source: trunk/doc/src/docbook/userdoc/webclient.xml @ 3221

Last change on this file since 3221 was 3221, checked in by Nicklas Nordborg, 16 years ago

References #525: Write "Using the web client"

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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 3221 2007-04-02 10:58:49Z 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 page
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.preferences.mostrecent"/>
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       
273        <para>
274          Use the <menuchoice><guimenu>File</guimenu>
275          <guimenuitem>Contact information</guimenuitem></menuchoice>
276          menu to bring up the contact information dialog. It contains
277          the following information:
278        </para>
279       
280        <helptext external_id="userpreferences.contact" title="Contact information">
281          <variablelist>
282            <varlistentry>
283              <term>
284                <guilabel>Email</guilabel>
285              </term>
286              <listitem>
287                Your email address (optional).
288              </listitem>
289            </varlistentry>
290            <varlistentry>
291              <term>
292                <guilabel>Organisation</guilabel>
293              </term>
294              <listitem>
295                The name of the organisation you work for or represent (optional).
296              </listitem>
297            </varlistentry>
298            <varlistentry>
299              <term>
300                <guilabel>Address</guilabel>
301              </term>
302              <listitem>
303                Your postal address as it should be printed on letters to you
304                (optional).
305              </listitem>
306            </varlistentry>
307            <varlistentry>
308              <term>
309                <guilabel>Phone</guilabel>
310              </term>
311              <listitem>
312                Your phone number (optional). You may enter multiple phone numbers,
313                for example your work phone number and a mobile number.
314              </listitem>
315            </varlistentry>
316            <varlistentry>
317              <term>
318                <guilabel>Fax</guilabel>
319              </term>
320              <listitem>
321                Your fax number (optional).
322              </listitem>
323            </varlistentry>
324            <varlistentry>
325              <term>
326                <guilabel>Url</guilabel>
327              </term>
328              <listitem>
329                An URL to your home page or your organisations home page (optional).
330              </listitem>
331            </varlistentry>
332          </variablelist>
333         
334          <note>
335            If you are using a multi-user account, for example a demo-account, you
336            are not able to change theese settings.
337          </note>
338         
339        </helptext>
340      </sect2>
341
342      <sect2 id="webclient.configuration.password">
343        <title>Changing password</title>
344       
345        <para>
346          Use the <menuchoice><guimenu>File</guimenu>
347          <guimenuitem>Change password</guimenuitem></menuchoice>
348          menu to bring up the change password dialog.
349        </para>
350       
351        <helptext external_id="userpreferences.password" title="Change password">
352          <variablelist>
353            <varlistentry>
354              <term>
355                <guilabel>New password</guilabel>
356              </term>
357              <listitem>
358                Enter the new password.
359              </listitem>
360            </varlistentry>
361            <varlistentry>
362              <term>
363                <guilabel>Retype password</guilabel>
364              </term>
365              <listitem>
366                Retype the same password. You must do this to
367                avoid spelling mistakes.
368              </listitem>
369            </varlistentry>
370          </variablelist>
371         
372          <note>
373            If you leave both fields empty the password will not be changed. It
374            is not possible to have an empty password.
375          </note>
376         
377          <note>
378            If you are using a multi-user account, for example a demo-account, you
379            are not able to change theese settings.
380          </note>
381         
382        </helptext>
383      </sect2>
384
385      <sect2 id="webclient.configuration.preferences">
386        <title>Preferences</title>
387       
388        <para>
389          Use the <menuchoice><guimenu>File</guimenu>
390          <guimenuitem>Preferences</guimenuitem></menuchoice>
391          menu to bring up the preferences dialog. It is divided into
392          three tabs.
393        </para>
394       
395        <sect3 id="webclient.configuration.preferences.appearance">
396          <title>Appearance</title>
397         
398          <helptext external_id="userpreferences.appearance" title="Preferences - Appearance">
399         
400          <para>
401          This tab contains settings that affect the appearance of the
402          web client.
