source: branches/3.2-stable/doc/src/docbook/user/webclient.xml @ 6252

Last change on this file since 6252 was 6252, checked in by Nicklas Nordborg, 9 years ago

Fixes #1747: Change the meaning of 'Decimals' setting to 'Precision'

Added AdaptiveNumberFormatter implementation that dynamically calculates the number of decimals to use. The FormatterFactory implementation now uses the new formatter instead of the old one.

Also changed the formatting original and remaining quantity display on a several places to use a Formatter implementation (eg. a better fix for #1746) so now the setting should automatically be applied everywhere numbers are displayed. The only exception is file sizes which now always use 2 decimals and dynamic switching between kb, Mb and Gb (this was not consistent before).

  • Property svn:eol-style set to native
  • Property svn:keywords set to Date Id
File size: 93.4 KB
Line 
1<?xml version="1.0" encoding="UTF-8"?>
2<!DOCTYPE chapter PUBLIC
3    "-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN"
4    "../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd">
5<!--
6  $Id: webclient.xml 6252 2013-03-14 11:46:14Z nicklas $
7
8  Copyright (C) 2007 Jari Häkkinen, Peter Johansson, Nicklas Nordborg, Martin Svensson
9
10  This file is part of BASE - BioArray Software Environment.
11  Available at http://base.thep.lu.se/
12
13  BASE is free software; you can redistribute it and/or
14  modify it under the terms of the GNU General Public License
15  as published by the Free Software Foundation; either version 3
16  of the License, or (at your option) any later version.
17
18  BASE is distributed in the hope that it will be useful,
19  but WITHOUT ANY WARRANTY; without even the implied warranty of
20  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
21  GNU General Public License for more details.
22
23  You should have received a copy of the GNU General Public License
24  along with BASE. If not, see <http://www.gnu.org/licenses/>.
25-->
26
27<chapter id="webclient">
28  <?dbhtml dir="webclient" filename="index.html" ?>
29  <title>Using the web client</title>
30    <sect1 id="webclient.introduction">
31      <?dbhtml filename="introduction.html" ?>
32      <title>Introduction</title>
33     
34      <sect2 id="webclient.intro.login">
35        <title>Logging in</title>
36        <para>
37          There are three things that you need to know
38          before you can use BASE:
39        </para>
40       
41        <orderedlist>
42        <listitem><simpara>The address (URL) to a BASE server</simpara></listitem>
43        <listitem><simpara>A username to login with</simpara></listitem>
44        <listitem><simpara>A password</simpara></listitem>
45        </orderedlist>
46       
47        <para>
48          You may, for example, try the BASE demo server. Go to the
49          URL <ulink url="http://base2.thep.lu.se/demo/">http://base2.thep.lu.se/demo/</ulink>
50          and enter <userinput>base2</userinput> for the login and <userinput>base2</userinput>
51          for the password.
52        </para>
53       
54        <para>
55          You need to get all three things from an administrator
56          of the BASE server. If you know only the address to the
57          BASE server, you may check the front page if the administrator
58          has added any information about how to get a username/password
59          there. Look for the <guilabel>Get an account!</guilabel> link on
60          the front page.
61        </para>
62       
63        <para>
64          Logging in is simple, just enter your <guilabel>login</guilabel> 
65          and <guilabel>password</guilabel> in the form on the front page
66          and click the <guibutton>Login</guibutton> button.
67        </para>
68      </sect2>
69     
70      <sect2 id="webclient.intro.forgotten_password">
71        <title>Forgotten password</title>
72        <para>
73          If you forget your password you will need to get a new one.
74          BASE stores the passwords in an encrypted form that does not allow
75          anyone, not even the server administrator, to find out the
76          un-encrypted password.
77        </para>
78        <para>
79          To get a new password you will have to contact the server
80          administrator. There may be a <guilabel>Forgot your password?</guilabel>
81          link on the front page where the server administrator has entered
82          information about how to get a new password.
83        </para>
84      </sect2>
85
86      <sect2 id="webclient.intro.homepage">
87        <title>The home page</title>
88     
89      <para>
90        When you have been logged in the home page will be displayed. It
91        displays some useful information. You can also go to the home page
92        using the
93        <menuchoice><guimenu>View</guimenu><guimenuitem>Home</guimenuitem></menuchoice>
94        menu.
95      </para>
96       
97      <figure id="webclient.figures.homepage">
98        <title>The home page</title>
99        <screenshot>
100          <mediaobject>
101            <imageobject><imagedata fileref="figures/homepage.png" format="PNG"
102              scalefit="1" width="100%"/></imageobject>
103          </mediaobject>
104        </screenshot>
105      </figure>
106       
107      <variablelist>
108        <varlistentry>
109          <term><interface>New messages</interface></term>
110          <listitem>
111            <para>
112            Messages are, for example, sent by plug-ins to notify you about finished jobs. In the
113            future, you may get messages from other sources as well. As of today,
114            messages are not used for communication between users.
115            </para>
116          </listitem>
117        </varlistentry>
118       
119        <varlistentry>
120          <term><interface>Projects</interface></term>
121          <listitem>
122            <para>
123            A list of projects that you are a member of. Projects are an important
124            part of BASE and are the best way to share data when you are
125            cooperating with other users. We recommend
126            that you always use a project when working with BASE.
127            For more information read <xref linkend="project_permission"/>. The list
128            displays the most recently used projects first and then fills up
129            with the rest sorted by name.
130            </para>
131          </listitem>
132        </varlistentry>
133       
134        <varlistentry>
135          <term><interface>Disk usage</interface></term>
136          <listitem>
137            <para>
138            An overview of how much disk space you have been assigned and
139            how much you are using.
140            </para>
141          </listitem>
142        </varlistentry>
143       
144        <varlistentry>
145          <term><interface>Help</interface></term>
146          <listitem>
147            <para>
148            Links for getting help and reporting bugs. The number
149            of links displayed here may vary depending on the server
150            configuration.
151            </para>
152          </listitem>
153        </varlistentry>
154       
155        <varlistentry>
156          <term><interface>News and announcements</interface></term>
157          <listitem>
158            <para>
159            A list of important news and announcements from the
160            server administrator. Here you may, for example, find
161            information about server upgrades and maintenance.
162            </para>
163           
164            <tip>
165              <title>Subscribe to the RSS news feed.</title>
166              <para>
167                Click on the RSS icon <guiicon>
168              <inlinemediaobject>
169              <imageobject><imagedata fileref="figures/rss.png" format="PNG" /></imageobject>
170              </inlinemediaobject>
171            </guiicon> in the <interface>News and announcements</interface>
172                title bar. This allows you to subscribe to the news feed
173                from the BASE server so that you don't miss anything interesting.
174              </para>
175            </tip>
176          </listitem>
177        </varlistentry>
178      </variablelist>
179       
180      </sect2>
181     
182      <sect2 id="webclient.intro.menubar">
183        <title>Using the menu bar</title>
184        <para>
185          On the top of the home page is the <interface>Menu bar</interface>.
186          This is the main navigation tool in BASE. It works the same way
187          as the regular menu system found in most other applications. Use
188          the mouse to click and select an item from the menu.
189        </para>
190       
191        <para>
192          Most of the menu is in two levels, ie. clicking on a top-level menu
193          will open a submenu just below it. Clicking on something in the
194          submenu will take you to another page or open a pop-up dialog window.
195          For example, the
196          <menuchoice><guimenu>Biomaterial LIMS</guimenu><guimenuitem>Samples</guimenuitem></menuchoice>
197          menu will take you to the page listing samples and
198          <menuchoice><guimenu>BASE</guimenu><guimenuitem>Contact information</guimenuitem></menuchoice>
199          opens a dialog where you can modify your contact information details.
200        </para>
201       
202        <para>
203          The menu bar also contains shortcuts to some often-used
204          actions:
205        </para>
206       
207       
208      <variablelist>
209        <varlistentry>
210          <term>
211            <guiicon>
212              <inlinemediaobject>
213              <imageobject><imagedata fileref="figures/project.png" format="PNG" /></imageobject>
214              </inlinemediaobject>
215            </guiicon>
216            <interface>
217            Projects
218            </interface>
219          </term>
220          <listitem>
221            <para>
222            A list of all projects you are a member of. The most recently used projects are
223            listed first, then the list is filled with the rest of your projects up to a
224            maximum of 15. If you have more projects an option to display the remaining
225            projects is activated. Selecting a project in the list will make that project
226            the active project.
227            </para>
228            <tip>
229              <para>
230              The sort order in the menu of non-recent projects is the same as the sort order on the
231              projects list page. If you, for example, want to sort the newest
232              project first (after the most recently used ones), select to sort by the
233              <guilabel>Registered</guilabel> column in descending order on the list page.
234              The menu will automatically use the same order.
235              </para>
236            </tip>
237          </listitem>
238        </varlistentry>
239        <varlistentry>
240          <term>           
241            <guiicon>
242              <inlinemediaobject>
243              <imageobject><imagedata fileref="figures/refresh.png" format="PNG" 
244                /></imageobject>
245              </inlinemediaobject>
246            </guiicon> 
247            <interface>
248            Refresh page
249            </interface>
250          </term>
251          <listitem>
252            <para>
253            Refresh/reload the current page. This is useful when you add
254            or modify items in BASE. Most of the time the page is refreshed
255            automatically, but in some cases you will have to use
256            this button to refresh the page.
257            </para>
258           
259            <warning>
260              <para>
261              Do not use your browser's <guibutton>Refresh</guibutton> button.
262              Most browsers will take you to the login page again.
263              </para>
264            </warning>
265          </listitem>
266        </varlistentry>
267       
268        <varlistentry>
269          <term>     
270            <guiicon>     
271              <inlinemediaobject>
272              <imageobject><imagedata fileref="figures/recent.png" format="PNG"/></imageobject>
273              </inlinemediaobject>
274            </guiicon>
275            <interface>
276            Recent items
277            </interface>
278          </term>
279          <listitem>
280            <para>
281            Shortcut to the most recently viewed items. The number of items are
282            configurable and you can also make some item types
283            <emphasis>sticky</emphasis>. This will for example keep the shortcut
284            to the last experiment even if you have viewed lots of other items
285            more recently.
286            See <xref linkend="webclient.configuration.preferences.mostrecent"/>
287            for configuration information.
288            </para>
289          </listitem>
290        </varlistentry>
291       
292        <varlistentry>
293          <term>
294            <guiicon>
295              <inlinemediaobject>
296              <imageobject><imagedata fileref="figures/user.png" format="PNG" /></imageobject>
297              </inlinemediaobject>
298            </guiicon>
299            <interface>
300            Logged in user
301            </interface>
302          </term>
303          <listitem>
304            <para>
305            Displays the name of the currently logged in user and allows
306            you to quickly log out and switch to another user.
307            </para>
308          </listitem>
309        </varlistentry>
310       
311      </variablelist>
312       
313      </sect2>
314     
315      <sect2 id="webclient.intro.help">
316        <title>Getting help</title>
317        <para>
318          Besides reading this document there are more ways to get help:
319        </para>
320        <variablelist>
321          <varlistentry>
322            <term>
323              On-line context-sensitive help
324            </term>
325            <listitem>
326              <para>
327              Whenever you find a small help icon
328              <guiicon>
329                <inlinemediaobject>
330                <imageobject><imagedata fileref="figures/help.png" format="PNG" /></imageobject>
331                </inlinemediaobject>
332              </guiicon>
333              or button you may
334              click it to get help about the part of the page
335              you are currently viewing. The icon is located in the title
336              bar in most pop-up dialog windows and in the toolbar in most
337              other pages.
