storage: Remove extra system.out #TASK-5663

opencb · Feb 16, 2024 · 51f1bbd · 51f1bbd
1 parent 6ffb513
commit 51f1bbd
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Showing 4 changed files with 2 additions and 9 deletions.
diff --git a/...src/main/java/org/opencb/opencga/storage/core/metadata/VariantStorageMetadataManager.java b/...src/main/java/org/opencb/opencga/storage/core/metadata/VariantStorageMetadataManager.java
@@ -1650,8 +1650,6 @@ public int registerSecondaryIndexSamples(int studyId, List<String> samples, bool
                 CohortMetadata secondaryIndexCohort = getCohortMetadata(studyId, id);
                 if (secondaryIndexCohort.getSamples().size() != sampleIds.size()
                         || !secondaryIndexCohort.getSamples().containsAll(sampleIds)) {
-                    System.out.println("secondaryIndexCohort = " + secondaryIndexCohort.getSamples());
-                    System.out.println("sampleIds = " + sampleIds);
                     throw new StorageEngineException("Must provide all the samples from the secondary index: "
                             + secondaryIndexCohort.getSamples()
                             .stream()

diff --git a/.../java/org/opencb/opencga/storage/core/variant/adaptors/VariantDBAdaptorMultiFileTest.java b/.../java/org/opencb/opencga/storage/core/variant/adaptors/VariantDBAdaptorMultiFileTest.java
@@ -145,10 +145,6 @@ public void testRelease() throws Exception {
             Integer minFileId = variant.getStudies().stream()
                     .flatMap(s -> s.getFiles().stream())
                     .map(FileEntry::getFileId)
-                    .map(s->{
-                        System.out.println("s = " + s);
-                        return s;
-                    })
                     .map(s -> StringUtils.removeStart(s, "1K.end.platinum-genomes-vcf-NA"))
                     .map(s -> StringUtils.removeEnd(s, "_S1.genome.vcf.gz"))
                     .map(Integer::valueOf)

diff --git a/...re/src/test/java/org/opencb/opencga/storage/core/variant/io/VariantWriterFactoryTest.java b/...re/src/test/java/org/opencb/opencga/storage/core/variant/io/VariantWriterFactoryTest.java
@@ -30,7 +30,6 @@
 import org.opencb.opencga.storage.core.exceptions.StorageEngineException;
 import org.opencb.opencga.storage.core.metadata.models.StudyMetadata;
 import org.opencb.opencga.storage.core.variant.dummy.DummyVariantDBAdaptor;
-import org.opencb.opencga.storage.core.variant.dummy.DummyVariantStorageEngine;
 import org.opencb.opencga.storage.core.variant.dummy.DummyVariantStorageMetadataDBAdaptorFactory;
 
 import java.io.ByteArrayOutputStream;
@@ -101,7 +100,6 @@ public void testContigLengthNull() throws IOException, StorageEngineException {
         writer.close();
 
         String s = outputStream.toString();
-        System.out.println("s = " + s);
         assertThat(s, containsString("##contig=<ID=chr1>"));
         assertThat(s, containsString("##contig=<ID=chr2>"));
         assertThat(s, containsString("##contig=<ID=chr3>"));

diff --git a/...re/src/test/java/org/opencb/opencga/storage/hadoop/utils/PersistentResultScannerTest.java b/...re/src/test/java/org/opencb/opencga/storage/hadoop/utils/PersistentResultScannerTest.java
@@ -63,7 +63,8 @@ public void test() throws Exception {
         int i = 0;
         for (Iterator<Result> iterator = scanner.iterator(); iterator.hasNext(); ) {
             Result result = iterator.next();
-            System.out.println(Bytes.toString(result.getRow()));
+            assertNotNull(result);
+            assertNotNull(result.getRow());
             i++;
             if (i == 50 || i == 99) {
                 int scannersCount = persistentScanner.getScannersCount();