Merge pull request #199 from ebi-uniprot/TRM-29989-proteome-hdfs-writer

Trm 29989 proteome hdfs writer
ebi-uniprot · Oct 18, 2023 · 11bd177 · 11bd177
2 parents e3d4e87 + 9e966bc
commit 11bd177
Show file tree

Hide file tree

Showing 7 changed files with 55 additions and 34 deletions.
diff --git a/core-domain/src/main/java/org/uniprot/core/proteome/ProteomeEntry.java b/core-domain/src/main/java/org/uniprot/core/proteome/ProteomeEntry.java
@@ -50,4 +50,6 @@ public interface ProteomeEntry extends Serializable {
     GenomeAnnotation getGenomeAnnotation();
 
     List<ExclusionReason> getExclusionReasons();
+
+    ProteomeStatistics getProteomeStatistics();
 }
diff --git a/core-domain/src/main/java/org/uniprot/core/proteome/impl/ProteomeEntryBuilder.java b/core-domain/src/main/java/org/uniprot/core/proteome/impl/ProteomeEntryBuilder.java
@@ -35,6 +35,7 @@ public class ProteomeEntryBuilder implements Builder<ProteomeEntry> {
     private GenomeAnnotation genomeAnnotation;
     private List<ExclusionReason> exclusionReasons = new ArrayList<>();
     private Integer proteinCount;
+    private ProteomeStatistics proteomeStatistics;
 
     @Override
     public @Nonnull ProteomeEntry build() {
@@ -59,7 +60,8 @@ public class ProteomeEntryBuilder implements Builder<ProteomeEntry> {
                 genomeAssembly,
                 genomeAnnotation,
                 exclusionReasons,
-                proteinCount);
+                proteinCount,
+                proteomeStatistics);
     }
 
     public static @Nonnull ProteomeEntryBuilder from(@Nonnull ProteomeEntry instance) {
@@ -84,7 +86,8 @@ public class ProteomeEntryBuilder implements Builder<ProteomeEntry> {
                 .genomeAssembly(instance.getGenomeAssembly())
                 .genomeAnnotation(instance.getGenomeAnnotation())
                 .exclusionReasonsSet(instance.getExclusionReasons())
-                .proteinCount(instance.getProteinCount());
+                .proteinCount(instance.getProteinCount())
+                .proteomeStatistics(instance.getProteomeStatistics());
     }
 
     public @Nonnull ProteomeEntryBuilder proteomeId(ProteomeId id) {
@@ -225,4 +228,9 @@ public class ProteomeEntryBuilder implements Builder<ProteomeEntry> {
         Utils.addOrIgnoreNull(exclusionReason, exclusionReasons);
         return this;
     }
+
+    public @Nonnull ProteomeEntryBuilder proteomeStatistics(ProteomeStatistics proteomeStatistics) {
+        this.proteomeStatistics = proteomeStatistics;
+        return this;
+    }
 }
diff --git a/core-domain/src/main/java/org/uniprot/core/proteome/impl/ProteomeEntryImpl.java b/core-domain/src/main/java/org/uniprot/core/proteome/impl/ProteomeEntryImpl.java
@@ -34,12 +34,13 @@ public class ProteomeEntryImpl implements ProteomeEntry {
     private final GenomeAnnotation genomeAnnotation;
     private final List<TaxonomyLineage> taxonLineage;
     private final List<ExclusionReason> exclusionReasons;
+    private final ProteomeStatistics proteomeStatistics;
 
     // no arg constructor for JSON deserialization
     ProteomeEntryImpl() {
         this(
                 null, null, null, null, null, null, null, null, null, null, null, null, null, null,
-                null, null, null, null, null, null, null);
+                null, null, null, null, null, null, null, null);
     }
 
     ProteomeEntryImpl(
@@ -63,7 +64,8 @@ public class ProteomeEntryImpl implements ProteomeEntry {
             GenomeAssembly genomeAssembly,
             GenomeAnnotation genomeAnnotation,
             List<ExclusionReason> exclusionReasons,
-            Integer proteinCount) {
+            Integer proteinCount,
+            ProteomeStatistics proteomeStatistics) {
         super();
         this.id = id;
         this.taxonomy = taxonomy;
@@ -88,6 +90,7 @@ public class ProteomeEntryImpl implements ProteomeEntry {
         this.genomeAnnotation = genomeAnnotation;
         this.exclusionReasons = Utils.unmodifiableList(exclusionReasons);
         this.proteinCount = proteinCount;
+        this.proteomeStatistics = proteomeStatistics;
     }
 
