source: trunk/doc/src/docbook/userdoc/webclient.xml @ 4771

Last change on this file since 4771 was 4771, checked in by Nicklas Nordborg, 14 years ago

Fixes #1193: Generic tree-like item overview

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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 4771 2009-02-19 08:48:56Z nicklas $
7
8  Copyright (C) 2007 Jari Hakkinen, 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"?>
29  <title>Using the web client</title>
30    <sect1 id="webclient.introduction">
31      <title>Introduction</title>
32     
33      <sect2 id="webclient.intro.login">
34        <title>Logging in</title>
35        <para>
36          There are three things that you need to know
37          before you can use BASE:
38        </para>
39       
40        <orderedlist>
41        <listitem><simpara>The address (URL) to a BASE server</simpara></listitem>
42        <listitem><simpara>A username to login with</simpara></listitem>
43        <listitem><simpara>A password</simpara></listitem>
44        </orderedlist>
45       
46        <para>
47          You may, for example, try the BASE demo server. Go to the
48          URL <ulink url="http://base2.thep.lu.se:8080/demo/">http://base2.thep.lu.se:8080/demo/</ulink>
49          and enter <userinput>base2</userinput> for the login and <userinput>base2</userinput>
50          for the password.
51        </para>
52       
53        <para>
54          You need to get all three things from an administrator
55          of the BASE server. If you know only the address to the
56          BASE server, you may check the front page if the administrator
57          has added any information about how to get a username/password
58          there. Look for the <guilabel>Get an account!</guilabel> link on
59          the front page.
60        </para>
61       
62        <para>
63          Logging in is simple, just enter your <guilabel>login</guilabel> 
64          and <guilabel>password</guilabel> in the form on the front page
65          and click the <guibutton>Login</guibutton> button. There is
66          a checkbox which allows you to <guilabel>encrypt the password</guilabel>
67          before it is sent to the BASE server. It is checked by default, and
68          it is a good idea to leave it checked unless you have problems logging
69          in. If you are sure you are entering the correct login and password,
70          but still cannot log in, try unchecking the encryption option.
71          If the checkbox is not visible, which happens if the server is
72          using an external authentication server, the password is not encrypted.
73        </para>
74      </sect2>
75     
76      <sect2 id="webclient.intro.forgotten_password">
77        <title>Forgotten password</title>
78        <para>
79          If you forget your password you will need to get a new one.
80          BASE stores the passwords in an encrypted form that does not allow
81          anyone, not even the server administrator, to find out the
82          un-encrypted password.
83        </para>
84        <para>
85          To get a new password you will have to contact the server
86          administrator. There may be a <guilabel>Forgot your password?</guilabel>
87          link on the front page where the server administrator has entered
88          information about how to get a new password.
89        </para>
90      </sect2>
91
92      <sect2 id="webclient.intro.homepage">
93        <title>The home page</title>
94     
95      <para>
96        When you have been logged in the home page will be displayed. It
97        displays some useful information. You can also go to the home page
98        using the
99        <menuchoice><guimenu>View</guimenu><guimenuitem>Home</guimenuitem></menuchoice>
100      </para>
101       
102      <figure id="webclient.figures.homepage">
103        <title>The home page</title>
104        <screenshot>
105          <mediaobject>
106            <imageobject><imagedata fileref="figures/homepage.png" format="PNG"
107              scalefit="1" width="100%"/></imageobject>
108          </mediaobject>
109        </screenshot>
110      </figure>
111       
112      <variablelist>
113        <varlistentry>
114          <term><interface>New messages</interface></term>
115          <listitem>
116            <para>
117            Messages are sent by plug-ins to notify you about finished jobs. In the
118            future, you may get messages from other sources as well. As of today,
119            messages are not used for communication between users.
120            </para>
121          </listitem>
122        </varlistentry>
123       
124        <varlistentry>
125          <term><interface>Projects</interface></term>
126          <listitem>
127            <para>
128            A list of projects that you are a member of. Projects are an important
129            part of BASE and are the best way to share data when you are
130            cooperating with other users. We recommend
131            that you always use a project when working with BASE.
132            For more information read <xref linkend="project_permission"/>.
133            </para>
134          </listitem>
135        </varlistentry>
136       
137        <varlistentry>
138          <term><interface>Disk usage</interface></term>
139          <listitem>
140            <para>
141            An overview of how much disk space you have been assigned and
142            how much you are using.
143            </para>
144          </listitem>
145        </varlistentry>
146       
147        <varlistentry>
148          <term><interface>Help</interface></term>
149          <listitem>
150            <para>
151            Links for getting help and reporting bugs. The number
152            of links displayed here may vary depending on the server
153            configuration.
154            </para>
155          </listitem>
156        </varlistentry>
157       
158        <varlistentry>
159          <term><interface>News and announcements</interface></term>
160          <listitem>
161            <para>
162            A list of important news and announcements from the
163            server administrator. Here you may, for example, find
164            information about server upgrades and maintenance.
165            </para>
166          </listitem>
167        </varlistentry>
168      </variablelist>
169       
170      </sect2>
171     
172      <sect2 id="webclient.intro.menubar">
173        <title>Using the menu bar</title>
174        <para>
175          On the top of the home page is the <interface>Menu bar</interface>.
176          This is the main navigation tool in BASE. It works the same way
177          as the regular menu system found in most other applications. Use
178          the mouse to click and select an item from the menu.
179        </para>
180       
181        <para>
182          Most of the menu is in two levels, ie. clicking on a top-level menu
183          will open a submenu just below it. Clicking on something in the
184          submenu will take you to another page or open a pop-up dialog window.
185          For example, the
186          <menuchoice><guimenu>Biomaterial LIMS</guimenu><guimenuitem>Samples</guimenuitem></menuchoice>
187          menu will take you to the page listing samples and
188          <menuchoice><guimenu>File</guimenu><guimenuitem>Contact information</guimenuitem></menuchoice>
189          opens a dialog where you can modify your contact information details.
190        </para>
191       
192        <para>
193          The menu bar also contains shortcuts to some often-used
194          actions:
195        </para>
196       
197       
198      <variablelist>
199        <varlistentry>
200          <term>           
201            <guiicon>
202              <inlinemediaobject>
203              <imageobject><imagedata fileref="figures/refresh.gif" format="GIF" align="left"
204                /></imageobject>
205              </inlinemediaobject>
206            </guiicon>
207            <interface>
208            Refresh page
209            </interface>
210          </term>
211          <listitem>
212            <para>
213            Refresh/reload the current page. This is useful when you add
214            or modify items in BASE. Most of the time the page is refreshed
215            automatically, but in some cases you will have to use
216            this button to refresh the page.
217            </para>
218           
219            <warning>
220              <para>
221              Do not use your browser's <guibutton>Refresh</guibutton> button.
222              Most browsers will take you to the login page again.
223              </para>
224            </warning>
225          </listitem>
226        </varlistentry>
227       
228        <varlistentry>
229          <term>     
230            <guiicon>     
231              <inlinemediaobject>
232              <imageobject><imagedata fileref="figures/recent.png" format="PNG" align="left"/></imageobject>
233              </inlinemediaobject>
234            </guiicon>
235            <interface>
236            Recent items
237            </interface>
238          </term>
239          <listitem>
240            <para>
241            Shortcut to the most recently viewed items. The number of items are
242            configurable and you can also make some item types
243            <emphasis>sticky</emphasis>. This will for example keep the shortcut
244            to the last experiment even if you have viewed lots of other items
245            more recently.
246            See <xref linkend="webclient.configuration.preferences.mostrecent"/>
247            for configuration information.
248            </para>
249          </listitem>
250        </varlistentry>
251       
252        <varlistentry>
253          <term>
254            <guiicon>
255              <inlinemediaobject>
256              <imageobject><imagedata fileref="figures/project.gif" format="GIF" align="left"/></imageobject>
257              </inlinemediaobject>
258            </guiicon>
259            <interface>
260            Projects
261            </interface>
262          </term>
263          <listitem>
264            <para>
265            A list of all projects you are a member of. Selecting a project in the
266            list will make that project the active project.
267            </para>
268          </listitem>
269        </varlistentry>
270       
271        <varlistentry>
272          <term>
273            <guiicon>
274              <inlinemediaobject>
275              <imageobject><imagedata fileref="figures/user.png" format="PNG" align="left"/></imageobject>
276              </inlinemediaobject>
277            </guiicon>
278            <interface>
279            Logged in user
280            </interface>
281          </term>
282          <listitem>
283            <para>
284            Displays the name of the currently logged in user and allows
285            you to quickly log out and switch to another user.
286            </para>
287          </listitem>
288        </varlistentry>
289       
290      </variablelist>
291       
292      </sect2>
293     
294      <sect2 id="webclient.intro.help">
295        <title>Getting help</title>
296        <para>
297          Besides reading this document there are more ways to get help:
298        </para>
299        <variablelist>
300          <varlistentry>
301            <term>
302              On-line context-sensitive help
303            </term>
304            <listitem>
305              <para>
306              Whenever you find a small help icon
307              (<guiicon>
308                <inlinemediaobject>
309                <imageobject><imagedata fileref="figures/help.gif" format="GIF" /></imageobject>
310                </inlinemediaobject>
311              </guiicon>)
312              or button you may
313              click it to get help about the part of the page
314              you are currently viewing. The icon is located in the title
315              bar in most pop-up dialog windows and in the toolbar in most
316              other pages.
317              </para>
318            </listitem>
319          </varlistentry>
320
321          <varlistentry>
322            <term>
323              Using the <menuchoice><guimenu>Help</guimenu></menuchoice> menu
324            </term>
325            <listitem>
326              <para>
327              The <menuchoice><guimenu>Help</guimenu></menuchoice> menu
328              contains links for getting on-line help. These links
329              may be configured by a server administrator, so they may be
330              different from server to server. By default links for reporting
331              a bug and accessing this document are installed.
332              </para>
333            </listitem>
334          </varlistentry>
335
336          <varlistentry>
337            <term>
338              Mailing lists and other resources
339            </term>
340            <listitem>
341              <para>
342              See <xref linkend="resources" />.
343              </para>
344            </listitem>
345          </varlistentry>
346
347        </variablelist>
348       
349      </sect2>
350   
351    </sect1>
352   
353    <sect1 id="webclient.configuration">
354      <title>Configuring your account</title>
355     
356      <sect2 id="webclient.configuration.contact">
357        <title>Contact information</title>
358       
359        <para>
360          Use the <menuchoice><guimenu>File</guimenu>
361          <guimenuitem>Contact information</guimenuitem></menuchoice>
362          menu to bring up the user information dialog.
