source: trunk/doc/src/docbook/userdoc/webclient.xml @ 3242

Last change on this file since 3242 was 3242, checked in by Martin Svensson, 15 years ago

Changing the docbook output files to no longer be organized into folders because of some difficulties to get the relative
path to css-files, figures etc.

  • Property svn:eol-style set to native
  • Property svn:keywords set to Date Id
File size: 37.3 KB
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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 3242 2007-04-13 12:56:43Z martin $
7
8  Copyright (C) Authors contributing to this file.
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      <para></para>
35     
36      <sect2 id="webclient.intro.login">
37        <title>Logging in</title>
38        <para>
39          There are three things that you need to know
40          before you can use BASE:
41        </para>
42       
43        <orderedlist>
44        <listitem>The address (URL) to a BASE server</listitem>
45        <listitem>A username to login with</listitem>
46        <listitem>A password</listitem>
47        </orderedlist>
48       
49        <para>
50          You may, for example, try the BASE 2 demo server. Go to the
51          URL <ulink url="http://base2.thep.lu.se:8080/demo/">http://base2.thep.lu.se:8080/demo/</ulink>
52          and enter <userinput>base2</userinput> for the login and <userinput>base2</userinput>
53          for the password.
54        </para>
55       
56        <para>
57          You will need to get all three things from a adminstrator
58          of the BASE server. If you know only the address to the
59          BASE server, you may check the front page if the administrator
60          has added any information about how to get a username/password
61          there. Look for a link named <guilabel>Get an account!</guilabel>.
62        </para>
63       
64        <para>
65          Logging in is simple, just enter your <guilabel>login</guilabel> 
66          and <guilabel>password</guilabel> in the input fields. There is
67          a checkbox which allows you to <guilabel>encrypt the password</guilabel>
68          before it is sent to the BASE server. It is enabled by default, and
69          it is a good idea to leave it checked unless you have problems logging
70          in. If you are sure you are entering the correct login and password,
71          but still can't log in, try unchecking the encyption option.
72        </para>
73      </sect2>
74 
75      <sect2 id="webclient.intro.homepage">
76        <title>The home page</title>
77     
78      <para>
79        When you have been logged in the home page will be displayed. It
80        displays some useful information.
81      </para>
82       
83      <figure id="webclient.figures.homepage">
84        <title>The home page</title>
85        <screenshot>
86          <mediaobject>
87            <imageobject><imagedata fileref="figures/homepage.png" format="PNG"/></imageobject>
88          </mediaobject>
89        </screenshot>
90      </figure>
91       
92      <variablelist>
93        <varlistentry>
94          <term><interface>New messages</interface></term>
95          <listitem>
96            <para>
97            Messages are sent by plugins to notify you about finished jobs. In the
98            future, you may get messages from other sources as well. As of today,
99            messages are not used for communication between users.
100            </para>
101          </listitem>
102        </varlistentry>
103       
104        <varlistentry>
105          <term><interface>Projects</interface></term>
106          <listitem>
107            <para>
108            A list of projects that you are a member of. It is possible
109            to activate a project from this list. We recommend
110            that you always use a project when working with BASE. It will
111            make your life much easier once you start to cooperate with
112            other users. For more information read <xref linkend="project_permission"/>.
113            </para>
114          </listitem>
115        </varlistentry>
116       
117        <varlistentry>
118          <term><interface>Disk usage</interface></term>
119          <listitem>
120            <para>
121            An overview of how much disk space you have been assigned and
122            how much you are using.
123            </para>
124          </listitem>
125        </varlistentry>
126       
127        <varlistentry>
128          <term><interface>Help</interface></term>
129          <listitem>
130            <para>
131            Links for getting help and reporting bugs. The number
132            of links displayed here may vary depending on how the administrator
133            have set up the server.
134            </para>
135          </listitem>
136        </varlistentry>
137       
138        <varlistentry>
139          <term><interface>News and announcements</interface></term>
140          <listitem>
141            <para>
142            A list of important news and announcements from the
143            server administrator. Here you may, for example, find
144            information about server upgrades and maintenance.
145            </para>
146          </listitem>
147        </varlistentry>
148      </variablelist>
149       
150      </sect2>
151     
152      <sect2 id="webclient.intro.menubar">
153        <title>Using the menu bar</title>
154        <para>
155          On the top of the home page is the <interface>Menu bar</interface>.
156          This is the main navigation tool in BASE. It works the same way
157          as the regular menu system found in most other applications. Use
158          the mouse to click and select an item from the menu.
