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menu.jsp @ 4022

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Last change on this file since 4022 was 4022, checked in by Nicklas Nordborg, 16 years ago

Fixes #855: &hellip is displayed in some menu items with IE

Was missing the final ;

Property svn:eol-style set to native
Property svn:keywords set to Id

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1	<%-- $Id: menu.jsp 4022 2007-11-30 08:10:05Z nicklas $
2	------------------------------------------------------------------
3	Copyright (C) 2005 Nicklas Nordborg, Gregory Vincic
4	Copyright (C) 2006 Jari Hakkinen, Nicklas Nordborg, Martin Svensson, Gregory Vincic
5	Copyright (C) 2007 Nicklas Nordborg
6
7	This file is part of BASE - BioArray Software Environment.
8	Available at http://base.thep.lu.se/
9
10	BASE is free software; you can redistribute it and/or
11	modify it under the terms of the GNU General Public License
12	as published by the Free Software Foundation; either version 2
13	of the License, or (at your option) any later version.
14
15	BASE is distributed in the hope that it will be useful,
16	but WITHOUT ANY WARRANTY; without even the implied warranty of
17	MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
18	GNU General Public License for more details.
19
20	You should have received a copy of the GNU General Public License
21	along with this program; if not, write to the Free Software
22	Foundation, Inc., 59 Temple Place - Suite 330,
23	Boston, MA 02111-1307, USA.
24	------------------------------------------------------------------
25
26	This page is included from the <base:page> taglib to display the
27	meny.
28
29	@param name
30	The name of the menu to display:
31	- standard: The standard menu for a logged in user
32	- login: The menu used on pages where no user is logged in
33	- exception: Used on error pages, does not display a menu at all
34	- auto: Will display either the "standard" or "login" menu
35
36	@author Nicklas
37	@version 2.0
38	--%>
39	<%@ page session="false"
40	import="net.sf.basedb.core.SessionControl"
41	import="net.sf.basedb.core.DbControl"
42	import="net.sf.basedb.core.BasicItem"
43	import="net.sf.basedb.core.Nameable"
44	import="net.sf.basedb.core.Permission"
45	import="net.sf.basedb.core.Item"
46	import="net.sf.basedb.core.ItemContext"
47	import="net.sf.basedb.core.User"
48	import="net.sf.basedb.core.Project"
49	import="net.sf.basedb.core.Client"
50	import="net.sf.basedb.core.StringUtil"
51	import="net.sf.basedb.core.ItemQuery"
52	import="net.sf.basedb.core.Include"
53	import="net.sf.basedb.core.ItemResultList"
54	import="net.sf.basedb.core.query.Orders"
55	import="net.sf.basedb.core.query.Hql"
56	import="net.sf.basedb.clients.web.Base"
57	import="net.sf.basedb.clients.web.util.HTML"
58	import="net.sf.basedb.util.Values"
59	import="java.util.HashMap"
60	import="java.util.ArrayList"
61	import="java.util.List"
62	import="java.util.Arrays"
63	%>
64	<%@ taglib prefix="m" uri="/WEB-INF/menu.tld" %>
65	<%
66	final SessionControl sc = Base.getSessionControl(pageContext, false);
67	final String ID = sc == null ? "" : sc.getId();
68	String name = Values.getString(request.getParameter("name"), "login");
69	final String root = request.getContextPath()+"/";
70	if ("exception".equals(name) && sc != null && sc.isLoggedIn()) name = "standard";
71
72	if ("login".equals(name))
73	{
74	}
75	else if ("recentItems".equals(name) && sc != null && sc.isLoggedIn())
76	{
77	// Recently used items menu
78	String stickyItems = Values.getString(sc.getUserClientSetting("menu.mostRecent"),
79	"EXPERIMENT:BIOASSAYSET:TRANSFORMATION");
80	boolean loadNames = Values.getBoolean(sc.getUserClientSetting("menu.mostRecent.loadNames"),
81	true);
82	String recentItems = sc.getUserClientSetting("menu.mostRecent.viewed");
83	DbControl dc = loadNames ? sc.newDbControl() : null;
84	try
85	{
86	%>
87	<m:menu
88	id="mostRecent"
89	style="display: none;"
90	>
91	<%
92	int numItems = 0;
