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EVA-4070: Remove index name in VariantSourceWriter, run tests using Mongo 6 #114

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Merged
apriltuesday merged 3 commits into from
Feb 5, 2026
Merged

EVA-4070: Remove index name in VariantSourceWriter, run tests using Mongo 6 #114

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10ccc84
remove index name in VariantSourceWriter, run tests using Mongo 6
apriltuesday Feb 4, 2026
c733191
fix test
apriltuesday Feb 4, 2026
665d9d8
Update .github/workflows/run-tests.yml
apriltuesday Feb 4, 2026
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8 changes: 4 additions & 4 deletions .github/workflows/run-tests.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
mongodb-version: [4.0.18]
mongodb-version: [6.0.6]
java-version: [1.8]

steps:
Expand All @@ -23,9 +23,9 @@ jobs:
java-version: ${{ matrix.java-version }}
- name: Install and Start MongoDB
run: |
wget http://fastdl.mongodb.org/linux/mongodb-linux-x86_64-${{ matrix.mongodb-version }}.tgz
tar xfz mongodb-linux-x86_64-${{ matrix.mongodb-version }}.tgz
export PATH=`pwd`/mongodb-linux-x86_64-${{ matrix.mongodb-version }}/bin:$PATH
wget http://fastdl.mongodb.org/linux/mongodb-linux-x86_64-ubuntu2204-${{ matrix.mongodb-version }}.tgz
tar xfz mongodb-linux-x86_64-ubuntu2204-${{ matrix.mongodb-version }}.tgz
export PATH=`pwd`/mongodb-linux-x86_64-ubuntu2204-${{ matrix.mongodb-version }}/bin:$PATH
mkdir -p data/db
mongod --dbpath=data/db &
mongod --version
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4 changes: 1 addition & 3 deletions ...mongodb/src/main/java/uk/ac/ebi/eva/commons/mongodb/writers/VariantSourceMongoWriter.java
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Expand Up @@ -33,8 +33,6 @@
*/
public class VariantSourceMongoWriter extends MongoItemWriter<IVariantSource> {

public static final String UNIQUE_FILE_INDEX_NAME = "unique_file";

private MongoOperations mongoOperations;

private String collection;
Expand All @@ -53,7 +51,7 @@ public VariantSourceMongoWriter(MongoOperations mongoOperations, String collecti
}

private void createIndexes() {
IndexOptions indexOptions = new IndexOptions().background(true).unique(true).name(UNIQUE_FILE_INDEX_NAME);
IndexOptions indexOptions = new IndexOptions().background(true).unique(true);
mongoOperations.getCollection(collection).createIndex(
new Document(VariantSourceMongo.STUDYID_FIELD, 1).append(VariantSourceMongo.FILEID_FIELD, 1)
.append(VariantSourceMongo.FILENAME_FIELD, 1),
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4 changes: 2 additions & 2 deletions ...odb/src/test/java/uk/ac/ebi/eva/commons/mongodb/writers/VariantSourceMongoWriterTest.java
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Expand Up @@ -170,11 +170,11 @@ public void shouldCreateUniqueFileIndex() throws Exception {
indexesInfo.map(index -> index.get("name").toString()).spliterator(), false)
.collect(Collectors.toSet());
Set<String> expectedIndexes = new HashSet<>();
expectedIndexes.addAll(Arrays.asList(VariantSourceMongoWriter.UNIQUE_FILE_INDEX_NAME, "_id_"));
expectedIndexes.addAll(Arrays.asList("sid_1_fid_1_fname_1", "_id_"));
assertEquals(expectedIndexes, createdIndexes);

for(Document indexInfo: indexesInfo) {
if (VariantSourceMongoWriter.UNIQUE_FILE_INDEX_NAME.equals(indexInfo.get("name").toString())) {
if ("sid_1_fid_1_fname_1".equals(indexInfo.get("name").toString())) {
assertNotNull(indexInfo);
assertEquals("true", indexInfo.get(UNIQUE_INDEX).toString());
assertEquals("true", indexInfo.get(BACKGROUND_INDEX).toString());
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