159        </para>
160       
161        <para>
162          Most of the menu is in two levels, ie. clicking on a top-level menu
163          will open a submenu just below it. Clicking on something in the
164          submenu will take you to another page or open a popup. For example, the
165          <menuchoice><guimenu>View</guimenu><guimenuitem>Samples</guimenuitem></menuchoice>
166          menu will take you to the page listing
167          samples.
168        </para>
169       
170        <para>
171          The menu bar also contains shortcuts to some often-used
172          actions:
173        </para>
174       
175       
176      <variablelist>
177        <varlistentry>
178          <term>
179            <interface>
180            <inlinemediaobject>
181            <imageobject><imagedata fileref="figures/refresh.gif" format="GIF" align="left"/></imageobject>
182            </inlinemediaobject>
183            Refresh page
184            </interface>
185          </term>
186          <listitem>
187            <para>
188            Refresh/reload the current page. This is useful when you add
189            or modify items in BASE. Most of the time the page is refreshed
190            automatically, but in some cases you will have to use
191            this button to refresh the page.
192            </para>
193           
194            <warning>
195              <para>
196              Do not use your browser's <guibutton>Refresh</guibutton> button
197              since it will take you to the login page again.
198              </para>
199            </warning>
200          </listitem>
201        </varlistentry>
202       
203        <varlistentry>
204          <term>
205            <interface>
206            <inlinemediaobject>
207            <imageobject><imagedata fileref="figures/recent.png" format="PNG" align="left"/></imageobject>
208            </inlinemediaobject>
209            Recent items
210            </interface>
211          </term>
212          <listitem>
213            <para>
214            Goto the most recently viewed item. By default, the list contains links to
215            the most recently viewed experiment and bioassayset, but this
216            is configurable. If you, for example, work a lot with protocols, you may
217            add a link to the most recently viewed protocol.
218            See <xref linkend="webclient.configuration.preferences.mostrecent"/>
219            </para>
220          </listitem>
221        </varlistentry>
222       
223        <varlistentry>
224          <term>
225            <interface>
226            <inlinemediaobject>
227            <imageobject><imagedata fileref="figures/project.gif" format="GIF" align="left"/></imageobject>
228            </inlinemediaobject>
229            Projects
230            </interface>
231          </term>
232          <listitem>
233            <para>
234            A list of all projects you are a member of. Selecting a project in the
235            list will make that project the active project.
236            </para>
237          </listitem>
238        </varlistentry>
239       
240        <varlistentry>
241          <term>
242            <interface>
243            <inlinemediaobject>
244            <imageobject><imagedata fileref="figures/user.png" format="PNG" align="left"/></imageobject>
245            </inlinemediaobject>
246            Logged in user
247            </interface>
248          </term>
249          <listitem>
250            <para>
251            Displays the name of the currently logged in user and allows
252            you to quickly logout and switch to another user.
253            </para>
254          </listitem>
255        </varlistentry>
256       
257      </variablelist>
258       
259      </sect2>
260     
261      <sect2 id="webclient.intro.help">
262        <title>Getting help</title>
263        <para>TODO</para>
264      </sect2>
265   
266    </sect1>
267   
268    <sect1 id="webclient.configuration">
269      <title>Configuring your account</title>
270     
271      <sect2 id="webclient.configuration.contact">
272        <title>Contact information</title>
273       
274        <para>
275          Use the <menuchoice><guimenu>File</guimenu>
276          <guimenuitem>Contact information</guimenuitem></menuchoice>
277          menu to bring up the contact information dialog. It contains
278          the following information:
279        </para>
280       
281        <helptext external_id="userpreferences.contact" title="Contact information">
282          <variablelist>
283            <varlistentry>
284              <term>
285                <guilabel>Email</guilabel>
286              </term>
287              <listitem>
288                Your email address (optional).
289              </listitem>
290            </varlistentry>
291            <varlistentry>
292              <term>
293                <guilabel>Organisation</guilabel>
294              </term>
295              <listitem>
296                The name of the organisation you work for or represent (optional).
297              </listitem>
298            </varlistentry>
299            <varlistentry>
300              <term>
301                <guilabel>Address</guilabel>
302              </term>
303              <listitem>
304                Your postal address as it should be printed on letters to you
305                (optional).
306              </listitem>
307            </varlistentry>
308            <varlistentry>
309              <term>
310                <guilabel>Phone</guilabel>
311              </term>
312              <listitem>
313                Your phone number (optional). You may enter multiple phone numbers,
314                for example your work phone number and a mobile number.
