Cleaning up code

Editing cdode according to the comments

src/main/java/org/broadinstitute/hellbender/tools/variantdb/SampleList.java

@@ -13,7 +13,7 @@
 import org.apache.logging.log4j.Logger;
 import org.broadinstitute.hellbender.utils.bigquery.BigQueryUtils;
 import org.broadinstitute.hellbender.utils.bigquery.TableReference;
-import org.broadinstitute.hellbender.utils.bigquery.UID;
+
 
 public class SampleList {
     static final Logger logger = LogManager.getLogger(SampleList.class);
@@ -120,7 +120,7 @@ private TableResult querySampleTable(String fqSampleTableName, String whereClaus
 
     // Create labels
     private TableResult querySampleTable(String fqSampleTableName, String whereClause, boolean printDebugInformation) {
-        UID run_uid = new UID();
+        UUID run_uid = UUID.randomUUID();
         Map<String, String> labels = new HashMap<String, String>();
         labels.put("query", "Run_SampleTable_" + run_uid.toString() );
         TableResult result = querySampleTable(fqSampleTableName, whereClause, printDebugInformation, labels);

src/main/java/org/broadinstitute/hellbender/tools/variantdb/nextgen/ExtractCohortEngine.java

@@ -172,7 +172,7 @@ public void traverse() {
                     logger.debug("using query api with order by");
                 }
                 // create the query string
-                UID run_uid = new UID();
+                UUID run_uid = UUID.randomUUID();
                 Map<String, String> labels = new HashMap<String, String>();
                 labels.put("query", "extract_cohort_"+ run_uid.toString());
                 String q = "SELECT " + StringUtils.join(SchemaUtils.COHORT_FIELDS,",") + " FROM " + cohortTableRef.getFQTableName() + " ORDER BY " + SchemaUtils.LOCATION_FIELD_NAME;

src/main/java/org/broadinstitute/hellbender/tools/variantdb/nextgen/ExtractFeaturesEngine.java

@@ -100,7 +100,7 @@ public void traverse() {
         final String featureQueryString =
 
         ExtractFeaturesBQ.getVQSRFeatureExtractQueryString(altAlleleTable, sampleListTable, minLocation, maxLocation, trainingSitesOnly, SNP_QUAL_THRESHOLD, INDEL_QUAL_THRESHOLD);
-        UID run_uid = new UID();
+        UUID run_uid = UUID.randomUUID();
         Map<String, String> labels = new HashMap<String, String>();
         labels.put("query", "extract_features_"+ run_uid.toString());
         logger.info(featureQueryString);

src/main/java/org/broadinstitute/hellbender/utils/bigquery/BigQueryUtils.java

@@ -45,6 +45,7 @@ public static BigQuery getBigQueryEndPoint() {
      * Will block until results are returned.
      * For more information on querying BigQuery tables, see: https://cloud.google.com/bigquery/sql-reference/
      * @param queryString The {@link BigQuery} query string to execute.  Must use standard SQL syntax.  Must contain the project ID, data set, and table name in the `FROM` clause for the table from which to retrieve data.
+     * @param labels The {@link BigQuery} label to add the job run.  Must use Map<String, String>.  Must contain Job label and gatk_execution_id.
      * @return A {@link TableResult} object containing the results of the query executed.
      */
     public static TableResult executeQuery(final String queryString, final Map<String, String> labels) {
@@ -56,15 +57,11 @@ public static TableResult executeQuery(final String queryString, final Map<Strin
      * Will block until results are returned.
      * For more information on querying BigQuery tables, see: https://cloud.google.com/bigquery/sql-reference/
      * @param queryString The {@link BigQuery} query string to execute.  Must use standard SQL syntax.  Must contain the project ID, data set, and table name in the `FROM` clause for the table from which to retrieve data.
+     * @param labels The {@link BigQuery} label to add the job run.  Must use Map<String, String>.  Must contain Job label and gatk_execution_id.
      * @param runQueryInBatchMode If true, run the query in batch mode, which is lower priority but has no limit on the number of concurrent queries
      * @return A {@link TableResult} object containing the results of the query executed.
      */
 
