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menu.jsp @ 5267

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Last change on this file since 5267 was 5267, checked in by Nicklas Nordborg, 12 years ago

Fixes #1463: HTTP Status 500 when logging in

Added update scripts that removes the bad 'null' values in the sort_property column.

Made the menu script more robust in case an error occurs.

NOTE! This update conflicts with the schema version change in the trunk for #1442 [5260]. This needs to be fixed in the trunk when we have merged 2.15 back to it.

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

File size: 44.6 KB

Line
1	<%-- $Id: menu.jsp 5267 2010-03-12 07:59:58Z nicklas $
2	------------------------------------------------------------------
3	Copyright (C) 2005 Nicklas Nordborg, Gregory Vincic
4	Copyright (C) 2006 Jari Häkkinen, 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 3
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 BASE. If not, see <http://www.gnu.org/licenses/>.
22	------------------------------------------------------------------
23
24	This page is included from the <base:page> taglib to display the
25	meny.
26
27	@param name
28	The name of the menu to display:
29	- standard: The standard menu for a logged in user
30	- login: The menu used on pages where no user is logged in
31	- exception: Used on error pages, does not display a menu at all
32	- auto: Will display either the "standard" or "login" menu
33
34	@author Nicklas
35	@version 2.0
36	--%>
37	<%@ page session="false"
38	import="net.sf.basedb.core.SessionControl"
39	import="net.sf.basedb.core.DbControl"
40	import="net.sf.basedb.core.BasicItem"
41	import="net.sf.basedb.core.Nameable"
42	import="net.sf.basedb.core.Permission"
43	import="net.sf.basedb.core.Item"
44	import="net.sf.basedb.core.ItemContext"
45	import="net.sf.basedb.core.User"
46	import="net.sf.basedb.core.Project"
47	import="net.sf.basedb.core.BioAssaySet"
48	import="net.sf.basedb.core.Client"
49	import="net.sf.basedb.core.StringUtil"
50	import="net.sf.basedb.core.ItemQuery"
51	import="net.sf.basedb.core.Include"
52	import="net.sf.basedb.core.ItemResultList"
53	import="net.sf.basedb.core.query.Orders"
54	import="net.sf.basedb.core.query.Order"
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="net.sf.basedb.clients.web.extensions.ExtensionsControl"
60	import="net.sf.basedb.clients.web.extensions.JspContext"
61	import="net.sf.basedb.clients.web.extensions.menu.MenuItemAction"
62	import="net.sf.basedb.util.extensions.Extension"
63	import="net.sf.basedb.util.extensions.ExtensionsInvoker"
64	import="net.sf.basedb.util.extensions.ActionIterator"
65	import="java.util.HashMap"
66	import="java.util.Map"
67	import="java.util.ArrayList"
68	import="java.util.LinkedList"
69	import="java.util.List"
70	import="java.util.Arrays"
71	import="java.util.Iterator"
72	%>
73	<%@ taglib prefix="m" uri="/WEB-INF/menu.tld" %>
74	<%
75	final SessionControl sc = Base.getSessionControl(pageContext, false);
76	final String ID = sc == null ? "" : sc.getId();
77	String name = Values.getString(request.getParameter("name"), "login");
78	final String root = request.getContextPath()+"/";
79	if ("exception".equals(name) && sc != null && sc.isLoggedIn()) name = "standard";
80
81	if ("login".equals(name))
82	{
83	}
84	else if ("projects".equals(name) && sc != null && sc.isLoggedIn())
85	{
86	// Projects menu
87	int activeProjectId = sc.getActiveProjectId();
88	%>
89	<m:menu
90	id="projects"
91	style="display: none"
92	>
93	<m:menuitem
94	title="<i>- no active project -</i>"
95	onclick="<%="Main.openPopup('"+root+"my_base/projects/set_active.jsp?ID="+ID+"', 'ActivateProject', 300, 140)"%>"
96	icon="<%=activeProjectId == 0 ? "checkedmenu.gif" : null%>"
97	enabled="<%=activeProjectId != 0%>"
98	tooltip="<%=activeProjectId == 0 ? "No project is active" : "Disable the currently active project"%>"
99	/>
100	<%
101	final DbControl dc = sc.newDbControl();
102	try
103	{
104	final ItemContext projectCC = sc.getCurrentContext(Item.PROJECT);
105	final ItemQuery<Project> projectQuery = Project.getQuery();
106	projectQuery.include(Include.MINE, Include.SHARED);
107	Order projectSortOrder = projectCC.getSortOrder();
108	if (projectSortOrder != null) projectQuery.order(projectSortOrder);
109	projectQuery.order(Orders.asc(Hql.property("name")));
110	projectQuery.setCacheResult(true);
111	ItemResultList<Project> projects = projectQuery.list(dc);
112	boolean breakAt20 = projects.size() > 25;
113	int index = 0;
114	for (Project p : projects)
115	{
116	if (index == 20 && breakAt20) break;
117	index++;
118	int projectId = p.getId();
119	boolean active = activeProjectId == projectId;
120	%>
121	<m:menuitem
122	title="<%=HTML.encodeTags(p.getName())%>"
123	style="<%=active ? "color: #000000; font-weight: bold;" : null %>"
124	onclick="<%="Main.openPopup('"+root+"my_base/projects/set_active.jsp?ID="+ID+"&project_id="+p.getId()+"', 'ActivateProject', 300, 140)"%>"
125	icon="<%=active ? "checkedmenu.gif" : null%>"
126	enabled="<%=!active%>"
127	tooltip="<%=active ? "This is the active project" : "Set this project to the active project"%>"
128	/>
129	<%
130	}
131	if (breakAt20)
132	{
133	int more = projects.size() - 20;
134	%>
135	<m:menuseparator />
136	<m:menuitem
137	title="<%=more + " more" %>"
138	onclick="<%="Menu.openUrl('"+root+"my_base/projects/index.jsp?ID="+ID+"')"%>"
139	tooltip="Show more projects"
140	/>
141	<%
142	}
143	}
144	catch (Throwable t)
145	{
146	t.printStackTrace();
147	%>
148	<m:menuitem
149	title="Error loading projects"
150	tooltip="<%=t.getMessage() + ": Check log file for more details"%>"
151	enabled="false"
152	icon="error.gif"
153	/>
154	<%
155	}
156	finally
157	{
158	if (dc != null) dc.close();
159	}
160	%>
161	</m:menu>
162	<%
163	}
164	else if ("recentItems".equals(name) && sc != null && sc.isLoggedIn())
165	{
166	// Recently used items menu
167	String stickyItems = Values.getString(sc.getUserClientSetting("menu.mostRecent"),
168	"EXPERIMENT:BIOASSAYSET:TRANSFORMATION");
169	boolean loadNames = Values.getBoolean(sc.getUserClientSetting("menu.mostRecent.loadNames"),
170	true);
171	String recentItems = sc.getUserClientSetting("menu.mostRecent.viewed");
172	DbControl dc = loadNames ? sc.newDbControl() : null;
173	try
174	{
175	%>
176	<m:menu
177	id="mostRecent"
178	style="display: none;"
179	>
180	<%
181	int numItems = 0;
