Fix variant stats - avoid failure if no variants in the batch has sta…

…ts (#199)

* fix variant stats

src/main/java/uk/ac/ebi/eva/pipeline/io/processors/VariantStatsProcessor.java

@@ -39,6 +39,10 @@ public VariantStatsProcessor(String studyId) {
     @Override
     public VariantDocument process(VariantDocument variant) {
         Map<String, Integer> filesIdNumberOfSamplesMap = VariantStatsReader.getFilesIdAndNumberOfSamplesMap();
+        if (filesIdNumberOfSamplesMap.isEmpty()) {
+            // No new stats can be calculated, no processing required
+            return variant;
+        }
         Set<String> fidSet = filesIdNumberOfSamplesMap.keySet();
 
         String variantRef = variant.getReference();

src/main/java/uk/ac/ebi/eva/pipeline/io/writers/VariantStatsWriter.java

@@ -9,9 +9,12 @@
 import org.springframework.data.mongodb.core.query.Query;
 import org.springframework.data.mongodb.core.query.Update;
 import uk.ac.ebi.eva.commons.models.mongo.entity.VariantDocument;
+import uk.ac.ebi.eva.pipeline.io.readers.VariantStatsReader;
 import uk.ac.ebi.eva.pipeline.parameters.DatabaseParameters;
 
 import java.util.List;
+import java.util.Map;
+import java.util.stream.Collectors;
 
 public class VariantStatsWriter implements ItemWriter<VariantDocument> {
     private static final Logger logger = LoggerFactory.getLogger(VariantStatsWriter.class);
@@ -25,20 +28,30 @@ public VariantStatsWriter(DatabaseParameters databaseParameters, MongoTemplate m
 
     @Override
     public void write(List<? extends VariantDocument> variants) {
-        BulkOperations bulkOperations = mongoTemplate.bulkOps(BulkOperations.BulkMode.UNORDERED, VariantDocument.class,
-                databaseParameters.getCollectionVariantsName());
-        for (VariantDocument variant : variants) {
-            if (variant.getVariantStatsMongo() == null || variant.getVariantStatsMongo().isEmpty()) {
-                continue;
+        Map<String, Integer> filesIdNumberOfSamplesMap = VariantStatsReader.getFilesIdAndNumberOfSamplesMap();
+        if (filesIdNumberOfSamplesMap.isEmpty()) {
+            // No new stats would have been calculated, no need to write anything
+            return;
+        }
+
+        variants = variants.stream()
+                .filter(v -> v.getVariantStatsMongo() != null && !v.getVariantStatsMongo().isEmpty())
+                .collect(Collectors.toList());
+
+        if (!variants.isEmpty()) {
+            BulkOperations bulkOperations = mongoTemplate.bulkOps(BulkOperations.BulkMode.UNORDERED, VariantDocument.class,
+                    databaseParameters.getCollectionVariantsName());
+
+            for (VariantDocument variant : variants) {
+                Query query = new Query(Criteria.where("_id").is(variant.getId()));
+                Update update = new Update();
+                update.set("st", variant.getVariantStatsMongo());
+
+                bulkOperations.updateOne(query, update);
             }
-            Query query = new Query(Criteria.where("_id").is(variant.getId()));
-            Update update = new Update();
-            update.set("st", variant.getVariantStatsMongo());
 
-            bulkOperations.updateOne(query, update);
+            bulkOperations.execute();
         }
-
-        bulkOperations.execute();
     }
 
 }

src/main/java/uk/ac/ebi/eva/pipeline/jobs/steps/tasklets/FileStatsTasklet.java

@@ -75,18 +75,21 @@ public FileStatsTasklet(DatabaseParameters databaseParameters, MongoTemplate mon
     @Override
     public RepeatStatus execute(StepContribution stepContribution, ChunkContext chunkContext) throws Exception {
         populateFilesIdAndNumberOfSamplesMap();
-        initializeFileIdCountsMap();
-        cursor = initializeCursor();
-        try {
-            while (cursor.hasNext()) {
-                VariantDocument variantDocument = getVariant(cursor.next());
-                processCounts(variantDocument);
+
+        if (!fileIdNumberOfSamplesMap.isEmpty()) {
+            initializeFileIdCountsMap();
+            cursor = initializeCursor();
+            try {
+                while (cursor.hasNext()) {
+                    VariantDocument variantDocument = getVariant(cursor.next());
+                    processCounts(variantDocument);
+                }
+            } finally {
+                cursor.close();
             }
-        } finally {
-            cursor.close();
-        }
 
