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* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package tool.util;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
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 tool.Main;
import tool.sieves.CompoundPhraseSieve;
import tool.sieves.SimpleNameSieve;
/**
*
* @author
*/
public class Terminology {
public static File terminologyFile;
private Map<String, List<String>> tokenToNameListMap = new HashMap<>();
private Map<String, List<String>> nameToCuiListMap = new HashMap<>();
private Map<String, List<String>> simpleNameToCuiListMap = new HashMap<>();
private Map<String, List<String>> compoundNameToCuiListMap = new HashMap<>();
private Map<String, List<String>> cuiToNameListMap = new HashMap<>();
private Map<String, List<String>> stemmedNameToCuiListMap = new HashMap<>();
private Map<String, List<String>> cuiToStemmedNameListMap = new HashMap<>();
private Map<String, List<String>> cuiAlternateCuiMap = new HashMap<>();
public static Map<String, Map<String, List<String>>> cuiNameFileListMap = new HashMap<>();
public Map<String, List<String>> getTokenToNameListMap() {
return tokenToNameListMap;
}
public Map<String, List<String>> getNameToCuiListMap()
{
return nameToCuiListMap;
}
public Map<String, List<String>> getSimpleNameToCuiListMap() {
return simpleNameToCuiListMap;
}
public Map<String, List<String>> getCompoundNameToCuiListMap() {
return compoundNameToCuiListMap;
}
public void setCompoundNameToCuiListMap(String name, String cui) {
compoundNameToCuiListMap = Util.setMap(compoundNameToCuiListMap, name, cui);
}
public Map<String, List<String>> getCuiToNameListMap() {
return cuiToNameListMap;
}
public Map<String, List<String>> getStemmedNameToCuiListMap() {
return stemmedNameToCuiListMap;
}
public Map<String, List<String>> getCuiToStemmedNameListMap() {
return cuiToStemmedNameListMap;
}
public Map<String, List<String>> getCuiAlternateCuiMap() {
return cuiAlternateCuiMap;
}
private String get_preferredID_set_altID(String[] identifiers) {
String preferredID = "";
boolean set = false;
List<String> altIDs = new ArrayList<>();
for (int i = 0; i < identifiers.length; i++) {
if (identifiers[i].contains("OMIM"))
identifiers[i] = identifiers[i].split(":")[1];
if (i == 0)
preferredID = identifiers[i];
if (Character.isLetter(identifiers[i].charAt(0)) && set == false) {
preferredID = identifiers[i];
set = true;
continue;
}
altIDs.add(identifiers[i]);
}
if (!altIDs.isEmpty()) {
cuiAlternateCuiMap.put(preferredID, altIDs);
}
return preferredID;
}
private void loadMaps(String conceptName, String cui) {
nameToCuiListMap = Util.setMap(nameToCuiListMap, conceptName, cui);
cuiToNameListMap = Util.setMap(cuiToNameListMap, cui, conceptName);
String stemmedConceptName = Ling.getStemmedPhrase(conceptName);
stemmedNameToCuiListMap = Util.setMap(stemmedNameToCuiListMap, stemmedConceptName, cui);
cuiToStemmedNameListMap = Util.setMap(cuiToStemmedNameListMap, cui, stemmedConceptName);
String[] conceptNameTokens = conceptName.split("\\s");
for (String conceptNameToken : conceptNameTokens) {
if (Ling.getStopwordsList().contains(conceptNameToken))
continue;
tokenToNameListMap = Util.setMap(tokenToNameListMap, conceptNameToken, conceptName);
}
if (Main.training_data_dir.toString().contains("semeval")) {
CompoundPhraseSieve.setCompoundNameTerminology(this, conceptName, conceptNameTokens, cui);
}
else if (cui.contains("|")) {
nameToCuiListMap.remove(conceptName);
stemmedNameToCuiListMap.remove(stemmedConceptName);
for (String conceptNameToken : conceptNameTokens) {
if (Ling.getStopwordsList().contains(conceptNameToken))
continue;
tokenToNameListMap.get(conceptNameToken).remove(conceptName);
}
compoundNameToCuiListMap = Util.setMap(compoundNameToCuiListMap, conceptName, cui);
}
}
public void loadTerminology() throws IOException {
String cui = "";
try (BufferedReader br = new BufferedReader(new FileReader(terminologyFile))) {
String line;
while ((line = br.readLine()) != null) {
line = line.trim();
if (line.equals(""))
continue;
String[] token = line.split("\\|\\|");
cui = token[0].contains("|") ? get_preferredID_set_altID(token[0].split("\\|")) : token[0];
String[] conceptNames = token[1].toLowerCase().split("\\|");
for (String conceptName : conceptNames)
loadMaps(conceptName, cui);
}
}
}
private void setOMIM(String cuis, String MeSHorSNOMEDcuis, String conceptName) {
if (MeSHorSNOMEDcuis.equals("")) {
cuis = cuis.replaceAll("OMIM:", "");
loadMaps(conceptName, cuis);
}
else {
String[] cuis_arr = cuis.split("\\|");