338              </para>
339            </listitem>
340          </varlistentry>
341
342          <varlistentry>
343            <term>
344              Using the <menuchoice><guimenu>Help</guimenu></menuchoice> menu
345            </term>
346            <listitem>
347              <para>
348              The <menuchoice><guimenu>Help</guimenu></menuchoice> menu
349              contains links for getting on-line help. These links
350              may be configured by a server administrator, so they may be
351              different from server to server. By default links for reporting
352              a bug and accessing this document are installed.
353              </para>
354            </listitem>
355          </varlistentry>
356
357          <varlistentry>
358            <term>
359              Mailing lists and other resources
360            </term>
361            <listitem>
362              <para>
363              See <xref linkend="resources" />.
364              </para>
365            </listitem>
366          </varlistentry>
367
368        </variablelist>
369       
370      </sect2>
371   
372    </sect1>
373   
374    <sect1 id="webclient.configuration">
375      <?dbhtml filename="configuration.html" ?>
376      <title>Configuring your account</title>
377     
378      <sect2 id="webclient.configuration.contact">
379        <title>Contact information</title>
380       
381        <para>
382          Use the <menuchoice><guimenu>BASE</guimenu>
383          <guimenuitem>Contact information</guimenuitem></menuchoice>
384          menu to bring up the user information dialog.
385        </para>
386         
387          <figure id="webclient.figures.contactinformation">
388            <title>Contact information</title>
389            <screenshot>
390              <mediaobject>
391                <imageobject><imagedata fileref="figures/contact_information.png" format="PNG" /></imageobject>
392              </mediaobject>
393            </screenshot>
394          </figure>
395       
396        <helptext external_id="userpreferences.contact" title="Contact information">
397       
398          <para>
399          This dialog has three tabs, <guilabel>Contact information</guilabel>
400          (selected), <guilabel>Password</guilabel> and <guilabel>Other information</guilabel>.
401          The logged in user can update the following contact information
402          details.
403          </para>
404       
405          <note>
406            <title>Multi-user accounts</title>
407            <para>
408              If you are using a multi-user account, for example a demo-account, you
409              do not have permission to change the contact information.
410            </para>
411          </note>
412       
413          <variablelist>
414            <varlistentry>
415              <term>
416                <guilabel>Full name</guilabel>
417              </term>
418              <listitem>
419                <para>
420                Your full name. You are not allowed to change this. If
421                it is not correct, contact an administrator to do it for
422                you.
423                </para>
424              </listitem>
425            </varlistentry>
426            <varlistentry>
427              <term>
428                <guilabel>Email</guilabel>
429              </term>
430              <listitem>
431                <para>
432                Your email address (optional). If an email has been specified and if the
433                server administrator has enabled email notifications, you also have the
434                option to select if messages should be sent as emails. This can be useful
435                to keep track of jobs that take a long time to complete.
436                </para>
437              </listitem>
438            </varlistentry>
439            <varlistentry>
440              <term>
441                <guilabel>Organisation</guilabel>
442              </term>
443              <listitem>
444                <para>
445                The name of the organisation you work for or represent (optional).
446                </para>
447              </listitem>
448            </varlistentry>
449            <varlistentry>
450              <term>
451                <guilabel>Address</guilabel>
452              </term>
453              <listitem>
454                <para>
455                Your postal address as it should be printed on letters to you
456                (optional).
457                </para>
458              </listitem>
459            </varlistentry>
460            <varlistentry>
461              <term>
462                <guilabel>Phone</guilabel>
463              </term>
464              <listitem>
465                <para>
466                Your phone number (optional). You may enter multiple phone numbers,
467                for example your work phone number and a mobile number.
468                </para>
469              </listitem>
470            </varlistentry>
471            <varlistentry>
472              <term>
473                <guilabel>Fax</guilabel>
474              </term>
475              <listitem>
476                <para>
477                Your fax number (optional).
478                </para>
479              </listitem>
480            </varlistentry>
481            <varlistentry>
482              <term>
483                <guilabel>Url</guilabel>
484              </term>
485              <listitem>
486                <para>
487                An URL to your home page or your organisation's home page (optional).
488                </para>
489              </listitem>
490            </varlistentry>
491          </variablelist>
492         
493          <para>
494            Press &gbSave; to save the changes or
495            &gbCancel; to abort.
496          </para>
497         
498          <seeother>
499            <other external_id="userpreferences.password">Change password</other>
500            <other external_id="userpreferences.other">Other information</other>
501          </seeother>
502        </helptext>
503       
504      </sect2>
505     
506      <sect2 id="webclient.configuration.other">
507        <title>Other information</title>
508        <para>
509          Use the
510          <menuchoice>
511            <guimenu>BASE</guimenu>
512            <guimenuitem>Other information&hellip;</guimenuitem>
513          </menuchoice>
514          menu to bring up the other information dialog.
515        </para>
516
517          <figure id="webclient.figures.otherinformation">
518            <title>Other information</title>
519            <screenshot>
520              <mediaobject>
521                <imageobject><imagedata fileref="figures/other_information.png" format="PNG" /></imageobject>
522              </mediaobject>
523            </screenshot>
524          </figure>
525
526
527        <helptext external_id="userpreferences.other" title="Other information">
528          <para>
529            This dialog has three tabs,
530            <guilabel>Contact information</guilabel>,
531            <guilabel>Password</guilabel> and
532            <guilabel>Other information</guilabel>
533            (selected).
534          </para>
535          <para>
536            The look of the
537            <guilabel>Other information</guilabel>
538            tab can differ a bit between different servers, depending on what settings
539            the server is installed with. There are three inputs in a fresh BASE
540            installation but it is only the
541            <guilabel>Description</guilabel>
542            text area that is static, the others can be removed or more fields can be
543            added (managed by the server administrator). The three fields, included in a
544            the BASE installation, are
545            <variablelist>
546              <varlistentry>
547                <term>
548                  <guilabel>Mobile</guilabel>
549                </term>
550                <listitem>
551                  <para>Your mobile number(Optional).</para>
552                </listitem>
553              </varlistentry>
554              <varlistentry>
555                <term>
556                  <guilabel>Skype</guilabel>
557                </term>
558                <listitem>
559                  <para>Your Skype contact information(Optional).</para>
560                </listitem>
561              </varlistentry>
562              <varlistentry>
563                <term>
564                  <guilabel>Description</guilabel>
565                </term>
566                <listitem>
567                  <para>
568                    Text area where you can put useful information that couldn't
569                    be stored anywhere else(Optional).
570                  </para>
571                </listitem>
572              </varlistentry>
573            </variablelist>
574          </para>
575          <para>Press &gbSave; to save the changes or &gbCancel; to abort.</para>
576          <seeother>
577            <other external_id="userpreferences.contact">Contact information</other>
578            <other external_id="userpreferences.password">Change password</other>
579          </seeother>
580        </helptext>
581      </sect2>
582
583      <sect2 id="webclient.configuration.password">
584        <title>Changing password</title>
585       
586        <para>
587          Use the <menuchoice><guimenu>BASE</guimenu>
588          <guimenuitem>Change password</guimenuitem></menuchoice>
589          menu to bring up the change password dialog.
590        </para>
591       
592          <figure id="webclient.figures.changepassword">
593            <title>Change password</title>
594            <screenshot>
595              <mediaobject>
596                <imageobject><imagedata fileref="figures/change_password.png" format="PNG" /></imageobject>
597              </mediaobject>
598            </screenshot>
599          </figure>
600       
601        <helptext external_id="userpreferences.password" title="Change password">
602
603          <para>
604          This dialog has three tabs, <guilabel>Contact information</guilabel>,
605          <guilabel>Password</guilabel> (selected) and <guilabel>Other information</guilabel>.
606          </para>
607
608          <variablelist>
609            <varlistentry>
610              <term>
611                <guilabel>New password</guilabel>
612              </term>
613              <listitem>
614                <para>
615                Enter the new password.
616                </para>
617              </listitem>
618            </varlistentry>
619            <varlistentry>
620              <term>
621                <guilabel>Retype password</guilabel>
622              </term>
623              <listitem>
624                <para>
625                Retype the same password. You must do this to
626                avoid spelling mistakes.
627                </para>
628              </listitem>
629            </varlistentry>
630          </variablelist>
631
632          <note>
633            <title>Multi-user accounts</title>
634            <para>
635              If you are using a multi-user account, for example a demo-account, you
636              do not have permission to change the password.
637            </para>
638          </note>
639       
640          <note>
641            <title>Empty passwords</title>
642            <para>
643              If you leave both fields empty the password will not be changed. It
644              is not possible to have an empty password.
645            </para>
646          </note>
647         
648          <seeother>
649            <other external_id="userpreferences.contact">Contact information</other>
650            <other external_id="userpreferences.other">Other information</other>
651          </seeother>
652         
653        </helptext>
654      </sect2>
655
656      <sect2 id="webclient.configuration.preferences">
657        <title>Preferences</title>
658       
659        <para>
660          Use the <menuchoice><guimenu>BASE</guimenu>
661          <guimenuitem>Preferences</guimenuitem></menuchoice>
662          menu to bring up the preferences dialog.
663          This dialog has three tabs, <guilabel>Appearance</guilabel>,
664          <guilabel>Plugins</guilabel> and <guilabel>Recent items</guilabel>.
665        </para>
666       
667        <sect3 id="webclient.configuration.preferences.appearance">
668          <title>The Appearance tab</title>
669
670          <figure id="webclient.figures.appearance">
671            <title>The Appearance tab</title>
672            <screenshot>
673              <mediaobject>
674                <imageobject><imagedata fileref="figures/preferences_appearance.png" format="PNG" /></imageobject>
675              </mediaobject>
676            </screenshot>
677          </figure>
678         
679          <helptext external_id="userpreferences.appearance" title="Preferences - Appearance">
680         
681          <para>
682          This tab contains settings that affect the appearance of the
683          web client.
684          </para>
685         
686          <variablelist>
687            <varlistentry>
688              <term>
689                <guilabel>Font size</guilabel>
690              </term>
691              <listitem>
692                <para>
693                Select a basic font size. You can choose between
694                five sizes: extra small (XS), small (S), medium (M),
695                large (L) and extra large (XL). The default font size is
696                medium.
697                </para>
698              </listitem>
699            </varlistentry>
700            <varlistentry>
701              <term>
702                <guilabel>Scale factor</guilabel>
703              </term>
704              <listitem>
705                <para>
706                The scale factor affects the size of pop-up windows.
707                This setting exists because different browsers render
708                pages differently. If you often find that pop-up windows
709                are too small you can change this setting to make them
710                bigger.
711                </para>
712                <note>
713                  <para>
714                    The scale factor is automatically changed if the
715                    font size is changed.
716                  </para>
717                </note>
718              </listitem>
719            </varlistentry>
720            <varlistentry>
721              <term>
722                <guilabel>Display long texts</guilabel>
723              </term>
724              <listitem>
725                <para>
726                This setting is used to control how long description texts
727                are displayed in tables and other places with limited space.
728                There are three settings:
729                </para>
730                <itemizedlist>
731                  <listitem>
732                    <simpara>
733                    <guilabel>Always</guilabel>: The full text is always displayed. This may
734                    cause tables, etc. to become hard to read since cells will automatically
735                    grow to be able to display the full text.
736                    </simpara>
737                  </listitem>
738                  <listitem>
739                    <simpara>
740                    <guilabel>On hover</guilabel>: A short version of the text is
741                    displayed and the full text is automatically displayed when
742                    the mouse is moved over the text. Texts that are not fully
743                    visible are indicated with a dotted line to the right.
744                    </simpara>
745                  </listitem>
746                  <listitem>
747                    <simpara>
748                    <guilabel>On click</guilabel>: A short version of the text is
749                    displayed and the full text is displayed when the mouse is clicked
750                    somewhere on the short text. Texts that are not fully visible
751                    are indicated with a grey line to the right.