315              </listitem>
316            </varlistentry>
317            <varlistentry>
318              <term>
319                <guilabel>Fax</guilabel>
320              </term>
321              <listitem>
322                Your fax number (optional).
323              </listitem>
324            </varlistentry>
325            <varlistentry>
326              <term>
327                <guilabel>Url</guilabel>
328              </term>
329              <listitem>
330                An URL to your home page or your organisations home page (optional).
331              </listitem>
332            </varlistentry>
333          </variablelist>
334         
335          <note>
336            If you are using a multi-user account, for example a demo-account, you
337            are not able to change theese settings.
338          </note>
339         
340        </helptext>
341      </sect2>
342
343      <sect2 id="webclient.configuration.password">
344        <title>Changing password</title>
345       
346        <para>
347          Use the <menuchoice><guimenu>File</guimenu>
348          <guimenuitem>Change password</guimenuitem></menuchoice>
349          menu to bring up the change password dialog.
350        </para>
351       
352        <helptext external_id="userpreferences.password" title="Change password">
353          <variablelist>
354            <varlistentry>
355              <term>
356                <guilabel>New password</guilabel>
357              </term>
358              <listitem>
359                Enter the new password.
360              </listitem>
361            </varlistentry>
362            <varlistentry>
363              <term>
364                <guilabel>Retype password</guilabel>
365              </term>
366              <listitem>
367                Retype the same password. You must do this to
368                avoid spelling mistakes.
369              </listitem>
370            </varlistentry>
371          </variablelist>
372         
373          <note>
374            If you leave both fields empty the password will not be changed. It
375            is not possible to have an empty password.
376          </note>
377         
378          <note>
379            If you are using a multi-user account, for example a demo-account, you
380            are not able to change theese settings.
381          </note>
382         
383        </helptext>
384      </sect2>
385
386      <sect2 id="webclient.configuration.preferences">
387        <title>Preferences</title>
388       
389        <para>
390          Use the <menuchoice><guimenu>File</guimenu>
391          <guimenuitem>Preferences</guimenuitem></menuchoice>
392          menu to bring up the preferences dialog. It is divided into
393          three tabs.
394        </para>
395       
396        <sect3 id="webclient.configuration.preferences.appearance">
397          <title>Appearance</title>
398         
399          <helptext external_id="userpreferences.appearance" title="Preferences - Appearance">
400         
401          <para>
402          This tab contains settings that affect the appearance of the
403          web client.
404          </para>
405         
406          <variablelist>
407            <varlistentry>
408              <term>
409                <guilabel>Font size</guilabel>
410              </term>
411              <listitem>
412                Select a basic font size. You can choose between
413                five sizes: extra small (XS), small (S), medium (M),
414                large (L) and extra large (XL). The default font size is
415                medium.
416              </listitem>
417            </varlistentry>
418            <varlistentry>
419              <term>
420                <guilabel>Scale factor</guilabel>
421              </term>
422              <listitem>
423                The scale factor affects the size of popup windows.
424                This setting exists because different browsers render
425                pages differently. If you often find that popup windows
426                are too small you can change this setting to make them
427                bigger.
428                <note>
429                  The scale factor is automatically changed if the
430                  font size is changed.
431                </note>
432              </listitem>
433            </varlistentry>
434            <varlistentry>
435              <term>
436                <guilabel>Toolbar</guilabel>
437              </term>
438              <listitem>
439                You may choose if the toolbar buttons should
440                have only images, only text or both images and text.
441                The default is that they have both images and text.
442              </listitem>
443            </varlistentry>
444            <varlistentry>
445              <term>
446                <guilabel>Recently used items</guilabel>
447              </term>
448              <listitem>
449                The number of items to remember in the list
450                of recently used items. This will make data input
451                faster since fewer clicks are required to select
452                items. The default is to remember 4 items.
453              </listitem>
454            </varlistentry>
455            <varlistentry>
456              <term>
457                <guilabel>Ratio color range</guilabel>
458              </term>
459              <listitem>
460                Select three colors to use when displaying
461                data that is suitable for color coding, for
462                example the intensity ratio in two-color
463                experiments. The default setting is blue-black-yellow.
464                The list of presets contains other useful color combinations
465                (for example, the BASE 1 red-yellow-green) and the most
466                recently used color combinations.