403          </para>
404         
405          <variablelist>
406            <varlistentry>
407              <term>
408                <guilabel>Font size</guilabel>
409              </term>
410              <listitem>
411                Select a basic font size. You can choose between
412                five sizes: extra small (XS), small (S), medium (M),
413                large (L) and extra large (XL). The default font size is
414                medium.
415              </listitem>
416            </varlistentry>
417            <varlistentry>
418              <term>
419                <guilabel>Scale factor</guilabel>
420              </term>
421              <listitem>
422                The scale factor affects the size of popup windows.
423                This setting exists because different browsers render
424                pages differently. If you often find that popup windows
425                are too small you can change this setting to make them
426                bigger.
427                <note>
428                  The scale factor is automatically changed if the
429                  font size is changed.
430                </note>
431              </listitem>
432            </varlistentry>
433            <varlistentry>
434              <term>
435                <guilabel>Toolbar</guilabel>
436              </term>
437              <listitem>
438                You may choose if the toolbar buttons should
439                have only images, only text or both images and text.
440                The default is that they have both images and text.
441              </listitem>
442            </varlistentry>
443            <varlistentry>
444              <term>
445                <guilabel>Recently used items</guilabel>
446              </term>
447              <listitem>
448                The number of items to remember in the list
449                of recently used items. This will make data input
450                faster since fewer clicks are required to select
451                items. The default is to remember 4 items.
452              </listitem>
453            </varlistentry>
454            <varlistentry>
455              <term>
456                <guilabel>Ratio color range</guilabel>
457              </term>
458              <listitem>
459                Select three colors to use when displaying
460                data that is suitable for color coding, for
461                example the intensity ratio in two-color
462                experiments. The default setting is blue-black-yellow.
463                The list of presets contains other useful color combinations
464                (for example, the BASE 1 red-yellow-green) and the most
465                recently used color combinations.
466              </listitem>
467            </varlistentry>
468            <varlistentry>
469              <term>
470                <guilabel>Date format</guilabel>
471              </term>
472              <listitem>
473                <para>
474                A format string describing how dates should be displayed.
475                We support all formatting options supported by the Java
476                language. For more information see:
477                <ulink url="http://java.sun.com/j2se/1.5.0/docs/api/java/text/SimpleDateFormat.html">SimpleDateFormat documentation</ulink>
478                The most useful format patterns are:
479                </para>
480               
481                <itemizedlist>
482                  <listitem>yy: two-digit year</listitem>
483                  <listitem>yyyy: four-digit year</listitem>
484                  <listitem>MM: two-digit month</listitem>
485                  <listitem>MMM: month name (short)</listitem>
486                  <listitem>MMMM: month name (full)</listitem>
487                  <listitem>dd: two-digit day in month</listitem>
488                </itemizedlist>
489               
490                <para>
491                The list of presets contains the most commonly/recently
492                used date formats.
493                </para>
494               
495              </listitem>
496            </varlistentry>
497           
498            <varlistentry>
499              <term>
500                <guilabel>Date-time format</guilabel>
501              </term>
502              <listitem>
503                <para>
504                A format string describing how dates with times should be displayed.
505                We support all formatting options supported by the Java
506                language. For more information see:
507                <ulink url="http://java.sun.com/j2se/1.5.0/docs/api/java/text/SimpleDateFormat.html">SimpleDateFormat documentations</ulink>
508                The most useful time-format patterns are:
509                </para>
510               
511                <itemizedlist>
512                  <listitem>HH: two-digit hour (0-23)</listitem>
513                  <listitem>hh: two-digit hour (1-12)</listitem>
514                  <listitem>a: AM/PM marker</listitem>
515                  <listitem>mm: two-digit minute</listitem>
516                  <listitem>ss: two-digit second</listitem>
517                </itemizedlist>
518               
519              </listitem>
520            </varlistentry>
521           
522            <varlistentry>
523              <term>
524                <guilabel>Decimals</guilabel>
525              </term>
526              <listitem>
527                The number of decimals to display for numeric values.
528                The default is 2.
529              </listitem>
530            </varlistentry>
531           
532          </variablelist>
533       
534          </helptext>
535       
536        </sect3>
537       
538        <sect3 id="webclient.configuration.preferences.plugins">
539          <title>Plugins</title>
540         
541          <helptext external_id="userpreferences.plugins" title="Preferences - Plugins">
542         
543          <para>
544            This tab contains settings that affect plugin execution.
545          </para>
546         
547          <variablelist>
548            <varlistentry>
549              <term>
550                <guilabel>Messages</guilabel>
551              </term>
552              <listitem>
553                Mark the checkbox if you want to have a message sent
554                to you when a plugin completes execution. This setting
555                can be overridden each time you start a plugin.