93	// Recently viewed items
94	List<String> recentlyViewed = recentItems == null ?
95	new ArrayList<String>() : Arrays.asList(recentItems.split(":"));
96	if (recentlyViewed.size() > 0)
97	{
98	%>
99	<m:menuitem
100	title="Recently viewed items"
101	style="font-weight: bold; color: #000000; background: #e8e8e8;"
102	enabled="false"
103	/>
104	<m:menuseparator />
105	<%
106	for (String recent : recentlyViewed)
107	{
108	try
109	{
110	String[] tmp = recent.split("=");
111	Item itemType = Item.valueOf(tmp[0]);
112	int itemId = Values.getInt(tmp[1], 0);
113	if (itemId != 0)
114	{
115	String shortName = "";
116	String fullName = "";
117	if (loadNames)
118	{
119	try
120	{
121	BasicItem item = itemType.getById(dc, itemId);
122	fullName = ((Nameable)item).getName();
123	shortName = HTML.encodeTags(StringUtil.trimString(fullName, 35));
124	}
125	catch (Throwable t)
126	{
127	continue;
128	}
129	}
130	else
131	{
132	fullName = itemType.toString() + "; id=" + itemId;
133	shortName = itemType + " (id=" + itemId + ")";
134	}
135	numItems++;
136	%>
137	<m:menuitem
138	title="<%=numItems + ". " + shortName%>"
139	onclick="<%="Main.viewOrEditItem('" + ID + "', '" + itemType.name() + "', " + itemId + ")"%>"
140	tooltip="<%="Go to " + HTML.encodeTags(fullName) + " (" + itemType + ")"%>"
141	/>
142	<%
143	}
144	}
145	catch (Throwable t)
146	{}
147	}
148	}
149	if (stickyItems != null && stickyItems.length() > 0)
150	{
151	int numSticky = 0;
152	if (numItems > 0)
153	{
154	%>
155	<m:menuseparator />
156	<%
157	}
158	%>
159	<m:menuitem
160	title="Sticky items"
161	style="font-weight: bold; color: #000000; background: #e8e8e8;"
162	enabled="false"
163	/>
164	<m:menuseparator />
165	<%
166	// Sticky items
167	for (String recentItem : stickyItems.split(":"))
168	{
169	try
170	{
171	Item itemType = Item.valueOf(recentItem);
172	ItemContext cc = sc.getCurrentContext(itemType);
173	if (cc.getId() != 0)
174	{
175	String shortName = "";
176	String fullName = "";
177	if (loadNames)
178	{
179	try
180	{
181	BasicItem item = itemType.getById(dc, cc.getId());
182	fullName = ((Nameable)item).getName();
183	shortName = ": " + HTML.encodeTags(StringUtil.trimString(fullName, 30));
184	}
185	catch (Throwable t)
186	{
187	continue;
188	}
189	}
190	else
191	{
192	fullName = itemType.toString() + "; id=" + cc.getId();
193	shortName = " (id=" + cc.getId() + ")";
194	}
195	numItems++;
196	numSticky++;
197	%>
198	<m:menuitem
199	title="<%=itemType + shortName%>"
200	onclick="<%="Main.viewOrEditItem('" + ID + "', '" + itemType.name() + "', " + cc.getId() + ")"%>"
201	tooltip="<%="Go to " + HTML.encodeTags(fullName) + " (" + itemType + ")"%>"
202	/>
203	<%
204	if (itemType == Item.BIOASSAYSET)
205	{
206	// Add menu for Experiment explorer as well
207	%>
208	<m:menuitem
209	title="<%="Experiment explorer"+HTML.encodeTags(shortName)%>"
210	onclick="<%="location.href = '"+root+"views/experiments/explorer/view/index.jsp?ID=" + ID + "&bioassayset_id="+cc.getId()+"'"%>"
211	tooltip="Go to experiment explorer"
212	/>
213	<%
214	}
215	}
216	}
217	catch (Throwable t)
218	{}
219	}
220	if (numSticky == 0)
221	{
222	%>
223	<m:menuitem
224	title="<i>- no sticky items -</i>"
225	enabled="false"
226	/>
227	<%
228	}
229	}
230	%>
231	<m:menuseparator />
232	<m:menuitem
233	title="Options…"
234	onclick="<%="Main.openPopup('"+root+"my_base/user/preferences.jsp?ID="+ID+"&page=mostRecent', 'Preferences', 500, 400);"%>"
235	tooltip="Change options for this menu"
236	/>
237	</m:menu>
238	<%
239	}
240	finally
241	{
242	if (dc != null) dc.close();
243	}
244	}
245	else if ("standard".equals(name))
246	{
247	final DbControl dc = sc.newDbControl();
248	ItemResultList<Project> projects = null;
249	StringBuilder fillText = new StringBuilder();
250	try
251	{
252	fillText.append("<a href=\"javascript:void(0)\" title=\"Refresh current page\"");
253	fillText.append(" onclick=\"location.reload()\">");
254	fillText.append("<img src=\""+root+"images/refresh.gif\" border=\"0\"></a><span class=\"menuseparator\">  </span>");
255
256	fillText.append("<a href=\"javascript:void(0)\" title=\"Go to the most recently viewed item\"");
257	fillText.append(" onclick=\"Menu.toggleTopMenu(document.getElementById('mostRecent'), event.clientX-20, event.clientY); event.cancelBubble = true;\">");
258	fillText.append(" <img src=\""+root+"images/recent.png\" border=\"0\"><img src=\""+root+"images/sort_asc.gif\" border=\"0\"></a><span class=\"menuseparator\">  </span>");
259
260	Project activeProject = sc.getActiveProjectId() == 0 ? null : Project.getById(dc, sc.getActiveProjectId());
261	fillText.append("<img src=\""+root+"images/project.gif\" border=\"0\"> <a href=\"javascript:void(0)\" title=\"Switch project\"");
262	fillText.append(" onclick=\"Menu.toggleTopMenu(document.getElementById('projects'), event.clientX-100, event.clientY); event.cancelBubble = true;\">");