182	// Recently viewed items
183	List<String> recentlyViewed = recentItems == null ?
184	new ArrayList<String>() : Arrays.asList(recentItems.split(":"));
185	if (recentlyViewed.size() > 0)
186	{
187	%>
188	<m:menuitem
189	title="Recently viewed items"
190	style="font-weight: bold; color: #000000; background: #e8e8e8;"
191	enabled="false"
192	/>
193	<m:menuseparator />
194	<%
195	for (String recent : recentlyViewed)
196	{
197	try
198	{
199	String[] tmp = recent.split("=");
200	Item itemType = Item.valueOf(tmp[0]);
201	int itemId = Values.getInt(tmp[1], 0);
202	if (itemId != 0)
203	{
204	String shortName = "";
205	String fullName = "";
206	if (loadNames)
207	{
208	try
209	{
210	BasicItem item = itemType.getById(dc, itemId);
211	fullName = ((Nameable)item).getName();
212	shortName = HTML.encodeTags(StringUtil.trimString(fullName, 35));
213	}
214	catch (Throwable t)
215	{
216	continue;
217	}
218	}
219	else
220	{
221	fullName = itemType.toString() + "; id=" + itemId;
222	shortName = itemType + " (id=" + itemId + ")";
223	}
224	numItems++;
225	%>
226	<m:menuitem
227	title="<%=numItems + ". " + shortName%>"
228	onclick="<%="Main.viewOrEditItem('" + ID + "', '" + itemType.name() + "', " + itemId + ")"%>"
229	tooltip="<%="Go to " + HTML.encodeTags(fullName) + " (" + itemType + ")"%>"
230	/>
231	<%
232	}
233	}
234	catch (Throwable t)
235	{}
236	}
237	}
238	if (stickyItems != null && stickyItems.length() > 0)
239	{
240	int numSticky = 0;
241	if (numItems > 0)
242	{
243	%>
244	<m:menuseparator />
245	<%
246	}
247	%>
248	<m:menuitem
249	title="Sticky items"
250	style="font-weight: bold; color: #000000; background: #e8e8e8;"
251	enabled="false"
252	/>
253	<m:menuseparator />
254	<%
255	// Sticky items
256	for (String recentItem : stickyItems.split(":"))
257	{
258	try
259	{
260	BasicItem item = null;
261	Item itemType = Item.valueOf(recentItem);
262	ItemContext cc = sc.getCurrentContext(itemType);
263	if (cc.getId() != 0)
264	{
265	String shortName = "";
266	String fullName = "";
267	if (loadNames)
268	{
269	try
270	{
271	item = itemType.getById(dc, cc.getId());
272	fullName = ((Nameable)item).getName();
273	shortName = ": " + HTML.encodeTags(StringUtil.trimString(fullName, 30));
274	}
275	catch (Throwable t)
276	{
277	continue;
278	}
279	}
280	else
281	{
282	fullName = itemType.toString() + "; id=" + cc.getId();
283	shortName = " (id=" + cc.getId() + ")";
284	}
285	numItems++;
286	numSticky++;
287	%>
288	<m:menuitem
289	title="<%=itemType + shortName%>"
290	onclick="<%="Main.viewOrEditItem('" + ID + "', '" + itemType.name() + "', " + cc.getId() + ")"%>"
291	tooltip="<%="Go to " + HTML.encodeTags(fullName) + " (" + itemType + ")"%>"
292	/>
293	<%
294	if (itemType == Item.BIOASSAYSET)
295	{
296	// Add menu for Experiment explorer as well
297	%>
298	<m:menuitem
299	title="<%="Experiment explorer"+HTML.encodeTags(shortName)%>"
300	onclick="<%="location.href = '"+root+"views/experiments/explorer/view/index.jsp?ID=" + ID + "&bioassayset_id="+cc.getId()+"'"%>"
301	tooltip="Go to experiment explorer"
302	visible="<%=item == null \|\| ((BioAssaySet)item).getNumSpots() > 0 %>"
303	/>
304	<%
305	}
306	}
307	}
308	catch (Throwable t)
309	{}
310	}
311	if (numSticky == 0)
312	{
313	%>
314	<m:menuitem
315	title="<i>- no sticky items -</i>"
316	enabled="false"
317	/>
318	<%
319	}
320	}
321	%>
322	<m:menuseparator />
323	<m:menuitem
324	title="Options…"
325	onclick="<%="Main.openPopup('"+root+"my_base/user/preferences.jsp?ID="+ID+"&page=mostRecent', 'Preferences', 500, 400);"%>"
326	tooltip="Change options for this menu"
327	/>
328	</m:menu>
329	<%
330	}
331	finally
332	{
333	if (dc != null) dc.close();
334	}
335	}
336	else if ("standard".equals(name))
337	{
338	final DbControl dc = sc.newDbControl();
339	StringBuilder fillText = new StringBuilder();
340	try
341	{
342	Project activeProject = sc.getActiveProjectId() == 0 ? null : Project.getById(dc, sc.getActiveProjectId());
343	if (activeProject == null)
344	{
345	fillText.append("<img src=\""+root+"images/no_active_project.gif\" border=\"0\"> ");
346	fillText.append("<a href=\"javascript:void(0)\" style=\"color:#FF0000;\" title=\"Set active project\"");
347	}
348	else
349	{
350	fillText.append("<img src=\""+root+"images/project.gif\" border=\"0\"> ");
351	fillText.append("<a href=\"javascript:void(0)\" title=\"Switch active project\"");
352	}
353
354	fillText.append(" onclick=\"Menu.toggleTopMenu(document.getElementById('projects'), event.clientX-50, event.clientY); event.cancelBubble = true;\">");
355	fillText.append(activeProject == null ? "<i>- no active project -</i>" : HTML.encodeTags(activeProject.getName()));
356	fillText.append(" <img src=\""+root+"images/sort_asc.gif\" border=\"0\"></a><span class=\"menuseparator\">  </span>");
357
358	fillText.append("<a href=\"javascript:void(0)\" title=\"Refresh current page\"");
359	fillText.append(" onclick=\"location.reload()\">");
360	fillText.append("<img src=\""+root+"images/refresh.gif\" border=\"0\"></a><span class=\"menuseparator\">  </span>");
361
362	fillText.append("<a href=\"javascript:void(0)\" title=\"Go to the most recently viewed item\"");
363	fillText.append(" onclick=\"Menu.toggleTopMenu(document.getElementById('mostRecent'), event.clientX-200, event.clientY); event.cancelBubble = true;\">");
364	fillText.append(" <img src=\""+root+"images/recent.png\" border=\"0\"><img src=\""+root+"images/sort_asc.gif\" border=\"0\"></a><span class=\"menuseparator\">  </span>");
365
366	User user = User.getById(dc, sc.getLoggedInUserId());
367	String userPrompt = sc.isImpersonated() ? "Impersonated" : "User";
368	fillText.append("<img src=\""+root+"images/take_ownership.png\" border=\"0\"> <a href=\"javascript:void(0)\" title=\"Switch user/logout\"");
369	fillText.append(" onclick=\"javascript:Menu.toggleTopMenu(document.getElementById('switchuser'), event.clientX-100, event.clientY); event.cancelBubble = true;\">");
370	fillText.append(HTML.encodeTags(user.getLogin()));
371	fillText.append(" (").append(user.getName()).append(") <img src=\""+root+"images/sort_asc.gif\" border=\"0\"></a>");
