Merge pull request #2201 from opencb/TASK-2420

TASK-2420 - Sample-variant-stats error 'Unable to index with indexId='ALL' if query is not empty'

opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/manager/VariantCatalogQueryUtils.java

@@ -719,6 +719,9 @@ public Query parseQuery(Query query, QueryOptions queryOptions, CellBaseUtils ce
                 panelGenes.addAll(xrefs.getGenes());
                 query.put(GENE.key(), panelGenes);
                 query.put(SKIP_MISSING_GENES, true);
+
+                // Remove "false" value if exists
+                query.remove(PANEL_INTERSECTION.key());
             } else {
                 logger.info("Panel intersection");
                 // Intersect panel with query!

opencga-analysis/src/test/java/org/opencb/opencga/analysis/variant/VariantAnalysisTest.java

@@ -119,7 +119,7 @@ public class VariantAnalysisTest {
     public static Object[][] parameters() {
         return new Object[][]{
                 {MongoDBVariantStorageEngine.STORAGE_ENGINE_ID},
-//                {HadoopVariantStorageEngine.STORAGE_ENGINE_ID}
+                {HadoopVariantStorageEngine.STORAGE_ENGINE_ID}
         };
     }
 

opencga-core/src/main/java/org/opencb/opencga/core/models/variant/AnnotationVariantQueryParams.java

@@ -1,5 +1,6 @@
 package org.opencb.opencga.core.models.variant;
 
+import com.fasterxml.jackson.annotation.JsonInclude;
 import org.opencb.commons.datastore.core.Query;
 import org.opencb.opencga.core.tools.ToolParams;
 
@@ -12,6 +13,7 @@ public class AnnotationVariantQueryParams extends ToolParams {
     private String panelModeOfInheritance;
     private String panelConfidence;
     private String panelRoleInCancer;
+    @JsonInclude(JsonInclude.Include.NON_DEFAULT)
     private boolean panelIntersection;
     private String cohortStatsRef;
     private String cohortStatsAlt;
@@ -28,6 +30,7 @@ public class AnnotationVariantQueryParams extends ToolParams {
     private String functionalScore;
     private String clinical;
     private String clinicalSignificance;
+    @JsonInclude(JsonInclude.Include.NON_DEFAULT)
     private boolean clinicalConfirmedStatus;
 
     public AnnotationVariantQueryParams() {

opencga-core/src/main/java/org/opencb/opencga/core/models/variant/VariantExportParams.java

@@ -16,6 +16,7 @@
 
 package org.opencb.opencga.core.models.variant;
 
+import com.fasterxml.jackson.annotation.JsonInclude;
 import org.opencb.commons.datastore.core.Query;
 
 public class VariantExportParams extends VariantQueryParams {
@@ -28,6 +29,7 @@ public class VariantExportParams extends VariantQueryParams {
     private String exclude;
     private Integer limit;
     private Integer skip;
+    @JsonInclude(JsonInclude.Include.NON_DEFAULT)
     private boolean summary;
 
     public VariantExportParams() {

opencga-core/src/main/java/org/opencb/opencga/core/models/variant/VariantIndexParams.java

@@ -17,8 +17,6 @@
 package org.opencb.opencga.core.models.variant;
 
 import org.opencb.biodata.models.variant.metadata.Aggregation;
-import org.opencb.opencga.core.api.ParamConstants;
-import org.opencb.opencga.core.common.YesNoAuto;
 import org.opencb.opencga.core.tools.ToolParams;
 
 public class VariantIndexParams extends ToolParams {
@@ -98,12 +96,12 @@ public VariantIndexParams(String file,
     private String loadHomRef;
     private String postLoadCheck;
     private String includeGenotypes;
-    private String includeSampleData = ParamConstants.ALL;
+    private String includeSampleData;
     private String merge;
     private String deduplicationPolicy;
 
     private boolean calculateStats;
-    private Aggregation aggregated = Aggregation.NONE;
+    private Aggregation aggregated;
     private String aggregationMappingFile;
 
     private boolean annotate;

opencga-core/src/main/java/org/opencb/opencga/core/models/variant/VariantQueryParams.java

@@ -16,10 +16,12 @@
 
 package org.opencb.opencga.core.models.variant;
 
+import com.fasterxml.jackson.annotation.JsonInclude;
 import org.opencb.commons.datastore.core.Query;
 
