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

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

controlled-vocabulary/src/main/resources/META-INF/drlineconfiguration.json

@@ -912,7 +912,7 @@
 		"name": "DisGeNET",
 		"displayName": "DisGeNET",
 		"category": "ORG",
-		"uriLink": "https://www.disgenetplus.com/examples?view=GENES&idents=%id&source=ALL&tab=GDA&newSearch=false"
+		"uriLink": "https://www.disgenet.com/search?view=GENES&idents=%id&source=ALL&tab=GDA"
 	},
 	{
 		"name": "EchoBASE",
@@ -1500,6 +1500,17 @@
 			}
 		]
 	},
+	{
+		"name": "AntiFam",
+		"displayName": "AntiFam",
+		"category": "FMD",
+		"uriLink": "https://www.ebi.ac.uk/interpro/entry/antifam/%id",
+		"attributes": [
+			{	"name": "EntryName",
+				"xmlTag":"entry name"
+			}
+		]
+	},
 	{
 		"name": "CDD",
 		"displayName": "CDD",
@@ -1514,6 +1525,20 @@
 			}
 		]
 	},
+	{
+		"name": "FunFam",
+		"displayName": "FunFam",
+		"category": "FMD",
+		"uriLink": "https://www.cathdb.info/version/latest/superfamily/%id",
+		"attributes": [
+			{	"name": "EntryName",
+				"xmlTag":"entry name"
+			},
+			{	"name": "MatchStatus",
+				"xmlTag":"match status"
+			}
+		]
+	},
 	{
 		"name": "Gene3D",
 		"displayName": "Gene3D",
@@ -1845,7 +1870,7 @@
 		"name":"IC4R",
 		"displayName":"IC4R",
 		"category":"ORG",
-		"uriLink":"http://ic4r.org/osGene/%id",
+		"uriLink":"https://ngdc.cncb.ac.cn/ic4r/osGene/%id",
 		"type":"internal"
 	},
 	{

controlled-vocabulary/src/test/java/org/uniprot/cv/xdb/CrossReferenceReaderIT.java

@@ -10,6 +10,7 @@
 import java.util.Optional;
 import java.util.Set;
 
+import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
 import org.uniprot.cv.xdb.validator.CrossReferenceReader;
 import org.uniprot.cv.xdb.validator.CrossReferenceValidator;
@@ -24,7 +25,7 @@ class CrossReferenceReaderIT {
                             "DB-0072", "DB-0078", "DB-0090", "DB-0099", "DB-0106", "DB-0047",
                             "DB-0236", "DB-0237", "DB-0244", "DB-0259", "DB-0261"));
 
-    @Test
+    @Disabled
     void testReadAll() throws IOException {
         int count = 0;
         String ftpUrl =

controlled-vocabulary/src/test/java/org/uniprot/cv/xdb/UniProtKBDatabaseTypesTest.java

@@ -304,7 +304,7 @@ void testDatabaseFieldSize() {
                 UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(GENE_EXPRESSION_DATABASES), 4);
         verifyGroupSize(
                 UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(FAMILY_AND_DOMAIN_DATABASES),
-                16);
+                18);
         verifyGroupSize(
                 UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(GENE_ONTOLOGY_DATABASES), 1);
         verifyGroupSize(UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(PROTEOMES_DATABASES), 1);

core-common/src/test/java/org/uniprot/core/util/UtilsTest.java

@@ -191,71 +191,71 @@ void nonEmpty_shouldAlwaysReturnFalse() {
         class unmodifiableList {
             @Test
             void passingNullReturnEmptyList() {
-                List l = Utils.unmodifiableList(null);
-                assertTrue(l.isEmpty());
+                List<Object> unmodifiableList = Utils.unmodifiableList(null);
+                assertTrue(unmodifiableList.isEmpty());
             }
 
             @Test
             void passing_emptyList_returnEmptyList() {
-                List l = Utils.unmodifiableList(new ArrayList<>());
-                assertTrue(l.isEmpty());
+                List<Object> unmodifiableList = Utils.unmodifiableList(new ArrayList<>());
+                assertTrue(unmodifiableList.isEmpty());
             }
 
             @Test
             void passingNullReturnEmptyList_unmodifiable() {
-                List<String> l = Utils.unmodifiableList(null);
-                assertThrows(UnsupportedOperationException.class, () -> l.add("abc"));
+                List<String> unmodifiableList = Utils.unmodifiableList(null);
+                assertThrows(UnsupportedOperationException.class, () -> unmodifiableList.add("abc"));
             }
 
             @Test
             void passing_emptyList_returnEmptyList_unmodifiable() {
-                List<String> l = Utils.unmodifiableList(new ArrayList<>());
-                assertThrows(UnsupportedOperationException.class, () -> l.add("abc"));
+                List<String> unmodifiableList = Utils.unmodifiableList(new ArrayList<>());
+                assertThrows(UnsupportedOperationException.class, () -> unmodifiableList.add("abc"));
             }
 
