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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 3675 2007-08-16 14:16:43Z jari $
7
8  Copyright (C) 2007 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            <interface>
204            <inlinemediaobject>
205            <imageobject><imagedata fileref="figures/refresh.gif" format="GIF" align="left"
206              /></imageobject>
207            </inlinemediaobject>
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            <interface>
231            <inlinemediaobject>
232            <imageobject><imagedata fileref="figures/recent.png" format="PNG" align="left"/></imageobject>
233            </inlinemediaobject>
234            Recent items
235            </interface>
236          </term>
237          <listitem>
238            <para>
239            Shortcut to the most recently viewed items. The number of items are
240            configurable and you can also make some item types
241            <emphasis>sticky</emphasis>. This will for example keep the shortcut
242            to the last experiment even if you have viewed lots of other items
243            more recently.
244            See <xref linkend="webclient.configuration.preferences.mostrecent"/>
245            for configuration information.
246            </para>
247          </listitem>
248        </varlistentry>
249       
250        <varlistentry>
251          <term>
252            <interface>
253            <inlinemediaobject>
254            <imageobject><imagedata fileref="figures/project.gif" format="GIF" align="left"/></imageobject>
255            </inlinemediaobject>
256            Projects
257            </interface>
258          </term>
259          <listitem>
260            <para>
261            A list of all projects you are a member of. Selecting a project in the
262            list will make that project the active project.
263            </para>
264          </listitem>
265        </varlistentry>
266       
267        <varlistentry>
268          <term>
269            <interface>
270            <inlinemediaobject>
271            <imageobject><imagedata fileref="figures/user.png" format="PNG" align="left"/></imageobject>
272            </inlinemediaobject>
273            Logged in user
274            </interface>
275          </term>
276          <listitem>
277            <para>
278            Displays the name of the currently logged in user and allows
279            you to quickly logout and switch to another user.
280            </para>
281          </listitem>
282        </varlistentry>
283       
284      </variablelist>
285       
286      </sect2>
287     
288      <sect2 id="webclient.intro.help">
289        <title>Getting help</title>
290        <para>
291          Besides reading this document there are more ways to get help:
292        </para>
293        <variablelist>
294          <varlistentry>
295            <term>
296              Online context-sensitive help
297            </term>
298            <listitem>
299              <para>
300              Whenever you find a small help icon (
301              <inlinemediaobject>
302              <imageobject><imagedata fileref="figures/help.gif" format="GIF" /></imageobject>
303              </inlinemediaobject>
304              ) or button you may
305              click it to get help about the part of the page
306              you are currently viewing. The icon is located in the title
307              bar in most popup dialog windows and in the toolbar in most
308              other pages.
309              </para>
310            </listitem>
311          </varlistentry>
312
313          <varlistentry>
314            <term>
315              Using the <menuchoice><guimenu>Help</guimenu></menuchoice> menu
316            </term>
317            <listitem>
318              <para>
319              The <menuchoice><guimenu>Help</guimenu></menuchoice> menu
320              contains links for getting online help. These links
321              may be configured by a server administrator, so they may be
322              different from server to server. By default links for reporting
323              a bug and accessing this document are installed.
324              </para>
325            </listitem>
326          </varlistentry>
327
328          <varlistentry>
329            <term>
330              Mailing lists and other resources
331            </term>
332            <listitem>
333              <para>
334              See <xref linkend="resources" />.
335              </para>
336            </listitem>
337          </varlistentry>
338
339        </variablelist>
340       
341      </sect2>
342   
343    </sect1>
344   
345    <sect1 id="webclient.configuration">
346      <title>Configuring your account</title>
347     
348      <sect2 id="webclient.configuration.contact">
349        <title>Contact information</title>
350       
351        <para>
352          Use the <menuchoice><guimenu>File</guimenu>
353          <guimenuitem>Contact information</guimenuitem></menuchoice>
354          menu to bring up the user information dialog.
355        </para>
356       
357        <helptext external_id="userpreferences.contact" title="Contact information">
358       
359          <para>
360          This dialog has three tabs, <guilabel>Contact information</guilabel>
361          (selected), <guilabel>Password</guilabel> and <guilabel>Other information</guilabel>.
362          The logged in user can update the following contact information
363          details.
364          </para>
365       
366          <note>
367            <title>Multi-user accounts</title>
368            <para>
369              If you are using a multi-user account, for example a demo-account, you
370              do not have permission to change the contact information.
371            </para>
372          </note>
373       
374          <variablelist>
375            <varlistentry>
376              <term>
377                <guilabel>Full name</guilabel>
378              </term>
379              <listitem>
380                <para>
381                Your full name. You are not allowed to change this. If
382                it is not correct, contact an administrator to do it for
383                you.
384                </para>
385              </listitem>
386            </varlistentry>
387            <varlistentry>
388              <term>
389                <guilabel>Email</guilabel>
390              </term>
391              <listitem>
392                <para>
393                Your email address (optional).
394                </para>
395              </listitem>
396            </varlistentry>
397            <varlistentry>
398              <term>
399                <guilabel>Organisation</guilabel>
400              </term>
401              <listitem>
402                <para>
403                The name of the organisation you work for or represent (optional).
404                </para>
405              </listitem>
406            </varlistentry>
407            <varlistentry>
408              <term>
409                <guilabel>Address</guilabel>
410              </term>
411              <listitem>
412                <para>
413                Your postal address as it should be printed on letters to you
414                (optional).
415                </para>
416              </listitem>
417            </varlistentry>
418            <varlistentry>
419              <term>
420                <guilabel>Phone</guilabel>
421              </term>
422              <listitem>
423                <para>
424                Your phone number (optional). You may enter multiple phone numbers,
425                for example your work phone number and a mobile number.
426                </para>
427              </listitem>
428            </varlistentry>
429            <varlistentry>
430              <term>
431                <guilabel>Fax</guilabel>
432              </term>
433              <listitem>
434                <para>
435                Your fax number (optional).
436                </para>
437              </listitem>
438            </varlistentry>
439            <varlistentry>
440              <term>
441                <guilabel>Url</guilabel>
442              </term>
443              <listitem>
444                <para>
445                An URL to your home page or your organisation's home page (optional).
446                </para>
447              </listitem>
448            </varlistentry>
449          </variablelist>
450         
451          <para>
452            Press &gbSave; to save the changes or
453            &gbCancel; to abort.
454          </para>
455         
456          <seeother>
457            <other external_id="userpreferences.password">Change password</other>
458            <other external_id="userpreferences.other">Other information</other>
459          </seeother>
460        </helptext>
461       
462      </sect2>
463     
464      <sect2 id="webclient.configuration.other">
465        <title>Other information</title>
466        <para>
467          Use the
468          <menuchoice>
469            <guimenu>File</guimenu>
470            <guimenuitem>Other information&hellip;</guimenuitem>
471          </menuchoice>
472          menu to bring up the other information dialog.