-        writeStatsInTheDB();
+            writeStatsInTheDB();
+        }
 
         return RepeatStatus.FINISHED;
     }

src/test/java/uk/ac/ebi/eva/pipeline/configuration/jobs/steps/variantstats/VariantStatsStepTestNoNewStatsCalculated.java

@@ -0,0 +1,163 @@
+/*
+ * Copyright 2024 EMBL - European Bioinformatics Institute
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package uk.ac.ebi.eva.pipeline.configuration.jobs.steps.variantstats;
+
+import com.mongodb.client.MongoCollection;
+import org.bson.Document;
+import org.junit.After;
+import org.junit.Assert;
+import org.junit.Before;
+import org.junit.Rule;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.springframework.batch.core.JobExecution;
+import org.springframework.batch.core.JobParameters;
+import org.springframework.batch.test.JobLauncherTestUtils;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.test.context.ContextConfiguration;
+import org.springframework.test.context.TestPropertySource;
+import org.springframework.test.context.junit4.SpringRunner;
+import uk.ac.ebi.eva.pipeline.configuration.BeanNames;
+import uk.ac.ebi.eva.pipeline.configuration.MongoConfiguration;
+import uk.ac.ebi.eva.pipeline.configuration.jobs.VariantStatsJobConfiguration;
+import uk.ac.ebi.eva.pipeline.configuration.jobs.steps.VariantStatsStepConfiguration;
+import uk.ac.ebi.eva.test.configuration.BatchTestConfiguration;
+import uk.ac.ebi.eva.test.configuration.TemporaryRuleConfiguration;
+import uk.ac.ebi.eva.test.rules.PipelineTemporaryFolderRule;
+import uk.ac.ebi.eva.test.rules.TemporaryMongoRule;
+import uk.ac.ebi.eva.utils.EvaJobParameterBuilder;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import static org.junit.Assert.assertEquals;
+import static uk.ac.ebi.eva.test.utils.JobTestUtils.assertCompleted;
+
+/**
+ * Test for {@link VariantStatsStepConfiguration}
+ */
+@RunWith(SpringRunner.class)
+@TestPropertySource({"classpath:test-stats.properties"})
+@ContextConfiguration(classes = {VariantStatsJobConfiguration.class, BatchTestConfiguration.class,
+        TemporaryRuleConfiguration.class, MongoConfiguration.class})
+public class VariantStatsStepTestNoNewStatsCalculated {
+    private static final String COLLECTION_VARIANTS_NAME = "variants";
+
+    private static final String COLLECTION_FILES_NAME = "files";
+
+    private static final String DATABASE_NAME = "variant_stats_test_db";
+
+    @Autowired
+    @Rule
+    public TemporaryMongoRule mongoRule;
+
+    @Rule
+    public PipelineTemporaryFolderRule temporaryFolderRule = new PipelineTemporaryFolderRule();
+
+    @Autowired
+    private JobLauncherTestUtils jobLauncherTestUtils;
+
+    @Before
+    public void setUp() throws Exception {
+        mongoRule.getTemporaryDatabase(DATABASE_NAME).drop();
+    }
+
+    @After
+    public void cleanUp() {
+        mongoRule.getTemporaryDatabase(DATABASE_NAME).drop();
+    }
+
+    @Test
+    public void variantStatsStepShouldCalculateAndLoadStats_NoNewStatsCanbeCalculated() throws Exception {
+        MongoCollection<Document> filesCollection = mongoRule.getCollection(DATABASE_NAME, COLLECTION_FILES_NAME);
+        MongoCollection<Document> variantsCollection = mongoRule.getCollection(DATABASE_NAME, COLLECTION_VARIANTS_NAME);
+
+        filesCollection.insertMany(Arrays.asList(
+                // multiple entries for fid2 in the files collection
+                new Document("sid", "sid1").append("fid", "fid2").append("fname", "fname21")
+                        .append("samp", new Document("samp21", 0).append("samp22", 1)).append("samp23", 2),
+                new Document("sid", "sid1").append("fid", "fid2").append("fname", "fname22")
+                        .append("samp", new Document("samp31", 0).append("samp32", 1)).append("samp33", 2)
+        ));
+
+        variantsCollection.insertMany(Arrays.asList(
+                new Document("_id", "chr1_11111111_A_G").append("ref", "A").append("alt", "G")
+                        .append("files", Arrays.asList(