752                    </simpara>
753                  </listitem>
754                </itemizedlist>
755               
756                <warning>
757                  The 'On click' mode may not perform so well if lots of items are
758                  displayed in a single list. This is particularly so with Internet
759                  Explorer (version 7) which is 5-10 times slower than Firefox to
760                  render the page. If you experience problems with this mode you should
761                  either use a different mode or display less items on a single page.
762                </warning>
763               
764              </listitem>
765            </varlistentry>
766            <varlistentry>
767              <term>
768                <guilabel>Toolbar</guilabel>
769              </term>
770              <listitem>
771                <para>
772                You may choose if the toolbar buttons should
773                have only images, only text or both images and text.
774                The default is that they have both images and text.
775                </para>
776              </listitem>
777            </varlistentry>
778            <varlistentry>
779              <term>
780                <guilabel>Ratio color range</guilabel>
781              </term>
782              <listitem>
783                <para>
784                Select three colors to use when displaying
785                data that is suitable for color coding, for
786                example the intensity ratio in two-color
787                experiments. The default setting is blue-white-yellow.
788                The list of presets contains other useful color combinations
789                (for example, the BASE version 1 red-yellow-green) and the most
790                recently used color combinations.
791                </para>
792              </listitem>
793            </varlistentry>
794            <varlistentry>
795              <term>
796                <guilabel>Date format</guilabel>
797              </term>
798              <listitem>
799                <para>
800                A format string describing how dates should be displayed.
801                We support all formatting options supported by the Java
802                language. For more information see:
803                <ulink url="http://download.oracle.com/javase/6/docs/api/java/text/SimpleDateFormat.html">SimpleDateFormat documentation</ulink>
804                The most useful format patterns are:
805                </para>
806               
807                <itemizedlist>
808                  <listitem><simpara>yy: two-digit year</simpara></listitem>
809                  <listitem><simpara>yyyy: four-digit year</simpara></listitem>
810                  <listitem><simpara>MM: two-digit month</simpara></listitem>
811                  <listitem><simpara>MMM: month name (short)</simpara></listitem>
812                  <listitem><simpara>MMMM: month name (full)</simpara></listitem>
813                  <listitem><simpara>dd: two-digit day in month</simpara></listitem>
814                </itemizedlist>
815               
816                <para>
817                The list of presets contains the most commonly/recently
818                used date formats.
819                </para>
820               
821              </listitem>
822            </varlistentry>
823           
824            <varlistentry>
825              <term>
826                <guilabel>Date-time format</guilabel>
827              </term>
828              <listitem>
829                <para>
830                A format string describing how dates with times should be displayed.
831                We support all formatting options supported by the Java
832                language. For more information see:
833                <ulink url="http://download.oracle.com/javase/6/docs/api/java/text/SimpleDateFormat.html">SimpleDateFormat documentations</ulink>
834                The most useful time-format patterns are:
835                </para>
836               
837                <itemizedlist>
838                  <listitem><simpara>HH: two-digit hour (0-23)</simpara></listitem>
839                  <listitem><simpara>hh: two-digit hour (1-12)</simpara></listitem>
840                  <listitem><simpara>a: AM/PM marker</simpara></listitem>
841                  <listitem><simpara>mm: two-digit minute</simpara></listitem>
842                  <listitem><simpara>ss: two-digit second</simpara></listitem>
843                </itemizedlist>
844               
845              </listitem>
846            </varlistentry>
847           
848            <varlistentry>
849              <term>
850                <guilabel>Decimals</guilabel>
851              </term>
852              <listitem>
853                <para>
854                The base number of decimals to display for numerical floating point values.
855                The default is 2. This setting is used for values between 1 and 10. For higher
856                or lower values, the number of decimals is adapted in order to not loose
857                information (eg. 0.0059 instead of 0.01) or give the impression of very
858                high precision (eg. 135000 instead of 135000.00).
859                </para>
860              </listitem>
861            </varlistentry>
862           
863          </variablelist>
864       
865          </helptext>
866       
867        </sect3>
868       
869        <sect3 id="webclient.configuration.preferences.plugins">
870          <title>The Plugins tab</title>
871         
872          <figure id="webclient.figures.preferences.plugins">
873            <title>The Plugins tab</title>
874            <screenshot>
875              <mediaobject>
876                <imageobject><imagedata fileref="figures/preferences_plugins.png" format="PNG" /></imageobject>
877              </mediaobject>
878            </screenshot>
879          </figure>
880         
881          <helptext external_id="userpreferences.plugins" title="Preferences - Plugins">
882         
883          <para>
884            This tab contains settings that affect plug-in execution.
885          </para>
886         
887          <variablelist>
888            <varlistentry>
889              <term>
890                <guilabel>Messages</guilabel>
891              </term>
892              <listitem>
893                <para>
894                Mark the checkbox if you want to have a message sent
895                to you when a plug-in completes execution. This setting
896                can be overridden each time you start a plug-in. You'll
897                receive the message as a notification in BASE, but it may
898                also be possible to get the message as an email.
899                </para>
900              </listitem>
901            </varlistentry>
902            <varlistentry>
903              <term>
904                <guilabel>Remove jobs</guilabel>
905              </term>
906              <listitem>
907                <para>
908                  This checkbox should be marked if you want the jobs, done by
909                  import or export plug-ins, to be marked as removed if they
910                  finished successfully. This setting can be overridden each time
911                  you start a plug-in.
912                </para>
913              </listitem>
914            </varlistentry>
915            <varlistentry>
916              <term>
917                <guilabel>Show warnings</guilabel>
918              </term>
919              <listitem>
920                <para>
921                  This checkbox should be marked if you want to show warning
922                  messages from plug-ins in the <guilabel>Select plug-in</guilabel>
923                  dialog. Warning-level messages usually originates from plug-ins
924                  that are unrelated to the current task and are only of interest to
925                  plug-in developers. Error messages that are related to the
926                  current task are always shown.
927                </para>
928              </listitem>
929            </varlistentry>
930          </variablelist>
931          </helptext>
932         
933        </sect3>
934       
935        <sect3 id="webclient.configuration.preferences.mostrecent">
936          <title>The Recent items tab</title>
937         
938          <figure id="webclient.figures.preferences.recentitems">
939            <title>The Recent items tab</title>
940            <screenshot>
941              <mediaobject>
942                <imageobject><imagedata fileref="figures/preferences_recentitems.png" format="PNG" /></imageobject>
943              </mediaobject>
944            </screenshot>
945          </figure>
946         
947          <helptext external_id="userpreferences.mostrecent" 
948            title="Preferences - Recent items">
949         
950          <para>
951            This tab contains settings that affect the <guilabel>Recent
952            items</guilabel> menu and selection lists in many edit dialogs.
953          </para>
954         
955          <variablelist>
956          <varlistentry>
957            <term>
958              <guilabel>Recently viewed items</guilabel>
959            </term>
960            <listitem>
961              <para>
962              The number of recently <emphasis>viewed</emphasis> items to remember.
963              The default is to remember 6 items. The remembered items
964              will be displayed in the <guilabel>Recent items</guilabel>
965              menu in the menu bar.
966              </para>
967            </listitem>
968          </varlistentry>
969          <varlistentry>
970            <term>
971              <guilabel>Recently used items</guilabel>
972            </term>
973            <listitem>
974              <para>
975              The number of recently <emphasis>used</emphasis> items to remember.
976              The default is to remember 4 items. The remembered items will
977              be displayed in edit dialogs where they have been used before.
978              Each type of edit operation has it's own list of remembered items.
979              For example, there is one list that remembers the most recently used
980              protocols when creating a sample, and there is another list that
981              remembers the most recently used scanners when creating a scan.
982              </para>
983            </listitem>
984          </varlistentry>
985         
986          <varlistentry>
987            <term>
988              <guilabel>Load the names of all items</guilabel>
989            </term>
990            <listitem>
991              <para>
992              If checked, the names of the items will be loaded and
993              displayed in the menu, otherwise only the ID and type of item
994              is displayed.
995              </para>
996            </listitem>
997          </varlistentry>
998         
999          <varlistentry>
1000            <term>
1001              <guilabel>Sticky items</guilabel>
1002            </term>
1003            <listitem>
1004              <para>
1005              Always remember the last viewed item of the selected types.
1006              For example, if you have selected <emphasis>Experiment</emphasis>
1007              as a sticky item, the last viewed experiment will be remembered
1008              even if you view hundreds of other items. Use the arrow buttons
1009              to move item types between the lists and sort the sticky items list.
1010              Sticky items will be displayed in the <guilabel>Recent items</guilabel>
1011              menu in the menu bar.             
1012              </para>
1013            </listitem>
1014          </varlistentry>
1015          </variablelist>
1016          </helptext>
1017         
1018        </sect3>
1019      </sect2>
1020 
1021    </sect1>
1022   
1023    <sect1 id="webclient.items">
1024      <?dbhtml filename="items.html" ?>
1025      <title>Working with items</title>
1026     
1027      <para>
1028        No matter what you are doing in BASE some things works more
1029        or less in the same way. This section covers things that are
1030        common for most parts of BASE.
1031      </para>
1032     
1033      <para>
1034        You mostly work with a single type of item at a time. This is
1035        reflected in the menu system. For example, use
1036        <menuchoice>
1037          <guimenu>Biomaterial LIMS</guimenu>
1038          <guimenuitem>Samples</guimenuitem>
1039        </menuchoice>
1040        to work with samples, and
1041        <menuchoice>
1042          <guimenu>View</guimenu>
1043          <guimenuitem>Experiments</guimenuitem>
1044        </menuchoice>
1045        to work with experiments. In most cases the list view for that type
1046        of item is displayed. The list view, as the name says,
1047        is used to list all items. There are two more standard views, the
1048        single-item view and the edit view.
1049      </para>
1050     
1051      <variablelist>
1052        <varlistentry>
1053          <term>List view</term>
1054          <listitem>
1055            <para>
1056            This view lists all items of a certain type. The view allows you to search
1057            and it is possible to configure which information to show
1058            for each item. It also contains functions that
1059            can be used on multiple items at the same time, for example,
1060            delete, share and export. See <xref linkend="webclient.itemlist"/> for more information.
1061            </para>
1062          </listitem>
1063        </varlistentry>
1064     
1065        <varlistentry>
1066          <term>Single-item view</term>
1067          <listitem>
1068            <para>
1069            Displays information about a single item. For some items it is very little,
1070            but for some it is very much and the information may be divided
1071            into multiple tabs.
1072            </para>
1073          </listitem>
1074        </varlistentry>
1075     
1076        <varlistentry>
1077          <term>Edit view</term>
1078          <listitem>
1079            <para>
1080            This view is used for editing the information about a single item.
1081            It is always displayed as a pop-up window. Quite often the popup has
1082            multiple tabs, but the most important information is found on the
1083            first tab. Information that is required is always found on the
1084            first tab.
1085            </para>
1086          </listitem>
1087        </varlistentry>
1088      </variablelist> 
1089             
1090      <sect2 id="webclient.items.new">
1091        <title>Create a new item</title>
1092       
1093        <para>
1094          New items are mostly created from the list view. For example,
1095          to create a new experiment go to the
1096          <menuchoice><guimenu>View</guimenu> <guimenuitem>Experiments</guimenuitem></menuchoice>
1097          page. Here you will find a &gbNew; button in the
1098          toolbar. The button is disabled if you do not have permission to create new experiments.
1099          Otherwise, click on it and enter any required information in the pop-up dialog.
1100          Sometimes there are multiple tabs in this dialog. In the case of experiments
1101          there are three tabs: <guilabel>Experiment</guilabel>, <guilabel>Publication</guilabel>
1102          and <guilabel>Experimental factors</guilabel>.
