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Using the menu bar section.
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1	<?xml version="1.0" encoding="UTF-8"?>
2	<!DOCTYPE chapter PUBLIC
3	"-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN"
4	"../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd">
5	<!--
6	$Id: webclient.xml 3214 2007-03-26 14:01:26Z nicklas $
7
8	Copyright (C) Authors contributing to this file.
9
10	This file is part of BASE - BioArray Software Environment.
11	Available at http://base.thep.lu.se/
12
13	BASE is free software; you can redistribute it and/or
14	modify it under the terms of the GNU General Public License
15	as published by the Free Software Foundation; either version 2
16	of the License, or (at your option) any later version.
17
18	BASE is distributed in the hope that it will be useful,
19	but WITHOUT ANY WARRANTY; without even the implied warranty of
20	MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
21	GNU General Public License for more details.
22
23	You should have received a copy of the GNU General Public License
24	along with this program; if not, write to the Free Software
25	Foundation, Inc., 59 Temple Place - Suite 330,
26	Boston, MA 02111-1307, USA.
27	-->
28
29	<chapter id="webclient">
30	<title>Using the web client</title>
31	<sect1 id="webclient.introduction">
32	<title>Introduction</title>
33	<para></para>
34
35	<sect2 id="webclient.intro.login">
36	<title>Logging in</title>
37	<para>
38	There are three things that you need to know
39	before you can use BASE:
40	</para>
41
42	<orderedlist>
43	<listitem>The address (URL) to a BASE server</listitem>
44	<listitem>A username to login with</listitem>
45	<listitem>A password</listitem>
46	</orderedlist>
47
48	<para>
49	You may, for example, try the BASE 2 demo server. Go to the
50	URL <ulink url="http://base2.thep.lu.se:8080/demo/">http://base2.thep.lu.se:8080/demo/</ulink>
51	and enter <userinput>base2</userinput> for the login and <userinput>base2</userinput>
52	for the password.
53	</para>
54
55	<para>
56	You will need to get all three things from a adminstrator
57	of the BASE server. If you know only the address to the
58	BASE server, you may check the front page if the administrator
59	has added any information about how to get a username/password
60	there. Look for a link named <guilabel>Get an account!</guilabel>.
61	</para>
62
63	<para>
64	Logging in is simple, just enter your <guilabel>login</guilabel>
65	and <guilabel>password</guilabel> in the input fields. There is
66	a checkbox which allows you to <guilabel>encrypt the password</guilabel>
67	before it is sent to the BASE server. It is enabled by default, and
68	it is a good idea to leave it checked unless you have problems logging
69	in. If you are sure you are entering the correct login and password,
70	but still can't log in, try unchecking the encyption option.
71	</para>
72	</sect2>
73
74	<sect2 id="webclient.intro.homepage">
75	<title>The home page</title>
76
77	<para>
78	When you have been logged in the home page will be displayed. It
79	displays some useful information.
80	</para>
81
82	<figure id="webclient.figures.homepage">
83	<title>The home page</title>
84	<screenshot>
85	<mediaobject>
86	<imageobject><imagedata fileref="figures/homepage.png" format="PNG"/></imageobject>
87	</mediaobject>
88	</screenshot>
89	</figure>
90
91	<variablelist>
92	<varlistentry>
93	<term><interface>New messages</interface></term>
94	<listitem>
95	<para>
96	Messages are sent by plugins to notify you about finished jobs. In the
97	future, you may get messages from other sources as well. As of today,
98	messages are not used for communication between users.
99	</para>
100	</listitem>
101	</varlistentry>
102
103	<varlistentry>
104	<term><interface>Projects</interface></term>
105	<listitem>
106	<para>
107	A list of projects that you are a member of. It is possible
108	to activate a project from this list. We recommend
109	that you always use a project when working with BASE. It will
110	make your life much easier once you start to cooperate with
111	other users. For more information read <xref linkend="project_permission"/>.
112	</para>
113	</listitem>
114	</varlistentry>
115
116	<varlistentry>
117	<term><interface>Disk usage</interface></term>
118	<listitem>
119	<para>
120	An overview of how much disk space you have been assigned and
121	how much you are using.
