Changeset 6334

Timestamp:

Oct 16, 2013, 4:39:55 PM (10 years ago)

Author:

olle

Message:

Refs #1772. Support for annotatable Software items added.

Location:

trunk

Files:

• src/core/net/sf/basedb/core/DerivedBioAssay.java (modified) (1 diff)
• src/core/net/sf/basedb/core/RawBioAssay.java (modified) (1 diff)
• src/core/net/sf/basedb/core/Software.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/data/SoftwareData.java (modified) (1 diff)
• src/core/net/sf/basedb/util/overview/loader/SoftwareLoader.java (modified) (1 diff)
• www/admin/software/edit_software.jsp (modified) (2 diffs)
• www/admin/software/index.jsp (modified) (3 diffs)
• www/admin/software/list_software.jsp (modified) (4 diffs)
• www/admin/software/software.js (modified) (3 diffs)
• www/admin/software/view_software.jsp (modified) (1 diff)
• www/include/scripts/main.js (modified) (1 diff)
• www/views/derivedbioassays/bioassays.js (modified) (1 diff)
• www/views/rawbioassays/bioassays.js (modified) (1 diff)

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

@@ -368 +368 @@
       if (getData().getExtract() != null) annotatable.add(getExtract());
       if (getData().getHardware() != null) annotatable.add(getHardware());
+      if (getData().getSoftware() != null) annotatable.add(getSoftware());
     }
     catch (PermissionDeniedException ex)

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

@@ -244 +244 @@
       if (getData().getParentBioAssay() != null) annotatable.add(getParentBioAssay());
       if (getData().getParentExtract() != null) annotatable.add(getParentExtract());
+      if (getData().getSoftware() != null) annotatable.add(getSoftware());
     }
     catch (PermissionDeniedException ex)

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

@@ -38 +38 @@
 */
 public class Software
-  extends CommonItem<SoftwareData>
+  extends AnnotatedItem<SoftwareData>
   implements Registered, Subtypable
 {
@@ -171 +171 @@
   {
     return DateUtil.copy(getData().getEntryDate());
+  }
+  // -------------------------------------------
+  /*
+    From the Annotatable interface
+    -------------------------------------------
+  */
+  /**
+    @return Always null
+    @since 3.3
+  */
+  @Override
+  public Set<Annotatable> getAnnotatableParents()
+  {
+    return null;
   }
   // -------------------------------------------

trunk/src/core/net/sf/basedb/core/data/SoftwareData.java

@@ -36 +36 @@
 */
 public class SoftwareData
-  extends CommonData
+  extends AnnotatedData
   implements RegisteredData, SubtypableData
 {

trunk/src/core/net/sf/basedb/util/overview/loader/SoftwareLoader.java

@@ -84 +84 @@
     }
     Node softwareNode = createItemNode(nf, software, software, denied, 
-        parentNode, ChildNodeDirection.NONE);
+        parentNode, ChildNodeDirection.PROPERTY);
     return softwareNode;
   }
   // -----------------------------------
-  
+  /*
+    From the AbstractNodeLoader class
+    ----------------------------------
+  */
+  /**
+    Loads annotations and software parameters for the given software node.
+    @see RawBioAssayLoader#createForwardNode(DbControl, OverviewContext, Node)
+  */
+  @Override
+  protected void loadPropertyChildNodes(DbControl dc, OverviewContext context, Node softwareNode)
+  {
+    getNodeLoader(context, Item.ANNOTATION).createPropertyNode(dc, context, softwareNode);
+  }
+  // -------------------------------------  
 }

trunk/www/admin/software/edit_software.jsp

@@ -26 +26 @@
 --%>
 <%@ page pageEncoding="UTF-8" session="false"
+  import="net.sf.basedb.core.AnnotationType"
   import="net.sf.basedb.core.SessionControl"
   import="net.sf.basedb.core.DbControl"
@@ -197 +198 @@
       </table>
     </t:tab>
+    <t:tab id="annotations" title="Annotations" helpid="annotations.edit">
+      <jsp:include page="../../common/annotations/annotate_frameset.jsp">
+        <jsp:param name="item_type" value="<%=itemType.name()%>" />
+        <jsp:param name="item_id" value="<%=itemId%>" />
+        <jsp:param name="ID" value="<%=ID%>" />
+      </jsp:include>
+    </t:tab>
     </t:tabcontrol>
     </form>

