source: branches/2.6-stable/doc/src/docbook/userdoc/webclient.xml @ 4175

Last change on this file since 4175 was 4175, checked in by Nicklas Nordborg, 14 years ago

Fixes #949: Installation documentation has incorrect information about which Java version to use

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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 4175 2008-03-14 08:47:48Z 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 2
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 this program; if not, write to the Free Software
25  Foundation, Inc., 59 Temple Place - Suite 330,
26  Boston, MA  02111-1307, USA.
27-->
28
29<chapter id="webclient">
30  <?dbhtml dir="webclient"?>
31  <title>Using the web client</title>
32    <sect1 id="webclient.introduction">
33      <title>Introduction</title>
34     
35      <sect2 id="webclient.intro.login">
36        <title>Logging in</title>
37        <para>
38          There are three things that you need to know
39          before you can use BASE:
40        </para>
41       
42        <orderedlist>
43        <listitem><simpara>The address (URL) to a BASE server</simpara></listitem>
44        <listitem><simpara>A username to login with</simpara></listitem>
45        <listitem><simpara>A password</simpara></listitem>
46        </orderedlist>
47       
48        <para>
49          You may, for example, try the BASE 2 demo server. Go to the
50          URL <ulink url="http://base2.thep.lu.se:8080/demo/">http://base2.thep.lu.se:8080/demo/</ulink>
51          and enter <userinput>base2</userinput> for the login and <userinput>base2</userinput>
52          for the password.
53        </para>
54       
55        <para>
56          You need to get all three things from an administrator
57          of the BASE server. If you know only the address to the
58          BASE server, you may check the front page if the administrator
59          has added any information about how to get a username/password
60          there. Look for the <guilabel>Get an account!</guilabel> link on
61          the front page.
62        </para>
63       
64        <para>
65          Logging in is simple, just enter your <guilabel>login</guilabel> 
66          and <guilabel>password</guilabel> in the form on the front page
67          and click the <guibutton>Login</guibutton> button. There is
68          a checkbox which allows you to <guilabel>encrypt the password</guilabel>
69          before it is sent to the BASE server. It is checked by default, and
70          it is a good idea to leave it checked unless you have problems logging
71          in. If you are sure you are entering the correct login and password,
72          but still cannot log in, try unchecking the encryption option.
73          If the checkbox is not visible, which happens if the server is
74          using an external authentication server, the password is not encrypted.
75        </para>
76      </sect2>
77     
78      <sect2 id="webclient.intro.forgotten_password">
79        <title>Forgotten password</title>
80        <para>
81          If you forget your password you will need to get a new one.
82          BASE stores the passwords in an encrypted form that does not allow
83          anyone, not even the server administrator, to find out the
84          un-encrypted password.
85        </para>
86        <para>
87          To get a new password you will have to contact the server
88          administrator. There may be a <guilabel>Forgot your password?</guilabel>
89          link on the front page where the server administrator has entered
90          information about how to get a new password.
91        </para>
92      </sect2>
93
94      <sect2 id="webclient.intro.homepage">
95        <title>The home page</title>
96     
97      <para>
98        When you have been logged in the home page will be displayed. It
99        displays some useful information. You can also go to the home page
100        using the
101        <menuchoice><guimenu>View</guimenu><guimenuitem>Home</guimenuitem></menuchoice>
102      </para>
103       
104      <figure id="webclient.figures.homepage">
105        <title>The home page</title>
106        <screenshot>
107          <mediaobject>
108            <imageobject><imagedata fileref="figures/homepage.png" format="PNG"
109              scalefit="1" width="100%"/></imageobject>
110          </mediaobject>
111        </screenshot>
112      </figure>
113       
114      <variablelist>
115        <varlistentry>
116          <term><interface>New messages</interface></term>
117          <listitem>
118            <para>
119            Messages are sent by plug-ins to notify you about finished jobs. In the
120            future, you may get messages from other sources as well. As of today,
121            messages are not used for communication between users.
122            </para>
123          </listitem>
124        </varlistentry>
125       
126        <varlistentry>
127          <term><interface>Projects</interface></term>
128          <listitem>
129            <para>
130            A list of projects that you are a member of. Projects are an important
131            part of BASE and are the best way to share data when you are
132            cooperating with other users. We recommend
133            that you always use a project when working with BASE.
134            For more information read <xref linkend="project_permission"/>.
135            </para>
136          </listitem>
137        </varlistentry>
138       
139        <varlistentry>
140          <term><interface>Disk usage</interface></term>
141          <listitem>
142            <para>
143            An overview of how much disk space you have been assigned and
144            how much you are using.
145            </para>
146          </listitem>
147        </varlistentry>
148       
149        <varlistentry>
150          <term><interface>Help</interface></term>
151          <listitem>
152            <para>
153            Links for getting help and reporting bugs. The number
154            of links displayed here may vary depending on the server
155            configuration.
156            </para>
157          </listitem>
158        </varlistentry>
159       
160        <varlistentry>
161          <term><interface>News and announcements</interface></term>
162          <listitem>
163            <para>
164            A list of important news and announcements from the
165            server administrator. Here you may, for example, find
166            information about server upgrades and maintenance.
167            </para>
168          </listitem>
169        </varlistentry>
170      </variablelist>
171       
172      </sect2>
173     
174      <sect2 id="webclient.intro.menubar">
175        <title>Using the menu bar</title>
176        <para>
177          On the top of the home page is the <interface>Menu bar</interface>.
178          This is the main navigation tool in BASE. It works the same way
179          as the regular menu system found in most other applications. Use
180          the mouse to click and select an item from the menu.
181        </para>
182       
183        <para>
184          Most of the menu is in two levels, ie. clicking on a top-level menu
185          will open a submenu just below it. Clicking on something in the
186          submenu will take you to another page or open a popup dialog window.
187          For example, the
188          <menuchoice><guimenu>View</guimenu><guimenuitem>Samples</guimenuitem></menuchoice>
189          menu will take you to the page listing samples and
190          <menuchoice><guimenu>File</guimenu><guimenuitem>Contact information</guimenuitem></menuchoice>
191          opens a dialog where you can modify your contact information details.
192        </para>
193       
194        <para>
195          The menu bar also contains shortcuts to some often-used
196          actions:
197        </para>
198       
199       
200      <variablelist>
201        <varlistentry>
202          <term>           
203            <guiicon>
204              <inlinemediaobject>
205              <imageobject><imagedata fileref="figures/refresh.gif" format="GIF" align="left"
206                /></imageobject>
207              </inlinemediaobject>
208            </guiicon>
209            <interface>
210            Refresh page
211            </interface>
212          </term>
213          <listitem>
214            <para>
215            Refresh/reload the current page. This is useful when you add
216            or modify items in BASE. Most of the time the page is refreshed
217            automatically, but in some cases you will have to use
218            this button to refresh the page.
219            </para>
220           
221            <warning>
222              <para>
223              Do not use your browser's <guibutton>Refresh</guibutton> button.
224              Most browsers will take you to the login page again.
225              </para>
226            </warning>
227          </listitem>
228        </varlistentry>
229       
230        <varlistentry>
231          <term>     
232            <guiicon>     
233              <inlinemediaobject>
234              <imageobject><imagedata fileref="figures/recent.png" format="PNG" align="left"/></imageobject>
235              </inlinemediaobject>
236            </guiicon>
237            <interface>
238            Recent items
239            </interface>
240          </term>
241          <listitem>
242            <para>
243            Shortcut to the most recently viewed items. The number of items are
244            configurable and you can also make some item types
245            <emphasis>sticky</emphasis>. This will for example keep the shortcut
246            to the last experiment even if you have viewed lots of other items
247            more recently.
248            See <xref linkend="webclient.configuration.preferences.mostrecent"/>
249            for configuration information.
250            </para>
251          </listitem>
252        </varlistentry>
253       
254        <varlistentry>
255          <term>
256            <guiicon>
257              <inlinemediaobject>
258              <imageobject><imagedata fileref="figures/project.gif" format="GIF" align="left"/></imageobject>
259              </inlinemediaobject>
260            </guiicon>
261            <interface>
262            Projects
263            </interface>
264          </term>
265          <listitem>
266            <para>
267            A list of all projects you are a member of. Selecting a project in the
268            list will make that project the active project.
