Skip to content

EVA-4082 update write method on VariantSourceMongoWriter to do upsert #115

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
nitin-ebi merged 1 commit into from
Feb 20, 2026
Merged

EVA-4082 update write method on VariantSourceMongoWriter to do upsert #115

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
26 changes: 24 additions & 2 deletions ...mongodb/src/main/java/uk/ac/ebi/eva/commons/mongodb/writers/VariantSourceMongoWriter.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,9 @@
package uk.ac.ebi.eva.commons.mongodb.writers;

import com.mongodb.client.model.IndexOptions;
import com.mongodb.client.model.UpdateOneModel;
import com.mongodb.client.model.UpdateOptions;
import com.mongodb.client.model.WriteModel;
import org.bson.Document;
import org.springframework.batch.item.data.MongoItemWriter;
import org.springframework.data.mongodb.core.MongoOperations;
Expand All @@ -25,6 +28,7 @@
import uk.ac.ebi.eva.commons.core.models.IVariantSource;
import uk.ac.ebi.eva.commons.mongodb.entities.VariantSourceMongo;

import java.util.ArrayList;
import java.util.List;
import java.util.stream.Collectors;

Expand Down Expand Up @@ -60,9 +64,27 @@ private void createIndexes() {

@Override
public void write(List<? extends IVariantSource> items) throws Exception {
List<VariantSourceMongo> convertedList = items.stream()
List<VariantSourceMongo> variantSourceMongoList = items.stream()
.map(VariantSourceMongo::new)
.collect(Collectors.toList());
super.write(convertedList);

List<WriteModel<Document>> writes = new ArrayList<>();
for (VariantSourceMongo variantSourceMongo : variantSourceMongoList) {
// include only shard keys as part of query
Document query = new Document()
.append(VariantSourceMongo.STUDYID_FIELD, variantSourceMongo.getStudyId())
.append(VariantSourceMongo.FILEID_FIELD, variantSourceMongo.getFileId())
.append(VariantSourceMongo.FILENAME_FIELD, variantSourceMongo.getFileName());
Document update = new Document("$set", convertToMongo(variantSourceMongo));
writes.add(new UpdateOneModel<>(query, update, new UpdateOptions().upsert(true)));
}

if (!writes.isEmpty()) {
mongoOperations.getCollection(collection).bulkWrite(writes);
}
}

private Document convertToMongo(VariantSourceMongo variantSourceMongo) {
return (Document) mongoOperations.getConverter().convertToMongoType(variantSourceMongo);
}
}
81 changes: 68 additions & 13 deletions ...odb/src/test/java/uk/ac/ebi/eva/commons/mongodb/writers/VariantSourceMongoWriterTest.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -45,9 +45,7 @@
import java.util.stream.Collectors;
import java.util.stream.StreamSupport;


import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.*;


/**
Expand All @@ -73,6 +71,8 @@ public class VariantSourceMongoWriterTest {

private static final String STUDY_ID = "1";

private static final String FILE_NAME = "CHICKEN_SNPS_LAYER";

private static final String STUDY_NAME = "small";

private static final StudyType STUDY_TYPE = StudyType.COLLECTION;
Expand All @@ -98,7 +98,7 @@ public void tearDown() throws Exception {

@Test
public void shouldWriteAllFieldsIntoMongoDb() throws Exception {
MongoCollection<Document> fileCollection = mongoOperations.getCollection (COLLECTION_FILES_NAME);
MongoCollection<Document> fileCollection = mongoOperations.getCollection(COLLECTION_FILES_NAME);
VariantSourceMongoWriter filesWriter = new VariantSourceMongoWriter(
mongoOperations, COLLECTION_FILES_NAME);

Expand All @@ -108,7 +108,7 @@ public void shouldWriteAllFieldsIntoMongoDb() throws Exception {
FindIterable<Document> cursor = fileCollection.find();
int count = 0;

for (Document next: cursor) {
for (Document next : cursor) {
count++;
assertNotNull(next.get(VariantSourceMongo.FILEID_FIELD));
assertNotNull(next.get(VariantSourceMongo.FILENAME_FIELD));
Expand All @@ -129,6 +129,61 @@ public void shouldWriteAllFieldsIntoMongoDb() throws Exception {
assertEquals(1, count);
}

@Test
public void shouldDoUpdateInCaseOfExistingDocument() throws Exception {
MongoCollection<Document> fileCollection = mongoOperations.getCollection(COLLECTION_FILES_NAME);
VariantSourceMongoWriter filesWriter = new VariantSourceMongoWriter(
mongoOperations, COLLECTION_FILES_NAME);