+                                // should not calculate stats - fid2 has more than one entry in the files collection
+                                new Document("sid", "sid1").append("fid", "fid2")
+                                        .append("samp", new Document("def", "0|0").append("0|1", Arrays.asList(1))),
+                                // should not calculate stats - no entry for fid3 in files collection
+                                new Document("sid", "sid1").append("fid", "fid3")
+                                        .append("samp", new Document("def", "0|0").append("0|1", Arrays.asList(1))),
+                                // should not calculate stats - different study
+                                new Document("sid", "sid2").append("fid", "fid1")
+                                        .append("samp", new Document("def", "0|0").append("0|1", Arrays.asList(1)))
+                        ))
+                        .append("st", Arrays.asList(
+                                // should not calculate or add anything for sid1 and fid2 since fid2 has more than one file
+
+                                // should not change as it belongs to different study id
+                                new Document("sid", "sid2").append("fid", "fid1")
+                                        .append("maf", 0.20000000298023224).append("mgf", 0.20000000298023224)
+                                        .append("mafAl", "A").append("mgfGt", "0|0"),
+                                // should not change as it belongs to different fid
+                                new Document("sid", "sid1").append("fid", "fid3")
+                                        .append("maf", 0.30000001192092896).append("mgf", 0.30000001192092896)
+                                        .append("mafAl", "A").append("mgfGt", "0|0")
+
+                        ))
+        ));
+
+        JobParameters jobParameters = new EvaJobParameterBuilder()
+                .collectionFilesName(COLLECTION_FILES_NAME)
+                .collectionVariantsName(COLLECTION_VARIANTS_NAME)
+                .databaseName(DATABASE_NAME)
+                .inputStudyId("sid1")
+                .chunkSize("100")
+                .toJobParameters();
+
+        JobExecution jobExecution = jobLauncherTestUtils.launchStep(BeanNames.VARIANT_STATS_STEP, jobParameters);
+
+        // check job completed successfully
+        assertCompleted(jobExecution);
+        List<Document> documents = mongoRule.getTemporaryDatabase(DATABASE_NAME).getCollection(COLLECTION_VARIANTS_NAME)
+                .find().into(new ArrayList<>());
+        Assert.assertTrue(documents.size() == 1);
+
+        // assert data
+        ArrayList<Document> variantStatsList = documents.stream().filter(doc -> doc.get("_id").equals("chr1_11111111_A_G"))
+                .findFirst().get().get("st", ArrayList.class);
+        assertEquals(2, variantStatsList.size());
+
+        // assert remained unchanged
+        Document variantStatsForSid2Fid1 = variantStatsList.stream()
+                .filter(st -> st.get("sid").equals("sid2") && st.get("fid").equals("fid1")).findFirst().get();
+        assertEquals(0.20000000298023224, variantStatsForSid2Fid1.get("maf"));
+        assertEquals(0.20000000298023224, variantStatsForSid2Fid1.get("mgf"));
+        assertEquals("A", variantStatsForSid2Fid1.get("mafAl"));
+        assertEquals("0|0", variantStatsForSid2Fid1.get("mgfGt"));
+
+        // assert remained unchanged
+        Document variantStatsForSid1Fid3 = variantStatsList.stream()
+                .filter(st -> st.get("sid").equals("sid1") && st.get("fid").equals("fid3")).findFirst().get();
+        assertEquals(0.30000001192092896, variantStatsForSid1Fid3.get("maf"));
+        assertEquals(0.30000001192092896, variantStatsForSid1Fid3.get("mgf"));
+        assertEquals("A", variantStatsForSid1Fid3.get("mafAl"));
+        assertEquals("0|0", variantStatsForSid1Fid3.get("mgfGt"));
+    }
+
+}