private void setRefsAndCollections(List<String> parents, Item feature) {
String clsName = feature.getClassName();
Map<String, String> refsAndCollections = handler.getRefsAndCollections();
if (refsAndCollections != null
&& refsAndCollections.containsKey(clsName)
&& parents != null
&& !parents.isEmpty()) {
ClassDescriptor cld =
tgtModel.getClassDescriptorByName(tgtModel.getPackageName() + "." + clsName);
String refName = refsAndCollections.get(clsName);
Iterator<String> parentIter = parents.iterator();
if (cld.getReferenceDescriptorByName(refName, true) != null) {
String parent = parentIter.next();
feature.setReference(refName, getRefId(parent));
if (parentIter.hasNext()) {
String primaryIdent = feature.getAttribute("primaryIdentifier").getValue();
throw new RuntimeException(
"Feature has multiple relations for reference: "
+ refName
+ " for feature: "
+ feature.getClassName()
+ ", "
+ feature.getIdentifier()
+ ", "
+ primaryIdent);
}
} else if (cld.getCollectionDescriptorByName(refName, true) != null) {
List<String> refIds = new ArrayList<String>();
while (parentIter.hasNext()) {
refIds.add(getRefId(parentIter.next()));
}
feature.setCollection(refName, refIds);
} else if (parentIter.hasNext()) {
throw new RuntimeException(
"No '"
+ refName
+ "' reference/collection found in "
+ "class: "
+ clsName
+ " - is map configured correctly?");
}
}
}
/**
* Search for the classes in a collection for a given InterMineObject, for example find all of the
* sub-classes of Employee in the Department.employees collection of a given Department. If there
* are no subclasses or the collection is empty a list with the type of the collection is
* returned.
*
* @param object an InterMineObject to inspect
* @param field the name if the collection to check
* @param os the ObjectStore in which to execute the query
* @return a list of classes in the collection
*/
public static List<Class<?>> queryForTypesInCollection(
InterMineObject object, String field, ObjectStore os) {
List<Class<?>> typesInCollection = new ArrayList<Class<?>>();
// if there are no subclasses there can only be one type in the collection
Model model = os.getModel();
ClassDescriptor startCld =
model.getClassDescriptorByName(DynamicUtil.getSimpleClassName(object));
CollectionDescriptor col = startCld.getCollectionDescriptorByName(field, true);
ClassDescriptor colCld = col.getReferencedClassDescriptor();
if (model.getAllSubs(colCld).isEmpty()) {
// there aren't any subclasses, so no need to do a query
typesInCollection.add(colCld.getType());
} else {
// there may be multiple subclasses in the collection, need to run a query
Query query = new Query();
QueryClass qc = new QueryClass(colCld.getType());
query.addFrom(qc);
query.addToSelect(new QueryField(qc, "class"));
query.setDistinct(true);
query.setConstraint(
new ContainsConstraint(
new QueryCollectionReference(object, field), ConstraintOp.CONTAINS, qc));
for (Object o : os.executeSingleton(query)) {
typesInCollection.add((Class<?>) o);
}
// Collection was empty but add collection type to be consistent with collection types
// without subclasses.
if (typesInCollection.isEmpty()) {
typesInCollection.add(colCld.getType());
}
}
return typesInCollection;
}
/**
* 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);
}
}