269            </para>
270          </listitem>
271        </varlistentry>
272       
273        <varlistentry>
274          <term>
275            <guiicon>
276              <inlinemediaobject>
277              <imageobject><imagedata fileref="figures/user.png" format="PNG" align="left"/></imageobject>
278              </inlinemediaobject>
279            </guiicon>
280            <interface>
281            Logged in user
282            </interface>
283          </term>
284          <listitem>
285            <para>
286            Displays the name of the currently logged in user and allows
287            you to quickly logout and switch to another user.
288            </para>
289          </listitem>
290        </varlistentry>
291       
292      </variablelist>
293       
294      </sect2>
295     
296      <sect2 id="webclient.intro.help">
297        <title>Getting help</title>
298        <para>
299          Besides reading this document there are more ways to get help:
300        </para>
301        <variablelist>
302          <varlistentry>
303            <term>
304              Online context-sensitive help
305            </term>
306            <listitem>
307              <para>
308              Whenever you find a small help icon
309              (<guiicon>
310                <inlinemediaobject>
311                <imageobject><imagedata fileref="figures/help.gif" format="GIF" /></imageobject>
312                </inlinemediaobject>
313              </guiicon>)
314              or button you may
315              click it to get help about the part of the page
316              you are currently viewing. The icon is located in the title
317              bar in most popup dialog windows and in the toolbar in most
318              other pages.
319              </para>
320            </listitem>
321          </varlistentry>
322
323          <varlistentry>
324            <term>
325              Using the <menuchoice><guimenu>Help</guimenu></menuchoice> menu
326            </term>
327            <listitem>
328              <para>
329              The <menuchoice><guimenu>Help</guimenu></menuchoice> menu
330              contains links for getting online help. These links
331              may be configured by a server administrator, so they may be
332              different from server to server. By default links for reporting
333              a bug and accessing this document are installed.
334              </para>
335            </listitem>
336          </varlistentry>
337
338          <varlistentry>
339            <term>
340              Mailing lists and other resources
341            </term>
342            <listitem>
343              <para>
344              See <xref linkend="resources" />.
345              </para>
346            </listitem>
347          </varlistentry>
348
349        </variablelist>
350       
351      </sect2>
352   
353    </sect1>
354   
355    <sect1 id="webclient.configuration">
356      <title>Configuring your account</title>
357     
358      <sect2 id="webclient.configuration.contact">
359        <title>Contact information</title>
360       
361        <para>
362          Use the <menuchoice><guimenu>File</guimenu>
363          <guimenuitem>Contact information</guimenuitem></menuchoice>
364          menu to bring up the user information dialog.
365        </para>
366       
367        <helptext external_id="userpreferences.contact" title="Contact information">
368       
369          <para>
370          This dialog has three tabs, <guilabel>Contact information</guilabel>
371          (selected), <guilabel>Password</guilabel> and <guilabel>Other information</guilabel>.
372          The logged in user can update the following contact information
373          details.
374          </para>
375       
376          <note>
377            <title>Multi-user accounts</title>
378            <para>
379              If you are using a multi-user account, for example a demo-account, you
380              do not have permission to change the contact information.
381            </para>
382          </note>
383       
384          <variablelist>
385            <varlistentry>
386              <term>
387                <guilabel>Full name</guilabel>
388              </term>
389              <listitem>
390                <para>
391                Your full name. You are not allowed to change this. If
392                it is not correct, contact an administrator to do it for
393                you.
394                </para>
395              </listitem>
396            </varlistentry>
397            <varlistentry>
398              <term>
399                <guilabel>Email</guilabel>
400              </term>
401              <listitem>
402                <para>
403                Your email address (optional).
404                </para>
405              </listitem>
406            </varlistentry>
407            <varlistentry>
408              <term>
409                <guilabel>Organisation</guilabel>
410              </term>
411              <listitem>
412                <para>
413                The name of the organisation you work for or represent (optional).
414                </para>
415              </listitem>
416            </varlistentry>
417            <varlistentry>
418              <term>
419                <guilabel>Address</guilabel>
420              </term>
421              <listitem>
422                <para>
423                Your postal address as it should be printed on letters to you
424                (optional).
425                </para>
426              </listitem>
427            </varlistentry>
428            <varlistentry>
429              <term>
430                <guilabel>Phone</guilabel>
431              </term>
432              <listitem>
433                <para>
434                Your phone number (optional). You may enter multiple phone numbers,
435                for example your work phone number and a mobile number.
436                </para>
437              </listitem>
438            </varlistentry>
439            <varlistentry>
440              <term>
441                <guilabel>Fax</guilabel>
442              </term>
443              <listitem>
444                <para>
445                Your fax number (optional).
446                </para>
447              </listitem>
448            </varlistentry>
449            <varlistentry>
450              <term>
451                <guilabel>Url</guilabel>
452              </term>
453              <listitem>
454                <para>
455                An URL to your home page or your organisation's home page (optional).
456                </para>
457              </listitem>
458            </varlistentry>
459          </variablelist>
460         
461          <para>
462            Press &gbSave; to save the changes or
463            &gbCancel; to abort.
464          </para>
465         
466          <seeother>
467            <other external_id="userpreferences.password">Change password</other>
468            <other external_id="userpreferences.other">Other information</other>
469          </seeother>
470        </helptext>
471       
472      </sect2>
473     
474      <sect2 id="webclient.configuration.other">
475        <title>Other information</title>
476        <para>
477          Use the
478          <menuchoice>
479            <guimenu>File</guimenu>
480            <guimenuitem>Other information&hellip;</guimenuitem>
481          </menuchoice>
482          menu to bring up the other information dialog.
483        </para>
484        <helptext external_id="userpreferences.other" title="Other information">
485          <para>
486            This dialog has three tabs,
487            <guilabel>Contact information</guilabel>
488            ,
489            <guilabel>Password</guilabel>
490            and
491            <guilabel>Other information</guilabel>
492            (selected) .
493          </para>
494          <para>
495            The look of the
496            <guilabel>Other information</guilabel>
497            tab can differe abit between different servers, depending on what settings
498            the server is installed with. There are three inputs in a fresh BASE2
499            installation but it is only the
500            <guilabel>Description</guilabel>
501            textarea that is static, the others can be removed or more fields can be
502            added (managed by the server administrator). The three fields, included in a
503            the BASE2 installation, are
504            <variablelist>
505              <varlistentry>
506                <term>
507                  <guilabel>Mobile</guilabel>
508                </term>
509                <listitem>
510                  <para>Your mobile number(Optional).</para>
511                </listitem>
512              </varlistentry>
513              <varlistentry>
514                <term>
515                  <guilabel>Skype</guilabel>
516                </term>
517                <listitem>
518                  <para>Your skype contact information(Optional).</para>
519                </listitem>
520              </varlistentry>
521              <varlistentry>
522                <term>
523                  <guilabel>Description</guilabel>
524                </term>
525                <listitem>
526                  <para>
527                    Text area where you can put useful information that couldn't
528                    be stored anywhere else(Optional).
529                  </para>
530                </listitem>
531              </varlistentry>
532            </variablelist>
533          </para>
534          <para>Press &gbSave; to save the changes or &gbCancel; to abort.</para>
535          <seeother>
536            <other external_id="userpreferences.contact">Contact information</other>
537            <other external_id="userpreferences.password">Change password</other>
538          </seeother>
539        </helptext>
540      </sect2>
541
542      <sect2 id="webclient.configuration.password">
543        <title>Changing password</title>
544       
545        <para>
546          Use the <menuchoice><guimenu>File</guimenu>
547          <guimenuitem>Change password</guimenuitem></menuchoice>
548          menu to bring up the change password dialog.
549        </para>
550       
551        <helptext external_id="userpreferences.password" title="Change password">
552
553          <para>
554          This dialog has three tabs, <guilabel>Contact information</guilabel>,
555          <guilabel>Password</guilabel> (selected) and <guilabel>Other information</guilabel>.
556          </para>
557
558          <variablelist>
559            <varlistentry>
560              <term>
561                <guilabel>New password</guilabel>
562              </term>
563              <listitem>
564                <para>
565                Enter the new password.
566                </para>
567              </listitem>
568            </varlistentry>
569            <varlistentry>
570              <term>
571                <guilabel>Retype password</guilabel>
572              </term>
573              <listitem>
574                <para>
575                Retype the same password. You must do this to
576                avoid spelling mistakes.