for (String cui : cuis_arr) {
if (!cui.contains("OMIM"))
continue;
cui = cui.split(":")[1];
cuiAlternateCuiMap = Util.setMap(cuiAlternateCuiMap, MeSHorSNOMEDcuis, cui);
}
}
}
public static List<String> getOMIMCuis(String[] cuis) {
List<String> OMIMcuis = new ArrayList<>();
for (String cui : cuis) {
if (!cui.contains("OMIM"))
continue;
cui = cui.split(":")[1];
OMIMcuis = Util.setList(OMIMcuis, cui);
}
return OMIMcuis;
}
public static String getMeSHorSNOMEDCuis(String[] cuis) {
String cuiStr = "";
for (String cui : cuis) {
if (cui.contains("OMIM"))
continue;
cuiStr = cuiStr.equals("") ? cui : cuiStr+"|"+cui;
}
return cuiStr;
}
public void loadTrainingDataTerminology(File dir) throws IOException {
Map<String, List<String>> cuiNamesMap = new HashMap<>();
for (File file : dir.listFiles()) {
if (!file.toString().contains(".concept"))
continue;
cuiNamesMap = new HashMap<>();
try (BufferedReader br = new BufferedReader(new FileReader(file))) {
String line;
while ((line = br.readLine()) != null) {
line = line.trim();
String[] tokens = line.split("\\|\\|");
String conceptName = Ling.correctSpelling(tokens[3].toLowerCase().trim());
String[] cuis = tokens[4].contains("+") ? tokens[4].split("\\+") : tokens[4].split("\\|");
String MeSHorSNOMEDcuis = getMeSHorSNOMEDCuis(cuis);
if (!MeSHorSNOMEDcuis.equals(""))
loadMaps(conceptName, MeSHorSNOMEDcuis);
setOMIM(tokens[4], MeSHorSNOMEDcuis, conceptName);
String cui = !MeSHorSNOMEDcuis.equals("") ? MeSHorSNOMEDcuis : tokens[4].replaceAll("OMIM:", "");
cuiNamesMap = Util.setMap(cuiNamesMap, cui, conceptName);
//-------------remove-------------------------------
Map<String, List<String>> nameFileListMap = cuiNameFileListMap.get(MeSHorSNOMEDcuis);
if (nameFileListMap == null)
cuiNameFileListMap.put(MeSHorSNOMEDcuis, nameFileListMap = new HashMap<>());
nameFileListMap = Util.setMap(nameFileListMap, conceptName, tokens[0]);
//-------------remove-------------------------------
List<String> simpleConceptNames = SimpleNameSieve.getTerminologySimpleNames(conceptName.split("\\s+"));
for (String simpleConceptName : simpleConceptNames)
simpleNameToCuiListMap = Util.setMap(simpleNameToCuiListMap, simpleConceptName, cui);
}
}
if (Main.training_data_dir.toString().contains("ncbi"))
continue;
for (String cui : cuiNamesMap.keySet()) {
List<String> names = cuiNamesMap.get(cui);
List<String> namesToPrune = new ArrayList<>();
for (String name : names) {
String[] nameTokens = name.split("\\s+");
if (nameTokens.length < 3)
continue;
if (names.contains(nameTokens[0]+" "+nameTokens[1]))
namesToPrune = Util.setList(namesToPrune, nameTokens[0]+" "+nameTokens[1]);
else if (names.contains(nameTokens[nameTokens.length-2]+" "+nameTokens[nameTokens.length-1]))
namesToPrune = Util.setList(namesToPrune, nameTokens[nameTokens.length-2]+" "+nameTokens[nameTokens.length-1]);
}
for (String nameToPrune : namesToPrune) {
nameToCuiListMap.remove(nameToPrune);
cuiToNameListMap.get(cui).remove(nameToPrune);
stemmedNameToCuiListMap.remove(Ling.getStemmedPhrase(nameToPrune));
cuiToStemmedNameListMap.get(cui).remove(Ling.getStemmedPhrase(nameToPrune));
String[] nameToPruneTokens = nameToPrune.split("\\s+");
for (String nameToPruneToken : nameToPruneTokens) {
if (Ling.getStopwordsList().contains(nameToPruneToken))
continue;
tokenToNameListMap.get(nameToPruneToken).remove(nameToPrune);
}
}
}
}
}
private static Map<String, List<String>> normalizedNameToCuiListMap = new HashMap<>();
public static void setNormalizedNameToCuiListMap(String name, String cui) {
normalizedNameToCuiListMap = Util.setMap(normalizedNameToCuiListMap, name, cui);
}
public static Map<String, List<String>> getNormalizedNameToCuiListMap() {
return normalizedNameToCuiListMap;
}
private static Map<String, List<String>> stemmedNormalizedNameToCuiListMap = new HashMap<>();
public static void setStemmedNormalizedNameToCuiListMap(String stemmedName, String cui) {
stemmedNormalizedNameToCuiListMap = Util.setMap(stemmedNormalizedNameToCuiListMap, stemmedName, cui);
}
public static Map<String, List<String>> getStemmedNormalizedNameToCuiListMap() {
return stemmedNormalizedNameToCuiListMap;
}
public static void storeNormalizedConcept(Concept concept) {
setNormalizedNameToCuiListMap(concept.getNormalizingSieve() == 2 ? concept.getNameExpansion() : concept.getName(), concept.getCui());
setStemmedNormalizedNameToCuiListMap(concept.getNormalizingSieve() == 2 ? Ling.getStemmedPhrase(concept.getNameExpansion()) : concept.getStemmedName(), concept.getCui());
}
}
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