363        </para>
364       
365        <helptext external_id="userpreferences.contact" title="Contact information">
366       
367          <para>
368          This dialog has three tabs, <guilabel>Contact information</guilabel>
369          (selected), <guilabel>Password</guilabel> and <guilabel>Other information</guilabel>.
370          The logged in user can update the following contact information
371          details.
372          </para>
373       
374          <note>
375            <title>Multi-user accounts</title>
376            <para>
377              If you are using a multi-user account, for example a demo-account, you
378              do not have permission to change the contact information.
379            </para>
380          </note>
381       
382          <variablelist>
383            <varlistentry>
384              <term>
385                <guilabel>Full name</guilabel>
386              </term>
387              <listitem>
388                <para>
389                Your full name. You are not allowed to change this. If
390                it is not correct, contact an administrator to do it for
391                you.
392                </para>
393              </listitem>
394            </varlistentry>
395            <varlistentry>
396              <term>
397                <guilabel>Email</guilabel>
398              </term>
399              <listitem>
400                <para>
401                Your email address (optional).
402                </para>
403              </listitem>
404            </varlistentry>
405            <varlistentry>
406              <term>
407                <guilabel>Organisation</guilabel>
408              </term>
409              <listitem>
410                <para>
411                The name of the organisation you work for or represent (optional).
412                </para>
413              </listitem>
414            </varlistentry>
415            <varlistentry>
416              <term>
417                <guilabel>Address</guilabel>
418              </term>
419              <listitem>
420                <para>
421                Your postal address as it should be printed on letters to you
422                (optional).
423                </para>
424              </listitem>
425            </varlistentry>
426            <varlistentry>
427              <term>
428                <guilabel>Phone</guilabel>
429              </term>
430              <listitem>
431                <para>
432                Your phone number (optional). You may enter multiple phone numbers,
433                for example your work phone number and a mobile number.
434                </para>
435              </listitem>
436            </varlistentry>
437            <varlistentry>
438              <term>
439                <guilabel>Fax</guilabel>
440              </term>
441              <listitem>
442                <para>
443                Your fax number (optional).
444                </para>
445              </listitem>
446            </varlistentry>
447            <varlistentry>
448              <term>
449                <guilabel>Url</guilabel>
450              </term>
451              <listitem>
452                <para>
453                An URL to your home page or your organisation's home page (optional).
454                </para>
455              </listitem>
456            </varlistentry>
457          </variablelist>
458         
459          <para>
460            Press &gbSave; to save the changes or
461            &gbCancel; to abort.
462          </para>
463         
464          <seeother>
465            <other external_id="userpreferences.password">Change password</other>
466            <other external_id="userpreferences.other">Other information</other>
467          </seeother>
468        </helptext>
469       
470      </sect2>
471     
472      <sect2 id="webclient.configuration.other">
473        <title>Other information</title>
474        <para>
475          Use the
476          <menuchoice>
477            <guimenu>File</guimenu>
478            <guimenuitem>Other information&hellip;</guimenuitem>
479          </menuchoice>
480          menu to bring up the other information dialog.
481        </para>
482        <helptext external_id="userpreferences.other" title="Other information">
483          <para>
484            This dialog has three tabs,
485            <guilabel>Contact information</guilabel>
486            ,
487            <guilabel>Password</guilabel>
488            and
489            <guilabel>Other information</guilabel>
490            (selected) .
491          </para>
492          <para>
493            The look of the
494            <guilabel>Other information</guilabel>
495            tab can differ a bit between different servers, depending on what settings
496            the server is installed with. There are three inputs in a fresh BASE
497            installation but it is only the
498            <guilabel>Description</guilabel>
499            text area that is static, the others can be removed or more fields can be
500            added (managed by the server administrator). The three fields, included in a
501            the BASE installation, are
502            <variablelist>
503              <varlistentry>
504                <term>
505                  <guilabel>Mobile</guilabel>
506                </term>
507                <listitem>
508                  <para>Your mobile number(Optional).</para>
509                </listitem>
510              </varlistentry>
511              <varlistentry>
512                <term>
513                  <guilabel>Skype</guilabel>
514                </term>
515                <listitem>
516                  <para>Your Skype contact information(Optional).</para>
517                </listitem>
518              </varlistentry>
519              <varlistentry>
520                <term>
521                  <guilabel>Description</guilabel>
522                </term>
523                <listitem>
524                  <para>
525                    Text area where you can put useful information that couldn't
526                    be stored anywhere else(Optional).
527                  </para>
528                </listitem>
529              </varlistentry>
530            </variablelist>
531          </para>
532          <para>Press &gbSave; to save the changes or &gbCancel; to abort.</para>
533          <seeother>
534            <other external_id="userpreferences.contact">Contact information</other>
535            <other external_id="userpreferences.password">Change password</other>
536          </seeother>
537        </helptext>
538      </sect2>
539
540      <sect2 id="webclient.configuration.password">
541        <title>Changing password</title>
542       
543        <para>
544          Use the <menuchoice><guimenu>File</guimenu>
545          <guimenuitem>Change password</guimenuitem></menuchoice>
546          menu to bring up the change password dialog.
547        </para>
548       
549        <helptext external_id="userpreferences.password" title="Change password">
550
551          <para>
552          This dialog has three tabs, <guilabel>Contact information</guilabel>,
553          <guilabel>Password</guilabel> (selected) and <guilabel>Other information</guilabel>.
554          </para>
555
556          <variablelist>
557            <varlistentry>
558              <term>
559                <guilabel>New password</guilabel>
560              </term>
561              <listitem>
562                <para>
563                Enter the new password.
564                </para>
565              </listitem>
566            </varlistentry>
567            <varlistentry>
568              <term>
569                <guilabel>Retype password</guilabel>
570              </term>
571              <listitem>
572                <para>
573                Retype the same password. You must do this to
574                avoid spelling mistakes.
575                </para>
576              </listitem>
577            </varlistentry>
578          </variablelist>
579
580          <note>
581            <title>Multi-user accounts</title>
582            <para>
583              If you are using a multi-user account, for example a demo-account, you
584              do not have permission to change the password.
585            </para>
586          </note>
587       
588          <note>
589            <title>Empty passwords</title>
590            <para>
591              If you leave both fields empty the password will not be changed. It
592              is not possible to have an empty password.
593            </para>
594          </note>
595         
596          <seeother>
597            <other external_id="userpreferences.contact">Contact information</other>
598            <other external_id="userpreferences.other">Other information</other>
599          </seeother>
600         
601        </helptext>
602      </sect2>
603
604      <sect2 id="webclient.configuration.preferences">
605        <title>Preferences</title>
606       
607        <para>
608          Use the <menuchoice><guimenu>File</guimenu>
609          <guimenuitem>Preferences</guimenuitem></menuchoice>
610          menu to bring up the preferences dialog.
611          This dialog has three tabs, <guilabel>Appearance</guilabel>,
612          <guilabel>Plugins</guilabel> and <guilabel>Most recent</guilabel>.
613        </para>
614       
615        <sect3 id="webclient.configuration.preferences.appearance">
616          <title>The Appearance tab</title>
617         
618          <helptext external_id="userpreferences.appearance" title="Preferences - Appearance">
619         
620          <para>
621          This tab contains settings that affect the appearance of the
622          web client.
623          </para>
624         
625          <variablelist>
626            <varlistentry>
627              <term>
628                <guilabel>Font size</guilabel>
629              </term>
630              <listitem>
631                <para>
632                Select a basic font size. You can choose between
633                five sizes: extra small (XS), small (S), medium (M),
634                large (L) and extra large (XL). The default font size is
635                medium.
636                </para>
637              </listitem>
638            </varlistentry>
639            <varlistentry>
640              <term>
641                <guilabel>Scale factor</guilabel>
642              </term>
643              <listitem>
644                <para>
645                The scale factor affects the size of pop-up windows.
646                This setting exists because different browsers render
647                pages differently. If you often find that pop-up windows
648                are too small you can change this setting to make them
649                bigger.
650                </para>
651                <note>
652                  <para>
653                    The scale factor is automatically changed if the
654                    font size is changed.
655                  </para>
656                </note>
657              </listitem>
658            </varlistentry>
659            <varlistentry>
660              <term>
661                <guilabel>Display long texts</guilabel>
662              </term>
663              <listitem>
664                <para>
665                This setting is used to control how long description texts
666                are displayed in tables and other places with limited space.
667                There are three settings:
668                </para>
669                <itemizedlist>
670                  <listitem>
671                    <simpara>
672                    <guilabel>Always</guilabel>: The full text is always displayed.
673                    </simpara>
674                  </listitem>
675                  <listitem>
676                    <simpara>
677                    <guilabel>On hover</guilabel>: A short version of the text is
678                    displayed and the full text is automatically displayed when
679                    the mouse is moved over the text. Texts that are not fully
680                    visible are indicated with a dotted line to the right.
681                    </simpara>
682                  </listitem>
683                  <listitem>
684                    <simpara>
685                    <guilabel>On click</guilabel>: A short version of the text is
686                    displayed and the full text is displayed when the mouse is clicked
687                    somewhere on the short text. Texts that are not fully visible
688                    are indicated with a grey line to the right.
689                    </simpara>
690                  </listitem>
691                </itemizedlist>
692               
693                <warning>
694                  The 'On click' mode may not perform so well if lots of items are
695                  displayed in a single list. This is particularly so with Internet
696                  Explorer (version 7) which is 5-10 times slower than Firefox to
697                  render the page. If you experience problems with this mode you should
698                  either use a different mode or display less items on a single page.
699                </warning>
700               
701              </listitem>
702            </varlistentry>
703            <varlistentry>
704              <term>
705                <guilabel>Toolbar</guilabel>
706              </term>
707              <listitem>
708                <para>
709                You may choose if the toolbar buttons should
710                have only images, only text or both images and text.
711                The default is that they have both images and text.
712                </para>
713              </listitem>
714            </varlistentry>
715            <varlistentry>
716              <term>
717                <guilabel>Ratio color range</guilabel>
718              </term>
719              <listitem>
720                <para>
721                Select three colors to use when displaying
722                data that is suitable for color coding, for
723                example the intensity ratio in two-color
724                experiments. The default setting is blue-black-yellow.
725                The list of presets contains other useful color combinations
726                (for example, the BASE version 1 red-yellow-green) and the most
727                recently used color combinations.
