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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.
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10	This file is part of BASE - BioArray Software Environment.
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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…</guibutton> for creating a new item,
630	<guibutton>Delete</guibutton> for deleting items and
631	<guibutton>Columns…</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><=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><</keycap></term>
747	<listitem>Less than</listitem>
748	</varlistentry>
749	<varlistentry>
750	<term><keycap><=</keycap></term>
751	<listitem>Less than or equal to</listitem>
752	</varlistentry>
753	<varlistentry>
754	<term><keycap>></keycap></term>
755	<listitem>Greater than</listitem>
756	</varlistentry>
757	<varlistentry>
758	<term><keycap>>=</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><></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…</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…</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…</guilabel> - Save the
933	current configuration as a preset.</para>
934	</listitem>
935
936	<listitem>
937	<para><guilabel>Manage…</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…</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…</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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