467              </listitem>
468            </varlistentry>
469            <varlistentry>
470              <term>
471                <guilabel>Date format</guilabel>
472              </term>
473              <listitem>
474                <para>
475                A format string describing how dates should be displayed.
476                We support all formatting options supported by the Java
477                language. For more information see:
478                <ulink url="http://java.sun.com/j2se/1.5.0/docs/api/java/text/SimpleDateFormat.html">SimpleDateFormat documentation</ulink>
479                The most useful format patterns are:
480                </para>
481               
482                <itemizedlist>
483                  <listitem>yy: two-digit year</listitem>
484                  <listitem>yyyy: four-digit year</listitem>
485                  <listitem>MM: two-digit month</listitem>
486                  <listitem>MMM: month name (short)</listitem>
487                  <listitem>MMMM: month name (full)</listitem>
488                  <listitem>dd: two-digit day in month</listitem>
489                </itemizedlist>
490               
491                <para>
492                The list of presets contains the most commonly/recently
493                used date formats.
494                </para>
495               
496              </listitem>
497            </varlistentry>
498           
499            <varlistentry>
500              <term>
501                <guilabel>Date-time format</guilabel>
502              </term>
503              <listitem>
504                <para>
505                A format string describing how dates with times should be displayed.
506                We support all formatting options supported by the Java
507                language. For more information see:
508                <ulink url="http://java.sun.com/j2se/1.5.0/docs/api/java/text/SimpleDateFormat.html">SimpleDateFormat documentations</ulink>
509                The most useful time-format patterns are:
510                </para>
511               
512                <itemizedlist>
513                  <listitem>HH: two-digit hour (0-23)</listitem>
514                  <listitem>hh: two-digit hour (1-12)</listitem>
515                  <listitem>a: AM/PM marker</listitem>
516                  <listitem>mm: two-digit minute</listitem>
517                  <listitem>ss: two-digit second</listitem>
518                </itemizedlist>
519               
520              </listitem>
521            </varlistentry>
522           
523            <varlistentry>
524              <term>
525                <guilabel>Decimals</guilabel>
526              </term>
527              <listitem>
528                The number of decimals to display for numeric values.
529                The default is 2.
530              </listitem>
531            </varlistentry>
532           
533          </variablelist>
534       
535          </helptext>
536       
537        </sect3>
538       
539        <sect3 id="webclient.configuration.preferences.plugins">
540          <title>Plugins</title>
541         
542          <helptext external_id="userpreferences.plugins" title="Preferences - Plugins">
543         
544          <para>
545            This tab contains settings that affect plugin execution.
546          </para>
547         
548          <variablelist>
549            <varlistentry>
550              <term>
551                <guilabel>Messages</guilabel>
552              </term>
553              <listitem>
554                Mark the checkbox if you want to have a message sent
555                to you when a plugin completes execution. This setting
556                can be overridden each time you start a plugin.
557              </listitem>
558            </varlistentry>
559          </variablelist>
560          </helptext>
561         
562        </sect3>
563       
564        <sect3 id="webclient.configuration.preferences.mostrecent">
565          <title>Most recent</title>
566         
567          <helptext external_id="userpreferences.mostrecent" title="Preferences - Most recent">
568         
569          <para>
570            This tab contains settings that affect the <guilabel>Most
571            recent</guilabel> menu. You can select which items should
572            appear in the menu by moving them to the left list. Use
573            the up and down arrows to change the order in which they appear.
574          </para>
575         
576          <para>
577            If the <guilabel>Load the names of all recent items</guilabel> checkbox
578            is checked the name of the items will be displayed in the menu (for example,
579            Experiment: My experiment). Otherwise only the type of the item is
580            displayed (for example, Experiment).
581          </para>
582          </helptext>
583         
584        </sect3>
585      </sect2>
586 
587    </sect1>
588   
589    <sect1 id="webclient.itemlist">
590      <title>Listing items</title>
591     
592      <para>
593        All pages that lists items are very similar in their appearance and
594        functionality. In this section we will describe the things that are
595        common for most (if not all) list pages.
596      </para>
597     
598      <para>
599        Use the <link linkend="webclient.intro.menubar">menu</link> to
600        open a page listing items. Most list pages can only
601        list one type of items. For example: use the
602        <menuchoice><guimenu>View</guimenu><guimenuitem>Samples</guimenuitem></menuchoice>
603        menu to list samples and the
604        <menuchoice><guimenu>View</guimenu><guimenuitem>Experiments</guimenuitem></menuchoice>
605        menu to list experiments. An example of a list page that can list
606        items of several types is the <link linkend="trashcan">Trashcan</link>.     