1103         
1104          As a general rule, only the first tab has information that is required.
1105          The information in all other tabs are optional.
1106        </para>
1107       
1108        <para>
1109          In some places you will also find actions that create items
1110          directly in the list. For example in the list of samples or on
1111          the single-item view for a sample you can create an extract using that
1112          sample as the parent. If you use such links the parent
1113          item will in most cases be selected automatically, which saves
1114          you a few clicks when creating new items.
1115        </para>
1116       
1117        <para>
1118          Click on the &gbSave; button to save the new
1119          item to the database or on the &gbCancel; button
1120          to abort.
1121        </para>
1122
1123        <note>
1124          <para>
1125          To speed up data entry when adding multiple new items there
1126          are a few tricks you can use to make the web client supply
1127          default values for most properties. To find a default value
1128          the following checklist is used in this order:
1129          </para>
1130       
1131        <orderedlist>         
1132          <listitem>
1133            <para>
1134            If the list have an active filter the filter values are
1135            used as default property values for the new item. For example,
1136            if you are listing experiments with <guilabel>Genepix</guilabel>
1137            raw data type the new experiment will automatically have
1138            <guilabel>Genepix</guilabel> selected. This trick should work
1139            for all properties except annotations, if it does not
1140            report it as a bug to the development team.
1141            </para>
1142          </listitem>
1143         
1144          <listitem>
1145            <para>
1146            When you link to other items the same item will be used the next time.
1147            For example, if you create an extract and selects an extraction protocol
1148            the same protocol is used the next time you create another extract.
1149            In fact, BASE will remember as many items as specified by
1150            the
1151            <guilabel>Recently used items</guilabel> setting (default is 4),
1152            allowing you to quickly select one of those protocols.
1153            <xref linkend="webclient.configuration.preferences.mostrecent" /> 
1154            contains more information about the setting.
1155            </para>
1156          </listitem>
1157         
1158          <listitem>
1159            <para>
1160            If you have a project active and that project has specified default
1161            values those values will be used for new items. A project can specify
1162            defaults for protocols, hardware and software and a few other settings.
1163            </para>
1164          </listitem>
1165         
1166        </orderedlist>
1167       
1168        </note>
1169       
1170      </sect2>
1171     
1172      <sect2 id="webclient.items.edit">
1173        <title>Edit an existing item</title>
1174       
1175        <para>
1176          On all single-item views there is an &gbEdit;
1177          button in the toolbar that opens a pop-up dialog for editing the properties
1178          of the item. This button is disabled if the logged in user does not have
1179          write permission for the item.
1180        </para>
1181       
1182        <para>
1183          You can also open the edit pop-up in most other places where
1184          the item appears, for example, in lists or the single-item view
1185          of a related item. Press and hold one of the <keycap>CTRL</keycap>,
1186          <keycap>ALT</keycap> or <keycap>SHIFT</keycap> keys while clicking
1187          on the link and the edit window will open in a pop-up.
1188          If you do not have write permission
1189          on the item there is no meaning to open the edit pop-up and you will
1190          be taken to the single-item view page instead.
1191        </para>
1192
1193        <para>
1194          Click on the &gbSave; button to save the changes
1195          to the database or on the &gbCancel; button
1196          to abort.
1197        </para>
1198     
1199      </sect2>
1200
1201      <sect2 id="webclient.items.delete">
1202        <title>Delete items</title>
1203
1204        <para>
1205          You can delete items either from the list view or from
1206          a single-item view. In both cases, deleted items are only moved to
1207          the trashcan. No information is removed from the database. This allows
1208          you to restore items if you later find out that you need them again.
1209          In fact, there is nothing special about a removed item. It can still be
1210          used for the same things as any non-removed item can.
1211        </para>
1212
1213        <important>
1214          <para>
1215          To really delete items from the database you have two options:
1216          <orderedlist>
1217          <listitem>
1218            <para>
1219            Go to the trashcan
1220            <menuchoice><guimenu>View</guimenu><guimenuitem>Trashcan</guimenuitem></menuchoice>
1221            and delete it from there. From the trashcan you can delete several items
1222            in one go. See <xref linkend="webclient.trashcan"/>.
1223            </para>
1224          </listitem>
1225          <listitem>
1226            <para>
1227            Click on the small trashcan icon in the list or single-item view.
1228            You can only delete one item at a time.
1229            </para>
1230          </listitem>
1231          </orderedlist>
1232          </para>
1233        </important>
1234       
1235        <para>
1236          To delete items from the list view you must first mark
1237          the checkbox for each item you want to delete. Then, click on
1238          the &gbDelete; button. The list should refresh itself
1239          automatically. If you want to confirm that the items have been removed
1240          use the <guilabel>view / presets</guilabel> dropdown and select
1241          the <guilabel>Removed</guilabel> option. The removed items should now
1242          be displayed in the list with a small trashcan icon to indicate that
1243          they are located in the trashcan.
1244        </para>
1245
1246        <para>
1247          To delete items from the single-item view, click on the
1248          &gbDelete; button in the toolbar. The page will refresh
1249          itself automatically and a small trashcan icon should be displayed.
1250          If you do not have permission to delete the item the delete button
1251          is disabled.
1252        </para>
1253
1254      </sect2>
1255     
1256      <sect2 id="webclient.items.restore">
1257        <title>Restore deleted items</title>
1258       
1259        <para>
1260          You can restore deleted items either from the trashcan, from
1261          the list view, or from the single-item view. This section
1262          only covers the last two cases. The trashcan is described in
1263          <xref linkend="webclient.trashcan"/>.
1264        </para>
1265
1266        <para>
1267          To delete items from the list view you must first make the deleted
1268          items appear in the list. This is easy, just use the <guilabel>view / presets</guilabel> 
1269          dropdown and select the <guilabel>Removed</guilabel> option. The list should
1270          refresh itself automatically. The removed items are
1271          displayed in the list with a small trashcan icon to indicate that
1272          they are located in the trashcan. Then, mark the checkbox for each item that you want
1273          to restore and click the &gbRestore; button. The list should
1274          refresh itself automatically and the trashcan icon should be gone from the
1275          restored items.
1276        </para>
1277       
1278        <para>
1279          To restore items from the single-item view, click on the
1280          &gbRestore; button in the toolbar. The page will refresh
1281          itself automatically and the small trashcan icon should be gone.
1282          If you do not have permission to restore the item the restore button
1283          is disabled.
1284        </para>
1285
1286      </sect2>
1287
1288      <sect2 id="webclient.items.share">
1289        <title>Share items to other users</title>
1290        <para>
1291          Sharing data with other users is an important feature
1292          of BASE, which allows you cooperate in teams. If you
1293          follow the instructions in <xref linkend="project_permission" />
1294          you will find that you almost never have to share items manually
1295          to other users. This is because whenever you work with an active
1296          project each new item you create will automatically be shared
1297          according to the settings of that project. In most cases, this
1298          is all you need.
1299        </para>
1300       
1301        <para>
1302          If you still need to manually share your data with other users,
1303          here is how to do it.
1304        </para>
1305       
1306        <para>
1307          From a list view, mark the checkbox for each item you want to share.
1308          Then, click on the &gbShare; button.
1309          If you are on a single-item page, click on the &gbShare; 
1310          button on that page. In both cases, this will open the
1311          <guilabel>Set access permissions</guilabel>
1312          dialog window.
1313        </para>
1314       
1315        <figure id="webclient.items.share.set_permissions">
1316          <title>Sharing items to other users</title>
1317          <screenshot>
1318          <mediaobject>
1319            <imageobject>
1320              <imagedata fileref="figures/set_permissions.png" format="PNG" />
1321            </imageobject>
1322          </mediaobject>
1323          </screenshot>
1324        </figure>
1325       
1326        <helptext external_id="share.setpermissions" title="Set access permissions">
1327          <variablelist>
1328            <varlistentry>
1329              <term><guilabel>Members</guilabel></term>
1330              <listitem>
1331                <para>
1332                The list displays the users, groups and projects
1333                that already has access to the items you selected.
1334                The list shows the name and the permission level.
1335                The permission level uses a one-letter code as follows:
1336                </para>
1337               
1338                <itemizedlist>
1339                <listitem><simpara><guilabel>R</guilabel> = Read</simpara></listitem>
1340                <listitem><simpara><guilabel>U</guilabel> = Use</simpara></listitem>
1341                <listitem><simpara><guilabel>W</guilabel> = Write</simpara></listitem>
1342                <listitem><simpara><guilabel>D</guilabel> = Delete</simpara></listitem>
1343                <listitem><simpara><guilabel>O</guilabel> = Set owner</simpara></listitem>
1344                <listitem><simpara><guilabel>P</guilabel> = Set permission</simpara></listitem>
1345                </itemizedlist>
1346               
1347                <para>
1348                  Instead of a permission code, the word <guilabel>varying</guilabel>
1349                  may be displayed. This happens if the items you selected have been
1350                  shared with different permission.
1351                </para>
1352               
1353                <para>
1354                  The <guilabel>Permission templates</guilabel> part of the list
1355                  is always empty to begin with.
1356                </para>
1357               
1358              </listitem>
1359            </varlistentry>
1360           
1361            <varlistentry>
1362              <term><guilabel>Permissions</guilabel></term>
1363              <listitem>
1364                <para>
1365                When you select a user, group or project in the
1366                list, the checkboxes will change to indicate the current permissions.
1367                The exception is if the permissions are varying, in which
1368                case no checkboxes are checked.
1369                To change the permissions just check the permissions you want to
1370                grant or uncheck the permissions you want to revoke.
1371                You can select more than one user, group or project
1372                and change the permissions for all of them at once.
1373                </para>
1374                <para>
1375                The permission boxes are disabled if a permission template
1376                is selected. The permissions are already part of the template
1377                and can't be changed here.
1378                </para>
1379              </listitem>
1380            </varlistentry>           
1381
1382            <varlistentry>
1383              <term><guibutton>Add users</guibutton></term>
1384              <listitem>
1385                <para>
1386                Opens a pop-up window that allows you to select
1387                users to share the items to. In the pop-up window, mark
1388                one or more users and click on the &gbOk;
1389                button. The pop-up window will only list users that you have
1390                permission to read. Unless you are an administrator, this
1391                usually means that you can only see users that:
1392                </para>
1393                <itemizedlist>
1394                  <listitem>
1395                    <para>
1396                    you share group memberships with  (the <emphasis>Everyone</emphasis> 
1397                    group or groups with hidden members doesn't count)
1398                    </para>
1399                  </listitem>
1400                  <listitem>
1401                    <para>
1402                    are members of the currently active project, if any.
1403                    </para>
1404                  </listitem>
1405                </itemizedlist>
1406                <para>
1407                Users that already have access to the item are not included in the
1408                list. If you don't see a user that you want to share an item to,
1409                you'll need to talk to an administrator for setting up the proper
1410                group membership.
1411                </para>
1412              </listitem>
1413            </varlistentry>
1414
1415            <varlistentry>
1416              <term><guibutton>Add groups</guibutton></term>
1417              <listitem>
1418                <para>
1419                Opens a pop-up window that allows you to select
1420                groups to share the items to. In the pop-up window, mark
1421                one or more groups and click on the &gbOk;
1422                button. Unless you are an administrator, the pop-up window
1423                will only list groups where you are a member. It will not list
1424                groups that already have access to the items. The
1425                <emphasis>Everyone</emphasis> groups is normally not visible unless
1426                have a specific permission to share items with this group.