122	</para>
123	</listitem>
124	</varlistentry>
125
126	<varlistentry>
127	<term><interface>Help</interface></term>
128	<listitem>
129	<para>
130	Links for getting help and reporting bugs. The number
131	of links displayed here may vary depending on how the administrator
132	have set up the server.
133	</para>
134	</listitem>
135	</varlistentry>
136
137	<varlistentry>
138	<term><interface>News and announcements</interface></term>
139	<listitem>
140	<para>
141	A list of important news and announcements from the
142	server administrator. Here you may, for example, find
143	information about server upgrades and maintenance.
144	</para>
145	</listitem>
146	</varlistentry>
147	</variablelist>
148
149	</sect2>
150
151	<sect2 id="webclient.intro.menubar">
152	<title>Using the menu bar</title>
153	<para>
154	On the top of the home page is the <interface>Menu bar</interface>.
155	This is the main navigation tool in BASE. It works the same way
156	as the regular menu system found in most other applications. Use
157	the mouse to click and select an item from the menu.
158	</para>
159
160	<para>
161	Most of the menu is in two levels, ie. clicking on a top-level menu
162	will open a submenu just below it. Clicking on something in the
163	submenu will take you to another page or open a popup. For example, the
164	<menuchoice><guimenu>View</guimenu><guimenuitem>Samples</guimenuitem></menuchoice>
165	menu will take you to the page listing
166	samples.
167	</para>
168
169	<para>
170	The menu bar also contains shortcuts to some often-used
171	actions:
172	</para>
173
174
175	<variablelist>
176	<varlistentry>
177	<term>
178	<interface>
179	<inlinemediaobject>
180	<imageobject><imagedata fileref="figures/refresh.gif" format="GIF" align="left"/></imageobject>
181	</inlinemediaobject>
182	Refresh button
183	</interface>
184	</term>
185	<listitem>
186	<para>
187	Refresh/reload the current page. This is useful when you add
188	or modify items in BASE. Most of the time the page is refreshed
189	automatically, but in some cases you will have to use
190	this button to refresh the page.
191	</para>
192
193	<warning>
194	<para>
195	Do not use your browser's <guibutton>Refresh</guibutton> button
196	since it will take you to the login page again.
197	</para>
198	</warning>
199	</listitem>
200	</varlistentry>
201
202	<varlistentry>
203	<term>
204	<interface>
205	<inlinemediaobject>
206	<imageobject><imagedata fileref="figures/recent.png" format="PNG" align="left"/></imageobject>
207	</inlinemediaobject>
208	Recent items
209	</interface>
210	</term>
211	<listitem>
212	<para>
213	Goto the most recently viewed item. By default, the list contains links to
214	the most recently viewed experiment and bioassayset, but this
215	is configurable. If you, for example, work a lot with protocols, you may
216	add a link to the most recently viewed protocol.
217	See <xref linkend="webclient.configuration.other"/>
218	</para>
219	</listitem>
220	</varlistentry>
221
222	<varlistentry>
223	<term>
224	<interface>
225	<inlinemediaobject>
226	<imageobject><imagedata fileref="figures/project.gif" format="GIF" align="left"/></imageobject>
227	</inlinemediaobject>
228	Projects
229	</interface>
230	</term>
231	<listitem>
232	<para>
233	A list of all projects you are a member of. Selecting a project in the
234	list will make that project the active project.
235	</para>
236	</listitem>
237	</varlistentry>
238
239	<varlistentry>
240	<term>
241	<interface>
242	<inlinemediaobject>
243	<imageobject><imagedata fileref="figures/user.png" format="PNG" align="left"/></imageobject>
244	</inlinemediaobject>
245	Logged in user
246	</interface>
247	</term>
248	<listitem>
249	<para>
250	Displays the name of the currently logged in user and allows
251	you to quickly logout and switch to another user.
252	</para>
253	</listitem>
254	</varlistentry>
255
256	</variablelist>
257
258	</sect2>
259
260	<sect2 id="webclient.intro.help">
261	<title>Getting help</title>
262	<para>TODO</para>
263	</sect2>
264
265	</sect1>
266
267	<sect1 id="webclient.configuration">
268	<title>Configuring your account</title>
269
270	<sect2 id="webclient.configuration.contact">
271	<title>Contact information</title>
272	</sect2>
273
274	<sect2 id="webclient.configuration.password">
275	<title>Changing password</title>
276	</sect2>
277
278	<sect2 id="webclient.configuration.other">
279	<title>Other settings</title>
280	</sect2>
281
282	</sect1>
283
284	<sect1 id="webclient.itemlist">
285	<title>Listing items</title>
286
287	<para>
288	All pages that lists items are very similar in their appearance and
289	functionality. In this section we will describe the things that are
290	common for most (if not all) list pages.
