Program: 79480
Project: 79480
Buggy source:
/** 
 * Counts the number of files in a pack and does some basic verification to ensure files are in order.
 */
private boolean countFiles(ZipInputStream zis,Realm realm) throws IOException {
  actionSubject.onNext(LanguageImportFragment.ACTION_COUNTING_SENTENCES);
  final byte[] buffer=new byte[BUFFER_SIZE];
  ZipEntry zipEntry;
  int numFiles=0;
  int bytesRead;
  ByteArrayOutputStream baos=new ByteArrayOutputStream();
  String baseLanguage="String_Node_Str";
  String targetLanguage="String_Node_Str";
  String packName="String_Node_Str";
  while ((zipEntry=zis.getNextEntry()) != null) {
    if (zipEntry.getName().endsWith("String_Node_Str")) {
      packName=zipEntry.getName().split("String_Node_Str")[1];
      numFiles++;
      actionSubject.onNext(LanguageImportFragment.ACTION_COUNTING_SENTENCES);
      totalSubject.onNext(numFiles);
    }
 else     if (zipEntry.getName().endsWith("String_Node_Str")) {
      actionSubject.onNext(LanguageImportFragment.ACTION_READING_SENTENCES);
      String[] nameParts=zipEntry.getName().split("String_Node_Str");
      baseLanguage=nameParts[0].trim();
      targetLanguage=nameParts[1].trim();
      while ((bytesRead=zis.read(buffer,0,BUFFER_SIZE)) >= 0) {
        baos.write(buffer,0,bytesRead);
      }
    }
  }
  LanguageType baseType=LanguageData.getLanguageById(baseLanguage);
  LanguageType targetType=LanguageData.getLanguageById(targetLanguage);
  if (baseLanguage.length() < 2 || targetLanguage.length() < 2 || baseType == null || targetType == null)   return false;
  realm.beginTransaction();
  Language base=realm.where(Language.class).equalTo("String_Node_Str",baseLanguage).findFirst();
  if (base == null) {
    base=realm.createObject(Language.class,baseLanguage);
  }
  Pack basePack=base.getPack(packName);
  if (basePack == null) {
    basePack=realm.createObject(Pack.class,UUID.randomUUID().toString());
    basePack.setBook(packName);
    base.getPacks().add(basePack);
  }
  Language target=realm.where(Language.class).equalTo("String_Node_Str",targetLanguage).findFirst();
  if (target == null) {
    target=realm.createObject(Language.class,targetLanguage);
  }
  Pack targetPack=target.getPack(packName);
  if (targetPack == null) {
    targetPack=realm.createObject(Pack.class,UUID.randomUUID().toString());
    targetPack.setBook(packName);
    target.getPacks().add(targetPack);
  }
  realm.commitTransaction();
  actionSubject.onNext(LanguageImportFragment.ACTION_EXTRACTING_TEXT);
  progressSubject.onNext(0);
  totalSubject.onNext(numFiles / 2);
  String[] sentenceList=baos.toString("String_Node_Str").split("String_Node_Str");
  String[] sections=sentenceList[0].split("String_Node_Str");
  realm.beginTransaction();
  for (int i=1; i < sentenceList.length; i++) {
    progressSubject.onNext(i);
    String[] sentenceParts=sentenceList[i].split("String_Node_Str");
    int index=Integer.parseInt(sentenceParts[0]);
    String sentence=null;
    String translation=null;
    String ipa=null;
    String romanization=null;
    for (int j=0; j < sentenceParts.length; j++) {
      String value=sentenceParts[j];
switch (sections[j]) {
case "String_Node_Str":
        break;
case "String_Node_Str":
      sentence=value;
    break;
case "String_Node_Str":
  translation=value;
break;
case "String_Node_Str":
ipa=value;
break;
case "String_Node_Str":
romanization=value;
break;
}
}
targetPack.createSentenceOrUpdate(realm,index,translation,ipa,romanization,null);
basePack.createSentenceOrUpdate(realm,index,sentence,null,null,null);
}
realm.commitTransaction();
actionSubject.onNext(LanguageImportFragment.ACTION_EXTRACTING_AUDIO);
progressSubject.onNext(0);
totalSubject.onNext(numFiles);
return true;
}

Fixed version (ground truth):
/** 
 * Counts the number of files in a pack and does some basic verification to ensure files are in order.
