Merge branch 'main' into 2023_05_CHANGES

.gitlab-ci.yml

@@ -30,15 +30,15 @@ core:settings:
     - 'wget --no-cache --no-cookies -O ${MAVEN_SETTINGS} "${URL_MAVEN_SETTINGS}"'
   script:
     - if [ ! -f ${MAVEN_SETTINGS} ];
-        then echo "CI settings missing";
+        then echo "CI settings file missing";
       fi
   artifacts:
     when: always
     expire_in: 2 days
     paths:
       - ./${MAVEN_SETTINGS}
   rules:
-    - if: '$CI_COMMIT_REF_NAME == "master"'
+    - if: '$CI_COMMIT_REF_NAME == "main"'
     - when: manual
       allow_failure: true
 
@@ -59,7 +59,7 @@ core:test:
       junit:
         - ./*/target/surefire-reports/TEST-*.xml
   rules:
-    - if: '$CI_COMMIT_REF_NAME == "master"'
+    - if: '$CI_COMMIT_REF_NAME == "main"'
     - when: manual
       allow_failure: true
 
@@ -76,7 +76,7 @@ core:sonar:
       - ./target
       - ./*/target
   rules:
-    - if: '$CI_COMMIT_REF_NAME == "master"'
+    - if: '$CI_COMMIT_REF_NAME == "main"'
     - when: manual
       allow_failure: true
 
@@ -87,18 +87,11 @@ core:deploy:
     - core:settings
     - core:sonar
   only:
-    - master
-
-#after_script:
-#  - 'pwd'
-#  - 'ls -al'
-#  - 'ls -al */'
-#  - 'ls -al */*/'
-#  - 'ls -al */*/*/'
+    - main
 
 store:downstream:
   stage: bridge
-  trigger: uniprot/deployment/mirror-uniprot-store
+  trigger: uniprot/deployment/uniprot-store
   when: on_success
   only:
-    - master
+    - main

controlled-vocabulary/src/main/java/org/uniprot/cv/xdb/UniProtDatabaseTypes.java

@@ -50,6 +50,12 @@ public List<UniProtDatabaseDetail> getDBTypesByCategory(UniProtDatabaseCategory
                 .collect(Collectors.toList());
     }
 
+    public List<UniProtDatabaseDetail> getInternalDatabaseDetails() {
+        return UniProtDatabaseTypes.INSTANCE.getAllDbTypes().stream()
+                .filter(dbDetail -> "internal".equals(dbDetail.getType()))
+                .collect(Collectors.toList());
+    }
+
     private void init() {
 
         String source =
@@ -72,6 +78,7 @@ private void init() {
 
                     String linkedReason = item.optString("linkedReason", null);
                     String idMappingName = item.optString("idMappingName", null);
+                    String type = item.optString("type", null);
 
                     List<UniProtDatabaseAttribute> attributes = new ArrayList<>();
                     List<Property> properties = item.getProperties("attributes");
@@ -97,7 +104,8 @@ private void init() {
                                     attributes,
                                     isImplicit,
                                     linkedReason,
-                                    idMappingName);
+                                    idMappingName,
+                                    type);
                     types.add(xdbType);
                 });
         typeMap =

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

@@ -1224,7 +1224,7 @@
 		"name": "TAIR",
 		"displayName": "TAIR",
 		"category": "ORG",
-		"uriLink": "https://www.arabidopsis.org/servlets/TairObject?accession=%id",
+		"uriLink": "https://www.arabidopsis.org/servlets/TairObject?type=locus&name=%id",
 		"attributes": [
 			{
 				"name": "GeneName",
@@ -1904,5 +1904,54 @@
       "displayName": "AlphaFoldDB",
       "category": "3DS",
       "uriLink": "https://alphafold.ebi.ac.uk/entry/%id"
-    }
+    },
+	{
+		"name": "eMIND",
+		"displayName": "eMIND",
+		"category": "MISC",
+		"uriLink": "https://research.bioinformatics.udel.edu/itextmine/integrate/doc/emind/medline/%id",
+		"type": "internal"
+	},
+	{
+		"name":"PGenN",
+		"displayName":"PGenN",
+		"category":"MISC",
+		"uriLink":"https://research.bioinformatics.udel.edu/itextmine/pgenn/doc/pgenn/medline/%id",
+		"type":"internal"
+	},
+	{
+		"name":"Alzforum",
+		"displayName":"Alzforum",
+		"category":"GVD",
+		"uriLink":"https://www.alzforum.org/node/%id",
+		"type":"internal"
+	},
+	{
+		"name":"GeneRIF",
+		"displayName":"GeneRIF",
+		"category":"SEQ",
+		"uriLink":"https://www.ncbi.nlm.nih.gov/gene?Db=gene&Cmd=DetailsSearch&Term=%id",
+		"type":"internal"
+	},
+	{
+		"name":"IC4R",
+		"displayName":"IC4R",
+		"category":"ORG",
+		"uriLink":"http://ic4r.org/osGene/%id",
+		"type":"internal"
+	},
+	{
+		"name":"ORCID",
+		"displayName":"ORCID",
+		"category":"MISC",
+		"uriLink":"https://orcid.org/%id",
+		"type":"internal"
+	},
+	{
+		"name":"PubTator",
+		"displayName":"PubTator",
+		"category":"MISC",
+		"uriLink":"https://www.ncbi.nlm.nih.gov/research/pubtator/?query=%id",
+		"type":"internal"
+	}
 ]

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

@@ -69,6 +69,7 @@ void testFailedValidation() {
                         opType.getAttributes(),
                         false,
                         null,
+                        null,
                         null);
 
