Changeset 3400 for trunk


Ignore:
Timestamp:
May 29, 2007, 8:47:04 AM (15 years ago)
Author:
Nicklas Nordborg
Message:

Fixes #534.

Location:
trunk
Files:
7 edited

Legend:

Unmodified
Added
Removed
  • trunk/doc/src/docbook/userdoc/annotations.xml

    r3396 r3400  
    3434    <title>Annotation Types</title>
    3535
    36     <helptext id="annotationtype.view.properties"
     36    <helptext external_id="annotationtype.view.properties"
    3737      title="Annotation types">
    3838    <para>
     
    565565     
    566566      <para>
    567         Annotation types marked with angle brackets are protocol
    568         parameters.
     567        Annotation types marked with angle brackets
     568        <nohelp>
     569        (<inlinemediaobject>
     570          <imageobject><imagedata fileref="figures/parameter.gif" format="GIF"
     571          /></imageobject>
     572        </inlinemediaobject>)</nohelp>
     573        are protocol parameters.
    569574      </para>
    570575     
     
    589594        <listitem>
    590595          <para>
    591           <guilabel>uncategorized</guilabel>: Display only annoatation types
     596          <guilabel>uncategorized</guilabel>: Display only annotation types
    592597          that hasn't been put into a category.
    593598          </para>
     
    596601      </para>
    597602     
     603      <seeother>
     604        <other external_id="annotations.edit.inherited">Inherit annotations</other>
     605      </seeother>
    598606     
    599607    </helptext>
     
    601609    <sect2 id="annotations.inheriting">
    602610      <title>Inheriting annotations from other items</title>
     611     
     612      <helptext external_id="annotations.edit.inherited"
     613        title="Inherit annotations">
     614        <para>
     615          An item may inherit annotations from any of it's parent items.
     616          E.g. an extract can inherit annotations from the sample or biosource
     617          it was created from. This is an important feature to make the
     618          experimental factors work. Annotations that should be used as
     619          experimental factors must be inherited to the raw bioassay level.
     620          <nohelp>See <xref linkend="experiments_analysis.experiment.factors" /> for more
     621          information about experimental factors.</nohelp>
     622        </para>
     623       
     624        <nohelp>
     625        <figure
     626          id="annotations.figures.inherit">
     627          <title>Inheriting annotations from a parent item</title>
     628          <screenshot>
     629            <mediaobject>
     630              <imageobject>
     631                <imagedata
     632                  fileref="figures/inherit_annotations.png" format="PNG" />
     633              </imageobject>
     634            </mediaobject>
     635          </screenshot>
     636        </figure>
     637        </nohelp>
     638   
     639        <para>
     640          On this screen is a tree-like structure in two levels. The first level
     641          lists all parent items which has at least one annotations. The second
     642          level lists the annotations and protocol parameters for the item.
     643          Selecting an item in the first level will inherit all annotations
     644          from that item, including those that you maybe add later.
     645          Selecting an annotation or protocol parameter at the second level
     646          will inherit only the selected one.
     647        </para>
     648       
     649        <note>
     650          <itemizedlist>
     651          <listitem>
     652            <para>
     653            The inheritance is implemented by reference. This means that if
     654            you change the value of an annotation the new value is automatically
     655            picked up by those inheriting it.
     656            </para>
     657          </listitem>
     658          <listitem>
     659            <para>
     660            You can't inherit annotations from an item which doesn't have
     661            annotations.
     662            </para>
     663          </listitem>
     664          <listitem>
     665            <para>
     666            If you delete an annotation from a parent item, the inheritance will
     667            be lost, even if you later add a value again.
     668            </para>
     669          </listitem>
     670          </itemizedlist>
     671        </note>
     672       
     673        <warning>
     674          <para>
     675          If you rearrange links to parent items after you have
     676          specified inheritance, it may happen that you are inheriting
     677          annotation from non-parent items. This will be flagged with a warning
     678          icon in the list, and must be fixed manually. The experiment validation
     679          tool is an excellent help for locating this kind of problems.
     680          <nohelp>See <xref linkend="experiments_analysis.experiment.overview" />.</nohelp>
     681          </para>
     682        </warning>
     683   
     684        <seeother>
     685          <other external_id="annotations.edit">Annotations and parameters</other>
     686          <other external_id="experiment.edit.factors">Experimental factors</other>
     687          <other external_id="experiment.overview">Experiment validation tool</other>
     688        </seeother>
     689     
     690      </helptext>     
     691     
    603692    </sect2>
    604693   
  • trunk/doc/src/docbook/userdoc/experiments.xml