728                </para>
729              </listitem>
730            </varlistentry>
731            <varlistentry>
732              <term>
733                <guilabel>Date format</guilabel>
734              </term>
735              <listitem>
736                <para>
737                A format string describing how dates should be displayed.
738                We support all formatting options supported by the Java
739                language. For more information see:
740                <ulink url="http://java.sun.com/javase/6/docs/api/java/text/SimpleDateFormat.html">SimpleDateFormat documentation</ulink>
741                The most useful format patterns are:
742                </para>
743               
744                <itemizedlist>
745                  <listitem><simpara>yy: two-digit year</simpara></listitem>
746                  <listitem><simpara>yyyy: four-digit year</simpara></listitem>
747                  <listitem><simpara>MM: two-digit month</simpara></listitem>
748                  <listitem><simpara>MMM: month name (short)</simpara></listitem>
749                  <listitem><simpara>MMMM: month name (full)</simpara></listitem>
750                  <listitem><simpara>dd: two-digit day in month</simpara></listitem>
751                </itemizedlist>
752               
753                <para>
754                The list of presets contains the most commonly/recently
755                used date formats.
756                </para>
757               
758              </listitem>
759            </varlistentry>
760           
761            <varlistentry>
762              <term>
763                <guilabel>Date-time format</guilabel>
764              </term>
765              <listitem>
766                <para>
767                A format string describing how dates with times should be displayed.
768                We support all formatting options supported by the Java
769                language. For more information see:
770                <ulink url="http://java.sun.com/javase/6/docs/api/java/text/SimpleDateFormat.html">SimpleDateFormat documentations</ulink>
771                The most useful time-format patterns are:
772                </para>
773               
774                <itemizedlist>
775                  <listitem><simpara>HH: two-digit hour (0-23)</simpara></listitem>
776                  <listitem><simpara>hh: two-digit hour (1-12)</simpara></listitem>
777                  <listitem><simpara>a: AM/PM marker</simpara></listitem>
778                  <listitem><simpara>mm: two-digit minute</simpara></listitem>
779                  <listitem><simpara>ss: two-digit second</simpara></listitem>
780                </itemizedlist>
781               
782              </listitem>
783            </varlistentry>
784           
785            <varlistentry>
786              <term>
787                <guilabel>Decimals</guilabel>
788              </term>
789              <listitem>
790                <para>
791                The number of decimals to display for numeric values.
792                The default is 2.
793                </para>
794              </listitem>
795            </varlistentry>
796           
797          </variablelist>
798       
799          </helptext>
800       
801        </sect3>
802       
803        <sect3 id="webclient.configuration.preferences.plugins">
804          <title>The Plugins tab</title>
805         
806          <helptext external_id="userpreferences.plugins" title="Preferences - Plugins">
807         
808          <para>
809            This tab contains settings that affect plug-in execution.
810          </para>
811         
812          <variablelist>
813            <varlistentry>
814              <term>
815                <guilabel>Messages</guilabel>
816              </term>
817              <listitem>
818                <para>
819                Mark the checkbox if you want to have a message sent
820                to you when a plug-in completes execution. This setting
821                can be overridden each time you start a plug-in.
822                </para>
823              </listitem>
824            </varlistentry>
825            <varlistentry>
826              <term>
827                <guilabel>Remove jobs</guilabel>
828              </term>
829              <listitem>
830                <para>
831                  This checkbox should be marked if you want the jobs, done by
832                  import or export plug-ins, to be marked as removed if they
833                  finished successfully. This setting can be overridden each time
834                  you start a plug-in.
835                </para>
836              </listitem>
837            </varlistentry>
838            <varlistentry>
839              <term>
840                <guilabel>Show warnings</guilabel>
841              </term>
842              <listitem>
843                <para>
844                  This checkbox should be marked if you want to show warning
845                  messages from plug-ins in the <guilabel>Select plug-in</guilabel>
846                  dialog. Warning-level messages usually originates from plug-ins
847                  that are unrelated to the current task and are only of interest to
848                  plug-in developers. Error messages that are related to the
849                  current task are always shown.
850                </para>
851              </listitem>
852            </varlistentry>
853          </variablelist>
854          </helptext>
855         
856        </sect3>
857       
858        <sect3 id="webclient.configuration.preferences.mostrecent">
859          <title>The Recent items tab</title>
860         
861          <helptext external_id="userpreferences.mostrecent" 
862            title="Preferences - Recent items">
863         
864          <para>
865            This tab contains settings that affect the <guilabel>Recent
866            items</guilabel> menu.
867          </para>
868         
869          <variablelist>
870          <varlistentry>
871            <term>
872              <guilabel>Recently viewed items</guilabel>
873            </term>
874            <listitem>
875              <para>
876              The number of recently <emphasis>viewed</emphasis> items to remember.
877              The default is to remember 6 items. The remembered items
878              will be displayed in the <guilabel>Recent items</guilabel>
879              menu in the menu bar.
880              </para>
881            </listitem>
882          </varlistentry>
883          <varlistentry>
884            <term>
885              <guilabel>Recently used items</guilabel>
886            </term>
887            <listitem>
888              <para>
889              The number of recently <emphasis>used</emphasis> items to remember.
890              The default is to remember 4 items. The remembered items will
891              be displayed in edit dialogs where they have been used before.
892              Each type of edit operation has it's own list of remembered items.
893              For example, there is one list that remembers the most recently used
894              protocols when creating a sample, and there is another list that
895              remembers the most recently used scanners when creating a scan.
896              </para>
897            </listitem>
898          </varlistentry>
899         
900          <varlistentry>
901            <term>
902              <guilabel>Load the names of all items</guilabel>
903            </term>
904            <listitem>
905              <para>
906              If checked, the names of the items will be loaded and
907              displayed in the menu, otherwise only the ID and type of item
908              is displayed.
909              </para>
910            </listitem>
911          </varlistentry>
912         
913          <varlistentry>
914            <term>
915              <guilabel>Sticky items</guilabel>
916            </term>
917            <listitem>
918              <para>
919              Always remember the last viewed item of the selected types.
920              For example, if you have selected <emphasis>Experiment</emphasis>
921              as a sticky item, the last viewed experiment will be remembered
922              even if you view hundreds of other items. Use the arrow buttons
923              to move item types between the lists and sort the sticky items list.
924              Sticky items will be displayed in the <guilabel>Recent items</guilabel>
925              menu in the menu bar.             
926              </para>
927            </listitem>
928          </varlistentry>
929          </variablelist>
930          </helptext>
931         
932        </sect3>
933      </sect2>
934 
935    </sect1>
936   
937    <sect1 id="webclient.items">
938      <title>Working with items</title>
939     
940      <para>
941        No matter what you are doing in BASE some things works more
942        or less in the same way. This section covers things that are
943        common for most parts of BASE.
944      </para>
945     
946      <para>
947        You mostly work with a single type of item at a time. This is
948        reflected in the menu system. For example, use
949        <menuchoice>
950          <guimenu>Biomaterial LIMS</guimenu>
951          <guimenuitem>Samples</guimenuitem>
952        </menuchoice>
953        to work with samples, and
954        <menuchoice>
955          <guimenu>View</guimenu>
956          <guimenuitem>Experiments</guimenuitem>
957        </menuchoice>
958        to work with experiments. In most cases the list view for that type
959        of item is displayed. The list view, as the name says,
960        is used to list all items. There are two more standard views, the
961        single-item view and the edit view.
962      </para>
963     
964      <variablelist>
965        <varlistentry>
966          <term>List view</term>
967          <listitem>
968            <para>
969            This view lists all items of a certain type. The view allows you to search
970            and it is possible to configure which information to show
971            for each item. It also contains functions that
972            can be used on multiple items at the same time, for example,
973            delete, share and export. See <xref linkend="webclient.itemlist"/> for more information.
974            </para>
975          </listitem>
976        </varlistentry>
977     
978        <varlistentry>
979          <term>Single-item view</term>
980          <listitem>
981            <para>
982            Displays information about a single item. Sometimes it is very little,
983            sometimes it is very much and the information may be divided
984            into multiple tabs.
985            </para>
986          </listitem>
987        </varlistentry>
988     
989        <varlistentry>
990          <term>Edit view</term>
991          <listitem>
992            <para>
993            This view is used for editing the information
994            about a single item. It is always displayed as a pop-up window.
995            </para>
996          </listitem>
997        </varlistentry>
998      </variablelist> 
999             
1000      <sect2 id="webclient.items.new">
1001        <title>Create a new item</title>
1002       
1003        <para>
1004          New items are mostly created from the list view. For example,
1005          to create a new experiment go to the
1006          <menuchoice><guimenu>View</guimenu> <guimenuitem>Experiments</guimenuitem></menuchoice>
1007          page. Here you will find a &gbNew; button in the
1008          toolbar. The button is disabled if you do not have permission to create new experiments.
1009          Otherwise, click on it and enter any required information in the pop-up dialog.
1010          Sometimes there are multiple tabs in this dialog. In the case of experiments
1011          there are three tabs: <guilabel>Experiment</guilabel>, <guilabel>Publication</guilabel>
1012          and <guilabel>Experimental factors</guilabel>.
1013         
1014          As a general rule, only the first tab has information that is required.
1015          The information in all other tabs are optional.
1016        </para>
1017       
1018        <para>
1019          In some places you will also find actions that create items
1020          directly in the list. For example in the list of samples or on
1021          the single-item view for a sample you can create an extract using that
1022          sample as the parent. If you use such links the parent
1023          item will in most cases be selected automatically, which saves
1024          you a few clicks when creating new items.
1025        </para>
1026       
1027        <para>
1028          Click on the &gbSave; button to save the new
1029          item to the database or on the &gbCancel; button
1030          to abort.
1031        </para>
1032
1033        <note>
1034          <para>
1035          To speed up data entry when adding multiple new items there
1036          are a few tricks you can use to make the web client supply
1037          default values for most properties. To find a default value
1038          the following checklist is used in this order:
1039          </para>
1040       
1041        <orderedlist>         
1042          <listitem>
1043            <para>
1044            If the list have an active filter the filter values are
1045            used as default property values for the new item. For example,
1046            if you are listing experiments with <guilabel>Genepix</guilabel>
1047            raw data type the new experiment will automatically have
1048            <guilabel>Genepix</guilabel> selected. This trick should work
1049            for all properties except annotations, if it does not
1050            report it as a bug to the development team.
1051            </para>
1052          </listitem>
1053         
1054          <listitem>
1055            <para>
1056            When you link to other items the same item will be used the next time.
1057            For example, if you create an extract and selects an extraction protocol
1058            the same protocol is used the next time you create another extract.