556              </listitem>
557            </varlistentry>
558          </variablelist>
559          </helptext>
560         
561        </sect3>
562       
563        <sect3 id="webclient.configuration.preferences.mostrecent">
564          <title>Most recent</title>
565         
566          <helptext external_id="userpreferences.mostrecent" title="Preferences - Most recent">
567         
568          <para>
569            This tab contains settings that affect the <guilabel>Most
570            recent</guilabel> menu. You can select which items should
571            appear in the menu by moving them to the left list. Use
572            the up and down arrows to change the order in which they appear.
573          </para>
574         
575          <para>
576            If the <guilabel>Load the names of all recent items</guilabel> checkbox
577            is checked the name of the items will be displayed in the menu (for example,
578            Experiment: My experiment). Otherwise only the type of the item is
579            displayed (for example, Experiment).
580          </para>
581          </helptext>
582         
583        </sect3>
584      </sect2>
585 
586    </sect1>
587   
588    <sect1 id="webclient.itemlist">
589      <title>Listing items</title>
590     
591      <para>
592        All pages that lists items are very similar in their appearance and
593        functionality. In this section we will describe the things that are
594        common for most (if not all) list pages.
595      </para>
596     
597      <para>
598        Use the <link linkend="webclient.intro.menubar">menu</link> to
599        open a page listing items. Most list pages can only
600        list one type of items. For example: use the
601        <menuchoice><guimenu>View</guimenu><guimenuitem>Samples</guimenuitem></menuchoice>
602        menu to list samples and the
603        <menuchoice><guimenu>View</guimenu><guimenuitem>Experiments</guimenuitem></menuchoice>
604        menu to list experiments. An example of a list page that can list
605        items of several types is the <link linkend="trashcan">Trashcan</link>.     
606        A typical list page is shown below.
607      </para>
608     
609      <figure id="webclient.figures.listpage">
610        <title>Example of a list page</title>
611        <screenshot>
612          <mediaobject>
613            <imageobject><imagedata fileref="figures/listpage.png" format="PNG"/></imageobject>
614          </mediaobject>
615        </screenshot>
616      </figure>
617     
618      <para>
619        The typical list page contains the following important
620        elements:
621      </para>
622
623      <variablelist>
624        <varlistentry>
625          <term><interface>1. Toolbar</interface></term>
626          <listitem>
627            <para>
628            A toolbar with buttons for various actions such as
629            <guibutton>New&hellip;</guibutton> for creating a new item,
630            <guibutton>Delete</guibutton> for deleting items and
631            <guibutton>Columns&hellip;</guibutton> for configuring columns.
632            Depending on the permissions of the logged in user
633            some buttons may be disabled (greyed out) or not shown at all.
634            </para>
635          </listitem>
636        </varlistentry>
637       
638        <varlistentry>
639          <term><interface>2. Navigation bar</interface></term>
640          <listitem>
641            <para>
642            If there are many items the list will be divided into
643            pages showin a limited number of items at the same time.
644            The navigation bar allows you to
645            move to other pages and specify how many items each page
646            should display. The navigation bar is repeated at the
647            bottom of the list so you don't have to scroll back to the
648            top of a long list just to get to another page.
649            </para>
650          </listitem>
651        </varlistentry>
652       
653        <varlistentry>
654          <term><interface>3. List of presets</interface></term>
655          <listitem>
656            <para>
657            A list with preconfigured settings allowing you to
658            quickly switch between different layouts (sort order, visible
659            columns, filter settings, etc).