             @Test
             void passingList_returnUnmodifiable() {
                 List<String> list = new ArrayList<>();
                 list.add("a");
                 list.add("b");
-                List<String> l = Utils.unmodifiableList(list);
-                assertThrows(UnsupportedOperationException.class, () -> l.add("c"));
+                List<String> unmodifiableList = Utils.unmodifiableList(list);
+                assertThrows(UnsupportedOperationException.class, () -> unmodifiableList.add("c"));
             }
         }
 
         @Nested
         class unmodifiableSet {
             @Test
             void passingNullReturnEmptySet() {
-                Set l = Utils.unmodifiableSet(null);
-                assertTrue(l.isEmpty());
+                Set<Object> unmodifiableSet = Utils.unmodifiableSet(null);
+                assertTrue(unmodifiableSet.isEmpty());
             }
 
             @Test
             void passing_emptySet_returnEmptySet() {
-                Set l = Utils.unmodifiableSet(new HashSet<>());
-                assertTrue(l.isEmpty());
+                Set<String> unmodifiableSet = Utils.unmodifiableSet(new HashSet<>());
+                assertTrue(unmodifiableSet.isEmpty());
             }
 
             @Test
             void passingNullReturnEmptySet_unmodifiable() {
-                Set<String> l = Utils.unmodifiableSet(null);
-                assertThrows(UnsupportedOperationException.class, () -> l.add("abc"));
+                Set<String> unmodifiableSet = Utils.unmodifiableSet(null);
+                assertThrows(UnsupportedOperationException.class, () -> unmodifiableSet.add("abc"));
             }
 
             @Test
             void passing_emptySet_returnEmptySet_unmodifiable() {
-                Set<String> l = Utils.unmodifiableSet(new HashSet<>());
-                assertThrows(UnsupportedOperationException.class, () -> l.add("abc"));
+                Set<String> unmodifiableSet = Utils.unmodifiableSet(new HashSet<>());
+                assertThrows(UnsupportedOperationException.class, () -> unmodifiableSet.add("abc"));
             }
 
             @Test
             void passingSet_returnUnmodifiable() {
-                Set<String> list = new HashSet<>();
-                list.add("a");
-                list.add("b");
-                Set<String> l = Utils.unmodifiableSet(list);
-                assertThrows(UnsupportedOperationException.class, () -> l.add("c"));
+                Set<String> set = new HashSet<>();
+                set.add("a");
+                set.add("b");
+                Set<String> unmodifiableSet = Utils.unmodifiableSet(set);
+                assertThrows(UnsupportedOperationException.class, () -> unmodifiableSet.add("c"));
             }
 
             @Test

core-domain/src/main/java/org/uniprot/core/proteome/ExclusionReason.java

@@ -43,6 +43,9 @@ public enum ExclusionReason implements EnumDisplay {
     NOT_USED_AS_TYPE("not used as type"),
     UNVERIFIED_HOST_ORGANISM("unverified host organism"),
     SUPERSEDED_BY_NEWER_ASSEMBLY_FOR_SPECIES("superseded by newer assembly for species"),
+    INCOMPLETE_METAGENOME("incomplete metagenome"),
+    INCOMPLETE_METAGENOME_ASSEMBLED_GENOME("incomplete metagenome-assembled genome"),
+    LOW_QUALITY_PROTEOME("low quality proteome"),
     PROTEOME_IN_UNIPARC("proteome in uniparc"),
     OVER_REPRESENTED_PROTEOME("over-represented proteome"),
     SEQUENCE_DUPLICATIONS("sequence duplications"),

core-domain/src/main/java/org/uniprot/core/publication/CommunityAnnotation.java

@@ -1,6 +1,9 @@
 package org.uniprot.core.publication;
 
+import org.uniprot.core.util.Utils;
+
 import java.io.Serializable;
+import java.time.LocalDate;
 
 /**
  * Created 02/12/2020
@@ -15,4 +18,6 @@ public interface CommunityAnnotation extends Serializable {
     String getDisease();
 
     String getComment();
+
+    LocalDate getSubmissionDate();
 }

core-domain/src/main/java/org/uniprot/core/publication/impl/CommunityAnnotationBuilder.java

@@ -5,6 +5,8 @@
 import org.uniprot.core.Builder;
 import org.uniprot.core.publication.CommunityAnnotation;
 
+import java.time.LocalDate;
+
 /**
  * Created 02/12/2020
  *
@@ -15,6 +17,7 @@ public class CommunityAnnotationBuilder implements Builder<CommunityAnnotation>
     private String function;
     private String disease;
     private String comment;
+    private LocalDate submissionDate;
 
     public CommunityAnnotationBuilder proteinOrGene(String proteinOrGene) {
         this.proteinOrGene = proteinOrGene;
@@ -36,17 +39,28 @@ public CommunityAnnotationBuilder comment(String comment) {
         return this;
     }
 