263	fillText.append(activeProject == null ? "<i>- none -</i>" : HTML.encodeTags(activeProject.getName()));
264	fillText.append(" <img src=\""+root+"images/sort_asc.gif\" border=\"0\"></a><span class=\"menuseparator\">  </span>");
265
266	User user = User.getById(dc, sc.getLoggedInUserId());
267	String userPrompt = sc.isImpersonated() ? "Impersonated" : "User";
268	fillText.append("<img src=\""+root+"images/take_ownership.png\" border=\"0\"> <a href=\"javascript:void(0)\" title=\"Switch user/logout\"");
269	fillText.append(" onclick=\"javascript:Menu.toggleTopMenu(document.getElementById('switchuser'), event.clientX-100, event.clientY); event.cancelBubble = true;\">");
270	fillText.append(HTML.encodeTags(user.getLogin()));
271	fillText.append(" (").append(user.getName()).append(") <img src=\""+root+"images/sort_asc.gif\" border=\"0\"></a>");
272	%>
273	<%
274	// Permission settings
275	final boolean hasFiles = !sc.hasPermission(Permission.DENIED, Item.FILE);
276	final boolean createFiles = sc.hasPermission(Permission.CREATE, Item.FILE);
277
278	final boolean hasProjects = !sc.hasPermission(Permission.DENIED, Item.PROJECT);
279	final boolean createProjects = sc.hasPermission(Permission.CREATE, Item.PROJECT);
280
281	final boolean hasMessages = !sc.hasPermission(Permission.DENIED, Item.MESSAGE);
282	final boolean createMessages = sc.hasPermission(Permission.CREATE, Item.MESSAGE);
283
284	final boolean hasLabels = !sc.hasPermission(Permission.DENIED, Item.LABEL);
285	final boolean createLabels = sc.hasPermission(Permission.CREATE, Item.LABEL);
286
287	final boolean hasBioSources = !sc.hasPermission(Permission.DENIED, Item.BIOSOURCE);
288	final boolean createBioSources = sc.hasPermission(Permission.CREATE, Item.BIOSOURCE);
289
290	final boolean hasSamples = !sc.hasPermission(Permission.DENIED, Item.SAMPLE);
291	final boolean createSamples = sc.hasPermission(Permission.CREATE, Item.SAMPLE);
292
293	final boolean hasExtracts = !sc.hasPermission(Permission.DENIED, Item.EXTRACT);
294	final boolean createExtracts = sc.hasPermission(Permission.CREATE, Item.EXTRACT);
295
296	final boolean hasLabeledExtracts = !sc.hasPermission(Permission.DENIED, Item.LABELEDEXTRACT);
297	final boolean createLabeledExtracts = sc.hasPermission(Permission.CREATE, Item.LABELEDEXTRACT);
298
299	final boolean hasHybridizations = !sc.hasPermission(Permission.DENIED, Item.HYBRIDIZATION);
300	final boolean createHybridizations = sc.hasPermission(Permission.CREATE, Item.HYBRIDIZATION);
301
302	final boolean hasScans = !sc.hasPermission(Permission.DENIED, Item.SCAN);
303	final boolean createScans = sc.hasPermission(Permission.CREATE, Item.SCAN);
304	final boolean hasRawBioAssays = !sc.hasPermission(Permission.DENIED, Item.RAWBIOASSAY);
305	final boolean createRawBioAssays = sc.hasPermission(Permission.CREATE, Item.RAWBIOASSAY);
306	final boolean hasExperiments = !sc.hasPermission(Permission.DENIED, Item.EXPERIMENT);
307	final boolean createExperiments = sc.hasPermission(Permission.CREATE, Item.EXPERIMENT);
308	final boolean hasFormulas = !sc.hasPermission(Permission.DENIED, Item.FORMULA);
309	final boolean createFormulas = sc.hasPermission(Permission.CREATE, Item.FORMULA);
310
311	final boolean hasReporters = !sc.hasPermission(Permission.DENIED, Item.REPORTER);
312	final boolean hasReporterLists = !sc.hasPermission(Permission.DENIED, Item.REPORTERLIST);
313	final boolean createReporters = sc.hasPermission(Permission.CREATE, Item.REPORTER);
314	final boolean hasJobs = !sc.hasPermission(Permission.DENIED, Item.JOB);
315	final boolean hasSessions = !sc.hasPermission(Permission.DENIED, Item.SESSION);
316	%>
317	<m:menu
318	id="view"
319	style="display: none"
320	>
321	<m:menuitem
322	title="Home"
323	onclick="<%="Menu.openUrl('"+root+"my_base/index.jsp?ID="+ID+"')"%>"
324	/>
325	<m:menuitem
326	title="All items"
327	tooltip="View all items that you are the owner of"
328	onclick="<%="Menu.openUrl('"+root+"views/items/index.jsp?ID="+ID+"')"%>"
329	/>
330	<m:menuitem
331	title="Trashcan"
332	tooltip="View all items that have been marked for deletion"
333	onclick="<%="Menu.openUrl('"+root+"views/trashcan/index.jsp?ID="+ID+"')"%>"
334	/>
335	<m:menuseparator />
336	<m:menuitem
337	title="Files"
338	onclick="<%="Menu.openUrl('"+root+"filemanager/index.jsp?ID="+ID+"')"%>"
339	tooltip="<%=hasFiles ? "Manage files" : "You do not have permission to manage files"%>"
340	enabled="<%=hasFiles%>"
341	/>
342	<m:menuitem
343	title="Projects"
344	onclick="<%="Menu.openUrl('"+root+"my_base/projects/index.jsp?ID="+ID+"')"%>"
345	tooltip="Manage projects"
346	enabled="<%=hasProjects%>"
347	/>
348	<m:menuitem
349	title="Messages"
350	onclick="<%="Menu.openUrl('"+root+"my_base/messages/index.jsp?ID="+ID+"')"%>"
351	tooltip="<%=hasMessages ? "Read your messages" : "You do not have permission to read messages"%>"
352	enabled="<%=hasMessages%>"
353	/>
354	<m:menuitem
355	title="Jobs"
