Changeset 6319

Timestamp:

Sep 9, 2013, 9:56:59 AM (9 years ago)

Author:

Nicklas Nordborg

Message:

Merged patch release 3.2.3 to the trunk.

Location:

trunk

Files:

• . (modified) (1 prop)
• credits.txt (modified) (1 diff)
• src/clients/web/net/sf/basedb/clients/web/extensions/plot/MAPlotFactory.java (modified) (5 diffs)
• src/clients/web/net/sf/basedb/clients/web/formatter/ColorFormatter.java (modified) (2 diffs)
• src/clients/web/net/sf/basedb/clients/web/plugins/SimpleExport.java (modified) (1 diff)
• src/core/net/sf/basedb/core/AnnotationSet.java (modified) (1 diff)
• src/core/net/sf/basedb/core/log/EntityDetails.java (modified) (7 diffs)
• src/core/net/sf/basedb/core/log/LoggingInterceptor.java (modified) (1 diff)
• src/core/net/sf/basedb/core/log/db/AnnotationSetLogger.java (modified) (1 diff)
• www/admin/itemsubtypes/index.jsp (modified) (3 diffs)
• www/admin/itemsubtypes/list_subtypes.jsp (modified) (2 diffs)
• www/biomaterials/extracts/list_extracts.jsp (modified) (2 diffs)
• www/biomaterials/samples/list_samples.jsp (modified) (2 diffs)
• www/common/annotations/annotate.jsp (modified) (2 diffs)
• www/common/plugin/index.jsp (modified) (1 diff)
• www/filemanager/directories/list_directories.jsp (modified) (1 diff)
• www/include/styles/main.css (modified) (2 diffs)
• www/plugins/net/sf/basedb/plugins/executor/external_plugin_parameters.jsp (modified) (1 diff)
• www/views/physicalbioassays/list_bioassays.jsp (modified) (2 diffs)

trunk/credits.txt

@@ -1 +1 @@
 $Id$
 
-The current BASE team is (at BASE 3.2.2 release)
+The current BASE team is (at BASE 3.2.3 release)
 {{{
 Jari Häkkinen

trunk/src/clients/web/net/sf/basedb/clients/web/extensions/plot/MAPlotFactory.java

@@ -22 +22 @@
 package net.sf.basedb.clients.web.extensions.plot;
 
+import java.util.ArrayList;
 import java.util.List;
 
@@ -30 +31 @@
 import net.sf.basedb.core.BioAssaySet;
 import net.sf.basedb.core.DbControl;
+import net.sf.basedb.core.ItemQuery;
+import net.sf.basedb.core.query.Hql;
+import net.sf.basedb.core.query.Orders;
 import net.sf.basedb.util.Values;
 import net.sf.basedb.util.extensions.InvokationContext;
@@ -86 +90 @@
     DbControl dc = context.getClientContext().getDbControl();
     BioAssaySet source = (BioAssaySet)context.getClientContext().getCurrentItem();
-    boolean hasCfPlot = source.getTransformation().getSource() != null;
-    List<BioAssay> bioAssays = source.getBioAssays().list(dc);
-    OverviewPlotAction[] actions = new OverviewPlotAction[hasCfPlot ? 2 : 1];
+    BioAssaySet parent = source.getTransformation().getSource();
+    boolean hasCfPlot = parent != null && parent.getDataCubeNo() == source.getDataCubeNo();
+    ItemQuery<BioAssay> baQuery = source.getBioAssays();
+    baQuery.order(Orders.asc(Hql.property("name")));
+    List<BioAssay> bioAssays = baQuery.list(dc);
     