 /**
- * Do not use native values (like boolean or int), so they are null by default.
+ * When using native values (like boolean or int), set add
+ * {@code @JsonInclude(JsonInclude.Include.NON_DEFAULT)} so they are null by default.
  */
 public class VariantQueryParams extends BasicVariantQueryParams {
 
@@ -34,7 +36,9 @@ public class VariantQueryParams extends BasicVariantQueryParams {
     private String includeSample;
     private String includeFile;
     private String includeSampleData;
+    @JsonInclude(JsonInclude.Include.NON_DEFAULT)
     private boolean includeSampleId;
+    @JsonInclude(JsonInclude.Include.NON_DEFAULT)
     private boolean includeGenotype;
 
     private String file;
@@ -79,7 +83,9 @@ public class VariantQueryParams extends BasicVariantQueryParams {
     private String customAnnotation;
 
     private String unknownGenotype;
+    @JsonInclude(JsonInclude.Include.NON_DEFAULT)
     private boolean sampleMetadata = false;
+    @JsonInclude(JsonInclude.Include.NON_DEFAULT)
     private boolean sort = false;
 
 

opencga-core/src/test/java/org/opencb/opencga/core/models/variant/VariantQueryParamsTest.java

@@ -0,0 +1,15 @@
+package org.opencb.opencga.core.models.variant;
+
+import org.junit.Test;
+
+import static org.junit.Assert.*;
+
+public class VariantQueryParamsTest {
+
+    @Test
+    public void test() {
+        VariantQueryParams params = new VariantQueryParams();
+        assertEquals(0, params.toObjectMap().size());
+        assertEquals(0, params.toParams().size());
+    }
+}

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

@@ -125,7 +125,7 @@ public final class VariantQueryParam implements QueryParam {
 
     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.";
-    public static final VariantQueryParam SAMPLE_METADATA = new VariantQueryParam("sampleMetadata", TEXT_ARRAY, SAMPLE_METADATA_DESCR);
+    public static final VariantQueryParam SAMPLE_METADATA = new VariantQueryParam("sampleMetadata", BOOLEAN, SAMPLE_METADATA_DESCR);
 
     public static final String INCLUDE_SAMPLE_DATA_DESCR
             = "List of Sample Data keys (i.e. FORMAT column from VCF file) from Sample Data to include in the output. e.g: DP,AD. "

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

@@ -9,10 +9,10 @@
 import org.opencb.biodata.models.variant.avro.ClinicalSignificance;
 import org.opencb.biodata.models.variant.avro.VariantType;
 import org.opencb.biodata.models.variant.metadata.VariantFileHeaderComplexLine;
-import org.opencb.opencga.core.models.variant.VariantAnnotationConstants;
 import org.opencb.commons.datastore.core.Query;
 import org.opencb.commons.datastore.core.QueryOptions;
 import org.opencb.commons.datastore.core.QueryParam;
+import org.opencb.opencga.core.models.variant.VariantAnnotationConstants;
 import org.opencb.opencga.storage.core.metadata.VariantStorageMetadataManager;
 import org.opencb.opencga.storage.core.metadata.models.SampleMetadata;
 import org.opencb.opencga.storage.core.metadata.models.StudyMetadata;
@@ -272,6 +272,11 @@ protected void preProcessAnnotationParams(Query query) {
             query.put(TYPE.key(), new ArrayList<>(types));
         }
 
+        if (VariantQueryUtils.isValidParam(query, ANNOT_CLINICAL_CONFIRMED_STATUS)
+                && !query.getBoolean(ANNOT_CLINICAL_CONFIRMED_STATUS.key())) {
+            // Remove false value if exists
+            query.remove(ANNOT_CLINICAL_CONFIRMED_STATUS.key());
+        }
         if (VariantQueryUtils.isValidParam(query, ANNOT_CLINICAL_SIGNIFICANCE)) {
             String v = query.getString(ANNOT_CLINICAL_SIGNIFICANCE.key());
             QueryOperation operator = VariantQueryUtils.checkOperator(v);
@@ -716,6 +721,10 @@ protected void preProcessStudyParams(Query query, QueryOptions options) {
             formats = Collections.singletonList(NONE);
         }
 
+        if (VariantQueryUtils.isValidParam(query, SAMPLE_METADATA) && !query.getBoolean(SAMPLE_METADATA.key())) {
+            // Remove false value if exists
+            query.remove(SAMPLE_METADATA.key());
+        }
         query.put(INCLUDE_SAMPLE_DATA.key(), formats);
         query.remove(INCLUDE_GENOTYPE.key(), formats);
     }