Merge branch 'uniparc_light_vd_v2' into TRM-30823-REDUNDANT-FASTA_TST

ebi-uniprot · Sep 24, 2024 · 01539d9 · 01539d9
2 parents 149a8cf + 5e991c9
commit 01539d9
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Showing 40 changed files with 379 additions and 124 deletions.
diff --git a/controlled-vocabulary/pom.xml b/controlled-vocabulary/pom.xml
@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>org.uniprot</groupId>
 		<artifactId>core-parent</artifactId>
-		<version>1.0.33-SNAPSHOT</version>
+		<version>1.0.35-SNAPSHOT</version>
 		<relativePath>../</relativePath>
 	</parent>
 

diff --git a/core-common/pom.xml b/core-common/pom.xml
@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>org.uniprot</groupId>
 		<artifactId>core-parent</artifactId>
-		<version>1.0.33-SNAPSHOT</version>
+		<version>1.0.35-SNAPSHOT</version>
 		<relativePath>../</relativePath>
 	</parent>
 

diff --git a/core-domain-utils/pom.xml b/core-domain-utils/pom.xml
@@ -5,7 +5,7 @@
 	<parent>
 		<artifactId>core-parent</artifactId>
 		<groupId>org.uniprot</groupId>
-		<version>1.0.33-SNAPSHOT</version>
+		<version>1.0.35-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 

diff --git a/core-domain/pom.xml b/core-domain/pom.xml
@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>org.uniprot</groupId>
 		<artifactId>core-parent</artifactId>
-		<version>1.0.33-SNAPSHOT</version>
+		<version>1.0.35-SNAPSHOT</version>
 		<relativePath>../</relativePath>
 	</parent>
 

diff --git a/core-domain/src/main/java/org/uniprot/core/uniparc/SequenceFeature.java b/core-domain/src/main/java/org/uniprot/core/uniparc/SequenceFeature.java
@@ -3,8 +3,6 @@
 import java.io.Serializable;
 import java.util.List;
 
-import org.uniprot.core.Location;
-
 /**
  * @author jluo
  * @date: 22 May 2019
@@ -16,5 +14,5 @@ public interface SequenceFeature extends Serializable {
 
     String getSignatureDbId();
 
-    List<Location> getLocations();
+    List<SequenceFeatureLocation> getLocations();
 }
diff --git a/core-domain/src/main/java/org/uniprot/core/uniparc/SequenceFeatureLocation.java b/core-domain/src/main/java/org/uniprot/core/uniparc/SequenceFeatureLocation.java
@@ -0,0 +1,11 @@
+package org.uniprot.core.uniparc;
+
+import java.io.Serializable;
+
+public interface SequenceFeatureLocation extends Serializable {
+    int getStart();
+
+    int getEnd();
+
+    String getAlignment();
+}
diff --git a/core-domain/src/main/java/org/uniprot/core/uniparc/SignatureDbType.java b/core-domain/src/main/java/org/uniprot/core/uniparc/SignatureDbType.java
@@ -1,9 +1,9 @@
 package org.uniprot.core.uniparc;
 
-import javax.annotation.Nonnull;
-
 import org.uniprot.core.util.EnumDisplay;
 
+import javax.annotation.Nonnull;
+
 public enum SignatureDbType implements EnumDisplay {
     CDD("CDD"),
     GENE3D("Gene3D"),
@@ -16,7 +16,8 @@ public enum SignatureDbType implements EnumDisplay {
     SFLD("SFLD"),
     SMART("SMART"),
     SUPFAM("SUPFAM"),
-    NCBIFAM("NCBIfam");
+    NCBIFAM("NCBIfam"),
+    FUNFAM("FUNFAM");
 
     private final String name;
 

diff --git a/core-domain/src/main/java/org/uniprot/core/uniparc/UniParcEntryLight.java b/core-domain/src/main/java/org/uniprot/core/uniparc/UniParcEntryLight.java
@@ -6,6 +6,7 @@
 import java.io.Serializable;
 import java.time.LocalDate;
 import java.util.List;
+import java.util.Map;
 import java.util.Set;
 
 public interface UniParcEntryLight extends Serializable {
@@ -25,6 +26,8 @@ public interface UniParcEntryLight extends Serializable {
 
     LocalDate getMostRecentCrossRefUpdated();
 
+    Map<String, Object> getExtraAttributes();
+
     // lazily loaded fields
     Set<Organism> getOrganisms();// organism id and name pair
 

diff --git a/core-domain/src/main/java/org/uniprot/core/uniparc/impl/SequenceFeatureBuilder.java b/core-domain/src/main/java/org/uniprot/core/uniparc/impl/SequenceFeatureBuilder.java
@@ -6,9 +6,9 @@
 import javax.annotation.Nonnull;
 
 import org.uniprot.core.Builder;
-import org.uniprot.core.Location;
 import org.uniprot.core.uniparc.InterProGroup;
 import org.uniprot.core.uniparc.SequenceFeature;
+import org.uniprot.core.uniparc.SequenceFeatureLocation;
 import org.uniprot.core.uniparc.SignatureDbType;
 import org.uniprot.core.util.Utils;
 
