Changeset 5319

Timestamp:

Feb 28, 2019, 10:51:14 AM (3 years ago)

Author:

Nicklas Nordborg

Message:

References #1113: Switch to JSON.simple 1.1.1-1

Switched to the new version. Compilation errors have been fixed. There are now over 200 warnings about Unnecessary @SuppressWarnings("unchecked").

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• .classpath (modified) (2 diffs)
• lib/compile/json-simple-1.1.1-1.jar (added)
• lib/compile/json_simple-1.1.jar (deleted)
• src/net/sf/basedb/reggie/json/FilteredJSONObject.java (modified) (4 diffs)
• src/net/sf/basedb/reggie/servlet/DemuxMergeServlet.java (modified) (1 diff)
• src/net/sf/basedb/reggie/servlet/GenotypeServlet.java (modified) (1 diff)
• src/net/sf/basedb/reggie/servlet/MRnaServlet.java (modified) (1 diff)
• src/net/sf/basedb/reggie/servlet/SampleReportServlet.java (modified) (1 diff)

extensions/net.sf.basedb.reggie/trunk/.classpath

@@ -3 +3 @@
   <classpathentry kind="src" path="src"/>
   <classpathentry kind="lib" path="lib/compile/servlet-api.jar"/>
-  <classpathentry kind="lib" path="lib/compile/json_simple-1.1.jar"/>
   <classpathentry kind="lib" path="lib/compile/slf4j-api-1.6.4.jar"/>
   <classpathentry kind="lib" path="META-INF/lib/itextpdf-5.5.3.jar"/>
@@ -17 +16 @@
   <classpathentry kind="lib" path="META-INF/lib/poi-ooxml-4.0.1.jar"/>
   <classpathentry kind="lib" path="lib/compile/commons-io-1.4.jar"/>
+  <classpathentry kind="lib" path="lib/compile/json-simple-1.1.1-1.jar"/>
   <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8"/>
   <classpathentry kind="output" path=".build"/>

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/json/FilteredJSONObject.java

@@ -15 +15 @@
   @since 4.10
 */
-@SuppressWarnings({"rawtypes", "unchecked"})
 public class FilteredJSONObject 
   extends JSONObject 
@@ -21 +20 @@
 
   private static final long serialVersionUID = -5032543945179269026L;
-  private final Filter filter;
+  private final Filter<Object> filter;
   
-  public FilteredJSONObject(Filter filter)
+  public FilteredJSONObject(Filter<Object> filter)
   {
     this.filter = filter;
@@ -29 +28 @@
 
   @Override
-  public Object put(Object key, Object value) 
+  public Object put(String key, Object value) 
   {
     return filter.evaluate(value) ? super.put(key, value) : null;
@@ -35 +34 @@
 
   @Override
-  public void putAll(Map m) 
+  public void putAll(Map<? extends String, ? extends Object> m) 
   {
-    for (Object entry : m.entrySet())
+    for (Map.Entry<? extends String, ? extends Object> entry : m.entrySet())
     {
-      Map.Entry e = (Map.Entry)entry; 
-      if (filter.evaluate(e.getValue())) super.put(e.getKey(),  e.getValue());
+      if (filter.evaluate(entry.getValue())) super.put(entry.getKey(),  entry.getValue());
     }
     super.putAll(m);

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/DemuxMergeServlet.java

@@ -345 +345 @@
           Number seqRunId = (Number)jsonSeqRun.get("id");
           String readString = (String)jsonSeqRun.get("ReadString");
-          JSONArray jsonOmitLanes = (JSONArray)jsonSeqRun.get("OmitLanes");
+          List<Number> jsonOmitLanes = (List<Number>)jsonSeqRun.get("OmitLanes");
           boolean excludeDoNotUse = Boolean.TRUE.equals(jsonSeqRun.get("excludeDoNotUse"));
           

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/GenotypeServlet.java

@@ -498 +498 @@
         JSONObject jsonReq = JsonUtil.parseRequest(req);
         JSONArray jsonItems = (JSONArray)jsonReq.get("items");
-        Set<Number> jsonPaired = new HashSet<Number>((JSONArray)jsonReq.get("paired"));
+        Set<Number> jsonPaired = new HashSet<Number>((List<Number>)jsonReq.get("paired"));
         
         ItemSubtype mergedType = Subtype.MERGED_SEQUENCES.get(dc);

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/MRnaServlet.java

@@ -392 +392 @@
         
         JSONObject jsonReq = JsonUtil.parseRequest(req);
-        JSONArray jsonIgnore = (JSONArray)jsonReq.get("ignore");
+        List<Long> jsonIgnore = (List<Long>)jsonReq.get("ignore");
         boolean preNormalized = jsonReq.get("preNormalized") != null;
         boolean flagNotSelected = !preNormalized && jsonReq.get("flag") != null;

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/SampleReportServlet.java

@@ -1941 +1941 @@
                 DateToStringConverter converter = new DateToStringConverter(new SimpleDateFormat("yyyy-MM-dd"));
                 String dateStr = converter.convert(date);
-                jsonMultipleDates.put(dateCounter, dateStr);
+                jsonMultipleDates.put(Integer.toString(dateCounter), dateStr);
                 dateCounter++;
               }