607        A typical list page is shown below.
608      </para>
609     
610      <figure id="webclient.figures.listpage">
611        <title>Example of a list page</title>
612        <screenshot>
613          <mediaobject>
614            <imageobject><imagedata fileref="figures/listpage.png" format="PNG"/></imageobject>
615          </mediaobject>
616        </screenshot>
617      </figure>
618     
619      <para>
620        The typical list page contains the following important
621        elements:
622      </para>
623
624      <variablelist>
625        <varlistentry>
626          <term><interface>1. Toolbar</interface></term>
627          <listitem>
628            <para>
629            A toolbar with buttons for various actions such as
630            <guibutton>New&hellip;</guibutton> for creating a new item,
631            <guibutton>Delete</guibutton> for deleting items and
632            <guibutton>Columns&hellip;</guibutton> for configuring columns.
633            Depending on the permissions of the logged in user
634            some buttons may be disabled (greyed out) or not shown at all.
635            </para>
636          </listitem>
637        </varlistentry>
638       
639        <varlistentry>
640          <term><interface>2. Navigation bar</interface></term>
641          <listitem>
642            <para>
643            If there are many items the list will be divided into
644            pages showin a limited number of items at the same time.
645            The navigation bar allows you to
646            move to other pages and specify how many items each page
647            should display. The navigation bar is repeated at the
648            bottom of the list so you don't have to scroll back to the
649            top of a long list just to get to another page.
650            </para>
651          </listitem>
652        </varlistentry>
653       
654        <varlistentry>
655          <term><interface>3. List of presets</interface></term>
656          <listitem>
657            <para>
658            A list with preconfigured settings allowing you to
659            quickly switch between different layouts (sort order, visible
660            columns, filter settings, etc).
661            </para>
662          </listitem>
663        </varlistentry>
664       
665        <varlistentry>
666          <term><interface>4. Column headers</interface></term>
667          <listitem>
668            <para>
669            The columns headers can be used for selecting sort order.
670            </para>
671          </listitem>
672        </varlistentry>
673       
674        <varlistentry>
675          <term><interface>5. Filter bar</interface></term>
676          <listitem>
677            <para>
678            The filter bar allows you to search for items.
679            </para>
680          </listitem>
681        </varlistentry>
682       
683      </variablelist>
684     
685     
686      <sect2 id="webclient.itemlist.order">
687        <title>Ordering the list</title>
688       
689        <para>
690          Most lists are by default sorted by the name of the item. This can
691          be changed by clicking on the column header of another column.
692          If you click on the same column twice the sort order is reversed.
693          A downwards or upwards pointing arrow is displayed next to the
694          column header in the column that is currently used for sorting.
695          Column headers that are black can't be used for sorting.
696        </para>
697       
698        <para>
699          It is possible to use more than one column for sorting. Press
700          and hold one of the <keycap>CTRL</keycap>,
701          <keycap>ALT</keycap> or <keycap>SHIFT</keycap> keys while clicking
702          on another column header. The original sorting is kept and the new
703          column is used for sub-sorting the list. The procedure can be
704          repeated with more columns if you need to sort on three or more
705          columns. To revert to sort by only one column again click the
706          column header without holding down any key.
707        </para> 
708      </sect2>
709   
710      <sect2 id="webclient.itemlist.filter">
711        <title>Filtering the list</title>
712       
713        <para>
714          If the list contains many items you may need to use a filter to be
715          able to find the item you are looking for. The input boxes on the
716          line below the column headers are used for filtering. Most columns
717          are filtered using a free-text input box, but some columns that can
718          only take a few distinct values use a selection list or radio buttons
719          instead. The selection list and radio buttons are very simple to use.
720          Just select the alternative that you want to filter on. The list
721          will be automatically updated when the selection has been made.
722        </para>
723       
724        <para>
725          The free-text filter is a bit more complex. By default, an exact match is
726          required, use % as a wildcard that matches any character.
727          For example, the filter <informalexample>Experiment A</informalexample> 
728          only matches the same exact string, but the filter
729          <informalexample>Exp%</informalexample> matches
730          <informalexample>Experiment A, Experiment B, etc.</informalexample>
731        </para>
732       
733        <para>
734          You can also use operators to find items which has a value that
735          is greater than, less than or not equal to a specific value. This is
736          mostly useful on numeric or date columns but also works on text
737          columns. The operator must be entered first in the
738          free-text box, for example
739          <informalexample>&lt;=10</informalexample>
740          to find items which has a value less than or equal to 10.   