1059            In fact, BASE will remember as many items as specified by
1060            the
1061            <guilabel>Recently used items</guilabel> setting (default is 4),
1062            allowing you to quickly select one of those protocols.
1063            <xref linkend="webclient.configuration.preferences.appearance"/> 
1064            contains more information about the setting.
1065            </para>
1066          </listitem>
1067         
1068          <listitem>
1069            <para>
1070            If you have a project active and that project has specified default
1071            values those values will be used for new items. A project can specify
1072            defaults for protocols, hardware and software and a few other settings.
1073            </para>
1074          </listitem>
1075         
1076        </orderedlist>
1077       
1078        </note>
1079       
1080      </sect2>
1081     
1082      <sect2 id="webclient.items.edit">
1083        <title>Edit an existing item</title>
1084       
1085        <para>
1086          On all single-item views there is an &gbEdit;
1087          button in the toolbar that opens a pop-up dialog for editing the properties
1088          of the item. This button is disabled if the logged in user does not have
1089          write permission for the item.
1090        </para>
1091       
1092        <para>
1093          You can also open the edit pop-up in most other places where
1094          the item appears, for example, in lists or the single-item view
1095          of a related item. Press and hold one of the <keycap>CTRL</keycap>,
1096          <keycap>ALT</keycap> or <keycap>SHIFT</keycap> keys while clicking
1097          on the link and the edit window will open in a pop-up.
1098          If you do not have write permission
1099          on the item there is no meaning to open the edit pop-up and you will
1100          be taken to the single-item view page instead.
1101        </para>
1102
1103        <para>
1104          Click on the &gbSave; button to save the changes
1105          to the database or on the &gbCancel; button
1106          to abort.
1107        </para>
1108     
1109      </sect2>
1110
1111      <sect2 id="webclient.items.delete">
1112        <title>Delete items</title>
1113
1114        <para>
1115          You can delete items either from the list view or from
1116          a single-item view. In both cases, deleted items are only moved to
1117          the trashcan. No information is removed from the database. This allows
1118          you to restore items if you later find out that you need them again.
1119          In fact, there is nothing special about a removed item. It can still be
1120          used for the same things as any non-removed item can.
1121        </para>
1122
1123        <important>
1124          <para>
1125          To really delete items from the database you have two options:
1126          <orderedlist>
1127          <listitem>
1128            <para>
1129            Go to the trashcan
1130            <menuchoice><guimenu>View</guimenu><guimenuitem>Trashcan</guimenuitem></menuchoice>
1131            and delete it from there. From the trashcan you can delete several items
1132            in one go. See <xref linkend="webclient.trashcan"/>.
1133            </para>
1134          </listitem>
1135          <listitem>
1136            <para>
1137            Click on the small trashcan icon in the list or single-item view.
1138            You can only delete one item at a time.
1139            </para>
1140          </listitem>
1141          </orderedlist>
1142          </para>
1143        </important>
1144       
1145        <para>
1146          To delete items from the list view you must first mark
1147          the checkbox for each item you want to delete. Then, click on
1148          the &gbDelete; button. The list should refresh itself
1149          automatically. If you want to confirm that the items have been removed
1150          use the <guilabel>view / presets</guilabel> dropdown and select
1151          the <guilabel>Removed</guilabel> option. The removed items should now
1152          be displayed in the list with a small trashcan icon to indicate that
1153          they are located in the trashcan.
1154        </para>
1155
1156        <para>
1157          To delete items from the single-item view, click on the
1158          &gbDelete; button in the toolbar. The page will refresh
1159          itself automatically and a small trashcan icon should be displayed.
1160          If you do not have permission to delete the item the delete button
1161          is disabled.
1162        </para>
1163
1164      </sect2>
1165     
1166      <sect2 id="webclient.items.restore">
1167        <title>Restore deleted items</title>
1168       
1169        <para>
1170          You can restore deleted items either from the trashcan, from
1171          the list view, or from the single-item view. This section
1172          only covers the last two cases. The trashcan is described in
1173          another section (<xref linkend="webclient.trashcan"/>).
1174        </para>
1175
1176        <para>
1177          To delete items from the list view you must first make the deleted
1178          items appear in the list. This is easy, just use the <guilabel>view / presets</guilabel> 
1179          dropdown and select the <guilabel>Removed</guilabel> option. The list should
1180          refresh itself automatically. The removed items are
1181          displayed in the list with a small trashcan icon to indicate that
1182          they are located in the trashcan. Then, mark the checkbox for each item that you want
1183          to restore and click the &gbRestore; button. The list should
1184          refresh itself automatically and the trashcan icon should be gone from the
1185          restored items.
1186        </para>
1187       
1188        <para>
1189          To restore items from the single-item view, click on the
1190          &gbRestore; button in the toolbar. The page will refresh
1191          itself automatically and the small trashcan icon should be gone.
1192          If you do not have permission to restore the item the restore button
1193          is disabled.
1194        </para>
1195
1196      </sect2>
1197
1198      <sect2 id="webclient.items.share">
1199        <title>Share items to other users</title>
1200        <para>
1201          Sharing data with other users is an important feature
1202          of BASE, which allows you cooperate in teams. If you
1203          follow the instructions in <xref linkend="project_permission" />
1204          you will find that you almost never have to share items manually
1205          to other users. This is because whenever you work with an active
1206          project each new item you create will automatically be shared
1207          to that project. In most cases, this is all you need.
1208        </para>
1209       
1210        <para>
1211          If you still need to manually share your data with other users,
1212          here is how to do it.
1213        </para>
1214       
1215        <para>
1216          From a list view, mark the checkbox for each item you want to share.
1217          Then, click on the &gbShare; button.
1218          If you are on a single-item page, click on the &gbShare; 
1219          button on that page. In both cases, this will open the
1220          <guilabel>Set access permissions</guilabel>
1221          dialog window.
1222        </para>
1223       
1224        <figure id="webclient.items.share.set_permissions">
1225          <title>Sharing items to other users</title>
1226          <screenshot>
1227          <mediaobject>
1228            <imageobject>
1229              <imagedata fileref="figures/set_permissions.png" format="PNG" />
1230            </imageobject>
1231          </mediaobject>
1232          </screenshot>
1233        </figure>
1234       
1235        <helptext external_id="share.setpermissions" title="Set access permissions">
1236          <variablelist>
1237            <varlistentry>
1238              <term><guilabel>Members</guilabel></term>
1239              <listitem>
1240                <para>
1241                The list displays the users, groups and projects
1242                that already has access to the items you selected.
1243                The list shows the name and the permission level.
1244                The permission level uses a one-letter code as follows:
1245                </para>
1246               
1247                <itemizedlist>
1248                <listitem><simpara><guilabel>R</guilabel> = Read</simpara></listitem>
1249                <listitem><simpara><guilabel>U</guilabel> = Use</simpara></listitem>
1250                <listitem><simpara><guilabel>W</guilabel> = Write</simpara></listitem>
1251                <listitem><simpara><guilabel>D</guilabel> = Delete</simpara></listitem>
1252                <listitem><simpara><guilabel>O</guilabel> = Set owner</simpara></listitem>
1253                <listitem><simpara><guilabel>P</guilabel> = Set permission</simpara></listitem>
1254                </itemizedlist>
1255               
1256                <para>
1257                  Instead of a permission code, the word <guilabel>varying</guilabel>
1258                  may be displayed. This happens if the items you selected have been
1259                  shared with different permission.
1260                </para>
1261               
1262              </listitem>
1263            </varlistentry>
1264           
1265            <varlistentry>
1266              <term><guilabel>Permissions</guilabel></term>
1267              <listitem>
1268                <para>
1269                When you select a user, group or project in the
1270                list, the checkboxes will display the current permission.
1271                The exception is if the permissions are varying, in which
1272                case no checkboxes are checked.
1273                To change the permissions just check the permissions you want to
1274                grant or uncheck the permissions you want to revoke.
1275                You can select more than one user, group or project
1276                and change the permissions for all of them at once.
1277                </para>
1278              </listitem>
1279            </varlistentry>           
1280
1281            <varlistentry>
1282              <term><guibutton>Add users</guibutton></term>
1283              <listitem>
1284                <para>
1285                Opens a pop-up window that allows you to select
1286                users to share the items to. In the pop-up window, mark
1287                one or more users and click on the &gbOk;
1288                button. The pop-up window will only list users that you have
1289                permission to read. Unless you are an administrator, this
1290                usually means that you can only see users that:
1291                </para>
1292                <itemizedlist>
1293                  <listitem>
1294                    <para>
1295                    you share group memberships with
1296                    (the <emphasis>Everyone</emphasis> group doesn't count)
1297                    </para>
1298                  </listitem>
1299                  <listitem>
1300                    <para>
1301                    are members of the currently active project, if any.
1302                    </para>
1303                  </listitem>
1304                </itemizedlist>
1305                <para>
1306                Users that already have access to the item are not included in the
1307                list. If you don't see a user that you want to share an item to,
1308                you'll need to talk to an administrator for setting up the proper
1309                group membership.
1310                </para>
1311              </listitem>
1312            </varlistentry>
1313
1314            <varlistentry>
1315              <term><guibutton>Add groups</guibutton></term>
1316              <listitem>
1317                <para>
1318                Opens a pop-up window that allows you to select
1319                groups to share the items to. In the pop-up window, mark
1320                one or more groups and click on the &gbOk;
1321                button. Unless you are an administrator, the pop-up window
1322                will only list groups where you are a member. It will not list
1323                groups that already have access to the items.
1324                </para>
1325              </listitem>
1326            </varlistentry>
1327           
1328            <varlistentry>
1329              <term><guibutton>Add projects</guibutton></term>
1330              <listitem>
1331                <para>
1332                Opens a pop-up window that allows you to select
1333                projects to share the items to. In the pop-up window, mark
1334                one or more projects and click on the &gbOk;
1335                button. Unless you are an administrator, the pop-up window
1336                will only list projects where you are a member. It will not list
1337                projects that already have access to the items.
1338                </para>
1339              </listitem>
1340            </varlistentry>
1341
1342            <varlistentry>
1343              <term>&gbRemove;</term>
1344              <listitem>
1345                <para>
1346                Click on this button to revoke access permissions from
1347                the selected users, groups and projects.
1348                </para>
1349              </listitem>   
1350            </varlistentry>
1351           
1352            <varlistentry>
1353              <term><guilabel>Apply permissions to all sub-directories and their files</guilabel></term>
1354              <listitem>
1355                <para>
1356                This option shows up if at least one of the selected items
1357                is a directory. If this option is selected the permissions given
1358                to the directory will recursively be copied to all files and
1359                sub-directories. Existing permissions on those items will be
1360                overwritten with the new permissions.