473        </para>
474        <helptext external_id="userpreferences.other" title="Other information">
475          <para>
476            This dialog has three tabs,
477            <guilabel>Contact information</guilabel>
478            ,
479            <guilabel>Password</guilabel>
480            and
481            <guilabel>Other information</guilabel>
482            (selected) .
483          </para>
484          <para>
485            The look of the
486            <guilabel>Other information</guilabel>
487            tab can differe abit between different servers, depending on what settings
488            the server is installed with. There are three inputs in a fresh BASE2
489            installation but it is only the
490            <guilabel>Description</guilabel>
491            textarea that is static, the others can be removed or more fields can be
492            added (managed by the server administrator). The three fields, included in a
493            the BASE2 installation, are
494            <variablelist>
495              <varlistentry>
496                <term>
497                  <guilabel>Mobile</guilabel>
498                </term>
499                <listitem>
500                  <para>Your mobile number(Optional).</para>
501                </listitem>
502              </varlistentry>
503              <varlistentry>
504                <term>
505                  <guilabel>Skype</guilabel>
506                </term>
507                <listitem>
508                  <para>Your skype contact information(Optional).</para>
509                </listitem>
510              </varlistentry>
511              <varlistentry>
512                <term>
513                  <guilabel>Description</guilabel>
514                </term>
515                <listitem>
516                  <para>
517                    Text area where you can put useful information that couldn't
518                    be stored anywhere else(Optional).
519                  </para>
520                </listitem>
521              </varlistentry>
522            </variablelist>
523          </para>
524          <para>Press &gbSave; to save the changes or &gbCancel; to abort.</para>
525          <seeother>
526            <other external_id="userpreferences.contact">Contact information</other>
527            <other external_id="userpreferences.password">Change password</other>
528          </seeother>
529        </helptext>
530      </sect2>
531
532      <sect2 id="webclient.configuration.password">
533        <title>Changing password</title>
534       
535        <para>
536          Use the <menuchoice><guimenu>File</guimenu>
537          <guimenuitem>Change password</guimenuitem></menuchoice>
538          menu to bring up the change password dialog.
539        </para>
540       
541        <helptext external_id="userpreferences.password" title="Change password">
542
543          <para>
544          This dialog has three tabs, <guilabel>Contact information</guilabel>,
545          <guilabel>Password</guilabel> (selected) and <guilabel>Other information</guilabel>.
546          </para>
547
548          <variablelist>
549            <varlistentry>
550              <term>
551                <guilabel>New password</guilabel>
552              </term>
553              <listitem>
554                <para>
555                Enter the new password.
556                </para>
557              </listitem>
558            </varlistentry>
559            <varlistentry>
560              <term>
561                <guilabel>Retype password</guilabel>
562              </term>
563              <listitem>
564                <para>
565                Retype the same password. You must do this to
566                avoid spelling mistakes.
567                </para>
568              </listitem>
569            </varlistentry>
570          </variablelist>
571
572          <note>
573            <title>Multi-user accounts</title>
574            <para>
575              If you are using a multi-user account, for example a demo-account, you
576              do not have permission to change the password.
577            </para>
578          </note>
579       
580          <note>
581            <title>Empty passwords</title>
582            <para>
583              If you leave both fields empty the password will not be changed. It
584              is not possible to have an empty password.
585            </para>
586          </note>
587         
588          <seeother>
589            <other external_id="userpreferences.contact">Contact information</other>
590            <other external_id="userpreferences.other">Other information</other>
591          </seeother>
592         
593        </helptext>
594      </sect2>
595
596      <sect2 id="webclient.configuration.preferences">
597        <title>Preferences</title>
598       
599        <para>
600          Use the <menuchoice><guimenu>File</guimenu>
601          <guimenuitem>Preferences</guimenuitem></menuchoice>
602          menu to bring up the preferences dialog.
603          This dialog has three tabs, <guilabel>Appearance</guilabel>,
604          <guilabel>Plugins</guilabel> and <guilabel>Most recent</guilabel>.
605        </para>
606       
607        <sect3 id="webclient.configuration.preferences.appearance">
608          <title>The Appearance tab</title>
609         
610          <helptext external_id="userpreferences.appearance" title="Preferences - Appearance">
611         
612          <para>
613          This tab contains settings that affect the appearance of the
614          web client.
615          </para>
616         
617          <variablelist>
618            <varlistentry>
619              <term>
620                <guilabel>Font size</guilabel>
621              </term>
622              <listitem>
623                <para>
624                Select a basic font size. You can choose between
625                five sizes: extra small (XS), small (S), medium (M),
626                large (L) and extra large (XL). The default font size is
627                medium.
628                </para>
629              </listitem>
630            </varlistentry>
631            <varlistentry>
632              <term>
633                <guilabel>Scale factor</guilabel>
634              </term>
635              <listitem>
636                <para>
637                The scale factor affects the size of popup windows.
638                This setting exists because different browsers render
639                pages differently. If you often find that popup windows
640                are too small you can change this setting to make them
641                bigger.
642                </para>
643                <note>
644                  <para>
645                    The scale factor is automatically changed if the
646                    font size is changed.
647                  </para>
648                </note>
649              </listitem>
650            </varlistentry>
651            <varlistentry>
652              <term>
653                <guilabel>Toolbar</guilabel>
654              </term>
655              <listitem>
656                <para>
657                You may choose if the toolbar buttons should
658                have only images, only text or both images and text.
659                The default is that they have both images and text.
660                </para>
661              </listitem>
662            </varlistentry>
663            <varlistentry>
664              <term>
665                <guilabel>Ratio color range</guilabel>
666              </term>
667              <listitem>
668                <para>
669                Select three colors to use when displaying
670                data that is suitable for color coding, for
671                example the intensity ratio in two-color
672                experiments. The default setting is blue-black-yellow.
673                The list of presets contains other useful color combinations
674                (for example, the BASE 1 red-yellow-green) and the most
675                recently used color combinations.
676                </para>
677              </listitem>
678            </varlistentry>
679            <varlistentry>
680              <term>
681                <guilabel>Date format</guilabel>
682              </term>
683              <listitem>
684                <para>
685                A format string describing how dates should be displayed.
686                We support all formatting options supported by the Java
687                language. For more information see:
688                <ulink url="http://java.sun.com/j2se/1.5.0/docs/api/java/text/SimpleDateFormat.html">SimpleDateFormat documentation</ulink>
689                The most useful format patterns are:
690                </para>
691               
692                <itemizedlist>
693                  <listitem><simpara>yy: two-digit year</simpara></listitem>
694                  <listitem><simpara>yyyy: four-digit year</simpara></listitem>
695                  <listitem><simpara>MM: two-digit month</simpara></listitem>
696                  <listitem><simpara>MMM: month name (short)</simpara></listitem>
697                  <listitem><simpara>MMMM: month name (full)</simpara></listitem>
698                  <listitem><simpara>dd: two-digit day in month</simpara></listitem>
699                </itemizedlist>
700               
701                <para>
702                The list of presets contains the most commonly/recently
703                used date formats.
