address review comment

ebi-uniprot · Sep 24, 2024 · f9426f3 · f9426f3
1 parent 5e991c9
commit f9426f3
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Showing 9 changed files with 78 additions and 85 deletions.
diff --git a/core-domain/src/main/java/org/uniprot/core/uniparc/impl/UniParcCrossReferenceImpl.java b/core-domain/src/main/java/org/uniprot/core/uniparc/impl/UniParcCrossReferenceImpl.java
@@ -30,7 +30,7 @@ public class UniParcCrossReferenceImpl extends CrossReferenceImpl<UniParcDatabas
     private final String proteomeId;
     private final String component;
 
-    protected UniParcCrossReferenceImpl() {
+    UniParcCrossReferenceImpl() {
         this(
                 null, null, null, 0, null, false, null, null, null, null, null, null, null, null,
                 null);

diff --git a/core-domain/src/main/java/org/uniprot/core/uniparc/impl/UniParcCrossReferencePair.java b/core-domain/src/main/java/org/uniprot/core/uniparc/impl/UniParcCrossReferencePair.java
@@ -12,16 +12,13 @@ public class UniParcCrossReferencePair implements Pair<String, List<UniParcCross
     private static final long serialVersionUID = 7906365717659009263L;
     private String key;
     private List<UniParcCrossReference> value;
-    public UniParcCrossReferencePair(){
-        this(null, null);
-    }
+
 
     public UniParcCrossReferencePair(String key, List<UniParcCrossReference> value) {
         this.key = key;
         this.value = value;
     }
 
-
     @Override
     public String getKey() {
         return key;

diff --git a/core-domain/src/main/java/org/uniprot/core/uniparc/impl/UniParcEntryLightBuilder.java b/core-domain/src/main/java/org/uniprot/core/uniparc/impl/UniParcEntryLightBuilder.java
@@ -20,7 +20,7 @@ public class UniParcEntryLightBuilder implements Builder<UniParcEntryLight> {
     private String uniParcId;
     private int crossReferenceCount;
     private List<CommonOrganism> commonTaxons = new ArrayList<>();
-    private LinkedHashSet<String> uniProtKBAccessions = new LinkedHashSet<>();
+    private Set<String> uniProtKBAccessions = new LinkedHashSet<>();
 
     private Sequence sequence;
 
@@ -45,8 +45,8 @@ public class UniParcEntryLightBuilder implements Builder<UniParcEntryLight> {
     public UniParcEntryLight build() {
         return new UniParcEntryLightImpl(uniParcId, crossReferenceCount, commonTaxons, uniProtKBAccessions,
                 sequence, sequenceFeatures, oldestCrossRefCreated,
-                mostRecentCrossRefUpdated, (LinkedHashSet<Organism>) organisms, (LinkedHashSet<String>) proteinNames,
-                (LinkedHashSet<String>) geneNames, (LinkedHashSet<Proteome>) proteomes, extraAttributes);
+                mostRecentCrossRefUpdated, organisms, proteinNames,
+                geneNames, proteomes, extraAttributes);
     }
 
     public  @Nonnull UniParcEntryLightBuilder uniParcId(String uniParcId) {
@@ -149,6 +149,11 @@ public UniParcEntryLight build() {
         return this;
     }
 
