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source: trunk/www/include/menu.jsp @ 3679

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Last change on this file since 3679 was 3679, checked in by Jari Häkkinen, 16 years ago
Changing the pesky "a (ä) character to a.
Property svn:eol-style set to `native` Property svn:keywords set to `Id`
File size: 36.2 KB

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1	<%-- $Id: menu.jsp 3679 2007-08-17 07:18:29Z jari $
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	String[] tmp = recent.split("=");
109	Item itemType = Item.valueOf(tmp[0]);
110	int itemId = Values.getInt(tmp[1], 0);
111	if (itemId != 0)
112	{
113	String shortName = "";
114	String fullName = "";
115	if (loadNames)
116	{
117	try
118	{
119	BasicItem item = itemType.getById(dc, itemId);
120	fullName = ((Nameable)item).getName();
121	shortName = HTML.encodeTags(StringUtil.trimString(fullName, 35));
122	}
123	catch (Throwable t)
124	{
125	continue;
126	}
127	}
128	else
129	{
130	fullName = itemType.toString() + "; id=" + itemId;
131	shortName = itemType + " (id=" + itemId + ")";
132	}
133	numItems++;
134	%>
135	<m:menuitem
136	title="<%=numItems + ". " + shortName%>"
137	onclick="<%="Main.viewOrEditItem('" + ID + "', '" + itemType.name() + "', " + itemId + ")"%>"
138	tooltip="<%="Go to " + HTML.encodeTags(fullName) + " (" + itemType + ")"%>"
139	/>
140	<%
141	}
142	}
143	}
144	if (stickyItems != null && stickyItems.length() > 0)
145	{
146	int numSticky = 0;
147	if (numItems > 0)
148	{
149	%>
150	<m:menuseparator />
151	<%
152	}
153	%>
154	<m:menuitem
155	title="Sticky items"
156	style="font-weight: bold; color: #000000; background: #e8e8e8;"
157	enabled="false"
158	/>
159	<m:menuseparator />
160	<%
161	// Sticky items
162	for (String recentItem : stickyItems.split(":"))
163	{
164	Item itemType = Item.valueOf(recentItem);
165	ItemContext cc = sc.getCurrentContext(itemType);
166	if (cc.getId() != 0)
167	{
168	String shortName = "";
169	String fullName = "";
170	if (loadNames)
171	{
172	try
173	{
174	BasicItem item = itemType.getById(dc, cc.getId());
175	fullName = ((Nameable)item).getName();
176	shortName = ": " + HTML.encodeTags(StringUtil.trimString(fullName, 30));
177	}
178	catch (Throwable t)
179	{
180	continue;
181	}
182	}
183	else
184	{
185	fullName = itemType.toString() + "; id=" + cc.getId();
186	shortName = " (id=" + cc.getId() + ")";
187	}
188	numItems++;
189	numSticky++;
190	%>
191	<m:menuitem
192	title="<%=itemType + shortName%>"
193	onclick="<%="Main.viewOrEditItem('" + ID + "', '" + itemType.name() + "', " + cc.getId() + ")"%>"
194	tooltip="<%="Go to " + HTML.encodeTags(fullName) + " (" + itemType + ")"%>"
195	/>
196	<%
197	if (itemType == Item.BIOASSAYSET)
198	{
199	// Add menu for Experiment explorer as well
200	%>
201	<m:menuitem
202	title="<%="Experiment explorer"+HTML.encodeTags(shortName)%>"
203	onclick="<%="location.href = '"+root+"views/experiments/explorer/view/index.jsp?ID=" + ID + "&bioassayset_id="+cc.getId()+"'"%>"
204	tooltip="Go to experiment explorer"
205	/>
206	<%
207	}
208	}
209	}
210	if (numSticky == 0)
211	{
212	%>
213	<m:menuitem
214	title="<i>- no sticky items -</i>"
215	enabled="false"
216	/>
217	<%
218	}
219	}
220	%>
221	<m:menuseparator />
222	<m:menuitem
223	title="Options…"
224	onclick="<%="Main.openPopup('"+root+"my_base/user/preferences.jsp?ID="+ID+"&page=mostRecent', 'Preferences', 500, 400);"%>"
225	tooltip="Change options for this menu"
226	/>
227	</m:menu>
228	<%
229	}
230	finally
231	{