 */
private boolean countFiles(ZipInputStream zis,Realm realm) throws IOException {
  actionSubject.onNext(LanguageImportFragment.ACTION_COUNTING_SENTENCES);
  final byte[] buffer=new byte[BUFFER_SIZE];
  ZipEntry zipEntry;
  int numFiles=0;
  int bytesRead;
  ByteArrayOutputStream baos=new ByteArrayOutputStream();
  String baseLanguage="String_Node_Str";
  String targetLanguage="String_Node_Str";
  String packName="String_Node_Str";
  while ((zipEntry=zis.getNextEntry()) != null) {
    if (zipEntry.getName().endsWith("String_Node_Str")) {
      packName=zipEntry.getName().split("String_Node_Str")[1];
      numFiles++;
      actionSubject.onNext(LanguageImportFragment.ACTION_COUNTING_SENTENCES);
      totalSubject.onNext(numFiles);
    }
 else     if (zipEntry.getName().endsWith("String_Node_Str")) {
      actionSubject.onNext(LanguageImportFragment.ACTION_READING_SENTENCES);
      String[] nameParts=zipEntry.getName().split("String_Node_Str");
      baseLanguage=nameParts[0].trim();
      targetLanguage=nameParts[1].trim();
      while ((bytesRead=zis.read(buffer,0,BUFFER_SIZE)) >= 0) {
        baos.write(buffer,0,bytesRead);
      }
    }
  }
  LanguageType baseType=LanguageData.getLanguageById(baseLanguage);
  LanguageType targetType=LanguageData.getLanguageById(targetLanguage);
  if (baseLanguage.length() < 2 || targetLanguage.length() < 2 || baseType == null || targetType == null)   return false;
  realm.beginTransaction();
  Language base=realm.where(Language.class).equalTo("String_Node_Str",baseLanguage).findFirst();
  if (base == null) {
    base=realm.createObject(Language.class,baseLanguage);
  }
  Pack basePack=base.getPack(packName);
  if (basePack == null) {
    basePack=realm.createObject(Pack.class,UUID.randomUUID().toString());
    basePack.setBook(packName);
    base.getPacks().add(basePack);
  }
  Language target=realm.where(Language.class).equalTo("String_Node_Str",targetLanguage).findFirst();
  if (target == null) {
    target=realm.createObject(Language.class,targetLanguage);
  }
  Pack targetPack=target.getPack(packName);
  if (targetPack == null) {
    targetPack=realm.createObject(Pack.class,UUID.randomUUID().toString());
    targetPack.setBook(packName);
    target.getPacks().add(targetPack);
  }
  realm.commitTransaction();
  actionSubject.onNext(LanguageImportFragment.ACTION_EXTRACTING_TEXT);
  progressSubject.onNext(0);
  totalSubject.onNext(numFiles / 2);
  String[] sentenceList=baos.toString("String_Node_Str").split("String_Node_Str");
  String[] sections=sentenceList[0].split("String_Node_Str");
  for (int i=1; i < sentenceList.length; i++) {
    progressSubject.onNext(i);
    String[] sentenceParts=sentenceList[i].split("String_Node_Str");
    int index=Integer.parseInt(sentenceParts[0]);
    String sentence=null;
    String translation=null;
    String ipa=null;
    String romanization=null;
    for (int j=0; j < sentenceParts.length; j++) {
      String value=sentenceParts[j];
switch (sections[j]) {
case "String_Node_Str":
        break;
case "String_Node_Str":
      sentence=value;
    break;
case "String_Node_Str":
  translation=value;
break;
case "String_Node_Str":
ipa=value;
break;
case "String_Node_Str":
romanization=value;
break;
}
}
targetPack.createSentenceOrUpdate(realm,index,translation,ipa,romanization,null);
basePack.createSentenceOrUpdate(realm,index,sentence,null,null,null);
}
actionSubject.onNext(LanguageImportFragment.ACTION_EXTRACTING_AUDIO);
progressSubject.onNext(0);
totalSubject.onNext(numFiles);
return true;
}