1361                </para>
1362              </listitem>   
1363            </varlistentry>
1364          </variablelist>
1365       
1366          <para>
1367            Use the &gbSave; button to save your
1368            changes or the &gbCancel; button to
1369            close the pop-up without saving.
1370          </para>
1371        </helptext>
1372
1373      </sect2>
1374
1375      <sect2 id="webclient.items.changeowner">
1376        <title>Change owner of items</title>
1377        <para>
1378          Sometimes it may be necessary to change the owner of an item.
1379          This can be done by everyone with <emphasis>Set owner</emphasis>
1380          permission on the item.
1381          For a user to have the rights to change owner of an item, the item must
1382          either be owned by or shared with <emphasis>Set owner</emphasis> 
1383          permission to the user .
1384          See <xref linkend="webclient.items.share" />.
1385        </para>
1386       
1387        <para>
1388          An user with <emphasis>Set owner</emphasis> permission can go to a list view
1389          (or the single-item view), mark the checkboxes for the items to change owner of,
1390          and click on the <guibutton>Set owner</guibutton> button. 
1391          A dialog window, like the screen-shot below, will appear.
1392        </para>
1393        <helptext external_id="ownership.configure" title="Change owner">
1394        <variablelist>
1395        <varlistentry>
1396          <term><guilabel>New owner</guilabel></term>
1397          <listitem>
1398          <para>
1399            The user to be the new owner of selected item(s).
1400            By default the current user will be selected but other
1401            users can be picked from the <emphasis>currently used</emphasis> part of the drop-down
1402            list or by clicking on <guibutton>Select</guibutton>.
1403          </para>
1404          </listitem>
1405        </varlistentry>
1406        </variablelist>
1407        <para>
1408          Use the &gbSave; button to set the new owner
1409          or the &gbCancel; button to
1410          close the pop-up without saving.
1411        </para>
1412        </helptext> 
1413        <figure id="webclient.figures.selectowner">
1414          <title>Select a new owner</title>
1415          <screenshot>
1416            <mediaobject>
1417              <imageobject><imagedata fileref="figures/select_owner.png" format="PNG"
1418                scalefit="1" width="100%" /></imageobject>
1419            </mediaobject>
1420          </screenshot>
1421        </figure>
1422       
1423        <note>
1424          <para>
1425          The original owner may not have access permissions to the items
1426          any longer. If that is desired, the new owner must share the items
1427          to the original owner.
1428          </para>
1429        </note>
1430       
1431      </sect2>
1432     
1433      <sect2 id="webclient.items.export">
1434        <title>Export items</title>
1435        <para>
1436          This has a chapter of it's own. See <xref linkend="export_data"/>.
1437        </para>
1438      </sect2>
1439
1440    </sect1>
1441   
1442    <sect1 id="webclient.itemlist">
1443      <title>Listing items</title>
1444     
1445      <para>
1446        All pages that lists items are very similar in their appearance and
1447        functionality. In this section we will describe the things that are
1448        common for most (if not all) list pages.
1449      </para>
1450     
1451      <para>
1452        Use the menu to open a page listing items. Most list pages can only list one type of
1453        items. For example: use the
1454        <menuchoice>
1455          <guimenu>View</guimenu>
1456          <guimenuitem>Samples</guimenuitem>
1457        </menuchoice>
1458        menu to list samples and the
1459        <menuchoice>
1460          <guimenu>View</guimenu>
1461          <guimenuitem>Experiments</guimenuitem>
1462        </menuchoice>
1463        menu to list experiments.
1464      </para>
1465
1466      <tip>
1467        An example of a list page that can list
1468        items of several types is found by going to
1469        <menuchoice>
1470          <guimenu>View</guimenu>
1471          <guimenuitem>All items</guimenuitem>
1472        </menuchoice>.
1473        This page lists all items that you are the owner of. It has a few limitations:
1474       
1475        <itemizedlist>
1476          <listitem>
1477            <para>
1478              It support only a limited set of columns (type, name and description)
1479              since these are the only properties that are common
1480              among all items.
1481            </para>
1482          </listitem>
1483         
1484          <listitem>
1485            <para>
1486              The list cannot be filtered (except by item type)
1487              or sorted. This is due to a limitation in the query system
1488              used to generate the list.
1489            </para>
1490          </listitem>
1491        </itemizedlist>
1492       
1493        <para>
1494          There are also several similarities:
1495        </para>
1496       
1497        <itemizedlist>
1498          <listitem>
1499            <para>
1500              It supports all of the regular multi-item
1501              operations such as delete, restore, share
1502              and change owner.
1503            </para>
1504          </listitem>
1505         
1506          <listitem>
1507            <para>
1508              Clicking on the name of the item will take you to the
1509              single-item view of that item. Holding down <keycap>CTRL</keycap>,
1510              <keycap>ALT</keycap> or <keycap>SHIFT</keycap> while clicking,
1511              will open the edit pop-up.
1512            </para>
1513          </listitem>
1514        </itemizedlist>       
1515       
1516      </tip>
1517     
1518      <figure id="webclient.figures.listpage">
1519        <title>A typical list page</title>
1520        <screenshot>
1521          <mediaobject>
1522            <imageobject><imagedata fileref="figures/listpage.png" format="PNG"
1523              scalefit="1" width="100%" /></imageobject>
1524          </mediaobject>
1525        </screenshot>
1526      </figure>
1527     
1528      <para>
1529        The typical list page contains the following important
1530        elements:
1531      </para>
1532
1533      <variablelist>
1534        <varlistentry>
1535          <term><interface>1. Toolbar</interface></term>
1536          <listitem>
1537            <para>
1538            A toolbar with buttons for various actions such as
1539            &gbNew; for creating a new item,
1540            &gbDelete; for deleting items and
1541            <guibutton>Columns&hellip;</guibutton> for configuring columns.
1542            Depending on the permissions of the logged in user
1543            some buttons may be disabled (greyed out) or not shown at all.
1544            </para>
1545          </listitem>
1546        </varlistentry>
1547       
1548        <varlistentry>
1549          <term><interface>2. Navigation bar</interface></term>
1550          <listitem>
1551            <para>
1552            If there are many items the list will be divided into
1553            pages, each one showing a limited number of items.
1554            The navigation bar allows you to
1555            move to other pages and specify how many items each page
1556            should display. The navigation bar is repeated at the
1557            bottom of the list so you do not have to scroll back to the
1558            top of a long list just to get to another page.
1559            </para>
1560          </listitem>
1561        </varlistentry>
1562       
1563        <varlistentry>
1564          <term><interface>3. List of presets</interface></term>
1565          <listitem>
1566            <para>
1567            A list with preconfigured settings which allows you to
1568            quickly switch between different layouts (sort order, visible
1569            columns, filter settings, etc).
1570            </para>
1571          </listitem>
1572        </varlistentry>
1573       
1574        <varlistentry>
1575          <term><interface>4. Column headers</interface></term>
1576          <listitem>
1577            <para>
1578            The columns headers can be used for selecting sort order.
1579            </para>
1580          </listitem>
1581        </varlistentry>
1582       
1583        <varlistentry>
1584          <term><interface>5. Filter bar</interface></term>
1585          <listitem>
1586            <para>
1587            The filter bar allows you to search for items.
1588            </para>
1589          </listitem>
1590        </varlistentry>
1591       
1592      </variablelist>
1593     
1594     
1595      <sect2 id="webclient.itemlist.order">
1596        <title>Ordering the list</title>
1597       
1598        <para>
1599          Most lists are by default sorted by the name of the item. This can
1600          be changed by clicking on the column header of another column.
1601          If you click on the same column twice the sort order is reversed.
1602          A downwards or upwards pointing arrow is displayed next to the
1603          column header in the column that is currently used for sorting.
1604          Column headers that are black cannot be used for sorting.
1605        </para>
1606       
1607        <para>
1608          It is possible to use more than one column for sorting. Press
1609          and hold one of the <keycap>CTRL</keycap>,
1610          <keycap>ALT</keycap> or <keycap>SHIFT</keycap> keys while clicking
1611          on another column header. The original sorting is kept and the new
1612          column is used for sub-sorting the list. The procedure can be
1613          repeated with more columns if you need to sort on three or more
1614          columns. To revert to sort by only one column again click a
1615          column header without holding down any key.
1616        </para> 
1617      </sect2>
1618   
1619      <sect2 id="webclient.itemlist.filter">
1620        <title>Filtering the list</title>
1621       
1622        <para>
1623          If the list contains many items you may need to use a filter to be
1624          able to find the item you are looking for. The input boxes on the
1625          line below the column headers are used for filtering. Most columns
1626          are filtered using a free-text input box, but some columns that can
1627          only take a few distinct values use a selection list or radio buttons
1628          instead. The selection list and radio buttons are very simple to use.
1629          Just select the alternative that you want to filter on. The list
1630          will be automatically updated when the selection has been made.
1631        </para>
1632       
1633        <para>
1634          The free-text filter is a bit more complex. By default, an exact match is
1635          required, use % as a wildcard character that matches any character.
1636          For example, the filter <informalexample>Experiment A</informalexample> 
1637          only matches the same exact string, but the filter
1638          <informalexample>Exp%</informalexample> matches
1639          <informalexample>Experiment A, Experiment B, etc.</informalexample>
1640        </para>
1641        <para>
1642          If you want to filter on several values at the same time, separate the
1643          values in the filter input box with the <quote>|</quote> character.
1644          For example, a filter text like <informalexample>Experiment A|C%</informalexample>
1645          matches both <quote>Experiment A</quote> and values 
1646          that begin with <quote>C</quote>.
1647        </para>       
1648        <para>
1649          You can also use operators to find items which has a value that
1650          is greater than, less than or not equal to a specific value. This is
1651          mostly useful on numeric or date columns but also works on text
1652          columns. The operator must be entered first in the
1653          free-text box, for example
1654          <informalexample>&lt;=10</informalexample>
1655          to find items which has a value less than or equal to 10.   
