TASK-5878 - Unable to filter by dbSNP (rsIds) and HGVS id in variant browser

opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/utils/CellBaseUtils.java

@@ -343,6 +343,7 @@ public List<Variant> getVariants(List<String> variantsStr) {
         List<Variant> variants = new ArrayList<>(variantsStr.size());
         List<CellBaseDataResult<Variant>> response = null;
         try {
+            // FIXME: This method should call genomic/variant/snp/search
             response = checkNulls(cellBaseClient.getVariantClient().get(variantsStr,
                     new QueryOptions(QueryOptions.INCLUDE,
                             VariantField.CHROMOSOME.fieldName() + ","

opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/VariantStorageEngine.java

@@ -1192,8 +1192,36 @@ public VariantQueryResult<Variant> getCompoundHeterozygous(String study, String
         return get(query, options);
     }
 
-    public DataResult<Variant> getSampleData(String variant, String study, QueryOptions options) throws StorageEngineException {
-        return new VariantSampleDataManager(getDBAdaptor()).getSampleData(variant, study, options);
+    public DataResult<Variant> getSampleData(String variantStr, String study, QueryOptions options) throws StorageEngineException {
+        final Variant variant = getVariant(variantStr);
+        return getVariantSampleDataManager().getSampleData(variant, study, options);
+    }
+
+    public Variant getVariant(String variantStr) {
+        final Variant variant;
+        if (VariantQueryUtils.isVariantId(variantStr)) {
+            variant = new Variant(variantStr);
+        } else if (VariantQueryUtils.isVariantAccession(variantStr)) {
+            VariantQueryResult<Variant> result = get(new Query(VariantQueryParam.ANNOT_XREF.key(), variantStr),
+                    new QueryOptions(QueryOptions.INCLUDE, VariantField.ID).append(QueryOptions.LIMIT, 1).append(QueryOptions.COUNT, true));
+            if (result.getNumMatches() > 1) {
+                throw new VariantQueryException("Not unique variant identifier '" + variantStr + "'."
+                        + " Found " + result.getNumMatches() + " results");
+            } else if (result.getNumResults() == 1) {
+                variant = result.first();
+            } else {
+                throw VariantQueryException.variantNotFound(variantStr);
+            }
+        } else {
+            throw new VariantQueryException("Variant not valid. Variant = '" + variantStr + "'. Supported values:"
+                    + " {chr}:{start}:{end}:{ref}:{alt}, rs{id}");
+        }
+        variant.setId(variant.toString());
+        return variant;
+    }
+
+    protected VariantSampleDataManager getVariantSampleDataManager() throws StorageEngineException {
+        return new VariantSampleDataManager(getDBAdaptor());
     }
 
     public VariantQueryResult<Variant> get(Query query, QueryOptions options) {

opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/adaptors/VariantQuery.java

@@ -105,6 +105,15 @@ public VariantQuery sample(String value) {
         return sample(VariantQueryUtils.QueryOperation.OR, value);
     }
 
+    public VariantQuery sample(List<String> value) {
+        return sample(VariantQueryUtils.QueryOperation.OR, value);
+    }
+
+    public VariantQuery sample(VariantQueryUtils.QueryOperation operation, List<String> value) {
+        put(VariantQueryParam.SAMPLE.key(), value.stream().collect(Collectors.joining(operation.separator())));
+        return this;
+    }
+
     public VariantQuery sample(String... value) {
         return sample(VariantQueryUtils.QueryOperation.OR, value);
     }
@@ -178,8 +187,9 @@ public VariantQuery includeSampleId(boolean value) {
         put(VariantQueryParam.INCLUDE_SAMPLE_ID.key(), value);
         return this;
     }
-    public String includeSampleId() {
-        return getString(VariantQueryParam.INCLUDE_SAMPLE_ID.key());
+
+    public boolean includeSampleId() {
+        return getBoolean(VariantQueryParam.INCLUDE_SAMPLE_ID.key());
     }
 
     public VariantQuery sampleMetadata(boolean value) {

opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/adaptors/VariantQueryParam.java

