source: trunk/doc/src/docbook/userdoc/webclient.xml @ 3214

Last change on this file since 3214 was 3214, checked in by Nicklas Nordborg, 16 years ago

Using the menu bar section.

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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 3214 2007-03-26 14:01:26Z nicklas $
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  <title>Using the web client</title>
31    <sect1 id="webclient.introduction">
32      <title>Introduction</title>
33      <para></para>
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>The address (URL) to a BASE server</listitem>
44        <listitem>A username to login with</listitem>
45        <listitem>A password</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 will need to get all three things from a adminstrator
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 a link named <guilabel>Get an account!</guilabel>.
61        </para>
62       
63        <para>
64          Logging in is simple, just enter your <guilabel>login</guilabel> 
65          and <guilabel>password</guilabel> in the input fields. There is
66          a checkbox which allows you to <guilabel>encrypt the password</guilabel>
67          before it is sent to the BASE server. It is enabled by default, and
68          it is a good idea to leave it checked unless you have problems logging
69          in. If you are sure you are entering the correct login and password,
70          but still can't log in, try unchecking the encyption option.
71        </para>
72      </sect2>
73 
74      <sect2 id="webclient.intro.homepage">
75        <title>The home page</title>
76     
77      <para>
78        When you have been logged in the home page will be displayed. It
79        displays some useful information.
80      </para>
81       
82      <figure id="webclient.figures.homepage">
83        <title>The home page</title>
84        <screenshot>
85          <mediaobject>
86            <imageobject><imagedata fileref="figures/homepage.png" format="PNG"/></imageobject>
87          </mediaobject>
88        </screenshot>
89      </figure>
90       
91      <variablelist>
92        <varlistentry>
93          <term><interface>New messages</interface></term>
94          <listitem>
95            <para>
96            Messages are sent by plugins to notify you about finished jobs. In the
97            future, you may get messages from other sources as well. As of today,
98            messages are not used for communication between users.
99            </para>
100          </listitem>
101        </varlistentry>
102       
103        <varlistentry>
104          <term><interface>Projects</interface></term>
105          <listitem>
106            <para>
107            A list of projects that you are a member of. It is possible
108            to activate a project from this list. We recommend
109            that you always use a project when working with BASE. It will
110            make your life much easier once you start to cooperate with
111            other users. For more information read <xref linkend="project_permission"/>.
112            </para>
113          </listitem>
114        </varlistentry>
115       
116        <varlistentry>
117          <term><interface>Disk usage</interface></term>
118          <listitem>
119            <para>
120            An overview of how much disk space you have been assigned and
121            how much you are using.
122            </para>
123          </listitem>
124        </varlistentry>
125       
126        <varlistentry>
127          <term><interface>Help</interface></term>
128          <listitem>
129            <para>
130            Links for getting help and reporting bugs. The number
131            of links displayed here may vary depending on how the administrator
132            have set up the server.
133            </para>
134          </listitem>
135        </varlistentry>
136       
137        <varlistentry>
138          <term><interface>News and announcements</interface></term>
139          <listitem>
140            <para>
141            A list of important news and announcements from the
142            server administrator. Here you may, for example, find
143            information about server upgrades and maintenance.
144            </para>
145          </listitem>
146        </varlistentry>
147      </variablelist>
148       
149      </sect2>
150     
151      <sect2 id="webclient.intro.menubar">
152        <title>Using the menu bar</title>
153        <para>
154          On the top of the home page is the <interface>Menu bar</interface>.
155          This is the main navigation tool in BASE. It works the same way
156          as the regular menu system found in most other applications. Use
157          the mouse to click and select an item from the menu.
158        </para>
159       
160        <para>
161          Most of the menu is in two levels, ie. clicking on a top-level menu
162          will open a submenu just below it. Clicking on something in the
163          submenu will take you to another page or open a popup. For example, the
164          <menuchoice><guimenu>View</guimenu><guimenuitem>Samples</guimenuitem></menuchoice>
165          menu will take you to the page listing
166          samples.
