Fix compiler warnings

Author: ryanrdoherty

Model/src/main/java/org/gusdb/wdk/model/ThreadMonitor.java

@@ -88,7 +88,7 @@ public void run() {
   public void monitorThreads(ThreadMXBean thbean) {
 
     String siteInfo = _config.getAppName() + ", " + ManagementFactory.getRuntimeMXBean().getName();
-    LOG.info("Thread Monitor started on thread #" + Thread.currentThread().getId() + " - " + siteInfo);
+    LOG.info("Thread Monitor started on thread #" + Thread.currentThread().threadId() + " - " + siteInfo);
     thbean.setThreadContentionMonitoringEnabled(true);
 
     int blockedCycles = 0; // keeps track of amount of time since last report
@@ -119,7 +119,7 @@ public void monitorThreads(ThreadMXBean thbean) {
         break;
       }
     }
-    LOG.info("Thread monitor stopped on Thread " + Thread.currentThread().getId() + " - " + siteInfo);
+    LOG.info("Thread monitor stopped on Thread " + Thread.currentThread().threadId() + " - " + siteInfo);
   }
 
   private static ThreadState getThreadState(ThreadMXBean thbean) {
@@ -181,7 +181,7 @@ private String getEmailBody(ThreadMXBean thbean, String siteInfo, String stateTe
     // get thread infos
     long[] ids = new long[blockedThreads.size()];
     for (int i = 0; i < ids.length; i++) {
-      ids[i] = blockedThreads.get(i).getId();
+      ids[i] = blockedThreads.get(i).threadId();
     }
     ThreadInfo[] infos = thbean.getThreadInfo(ids);
 
@@ -194,7 +194,7 @@ private String getEmailBody(ThreadMXBean thbean, String siteInfo, String stateTe
       Thread thread = blockedThreads.get(i);
       ThreadInfo info = infos[i];
       if (info != null) {
-        buffer.append("<div><div>Thread id=").append(thread.getId())
+        buffer.append("<div><div>Thread id=").append(thread.threadId())
               .append(", name='").append(thread.getName()).append("'</div>\n")
               .append("<div>\tblocked count=").append(info.getBlockedCount())
               .append(", blocked time=").append(info.getBlockedTime() + "</div>\n")

Model/src/main/java/org/gusdb/wdk/model/Utilities.java

@@ -6,6 +6,10 @@
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
+import java.net.MalformedURLException;
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.net.URL;
 import java.sql.Clob;
 import java.sql.SQLException;
 import java.util.Date;
@@ -350,4 +354,12 @@ public static Map<String, Boolean> parseSortList(String sortList) throws WdkMode
     return sortingMap;
   }
 
+  public static URL newURL(String urlString) {
+    try {
+      return new URI(urlString).toURL();
+    }
+    catch (MalformedURLException | URISyntaxException e) {
+      throw new RuntimeException("Attempt to use malformed URL: " + urlString, e);
+    }
+  }
 }

Model/src/main/java/org/gusdb/wdk/model/answer/SummaryViewHandler.java

@@ -27,6 +27,7 @@ public interface SummaryViewHandler {
      * @throws WdkModelException if system exception occurs
      * @throws WdkUserException if input parameters are invalid
      */
+    @Deprecated
     Map<String, Object> process(RunnableObj<AnswerSpec> answerSpec, Map<String, String[]> parameters, User user)
         throws WdkModelException, WdkUserException;
 
@@ -41,6 +42,7 @@ Map<String, Object> process(RunnableObj<AnswerSpec> answerSpec, Map<String, Stri
      * @throws WdkModelException if system exception occurs
      * @throws WdkUserException if input parameters are invalid
      */
+    @Deprecated
     String processUpdate(RunnableObj<AnswerSpec> answerSpec, Map<String, String[]> parameters, User user)
         throws WdkModelException, WdkUserException;
 }

Model/src/main/java/org/gusdb/wdk/model/fix/StepParamExpander.java

@@ -46,9 +46,11 @@ public class StepParamExpander extends BaseCLI {
 
   private static final String ARG_THREADED = "threaded";
   private static final String ARG_DROP = "dropTablesOnly";
+  @Deprecated
   static final String STEP_PARAMS_TABLE = "step_params";
   private static final String UPDATED_STEPS_TABLE = "wdk_updated_steps";
 
+  @Deprecated
   public static void main(String[] args) {
     String cmdName = System.getProperty("cmdName");
     StepParamExpander expender = new StepParamExpander(cmdName);
@@ -65,11 +67,13 @@ public static void main(String[] args) {
   /**
    * @param command
    */
+  @Deprecated
   protected StepParamExpander(String command) {
     super((command != null) ? command : "stepParamExpander",
         "expand the param clob into its own rows in " + STEP_PARAMS_TABLE + " table");
   }
 