+    public @Nonnull UniParcEntryLightBuilder extraAttributesSet(Map<String, Object> extraAttributes) {
+        this.extraAttributes = new LinkedHashMap<>(extraAttributes);
+        return this;
+    }
+
     public static @Nonnull UniParcEntryLightBuilder from(UniParcEntryLight uniParcEntryLight){
         LinkedHashSet<String> uniProtKBAccessions = new LinkedHashSet<>(uniParcEntryLight.getUniProtKBAccessions());
         LinkedHashSet<Organism> organisms = new LinkedHashSet<>(uniParcEntryLight.getOrganisms());
@@ -167,8 +172,8 @@ public UniParcEntryLight build() {
                 .organismsSet(organisms)
                 .proteinNamesSet(proteinNames)
                 .geneNamesSet(geneNames)
-                .proteomesSet(proteomes);
-        builder.extraAttributes = new LinkedHashMap<>(uniParcEntryLight.getExtraAttributes());
+                .proteomesSet(proteomes)
+                .extraAttributesSet(uniParcEntryLight.getExtraAttributes());
         return builder;
     }
 }
diff --git a/core-domain/src/main/java/org/uniprot/core/uniparc/impl/UniParcEntryLightImpl.java b/core-domain/src/main/java/org/uniprot/core/uniparc/impl/UniParcEntryLightImpl.java
@@ -43,11 +43,11 @@ public class UniParcEntryLightImpl implements UniParcEntryLight {
                 null, null, null, null, null);
     }
     UniParcEntryLightImpl(String uniParcId, int crossReferenceCount,
-                          List<CommonOrganism> commonTaxons, LinkedHashSet<String> uniProtKBAccessions,
+                          List<CommonOrganism> commonTaxons, Set<String> uniProtKBAccessions,
                                   Sequence sequence, List<SequenceFeature> sequenceFeatures,
                                  LocalDate oldestCrossRefCreated, LocalDate mostRecentCrossRefUpdated,
-                          LinkedHashSet<Organism> organisms, LinkedHashSet<String> proteinNames, LinkedHashSet<String> geneNames,
-                          LinkedHashSet<Proteome> proteomes, Map<String, Object> extraAttributes) {
+                          Set<Organism> organisms, Set<String> proteinNames, Set<String> geneNames,
+                          Set<Proteome> proteomes, Map<String, Object> extraAttributes) {
         this.uniParcId = uniParcId;
         this.crossReferenceCount = crossReferenceCount;
         this.commonTaxons = Utils.unmodifiableList(commonTaxons);

diff --git a/core-domain/src/test/java/org/uniprot/core/uniparc/impl/UniParcEntryLightBuilderTest.java b/core-domain/src/test/java/org/uniprot/core/uniparc/impl/UniParcEntryLightBuilderTest.java
@@ -14,6 +14,7 @@
 import java.time.LocalDate;
 import java.util.LinkedHashSet;
 import java.util.List;
+import java.util.Map;
 
 import static org.junit.jupiter.api.Assertions.*;
 import static org.uniprot.core.ObjectsForTests.sequenceFeatures;
@@ -224,6 +225,20 @@ void testProteomeIdsAdd() {
         assertTrue(entry.getProteomes().contains(proteomeId));
     }
 
+    @Test
+    void testProteomesSetThenAdd() {
+        Proteome proteome1 = new ProteomeBuilder().id("UP000005640").component("chromosome").build();
+        LinkedHashSet<Proteome> proteomes = new LinkedHashSet<>(List.of(proteome1));
+        Proteome proteome2 = new ProteomeBuilder().id("UP000002494").component("chromosome").build();
+
+        UniParcEntryLight entry = new UniParcEntryLightBuilder()
+                .proteomesSet(proteomes)
+                .proteomesAdd(proteome2)
+                .build();
+        assertEquals(2, entry.getProteomes().size());
+        assertTrue(entry.getProteomes().containsAll(List.of(proteome1, proteome2)));
+    }
+
     @Test
     void testOrganismsSetThenAdd() {
         Organism organism1 = new OrganismBuilder().taxonId(9606).scientificName("Homo sapiens").build();
@@ -261,20 +276,6 @@ void testGeneNamesSetThenAdd() {
         assertTrue(entry.getGeneNames().containsAll(List.of("Gene1", "Gene2")));
     }
 