167        </para>
168       
169        <para>
170          The menu bar also contains shortcuts to some often-used
171          actions:
172        </para>
173       
174       
175      <variablelist>
176        <varlistentry>
177          <term>
178            <interface>
179            <inlinemediaobject>
180            <imageobject><imagedata fileref="figures/refresh.gif" format="GIF" align="left"/></imageobject>
181            </inlinemediaobject>
182            Refresh button
183            </interface>
184          </term>
185          <listitem>
186            <para>
187            Refresh/reload the current page. This is useful when you add
188            or modify items in BASE. Most of the time the page is refreshed
189            automatically, but in some cases you will have to use
190            this button to refresh the page.
191            </para>
192           
193            <warning>
194              <para>
195              Do not use your browser's <guibutton>Refresh</guibutton> button
196              since it will take you to the login page again.
197              </para>
198            </warning>
199          </listitem>
200        </varlistentry>
201       
202        <varlistentry>
203          <term>
204            <interface>
205            <inlinemediaobject>
206            <imageobject><imagedata fileref="figures/recent.png" format="PNG" align="left"/></imageobject>
207            </inlinemediaobject>
208            Recent items
209            </interface>
210          </term>
211          <listitem>
212            <para>
213            Goto the most recently viewed item. By default, the list contains links to
214            the most recently viewed experiment and bioassayset, but this
215            is configurable. If you, for example, work a lot with protocols, you may
216            add a link to the most recently viewed protocol.
217            See <xref linkend="webclient.configuration.other"/>
218            </para>
219          </listitem>
220        </varlistentry>
221       
222        <varlistentry>
223          <term>
224            <interface>
225            <inlinemediaobject>
226            <imageobject><imagedata fileref="figures/project.gif" format="GIF" align="left"/></imageobject>
227            </inlinemediaobject>
228            Projects
229            </interface>
230          </term>
231          <listitem>
232            <para>
233            A list of all projects you are a member of. Selecting a project in the
234            list will make that project the active project.
235            </para>
236          </listitem>
237        </varlistentry>
238       
239        <varlistentry>
240          <term>
241            <interface>
242            <inlinemediaobject>
243            <imageobject><imagedata fileref="figures/user.png" format="PNG" align="left"/></imageobject>
244            </inlinemediaobject>
245            Logged in user
246            </interface>
247          </term>
248          <listitem>
249            <para>
250            Displays the name of the currently logged in user and allows
251            you to quickly logout and switch to another user.
252            </para>
253          </listitem>
254        </varlistentry>
255       
256      </variablelist>
257       
258      </sect2>
259     
260      <sect2 id="webclient.intro.help">
261        <title>Getting help</title>
262        <para>TODO</para>
263      </sect2>
264   
265    </sect1>
266   
267    <sect1 id="webclient.configuration">
268      <title>Configuring your account</title>
269     
270      <sect2 id="webclient.configuration.contact">
271        <title>Contact information</title>
272      </sect2>
273
274      <sect2 id="webclient.configuration.password">
275        <title>Changing password</title>
276      </sect2>
277
278      <sect2 id="webclient.configuration.other">
279        <title>Other settings</title>
280      </sect2>
281 
282    </sect1>
283   
284    <sect1 id="webclient.itemlist">
285      <title>Listing items</title>
286     
287      <para>
288        All pages that lists items are very similar in their appearance and
289        functionality. In this section we will describe the things that are
290        common for most (if not all) list pages.
291      </para>
292     
293      <para>
294        Use the <link linkend="webclient.intro.menubar">menu</link> to
295        open a page listing items. Most list pages can only
296        list one type of items. For example: use the
297        <menuchoice><guimenu>View</guimenu><guimenuitem>Samples</guimenuitem></menuchoice>
298        menu to list samples and the
299        <menuchoice><guimenu>View</guimenu><guimenuitem>Experiments</guimenuitem></menuchoice>
300        menu to list experiments. A typical list
301        page is shown below.