-    // MA plot
-    OverviewPlotBean maBean = new OverviewPlotBean();
-    maBean.setTitle("MA plots");
-    maBean.setDescription("MA plots for each bioassay in this bioassay set");
-    maBean.setId("maplots");
-    String M = HTML.urlEncode("log2(ch(1) / ch(2))");
-    String A = HTML.urlEncode("log(ch(1) * ch(2)) / 2");
-    String maFilter = HTML.urlEncode("ch(1) > 0 && ch(2) > 0");
+    // Plot generators for each bioassay
     PlotGenerator[] maGenerators = new PlotGenerator[bioAssays.size()];
-    maBean.setPlotGenerators(maGenerators);
-    actions[0] = maBean;
-    
-    // Correction factor plot
-    PlotGenerator[] cfGenerators = null;
-    if (hasCfPlot)
-    {
-      OverviewPlotBean cfBean = new OverviewPlotBean();
-      cfBean.setTitle("Correction factor plots");
-      cfBean.setDescription("MA-plot of the parent bioassays together " +
-          "with a correction factor for each spot in the current bioassayset.");
-      cfBean.setId("cfplots");
-      cfGenerators = new PlotGenerator[bioAssays.size()];
-      cfBean.setPlotGenerators(cfGenerators);
-      actions[1] = cfBean;
-    }
+    List<PlotGenerator> cfGenerators = hasCfPlot ? new ArrayList<PlotGenerator>(bioAssays.size()) : null;
     
     // Generate plot url:s for each bioassay
     String xLabel = HTML.urlEncode("A, log10(ch1 * ch2) / 2");
     String yLabel = HTML.urlEncode("M, log2(ch1 / ch2)");
+    String M = HTML.urlEncode("log2(ch(1) / ch(2))");
+    String A = HTML.urlEncode("log(ch(1) * ch(2)) / 2");
+    String maFilter = HTML.urlEncode("ch(1) > 0 && ch(2) > 0");
     int index = 0;
     for (BioAssay ba : bioAssays)
@@ -143 +130 @@
       maGenerators[index] = maPlot;
       // Correction factor plot
-      if (hasCfPlot)
+      if (hasCfPlot && ba.getParents().count(dc) == 1)
       {
         PlotGeneratorBean cfPlot = new PlotGeneratorBean();
@@ -159 +146 @@
             "&title="+HTML.urlEncode(ba.getName())
         );
-        cfGenerators[index] = cfPlot;
+        cfGenerators.add(cfPlot);
       }
       ++index;
     }
+
+    // Main plot actions
+    hasCfPlot = cfGenerators != null && cfGenerators.size() > 0;
+    OverviewPlotAction[] actions = new OverviewPlotAction[hasCfPlot ? 2 : 1];
+
+    // MA plot
+    OverviewPlotBean maBean = new OverviewPlotBean();
+    maBean.setTitle("MA plots");
+    maBean.setDescription("MA plots for each bioassay in this bioassay set");
+    maBean.setId("maplots");
+    maBean.setPlotGenerators(maGenerators);
+    actions[0] = maBean;
+    
+    if (hasCfPlot)
+    {
+      OverviewPlotBean cfBean = new OverviewPlotBean();
+      cfBean.setTitle("Correction factor plots");
+      cfBean.setDescription("MA-plot of the parent bioassays together " +
+          "with a correction factor for each spot in the current bioassayset.");
+      cfBean.setId("cfplots");
+      cfBean.setPlotGenerators(cfGenerators.toArray(new PlotGenerator[cfGenerators.size()]));
+      actions[1] = cfBean;
+    }
+    
     return actions;
   }

trunk/src/clients/web/net/sf/basedb/clients/web/formatter/ColorFormatter.java

@@ -68 +68 @@
     if (color != null)
     {
-      sb.append("class=\"colorbox\" style=\"background: #");
+      sb.append("class=\"colorbox inline\" style=\"background: #");
       sb.append(ColorGenerator.toHex(color));
       sb.append(";\"");
@@ -74 +74 @@
     else
     {
-      sb.append("class=\"colorbox nan\"");
+      sb.append("class=\"colorbox inline nan\"");
     }
-    sb.append("></div>");
+    sb.append("></div> ");
     sb.append(numberFormatter.format(value));
     return sb.toString();

