Program: 112323
Project: 112323
Buggy source:
protected List<ResourceLink> extractResourceLinks(ResourceTable theEntity,IResource theResource){
  ArrayList<ResourceLink> retVal=new ArrayList<ResourceLink>();
  RuntimeResourceDefinition def=getContext().getResourceDefinition(theResource);
  FhirTerser t=getContext().newTerser();
  for (  RuntimeSearchParam nextSpDef : def.getSearchParams()) {
    if (nextSpDef.getParamType() != SearchParamTypeEnum.REFERENCE) {
      continue;
    }
    String nextPath=nextSpDef.getPath();
    boolean multiType=false;
    if (nextPath.endsWith("String_Node_Str")) {
      multiType=true;
    }
    List<Object> values=t.getValues(theResource,nextPath);
    for (    Object nextObject : values) {
      if (nextObject == null) {
        continue;
      }
      ResourceLink nextEntity;
      if (nextObject instanceof ResourceReferenceDt) {
        ResourceReferenceDt nextValue=(ResourceReferenceDt)nextObject;
        if (nextValue.isEmpty()) {
          continue;
        }
        if (nextValue.getReference().getValue().startsWith("String_Node_Str")) {
          continue;
        }
        String typeString=nextValue.getReference().getResourceType();
        if (isBlank(typeString)) {
          throw new InvalidRequestException("String_Node_Str" + nextPath + "String_Node_Str"+ nextValue.getReference().getValue());
        }
        Class<? extends IResource> type=getContext().getResourceDefinition(typeString).getImplementingClass();
        String id=nextValue.getReference().getIdPart();
        if (StringUtils.isBlank(id)) {
          continue;
        }
        IFhirResourceDao<?> dao=getDao(type);
        if (dao == null) {
          throw new InvalidRequestException("String_Node_Str" + nextValue.getReference().getResourceType());
        }
        Long valueOf;
        try {
          valueOf=translateForcedIdToPid(nextValue.getReference());
        }
 catch (        Exception e) {
          String resName=getContext().getResourceDefinition(type).getName();
          throw new InvalidRequestException("String_Node_Str" + resName + "String_Node_Str"+ id+ "String_Node_Str"+ nextPath+ "String_Node_Str");
        }
        ResourceTable target=myEntityManager.find(ResourceTable.class,valueOf);
        if (target == null) {
          String resName=getContext().getResourceDefinition(type).getName();
          throw new InvalidRequestException("String_Node_Str" + resName + "String_Node_Str"+ id+ "String_Node_Str"+ nextPath);
        }
        nextEntity=new ResourceLink(nextPath,theEntity,target);
      }
 else {
        if (!multiType) {
          throw new ConfigurationException("String_Node_Str" + nextSpDef.getName() + "String_Node_Str"+ nextObject.getClass());
        }
 else {
          continue;
        }
      }
      if (nextEntity != null) {
        retVal.add(nextEntity);
      }
    }
  }
  theEntity.setHasLinks(retVal.size() > 0);
  return retVal;
}

Fixed version (ground truth):
protected List<ResourceLink> extractResourceLinks(ResourceTable theEntity,IResource theResource){
  ArrayList<ResourceLink> retVal=new ArrayList<ResourceLink>();
  RuntimeResourceDefinition def=getContext().getResourceDefinition(theResource);
  FhirTerser t=getContext().newTerser();
  for (  RuntimeSearchParam nextSpDef : def.getSearchParams()) {
    if (nextSpDef.getParamType() != SearchParamTypeEnum.REFERENCE) {
      continue;
    }
    String nextPath=nextSpDef.getPath();
    if (isBlank(nextPath)) {
      continue;
    }
    boolean multiType=false;
    if (nextPath.endsWith("String_Node_Str")) {
      multiType=true;
    }
    List<Object> values=t.getValues(theResource,nextPath);
    for (    Object nextObject : values) {
      if (nextObject == null) {
        continue;
      }
      ResourceLink nextEntity;
      if (nextObject instanceof ResourceReferenceDt) {
        ResourceReferenceDt nextValue=(ResourceReferenceDt)nextObject;
        if (nextValue.isEmpty()) {
          continue;
        }
        if (nextValue.getReference().getValue().startsWith("String_Node_Str")) {
          continue;
        }
        String typeString=nextValue.getReference().getResourceType();
        if (isBlank(typeString)) {
          throw new InvalidRequestException("String_Node_Str" + nextPath + "String_Node_Str"+ nextValue.getReference().getValue());
        }
        Class<? extends IResource> type=getContext().getResourceDefinition(typeString).getImplementingClass();
        String id=nextValue.getReference().getIdPart();
        if (StringUtils.isBlank(id)) {
          continue;
        }
        IFhirResourceDao<?> dao=getDao(type);
        if (dao == null) {
          throw new InvalidRequestException("String_Node_Str" + nextValue.getReference().getResourceType());
        }
        Long valueOf;
        try {
          valueOf=translateForcedIdToPid(nextValue.getReference());
        }
 catch (        Exception e) {
          String resName=getContext().getResourceDefinition(type).getName();
          throw new InvalidRequestException("String_Node_Str" + resName + "String_Node_Str"+ id+ "String_Node_Str"+ nextPath+ "String_Node_Str");
        }
        ResourceTable target=myEntityManager.find(ResourceTable.class,valueOf);
        if (target == null) {
          String resName=getContext().getResourceDefinition(type).getName();
          throw new InvalidRequestException("String_Node_Str" + resName + "String_Node_Str"+ id+ "String_Node_Str"+ nextPath);
        }
        nextEntity=new ResourceLink(nextPath,theEntity,target);
      }
 else {
        if (!multiType) {
          throw new ConfigurationException("String_Node_Str" + nextSpDef.getName() + "String_Node_Str"+ nextObject.getClass());
        }
 else {
          continue;
        }
      }
      if (nextEntity != null) {
        retVal.add(nextEntity);
      }
    }
  }
  theEntity.setHasLinks(retVal.size() > 0);
  return retVal;
}