Merge pull request #678 from opencb/TASK-5212

TASK-5212 Fix 'cellbase-admin.sh build' for clinical variants

Author: jtarraga

cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/HGMDIndexer.java

@@ -167,7 +167,7 @@ private boolean updateRocksDB(Variant variant) throws RocksDBException, IOExcept
 
         if (normalisedVariantStringList != null) {
             for (String normalisedVariantString : normalisedVariantStringList) {
-                VariantAnnotation variantAnnotation = getVariantAnnotation(variant.toString().getBytes());
+                VariantAnnotation variantAnnotation = getVariantAnnotation(normalisedVariantString.getBytes());
 
                 // Add haplotype property to all EvidenceEntry objects in variant if there are more than 1 variants in
                 // normalisedVariantStringList, i.e. if this variant is part of an MNV (haplotype)

cellbase-lib/src/main/java/org/opencb/cellbase/lib/variant/annotation/VariantAnnotationCalculator.java

@@ -431,6 +431,7 @@ private List<GeneMirnaTarget> getTargets(Gene mirna) throws QueryException, Ille
             }
         }
         GeneQuery geneQuery = new GeneQuery();
+        geneQuery.setDataRelease(dataRelease);
         geneQuery.setAnnotationTargets(new LogicalList<>(mirnas, false));
         List<GeneMirnaTarget> geneMirnaTargets = new ArrayList<>();
         List<Gene> genes = (geneManager.search(geneQuery)).getResults();
@@ -679,9 +680,9 @@ public List<Gene> getBatchGeneList(List<Variant> variantList)
 
         List<Gene> geneList = new ArrayList<>();
         GeneQuery geneQuery = new GeneQuery();
+        geneQuery.setDataRelease(dataRelease);
         geneQuery.setIncludes(includeGeneFields);
         geneQuery.setRegions(regionList);
-        geneQuery.setDataRelease(dataRelease);
 
         if (StringUtils.isNotEmpty(consequenceTypeSource)) {
             // sources can be "ensembl" and/or "refseq". query is validated before execution, will fail if invalid value
@@ -1354,6 +1355,7 @@ private boolean[] getRegulatoryRegionOverlaps(String chromosome, Integer start,
         boolean[] overlapsRegulatoryRegion = {false, false};
 
         RegulationQuery query = new RegulationQuery();
+        query.setDataRelease(dataRelease);
         query.setExcludes(Collections.singletonList("_id"));
         query.setIncludes(Collections.singletonList("chromosome"));
         query.setLimit(1);