1427                </para>
1428              </listitem>
1429            </varlistentry>
1430           
1431            <varlistentry>
1432              <term><guibutton>Add projects</guibutton></term>
1433              <listitem>
1434                <para>
1435                Opens a pop-up window that allows you to select
1436                projects to share the items to. In the pop-up window, mark
1437                one or more projects and click on the &gbOk;
1438                button. Unless you are an administrator, the pop-up window
1439                will only list projects where you are a member. It will not list
1440                projects that already have access to the items.
1441                </para>
1442              </listitem>
1443            </varlistentry>
1444           
1445            <varlistentry>
1446              <term><guibutton>Templates</guibutton></term>
1447              <listitem>
1448                <para>
1449                Opens a pop-up window that allows you to select
1450                permission templates. In the pop-up window, mark
1451                one or more templates and click on the &gbOk;
1452                button. Unless you are an administrator, the pop-up window
1453                will only list templates that you are allowed to use. It will
1454                not list templates that have already been added.
1455                </para>
1456               
1457                <note>
1458                  <para>
1459                  The permissions from the selected templates are <emphasis>copied</emphasis>
1460                  to the items when the access permissions are saved. If you re-open the share dialog,
1461                  the actual permissions are shown and the permission templates
1462                  section is empty. Modifying the permission template later doesn't
1463                  affect the permissions on existing items. See <xref linkend="project_permission.templates" /> 
1464                  for more information about permission templates.
1465                  </para>
1466                </note>
1467               
1468              </listitem>
1469            </varlistentry>
1470
1471            <varlistentry>
1472              <term>&gbRemove;</term>
1473              <listitem>
1474                <para>
1475                Click on this button to revoke access permissions from
1476                the selected users, groups and projects.
1477                </para>
1478              </listitem>   
1479            </varlistentry>
1480           
1481            <varlistentry>
1482              <term><guilabel>Apply permissions to all sub-directories and their files</guilabel></term>
1483              <listitem>
1484                <para>
1485                This option shows up if at least one of the selected items
1486                is a directory. If this option is selected the permissions given
1487                to the directory will recursively be copied to all files and
1488                sub-directories. Existing permissions on those items will be
1489                overwritten with the new permissions.
1490                </para>
1491              </listitem>   
1492            </varlistentry>
1493          </variablelist>
1494       
1495          <para>
1496            Use the &gbSave; button to save your
1497            changes or the &gbCancel; button to
1498            close the pop-up without saving.
1499          </para>
1500        </helptext>
1501
1502      </sect2>
1503
1504      <sect2 id="webclient.items.changeowner">
1505        <title>Change owner of items</title>
1506        <para>
1507          Sometimes it may be necessary to change the owner of an item.
1508          This can be done by everyone with <emphasis>Set owner</emphasis>
1509          permission on the item.
1510          For a user to have the rights to change owner of an item, the item must
1511          either be owned by or shared with <emphasis>Set owner</emphasis> 
1512          permission to the user .
1513          See <xref linkend="webclient.items.share" />.
1514        </para>
1515       
1516        <para>
1517          An user with <emphasis>Set owner</emphasis> permission can go to a list view
1518          (or the single-item view), mark the checkboxes for the items to change owner of,
1519          and click on the <guibutton>Set owner</guibutton> button. 
1520          A dialog window, like the screen-shot below, will appear.
1521        </para>
1522        <helptext external_id="ownership.configure" title="Change owner">
1523        <variablelist>
1524        <varlistentry>
1525          <term><guilabel>New owner</guilabel></term>
1526          <listitem>
1527          <para>
1528            The user to be the new owner of selected item(s).
1529            By default the current user will be selected but other
1530            users can be picked from the <emphasis>currently used</emphasis> part of the drop-down
1531            list or by clicking on <guibutton>Select</guibutton>.
1532          </para>
1533          </listitem>
1534        </varlistentry>
1535        </variablelist>
1536        <para>
1537          Use the &gbSave; button to set the new owner
1538          or the &gbCancel; button to
1539          close the pop-up without saving.
1540        </para>
1541        </helptext> 
1542        <figure id="webclient.figures.selectowner">
1543          <title>Select a new owner</title>
1544          <screenshot>
1545            <mediaobject>
1546              <imageobject><imagedata fileref="figures/select_owner.png" format="PNG"
1547                scalefit="1" width="100%" /></imageobject>
1548            </mediaobject>
1549          </screenshot>
1550        </figure>
1551       
1552        <warning>
1553          <para>
1554          If you are the original owner of the items, you should be aware of that
1555          after the change you may no longer have access to the items. If you
1556          make a mistake you may have to talk to an administrator to correct it.
1557          </para>
1558        </warning>
1559       
1560      </sect2>
1561     
1562    </sect1>
1563   
1564    <sect1 id="webclient.itemlist">
1565      <?dbhtml filename="lists.html" ?>
1566      <title>Listing items</title>
1567     
1568      <para>
1569        All pages that lists items are very similar in their appearance and
1570        functionality. In this section we will describe the things that are
1571        common for most (if not all) list pages.
1572      </para>
1573     
1574      <para>
1575        Use the menu to open a page listing items. Most list pages can only list one type of
1576        items. For example: use the
1577        <menuchoice>
1578          <guimenu>View</guimenu>
1579          <guimenuitem>Samples</guimenuitem>
1580        </menuchoice>
1581        menu to list samples and the
1582        <menuchoice>
1583          <guimenu>View</guimenu>
1584          <guimenuitem>Experiments</guimenuitem>
1585        </menuchoice>
1586        menu to list experiments.
1587      </para>
1588
1589      <tip>
1590        An example of a list page that can list
1591        items of several types is found by going to
1592        <menuchoice>
1593          <guimenu>View</guimenu>
1594          <guimenuitem>All items</guimenuitem>
1595        </menuchoice>.
1596        This page lists all items that you are the owner of. It has a few limitations:
1597       
1598        <itemizedlist>
1599          <listitem>
1600            <para>
1601              It support only a limited set of columns (id, item type, name and description)
1602              since these are the only properties that are common among all items. It is also
1603              possible to display sharing information.
1604            </para>
1605          </listitem>
1606         
1607          <listitem>
1608            <para>
1609              The list may have not have full support for filtering and
1610              sorting. This is due to a limitation in the
1611              query system used to generate the list.
1612            </para>
1613          </listitem>
1614        </itemizedlist>
1615       
1616        <para>
1617          There are also several similarities:
1618        </para>
1619       
1620        <itemizedlist>
1621          <listitem>
1622            <para>
1623              It supports all of the regular multi-item
1624              operations such as delete, restore, share
1625              and change owner.
1626            </para>
1627          </listitem>
1628         
1629          <listitem>
1630            <para>
1631              Clicking on the name of the item will take you to the
1632              single-item view of that item. Holding down <keycap>CTRL</keycap>,
1633              <keycap>ALT</keycap> or <keycap>SHIFT</keycap> while clicking,
1634              will open the edit pop-up.
1635            </para>
1636          </listitem>
1637        </itemizedlist>       
1638       
1639      </tip>
1640     
1641      <figure id="webclient.figures.listpage">
1642        <title>A typical list page</title>
1643        <screenshot>
1644          <mediaobject>
1645            <imageobject><imagedata fileref="figures/listpage.png" format="PNG"
1646              scalefit="1" width="100%" /></imageobject>
1647          </mediaobject>
1648        </screenshot>
1649      </figure>
1650     
1651      <para>
1652        The typical list page contains the following important
1653        elements:
1654      </para>
1655
1656      <variablelist>
1657        <varlistentry>
1658          <term><interface>1. Toolbar</interface></term>
1659          <listitem>
1660            <para>
1661            A toolbar with buttons for various actions such as
1662            &gbNew; for creating a new item,
1663            &gbDelete; for deleting items and
1664            <guibutton>Columns&hellip;</guibutton> for configuring columns.
1665            Depending on the permissions of the logged in user
1666            some buttons may be disabled (greyed out) or not shown at all.
1667            </para>
1668          </listitem>
1669        </varlistentry>
1670       
1671        <varlistentry>
1672          <term><interface>2. Navigation bar</interface></term>
1673          <listitem>
1674            <para>
1675            If there are many items the list will be divided into
1676            pages, each one showing a limited number of items.
1677            The navigation bar allows you to
1678            move to other pages and specify how many items each page
1679            should display. The navigation bar is repeated at the
1680            bottom of the list so you do not have to scroll back to the
1681            top of a long list just to get to another page.
1682            </para>
1683          </listitem>
1684        </varlistentry>
1685       
1686        <varlistentry>
1687          <term><interface>3. List of presets</interface></term>
1688          <listitem>
1689            <para>
1690            A list with preconfigured settings which allows you to
1691            quickly switch between different layouts (sort order, visible
1692            columns, filter settings, etc).
1693            </para>
1694          </listitem>
1695        </varlistentry>
1696       
1697        <varlistentry>
1698          <term><interface>4. Column headers</interface></term>
1699          <listitem>
1700            <para>
1701            The columns headers can be used for selecting sort order.
1702            </para>
1703          </listitem>
1704        </varlistentry>
1705       
1706        <varlistentry>
1707          <term><interface>5. Filter bar</interface></term>
1708          <listitem>
1709            <para>
1710            The filter bar allows you to search for items.
1711            </para>
1712          </listitem>
1713        </varlistentry>
1714       
1715      </variablelist>
1716     
1717     
1718      <sect2 id="webclient.itemlist.order">
1719        <title>Ordering the list</title>
1720       
1721        <para>
1722          Most lists are by default sorted by the name of the item. This can
1723          be changed by clicking on the column header of another column.
1724          If you click on the same column twice the sort order is reversed.
1725          A downwards or upwards pointing arrow is displayed next to the
1726          column header in the column that is currently used for sorting.
1727          Column headers that are black cannot be used for sorting.
1728        </para>
1729       
1730        <para>
1731          It is possible to use more than one column for sorting. Press
1732          and hold one of the <keycap>CTRL</keycap>,
1733          <keycap>ALT</keycap> or <keycap>SHIFT</keycap> keys while clicking
1734          on another column header. The original sorting is kept and the new
1735          column is used for sub-sorting the list. The procedure can be
1736          repeated with more columns if you need to sort on three or more
1737          columns. To revert to sort by only one column again click a
1738          column header without holding down any key.
1739        </para> 
1740      </sect2>
1741   
1742      <sect2 id="webclient.itemlist.filter">
1743        <title>Filtering the list</title>
1744       
1745        <para>
1746          If the list contains many items you may need to use a filter to be
1747          able to find the item you are looking for. The input boxes on the
1748          line below the column headers are used for filtering. Most columns
1749          are filtered using a free-text input box, but some columns that can
1750          only take a few distinct values use a selection list or radio buttons
1751          instead. The selection list and radio buttons are very simple to use.
1752          Just select the alternative that you want to filter on. The list
1753          will be automatically updated when the selection has been made.
1754        </para>
1755       
1756        <para>
1757          The free-text filter is a bit more complex. By default, an exact match is
1758          required, use % as a wildcard character that matches any character.
1759          For example, the filter <informalexample>Experiment A</informalexample> 
1760          only matches the same exact string, but the filter
1761          <informalexample>Exp%</informalexample> matches
1762          <informalexample>Experiment A, Experiment B, etc.</informalexample>
1763        </para>
1764        <para>
1765          If you want to filter on several values at the same time, separate the
1766          values in the filter input box with the <quote>|</quote> character.
1767          For example, a filter text like <informalexample>Experiment A|C%</informalexample>
1768          matches both <quote>Experiment A</quote> and values 
1769          that begin with <quote>C</quote>.
1770        </para>       
1771        <para>
1772          You can also use operators to find items which has a value that
1773          is greater than, less than or not equal to a specific value. This is
1774          mostly useful on numeric or date columns but also works on text
1775          columns. The operator must be entered first in the
1776          free-text box, for example
1777          <informalexample>&lt;=10</informalexample>
1778          to find items which has a value less than or equal to 10.   
