EVA-3425 make sure reference and alternate are always uppercase (#107)

* make sure reference and alternate are always uppercase
EBIvariation · Oct 26, 2023 · 923accf · 923accf
1 parent 1a8ff72
commit 923accf
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Showing 17 changed files with 156 additions and 24 deletions.
diff --git a/variation-commons-core/src/main/java/uk/ac/ebi/eva/commons/core/models/AbstractVariant.java b/variation-commons-core/src/main/java/uk/ac/ebi/eva/commons/core/models/AbstractVariant.java
@@ -124,6 +124,8 @@ public AbstractVariant(String chromosome, long start, long end, String reference
         if (chromosome == null || chromosome.trim().equals("")) {
             throw new IllegalArgumentException("Chromosome name cannot be empty");
         }
+        reference = Objects.nonNull(reference) ? reference.toUpperCase() : null;
+        alternate = Objects.nonNull(alternate) ? alternate.toUpperCase() : null;
         this.chromosome = chromosome;
         this.setCoordinates(start, end);
         this.setReference(reference);
@@ -200,11 +202,11 @@ public String getMainId() {
     }
 
     private void setReference(String reference) {
-        this.reference = (reference != null) ? reference : "";
+        this.reference = (reference != null) ? reference.toUpperCase() : "";
     }
 
     private void setAlternate(String alternate) {
-        this.alternate = (alternate != null) ? alternate : "";
+        this.alternate = (alternate != null) ? alternate.toUpperCase() : "";
     }
 
     private void setCoordinates(long start, long end) {

diff --git a/...mons-core/src/main/java/uk/ac/ebi/eva/commons/core/models/AbstractVariantSourceEntry.java b/...mons-core/src/main/java/uk/ac/ebi/eva/commons/core/models/AbstractVariantSourceEntry.java
@@ -19,6 +19,7 @@
 import java.util.HashMap;
 import java.util.LinkedHashMap;
 import java.util.Map;
+import java.util.stream.Collectors;
 
 /**
  * Entry that associates a variant and a file in a variant archive. It contains
@@ -65,7 +66,7 @@ public AbstractVariantSourceEntry(String fileId, String studyId, String[] second
         this.fileId = fileId;
         this.studyId = studyId;
         if (secondaryAlternates != null) {
-            this.secondaryAlternates = Arrays.copyOf(secondaryAlternates, secondaryAlternates.length);
+            setSecondaryAlternates(secondaryAlternates);
         } else {
             this.secondaryAlternates = new String[]{};
         }
@@ -105,7 +106,10 @@ public String[] getSecondaryAlternates() {
     }
 
     public void setSecondaryAlternates(String[] secondaryAlternates) {
-        this.secondaryAlternates = secondaryAlternates;
+        this.secondaryAlternates = Arrays.stream(secondaryAlternates)
+                .map(a->a.toUpperCase())
+                .collect(Collectors.toList())
+                .toArray(new String[0]);
     }
 
     @Override

diff --git a/...ation-commons-core/src/main/java/uk/ac/ebi/eva/commons/core/models/VariantStatistics.java b/...ation-commons-core/src/main/java/uk/ac/ebi/eva/commons/core/models/VariantStatistics.java
@@ -112,8 +112,8 @@ public VariantStatistics(String referenceAllele, String alternateAlleles,
                              int numMissingAlleles, int numMissingGenotypes, int numMendelErrors,
                              float percentCasesDominant,
                              float percentControlsDominant, float percentCasesRecessive, float percentControlsRecessive) {
-        this.refAllele = referenceAllele;
-        this.altAllele = alternateAlleles;
+        this.refAllele = Objects.nonNull(referenceAllele) ? referenceAllele.toUpperCase() : null;
+        this.altAllele = Objects.nonNull(alternateAlleles) ? alternateAlleles.toUpperCase() : null;
         this.variantType = variantType;
 
         this.maf = maf;
@@ -142,15 +142,15 @@ public String getRefAllele() {
     }
 
     public void setRefAllele(String refAllele) {
-        this.refAllele = refAllele;
+        this.refAllele = Objects.nonNull(refAllele) ? refAllele.toUpperCase() : null;
     }
 
