Fix HPO gene queries

Author: imedina

cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/GeneMongoDBAdaptor.java

@@ -257,6 +257,7 @@ private void createDiseaseQuery(Object queryValues, List<Bson> andBsonList) {
             List<Bson> orBsonList = new ArrayList<>();
             orBsonList.add(getLogicalListFilter(queryValues, "annotation.diseases.id"));
             orBsonList.add(getLogicalListFilter(queryValues, "annotation.diseases.name"));
+            orBsonList.add(getLogicalListFilter(queryValues, "annotation.diseases.hpo"));
             andBsonList.add(Filters.or(orBsonList));
         }
     }

cellbase-lib/src/main/resources/mongodb-indexes.json

@@ -43,6 +43,7 @@
 {"collection": "gene", "fields": {"mirna.matures.id": 1}, "options": {"background": true, "sparse": true}}
 {"collection": "gene", "fields": {"annotation.diseases.id": 1}, "options": {"background": true}}
 {"collection": "gene", "fields": {"annotation.diseases.name": 1}, "options": {"background": true}}
+{"collection": "gene", "fields": {"annotation.diseases.hpo": 1}, "options": {"background": true}}
 {"collection": "gene", "fields": {"annotation.expression.expression": 1}, "options": {"background": true}}
 {"collection": "gene", "fields": {"annotation.expression.factorValue": 1}, "options": {"background": true}}
 {"collection": "gene", "fields": {"annotation.drugs.drugName": 1}, "options": {"background": true}}

pom.xml

@@ -23,8 +23,8 @@
 
     <properties>
         <pycellbase.version>${project.version}</pycellbase.version>
-        <java-common-libs.version>4.12.1-SNAPSHOT</java-common-libs.version>
-        <biodata.version>2.12.4-SNAPSHOT</biodata.version>
+        <java-common-libs.version>4.12.0</java-common-libs.version>
+        <biodata.version>2.12.4</biodata.version>
         <bionetdb.version>0.1.0</bionetdb.version>
         <jackson.version>2.11.4</jackson.version>
         <jackson-asl.version>1.9.13</jackson-asl.version>
@@ -39,7 +39,7 @@
         <swagger-annotations.version>1.6.5</swagger-annotations.version>
         <javax.servlet-api.version>3.1.0</javax.servlet-api.version>
         <poi.version>4.1.2</poi.version>
-        <mongodb.version>4.8.2</mongodb.version>
+        <mongodb.version>4.11.5</mongodb.version>
         <junit.version>4.12</junit.version>
         <commons-codec.version>1.13</commons-codec.version>
         <jakarta.xml.bind-api.version>2.3.3</jakarta.xml.bind-api.version>