSiteSpecificSurgeryDataXstream() {
XStream xstream = new XStream(new XppDriver());
xstream.autodetectAnnotations(true);
xstream.alias("surgery-tables", SurgeryTablesXmlDto.class);
return xstream;
}
/**
* Constructor.
*
* Created on Jul 18, 2012 by depryf
* @param data a SurgeryTablesXmlDto, cannot be null
*/
SiteSpecificSurgeryUtils(SurgeryTablesXmlDto data) {
_version = data.getVersion();
_versionName = data.getVersionName();
_tables = new ArrayList<>();
for (SurgeryTableXmlDto table : data.getSurgeryTable()) {
SurgeryTableDto dto = new SurgeryTableDto();
dto.setTitle(table.getTitle());
dto.setSiteInclusion(table.getSiteInclusion());
dto.setHistInclusion(table.getHistInclusion());
dto.setHistExclusion(table.getHistExclusion());
dto.setPreNote(table.getPreNote());
dto.setPostNote(table.getPostNote());
List rows = new ArrayList<>();
for (SurgeryRowXmlDto row : table.getRow()) {
SurgeryRowDto rowDto = new SurgeryRowDto();
rowDto.setCode(row.getCode());
rowDto.setDescription(row.getDescription());
rowDto.setLevel(row.getLevel() == null ? Integer.valueOf(0) : row.getLevel());
rowDto.setLineBreak(row.isBreak() == null ? Boolean.FALSE : row.isBreak());
rows.add(rowDto);
}
dto.setRow(rows);
_tables.add(dto);
}
}
/**
* Returns the data version.
*
* Created on Jul 18, 2012 by depryf
* @return the data version
*/
public String getVersion() {
return _version;
}
/**
* Returns the data version name.
*
* Created on Jul 18, 2012 by depryf
* @return the data version name
*/
public String getVersionName() {
return _versionName;
}
/**
* Returns all the available site-specific surgery tables.
*
* Created on Jul 18, 2012 by depryf
* @return all the available site-specific surgery table
*/
public Collection getAllTables() {
return Collections.unmodifiableList(_tables);
}
/**
* Returns all the available site-specific surgery table titles in alphabetical order.
*
* Created on Jul 18, 2012 by depryf
* @return all the available site-specific surgery table titles in alphabetical order
*/
public List getAllTableTitles() {
List result = new ArrayList<>();
for (SurgeryTableDto table : _tables)
result.add(table.getTitle());
// just for convenience...
Collections.sort(result);
return result;
}
/**
* Returns the site-specific surgery table corresponding to the requested title, null if not found.
*
* Created on Jul 18, 2012 by depryf
* @param title requested table title
* @return the site-specific surgery table corresponding to the requested title, null if not found
*/
public SurgeryTableDto getTable(String title) {
for (SurgeryTableDto table : _tables)
if (table.getTitle().equals(title))
return table;
return null;
}
/**
* Returns the site-specific surgery table corresponding to the requested site/histology, null if the table is not found.
*
* Created on Jul 18, 2012 by depryf
* @param site primary site, cannot be null, format must be Cxxx
* @param histology histology, cannot be null, format must be xxxx
* @return the site-specific surgery table corresponding to the requested site/histology, null if the table is not found
*/
public SurgeryTableDto getTable(String site, String histology) {
if (site == null || !site.matches("C\\d\\d\\d") || histology == null || !histology.matches("\\d\\d\\d\\d"))
return null;
SurgeryTableDto result = null;
for (SurgeryTableDto table : _tables) {
// if the table has an histology inclusion, check it first
boolean includeHist = false;
String histInc = table.getHistInclusion();
if (histInc != null) {
for (String s : histInc.split(",")) {
s = s.trim();
if (s.contains("-")) {
String[] parts = s.split("\\-");
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 : table.getSiteInclusion().split(",")) {
s = s.trim();
if (s.contains("-")) {
String[] parts = s.split("\\-");
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 : histExc.split(",")) {
s = s.trim();
if (s.contains("-")) {
String[] parts = s.split("\\-");
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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