372	%>
373	<%
374	// Permission settings
375	final boolean hasFiles = !sc.hasPermission(Permission.DENIED, Item.FILE);
376	final boolean createFiles = sc.hasPermission(Permission.CREATE, Item.FILE);
377
378	final boolean hasProjects = !sc.hasPermission(Permission.DENIED, Item.PROJECT);
379	final boolean createProjects = sc.hasPermission(Permission.CREATE, Item.PROJECT);
380
381	final boolean hasMessages = !sc.hasPermission(Permission.DENIED, Item.MESSAGE);
382	final boolean createMessages = sc.hasPermission(Permission.CREATE, Item.MESSAGE);
383
384	final boolean hasHybridizations = !sc.hasPermission(Permission.DENIED, Item.HYBRIDIZATION);
385	final boolean createHybridizations = sc.hasPermission(Permission.CREATE, Item.HYBRIDIZATION);
386
387	final boolean hasScans = !sc.hasPermission(Permission.DENIED, Item.SCAN);
388	final boolean createScans = sc.hasPermission(Permission.CREATE, Item.SCAN);
389	final boolean hasRawBioAssays = !sc.hasPermission(Permission.DENIED, Item.RAWBIOASSAY);
390	final boolean createRawBioAssays = sc.hasPermission(Permission.CREATE, Item.RAWBIOASSAY);
391	final boolean hasExperiments = !sc.hasPermission(Permission.DENIED, Item.EXPERIMENT);
392	final boolean createExperiments = sc.hasPermission(Permission.CREATE, Item.EXPERIMENT);
393	final boolean hasFormulas = !sc.hasPermission(Permission.DENIED, Item.FORMULA);
394	final boolean createFormulas = sc.hasPermission(Permission.CREATE, Item.FORMULA);
395
396	final boolean hasReporters = !sc.hasPermission(Permission.DENIED, Item.REPORTER);
397	final boolean hasReporterLists = !sc.hasPermission(Permission.DENIED, Item.REPORTERLIST);
398	final boolean createReporters = sc.hasPermission(Permission.CREATE, Item.REPORTER);
399	final boolean hasJobs = !sc.hasPermission(Permission.DENIED, Item.JOB);
400	final boolean hasSessions = !sc.hasPermission(Permission.DENIED, Item.SESSION);
401	%>
402	<m:menu
403	id="view"
404	style="display: none"
405	>
406	<m:menuitem
407	title="Home"
408	onclick="<%="Menu.openUrl('"+root+"my_base/index.jsp?ID="+ID+"')"%>"
409	/>
410	<m:menuitem
411	title="All items"
412	tooltip="View all items that you are the owner of"
413	onclick="<%="Menu.openUrl('"+root+"views/items/index.jsp?ID="+ID+"')"%>"
414	/>
415	<m:menuitem
416	title="Trashcan"
417	tooltip="View all items that have been marked for deletion"
418	onclick="<%="Menu.openUrl('"+root+"views/trashcan/index.jsp?ID="+ID+"')"%>"
419	/>
420	<m:menuseparator />
421	<m:menuitem
422	title="Files"
423	onclick="<%="Menu.openUrl('"+root+"filemanager/index.jsp?ID="+ID+"')"%>"
424	tooltip="<%=hasFiles ? "Manage files" : "You do not have permission to manage files"%>"
425	enabled="<%=hasFiles%>"
426	/>
427	<m:menuitem
428	title="Projects"
429	onclick="<%="Menu.openUrl('"+root+"my_base/projects/index.jsp?ID="+ID+"')"%>"
430	tooltip="Manage projects"
431	enabled="<%=hasProjects%>"
432	/>
433	<m:menuitem
434	title="Messages"
435	onclick="<%="Menu.openUrl('"+root+"my_base/messages/index.jsp?ID="+ID+"')"%>"
436	tooltip="<%=hasMessages ? "Read your messages" : "You do not have permission to read messages"%>"
437	enabled="<%=hasMessages%>"
438	/>
439	<m:menuitem
440	title="Jobs"
441	onclick="<%="Menu.openUrl('"+root+"views/jobs/index.jsp?ID="+ID+"')"%>"
442	tooltip="<%=hasJobs ? "Check the status of your jobs" : "You do not have permission to access jobs"%>"
443	enabled="<%=hasJobs%>"
444	/>
445	<m:menuitem
446	title="Sessions"
447	onclick="<%="Menu.openUrl('"+root+"views/sessions/index.jsp?ID="+ID+"')"%>"
448	tooltip="<%=hasSessions ? "Check you login sessions" : "You do not have permission to access sessions"%>"
449	enabled="<%=hasSessions%>"
450	/>
451	<m:menuseparator />
452	<m:menuitem
453	title="Hybridizations"
454	onclick="<%="Menu.openUrl('"+root+"views/hybridizations/index.jsp?ID="+ID+"')"%>"
455	tooltip="<%=hasHybridizations ? "Manage hybridizations" : "You do not have permission to manage hybridizations"%>"
456	enabled="<%=hasHybridizations%>"
457	/>
458	<m:menuitem
459	title="Scans"
460	onclick="<%="Menu.openUrl('"+root+"views/scans/index.jsp?ID="+ID+"')"%>"
461	tooltip="<%=hasScans ? "Manage scans" : "You do not have permission to manage scans"%>"
462	enabled="<%=hasScans%>"
463	/>
464	<m:menuitem
465	title="Raw bioassays"
466	onclick="<%="Menu.openUrl('"+root+"views/rawbioassays/index.jsp?ID="+ID+"')"%>"
467	tooltip="<%=hasRawBioAssays ? "Manage raw bioassays" : "You do not have permission to manage raw bioassays"%>"
468	enabled="<%=hasRawBioAssays%>"
469	/>
470	<m:menuitem
471	title="Experiments"
472	onclick="<%="Menu.openUrl('"+root+"views/experiments/index.jsp?ID="+ID+"')"%>"
473	tooltip="<%=hasExperiments ? "Manage experiments" : "You do not have permission to manage experiments"%>"
474	enabled="<%=hasExperiments%>"
475	/>
476	<m:menuitem
477	title="Formulas"
478	onclick="<%="Menu.openUrl('"+root+"views/formulas/index.jsp?ID="+ID+"')"%>"
479	tooltip="<%=hasFormulas ? "Manage formulas" : "You do not have permission to manage formulas"%>"
480	enabled="<%=hasFormulas%>"
481	/>
482	<m:menuseparator />
483	<m:menuitem
484	title="Reporters"
485	onclick="<%="Menu.openUrl('"+root+"views/reporters/index.jsp?ID="+ID+"')"%>"
486	tooltip="<%=hasReporters ? "Manage reporters" : "You do not have permission to manage reporters"%>"
487	enabled="<%=hasReporters%>"
488	/>
489	<m:menuitem
490	title="Reporter lists"
491	onclick="<%="Menu.openUrl('"+root+"views/reporterlists/index.jsp?ID="+ID+"')"%>"
492	tooltip="<%=hasReporterLists ? "Manage reporter lists" : "You do not have permission to manage reporter lists"%>"
493	enabled="<%=hasReporterLists%>"
494	/>
495	</m:menu>
496
497	<m:menu
498	id="base"
499	style="display: none"
500	>
501	<m:submenu
502	subid="projects"
503	title="Select project"
504	enabled="<%=hasProjects%>"
505	/>
506	<m:menuseparator />
507	<m:menuitem
508	title="Contact information…"
509	onclick="<%="Main.openPopup('"+root+"my_base/user/settings.jsp?ID="+ID+"&page=contact', 'Settings', 500, 360);"%>"
510	tooltip="Set your address, phone, email, etc."