1656          Here is a list of the supported operators:
1657        </para>
1658       
1659        <variablelist id="webclient.itemlist.filter.operators">
1660          <title>List of operators supported by the free-text filter</title>
1661          <varlistentry>
1662            <term><keycap>&lt;</keycap></term>
1663            <listitem><simpara>Less than</simpara></listitem>
1664          </varlistentry>
1665          <varlistentry>
1666            <term><keycap>&lt;=</keycap></term>
1667            <listitem><simpara>Less than or equal to</simpara></listitem>
1668          </varlistentry>
1669          <varlistentry>
1670            <term><keycap>&gt;</keycap></term>
1671            <listitem><simpara>Greater than</simpara></listitem>
1672          </varlistentry>
1673          <varlistentry>
1674            <term><keycap>&gt;=</keycap></term>
1675            <listitem><simpara>Greater than or equal to</simpara></listitem>
1676          </varlistentry>
1677          <varlistentry>
1678            <term><keycap>=</keycap></term>
1679            <listitem>
1680              <simpara>
1681                Equal to (useful to find items with a null value). Supports
1682                filtering on more then one value.
1683              </simpara>
1684            </listitem>
1685          </varlistentry>
1686          <varlistentry>
1687            <term><keycap>&lt;&gt;</keycap></term>
1688            <term><keycap>!=</keycap></term>
1689            <listitem>
1690              <simpara>
1691                Not equal to (useful to find items with a non-null value). Supports
1692                filtering on more then one value.
1693              </simpara>
1694            </listitem>
1695          </varlistentry>
1696          <varlistentry>
1697            <term><keycap>==</keycap></term>
1698            <listitem>
1699              <simpara>
1700                Same as <keycap>=</keycap> but interprets <quote>|</quote>, <quote>%</quote> 
1701                and other special characters literally. Use this when you need an exact
1702                string match.
1703              </simpara>
1704            </listitem>
1705          </varlistentry>
1706        </variablelist>
1707       
1708        <sect3 id="webclient.itemlist.filter.units">
1709          <title>Units</title>
1710          <para>
1711            Some (numeric) columns have values with units. There are, for example,
1712            the <emphasis>Original quantity</emphasis> and <emphasis>Remaining quantity</emphasis>
1713            columns for biomaterials, which have values in micrograms (µg), and
1714            annotations which may have any unit.
1715          </para>
1716          <para>
1717            When filtering on a column that has a unit, numeric values without units are
1718            interpreted as the default unit for that column. But it is also possible to
1719            add a unit to the filter value. The examples below are filtering on the
1720            original quantity column of a biomaterial:
1721          </para>
1722          <para>
1723            <informalexample>&gt;=0.5mg</informalexample> matches biomaterials with
1724            an original quantity &gt;=500µg.
1725          </para>
1726          <para>
1727            <informalexample>=100|200|300µg</informalexample> matches biomaterials with
1728            exactly 100, 200 or 300 micrograms.
1729          </para>
1730          <para>
1731            It is also possible to mix units in a single filter:
1732            <informalexample>=100|200|300µg|0.5|1mg</informalexample> which matches
1733            100, 200, 300, 500 and 1000 micrograms.
1734          </para>
1735         
1736          <warning>
1737            <title>Be aware of rounding errors</title>
1738            <para>
1739              All filter values with a unit that is different from the default
1740              unit are converted to the default unit before being applied. Since
1741              numeric conversions are never exact down to the last decimal, this may
1742              result in problems to filter with an exact match. The last example above
1743              could, for example, be converted to: 100, 200, 300, 500.000001 and
1744              999.99999998.
1745            </para>
1746          </warning>
1747         
1748          <tip>
1749            <title>Hard-to-type characters</title>
1750            <para>
1751              Some units contains hard-to-type characters. For example,
1752              the greek letter µ in µg, and m² and m³ for areas and volumes.
1753              In all those cases it is also possible to use ug, m2 and m3,
1754              respectively.
1755            </para>
1756          </tip>
1757         
1758          <note>
1759            <title>Units are case-sensitive</title>
1760            <para>
1761              All units are case sensitive. The main reason for this is that
1762              it must be possible to tell the difference between
1763              <emphasis>milli (m)</emphasis> and <emphasis>mega (M)</emphasis> 
1764              prefixes, for example, <emphasis>mJ</emphasis> and <emphasis>MJ</emphasis>.
1765            </para>
1766          </note>
1767         
1768        </sect3>
1769      </sect2>
1770     
1771      <sect2 id="webclient.itemlist.columns">
1772        <title>Configuring which columns to show</title>
1773       
1774        <para>
1775          Most lists show only a small subset of the columns it
1776          is capable of showing. Use the
1777          <guibutton>Columns&hellip;</guibutton> button to open
1778          a dialog that allows you to select which columns to show
1779          and the order in which they are shown.
1780        </para>
1781       
1782        <figure id="webclient.figures.configure_columns">
1783          <title>Configuring which columns to show</title>
1784          <screenshot>
1785          <mediaobject>
1786            <imageobject>
1787              <imagedata fileref="figures/configure_columns.png" format="PNG"/>
1788            </imageobject>
1789          </mediaobject>
1790          </screenshot>
1791        </figure>
1792       
1793        <helptext external_id="columns.configure" 
1794          title="Set column order and visiblity">
1795       
1796        <variablelist>
1797        <varlistentry>
1798          <term><guilabel>Visible columns</guilabel></term>
1799          <listitem>
1800            <para>
1801              Shows the columns that are currently visible.
1802              Use the up/down arrow buttons to arrange the order of the
1803              visible columns. The topmost column is shown to the left.
1804              Use the right arrow button to move columns from this list
1805              to the hidden columns list. Columns marked with an <guilabel>×</guilabel> 
1806              are required
1807              and cannot be hidden. In most lists the <guilabel>Name</guilabel> column
1808              is the only column that is required.
1809            </para>
1810          </listitem>
1811        </varlistentry>
1812         
1813        <varlistentry>
1814          <term><guilabel>Hidden columns</guilabel></term>
1815          <listitem>
1816            <para>
1817              Shows columns that are not currently visible in the
1818              list. Use the left arrow button to move columns from
1819              this list to the visible columns list.
1820            </para>
1821          </listitem>
1822        </varlistentry>
1823       
1824       
1825        <varlistentry>
1826          <term><guilabel>Presets</guilabel></term>
1827          <listitem>
1828            <para>
1829              A dropdown list that allows you to
1830              select a set of preconfigured columns. You may also create
1831              your own preset if you often need to switch between different
1832              configurations. The list of presets is the same as the one
1833              described <link linkend="webclient.itemlist.presets">below</link>,
1834              but if used from this dialog the presets does not affect filters,
1835              sort order, etc.
1836            </para>
1837          </listitem>
1838        </varlistentry>
1839        </variablelist>
1840       
1841          <para>
1842            Use the &gbSave; button to apply your
1843            changes or the &gbCancel; button to
1844            close the pop-up without saving.
1845          </para>
1846
1847        </helptext>
1848
1849      </sect2>
1850     
1851      <sect2 id="webclient.itemlist.presets">
1852        <title>Presets</title>
1853       
1854        <para>
1855          The <guilabel>view / presets</guilabel> dropdown has three
1856          main functions:
1857        </para>
1858       
1859        <figure id="webclient.figures.viewpresets">
1860          <title>The view / presets dropdown</title>
1861          <screenshot>
1862            <mediaobject>
1863              <imageobject><imagedata fileref="figures/view_presets.png" format="PNG" 
1864                /></imageobject>
1865            </mediaobject>
1866          </screenshot>
1867        </figure>
1868        <orderedlist>
1869          <listitem>
1870            <para>
1871              Switch between different configuration presets.
1872              The top of the dropdown contains user-defined presets (<guilabel>Saved preset #1</guilabel> and
1873              <guilabel>#2</guilabel>) and a few preconfigured presets.
1874              The user-defined presets are used to store a complete table configuration,
1875              including:
1876            </para>
1877           
1878            <itemizedlist>
1879              <listitem><simpara>Which columns are visible and their order</simpara></listitem>
1880              <listitem><simpara>The column (or columns) used for sorting</simpara></listitem>
1881              <listitem><simpara>Filter settings</simpara></listitem>
1882              <listitem><simpara>The number of items per page and the current page</simpara></listitem>
1883            </itemizedlist>
1884           
1885            <para>             
1886              The preconfigured presets only affects
1887              the visible columns as follows:
1888            </para>
1889           
1890            <itemizedlist>
1891              <listitem>
1892                <para><guilabel>All columns</guilabel> - Show all columns.</para>
1893              </listitem>
1894              <listitem>
1895                <para><guilabel>Required columns</guilabel> - Show only the required columns.
1896                  Usually only the <guilabel>Name</guilabel> column is required.</para>
1897              </listitem>
1898              <listitem>
1899                <para><guilabel>Default columns</guilabel> - Show the default set of columns.</para>
1900              </listitem>
1901              <listitem>
1902                <para><guilabel>Other&hellip;</guilabel> -
1903                  Open the configure columns dialog box, described in
1904                  <xref linkend="webclient.itemlist.columns"/>.</para>
1905              </listitem>
1906            </itemizedlist>
1907           
1908          </listitem>
1909         
1910          <listitem>
1911            <para>
1912              Filter items by the removed status and the access
1913              permissions to an item.
1914            </para>
1915           
1916            <itemizedlist>
1917              <listitem>
1918                <para><guilabel>Removed</guilabel> - If checked, items that have been
1919                moved to the trashcan are shown, otherwise they are hidden.</para>
1920              </listitem>
1921              <listitem>
1922                <para><guilabel>Owned by me</guilabel> - If checked, items that the logged in user
1923                owns are displayed, otherwise they are hidden.</para>
1924              </listitem>
1925              <listitem>
1926                <para><guilabel>Shared to me</guilabel> - If checked, items that are owned
1927                by other users but shared to the logged in user are displayed, otherwise
1928                they are hidden.</para>
1929              </listitem>
1930              <listitem>
1931                <para><guilabel>In current project</guilabel> -
1932                  If checked, items that are linked with the current project are displayed,
1933                  otherwise they are hidden. It does not matter if the logged in user is the
1934                  owner or not. This option is only available if a project is active.
1935                </para>
1936              </listitem>
1937              <listitem>
1938                <para><guilabel>Owned by others</guilabel> -
1939                  This option is only available to administrators and will display
1940                  items that are owned by other users.
1941                </para>
1942              </listitem>
1943            </itemizedlist>
1944           
1945            <para>
1946              The default is to display item that the current user
1947              owns and, if a project is active, items in that project.
