Changeset 7603

Timestamp:

Feb 22, 2019, 1:50:40 PM (5 years ago)

Author:

Nicklas Nordborg

Message:

References #2151: Pre-compile all JSP pages before releases

Getting rid of deprecation warnings except those that are related to spot images since they should be fixed by #2136.

Location:

trunk/www

Files:

• common/overview/index.jsp (modified) (1 diff)
• views/derivedbioassays/ajax.jsp (modified) (1 diff)
• views/experiments/reporters/index.jsp (modified) (5 diffs)
• views/experiments/reporters/list_reporters.jsp (modified) (3 diffs)
• views/experiments/rootrawbioassays/view_bioassay.jsp (modified) (1 diff)
• views/experiments/spotdata/index.jsp (modified) (3 diffs)
• views/experiments/spotdata/list_spotdata.jsp (modified) (3 diffs)
• views/itemlists/members/index.jsp (modified) (1 diff)

trunk/www/common/overview/index.jsp

@@ -101 +101 @@
       }
     }
-    options.setOption(Validator.NONMATCHING_SPOTCOUNT, "threshold", request.getParameter("threshold"));
+    options.setOption((ValidationRuleAction)Validator.NONMATCHING_SPOTCOUNT, "threshold", request.getParameter("threshold"));
     options.saveToPreset(presets.getDefault());
     OverviewUtil.saveValidationPresets(sc);

trunk/www/views/derivedbioassays/ajax.jsp

@@ -69 +69 @@
 try
 {
-  if ("GetExtracts".equals(cmd))
-  {
-    dc = sc.newDbControl();
-    DerivedBioAssay dba = DerivedBioAssay.getById(dc, itemId);
-    json.put("id", dba.getId());
-    json.put("name", dba.getName());
-
-    JSONArray jsonSources = new JSONArray();
-    try
-    {
-      Extract extract = dba.getExtract();
-      if (extract != null)
-      {
-        JSONObject jsonSrc = new JSONObject();
-        jsonSrc.put("id", extract.getId());
-        jsonSrc.put("name", extract.getName());
-        jsonSources.add(jsonSrc);
-      }
-      else
-      {
-        SpecialQuery<BioMaterialEventSource> sourceQuery = dba.getPhysicalBioAssay().getCreationEvent().getEventSources();
-        sourceQuery.order(Orders.asc(Hql.property("position")));
-        sourceQuery.order(Orders.asc(Hql.property("bioMaterial.name")));
-        for (BioMaterialEventSource src : sourceQuery.list(dc))
-        {
-          JSONObject jsonSrc = new JSONObject();
-          try
-          {
-            extract = (Extract)src.getBioMaterial();
-            jsonSrc.put("id", extract.getId());
-            jsonSrc.put("name", extract.getName());
-            jsonSrc.put("position", src.getPosition());
-            jsonSources.add(jsonSrc);
-          }
-          catch (PermissionDeniedException ex)
-          {}
-        }
-      }
-    }
-    catch (PermissionDeniedException ex)
-    {}
-    json.put("sources", jsonSources);
-
-    
-    dc.commit();
-  }
-  else if ("GetArrayDesign".equals(cmd))
+  if ("GetArrayDesign".equals(cmd))
   {
     dc = sc.newDbControl();

trunk/www/views/experiments/reporters/index.jsp

@@ -37 +37 @@
   import="net.sf.basedb.core.User"
   import="net.sf.basedb.core.ItemQuery"
-  import="net.sf.basedb.core.DynamicReporterQuery"
   import="net.sf.basedb.core.ItemResultIterator"
   import="net.sf.basedb.core.Permission"
@@ -46 +45 @@
   import="net.sf.basedb.core.ItemAlreadyExistsException"
   import="net.sf.basedb.core.query.Restriction"
+  import="net.sf.basedb.core.query.SqlQuery"
   import="net.sf.basedb.plugins.CloneReportersPlugin"
   import="net.sf.basedb.clients.web.Base"
@@ -109 +109 @@
     dc = sc.newDbControl();
     final Experiment experiment = Experiment.getById(dc, experimentId);
-    final DynamicReporterQuery query = Reporter.getDynamicQuery(experiment);
+    final SqlQuery query = Reporter.getDynamicQuery(experiment);
     dc.close();
     cc.setQuery(query);
@@ -120 +120 @@
     dc = sc.newDbControl();
     final Experiment experiment = Experiment.getById(dc, experimentId);
-    final DynamicReporterQuery query = Reporter.getDynamicQuery(experiment);
+    final SqlQuery query = Reporter.getDynamicQuery(experiment);
     dc.close();
     cc.setQuery(query);
@@ -130 +130 @@
     dc = sc.newDbControl();
     final Experiment experiment = Experiment.getById(dc, experimentId);
-    final DynamicReporterQuery query = Reporter.getDynamicQuery(experiment);
+    final SqlQuery query = Reporter.getDynamicQuery(experiment);
     cc.configureQuery(dc, query, Collections.singletonList("@id"));
     dc.close();