302      </para>
303     
304      <figure id="webclient.figures.listpage">
305        <title>Example of a list page</title>
306        <screenshot>
307          <mediaobject>
308            <imageobject><imagedata fileref="figures/listpage.png" format="PNG"/></imageobject>
309          </mediaobject>
310        </screenshot>
311      </figure>
312     
313      <para>
314        The typical list page contains the following important
315        elements:
316      </para>
317
318      <variablelist>
319        <varlistentry>
320          <term><interface>1. Toolbar</interface></term>
321          <listitem>
322            <para>
323            A toolbar with buttons for various actions such as
324            <guibutton>New&hellip;</guibutton> for creating a new item,
325            <guibutton>Delete</guibutton> for deleting items and
326            <guibutton>Columns&hellip;</guibutton> for configuring columns.
327            Depending on the permissions of the logged in user
328            some buttons may be disabled (greyed out) or not shown at all.
329            </para>
330          </listitem>
331        </varlistentry>
332       
333        <varlistentry>
334          <term><interface>2. Navigation bar</interface></term>
335          <listitem>
336            <para>
337            If there are many items the list will be divided into
338            pages showin a limited number of items at the same time.
339            The navigation bar allows you to
340            move to other pages and specify how many items each page
341            should display. The navigation bar is repeated at the
342            bottom of the list so you don't have to scroll back to the
343            top of a long list just to get to another page.
344            </para>
345          </listitem>
346        </varlistentry>
347       
348        <varlistentry>
349          <term><interface>3. List of presets</interface></term>
350          <listitem>
351            <para>
352            A list with preconfigured settings allowing you to
353            quickly switch between different layouts (sort order, visible
354            columns, filter settings, etc).
355            </para>
356          </listitem>
357        </varlistentry>
358       
359        <varlistentry>
360          <term><interface>4. Column headers</interface></term>
361          <listitem>
362            <para>
363            The columns headers can be used for selecting sort order.
364            </para>
365          </listitem>
366        </varlistentry>
367       
368        <varlistentry>
369          <term><interface>5. Filter bar</interface></term>
370          <listitem>
371            <para>
372            The filter bar allows you to search for items.
373            </para>
374          </listitem>
375        </varlistentry>
376       
377      </variablelist>
378     
379     
380      <sect2 id="webclient.itemlist.order">
381        <title>Ordering the list</title>
382       
383        <para>
384          Most lists are by default sorted by the name of the item. This can
385          be changed by clicking on the column header of another column.
386          If you click on the same column twice the sort order is reversed.
387          A downwards or upwards pointing arrow is displayed next to the
388          column header in the column that is currently used for sorting.
389          Column headers that are black can't be used for sorting.
390        </para>
391       
392        <para>
393          It is possible to use more than one column for sorting. Press
394          and hold one of the <keycap>CTRL</keycap>,
395          <keycap>ALT</keycap> or <keycap>SHIFT</keycap> keys while clicking
396          on another column header. The original sorting is kept and the new
397          column is used for sub-sorting the list. The procedure can be
398          repeated with more columns if you need to sort on three or more
399          columns. To revert to sort by only one column again click the
400          column header without holding down any key.
401        </para> 
402      </sect2>
403   
404      <sect2 id="webclient.itemlist.filter">
405        <title>Filtering the list</title>
406       
407        <para>
408          If the list contains many items you may need to use a filter to be
409          able to find the item you are looking for. The input boxes on the
410          line below the column headers are used for filtering. Most columns
411          are filtered using a free-text input box, but some columns that can
412          only take a few distinct values use a selection list or radio buttons
413          instead. The selection list and radio buttons are very simple to use.
414          Just select the alternative that you want to filter on. The list
415          will be automatically updated when the selection has been made.
416        </para>
417       
418        <para>
419          The free-text filter is a bit more complex. By default, an exact match is
420          required, use % as a wildcard that matches any character.