1948            </para>
1949           
1950          </listitem>
1951
1952          <listitem>
1953            <para>
1954              Administrate the presets
1955            </para>
1956            <itemizedlist>
1957              <listitem>
1958                <para><guilabel>Clear filter</guilabel> - Clears
1959                all filters.</para>
1960              </listitem>
1961             
1962              <listitem>
1963                <para><guilabel>Save as&hellip;</guilabel> - Save the
1964                current configuration as a preset.</para>
1965              </listitem>
1966
1967              <listitem>
1968                <para><guilabel>Manage&hellip;</guilabel> - Opens a dialog
1969                where you can remove saved presets. You can also load
1970                saved presets from the dialog, but it is quicker to just
1971                use the dropdown list for this.</para>
1972              </listitem>
1973            </itemizedlist>
1974          </listitem>
1975        </orderedlist>
1976       
1977        <sect3 id="webclient.itemlist.presets.saveas">
1978          <title>Save a preset</title>
1979         
1980          <para>
1981            If you select the <guilabel>Save as&hellip;</guilabel>
1982            option from the <guilabel>view / presets</guilabel> dropdown
1983            the <guilabel>Save preset as</guilabel> dialog is opened.
1984          </para>
1985         
1986          <figure id="webclient.figures.savepresetas">
1987            <title>Save preset as</title>
1988            <screenshot>
1989              <mediaobject>
1990                <imageobject><imagedata fileref="figures/save_preset.png" format="PNG" /></imageobject>
1991              </mediaobject>
1992            </screenshot>
1993          </figure>
1994         
1995          <helptext external_id="contexts.saveas" title="Save preset as">
1996         
1997          <variablelist>
1998          <varlistentry>
1999            <term><guilabel>For item</guilabel></term>
2000            <listitem>
2001              <para>
2002              The type of item the preset is saved for.
2003              </para>
2004            </listitem>
2005          </varlistentry>
2006          <varlistentry>
2007            <term><guilabel >Name</guilabel></term>
2008            <listitem>
2009              <para>
2010              The name of the preset. The name must be unique.
2011              </para>
2012            </listitem>
2013          </varlistentry>
2014          <varlistentry>
2015            <term><guilabel>Overwrite existing</guilabel></term>
2016            <listitem>
2017              <para>
2018              If a preset with the same name already exists, it is
2019              overwritten if this checkbox is checked.
2020              </para>
2021            </listitem>
2022          </varlistentry>
2023          <varlistentry>
2024            <term><guilabel>Public</guilabel></term>
2025            <listitem>
2026              <para>
2027              This options is only available for users
2028              which has the <emphasis>SHARE_TO_EVERYONE</emphasis>
2029              permission. If checked the preset is visible to
2030              all users.
2031              </para>
2032            </listitem>
2033          </varlistentry>
2034          </variablelist>
2035         
2036          <para>
2037            Use the &gbOk; button to save the preset
2038            or the &gbCancel; button to
2039            close the pop-up without saving.
2040          </para>
2041         
2042         
2043          </helptext>
2044         
2045        </sect3>
2046       
2047        <sect3 id="webclient.itemlist.presets.manage">
2048          <title>Manage presets</title>
2049         
2050          <para>
2051            If you select the <guilabel>Manage&hellip;</guilabel>
2052            option from the <guilabel>view / presets</guilabel> dropdown
2053            the <guilabel>Manage presets</guilabel> dialog is opened.
2054          </para>
2055         
2056          <figure id="webclient.figures.managepresets">
2057            <title>Manage presets</title>
2058            <screenshot>
2059              <mediaobject>
2060                <imageobject><imagedata fileref="figures/manage_presets.png" format="PNG" /></imageobject>
2061              </mediaobject>
2062            </screenshot>
2063          </figure>
2064         
2065          <helptext external_id="contexts.manage" title="Manage presets">
2066         
2067          <para>
2068            From this dialog you can delete or load presets.
2069          </para>
2070         
2071          <para>
2072            To delete presets, first mark the checkbox in front of
2073            each preset you want to delete. Then, click on the
2074            <guibutton>Delete&hellip;</guibutton> button. You will get
2075            a warning about that the action cannot be undone. Unlike other
2076            items, the presets are not moved to the trashcan. Click on
2077            &gbOk; to delete the preset.
2078          </para>
2079         
2080          <note>
2081            <title>Edit a preset</title>
2082            <para>
2083            It is not possible to edit a preset directly. To change an
2084            existing preset you must:
2085           
2086            <orderedlist>
2087            <listitem><simpara>Load the preset.</simpara></listitem>
2088            <listitem><simpara>Use the interface to change column settings, filter,
2089              sort order, etc.</simpara></listitem>
2090            <listitem><simpara>Save the preset with the same name.</simpara></listitem>
2091            </orderedlist>
2092            </para>
2093          </note>
2094         
2095          <para>
2096            Use the &gbClose; button to
2097            close the pop-up.
2098          </para>
2099         
2100         
2101          </helptext>
2102         
2103        </sect3>
2104       
2105      </sect2>
2106    </sect1>
2107
2108
2109    <sect1 id="webclient.trashcan">
2110      <title>Trashcan</title>
2111      <para>
2112        All items that have been deleted, and are owned by you, are
2113        listed in your trashcan. This list page is accessed with
2114        <menuchoice>
2115          <guimenu>View</guimenu>
2116          <guimenuitem>Trashcan</guimenuitem>
2117        </menuchoice>
2118        and it differs a bit from the other common list pages. The
2119        most significant difference is that the trashcan page can
2120        contain more then one item type, actually all removable item
2121        types in BASE can be listed in the trashcan. Items that neither
2122        can be removed or deleted, <emphasis>i.e.,</emphasis> items
2123        like sessions, nor clients' help texts since these are deleted
2124        from the database immediately in list/item view will be shown
2125        in the trashcan page.
2126      </para>
2127      <warning>
2128        <para>
2129          Some item types do not have any owner and these are listed
2130          in the trashcans for everyone with delete permission on that
2131          specific item type.
2132        </para>
2133      </warning>
2134
2135      <para>
2136        Things that the trashcan page have in common with other list
2137        pages are the possibility to restore and view/edit items, see
2138        <xref linkend="webclient.items.restore" /> and
2139        <xref linkend="webclient.items.edit" /> . If an item is
2140        restored, it will of course disappear from the trashcan.
2141      </para>
2142
2143      <sect2 id="webclient.trashcan.deleteitem">
2144        <title>Delete items permanently</title>
2145        <para>
2146          Items can be permanently deleted from BASE only if they are
2147          not used by other items.  Items that are used have the icon
2148          <inlinemediaobject>
2149            <imageobject>
2150              <imagedata fileref="figures/isused.gif" format="GIF" />
2151            </imageobject>
2152          </inlinemediaobject>
2153          in the first column and by clicking on it you can get more
2154          information about the dependencies, see
2155          <xref linkend="webclient.trashcan.viewdependencies" /> .
2156          <note>
2157            <simpara>
2158              This view is NOT the same view page as when clicking on
2159              the item's name, which brings you to the item's view
2160              page.
2161            </simpara>
2162          </note>
2163        </para>
2164        <para>
2165          To delete one or several items permanently from the trashcan
2166          you first have to select them and then to click on the
2167          &gbDelete; button. Press then on either &gbOk; (completes
2168          the deletion) or &gbCancel; (no items will be deleted) in
2169          the dialog window that appears.
2170        </para>
2171
2172        <sect3 id="webclient.trashcan.deleteitem.empty">
2173          <title>Empty trashcan</title>
2174          <para>
2175            If all items in the trashcan should be deleted permanently
2176            the <guibutton>Empty trash</guibutton> button can be
2177            used. This function will remove all items that are listed
2178            in your trashcan, except those items which other items,
2179            not marked for deletion or cannot be deleted, are
2180            dependent on.
2181          </para>
2182        </sect3>
2183      </sect2>
2184
2185      <sect2 id="webclient.trashcan.viewdependencies">
2186        <title>View dependencies of a trashed item</title>
2187        <helptext external_id="trash.view.properties" title="Properties for a trashed item">
2188          <para>
2189            This view can only be accessed from trashed items that are
2190            linked together with other items. Beside the item's
2191            <guilabel>item type</guilabel>, <guilabel>name</guilabel>,
2192            and <guilabel>description</guilabel> there is a list at
2193            the bottom of the view page with those items that are
2194            using the current item in some way.
2195          </para>
2196        </helptext>
2197        <para>
2198          <nohelp>
2199            <figure id="webclient.trashcan.figures.viewtrasheditem">
2200              <title>Item view of a trashed item.</title>
2201              <screenshot>
2202                <mediaobject>
2203                  <imageobject>
2204                    <imagedata fileref="figures/trashview.png" format="PNG" 
2205                               scalefit="1" width="100%" />
2206                  </imageobject>
2207                </mediaobject>
2208              </screenshot>
2209            </figure>
2210          </nohelp>
2211          <orderedlist>
2212            <listitem>
2213              <para>
2214                This icon indicates that the item cannot be deleted
2215                permanently cause of some dependencies, see
2216                #<xref linkend="webclient.trashcan.lists.dependentitem3" />.
2217              </para>
2218            </listitem>
2219            <listitem>
2220              <para>Common properties for all removable items.</para>
2221            </listitem>
2222            <listitem id="webclient.trashcan.lists.dependentitem3">
2223              <para>A list of other items that are using the current item.</para>
2224            </listitem>
2225          </orderedlist>
2226        </para>
2227      </sect2>
2228    </sect1>
2229   
2230  <sect1 id="webclient.itemoverview">
2231    <title>Item overview</title>
2232
2233    <helptext external_id="item.overview" 
2234      title="Item overview">
2235   
2236    <para>
2237      With the <guilabel>Item overview</guilabel> 
2238      function you can get an overview of all hybridizations,
2239      extracts, samples, annotations, raw data sets, etc. that are
2240      related to a given item. The overview includes a lot of checks
2241      that validates the data for missing or possibly incorrect information.
2242    </para>
2243   
2244    <nohelp>
2245    <para>
2246      You can access the overview for an item by navigating
2247      to the single-item view of the item you are interested in.
2248      Then, switch to the <guilabel>Overview</guilabel> tab that
2249      is present on that page. Here is an example of what is displayed:
2250    </para>
2251   
2252    <figure id="webclient.figures.itemoverview">
2253      <title>The item overview</title>
2254      <screenshot>
2255        <mediaobject>
2256          <imageobject><imagedata 
2257            scalefit="1" width="100%"
2258            fileref="figures/item_overview.png" format="PNG"
2259            /></imageobject>
2260        </mediaobject>
2261      </screenshot>
2262    </figure>
2263    </nohelp>
2264   
2265    <para>
2266      The page is divided into three sections:
2267    </para>
2268   
2269    <itemizedlist>
2270      <listitem>
2271        <para>
2272        To the left is a tree displaying all items
2273        that are related to the current item.
