added tests

variation-commons-core/src/test/java/uk/ac/ebi/eva/commons/core/models/AbstractVariantTest.java

@@ -99,6 +99,13 @@ public void testRefAltAssignmentInConstructor() {
         assertEquals("T", variant.getAlternate());
     }
 
+    @Test
+    public void testChangeRefAltToUpperCase() {
+        Variant variant = new Variant("1", 1, 1, "c", "t");
+        assertEquals("C", variant.getReference());
+        assertEquals("T", variant.getAlternate());
+    }
+
     @Test
     public void testRefAltAssignmentInRenormalization() {
         Variant variant = new Variant("1", 1, 1, "", "T");

variation-commons-core/src/test/java/uk/ac/ebi/eva/commons/core/models/GenotypeTest.java

@@ -0,0 +1,19 @@
+package uk.ac.ebi.eva.commons.core.models;
+
+import org.junit.Test;
+import uk.ac.ebi.eva.commons.core.models.genotype.Genotype;
+
+import static org.junit.Assert.assertEquals;
+
+public class GenotypeTest {
+
+    @Test
+    public void testChangeRefAltToUpperCase() {
+        Genotype genotype = new Genotype("", "a", "t");
+
+        assertEquals("A", genotype.getReference());
+        assertEquals("T", genotype.getAlternate());
+    }
+
+
+}

variation-commons-core/src/test/java/uk/ac/ebi/eva/commons/core/models/VariantStatisticsTest.java

@@ -0,0 +1,18 @@
+package uk.ac.ebi.eva.commons.core.models;
+
+import org.junit.Test;
+
+import static org.junit.Assert.assertEquals;
+
+public class VariantStatisticsTest {
+
+    @Test
+    public void testChangeRefAltToUpperCase() {
+        VariantStatistics variantStatistics = new VariantStatistics("a", "t", null,
+                -1, -1, "", "", -1, -1, -1,
+                -1, -1, -1, -1);
+        assertEquals("A", variantStatistics.getRefAllele());
+        assertEquals("T", variantStatistics.getAltAllele());
+    }
+
+}

variation-commons-core/src/test/java/uk/ac/ebi/eva/commons/core/models/factories/VariantVcfFactoryTest.java

@@ -250,6 +250,14 @@ public void testVariantIds() {
                  Collections.singleton("rs123,rs456"));
     }
 
+    @Test
+    public void testChangeRefAltToUpperCase(){
+       String line = "chr1\t1000\t.\tt\tg\t.\t.\t.";
+        List<Variant> expResult = Collections.singletonList(new Variant("chr1", 1000, 1000, "T", "G"));
+        List<Variant> result = factory.create(FILE_ID, STUDY_ID, line);
+        assertEquals(expResult, result);
+    }
+
     private void checkIds(VariantVcfFactory variantVcfFactory, String vcfLine, Set<String> expectedIds) {
         List<Variant> expectedVariants = new LinkedList<>();
         expectedVariants.add(new Variant("1", 1000, 1000, "C", "T"));

variation-commons-mongodb/src/test/java/uk/ac/ebi/eva/commons/mongodb/MongoVariantConversionTest.java

@@ -17,7 +17,6 @@
 
 import com.lordofthejars.nosqlunit.mongodb.MongoDbConfigurationBuilder;
 import com.lordofthejars.nosqlunit.mongodb.MongoDbRule;
-
 import org.bson.BsonArray;
 import org.bson.BsonString;
 import org.bson.Document;
@@ -31,7 +30,6 @@
 import org.springframework.test.context.ContextConfiguration;
 import org.springframework.test.context.TestPropertySource;
 import org.springframework.test.context.junit4.SpringRunner;
-
 import uk.ac.ebi.eva.commons.core.models.pipeline.VariantSourceEntry;
 import uk.ac.ebi.eva.commons.core.models.ws.VariantSourceEntryWithSampleNames;
 import uk.ac.ebi.eva.commons.core.models.ws.VariantWithSamplesAndAnnotation;
@@ -180,7 +178,7 @@ private Document buildMongoVariantWithFiles() {
 
