improve test in UniParcProteomeFastaParser.java

ebi-uniprot · Nov 28, 2024 · a13cefc · a13cefc
1 parent 97d68a9
commit a13cefc
Show file tree

Hide file tree

Showing 7 changed files with 87 additions and 227 deletions.
diff --git a/...ser/fasta/uniparc/UniParcFastaParser.java → ...uniparc/UniParcEntryLightFastaParser.java b/...ser/fasta/uniparc/UniParcFastaParser.java → ...uniparc/UniParcEntryLightFastaParser.java
@@ -1,8 +1,6 @@
-package org.uniprot.core.parser.fasta;
+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;
@@ -11,19 +9,8 @@
  * @author jluo
  * @date: 24 Jun 2019
  */
-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 class UniParcEntryLightFastaParser {
+    private UniParcEntryLightFastaParser(){}
 
     public static String toFasta(UniParcEntryLight entry) {
         String status = "active";

diff --git a/...arser/src/main/java/org/uniprot/core/parser/fasta/uniparc/UniParcProteomeFastaParser.java b/...arser/src/main/java/org/uniprot/core/parser/fasta/uniparc/UniParcProteomeFastaParser.java
@@ -110,7 +110,7 @@ private static StringBuilder getFastaHeader(List<UniParcCrossReference> xrefs, b
         if(!sourceIds.isEmpty()){
             sb.append(" SS=").append(String.join("|", sourceIds));
         }
-        sb.append(" UP=").append(proteomeId);
+        sb.append(" PC=").append(proteomeId);
         if(!component.isEmpty()){
             sb.append(":").append(String.join("|", component));
         }

diff --git a/core-parser/src/test/java/org/uniprot/core/parser/fasta/UniParcFastaParserTest.java b/core-parser/src/test/java/org/uniprot/core/parser/fasta/UniParcFastaParserTest.java
diff --git a/...src/test/java/org/uniprot/core/parser/fasta/uniparc/UniParcEntryLightFastaParserTest.java b/...src/test/java/org/uniprot/core/parser/fasta/uniparc/UniParcEntryLightFastaParserTest.java
@@ -0,0 +1,49 @@
+package org.uniprot.core.parser.fasta.uniparc;
+
+import static org.junit.jupiter.api.Assertions.*;
+import static org.uniprot.core.parser.fasta.uniparc.UniParcFastaParserTestUtils.*;
+import static org.uniprot.core.uniparc.impl.UniParcEntryLightBuilder.HAS_ACTIVE_CROSS_REF;
+
+import org.junit.jupiter.api.Test;
+import org.uniprot.core.uniparc.*;
+import org.uniprot.core.uniparc.impl.UniParcEntryLightBuilder;
+
+/**
+ * @author jluo
+ * @date: 24 Jun 2019
+ */
+class UniParcEntryLightFastaParserTest {
+
+    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 testUniParcEntryLightToFasta() {
+        UniParcEntryLight entry = createEntryLight();
+        String fasta = UniParcEntryLightFastaParser.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 = UniParcEntryLightFastaParser.toFasta(entry);
+        assertEquals(EXPECTED_FASTA_RESULT_INACTIVE, fasta);
+    }
+
+    private UniParcEntryLight createEntryLight() {
+        return new UniParcEntryLightBuilder()
+                .uniParcId("UPI0000083A08")
+                .sequence(getSequence())
+                .build();
+    }
+
+}
diff --git a/core-parser/src/test/java/org/uniprot/core/parser/fasta/uniparc/UniParcFastaParserTest.java b/core-parser/src/test/java/org/uniprot/core/parser/fasta/uniparc/UniParcFastaParserTest.java
diff --git a/...rser/src/test/java/org/uniprot/core/parser/fasta/uniparc/UniParcFastaParserTestUtils.java b/...rser/src/test/java/org/uniprot/core/parser/fasta/uniparc/UniParcFastaParserTestUtils.java
@@ -1,5 +1,6 @@
 package org.uniprot.core.parser.fasta.uniparc;
 
+import org.uniprot.core.Property;
 import org.uniprot.core.Sequence;
 import org.uniprot.core.impl.SequenceBuilder;
 import org.uniprot.core.uniparc.*;
@@ -33,7 +34,7 @@ static List<UniParcCrossReference> getUniProtXrefs(boolean active) {
         List<UniParcCrossReference> result = new ArrayList<>();
         Organism human = getOrganism(9606, "Homo sapiens");
 
-        result.add(getXref(UniParcDatabase.SWISSPROT, "P12345", active, human, null, null, "Protein Name One", "Gene Name One"));
+        result.add(getXref(UniParcDatabase.SWISSPROT, "P12345", active, human, null, null, "Protein Name One", "Gene Name One", new Property(UniParcCrossReference.PROPERTY_SOURCES, "ABC01415:UP000005640:Chromosome 1")));
 
         return result;
     }
@@ -47,10 +48,14 @@ static UniParcCrossReference getXref(UniParcDatabase database, String id, boolea
     }
 
     static UniParcCrossReference getXref(UniParcDatabase database, String id, boolean active, Organism organism, String proteomeId, String component) {
-        return getXref(database,id, active, organism, proteomeId, component, null, null);
+        return getXref(database,id, active, organism, proteomeId, component, null, null,null);
     }
 
-    static UniParcCrossReference getXref(UniParcDatabase database, String id, boolean active, Organism organism, String proteomeId, String component, String proteinName, String geneName) {
+    static UniParcCrossReference getXref(UniParcDatabase database, String id, boolean active, Organism organism, String geneName, String proteinName, Property property) {
+        return getXref(database,id, active, organism, null, null, proteinName, geneName, property);
+    }
+
+    static UniParcCrossReference getXref(UniParcDatabase database, String id, boolean active, Organism organism, String proteomeId, String component, String proteinName, String geneName, Property property) {
         return new UniParcCrossReferenceBuilder()
                 .database(database)
                 .id(id)
@@ -60,6 +65,7 @@ static UniParcCrossReference getXref(UniParcDatabase database, String id, boolea
                 .geneName(geneName)
                 .proteomeId(proteomeId)
                 .component(component)
+                .propertiesAdd(property)
                 .build();
     }
 }