storage: Fix compilation issues #TASK-6765

opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_4_0/storage/EnsureSampleIndexConfigurationIsAlwaysDefined.java

@@ -13,7 +13,7 @@
 import java.util.List;
 
 @Migration(id = "ensure_sample_index_configuration_is_defined",
-        description = "Ensure that the SampleIndexConfiguration object is correctly defined. #TASK-6765", version = "3.4.0",
+        description = "Ensure that the SampleIndexConfiguration object is correctly defined. #TASK-6765", version = "4.0.0",
         language = Migration.MigrationLanguage.JAVA,
         domain = Migration.MigrationDomain.STORAGE,
         patch = 1,

opencga-client/src/main/R/R/Clinical-methods.R

@@ -42,8 +42,6 @@
 #' | queryRgaVariant | /{apiVersion}/analysis/clinical/rga/variant/query | include, exclude, limit, skip, count, includeIndividual, skipIndividual, limitIndividual, sampleId, individualId, sex, phenotypes, disorders, numParents, geneId, geneName, chromosome, start, end, transcriptId, variants, dbSnps, knockoutType, filter, type, clinicalSignificance, populationFrequency, consequenceType, study |
 #' | summaryRgaVariant | /{apiVersion}/analysis/clinical/rga/variant/summary | limit, skip, count, sampleId, individualId, sex, phenotypes, disorders, numParents, geneId, geneName, chromosome, start, end, transcriptId, variants, dbSnps, knockoutType, filter, type, clinicalSignificance, populationFrequency, consequenceType, study |
 #' | search | /{apiVersion}/analysis/clinical/search | include, exclude, limit, skip, count, flattenAnnotations, study, id, uuid, type, disorder, files, sample, individual, proband, probandSamples, family, familyMembers, familyMemberSamples, panels, locked, analystId, priority, flags, creationDate, modificationDate, dueDate, qualityControlSummary, release, status, internalStatus, annotation, deleted |
-#' | queryVariant | /{apiVersion}/analysis/clinical/variant/query | include, exclude, limit, skip, count, approximateCount, approximateCountSamplingSize, savedFilter, includeInterpretation, id, region, type, study, file, filter, qual, fileData, sample, sampleData, sampleAnnotation, cohort, cohortStatsRef, cohortStatsAlt, cohortStatsMaf, cohortStatsMgf, cohortStatsPass, missingAlleles, missingGenotypes, score, family, familyDisorder, familySegregation, familyMembers, familyProband, gene, ct, xref, biotype, proteinSubstitution, conservation, populationFrequencyAlt, populationFrequencyRef, populationFrequencyMaf, transcriptFlag, geneTraitId, go, expression, proteinKeyword, drug, functionalScore, clinical, clinicalSignificance, clinicalConfirmedStatus, customAnnotation, panel, panelModeOfInheritance, panelConfidence, panelRoleInCancer, panelFeatureType, panelIntersection, trait |
-#' | search | /{apiVersion}/analysis/clinical/search | include, exclude, limit, skip, count, flattenAnnotations, study, id, uuid, type, disorder, files, sample, individual, proband, probandSamples, family, familyMembers, familyMemberSamples, panels, locked, analystId, priority, flags, creationDate, modificationDate, dueDate, qualityControlSummary, release, snapshot, status, internalStatus, annotation, deleted |
 #' | queryVariant | /{apiVersion}/analysis/clinical/variant/query | include, exclude, limit, skip, count, approximateCount, approximateCountSamplingSize, savedFilter, includeInterpretation, id, region, type, study, file, filter, qual, fileData, sample, sampleData, sampleAnnotation, cohort, cohortStatsRef, cohortStatsAlt, cohortStatsMaf, cohortStatsMgf, cohortStatsPass, missingAlleles, missingGenotypes, score, family, familyDisorder, familySegregation, familyMembers, familyProband, gene, ct, xref, biotype, proteinSubstitution, conservation, populationFrequencyAlt, populationFrequencyRef, populationFrequencyMaf, transcriptFlag, geneTraitId, go, expression, proteinKeyword, drug, functionalScore, clinical, clinicalSignificance, clinicalConfirmedStatus, customAnnotation, panel, panelModeOfInheritance, panelConfidence, panelRoleInCancer, panelFeatureType, panelIntersection, source, trait |
 #' | acl | /{apiVersion}/analysis/clinical/{clinicalAnalyses}/acl | clinicalAnalyses[*], study, member, silent |
 #' | delete | /{apiVersion}/analysis/clinical/{clinicalAnalyses}/delete | study, force, clinicalAnalyses[*] |