356	onclick="<%="Menu.openUrl('"+root+"views/jobs/index.jsp?ID="+ID+"')"%>"
357	tooltip="<%=hasJobs ? "Check the status of your jobs" : "You do not have permission to access jobs"%>"
358	enabled="<%=hasJobs%>"
359	/>
360	<m:menuitem
361	title="Sessions"
362	onclick="<%="Menu.openUrl('"+root+"views/sessions/index.jsp?ID="+ID+"')"%>"
363	tooltip="<%=hasSessions ? "Check you login sessions" : "You do not have permission to access sessions"%>"
364	enabled="<%=hasSessions%>"
365	/>
366	<m:menuseparator />
367	<m:menuitem
368	title="Biosources"
369	onclick="<%="Menu.openUrl('"+root+"biomaterials/biosources/index.jsp?ID="+ID+"')"%>"
370	tooltip="<%=hasBioSources ? "Manage biosources" : "You do not have permission to manage biosources"%>"
371	enabled="<%=hasBioSources%>"
372	/>
373	<m:menuitem
374	title="Samples"
375	onclick="<%="Menu.openUrl('"+root+"biomaterials/samples/index.jsp?ID="+ID+"')"%>"
376	tooltip="<%=hasSamples ? "Manage samples" : "You do not have permission to manage samples"%>"
377	enabled="<%=hasSamples%>"
378	/>
379	<m:menuitem
380	title="Extracts"
381	onclick="<%="Menu.openUrl('"+root+"biomaterials/extracts/index.jsp?ID="+ID+"')"%>"
382	tooltip="<%=hasExtracts ? "Manage extracts" : "You do not have permission to manage extracts"%>"
383	enabled="<%=hasExtracts%>"
384	/>
385	<m:menuitem
386	title="Labeled extracts"
387	onclick="<%="Menu.openUrl('"+root+"biomaterials/labeledextracts/index.jsp?ID="+ID+"')"%>"
388	tooltip="<%=hasLabeledExtracts ? "Manage labeled extracts" : "You do not have permission to manage labeled extracts"%>"
389	enabled="<%=hasLabeledExtracts%>"
390	/>
391	<m:menuitem
392	title="Labels"
393	onclick="<%="Menu.openUrl('"+root+"biomaterials/labels/index.jsp?ID="+ID+"')"%>"
394	tooltip="<%=hasLabels ? "Manage labels" : "You do not have permission to manage labels"%>"
395	enabled="<%=hasLabels%>"
396	/>
397	<m:menuseparator />
398	<m:menuitem
399	title="Hybridizations"
400	onclick="<%="Menu.openUrl('"+root+"views/hybridizations/index.jsp?ID="+ID+"')"%>"
401	tooltip="<%=hasHybridizations ? "Manage hybridizations" : "You do not have permission to manage hybridizations"%>"
402	enabled="<%=hasHybridizations%>"
403	/>
404	<m:menuitem
405	title="Scans"
406	onclick="<%="Menu.openUrl('"+root+"views/scans/index.jsp?ID="+ID+"')"%>"
407	tooltip="<%=hasScans ? "Manage scans" : "You do not have permission to manage scans"%>"
408	enabled="<%=hasScans%>"
409	/>
410	<m:menuitem
411	title="Raw bioassays"
412	onclick="<%="Menu.openUrl('"+root+"views/rawbioassays/index.jsp?ID="+ID+"')"%>"
413	tooltip="<%=hasRawBioAssays ? "Manage raw bioassays" : "You do not have permission to manage raw bioassays"%>"
414	enabled="<%=hasRawBioAssays%>"
415	/>
416	<m:menuitem
417	title="Experiments"
418	onclick="<%="Menu.openUrl('"+root+"views/experiments/index.jsp?ID="+ID+"')"%>"
419	tooltip="<%=hasExperiments ? "Manage experiments" : "You do not have permission to manage experiments"%>"
420	enabled="<%=hasExperiments%>"
421	/>
422	<m:menuitem
423	title="Formulas"
424	onclick="<%="Menu.openUrl('"+root+"views/formulas/index.jsp?ID="+ID+"')"%>"
425	tooltip="<%=hasFormulas ? "Manage formulas" : "You do not have permission to manage formulas"%>"
426	enabled="<%=hasFormulas%>"
427	/>
428	<m:menuseparator />
429	<m:menuitem
430	title="Reporters"
431	onclick="<%="Menu.openUrl('"+root+"views/reporters/index.jsp?ID="+ID+"')"%>"
432	tooltip="<%=hasReporters ? "Manage reporters" : "You do not have permission to manage reporters"%>"
433	enabled="<%=hasReporters%>"
434	/>
435	<m:menuitem
436	title="Reporter lists"
437	onclick="<%="Menu.openUrl('"+root+"views/reporterlists/index.jsp?ID="+ID+"')"%>"
438	tooltip="<%=hasReporterLists ? "Manage reporter lists" : "You do not have permission to manage reporter lists"%>"
439	enabled="<%=hasReporterLists%>"
440	/>
441
442	</m:menu>
443
444
445	<m:menu
446	id="file"
447	style="display: none"
448	>
449	<m:submenu
450	subid="projects"
451	title="Select project"
452	enabled="<%=hasProjects%>"
453	/>
454	<m:menuseparator />
455	<m:menuitem
456	title="Contact information…"
457	onclick="<%="Main.openPopup('"+root+"my_base/user/settings.jsp?ID="+ID+"&page=contact', 'Settings', 500, 360);"%>"
458	tooltip="Set your address, phone, email, etc."
459	/>
460	<m:menuitem
461	title="Change password…"
462	onclick="<%="Main.openPopup('"+root+"my_base/user/settings.jsp?ID="+ID+"&page=password', 'Settings', 500, 360);"%>"
463	tooltip="Set your password"
464	/>
465	<m:menuitem
466	title="Other information…"
467	onclick="<%="Main.openPopup('"+root+"my_base/user/settings.jsp?ID="+ID+"&page=other', 'Settings', 500, 360);"%>"
468	tooltip="Other user-related information"
469	/>
470	<m:menuseparator />
471	<m:menuitem
472	title="Preferences…"
473	onclick="<%="Main.openPopup('"+root+"my_base/user/preferences.jsp?ID="+ID+"', 'Preferences', 500, 400);"%>"
474	tooltip="Change font sizes, etc."