2274        </para>
2275      </listitem>
2276     
2277      <listitem>
2278        <para>
2279        The lower right shows a list of warnings and error
2280        messages that was found when validating the data.
2281        <nohelp>
2282        In the example you can see that we have failed to
2283        specify a value for the <guilabel>Temperature</guilabel>
2284        protocol parameter for one of the samples.
2285        </nohelp>
2286        </para>
2287      </listitem>
2288       
2289      <listitem>
2290        <para>
2291          The upper right shows information about the
2292          currently selected item in the tree. This part also
2293          contains more information errors or warnings for this
2294          item. It may also present you with one or more suggestions
2295          about how to fix the problem and with a link that
2296          takes you to the most probable location where you can fix
2297          the error or warning.
2298        </para>
2299       
2300        <note>
2301          <title>No links?</title>
2302          If you do not have permission to change things no links
2303          will be shown.
2304        </note>
2305       
2306      </listitem>
2307       
2308    </itemizedlist>
2309   
2310    <seeother>
2311      <other external_id="item.overview.validationoptions"
2312        >Validation options</other>
2313      <other external_id="item.overview.fixfailures"
2314        >How to fix validation failures</other>
2315    </seeother>
2316   
2317    </helptext>
2318   
2319    <sect2 id="webclient.itemoverview.validationoptions">
2320      <title>Validation options</title>
2321      <para>
2322        Click on the <guibutton>Validation options</guibutton>
2323        button in the toolbar to open the <guilabel>Validation
2324        options</guilabel> dialog.
2325      </para>
2326     
2327      <figure id="webclient.figures.validationoptions">
2328        <title>Validation options</title>
2329        <screenshot>
2330          <mediaobject>
2331            <imageobject><imagedata 
2332              fileref="figures/validation_options.png" format="PNG"
2333              /></imageobject>
2334          </mediaobject>
2335        </screenshot>
2336      </figure>         
2337     
2338      <helptext external_id="item.overview.validationoptions" 
2339        title="Validation options">
2340        <para>
2341          The validation procedure is highly
2342          configurable and you can select what you want to
2343          ignore, or something should be displayed as an error
2344          or warning.
2345        </para>
2346       
2347        <variablelist>
2348          <varlistentry>
2349            <term>
2350            <guilabel>Presets</guilabel></term>
2351            <listitem>
2352              <para>
2353              The list contains predefined and
2354              user defined validation options.
2355              Use the <guibutton>Save as&hellip;</guibutton>
2356              button to save the current options as a user defined
2357              preset. The <guibutton>Remove&hellip;</guibutton>
2358              button is used to remove the currently selected
2359              preset. Predefined presets cannot be deleted.
2360              </para>
2361            </listitem>
2362          </varlistentry>
2363         
2364          <varlistentry>
2365            <term><guilabel>Project defaults</guilabel></term>
2366            <listitem>
2367              <para>
2368              The options in this section are used to check
2369              if your experiment uses the same values as set
2370              by the project default values of the currently active
2371              project<nohelp>
2372              (see <xref linkend="project_permission.projects" />)</nohelp>.
2373              If no project is active or if the active project does not
2374              have default values these options are ignored.
2375              </para>
2376            </listitem>
2377           
2378          </varlistentry>
2379         
2380          <varlistentry>
2381            <term><guilabel>Missing items</guilabel></term>
2382            <listitem>
2383              <para>
2384              The options in this section are used to check if
2385              you have specified values for optional items.
2386              For example, there is an option that warns you if
2387              you have not specified a protocol.
2388              </para>
2389            </listitem>
2390          </varlistentry>
2391         
2392          <varlistentry>
2393            <term><guilabel>Annotations</guilabel></term>
2394            <listitem>
2395              <para>
2396              The options in this section are used to check
2397              problems related to annotations. The most
2398              important ones are listed here:
2399              </para>
2400             
2401              <itemizedlist>
2402              <listitem>
2403                <simpara>
2404                <emphasis>Missing MIAME annotation value</emphasis>:
2405                Checks that you have specified values
2406                for all annotations marked as
2407                <guilabel>Required for MIAME</guilabel>.
2408                </simpara>
2409              </listitem>
2410             
2411              <listitem>
2412                <simpara>
2413                <emphasis>Missing factor value</emphasis>:
2414                Checks that you have specified values for
2415                all annotations used as experimental factors in
2416                the experiment. This is only checked when an experiment
2417                is selected as the root item.
2418                </simpara>
2419              </listitem>
2420             
2421              <listitem>
2422                <simpara>
2423                <emphasis>Missing parameter value</emphasis>:
2424                Checks that you have specified values
2425                for all protocol parameters.
2426                </simpara>
2427              </listitem>
2428
2429              <listitem>
2430                <simpara>
2431                <emphasis>Annotation is protocol parameter</emphasis>:
2432                Checks if an item has been annotated with a
2433                an annotation that is actually a protocol parameter.
2434                </simpara>
2435              </listitem>
2436
2437              <listitem>
2438                <simpara>
2439                <emphasis>Annotation has invalid value</emphasis>:
2440                Checks if annotation values are correct with
2441                respect to the rules given by the annotation type.
2442                This might include numeric values that are outside
2443                the valid range, or values not in the list
2444                of allows values for an enumerated annotation type.
2445                </simpara>
2446              </listitem>
2447
2448              <listitem>
2449                <simpara>
2450                <emphasis>Inheriting annotation from non-parent</emphasis>:
2451                Checks if inherited annotations really comes from a
2452                parent item. This might happen if you rearrange
2453                parent-child relationship because you found that
2454                they were incorrectly linked.
2455                </simpara>
2456              </listitem>
2457              </itemizedlist>
2458             
2459           
2460            </listitem>
2461          </varlistentry>
2462         
2463          <varlistentry>
2464            <term><guilabel>Denied access</guilabel></term>
2465            <listitem>
2466              <para>
2467              The options in this section are used to
2468              check if you do not have access (read permission)
2469              to an item in the experiment hierarchy. If this
2470              happens the validation cannot proceed in that branch.
2471              This might mask other validation problems.
2472              </para>
2473            </listitem>
2474          </varlistentry>
2475         
2476          <varlistentry>
2477            <term><guilabel>Other</guilabel></term>
2478            <listitem>
2479              <para>
2480              This section collects options that does not fit
2481              into any of the other sections. The most
2482              important options are:
2483              </para>
2484             
2485              <itemizedlist>
2486                <listitem>
2487                  <simpara>
2488                  <emphasis>Array deign mismatch</emphasis>:
2489                  Checks if the array design specified for
2490                  a raw bioassay is the same array design
2491                  specified for the hybridization.
2492                  </simpara>
2493                </listitem>
2494               
2495                <listitem>
2496                  <simpara>
2497                  <emphasis>Multiple array designs</emphasis>:
2498                  Checks if all raw bioassays in an experiment
2499                  use the same array design or not. This is only
2500                  checked when the root item is an experiment.
2501                  </simpara>
2502                </listitem>
2503             
2504                <listitem>
2505                  <simpara>
2506                  <emphasis>Incorrect number of labled extracts</emphasis>:
2507                  Checks if the number of labeled extracts
2508                  match the number of channels for the experiment.
2509                  This is only checked when the root item is an experiment.
2510                  </simpara>
2511                </listitem>
2512
2513                <listitem>
2514                  <simpara>
2515                  <emphasis>Non-unique name</emphasis>:
2516                  Checks if two items of the same type
2517                  have the same name. A unique name if important
2518                  when exporting data in Tab2Mage format.
2519                  </simpara>
2520                </listitem>
2521
2522                <listitem>
2523                  <simpara>
2524                  <emphasis>Circular reference to pooled item</emphasis>:
2525                  If you have used pooling, checks that no
2526                  circular references have been created.
2527                  </simpara>
2528                </listitem>
2529             
2530              </itemizedlist>
2531             
2532            </listitem>
2533          </varlistentry>
2534         
2535        </variablelist>
2536       
2537        <para>
2538          Click on the &gbSave; button
2539          to use the current settings. The display will
2540          automatically refresh itself.
2541        </para>
2542       
2543      </helptext>
2544     
2545      <helptext external_id="item.overview.validationoptions.savepreset" 
2546        title="Save preset" webonly="1">
2547       
2548        <para>
2549        Saves all validation options as a preset.
2550        </para>
2551       
2552        <variablelist>
2553          <varlistentry>
2554            <term><guilabel>Name</guilabel></term>
2555            <listitem>
2556              <para>
2557                The name of the preset. The name must be unique
2558                and if a preset with the same name already exists
2559                you will be asked if you want to overwrite it or not.
2560              </para>
2561            </listitem>
2562          </varlistentry>
2563        </variablelist>
2564       
2565        <para>
2566          Click on the &gbSave; button
2567          to save the preset or &gbCancel;
2568          to abort.
2569        </para>
2570      </helptext>
2571     
2572    </sect2>
2573   
2574    <sect2 id="webclient.itemoverview.fixfailures">
2575      <title>Fixing validation failures</title>
2576      <helptext external_id="item.overview.fixfailures" 
2577        title="How to fix validation failures">
2578       
2579        <para>
2580        The overview includes a function that allows
2581        you to quickly fix most of the problems found during the
2582        validation. The easiest way to use the function is:
2583        </para>
2584       
2585        <orderedlist>
2586          <listitem>
2587            <simpara>
2588            Click on an error or warning in the list of failures in
2589            the lower right
2590            pane. The tree in the left pane and the item overview in the
2591            top right pane will automatically be updated to show the
2592            exact location of the faulty item.
2593            </simpara>
2594          </listitem>
2595          <listitem>
2596            <simpara>
2597            The upper right pane should contain a list labeled
2598            <guilabel>Failure details</guilabel> with more information
2599            about each failure and also one or more suggestions for fixing
2600            the problem. For example, a failure due to a missing item
2601            should suggest that you add or select an item.
2602            </simpara>
2603          </listitem>
2604         
2605          <listitem>
2606            <simpara>
2607            The suggestions should also have links that takes
2608            you to an edit view where you can do the changes.
2609            </simpara>
2610          </listitem>
2611         
2612          <listitem>
2613            <simpara>
2614            After saving the changes you must click on the
2615            <guibutton>Revalidate</guibutton> button to update
2616            interface. If you want, you can fix more than one
2617            failure before clicking on the button.
2618            </simpara>
2619          </listitem>
2620           
2621        </orderedlist>
2622     
2623      </helptext>
2624    </sect2>
2625   
2626  </sect1>
2627
2628</chapter>
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