-    @Test
-    void testProteomeIdsSetThenAdd() {
-        Proteome proteome1 = new ProteomeBuilder().id("UP000005640").component("chromosome").build();
-        LinkedHashSet<Proteome> proteomes = new LinkedHashSet<>(List.of(proteome1));
-        Proteome proteome2 = new ProteomeBuilder().id("UP000002494").component("chromosome").build();
-
-        UniParcEntryLight entry = new UniParcEntryLightBuilder()
-                .proteomesSet(proteomes)
-                .proteomesAdd(proteome2)
-                .build();
-        assertEquals(2, entry.getProteomes().size());
-        assertTrue(entry.getProteomes().containsAll(List.of(proteome1, proteome2)));
-    }
-
 
     @Test
     void testFrom() {
@@ -313,18 +314,7 @@ void testFrom() {
 
         UniParcEntryLight newEntry = UniParcEntryLightBuilder.from(originalEntry).build();
 
-        assertEquals(originalEntry.getUniParcId(), newEntry.getUniParcId());
-        assertEquals(originalEntry.getCrossReferenceCount(), newEntry.getCrossReferenceCount());
-        assertEquals(originalEntry.getCommonTaxons(), newEntry.getCommonTaxons());
-        assertEquals(originalEntry.getSequence(), newEntry.getSequence());
-        assertEquals(originalEntry.getSequenceFeatures(), newEntry.getSequenceFeatures());
-        assertEquals(originalEntry.getOldestCrossRefCreated(), newEntry.getOldestCrossRefCreated());
-        assertEquals(originalEntry.getMostRecentCrossRefUpdated(), newEntry.getMostRecentCrossRefUpdated());
-        assertEquals(originalEntry.getOrganisms(), newEntry.getOrganisms());
-        assertEquals(originalEntry.getProteinNames(), newEntry.getProteinNames());
-        assertEquals(originalEntry.getGeneNames(), newEntry.getGeneNames());
-        assertEquals(originalEntry.getProteomes(), newEntry.getProteomes());
-        assertEquals(originalEntry, newEntry);
+        verifyOriginalAndNewEntry(originalEntry, newEntry);
     }
 
     @Test
@@ -361,4 +351,33 @@ void testAddExtraAttributes(){
         assertEquals(false, updatedEntry.getExtraAttributes().get("hasActiveCrossRef"));
     }
 
+    @Test
+    void testSetExtraAttributes(){
+        UniParcEntryLight entry = new UniParcEntryLightBuilder().uniParcId("UPI0000083A08").build();
+        assertEquals("UPI0000083A08", entry.getUniParcId());
+        assertTrue(entry.getExtraAttributes().isEmpty());
+        // set extra attribute
+        UniParcEntryLight updatedEntry = UniParcEntryLightBuilder.from(entry)
+                .extraAttributesSet(Map.of("hasActiveCrossRef", false, "another", "random")).build();
+        assertEquals("UPI0000083A08", updatedEntry.getUniParcId());
+        assertEquals(2, updatedEntry.getExtraAttributes().size());
+        assertEquals(false, updatedEntry.getExtraAttributes().get("hasActiveCrossRef"));
+        assertEquals("random", updatedEntry.getExtraAttributes().get("another"));
+    }
+
+    private void verifyOriginalAndNewEntry(UniParcEntryLight originalEntry, UniParcEntryLight newEntry) {
+        assertEquals(originalEntry.getUniParcId(), newEntry.getUniParcId());
+        assertEquals(originalEntry.getCrossReferenceCount(), newEntry.getCrossReferenceCount());
+        assertEquals(originalEntry.getCommonTaxons(), newEntry.getCommonTaxons());
+        assertEquals(originalEntry.getSequence(), newEntry.getSequence());
+        assertEquals(originalEntry.getSequenceFeatures(), newEntry.getSequenceFeatures());
+        assertEquals(originalEntry.getOldestCrossRefCreated(), newEntry.getOldestCrossRefCreated());
+        assertEquals(originalEntry.getMostRecentCrossRefUpdated(), newEntry.getMostRecentCrossRefUpdated());
+        assertEquals(originalEntry.getOrganisms(), newEntry.getOrganisms());
+        assertEquals(originalEntry.getProteinNames(), newEntry.getProteinNames());
+        assertEquals(originalEntry.getGeneNames(), newEntry.getGeneNames());
+        assertEquals(originalEntry.getProteomes(), newEntry.getProteomes());
+        assertEquals(originalEntry, newEntry);
+    }
+
 }
diff --git a/core-domain/src/test/java/org/uniprot/core/uniparc/impl/UniParcEntryLightImplTest.java b/core-domain/src/test/java/org/uniprot/core/uniparc/impl/UniParcEntryLightImplTest.java
@@ -24,7 +24,6 @@ class UniParcEntryLightImplTest {
     void needDefaultConstructorForJsonDeserialization() {
         UniParcEntryLight lightObject = new UniParcEntryLightImpl();
         assertNotNull(lightObject);
-        UniParcEntryLightBuilder.from(lightObject);
     }
 