704                </para>
705               
706              </listitem>
707            </varlistentry>
708           
709            <varlistentry>
710              <term>
711                <guilabel>Date-time format</guilabel>
712              </term>
713              <listitem>
714                <para>
715                A format string describing how dates with times should be displayed.
716                We support all formatting options supported by the Java
717                language. For more information see:
718                <ulink url="http://java.sun.com/j2se/1.5.0/docs/api/java/text/SimpleDateFormat.html">SimpleDateFormat documentations</ulink>
719                The most useful time-format patterns are:
720                </para>
721               
722                <itemizedlist>
723                  <listitem><simpara>HH: two-digit hour (0-23)</simpara></listitem>
724                  <listitem><simpara>hh: two-digit hour (1-12)</simpara></listitem>
725                  <listitem><simpara>a: AM/PM marker</simpara></listitem>
726                  <listitem><simpara>mm: two-digit minute</simpara></listitem>
727                  <listitem><simpara>ss: two-digit second</simpara></listitem>
728                </itemizedlist>
729               
730              </listitem>
731            </varlistentry>
732           
733            <varlistentry>
734              <term>
735                <guilabel>Decimals</guilabel>
736              </term>
737              <listitem>
738                <para>
739                The number of decimals to display for numeric values.
740                The default is 2.
741                </para>
742              </listitem>
743            </varlistentry>
744           
745          </variablelist>
746       
747          </helptext>
748       
749        </sect3>
750       
751        <sect3 id="webclient.configuration.preferences.plugins">
752          <title>The Plugins tab</title>
753         
754          <helptext external_id="userpreferences.plugins" title="Preferences - Plugins">
755         
756          <para>
757            This tab contains settings that affect plug-in execution.
758          </para>
759         
760          <variablelist>
761            <varlistentry>
762              <term>
763                <guilabel>Messages</guilabel>
764              </term>
765              <listitem>
766                <para>
767                Mark the checkbox if you want to have a message sent
768                to you when a plug-in completes execution. This setting
769                can be overridden each time you start a plug-in.
770                </para>
771              </listitem>
772            </varlistentry>
773            <varlistentry>
774              <term>
775                <guilabel>Remove jobs</guilabel>
776              </term>
777              <listitem>
778                <para>
779                  This checkbox should be marked if you want the jobs, done by
780                  import or export plug-ins, to be marked as removed if they
781                  finished successfully. This setting can be overridden each time
782                  you start a plug-in.
783                </para>
784              </listitem>
785            </varlistentry>
786            <varlistentry>
787              <term>
788                <guilabel>Show warnings</guilabel>
789              </term>
790              <listitem>
791                <para>
792                  This checkbox should be marked if you want to show warning
793                  messages from plug-ins in the <guilabel>Select plug-in</guilabel>
794                  dialog. Warning-level messages usually originates from plug-ins
795                  that are unrelated to the current task and are only of interest to
796                  plug-in developers. Error messages that are related to the
797                  current task are always shown.
798                </para>
799              </listitem>
800            </varlistentry>
801          </variablelist>
802          </helptext>
803         
804        </sect3>
805       
806        <sect3 id="webclient.configuration.preferences.mostrecent">
807          <title>The Recent items tab</title>
808         
809          <helptext external_id="userpreferences.mostrecent" 
810            title="Preferences - Recent items">
811         
812          <para>
813            This tab contains settings that affect the <guilabel>Recent
814            items</guilabel> menu.
815          </para>
816         
817          <variablelist>
818          <varlistentry>
819            <term>
820              <guilabel>Recently viewed items</guilabel>
821            </term>
822            <listitem>
823              <para>
824              The number of recently <emphasis>viewed</emphasis> items to remember.
825              The default is to remember 6 items. The remembered items
826              will be displayed in the <guilabel>Recent items</guilabel>
827              menu in the menu bar.
828              </para>
829            </listitem>
830          </varlistentry>
831          <varlistentry>
832            <term>
833              <guilabel>Recently used items</guilabel>
834            </term>
835            <listitem>
836              <para>
837              The number of recently <emphasis>used</emphasis> items to remember.
838              The default is to remember 4 items. The remembered items will
839              be displayed in edit dialogs where they have been used before.
840              Each type of edit operation has it's own list of remembered items.
841              For example, there is one list that remembers the most recently used
842              protocols when creating a sample, and there is another list that
843              remembers the most recently used scanners when creating a scan.
844              </para>
845            </listitem>
846          </varlistentry>
847         
848          <varlistentry>
849            <term>
850              <guilabel>Load the names of all items</guilabel>
851            </term>
852            <listitem>
853              <para>
854              If checked, the names of the items will be loaded and
855              displayed in the menu, otherwise only the ID and type of item
856              is displayed.
857              </para>
858            </listitem>
859          </varlistentry>
860         
861          <varlistentry>
862            <term>
863              <guilabel>Sticky items</guilabel>
864            </term>
865            <listitem>
866              <para>
867              Always remember the last viewed item of the selected types.
868              For example, if you have selected <emphasis>Experiment</emphasis>
869              as a sticky item, the last viewed experiment will be remembered
870              even if you view hundreds of other items. Use the arrow buttons
871              to move item types between the lists and sort the sticky items list.
872              Sticky items will be displayed in the <guilabel>Recent items</guilabel>
873              menu in the menu bar.             
874              </para>
875            </listitem>
876          </varlistentry>
877          </variablelist>
878          </helptext>
879         
880        </sect3>
881      </sect2>
882 
883    </sect1>
884   
885    <sect1 id="webclient.items">
886      <title>Working with items</title>
887     
888      <para>
889        No matter what you are doing in BASE some things works more
890        or less in the same way. This section covers things that are
891        common for most parts of BASE.
892      </para>
893     
894      <para>
895        You mostly work with a single type of item at a time. This is
896        reflected in the menu system. For example, use
897        <menuchoice>
898          <guimenu>View</guimenu>
899          <guimenuitem>Samples</guimenuitem>
900        </menuchoice>
901        to work with samples, and
902        <menuchoice>
903          <guimenu>View</guimenu>
904          <guimenuitem>Experiments</guimenuitem>
905        </menuchoice>
906        to work with experiments. In most cases the list view for that type
907        of item is displayed. The list view, as the name says,
908        is used to list all items. There are two more standard views, the
909        single-item view and the edit view.