@@ -20,7 +20,7 @@ public class SequenceFeatureBuilder implements Builder<SequenceFeature> {
     private InterProGroup interproGroup;
     private SignatureDbType dbType;
     private String dbId;
-    private List<Location> locations = new ArrayList<>();
+    private List<SequenceFeatureLocation> locations = new ArrayList<>();
 
     @Override
     public @Nonnull SequenceFeature build() {
@@ -42,12 +42,12 @@ public class SequenceFeatureBuilder implements Builder<SequenceFeature> {
         return this;
     }
 
-    public @Nonnull SequenceFeatureBuilder locationsSet(List<Location> locations) {
+    public @Nonnull SequenceFeatureBuilder locationsSet(List<SequenceFeatureLocation> locations) {
         this.locations = Utils.modifiableList(locations);
         return this;
     }
 
-    public @Nonnull SequenceFeatureBuilder locationsAdd(Location location) {
+    public @Nonnull SequenceFeatureBuilder locationsAdd(SequenceFeatureLocation location) {
         Utils.addOrIgnoreNull(location, locations);
         return this;
     }

diff --git a/core-domain/src/main/java/org/uniprot/core/uniparc/impl/SequenceFeatureImpl.java b/core-domain/src/main/java/org/uniprot/core/uniparc/impl/SequenceFeatureImpl.java
@@ -4,9 +4,9 @@
 import java.util.List;
 import java.util.Objects;
 
-import org.uniprot.core.Location;
 import org.uniprot.core.uniparc.InterProGroup;
 import org.uniprot.core.uniparc.SequenceFeature;
+import org.uniprot.core.uniparc.SequenceFeatureLocation;
 import org.uniprot.core.uniparc.SignatureDbType;
 import org.uniprot.core.util.Utils;
 
@@ -17,19 +17,19 @@
 public class SequenceFeatureImpl implements SequenceFeature {
 
     /** */
-    private static final long serialVersionUID = -8511912268843073779L;
+    private static final long serialVersionUID = 5234475851615797849L;
 
     private InterProGroup interproGroup;
     private SignatureDbType database;
     private String databaseId;
-    private List<Location> locations;
+    private List<SequenceFeatureLocation> locations;
 
     SequenceFeatureImpl() {
         this.locations = Collections.emptyList();
     }
 
     SequenceFeatureImpl(
-            InterProGroup domain, SignatureDbType dbType, String dbId, List<Location> locations) {
+            InterProGroup domain, SignatureDbType dbType, String dbId, List<SequenceFeatureLocation> locations) {
         super();
         this.interproGroup = domain;
         this.database = dbType;
@@ -53,7 +53,7 @@ public String getSignatureDbId() {
     }
 
     @Override
-    public List<Location> getLocations() {
+    public List<SequenceFeatureLocation> getLocations() {
         return locations;
     }
 

diff --git a/core-domain/src/main/java/org/uniprot/core/uniparc/impl/SequenceFeatureLocationBuilder.java b/core-domain/src/main/java/org/uniprot/core/uniparc/impl/SequenceFeatureLocationBuilder.java
@@ -0,0 +1,47 @@
+package org.uniprot.core.uniparc.impl;
+
+import org.uniprot.core.Builder;
+import org.uniprot.core.uniparc.SequenceFeatureLocation;
+
+import javax.annotation.Nonnull;
+
+public class SequenceFeatureLocationBuilder implements Builder<SequenceFeatureLocation> {
+
+    private int start;
+    private int end;
+    private String alignment;
+
+    @Nonnull
+    @Override
+    public SequenceFeatureLocation build() {
+        return new SequenceFeatureLocationImpl(start,end,alignment);
+    }
+
+    public @Nonnull SequenceFeatureLocationBuilder range(int start, int end) {
+        this.start = start;
+        this.end = end;
+        return this;
+    }
+
+    public @Nonnull SequenceFeatureLocationBuilder start(int start) {
+        this.start = start;
+        return this;
+    }
+
+    public @Nonnull SequenceFeatureLocationBuilder end(int end) {
+        this.end = end;
+        return this;
+    }
+
+    public @Nonnull SequenceFeatureLocationBuilder alignment(String alignment) {
+        this.alignment = alignment;
+        return this;
+    }
+
+    public static @Nonnull SequenceFeatureLocationBuilder from(@Nonnull SequenceFeatureLocation instance) {
+        return new SequenceFeatureLocationBuilder()
+                .start(instance.getStart())
+                .end(instance.getEnd())
+                .alignment(instance.getAlignment());
+    }
+}
diff --git a/core-domain/src/main/java/org/uniprot/core/uniparc/impl/SequenceFeatureLocationImpl.java b/core-domain/src/main/java/org/uniprot/core/uniparc/impl/SequenceFeatureLocationImpl.java
@@ -0,0 +1,41 @@
+package org.uniprot.core.uniparc.impl;
+
+import org.uniprot.core.Location;
+import org.uniprot.core.uniparc.SequenceFeatureLocation;
+
+import java.util.Objects;
+
+public class SequenceFeatureLocationImpl extends Location implements SequenceFeatureLocation{
+
+    private static final long serialVersionUID = -4804406936471873484L;
+    private String alignment;
+
+    SequenceFeatureLocationImpl(){
+        super(0, 0);
+    }
+
+    SequenceFeatureLocationImpl(int start, int end, String alignment) {
+        super(start, end);
+        this.alignment = alignment;
+    }
+
+    @Override
+    public String getAlignment() {
+        return alignment;
+    }
+
+
+    @Override
+    public boolean equals(Object o) {
+        if (this == o) return true;
+        if (o == null || getClass() != o.getClass()) return false;
+        if (!super.equals(o)) return false;
+        SequenceFeatureLocationImpl that = (SequenceFeatureLocationImpl) o;
+        return Objects.equals(alignment, that.alignment);
+    }
+
+    @Override
+    public int hashCode() {
+        return Objects.hash(super.hashCode(), alignment);
+    }
+}
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
@@ -11,11 +11,12 @@
 