232	if (dc != null) dc.close();
233	}
234	}
235	else if ("standard".equals(name))
236	{
237	final DbControl dc = sc.newDbControl();
238	ItemResultList<Project> projects = null;
239	StringBuilder fillText = new StringBuilder();
240	try
241	{
242	fillText.append("<a href=\"javascript:void(0)\" title=\"Refresh current page\"");
243	fillText.append(" onclick=\"location.reload()\">");
244	fillText.append("<img src=\""+root+"images/refresh.gif\" border=\"0\"></a><span class=\"menuseparator\">  </span>");
245
246	fillText.append("<a href=\"javascript:void(0)\" title=\"Go to the most recently viewed item\"");
247	fillText.append(" onclick=\"Menu.toggleTopMenu(document.getElementById('mostRecent'), event.clientX-20, event.clientY); event.cancelBubble = true;\">");
248	fillText.append(" <img src=\""+root+"images/recent.png\" border=\"0\"><img src=\""+root+"images/sort_asc.gif\" border=\"0\"></a><span class=\"menuseparator\">  </span>");
249
250	Project activeProject = sc.getActiveProjectId() == 0 ? null : Project.getById(dc, sc.getActiveProjectId());
251	fillText.append("<img src=\""+root+"images/project.gif\" border=\"0\"> <a href=\"javascript:void(0)\" title=\"Switch project\"");
252	fillText.append(" onclick=\"Menu.toggleTopMenu(document.getElementById('projects'), event.clientX-100, event.clientY); event.cancelBubble = true;\">");
253	fillText.append(activeProject == null ? "<i>- none -</i>" : HTML.encodeTags(activeProject.getName()));
254	fillText.append(" <img src=\""+root+"images/sort_asc.gif\" border=\"0\"></a><span class=\"menuseparator\">  </span>");
255
256	User user = User.getById(dc, sc.getLoggedInUserId());
257	String userPrompt = sc.isImpersonated() ? "Impersonated" : "User";
258	fillText.append("<img src=\""+root+"images/take_ownership.png\" border=\"0\"> <a href=\"javascript:void(0)\" title=\"Switch user/logout\"");
259	fillText.append(" onclick=\"javascript:Menu.toggleTopMenu(document.getElementById('switchuser'), event.clientX-100, event.clientY); event.cancelBubble = true;\">");
260	fillText.append(HTML.encodeTags(user.getLogin()));
261	fillText.append(" (").append(user.getName()).append(") <img src=\""+root+"images/sort_asc.gif\" border=\"0\"></a>");
262	%>
263	<%
264	// Permission settings
265	final boolean hasFiles = !sc.hasPermission(Permission.DENIED, Item.FILE);
266	final boolean createFiles = sc.hasPermission(Permission.CREATE, Item.FILE);
267
268	final boolean hasProjects = !sc.hasPermission(Permission.DENIED, Item.PROJECT);
269	final boolean createProjects = sc.hasPermission(Permission.CREATE, Item.PROJECT);
270
271	final boolean hasMessages = !sc.hasPermission(Permission.DENIED, Item.MESSAGE);
272	final boolean createMessages = sc.hasPermission(Permission.CREATE, Item.MESSAGE);
273
274	final boolean hasLabels = !sc.hasPermission(Permission.DENIED, Item.LABEL);
275	final boolean createLabels = sc.hasPermission(Permission.CREATE, Item.LABEL);
276
277	final boolean hasBioSources = !sc.hasPermission(Permission.DENIED, Item.BIOSOURCE);
278	final boolean createBioSources = sc.hasPermission(Permission.CREATE, Item.BIOSOURCE);
279
280	final boolean hasSamples = !sc.hasPermission(Permission.DENIED, Item.SAMPLE);
281	final boolean createSamples = sc.hasPermission(Permission.CREATE, Item.SAMPLE);
282
283	final boolean hasExtracts = !sc.hasPermission(Permission.DENIED, Item.EXTRACT);
284	final boolean createExtracts = sc.hasPermission(Permission.CREATE, Item.EXTRACT);
285
286	final boolean hasLabeledExtracts = !sc.hasPermission(Permission.DENIED, Item.LABELEDEXTRACT);