741          Here is a list of the supported operators:
742        </para>
743       
744        <variablelist id="webclient.itemlist.filter.operators">
745          <title>List of operators supported by the free-text filter</title>
746          <varlistentry>
747            <term><keycap>&lt;</keycap></term>
748            <listitem>Less than</listitem>
749          </varlistentry>
750          <varlistentry>
751            <term><keycap>&lt;=</keycap></term>
752            <listitem>Less than or equal to</listitem>
753          </varlistentry>
754          <varlistentry>
755            <term><keycap>&gt;</keycap></term>
756            <listitem>Greater than</listitem>
757          </varlistentry>
758          <varlistentry>
759            <term><keycap>&gt;=</keycap></term>
760            <listitem>Greater than or equal to</listitem>
761          </varlistentry>
762          <varlistentry>
763            <term><keycap>=</keycap></term>
764            <listitem>Equal to (useful to find items with a null value)</listitem>
765          </varlistentry>
766          <varlistentry>
767            <term><keycap>&lt;&gt;</keycap></term>
768            <term><keycap>!=</keycap></term>
769            <listitem>Not equal to (useful to find items with a non-null value)</listitem>
770          </varlistentry>
771        </variablelist>
772      </sect2>
773     
774      <sect2 id="webclient.itemlist.columns">
775        <title>Configuring which columns to show</title>
776       
777        <para>
778          Most lists show only a small subset of the columns it
779          is capable of showing. Use the
780          <guibutton>Columns&hellip;</guibutton> button to open
781          a dialog that allows you to select which columns to show
782          and the order in which they are shown.
783        </para>
784       
785        <figure id="webclient.figures.configure_columns">
786          <title>Configuring which columns to show</title>
787          <screenshot>
788          <mediaobject>
789            <imageobject>
790              <imagedata fileref="figures/configure_columns.png" format="PNG"/>
791            </imageobject>
792          </mediaobject>
793          </screenshot>
794        </figure>
795       
796        <para>
797          Use the left/right arrow buttons to move columns between
798          the <guilabel>Visible columns</guilabel> list and the
799          <guilabel>Hidden columns</guilabel> list. Use the up/down arrow
800          buttons to arrange the order of the visible columns. The topmost column
801          will be shown to the left.
802        </para>
803       
804        <para>
805          Columns marked with an <guilabel>×</guilabel> are required
806          and can't be hidden. In mosts lists the <guilabel>Name</guilabel> column
807          is the only column that is required.
808        </para>
809       
810        <para>
811          The <guilabel>Presets</guilabel> dropdown list allows you to
812          select a set of preconfigured columns. You may also create
813          your own preset if you often need to switch between different
814          configurations. The list of presets is the same as the one
815          described <link linkend="webclient.itemlist.presets">below</link>,
816          but if used from this dialog the presets doesn't affect filters,
817          sort order, etc.
818        </para>
819       
820       
821      </sect2>
822     
823      <sect2 id="webclient.itemlist.presets">
824        <title>Presets</title>
825       
826        <para>
827          The <guilabel>view / presets</guilabel> dropdown has three
828          main functions:
829        </para>
830       
831        <figure id="webclient.figures.viewpresets" float="right">
832          <title>The view / presets dropdown</title>
833          <screenshot>
834            <mediaobject>
835              <imageobject><imagedata fileref="figures/view_presets.png" format="PNG" /></imageobject>
836            </mediaobject>
837          </screenshot>
838        </figure>
839        <orderedlist>
840          <listitem>
841            <para>
842              Switch between different configuration presets.
843              The top of the dropdown contains user-defined presets (<guilabel>Saved preset #1</guilabel> and
844              <guilabel>#2</guilabel>) and a few preconfigured presets.
845              The user-defined presets are used to store a complete table configuration,
846              including:
847            </para>
848           
849            <itemizedlist>
850              <listitem>Which columns are visible and their order</listitem>
851              <listitem>The column (or columns) used for sorting</listitem>
852              <listitem>Filter settings</listitem>
853              <listitem>The number of items per page and the current page</listitem>
854            </itemizedlist>
855           
856            <para>             
857              The preconfigured presets only affects
858              the visible columns as follows:
859            </para>
860           
861            <itemizedlist>
862              <listitem>
863                <para><guilabel>All columns</guilabel> - Show all columns.</para>
864              </listitem>
865              <listitem>
866                <para><guilabel>Required columns</guilabel> - Show only the required columns.