511	/>
512	<m:menuitem
513	title="Change password…"
514	onclick="<%="Main.openPopup('"+root+"my_base/user/settings.jsp?ID="+ID+"&page=password', 'Settings', 500, 360);"%>"
515	tooltip="Set your password"
516	/>
517	<m:menuitem
518	title="Other information…"
519	onclick="<%="Main.openPopup('"+root+"my_base/user/settings.jsp?ID="+ID+"&page=other', 'Settings', 500, 360);"%>"
520	tooltip="Other user-related information"
521	/>
522	<m:menuseparator />
523	<m:menuitem
524	title="Preferences…"
525	onclick="<%="Main.openPopup('"+root+"my_base/user/preferences.jsp?ID="+ID+"', 'Preferences', 500, 400);"%>"
526	tooltip="Change font sizes, etc."
527	/>
528	<m:menuitem
529	title="Reload permissions"
530	onclick="<%="Main.openPopup('"+root+"my_base/user/submit_user.jsp?ID="+ID+"&cmd=ReloadPermissions', 'ReloadPermissions', 300, 200);"%>"
531	tooltip="Reload permissions"
532	/>
533	<m:menuitem
534	title="Reset list settings…"
535	onclick="<%="Main.openPopup('"+root+"my_base/user/reset_filters.jsp?ID="+ID+"', 'ResetFilter', 400, 300);"%>"
536	tooltip="Reset visible columns, sort order, filters, etc. to default settings on all lists"
537	/>
538	<m:menuseparator />
539	<m:menuitem
540	title="Logout…"
541	onclick="<%="Main.openPopup('"+root+"logout.jsp?ID="+ID+"', 'Logout', 360, 200);"%>"
542	tooltip="Exit from BASE"
543	/>
544	</m:menu>
545
546	<%
547	// BioLIMS - menu
548	final boolean hasLabels = !sc.hasPermission(Permission.DENIED, Item.LABEL);
549	final boolean createLabels = sc.hasPermission(Permission.CREATE, Item.LABEL);
550
551	final boolean hasBioSources = !sc.hasPermission(Permission.DENIED, Item.BIOSOURCE);
552	final boolean createBioSources = sc.hasPermission(Permission.CREATE, Item.BIOSOURCE);
553
554	final boolean hasSamples = !sc.hasPermission(Permission.DENIED, Item.SAMPLE);
555	final boolean createSamples = sc.hasPermission(Permission.CREATE, Item.SAMPLE);
556
557	final boolean hasExtracts = !sc.hasPermission(Permission.DENIED, Item.EXTRACT);
558	final boolean createExtracts = sc.hasPermission(Permission.CREATE, Item.EXTRACT);
559
560	final boolean hasLabeledExtracts = !sc.hasPermission(Permission.DENIED, Item.LABELEDEXTRACT);
561	final boolean createLabeledExtracts = sc.hasPermission(Permission.CREATE, Item.LABELEDEXTRACT);
562
563	final boolean hasBioMaterialLists = !sc.hasPermission(Permission.DENIED, Item.BIOMATERIALLIST);
564
565	final boolean hasBioPlates = !sc.hasPermission(Permission.DENIED, Item.BIOPLATE);
566	final boolean createBioPlates = sc.hasPermission(Permission.CREATE, Item.BIOPLATE);
567	final boolean hasBioLims = hasLabels \|\| hasBioSources \|\| hasSamples \|\| hasExtracts \|\|
568	hasLabeledExtracts \|\| hasBioMaterialLists;
569
570	if (hasBioLims)
571	{
572	%>
573	<m:menu
574	id="biolims"
575	style="display: none"
576	>
577	<m:menuitem
578	title="Biosources"
579	onclick="<%="Menu.openUrl('"+root+"biomaterials/biosources/index.jsp?ID="+ID+"')"%>"
580	tooltip="<%=hasBioSources ? "Manage biosources" : "You do not have permission to manage biosources"%>"
581	enabled="<%=hasBioSources%>"
582	/>
583	<m:menuitem
584	title="Samples"
585	onclick="<%="Menu.openUrl('"+root+"biomaterials/samples/index.jsp?ID="+ID+"')"%>"
586	tooltip="<%=hasSamples ? "Manage samples" : "You do not have permission to manage samples"%>"
587	enabled="<%=hasSamples%>"
588	/>
589	<m:menuitem
590	title="Extracts"
591	onclick="<%="Menu.openUrl('"+root+"biomaterials/extracts/index.jsp?ID="+ID+"')"%>"
592	tooltip="<%=hasExtracts ? "Manage extracts" : "You do not have permission to manage extracts"%>"
593	enabled="<%=hasExtracts%>"
594	/>
595	<m:menuitem
596	title="Labeled extracts"
597	onclick="<%="Menu.openUrl('"+root+"biomaterials/labeledextracts/index.jsp?ID="+ID+"')"%>"
598	tooltip="<%=hasLabeledExtracts ? "Manage labeled extracts" : "You do not have permission to manage labeled extracts"%>"
599	enabled="<%=hasLabeledExtracts%>"
600	/>
601	<m:menuitem
602	title="Labels"
603	onclick="<%="Menu.openUrl('"+root+"biomaterials/labels/index.jsp?ID="+ID+"')"%>"
604	tooltip="<%=hasLabels ? "Manage labels" : "You do not have permission to manage labels"%>"
605	enabled="<%=hasLabels%>"
606	/>
607	<m:menuseparator />
608	<m:menuitem
609	title="Bioplates"
610	onclick="<%="Menu.openUrl('"+root+"biomaterials/bioplates/index.jsp?ID="+ID+"')"%>"
611	tooltip="<%=hasBioPlates ? "Manage bio plates" : "You do not have permission to manage bio plates"%>"
612	enabled="<%=hasBioPlates%>"
613	/>
614	<m:menuitem
615	title="Biomaterial lists"
616	onclick="<%="Menu.openUrl('"+root+"biomaterials/lists/index.jsp?ID="+ID+"')"%>"
617	tooltip="<%=hasBioMaterialLists ? "Manage biomaterial lists" : "You do not have permission to manage biomaterial lists"%>"
618	enabled="<%=hasBioMaterialLists%>"
619	/>
620	</m:menu>
621	<%
622	}
623
624	// Array LIMS - menu
625	final boolean hasPlateGeometries = sc.hasPermission(Permission.READ, Item.PLATEGEOMETRY);
626	final boolean hasPlateTypes = !sc.hasPermission(Permission.DENIED, Item.PLATETYPE);
627	final boolean hasPlates = !sc.hasPermission(Permission.DENIED, Item.PLATE);
628	final boolean hasPlateMappings = !sc.hasPermission(Permission.DENIED, Item.PLATEMAPPING);
629	final boolean hasArraySlides = !sc.hasPermission(Permission.DENIED, Item.ARRAYSLIDE);
630	final boolean hasArrayBatches = !sc.hasPermission(Permission.DENIED, Item.ARRAYBATCH);
631	final boolean hasArrayDesigns = !sc.hasPermission(Permission.DENIED, Item.ARRAYDESIGN);
