/**
* Populate the SequenceFeature.locatedFeatures() collection for: Gene, Transcript, Exon and CDS
*
* @throws Exception if anything goes wrong
*/
public void populateCollection() throws Exception {
Map<String, SOTerm> soTerms = populateSOTermMap(osw);
Query q = getAllParents();
Results res = osw.getObjectStore().execute(q);
Iterator<Object> resIter = res.iterator();
osw.beginTransaction();
int parentCount = 0;
int childCount = 0;
while (resIter.hasNext()) {
ResultsRow<InterMineObject> rr = (ResultsRow<InterMineObject>) resIter.next();
InterMineObject parent = rr.get(0);
SOTerm soTerm = (SOTerm) rr.get(1);
InterMineObject o = PostProcessUtil.cloneInterMineObject(parent);
Set<InterMineObject> newCollection = getChildFeatures(soTerms, soTerm, o);
if (newCollection != null && !newCollection.isEmpty()) {
o.setFieldValue(TARGET_COLLECTION, newCollection);
osw.store(o);
parentCount++;
childCount += newCollection.size();
}
}
osw.commitTransaction();
LOG.info("Stored " + childCount + " child features for " + parentCount + " parent features");
}
/**
* Read the UTRs collection of MRNA then set the fivePrimeUTR and threePrimeUTR fields with the
* corresponding UTRs.
*
* @throws Exception if anything goes wrong
*/
public void createUtrRefs() throws Exception {
long startTime = System.currentTimeMillis();
Query q = new Query();
q.setDistinct(false);
QueryClass qcMRNA = new QueryClass(model.getClassDescriptorByName("MRNA").getType());
q.addFrom(qcMRNA);
q.addToSelect(qcMRNA);
q.addToOrderBy(qcMRNA);
QueryClass qcUTR = new QueryClass(model.getClassDescriptorByName("UTR").getType());
q.addFrom(qcUTR);
q.addToSelect(qcUTR);
q.addToOrderBy(qcUTR);
QueryCollectionReference mrnaUtrsRef = new QueryCollectionReference(qcMRNA, "UTRs");
ContainsConstraint mrnaUtrsConstraint =
new ContainsConstraint(mrnaUtrsRef, ConstraintOp.CONTAINS, qcUTR);
QueryObjectReference fivePrimeRef = new QueryObjectReference(qcMRNA, "fivePrimeUTR");
ContainsConstraint fivePrimeNullConstraint =
new ContainsConstraint(fivePrimeRef, ConstraintOp.IS_NULL);
QueryObjectReference threePrimeRef = new QueryObjectReference(qcMRNA, "threePrimeUTR");
ContainsConstraint threePrimeNullConstraint =
new ContainsConstraint(threePrimeRef, ConstraintOp.IS_NULL);
ConstraintSet cs = new ConstraintSet(ConstraintOp.AND);
cs.addConstraint(mrnaUtrsConstraint);
cs.addConstraint(fivePrimeNullConstraint);
cs.addConstraint(threePrimeNullConstraint);
q.setConstraint(cs);
ObjectStore os = osw.getObjectStore();
((ObjectStoreInterMineImpl) os).precompute(q, Constants.PRECOMPUTE_CATEGORY);
Results res = os.execute(q, 500, true, true, true);
int count = 0;
InterMineObject lastMRNA = null;
InterMineObject fivePrimeUTR = null;
InterMineObject threePrimeUTR = null;
osw.beginTransaction();
Class<? extends FastPathObject> fivePrimeUTRCls =
model.getClassDescriptorByName("FivePrimeUTR").getType();
Iterator<?> resIter = res.iterator();
while (resIter.hasNext()) {
ResultsRow<?> rr = (ResultsRow<?>) resIter.next();
InterMineObject mrna = (InterMineObject) rr.get(0);
InterMineObject utr = (InterMineObject) rr.get(1);
if (lastMRNA != null && !mrna.getId().equals(lastMRNA.getId())) {
// clone so we don't change the ObjectStore cache
InterMineObject tempMRNA = PostProcessUtil.cloneInterMineObject(lastMRNA);
if (fivePrimeUTR != null) {
tempMRNA.setFieldValue("fivePrimeUTR", fivePrimeUTR);
fivePrimeUTR = null;
}
if (threePrimeUTR != null) {
tempMRNA.setFieldValue("threePrimeUTR", threePrimeUTR);
threePrimeUTR = null;
}
osw.store(tempMRNA);
count++;
}
if (DynamicUtil.isInstance(utr, fivePrimeUTRCls)) {
fivePrimeUTR = utr;
} else {
threePrimeUTR = utr;
}
lastMRNA = mrna;
}
if (lastMRNA != null) {
// clone so we don't change the ObjectStore cache
InterMineObject tempMRNA = PostProcessUtil.cloneInterMineObject(lastMRNA);
tempMRNA.setFieldValue("fivePrimeUTR", fivePrimeUTR);
tempMRNA.setFieldValue("threePrimeUTR", threePrimeUTR);
osw.store(tempMRNA);
count++;
}
LOG.info(
"Stored MRNA "
+ count
+ " times ("
+ count * 2
+ " fields set)"
+ " - took "
+ (System.currentTimeMillis() - startTime)
+ " ms.");
osw.commitTransaction();
// now ANALYSE tables relating to class that has been altered - may be rows added
// to indirection tables
if (osw instanceof ObjectStoreWriterInterMineImpl) {
ClassDescriptor cld = model.getClassDescriptorByName("MRNA");
DatabaseUtil.analyse(((ObjectStoreWriterInterMineImpl) osw).getDatabase(), cld, false);
}
}
/**
* 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 -> BioEntity2 -> BioEntity3 ==> BioEntitiy1
* -> 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);
}
}