291	</para>
292
293	<para>
294	Use the <link linkend="webclient.intro.menubar">menu</link> to
295	open a page listing items. Most list pages can only
296	list one type of items. For example: use the
297	<menuchoice><guimenu>View</guimenu><guimenuitem>Samples</guimenuitem></menuchoice>
298	menu to list samples and the
299	<menuchoice><guimenu>View</guimenu><guimenuitem>Experiments</guimenuitem></menuchoice>
300	menu to list experiments. A typical list
301	page is shown below.
302	</para>
303
304	<figure id="webclient.figures.listpage">
305	<title>Example of a list page</title>
306	<screenshot>
307	<mediaobject>
308	<imageobject><imagedata fileref="figures/listpage.png" format="PNG"/></imageobject>
309	</mediaobject>
310	</screenshot>
311	</figure>
312
313	<para>
314	The typical list page contains the following important
315	elements:
316	</para>
317
318	<variablelist>
319	<varlistentry>
320	<term><interface>1. Toolbar</interface></term>
321	<listitem>
322	<para>
323	A toolbar with buttons for various actions such as
324	<guibutton>New…</guibutton> for creating a new item,
325	<guibutton>Delete</guibutton> for deleting items and
326	<guibutton>Columns…</guibutton> for configuring columns.
327	Depending on the permissions of the logged in user
328	some buttons may be disabled (greyed out) or not shown at all.
329	</para>
330	</listitem>
331	</varlistentry>
332
333	<varlistentry>
334	<term><interface>2. Navigation bar</interface></term>
335	<listitem>
336	<para>
337	If there are many items the list will be divided into
338	pages showin a limited number of items at the same time.
339	The navigation bar allows you to
340	move to other pages and specify how many items each page
341	should display. The navigation bar is repeated at the
342	bottom of the list so you don't have to scroll back to the
343	top of a long list just to get to another page.
344	</para>
345	</listitem>
346	</varlistentry>
347
348	<varlistentry>
349	<term><interface>3. List of presets</interface></term>
350	<listitem>
351	<para>
352	A list with preconfigured settings allowing you to
353	quickly switch between different layouts (sort order, visible
354	columns, filter settings, etc).
355	</para>
356	</listitem>
357	</varlistentry>
358
359	<varlistentry>
360	<term><interface>4. Column headers</interface></term>
361	<listitem>
362	<para>
363	The columns headers can be used for selecting sort order.
364	</para>
365	</listitem>
366	</varlistentry>
367
368	<varlistentry>
369	<term><interface>5. Filter bar</interface></term>
370	<listitem>
371	<para>
372	The filter bar allows you to search for items.
373	</para>
374	</listitem>
375	</varlistentry>
376
377	</variablelist>
378
379
380	<sect2 id="webclient.itemlist.order">
381	<title>Ordering the list</title>
382
383	<para>
384	Most lists are by default sorted by the name of the item. This can
385	be changed by clicking on the column header of another column.
386	If you click on the same column twice the sort order is reversed.
387	A downwards or upwards pointing arrow is displayed next to the
388	column header in the column that is currently used for sorting.
389	Column headers that are black can't be used for sorting.
390	</para>
391
392	<para>
393	It is possible to use more than one column for sorting. Press
394	and hold one of the <keycap>CTRL</keycap>,
395	<keycap>ALT</keycap> or <keycap>SHIFT</keycap> keys while clicking
396	on another column header. The original sorting is kept and the new
397	column is used for sub-sorting the list. The procedure can be
398	repeated with more columns if you need to sort on three or more
399	columns. To revert to sort by only one column again click the
400	column header without holding down any key.
401	</para>
402	</sect2>
403
404	<sect2 id="webclient.itemlist.filter">
405	<title>Filtering the list</title>
406
407	<para>
408	If the list contains many items you may need to use a filter to be
409	able to find the item you are looking for. The input boxes on the
410	line below the column headers are used for filtering. Most columns
411	are filtered using a free-text input box, but some columns that can
412	only take a few distinct values use a selection list or radio buttons
413	instead. The selection list and radio buttons are very simple to use.