577                </para>
578              </listitem>
579            </varlistentry>
580          </variablelist>
581
582          <note>
583            <title>Multi-user accounts</title>
584            <para>
585              If you are using a multi-user account, for example a demo-account, you
586              do not have permission to change the password.
587            </para>
588          </note>
589       
590          <note>
591            <title>Empty passwords</title>
592            <para>
593              If you leave both fields empty the password will not be changed. It
594              is not possible to have an empty password.
595            </para>
596          </note>
597         
598          <seeother>
599            <other external_id="userpreferences.contact">Contact information</other>
600            <other external_id="userpreferences.other">Other information</other>
601          </seeother>
602         
603        </helptext>
604      </sect2>
605
606      <sect2 id="webclient.configuration.preferences">
607        <title>Preferences</title>
608       
609        <para>
610          Use the <menuchoice><guimenu>File</guimenu>
611          <guimenuitem>Preferences</guimenuitem></menuchoice>
612          menu to bring up the preferences dialog.
613          This dialog has three tabs, <guilabel>Appearance</guilabel>,
614          <guilabel>Plugins</guilabel> and <guilabel>Most recent</guilabel>.
615        </para>
616       
617        <sect3 id="webclient.configuration.preferences.appearance">
618          <title>The Appearance tab</title>
619         
620          <helptext external_id="userpreferences.appearance" title="Preferences - Appearance">
621         
622          <para>
623          This tab contains settings that affect the appearance of the
624          web client.
625          </para>
626         
627          <variablelist>
628            <varlistentry>
629              <term>
630                <guilabel>Font size</guilabel>
631              </term>
632              <listitem>
633                <para>
634                Select a basic font size. You can choose between
635                five sizes: extra small (XS), small (S), medium (M),
636                large (L) and extra large (XL). The default font size is
637                medium.
638                </para>
639              </listitem>
640            </varlistentry>
641            <varlistentry>
642              <term>
643                <guilabel>Scale factor</guilabel>
644              </term>
645              <listitem>
646                <para>
647                The scale factor affects the size of popup windows.
648                This setting exists because different browsers render
649                pages differently. If you often find that popup windows
650                are too small you can change this setting to make them
651                bigger.
652                </para>
653                <note>
654                  <para>
655                    The scale factor is automatically changed if the
656                    font size is changed.
657                  </para>
658                </note>
659              </listitem>
660            </varlistentry>
661            <varlistentry>
662              <term>
663                <guilabel>Toolbar</guilabel>
664              </term>
665              <listitem>
666                <para>
667                You may choose if the toolbar buttons should
668                have only images, only text or both images and text.
669                The default is that they have both images and text.
670                </para>
671              </listitem>
672            </varlistentry>
673            <varlistentry>
674              <term>
675                <guilabel>Ratio color range</guilabel>
676              </term>
677              <listitem>
678                <para>
679                Select three colors to use when displaying
680                data that is suitable for color coding, for
681                example the intensity ratio in two-color
682                experiments. The default setting is blue-black-yellow.
683                The list of presets contains other useful color combinations
684                (for example, the BASE 1 red-yellow-green) and the most
685                recently used color combinations.
686                </para>
687              </listitem>
688            </varlistentry>
689            <varlistentry>
690              <term>
691                <guilabel>Date format</guilabel>
692              </term>
693              <listitem>
694                <para>
695                A format string describing how dates should be displayed.
696                We support all formatting options supported by the Java
697                language. For more information see:
698                <ulink url="http://java.sun.com/javase/6/docs/api/java/text/SimpleDateFormat.html">SimpleDateFormat documentation</ulink>
699                The most useful format patterns are:
700                </para>
701               
702                <itemizedlist>
703                  <listitem><simpara>yy: two-digit year</simpara></listitem>
704                  <listitem><simpara>yyyy: four-digit year</simpara></listitem>
705                  <listitem><simpara>MM: two-digit month</simpara></listitem>
706                  <listitem><simpara>MMM: month name (short)</simpara></listitem>
707                  <listitem><simpara>MMMM: month name (full)</simpara></listitem>
708                  <listitem><simpara>dd: two-digit day in month</simpara></listitem>
709                </itemizedlist>
710               
711                <para>
712                The list of presets contains the most commonly/recently
713                used date formats.
714                </para>
715               
716              </listitem>
717            </varlistentry>
718           
719            <varlistentry>
720              <term>
721                <guilabel>Date-time format</guilabel>
722              </term>
723              <listitem>
724                <para>
725                A format string describing how dates with times should be displayed.
726                We support all formatting options supported by the Java
727                language. For more information see:
728                <ulink url="http://java.sun.com/javase/6/docs/api/java/text/SimpleDateFormat.html">SimpleDateFormat documentations</ulink>
729                The most useful time-format patterns are:
730                </para>
731               
732                <itemizedlist>
733                  <listitem><simpara>HH: two-digit hour (0-23)</simpara></listitem>
734                  <listitem><simpara>hh: two-digit hour (1-12)</simpara></listitem>
735                  <listitem><simpara>a: AM/PM marker</simpara></listitem>
736                  <listitem><simpara>mm: two-digit minute</simpara></listitem>
737                  <listitem><simpara>ss: two-digit second</simpara></listitem>
738                </itemizedlist>
739               
740              </listitem>
741            </varlistentry>
742           
743            <varlistentry>
744              <term>
745                <guilabel>Decimals</guilabel>
746              </term>
747              <listitem>
748                <para>
749                The number of decimals to display for numeric values.
750                The default is 2.
751                </para>
752              </listitem>
753            </varlistentry>
754           
755          </variablelist>
756       
757          </helptext>
758       
759        </sect3>
760       
761        <sect3 id="webclient.configuration.preferences.plugins">
762          <title>The Plugins tab</title>
763         
764          <helptext external_id="userpreferences.plugins" title="Preferences - Plugins">
765         
766          <para>
767            This tab contains settings that affect plug-in execution.
768          </para>
769         
770          <variablelist>
771            <varlistentry>
772              <term>
773                <guilabel>Messages</guilabel>
774              </term>
775              <listitem>
776                <para>
777                Mark the checkbox if you want to have a message sent
778                to you when a plug-in completes execution. This setting
779                can be overridden each time you start a plug-in.
780                </para>
781              </listitem>
782            </varlistentry>
783            <varlistentry>
784              <term>
785                <guilabel>Remove jobs</guilabel>
786              </term>
787              <listitem>
788                <para>
789                  This checkbox should be marked if you want the jobs, done by
790                  import or export plug-ins, to be marked as removed if they
791                  finished successfully. This setting can be overridden each time
792                  you start a plug-in.
793                </para>
794              </listitem>
795            </varlistentry>
796            <varlistentry>
797              <term>
798                <guilabel>Show warnings</guilabel>
799              </term>
800              <listitem>
801                <para>
802                  This checkbox should be marked if you want to show warning
803                  messages from plug-ins in the <guilabel>Select plug-in</guilabel>
804                  dialog. Warning-level messages usually originates from plug-ins
805                  that are unrelated to the current task and are only of interest to
806                  plug-in developers. Error messages that are related to the
807                  current task are always shown.
808                </para>
809              </listitem>
810            </varlistentry>
811          </variablelist>
812          </helptext>
813         
814        </sect3>
815       
816        <sect3 id="webclient.configuration.preferences.mostrecent">
817          <title>The Recent items tab</title>
818         
819          <helptext external_id="userpreferences.mostrecent" 
820            title="Preferences - Recent items">
821         
822          <para>
823            This tab contains settings that affect the <guilabel>Recent
824            items</guilabel> menu.
825          </para>
826         
827          <variablelist>
828          <varlistentry>
829            <term>
830              <guilabel>Recently viewed items</guilabel>
831            </term>
832            <listitem>
833              <para>
834              The number of recently <emphasis>viewed</emphasis> items to remember.
835              The default is to remember 6 items. The remembered items
836              will be displayed in the <guilabel>Recent items</guilabel>
837              menu in the menu bar.
838              </para>
839            </listitem>
840          </varlistentry>
841          <varlistentry>
842            <term>
843              <guilabel>Recently used items</guilabel>
844            </term>
845            <listitem>
846              <para>
847              The number of recently <emphasis>used</emphasis> items to remember.
848              The default is to remember 4 items. The remembered items will
849              be displayed in edit dialogs where they have been used before.