         // validate, the category should mismatch

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

@@ -288,7 +288,7 @@ void testProteomesType() {
 
     @Test
     void testDatabaseFieldSize() {
-        verifyGroupSize(UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(SEQUENCE_DATABASES), 6);
+        verifyGroupSize(UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(SEQUENCE_DATABASES), 7);
         verifyGroupSize(
                 UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(D3_STRUCTURE_DATABASES), 12);
         verifyGroupSize(
@@ -301,7 +301,7 @@ void testDatabaseFieldSize() {
                 13);
         verifyGroupSize(UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(PTM_DATABASES), 10);
         verifyGroupSize(
-                UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(GENERIC_VARIATION_DATABASES), 5);
+                UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(GENERIC_VARIATION_DATABASES), 6);
         verifyGroupSize(UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(D2_GEL_DATABASES), 7);
         verifyGroupSize(
                 UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(PROTEOMIC_DATABASES), 12);
@@ -314,13 +314,13 @@ void testDatabaseFieldSize() {
                 15);
         verifyGroupSize(
                 UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(ORGANISM_SPECIFIC_DATABASES),
-                40);
+                41);
         verifyGroupSize(
                 UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(PHYLOGENOMIC_DATABASES), 9);
         verifyGroupSize(
                 UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(ENZYME_AND_PATHWAY_DATABASES),
                 10);
-        verifyGroupSize(UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(MISCELLANEOUS), 11);
+        verifyGroupSize(UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(MISCELLANEOUS), 15);
         verifyGroupSize(
                 UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(GENE_EXPRESSION_DATABASES), 5);
         verifyGroupSize(
@@ -331,6 +331,14 @@ void testDatabaseFieldSize() {
         verifyGroupSize(UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(PROTEOMES_DATABASES), 1);
     }
 
+    @Test
+    void testInternalCrossRefs() {
+        List<UniProtDatabaseDetail> internalCrossRefs =
+                UniProtDatabaseTypes.INSTANCE.getInternalDatabaseDetails();
+
+        assertEquals(7, internalCrossRefs.size());
+    }
+
     private void verifyGroupSize(List<UniProtDatabaseDetail> dbTypesByCategory, int size) {
         assertEquals(size, dbTypesByCategory.size());
     }

core-domain/src/main/java/org/uniprot/core/cv/xdb/UniProtDatabaseDetail.java

@@ -9,7 +9,7 @@ public class UniProtDatabaseDetail implements Serializable {
 
     private static final long serialVersionUID = 8751881513996820892L;
 
-    private static final UniProtDatabaseAttribute DEFAULT_ATTRIBUTE =
+    public static final UniProtDatabaseAttribute DEFAULT_ATTRIBUTE =
             new UniProtDatabaseAttribute("Description", "description", null);
     private String name;
     private String displayName;
@@ -20,6 +20,7 @@ public class UniProtDatabaseDetail implements Serializable {
     private boolean implicit = false;
     private String linkedReason = null;
     private String idMappingName;
+    private String type;
 
     UniProtDatabaseDetail() {
         this.attributes = new ArrayList<>();
@@ -35,6 +36,28 @@ public UniProtDatabaseDetail(
             boolean implicit,
             String linkedReason,
             String idMappingName) {
+        this(
+                name,
+                displayName,
+                category,
+                uriLink,
+                attributes,
+                implicit,
+                linkedReason,
+                idMappingName,
+                null);
+    }
+
+    public UniProtDatabaseDetail(
+            String name,
+            String displayName,
+            UniProtDatabaseCategory category,
+            String uriLink,
+            List<UniProtDatabaseAttribute> attributes,
+            boolean implicit,
+            String linkedReason,
+            String idMappingName,
+            String type) {
         super();
         this.name = name;
         this.displayName = displayName;
@@ -47,6 +70,7 @@ public UniProtDatabaseDetail(
         if ((attributes != null) && !attributes.isEmpty()) this.attributes.addAll(attributes);
         else this.attributes.add(DEFAULT_ATTRIBUTE);
         this.idMappingName = idMappingName;
+        this.type = type;
     }
 
     public String getName() {
@@ -81,6 +105,10 @@ public String getIdMappingName() {
         return idMappingName;
     }
 
+    public String getType() {
+        return this.type;
+    }
+
     @Override
     public int hashCode() {
         return Objects.hash(
@@ -91,7 +119,8 @@ public int hashCode() {
                 this.uriLink,
                 this.implicit,
                 this.linkedReason,
-                this.idMappingName);
+                this.idMappingName,
+                this.type);
     }
 
     @Override
@@ -109,6 +138,7 @@ public boolean equals(Object obj) {
                 && Objects.equals(this.uriLink, other.uriLink)
                 && Objects.equals(this.implicit, other.implicit)
                 && Objects.equals(this.linkedReason, other.linkedReason)
-                && Objects.equals(this.idMappingName, other.idMappingName);
+                && Objects.equals(this.idMappingName, other.idMappingName)
+                && Objects.equals(this.type, other.type);
     }
 }

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

@@ -16,7 +16,7 @@ public enum GenomeAssemblySource implements EnumDisplay {
     ENSEMBLPROTISTS("EnsemblProtists"),
     ENSEMBLMETAZOA("EnsemblMetazoa"),
     ENSEMBL("Ensembl"),
-    REFSEQ("Refseq"),
+    REFSEQ("RefSeq"),
     WORMBASE("WormBase");
 
     private final String name;

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();
 }

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;
+    }
 }