     public String getAltAllele() {
         return altAllele;
     }
 
     public void setAltAllele(String altAllele) {
-        this.altAllele = altAllele;
+        this.altAllele = Objects.nonNull(altAllele) ? altAllele.toUpperCase() : null;
     }
 
     public VariantType getVariantType() {

diff --git a/...ons-core/src/main/java/uk/ac/ebi/eva/commons/core/models/factories/VariantVcfFactory.java b/...ons-core/src/main/java/uk/ac/ebi/eva/commons/core/models/factories/VariantVcfFactory.java
@@ -131,11 +131,14 @@ public boolean isIncludeIds() {
     }
 
     protected String getReference(String[] fields) {
-        return fields[3].equals(".") ? "" : fields[3];
+        return fields[3].equals(".") ? "" : fields[3].toUpperCase();
     }
 
     protected String[] getAlternateAlleles(String[] fields) {
-        return fields[4].split(",");
+        return Arrays.stream(fields[4].split(","))
+                .map(a->a.toUpperCase())
+                .collect(Collectors.toList())
+                .toArray(new String[0]);
     }
 
     protected float getQuality(String[] fields) {

diff --git a/...ation-commons-core/src/main/java/uk/ac/ebi/eva/commons/core/models/genotype/Genotype.java b/...ation-commons-core/src/main/java/uk/ac/ebi/eva/commons/core/models/genotype/Genotype.java
@@ -47,8 +47,8 @@ public Genotype(String genotype) {
     }
 
     public Genotype(String genotype, String ref, String alt) {
-        this.reference = ref;
-        this.alternate = alt;
+        this.reference = Objects.nonNull(ref) ? ref.toUpperCase() : null;
+        this.alternate = Objects.nonNull(alt) ? alt.toUpperCase() : null;
         this.phased = genotype.contains("|");
         this.count = 0;
         parseGenotype(genotype);
@@ -96,15 +96,15 @@ public String getReference() {
     }
 
     void setReference(String reference) {
-        this.reference = reference;
+        this.reference = Objects.nonNull(reference) ? reference.toUpperCase() : null;
     }
 
     public String getAlternate() {
         return alternate;
     }
 
     void setAlternate(String alternate) {
-        this.alternate = alternate;
+        this.alternate = Objects.nonNull(alternate) ? alternate.toUpperCase() : null;
     }
 
     public int getAllele(int i) {

diff --git a/...ion-commons-core/src/test/java/uk/ac/ebi/eva/commons/core/models/AbstractVariantTest.java b/...ion-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");

diff --git a/variation-commons-core/src/test/java/uk/ac/ebi/eva/commons/core/models/GenotypeTest.java b/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());
+    }
+
+
+}
diff --git a/...n-commons-core/src/test/java/uk/ac/ebi/eva/commons/core/models/VariantStatisticsTest.java b/...n-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());
+    }
+
+}
diff --git a/...core/src/test/java/uk/ac/ebi/eva/commons/core/models/factories/VariantVcfFactoryTest.java b/...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"));

diff --git a/...on-commons-mongodb/src/main/java/uk/ac/ebi/eva/commons/mongodb/entities/VariantMongo.java b/...on-commons-mongodb/src/main/java/uk/ac/ebi/eva/commons/mongodb/entities/VariantMongo.java
@@ -34,6 +34,7 @@
 import java.util.LinkedHashMap;
 import java.util.LinkedHashSet;
 import java.util.Map;
+import java.util.Objects;
 import java.util.Set;
 
 /**
@@ -201,8 +202,8 @@ public VariantMongo(String id, VariantType type, String chromosome, long start,
         this.start = start;
         this.end = end;
         this.length = length;
-        this.reference = reference;
-        this.alternate = alternate;
+        this.reference = Objects.nonNull(reference) ? reference.toUpperCase() : null;
+        this.alternate = Objects.nonNull(alternate) ? alternate.toUpperCase() : null;
         this.at = at;
         this.hgvs = new LinkedHashSet<>();
         if (hgvs != null && !hgvs.isEmpty()) {
@@ -229,6 +230,8 @@ public VariantMongo(String id, VariantType type, String chromosome, long start,
 
     public static String buildVariantId(String chromosome, long start, String reference, String alternate) {
         StringBuilder builder = new StringBuilder(chromosome);
+        reference = reference.toUpperCase();
+        alternate = alternate.toUpperCase();
         builder.append("_");
         builder.append(start);
         builder.append("_");

diff --git a/...b/src/main/java/uk/ac/ebi/eva/commons/mongodb/entities/projections/SimplifiedVariant.java b/...b/src/main/java/uk/ac/ebi/eva/commons/mongodb/entities/projections/SimplifiedVariant.java
@@ -23,6 +23,7 @@
 
 import java.util.HashSet;
 import java.util.Map;
+import java.util.Objects;
 import java.util.Set;
 
 import static uk.ac.ebi.eva.commons.mongodb.entities.VariantMongo.ALTERNATE_FIELD;
@@ -79,6 +80,8 @@ public class SimplifiedVariant {
 
     public SimplifiedVariant(VariantType variantType, String chromosome, long start, long end, int length,
                              String reference, String alternate, Map<String, Set<String>> hgvs) {
+        reference = Objects.nonNull(reference) ? reference.toUpperCase() : null;
+        alternate = Objects.nonNull(alternate) ? alternate.toUpperCase() : null;
         this.id = buildVariantId(chromosome, start, reference, alternate);
         this.variantType = variantType;
         this.chromosome = chromosome;

diff --git a/...ain/java/uk/ac/ebi/eva/commons/mongodb/entities/subdocuments/VariantSourceEntryMongo.java b/...ain/java/uk/ac/ebi/eva/commons/mongodb/entities/subdocuments/VariantSourceEntryMongo.java
@@ -27,6 +27,7 @@
 
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Collection;
 import java.util.HashMap;
 import java.util.List;
@@ -100,8 +101,10 @@ public VariantSourceEntryMongo(String fileId, String studyId, String[] alternate
         this.fileId = fileId;
         this.studyId = studyId;
         if (alternates != null && alternates.length > 0) {
-            this.alternates = new String[alternates.length];
-            System.arraycopy(alternates, 0, this.alternates, 0, alternates.length);
+            this.alternates = Arrays.stream(alternates)
+                    .map(a->a.toUpperCase())
+                    .collect(Collectors.toList())
+                    .toArray(new String[0]);
         }
 
         if (attributes != null) {

diff --git a/...ion-commons-mongodb/src/main/java/uk/ac/ebi/eva/commons/mongodb/filter/FilterBuilder.java b/...ion-commons-mongodb/src/main/java/uk/ac/ebi/eva/commons/mongodb/filter/FilterBuilder.java
@@ -23,6 +23,7 @@
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
+import java.util.stream.Collectors;
 
 /**
  * Class for building filters for querying using the VariantRepository
@@ -114,21 +115,22 @@ public FilterBuilder withVariantTypes(VariantType variantType) {
 
     public FilterBuilder withAlternates(List<String> alternates) {
         if (alternates != null && !alternates.isEmpty()) {
-            filters.add(new VariantRepositoryAlternateFilter(alternates));
+            List<String> alternatesUppercase = alternates.stream().map(a->a.toUpperCase()).collect(Collectors.toList());
+            filters.add(new VariantRepositoryAlternateFilter(alternatesUppercase));
         }
         return this;
     }
 
     public FilterBuilder withAlternates(String alternate) {
         if (alternate != null) {
-            filters.add(new VariantRepositoryAlternateFilter(Collections.singletonList(alternate)));
+            filters.add(new VariantRepositoryAlternateFilter(Collections.singletonList(alternate.toUpperCase())));
         }
         return this;
     }
 
     public FilterBuilder withReferenceBases(String referenceBases) {
         if (referenceBases != null) {
-            filters.add(new VariantRepositoryReferenceBasesFilter(Collections.singletonList(referenceBases)));
+            filters.add(new VariantRepositoryReferenceBasesFilter(Collections.singletonList(referenceBases.toUpperCase())));
         }
         return this;
     }

diff --git a/...mmons-mongodb/src/test/java/uk/ac/ebi/eva/commons/mongodb/MongoVariantConversionTest.java b/...mmons-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());
+    }
+
 }
diff --git a/...on-commons-mongodb/src/test/java/uk/ac/ebi/eva/commons/mongodb/SimplifiedVariantTest.java b/...on-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);
+
+    }
+}
diff --git a/...mongodb/src/test/java/uk/ac/ebi/eva/commons/mongodb/VariantSourceEntryConversionTest.java b/...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]);
+    }
 
 }