trunk/www/admin/software/index.jsp

@@ -179 +179 @@
       }
       
+      Base.updateAnnotations(dc, software, software, request);
       // OnSave extensions
       invoker.render(OnSaveRenderer.ON_SAVE);
@@ -215 +216 @@
       message = (numRemoved == 0 ? "No" : "Only "+numRemoved+" of "+numTotal) + " items could be deleted, because you have no DELETE permission";
     }
-    redirect = listPage;
+    redirect = listPage+(message != null ? "&popmessage="+HTML.urlEncode(message) : "");
   }
   else if ("RestoreItem".equals(cmd))
@@ -238 +239 @@
       message = (numRemoved == 0 ? "No" : "Only "+numRemoved+" of "+numTotal) + " items could be restored, because you have no WRITE permission";
     }
-    redirect = listPage;
+    redirect = listPage+(message != null ? "&popmessage="+HTML.urlEncode(message) : "");
   }
   else if ("ShareItem".equals(cmd))

trunk/www/admin/software/list_software.jsp

@@ -30 +30 @@
   import="net.sf.basedb.core.Software"
   import="net.sf.basedb.core.ItemSubtype"
+  import="net.sf.basedb.core.Annotation"
+  import="net.sf.basedb.core.AnnotationType"
+  import="net.sf.basedb.core.AnnotationSet"
   import="net.sf.basedb.core.ItemQuery"
   import="net.sf.basedb.core.Include"
@@ -80 +83 @@
 final DbControl dc = sc.newDbControl();
 ItemResultIterator<Software> software = null;
+ItemResultList<AnnotationType> annotationTypes = null;
 try
 {
   Formatter<Date> dateFormatter = FormatterFactory.getDateFormatter(sc);
   final ItemQuery<ItemSubtype> subtypesQuery = Base.getSubtypesQuery(itemType);
+  final ItemQuery<AnnotationType> annotationTypeQuery = Base.getAnnotationTypesQuery(itemType);
+  annotationTypes = annotationTypeQuery.list(dc);
 
   Map<Plugin.MainType, Integer> pluginCount = PluginDefinition.countPlugins(dc, guiContext);
@@ -197 +203 @@
         exportable="true"
       />
+      <%
+      for (AnnotationType at : annotationTypes)
+      {
+        Enumeration<String, String> annotationEnum = null;
+        Formatter formatter = FormatterFactory.getTypeFormatter(sc, at.getValueType());
+        if (at.isEnumeration())
+        {
+          annotationEnum = new Enumeration<String, String>();
+          List<?> values = at.getValues();
+          for (Object value : values)
+          {
+            String encoded = formatter.format(value);
+            annotationEnum.add(encoded, encoded);
+          }
+        }
+        %>
+        <tbl:columndef 
+          id="<%="at"+at.getId()%>"
+          title="<%=HTML.encodeTags(at.getName())+" [A]"%>" 
+          property="<%="#"+at.getId()%>"
+          annotation="true"
+          datatype="<%=at.getValueType().getStringValue()%>"
+          enumeration="<%=annotationEnum%>"
+          smartenum="<%=at.getDisplayAsList() %>"
+          sortable="<%=at.getMultiplicity() == 1%>" 
+          filterable="true" 
+          exportable="true"
+          formatter="<%=formatter%>"
+          unit="<%=at.getDefaultUnit()%>"
+        />
+        <%
+      }
+      %>  
       <tbl:columndef
         id="permission"
@@ -416 +455 @@
                   /></tbl:cell>
                 <tbl:cell column="description"><%=HTML.encodeTags(item.getDescription())%></tbl:cell>
+                <%
+                AnnotationSet as = item.isAnnotated() ? item.getAnnotationSet() : null;
+                if (as != null)
+                {
+                  for (AnnotationType at : annotationTypes)
+                  {
+                    if (as.hasAnnotation(at))
+                    {
+                      Annotation a = as.getAnnotation(at);
+                      String suffix = a.getUnitSymbol(null);
+                      if (suffix != null) suffix = "&nbsp;" + suffix;
+                      %>
+                      <tbl:cell 
+                        column="<%="at"+at.getId()%>"
+                        ><tbl:cellvalue 
+                          list="<%=a.getValues(null)%>"
+                          suffix="<%=suffix%>"
+                      /></tbl:cell>
+                      <%
+                    }
+                  }
+                }
+                %>
                 <tbl:cell column="permission"><%=PermissionUtil.getShortPermissions(item)%></tbl:cell>
                 <tbl:cell column="sharedTo">

