From 10ccc8479c87b28234e3e9c25239baa49455ffc3 Mon Sep 17 00:00:00 2001 From: April Shen Date: Wed, 4 Feb 2026 10:06:13 +0000 Subject: [PATCH 1/3] remove index name in VariantSourceWriter, run tests using Mongo 6 --- .github/workflows/run-tests.yml | 8 ++++---- .../commons/mongodb/writers/VariantSourceMongoWriter.java | 4 +--- 2 files changed, 5 insertions(+), 7 deletions(-) diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml index 88b715b0..8fdf1a94 100644 --- a/.github/workflows/run-tests.yml +++ b/.github/workflows/run-tests.yml @@ -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: @@ -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 diff --git a/variation-commons-mongodb/src/main/java/uk/ac/ebi/eva/commons/mongodb/writers/VariantSourceMongoWriter.java b/variation-commons-mongodb/src/main/java/uk/ac/ebi/eva/commons/mongodb/writers/VariantSourceMongoWriter.java index bb7db4cc..6b602128 100644 --- a/variation-commons-mongodb/src/main/java/uk/ac/ebi/eva/commons/mongodb/writers/VariantSourceMongoWriter.java +++ b/variation-commons-mongodb/src/main/java/uk/ac/ebi/eva/commons/mongodb/writers/VariantSourceMongoWriter.java @@ -33,8 +33,6 @@ */ public class VariantSourceMongoWriter extends MongoItemWriter { - public static final String UNIQUE_FILE_INDEX_NAME = "unique_file"; - private MongoOperations mongoOperations; private String collection; @@ -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), From c73319148f0f25c515971f128c2b393cce414980 Mon Sep 17 00:00:00 2001 From: April Shen Date: Wed, 4 Feb 2026 10:14:49 +0000 Subject: [PATCH 2/3] fix test --- .../commons/mongodb/writers/VariantSourceMongoWriterTest.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/variation-commons-mongodb/src/test/java/uk/ac/ebi/eva/commons/mongodb/writers/VariantSourceMongoWriterTest.java b/variation-commons-mongodb/src/test/java/uk/ac/ebi/eva/commons/mongodb/writers/VariantSourceMongoWriterTest.java index cd55bdde..228fe896 100644 --- a/variation-commons-mongodb/src/test/java/uk/ac/ebi/eva/commons/mongodb/writers/VariantSourceMongoWriterTest.java +++ b/variation-commons-mongodb/src/test/java/uk/ac/ebi/eva/commons/mongodb/writers/VariantSourceMongoWriterTest.java @@ -170,11 +170,11 @@ public void shouldCreateUniqueFileIndex() throws Exception { indexesInfo.map(index -> index.get("name").toString()).spliterator(), false) .collect(Collectors.toSet()); Set 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()); From 665d9d8040c0016ae475a64cc2f7f62b7420fe25 Mon Sep 17 00:00:00 2001 From: April Shen Date: Wed, 4 Feb 2026 10:37:19 +0000 Subject: [PATCH 3/3] Update .github/workflows/run-tests.yml Co-authored-by: nitin-ebi <79518737+nitin-ebi@users.noreply.github.com> --- .github/workflows/run-tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml index 8fdf1a94..ddab2acb 100644 --- a/.github/workflows/run-tests.yml +++ b/.github/workflows/run-tests.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - mongodb-version: [6.0.6] + mongodb-version: [6.0.24] java-version: [1.8] steps: