improve uniparc xref voldemort index

core-parser/src/main/java/org/uniprot/core/parser/fasta/uniparc/UniParcEntryLightFastaParser.java → core-parser/src/main/java/org/uniprot/core/parser/fasta/uniparc/UniParcFastaParser.java

@@ -1,6 +1,8 @@
 package org.uniprot.core.parser.fasta.uniparc;
 
 import org.uniprot.core.Sequence;
+import org.uniprot.core.uniparc.UniParcCrossReference;
+import org.uniprot.core.uniparc.UniParcEntry;
 import org.uniprot.core.uniparc.UniParcEntryLight;
 
 import static org.uniprot.core.uniparc.impl.UniParcEntryLightBuilder.HAS_ACTIVE_CROSS_REF;
@@ -9,8 +11,20 @@
  * @author jluo
  * @date: 24 Jun 2019
  */
-public class UniParcEntryLightFastaParser {
-    private UniParcEntryLightFastaParser(){}
+public class UniParcFastaParser {
+    private UniParcFastaParser(){}
+
+
+    public static String toFasta(UniParcEntry entry) {
+        String status = "active";
+        boolean isActive = entry.getUniParcCrossReferences()
+                .stream()
+                .anyMatch(UniParcCrossReference::isActive);
+        if (!isActive) {
+            status = "inactive";
+        }
+        return getFastaString(entry.getUniParcId().getValue(), status, entry.getSequence());
+    }
 
     public static String toFasta(UniParcEntryLight entry) {
         String status = "active";

core-parser/src/test/java/org/uniprot/core/parser/fasta/uniparc/UniParcFastaParserTest.java

@@ -0,0 +1,123 @@
+package org.uniprot.core.parser.fasta.uniparc;
+
+import static org.junit.jupiter.api.Assertions.*;
+import static org.uniprot.core.uniparc.impl.UniParcEntryLightBuilder.HAS_ACTIVE_CROSS_REF;
+
+import org.junit.jupiter.api.Test;
+import org.uniprot.core.Property;
+import org.uniprot.core.Sequence;
+import org.uniprot.core.impl.SequenceBuilder;
+import org.uniprot.core.uniparc.*;
+import org.uniprot.core.uniparc.impl.*;
+import org.uniprot.core.uniprotkb.taxonomy.Organism;
+import org.uniprot.core.uniprotkb.taxonomy.impl.OrganismBuilder;
+
+import java.time.LocalDate;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+/**
+ * @author jluo
+ * @date: 24 Jun 2019
+ */
+class UniParcFastaParserTest {
+
+    public static final String EXPECTED_FASTA_RESULT = """
+            >UPI0000083A08 status=active
+            MSMAMARALATLGRLRYRVSGQLPLLDETAIEVMAGGQFLDGRKAREELGFFSTTALDDT
+            LLRAIDWFRDNGYFNA""";
+    public static final String EXPECTED_FASTA_RESULT_INACTIVE = """
+            >UPI0000083A08 status=inactive
+            MSMAMARALATLGRLRYRVSGQLPLLDETAIEVMAGGQFLDGRKAREELGFFSTTALDDT
+            LLRAIDWFRDNGYFNA""";
+    @Test
+    void testUniParcEntryToFasta() {
+        UniParcEntry entry = create();
+        String fasta = UniParcFastaParser.toFasta(entry);
+        assertEquals(EXPECTED_FASTA_RESULT, fasta);
+    }
+
+    @Test
+    void testUniParcEntryLightToFasta() {
+        UniParcEntryLight entry = createEntryLight();
+        String fasta = UniParcFastaParser.toFasta(entry);
+        assertEquals(EXPECTED_FASTA_RESULT, fasta);
+    }
+
+    @Test
+    void testUniParcEntryLightToFastaInactive() {
+        UniParcEntryLight entry = createEntryLight();
+        entry = UniParcEntryLightBuilder.from(entry).extraAttributesAdd(HAS_ACTIVE_CROSS_REF, false).build();
+        String fasta = UniParcFastaParser.toFasta(entry);
+        assertEquals(EXPECTED_FASTA_RESULT_INACTIVE, fasta);
+    }
+
+    private UniParcEntry create() {
+        Sequence sequence = getSequence();
+        List<UniParcCrossReference> xrefs = getXrefs();
+        return new UniParcEntryBuilder()
+                        .uniParcId(new UniParcIdBuilder("UPI0000083A08").build())
+                        .uniParcCrossReferencesSet(xrefs)
+                        .sequence(sequence)
+                        .build();
+    }
+
+    private UniParcEntryLight createEntryLight() {
+        return new UniParcEntryLightBuilder()
+                .uniParcId("UPI0000083A08")
+                .sequence(getSequence())
+                .build();
+    }
+
+    private static Sequence getSequence() {
+        String seq =
+                "MSMAMARALATLGRLRYRVSGQLPLLDETAIEVMAGGQFLDGRKAREELGFFSTTALDDT" + "LLRAIDWFRDNGYFNA";
+        Sequence sequence = new SequenceBuilder(seq).build();
+        return sequence;
+    }
+
+    private List<UniParcCrossReference> getXrefs() {
+        Organism taxonomy =
+                new OrganismBuilder().taxonId(9606).scientificName("Homo sapiens").build();
+        List<Property> properties = new ArrayList<>();
+        properties.add(new Property("prop1", "pvalue"));
+        UniParcCrossReference xref =
+                new UniParcCrossReferenceBuilder()
+                        .versionI(3)
+                        .database(UniParcDatabase.SWISSPROT)
+                        .id("P12345")
+                        .version(7)
+                        .active(true)
+                        .created(LocalDate.of(2017, 5, 17))
+                        .lastUpdated(LocalDate.of(2017, 2, 27))
+                        .propertiesSet(properties)
+                        .organism(taxonomy)
+                        .proteinName("some pname")
+                        .geneName("some gname")
+                        .build();
+
+        List<Property> properties2 = new ArrayList<>();
+        properties.add(new Property("prop2", "pvalue2"));
+        Organism taxonomy2 = new OrganismBuilder().taxonId(10090).scientificName("MOUSE").build();
+
+        UniParcCrossReference xref2 =
+                new UniParcCrossReferenceBuilder()
+                        .versionI(1)
+                        .database(UniParcDatabase.TREMBL)
+                        .id("P52346")
+                        .version(7)
+                        .active(true)
+                        .created(LocalDate.of(2017, 2, 12))
+                        .lastUpdated(LocalDate.of(2017, 4, 23))
+                        .propertiesSet(properties2)
+                        .organism(taxonomy2)
+                        .proteinName("some pname")
+                        .proteomeId("UP00000564")
+                        .component("chromosome 1")
+                        .build();
+
+        return Arrays.asList(xref, xref2);
+    }
+
+}