+  @Deprecated
   public void expand(WdkModel wdkModel) throws SQLException, WdkModelException {
     String userSchema = wdkModel.getModelConfig().getUserDB().getUserSchema();
     DatabaseInstance database = wdkModel.getUserDb();
@@ -171,6 +175,7 @@ private static String getSelectSql(String userSchema, String projectId) {
     return getSelectForColumns(userSchema, projectId, "step_id,display_params");
   }
 
+  @Deprecated
   public static String getSelectForColumns(String userSchema, String projectId, String columns) {
     String projectIdCondition = (projectId != null ? " AND s.project_id = '" + projectId + "'" : "");
     return
@@ -180,6 +185,7 @@ public static String getSelectForColumns(String userSchema, String projectId, St
         "   AND s.step_id NOT IN (SELECT step_id FROM " + STEP_PARAMS_TABLE + ")";
   }
 
+  @Deprecated
   public static void createParamTable(WdkModel wdkModel) throws SQLException {
     DatabaseInstance database = wdkModel.getUserDb();
     DataSource dataSource = database.getDataSource();
@@ -224,10 +230,12 @@ public static void createParamTable(WdkModel wdkModel) throws SQLException {
     }
   }
 
+  @Deprecated
   public static String getInsertSql() {
     return "INSERT INTO " + STEP_PARAMS_TABLE + " (step_id, param_name, param_value) VALUES (?, ?, ?)";
   }
 
+  @Deprecated
   public static Map<String, Set<String>> parseClob(int stepId, String clob)
       throws JSONException {
     if (clob == null || clob.trim().isEmpty()) {
@@ -243,6 +251,7 @@ public static Map<String, Set<String>> parseClob(int stepId, String clob)
     }
   }
 
+  @Deprecated
   public static Map<String, Set<String>> parseDisplayParams(int stepId, JSONObject displayParams) {
     return parseParams(stepId, displayParams.has(ParamsAndFiltersDbColumnFormat.KEY_PARAMS) ?
         // new displayParams format, fetch params object from params property
@@ -277,6 +286,7 @@ private static Map<String, Set<String>> parseParams(int stepId, JSONObject param
     return newValues;
   }
 
+  @Deprecated
   public static String truncateTerm(String term) {
     return (term.length() <= 4000 ? term : term.substring(0, 4000));
   }
@@ -286,6 +296,7 @@ public static String truncateTerm(String term) {
    * 
    * @see org.gusdb.fgputil.BaseCLI#declareOptions()
    */
+  @Deprecated
   @Override
   protected void declareOptions() {
     addSingleValueOption(ARG_PROJECT_ID, true, null, "ProjectId, which" +
@@ -299,6 +310,7 @@ protected void declareOptions() {
    * 
    * @see org.gusdb.fgputil.BaseCLI#execute()
    */
+  @Deprecated
   @Override
   protected void execute() throws Exception {
     String projectId = (String)getOptionValue(ARG_PROJECT_ID);

Model/src/main/java/org/gusdb/wdk/model/fix/StepParamExpanderPlugin.java

@@ -27,12 +27,15 @@ public class StepParamExpanderPlugin implements TableRowUpdaterPlugin<StepData>
 
   private static final Logger LOG = Logger.getLogger(StepParamExpanderPlugin.class);
 
+  @Deprecated
   public static class ParamExpanderLoader extends StepDataFactory {
 
+    @Deprecated
     public ParamExpanderLoader() {
       super(true);
     }
 
+    @Deprecated
     @Override
     public String getRecordsSql(String schema, String projectId) {
       // ignore projectId for now; must select cols from StepDataFactory so we can properly load StepData objs
@@ -42,13 +45,17 @@ public String getRecordsSql(String schema, String projectId) {
     }
   }
 
+  @Deprecated
   public static class StepWithParams extends StepData {
 
     private static final int MAX_PARAM_VALUE_LENGTH = 4000;
 
+    @Deprecated
     public Map<String, Set<String>> params = new HashMap<>();
+    @Deprecated
     public int valueCount;
 
+    @Deprecated
     public StepWithParams(StepData base) {
       super(base);
       Map<String, Set<String>> fullParams = StepParamExpander.parseDisplayParams(getStepId().intValue(), getParamFilters());
@@ -118,23 +125,27 @@ public List<String> getTableNamesForBackup(String schema) {
 
   private AtomicInteger _numParams = new AtomicInteger(0);
 
+  @Deprecated
   @Override
   public void configure(WdkModel wdkModel, List<String> additionalArgs) throws Exception {
     // no configuration needed
   }
 