@@ -41,7 +41,7 @@ public final class VariantQueryParam implements QueryParam {
     private static final String ACCEPTS_AND_OR = "Accepts AND (" + AND + ") and OR (" + OR + ") operators.";
 
     public static final String ID_DESCR
-            = "List of IDs, these can be rs IDs (dbSNP) or variants in the format chrom:start:ref:alt, e.g. rs116600158,19:7177679:C:T";
+            = "List of variant IDs in the format chrom:start:ref:alt, e.g. 19:7177679:C:T";
     public static final VariantQueryParam ID = new VariantQueryParam("id", TEXT_ARRAY, ID_DESCR);
 
     public static final String REGION_DESCR
@@ -121,7 +121,7 @@ public final class VariantQueryParam implements QueryParam {
 
     public static final String INCLUDE_SAMPLE_ID_DESCR
             = "Include sampleId on each result";
-    public static final VariantQueryParam INCLUDE_SAMPLE_ID = new VariantQueryParam("includeSampleId", TEXT_ARRAY, INCLUDE_SAMPLE_ID_DESCR);
+    public static final VariantQueryParam INCLUDE_SAMPLE_ID = new VariantQueryParam("includeSampleId", BOOLEAN, INCLUDE_SAMPLE_ID_DESCR);
 
     public static final String SAMPLE_METADATA_DESCR
             = "Return the samples metadata group by study. Sample names will appear in the same order as their corresponding genotypes.";
@@ -215,7 +215,7 @@ public final class VariantQueryParam implements QueryParam {
 
     public static final String ANNOT_XREF_DESCR
             = "List of any external reference, these can be genes, proteins or variants. "
-            + "Accepted IDs include HGNC, Ensembl genes, dbSNP, ClinVar, HPO, Cosmic, ...";
+            + "Accepted IDs include HGNC, Ensembl genes, dbSNP, ClinVar, HPO, Cosmic, HGVS ...";
     public static final VariantQueryParam ANNOT_XREF = new VariantQueryParam("xref", TEXT_ARRAY, ANNOT_XREF_DESCR);
 
     public static final String GENE_DESCR

opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/adaptors/sample/VariantSampleDataManager.java

@@ -40,13 +40,13 @@ public VariantSampleDataManager(VariantDBAdaptor dbAdaptor) {
 
     }
 
-    public final DataResult<Variant> getSampleData(String variant, String study, QueryOptions options) {
+    public final DataResult<Variant> getSampleData(Variant variant, String study, QueryOptions options) {
         options = options == null ? new QueryOptions() : options;
         int sampleLimit = options.getInt(SAMPLE_BATCH_SIZE, SAMPLE_BATCH_SIZE_DEFAULT);
         return getSampleData(variant, study, options, sampleLimit);
     }
 
-    public final DataResult<Variant> getSampleData(String variant, String study, QueryOptions options, int sampleLimit) {
+    public final DataResult<Variant> getSampleData(Variant variant, String study, QueryOptions options, int sampleLimit) {
         options = options == null ? new QueryOptions() : options;
 
 
@@ -77,7 +77,7 @@ public final DataResult<Variant> getSampleData(String variant, String study, Que
     }
 
     protected DataResult<Variant> getSampleData(
-            String variantStr, String study, QueryOptions options, List<String> includeSamples, Set<String> genotypes,
+            Variant variant, String study, QueryOptions options, List<String> includeSamples, Set<String> genotypes,
             int sampleLimit) {
         options = options == null ? new QueryOptions() : options;
         Set<VariantField> includeFields = VariantField.getIncludeFields(options);
@@ -98,7 +98,7 @@ protected DataResult<Variant> getSampleData(
         int queries = 0;
         while (true) {
             queries++;
-            Query query = new Query(VariantQueryParam.ID.key(), variantStr)
+            Query query = new Query(VariantQueryParam.ID.key(), variant.toString())
                     .append(VariantQueryParam.STUDY.key(), study)
                     .append(VariantQueryParam.INCLUDE_GENOTYPE.key(), options.get(VariantQueryParam.INCLUDE_GENOTYPE.key()))
                     .append(VariantQueryParam.INCLUDE_SAMPLE_DATA.key(), options.get(VariantQueryParam.INCLUDE_SAMPLE_DATA.key()))
@@ -130,7 +130,7 @@ protected DataResult<Variant> getSampleData(
 