867                  Usually only the <guilabel>Name</guilabel> column is required.</para>
868              </listitem>
869              <listitem>
870                <para><guilabel>Default columns</guilabel> - Show the default set of columns.</para>
871              </listitem>
872              <listitem>
873                <para><guilabel>Other&hellip;</guilabel> -
874                  Open the <link linkend="webclient.itemlist.columns">configure columns dialog box</link>.</para>
875              </listitem>
876            </itemizedlist>
877           
878          </listitem>
879         
880          <listitem>
881            <para>
882              Filter items by the removed status and the access
883              permissions to an item.
884            </para>
885           
886            <itemizedlist>
887              <listitem>
888                <para><guilabel>Removed</guilabel> - If checked, items that have been
889                marked for deletion are shown, otherwise they are hidden.</para>
890              </listitem>
891              <listitem>
892                <para><guilabel>Owned by me</guilabel> - If checked, items that the logged in user
893                owns are displayed, otherwise they are hidden.</para>
894              </listitem>
895              <listitem>
896                <para><guilabel>Shared to me</guilabel> - If checked, items that are owned
897                by other users but shared to the logged in user are displayed, otherwise
898                they are hidden.</para>
899              </listitem>
900              <listitem>
901                <para><guilabel>In current project</guilabel> -
902                  If checked, items that are linked with the current project are displayed,
903                  otherwise they are hidden. It doesn't matter if the logged in user is the
904                  owner or not. This option is only available if a project is active.
905                </para>
906              </listitem>
907              <listitem>
908                <para><guilabel>Owned by others</guilabel> -
909                  This option is only avilable to administrators and will display
910                  items that are owned by other users.
911                </para>
912              </listitem>
913            </itemizedlist>
914           
915            <para>
916              The default options are to only display items that the current
917              user owns and, if a project is active, items in that project.
918            </para>
919           
920          </listitem>
921
922          <listitem>
923            <para>
924              Administrate the presets
925            </para>
926            <itemizedlist>
927              <listitem>
928                <para><guilabel>Clear filter</guilabel> - Clears
929                all filters.</para>
930              </listitem>
931             
932              <listitem>
933                <para><guilabel>Save as&hellip;</guilabel> - Save the
934                current configuration as a preset.</para>
935              </listitem>
936
937              <listitem>
938                <para><guilabel>Manage&hellip;</guilabel> - Opens a dialog
939                where you can remove saved presets. You can also load
940                saved presets from the dialog, but it is quicker to just
941                use the dropdown list for this.</para>
942              </listitem>
943             
944            </itemizedlist>
945         
946         
947          </listitem>
948
949        </orderedlist>
950      </sect2>
951     
952    </sect1>
953   
954    <sect1 id="webclient.items">
955      <title>Working with items</title>
956     
957      <para>
958        No matter what you are doing in BASE some things works more
959        or less in the same way. This section convers things that are
960        common for most parts of BASE.
961      </para>
962             
963      <sect2 id="webclient.items.new">
964        <title>Create a new item</title>
965       
966        <para>
967          New items are mostly created from the list view. For example,
968          to create a new experiment go to the
969          <menuchoice><guimenu>View</guimenu> <guimenuitem>Experiments</guimenuitem></menuchoice>
970          page. Here you will find a <guibutton>New&hellip;</guibutton> button in the
971          toolbar. The button is disabled if you don't have permission to create new experiments.
972          Otherwise, click on it and enter any required information in the popup dialog.
973          Sometimes there are multiple tabs in this dialog. In the case of experiments
974          there are three tabs: <guilabel>Experiment</guilabel>, <guilabel>Publication</guilabel>
975          and <guilabel>Experimental factors</guilabel>.
976         
977          As a general rule, only the first tab has information that is required.
978          The information in all other tabs are optional.
979        </para>
980       
981        <para>
982          Click on the <guibutton>Save</guibutton> button to save the new
983          experiment to the database or on the <guibutton>Cancel</guibutton> button
984          to abort.
985        </para>
986
987        <note>
988          <para>
989          To speed up data entry when adding multiple new items there
990          are a few tricks you can use to make the web client to enter
991          default values for most properties. To find a default value
992          the following checklist is used in this order.
993          </para>
994       
995        <orderedlist>         
996          <listitem>
997            If the list have an active filter the filter values are
998            used as default property values for the new item. For example,
999            if you are listing experiments with <guilabel>Genepix</guilabel>
1000            raw data type the new experiment will automatically have
1001            <guilabel>Genepix</guilabel> selected. This trick should work
1002            for all properties except annotations.       