850              Each type of edit operation has it's own list of remembered items.
851              For example, there is one list that remembers the most recently used
852              protocols when creating a sample, and there is another list that
853              remembers the most recently used scanners when creating a scan.
854              </para>
855            </listitem>
856          </varlistentry>
857         
858          <varlistentry>
859            <term>
860              <guilabel>Load the names of all items</guilabel>
861            </term>
862            <listitem>
863              <para>
864              If checked, the names of the items will be loaded and
865              displayed in the menu, otherwise only the ID and type of item
866              is displayed.
867              </para>
868            </listitem>
869          </varlistentry>
870         
871          <varlistentry>
872            <term>
873              <guilabel>Sticky items</guilabel>
874            </term>
875            <listitem>
876              <para>
877              Always remember the last viewed item of the selected types.
878              For example, if you have selected <emphasis>Experiment</emphasis>
879              as a sticky item, the last viewed experiment will be remembered
880              even if you view hundreds of other items. Use the arrow buttons
881              to move item types between the lists and sort the sticky items list.
882              Sticky items will be displayed in the <guilabel>Recent items</guilabel>
883              menu in the menu bar.             
884              </para>
885            </listitem>
886          </varlistentry>
887          </variablelist>
888          </helptext>
889         
890        </sect3>
891      </sect2>
892 
893    </sect1>
894   
895    <sect1 id="webclient.items">
896      <title>Working with items</title>
897     
898      <para>
899        No matter what you are doing in BASE some things works more
900        or less in the same way. This section covers things that are
901        common for most parts of BASE.
902      </para>
903     
904      <para>
905        You mostly work with a single type of item at a time. This is
906        reflected in the menu system. For example, use
907        <menuchoice>
908          <guimenu>View</guimenu>
909          <guimenuitem>Samples</guimenuitem>
910        </menuchoice>
911        to work with samples, and
912        <menuchoice>
913          <guimenu>View</guimenu>
914          <guimenuitem>Experiments</guimenuitem>
915        </menuchoice>
916        to work with experiments. In most cases the list view for that type
917        of item is displayed. The list view, as the name says,
918        is used to list all items. There are two more standard views, the
919        single-item view and the edit view.
920      </para>
921     
922      <variablelist>
923        <varlistentry>
924          <term>List view</term>
925          <listitem>
926            <para>
927            This view lists all items of a certain type. The view allows you to search
928            and it is possible to configure which information to show
929            for each item. It also contains functions that
930            can be used on multiple items at the same time, for example,
931            delete, share and export. See <xref linkend="webclient.itemlist"/> for more information.
932            </para>
933          </listitem>
934        </varlistentry>
935     
936        <varlistentry>
937          <term>Single-item view</term>
938          <listitem>
939            <para>
940            Displays information about a single item. Sometimes it is very little,
941            sometimes it is very much and the information may be divided
942            into multiple tabs.
943            </para>
944          </listitem>
945        </varlistentry>
946     
947        <varlistentry>
948          <term>Edit view</term>
949          <listitem>
950            <para>
951            This view is used for editing the information
952            about a single item. It is always displayed as a popup window.
953            </para>
954          </listitem>
955        </varlistentry>
956      </variablelist> 
957             
958      <sect2 id="webclient.items.new">
959        <title>Create a new item</title>
960       
961        <para>
962          New items are mostly created from the list view. For example,
963          to create a new experiment go to the
964          <menuchoice><guimenu>View</guimenu> <guimenuitem>Experiments</guimenuitem></menuchoice>
965          page. Here you will find a &gbNew; button in the
966          toolbar. The button is disabled if you do not have permission to create new experiments.
967          Otherwise, click on it and enter any required information in the popup dialog.
968          Sometimes there are multiple tabs in this dialog. In the case of experiments
969          there are three tabs: <guilabel>Experiment</guilabel>, <guilabel>Publication</guilabel>
970          and <guilabel>Experimental factors</guilabel>.
971         
972          As a general rule, only the first tab has information that is required.
973          The information in all other tabs are optional.
974        </para>
975       
976        <para>
977          In some places you will also find actions that create items
978          directly in the list. For example in the list of samples or on
979          the single-item view for a sample you can create an extract using that
980          sample as the parent. If you use such links the parent
981          item will in most cases be selected automatically, which saves
982          you a few clicks when creating new items.
983        </para>
984       
985        <para>
986          Click on the &gbSave; button to save the new
987          item to the database or on the &gbCancel; button
988          to abort.
989        </para>
990
991        <note>
992          <para>
993          To speed up data entry when adding multiple new items there
994          are a few tricks you can use to make the web client supply
995          default values for most properties. To find a default value
996          the following checklist is used in this order:
997          </para>
998       
999        <orderedlist>         
1000          <listitem>
1001            <para>
1002            If the list have an active filter the filter values are
1003            used as default property values for the new item. For example,
1004            if you are listing experiments with <guilabel>Genepix</guilabel>
1005            raw data type the new experiment will automatically have
1006            <guilabel>Genepix</guilabel> selected. This trick should work
1007            for all properties except annotations, if it does not
1008            report it as a bug to the development team.
1009            </para>
1010          </listitem>
1011         
1012          <listitem>
1013            <para>
1014            When you link to other items the same item will be used the next time.
1015            For example, if you create an extract and selects an extraction protocol
1016            the same protocol is used the next time you create another extract.
1017            In fact, BASE will remember as many items as specified by
1018            the
1019            <guilabel>Recently used items</guilabel> setting (default is 4),
1020            allowing you to quickly select one of those protocols.
1021            <xref linkend="webclient.configuration.preferences.appearance"/> 
1022            contains more information about the setting.
1023            </para>
1024          </listitem>
1025         
1026          <listitem>
1027            <para>
1028            If you have a project active and that project has specified default
1029            values those values will be used for new items. A project can specify
1030            defaults for protocols, hardware and software and a few other settings.
1031            </para>
1032          </listitem>
1033         
1034        </orderedlist>
1035       
1036        </note>
1037       
1038      </sect2>
1039     
1040      <sect2 id="webclient.items.edit">
1041        <title>Edit an existing item</title>
1042       
1043        <para>
1044          On all single-item views there is an &gbEdit;
1045          button in the toolbar that opens a popup dialog for editing the properties
1046          of the item. This button is disabled if the logged in user does not have
1047          write permission for the item.
1048        </para>
1049       
1050        <para>
1051          You can also open the edit popup in most other places where
1052          the item appears, for example, in lists or the single-item view
1053          of a related item. Press and hold one of the <keycap>CTRL</keycap>,
1054          <keycap>ALT</keycap> or <keycap>SHIFT</keycap> keys while clicking
1055          on the link and the edit window will open in a popup.
1056          If you do not have write permission
1057          on the item there is no meaning to open the edit popup and you will
1058          be taken to the single-item view page instead.
1059        </para>
1060
1061        <para>
1062          Click on the &gbSave; button to save the changes
1063          to the database or on the &gbCancel; button
1064          to abort.
1065        </para>
1066     
1067      </sect2>
1068
1069      <sect2 id="webclient.items.delete">
1070        <title>Delete items</title>
1071
1072        <para>
1073          You can delete items either from the list view or from
1074          a single-item view. In both cases, deleted items are only moved to
1075          the trashcan. No information is removed from the database. This allows
1076          you to restore items if you later find out that you need them again.
1077          In fact, there is nothing special about a removed item. It can still be
1078          used for the same things as any non-removed item can.
1079        </para>
1080
1081        <important>
1082          <para>
1083          To really delete items from the database you have two options:
1084          <orderedlist>
1085          <listitem>
1086            <para>
1087            Go to the trashcan
1088            <menuchoice><guimenu>View</guimenu><guimenuitem>Trashcan</guimenuitem></menuchoice>
1089            and delete it from there. From the trashcan you can delete several items
1090            in one go. See <xref linkend="webclient.trashcan"/>.
1091            </para>
1092          </listitem>
1093          <listitem>
1094            <para>
1095            Click on the small trashcan icon in the list or single-item view.
1096            You can only delete one item at a time.
1097            </para>
1098          </listitem>
1099          </orderedlist>
1100          </para>
1101        </important>
1102       
1103        <para>
1104          To delete items from the list view you must first mark
1105          the checkbox for each item you want to delete. Then, click on
1106          the &gbDelete; button. The list should refresh itself
1107          automatically. If you want to confirm that the items have been removed
1108          use the <guilabel>view / presets</guilabel> dropdown and select
1109          the <guilabel>Removed</guilabel> option. The removed items should now
1110          be displayed in the list with a small trashcan icon to indicate that
1111          they are located in the trashcan.