475	/>
476	<m:menuitem
477	title="Reload permissions"
478	onclick="<%="Main.openPopup('"+root+"my_base/user/submit_user.jsp?ID="+ID+"&cmd=ReloadPermissions', 'ReloadPermissions', 300, 200);"%>"
479	tooltip="Reload permissions"
480	/>
481	<m:menuseparator />
482	<m:menuitem
483	title="Logout…"
484	onclick="<%="Main.openPopup('"+root+"logout.jsp?ID="+ID+"', 'Logout', 360, 200);"%>"
485	tooltip="Exit from BASE"
486	/>
487	</m:menu>
488	<%
489	// Projects menu
490	int activeProjectId = sc.getActiveProjectId();
491	final ItemQuery<Project> projectQuery = Project.getQuery();
492	projectQuery.include(Include.MINE, Include.SHARED);
493	projectQuery.order(Orders.asc(Hql.property("name")));
494	projectQuery.setCacheResult(true);
495	%>
496	<m:menu
497	id="projects"
498	style="display: none"
499	>
500	<m:menuitem
501	title="<i>- no active project -</i>"
502	onclick="<%="Main.openPopup('"+root+"my_base/projects/set_active.jsp?ID="+ID+"', 'ActivateProject', 300, 140)"%>"
503	icon="<%=activeProjectId == 0 ? "checkedmenu.gif" : null%>"
504	enabled="<%=activeProjectId != 0%>"
505	tooltip="<%=activeProjectId == 0 ? "No project is active" : "Disable the currently active project"%>"
506	/>
507	<%
508	projects = projectQuery.list(dc);
509	for (Project p : projects)
510	{
511	int projectId = p.getId();
512	boolean active = activeProjectId == projectId;
513	%>
514	<m:menuitem
515	title="<%=HTML.encodeTags(p.getName())%>"
516	style="<%=active ? "color: #000000; font-weight: bold;" : null %>"
517	onclick="<%="Main.openPopup('"+root+"my_base/projects/set_active.jsp?ID="+ID+"&project_id="+p.getId()+"', 'ActivateProject', 300, 140)"%>"
518	icon="<%=active ? "checkedmenu.gif" : null%>"
519	enabled="<%=!active%>"
520	tooltip="<%=active ? "This is the active project" : "Set this project to the active project"%>"
521	/>
522	<%
523	}
524	%>
525	</m:menu>
526
527	<%
528	// Array LIMS - menu
529	final boolean hasPlateGeometries = sc.hasPermission(Permission.READ, Item.PLATEGEOMETRY);
530	final boolean hasPlateTypes = !sc.hasPermission(Permission.DENIED, Item.PLATETYPE);
531	final boolean hasPlates = !sc.hasPermission(Permission.DENIED, Item.PLATE);
532	final boolean hasPlateMappings = !sc.hasPermission(Permission.DENIED, Item.PLATEMAPPING);
533	final boolean hasArraySlides = !sc.hasPermission(Permission.DENIED, Item.ARRAYSLIDE);
534	final boolean hasArrayBatches = !sc.hasPermission(Permission.DENIED, Item.ARRAYBATCH);
535	final boolean hasArrayDesigns = !sc.hasPermission(Permission.DENIED, Item.ARRAYDESIGN);
536	final boolean hasLims = hasPlateGeometries \|\| hasPlateTypes \|\| hasPlates \|\| hasPlateMappings \|\|
537	hasArraySlides \|\| hasArrayBatches \|\| hasArrayDesigns;
538	if (hasLims)
539	{
540	%>
541	<m:menu
542	id="lims"
543	style="display: none"
544	>
545	<m:menuitem
546	title="Plate geometries"
547	onclick="<%="Menu.openUrl('"+root+"lims/geometries/index.jsp?ID="+ID+"')"%>"
548	tooltip="<%=hasPlateGeometries ? "Manage plate geometries" : "You do not have permission to manage plate geometries"%>"
549	enabled="<%=hasPlateGeometries%>"
550	/>
551	<m:menuitem
552	title="Plate types"
553	onclick="<%="Menu.openUrl('"+root+"lims/platetypes/index.jsp?ID="+ID+"')"%>"
554	tooltip="<%=hasPlateTypes ? "Manage plate types" : "You do not have permission to manage plate types"%>"
555	enabled="<%=hasPlateTypes%>"
556	/>
557	<m:menuitem
558	title="Plates"
559	onclick="<%="Menu.openUrl('"+root+"lims/plates/index.jsp?ID="+ID+"')"%>"
560	tooltip="<%=hasPlates ? "Manage plates" : "You do not have permission to manage plates"%>"
561	enabled="<%=hasPlates%>"
562	/>
563	<m:menuitem
564	title="Plate mappings"
565	onclick="<%="Menu.openUrl('"+root+"lims/platemappings/index.jsp?ID="+ID+"')"%>"
566	tooltip="<%=hasPlateTypes ? "Manage plate mappings" : "You do not have permission to manage plate mappings"%>"
567	enabled="<%=hasPlateTypes%>"
568	/>
569	<m:menuseparator />
570	<m:menuitem
571	title="Array designs"
572	onclick="<%="Menu.openUrl('"+root+"lims/arraydesigns/index.jsp?ID="+ID+"')"%>"
573	tooltip="<%=hasArrayDesigns ? "Manage array designs" : "You do not have permission to manage array designs"%>"
574	enabled="<%=hasArrayDesigns%>"
575	/>
576	<m:menuitem
577	title="Array batches"
578	onclick="<%="Menu.openUrl('"+root+"lims/arraybatches/index.jsp?ID="+ID+"')"%>"
579	tooltip="<%=hasArrayBatches ? "Manage array batches" : "You do not have permission to manage array batches"%>"
580	enabled="<%=hasArrayBatches%>"
581	/>
582	<m:menuitem
583	title="Array slides"
584	onclick="<%="Menu.openUrl('"+root+"lims/arrayslides/index.jsp?ID="+ID+"')"%>"
585	tooltip="<%=hasArraySlides ? "Manage array slides" : "You do not have permission to manage array slides"%>"
586	enabled="<%=hasArraySlides%>"
587	/>
588	</m:menu>
589	<%
590	}
591	%>
592	<%
593	// Administrate -> Types menu
594	final boolean hasQuotaTypes = sc.hasPermission(Permission.READ, Item.QUOTATYPE);
595	final boolean hasProtocolTypes = sc.hasPermission(Permission.READ, Item.PROTOCOLTYPE);
596	final boolean hasFileTypes = sc.hasPermission(Permission.READ, Item.FILETYPE);