660            </para>
661          </listitem>
662        </varlistentry>
663       
664        <varlistentry>
665          <term><interface>4. Column headers</interface></term>
666          <listitem>
667            <para>
668            The columns headers can be used for selecting sort order.
669            </para>
670          </listitem>
671        </varlistentry>
672       
673        <varlistentry>
674          <term><interface>5. Filter bar</interface></term>
675          <listitem>
676            <para>
677            The filter bar allows you to search for items.
678            </para>
679          </listitem>
680        </varlistentry>
681       
682      </variablelist>
683     
684     
685      <sect2 id="webclient.itemlist.order">
686        <title>Ordering the list</title>
687       
688        <para>
689          Most lists are by default sorted by the name of the item. This can
690          be changed by clicking on the column header of another column.
691          If you click on the same column twice the sort order is reversed.
692          A downwards or upwards pointing arrow is displayed next to the
693          column header in the column that is currently used for sorting.
694          Column headers that are black can't be used for sorting.
695        </para>
696       
697        <para>
698          It is possible to use more than one column for sorting. Press
699          and hold one of the <keycap>CTRL</keycap>,
700          <keycap>ALT</keycap> or <keycap>SHIFT</keycap> keys while clicking
701          on another column header. The original sorting is kept and the new
702          column is used for sub-sorting the list. The procedure can be
703          repeated with more columns if you need to sort on three or more
704          columns. To revert to sort by only one column again click the
705          column header without holding down any key.
706        </para> 
707      </sect2>
708   
709      <sect2 id="webclient.itemlist.filter">
710        <title>Filtering the list</title>
711       
712        <para>
713          If the list contains many items you may need to use a filter to be
714          able to find the item you are looking for. The input boxes on the
715          line below the column headers are used for filtering. Most columns
716          are filtered using a free-text input box, but some columns that can
717          only take a few distinct values use a selection list or radio buttons
718          instead. The selection list and radio buttons are very simple to use.
719          Just select the alternative that you want to filter on. The list
720          will be automatically updated when the selection has been made.
721        </para>
722       
723        <para>
724          The free-text filter is a bit more complex. By default, an exact match is
725          required, use % as a wildcard that matches any character.
726          For example, the filter <informalexample>Experiment A</informalexample> 
727          only matches the same exact string, but the filter
728          <informalexample>Exp%</informalexample> matches
729          <informalexample>Experiment A, Experiment B, etc.</informalexample>
730        </para>
731       
732        <para>
733          You can also use operators to find items which has a value that
734          is greater than, less than or not equal to a specific value. This is
735          mostly useful on numeric or date columns but also works on text
736          columns. The operator must be entered first in the
737          free-text box, for example
738          <informalexample>&lt;=10</informalexample>
739          to find items which has a value less than or equal to 10.   
740          Here is a list of the supported operators:
741        </para>
742       
743        <variablelist id="webclient.itemlist.filter.operators">
744          <title>List of operators supported by the free-text filter</title>
745          <varlistentry>
746            <term><keycap>&lt;</keycap></term>
747            <listitem>Less than</listitem>
748          </varlistentry>
749          <varlistentry>
750            <term><keycap>&lt;=</keycap></term>
751            <listitem>Less than or equal to</listitem>
752          </varlistentry>
753          <varlistentry>
754            <term><keycap>&gt;</keycap></term>
755            <listitem>Greater than</listitem>
756          </varlistentry>
757          <varlistentry>
758            <term><keycap>&gt;=</keycap></term>
759            <listitem>Greater than or equal to</listitem>
760          </varlistentry>
761          <varlistentry>
762            <term><keycap>=</keycap></term>
763            <listitem>Equal to (useful to find items with a null value)</listitem>
764          </varlistentry>
765          <varlistentry>
766            <term><keycap>&lt;&gt;</keycap></term>
767            <term><keycap>!=</keycap></term>
768            <listitem>Not equal to (useful to find items with a non-null value)</listitem>
769          </varlistentry>
770        </variablelist>
771      </sect2>
772     
773      <sect2 id="webclient.itemlist.columns">
774        <title>Configuring which columns to show</title>
775       
776        <para>
777          Most lists show only a small subset of the columns it
778          is capable of showing. Use the
779          <guibutton>Columns&hellip;</guibutton> button to open
780          a dialog that allows you to select which columns to show
781          and the order in which they are shown.