1112        </para>
1113
1114        <para>
1115          To delete items from the single-item view, click on the
1116          &gbDelete; button in the toolbar. The page will refresh
1117          itself automatically and a small trashcan icon should be displayed.
1118          If you do not have permission to delete the item the delete button
1119          is disabled.
1120        </para>
1121
1122      </sect2>
1123     
1124      <sect2 id="webclient.items.restore">
1125        <title>Restore deleted items</title>
1126       
1127        <para>
1128          You can restore deleted items either from the trashcan, from
1129          the list view, or from the single-item view. This section
1130          only covers the last two cases. The trashcan is described in
1131          another section (<xref linkend="webclient.trashcan"/>).
1132        </para>
1133
1134        <para>
1135          To delete items from the list view you must first make the deleted
1136          items appear in the list. This is easy, just use the <guilabel>view / presets</guilabel> 
1137          dropdown and select the <guilabel>Removed</guilabel> option. The list should
1138          refresh itself automatically. The removed items are
1139          displayed in the list with a small trashcan icon to indicate that
1140          they are located in the trashcan. Then, mark the checkbox for each item that you want
1141          to restore and click the &gbRestore; button. The list should
1142          refresh itself automatically and the trashcan icon should be gone from the
1143          restored items.
1144        </para>
1145       
1146        <para>
1147          To restore items from the single-item view, click on the
1148          &gbRestore; button in the toolbar. The page will refresh
1149          itself automatically and the small trashcan icon should be gone.
1150          If you do not have permission to restore the item the restore button
1151          is disabled.
1152        </para>
1153
1154      </sect2>
1155
1156      <sect2 id="webclient.items.share">
1157        <title>Share items to other users</title>
1158        <para>
1159          Sharing data with other users is an important feature
1160          of BASE, which allows you cooperate in teams. If you have
1161          followed the instructions in <xref linkend="project_permission" />
1162          you will find that you almost never have to share items manually
1163          to other users. This is because whenever you work with an active
1164          project each new item you create will automatically be shared
1165          to that project. In most cases, this is all you need.
1166        </para>
1167       
1168        <para>
1169          If you still need to manually share your data with other users,
1170          here is how to do it.
1171        </para>
1172       
1173        <para>
1174          From a list view, mark the checkbox for each item you want to share.
1175          Then, click on the &gbShare; button.
1176          If you are on a single-item page, click on the &gbShare; 
1177          button on that page. In both cases, this will open the
1178          <guilabel>Set access permissions</guilabel>
1179          dialog window.
1180        </para>
1181       
1182        <figure id="webclient.items.share.set_permissions">
1183          <title>Sharing items to other users</title>
1184          <screenshot>
1185          <mediaobject>
1186            <imageobject>
1187              <imagedata fileref="figures/set_permissions.png" format="PNG" />
1188            </imageobject>
1189          </mediaobject>
1190          </screenshot>
1191        </figure>
1192       
1193        <helptext external_id="share.setpermissions" title="Set access permissions">
1194          <variablelist>
1195            <varlistentry>
1196              <term><guilabel>Members</guilabel></term>
1197              <listitem>
1198                <para>
1199                The list displays the users, groups and projects
1200                that already has access to the items you selected.
1201                The list shows the name and the permission level.
1202                The permission level uses a one-letter code as follows:
1203                </para>
1204               
1205                <itemizedlist>
1206                <listitem><simpara><guilabel>R</guilabel> = Read</simpara></listitem>
1207                <listitem><simpara><guilabel>U</guilabel> = Use</simpara></listitem>
1208                <listitem><simpara><guilabel>W</guilabel> = Write</simpara></listitem>
1209                <listitem><simpara><guilabel>D</guilabel> = Delete</simpara></listitem>
1210                <listitem><simpara><guilabel>O</guilabel> = Take ownership</simpara></listitem>
1211                <listitem><simpara><guilabel>P</guilabel> = Set permission</simpara></listitem>
1212                </itemizedlist>
1213               
1214                <para>
1215                  Instead of a permission code, the word <guilabel>varying</guilabel>
1216                  may be displayed. This happens if the items you selected have been
1217                  shared with different permission.
1218                </para>
1219               
1220              </listitem>
1221            </varlistentry>
1222           
1223            <varlistentry>
1224              <term><guilabel>Permissions</guilabel></term>
1225              <listitem>
1226                <para>
1227                When you select a user, group or project in the
1228                list, the checkboxes will display the current permission.
1229                The exception is if the permissions are varying, in which
1230                case no checkboxes are checked.
1231                To change the permissions just check the permissions you want to
1232                grant or uncheck the permissions you want to revoke.
1233                You can select more than one user, group or project
1234                and change the permissions for all of them at once.
1235                </para>
1236              </listitem>
1237            </varlistentry>           
1238
1239            <varlistentry>
1240              <term><guibutton>Add users</guibutton></term>
1241              <listitem>
1242                <para>
1243                Opens a popup window that allows you to select
1244                users to share the items to. In the popup window, mark
1245                one or more users and click on the &gbOk;
1246                button. Unless you are an administrator, the popup window
1247                will only list users that are members of at least one of the
1248                groups where you also are a member. It will not list users that
1249                already have access to the items.
1250                </para>
1251              </listitem>
1252            </varlistentry>
1253
1254            <varlistentry>
1255              <term><guibutton>Add groups</guibutton></term>
1256              <listitem>
1257                <para>
1258                Opens a popup window that allows you to select
1259                groups to share the items to. In the popup window, mark
1260                one or more groups and click on the &gbOk;
1261                button. Unless you are an administrator, the popup window
1262                will only list groups where you are a member. It will not list
1263                groups that already have access to the items.
1264                </para>
1265              </listitem>
1266            </varlistentry>
1267           
1268            <varlistentry>
1269              <term><guibutton>Add projects</guibutton></term>
1270              <listitem>
1271                <para>
1272                Opens a popup window that allows you to select
1273                projects to share the items to. In the popup window, mark
1274                one or more projects and click on the &gbOk;
1275                button. Unless you are an administrator, the popup window
1276                will only list projects where you are a member. It will not list
1277                projects that already have access to the items.
1278                </para>
1279              </listitem>
1280            </varlistentry>
1281
1282            <varlistentry>
1283              <term>&gbRemove;</term>
1284              <listitem>
1285                <para>
1286                Click on this button to revoke access permissions from
1287                the selected users, groups and projects.
1288                </para>
1289              </listitem>   
1290            </varlistentry>
1291          </variablelist>
1292       
1293          <para>
1294            Use the &gbSave; button to save your
1295            changes or the &gbCancel; button to
1296            close the popup without saving.
1297          </para>
1298        </helptext>
1299
1300      </sect2>
1301
1302      <sect2 id="webclient.items.takeownership">
1303        <title>Take ownership of items</title>
1304        <para>
1305          Sometime it may be necessary to change the owner of an item.
1306          As an user you cannot give the ownership of your items to another
1307          user. It is instead the other user that must take the ownership
1308          of your items. For this to work, you must first give the other user
1309          permission to do so. That it, you must share your items with
1310          <guilabel>Take ownership</guilabel> permission to other user.
1311          See <xref linkend="webclient.items.share" />.
1312        </para>
1313       
1314        <para>
1315          When the items have been shared, the other user has to go to the
1316          list view (or the single-item view), mark the checkboxes for
1317          the items, and click in the <guibutton>Take ownership</guibutton>
1318          button. A warning message about not being able to undo the action
1319          is displayed. Click on &gbOk; to continue or
1320          &gbCancel; to abort.
1321        </para>
1322       
1323        <note>
1324          <para>
1325          The original owner may not have access permissions to the items
1326          any longer. If that is desired, the new owner must share the items
1327          to the original owner.
1328          </para>
1329        </note>
1330       
1331      </sect2>
1332     
1333      <sect2 id="webclient.items.export">
1334        <title>Export items</title>
1335        <para>
1336          This has a chapter of it's own. See <xref linkend="import_export_data.export"/>.
1337        </para>
1338      </sect2>
1339
1340    </sect1>
1341   
1342    <sect1 id="webclient.itemlist">
1343      <title>Listing items</title>
1344     
1345      <para>
1346        All pages that lists items are very similar in their appearance and
1347        functionality. In this section we will describe the things that are
1348        common for most (if not all) list pages.