414	Just select the alternative that you want to filter on. The list
415	will be automatically updated when the selection has been made.
416	</para>
417
418	<para>
419	The free-text filter is a bit more complex. By default, an exact match is
420	required, use % as a wildcard that matches any character.
421	For example, the filter <informalexample>Experiment A</informalexample>
422	only matches the same exact string, but the filter
423	<informalexample>Exp%</informalexample> matches
424	<informalexample>Experiment A, Experiment B, etc.</informalexample>
425	</para>
426
427	<para>
428	You can also use operators to find items which has a value that
429	is greater than, less than or not equal to a specific value. This is
430	mostly useful on numeric or date columns but also works on text
431	columns. The operator must be entered first in the
432	free-text box, for example
433	<informalexample><=10</informalexample>
434	to find items which has a value less than or equal to 10.
435	Here is a list of the supported operators:
436	</para>
437
438	<variablelist id="webclient.itemlist.filter.operators">
439	<title>List of operators supported by the free-text filter</title>
440	<varlistentry>
441	<term><keycap><</keycap></term>
442	<listitem>Less than</listitem>
443	</varlistentry>
444	<varlistentry>
445	<term><keycap><=</keycap></term>
446	<listitem>Less than or equal to</listitem>
447	</varlistentry>
448	<varlistentry>
449	<term><keycap>></keycap></term>
450	<listitem>Greater than</listitem>
451	</varlistentry>
452	<varlistentry>
453	<term><keycap>>=</keycap></term>
454	<listitem>Greater than or equal to</listitem>
455	</varlistentry>
456	<varlistentry>
457	<term><keycap>=</keycap></term>
458	<listitem>Equal to (useful to find items with a null value)</listitem>
459	</varlistentry>
460	<varlistentry>
461	<term><keycap><></keycap></term>
462	<term><keycap>!=</keycap></term>
463	<listitem>Not equal to (useful to find items with a non-null value)</listitem>
464	</varlistentry>
465	</variablelist>
466	</sect2>
467
468	<sect2 id="webclient.itemlist.columns">
469	<title>Configuring which columns to show</title>
470
471	<para>
472	Most lists show only a small subset of the columns it
473	is capable of showing. Use the
474	<guibutton>Columns…</guibutton> button to open
475	a dialog that allows you to select which columns to show
476	and the order in which they are shown.
477	</para>
478
479	<figure id="webclient.figures.configure_columns">
480	<title>Configuring which columns to show</title>
481	<screenshot>
482	<mediaobject>
483	<imageobject>
484	<imagedata fileref="figures/configure_columns.png" format="PNG"/>
485	</imageobject>
486	</mediaobject>
487	</screenshot>
488	</figure>
489
490	<para>
491	Use the left/right arrow buttons to move columns between
492	the <guilabel>Visible columns</guilabel> list and the
493	<guilabel>Hidden columns</guilabel> list. Use the up/down arrow
494	buttons to arrange the order of the visible columns. The topmost column
495	will be shown to the left.
496	</para>
497
498	<para>
499	Columns marked with an <guilabel>×</guilabel> are required
500	and can't be hidden. In mosts lists the <guilabel>Name</guilabel> column
501	is the only column that is required.
502	</para>
503
504	<para>
505	The <guilabel>Presets</guilabel> dropdown list allows you to
506	select a set of preconfigured columns. You may also create
507	your own preset if you often need to switch between different
508	configurations. The list of presets is the same as the one
509	described <link linkend="webclient.itemlist.presets">below</link>,
510	but if used from this dialog the presets doesn't affect filters,
511	sort order, etc.
512	</para>
513
514
515	</sect2>
516
517	<sect2 id="webclient.itemlist.presets">
518	<title>Presets</title>
519
520	<para>
521	The <guilabel>view / presets</guilabel> dropdown has three
522	main functions:
523	</para>
524
525	<figure id="webclient.figures.viewpresets" float="right">
526	<title>The view / presets dropdown</title>
527	<screenshot>
528	<mediaobject>
529	<imageobject><imagedata fileref="figures/view_presets.png" format="PNG" /></imageobject>
530	</mediaobject>
531	</screenshot>
532	</figure>
533	<orderedlist>
534	<listitem>
535	<para>
536	Switch between different configuration presets.
537	The top of the dropdown contains user-defined presets (<guilabel>Saved preset #1</guilabel> and
538	<guilabel>#2</guilabel>) and a few preconfigured presets.