 import javax.annotation.Nonnull;
 import java.time.LocalDate;
-import java.util.ArrayList;
-import java.util.LinkedHashSet;
-import java.util.List;
-import java.util.Set;
+import java.util.*;
+
+import static org.uniprot.core.util.Utils.putOrIgnoreNull;
+
 public class UniParcEntryLightBuilder implements Builder<UniParcEntryLight> {
+    public static final String HAS_ACTIVE_CROSS_REF = "hasActiveCrossRef";
     private String uniParcId;
     private int crossReferenceCount;
     private List<CommonOrganism> commonTaxons = new ArrayList<>();
@@ -37,12 +38,15 @@ public class UniParcEntryLightBuilder implements Builder<UniParcEntryLight> {
 
     private Set<Proteome> proteomes = new LinkedHashSet<>();
 
+    private Map<String, Object> extraAttributes = new LinkedHashMap<>();
+
     @Nonnull
     @Override
     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);
+                mostRecentCrossRefUpdated, (LinkedHashSet<Organism>) organisms, (LinkedHashSet<String>) proteinNames,
+                (LinkedHashSet<String>) geneNames, (LinkedHashSet<Proteome>) proteomes, extraAttributes);
     }
 
     public  @Nonnull UniParcEntryLightBuilder uniParcId(String uniParcId) {
@@ -140,16 +144,22 @@ public UniParcEntryLight build() {
         return this;
     }
 
+    public @Nonnull UniParcEntryLightBuilder extraAttributesAdd(String name, Object value) {
+        putOrIgnoreNull(name, value, this.extraAttributes);
+        return this;
+    }
+
     public static @Nonnull UniParcEntryLightBuilder from(UniParcEntryLight uniParcEntryLight){
-        LinkedHashSet<String> uniprotKbAccessions = new LinkedHashSet<>(uniParcEntryLight.getUniProtKBAccessions());
+        LinkedHashSet<String> uniProtKBAccessions = new LinkedHashSet<>(uniParcEntryLight.getUniProtKBAccessions());
         LinkedHashSet<Organism> organisms = new LinkedHashSet<>(uniParcEntryLight.getOrganisms());
         LinkedHashSet<String> proteinNames = new LinkedHashSet<>(uniParcEntryLight.getProteinNames());
         LinkedHashSet<String> geneNames = new LinkedHashSet<>(uniParcEntryLight.getGeneNames());
         LinkedHashSet<Proteome> proteomes = new LinkedHashSet<>(uniParcEntryLight.getProteomes());
-        return new UniParcEntryLightBuilder().uniParcId(uniParcEntryLight.getUniParcId())
+        UniParcEntryLightBuilder builder = new UniParcEntryLightBuilder();
+        builder.uniParcId(uniParcEntryLight.getUniParcId())
                 .crossReferenceCount(uniParcEntryLight.getCrossReferenceCount())
                 .commonTaxonsSet(uniParcEntryLight.getCommonTaxons())
-                .uniProtKBAccessionsSet(uniprotKbAccessions)
+                .uniProtKBAccessionsSet(uniProtKBAccessions)
                 .sequence(uniParcEntryLight.getSequence())
                 .sequenceFeaturesSet(uniParcEntryLight.getSequenceFeatures())
                 .oldestCrossRefCreated(uniParcEntryLight.getOldestCrossRefCreated())
@@ -158,5 +168,7 @@ public UniParcEntryLight build() {
                 .proteinNamesSet(proteinNames)
                 .geneNamesSet(geneNames)
                 .proteomesSet(proteomes);
+        builder.extraAttributes = new LinkedHashMap<>(uniParcEntryLight.getExtraAttributes());
+        return builder;
     }
 }