1349      </para>
1350     
1351      <para>
1352        Use the menu to open a page listing items. Most list pages can only list one type of
1353        items. For example: use the
1354        <menuchoice>
1355          <guimenu>View</guimenu>
1356          <guimenuitem>Samples</guimenuitem>
1357        </menuchoice>
1358        menu to list samples and the
1359        <menuchoice>
1360          <guimenu>View</guimenu>
1361          <guimenuitem>Experiments</guimenuitem>
1362        </menuchoice>
1363        menu to list experiments.
1364      </para>
1365
1366      <tip>
1367        An example of a list page that can list
1368        items of several types is found by going to
1369        <menuchoice>
1370          <guimenu>View</guimenu>
1371          <guimenuitem>All items</guimenuitem>
1372        </menuchoice>.
1373        This page lists all items that you are the owner of. It has a few limitations:
1374       
1375        <itemizedlist>
1376          <listitem>
1377            <para>
1378              It support only a limited set of columns (type, name and description)
1379              since these are the only properties that are common
1380              among all items.
1381            </para>
1382          </listitem>
1383         
1384          <listitem>
1385            <para>
1386              The list cannot be filtered (except by item type)
1387              or sorted. This is due to a limitation in the query system
1388              used to generate the list.
1389            </para>
1390          </listitem>
1391        </itemizedlist>
1392       
1393        <para>
1394          There are also several similarities:
1395        </para>
1396       
1397        <itemizedlist>
1398          <listitem>
1399            <para>
1400              It supports all of the regular multi-item
1401              operations such as delete, restore, share
1402              and take ownership.
1403            </para>
1404          </listitem>
1405         
1406          <listitem>
1407            <para>
1408              Clicking on the name of the item will take you to the
1409              single-item view of that item. Holding down <keycap>CTRL</keycap>,
1410              <keycap>ALT</keycap> or <keycap>SHIFT</keycap> while clicking,
1411              will open the edit popup.
1412            </para>
1413          </listitem>
1414        </itemizedlist>       
1415       
1416      </tip>
1417     
1418      <figure id="webclient.figures.listpage">
1419        <title>A typical list page</title>
1420        <screenshot>
1421          <mediaobject>
1422            <imageobject><imagedata fileref="figures/listpage.png" format="PNG"
1423              scalefit="1" width="100%" /></imageobject>
1424          </mediaobject>
1425        </screenshot>
1426      </figure>
1427     
1428      <para>
1429        The typical list page contains the following important
1430        elements:
1431      </para>
1432
1433      <variablelist>
1434        <varlistentry>
1435          <term><interface>1. Toolbar</interface></term>
1436          <listitem>
1437            <para>
1438            A toolbar with buttons for various actions such as
1439            &gbNew; for creating a new item,
1440            &gbDelete; for deleting items and
1441            <guibutton>Columns&hellip;</guibutton> for configuring columns.
1442            Depending on the permissions of the logged in user
1443            some buttons may be disabled (greyed out) or not shown at all.
1444            </para>
1445          </listitem>
1446        </varlistentry>
1447       
1448        <varlistentry>
1449          <term><interface>2. Navigation bar</interface></term>
1450          <listitem>
1451            <para>
1452            If there are many items the list will be divided into
1453            pages, each one showing a limited number of items.
1454            The navigation bar allows you to
1455            move to other pages and specify how many items each page
1456            should display. The navigation bar is repeated at the
1457            bottom of the list so you do not have to scroll back to the
1458            top of a long list just to get to another page.
1459            </para>
1460          </listitem>
1461        </varlistentry>
1462       
1463        <varlistentry>
1464          <term><interface>3. List of presets</interface></term>
1465          <listitem>
1466            <para>
1467            A list with preconfigured settings which allows you to
1468            quickly switch between different layouts (sort order, visible
1469            columns, filter settings, etc).
1470            </para>
1471          </listitem>
1472        </varlistentry>
1473       
1474        <varlistentry>
1475          <term><interface>4. Column headers</interface></term>
1476          <listitem>
1477            <para>
1478            The columns headers can be used for selecting sort order.
1479            </para>
1480          </listitem>
1481        </varlistentry>
1482       
1483        <varlistentry>
1484          <term><interface>5. Filter bar</interface></term>
1485          <listitem>
1486            <para>
1487            The filter bar allows you to search for items.
1488            </para>
1489          </listitem>
1490        </varlistentry>
1491       
1492      </variablelist>
1493     
1494     
1495      <sect2 id="webclient.itemlist.order">
1496        <title>Ordering the list</title>
1497       
1498        <para>
1499          Most lists are by default sorted by the name of the item. This can
1500          be changed by clicking on the column header of another column.
1501          If you click on the same column twice the sort order is reversed.
1502          A downwards or upwards pointing arrow is displayed next to the
1503          column header in the column that is currently used for sorting.
1504          Column headers that are black cannot be used for sorting.
1505        </para>
1506       
1507        <para>
1508          It is possible to use more than one column for sorting. Press
1509          and hold one of the <keycap>CTRL</keycap>,
1510          <keycap>ALT</keycap> or <keycap>SHIFT</keycap> keys while clicking
1511          on another column header. The original sorting is kept and the new
1512          column is used for sub-sorting the list. The procedure can be
1513          repeated with more columns if you need to sort on three or more
1514          columns. To revert to sort by only one column again click a
1515          column header without holding down any key.
1516        </para> 
1517      </sect2>
1518   
1519      <sect2 id="webclient.itemlist.filter">
1520        <title>Filtering the list</title>
1521       
1522        <para>
1523          If the list contains many items you may need to use a filter to be
1524          able to find the item you are looking for. The input boxes on the
1525          line below the column headers are used for filtering. Most columns
1526          are filtered using a free-text input box, but some columns that can
1527          only take a few distinct values use a selection list or radio buttons
1528          instead. The selection list and radio buttons are very simple to use.
1529          Just select the alternative that you want to filter on. The list
1530          will be automatically updated when the selection has been made.
1531        </para>
1532       
1533        <para>
1534          The free-text filter is a bit more complex. By default, an exact match is
1535          required, use % as a wildcard that matches any character.
1536          For example, the filter <informalexample>Experiment A</informalexample> 
1537          only matches the same exact string, but the filter
1538          <informalexample>Exp%</informalexample> matches
1539          <informalexample>Experiment A, Experiment B, etc.</informalexample>
1540        </para>
1541        <para>
1542          If you want to filter on several values at the same time, separate the
1543          values in the filter input box with the <quote>|</quote> character.
1544          For example, a filter text like <informalexample>Experiment A|C%</informalexample>
1545          matches both <quote>Experiment A</quote> and values 
1546          that begin with <quote>C</quote>.
1547        </para>       
1548        <para>
1549          You can also use operators to find items which has a value that
1550          is greater than, less than or not equal to a specific value. This is
1551          mostly useful on numeric or date columns but also works on text
1552          columns. The operator must be entered first in the
1553          free-text box, for example
1554          <informalexample>&lt;=10</informalexample>
1555          to find items which has a value less than or equal to 10.   
1556          Here is a list of the supported operators:
1557        </para>
1558       
1559        <variablelist id="webclient.itemlist.filter.operators">
1560          <title>List of operators supported by the free-text filter</title>
1561          <varlistentry>
1562            <term><keycap>&lt;</keycap></term>
1563            <listitem><simpara>Less than</simpara></listitem>
1564          </varlistentry>
1565          <varlistentry>
1566            <term><keycap>&lt;=</keycap></term>
1567            <listitem><simpara>Less than or equal to</simpara></listitem>
1568          </varlistentry>
1569          <varlistentry>
1570            <term><keycap>&gt;</keycap></term>
1571            <listitem><simpara>Greater than</simpara></listitem>
1572          </varlistentry>
1573          <varlistentry>
1574            <term><keycap>&gt;=</keycap></term>
1575            <listitem><simpara>Greater than or equal to</simpara></listitem>
1576          </varlistentry>
1577          <varlistentry>
1578            <term><keycap>=</keycap></term>
1579            <listitem>
1580              <simpara>
1581                Equal to (useful to find items with a null value). Supports
1582                filtering on more then one value.