1003          </listitem>
1004         
1005          <listitem>
1006            When you link to other items the same item will be used the next time.
1007            For example the extraction protocol used to create an extract from a sample
1008            is remembered and the same protocol is used the next time you create an extract.
1009            In fact, BASE will remember as many items as specified by
1010            the <link linkend="webclient.configuration.preferences.appearance">
1011            <guilabel>Recently used items</guilabel></link> setting (default is 4).
1012          </listitem>
1013         
1014          <listitem>
1015            If you have a project active and that project has specified default
1016            values those values will be used for new items. A project can specify
1017            defaults for protocols, hardware and software and a few other settings.
1018          </listitem>
1019         
1020        </orderedlist>
1021       
1022        </note>
1023       
1024      </sect2>
1025     
1026      <sect2 id="webclient.items.edit">
1027        <title>Edit an existing item</title>
1028       
1029        <para>
1030          On all single-item views there is an <guibutton>Edit&hellip;</guibutton>
1031          button in the toolbar that opens a popup dialog for editing the properties
1032          of the item. This button is disabled if the logged in user doesn't have
1033          write permission for the item.
1034        </para>
1035       
1036        <para>
1037          You don't have to go to the single-item view to edit an item.
1038          Whenever an item appear in a list or another place and has a link
1039          on it, you can use a shortcut to open it's edit popup. Press
1040          and hold one of the <keycap>CTRL</keycap>,
1041          <keycap>ALT</keycap> or <keycap>SHIFT</keycap> keys while clicking on the
1042          link. This will open the edit popup dialog for the item. If you don't
1043          have write permission you will be taken to the single-item view of
1044          that item instead.
1045        </para>
1046
1047     
1048      </sect2>
1049
1050      <sect2 id="webclient.items.delete">
1051        <title>Delete items</title>
1052
1053        <para>
1054          You can delete items either from the list view or from
1055          a single-item view. In both cases, the item is only marked
1056          as beeing removed. It is not deleted from the database. This allows
1057          you to restore the item if you later find out that you need it again.
1058          In fact, there is nothing special about a removed item. It can still be
1059          used for the same things as any non-removed item can.
1060        </para>
1061
1062        <important>
1063          To really delete an item from the database you must use
1064          the <link linkend="trashcan">trashcan</link>.
1065        </important>
1066       
1067        <para>
1068          To delete items from the list view you must first mark
1069          the checkbox for each item you want to delete. Then, click on
1070          the <guibutton>Delete</guibutton> button. The list should refresh iteself
1071          automatically. If you want to confirm that the items have been removed
1072          use the <guilabel>view / presets</guilabel> dropdown and select
1073          the <guilabel>Removed</guilabel> option. The removed items should now
1074          be displayed in the list with a small trashcan icon to indicate that
1075          they have been removed.
1076        </para>
1077
1078        <para>
1079          To delete items from the single-item view you just click on the
1080          <guibutton>Delete</guibutton> in the toolbar. The page will refresh
1081          itself automatically and a small trashcan icon should be displayed.
1082          If you don't have permission to delete the item the delete button
1083          will be disabled.
1084        </para>
1085
1086      </sect2>
1087     
1088      <sect2 id="webclient.items.restore">
1089        <title>Restore deleted items</title>
1090       
1091        <para>
1092          You can restore deleted items either from the <link linkend="trashcan">trashcan</link>,
1093          from the list view or from the single-item view. This section only covers the last two
1094          cases. The trashcan has a chapter of it's own.
1095        </para>
1096
1097        <para>
1098          To delete items from the list view you must first make the deleted
1099          items appear in the list. This is easy, just use the <guilabel>view / presets</guilabel> 
1100          dropdown and select the <guilabel>Removed</guilabel> option. This list should
1101          refresh itself automatically. The removed items should now
1102          be displayed in the list with a small trashcan icon to indicate that
1103          they have been removed. Then, mark the checkbox for each item that you want
1104          to restore and click the <guibutton>Restore</guibutton> button. The list should
1105          refresh iteself automatically and the trashcan icon should be gone from the
1106          restored items.
1107        </para>
1108       
1109        <para>
1110          To restore items from the single-item view you just click on the
1111          <guibutton>Restore</guibutton> in the toolbar. The page will refresh
1112          itself automatically and the small trashcan icon should be gone.
1113          If you don't have permission to restore the item the restore button
1114          will be disabled.
1115        </para>
1116
1117      </sect2>
1118
1119    </sect1>
1120   
1121   
1122</chapter>
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