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

@@ -14,6 +14,7 @@
 import org.opencb.commons.datastore.core.QueryParam;
 import org.opencb.opencga.storage.core.exceptions.StorageEngineException;
 import org.opencb.opencga.storage.core.variant.adaptors.VariantDBAdaptor;
+import org.opencb.opencga.storage.core.variant.adaptors.VariantQuery;
 import org.opencb.opencga.storage.core.variant.adaptors.VariantQueryException;
 import org.opencb.opencga.storage.core.variant.adaptors.VariantQueryParam;
 import org.opencb.opencga.storage.core.variant.adaptors.iterators.VariantDBIterator;
@@ -40,7 +41,8 @@ public BreakendVariantQueryExecutor(String storageEngineId, ObjectMap options,
     }
 
     @Override
-    public boolean canUseThisExecutor(Query query, QueryOptions options) throws StorageEngineException {
+    public boolean canUseThisExecutor(ParsedVariantQuery variantQuery, QueryOptions options) throws StorageEngineException {
+        VariantQuery query = variantQuery.getQuery();
         return query.getString(VariantQueryParam.TYPE.key()).equals(VariantType.BREAKEND.name())
                 && VariantQueryUtils.isValidParam(query, VariantQueryParam.GENOTYPE);
     }

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

@@ -12,10 +12,7 @@
 import org.opencb.opencga.storage.core.metadata.models.SampleMetadata;
 import org.opencb.opencga.storage.core.metadata.models.Trio;
 import org.opencb.opencga.storage.core.variant.VariantStorageOptions;
-import org.opencb.opencga.storage.core.variant.adaptors.VariantField;
-import org.opencb.opencga.storage.core.variant.adaptors.VariantIterable;
-import org.opencb.opencga.storage.core.variant.adaptors.VariantQueryException;
-import org.opencb.opencga.storage.core.variant.adaptors.VariantQueryParam;
+import org.opencb.opencga.storage.core.variant.adaptors.*;
 import org.opencb.opencga.storage.core.variant.adaptors.iterators.UnionMultiVariantKeyIterator;
 import org.opencb.opencga.storage.core.variant.adaptors.iterators.VariantDBIterator;
 import org.opencb.opencga.storage.core.variant.adaptors.iterators.VariantDBIteratorWithCounts;
@@ -64,8 +61,8 @@ public CompoundHeterozygousQueryExecutor(VariantStorageMetadataManager metadataM
     }
 
     @Override
-    public boolean canUseThisExecutor(Query query, QueryOptions options) throws StorageEngineException {
-        return isValidParam(query, VariantQueryUtils.SAMPLE_COMPOUND_HETEROZYGOUS);
+    public boolean canUseThisExecutor(ParsedVariantQuery variantQuery, QueryOptions options) throws StorageEngineException {
+        return isValidParam(variantQuery.getQuery(), VariantQueryUtils.SAMPLE_COMPOUND_HETEROZYGOUS);
     }
 
