Changeset 5801

Timestamp:

Oct 12, 2011, 1:26:21 PM (12 years ago)

Author:

Nicklas Nordborg

Message:

References #1590: Documentation cleanup

New and updated screenshots for chapters 20-22 - Admin documentation.

Location:

trunk

Files:

• doc/src/docbook/admin/accounts.xml (modified) (36 diffs)
• doc/src/docbook/admin/installation.xml (modified) (9 diffs)
• doc/src/docbook/admin/plugins.xml (modified) (3 diffs)
• doc/src/docbook/figures/bioplate.png (deleted)
• doc/src/docbook/figures/broadcast_message.png (added)
• doc/src/docbook/figures/default_membership.png (added)
• doc/src/docbook/figures/group_edit.png (added)
• doc/src/docbook/figures/group_members.png (added)
• doc/src/docbook/figures/installed_extensions.png (modified) (previous)
• doc/src/docbook/figures/plugin_configuration.png (modified) (previous)
• doc/src/docbook/figures/plugin_jobagents.png (modified) (previous)
• doc/src/docbook/figures/plugin_permissions.png (modified) (previous)
• doc/src/docbook/figures/plugin_wizard.png (modified) (previous)
• doc/src/docbook/figures/plugins_install_manual.png (modified) (previous)
• doc/src/docbook/figures/plugins_install_wizard.png (modified) (previous)
• doc/src/docbook/figures/plugins_install_wizard_2.png (modified) (previous)
• doc/src/docbook/figures/quota_edit.png (added)
• doc/src/docbook/figures/quota_values.png (added)
• doc/src/docbook/figures/role_edit.png (added)
• doc/src/docbook/figures/role_members.png (added)
• doc/src/docbook/figures/role_permissions.png (added)
• doc/src/docbook/figures/server_configuration.png (added)
• doc/src/docbook/figures/test_with_file.png (modified) (previous)
• doc/src/docbook/figures/test_with_file_mappings.png (modified) (previous)
• doc/src/docbook/figures/user_contact.png (added)
• doc/src/docbook/figures/user_edit.png (added)
• doc/src/docbook/figures/user_extra.png (added)
• doc/src/docbook/figures/user_membership.png (added)
• www/admin/plugindefinitions/edit_plugin.jsp (modified) (1 diff)
• www/common/plugin/test_with_file.jsp (modified) (1 diff)