421          For example, the filter <informalexample>Experiment A</informalexample> 
422          only matches the same exact string, but the filter
423          <informalexample>Exp%</informalexample> matches
424          <informalexample>Experiment A, Experiment B, etc.</informalexample>
425        </para>
426       
427        <para>
428          You can also use operators to find items which has a value that
429          is greater than, less than or not equal to a specific value. This is
430          mostly useful on numeric or date columns but also works on text
431          columns. The operator must be entered first in the
432          free-text box, for example
433          <informalexample>&lt;=10</informalexample>
434          to find items which has a value less than or equal to 10.   
435          Here is a list of the supported operators:
436        </para>
437       
438        <variablelist id="webclient.itemlist.filter.operators">
439          <title>List of operators supported by the free-text filter</title>
440          <varlistentry>
441            <term><keycap>&lt;</keycap></term>
442            <listitem>Less than</listitem>
443          </varlistentry>
444          <varlistentry>
445            <term><keycap>&lt;=</keycap></term>
446            <listitem>Less than or equal to</listitem>
447          </varlistentry>
448          <varlistentry>
449            <term><keycap>&gt;</keycap></term>
450            <listitem>Greater than</listitem>
451          </varlistentry>
452          <varlistentry>
453            <term><keycap>&gt;=</keycap></term>
454            <listitem>Greater than or equal to</listitem>
455          </varlistentry>
456          <varlistentry>
457            <term><keycap>=</keycap></term>
458            <listitem>Equal to (useful to find items with a null value)</listitem>
459          </varlistentry>
460          <varlistentry>
461            <term><keycap>&lt;&gt;</keycap></term>
462            <term><keycap>!=</keycap></term>
463            <listitem>Not equal to (useful to find items with a non-null value)</listitem>
464          </varlistentry>
465        </variablelist>
466      </sect2>
467     
468      <sect2 id="webclient.itemlist.columns">
469        <title>Configuring which columns to show</title>
470       
471        <para>
472          Most lists show only a small subset of the columns it
473          is capable of showing. Use the
474          <guibutton>Columns&hellip;</guibutton> button to open
475          a dialog that allows you to select which columns to show
476          and the order in which they are shown.
477        </para>
478       
479        <figure id="webclient.figures.configure_columns">
480          <title>Configuring which columns to show</title>
481          <screenshot>
482          <mediaobject>
483            <imageobject>
484              <imagedata fileref="figures/configure_columns.png" format="PNG"/>
485            </imageobject>
486          </mediaobject>
487          </screenshot>
488        </figure>
489       
490        <para>
491          Use the left/right arrow buttons to move columns between
492          the <guilabel>Visible columns</guilabel> list and the
493          <guilabel>Hidden columns</guilabel> list. Use the up/down arrow
494          buttons to arrange the order of the visible columns. The topmost column
495          will be shown to the left.
496        </para>
497       
498        <para>
499          Columns marked with an <guilabel>×</guilabel> are required
500          and can't be hidden. In mosts lists the <guilabel>Name</guilabel> column
501          is the only column that is required.
502        </para>
503       
504        <para>
505          The <guilabel>Presets</guilabel> dropdown list allows you to
506          select a set of preconfigured columns. You may also create
507          your own preset if you often need to switch between different
508          configurations. The list of presets is the same as the one
509          described <link linkend="webclient.itemlist.presets">below</link>,
510          but if used from this dialog the presets doesn't affect filters,
511          sort order, etc.
512        </para>
513       
514       
515      </sect2>
516     
517      <sect2 id="webclient.itemlist.presets">
518        <title>Presets</title>
519       
520        <para>
521          The <guilabel>view / presets</guilabel> dropdown has three
522          main functions:
523        </para>
524       
525        <figure id="webclient.figures.viewpresets" float="right">
526          <title>The view / presets dropdown</title>
527          <screenshot>
528            <mediaobject>
529              <imageobject><imagedata fileref="figures/view_presets.png" format="PNG" /></imageobject>
530            </mediaobject>
531          </screenshot>
532        </figure>
533        <orderedlist>
534          <listitem>
535            <para>
536              Switch between different configuration presets.
537              The top of the dropdown contains user-defined presets (<guilabel>Saved preset #1</guilabel> and
538              <guilabel>#2</guilabel>) and a few preconfigured presets.