632	final boolean hasLims = hasPlateGeometries \|\| hasPlateTypes \|\| hasPlates \|\| hasPlateMappings \|\|
633	hasArraySlides \|\| hasArrayBatches \|\| hasArrayDesigns;
634	if (hasLims)
635	{
636	%>
637	<m:menu
638	id="lims"
639	style="display: none"
640	>
641	<m:menuitem
642	title="Plate geometries"
643	onclick="<%="Menu.openUrl('"+root+"lims/geometries/index.jsp?ID="+ID+"')"%>"
644	tooltip="<%=hasPlateGeometries ? "Manage plate geometries" : "You do not have permission to manage plate geometries"%>"
645	enabled="<%=hasPlateGeometries%>"
646	/>
647	<m:menuitem
648	title="Plate types"
649	onclick="<%="Menu.openUrl('"+root+"lims/platetypes/index.jsp?ID="+ID+"')"%>"
650	tooltip="<%=hasPlateTypes ? "Manage plate types" : "You do not have permission to manage plate types"%>"
651	enabled="<%=hasPlateTypes%>"
652	/>
653	<m:menuitem
654	title="Plates"
655	onclick="<%="Menu.openUrl('"+root+"lims/plates/index.jsp?ID="+ID+"')"%>"
656	tooltip="<%=hasPlates ? "Manage plates" : "You do not have permission to manage plates"%>"
657	enabled="<%=hasPlates%>"
658	/>
659	<m:menuitem
660	title="Plate mappings"
661	onclick="<%="Menu.openUrl('"+root+"lims/platemappings/index.jsp?ID="+ID+"')"%>"
662	tooltip="<%=hasPlateTypes ? "Manage plate mappings" : "You do not have permission to manage plate mappings"%>"
663	enabled="<%=hasPlateTypes%>"
664	/>
665	<m:menuseparator />
666	<m:menuitem
667	title="Array designs"
668	onclick="<%="Menu.openUrl('"+root+"lims/arraydesigns/index.jsp?ID="+ID+"')"%>"
669	tooltip="<%=hasArrayDesigns ? "Manage array designs" : "You do not have permission to manage array designs"%>"
670	enabled="<%=hasArrayDesigns%>"
671	/>
672	<m:menuitem
673	title="Array batches"
674	onclick="<%="Menu.openUrl('"+root+"lims/arraybatches/index.jsp?ID="+ID+"')"%>"
675	tooltip="<%=hasArrayBatches ? "Manage array batches" : "You do not have permission to manage array batches"%>"
676	enabled="<%=hasArrayBatches%>"
677	/>
678	<m:menuitem
679	title="Array slides"
680	onclick="<%="Menu.openUrl('"+root+"lims/arrayslides/index.jsp?ID="+ID+"')"%>"
681	tooltip="<%=hasArraySlides ? "Manage array slides" : "You do not have permission to manage array slides"%>"
682	enabled="<%=hasArraySlides%>"
683	/>
684	</m:menu>
685	<%
686	}
687	%>
688	<%
689	// Administrate -> Types menu
690	final boolean hasQuotaTypes = sc.hasPermission(Permission.READ, Item.QUOTATYPE);
691	final boolean hasProtocolTypes = sc.hasPermission(Permission.READ, Item.PROTOCOLTYPE);
692	final boolean hasFileTypes = sc.hasPermission(Permission.READ, Item.FILETYPE);
693	final boolean hasMimeTypes = sc.hasPermission(Permission.READ, Item.MIMETYPE);
694	final boolean hasHardwareTypes = sc.hasPermission(Permission.READ, Item.HARDWARETYPE);
695	final boolean hasSoftwareTypes = sc.hasPermission(Permission.READ, Item.SOFTWARETYPE);
696	final boolean hasAnnotationTypeCategories = !sc.hasPermission(Permission.DENIED, Item.ANNOTATIONTYPECATEGORY);
697	final boolean hasAnnotationTypes = !sc.hasPermission(Permission.DENIED, Item.ANNOTATIONTYPE);
698	final boolean hasReporterTypes = !sc.hasPermission(Permission.DENIED, Item.REPORTERTYPE);
699	final boolean hasExtraValueTypes = !sc.hasPermission(Permission.DENIED, Item.EXTRAVALUETYPE);
700	final boolean hasQuantities = !sc.hasPermission(Permission.DENIED, Item.QUANTITY);
701	final boolean hasTypes = hasFileTypes \|\| hasProtocolTypes \|\| hasMimeTypes \|\| hasQuotaTypes \|\|
702	hasSoftwareTypes \|\| hasHardwareTypes \|\| hasAnnotationTypeCategories \|\| hasAnnotationTypes \|\|
703	hasReporterTypes \|\| hasExtraValueTypes \|\| hasQuantities;
704	if (hasTypes)
705	{
706	%>
707	<m:menu
708	id="types"
709	style="display: none"
710	>
711	<m:menuitem
712	title="Quota types"
713	onclick="<%="Menu.openUrl('"+root+"admin/quotatypes/index.jsp?ID="+ID+"')"%>"
714	tooltip="<%=hasQuotaTypes ? "Administrate quota types" : "You do not have permission to administrate quota types"%>"
715	enabled="<%=hasQuotaTypes%>"
716	/>
717	<m:menuitem
718	title="Protocol types"
719	onclick="<%="Menu.openUrl('"+root+"admin/protocoltypes/index.jsp?ID="+ID+"')"%>"
720	tooltip="<%=hasProtocolTypes ? "Administrate protocol types" : "You do not have permission to administrate protocol types"%>"
721	enabled="<%=hasProtocolTypes%>"
722	/>
723	<m:menuitem
724	title="File types"
725	onclick="<%="Menu.openUrl('"+root+"admin/filetypes/index.jsp?ID="+ID+"')"%>"
726	tooltip="<%=hasFileTypes ? "Administrate file types" : "You do not have permission to administrate file types"%>"
727	enabled="<%=hasFileTypes%>"
728	/>
729	<m:menuitem
730	title="MIME types"
731	onclick="<%="Menu.openUrl('"+root+"admin/mimetypes/index.jsp?ID="+ID+"')"%>"
732	tooltip="<%=hasMimeTypes ? "Administrate MIME types" : "You do not have permission to administrate mime types"%>"
733	enabled="<%=hasMimeTypes%>"
734	/>
735	<m:menuitem
736	title="Software types"
737	onclick="<%="Menu.openUrl('"+root+"admin/softwaretypes/index.jsp?ID="+ID+"')"%>"
738	tooltip="<%=hasSoftwareTypes ? "Administrate software types" : "You do not have permission to administrate software types"%>"
739	enabled="<%=hasSoftwareTypes%>"
740	/>
741	<m:menuitem
742	title="Hardware types"
743	onclick="<%="Menu.openUrl('"+root+"admin/hardwaretypes/index.jsp?ID="+ID+"')"%>"
744	tooltip="<%=hasHardwareTypes ? "Administrate hardware types" : "You do not have permission to administrate hardware types"%>"
745	enabled="<%=hasHardwareTypes%>"
746	/>
747	<m:menuitem