     @Override

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

@@ -1,12 +1,14 @@
 package org.opencb.opencga.storage.core.variant.query.executors;
 
 import org.opencb.biodata.models.variant.Variant;
-import org.opencb.commons.datastore.core.*;
+import org.opencb.commons.datastore.core.ObjectMap;
+import org.opencb.commons.datastore.core.QueryOptions;
+import org.opencb.commons.datastore.core.QueryParam;
 import org.opencb.opencga.storage.core.exceptions.StorageEngineException;
-import org.opencb.opencga.storage.core.variant.query.ParsedVariantQuery;
-import org.opencb.opencga.storage.core.variant.query.VariantQueryResult;
 import org.opencb.opencga.storage.core.variant.adaptors.VariantDBAdaptor;
 import org.opencb.opencga.storage.core.variant.adaptors.VariantQueryParam;
+import org.opencb.opencga.storage.core.variant.query.ParsedVariantQuery;
+import org.opencb.opencga.storage.core.variant.query.VariantQueryResult;
 import org.opencb.opencga.storage.core.variant.query.VariantQueryUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -52,9 +54,9 @@ protected Object getOrIterator(ParsedVariantQuery variantQuery, boolean iterator
     }
 
     @Override
-    public boolean canUseThisExecutor(Query query, QueryOptions options) {
+    public boolean canUseThisExecutor(ParsedVariantQuery variantQuery, QueryOptions options) throws StorageEngineException {
         for (QueryParam unsupportedParam : UNSUPPORTED_PARAMS) {
-            if (VariantQueryUtils.isValidParam(query, unsupportedParam)) {
+            if (VariantQueryUtils.isValidParam(variantQuery.getQuery(), unsupportedParam)) {
                 logger.warn("Unsupported variant query param {} in {}",
                         unsupportedParam.key(),
                         DBAdaptorVariantQueryExecutor.class.getSimpleName());

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

@@ -8,6 +8,7 @@
 import org.opencb.opencga.storage.core.metadata.models.CohortMetadata;
 import org.opencb.opencga.storage.core.metadata.models.StudyMetadata;
 import org.opencb.opencga.storage.core.variant.adaptors.GenotypeClass;
+import org.opencb.opencga.storage.core.variant.adaptors.VariantQuery;
 import org.opencb.opencga.storage.core.variant.adaptors.VariantQueryParam;
 import org.opencb.opencga.storage.core.variant.adaptors.iterators.VariantDBIterator;
 import org.opencb.opencga.storage.core.variant.query.*;
@@ -34,7 +35,8 @@ public NoOpVariantQueryExecutor(VariantStorageMetadataManager metadataManager, S
     }
 
     @Override
-    public boolean canUseThisExecutor(Query query, QueryOptions options) throws StorageEngineException {
+    public boolean canUseThisExecutor(ParsedVariantQuery variantQuery, QueryOptions options) throws StorageEngineException {
+        VariantQuery query = variantQuery.getQuery();
         boolean sampleQuery = false;
         String sample = null;
         if (VariantQueryUtils.isValidParam(query, VariantQueryParam.GENOTYPE)) {

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

@@ -63,6 +63,12 @@ public static void setDefaultTimeout(QueryOptions queryOptions, ObjectMap config
         queryOptions.put(QueryOptions.TIMEOUT, timeout);
     }
 
+    /**
+     * Determine if this VariantQueryExecutor can run the given query.
+     * @param variantQuery    Query to execute
+     * @return         True if this variant query executor is valid for the query
+     * @throws StorageEngineException if there is an error
+     */
     public final boolean canUseThisExecutor(ParsedVariantQuery variantQuery) throws StorageEngineException {
         boolean canUseThisExecutor = canUseThisExecutor(variantQuery, variantQuery.getInputOptions());
         if (canUseThisExecutor) {
@@ -77,7 +83,7 @@ public final boolean canUseThisExecutor(ParsedVariantQuery variantQuery) throws
     }
 
     /**
-     * Determine if this VariantQueryExecutor can run the given query.
+     * Internal method to determine if this VariantQueryExecutor can run the given query.
      * @param variantQuery    Query to execute
      * @param options  Options for the query
      * @return         True if this variant query executor is valid for the query