597	final boolean hasMimeTypes = sc.hasPermission(Permission.READ, Item.MIMETYPE);
598	final boolean hasHardwareTypes = sc.hasPermission(Permission.READ, Item.HARDWARETYPE);
599	final boolean hasSoftwareTypes = sc.hasPermission(Permission.READ, Item.SOFTWARETYPE);
600	final boolean hasAnnotationTypeCategories = !sc.hasPermission(Permission.DENIED, Item.ANNOTATIONTYPECATEGORY);
601	final boolean hasAnnotationTypes = !sc.hasPermission(Permission.DENIED, Item.ANNOTATIONTYPE);
602	final boolean hasReporterTypes = !sc.hasPermission(Permission.DENIED, Item.REPORTERTYPE);
603	final boolean hasExtraValueTypes = !sc.hasPermission(Permission.DENIED, Item.EXTRAVALUETYPE);
604	final boolean hasTypes = hasFileTypes \|\| hasProtocolTypes \|\| hasMimeTypes \|\| hasQuotaTypes \|\|
605	hasSoftwareTypes \|\| hasHardwareTypes \|\| hasAnnotationTypeCategories \|\| hasAnnotationTypes \|\|
606	hasReporterTypes \|\| hasExtraValueTypes;
607	if (hasTypes)
608	{
609	%>
610	<m:menu
611	id="types"
612	style="display: none"
613	>
614	<m:menuitem
615	title="Quota types"
616	onclick="<%="Menu.openUrl('"+root+"admin/quotatypes/index.jsp?ID="+ID+"')"%>"
617	tooltip="<%=hasQuotaTypes ? "Administrate quota types" : "You do not have permission to administrate quota types"%>"
618	enabled="<%=hasQuotaTypes%>"
619	/>
620	<m:menuitem
621	title="Protocol types"
622	onclick="<%="Menu.openUrl('"+root+"admin/protocoltypes/index.jsp?ID="+ID+"')"%>"
623	tooltip="<%=hasProtocolTypes ? "Administrate protocol types" : "You do not have permission to administrate protocol types"%>"
624	enabled="<%=hasProtocolTypes%>"
625	/>
626	<m:menuitem
627	title="File types"
628	onclick="<%="Menu.openUrl('"+root+"admin/filetypes/index.jsp?ID="+ID+"')"%>"
629	tooltip="<%=hasFileTypes ? "Administrate file types" : "You do not have permission to administrate file types"%>"
630	enabled="<%=hasFileTypes%>"
631	/>
632	<m:menuitem
633	title="MIME types"
634	onclick="<%="Menu.openUrl('"+root+"admin/mimetypes/index.jsp?ID="+ID+"')"%>"
635	tooltip="<%=hasMimeTypes ? "Administrate MIME types" : "You do not have permission to administrate mime types"%>"
636	enabled="<%=hasMimeTypes%>"
637	/>
638	<m:menuitem
639	title="Software types"
640	onclick="<%="Menu.openUrl('"+root+"admin/softwaretypes/index.jsp?ID="+ID+"')"%>"
641	tooltip="<%=hasSoftwareTypes ? "Administrate software types" : "You do not have permission to administrate software types"%>"
642	enabled="<%=hasSoftwareTypes%>"
643	/>
644	<m:menuitem
645	title="Hardware types"
646	onclick="<%="Menu.openUrl('"+root+"admin/hardwaretypes/index.jsp?ID="+ID+"')"%>"
647	tooltip="<%=hasHardwareTypes ? "Administrate hardware types" : "You do not have permission to administrate hardware types"%>"
648	enabled="<%=hasHardwareTypes%>"
649	/>
650	<m:menuitem
651	title="Annotation type categories"
652	onclick="<%="Menu.openUrl('"+root+"admin/annotationtypecategories/index.jsp?ID="+ID+"')"%>"
653	tooltip="<%=hasAnnotationTypeCategories ? "Administrate annotation type categories" : "You do not have permission to administrate annotation types categories"%>"
654	enabled="<%=hasAnnotationTypeCategories%>"
655	/>
656	<m:menuitem
657	title="Annotation types"
658	onclick="<%="Menu.openUrl('"+root+"admin/annotationtypes/index.jsp?ID="+ID+"')"%>"
659	tooltip="<%=hasAnnotationTypes ? "Administrate annotation types" : "You do not have permission to administrate annotation types"%>"
660	enabled="<%=hasAnnotationTypes%>"
661	/>
662	<m:menuitem
663	title="Reporter types"
664	onclick="<%="Menu.openUrl('"+root+"admin/reportertypes/index.jsp?ID="+ID+"')"%>"
665	tooltip="<%=hasReporterTypes ? "Administrate reporter types" : "You do not have permission to administrate reporter types"%>"
666	enabled="<%=hasReporterTypes%>"
667	/>
668	<m:menuitem
669	title="Extra value types"
670	onclick="<%="Menu.openUrl('"+root+"admin/extravaluetypes/index.jsp?ID="+ID+"')"%>"
671	tooltip="<%=hasExtraValueTypes ? "Administrate extra value types" : "You do not have permission to administrate extra value types"%>"
672	enabled="<%=hasExtraValueTypes%>"
673	/>
674	</m:menu>
675	<%
676	}
677	%>
678	<%
679	// Administrate -> Platforms menu
680	final boolean hasPlatforms = sc.hasPermission(Permission.READ, Item.PLATFORM);
681	final boolean hasFileSetMemberTypes = sc.hasPermission(Permission.READ, Item.DATAFILETYPE);
682	final boolean hasTopPlatforms = hasPlatforms \|\| hasFileSetMemberTypes;
683	if (hasTopPlatforms)
684	{
685	%>
686	<m:menu
687	id="platforms"
688	style="display: none"
689	>
690	<m:menuitem
691	title="Experimental platforms"
692	onclick="<%="Menu.openUrl('"+root+"admin/platforms/index.jsp?ID="+ID+"')"%>"
693	tooltip="<%=hasPlatforms ? "Administrate experimental platforms" : "You do not have permission to administrate experimental platforms"%>"
694	enabled="<%=hasPlatforms%>"
695	/>
696	<m:menuitem
697	title="Data file types"
698	onclick="<%="Menu.openUrl('"+root+"admin/datafiletypes/index.jsp?ID="+ID+"')"%>"
699	tooltip="<%=hasFileSetMemberTypes ? "Administrate data file types" : "You do not have permission to administrate data file types"%>"