1583              </simpara>
1584            </listitem>
1585          </varlistentry>
1586          <varlistentry>
1587            <term><keycap>&lt;&gt;</keycap></term>
1588            <term><keycap>!=</keycap></term>
1589            <listitem>
1590              <simpara>
1591                Not equal to (useful to find items with a non-null value). Supports
1592                filtering on more then one value.
1593              </simpara>
1594            </listitem>
1595          </varlistentry>
1596          <varlistentry>
1597            <term><keycap>==</keycap></term>
1598            <listitem>
1599              <simpara>
1600                Same as <keycap>=</keycap> but this will ignore <quote>|</quote> as a value separator.
1601              </simpara>
1602            </listitem>
1603          </varlistentry>
1604        </variablelist>
1605      </sect2>
1606     
1607      <sect2 id="webclient.itemlist.columns">
1608        <title>Configuring which columns to show</title>
1609       
1610        <para>
1611          Most lists show only a small subset of the columns it
1612          is capable of showing. Use the
1613          <guibutton>Columns&hellip;</guibutton> button to open
1614          a dialog that allows you to select which columns to show
1615          and the order in which they are shown.
1616        </para>
1617       
1618        <figure id="webclient.figures.configure_columns">
1619          <title>Configuring which columns to show</title>
1620          <screenshot>
1621          <mediaobject>
1622            <imageobject>
1623              <imagedata fileref="figures/configure_columns.png" format="PNG"/>
1624            </imageobject>
1625          </mediaobject>
1626          </screenshot>
1627        </figure>
1628       
1629        <helptext external_id="columns.configure" 
1630          title="Set column order and visiblity">
1631       
1632        <variablelist>
1633        <varlistentry>
1634          <term><guilabel>Visible columns</guilabel></term>
1635          <listitem>
1636            <para>
1637              Shows the columns that are currently visible.
1638              Use the up/down arrow buttons to arrange the order of the
1639              visible columns. The topmost column is shown to the left.
1640              Use the right arrow button to move columns from this list
1641              to the hidden columns list. Columns marked with an <guilabel>×</guilabel> 
1642              are required
1643              and cannot be hidden. In most lists the <guilabel>Name</guilabel> column
1644              is the only column that is required.
1645            </para>
1646          </listitem>
1647        </varlistentry>
1648         
1649        <varlistentry>
1650          <term><guilabel>Hidden columns</guilabel></term>
1651          <listitem>
1652            <para>
1653              Shows columns that are not currently visible in the
1654              list. Use the left arrow button to move columns from
1655              this list to the visible columns list.
1656            </para>
1657          </listitem>
1658        </varlistentry>
1659       
1660       
1661        <varlistentry>
1662          <term><guilabel>Presets</guilabel></term>
1663          <listitem>
1664            <para>
1665              A dropdown list that allows you to
1666              select a set of preconfigured columns. You may also create
1667              your own preset if you often need to switch between different
1668              configurations. The list of presets is the same as the one
1669              described <link linkend="webclient.itemlist.presets">below</link>,
1670              but if used from this dialog the presets does not affect filters,
1671              sort order, etc.
1672            </para>
1673          </listitem>
1674        </varlistentry>
1675        </variablelist>
1676       
1677          <para>
1678            Use the &gbSave; button to apply your
1679            changes or the &gbCancel; button to
1680            close the popup without saving.
1681          </para>
1682
1683        </helptext>
1684
1685      </sect2>
1686     
1687      <sect2 id="webclient.itemlist.presets">
1688        <title>Presets</title>
1689       
1690        <para>
1691          The <guilabel>view / presets</guilabel> dropdown has three
1692          main functions:
1693        </para>
1694       
1695        <figure id="webclient.figures.viewpresets">
1696          <title>The view / presets dropdown</title>
1697          <screenshot>
1698            <mediaobject>
1699              <imageobject><imagedata fileref="figures/view_presets.png" format="PNG" 
1700                /></imageobject>
1701            </mediaobject>
1702          </screenshot>
1703        </figure>
1704        <orderedlist>
1705          <listitem>
1706            <para>
1707              Switch between different configuration presets.
1708              The top of the dropdown contains user-defined presets (<guilabel>Saved preset #1</guilabel> and
1709              <guilabel>#2</guilabel>) and a few preconfigured presets.
1710              The user-defined presets are used to store a complete table configuration,
1711              including:
1712            </para>
1713           
1714            <itemizedlist>
1715              <listitem><simpara>Which columns are visible and their order</simpara></listitem>
1716              <listitem><simpara>The column (or columns) used for sorting</simpara></listitem>
1717              <listitem><simpara>Filter settings</simpara></listitem>
1718              <listitem><simpara>The number of items per page and the current page</simpara></listitem>
1719            </itemizedlist>
1720           
1721            <para>             
1722              The preconfigured presets only affects
1723              the visible columns as follows:
1724            </para>
1725           
1726            <itemizedlist>
1727              <listitem>
1728                <para><guilabel>All columns</guilabel> - Show all columns.</para>
1729              </listitem>
1730              <listitem>
1731                <para><guilabel>Required columns</guilabel> - Show only the required columns.
1732                  Usually only the <guilabel>Name</guilabel> column is required.</para>
1733              </listitem>
1734              <listitem>
1735                <para><guilabel>Default columns</guilabel> - Show the default set of columns.</para>
1736              </listitem>
1737              <listitem>
1738                <para><guilabel>Other&hellip;</guilabel> -
1739                  Open the configure columns dialog box, described in
1740                  <xref linkend="webclient.itemlist.columns"/>.</para>
1741              </listitem>
1742            </itemizedlist>
1743           
1744          </listitem>
1745         
1746          <listitem>
1747            <para>
1748              Filter items by the removed status and the access
1749              permissions to an item.
1750            </para>
1751           
1752            <itemizedlist>
1753              <listitem>
1754                <para><guilabel>Removed</guilabel> - If checked, items that have been
1755                moved to the trashcan are shown, otherwise they are hidden.</para>
1756              </listitem>
1757              <listitem>
1758                <para><guilabel>Owned by me</guilabel> - If checked, items that the logged in user
1759                owns are displayed, otherwise they are hidden.</para>
1760              </listitem>
1761              <listitem>
1762                <para><guilabel>Shared to me</guilabel> - If checked, items that are owned
1763                by other users but shared to the logged in user are displayed, otherwise
1764                they are hidden.</para>
1765              </listitem>
1766              <listitem>
1767                <para><guilabel>In current project</guilabel> -
1768                  If checked, items that are linked with the current project are displayed,
1769                  otherwise they are hidden. It does not matter if the logged in user is the
1770                  owner or not. This option is only available if a project is active.
1771                </para>
1772              </listitem>
1773              <listitem>
1774                <para><guilabel>Owned by others</guilabel> -
1775                  This option is only available to administrators and will display
1776                  items that are owned by other users.
1777                </para>
1778              </listitem>
1779            </itemizedlist>
1780           
1781            <para>
1782              The default is to display item that the current user
1783              owns and, if a project is active, items in that project.
1784            </para>
1785           
1786          </listitem>
1787
1788          <listitem>
1789            <para>
1790              Administrate the presets
1791            </para>
1792            <itemizedlist>
1793              <listitem>
1794                <para><guilabel>Clear filter</guilabel> - Clears
1795                all filters.</para>
1796              </listitem>
1797             
1798              <listitem>
1799                <para><guilabel>Save as&hellip;</guilabel> - Save the
1800                current configuration as a preset.</para>
1801              </listitem>
1802
1803              <listitem>
1804                <para><guilabel>Manage&hellip;</guilabel> - Opens a dialog
1805                where you can remove saved presets. You can also load
1806                saved presets from the dialog, but it is quicker to just
1807                use the dropdown list for this.</para>
1808              </listitem>
1809            </itemizedlist>
1810          </listitem>
1811        </orderedlist>
1812       
1813        <sect3 id="webclient.itemlist.presets.saveas">
1814          <title>Save a preset</title>
1815         
1816          <para>
1817            If you select the <guilabel>Save as&hellip;</guilabel>
1818            option from the <guilabel>view / presets</guilabel> dropdown
1819            the <guilabel>Save preset as</guilabel> dialog is opened.
