/**
   * Add a collection of objects of type X to objects of type Y by using a connecting class. Eg. Add
   * a collection of Protein objects to Gene by examining the Transcript objects in the transcripts
   * collection of the Gene, which would use a query like: SELECT DISTINCT gene FROM Gene AS gene,
   * Transcript AS transcript, Protein AS protein WHERE (gene.transcripts CONTAINS transcript AND
   * transcript.protein CONTAINS protein) ORDER BY gene and then set protected gene.protein (if
   * created BioEntity1 -> BioEntity2 -> BioEntity3 ==> BioEntity1 -> BioEntity3
   *
   * @param firstClsName the first class in the query
   * @param firstClassFieldName the field in the firstClass which should contain the connectingClass
   * @param connectingClsName the class referred to by firstClass.sourceFieldName
   * @param connectingClassFieldName the field in connectingClass which should contain secondClass
   * @param secondClsName the class referred to by connectingClass.connectingClassFieldName
   * @param createFieldName the collection field in the secondClass - the collection to create/set
   * @param createInFirstClass if true create the new collection field in firstClass, otherwise
   *     create in secondClass
   * @throws Exception if anything goes wrong
   */
  protected void insertCollectionField(
      String firstClsName,
      String firstClassFieldName,
      String connectingClsName,
      String connectingClassFieldName,
      String secondClsName,
      String createFieldName,
      boolean createInFirstClass)
      throws Exception {
    InterMineObject lastDestObject = null;
    Set<InterMineObject> newCollection = new HashSet<InterMineObject>();

    String insertMessage =
        "insertCollectionField("
            + firstClsName
            + ", "
            + firstClassFieldName
            + ", "
            + connectingClsName
            + ", "
            + connectingClassFieldName
            + ","
            + secondClsName
            + ", "
            + createFieldName
            + ", "
            + createInFirstClass
            + ")";

    // Check that classes and fields specified exist in model
    try {
      String errorMessage = "Not performing " + insertMessage;
      PostProcessUtil.checkFieldExists(model, firstClsName, firstClassFieldName, errorMessage);
      PostProcessUtil.checkFieldExists(
          model, connectingClsName, connectingClassFieldName, errorMessage);
      PostProcessUtil.checkFieldExists(model, secondClsName, createFieldName, errorMessage);
    } catch (MetaDataException e) {
      return;
    }

    LOG.info("Beginning " + insertMessage);
    long startTime = System.currentTimeMillis();

    // if this is a many to many collection we can use ObjectStore.addToCollection which will
    // write directly to the database.
    boolean manyToMany = false;
    ClassDescriptor destCld;
    if (createInFirstClass) {
      destCld = model.getClassDescriptorByName(firstClsName);
    } else {
      destCld = model.getClassDescriptorByName(secondClsName);
    }
    CollectionDescriptor col = destCld.getCollectionDescriptorByName(createFieldName);
    if (col == null) {
      String msg =
          "Error running post-process `create-references` for `"
              + createFieldName
              + "` since this collection doesn't exist in the model.";
      LOG.error(msg);
      return;
    }

    if (col.relationType() == CollectionDescriptor.M_N_RELATION) {
      manyToMany = true;
    }

    Iterator<ResultsRow<InterMineObject>> resIter =
        PostProcessUtil.findConnectingClasses(
            osw.getObjectStore(),
            model.getClassDescriptorByName(firstClsName).getType(),
            firstClassFieldName,
            model.getClassDescriptorByName(connectingClsName).getType(),
            connectingClassFieldName,
            model.getClassDescriptorByName(secondClsName).getType(),
            createInFirstClass);

    // results will be firstClass ; destClass (ordered by firstClass)
    osw.beginTransaction();
    int count = 0;

    while (resIter.hasNext()) {
      ResultsRow<InterMineObject> rr = resIter.next();

      InterMineObject thisSourceObject;
      InterMineObject thisDestObject;

      if (createInFirstClass) {
        thisDestObject = rr.get(0);
        thisSourceObject = rr.get(1);
      } else {
        thisDestObject = rr.get(1);
        thisSourceObject = rr.get(0);
      }

      if (!manyToMany
          && (lastDestObject == null || !thisDestObject.getId().equals(lastDestObject.getId()))) {

        if (lastDestObject != null) {
          try {
            InterMineObject tempObject = PostProcessUtil.cloneInterMineObject(lastDestObject);
            Set<InterMineObject> oldCollection =
                (Set<InterMineObject>) tempObject.getFieldValue(createFieldName);
            newCollection.addAll(oldCollection);
            tempObject.setFieldValue(createFieldName, newCollection);
            count += newCollection.size();
            osw.store(tempObject);
          } catch (IllegalAccessException e) {
            LOG.error(
                "Object with ID "
                    + thisDestObject.getId()
                    + " has no "
                    + createFieldName
                    + " field",
                e);
          }
        }

        newCollection = new HashSet<InterMineObject>();
      }

      if (manyToMany) {
        osw.addToCollection(
            thisDestObject.getId(), destCld.getType(), createFieldName, thisSourceObject.getId());
      } else {
        newCollection.add(thisSourceObject);
      }

      lastDestObject = thisDestObject;
    }

    if (!manyToMany && lastDestObject != null) {
      // clone so we don't change the ObjectStore cache
      InterMineObject tempObject = PostProcessUtil.cloneInterMineObject(lastDestObject);
      tempObject.setFieldValue(createFieldName, newCollection);
      count += newCollection.size();
      osw.store(tempObject);
    }
    LOG.info(
        "Finished: created "
            + count
            + " references in "
            + secondClsName
            + " to "
            + firstClsName
            + " via "
            + connectingClsName
            + " - took "
            + (System.currentTimeMillis() - startTime)
            + " ms.");
    osw.commitTransaction();