     private Document buildMongoBasicVariant() {
         VariantWithSamplesAndAnnotation variant = new VariantWithSamplesAndAnnotation(CHROMOSOME, START, END, REFERENCE,
-                                                                                      ALTERNATE, null);
+                ALTERNATE, null);
         Document mongoVariant = new Document("_id", VARIANT_ID)
                 .append(VariantMongo.IDS_FIELD, Collections.singleton(RS_666))
                 .append(VariantMongo.TYPE_FIELD, variant.getType().name())
@@ -249,4 +247,13 @@ public void testConvertToDataModelTypeEmptyIds() {
         assertNotNull(variant.getIds());
         assertTrue(variant.getIds().isEmpty());
     }
+
+    @Test
+    public void testChangeRefAltToUpperCase() {
+        VariantMongo variantMongo = new VariantMongo(new VariantWithSamplesAndAnnotation("chr1", START,
+                END, "a", "t", null));
+        Assert.assertEquals("A", variantMongo.getReference());
+        Assert.assertEquals("T", variantMongo.getAlternate());
+    }
+
 }

variation-commons-mongodb/src/test/java/uk/ac/ebi/eva/commons/mongodb/SimplifiedVariantTest.java

@@ -0,0 +1,28 @@
+package uk.ac.ebi.eva.commons.mongodb;
+
+import org.junit.Test;
+import uk.ac.ebi.eva.commons.mongodb.entities.projections.SimplifiedVariant;
+
+import java.lang.reflect.Field;
+
+import static org.junit.Assert.assertEquals;
+
+public class SimplifiedVariantTest {
+
+    @Test
+    public void testChangeRefAltToUpperCase() throws NoSuchFieldException, IllegalAccessException {
+        SimplifiedVariant simplifiedVariant = new SimplifiedVariant(null, "", -1, -1,
+                -1, "a", "t", null);
+
+        Field refField = SimplifiedVariant.class.getDeclaredField("reference");
+        Field altField = SimplifiedVariant.class.getDeclaredField("alternate");
+        refField.setAccessible(true);
+        altField.setAccessible(true);
+        String refValue = (String) refField.get(simplifiedVariant);
+        String altValue = (String) altField.get(simplifiedVariant);
+
+        assertEquals("A", refValue);
+        assertEquals("T", altValue);
+
+    }
+}

variation-commons-mongodb/src/test/java/uk/ac/ebi/eva/commons/mongodb/VariantSourceEntryConversionTest.java

@@ -166,5 +166,19 @@ public void testConvertFromVariantSourceEntryMongoToVariantSourceEntry() {
         Assert.assertEquals("1/1", variantSourceEntryWithSampleNames.getSamplesDataMap().get("NA003").get("GT"));
     }
 
+    @Test
+    public void testChangeRefAltToUpperCaseVariantSourceEntry() {
+        VariantSourceEntry variantSourceEntry = new VariantSourceEntry(null, "", new String[]{"a"},
+                null, null, null, null);
+        Assert.assertEquals("A", variantSourceEntry.getSecondaryAlternates()[0]);
+
+    }
+
+    @Test
+    public void testChangeRefAltToUpperCaseVariantEntrySourceMongo() {
+        VariantSourceEntryMongo variantSourceEntryMongo = new VariantSourceEntryMongo(new VariantSourceEntry(null,
+                "", new String[]{"a"}, null, null, null, null));
+        Assert.assertEquals( "A", variantSourceEntryMongo.getSecondaryAlternates()[0]);
+    }
 
 }

variation-commons-mongodb/src/test/java/uk/ac/ebi/eva/commons/mongodb/filter/VariantRepositoryFilterTest.java

@@ -18,6 +18,7 @@
  */
 package uk.ac.ebi.eva.commons.mongodb.filter;
 
+import org.bson.Document;
 import org.junit.Test;
 import org.springframework.data.mongodb.core.query.Criteria;
 
@@ -67,4 +68,14 @@ public void getCriteriaIn() throws Exception {
         Criteria test = filter.getCriteria();
         assertEquals(expected, test);
     }
+
+    @Test
+    public void testChangeRefAltToUpperCase() {
+        List<VariantRepositoryFilter> filters = new FilterBuilder().getBeaconFilters("a", "t",
+                null, null);
+        assertEquals("A", ((List<String>) ((Document)filters.get(0).getCriteria().getCriteriaObject()
+                .get("ref")).get("$in")).get(0));
+        assertEquals("T", ((List<String>) ((Document)filters.get(1).getCriteria().getCriteriaObject()
+                .get("alt")).get("$in")).get(0));
+    }
 }