Changeset 3400

Timestamp:

May 29, 2007, 8:47:04 AM (14 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #534.

Location:

trunk

Files:

• doc/src/docbook/userdoc/annotations.xml (modified) (5 diffs)
• doc/src/docbook/userdoc/experiments.xml (modified) (5 diffs)
• www/lims/plates/edit_plate.jsp (modified) (1 diff)
• www/views/experiments/bioassays/edit_bioassay.jsp (modified) (1 diff)
• www/views/experiments/bioassaysets/edit_bioassayset.jsp (modified) (1 diff)
• www/views/rawbioassays/edit_rawbioassay.jsp (modified) (1 diff)
• www/views/scans/edit_scan.jsp (modified) (1 diff)

trunk/doc/src/docbook/userdoc/annotations.xml

@@ -34 +34 @@
     <title>Annotation Types</title>
 
-    <helptext id="annotationtype.view.properties" 
+    <helptext external_id="annotationtype.view.properties" 
       title="Annotation types">
     <para>
@@ -565 +565 @@
       
       <para>
-        Annotation types marked with angle brackets are protocol 
-        parameters.
+        Annotation types marked with angle brackets
+        <nohelp>
+        (<inlinemediaobject>
+          <imageobject><imagedata fileref="figures/parameter.gif" format="GIF"
+          /></imageobject>
+        </inlinemediaobject>)</nohelp>
+        are protocol parameters.
       </para>
       
@@ -589 +594 @@
         <listitem>
           <para>
-          <guilabel>uncategorized</guilabel>: Display only annoatation types
+          <guilabel>uncategorized</guilabel>: Display only annotation types
           that hasn't been put into a category.
           </para>
@@ -596 +601 @@
       </para>
       
+      <seeother>
+        <other external_id="annotations.edit.inherited">Inherit annotations</other>
+      </seeother>
       
     </helptext>
@@ -601 +609 @@
     <sect2 id="annotations.inheriting">
       <title>Inheriting annotations from other items</title>
+      
+      <helptext external_id="annotations.edit.inherited" 
+        title="Inherit annotations">
+        <para>
+          An item may inherit annotations from any of it's parent items.
+          E.g. an extract can inherit annotations from the sample or biosource
+          it was created from. This is an important feature to make the
+          experimental factors work. Annotations that should be used as 
+          experimental factors must be inherited to the raw bioassay level.
+          <nohelp>See <xref linkend="experiments_analysis.experiment.factors" /> for more 
+          information about experimental factors.</nohelp>
+        </para>
+        
+        <nohelp>
+        <figure
+          id="annotations.figures.inherit">
+          <title>Inheriting annotations from a parent item</title>
+          <screenshot>
+            <mediaobject>
+              <imageobject>
+                <imagedata
+                  fileref="figures/inherit_annotations.png" format="PNG" />
+              </imageobject>
+            </mediaobject>
+          </screenshot>
+        </figure>
+        </nohelp>
+    
+        <para>
+          On this screen is a tree-like structure in two levels. The first level 
+          lists all parent items which has at least one annotations. The second
+          level lists the annotations and protocol parameters for the item.
+          Selecting an item in the first level will inherit all annotations
+          from that item, including those that you maybe add later. 
+          Selecting an annotation or protocol parameter at the second level
+          will inherit only the selected one.
+        </para>
+        
+        <note>
+          <itemizedlist>
+          <listitem>
+            <para>
+            The inheritance is implemented by reference. This means that if
+            you change the value of an annotation the new value is automatically
+            picked up by those inheriting it.
+            </para>
+          </listitem>
+          <listitem>
+            <para>
+            You can't inherit annotations from an item which doesn't have 
+            annotations.
+            </para>
+          </listitem>
+          <listitem>
+            <para>
+            If you delete an annotation from a parent item, the inheritance will
+            be lost, even if you later add a value again.
+            </para>
+          </listitem>
+          </itemizedlist>
+        </note>
+        
+        <warning>
+          <para>
+          If you rearrange links to parent items after you have 
+          specified inheritance, it may happen that you are inheriting
+          annotation from non-parent items. This will be flagged with a warning
+          icon in the list, and must be fixed manually. The experiment validation
+          tool is an excellent help for locating this kind of problems.
+          <nohelp>See <xref linkend="experiments_analysis.experiment.overview" />.</nohelp>
+          </para>
+        </warning>
+    
+        <seeother>
+          <other external_id="annotations.edit">Annotations and parameters</other>
+          <other external_id="experiment.edit.factors">Experimental factors</other>
+          <other external_id="experiment.overview">Experiment validation tool</other>
+        </seeother>
+      
+      </helptext>     
+      
     </sect2>
     