782        </para>
783       
784        <figure id="webclient.figures.configure_columns">
785          <title>Configuring which columns to show</title>
786          <screenshot>
787          <mediaobject>
788            <imageobject>
789              <imagedata fileref="figures/configure_columns.png" format="PNG"/>
790            </imageobject>
791          </mediaobject>
792          </screenshot>
793        </figure>
794       
795        <para>
796          Use the left/right arrow buttons to move columns between
797          the <guilabel>Visible columns</guilabel> list and the
798          <guilabel>Hidden columns</guilabel> list. Use the up/down arrow
799          buttons to arrange the order of the visible columns. The topmost column
800          will be shown to the left.
801        </para>
802       
803        <para>
804          Columns marked with an <guilabel>×</guilabel> are required
805          and can't be hidden. In mosts lists the <guilabel>Name</guilabel> column
806          is the only column that is required.
807        </para>
808       
809        <para>
810          The <guilabel>Presets</guilabel> dropdown list allows you to
811          select a set of preconfigured columns. You may also create
812          your own preset if you often need to switch between different
813          configurations. The list of presets is the same as the one
814          described <link linkend="webclient.itemlist.presets">below</link>,
815          but if used from this dialog the presets doesn't affect filters,
816          sort order, etc.
817        </para>
818       
819       
820      </sect2>
821     
822      <sect2 id="webclient.itemlist.presets">
823        <title>Presets</title>
824       
825        <para>
826          The <guilabel>view / presets</guilabel> dropdown has three
827          main functions:
828        </para>
829       
830        <figure id="webclient.figures.viewpresets" float="right">
831          <title>The view / presets dropdown</title>
832          <screenshot>
833            <mediaobject>
834              <imageobject><imagedata fileref="figures/view_presets.png" format="PNG" /></imageobject>
835            </mediaobject>
836          </screenshot>
837        </figure>
838        <orderedlist>
839          <listitem>
840            <para>
841              Switch between different configuration presets.
842              The top of the dropdown contains user-defined presets (<guilabel>Saved preset #1</guilabel> and
843              <guilabel>#2</guilabel>) and a few preconfigured presets.
844              The user-defined presets are used to store a complete table configuration,
845              including:
846            </para>
847           
848            <itemizedlist>
849              <listitem>Which columns are visible and their order</listitem>
850              <listitem>The column (or columns) used for sorting</listitem>
851              <listitem>Filter settings</listitem>
852              <listitem>The number of items per page and the current page</listitem>
853            </itemizedlist>
854           
855            <para>             
856              The preconfigured presets only affects
857              the visible columns as follows:
858            </para>
859           
860            <itemizedlist>
861              <listitem>
862                <para><guilabel>All columns</guilabel> - Show all columns.</para>
863              </listitem>
864              <listitem>
865                <para><guilabel>Required columns</guilabel> - Show only the required columns.
866                  Usually only the <guilabel>Name</guilabel> column is required.</para>
867              </listitem>
868              <listitem>
869                <para><guilabel>Default columns</guilabel> - Show the default set of columns.</para>
870              </listitem>
871              <listitem>
872                <para><guilabel>Other&hellip;</guilabel> -
873                  Open the <link linkend="webclient.itemlist.columns">configure columns dialog box</link>.</para>
874              </listitem>
875            </itemizedlist>
876           
877          </listitem>
878         
879          <listitem>
880            <para>
881              Filter items by the removed status and the access
882              permissions to an item.