287	final boolean createLabeledExtracts = sc.hasPermission(Permission.CREATE, Item.LABELEDEXTRACT);
288
289	final boolean hasHybridizations = !sc.hasPermission(Permission.DENIED, Item.HYBRIDIZATION);
290	final boolean createHybridizations = sc.hasPermission(Permission.CREATE, Item.HYBRIDIZATION);
291
292	final boolean hasScans = !sc.hasPermission(Permission.DENIED, Item.SCAN);
293	final boolean createScans = sc.hasPermission(Permission.CREATE, Item.SCAN);
294	final boolean hasRawBioAssays = !sc.hasPermission(Permission.DENIED, Item.RAWBIOASSAY);
295	final boolean createRawBioAssays = sc.hasPermission(Permission.CREATE, Item.RAWBIOASSAY);
296	final boolean hasExperiments = !sc.hasPermission(Permission.DENIED, Item.EXPERIMENT);
297	final boolean createExperiments = sc.hasPermission(Permission.CREATE, Item.EXPERIMENT);
298	final boolean hasFormulas = !sc.hasPermission(Permission.DENIED, Item.FORMULA);
299	final boolean createFormulas = sc.hasPermission(Permission.CREATE, Item.FORMULA);
300
301	final boolean hasReporters = !sc.hasPermission(Permission.DENIED, Item.REPORTER);
302	final boolean hasReporterLists = !sc.hasPermission(Permission.DENIED, Item.REPORTERLIST);
303	final boolean createReporters = sc.hasPermission(Permission.CREATE, Item.REPORTER);
304	final boolean hasJobs = !sc.hasPermission(Permission.DENIED, Item.JOB);
305	final boolean hasSessions = !sc.hasPermission(Permission.DENIED, Item.SESSION);
306	%>
307	<m:menu
308	id="view"
309	style="display: none"
310	>
311	<m:menuitem
312	title="Home"
313	onclick="<%="Menu.openUrl('"+root+"my_base/index.jsp?ID="+ID+"')"%>"
314	/>
315	<m:menuitem
316	title="All items"
317	tooltip="View all items that you are the owner of"
318	onclick="<%="Menu.openUrl('"+root+"views/items/index.jsp?ID="+ID+"')"%>"
319	/>
320	<m:menuitem
321	title="Trashcan"
322	tooltip="View all items that have been marked for deletion"
323	onclick="<%="Menu.openUrl('"+root+"views/trashcan/index.jsp?ID="+ID+"')"%>"
324	/>
325	<m:menuseparator />
326	<m:menuitem
327	title="Files"
328	onclick="<%="Menu.openUrl('"+root+"filemanager/index.jsp?ID="+ID+"')"%>"
329	tooltip="<%=hasFiles ? "Manage files" : "You do not have permission to manage files"%>"
330	enabled="<%=hasFiles%>"
331	/>
332	<m:menuitem
333	title="Projects"
334	onclick="<%="Menu.openUrl('"+root+"my_base/projects/index.jsp?ID="+ID+"')"%>"
335	tooltip="Manage projects"
336	enabled="<%=hasProjects%>"
337	/>
338	<m:menuitem
339	title="Messages"
340	onclick="<%="Menu.openUrl('"+root+"my_base/messages/index.jsp?ID="+ID+"')"%>"
341	tooltip="<%=hasMessages ? "Read your messages" : "You do not have permission to read messages"%>"
342	enabled="<%=hasMessages%>"
343	/>
344	<m:menuitem
345	title="Jobs"
346	onclick="<%="Menu.openUrl('"+root+"views/jobs/index.jsp?ID="+ID+"')"%>"
347	tooltip="<%=hasJobs ? "Check the status of your jobs" : "You do not have permission to access jobs"%>"
348	enabled="<%=hasJobs%>"
349	/>
350	<m:menuitem
351	title="Sessions"
352	onclick="<%="Menu.openUrl('"+root+"views/sessions/index.jsp?ID="+ID+"')"%>"
353	tooltip="<%=hasSessions ? "Check you login sessions" : "You do not have permission to access sessions"%>"
354	enabled="<%=hasSessions%>"
355	/>
356	<m:menuseparator />
357	<m:menuitem
358	title="Biosources"
359	onclick="<%="Menu.openUrl('"+root+"biomaterials/biosources/index.jsp?ID="+ID+"')"%>"
360	tooltip="<%=hasBioSources ? "Manage biosources" : "You do not have permission to manage biosources"%>"
361	enabled="<%=hasBioSources%>"
362	/>