             DataResult<Variant> result = dbAdaptor.get(query, variantQueryOptions);
             if (result.getNumResults() == 0) {
-                throw VariantQueryException.variantNotFound(variantStr);
+                throw VariantQueryException.variantNotFound(variant.toString());
             }
             dbTime += result.getTime();
             Variant partialVariant = result.first();
@@ -199,7 +199,7 @@ protected DataResult<Variant> getSampleData(
             }
         }
 
-        Variant variant = new Variant(variantStr);
+        variant = new Variant(variant.toString());
         variant.setAnnotation(annotation);
         StudyEntry studyEntry = new StudyEntry(study);
         variant.addStudyEntry(studyEntry);

opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/annotation/converters/VariantAnnotationModelUtils.java

@@ -0,0 +1,106 @@
+package org.opencb.opencga.storage.core.variant.annotation.converters;
+
+import org.apache.commons.collections4.CollectionUtils;
+import org.opencb.biodata.models.variant.avro.*;
+
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+public class VariantAnnotationModelUtils {
+
+    /**
+     * Extracts all the XRefs from a VariantAnnotation object.
+     * Includes:
+     * - annotation.id
+     * - annotation.xrefs.id
+     * - annotation.hgvs
+     * - annotation.consequenceTypes.geneName
+     * - annotation.consequenceTypes.geneId
+     * - annotation.consequenceTypes.ensemblGeneId
+     * - annotation.consequenceTypes.transcriptId
+     * - annotation.consequenceTypes.ensemblTranscriptId
+     * - annotation.consequenceTypes.hgvs
+     * - annotation.consequenceTypes.proteinVariantAnnotation.uniprotAccession
+     * - annotation.consequenceTypes.proteinVariantAnnotation.uniprotName
+     * - annotation.consequenceTypes.proteinVariantAnnotation.uniprotVariantId
+     * - annotation.consequenceTypes.proteinVariantAnnotation.features.id
+     * - annotation.traitAssociation.id
+     * - annotation.geneTraitAssociation.hpo
+     * - annotation.geneTraitAssociation.id
+     *
+     * @param variantAnnotation VariantAnnotation object
+     * @return Set of XRefs
+     */
+    public Set<String> extractXRefs(VariantAnnotation variantAnnotation) {
+        Set<String> xrefs = new HashSet<>();
+
+        if (variantAnnotation == null) {
+            return xrefs;
+        }
+
+        xrefs.add(variantAnnotation.getId());
+
+        if (variantAnnotation.getXrefs() != null) {
+            for (Xref xref : variantAnnotation.getXrefs()) {
+                if (xref != null) {
+                    xrefs.add(xref.getId());
+                }
+            }
+        }
+
+        if (variantAnnotation.getHgvs() != null) {
+            xrefs.addAll(variantAnnotation.getHgvs());
+        }
+
+        List<ConsequenceType> consequenceTypes = variantAnnotation.getConsequenceTypes();
+        if (consequenceTypes != null) {
+            for (ConsequenceType conseqType : consequenceTypes) {
+                xrefs.add(conseqType.getGeneName());
+                xrefs.add(conseqType.getGeneId());
+                xrefs.add(conseqType.getEnsemblGeneId());
+                xrefs.add(conseqType.getTranscriptId());
+                xrefs.add(conseqType.getEnsemblTranscriptId());
+
+                if (conseqType.getHgvs() != null) {
+                    xrefs.addAll(conseqType.getHgvs());
+                }
+
+                ProteinVariantAnnotation protVarAnnotation = conseqType.getProteinVariantAnnotation();
+                if (protVarAnnotation != null) {
+
+                    xrefs.add(protVarAnnotation.getUniprotAccession());
+                    xrefs.add(protVarAnnotation.getUniprotName());
+                    xrefs.add(protVarAnnotation.getUniprotVariantId());
+
+                    if (protVarAnnotation.getFeatures() != null) {
+                        for (ProteinFeature proteinFeature : protVarAnnotation.getFeatures()) {
+                            xrefs.add(proteinFeature.getId());
+                        }
+                    }
+                }
+            }
+
+        }
+
+        if (CollectionUtils.isNotEmpty(variantAnnotation.getTraitAssociation())) {
+            for (EvidenceEntry evidenceEntry : variantAnnotation.getTraitAssociation()) {
+                xrefs.add(evidenceEntry.getId());
+            }
+        }
+
+        if (variantAnnotation.getGeneTraitAssociation() != null) {
+            for (GeneTraitAssociation geneTrait : variantAnnotation.getGeneTraitAssociation()) {
+                xrefs.add(geneTrait.getHpo());
+                xrefs.add(geneTrait.getId());
+            }
+        }
+
+        // Remove empty strings and nulls
+        xrefs.remove("");
+        xrefs.remove(null);
+
+        return xrefs;
+    }
+
+}

opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/query/ParsedVariantQuery.java

@@ -226,5 +226,16 @@ public List<String> getIDsAndXrefs() {
         public boolean isEmpty() {
             return genes.isEmpty() && variants.isEmpty() && ids.isEmpty() && otherXrefs.isEmpty();
         }
+
+        @Override
+        public String toString() {
+            final StringBuilder sb = new StringBuilder("VariantQueryXref{");
+            sb.append("genes=").append(genes);
+            sb.append(", variants=").append(variants);
+            sb.append(", ids=").append(ids);
+            sb.append(", otherXrefs=").append(otherXrefs);
+            sb.append('}');
+            return sb.toString();
+        }
     }
 }

opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/query/VariantQueryParser.java

@@ -851,7 +851,11 @@ public static ParsedVariantQuery.VariantQueryXref parseXrefs(Query query) {
                 if (variant != null) {
                     xrefs.getVariants().add(variant);
                 } else {
-                    if (isVariantAccession(value) || isClinicalAccession(value) || isGeneAccession(value)) {
+                    if (isVariantAccession(value)
+                            || isClinicalAccession(value)
+                            || isGeneAccession(value)
+                            || isHGVS(value)
+                            || isProteinFeatureId(value)) {
                         xrefs.getOtherXrefs().add(value);
                     } else {
                         genes.add(value);

opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/query/VariantQueryUtils.java

@@ -466,6 +466,20 @@ public static boolean isVariantAccession(String value) {
         return value.startsWith("rs") || value.startsWith("VAR_");
     }
 
+    /**
+     * Determines if the given value is a HGVS.
+     *
+     * @param value Value to check
+     * @return If is a known accession
+     */
+    public static boolean isHGVS(String value) {
+        // Check regex ':[cnpg].'
+        // HGVC examples :
+        //  - "1:g.65325832G>A"
+        //  - "1:g.65325832_65325833insA"
+        return value.contains(":c.") || value.contains(":n.") || value.contains(":p.") || value.contains(":g.");
+    }
+
     /**
      * Determines if the given value is a known clinical accession or not.
      * <p>
@@ -494,6 +508,18 @@ public static boolean isGeneAccession(String value) {
         return isHpo(value) || value.startsWith("OMIM:") || value.startsWith("umls:");
     }
 
+    /**
+     * Determines if the given value is a valid protein feature id.
+     * <p>
+     *     Protein feature id starts with 'PRO_', 'VAR_' or 'VSP_'
+     *
+     * @param value Value to check
+     * @return If is a known accession
+     */
+    public static boolean isProteinFeatureId(String value) {
+        return value.startsWith("PRO_") |  value.startsWith("VAR_") |  value.startsWith("VSP_");
+    }
+
     /**
      * Determines if the given value is a HPO term or not.
      * <p>

opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/query/executors/AbstractTwoPhasedVariantQueryExecutor.java

@@ -133,7 +133,7 @@ protected boolean shouldGetApproximateCount(QueryOptions options, boolean iterat
 //    }
 
     protected int getLimit(QueryOptions options) {
-        return options.getInt(QueryOptions.LIMIT);
+        return options.getInt(QueryOptions.LIMIT, -1);
     }
 
     protected int getSkip(QueryOptions options) {