     @Test

diff --git a/core-parser/src/main/java/org/uniprot/core/parser/tsv/uniparc/UniParcCrossReferenceMap.java b/core-parser/src/main/java/org/uniprot/core/parser/tsv/uniparc/UniParcCrossReferenceMap.java
@@ -1,23 +1,15 @@
 package org.uniprot.core.parser.tsv.uniparc;
 
-import java.time.LocalDate;
-import java.time.temporal.ChronoUnit;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Objects;
-import java.util.Optional;
-import java.util.stream.Collectors;
-
 import org.uniprot.core.parser.tsv.NamedValueMap;
 import org.uniprot.core.uniparc.UniParcCrossReference;
 import org.uniprot.core.uniparc.UniParcDatabase;
 import org.uniprot.core.util.Utils;
 
+import java.time.LocalDate;
+import java.time.temporal.ChronoUnit;
+import java.util.*;
+import java.util.stream.Collectors;
+
 /**
  * @author jluo
  * @date: 24 Jun 2019
@@ -36,8 +28,6 @@ public class UniParcCrossReferenceMap implements NamedValueMap {
                         "protein",
                         "proteome",
                         "accession",
-                        "first_seen",
-                        "last_seen",
                         "database",
                         "active",
                         "ncbiGi",
@@ -57,22 +47,17 @@ public UniParcCrossReferenceMap(List<UniParcCrossReference> uniParcCrossReferenc
     @Override
     public Map<String, String> attributeValues() {
         Map<String, String> map = new HashMap<>();
-        Optional<LocalDate> firstSeen = getFirstSeenDate();
-        Optional<LocalDate> lastSeen = getLastSeenDate();
         map.put(FIELDS.get(0), getGeneNames());
         map.put(FIELDS.get(1), getProteinNames());
         map.put(FIELDS.get(2), getProteomes());
         map.put(FIELDS.get(3), getUniProtKBAccessions());
-        map.put(FIELDS.get(4), firstSeen.map(LocalDate::toString).orElse(""));
-        map.put(FIELDS.get(5), lastSeen.map(LocalDate::toString).orElse(""));
-        map.put(FIELDS.get(6), getDatabases());
-        map.put(FIELDS.get(7), getActives());
-        map.put(FIELDS.get(8), getNcbiGis());
-        map.put(FIELDS.get(9), getTimelines());
-        map.put(FIELDS.get(10), getVersions());
-        map.put(FIELDS.get(11), getVersionIs());
+        map.put(FIELDS.get(4), getDatabases());
+        map.put(FIELDS.get(5), getActives());
+        map.put(FIELDS.get(6), getNcbiGis());
+        map.put(FIELDS.get(7), getTimelines());
+        map.put(FIELDS.get(8), getVersions());
+        map.put(FIELDS.get(9), getVersionIs());
         map.putAll(getDatabasesMap());
-
         return map;
     }
 