     @Override
@@ -195,6 +198,11 @@ public List<ExclusionReason> getExclusionReasons() {
         return exclusionReasons;
     }
 
+    @Override
+    public ProteomeStatistics getProteomeStatistics() {
+        return proteomeStatistics;
+    }
+
     @Override
     public int hashCode() {
         return Objects.hash(
@@ -214,7 +222,8 @@ public int hashCode() {
                 proteomeCompletenessReport,
                 genomeAssembly,
                 proteinCount,
-                genomeAnnotation);
+                genomeAnnotation,
+                proteomeStatistics);
     }
 
     @Override
@@ -240,6 +249,7 @@ public boolean equals(Object obj) {
                 && Objects.equals(genomeAssembly, other.genomeAssembly)
                 && Objects.equals(geneCount, other.geneCount)
                 && Objects.equals(proteinCount, other.proteinCount)
-                && Objects.equals(genomeAnnotation, other.genomeAnnotation);
+                && Objects.equals(genomeAnnotation, other.genomeAnnotation)
+                && Objects.equals(proteomeStatistics, other.proteomeStatistics);
     }
 }
diff --git a/core-domain/src/main/java/org/uniprot/core/proteome/impl/ProteomeStatisticsImpl.java b/core-domain/src/main/java/org/uniprot/core/proteome/impl/ProteomeStatisticsImpl.java
@@ -6,6 +6,7 @@
 import org.uniprot.core.proteome.ProteomeStatistics;
 
 public class ProteomeStatisticsImpl extends StatisticsImpl implements ProteomeStatistics {
+    private static final long serialVersionUID = -8585233468042758658L;
     private final long isoformProteinCount;
 
     ProteomeStatisticsImpl(
@@ -14,6 +15,10 @@ public class ProteomeStatisticsImpl extends StatisticsImpl implements ProteomeSt
         this.isoformProteinCount = isoformProteinCount;
     }
 
+    ProteomeStatisticsImpl() {
+        this(0, 0, 0);
+    }
+
     @Override
     public long getIsoformProteinCount() {
         return isoformProteinCount;

diff --git a/core-domain/src/test/java/org/uniprot/core/proteome/impl/ProteomeEntryBuilderTest.java b/core-domain/src/test/java/org/uniprot/core/proteome/impl/ProteomeEntryBuilderTest.java
@@ -11,7 +11,10 @@
 import java.util.List;
 
 import org.junit.jupiter.api.Test;
-import org.uniprot.core.citation.*;
+import org.uniprot.core.citation.Citation;
+import org.uniprot.core.citation.JournalArticle;
+import org.uniprot.core.citation.Submission;
+import org.uniprot.core.citation.SubmissionDatabase;
 import org.uniprot.core.citation.impl.JournalArticleBuilder;
 import org.uniprot.core.citation.impl.SubmissionBuilder;
 import org.uniprot.core.proteome.*;
@@ -350,4 +353,12 @@ void ExclusionReasons() {
         assertThat(proteome.getExclusionReasons(), hasItem(ExclusionReason.METAGENOME));
         assertThat(proteome.getExclusionReasons(), hasItem(ExclusionReason.MIXED_CULTURE));
     }
+
+    @Test
+    void testProteomeStatistics() {
+        ProteomeStatistics proteomeStatistics = new ProteomeStatisticsBuilder().build();
+        ProteomeEntry proteome =
+                new ProteomeEntryBuilder().proteomeStatistics(proteomeStatistics).build();
+        assertSame(proteomeStatistics, proteome.getProteomeStatistics());
+    }
 }
diff --git a/core-domain/src/test/java/org/uniprot/core/proteome/impl/ProteomeStatisticsImplTest.java b/core-domain/src/test/java/org/uniprot/core/proteome/impl/ProteomeStatisticsImplTest.java
@@ -1,6 +1,7 @@
 package org.uniprot.core.proteome.impl;
 