-    // TODO: add Collections.EMPTY_MAP
-//    public static TableResult executeQuery(final String queryString, final boolean runQueryInBatchMode) {
-//        return executeQuery(getBigQueryEndPoint(), queryString, runQueryInBatchMode, Collections.EMPTY_MAP);
-//    }
-
     public static TableResult executeQuery(final String queryString, final boolean runQueryInBatchMode, final Map<String, String> labels) {
         return executeQuery(getBigQueryEndPoint(), queryString, runQueryInBatchMode, labels);
     }
@@ -360,14 +357,13 @@ private static TableResult submitQueryAndWaitForResults( final BigQuery bigQuery
         return result;
     }
 
-    private static long getQueryCostBytesProcessedEstimate(String queryString, Map<String, String> labels) {
+    private static long getQueryCostBytesProcessedEstimate(String queryString) {
         final QueryJobConfiguration dryRunQueryConfig =
                 QueryJobConfiguration.newBuilder( queryString )
                         .setUseLegacySql(false)
                         .setDryRun(true)
                         .setUseQueryCache(false)
                         .setPriority(QueryJobConfiguration.Priority.INTERACTIVE)
-                        .setLabels(labels)
                         .build();
 
         Job dryRunJob = getBigQueryEndPoint().create(JobInfo.newBuilder(dryRunQueryConfig).build());
@@ -385,7 +381,7 @@ public static StorageAPIAvroReader executeQueryWithStorageAPI(final String query
         final String tempTableName = UUID.randomUUID().toString().replace('-', '_');
         final String tempTableFullyQualified = String.format("%s.%s.%s", projectID, tempTableDataset, tempTableName);
 
-        long bytesProcessed = getQueryCostBytesProcessedEstimate(queryString, labels);
+        long bytesProcessed = getQueryCostBytesProcessedEstimate(queryString);
         logger.info(String.format("Estimated %s MB scanned", bytesProcessed/1000000));
 
         final String queryStringIntoTempTable = "CREATE TABLE `" + tempTableFullyQualified + "`\n" +
@@ -394,8 +390,6 @@ public static StorageAPIAvroReader executeQueryWithStorageAPI(final String query
                 ") AS\n" +
                 queryString;
 
-        // TODO: add label
-
         executeQuery(queryStringIntoTempTable, runQueryInBatchMode, labels);
 
         final Table tableInfo = getBigQueryEndPoint().getTable( TableId.of(projectID, tempTableDataset, tempTableName) );

src/test/java/org/broadinstitute/hellbender/utils/bigquery/BigQueryUtilsUnitTest.java

@@ -21,13 +21,12 @@ public class BigQueryUtilsUnitTest extends GATKBaseTest {
     private static final String BIGQUERY_FULLY_QUALIFIED_TABLE = String.format("%s.%s.%s",
             BIGQUERY_TEST_PROJECT, BIGQUERY_TEST_DATASET, BIGQUERY_TEST_TABLE);
 
-    private static final UID run_uid = new UID();
+    private static final UUID run_uid = UUID.randomUUID();
 
     @Test(groups = {"cloud"})
     public void testExecuteQueryAllRecords() {
         final String query = String.format("SELECT * FROM `%s`", BIGQUERY_FULLY_QUALIFIED_TABLE);
         Map<String, String> labels = new HashMap<String, String>();
-        String test = run_uid.toString();
         labels.put("test_query", "get_all_records" + run_uid.toString() );
         final TableResult result = BigQueryUtils.executeQuery(query, labels);
 
@@ -123,6 +122,15 @@ public void testQueryWithEmptyDatasetStorageAPI() {
         Assert.assertTrue(retrievedNames.isEmpty(), "No Result expected");
     }
 
+    @Test(groups = {"cloud"})
+    public void testQueryWithNullLabel() {
+        final String query = String.format("SELECT * FROM `%s`", BIGQUERY_FULLY_QUALIFIED_TABLE);
+        Map<String, String> labels = null;
+        final TableResult result = BigQueryUtils.executeQuery(query, labels);
+
+        checkQueryResults(result, getAllExpectedNamesAndAges(), query);
+    }
+
     private Map<String, String> getAllExpectedNamesAndAges() {
         final Map<String, String> expectedNamesAndAges = new HashMap<>();
         expectedNamesAndAges.put("Fred", "35");