539              The user-defined presets are used to store a complete table configuration,
540              including:
541            </para>
542           
543            <itemizedlist>
544              <listitem>Which columns are visible and their order</listitem>
545              <listitem>The column (or columns) used for sorting</listitem>
546              <listitem>Filter settings</listitem>
547              <listitem>The number of items per page and the current page</listitem>
548            </itemizedlist>
549           
550            <para>             
551              The preconfigured presets only affects
552              the visible columns as follows:
553            </para>
554           
555            <itemizedlist>
556              <listitem>
557                <para><guilabel>All columns</guilabel> - Show all columns.</para>
558              </listitem>
559              <listitem>
560                <para><guilabel>Required columns</guilabel> - Show only the required columns.
561                  Usually only the <guilabel>Name</guilabel> column is required.</para>
562              </listitem>
563              <listitem>
564                <para><guilabel>Default columns</guilabel> - Show the default set of columns.</para>
565              </listitem>
566              <listitem>
567                <para><guilabel>Other&hellip;</guilabel> -
568                  Open the <link linkend="webclient.itemlist.columns">configure columns dialog box</link>.</para>
569              </listitem>
570            </itemizedlist>
571           
572          </listitem>
573         
574          <listitem>
575            <para>
576              Filter items by the removed status and the access
577              permissions to an item.
578            </para>
579           
580            <itemizedlist>
581              <listitem>
582                <para><guilabel>Removed</guilabel> - If checked, items that have been
583                marked for deletion are shown, otherwise they are hidden.</para>
584              </listitem>
585              <listitem>
586                <para><guilabel>Owned by me</guilabel> - If checked, items that the logged in user
587                owns are displayed, otherwise they are hidden.</para>
588              </listitem>
589              <listitem>
590                <para><guilabel>Shared to me</guilabel> - If checked, items that are owned
591                by other users but shared to the logged in user are displayed, otherwise
592                they are hidden.</para>
593              </listitem>
594              <listitem>
595                <para><guilabel>In current project</guilabel> -
596                  If checked, items that are linked with the current project are displayed,
597                  otherwise they are hidden. It doesn't matter if the logged in user is the
598                  owner or not. This option is only available if a project is active.
599                </para>
600              </listitem>
601              <listitem>
602                <para><guilabel>Owned by others</guilabel> -
603                  This option is only avilable to administrators and will display
604                  items that are owned by other users.
605                </para>
606              </listitem>
607            </itemizedlist>
608           
609            <para>
610              The default options are to only display items that the current
611              user owns and, if a project is active, items in that project.
612            </para>
613           
614          </listitem>
615
616          <listitem>
617            <para>
618              Administrate the presets
619            </para>
620            <itemizedlist>
621              <listitem>
622                <para><guilabel>Clear filter</guilabel> - Clears
623                all filters.</para>
624              </listitem>
625             
626              <listitem>
627                <para><guilabel>Save as&hellip;</guilabel> - Save the
628                current configuration as a preset.</para>
629              </listitem>
630
631              <listitem>
632                <para><guilabel>Manage&hellip;</guilabel> - Opens a dialog
633                where you can remove saved presets. You can also load
634                saved presets from the dialog, but it is quicker to just
635                use the dropdown list for this.</para>
636              </listitem>
637             
638            </itemizedlist>
639         
640         
641          </listitem>
642
643        </orderedlist>
644      </sect2>
645     
646    </sect1>
647   
648    <sect1 id="webclient.items">
649      <title>Working with items</title>
650     
651      <sect2 id="webclient.items.new">
652        <title>Creating a new item</title>
653      </sect2>
654     
655      <sect2 id="webclient.items.edit">
656        <title>Editing an existing item</title>
657      </sect2>
658
659      <sect2 id="webclient.items.delete">
660        <title>Delete an item</title>
661      </sect2>
662     
663      <sect2 id="webclient.items.restore">
664        <title>Restore a deleted item</title>
665      </sect2>
666
667    </sect1>
668   
669   
670</chapter>
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