700	enabled="<%=hasFileSetMemberTypes%>"
701	/>
702	</m:menu>
703	<%
704	}
705	%>
706
707	<%
708	// Plugins menu
709	final boolean hasPluginTypes = !sc.hasPermission(Permission.DENIED, Item.PLUGINTYPE);
710	final boolean hasPluginDefinitions = !sc.hasPermission(Permission.DENIED, Item.PLUGINDEFINITION);
711	final boolean hasPluginConfigurations = !sc.hasPermission(Permission.DENIED, Item.PLUGINCONFIGURATION);
712	final boolean hasJobAgents = sc.hasPermission(Permission.READ, Item.JOBAGENT);
713	final boolean hasPlugins = hasPluginTypes \|\| hasPluginDefinitions \|\|
714	hasPluginConfigurations \|\| hasJobAgents;
715
716	if (hasPlugins)
717	{
718	%>
719	<m:menu
720	id="plugins"
721	style="display: none"
722	>
723	<m:menuitem
724	title="Types"
725	onclick="<%="Menu.openUrl('"+root+"admin/plugintypes/index.jsp?ID="+ID+"')"%>"
726	tooltip="<%=hasPluginDefinitions ? "Administrate plugin types" : "You do not have permission to administrate plugin types"%>"
727	enabled="<%=hasPluginTypes%>"
728	/>
729	<m:menuitem
730	title="Definitions"
731	onclick="<%="Menu.openUrl('"+root+"admin/plugindefinitions/index.jsp?ID="+ID+"')"%>"
732	tooltip="<%=hasPluginDefinitions ? "Administrate plugin definitions" : "You do not have permission to administrate plugin definitions"%>"
733	enabled="<%=hasPluginDefinitions%>"
734	/>
735	<m:menuitem
736	title="Configurations"
737	onclick="<%="Menu.openUrl('"+root+"admin/pluginconfigurations/index.jsp?ID="+ID+"')"%>"
738	tooltip="<%=hasPluginConfigurations ? "Administrate plugin configurations" : "You do not have permission to administrate plugin configurations"%>"
739	enabled="<%=hasPluginConfigurations%>"
740	/>
741	<m:menuseparator />
742	<m:menuitem
743	title="Job agents"
744	onclick="<%="Menu.openUrl('"+root+"admin/jobagents/index.jsp?ID="+ID+"')"%>"
745	tooltip="<%=hasJobAgents ? "Administrate job agents" : "You do not have permission to administrate job agents"%>"
746	enabled="<%=hasJobAgents%>"
747	/>
748	</m:menu>
749	<%
750	}
751	%>
752
753	<%
754	// Administrate menu
755	final boolean hasUsers = sc.hasPermission(Permission.READ, Item.USER);
756	final boolean hasGroups = sc.hasPermission(Permission.READ, Item.GROUP);
757	final boolean hasRoles = sc.hasPermission(Permission.READ, Item.ROLE);
758	final boolean hasQuota = sc.hasPermission(Permission.READ, Item.QUOTA);
759	final boolean hasSoftware = !sc.hasPermission(Permission.DENIED, Item.SOFTWARE);
760	final boolean hasHardware = !sc.hasPermission(Permission.DENIED, Item.HARDWARE);
761	final boolean hasProtocols = !sc.hasPermission(Permission.DENIED, Item.PROTOCOL);
762	final boolean hasClients = sc.hasPermission(Permission.READ, Item.CLIENT);
763	final boolean hasNews = sc.hasPermission(Permission.READ, Item.NEWS);
764	final boolean hasDiskUsage = sc.hasPermission(Permission.READ, Item.DISKUSAGE);
765	final Client currentClient = Client.getById(dc, sc.getClientId());
766	final boolean hasServer = currentClient.hasPermission(Permission.WRITE);
767
768	final boolean hasAdministrate =
769	hasUsers \|\| hasGroups \|\| hasRoles \|\| hasQuota \|\| hasTypes \|\| hasPlugins \|\|
770	hasSoftware \|\| hasHardware \|\| hasProtocols \|\| hasClients \|\| hasNews \|\|
771	hasDiskUsage \|\| hasServer \|\| hasTopPlatforms;
772
773	if (hasAdministrate)
774	{
775	%>
776	<m:menu
777	id="administrate"
778	style="display: none"
779	>
780	<m:menuitem
781	title="Users"
782	onclick="<%="Menu.openUrl('"+root+"admin/users/index.jsp?ID="+ID+"')"%>"
783	tooltip="<%=hasUsers ? "Administrate users" : "You do not have permission to administrate users"%>"
784	enabled="<%=hasUsers%>"
785	/>
786	<m:menuitem
787	title="Groups"
788	onclick="<%="Menu.openUrl('"+root+"admin/groups/index.jsp?ID="+ID+"')"%>"
789	tooltip="<%=hasGroups ? "Administrate groups" : "You do not have permission to administrate groups"%>"
790	enabled="<%=hasGroups%>"
791	/>
792	<m:menuitem
793	title="Roles"
794	onclick="<%="Menu.openUrl('"+root+"admin/roles/index.jsp?ID="+ID+"')"%>"
795	tooltip="<%=hasRoles ? "Administrate roles" : "You do not have permission to administrate roles"%>"
796	enabled="<%=hasRoles%>"
797	/>
798	<m:menuseparator />
799	<m:submenu
800	subid="plugins"
801	title="Plugins"
802	tooltip="Administrate plugin definitions and configurations"
803	enabled="<%=hasPlugins%>"
804	/>
805	<m:menuseparator />
806	<m:menuitem
807	title="Quota"
808	onclick="<%="Menu.openUrl('"+root+"admin/quota/index.jsp?ID="+ID+"')"%>"
809	tooltip="<%=hasQuota ? "Administrate quota" : "You do not have permission to administrate quota"%>"
810	enabled="<%=hasQuota%>"
811	/>
812	<m:menuitem
813	title="Software"
814	onclick="<%="Menu.openUrl('"+root+"admin/software/index.jsp?ID="+ID+"')"%>"
815	tooltip="<%=hasSoftware ? "Administrate software" : "You do not have permission to administrate software"%>"
816	enabled="<%=hasSoftware%>"
817	/>
818	<m:menuitem
819	title="Hardware"
820	onclick="<%="Menu.openUrl('"+root+"admin/hardware/index.jsp?ID="+ID+"')"%>"