trunk/www/admin/software/software.js

@@ -44 +44 @@
       
       // Tab validation
+      TabControl.addTabActivateListener('settings.annotations', software.loadAnnotationsFrame);
       TabControl.addTabValidator('settings.info', software.validateSoftware);
     }
@@ -61 +62 @@
       Buttons.addClickHandler('btnImport', Buttons.runPlugin, attributes);
       Buttons.addClickHandler('btnRunPlugin', Buttons.runPlugin, attributes);
+
+      TabControl.addTabActivateListener('main.annotations', AnnotationsList.loadOnce);
     }
     else if (pageId == 'list-page')
@@ -99 +102 @@
     if (TabControl.validateActiveTab('settings'))
     {
+      Annotations.saveModifiedAnnotationsToForm(frm);
       frm.submit();
     }
+  }
+
+  software.loadAnnotationsFrame = function()
+  {
+    Annotations.autoLoadEditFrame(null, ItemSubtype.getSubtypeId('subtype_id'));
   }
 

trunk/www/admin/software/view_software.jsp

@@ -252 +252 @@
       </jsp:include>
     </t:tab>
+    <t:tab id="annotations" title="Annotations" 
+      tooltip="View annotation values" clazz="white">
+      <jsp:include page="../../common/annotations/list_frameset.jsp">
+        <jsp:param name="item_type" value="<%=itemType.name()%>" />
+        <jsp:param name="item_id" value="<%=itemId%>" />
+        <jsp:param name="ID" value="<%=ID%>" />
+      </jsp:include>
+    </t:tab>
     </t:tabcontrol>
   </base:body>

trunk/www/include/scripts/main.js

@@ -548 +548 @@
     this.controllers['SAMPLE'] = { url:'biomaterials/samples/index.jsp', width:750, height:500 };
     this.controllers['SESSION'] = { url:'views/sessions/index.jsp', width:450, height:300, popup:true, edit:false, noAnyToAny:true };
-    this.controllers['SOFTWARE'] = { url:'admin/software/index.jsp', width:450, height:300 };
+    this.controllers['SOFTWARE'] = { url:'admin/software/index.jsp', width:800, height:500 };
     this.controllers['TAG'] = { url:'biomaterials/tags/index.jsp', width:450, height:300 };
     this.controllers['TRANSFORMATION'] = { url:'views/experiments/transformations/index.jsp', width:450, height:300, noAnyToAny:true };

trunk/www/views/derivedbioassays/bioassays.js

@@ -240 +240 @@
     var hardwareId = Math.abs(parseInt(frm.hardware_id.value));
     if (hardwareId > 0) parents[parents.length] = 'HARDWARE:'+hardwareId;
+    var softwareId = Math.abs(parseInt(frm.software_id.value));
+    if (softwareId > 0) parents[parents.length] = 'SOFTWARE:'+softwareId;
     return parents;
   }

trunk/www/views/rawbioassays/bioassays.js

@@ -199 +199 @@
     var extractId = Math.abs(parseInt(frm.extract_id.value));
     if (extractId > 0) parents[parents.length] = 'EXTRACT:'+extractId;
+    var softwareId = Math.abs(parseInt(frm.software_id.value));
+    if (softwareId > 0) parents[parents.length] = 'SOFTWARE:'+softwareId;
     if (frm.arraydesign_id)
     {