trunk/doc/src/docbook/admin/accounts.xml

@@ -58 +58 @@
       <sect3 id="accounts.users.edit.properties">       
         <title>Properties</title>
+        
+        <figure id="accounts.figures.userproperties">
+          <title>User properties</title>
+          <screenshot>
+            <mediaobject>
+              <imageobject><imagedata fileref="figures/user_edit.png" format="PNG"
+                /></imageobject>
+            </mediaobject>
+          </screenshot>
+        </figure>
+          
         <helptext external_id="user.edit" title="Edit user account">
           <para>These are the properties for a user account.</para>
@@ -84 +95 @@
             <varlistentry>
               <term>
-                <optional>
                   <guilabel>External ID</guilabel>
-                </optional>
               </term>
               <listitem>
@@ -121 +130 @@
             <varlistentry>
               <term>
-                <optional>
                   <guilabel>Quota</guilabel>
-                </optional>
               </term>
               <listitem>
@@ -131 +138 @@
             <varlistentry>
               <term>
-                <optional>
                   <guilabel>Quota group</guilabel>
-                </optional>
               </term>
               <listitem>
@@ -146 +151 @@
             <varlistentry>
               <term>
-                <optional>
                   <guilabel>Home directory</guilabel>
-                </optional>
               </term>
               <listitem>
@@ -162 +165 @@
             <varlistentry>
               <term>
-                <optional>
                   <guilabel>Expiration date</guilabel>
-                </optional>
               </term>
               <listitem>
@@ -216 +217 @@
           <seeother>
             <other external_id="user.edit.contact">Edit contact information</other>
-            <other external_id="user.additional">Edit additional info</other>
+            <other external_id="user.edit.additional">Edit additional info</other>
             <other external_id="user.edit.membership">Group and role membership</other>
           </seeother>
@@ -224 +225 @@
       <sect3 id="user._administration.users.edit.contact">
         <title>Contact information</title>
+  
+        <figure id="accounts.figures.usercontact">
+          <title>Contact information</title>
+          <screenshot>
+            <mediaobject>
+              <imageobject><imagedata fileref="figures/user_contact.png" format="PNG"
+                /></imageobject>
+            </mediaobject>
+          </screenshot>
+        </figure>
+  
         <helptext external_id="user.edit.contact" title="Edit user's contact information">
           <para>
@@ -234 +246 @@
             <varlistentry>
               <term>
-                <optional>
                   <guilabel>Email</guilabel>
-                </optional>
               </term>
               <listitem>
@@ -247 +257 @@
             <varlistentry>
               <term>
-                <optional>
                   <guilabel>Organization</guilabel>
-                </optional>
               </term>
               <listitem>
@@ -257 +265 @@
             <varlistentry>
               <term>
-                <optional>
                   <guilabel>Address</guilabel>
-                </optional>
               </term>
               <listitem>
@@ -270 +276 @@
             <varlistentry>
               <term>
-                <optional>
                   <guilabel>Phone</guilabel>
-                </optional>
               </term>
               <listitem>
@@ -288 +292 @@
             <varlistentry>
               <term>
-                <optional>
                   <guilabel>Fax</guilabel>
-                </optional>
               </term>
               <listitem>
@@ -298 +300 @@
             <varlistentry>
               <term>
-                <optional>
                   <guilabel>Url</guilabel>
-                </optional>
               </term>
               <listitem>
@@ -308 +308 @@
             <varlistentry>
               <term>
-                <optional>
                   <guilabel>Description</guilabel>
-                </optional>
               </term>
               <listitem>
@@ -330 +328 @@
           <seeother>
             <other external_id="user.edit">Edit account</other>
-            <other external_id="user.additional">Edit additional info</other>
+            <other external_id="user.edit.additional">Edit additional info</other>
             <other external_id="user.edit.membership">Group and role membership</other>
           </seeother>
@@ -338 +336 @@
       <sect3 id="accounts.users.edit.additional">
         <title>Additional information</title>
+        <figure id="accounts.figures.userextra">
+          <title>Additional user information</title>
+          <screenshot>
+            <mediaobject>
+              <imageobject><imagedata fileref="figures/user_extra.png" format="PNG"
+                /></imageobject>
+            </mediaobject>
+          </screenshot>
+        </figure>
         <helptext external_id="user.edit.additional" title="Additional information">
           <para>
             This tab contains fields that hold various information about the user. There are
             by default two fields in BASE but this could easily be changed by the
-            server administrator. How this configuration is done can be read in
-            <xref linkend="appendix.extendedproperties" />
+            server administrator. <nohelp>How this configuration is done can be read in
+            <xref linkend="appendix.extendedproperties" />.</nohelp>
             <note>
               <para>
@@ -389 +396 @@
           <seeother>
             <other external_id="user.edit">Edit account</other>
-            <other external_id="user.contact">Edit contact</other>
+            <other external_id="user.edit.contact">Edit contact</other>
             <other external_id="user.edit.membership">Group and role membership</other>
           </seeother>
@@ -397 +404 @@
       <sect3 id="accounts.users.edit.membership">
         <title>Group and role membership</title>
+        <figure id="accounts.figures.usermembership">
+          <title>Group and role membership</title>
+          <screenshot>
+            <mediaobject>
+              <imageobject><imagedata fileref="figures/user_membership.png" format="PNG"
+                /></imageobject>
+            </mediaobject>
+          </screenshot>
+        </figure>
         <helptext external_id="user.edit.membership" title="Group and role membership">
           <para>
@@ -471 +487 @@
             <other external_id="user.edit">Edit user</other>
             <other external_id="user.edit.contact">Edit contact information</other>
-            <other external_id="user.additional">Edit additional info</other>
+            <other external_id="user.edit.additional">Edit additional info</other>
             <other external_id="user.edit.default_membership">Default group and role membership</other>
           </seeother>
@@ -481 +497 @@
       <title>Default group and role membership</title>
       