748	title="Annotation type categories"
749	onclick="<%="Menu.openUrl('"+root+"admin/annotationtypecategories/index.jsp?ID="+ID+"')"%>"
750	tooltip="<%=hasAnnotationTypeCategories ? "Administrate annotation type categories" : "You do not have permission to administrate annotation types categories"%>"
751	enabled="<%=hasAnnotationTypeCategories%>"
752	/>
753	<m:menuitem
754	title="Annotation types"
755	onclick="<%="Menu.openUrl('"+root+"admin/annotationtypes/index.jsp?ID="+ID+"')"%>"
756	tooltip="<%=hasAnnotationTypes ? "Administrate annotation types" : "You do not have permission to administrate annotation types"%>"
757	enabled="<%=hasAnnotationTypes%>"
758	/>
759	<m:menuitem
760	title="Units and quantities"
761	onclick="<%="Menu.openUrl('"+root+"admin/quantities/index.jsp?ID="+ID+"')"%>"
762	tooltip="<%=hasQuantities ? "Administrate quantities" : "You do not have permission to administrate quantities"%>"
763	enabled="<%=hasQuantities%>"
764	/>
765	<m:menuitem
766	title="Reporter types"
767	onclick="<%="Menu.openUrl('"+root+"admin/reportertypes/index.jsp?ID="+ID+"')"%>"
768	tooltip="<%=hasReporterTypes ? "Administrate reporter types" : "You do not have permission to administrate reporter types"%>"
769	enabled="<%=hasReporterTypes%>"
770	/>
771	<m:menuitem
772	title="Extra value types"
773	onclick="<%="Menu.openUrl('"+root+"admin/extravaluetypes/index.jsp?ID="+ID+"')"%>"
774	tooltip="<%=hasExtraValueTypes ? "Administrate extra value types" : "You do not have permission to administrate extra value types"%>"
775	enabled="<%=hasExtraValueTypes%>"
776	/>
777	</m:menu>
778	<%
779	}
780	%>
781	<%
782	// Administrate -> Platforms menu
783	final boolean hasPlatforms = sc.hasPermission(Permission.READ, Item.PLATFORM);
784	final boolean hasFileSetMemberTypes = sc.hasPermission(Permission.READ, Item.DATAFILETYPE);
785	final boolean hasTopPlatforms = hasPlatforms \|\| hasFileSetMemberTypes;
786	if (hasTopPlatforms)
787	{
788	%>
789	<m:menu
790	id="platforms"
791	style="display: none"
792	>
793	<m:menuitem
794	title="Experimental platforms"
795	onclick="<%="Menu.openUrl('"+root+"admin/platforms/index.jsp?ID="+ID+"')"%>"
796	tooltip="<%=hasPlatforms ? "Administrate experimental platforms" : "You do not have permission to administrate experimental platforms"%>"
797	enabled="<%=hasPlatforms%>"
798	/>
799	<m:menuitem
800	title="Data file types"
801	onclick="<%="Menu.openUrl('"+root+"admin/datafiletypes/index.jsp?ID="+ID+"')"%>"
802	tooltip="<%=hasFileSetMemberTypes ? "Administrate data file types" : "You do not have permission to administrate data file types"%>"
803	enabled="<%=hasFileSetMemberTypes%>"
804	/>
805	</m:menu>
806	<%
807	}
808	%>
809
810	<%
811	// Plugins menu
812	final boolean hasPluginTypes = !sc.hasPermission(Permission.DENIED, Item.PLUGINTYPE);
813	final boolean hasPluginDefinitions = !sc.hasPermission(Permission.DENIED, Item.PLUGINDEFINITION);
814	final boolean hasPluginConfigurations = !sc.hasPermission(Permission.DENIED, Item.PLUGINCONFIGURATION);
815	final boolean hasJobAgents = sc.hasPermission(Permission.READ, Item.JOBAGENT);
816	final boolean hasPlugins = hasPluginTypes \|\| hasPluginDefinitions \|\|
817	hasPluginConfigurations \|\| hasJobAgents;
818
819	if (hasPlugins)
820	{
821	%>
822	<m:menu
823	id="plugins"
824	style="display: none"
825	>
826	<m:menuitem
827	title="Types"
828	onclick="<%="Menu.openUrl('"+root+"admin/plugintypes/index.jsp?ID="+ID+"')"%>"
829	tooltip="<%=hasPluginDefinitions ? "Administrate plugin types" : "You do not have permission to administrate plugin types"%>"
830	enabled="<%=hasPluginTypes%>"
831	/>
832	<m:menuitem
833	title="Definitions"
834	onclick="<%="Menu.openUrl('"+root+"admin/plugindefinitions/index.jsp?ID="+ID+"')"%>"
835	tooltip="<%=hasPluginDefinitions ? "Administrate plugin definitions" : "You do not have permission to administrate plugin definitions"%>"
836	enabled="<%=hasPluginDefinitions%>"
837	/>
838	<m:menuitem
839	title="Configurations"
840	onclick="<%="Menu.openUrl('"+root+"admin/pluginconfigurations/index.jsp?ID="+ID+"')"%>"
841	tooltip="<%=hasPluginConfigurations ? "Administrate plugin configurations" : "You do not have permission to administrate plugin configurations"%>"
842	enabled="<%=hasPluginConfigurations%>"
843	/>
844	<m:menuseparator />
845	<m:menuitem
846	title="Job agents"
847	onclick="<%="Menu.openUrl('"+root+"admin/jobagents/index.jsp?ID="+ID+"')"%>"
848	tooltip="<%=hasJobAgents ? "Administrate job agents" : "You do not have permission to administrate job agents"%>"
849	enabled="<%=hasJobAgents%>"
850	/>
851	</m:menu>
852	<%
853	}
854	%>
855
856	<%
857	// Administrate menu
858	final boolean hasUsers = !sc.hasPermission(Permission.DENIED, Item.USER);
859	final boolean hasGroups = !sc.hasPermission(Permission.DENIED, Item.GROUP);
860	final boolean hasRoles = sc.hasPermission(Permission.READ, Item.ROLE);
861	final boolean hasQuota = sc.hasPermission(Permission.READ, Item.QUOTA);
862	final boolean hasSoftware = !sc.hasPermission(Permission.DENIED, Item.SOFTWARE);
863	final boolean hasHardware = !sc.hasPermission(Permission.DENIED, Item.HARDWARE);
864	final boolean hasProtocols = !sc.hasPermission(Permission.DENIED, Item.PROTOCOL);
865	final boolean hasClients = sc.hasPermission(Permission.READ, Item.CLIENT);
866	final boolean hasNews = sc.hasPermission(Permission.READ, Item.NEWS);
867	final boolean hasDiskUsage = sc.hasPermission(Permission.READ, Item.DISKUSAGE);