xml-parser/src/main/java/org/uniprot/core/xml/CrossReferenceConverterUtils.java

@@ -1,6 +1,7 @@
 package org.uniprot.core.xml;
 
 import com.google.common.base.Strings;
+import org.uniprot.core.uniparc.UniParcCrossReference;
 import org.uniprot.core.uniparc.impl.UniParcCrossReferenceBuilder;
 import org.uniprot.core.uniprotkb.taxonomy.Organism;
 import org.uniprot.core.uniprotkb.taxonomy.impl.OrganismBuilder;
@@ -18,6 +19,7 @@ public class CrossReferenceConverterUtils {
     public static final String PROPERTY_COMPONENT = "component";
     public static final String PROPERTY_NCBI_TAXONOMY_ID = "NCBI_taxonomy_id";
     public static final String PROPERTY_UNIPROTKB_ACCESSION = "UniProtKB_accession";
+    public static final String PROPERTY_SOURCES = UniParcCrossReference.PROPERTY_SOURCES;
 
     private CrossReferenceConverterUtils(){}
 
@@ -47,6 +49,9 @@ public static void populateUniParcCrossReferenceBuilder(String propertyType, Str
             case PROPERTY_UNIPROTKB_ACCESSION:
                 builder.propertiesAdd(PROPERTY_UNIPROTKB_ACCESSION, propertyValue);
                 break;
+            case PROPERTY_SOURCES:
+                builder.propertiesAdd(PROPERTY_SOURCES, propertyValue);
+                break;
             default:
                 throw new XmlReaderException(
                         "Unable to read xml property: "

xml-parser/src/main/java/org/uniprot/core/xml/uniparc/UniParcDBCrossReferenceConverter.java

@@ -32,7 +32,6 @@ public class UniParcDBCrossReferenceConverter
     public static final String PROPERTY_COMPONENT = "component";
     public static final String PROPERTY_NCBI_TAXONOMY_ID = "NCBI_taxonomy_id";
     public static final String PROPERTY_UNIPROTKB_ACCESSION = "UniProtKB_accession";
-    public static final String PROPERTY_SOURCE = "source";
 
     private final ObjectFactory xmlFactory;
     private final TaxonomyRepo taxonomyRepo;
@@ -57,13 +56,6 @@ public UniParcCrossReference fromXml(DbReferenceType xmlObj) {
                 .lastUpdated(XmlConverterHelper.dateFromXml(xmlObj.getLast()));
 
         for (PropertyType property : xmlObj.getProperty()) {
-
-            //TODO: Change it
-            /*
-                            case PROPERTY_SOURCE:
-                    builder.propertiesAdd(PROPERTY_SOURCE, property.getValue());
-                    break;
-             */
             CrossReferenceConverterUtils.populateUniParcCrossReferenceBuilder(property.getType(), property.getValue(), builder, taxonomyRepo);
         }
         if (xmlObj.getVersion() != null) builder.version(xmlObj.getVersion());