883            </para>
884           
885            <itemizedlist>
886              <listitem>
887                <para><guilabel>Removed</guilabel> - If checked, items that have been
888                marked for deletion are shown, otherwise they are hidden.</para>
889              </listitem>
890              <listitem>
891                <para><guilabel>Owned by me</guilabel> - If checked, items that the logged in user
892                owns are displayed, otherwise they are hidden.</para>
893              </listitem>
894              <listitem>
895                <para><guilabel>Shared to me</guilabel> - If checked, items that are owned
896                by other users but shared to the logged in user are displayed, otherwise
897                they are hidden.</para>
898              </listitem>
899              <listitem>
900                <para><guilabel>In current project</guilabel> -
901                  If checked, items that are linked with the current project are displayed,
902                  otherwise they are hidden. It doesn't matter if the logged in user is the
903                  owner or not. This option is only available if a project is active.
904                </para>
905              </listitem>
906              <listitem>
907                <para><guilabel>Owned by others</guilabel> -
908                  This option is only avilable to administrators and will display
909                  items that are owned by other users.
910                </para>
911              </listitem>
912            </itemizedlist>
913           
914            <para>
915              The default options are to only display items that the current
916              user owns and, if a project is active, items in that project.
917            </para>
918           
919          </listitem>
920
921          <listitem>
922            <para>
923              Administrate the presets
924            </para>
925            <itemizedlist>
926              <listitem>
927                <para><guilabel>Clear filter</guilabel> - Clears
928                all filters.</para>
929              </listitem>
930             
931              <listitem>
932                <para><guilabel>Save as&hellip;</guilabel> - Save the
933                current configuration as a preset.</para>
934              </listitem>
935
936              <listitem>
937                <para><guilabel>Manage&hellip;</guilabel> - Opens a dialog
938                where you can remove saved presets. You can also load
939                saved presets from the dialog, but it is quicker to just
940                use the dropdown list for this.</para>
941              </listitem>
942             
943            </itemizedlist>
944         
945         
946          </listitem>
947
948        </orderedlist>
949      </sect2>
950     
951    </sect1>
952   
953    <sect1 id="webclient.items">
954      <title>Working with items</title>
955     
956      <para>
957        No matter what you are doing in BASE some things works more
958        or less in the same way. This section convers things that are
959        common for most parts of BASE.
960      </para>
961             
962      <sect2 id="webclient.items.new">
963        <title>Create a new item</title>
964       
965        <para>
966          New items are mostly created from the list view. For example,
967          to create a new experiment go to the
968          <menuchoice><guimenu>View</guimenu> <guimenuitem>Experiments</guimenuitem></menuchoice>
969          page. Here you will find a <guibutton>New&hellip;</guibutton> button in the
970          toolbar. The button is disabled if you don't have permission to create new experiments.
971          Otherwise, click on it and enter any required information in the popup dialog.
972          Sometimes there are multiple tabs in this dialog. In the case of experiments
973          there are three tabs: <guilabel>Experiment</guilabel>, <guilabel>Publication</guilabel>
974          and <guilabel>Experimental factors</guilabel>.
975         
976          As a general rule, only the first tab has information that is required.
977          The information in all other tabs are optional.
978        </para>
979       
980        <para>
981          Click on the <guibutton>Save</guibutton> button to save the new
982          experiment to the database or on the <guibutton>Cancel</guibutton> button
983          to abort.
984        </para>
985
986        <note>
987          <para>
988          To speed up data entry when adding multiple new items there
989          are a few tricks you can use to make the web client to enter
990          default values for most properties. To find a default value
991          the following checklist is used in this order.
992          </para>
993       
994        <orderedlist>         
995          <listitem>
996            If the list have an active filter the filter values are
997            used as default property values for the new item. For example,
998            if you are listing experiments with <guilabel>Genepix</guilabel>
999            raw data type the new experiment will automatically have
1000            <guilabel>Genepix</guilabel> selected. This trick should work
1001            for all properties except annotations.       
1002          </listitem>
1003         
1004          <listitem>
1005            When you link to other items the same item will be used the next time.
1006            For example the extraction protocol used to create an extract from a sample
1007            is remembered and the same protocol is used the next time you create an extract.
1008            In fact, BASE will remember as many items as specified by
1009            the <link linkend="webclient.configuration.preferences.appearance">
1010            <guilabel>Recently used items</guilabel></link> setting (default is 4).
