TASK-5318 - Implement custom annotator to allow clients private files

cellbase-core/src/main/java/org/opencb/cellbase/core/exception/CellBaseException.java

@@ -22,5 +22,12 @@ public CellBaseException(String msg) {
         super(msg);
     }
 
+    public CellBaseException(String msg,  Throwable cause) {
+        super(msg, cause);
+    }
+
+    public CellBaseException(Throwable cause) {
+        super(cause);
+    }
 }
 

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

@@ -20,6 +20,7 @@
 import org.apache.commons.lang3.StringUtils;
 import org.opencb.biodata.formats.variant.clinvar.rcv.ClinvarParser;
 import org.opencb.biodata.formats.variant.clinvar.rcv.v64jaxb.*;
+import org.opencb.biodata.models.sequence.SequenceLocation;
 import org.opencb.biodata.models.variant.avro.*;
 import org.opencb.cellbase.lib.EtlCommons;
 import org.opencb.cellbase.lib.variant.VariantAnnotationUtils;

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

@@ -74,13 +74,12 @@ public abstract class ClinicalIndexer {
     protected VariantNormalizer normalizer;
 
     public ClinicalIndexer(Path genomeSequenceFilePath) throws IOException {
-        // Forcing decomposition here in all cases - assuming the way CellBase stores clinical variants from here
-        // onwards will be decomposed and Adaptors will deal with phased/no-phased queries
+        // Use the same OpenCGA normalization parameters
         VariantNormalizer.VariantNormalizerConfig variantNormalizerConfig
                 = (new VariantNormalizer.VariantNormalizerConfig())
                 .setReuseVariants(true)
-                .setNormalizeAlleles(false)
-                .setDecomposeMNVs(true);
+                .setNormalizeAlleles(true)
+                .setDecomposeMNVs(false);
 
         if (genomeSequenceFilePath != null) {
             logger.info("Enabling left aligning by using sequence at {}", genomeSequenceFilePath.toString());
@@ -231,92 +230,4 @@ protected void addHaplotypeProperty(List<EvidenceEntry> evidenceEntryList, List<
             }
         }
     }
-
-    class SequenceLocation {
-        private String chromosome;
-        private int start;
-        private int end;
-        private String reference;
-        private String alternate;
-        private String strand;
-
-        SequenceLocation() {
-        }
-
-        SequenceLocation(String chromosome, int start, int end, String reference, String alternate) {
-            this(chromosome, start, end, reference, alternate, "+");
-        }
-
-        SequenceLocation(String chromosome, int start, int end, String reference, String alternate, String strand) {
-            this.chromosome = chromosome;
-            this.start = start;
-            this.end = end;
-            this.reference = reference;
-            this.alternate = alternate;
-            this.strand = strand;
-        }
-
-        @Override
-        public String toString() {
-            final StringBuilder sb = new StringBuilder("SequenceLocation{");
-            sb.append("chromosome='").append(chromosome).append('\'');
-            sb.append(", start=").append(start);
-            sb.append(", end=").append(end);
-            sb.append(", reference='").append(reference).append('\'');
-            sb.append(", alternate='").append(alternate).append('\'');
-            sb.append(", strand='").append(strand).append('\'');
-            sb.append('}');
-            return sb.toString();
-        }
-
-        public String getChromosome() {
-            return chromosome;
-        }
-
-        public int getStart() {
-            return start;
-        }
-
-        public int getEnd() {
-            return end;
-        }
-
-        public String getReference() {
-            return reference;
-        }
-
-        public String getAlternate() {
-            return alternate;
-        }
-
-        public String getStrand() {
-            return strand;
-        }
-
-        public void setChromosome(String chromosome) {
-            this.chromosome = chromosome;
-        }
-
-        public void setStart(int start) {
-            this.start = start;
-        }
-
-        public void setEnd(int end) {
-            this.end = end;
-        }
-
-        public void setReference(String reference) {
-            this.reference = reference;
-        }
-
-        public void setAlternate(String alternate) {
-            this.alternate = alternate;
-        }
-
-        public void setStrand(String strand) {
-            this.strand = strand;
-        }
-    }
-
-
 }

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

@@ -19,6 +19,7 @@
 import com.fasterxml.jackson.databind.ObjectMapper;
 import org.opencb.biodata.models.variant.Variant;
 import org.opencb.biodata.models.variant.avro.VariantAnnotation;
+import org.opencb.cellbase.core.exception.CellBaseException;
 import org.opencb.cellbase.core.serializer.CellBaseSerializer;
 import org.opencb.cellbase.lib.EtlCommons;
 import org.opencb.cellbase.lib.builders.CellBaseBuilder;
@@ -99,7 +100,7 @@ public ClinicalVariantBuilder(Path clinvarXMLFile, Path clinvarSummaryFile, Path
         this.assembly = assembly;
     }
 
-    public void parse() throws IOException, RocksDBException {
+    public void parse() throws IOException, RocksDBException, CellBaseException {
 
         RocksDB rdb = null;
         Options dbOption = null;