    // now ANALYSE tables relation to class that has been altered - may be rows added
    // to indirection tables
    if (osw instanceof ObjectStoreWriterInterMineImpl) {
      ClassDescriptor cld = model.getClassDescriptorByName(secondClsName);
      DatabaseUtil.analyse(((ObjectStoreWriterInterMineImpl) osw).getDatabase(), cld, false);
    }
  }
  /**
   * Add a reference to and object of type X in objects of type Y by using a connecting class. Eg.
   * Add a reference to Gene objects in Exon by examining the Transcript objects in the transcripts
   * collection of the Gene, which would use a query like: SELECT DISTINCT gene FROM Gene AS gene,
   * Transcript AS transcript, Exon AS exon WHERE (gene.transcripts CONTAINS transcript AND
   * transcript.exons CONTAINS exon) ORDER BY gene and then set exon.gene
   *
   * <p>in overview we are doing: BioEntity1 -&gt; BioEntity2 -&gt; BioEntity3 ==&gt; BioEntitiy1
   * -&gt; BioEntity3
   *
   * @param sourceClsName the first class in the query
   * @param sourceClassFieldName the field in the sourceClass which should contain the
   *     connectingClass
   * @param connectingClsName the class referred to by sourceClass.sourceFieldName
   * @param connectingClassFieldName the field in connectingClass which should contain
   *     destinationClass
   * @param destinationClsName the class referred to by connectingClass.connectingClassFieldName
   * @param createFieldName the reference field in the destinationClass - the collection to
   *     create/set
   * @throws Exception if anything goes wrong
   */
  protected void insertReferenceField(
      String sourceClsName,
      String sourceClassFieldName,
      String connectingClsName,
      String connectingClassFieldName,
      String destinationClsName,
      String createFieldName)
      throws Exception {

    String insertMessage =
        "insertReferences("
            + sourceClsName
            + ", "
            + sourceClassFieldName
            + ", "
            + connectingClsName
            + ", "
            + connectingClassFieldName
            + ","
            + destinationClsName
            + ", "
            + createFieldName
            + ")";

    // Check that classes and fields specified exist in model
    try {
      String errorMessage = "Not performing " + insertMessage;
      PostProcessUtil.checkFieldExists(model, sourceClsName, sourceClassFieldName, errorMessage);
      PostProcessUtil.checkFieldExists(
          model, connectingClsName, connectingClassFieldName, errorMessage);
      PostProcessUtil.checkFieldExists(model, destinationClsName, createFieldName, errorMessage);
    } catch (MetaDataException e) {
      return;
    }

    LOG.info("Beginning " + insertMessage);
    long startTime = System.currentTimeMillis();

    Iterator<ResultsRow<InterMineObject>> resIter =
        PostProcessUtil.findConnectingClasses(
            osw.getObjectStore(),
            model.getClassDescriptorByName(sourceClsName).getType(),
            sourceClassFieldName,
            model.getClassDescriptorByName(connectingClsName).getType(),
            connectingClassFieldName,
            model.getClassDescriptorByName(destinationClsName).getType(),
            true);

    // results will be sourceClass ; destClass (ordered by sourceClass)
    osw.beginTransaction();

    int count = 0;

    while (resIter.hasNext()) {
      ResultsRow<InterMineObject> rr = resIter.next();
      InterMineObject thisSourceObject = rr.get(0);
      InterMineObject thisDestObject = rr.get(1);

      try {
        // clone so we don't change the ObjectStore cache
        InterMineObject tempObject = PostProcessUtil.cloneInterMineObject(thisDestObject);
        tempObject.setFieldValue(createFieldName, thisSourceObject);
        count++;
        if (count % 10000 == 0) {
          LOG.info(
              "Created "
                  + count
                  + " references in "
                  + destinationClsName
                  + " to "
                  + sourceClsName
                  + " via "
                  + connectingClsName);
        }
        osw.store(tempObject);
      } catch (IllegalAccessException e) {
        LOG.error(
            "Object with ID: " + thisDestObject.getId() + " has no " + createFieldName + " field");
      }
    }

    LOG.info(
        "Finished: created "
            + count
            + " references in "
            + destinationClsName
            + " to "
            + sourceClsName
            + " via "
            + connectingClsName
            + " - took "
            + (System.currentTimeMillis() - startTime)
            + " ms.");
    osw.commitTransaction();

    // now ANALYSE tables relation to class that has been altered - may be rows added
    // to indirection tables
    if (osw instanceof ObjectStoreWriterInterMineImpl) {
      ClassDescriptor cld = model.getClassDescriptorByName(destinationClsName);
      DatabaseUtil.analyse(((ObjectStoreWriterInterMineImpl) osw).getDatabase(), cld, false);
    }
  }