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

@@ -7,6 +7,7 @@
 import org.opencb.opencga.storage.core.exceptions.StorageEngineException;
 import org.opencb.opencga.storage.core.exceptions.VariantSearchException;
 import org.opencb.opencga.storage.core.variant.adaptors.VariantDBAdaptor;
+import org.opencb.opencga.storage.core.variant.adaptors.VariantQuery;
 import org.opencb.opencga.storage.core.variant.adaptors.VariantQueryException;
 import org.opencb.opencga.storage.core.variant.query.ParsedVariantQuery;
 import org.opencb.opencga.storage.core.variant.search.solr.VariantSearchManager;
@@ -28,7 +29,8 @@ public SamplesSearchIndexVariantQueryExecutor(VariantDBAdaptor dbAdaptor, Varian
     }
 
     @Override
-    public boolean canUseThisExecutor(Query query, QueryOptions options) throws StorageEngineException {
+    public boolean canUseThisExecutor(ParsedVariantQuery variantQuery, QueryOptions options) throws StorageEngineException {
+        VariantQuery query = variantQuery.getQuery();
         String samplesCollection = inferSpecificSearchIndexSamplesCollection(query, options, getMetadataManager(), dbName);
         return samplesCollection != null && searchActiveAndAlive(samplesCollection);
     }

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

@@ -11,10 +11,7 @@
 import org.opencb.opencga.storage.core.exceptions.StorageEngineException;
 import org.opencb.opencga.storage.core.exceptions.VariantSearchException;
 import org.opencb.opencga.storage.core.variant.VariantStorageEngine;
-import org.opencb.opencga.storage.core.variant.adaptors.VariantDBAdaptor;
-import org.opencb.opencga.storage.core.variant.adaptors.VariantField;
-import org.opencb.opencga.storage.core.variant.adaptors.VariantQueryException;
-import org.opencb.opencga.storage.core.variant.adaptors.VariantQueryParam;
+import org.opencb.opencga.storage.core.variant.adaptors.*;
 import org.opencb.opencga.storage.core.variant.query.ParsedVariantQuery;
 import org.opencb.opencga.storage.core.variant.query.VariantQueryResult;
 import org.opencb.opencga.storage.core.variant.query.VariantQueryUtils;
@@ -76,7 +73,8 @@ public SearchIndexVariantQueryExecutor setIntersectParamsThreshold(int intersect
     }
 
     @Override
-    public boolean canUseThisExecutor(Query query, QueryOptions options) throws StorageEngineException {
+    public boolean canUseThisExecutor(ParsedVariantQuery variantQuery, QueryOptions options) throws StorageEngineException {
+        VariantQuery query = variantQuery.getQuery();
         return doQuerySearchManager(query, options) || doIntersectWithSearch(query, options);
     }
 

opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/query/executors/VariantQueryExecutorTest.java

@@ -213,15 +213,15 @@ public VariantQueryResult<Variant> testQuery(Query query, QueryOptions options,
         logger.info("########## TEST QUERY :" + query.toJson());
         logger.info("####################################################");
         logger.info("## Allowed VariantQueryExecutors:");
+        ParsedVariantQuery variantQuery = variantStorageEngine.parseQuery(query, options);
         for (VariantQueryExecutor variantQueryExecutor : variantQueryExecutors) {
-            if (variantQueryExecutor.canUseThisExecutor(query, options)) {
+            if (variantQueryExecutor.canUseThisExecutor(variantQuery, options)) {
                 logger.info("## - " + variantQueryExecutor.getClass().getSimpleName());
             }
         }
         logger.info("## Using DBAdaptorVariantQueryExecutor for expected results");
-        Assert.assertTrue(dbQueryExecutor.canUseThisExecutor(query, options));
+        Assert.assertTrue(dbQueryExecutor.canUseThisExecutor(variantQuery, options));
 
-        ParsedVariantQuery variantQuery = variantStorageEngine.parseQuery(query, options);
         VariantQueryResult<Variant> expected = dbQueryExecutor.get(variantQuery);
 