910      </para>
911     
912      <variablelist>
913        <varlistentry>
914          <term>List view</term>
915          <listitem>
916            <para>
917            This view lists all items of a certain type. The view allows you to search
918            and it is possible to configure which information to show
919            for each item. It also contains functions that
920            can be used on multiple items at the same time, for example,
921            delete, share and export. See <xref linkend="webclient.itemlist"/> for more information.
922            </para>
923          </listitem>
924        </varlistentry>
925     
926        <varlistentry>
927          <term>Single-item view</term>
928          <listitem>
929            <para>
930            Displays information about a single item. Sometimes it is very little,
931            sometimes it is very much and the information may be divided
932            into multiple tabs.
933            </para>
934          </listitem>
935        </varlistentry>
936     
937        <varlistentry>
938          <term>Edit view</term>
939          <listitem>
940            <para>
941            This view is used for editing the information
942            about a single item. It is always displayed as a popup window.
943            </para>
944          </listitem>
945        </varlistentry>
946      </variablelist> 
947             
948      <sect2 id="webclient.items.new">
949        <title>Create a new item</title>
950       
951        <para>
952          New items are mostly created from the list view. For example,
953          to create a new experiment go to the
954          <menuchoice><guimenu>View</guimenu> <guimenuitem>Experiments</guimenuitem></menuchoice>
955          page. Here you will find a &gbNew; button in the
956          toolbar. The button is disabled if you do not have permission to create new experiments.
957          Otherwise, click on it and enter any required information in the popup dialog.
958          Sometimes there are multiple tabs in this dialog. In the case of experiments
959          there are three tabs: <guilabel>Experiment</guilabel>, <guilabel>Publication</guilabel>
960          and <guilabel>Experimental factors</guilabel>.
961         
962          As a general rule, only the first tab has information that is required.
963          The information in all other tabs are optional.
964        </para>
965       
966        <para>
967          In some places you will also find actions that create items
968          directly in the list. For example in the list of samples or on
969          the single-item view for a sample you can create an extract using that
970          sample as the parent. If you use such links the parent
971          item will in most cases be selected automatically, which saves
972          you a few clicks when creating new items.
973        </para>
974       
975        <para>
976          Click on the &gbSave; button to save the new
977          item to the database or on the &gbCancel; button
978          to abort.
979        </para>
980
981        <note>
982          <para>
983          To speed up data entry when adding multiple new items there
984          are a few tricks you can use to make the web client supply
985          default values for most properties. To find a default value
986          the following checklist is used in this order:
987          </para>
988       
989        <orderedlist>         
990          <listitem>
991            <para>
992            If the list have an active filter the filter values are
993            used as default property values for the new item. For example,
994            if you are listing experiments with <guilabel>Genepix</guilabel>
995            raw data type the new experiment will automatically have
996            <guilabel>Genepix</guilabel> selected. This trick should work
997            for all properties except annotations, if it does not
998            report it as a bug to the development team.
999            </para>
1000          </listitem>
1001         
1002          <listitem>
1003            <para>
1004            When you link to other items the same item will be used the next time.
1005            For example, if you create an extract and selects an extraction protocol
1006            the same protocol is used the next time you create another extract.
1007            In fact, BASE will remember as many items as specified by
1008            the <link linkend="webclient.configuration.preferences.appearance">
1009            <guilabel>Recently used items</guilabel></link> setting (default is 4),
1010            allowing you to quickly select one of those protocols.
1011            </para>
1012          </listitem>
1013         
1014          <listitem>
1015            <para>
1016            If you have a project active and that project has specified default
1017            values those values will be used for new items. A project can specify
1018            defaults for protocols, hardware and software and a few other settings.
1019            </para>
1020          </listitem>
1021         
1022        </orderedlist>
1023       
1024        </note>
1025       
1026      </sect2>
1027     
1028      <sect2 id="webclient.items.edit">
1029        <title>Edit an existing item</title>
1030       
1031        <para>
1032          On all single-item views there is an &gbEdit;
1033          button in the toolbar that opens a popup dialog for editing the properties
1034          of the item. This button is disabled if the logged in user does not have
1035          write permission for the item.
1036        </para>
1037       
1038        <para>
1039          You can also open the edit popup in most other places where
1040          the item appears, for example, in lists or the single-item view
1041          of a related item. Press and hold one of the <keycap>CTRL</keycap>,
1042          <keycap>ALT</keycap> or <keycap>SHIFT</keycap> keys while clicking
1043          on the link and the edit window will open in a popup.
1044          If you do not have write permission
1045          on the item there is no meaning to open the edit popup and you will
1046          be taken to the single-item view page instead.
1047        </para>
1048
1049        <para>
1050          Click on the &gbSave; button to save the changes
1051          to the database or on the &gbCancel; button
1052          to abort.
1053        </para>
1054     
1055      </sect2>
1056
1057      <sect2 id="webclient.items.delete">
1058        <title>Delete items</title>
1059
1060        <para>
1061          You can delete items either from the list view or from
1062          a single-item view. In both cases, the item is only moved to
1063          the trashcan. No information is deleted from the database. This allows
1064          you to restore the item if you later find out that you need it again.
1065          In fact, there is nothing special about a removed item. It can still be
1066          used for the same things as any non-removed item can.
1067        </para>
1068
1069        <important>
1070          <para>
1071          To really delete an item from the database you must use
1072          the trashcan. See <xref linkend="trashcan"/>.
1073          </para>
1074        </important>
1075       
1076        <para>
1077          To delete items from the list view you must first mark
1078          the checkbox for each item you want to delete. Then, click on
1079          the &gbDelete; button. The list should refresh itself
1080          automatically. If you want to confirm that the items have been removed
1081          use the <guilabel>view / presets</guilabel> dropdown and select
1082          the <guilabel>Removed</guilabel> option. The removed items should now
1083          be displayed in the list with a small trashcan icon to indicate that
1084          they are located in the trashcan.
1085        </para>
1086
1087        <para>
1088          To delete items from the single-item view, click on the
1089          &gbDelete; button in the toolbar. The page will refresh
1090          itself automatically and a small trashcan icon should be displayed.
1091          If you do not have permission to delete the item the delete button
1092          is disabled.
1093        </para>
1094
1095      </sect2>
1096     
1097      <sect2 id="webclient.items.restore">
1098        <title>Restore deleted items</title>
1099       
1100        <para>
1101          You can restore deleted items either from the trashcan,
1102          from the list view or from the single-item view. This section only covers the last two
1103          cases. The trashcan has a <link linkend="trashcan">chapter of it's own</link>.