    r3394 r3400  
    272272        in the analysis of your data the values must be accessible
    273273        from the raw bioassays. Since most of your annotations are
    274         probably made at the sample level the raw bioassays must
    275         inherit those annotations.
    276         <nohelp>Read <xref linkend="annotations" />
     274        probably made at the sample or biosource level the raw bioassays
     275        must inherit those annotations.
     276        <nohelp>Read <xref linkend="annotations.inheriting" />
    277277        for more information about this.</nohelp>
    278278      </para>
     
    300300  <sect2 id="experiments_analysis.experiment.overview">
    301301    <title>Experiment overview</title>
     302
     303    <helptext external_id="experiment.overview"
     304      title="Experiment overview">
    302305   
    303306    <para>
     
    310313    </para>
    311314   
     315    <nohelp>
    312316    <para>
    313317      You can access the overview of an experiment by navigating
     
    327331      </screenshot>
    328332    </figure>
    329    
    330     <helptext external_id="experiment.overview"
    331       title="Experiment overview">
     333    </nohelp>
     334   
    332335    <para>
    333336      The page is divided into three sections:
     
    416419          <varlistentry>
    417420            <term>
    418             <indexterm><primary>Presets</primary><secondary>experiment validation</secondary></indexterm>
    419421            <guilabel>Presets</guilabel></term>
    420422            <listitem>
  • trunk/www/lims/plates/edit_plate.jsp

    r2978 r3400  
    296296    </t:tab>
    297297   
    298     <t:tab id="inheritedAnnotations" title="Inherited annotations" helpid="annotations.edit.inerited">
     298    <t:tab id="inheritedAnnotations" title="Inherited annotations" helpid="annotations.edit.inherited">
    299299   
    300300      <iframe name="inheritedAnnotations" id="idInheritedAnnotations" src="../../common/annotations/wait.jsp"
  • trunk/www/views/experiments/bioassays/edit_bioassay.jsp

    r2978 r3400  
    181181    </t:tab>
    182182   
    183     <t:tab id="inheritedAnnotations" title="Inherited annotations" helpid="annotations.edit.inerited">
     183    <t:tab id="inheritedAnnotations" title="Inherited annotations" helpid="annotations.edit.inherited">
    184184      <iframe name="inheritedAnnotations" id="idInheritedAnnotations" src="../../../common/annotations/wait.jsp"
    185185        width="100%"  height="<%=(int)(scale*370)%>" frameborder=0 vspace=0 hspace=0
  • trunk/www/views/experiments/bioassaysets/edit_bioassayset.jsp

    r2978 r3400  
    193193    </t:tab>
    194194   
    195     <t:tab id="inheritedAnnotations" title="Inherited annotations" helpid="annotations.edit.inerited">
     195    <t:tab id="inheritedAnnotations" title="Inherited annotations" helpid="annotations.edit.inherited">
    196196      <iframe name="inheritedAnnotations" id="idInheritedAnnotations" src="../../../common/annotations/wait.jsp"
    197197        width="100%"  height="<%=(int)(scale*370)%>" frameborder=0 vspace=0 hspace=0
  • trunk/www/views/rawbioassays/edit_rawbioassay.jsp

    r2978 r3400  
    695695    </t:tab>
    696696   
    697     <t:tab id="inheritedAnnotations" title="Inherited annotations" helpid="annotations.edit.inerited">
     697    <t:tab id="inheritedAnnotations" title="Inherited annotations" helpid="annotations.edit.inherited">
    698698      <iframe name="inheritedAnnotations" id="idInheritedAnnotations" src="../../common/annotations/wait.jsp"
    699699        width="100%"  height="<%=(int)(scale*370)%>" frameborder=0 vspace=0 hspace=0
  • trunk/www/views/scans/edit_scan.jsp

    r2978 r3400  
    440440    </t:tab>
    441441   
    442     <t:tab id="inheritedAnnotations" title="Inherited annotations" helpid="annotations.edit.inerited">
     442    <t:tab id="inheritedAnnotations" title="Inherited annotations" helpid="annotations.edit.inherited">
    443443   
    444444      <iframe name="inheritedAnnotations" id="idInheritedAnnotations" src="../../common/annotations/wait.jsp"
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