diff --git a/core-parser/src/main/java/org/uniprot/core/parser/tsv/uniparc/UniParcEntryValueMapper.java b/core-parser/src/main/java/org/uniprot/core/parser/tsv/uniparc/UniParcEntryValueMapper.java
@@ -17,7 +17,7 @@
 public class UniParcEntryValueMapper implements EntityValueMapper<UniParcEntry> {
 
     private static final List<String> UNIPARC_FIELDS =
-            List.of("upi", "oldestCrossRefCreated", "mostRecentCrossRefUpdated");
+            List.of("upi", "first_seen", "last_seen");
 
     @Override
     public Map<String, String> mapEntity(UniParcEntry entry, List<String> fields) {
@@ -60,14 +60,14 @@ private Map<String, String> getSimpleAttributeValues(UniParcEntry entry, List<St
                 case "upi":
                     map.put(UNIPARC_FIELDS.get(0), entry.getUniParcId().getValue());
                     break;
-                case "oldestCrossRefCreated":
+                case "first_seen":
                     map.put(
                             UNIPARC_FIELDS.get(1),
                             Optional.of(entry.getOldestCrossRefCreated())
                                     .map(LocalDate::toString)
                                     .orElse(""));
                     break;
-                case "mostRecentCrossRefUpdated":
+                case "last_seen":
                     map.put(
                             UNIPARC_FIELDS.get(2),
                             Optional.of(entry.getMostRecentCrossRefUpdated())

diff --git a/...ser/src/test/java/org/uniprot/core/json/parser/uniparc/UniParcCrossRefJsonConfigTest.java b/...ser/src/test/java/org/uniprot/core/json/parser/uniparc/UniParcCrossRefJsonConfigTest.java
@@ -1,35 +1,23 @@
 package org.uniprot.core.json.parser.uniparc;
 
-import static org.junit.jupiter.api.Assertions.fail;
-import static org.uniprot.core.json.parser.uniparc.UniParcEntryTest.getCompleteUniParcEntry;
-
-import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
+import com.fasterxml.jackson.databind.ObjectMapper;
 import org.junit.jupiter.api.Test;
 import org.uniprot.core.json.parser.ValidateJson;
 import org.uniprot.core.uniparc.UniParcCrossReference;
-
-import com.fasterxml.jackson.databind.ObjectMapper;
 import org.uniprot.core.uniparc.UniParcEntry;
 import org.uniprot.core.uniparc.impl.UniParcCrossReferencePair;
 import org.uniprot.core.util.Pair;
-import org.uniprot.core.util.PairImpl;
 
-import java.util.ArrayList;
 import java.util.List;
 
+import static org.junit.jupiter.api.Assertions.fail;
+import static org.uniprot.core.json.parser.uniparc.UniParcEntryTest.getCompleteUniParcEntry;
+
 class UniParcCrossRefJsonConfigTest {
     @Test
     void test() {
         UniParcEntry completeUniParcEntry = getCompleteUniParcEntry();
         Pair<String, List<UniParcCrossReference>> entry = new UniParcCrossReferencePair(completeUniParcEntry.getUniParcId().getValue(), completeUniParcEntry.getUniParcCrossReferences());
-/*
-        ValidateJson.verifyJsonRoundTripParser(
-                UniParcCrossRefJsonConfig.getInstance().getFullObjectMapper(), completeUniParcEntry.getUniParcCrossReferences().get(0));
-
-        ValidateJson.verifyJsonRoundTripParser(
-                UniParcCrossRefJsonConfig.getInstance().getFullObjectMapper(), new ArrayList<>(completeUniParcEntry.getUniParcCrossReferences()));
-*/
-
         ValidateJson.verifyJsonRoundTripParser(
                 UniParcCrossRefJsonConfig.getInstance().getFullObjectMapper(), entry);
         ValidateJson.verifyEmptyFields(entry);