1779          Here is a list of the supported operators:
1780        </para>
1781       
1782        <variablelist id="webclient.itemlist.filter.operators">
1783          <title>List of operators supported by the free-text filter</title>
1784          <varlistentry>
1785            <term><keycap>&lt;</keycap></term>
1786            <listitem><simpara>Less than</simpara></listitem>
1787          </varlistentry>
1788          <varlistentry>
1789            <term><keycap>&lt;=</keycap></term>
1790            <listitem><simpara>Less than or equal to</simpara></listitem>
1791          </varlistentry>
1792          <varlistentry>
1793            <term><keycap>&gt;</keycap></term>
1794            <listitem><simpara>Greater than</simpara></listitem>
1795          </varlistentry>
1796          <varlistentry>
1797            <term><keycap>&gt;=</keycap></term>
1798            <listitem><simpara>Greater than or equal to</simpara></listitem>
1799          </varlistentry>
1800          <varlistentry>
1801            <term><keycap>=</keycap></term>
1802            <listitem>
1803              <simpara>
1804                Equal to (useful to find items with a null value). Supports
1805                filtering on more then one value.
1806              </simpara>
1807            </listitem>
1808          </varlistentry>
1809          <varlistentry>
1810            <term><keycap>&lt;&gt;</keycap></term>
1811            <term><keycap>!=</keycap></term>
1812            <listitem>
1813              <simpara>
1814                Not equal to (useful to find items with a non-null value). Supports
1815                filtering on more then one value.
1816              </simpara>
1817            </listitem>
1818          </varlistentry>
1819          <varlistentry>
1820            <term><keycap>==</keycap></term>
1821            <listitem>
1822              <simpara>
1823                Same as <keycap>=</keycap> but interprets <quote>|</quote>, <quote>%</quote> 
1824                and other special characters literally. Use this when you need an exact
1825                string match.
1826              </simpara>
1827            </listitem>
1828          </varlistentry>
1829          <varlistentry>
1830            <term><keycap>&gt;&lt;</keycap></term>
1831            <listitem>
1832              <simpara>
1833                Within a range. Two values separated by <quote>|</quote> are required.
1834                For example, <code>&gt;&lt;10|20</code> to find values between 10
1835                and 20 (inclusive).
1836              </simpara>
1837            </listitem>
1838          </varlistentry>
1839        </variablelist>
1840       
1841        <sect3 id="webclient.itemlist.filter.units">
1842          <title>Units</title>
1843          <para>
1844            Some (numeric) columns have values with units. There are, for example,
1845            the <emphasis>Original quantity</emphasis> and <emphasis>Remaining quantity</emphasis>
1846            columns for biomaterials, which have values in micrograms (µg), and
1847            annotations which may have any unit.
1848          </para>
1849          <para>
1850            When filtering on a column that has a unit, numeric values without units are
1851            interpreted as the default unit for that column. But it is also possible to
1852            add a unit to the filter value. The examples below are filtering on the
1853            original quantity column of a biomaterial:
1854          </para>
1855          <para>
1856            <informalexample>&gt;=0.5mg</informalexample> matches biomaterials with
1857            an original quantity &gt;=500µg.
1858          </para>
1859          <para>
1860            <informalexample>=100|200|300µg</informalexample> matches biomaterials with
1861            exactly 100, 200 or 300 micrograms.
1862          </para>
1863          <para>
1864            It is also possible to mix units in a single filter:
1865            <informalexample>=100|200|300µg|0.5|1mg</informalexample> which matches
1866            100, 200, 300, 500 and 1000 micrograms.
1867          </para>
1868         
1869          <warning>
1870            <title>Be aware of rounding errors</title>
1871            <para>
1872              All filter values with a unit that is different from the default
1873              unit are converted to the default unit before being applied. Since
1874              numeric conversions are never exact down to the last decimal, this may
1875              result in problems to filter with an exact match. The last example above
1876              could, for example, be converted to: 100, 200, 300, 500.000001 and
1877              999.99999998.
1878            </para>
1879          </warning>
1880         
1881          <tip>
1882            <title>Hard-to-type characters</title>
1883            <para>
1884              Some units contains hard-to-type characters. For example,
1885              the greek letter µ in µg, and m² and m³ for areas and volumes.
1886              In all those cases it is also possible to use ug, m2 and m3,
1887              respectively.
1888            </para>
1889          </tip>
1890         
1891          <note>
1892            <title>Units are case-sensitive</title>
1893            <para>
1894              All units are case sensitive. The main reason for this is that
1895              it must be possible to tell the difference between
1896              <emphasis>milli (m)</emphasis> and <emphasis>mega (M)</emphasis> 
1897              prefixes, for example, <emphasis>mJ</emphasis> and <emphasis>MJ</emphasis>.
1898            </para>
1899          </note>
1900         
1901        </sect3>
1902      </sect2>
1903     
1904      <sect2 id="webclient.itemlist.columns">
1905        <title>Configuring which columns to show</title>
1906       
1907        <para>
1908          Most lists show only a small subset of the columns it
1909          is capable of showing. Use the
1910          <guibutton>Columns&hellip;</guibutton> button to open
1911          a dialog that allows you to select which columns to show
1912          and the order in which they are shown.
1913        </para>
1914       
1915        <figure id="webclient.figures.configure_columns">
1916          <title>Configuring which columns to show</title>
1917          <screenshot>
1918          <mediaobject>
1919            <imageobject>
1920              <imagedata fileref="figures/configure_columns.png" format="PNG"/>
1921            </imageobject>
1922          </mediaobject>
1923          </screenshot>
1924        </figure>
1925       
1926        <helptext external_id="columns.configure" 
1927          title="Set column order and visiblity">
1928       
1929        <variablelist>
1930        <varlistentry>
1931          <term><guilabel>Visible columns</guilabel></term>
1932          <listitem>
1933            <para>
1934              Shows the columns that are currently visible.
1935              Use the up/down arrow buttons to arrange the order of the
1936              visible columns. The topmost column is shown to the left.
1937              Use the right arrow button to move columns from this list
1938              to the hidden columns list. Columns marked with an <guilabel>×</guilabel> 
1939              are required
1940              and cannot be hidden. In most lists the <guilabel>Name</guilabel> column
1941              is the only column that is required.
1942            </para>
1943          </listitem>
1944        </varlistentry>
1945         
1946        <varlistentry>
1947          <term><guilabel>Hidden columns</guilabel></term>
1948          <listitem>
1949            <para>
1950              Shows columns that are not currently visible in the
1951              list. Use the left arrow button to move columns from
1952              this list to the visible columns list.
1953            </para>
1954          </listitem>
1955        </varlistentry>
1956       
1957       
1958        <varlistentry>
1959          <term><guilabel>Presets</guilabel></term>
1960          <listitem>
1961            <para>
1962              A dropdown list that allows you to
1963              select a set of preconfigured columns. You may also create
1964              your own preset if you often need to switch between different
1965              configurations. The list of presets is the same as the one
1966              described <link linkend="webclient.itemlist.presets">below</link>,
1967              but if used from this dialog the presets only affects the visible columns
1968              and not filters or sort order.
1969            </para>
1970          </listitem>
1971        </varlistentry>
1972        </variablelist>
1973       
1974          <para>
1975            Use the &gbSave; button to apply your
1976            changes or the &gbCancel; button to
1977            close the pop-up without saving.
1978          </para>
1979
1980        </helptext>
1981
1982      </sect2>
1983     
1984      <sect2 id="webclient.itemlist.presets">
1985        <title>Presets</title>
1986       
1987        <para>
1988          The <guilabel>view / presets</guilabel> dropdown has three
1989          main functions:
1990        </para>
1991       
1992        <figure id="webclient.figures.viewpresets" float="right">
1993          <title>The view / presets dropdown</title>
1994          <screenshot>
1995            <mediaobject>
1996              <imageobject><imagedata fileref="figures/view_presets.png" format="PNG" 
1997                /></imageobject>
1998            </mediaobject>
1999          </screenshot>
2000        </figure>
2001        <orderedlist>
2002          <listitem>
2003            <para>
2004              Switch between different configuration presets.
2005              The top of the dropdown contains user-defined presets (<guilabel>Saved preset #1</guilabel> and
2006              <guilabel>#2</guilabel>) and a few preconfigured presets.
2007              The user-defined presets are used to store a complete table configuration,
2008              including:
2009            </para>
2010           
2011            <itemizedlist>
2012              <listitem><simpara>Which columns are visible and their order</simpara></listitem>
2013              <listitem><simpara>The column (or columns) used for sorting</simpara></listitem>
2014              <listitem><simpara>Filter settings</simpara></listitem>
2015              <listitem><simpara>The number of items per page and the current page</simpara></listitem>
2016            </itemizedlist>
2017           
2018            <para>             
2019              The preconfigured presets only affects
2020              the visible columns as follows:
2021            </para>
2022           
2023            <itemizedlist>
2024              <listitem>
2025                <para><guilabel>All columns</guilabel> - Show all columns.</para>
2026              </listitem>
2027              <listitem>
2028                <para><guilabel>Required columns</guilabel> - Show only the required columns.
2029                  Usually only the <guilabel>Name</guilabel> column is required.</para>
2030              </listitem>
2031              <listitem>
2032                <para><guilabel>Default columns</guilabel> - Show the default set of columns.</para>
2033              </listitem>
2034              <listitem>
2035                <para><guilabel>Other&hellip;</guilabel> -
2036                  Open the configure columns dialog box, described in
2037                  <xref linkend="webclient.itemlist.columns"/>.</para>
2038              </listitem>
2039            </itemizedlist>
2040           
2041          </listitem>
2042         
2043          <listitem>
2044            <para>
2045              Filter items by the removed status and the access
2046              permissions to an item.
2047            </para>
2048           
2049            <itemizedlist>
2050              <listitem>
2051                <para><guilabel>Removed</guilabel> - If checked, items that have been
2052                moved to the trashcan are shown, otherwise they are hidden.</para>
2053              </listitem>
2054              <listitem>
2055                <para><guilabel>Owned by me</guilabel> - If checked, items that the logged in user
2056                owns are displayed, otherwise they are hidden.</para>
2057              </listitem>
2058              <listitem>
2059                <para><guilabel>Shared to me</guilabel> - If checked, items that are owned
2060                by other users but shared to the logged in user are displayed, otherwise
2061                they are hidden.</para>
2062              </listitem>
2063              <listitem>
2064                <para><guilabel>In current project</guilabel> -
2065                  If checked, items that are linked with the current project are displayed,
2066                  otherwise they are hidden. It does not matter if the logged in user is the
2067                  owner or not. This option is only available if a project is active.
2068                </para>
2069              </listitem>
2070              <listitem>
2071                <para><guilabel>Owned by others</guilabel> -
2072                  This option is only available to administrators and will display
2073                  items that are owned by other users.
2074                </para>
2075              </listitem>
2076            </itemizedlist>
2077           
2078            <para>
2079              The default is to display item that the current user
2080              owns and, if a project is active, items in that project.
2081            </para>
2082           
2083          </listitem>
2084
2085          <listitem>
2086            <para>
2087              Administrate the presets
2088            </para>
2089            <itemizedlist>
2090              <listitem>
2091                <para><guilabel>Clear filter</guilabel> - Clears
2092                all filters.</para>
2093              </listitem>
2094             
2095              <listitem>
2096                <para><guilabel>Save as&hellip;</guilabel> - Save the
2097                current configuration as a preset.</para>
2098              </listitem>
2099
2100              <listitem>
2101                <para><guilabel>Manage&hellip;</guilabel> - Opens a dialog
2102                where you can remove saved presets. You can also load
2103                saved presets from the dialog, but it is quicker to just
2104                use the dropdown list for this.</para>
2105              </listitem>
2106            </itemizedlist>
2107          </listitem>
2108        </orderedlist>
2109       
2110        <sect3 id="webclient.itemlist.presets.saveas">
2111          <title>Save a preset</title>
2112         
2113          <para>
2114            If you select the <guilabel>Save as&hellip;</guilabel>
2115            option from the <guilabel>view / presets</guilabel> dropdown
2116            the <guilabel>Save preset as</guilabel> dialog is opened.