868	final Client currentClient = Client.getById(dc, sc.getClientId());
869	final boolean hasServer = currentClient.hasPermission(Permission.WRITE);
870
871	final boolean hasAdministrate =
872	hasUsers \|\| hasGroups \|\| hasRoles \|\| hasQuota \|\| hasTypes \|\| hasPlugins \|\|
873	hasSoftware \|\| hasHardware \|\| hasProtocols \|\| hasClients \|\| hasNews \|\|
874	hasDiskUsage \|\| hasServer \|\| hasTopPlatforms;
875
876	if (hasAdministrate)
877	{
878	%>
879	<m:menu
880	id="administrate"
881	style="display: none"
882	>
883	<m:menuitem
884	title="Users"
885	onclick="<%="Menu.openUrl('"+root+"admin/users/index.jsp?ID="+ID+"')"%>"
886	tooltip="<%=hasUsers ? "Administrate users" : "You do not have permission to administrate users"%>"
887	enabled="<%=hasUsers%>"
888	/>
889	<m:menuitem
890	title="Groups"
891	onclick="<%="Menu.openUrl('"+root+"admin/groups/index.jsp?ID="+ID+"')"%>"
892	tooltip="<%=hasGroups ? "Administrate groups" : "You do not have permission to administrate groups"%>"
893	enabled="<%=hasGroups%>"
894	/>
895	<m:menuitem
896	title="Roles"
897	onclick="<%="Menu.openUrl('"+root+"admin/roles/index.jsp?ID="+ID+"')"%>"
898	tooltip="<%=hasRoles ? "Administrate roles" : "You do not have permission to administrate roles"%>"
899	enabled="<%=hasRoles%>"
900	/>
901	<m:menuseparator />
902	<m:submenu
903	subid="plugins"
904	title="Plugins"
905	tooltip="Administrate plugin definitions and configurations"
906	enabled="<%=hasPlugins%>"
907	/>
908	<m:menuseparator />
909	<m:menuitem
910	title="Quota"
911	onclick="<%="Menu.openUrl('"+root+"admin/quota/index.jsp?ID="+ID+"')"%>"
912	tooltip="<%=hasQuota ? "Administrate quota" : "You do not have permission to administrate quota"%>"
913	enabled="<%=hasQuota%>"
914	/>
915	<m:menuitem
916	title="Software"
917	onclick="<%="Menu.openUrl('"+root+"admin/software/index.jsp?ID="+ID+"')"%>"
918	tooltip="<%=hasSoftware ? "Administrate software" : "You do not have permission to administrate software"%>"
919	enabled="<%=hasSoftware%>"
920	/>
921	<m:menuitem
922	title="Hardware"
923	onclick="<%="Menu.openUrl('"+root+"admin/hardware/index.jsp?ID="+ID+"')"%>"
924	tooltip="<%=hasHardware ? "Administrate hardware" : "You do not have permission to administrate hardware"%>"
925	enabled="<%=hasHardware%>"
926	/>
927	<m:menuitem
928	title="Protocols"
929	onclick="<%="Menu.openUrl('"+root+"admin/protocols/index.jsp?ID="+ID+"')"%>"
930	tooltip="<%=hasProtocols ? "Administrate protocols" : "You do not have permission to administrate protocols"%>"
931	enabled="<%=hasProtocols%>"
932	/>
933	<m:menuitem
934	title="Clients"
935	onclick="<%="Menu.openUrl('"+root+"admin/clients/index.jsp?ID="+ID+"')"%>"
936	tooltip="<%=hasClients ? "Administrate client applications" : "You do not have permission to administrate client applications"%>"
937	enabled="<%=hasClients%>"
938	/>
939	<m:menuitem
940	title="News"
941	onclick="<%="Menu.openUrl('"+root+"admin/news/index.jsp?ID="+ID+"')"%>"
942	tooltip="<%=hasNews ? "Administrate news" : "You do not have permission to administrate news"%>"
943	enabled="<%=hasNews%>"
944	/>
945	<m:menuseparator />
946	<m:submenu
947	subid="platforms"
948	title="Platforms"
949	tooltip="Administrate experimental platforms"
950	enabled="<%=hasTopPlatforms%>"
951	/>
952	<m:submenu
953	subid="types"
954	title="Types"
955	tooltip="Administrate quota, file, hardware and software types"
956	enabled="<%=hasTypes%>"
957	/>
958	<m:menuseparator />
959	<m:menuitem
960	title="Disk usage"
961	onclick="<%="Menu.openUrl('"+root+"admin/diskusage/index.jsp?ID="+ID+"')"%>"
962	tooltip="<%=hasDiskUsage ? "Check disk usage" : "You do not have permission to check disk usage"%>"
963	enabled="<%=hasDiskUsage%>"
964	/>
965	<m:menuitem
966	title="Server settings…"
967	onclick="<%="Main.openPopup('"+root+"admin/server/configure.jsp?ID="+ID+"', 'ServerSettings', 500, 400);"%>"
968	tooltip="<%=hasServer ? "Configure the server" : "You do not have permission to configure the server"%>"
969	enabled="<%=hasServer%>"
970	/>
971	<m:menuitem
972	title="Broadcast message…"
973	onclick="<%="Main.openPopup('"+root+"admin/server/broadcast.jsp?ID="+ID+"', 'BroadcastMessage', 640, 400);"%>"
974	tooltip="<%=hasServer ? "Broadcast a message to all logged in users" : "You do not have permission to send messages"%>"
975	enabled="<%=hasServer%>"
976	/>
977	<m:menuitem
978	title="Services"
979	tooltip="<%=hasServer ? "Manage service extensions" : "You do not have permission to manage services" %>"
980	onclick="<%="Menu.openUrl('"+root+"admin/services/index.jsp?ID="+ID+"')"%>"
981	enabled="<%=hasServer%>"
982	/>
983	</m:menu>
984	<%
985	}
986	%>
987	<%
988	// Help menu
989	final String helplink = Values.getStringOrNull(sc.getClientDefaultSetting("server.links.help"));
990	final String faqlink = Values.getStringOrNull(sc.getClientDefaultSetting("server.links.faq"));
991	final String reportbuglink = Values.getStringOrNull(sc.getClientDefaultSetting("server.links.reportbug"));
992	%>
993	<m:menu id="help" style="display: none">
994	<m:menuitem
995	visible="<%=HTML.isValidUrl(helplink)%>"
996	title="Help…"
997	onclick="<%="window.open('"+helplink+"','Help')"%>"
998	/>
999	<m:menuitem
1000	visible="<%=HTML.isValidUrl(faqlink)%>"
1001	title="FAQ…"
1002	onclick="<%="window.open('"+faqlink+"','FAQ')"%>"
1003	/>
1004	<m:menuseparator />
1005
1006	<m:menuitem
1007	title="About…"
1008	onclick="<%="Main.openPopup('"+root+"info/about.jsp?ID="+ID+"&page=about', 'About', 500, 350)"%>"