+        <figure id="accounts.figures.defaultmembership">
+          <title>Default group and role membership</title>
+          <screenshot>
+            <mediaobject>
+              <imageobject><imagedata fileref="figures/default_membership.png" format="PNG"
+                /></imageobject>
+            </mediaobject>
+          </screenshot>
+        </figure>
+        
       <helptext external_id="user.edit.default_membership" 
         title="Default group and role membership">
@@ -555 +581 @@
       <sect3 id="accounts.groups.edit.properties">
         <title>Properties</title>
+        <figure id="accounts.figures.group">
+          <title>Group properties</title>
+          <screenshot>
+            <mediaobject>
+              <imageobject><imagedata fileref="figures/group_edit.png" format="PNG"
+                /></imageobject>
+            </mediaobject>
+          </screenshot>
+        </figure>
         <helptext external_id="group.edit" title="Edit group">
           <variablelist>
@@ -591 +626 @@
             <varlistentry>
               <term>
-                <optional>
                   <guilabel>Description</guilabel>
-                </optional>
               </term>
               <listitem>
@@ -605 +638 @@
             <varlistentry>
               <term>
-                <optional>
                   <guilabel>Quota</guilabel>
-                </optional>
               </term>
               <listitem>
@@ -653 +684 @@
       <sect3 id="accounts.groups.edit.members">
         <title>Group members</title>
+        <figure id="accounts.figures.groupmembers">
+          <title>Group members</title>
+          <screenshot>
+            <mediaobject>
+              <imageobject><imagedata fileref="figures/group_members.png" format="PNG"
+                /></imageobject>
+            </mediaobject>
+          </screenshot>
+        </figure>
         <helptext external_id="group.edit.membership" title="Edit group members">
           <para>
@@ -820 +860 @@
       <sect3 id="accounts.roles.edit.properties">
         <title>Properties</title>
+        <figure id="accounts.figures.role">
+          <title>Role properties</title>
+          <screenshot>
+            <mediaobject>
+              <imageobject><imagedata fileref="figures/role_edit.png" format="PNG"
+                /></imageobject>
+            </mediaobject>
+          </screenshot>
+        </figure>
         <helptext external_id="role.edit" title="Edit role">
 
@@ -909 +958 @@
       <sect3 id="accounts.roles.edit.permissions">
         <title>Permissions</title>
+        <figure id="accounts.figures.rolepermissions">
+          <title>Role permissions</title>
+          <screenshot>
+            <mediaobject>
+              <imageobject><imagedata fileref="figures/role_permissions.png" format="PNG"
+                /></imageobject>
+            </mediaobject>
+          </screenshot>
+        </figure>
         <helptext external_id="role.edit.permissions" title="Edit role permissions">
           <para>
@@ -992 +1050 @@
       <sect3 id="accounts.roles.edit.members">
         <title>Members</title>
+        <figure id="accounts.figures.rolemembers">
+          <title>Role members</title>
+          <screenshot>
+            <mediaobject>
+              <imageobject><imagedata fileref="figures/role_members.png" format="PNG"
+                /></imageobject>
+            </mediaobject>
+          </screenshot>
+        </figure>
         <helptext external_id="role.edit.members" title="Role members">
         
@@ -1081 +1148 @@
       <sect3 id="accounts.quota.edit.properties">
         <title>Properties</title>
+        <figure id="accounts.figures.quota">
+          <title>Quota properties</title>
+          <screenshot>
+            <mediaobject>
+              <imageobject><imagedata fileref="figures/quota_edit.png" format="PNG"
+                /></imageobject>
+            </mediaobject>
+          </screenshot>
+        </figure>
         <helptext external_id="quota.edit" title="Edit properties">
           <variablelist>
@@ -1093 +1169 @@
             <varlistentry>
               <term>
-                <optional>
                   <guilabel>Description</guilabel>
-                </optional>
               </term>
               <listitem>
@@ -1113 +1187 @@
             to abort.
           </para>
+          
+          <seeother>
+            <other external_id="quota.edit.values">Quota values</other>
+          </seeother>
+          
         </helptext>
       </sect3>
@@ -1118 +1197 @@
       <sect3 id="accounts.quota.edit.values">
         <title>Values</title>
+        <figure id="accounts.figures.quotavalues">
+          <title>Quota values</title>
+          <screenshot>
+            <mediaobject>
+              <imageobject><imagedata fileref="figures/quota_values.png" format="PNG"
+                /></imageobject>
+            </mediaobject>
+          </screenshot>
+        </figure>
         <helptext external_id="quota.edit.values" title="Edit quota values">
           <para>
@@ -1141 +1229 @@
             <varlistentry>
               <term>
-                <optional>
                   <guilabel>Files</guilabel>
-                </optional>
               </term>
               <listitem>
@@ -1151 +1237 @@
             <varlistentry>
               <term>
-                <optional>
                   <guilabel>Raw data</guilabel>
-                </optional>
               </term>
               <listitem>
@@ -1161 +1245 @@
             <varlistentry>
               <term>
-                <optional>
                   <guilabel>Experiments</guilabel>
-                </optional>
               </term>
               <listitem>
@@ -1177 +1259 @@
             &gbCancel;.
           </para>
+          <seeother>
+            <other external_id="quota.edit">Quota properties</other>
+          </seeother>
         </helptext>
       </sect3>

trunk/doc/src/docbook/admin/installation.xml

@@ -45 +45 @@
 
     <important id="installation.upgrade.important">
-      <title>Important information for upgrading from BASE 2.17 to BASE 3.0-alfa</title>
+      <title>Important information for upgrading from BASE 2.17 to BASE 3.0-beta</title>
       
