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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.
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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…</guibutton> for creating a new item,
631	<guibutton>Delete</guibutton> for deleting items and
632	<guibutton>Columns…</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><=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><</keycap></term>
748	<listitem>Less than</listitem>
749	</varlistentry>
750	<varlistentry>
751	<term><keycap><=</keycap></term>
752	<listitem>Less than or equal to</listitem>
753	</varlistentry>
754	<varlistentry>
755	<term><keycap>></keycap></term>
756	<listitem>Greater than</listitem>
757	</varlistentry>
758	<varlistentry>
759	<term><keycap>>=</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><></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…</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…</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…</guilabel> - Save the
934	current configuration as a preset.</para>
935	</listitem>
936
937	<listitem>
938	<para><guilabel>Manage…</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…</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…</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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