1009	/>
1010
1011	<m:menuitem
1012	title="License…"
1013	onclick="<%="Main.openPopup('"+root+"info/about.jsp?ID="+ID+"&page=license', 'About', 500, 350)"%>"
1014
1015	/>
1016	<m:menuitem
1017	visible="<%=HTML.isValidUrl(reportbuglink)%>"
1018	title="Report a bug…"
1019	onclick="<%="window.open('"+reportbuglink+"','Reportbug')"%>"
1020	/>
1021	<m:menuseparator />
1022	<m:menuitem
1023	title="Base project site" onclick="<%="Menu.openUrl('http://base.thep.lu.se', 'basesite')"%>"
1024	/>
1025	</m:menu>
1026
1027	<%
1028	//Switch user/logout menu
1029	final boolean hasImpersonate =
1030	!sc.isImpersonated() && sc.hasSystemPermission(Permission.ACT_AS_ANOTHER_USER);
1031	%>
1032	<m:menu
1033	id="switchuser"
1034	style="display: none;"
1035	>
1036	<m:menuitem
1037	title="Switch user…"
1038	onclick="<%="Main.openPopup('"+root+"switch.jsp?ID="+ID+"', 'Switch', 360, 200);"%>"
1039	tooltip="Login as another user"
1040	/>
1041	<m:menuitem
1042	title="Impersonate…"
1043	onclick="<%="Main.openPopup('"+root+"impersonate.jsp?ID="+ID+"', 'Impersonate', 480, 240);"%>"
1044	tooltip="Login as another user without knowing the password"
1045	visible="<%=hasImpersonate%>"
1046	/>
1047	<m:menuitem
1048	title="Logout…"
1049	onclick="<%="Main.openPopup('"+root+"logout.jsp?ID="+ID+"', 'Logout', 360, 200);"%>"
1050	tooltip="Exit from BASE"
1051	/>
1052	</m:menu>
1053
1054	<%
1055	// Extensions menu
1056	JspContext context = ExtensionsControl.createContext(dc, pageContext);
1057	ExtensionsInvoker<MenuItemAction> invoker =
1058	(ExtensionsInvoker<MenuItemAction>)ExtensionsControl.useExtensions(context,
1059	"net.sf.basedb.clients.web.menu.extensions");
1060	ExtensionsControl ec = ExtensionsControl.get(dc);
1061	ActionIterator<MenuItemAction> it = invoker.iterate();
1062	Map<String, List<MenuItemAction>> menus = new HashMap<String, List<MenuItemAction>>();
1063	menus.put("extensions", new LinkedList<MenuItemAction>());
1064	while (it.hasNext())
1065	{
1066	MenuItemAction action = it.next();
1067	String menuId = action.getMenuId();
1068	menuId = menuId == null ? "extensions" : "extensions." + menuId;
1069	List<MenuItemAction> actions = menus.get(menuId);
1070	if (actions == null)
1071	{
1072	actions = new LinkedList<MenuItemAction>();
1073	menus.put(menuId, actions);
1074	}
1075	actions.add(action);
1076	}
1077
1078	for (Map.Entry<String, List<MenuItemAction>> entry : menus.entrySet())
1079	{
1080	String menuId = entry.getKey();
1081	List<MenuItemAction> actions = entry.getValue();
1082	%>
1083	<m:menu id="<%=menuId%>" style="display: none;">
1084	<%
1085	for (MenuItemAction action : actions)
1086	{
1087	if (action.getType() == MenuItemAction.MenuType.SEPARATOR)
1088	{
1089	%>
1090	<m:menuseparator style="<%=action.getStyle()%>" visible="<%=action.isVisible()%>" />
1091	<%
1092	}
1093	else if (action.getType() == MenuItemAction.MenuType.MENUITEM)
1094	{
1095	%>
1096	<m:menuitem
1097	style="<%=action.getStyle()%>"
1098	title="<%=action.getTitle()%>"
1099	icon="<%=action.getIcon()%>"
1100	iconabsolute="true"
1101	tooltip="<%=action.getTooltip()%>"
1102	enabled="<%=action.isEnabled()%>"
1103	visible="<%=action.isVisible()%>"
1104	onclick="<%=action.getOnClick()%>"
1105	/>
1106	<%
1107	}
1108	else if (action.getType() == MenuItemAction.MenuType.SUBMENU)
1109	{
1110	%>
1111	<m:submenu
1112	subid="<%="extensions." + action.getSubmenuId()%>"
1113	style="<%=action.getStyle()%>"
1114	title="<%=action.getTitle()%>"
1115	icon="<%=action.getIcon()%>"
1116	iconabsolute="true"
1117	tooltip="<%=action.getTooltip()%>"
1118	enabled="<%=action.isEnabled()%>"
1119	visible="<%=action.isVisible()%>"
1120	/>
1121	<%
1122	}
1123	}
1124	if ("extensions".equals(menuId))
1125	{
1126	if (actions.size() > 0)
1127	{
1128	%>
1129	<m:menuseparator />
1130	<%
1131	}
1132	%>
1133	<m:menuitem
1134	title="Installed extensions"
1135	onclick="<%="Menu.openUrl('"+root+"admin/extensions/index.jsp?ID="+ID+"')"%>"
1136	tooltip="Display and administrate installed extensions"
1137	/>
1138	<m:menuitem
1139	title="Manual scan…"
1140	onclick="<%="Main.openPopup('"+root+"admin/extensions/manual_scan.jsp?ID=" + ID + "', 'ManualScan', 500, 400);"%>"
1141	enabled="<%=ec.hasPermission(Permission.WRITE)%>"
1142	tooltip="Start a manual scan for new, updated and deleted extensions"
1143	/>
1144	<%
1145	}
1146	%>
1147	</m:menu>
1148	<%
1149	}
1150	%>
1151
1152	<%
1153	// Main menu
1154	%>
1155	<div style="position: fixed; top: 0px; left: 0px; width: 100%; height: 30px; background: #ffffff;">
1156	<m:menu
1157	type="horizontal"
1158	clazz="menu_horizontal"
1159	id="menubar"
1160	style="top: 5px; left: 8px; width: 98%"
1161	open="click"
1162	filltext="<%=fillText.toString()%>"
1163	>
1164	<m:submenu
1165	subid="base"
1166	title="BASE"
1167	/>
1168	<m:submenu
1169	subid="view"
1170	title="View"
1171	/>
1172	<m:submenu
1173	subid="biolims"
1174	title="Biomaterial LIMS"
1175	/>
1176	<m:submenu
1177	subid="lims"
1178	title="Array LIMS"
1179	/>
1180	<m:submenu
1181	subid="administrate"
1182	title="Administrate"
1183	visible="<%=hasAdministrate%>"
1184	/>
1185	<m:submenu
1186	subid="extensions"
1187	title="Extensions"
1188	/>
1189	<m:submenu
1190	subid="help"
1191	title="Help"
1192	/>
1193	</m:menu></div>
1194	<br><br>
1195	<%
1196	}
1197	finally
1198	{
1199	if (dc != null) dc.close();
1200	}
1201
1202	}
1203	%>
1204
1205
1206

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