2117          </para>
2118         
2119          <figure id="webclient.figures.savepresetas">
2120            <title>Save preset as</title>
2121            <screenshot>
2122              <mediaobject>
2123                <imageobject><imagedata fileref="figures/save_preset.png" format="PNG" /></imageobject>
2124              </mediaobject>
2125            </screenshot>
2126          </figure>
2127         
2128          <helptext external_id="contexts.saveas" title="Save preset as">
2129         
2130          <variablelist>
2131          <varlistentry>
2132            <term><guilabel>For item</guilabel></term>
2133            <listitem>
2134              <para>
2135              The type of item the preset is saved for.
2136              </para>
2137            </listitem>
2138          </varlistentry>
2139          <varlistentry>
2140            <term><guilabel >Name</guilabel></term>
2141            <listitem>
2142              <para>
2143              The name of the preset. The name must be unique.
2144              </para>
2145            </listitem>
2146          </varlistentry>
2147          <varlistentry>
2148            <term><guilabel>Overwrite existing</guilabel></term>
2149            <listitem>
2150              <para>
2151              If a preset with the same name already exists, it is
2152              overwritten if this checkbox is checked.
2153              </para>
2154            </listitem>
2155          </varlistentry>
2156          <varlistentry>
2157            <term><guilabel>Public</guilabel></term>
2158            <listitem>
2159              <para>
2160              This options is only available for users
2161              which has the <emphasis>SHARE_TO_EVERYONE</emphasis>
2162              permission. If checked the preset is visible to
2163              all users.
2164              </para>
2165            </listitem>
2166          </varlistentry>
2167          </variablelist>
2168         
2169          <para>
2170            Use the &gbOk; button to save the preset
2171            or the &gbCancel; button to
2172            close the pop-up without saving.
2173          </para>
2174         
2175         
2176          </helptext>
2177         
2178        </sect3>
2179       
2180        <sect3 id="webclient.itemlist.presets.manage">
2181          <title>Manage presets</title>
2182         
2183          <para>
2184            If you select the <guilabel>Manage&hellip;</guilabel>
2185            option from the <guilabel>view / presets</guilabel> dropdown
2186            the <guilabel>Manage presets</guilabel> dialog is opened.
2187          </para>
2188         
2189          <figure id="webclient.figures.managepresets">
2190            <title>Manage presets</title>
2191            <screenshot>
2192              <mediaobject>
2193                <imageobject><imagedata fileref="figures/manage_presets.png" format="PNG" /></imageobject>
2194              </mediaobject>
2195            </screenshot>
2196          </figure>
2197         
2198          <helptext external_id="contexts.manage" title="Manage presets">
2199         
2200          <para>
2201            From this dialog you can delete or load presets.
2202          </para>
2203         
2204          <para>
2205            To delete presets, first mark the checkbox in front of
2206            each preset you want to delete. Then, click on the
2207            <guibutton>Delete&hellip;</guibutton> button. You will get
2208            a warning about that the action cannot be undone. Unlike other
2209            items, the presets are not moved to the trashcan. Click on
2210            &gbOk; to delete the preset.
2211          </para>
2212         
2213          <note>
2214            <title>Edit a preset</title>
2215            <para>
2216            It is not possible to edit a preset directly. To change an
2217            existing preset you must:
2218           
2219            <orderedlist>
2220            <listitem><simpara>Load the preset.</simpara></listitem>
2221            <listitem><simpara>Use the interface to change column settings, filter,
2222              sort order, etc.</simpara></listitem>
2223            <listitem><simpara>Save the preset with the same name.</simpara></listitem>
2224            </orderedlist>
2225            </para>
2226          </note>
2227         
2228          <para>
2229            Use the &gbClose; button to
2230            close the pop-up.
2231          </para>
2232         
2233         
2234          </helptext>
2235         
2236        </sect3>
2237       
2238      </sect2>
2239    </sect1>
2240
2241
2242    <sect1 id="webclient.trashcan">
2243      <?dbhtml filename="trashcan.html" ?>
2244      <title>Trashcan</title>
2245      <para>
2246        All items that have been deleted, and are owned by you, are
2247        listed in your trashcan. This list page is accessed with
2248        <menuchoice>
2249          <guimenu>View</guimenu>
2250          <guimenuitem>Trashcan</guimenuitem>
2251        </menuchoice>
2252        and it differs a bit from the other common list pages. The
2253        most significant difference is that the trashcan page can
2254        contain more then one item type, actually all removable item
2255        types in BASE can be listed in the trashcan. Items that neither
2256        can be removed or deleted, <emphasis>i.e.,</emphasis> items
2257        like sessions, nor clients' help texts since these are deleted
2258        from the database immediately in list/item view will be shown
2259        in the trashcan page.
2260      </para>
2261      <warning>
2262        <para>
2263          Some item types do not have any owner and these are listed
2264          in the trashcans for everyone with delete permission on that
2265          specific item type.
2266        </para>
2267      </warning>
2268
2269      <para>
2270        Things that the trashcan page have in common with other list
2271        pages are the possibility to restore and view/edit items, see
2272        <xref linkend="webclient.items.restore" /> and
2273        <xref linkend="webclient.items.edit" /> . If an item is
2274        restored, it will of course disappear from the trashcan.
2275      </para>
2276
2277      <sect2 id="webclient.trashcan.deleteitem">
2278        <title>Delete items permanently</title>
2279        <para>
2280          Items can be permanently deleted from BASE only if they are
2281          not used by other items.  Items that are used have the icon
2282          <inlinemediaobject>
2283            <imageobject>
2284              <imagedata fileref="figures/used.png" format="PNG" />
2285            </imageobject>
2286          </inlinemediaobject>
2287          in the first column and by clicking on it you can get more
2288          information about the dependencies, see
2289          <xref linkend="webclient.trashcan.viewdependencies" /> .
2290          <note>
2291            <simpara>
2292              This view is NOT the same view page as when clicking on
2293              the item's name, which brings you to the item's view
2294              page.
2295            </simpara>
2296          </note>
2297        </para>
2298        <para>
2299          To delete one or several items permanently from the trashcan
2300          you first have to select them and then to click on the
2301          &gbDelete; button. Press then on either &gbOk; (completes
2302          the deletion) or &gbCancel; (no items will be deleted) in
2303          the dialog window that appears.
2304        </para>
2305
2306        <sect3 id="webclient.trashcan.deleteitem.empty">
2307          <title>Empty trashcan</title>
2308          <para>
2309            If all items in the trashcan should be deleted permanently
2310            the <guibutton>Empty trash</guibutton> button can be
2311            used. This function will remove all items that are listed
2312            in your trashcan, except those items which other items,
2313            not marked for deletion or cannot be deleted, are
2314            dependent on.
2315          </para>
2316        </sect3>
2317      </sect2>
2318
2319      <sect2 id="webclient.trashcan.viewdependencies">
2320        <title>View dependencies of a trashed item</title>
2321        <helptext external_id="trash.view.properties" title="Properties for a trashed item">
2322          <para>
2323            This view can only be accessed from trashed items that are
2324            linked together with other items. Beside the item's
2325            <guilabel>item type</guilabel>, <guilabel>name</guilabel>,
2326            and <guilabel>description</guilabel> there is a list at
2327            the bottom of the view page with those items that are
2328            using the current item in some way.
2329          </para>
2330        </helptext>
2331        <para>
2332          <nohelp>
2333            <figure id="webclient.trashcan.figures.viewtrasheditem">
2334              <title>Item view of a trashed item.</title>
2335              <screenshot>
2336                <mediaobject>
2337                  <imageobject>
2338                    <imagedata fileref="figures/trashview.png" format="PNG" 
2339                               scalefit="1" width="100%" />
2340                  </imageobject>
2341                </mediaobject>
2342              </screenshot>
2343            </figure>
2344          </nohelp>
2345          <orderedlist>
2346            <listitem>
2347              <para>
2348                This icon indicates that the item cannot be deleted
2349                permanently cause of some dependencies, listed below.
2350              </para>
2351            </listitem>
2352            <listitem>
2353              <para>Common properties for all removable items.</para>
2354            </listitem>
2355            <listitem id="webclient.trashcan.lists.dependentitem3">
2356              <para>
2357                A list of other items that are using the current item,
2358                blocking permanent removal.
2359              </para>
2360            </listitem>
2361          </orderedlist>
2362        </para>
2363      </sect2>
2364    </sect1>
2365   
2366  <sect1 id="webclient.itemoverview">
2367    <?dbhtml filename="itemoverview.html" ?>
2368    <title>Item overview</title>
2369
2370    <helptext external_id="item.overview" 
2371      title="Item overview">
2372   
2373    <para>
2374      With the <guilabel>Item overview</guilabel> 
2375      function you can get an overview of all bioassays,
2376      extracts, samples, annotations, raw data sets, etc. that are
2377      related to a given item. In the overview you can also validate
2378      the data to find possibly missing or incorrect information.
2379    </para>
2380   
2381    <nohelp>
2382    <para>
2383      You can access the overview for an item by navigating
2384      to the single-item view of the item you are interested in.
2385      Then, switch to the <guilabel>Overview</guilabel> tab that
2386      is present on that page. Here is an example of what is displayed:
2387    </para>
2388   
2389    <figure id="webclient.figures.itemoverview">
2390      <title>The item overview</title>
2391      <screenshot>
2392        <mediaobject>
2393          <imageobject><imagedata 
2394            scalefit="1" width="100%"
2395            fileref="figures/item_overview.png" format="PNG"
2396            /></imageobject>
2397        </mediaobject>
2398      </screenshot>
2399    </figure>
2400    </nohelp>
2401   
2402    <para>
2403      The page is divided into three sections:
2404    </para>
2405   
2406    <itemizedlist>
2407      <listitem>
2408        <para>
2409        To the left is a tree displaying items that are related
2410        to the current item. The tree is loaded gradually when
2411        you click your way through the sublevels.
2412        The only exception is after a validation has been done,
2413        in this case the whole tree is loaded through the validation-process.               
2414        </para>
2415      </listitem>
2416     
2417      <listitem>
2418        <para>
2419        The lower right shows a list of warnings and error
2420        messages that was found when validating the data.
2421        This section is empty if no validation has been done.
2422        Click on the <guibutton>Validate</guibutton> button
2423        to validate the data and load errors and warnings.       
2424        <nohelp>
2425          In the example you can see that we have failed to
2426          specify a value for the <guilabel>Temperature</guilabel> 
2427          protocol parameter for one of the samples.
2428        </nohelp> 
2429        </para>
2430      </listitem>
2431       
2432      <listitem>
2433        <para>
2434          The upper right shows information about the
2435          currently selected item in the tree. This part will also
2436          contain more information about errors or warnings for this
2437          item, but only if a validation has been done.
2438          It may also present you with one or more suggestions
2439          about how to fix the problem and with a link that
2440          takes you to the most probable location where you can fix
2441          the error or warning.
