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package org.intermine.bio.postprocess;
/*
* Copyright (C) 2002-2021 FlyMine
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. See the LICENSE file for more
* information or http://www.gnu.org/copyleft/lesser.html.
*
*/
import java.util.HashSet;
import java.util.Iterator;
import java.util.Set;
import org.apache.log4j.Logger;
import java.sql.SQLException;
import org.intermine.sql.DatabaseUtil;
import org.intermine.metadata.ClassDescriptor;
import org.intermine.metadata.CollectionDescriptor;
import org.intermine.metadata.MetaDataException;
import org.intermine.metadata.Model;
import org.intermine.model.InterMineObject;
import org.intermine.bio.util.PostProcessUtil;
import org.intermine.objectstore.ObjectStoreWriter;
import org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl;
import org.intermine.objectstore.ObjectStoreException;
import org.intermine.objectstore.query.ResultsRow;
import org.intermine.postprocess.PostProcessor;
/**
* Calculate additional mappings between annotation after loading into genomic ObjectStore.
* Currently designed to cope with situation after loading ensembl, may need to change
* as other annotation is loaded. New Locations (and updated BioEntities) are stored
* back in originating ObjectStore.
*
* @author Richard Smith
* @author Kim Rutherford
*/
public class CreateReferencesProcess extends PostProcessor
{
private Model model;
private static final Logger LOG = Logger.getLogger(CreateReferencesProcess.class);
/**
* Create a new instance
*
* @param osw object store writer
*/
public CreateReferencesProcess(ObjectStoreWriter osw) {
super(osw);
}
/**
* {@inheritDoc}
*
* Main post-processing routine.
* @throws ObjectStoreException if the objectstore throws an exception
*/
public void postProcess() throws ObjectStoreException {
model = Model.getInstanceByName("genomic");
LOG.info("insertReferences stage 1");
// fill in collections on Chromosome
insertCollectionField("ChromosomeBand", "locations",
"Location", "locatedOn",
"Chromosome", "chromosomeBands",
false);
LOG.info("insertReferences stage 2");
// Exon.gene / Gene.exons
insertReferenceField("Gene", "transcripts",
"Transcript", "exons",
"Exon", "gene");
LOG.info("insertReferences stage 3");
// UTR.gene / Gene.UTRs
insertReferenceField("Gene", "transcripts",
"Transcript", "UTRs",
"UTR", "gene");
LOG.info("insertReferences stage 4");
// CDS.gene / Gene.CDSs
insertReferenceField("Gene", "transcripts",
"Transcript", "CDSs",
"CDS", "gene");
}
/**
* 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
*
* 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 ObjectStoreException if anything goes wrong
*/
protected void insertReferenceField(String sourceClsName, String sourceClassFieldName,
String connectingClsName, String connectingClassFieldName, String destinationClsName,
String createFieldName) throws ObjectStoreException {
String insertMessage = "insertReferences("
+ sourceClsName + ", "
+ sourceClassFieldName + ", "
+ connectingClsName + ", "
+ connectingClassFieldName + ","
+ destinationClsName + ", "
+ createFieldName + ")";
// Check that classes and fields specified exist in model
if (model == null) {
model = Model.getInstanceByName("genomic");
}
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> resIter = null;
if (model == null) {
model = Model.getInstanceByName("genomic");
}
try {
resIter = PostProcessUtil.findConnectingClasses(
osw.getObjectStore(),
model.getClassDescriptorByName(sourceClsName).getType(),
sourceClassFieldName,
model.getClassDescriptorByName(connectingClsName).getType(),
connectingClassFieldName,
model.getClassDescriptorByName(destinationClsName).getType(), true);
} catch (IllegalAccessException e) {
throw new RuntimeException("couldn't find connecting classes " + e);
}
// results will be sourceClass ; destClass (ordered by sourceClass)
osw.beginTransaction();
int count = 0;
while (resIter.hasNext()) {
ResultsRow 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);
try {
DatabaseUtil.analyse(((ObjectStoreWriterInterMineImpl) osw).getDatabase(), cld,
false);
} catch (SQLException e) {
throw new RuntimeException("Couldn't analyse database " + e);
}
}
}
/**
* 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 ObjectStoreException if anything goes wrong
*/
protected void insertCollectionField(String firstClsName, String firstClassFieldName,
String connectingClsName, String connectingClassFieldName, String secondClsName,
String createFieldName, boolean createInFirstClass) throws ObjectStoreException {
InterMineObject lastDestObject = null;
Set newCollection = new HashSet();
String insertMessage = "insertCollectionField("
+ firstClsName + ", "
+ firstClassFieldName + ", "
+ connectingClsName + ", "
+ connectingClassFieldName + ","
+ secondClsName + ", "
+ createFieldName + ", "
+ createInFirstClass + ")";
// Check that classes and fields specified exist in model
if (model == null) {
model = Model.getInstanceByName("genomic");
}
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> resIter = null;
try {
resIter = PostProcessUtil.findConnectingClasses(
osw.getObjectStore(),
model.getClassDescriptorByName(firstClsName).getType(),
firstClassFieldName,
model.getClassDescriptorByName(connectingClsName).getType(),
connectingClassFieldName,
model.getClassDescriptorByName(secondClsName).getType(), createInFirstClass);
} catch (IllegalAccessException e) {
throw new RuntimeException("couldn't find connecting classes " + e);
}
// results will be firstClass ; destClass (ordered by firstClass)
osw.beginTransaction();
int count = 0;
while (resIter.hasNext()) {
ResultsRow 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 oldCollection
= (Set) 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();
}
if (manyToMany) {
osw.addToCollection(thisDestObject.getId(), destCld.getType(),
createFieldName, thisSourceObject.getId());
} else {
newCollection.add(thisSourceObject);
}
lastDestObject = thisDestObject;
}
if (!manyToMany && lastDestObject != null) {
try {
// clone so we don't change the ObjectStore cache
InterMineObject tempObject = PostProcessUtil.cloneInterMineObject(lastDestObject);
tempObject.setFieldValue(createFieldName, newCollection);
count += newCollection.size();
osw.store(tempObject);
} catch (IllegalAccessException e) {
throw new RuntimeException("Failed to clone " + e);
}
}
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);
try {
DatabaseUtil.analyse(((ObjectStoreWriterInterMineImpl) osw).getDatabase(), cld,
false);
} catch (SQLException e) {
throw new RuntimeException("Couldn't analyse database " + e);
}
}
}
}