1104        </para>
1105
1106        <para>
1107          To delete items from the list view you must first make the deleted
1108          items appear in the list. This is easy, just use the <guilabel>view / presets</guilabel> 
1109          dropdown and select the <guilabel>Removed</guilabel> option. The list should
1110          refresh itself automatically. The removed items are
1111          displayed in the list with a small trashcan icon to indicate that
1112          they are located in the trashcan. Then, mark the checkbox for each item that you want
1113          to restore and click the &gbRestore; button. The list should
1114          refresh itself automatically and the trashcan icon should be gone from the
1115          restored items.
1116        </para>
1117       
1118        <para>
1119          To restore items from the single-item view, click on the
1120          &gbRestore; button in the toolbar. The page will refresh
1121          itself automatically and the small trashcan icon should be gone.
1122          If you do not have permission to restore the item the restore button
1123          is disabled.
1124        </para>
1125
1126      </sect2>
1127
1128      <sect2 id="webclient.items.share">
1129        <title>Share items to other users</title>
1130        <para>
1131          Sharing data with other users is an important feature
1132          of BASE, which allows you cooperate in teams. If you have
1133          followed the instructions in <xref linkend="project_permission" />
1134          you will find that you almost never have to share items manually
1135          to other users. This is because whenever you work with an active
1136          project each new item you create will automatically be shared
1137          to that project. In most cases, this is all you need.
1138        </para>
1139       
1140        <para>
1141          If you still need to manually share your data with other users,
1142          here is how to do it.
1143        </para>
1144       
1145        <para>
1146          From a list view, mark the checkbox for each item you want to share.
1147          Then, click on the &gbShare; button.
1148          If you are on a single-item page, click on the &gbShare; 
1149          button on that page. In both cases, this will open the
1150          <guilabel>Set access permissions</guilabel>
1151          dialog window.
1152        </para>
1153       
1154        <figure id="webclient.items.share.set_permissions">
1155          <title>Sharing items to other users</title>
1156          <screenshot>
1157          <mediaobject>
1158            <imageobject>
1159              <imagedata fileref="figures/set_permissions.png" format="PNG" />
1160            </imageobject>
1161          </mediaobject>
1162          </screenshot>
1163        </figure>
1164       
1165        <helptext external_id="share.setpermissions" title="Set access permissions">
1166          <variablelist>
1167            <varlistentry>
1168              <term><guilabel>Members</guilabel></term>
1169              <listitem>
1170                <para>
1171                The list displays the users, groups and projects
1172                that already has access to the items you selected.
1173                The list shows the name and the permission level.
1174                The permission level uses a one-letter code as follows:
1175                </para>
1176               
1177                <itemizedlist>
1178                <listitem><simpara><guilabel>R</guilabel> = Read</simpara></listitem>
1179                <listitem><simpara><guilabel>U</guilabel> = Use</simpara></listitem>
1180                <listitem><simpara><guilabel>W</guilabel> = Write</simpara></listitem>
1181                <listitem><simpara><guilabel>D</guilabel> = Delete</simpara></listitem>
1182                <listitem><simpara><guilabel>O</guilabel> = Take ownership</simpara></listitem>
1183                <listitem><simpara><guilabel>P</guilabel> = Set permission</simpara></listitem>
1184                </itemizedlist>
1185               
1186                <para>
1187                  Instead of a permission code, the word <guilabel>varying</guilabel>
1188                  may be displayed. This happens if the items you selected have been
1189                  shared with different permission.
1190                </para>
1191               
1192              </listitem>
1193            </varlistentry>
1194           
1195            <varlistentry>
1196              <term><guilabel>Permissions</guilabel></term>
1197              <listitem>
1198                <para>
1199                When you select a user, group or project in the
1200                list, the checkboxes will display the current permission.
1201                The exception is if the permissions are varying, in which
1202                case no checkboxes are checked.
1203                To change the permissions just check the permissions you want to
1204                grant or uncheck the permissions you want to revoke.
1205                You can select more than one user, group or project
1206                and change the permissions for all of them at once.
1207                </para>
1208              </listitem>
1209            </varlistentry>           
1210
1211            <varlistentry>
1212              <term><guibutton>Add users</guibutton></term>
1213              <listitem>
1214                <para>
1215                Opens a popup window that allows you to select
1216                users to share the items to. In the popup window, mark
1217                one or more users and click on the &gbOk;
1218                button. Unless you are an administrator, the popup window
1219                will only list users that are members of at least one of the
1220                groups where you also are a member. It will not list users that
1221                already have access to the items.
1222                </para>
1223              </listitem>
1224            </varlistentry>
1225
1226            <varlistentry>
1227              <term><guibutton>Add groups</guibutton></term>
1228              <listitem>
1229                <para>
1230                Opens a popup window that allows you to select
1231                groups to share the items to. In the popup window, mark
1232                one or more groups and click on the &gbOk;
1233                button. Unless you are an administrator, the popup window
1234                will only list groups where you are a member. It will not list
1235                groups that already have access to the items.
1236                </para>
1237              </listitem>
1238            </varlistentry>
1239           
1240            <varlistentry>
1241              <term><guibutton>Add projects</guibutton></term>
1242              <listitem>
1243                <para>
1244                Opens a popup window that allows you to select
1245                projects to share the items to. In the popup window, mark
1246                one or more projects and click on the &gbOk;
1247                button. Unless you are an administrator, the popup window
1248                will only list projects where you are a member. It will not list
1249                projects that already have access to the items.
1250                </para>
1251              </listitem>
1252            </varlistentry>
1253
1254            <varlistentry>
1255              <term>&gbRemove;</term>
1256              <listitem>
1257                <para>
1258                Click on this button to revoke access permissions from
1259                the selected users, groups and projects.
1260                </para>
1261              </listitem>   
1262            </varlistentry>
1263          </variablelist>
1264       
1265          <para>
1266            Use the &gbSave; button to save your
1267            changes or the &gbCancel; button to
1268            close the popup without saving.
1269          </para>
1270        </helptext>
1271
1272      </sect2>
1273
1274      <sect2 id="webclient.items.takeownership">
1275        <title>Take ownership of items</title>
1276        <para>
1277          Sometime it may be necessary to change the owner of an item.
1278          As an user you cannot give the ownership of your items to another
1279          user. It is instead the other user that must take the ownership
1280          of your items. For this to work, you must first give the other user
1281          permission to do so. That it, you must share your items with
1282          <guilabel>Take ownership</guilabel> permission to other user.
1283          See <xref linkend="webclient.items.share" />.
1284        </para>
1285       
1286        <para>
1287          When the items have been shared, the other user has to go to the
1288          list view (or the single-item view), mark the checkboxes for
1289          the items, and click in the <guibutton>Take ownership</guibutton>
1290          button. A warning message about not being able to undo the action
1291          is displayed. Click on &gbOk; to continue or
1292          &gbCancel; to abort.