trunk/src/clients/web/net/sf/basedb/clients/web/plugins/SimpleExport.java

@@ -627 +627 @@
         if (progress != null)
         {
-          int percent = (int)(100L * numExported / totalItems);
+          int percent = (int)(99L * numExported / totalItems);
           progress.display(percent, numExported + " of " + totalItems + " done.");
         }
+      }
+      
+      if (progress != null)
+      {
+        progress.display(100, numExported + " of " + totalItems + " done.");
       }
       

trunk/src/core/net/sf/basedb/core/AnnotationSet.java

@@ -399 +399 @@
   {
     super.onBeforeCommit(action);
+    if (action == Action.CREATE && item != null && item.getId() != 0)
+    {
+      getData().setItemId(item.getId());
+    }
     if ((snapshotIsInvalid && action == Action.UPDATE) || action == Action.DELETE) 
     {

trunk/src/core/net/sf/basedb/core/log/EntityDetails.java

@@ -29 +29 @@
 import org.hibernate.collection.PersistentCollection;
 import org.hibernate.type.Type;
-import org.hibernate.type.VersionType;
 
 /**
@@ -66 +65 @@
     this.types = types;
     this.dirty = new int[types.length]; // 0 = not known, -1 = not dirty, 1 = dirty
-    findDirtyCollections();
+    initializeDirtynessForSomeProperties();
   }
     
@@ -124 +123 @@
     if (dirty[index] == 0)
     {
+      Type t = types[index];
       Object c = state[index];
       Object o = previousState[index];
-      dirty[index] = types[index].isEqual(c, o, EntityMode.POJO) ? -1 : 1;
+      dirty[index] = t.isEqual(c, o, EntityMode.POJO) ? -1 : 1;
     }
     return dirty[index];
@@ -152 +152 @@
     for (int i = 0; i < types.length; ++i)
     {
-      if (dirty[i] == 0)
-      {
-        Type t = types[i];
-        if (!t.isCollectionType() && !(t instanceof VersionType))
-        {
-          Object c = state[i];
-          Object o = previousState[i];
-          dirty[i] = t.isEqual(c, o, EntityMode.POJO) ? -1 : 1;
-        }
-      }
-      if (dirty[i] == 1)
+      if (getDirty(i) == 1)
       {
         modified.append(s).append(properties[i]);
@@ -171 +161 @@
     if (suffix != null) modified.append(suffix);
     return numModified == 0 ? null : modified.toString();
+  }
+  
+  /**
+    Checks if the given property is the only modified property. 
+    @param property
+    @return TRUE if the given property (but no other) is dirty, FALSE in
+      all other cases
+    @since 3.2.3
+  */
+  public boolean isOnlyDirty(String property)
+  {
+    boolean propertyIsDirty = false;
+    for (int i = 0; i < types.length; ++i)
+    {
+      if (getDirty(i) == 1)
+      {
+        if (property.equals(properties[i])) 
+        {
+          propertyIsDirty = true;
+        }
+        else
+        {
+          // Found another dirty property
+          return false;
+        }
+      }
+    }
+    return propertyIsDirty;
   }
   
@@ -211 +229 @@
   
   /**
-    We must do this from the constructor since the "dirtyness" of a
+    We must initialize "dirtyness" for collections and some other
+    properties from the constructor. The "dirtyness" of a
     collection is reset after flush the SQL to the database, which is 
     completed before the rest of the logging is done.
   */
-  private void findDirtyCollections()
+  private void initializeDirtynessForSomeProperties()
   {
     for (int i = 0; i < types.length; ++i)
@@ -227 +246 @@
           dirty[i] = ((PersistentCollection)c).isDirty() ? 1 : -1;
         }
+        else
+        {
+          dirty[i] = -1;
+        }
+      }
+      else if ("version".equals(properties[i]))
+      {
+        // Always ignore changes to the "version" property
+        dirty[i] = -1;
       }
     }

trunk/src/core/net/sf/basedb/core/log/LoggingInterceptor.java

@@ -149 +149 @@
   public void afterTransactionCompletion(Transaction tx)
   {
-    if (logHandlers == null)
+    if (logHandlers != null)
     {
       boolean rollback = tx.wasRolledBack();

trunk/src/core/net/sf/basedb/core/log/db/AnnotationSetLogger.java

@@ -66 +66 @@
     if (details.getChangeType() != ChangeType.UPDATE) return;
     