1011          </listitem>
1012         
1013          <listitem>
1014            If you have a project active and that project has specified default
1015            values those values will be used for new items. A project can specify
1016            defaults for protocols, hardware and software and a few other settings.
1017          </listitem>
1018         
1019        </orderedlist>
1020       
1021        </note>
1022       
1023      </sect2>
1024     
1025      <sect2 id="webclient.items.edit">
1026        <title>Edit an existing item</title>
1027       
1028        <para>
1029          On all single-item views there is an <guibutton>Edit&hellip;</guibutton>
1030          button in the toolbar that opens a popup dialog for editing the properties
1031          of the item. This button is disabled if the logged in user doesn't have
1032          write permission for the item.
1033        </para>
1034       
1035        <para>
1036          You don't have to go to the single-item view to edit an item.
1037          Whenever an item appear in a list or another place and has a link
1038          on it, you can use a shortcut to open it's edit popup. Press
1039          and hold one of the <keycap>CTRL</keycap>,
1040          <keycap>ALT</keycap> or <keycap>SHIFT</keycap> keys while clicking on the
1041          link. This will open the edit popup dialog for the item. If you don't
1042          have write permission you will be taken to the single-item view of
1043          that item instead.
1044        </para>
1045
1046     
1047      </sect2>
1048
1049      <sect2 id="webclient.items.delete">
1050        <title>Delete items</title>
1051
1052        <para>
1053          You can delete items either from the list view or from
1054          a single-item view. In both cases, the item is only marked
1055          as beeing removed. It is not deleted from the database. This allows
1056          you to restore the item if you later find out that you need it again.
1057          In fact, there is nothing special about a removed item. It can still be
1058          used for the same things as any non-removed item can.
1059        </para>
1060
1061        <important>
1062          To really delete an item from the database you must use
1063          the <link linkend="trashcan">trashcan</link>.
1064        </important>
1065       
1066        <para>
1067          To delete items from the list view you must first mark
1068          the checkbox for each item you want to delete. Then, click on
1069          the <guibutton>Delete</guibutton> button. The list should refresh iteself
1070          automatically. If you want to confirm that the items have been removed
1071          use the <guilabel>view / presets</guilabel> dropdown and select
1072          the <guilabel>Removed</guilabel> option. The removed items should now
1073          be displayed in the list with a small trashcan icon to indicate that
1074          they have been removed.
1075        </para>
1076
1077        <para>
1078          To delete items from the single-item view you just click on the
1079          <guibutton>Delete</guibutton> in the toolbar. The page will refresh
1080          itself automatically and a small trashcan icon should be displayed.
1081          If you don't have permission to delete the item the delete button
1082          will be disabled.
1083        </para>
1084
1085      </sect2>
1086     
1087      <sect2 id="webclient.items.restore">
1088        <title>Restore deleted items</title>
1089       
1090        <para>
1091          You can restore deleted items either from the <link linkend="trashcan">trashcan</link>,
1092          from the list view or from the single-item view. This section only covers the last two
1093          cases. The trashcan has a chapter of it's own.
1094        </para>
1095
1096        <para>
1097          To delete items from the list view you must first make the deleted
1098          items appear in the list. This is easy, just use the <guilabel>view / presets</guilabel> 
1099          dropdown and select the <guilabel>Removed</guilabel> option. This list should
1100          refresh itself automatically. The removed items should now
1101          be displayed in the list with a small trashcan icon to indicate that
1102          they have been removed. Then, mark the checkbox for each item that you want
1103          to restore and click the <guibutton>Restore</guibutton> button. The list should
1104          refresh iteself automatically and the trashcan icon should be gone from the
1105          restored items.
1106        </para>
1107       
1108        <para>
1109          To restore items from the single-item view you just click on the
1110          <guibutton>Restore</guibutton> in the toolbar. The page will refresh
1111          itself automatically and the small trashcan icon should be gone.
1112          If you don't have permission to restore the item the restore button
1113          will be disabled.
1114        </para>
1115
1116      </sect2>
1117
1118    </sect1>
1119   
1120   
1121</chapter>
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