1293        </para>
1294       
1295        <note>
1296          <para>
1297          The original owner may not have access permissions to the items
1298          any longer. If that is desired, the new owner must share the items
1299          to the original owner.
1300          </para>
1301        </note>
1302       
1303      </sect2>
1304     
1305      <sect2 id="webclient.items.export">
1306        <title>Export items</title>
1307        <para>
1308          This has a chapter of it's own. See <xref linkend="import_export_data.export"/>.
1309        </para>
1310      </sect2>
1311
1312    </sect1>
1313   
1314    <sect1 id="webclient.itemlist">
1315      <title>Listing items</title>
1316     
1317      <para>
1318        All pages that lists items are very similar in their appearance and
1319        functionality. In this section we will describe the things that are
1320        common for most (if not all) list pages.
1321      </para>
1322     
1323      <para>
1324        Use the <link linkend="webclient.intro.menubar">menu</link> to
1325        open a page listing items. Most list pages can only
1326        list one type of items. For example: use the
1327        <menuchoice><guimenu>View</guimenu><guimenuitem>Samples</guimenuitem></menuchoice>
1328        menu to list samples and the
1329        <menuchoice><guimenu>View</guimenu><guimenuitem>Experiments</guimenuitem></menuchoice>
1330        menu to list experiments.
1331      </para>
1332     
1333      <tip>
1334        An example of a list page that can list
1335        items of several types is found by going to
1336        <menuchoice>
1337          <guimenu>View</guimenu>
1338          <guimenuitem>All items</guimenuitem>
1339        </menuchoice>.
1340        This page lists all items that you are the owner of. It has a few limitations:
1341       
1342        <itemizedlist>
1343          <listitem>
1344            <para>
1345              It support only a limited set of columns (type, name and description)
1346              since these are the only properties that are common
1347              among all items.
1348            </para>
1349          </listitem>
1350         
1351          <listitem>
1352            <para>
1353              The list cannot be filtered (except by item type)
1354              or sorted. This is due to a limitation in the query system
1355              used to generate the list.
1356            </para>
1357          </listitem>
1358        </itemizedlist>
1359       
1360        <para>
1361          There are also several similarities:
1362        </para>
1363       
1364        <itemizedlist>
1365          <listitem>
1366            <para>
1367              It supports all of the regular multi-item
1368              operations such as delete, restore, share
1369              and take ownership.
1370            </para>
1371          </listitem>
1372         
1373          <listitem>
1374            <para>
1375              Clicking on the name of the item will take you to the
1376              single-item view of that item. Holding down <keycap>CTRL</keycap>,
1377              <keycap>ALT</keycap> or <keycap>SHIFT</keycap> while clicking,
1378              will open the edit popup.
1379            </para>
1380          </listitem>
1381        </itemizedlist>       
1382       
1383      </tip>
1384     
1385      <figure id="webclient.figures.listpage">
1386        <title>A typical list page</title>
1387        <screenshot>
1388          <mediaobject>
1389            <imageobject><imagedata fileref="figures/listpage.png" format="PNG"
1390              scalefit="1" width="100%" /></imageobject>
1391          </mediaobject>
1392        </screenshot>
1393      </figure>
1394     
1395      <para>
1396        The typical list page contains the following important
1397        elements:
1398      </para>
1399
1400      <variablelist>
1401        <varlistentry>
1402          <term><interface>1. Toolbar</interface></term>
1403          <listitem>
1404            <para>
1405            A toolbar with buttons for various actions such as
1406            &gbNew; for creating a new item,
1407            &gbDelete; for deleting items and
1408            <guibutton>Columns&hellip;</guibutton> for configuring columns.
1409            Depending on the permissions of the logged in user
1410            some buttons may be disabled (greyed out) or not shown at all.
1411            </para>
1412          </listitem>
1413        </varlistentry>
1414       
1415        <varlistentry>
1416          <term><interface>2. Navigation bar</interface></term>
1417          <listitem>
1418            <para>
1419            If there are many items the list will be divided into
1420            pages, each one showing a limited number of items.
1421            The navigation bar allows you to
1422            move to other pages and specify how many items each page
1423            should display. The navigation bar is repeated at the
1424            bottom of the list so you do not have to scroll back to the
1425            top of a long list just to get to another page.
1426            </para>
1427          </listitem>
1428        </varlistentry>
1429       
1430        <varlistentry>
1431          <term><interface>3. List of presets</interface></term>
1432          <listitem>
1433            <para>
1434            A list with preconfigured settings which allows you to
1435            quickly switch between different layouts (sort order, visible
1436            columns, filter settings, etc).
1437            </para>
1438          </listitem>
1439        </varlistentry>
1440       
1441        <varlistentry>
1442          <term><interface>4. Column headers</interface></term>
1443          <listitem>
1444            <para>
1445            The columns headers can be used for selecting sort order.
1446            </para>
1447          </listitem>
1448        </varlistentry>
1449       
1450        <varlistentry>
1451          <term><interface>5. Filter bar</interface></term>
1452          <listitem>
1453            <para>
1454            The filter bar allows you to search for items.
1455            </para>
1456          </listitem>
1457        </varlistentry>
1458       
1459      </variablelist>
1460     
1461     
1462      <sect2 id="webclient.itemlist.order">
1463        <title>Ordering the list</title>
1464       
1465        <para>
1466          Most lists are by default sorted by the name of the item. This can
1467          be changed by clicking on the column header of another column.
1468          If you click on the same column twice the sort order is reversed.
1469          A downwards or upwards pointing arrow is displayed next to the
1470          column header in the column that is currently used for sorting.
1471          Column headers that are black cannot be used for sorting.
1472        </para>
1473       
1474        <para>
1475          It is possible to use more than one column for sorting. Press
1476          and hold one of the <keycap>CTRL</keycap>,
1477          <keycap>ALT</keycap> or <keycap>SHIFT</keycap> keys while clicking
1478          on another column header. The original sorting is kept and the new
1479          column is used for sub-sorting the list. The procedure can be
1480          repeated with more columns if you need to sort on three or more
1481          columns. To revert to sort by only one column again click a
1482          column header without holding down any key.
1483        </para> 
1484      </sect2>
1485   
1486      <sect2 id="webclient.itemlist.filter">
1487        <title>Filtering the list</title>
1488       
1489        <para>
1490          If the list contains many items you may need to use a filter to be
1491          able to find the item you are looking for. The input boxes on the
1492          line below the column headers are used for filtering. Most columns
1493          are filtered using a free-text input box, but some columns that can
1494          only take a few distinct values use a selection list or radio buttons
1495          instead. The selection list and radio buttons are very simple to use.
1496          Just select the alternative that you want to filter on. The list
1497          will be automatically updated when the selection has been made.