+    // If the only modified property is the 'itemId' value, do not log it as a change
+    if (details.isOnlyDirty("itemId")) return;
+    
     LogControl logControl = logManager.getLogControl();
     AnnotationSetData as = (AnnotationSetData)details.getEntity();

trunk/www/admin/itemsubtypes/index.jsp

@@ -68 +68 @@
   private static final Item itemType = Item.ITEMSUBTYPE;
 
+  private static void registerExportUtils(ItemContext cc)
+  {
+    // Register formatters
+    cc.setObject("export.formatter.&fileTypes(dataFileType.name)", new NameableFormatter());
+    
+    // Register dataloaders
+    String subtypeParameter = "subtype";
+    // File types
+    final ItemQuery<DataFileType> fileTypesQuery = DataFileType.getQuery();
+    fileTypesQuery.include(cc.getInclude());
+    fileTypesQuery.join(Hql.innerJoin("itemSubtypes", "ist"));
+    fileTypesQuery.join(Hql.innerJoin("ist", "itemSubtype", "ist2"));
+    fileTypesQuery.restrict(Restrictions.eq(Hql.alias("ist2"), Expressions.parameter("subtype")));
+    fileTypesQuery.order(Orders.asc(Hql.property("name"))); 
+    cc.setObject("export.dataloader.&fileTypes(dataFileType.name)", new ItemQueryLoader(fileTypesQuery, subtypeParameter));
+  }
+
 %>
 <%
@@ -273 +290 @@
     cc.configureQuery(dc, query, true);
     cc.setQuery(query);
+    registerExportUtils(cc);
     JspContext jspContext = ExtensionsControl.createContext(dc, pageContext, GuiContext.list(itemType), null);
     ExtensionsInvoker listInvoker = ListColumnUtil.useExtensions(jspContext);
@@ -283 +301 @@
     // Run an export plugin in single-item context
     ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
+    registerExportUtils(cc);
     redirect = "../../common/export/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=ITEM&title=Export+item+subtype";
   }

trunk/www/admin/itemsubtypes/list_subtypes.jsp

@@ -103 +103 @@
   fileTypesQuery.include(cc.getInclude());
   fileTypesQuery.join(Hql.innerJoin("itemSubtypes", "ist"));
-  fileTypesQuery.restrict(Restrictions.eq(Hql.alias("ist"), Expressions.parameter("subtype")));
+  fileTypesQuery.join(Hql.innerJoin("ist", "itemSubtype", "ist2"));
+  fileTypesQuery.restrict(Restrictions.eq(Hql.alias("ist2"), Expressions.parameter("subtype")));
   fileTypesQuery.order(Orders.asc(Hql.property("name"))); 
 
@@ -220 +221 @@
         id="dataFileTypes"
         title="File types"
-        property="&dataFileTypes(name)"
+        property="&fileTypes(dataFileType.name)"
         datatype="string"
         filterable="true"

trunk/www/biomaterials/extracts/list_extracts.jsp

@@ -720 +720 @@
                     %>
                     <base:propertyvalue item="<%=item%>" property="parent" />
-                    <%=usedQuantity != null ? "(" + usedQuantity + "µg)" : ""%>
+                    <%=usedQuantity != null ? "(" + numericFormatter.format(usedQuantity) + "µg)" : ""%>
                     <%
                   }
@@ -741 +741 @@
                       if (usedQuantity != null)
                       {
-                        out.write(" (" + usedQuantity + "µg)");
+                        out.write(" (" + numericFormatter.format(usedQuantity) + "µg)");
                       }
                       separator = ", ";