// make an entry into the database
VariantSourceMongo variantSource = new VariantSourceMongo(FILE_ID, FILE_NAME, STUDY_ID, STUDY_NAME,
StudyType.AGGREGATE, Aggregation.BASIC, null, null, null);
filesWriter.write(Collections.singletonList(variantSource));
FindIterable<Document> cursor = fileCollection.find();
int count = 0;
for (Document next : cursor) {
count++;
assertTrue(next.get(VariantSourceMongo.FILEID_FIELD).equals(FILE_ID));
assertTrue(next.get(VariantSourceMongo.STUDYID_FIELD).equals(STUDY_ID));
assertTrue(next.get(VariantSourceMongo.FILENAME_FIELD).equals(FILE_NAME));
assertTrue(next.get(VariantSourceMongo.STUDYNAME_FIELD).equals(STUDY_NAME));
assertTrue(next.get(VariantSourceMongo.STUDYTYPE_FIELD).equals(StudyType.AGGREGATE.name()));
assertTrue(next.get(VariantSourceMongo.AGGREGATION_FIELD).equals(Aggregation.BASIC.name()));
assertNotNull(next.get(VariantSourceMongo.DATE_FIELD));
assertTrue(next.get(VariantSourceMongo.SAMPLES_FIELD).equals(new Document()));
assertTrue(next.get(VariantSourceMongo.METADATA_FIELD).equals(new Document()));
}
assertEquals(1, count);

// insert another document with same fileId, studyId and fileName
variantSource = getVariantSource();
filesWriter.write(Collections.singletonList(variantSource));
cursor = fileCollection.find();
count = 0;
for (Document next : cursor) {
count++;

assertTrue(next.get(VariantSourceMongo.FILEID_FIELD).equals(FILE_ID));
assertTrue(next.get(VariantSourceMongo.STUDYID_FIELD).equals(STUDY_ID));
assertTrue(next.get(VariantSourceMongo.FILENAME_FIELD).equals(FILE_NAME));
assertTrue(next.get(VariantSourceMongo.STUDYNAME_FIELD).equals(STUDY_NAME));

// existing document should be updated with new values from the document
assertTrue(next.get(VariantSourceMongo.STUDYTYPE_FIELD).equals(StudyType.COLLECTION.name()));
assertTrue(next.get(VariantSourceMongo.AGGREGATION_FIELD).equals(Aggregation.NONE.name()));
assertNotNull(next.get(VariantSourceMongo.SAMPLES_FIELD));
assertNotNull(next.get(VariantSourceMongo.DATE_FIELD));

Document meta = (Document) next.get(VariantSourceMongo.METADATA_FIELD);
assertNotNull(meta);
assertNotNull(meta.get("ALT"));
assertNotNull(meta.get("FILTER"));
assertNotNull(meta.get("INFO"));
assertNotNull(meta.get("FORMAT"));
}
assertEquals(1, count);
}

@Test
public void shouldWriteSamplesWithDotsInName() throws Exception {
MongoCollection<Document> fileCollection = mongoOperations.getCollection(COLLECTION_FILES_NAME);
Expand All @@ -147,7 +202,7 @@ public void shouldWriteSamplesWithDotsInName() throws Exception {

FindIterable<Document> cursor = fileCollection.find();

for (Document next: cursor) {
for (Document next : cursor) {
Document samples = (Document) next.get(VariantSourceMongo.SAMPLES_FIELD);
Set<String> keySet = samples.keySet();

Expand All @@ -158,22 +213,22 @@ public void shouldWriteSamplesWithDotsInName() throws Exception {

@Test
public void shouldCreateUniqueFileIndex() throws Exception {
MongoCollection<Document> fileCollection = mongoOperations.getCollection (COLLECTION_FILES_NAME);
VariantSourceMongoWriter filesWriter = new VariantSourceMongoWriter( mongoOperations, COLLECTION_FILES_NAME);
MongoCollection<Document> fileCollection = mongoOperations.getCollection(COLLECTION_FILES_NAME);
VariantSourceMongoWriter filesWriter = new VariantSourceMongoWriter(mongoOperations, COLLECTION_FILES_NAME);

VariantSourceMongo variantSource = getVariantSource();
filesWriter.write(Collections.singletonList(variantSource));

ListIndexesIterable<Document> indexesInfo = fileCollection.listIndexes();

Set<String> createdIndexes = StreamSupport.stream(
indexesInfo.map(index -> index.get("name").toString()).spliterator(), false)
.collect(Collectors.toSet());
indexesInfo.map(index -> index.get("name").toString()).spliterator(), false)
.collect(Collectors.toSet());
Set<String> expectedIndexes = new HashSet<>();
expectedIndexes.addAll(Arrays.asList("sid_1_fid_1_fname_1", "_id_"));
assertEquals(expectedIndexes, createdIndexes);

for(Document indexInfo: indexesInfo) {
for (Document indexInfo : indexesInfo) {
if ("sid_1_fid_1_fname_1".equals(indexInfo.get("name").toString())) {
assertNotNull(indexInfo);
assertEquals("true", indexInfo.get(UNIQUE_INDEX).toString());
Expand All @@ -196,9 +251,9 @@ private VariantSourceMongo getVariantSource() throws Exception {
metadata.put("FILTER", "All filters passed");
metadata.put("INFO", "INFO field");
metadata.put("FORMAT", "FORMAT field");
return new VariantSourceMongo(FILE_ID, "CHICKEN_SNPS_LAYER", STUDY_ID, STUDY_NAME, STUDY_TYPE,
return new VariantSourceMongo(FILE_ID, FILE_NAME, STUDY_ID, STUDY_NAME, STUDY_TYPE,
AGGREGATION, samplesPosition, metadata,
new VariantGlobalStatsMongo(0,0,0, 0,
new VariantGlobalStatsMongo(0, 0, 0, 0,
0, 0, 0, 0, 0));
}
}
Loading