1498        </para>
1499       
1500        <para>
1501          The free-text filter is a bit more complex. By default, an exact match is
1502          required, use % as a wildcard that matches any character.
1503          For example, the filter <informalexample>Experiment A</informalexample> 
1504          only matches the same exact string, but the filter
1505          <informalexample>Exp%</informalexample> matches
1506          <informalexample>Experiment A, Experiment B, etc.</informalexample>
1507        </para>
1508       
1509        <para>
1510          You can also use operators to find items which has a value that
1511          is greater than, less than or not equal to a specific value. This is
1512          mostly useful on numeric or date columns but also works on text
1513          columns. The operator must be entered first in the
1514          free-text box, for example
1515          <informalexample>&lt;=10</informalexample>
1516          to find items which has a value less than or equal to 10.   
1517          Here is a list of the supported operators:
1518        </para>
1519       
1520        <variablelist id="webclient.itemlist.filter.operators">
1521          <title>List of operators supported by the free-text filter</title>
1522          <varlistentry>
1523            <term><keycap>&lt;</keycap></term>
1524            <listitem><simpara>Less than</simpara></listitem>
1525          </varlistentry>
1526          <varlistentry>
1527            <term><keycap>&lt;=</keycap></term>
1528            <listitem><simpara>Less than or equal to</simpara></listitem>
1529          </varlistentry>
1530          <varlistentry>
1531            <term><keycap>&gt;</keycap></term>
1532            <listitem><simpara>Greater than</simpara></listitem>
1533          </varlistentry>
1534          <varlistentry>
1535            <term><keycap>&gt;=</keycap></term>
1536            <listitem><simpara>Greater than or equal to</simpara></listitem>
1537          </varlistentry>
1538          <varlistentry>
1539            <term><keycap>=</keycap></term>
1540            <listitem><simpara>Equal to (useful to find items with a null value)</simpara></listitem>
1541          </varlistentry>
1542          <varlistentry>
1543            <term><keycap>&lt;&gt;</keycap></term>
1544            <term><keycap>!=</keycap></term>
1545            <listitem><simpara>Not equal to (useful to find items with a non-null value)</simpara></listitem>
1546          </varlistentry>
1547        </variablelist>
1548      </sect2>
1549     
1550      <sect2 id="webclient.itemlist.columns">
1551        <title>Configuring which columns to show</title>
1552       
1553        <para>
1554          Most lists show only a small subset of the columns it
1555          is capable of showing. Use the
1556          <guibutton>Columns&hellip;</guibutton> button to open
1557          a dialog that allows you to select which columns to show
1558          and the order in which they are shown.
1559        </para>
1560       
1561        <figure id="webclient.figures.configure_columns">
1562          <title>Configuring which columns to show</title>
1563          <screenshot>
1564          <mediaobject>
1565            <imageobject>
1566              <imagedata fileref="figures/configure_columns.png" format="PNG"/>
1567            </imageobject>
1568          </mediaobject>
1569          </screenshot>
1570        </figure>
1571       
1572        <helptext external_id="columns.configure" 
1573          title="Set column order and visiblity">
1574       
1575        <variablelist>
1576        <varlistentry>
1577          <term><guilabel>Visible columns</guilabel></term>
1578          <listitem>
1579            <para>
1580              Shows the columns that are currently visible.
1581              Use the up/down arrow buttons to arrange the order of the
1582              visible columns. The topmost column is shown to the left.
1583              Use the right arrow button to move columns from this list
1584              to the hidden columns list. Columns marked with an <guilabel>×</guilabel> 
1585              are required
1586              and cannot be hidden. In most lists the <guilabel>Name</guilabel> column
1587              is the only column that is required.
1588            </para>
1589          </listitem>
1590        </varlistentry>
1591         
1592        <varlistentry>
1593          <term><guilabel>Hidden columns</guilabel></term>
1594          <listitem>
1595            <para>
1596              Shows columns that are not currently visible in the
1597              list. Use the left arrow button to move columns from
1598              this list to the visible columns list.
1599            </para>
1600          </listitem>
1601        </varlistentry>
1602       
1603       
1604        <varlistentry>
1605          <term><guilabel>Presets</guilabel></term>
1606          <listitem>
1607            <para>
1608              A dropdown list that allows you to
1609              select a set of preconfigured columns. You may also create
1610              your own preset if you often need to switch between different
1611              configurations. The list of presets is the same as the one
1612              described <link linkend="webclient.itemlist.presets">below</link>,
1613              but if used from this dialog the presets does not affect filters,
1614              sort order, etc.
1615            </para>
1616          </listitem>
1617        </varlistentry>
1618        </variablelist>
1619       
1620          <para>
1621            Use the &gbSave; button to apply your
1622            changes or the &gbCancel; button to
1623            close the popup without saving.
1624          </para>
1625
1626        </helptext>
1627
1628      </sect2>
1629     
1630      <sect2 id="webclient.itemlist.presets">
1631        <title>Presets</title>
1632       
1633        <para>
1634          The <guilabel>view / presets</guilabel> dropdown has three
1635          main functions:
1636        </para>
1637       
1638        <figure id="webclient.figures.viewpresets">
1639          <title>The view / presets dropdown</title>
1640          <screenshot>
1641            <mediaobject>
1642              <imageobject><imagedata fileref="figures/view_presets.png" format="PNG" 
1643                /></imageobject>
1644            </mediaobject>
1645          </screenshot>
1646        </figure>
1647        <orderedlist>
1648          <listitem>
1649            <para>
1650              Switch between different configuration presets.
1651              The top of the dropdown contains user-defined presets (<guilabel>Saved preset #1</guilabel> and
1652              <guilabel>#2</guilabel>) and a few preconfigured presets.
1653              The user-defined presets are used to store a complete table configuration,
1654              including:
1655            </para>
1656           
1657            <itemizedlist>
1658              <listitem><simpara>Which columns are visible and their order</simpara></listitem>
1659              <listitem><simpara>The column (or columns) used for sorting</simpara></listitem>
1660              <listitem><simpara>Filter settings</simpara></listitem>
1661              <listitem><simpara>The number of items per page and the current page</simpara></listitem>
1662            </itemizedlist>
1663           
1664            <para>             
1665              The preconfigured presets only affects
1666              the visible columns as follows:
1667            </para>
1668           
1669            <itemizedlist>
1670              <listitem>
1671                <para><guilabel>All columns</guilabel> - Show all columns.</para>
1672              </listitem>
1673              <listitem>
1674                <para><guilabel>Required columns</guilabel> - Show only the required columns.