         VariantQueryResult<Variant> unfilteredResult = null;
@@ -265,7 +265,7 @@ public VariantQueryResult<Variant> testQuery(Query query, QueryOptions options,
         }
 
         for (VariantQueryExecutor variantQueryExecutor : variantQueryExecutors) {
-            if (variantQueryExecutor.canUseThisExecutor(query, options)) {
+            if (variantQueryExecutor.canUseThisExecutor(variantQuery, options)) {
                 logger.info("");
                 logger.info("###################");
                 logger.info("### Testing " + variantQueryExecutor.getClass().getSimpleName());

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

@@ -7,6 +7,7 @@
 import org.opencb.commons.datastore.core.QueryOptions;
 import org.opencb.opencga.storage.core.variant.VariantStorageOptions;
 import org.opencb.opencga.storage.core.variant.adaptors.VariantDBAdaptor;
+import org.opencb.opencga.storage.core.variant.adaptors.VariantQuery;
 import org.opencb.opencga.storage.core.variant.query.ParsedQuery;
 import org.opencb.opencga.storage.core.variant.query.ParsedVariantQuery;
 import org.opencb.opencga.storage.core.variant.query.VariantQueryResult;
@@ -43,8 +44,8 @@ public HBaseColumnIntersectVariantQueryExecutor(VariantDBAdaptor dbAdaptor, Stri
     }
 
     @Override
-    public boolean canUseThisExecutor(Query query, QueryOptions options) {
-
+    public boolean canUseThisExecutor(ParsedVariantQuery variantQuery, QueryOptions options) {
+        VariantQuery query = variantQuery.getQuery();
         if (!options.getBoolean(HBASE_COLUMN_INTERSECT, ACTIVE_BY_DEFAULT)) {
             // HBase column intersect not active
             return false;

opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/SampleIndexMendelianErrorQueryExecutor.java

@@ -9,7 +9,6 @@
 import org.opencb.biodata.tools.pedigree.MendelianError;
 import org.opencb.commons.datastore.core.DataResult;
 import org.opencb.commons.datastore.core.ObjectMap;
-import org.opencb.commons.datastore.core.Query;
 import org.opencb.commons.datastore.core.QueryOptions;
 import org.opencb.opencga.storage.core.metadata.models.SampleMetadata;
 import org.opencb.opencga.storage.core.metadata.models.Trio;
@@ -33,10 +32,10 @@ public SampleIndexMendelianErrorQueryExecutor(VariantHadoopDBAdaptor dbAdaptor,
     }
 
     @Override
-    public boolean canUseThisExecutor(Query query, QueryOptions options) {
-        if (VariantQueryUtils.isValidParam(query, VariantQueryUtils.SAMPLE_MENDELIAN_ERROR)
-                || VariantQueryUtils.isValidParam(query, VariantQueryUtils.SAMPLE_DE_NOVO)
-                || VariantQueryUtils.isValidParam(query, VariantQueryUtils.SAMPLE_DE_NOVO_STRICT)) {
+    public boolean canUseThisExecutor(ParsedVariantQuery query, QueryOptions options) {
+        if (VariantQueryUtils.isValidParam(query.getQuery(), VariantQueryUtils.SAMPLE_MENDELIAN_ERROR)
+                || VariantQueryUtils.isValidParam(query.getQuery(), VariantQueryUtils.SAMPLE_DE_NOVO)
+                || VariantQueryUtils.isValidParam(query.getQuery(), VariantQueryUtils.SAMPLE_DE_NOVO_STRICT)) {
             return super.canUseThisExecutor(query, options);
         } else {
             return false;

opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/SampleIndexVariantQueryExecutor.java

@@ -58,9 +58,9 @@ public SampleIndexVariantQueryExecutor(VariantHadoopDBAdaptor dbAdaptor, SampleI
     }
 
     @Override
-    public boolean canUseThisExecutor(Query query, QueryOptions options) {
+    public boolean canUseThisExecutor(ParsedVariantQuery query, QueryOptions options) {
         if (options.getBoolean(SAMPLE_INDEX_INTERSECT, true)) {
-            return SampleIndexQueryParser.validSampleIndexQuery(query);
+            return SampleIndexQueryParser.validSampleIndexQuery(query.getQuery());
         }
         return false;
     }