storage: Add default limit to variant annotation query. #830

opencb · Jul 19, 2018 · 2141435 · 2141435
1 parent d3003fa
commit 2141435
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Showing 3 changed files with 29 additions and 22 deletions.
diff --git a/.../src/main/java/org/opencb/opencga/storage/core/manager/variant/VariantStorageManager.java b/.../src/main/java/org/opencb/opencga/storage/core/manager/variant/VariantStorageManager.java
@@ -68,12 +68,11 @@
 import static org.opencb.commons.datastore.core.QueryOptions.empty;
 import static org.opencb.opencga.catalog.db.api.StudyDBAdaptor.QueryParams.FQN;
 import static org.opencb.opencga.storage.core.variant.adaptors.VariantQueryParam.*;
+import static org.opencb.opencga.storage.core.variant.adaptors.VariantQueryUtils.addDefaultLimit;
+import static org.opencb.opencga.storage.core.variant.adaptors.VariantQueryUtils.getDefaultLimit;
 
 public class VariantStorageManager extends StorageManager {
 
-    public static final int LIMIT_DEFAULT = 1000;
-    public static final int LIMIT_MAX = 5000;
-
     private final VariantCatalogQueryUtils catalogUtils;
 
     public VariantStorageManager(CatalogManager catalogManager, StorageEngineFactory storageEngineFactory) {
@@ -562,25 +561,6 @@ Map<String, List<Sample>> checkSamplesPermissions(Query query, QueryOptions quer
 
     // Some aux methods
 
-    private int addDefaultLimit(QueryOptions queryOptions) {
-        return addDefaultLimit(queryOptions, LIMIT_MAX, LIMIT_DEFAULT);
-    }
-
-    private int addDefaultLimit(QueryOptions queryOptions, int limitMax, int limitDefault) {
-        // Add default limit
-        int limit = getDefaultLimit(queryOptions.getInt(QueryOptions.LIMIT, -1), limitMax, limitDefault);
-        queryOptions.put(QueryOptions.LIMIT,  limit);
-        return limit;
-    }
-
-    private int getDefaultLimit(int limit, int limitMax, int limitDefault) {
-        if (limit > limitMax) {
-            logger.info("Unable to return more than {} variants. Change limit from {} to {}", limitMax, limit, limitMax);
-        }
-        limit = (limit > 0) ? Math.min(limit, limitMax) : limitDefault;
-        return limit;
-    }
-
     private String[] getRegions(Query query) {
         String[] regions;
         String regionStr = query.getString(VariantQueryParam.REGION.key());

diff --git a/...rage-core/src/main/java/org/opencb/opencga/storage/core/variant/VariantStorageEngine.java b/...rage-core/src/main/java/org/opencb/opencga/storage/core/variant/VariantStorageEngine.java
@@ -80,6 +80,7 @@
 import static org.opencb.opencga.storage.core.variant.VariantStorageEngine.Options.*;
 import static org.opencb.opencga.storage.core.variant.adaptors.VariantQueryParam.ANNOT_CLINICAL_SIGNIFICANCE;
 import static org.opencb.opencga.storage.core.variant.adaptors.VariantQueryParam.ID;
+import static org.opencb.opencga.storage.core.variant.adaptors.VariantQueryUtils.addDefaultLimit;
 import static org.opencb.opencga.storage.core.variant.annotation.annotators.AbstractCellBaseVariantAnnotator.toCellBaseSpeciesName;
 import static org.opencb.opencga.storage.core.variant.search.solr.VariantSearchManager.SEARCH_ENGINE_ID;
 import static org.opencb.opencga.storage.core.variant.search.solr.VariantSearchUtils.*;
@@ -377,6 +378,7 @@ public void deleteAnnotation(String name, ObjectMap params) throws StorageEngine
     }
 
     public QueryResult<VariantAnnotation> getAnnotation(String name, Query query, QueryOptions options) throws StorageEngineException {
+        options = addDefaultLimit(options);
         return getDBAdaptor().getAnnotation(name, query, options);
     }
 

diff --git a/...ore/src/main/java/org/opencb/opencga/storage/core/variant/adaptors/VariantQueryUtils.java b/...ore/src/main/java/org/opencb/opencga/storage/core/variant/adaptors/VariantQueryUtils.java
@@ -66,6 +66,9 @@ public final class VariantQueryUtils {
     public static final String ALL = "all";
     public static final String GT = "GT";
 
+    private static final int LIMIT_DEFAULT = 1000;
+    private static final int LIMIT_MAX = 5000;
+
     public static final QueryParam ANNOT_EXPRESSION_GENES = QueryParam.create("annot_expression_genes", "", QueryParam.Type.TEXT_ARRAY);
     public static final QueryParam ANNOT_GO_GENES = QueryParam.create("annot_go_genes", "", QueryParam.Type.TEXT_ARRAY);
     public static final QueryParam ANNOT_GENE_REGIONS = QueryParam.create("annot_gene_regions", "", QueryParam.Type.TEXT_ARRAY);
@@ -1234,4 +1237,26 @@ public static String printQuery(Query query) {
         }
     }
 
+
+    public static QueryOptions addDefaultLimit(QueryOptions queryOptions) {
+        return addDefaultLimit(queryOptions, LIMIT_MAX, LIMIT_DEFAULT);
+    }
+
+    public static QueryOptions addDefaultLimit(QueryOptions queryOptions, int limitMax, int limitDefault) {
+        queryOptions = queryOptions == null ? new QueryOptions() : queryOptions;
+        // Add default limit
+        int limit = getDefaultLimit(queryOptions.getInt(QueryOptions.LIMIT, -1), limitMax, limitDefault);
+        queryOptions.put(QueryOptions.LIMIT,  limit);
+        return queryOptions;
+    }
+
+    public static int getDefaultLimit(int limit, int limitMax, int limitDefault) {
+        if (limit > limitMax) {
+            logger.info("Unable to return more than {} variants. Change limit from {} to {}", limitMax, limit, limitMax);
+        }
+        limit = (limit > 0) ? Math.min(limit, limitMax) : limitDefault;
+        return limit;
+    }
+
+
 }