2442        </para>
2443       
2444      </listitem>
2445       
2446    </itemizedlist>
2447   
2448    <seeother>
2449      <other external_id="item.overview.validationoptions"
2450        >Validation options</other>
2451      <other external_id="item.overview.fixfailures"
2452        >How to fix validation failures</other>
2453    </seeother>
2454   
2455    </helptext>
2456   
2457    <sect2 id="webclient.itemoverview.validationoptions">
2458      <title>Validation options</title>
2459      <para>
2460        Click on the <guibutton>Validation options</guibutton>
2461        button in the toolbar to open the <guilabel>Validation
2462        options</guilabel> dialog.
2463      </para>
2464     
2465      <figure id="webclient.figures.validationoptions">
2466        <title>Validation options</title>
2467        <screenshot>
2468          <mediaobject>
2469            <imageobject><imagedata 
2470              fileref="figures/validation_options.png" format="PNG"
2471              /></imageobject>
2472          </mediaobject>
2473        </screenshot>
2474      </figure>         
2475     
2476      <helptext external_id="item.overview.validationoptions" 
2477        title="Validation options">
2478        <para>
2479          The validation procedure is highly
2480          configurable and you can select what you want to
2481          ignore, and what should be displayed as an error
2482          or warning.
2483        </para>
2484       
2485        <variablelist>
2486          <varlistentry>
2487            <term>
2488            <guilabel>Presets</guilabel></term>
2489            <listitem>
2490              <para>
2491              The list contains predefined and
2492              user defined validation options.
2493              Use the <guibutton>Save as&hellip;</guibutton>
2494              button to save the current options as a user defined
2495              preset. The <guibutton>Remove&hellip;</guibutton>
2496              button is used to remove the currently selected
2497              preset. Predefined presets cannot be deleted.
2498              </para>
2499            </listitem>
2500          </varlistentry>
2501         
2502          <varlistentry>
2503            <term><guilabel>Project defaults</guilabel></term>
2504            <listitem>
2505              <para>
2506              The options in this section are used to check
2507              if your experiment uses the same values as set
2508              by the project default values of the currently active
2509              project<nohelp>
2510              (see <xref linkend="project_permission.projects" />)</nohelp>.
2511              If no project is active these options are ignored.
2512              The validation is only performed if the project has at least one
2513              item with a matching type. For example, if no default array
2514              design has been added to the project, all array designs
2515              are allowed. For items that can have a subtype, the
2516              subtype is also considered. For example, if only a default
2517              sampling protocol has been selected, no warnings are
2518              generated for extraction protocols.
2519              </para>
2520            </listitem>
2521           
2522          </varlistentry>
2523         
2524          <varlistentry>
2525            <term><guilabel>Missing items</guilabel></term>
2526            <listitem>
2527              <para>
2528              The options in this section are used to check if
2529              you have specified values for optional items.
2530              For example, there is an option that warns you if
2531              you have not specified a protocol. For items that
2532              can have a subtype, the rule here is to use the information
2533              about related subtypes before reporting a missing item.
2534              For example, the <emphasis>labeled extract</emphasis>
2535              subtype is related to the <emphasis>label</emphasis>
2536              subtype and if a label is missing it is reported as a
2537              warning. If there is no related subtype no warning is
2538              generated.
2539              </para>
2540            </listitem>
2541          </varlistentry>
2542         
2543          <varlistentry>
2544            <term><guilabel>Subtypes</guilabel></term>
2545            <listitem>
2546              <para>
2547              The options in this section are used to check that related items
2548              have a subtype that matches the subtype of the main item. For example,
2549              if we have an <emphasis>extract</emphasis>
2550              which is a <emphasis>labeled extract</emphasis> subtype the subtype for
2551              the related tag should be <emphasis>label</emphasis>, but if the extract
2552              is a <emphasis>library</emphasis> the subtype of the tag should be
2553              <emphasis>barcode</emphasis>.
2554              </para>
2555            </listitem>
2556          </varlistentry>
2557
2558          <varlistentry>
2559            <term><guilabel>Annotations</guilabel></term>
2560            <listitem>
2561              <para>
2562              The options in this section are used to check
2563              problems related to annotations. The most
2564              important ones are listed here:
2565              </para>
2566             
2567              <itemizedlist>
2568              <listitem>
2569                <simpara>
2570                <emphasis>Missing MIAME annotation value</emphasis>:
2571                Checks that you have specified values
2572                for all annotations marked as
2573                <guilabel>Required for MIAME</guilabel>.
2574                </simpara>
2575              </listitem>
2576             
2577              <listitem>
2578                <simpara>
2579                <emphasis>Missing factor value</emphasis>:
2580                Checks that you have specified values for
2581                all annotations used as experimental factors in
2582                the experiment. This is only checked when an experiment
2583                is selected as the root item.
2584                </simpara>
2585              </listitem>
2586             
2587              <listitem>
2588                <simpara>
2589                <emphasis>Missing parameter value</emphasis>:
2590                Checks that you have specified values
2591                for all protocol parameters.
2592                </simpara>
2593              </listitem>
2594
2595              <listitem>
2596                <simpara>
2597                <emphasis>Annotation is protocol parameter</emphasis>:
2598                Checks if an item has been annotated with a
2599                an annotation that is actually a protocol parameter.
2600                </simpara>
2601              </listitem>
2602
2603              <listitem>
2604                <simpara>
2605                <emphasis>Annotation has invalid value</emphasis>:
2606                Checks if annotation values are correct with
2607                respect to the rules given by the annotation type.
2608                This might include numeric values that are outside
2609                the valid range, or values not in the list
2610                of allows values for an enumerated annotation type.
2611                </simpara>
2612              </listitem>
2613
2614              <listitem>
2615                <simpara>
2616                <emphasis>Inheriting annotation from non-parent</emphasis>:
2617                Checks if inherited annotations really comes from a
2618                parent item. This might happen if you rearrange
2619                parent-child relationship because you found that
2620                they were incorrectly linked.
2621                </simpara>
2622              </listitem>
2623              </itemizedlist>
2624             
2625           
2626            </listitem>
2627          </varlistentry>
2628         
2629          <varlistentry>
2630            <term><guilabel>Files</guilabel></term>
2631            <listitem>
2632              <para>
2633              The options in this section are related to the validity of
2634              data files that can be attached to some items, for example,
2635              raw bioassays and array designs. The data files are usually
2636              validated immediately when they are used and the result is saved
2637              to the database. The options in this dialog can be used to find
2638              (or ignore) problems with data files.
2639              </para>
2640            </listitem>
2641          </varlistentry>
2642
2643         
2644          <varlistentry>
2645            <term><guilabel>Denied access</guilabel></term>
2646            <listitem>
2647              <para>
2648              The options in this section are used to
2649              check if you do not have access (read permission)
2650              to an item in the experiment hierarchy. If this
2651              happens the validation cannot proceed in that branch.
2652              This might mask other validation problems.
2653              </para>
2654            </listitem>
2655          </varlistentry>
2656         
2657          <varlistentry>
2658            <term><guilabel>Link consistency</guilabel></term>
2659            <listitem>
2660              <para>
2661              The options in this section are used to check
2662              that links between (multiple) items are consistent
2663              with each other. The most
2664              important options are:
2665              </para>
2666
2667              <itemizedlist>
2668                <listitem>
2669                  <simpara>
2670                  <emphasis>Array design mismatch</emphasis>:
2671                  Checks if the array design specified for
2672                  a raw bioassay is the same array design
2673                  specified for the physical bioassay.
2674                  </simpara>
2675                </listitem>
2676               
2677                <listitem>
2678                  <simpara>
2679                  <emphasis>Multiple array designs</emphasis>:
2680                  Checks if all raw bioassays in an experiment
2681                  use the same array design or not. This is only
2682                  checked when the root item is an experiment.
2683                  </simpara>
2684                </listitem>
2685               
2686                <listitem>
2687                  <simpara>
2688                  <emphasis>Circular reference to pooled item</emphasis>:
2689                  If you have used pooling, checks that no
2690                  circular references have been created.
2691                  </simpara>
2692                </listitem>
2693               
2694                <listitem>
2695                  <simpara>
2696                  <emphasis>Multiple extracts with same tag+position</emphasis>:
2697                  Checks if the extracts on a physical bioassay have a
2698                  unique combination of tag+position. This is usually
2699                  required to be able to assign measured data correctly
2700                  downstreams.
2701                  </simpara>
2702                </listitem>
2703               
2704              </itemizedlist>
2705
2706            </listitem>
2707          </varlistentry>
2708         
2709          <varlistentry>
2710            <term><guilabel>Other</guilabel></term>
2711            <listitem>
2712              <para>
2713              This section collects options that does not fit
2714              into any of the other sections. The most
2715              important options are:
2716              </para>
2717             
2718              <itemizedlist>
2719                <listitem>
2720                  <simpara>
2721                  <emphasis>Non-unique name</emphasis>:
2722                  Checks if two items of the same type
2723                  have the same name. It is usually a good idea to
2724                  have unique names within an experiment if the data is
2725                  going to be exported and in other circumstances.
2726                  </simpara>
2727                </listitem>
2728
2729              </itemizedlist>
2730             
2731            </listitem>
2732          </varlistentry>
2733         
2734        </variablelist>
2735       
2736        <para>
2737          Click on the &gbSave; button
2738          to use the current settings. The display will
2739          automatically refresh itself.
2740        </para>
2741       
2742      </helptext>
2743     
2744      <helptext external_id="item.overview.validationoptions.savepreset" 
2745        title="Save preset" webonly="1">
2746       
2747        <para>
2748        Saves all validation options as a preset.
2749        </para>
2750       
2751        <variablelist>
2752          <varlistentry>
2753            <term><guilabel>Name</guilabel></term>
2754            <listitem>
2755              <para>
2756                The name of the preset. The name must be unique
2757                and if a preset with the same name already exists
2758                you will be asked if you want to overwrite it or not.
2759              </para>
2760            </listitem>
2761          </varlistentry>
2762        </variablelist>
2763       
2764        <para>
2765          Click on the &gbSave; button
2766          to save the preset or &gbCancel;
2767          to abort.
2768        </para>
2769      </helptext>
2770     
2771    </sect2>
2772   
2773    <sect2 id="webclient.itemoverview.fixfailures">
2774      <title>Fixing validation failures</title>
2775      <helptext external_id="item.overview.fixfailures" 
2776        title="How to fix validation failures">
2777       
2778        <para>       
2779        The overview includes a function that allows
2780        you to quickly fix most of the problems found during the
2781        validation. The easiest way to use the function is:
2782        </para>
2783       
2784        <orderedlist>
2785          <listitem>
2786            <simpara>
2787            Click on an error or warning in the list of failures in
2788            the lower right
2789            pane. The tree in the left pane and the item overview in the
2790            top right pane will automatically be updated to show the
2791            exact location of the faulty item.
2792            </simpara>
2793          </listitem>
2794          <listitem>
2795            <simpara>
2796            The upper right pane should contain a list labeled
2797            <guilabel>Failure details</guilabel> with more information
2798            about each failure and also one or more suggestions for fixing
2799            the problem. For example, a failure due to a missing item
2800            should suggest that you add or select an item.
2801            </simpara>
2802          </listitem>
2803         
2804          <listitem>
2805            <simpara>
2806            The suggestions should also have links that takes
2807            you to an edit view where you can do the changes.
2808            </simpara>
2809          </listitem>
2810         
2811          <listitem>
2812            <simpara>
2813            After saving the changes you must click on the
2814            <guibutton>Validate</guibutton> button to update the
2815            interface. If you want, you can fix more than one
2816            failure before clicking on the button.
2817            </simpara>
2818          </listitem>
2819           
2820        </orderedlist>
2821       
2822        <note>
2823          <title>Inactive links?</title>
2824          If you do not have permission to fix a problem the links will be inactive
2825          and you'll have to talk to someone with more powers.
2826        </note>
2827     
2828      </helptext>
2829    </sect2>
2830   
2831  </sect1>
2832
2833</chapter>
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