       <bridgehead>Do not use on a production server!</bridgehead>
@@ -51 +51 @@
         The update has not been tested enough to consider this a safe option.
         The update may cause loss of data. Even if the update works, it is not
-        certain that the 3.0-alfa version can be updated to the 3.0-final
+        certain that the 3.0-beta version can be updated to the 3.0-final
         version. Before updating make sure that you have a backup of your
         BASE 2.17 database.
@@ -98 +98 @@
           <para>
             Labeled extract importer: This has been deprecated and it is recommended
-            that the Extract importer is used instead. Existing importer configurations 
-            should be re-created as extract importer configurations.
+            that the Extract importer is used instead. Existing labeled extract importer 
+            configurations should be re-created as extract importer configurations.
           </para>
         </listitem>
@@ -105 +105 @@
           <para>
             Hybridization importer: This has been deprecated and it is recommended
-            that the Physical bioassay importer is used instead. Existing importer configurations 
-            should be re-created as physical bioassay importer configurations.
+            that the Physical bioassay importer is used instead. Existing hybridization
+            importer configurations should be re-created as physical bioassay importer 
+            configurations.
           </para>
         </listitem>
@@ -112 +113 @@
           <para>
             Scan importer: This has been deprecated and it is recommended
-            that the Derived bioassay importer is used instead. Existing importer configurations 
-            should be re-created as derived bioassay importer configurations.
+            that the Derived bioassay importer is used instead. Existing scan 
+            importer configurations should be re-created as derived bioassay 
+            importer configurations.
           </para>
         </listitem>
@@ -354 +356 @@
               <para>
                 Enable headless mode if your are setting up a server which doesn't have
-                a display device connected to is. <code>-Djava.awt.headless=true</code>. 
+                a display device connected to it. <code>-Djava.awt.headless=true</code>. 
               </para>
             </listitem>
@@ -1131 +1133 @@
             <para>
               A list with the job agents where the plug-in is installed and 
-              allowed to be executed. Select a plug-in in this list to display 
+              allowed to be executed. Select a job agent in this list to display 
               more configuration options for the plug-in.
             </para>
@@ -1221 +1223 @@
       Each tab in the configuration dialog-window is described below.
     </para>
+    
+      <figure id="installation.figures.serverconfiguration">
+        <title>Server configuration</title>
+        <screenshot>
+          <mediaobject>
+            <imageobject><imagedata 
+              fileref="figures/server_configuration.png" format="PNG"
+              /></imageobject>
+          </mediaobject>
+        </screenshot>
+      </figure>
+      
     <variablelist>
       <varlistentry>
@@ -1405 +1419 @@
       </para>
       
+      <figure id="installation.figures.broadcast">
+        <title>Broadcast message</title>
+        <screenshot>
+          <mediaobject>
+            <imageobject><imagedata 
+              fileref="figures/broadcast_message.png" format="PNG"
+              /></imageobject>
+          </mediaobject>
+        </screenshot>
+      </figure>
+      
       <helptext external_id="broadcast.message" title="Broadcast message">
         <para>

trunk/doc/src/docbook/admin/plugins.xml

@@ -65 +65 @@
     <title>Managing plug-ins and extensions</title>
     
-    <note>
+    <important>
       <title>Changes since BASE 2</title>
       <para>
@@ -89 +89 @@
         </listitem>
       </itemizedlist>
-    </note>
+    </important>
     
     <para>
@@ -1261 +1261 @@
             <table frame="all" id="plugins.configuration.testwithfile.mappings">
               <title>Mapping expression examples</title>
-              <tgroup cols="2" align="left">
-                <colspec colname="expression" />
-                <colspec colname="explanation" />
+              <tgroup cols="2" align="center">
+                <colspec colname="expression" align="left"/>
+                <colspec colname="explanation" align="left"/>
                 <thead>
                   <row>

trunk/www/admin/plugindefinitions/edit_plugin.jsp

@@ -845 +845 @@
       {
         %>
-        <td>
+        <td style="background: #f8f8e0; border: 1px solid gray;">
         <b>Requested by plugin</b><br>
         <table>

trunk/www/common/plugin/test_with_file.jsp

@@ -322 +322 @@
             </td>
             <td>&nbsp;</td>
-            <td><base:button title="Parse the file" onclick="doParse()" /></td>
+            <td><base:button title="Parse the file" onclick="doParse()" image="gonext.gif"/></td>
             </tr>
           </table>