-import static org.junit.jupiter.api.Assertions.*;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNotEquals;
 
 import org.junit.jupiter.api.Test;
 
@@ -20,6 +21,12 @@ void getCountsAreAccurate() {
         assertEquals(ISOFORM_PROTEIN_COUNT, PROTEOME_STATISTICS.getIsoformProteinCount());
     }
 
+    @Test
+    void defaultConstructor() {
+        ProteomeStatisticsImpl that = new ProteomeStatisticsImpl();
+        assertEquals(new ProteomeStatisticsImpl(0, 0, 0), that);
+    }
+
     @Test
     void equals_whenTrue() {
         ProteomeStatisticsImpl that =

diff --git a/json-parser/src/main/java/org/uniprot/core/json/parser/proteome/ProteomeJsonConfig.java b/json-parser/src/main/java/org/uniprot/core/json/parser/proteome/ProteomeJsonConfig.java
@@ -5,37 +5,14 @@
 import org.uniprot.core.CrossReference;
 import org.uniprot.core.Database;
 import org.uniprot.core.Value;
-import org.uniprot.core.citation.Author;
-import org.uniprot.core.citation.Book;
-import org.uniprot.core.citation.ElectronicArticle;
-import org.uniprot.core.citation.Journal;
-import org.uniprot.core.citation.JournalArticle;
-import org.uniprot.core.citation.Locator;
-import org.uniprot.core.citation.Patent;
-import org.uniprot.core.citation.PublicationDate;
-import org.uniprot.core.citation.Submission;
-import org.uniprot.core.citation.Thesis;
-import org.uniprot.core.citation.Unpublished;
-import org.uniprot.core.citation.impl.AuthorImpl;
-import org.uniprot.core.citation.impl.BookImpl;
-import org.uniprot.core.citation.impl.ElectronicArticleImpl;
-import org.uniprot.core.citation.impl.JournalArticleImpl;
-import org.uniprot.core.citation.impl.JournalImpl;
-import org.uniprot.core.citation.impl.PatentImpl;
-import org.uniprot.core.citation.impl.PublicationDateImpl;
-import org.uniprot.core.citation.impl.SubmissionImpl;
-import org.uniprot.core.citation.impl.ThesisImpl;
-import org.uniprot.core.citation.impl.UnpublishedImpl;
+import org.uniprot.core.citation.*;
+import org.uniprot.core.citation.impl.*;
 import org.uniprot.core.impl.CrossReferenceImpl;
 import org.uniprot.core.impl.DefaultDatabase;
 import org.uniprot.core.impl.ValueImpl;
 import org.uniprot.core.json.parser.JsonConfig;
 import org.uniprot.core.json.parser.deserializer.LocalDateDeserializer;
-import org.uniprot.core.json.parser.serializer.AuthorSerializer;
-import org.uniprot.core.json.parser.serializer.JournalSerializer;
-import org.uniprot.core.json.parser.serializer.LocalDateSerializer;
-import org.uniprot.core.json.parser.serializer.LocatorSerializer;
-import org.uniprot.core.json.parser.serializer.PublicationDateSerializer;
+import org.uniprot.core.json.parser.serializer.*;
 import org.uniprot.core.json.parser.uniprot.serializer.UniProtKBAccessionSerializer;
 import org.uniprot.core.proteome.*;
 import org.uniprot.core.proteome.impl.*;
@@ -89,6 +66,7 @@ private ObjectMapper initObjectMapper() {
         mod.addAbstractTypeMapping(ProteomeId.class, ProteomeIdImpl.class);
         mod.addAbstractTypeMapping(Taxonomy.class, TaxonomyImpl.class);
         mod.addAbstractTypeMapping(TaxonomyLineage.class, TaxonomyLineageImpl.class);
+        mod.addAbstractTypeMapping(ProteomeStatistics.class, ProteomeStatisticsImpl.class);
 
         mod.addAbstractTypeMapping(Value.class, ValueImpl.class);
         mod.addAbstractTypeMapping(RedundantProteome.class, RedundantProteomeImpl.class);