trunk/doc/src/docbook/userdoc/experiments.xml

@@ -272 +272 @@
         in the analysis of your data the values must be accessible
         from the raw bioassays. Since most of your annotations are
-        probably made at the sample level the raw bioassays must 
-        inherit those annotations. 
-        <nohelp>Read <xref linkend="annotations" /> 
+        probably made at the sample or biosource level the raw bioassays 
+        must inherit those annotations. 
+        <nohelp>Read <xref linkend="annotations.inheriting" /> 
         for more information about this.</nohelp>
       </para>
@@ -300 +300 @@
   <sect2 id="experiments_analysis.experiment.overview">
     <title>Experiment overview</title>
+
+    <helptext external_id="experiment.overview" 
+      title="Experiment overview">
     
     <para>
@@ -310 +313 @@
     </para>
     
+    <nohelp>
     <para>
       You can access the overview of an experiment by navigating
@@ -327 +331 @@
       </screenshot>
     </figure>
-    
-    <helptext external_id="experiment.overview" 
-      title="Experiment overview">
+    </nohelp>
+    
     <para>
       The page is divided into three sections:
@@ -416 +419 @@
           <varlistentry>
             <term>
-            <indexterm><primary>Presets</primary><secondary>experiment validation</secondary></indexterm>
             <guilabel>Presets</guilabel></term>
             <listitem>

trunk/www/lims/plates/edit_plate.jsp

@@ -296 +296 @@
     </t:tab>
     
-    <t:tab id="inheritedAnnotations" title="Inherited annotations" helpid="annotations.edit.inerited">
+    <t:tab id="inheritedAnnotations" title="Inherited annotations" helpid="annotations.edit.inherited">
     
       <iframe name="inheritedAnnotations" id="idInheritedAnnotations" src="../../common/annotations/wait.jsp" 

trunk/www/views/experiments/bioassays/edit_bioassay.jsp

@@ -181 +181 @@
     </t:tab>
     
-    <t:tab id="inheritedAnnotations" title="Inherited annotations" helpid="annotations.edit.inerited">
+    <t:tab id="inheritedAnnotations" title="Inherited annotations" helpid="annotations.edit.inherited">
       <iframe name="inheritedAnnotations" id="idInheritedAnnotations" src="../../../common/annotations/wait.jsp" 
         width="100%"  height="<%=(int)(scale*370)%>" frameborder=0 vspace=0 hspace=0

trunk/www/views/experiments/bioassaysets/edit_bioassayset.jsp

@@ -193 +193 @@
     </t:tab>
     
-    <t:tab id="inheritedAnnotations" title="Inherited annotations" helpid="annotations.edit.inerited">
+    <t:tab id="inheritedAnnotations" title="Inherited annotations" helpid="annotations.edit.inherited">
       <iframe name="inheritedAnnotations" id="idInheritedAnnotations" src="../../../common/annotations/wait.jsp" 
         width="100%"  height="<%=(int)(scale*370)%>" frameborder=0 vspace=0 hspace=0

trunk/www/views/rawbioassays/edit_rawbioassay.jsp

@@ -695 +695 @@
     </t:tab>
     
-    <t:tab id="inheritedAnnotations" title="Inherited annotations" helpid="annotations.edit.inerited">
+    <t:tab id="inheritedAnnotations" title="Inherited annotations" helpid="annotations.edit.inherited">
       <iframe name="inheritedAnnotations" id="idInheritedAnnotations" src="../../common/annotations/wait.jsp" 
         width="100%"  height="<%=(int)(scale*370)%>" frameborder=0 vspace=0 hspace=0

trunk/www/views/scans/edit_scan.jsp

@@ -440 +440 @@
     </t:tab>
     
-    <t:tab id="inheritedAnnotations" title="Inherited annotations" helpid="annotations.edit.inerited">
+    <t:tab id="inheritedAnnotations" title="Inherited annotations" helpid="annotations.edit.inherited">
     
       <iframe name="inheritedAnnotations" id="idInheritedAnnotations" src="../../common/annotations/wait.jsp"