539	The user-defined presets are used to store a complete table configuration,
540	including:
541	</para>
542
543	<itemizedlist>
544	<listitem>Which columns are visible and their order</listitem>
545	<listitem>The column (or columns) used for sorting</listitem>
546	<listitem>Filter settings</listitem>
547	<listitem>The number of items per page and the current page</listitem>
548	</itemizedlist>
549
550	<para>
551	The preconfigured presets only affects
552	the visible columns as follows:
553	</para>
554
555	<itemizedlist>
556	<listitem>
557	<para><guilabel>All columns</guilabel> - Show all columns.</para>
558	</listitem>
559	<listitem>
560	<para><guilabel>Required columns</guilabel> - Show only the required columns.
561	Usually only the <guilabel>Name</guilabel> column is required.</para>
562	</listitem>
563	<listitem>
564	<para><guilabel>Default columns</guilabel> - Show the default set of columns.</para>
565	</listitem>
566	<listitem>
567	<para><guilabel>Other…</guilabel> -
568	Open the <link linkend="webclient.itemlist.columns">configure columns dialog box</link>.</para>
569	</listitem>
570	</itemizedlist>
571
572	</listitem>
573
574	<listitem>
575	<para>
576	Filter items by the removed status and the access
577	permissions to an item.
578	</para>
579
580	<itemizedlist>
581	<listitem>
582	<para><guilabel>Removed</guilabel> - If checked, items that have been
583	marked for deletion are shown, otherwise they are hidden.</para>
584	</listitem>
585	<listitem>
586	<para><guilabel>Owned by me</guilabel> - If checked, items that the logged in user
587	owns are displayed, otherwise they are hidden.</para>
588	</listitem>
589	<listitem>
590	<para><guilabel>Shared to me</guilabel> - If checked, items that are owned
591	by other users but shared to the logged in user are displayed, otherwise
592	they are hidden.</para>
593	</listitem>
594	<listitem>
595	<para><guilabel>In current project</guilabel> -
596	If checked, items that are linked with the current project are displayed,
597	otherwise they are hidden. It doesn't matter if the logged in user is the
598	owner or not. This option is only available if a project is active.
599	</para>
600	</listitem>
601	<listitem>
602	<para><guilabel>Owned by others</guilabel> -
603	This option is only avilable to administrators and will display
604	items that are owned by other users.
605	</para>
606	</listitem>
607	</itemizedlist>
608
609	<para>
610	The default options are to only display items that the current
611	user owns and, if a project is active, items in that project.
612	</para>
613
614	</listitem>
615
616	<listitem>
617	<para>
618	Administrate the presets
619	</para>
620	<itemizedlist>
621	<listitem>
622	<para><guilabel>Clear filter</guilabel> - Clears
623	all filters.</para>
624	</listitem>
625
626	<listitem>
627	<para><guilabel>Save as…</guilabel> - Save the
628	current configuration as a preset.</para>
629	</listitem>
630
631	<listitem>
632	<para><guilabel>Manage…</guilabel> - Opens a dialog
633	where you can remove saved presets. You can also load
634	saved presets from the dialog, but it is quicker to just
635	use the dropdown list for this.</para>
636	</listitem>
637
638	</itemizedlist>
639
640
641	</listitem>
642
643	</orderedlist>
644	</sect2>
645
646	</sect1>
647
648	<sect1 id="webclient.items">
649	<title>Working with items</title>
650
651	<sect2 id="webclient.items.new">
652	<title>Creating a new item</title>
653	</sect2>
654
655	<sect2 id="webclient.items.edit">
656	<title>Editing an existing item</title>
657	</sect2>
658
659	<sect2 id="webclient.items.delete">
660	<title>Delete an item</title>
661	</sect2>
662
663	<sect2 id="webclient.items.restore">
664	<title>Restore a deleted item</title>
665	</sect2>
666
667	</sect1>
668
669
670	</chapter>

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