1675                  Usually only the <guilabel>Name</guilabel> column is required.</para>
1676              </listitem>
1677              <listitem>
1678                <para><guilabel>Default columns</guilabel> - Show the default set of columns.</para>
1679              </listitem>
1680              <listitem>
1681                <para><guilabel>Other&hellip;</guilabel> -
1682                  Open the <link linkend="webclient.itemlist.columns">configure columns dialog box</link>.</para>
1683              </listitem>
1684            </itemizedlist>
1685           
1686          </listitem>
1687         
1688          <listitem>
1689            <para>
1690              Filter items by the removed status and the access
1691              permissions to an item.
1692            </para>
1693           
1694            <itemizedlist>
1695              <listitem>
1696                <para><guilabel>Removed</guilabel> - If checked, items that have been
1697                moved to the trashcan are shown, otherwise they are hidden.</para>
1698              </listitem>
1699              <listitem>
1700                <para><guilabel>Owned by me</guilabel> - If checked, items that the logged in user
1701                owns are displayed, otherwise they are hidden.</para>
1702              </listitem>
1703              <listitem>
1704                <para><guilabel>Shared to me</guilabel> - If checked, items that are owned
1705                by other users but shared to the logged in user are displayed, otherwise
1706                they are hidden.</para>
1707              </listitem>
1708              <listitem>
1709                <para><guilabel>In current project</guilabel> -
1710                  If checked, items that are linked with the current project are displayed,
1711                  otherwise they are hidden. It does not matter if the logged in user is the
1712                  owner or not. This option is only available if a project is active.
1713                </para>
1714              </listitem>
1715              <listitem>
1716                <para><guilabel>Owned by others</guilabel> -
1717                  This option is only available to administrators and will display
1718                  items that are owned by other users.
1719                </para>
1720              </listitem>
1721            </itemizedlist>
1722           
1723            <para>
1724              The default is to display item that the current user
1725              owns and, if a project is active, items in that project.
1726            </para>
1727           
1728          </listitem>
1729
1730          <listitem>
1731            <para>
1732              Administrate the presets
1733            </para>
1734            <itemizedlist>
1735              <listitem>
1736                <para><guilabel>Clear filter</guilabel> - Clears
1737                all filters.</para>
1738              </listitem>
1739             
1740              <listitem>
1741                <para><guilabel>Save as&hellip;</guilabel> - Save the
1742                current configuration as a preset.</para>
1743              </listitem>
1744
1745              <listitem>
1746                <para><guilabel>Manage&hellip;</guilabel> - Opens a dialog
1747                where you can remove saved presets. You can also load
1748                saved presets from the dialog, but it is quicker to just
1749                use the dropdown list for this.</para>
1750              </listitem>
1751            </itemizedlist>
1752          </listitem>
1753        </orderedlist>
1754       
1755        <sect3 id="webclient.itemlist.presets.saveas">
1756          <title>Save a preset</title>
1757         
1758          <para>
1759            If you select the <guilabel>Save as&hellip;</guilabel>
1760            option from the <guilabel>view / presets</guilabel> dropdown
1761            the <guilabel>Save preset as</guilabel> dialog is opened.
1762          </para>
1763         
1764          <figure id="webclient.figures.savepresetas">
1765            <title>Save preset as</title>
1766            <screenshot>
1767              <mediaobject>
1768                <imageobject><imagedata fileref="figures/save_preset.png" format="PNG" /></imageobject>
1769              </mediaobject>
1770            </screenshot>
1771          </figure>
1772         
1773          <helptext external_id="contexts.saveas" title="Save preset as">
1774         
1775          <variablelist>
1776          <varlistentry>
1777            <term><guilabel>For item</guilabel></term>
1778            <listitem>
1779              <para>
1780              The type of item the preset is saved for.
1781              </para>
1782            </listitem>
1783          </varlistentry>
1784          <varlistentry>
1785            <term><guilabel >Name</guilabel></term>
1786            <listitem>
1787              <para>
1788              The name of the preset. The name must be unique.
1789              </para>
1790            </listitem>
1791          </varlistentry>
1792          <varlistentry>
1793            <term><guilabel>Overwrite existing</guilabel></term>
1794            <listitem>
1795              <para>
1796              If a preset with the same name already exists, it is
1797              overwritten if this checkbox is checked.
1798              </para>
1799            </listitem>
1800          </varlistentry>
1801          <varlistentry>
1802            <term><guilabel>Public</guilabel></term>
1803            <listitem>
1804              <para>
1805              This options is only available for users
1806              which has the <emphasis>SHARE_TO_EVERYONE</emphasis>
1807              permission. If checked the preset is visible to
1808              all users.
1809              </para>
1810            </listitem>
1811          </varlistentry>
1812          </variablelist>
1813         
1814          <para>
1815            Use the &gbOk; button to save the preset
1816            or the &gbCancel; button to
1817            close the popup without saving.
1818          </para>
1819         
1820         
1821          </helptext>
1822         
1823        </sect3>
1824       
1825        <sect3 id="webclient.itemlist.presets.manage">
1826          <title>Manage presets</title>
1827         
1828          <para>
1829            If you select the <guilabel>Manage&hellip;</guilabel>
1830            option from the <guilabel>view / presets</guilabel> dropdown
1831            the <guilabel>Manage presets</guilabel> dialog is opened.
1832          </para>
1833         
1834          <figure id="webclient.figures.managepresets">
1835            <title>Manage presets</title>
1836            <screenshot>
1837              <mediaobject>
1838                <imageobject><imagedata fileref="figures/manage_presets.png" format="PNG" /></imageobject>
1839              </mediaobject>
1840            </screenshot>
1841          </figure>
1842         
1843          <helptext external_id="contexts.manage" title="Manage presets">
1844         
1845          <para>
1846            From this dialog you can delete or load presets.
1847          </para>
1848         
1849          <para>
1850            To delete presets, first mark the checkbox in front of
1851            each preset you want to delete. Then, click on the
1852            <guibutton>Delete&hellip;</guibutton> button. You will get
1853            a warning about that the action cannot be undone. Unlike other
1854            items, the presets are not moved to the trashcan. Click on
1855            &gbOk; to delete the preset.
1856          </para>
1857         
1858          <note>
1859            <title>Edit a preset</title>
1860            <para>
1861            It is not possible to edit a preset directly. To change an
1862            existing preset you must:
1863           
1864            <orderedlist>
1865            <listitem><simpara>Load the preset.</simpara></listitem>
1866            <listitem><simpara>Use the interface to change column settings, filter,
1867              sort order, etc.</simpara></listitem>
1868            <listitem><simpara>Save the preset with the same name.</simpara></listitem>
1869            </orderedlist>
1870            </para>
1871          </note>
1872         
1873          <para>
1874            Use the &gbClose; button to
1875            close the popup.
1876          </para>
1877         
1878         
1879          </helptext>
1880         
1881        </sect3>
1882       
1883      </sect2>
1884    </sect1>
1885   
1886</chapter>
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