trunk/www/views/experiments/reporters/list_reporters.jsp

@@ -31 +31 @@
   import="net.sf.basedb.core.VirtualDb"
   import="net.sf.basedb.core.BaseException"
-  import="net.sf.basedb.core.DynamicReporterQuery"
   import="net.sf.basedb.core.Reporter"
   import="net.sf.basedb.core.DynamicResultIterator"
@@ -43 +42 @@
   import="net.sf.basedb.core.query.Selects"
   import="net.sf.basedb.core.query.Dynamic"
+  import="net.sf.basedb.core.query.SqlQuery"
   import="net.sf.basedb.core.query.SqlResult"
   import="net.sf.basedb.util.Enumeration"
@@ -105 +105 @@
   try
   {
-    final DynamicReporterQuery query = Reporter.getDynamicQuery(experiment);
+    final SqlQuery query = Reporter.getDynamicQuery(experiment);
     query.select(Selects.expression(Dynamic.reporter("id"), "id", true));
     if (hasUpToDateColumn)

trunk/www/views/experiments/rootrawbioassays/view_bioassay.jsp

@@ -294 +294 @@
                     if (inherited != null)
                     {
-                      parentType = inherited.getItemType().toString();
+                      parentType = inherited.getThisItemType().toString();
                       if (lastModified == null)
                       {

trunk/www/views/experiments/spotdata/index.jsp

@@ -32 +32 @@
   import="net.sf.basedb.core.RawDataTypes"
   import="net.sf.basedb.core.ItemContext"
-  import="net.sf.basedb.core.DynamicSpotQuery"
+  import="net.sf.basedb.core.query.SqlQuery"
   import="net.sf.basedb.clients.web.Base"
   import="net.sf.basedb.clients.web.WebException"
@@ -139 +139 @@
     if (bas != null) dc.reattachItem(bas, false);
     if (ba != null) dc.reattachItem(ba, false);
-    final DynamicSpotQuery query = ba != null ? ba.getSpotData() : bas.getSpotData();
+    final SqlQuery query = ba != null ? ba.getSpotData() : bas.getSpotData();
     registerExportFormatters(dc, cc, bas, ba);
     dc.close();
@@ -151 +151 @@
     if (bas != null) dc.reattachItem(bas, false);
     if (ba != null) dc.reattachItem(ba, false);
-    final DynamicSpotQuery query = ba != null ? ba.getSpotData() : bas.getSpotData();
+    final SqlQuery query = ba != null ? ba.getSpotData() : bas.getSpotData();
     cc.configureQuery(dc, query, Collections.singletonList("@id"));
     dc.close();

trunk/www/views/experiments/spotdata/list_spotdata.jsp

@@ -36 +36 @@
   import="net.sf.basedb.core.RawDataType"
   import="net.sf.basedb.core.BaseException"
-  import="net.sf.basedb.core.DynamicSpotQuery"
   import="net.sf.basedb.core.DynamicResultIterator"
   import="net.sf.basedb.core.PluginDefinition"
@@ -43 +42 @@
   import="net.sf.basedb.core.plugin.GuiContext"
   import="net.sf.basedb.core.plugin.Plugin"
+  import="net.sf.basedb.core.query.SqlQuery"
   import="net.sf.basedb.core.query.SqlResult"
   import="net.sf.basedb.util.Enumeration"
@@ -127 +127 @@
   try
   {
-    final DynamicSpotQuery query = bioAssay != null ? bioAssay.getSpotData() : bioAssaySet.getSpotData();
+    final SqlQuery query = bioAssay != null ? bioAssay.getSpotData() : bioAssaySet.getSpotData();
     cc.configureQuery(dc, query, selected.selectedProperties);
     query.setFailSafe(true);

trunk/www/views/itemlists/members/index.jsp

@@ -232 +232 @@
     for (int itemId : cc.getSelected())
     {
-      list.remove((Listable)itemType.getById(dc, itemId));
+      list.removeItem((Listable)itemType.getById(dc, itemId));
     }
     dc.commit();