trunk/www/biomaterials/samples/list_samples.jsp

@@ -720 +720 @@
                     %>
                     <base:propertyvalue item="<%=item%>" property="parent"/>
-                    <%=usedQuantity != null ? "(" + usedQuantity + "µg)" : ""%>
+                    <%=usedQuantity != null ? "(" + numericFormatter.format(usedQuantity) + "µg)" : ""%>
                     <%
                   }
@@ -741 +741 @@
                       if (usedQuantity != null)
                       {
-                        out.write(" (" + usedQuantity + "µg)");
+                        out.write(" (" + numericFormatter.format(usedQuantity) + "µg)");
                       }
                       separator = ", ";

trunk/www/common/annotations/annotate.jsp

@@ -39 +39 @@
   import="net.sf.basedb.core.Subtypable"
   import="net.sf.basedb.core.ItemSubtype"
+  import="net.sf.basedb.core.BioPlateType"
+  import="net.sf.basedb.core.BioPlate"
   import="net.sf.basedb.core.AnnotationSet"
   import="net.sf.basedb.core.Annotation"
@@ -142 +144 @@
   {
     ItemSubtype subtype = null;
-    if (subtypeId == -1 && item != null && item instanceof Subtypable)
+    if (subtypeId > 0)
+    {
+      subtype = ItemSubtype.getById(dc, subtypeId);
+    }
+    else if (item instanceof Subtypable)
     {
       subtype = ((Subtypable)item).getItemSubtype();
     }
-    else if (subtypeId > 0)
-    {
-      subtype = ItemSubtype.getById(dc, subtypeId);
+    else if (item instanceof BioPlate)
+    {
+      BioPlateType bpt = ((BioPlate)item).getBioPlateType();
+      subtype = bpt.getItemSubtype();
+      if (subtype == null) selectedCategoryName = bpt.getName();
     }
     if (subtype != null) selectedCategoryName = subtype.getName();

trunk/www/common/plugin/index.jsp

@@ -589 +589 @@
   else if ("ExportImmediately".equals(cmd))
   {
+    out.clearBuffer();
     PluginResponse pluginResponse = (PluginResponse)sc.getSessionSetting("plugin.configure.response");
     ExportOutputStream exportStream = new ServletExportOutputStream(response);

trunk/www/filemanager/directories/list_directories.jsp

@@ -280 +280 @@
       if (window.top.setSelected)
       {
-        //window.top.setSelected('', path);
+        window.top.setSelected('', path);
       }
     }

trunk/www/include/styles/main.css

@@ -691 +691 @@
 }
 
-/* Otline for a colored box; background should be set on the element */
+/* Outline for a colored box; background should be set on the element */
 .colorbox 
 {
@@ -697 +697 @@
   height: 1em; 
   border: 1px solid #A0A0A0; 
+}
+
+/* Color box inline with other text */
+.colorbox.inline 
+{
+  display: inline-block;
 }
 

trunk/www/plugins/net/sf/basedb/plugins/executor/external_plugin_parameters.jsp

@@ -81 +81 @@
   {
     externalParameters = ParameterDefinition.parseXml(xml, false);
-    if (true) throw new RuntimeException("fff");
   }
   catch (Throwable ex)

trunk/www/views/physicalbioassays/list_bioassays.jsp

@@ -131 +131 @@
   int numListed = 0;
   Formatter<Date> dateFormatter = FormatterFactory.getDateFormatter(sc);
+  Formatter<Number> numericFormatter = FormatterFactory.getNumberFormatter(sc);
   JspContext jspContext = ExtensionsControl.createContext(dc, pageContext, guiContext, null);
   ExtensionsInvoker invoker = ToolbarUtil.useExtensions(jspContext);
@@ -571 +572 @@
                         if (usedQuantity != null)
                         {
-                          out.write(usedQuantity + "µg");
+                          out.write(numericFormatter.format(usedQuantity) + "µg");
                           if (tag != null) out.write("; ");
                         }