+  @Deprecated
   @Override
   public TableRowUpdater<StepData> getTableRowUpdater(WdkModel wdkModel) {
     return new TableRowUpdater<StepData>(new ParamExpanderLoader(), new ParamValueWriter(), this, wdkModel);
   }
 
+  @Deprecated
   @Override
   public RowResult<StepData> processRecord(StepData nextRow) throws Exception {
     StepWithParams replacement = new StepWithParams(nextRow);
     _numParams.addAndGet(replacement.valueCount);
     return new RowResult<StepData>(replacement).setShouldWrite(!replacement.params.isEmpty());
   }
 
+  @Deprecated
   @Override
   public void dumpStatistics() {
     LOG.info("Wrote " + _numParams.get() + " total param rows to the " + StepParamExpander.STEP_PARAMS_TABLE + " table.");

Model/src/main/java/org/gusdb/wdk/model/test/stress/UrlItem.java

@@ -5,6 +5,8 @@
 import java.net.MalformedURLException;
 import java.net.URL;
 
+import org.gusdb.wdk.model.Utilities;
+
 /**
  * @author Jerric
  */
@@ -27,11 +29,11 @@ public String getUrlType() {
     }
 
     public URL getUrl() throws MalformedURLException {
-        return new URL( urlPattern );
+        return Utilities.newURL( urlPattern );
     }
 
     public HttpURLConnection getConnection( String cookies ) throws IOException {
-        URL url = new URL( urlPattern );
+        URL url = Utilities.newURL( urlPattern );
         HttpURLConnection connection = ( HttpURLConnection ) url.openConnection();
         connection.setRequestProperty( "User-Agent",
                 "Mozilla/4.0 (compatible; MSIE 5.5; Windows NT 5.0)" );

Model/src/main/java/org/gusdb/wdk/model/user/BasketFactory.java

@@ -80,7 +80,7 @@ public BasketFactory(WdkModel wdkModel) {
   public void addEntireResultToBasket(User user, RunnableObj<AnswerSpec> spec) throws WdkModelException {
     AnswerValue answer = AnswerValueFactory.makeAnswer(spec);
     int recordCount = answer.getResultSizeFactory().getResultSize();
-    try (RecordStream records = RecordStreamFactory.getRecordStream(answer, Collections.EMPTY_LIST, Collections.EMPTY_LIST)) {
+    try (RecordStream records = RecordStreamFactory.getRecordStream(answer, Collections.emptyList(), Collections.emptyList())) {
       addToBasket(user, spec.get().getQuestion().get().getRecordClass(), recordCount, records);
     }
   }

Model/src/main/java/org/gusdb/wdk/model/user/dataset/irods/IrodsUserDatasetSession.java

@@ -658,7 +658,7 @@ private JsonUserDataset collectionToDataset(
           .orElseGet(Stream::empty)
           .map(ICatNode::getName)
           .map(s -> new JSONObject().put("name", s))
-          .reduce(new JSONArray(), JSONArray::put, (a, b) -> a)
+          .reduce(new JSONArray(), JSONArray::put, (a, _) -> a)
       ),
       metaJson,
       dsCol.getPath().resolve(DATAFILES_DIR),

Model/src/main/java/org/gusdb/wdk/model/user/dataset/irods/icat/ICatNode.java

@@ -75,7 +75,7 @@ public abstract class ICatNode {
    *   metadata value string
    */
   public void addMetadata(final String key, final String value) {
-    metadata.computeIfAbsent(key, __ -> new ArrayList<>()).add(value);
+    metadata.computeIfAbsent(key, _ -> new ArrayList<>()).add(value);
   }
 
   /**

Model/src/main/java/org/gusdb/wdk/model/xml/XmlQuestion.java

@@ -15,6 +15,7 @@
 import org.apache.log4j.Logger;
 import org.gusdb.fgputil.xml.TransformException;
 import org.gusdb.fgputil.xml.XmlTransformer;
+import org.gusdb.wdk.model.Utilities;
 import org.gusdb.wdk.model.WdkModel;
 import org.gusdb.wdk.model.WdkModelBase;
 import org.gusdb.wdk.model.WdkModelException;
@@ -275,7 +276,7 @@ public XmlAnswerValue makeAnswer(int startIndex, int endIndex) throws WdkModelEx
     private URL createURL(String data) throws MalformedURLException {
         if (data.startsWith("http://") || data.startsWith("ftp://")
                 || data.startsWith("https://")) {
-            return new URL(data);
+            return Utilities.newURL(data);
         } else {
             File xmlDataDir = _model.getXmlDataDir();
             File xmlDataFile = new File(xmlDataDir, data);