search: update according to java-common-libs changes, and recover the…

… deleled methods to mark them as deprecated for backward-compatibility, #TASK-6981

opencga-core/src/main/java/org/opencb/opencga/core/config/SearchConfiguration.java

@@ -23,6 +23,8 @@
 import java.util.Collections;
 import java.util.List;
 
+import static org.opencb.opencga.core.config.Configuration.reportUnusedField;
+
 /**
  * Created by wasim on 09/11/16.
  */
@@ -88,6 +90,17 @@ public String toString() {
         return sb.toString();
     }
 
+    @Deprecated
+    public String getHost() {
+        return null;
+    }
+
+    @Deprecated
+    public SearchConfiguration setHost(String host) {
+        reportUnusedField("search.configuration#host", host);
+        return this;
+    }
+
     public List<String> getHosts() {
         return hosts;
     }
@@ -169,6 +182,16 @@ public SearchConfiguration setWriteTimeout(int writeTimeout) {
         return this;
     }
 
+    @Deprecated
+    public int getRows() {
+        return 0;
+    }
+
+    @Deprecated
+    public SearchConfiguration setRows(int rows) {
+        reportUnusedField("search.configuration#rows", rows);
+        return this;
+    }
     public int getInsertBatchSize() {
         return insertBatchSize;
     }

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

@@ -693,11 +693,6 @@ public SolrClient getSolrClient() {
         return solrManager.getSolrClient();
     }
 
-    public VariantSearchManager setSolrClient(SolrClient solrClient) {
-        this.solrManager.setSolrClient(solrClient);
-        return this;
-    }
-
     public SolrQueryParser getSolrQueryParser() {
         return solrQueryParser;
     }

opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/VariantStorageSearchIntersectTest.java

@@ -31,6 +31,7 @@
 import org.opencb.commons.datastore.core.ObjectMap;
 import org.opencb.commons.datastore.core.Query;
 import org.opencb.commons.datastore.core.QueryOptions;
+import org.opencb.commons.datastore.solr.SolrManager;
 import org.opencb.opencga.core.api.ParamConstants;
 import org.opencb.opencga.storage.core.variant.query.VariantQueryResult;
 import org.opencb.opencga.storage.core.StoragePipelineResult;
@@ -92,8 +93,8 @@ public void before() throws Exception {
 //            new Exception().printStackTrace();
 //            return invocation.callRealMethod();
 //        }).when(solrClient).query(anyString(), any());
+        // Configure variant storage engine by using the current solrClient
         solr.configure(this.variantStorageEngine);
-        variantStorageEngine.getVariantSearchManager().setSolrClient(solrClient);
         for (VariantQueryExecutor variantQueryExecutor : variantStorageEngine.getVariantQueryExecutors()) {
             if (variantQueryExecutor instanceof SearchIndexVariantQueryExecutor) {
                 this.variantQueryExecutor = ((SearchIndexVariantQueryExecutor) variantQueryExecutor);

opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/solr/VariantSolrExternalResource.java

@@ -116,8 +116,8 @@ public VariantSearchManager configure(VariantStorageEngine variantStorageEngine)
         variantStorageEngine.getConfiguration().getSearch().setMode("core");
         variantStorageEngine.getConfiguration().getSearch().setActive(true);
         VariantSearchManager variantSearchManager = variantStorageEngine.getVariantSearchManager();
+        // Configure variant search manger by using the current solrClient
         variantSearchManager.setSolrManager(new SolrManager(solrClient, "localhost", "core"));
-        variantSearchManager.setSolrClient(solrClient);
         return variantSearchManager;
     }