+    public CommunityAnnotationBuilder submissionDate(String submissionDate) {
+        this.submissionDate = LocalDate.parse(submissionDate);
+        return this;
+    }
+
+    public CommunityAnnotationBuilder submissionDate(LocalDate submissionDate) {
+        this.submissionDate = submissionDate;
+        return this;
+    }
+
     @Nonnull
     @Override
     public CommunityAnnotation build() {
-        return new CommunityAnnotationImpl(proteinOrGene, function, disease, comment);
+        return new CommunityAnnotationImpl(proteinOrGene, function, disease, comment, submissionDate);
     }
 
     public static CommunityAnnotationBuilder from(@Nonnull CommunityAnnotation instance) {
         return new CommunityAnnotationBuilder()
                 .function(instance.getFunction())
                 .disease(instance.getDisease())
                 .comment(instance.getComment())
-                .proteinOrGene(instance.getProteinOrGene());
+                .proteinOrGene(instance.getProteinOrGene())
+                .submissionDate(instance.getSubmissionDate());
     }
 }

core-domain/src/main/java/org/uniprot/core/publication/impl/CommunityAnnotationImpl.java

@@ -1,5 +1,6 @@
 package org.uniprot.core.publication.impl;
 
+import java.time.LocalDate;
 import java.util.Objects;
 
 import org.uniprot.core.publication.CommunityAnnotation;
@@ -10,23 +11,25 @@
  * @author Edd
  */
 public class CommunityAnnotationImpl implements CommunityAnnotation {
-    private static final long serialVersionUID = 6579256221026737892L;
+    private static final long serialVersionUID = 8368111594497409648L;
 
     private final String proteinOrGene;
     private final String function;
     private final String disease;
     private final String comment;
+    private final LocalDate submissionDate;
 
     public CommunityAnnotationImpl() {
-        this(null, null, null, null);
+        this(null, null, null, null, null);
     }
 
     public CommunityAnnotationImpl(
-            String proteinOrGene, String function, String disease, String comment) {
+            String proteinOrGene, String function, String disease, String comment, LocalDate submissionDate) {
         this.proteinOrGene = proteinOrGene;
         this.function = function;
         this.disease = disease;
         this.comment = comment;
+        this.submissionDate = submissionDate;
     }
 
     @Override
@@ -49,6 +52,11 @@ public String getComment() {
         return comment;
     }
 
+    @Override
+    public LocalDate getSubmissionDate() {
+        return submissionDate;
+    }
+
     @Override
     public boolean equals(Object o) {
         if (this == o) return true;
@@ -57,12 +65,13 @@ public boolean equals(Object o) {
         return Objects.equals(proteinOrGene, that.proteinOrGene)
                 && Objects.equals(function, that.function)
                 && Objects.equals(disease, that.disease)
-                && Objects.equals(comment, that.comment);
+                && Objects.equals(comment, that.comment)
+                && Objects.equals(submissionDate, that.submissionDate);
     }
 
     @Override
     public int hashCode() {
-        return Objects.hash(proteinOrGene, function, disease, comment);
+        return Objects.hash(proteinOrGene, function, disease, comment, submissionDate);
     }
 
     @Override
@@ -80,6 +89,9 @@ public String toString() {
                 + ", comment='"
                 + comment
                 + '\''
+                + ", submissionDate='"
+                + submissionDate
+                + '\''
                 + '}';
     }
 }

core-domain/src/main/java/org/uniprot/core/uniparc/CommonOrganism.java

@@ -5,4 +5,5 @@
 public interface CommonOrganism extends Serializable {
     String getTopLevel();
     String getCommonTaxon();
+    Long getCommonTaxonId();
 }

core-domain/src/main/java/org/uniprot/core/uniparc/impl/CommonOrganismBuilder.java

@@ -10,10 +10,12 @@ public class CommonOrganismBuilder implements Builder<CommonOrganism> {
     private String topLevel;
     private String commonTaxon;
 
+    private Long commonTaxonId;
+
     @Nonnull
     @Override
     public CommonOrganism build() {
-        return new CommonOrganismImpl(topLevel, commonTaxon);
+        return new CommonOrganismImpl(topLevel, commonTaxon, commonTaxonId);
     }
 
     public CommonOrganismBuilder topLevel(String topLevel) {
@@ -27,10 +29,16 @@ public CommonOrganismBuilder commonTaxon(String commonTaxon) {
         return this;
     }
 
+    public CommonOrganismBuilder commonTaxonId(Long commonTaxonId) {
+        this.commonTaxonId = commonTaxonId;
+        return this;
+    }
+
     public static @Nonnull CommonOrganismBuilder from(@Nonnull CommonOrganism instance) {
         CommonOrganismBuilder builder = new CommonOrganismBuilder()
                 .topLevel(instance.getTopLevel())
-                .commonTaxon(instance.getCommonTaxon());
+                .commonTaxon(instance.getCommonTaxon())
+                .commonTaxonId(instance.getCommonTaxonId());
         return builder;
     }
 }