821	tooltip="<%=hasHardware ? "Administrate hardware" : "You do not have permission to administrate hardware"%>"
822	enabled="<%=hasHardware%>"
823	/>
824	<m:menuitem
825	title="Protocols"
826	onclick="<%="Menu.openUrl('"+root+"admin/protocols/index.jsp?ID="+ID+"')"%>"
827	tooltip="<%=hasProtocols ? "Administrate protocols" : "You do not have permission to administrate protocols"%>"
828	enabled="<%=hasProtocols%>"
829	/>
830	<m:menuitem
831	title="Clients"
832	onclick="<%="Menu.openUrl('"+root+"admin/clients/index.jsp?ID="+ID+"')"%>"
833	tooltip="<%=hasClients ? "Administrate client applications" : "You do not have permission to administrate client applications"%>"
834	enabled="<%=hasClients%>"
835	/>
836	<m:menuitem
837	title="News"
838	onclick="<%="Menu.openUrl('"+root+"admin/news/index.jsp?ID="+ID+"')"%>"
839	tooltip="<%=hasNews ? "Administrate news" : "You do not have permission to administrate news"%>"
840	enabled="<%=hasNews%>"
841	/>
842	<m:menuseparator />
843	<m:submenu
844	subid="platforms"
845	title="Platforms"
846	tooltip="Administrate experimental platforms"
847	enabled="<%=hasTopPlatforms%>"
848	/>
849	<m:submenu
850	subid="types"
851	title="Types"
852	tooltip="Administrate quota, file, hardware and software types"
853	enabled="<%=hasTypes%>"
854	/>
855	<m:menuseparator />
856	<m:menuitem
857	title="Disk usage"
858	onclick="<%="Menu.openUrl('"+root+"admin/diskusage/index.jsp?ID="+ID+"')"%>"
859	tooltip="<%=hasDiskUsage ? "Check disk usage" : "You do not have permission to check disk usage"%>"
860	enabled="<%=hasDiskUsage%>"
861	/>
862	<m:menuitem
863	title="Server settings…"
864	onclick="<%="Main.openPopup('"+root+"admin/server/configure.jsp?ID="+ID+"', 'ServerSettings', 500, 400);"%>"
865	tooltip="<%=hasServer ? "Configure the server" : "You do not have permission to configure the server"%>"
866	enabled="<%=hasServer%>"
867	/>
868	<m:menuitem
869	title="Restart BASE…"
870	onclick="<%="Main.openPopup('"+root+"admin/server/restart.jsp?ID="+ID+"', 'RestartServer', 360, 200);"%>"
871	tooltip="<%=hasServer ? "Restart the server" : "You do not have permission to restart the server"%>"
872	enabled="<%=hasServer%>"
873	/>
874	</m:menu>
875	<%
876	}
877	%>
878	<%
879	// Help menu
880	final String helplink = Values.getStringOrNull(sc.getClientDefaultSetting("server.links.help"));
881	final String faqlink = Values.getStringOrNull(sc.getClientDefaultSetting("server.links.faq"));
882	final String reportbuglink = Values.getStringOrNull(sc.getClientDefaultSetting("server.links.reportbug"));
883	%>
884	<m:menu id="help" style="display: none">
885	<m:menuitem
886	visible="<%=HTML.isValidUrl(helplink)%>"
887	title="Help…"
888	onclick="<%="window.open('"+helplink+"','Help')"%>"
889	/>
890	<m:menuitem
891	visible="<%=HTML.isValidUrl(faqlink)%>"
892	title="FAQ…"
893	onclick="<%="window.open('"+faqlink+"','FAQ')"%>"
894	/>
895	<m:menuseparator />
896
897	<m:menuitem
898	title="About…"
899	onclick="<%="Main.openPopup('"+root+"info/about.jsp?ID="+ID+"&page=about', 'About', 500, 350)"%>"
900	/>
901
902	<m:menuitem
903	title="License…"
904	onclick="<%="Main.openPopup('"+root+"info/about.jsp?ID="+ID+"&page=license', 'About', 500, 350)"%>"
905
906	/>
907	<m:menuitem
908	visible="<%=HTML.isValidUrl(reportbuglink)%>"
909	title="Report a bug…"
910	onclick="<%="window.open('"+reportbuglink+"','Reportbug')"%>"
911	/>
912	<m:menuseparator />
913	<m:menuitem
914	title="Base project site" onclick="<%="Menu.openUrl('http://base.thep.lu.se', 'basesite')"%>"
915	/>
916	</m:menu>
917
918	<%
919	//Switch user/logout menu
920	final boolean hasImpersonate =
921	!sc.isImpersonated() && sc.hasSystemPermission(Permission.ACT_AS_ANOTHER_USER);
922	%>
923	<m:menu
924	id="switchuser"
925	style="display: none;"
926	>
927	<m:menuitem
928	title="Switch user…"
929	onclick="<%="Main.openPopup('"+root+"switch.jsp?ID="+ID+"', 'Switch', 360, 200);"%>"
930	tooltip="Login as another user"
931	/>
932	<m:menuitem
933	title="Impersonate…"
934	onclick="<%="Main.openPopup('"+root+"impersonate.jsp?ID="+ID+"', 'Impersonate', 480, 240);"%>"
935	tooltip="Login as another user without knowing the password"
936	visible="<%=hasImpersonate%>"
937	/>
938	<m:menuitem
939	title="Logout…"
940	onclick="<%="Main.openPopup('"+root+"logout.jsp?ID="+ID+"', 'Logout', 360, 200);"%>"
941	tooltip="Exit from BASE"
942	/>
943	</m:menu>
944	<%
945	// Main menu
946	%>
947	<m:menu
948	type="horizontal"
949	clazz="menu_horizontal"
950	id="menubar"
951	style="top: 10px; left: 8px; width: 98%"
952	open="click"
953	filltext="<%=fillText.toString()%>"
954	>
955
956	<m:submenu
957	subid="file"
958	title="File"
959	/>
960	<m:submenu
961	subid="view"
962	title="View"
963	/>
964	<m:submenu
965	subid="lims"
966	title="Array LIMS"
967	/>
968	<m:submenu
969	subid="administrate"
970	title="Administrate"
971	visible="<%=hasAdministrate%>"
972	/>
973	<m:submenu
974	subid="help"
975	title="Help"
976	/>
977	</m:menu>
978	<br><br>
979	<%
980	}
981	finally
982	{
983	if (dc != null) dc.close();
984	}
985
986	}
987	%>
988
989
990

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