1820          </para>
1821         
1822          <figure id="webclient.figures.savepresetas">
1823            <title>Save preset as</title>
1824            <screenshot>
1825              <mediaobject>
1826                <imageobject><imagedata fileref="figures/save_preset.png" format="PNG" /></imageobject>
1827              </mediaobject>
1828            </screenshot>
1829          </figure>
1830         
1831          <helptext external_id="contexts.saveas" title="Save preset as">
1832         
1833          <variablelist>
1834          <varlistentry>
1835            <term><guilabel>For item</guilabel></term>
1836            <listitem>
1837              <para>
1838              The type of item the preset is saved for.
1839              </para>
1840            </listitem>
1841          </varlistentry>
1842          <varlistentry>
1843            <term><guilabel >Name</guilabel></term>
1844            <listitem>
1845              <para>
1846              The name of the preset. The name must be unique.
1847              </para>
1848            </listitem>
1849          </varlistentry>
1850          <varlistentry>
1851            <term><guilabel>Overwrite existing</guilabel></term>
1852            <listitem>
1853              <para>
1854              If a preset with the same name already exists, it is
1855              overwritten if this checkbox is checked.
1856              </para>
1857            </listitem>
1858          </varlistentry>
1859          <varlistentry>
1860            <term><guilabel>Public</guilabel></term>
1861            <listitem>
1862              <para>
1863              This options is only available for users
1864              which has the <emphasis>SHARE_TO_EVERYONE</emphasis>
1865              permission. If checked the preset is visible to
1866              all users.
1867              </para>
1868            </listitem>
1869          </varlistentry>
1870          </variablelist>
1871         
1872          <para>
1873            Use the &gbOk; button to save the preset
1874            or the &gbCancel; button to
1875            close the popup without saving.
1876          </para>
1877         
1878         
1879          </helptext>
1880         
1881        </sect3>
1882       
1883        <sect3 id="webclient.itemlist.presets.manage">
1884          <title>Manage presets</title>
1885         
1886          <para>
1887            If you select the <guilabel>Manage&hellip;</guilabel>
1888            option from the <guilabel>view / presets</guilabel> dropdown
1889            the <guilabel>Manage presets</guilabel> dialog is opened.
1890          </para>
1891         
1892          <figure id="webclient.figures.managepresets">
1893            <title>Manage presets</title>
1894            <screenshot>
1895              <mediaobject>
1896                <imageobject><imagedata fileref="figures/manage_presets.png" format="PNG" /></imageobject>
1897              </mediaobject>
1898            </screenshot>
1899          </figure>
1900         
1901          <helptext external_id="contexts.manage" title="Manage presets">
1902         
1903          <para>
1904            From this dialog you can delete or load presets.
1905          </para>
1906         
1907          <para>
1908            To delete presets, first mark the checkbox in front of
1909            each preset you want to delete. Then, click on the
1910            <guibutton>Delete&hellip;</guibutton> button. You will get
1911            a warning about that the action cannot be undone. Unlike other
1912            items, the presets are not moved to the trashcan. Click on
1913            &gbOk; to delete the preset.
1914          </para>
1915         
1916          <note>
1917            <title>Edit a preset</title>
1918            <para>
1919            It is not possible to edit a preset directly. To change an
1920            existing preset you must:
1921           
1922            <orderedlist>
1923            <listitem><simpara>Load the preset.</simpara></listitem>
1924            <listitem><simpara>Use the interface to change column settings, filter,
1925              sort order, etc.</simpara></listitem>
1926            <listitem><simpara>Save the preset with the same name.</simpara></listitem>
1927            </orderedlist>
1928            </para>
1929          </note>
1930         
1931          <para>
1932            Use the &gbClose; button to
1933            close the popup.
1934          </para>
1935         
1936         
1937          </helptext>
1938         
1939        </sect3>
1940       
1941      </sect2>
1942    </sect1>
1943
1944
1945    <sect1 id="webclient.trashcan">
1946      <title>Trashcan</title>
1947      <para>
1948        All items that have been deleted, and are owned by you, are
1949        listed in your trashcan. This list page is accessed with
1950        <menuchoice>
1951          <guimenu>View</guimenu>
1952          <guimenuitem>Trashcan</guimenuitem>
1953        </menuchoice>
1954        and it differs a bit from the other common list pages. The
1955        most significant difference is that the trashcan page can
1956        contain more then one item type, actually all removable item
1957        types in BASE can be listed in the trascan. Items that neither
1958        can be removed or deleted, <emphasis>i.e.,</emphasis> items
1959        like sessions, nor clients' help texts since these are deleted
1960        from the database immediately in list/item view will be shown
1961        in the trashcan page.
1962      </para>
1963      <warning>
1964        <para>
1965          Some item types do not have any owner and these are listed
1966          in the trashcans for everyone with delete permission on that
1967          specific item type.
1968        </para>
1969      </warning>
1970
1971      <para>
1972        Things that the trashcan page have in common with other list
1973        pages are the possibility to restore and view/edit items, see
1974        <xref linkend="webclient.items.restore" /> and
1975        <xref linkend="webclient.items.edit" /> . If an item is
1976        restored, it will of course disappear from the trashcan.
1977      </para>
1978
1979      <sect2 id="webclient.trashcan.deleteitem">
1980        <title>Delete items permanently</title>
1981        <para>
1982          Items can be permanently deleted from BASE only if they are
1983          not used by other items.  Items that are used have the icon
1984          <inlinemediaobject>
1985            <imageobject>
1986              <imagedata fileref="figures/isused.gif" format="GIF" />
1987            </imageobject>
1988          </inlinemediaobject>
1989          in the first column and by clicking on it you can get more
1990          information about the dependencies, see
1991          <xref linkend="webclient.trashcan.viewdependencies" /> .
1992          <note>
1993            <simpara>
1994              This view is NOT the same view page as when clicking on
1995              the item's name, which brings you to the item's view
1996              page.
1997            </simpara>
1998          </note>
1999        </para>
2000        <para>
2001          To delete one or several items permanently from the trashcan
2002          you first have to select them and then to click on the
2003          &gbDelete; button. Press then on either &gbOk; (completes
2004          the deletion) or &gbCancel; (no items will be deleted) in
2005          the dialog window that appears.
2006        </para>
2007
2008        <sect3 id="webclient.trashcan.deleteitem.empty">
2009          <title>Empty trashcan</title>
2010          <para>
2011            If all items in the trashcan should be deleted permanently
2012            the <guibutton>Empty trash</guibutton> button can be
2013            used. This function will remove all items that are listed
2014            in your trashcan, except those items which other items,
2015            not marked for deletion or cannot be deleted, are
2016            dependent on.
2017          </para>
2018        </sect3>
2019      </sect2>
2020
2021      <sect2 id="webclient.trashcan.viewdependencies">
2022        <title>View dependencies of a trashed item</title>
2023        <helptext external_id="trash.view.properties" title="Properties for a trashed item">
2024          <para>
2025            This view can only be accessed from trashed items that are
2026            linked together with other items. Beside the item's
2027            <guilabel>item type</guilabel>, <guilabel>name</guilabel>,
2028            and <guilabel>description</guilabel> there is a list at
2029            the bottom of the view page with those items that are
2030            using the current item in some way.
2031          </para>
2032        </helptext>
2033        <para>
2034          <nohelp>
2035            <figure id="webclient.trashcan.figures.viewtrasheditem">
2036              <title>Item view of a trashed item.</title>
2037              <screenshot>
2038                <mediaobject>
2039                  <imageobject>
2040                    <imagedata fileref="figures/trashview.png" format="PNG" 
2041                               scalefit="1" width="100%" />
2042                  </imageobject>
2043                </mediaobject>
2044              </screenshot>
2045            </figure>
2046          </nohelp>
2047          <orderedlist>
2048            <listitem>
2049              <para>
2050                This icon indicates that the item cannot be deleted
2051                permanently cause of some dependencies, see
2052                #<xref linkend="webclient.trashcan.lists.dependentitem3" />.
2053              </para>
2054            </listitem>
2055            <listitem>
2056              <para>Common properties for all removable items.</para>
2057            </listitem>
2058            <listitem id="webclient.trashcan.lists.dependentitem3">
2059              <para>A list of other items that are using the current item.</para>
2060            </listitem>
2061          </orderedlist>
2062        </para>
2063      </sect2>
2064    </sect1>
2065
2066</chapter>
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