363	<m:menuitem
364	title="Samples"
365	onclick="<%="Menu.openUrl('"+root+"biomaterials/samples/index.jsp?ID="+ID+"')"%>"
366	tooltip="<%=hasSamples ? "Manage samples" : "You do not have permission to manage samples"%>"
367	enabled="<%=hasSamples%>"
368	/>
369	<m:menuitem
370	title="Extracts"
371	onclick="<%="Menu.openUrl('"+root+"biomaterials/extracts/index.jsp?ID="+ID+"')"%>"
372	tooltip="<%=hasExtracts ? "Manage extracts" : "You do not have permission to manage extracts"%>"
373	enabled="<%=hasExtracts%>"
374	/>
375	<m:menuitem
376	title="Labeled extracts"
377	onclick="<%="Menu.openUrl('"+root+"biomaterials/labeledextracts/index.jsp?ID="+ID+"')"%>"
378	tooltip="<%=hasLabeledExtracts ? "Manage labeled extracts" : "You do not have permission to manage labeled extracts"%>"
379	enabled="<%=hasLabeledExtracts%>"
380	/>
381	<m:menuitem
382	title="Labels"
383	onclick="<%="Menu.openUrl('"+root+"biomaterials/labels/index.jsp?ID="+ID+"')"%>"
384	tooltip="<%=hasLabels ? "Manage labels" : "You do not have permission to manage labels"%>"
385	enabled="<%=hasLabels%>"
386	/>
387	<m:menuseparator />
388	<m:menuitem
389	title="Hybridizations"
390	onclick="<%="Menu.openUrl('"+root+"views/hybridizations/index.jsp?ID="+ID+"')"%>"
391	tooltip="<%=hasHybridizations ? "Manage hybridizations" : "You do not have permission to manage hybridizations"%>"
392	enabled="<%=hasHybridizations%>"
393	/>
394	<m:menuitem
395	title="Scans"
396	onclick="<%="Menu.openUrl('"+root+"views/scans/index.jsp?ID="+ID+"')"%>"
397	tooltip="<%=hasScans ? "Manage scans" : "You do not have permission to manage scans"%>"
398	enabled="<%=hasScans%>"
399	/>
400	<m:menuitem
401	title="Raw bioassays"
402	onclick="<%="Menu.openUrl('"+root+"views/rawbioassays/index.jsp?ID="+ID+"')"%>"
403	tooltip="<%=hasRawBioAssays ? "Manage raw bioassays" : "You do not have permission to manage raw bioassays"%>"
404	enabled="<%=hasRawBioAssays%>"
405	/>
406	<m:menuitem
407	title="Experiments"
408	onclick="<%="Menu.openUrl('"+root+"views/experiments/index.jsp?ID="+ID+"')"%>"
409	tooltip="<%=hasExperiments ? "Manage experiments" : "You do not have permission to manage experiments"%>"
410	enabled="<%=hasExperiments%>"
411	/>
412	<m:menuitem
413	title="Formulas"
414	onclick="<%="Menu.openUrl('"+root+"views/formulas/index.jsp?ID="+ID+"')"%>"
415	tooltip="<%=hasFormulas ? "Manage formulas" : "You do not have permission to manage formulas"%>"
416	enabled="<%=hasFormulas%>"
417	/>
418	<m:menuseparator />
419	<m:menuitem
420	title="Reporters"
421	onclick="<%="Menu.openUrl('"+root+"views/reporters/index.jsp?ID="+ID+"')"%>"
422	tooltip="<%=hasReporters ? "Manage reporters" : "You do not have permission to manage reporters"%>"
423	enabled="<%=hasReporters%>"
424	/>
425	<m:menuitem
426	title="Reporter lists"
427	onclick="<%="Menu.openUrl('"+root+"views/reporterlists/index.jsp?ID="+ID+"')"%>"
428	tooltip="<%=hasReporterLists ? "Manage reporter lists" : "You do not have permission to manage reporter lists"%>"
429	enabled="<%=hasReporterLists%>"
430	/>
431
432	</m:menu>
433
434
435	<m:menu
436	id="file"
437	style="display: none"
438	>
439	<m:submenu
440	subid="projects"
441	title="Select project"
442	enabled="<%=hasProjects%>"
443	/>
444	<m:menuseparator />
445	<m:menuitem
446	title="Contact information…"
447	onclick="<%="Main.openPopup('"+root+"my_base/user/settings.jsp?ID="+ID+"&page=contact', 'Settings', 500, 360);"%>"
448	tooltip="Set your address, phone, email, etc."
449	/>
450	<m:menuitem
451	title="Change password…"
452	onclick="<%="Main.openPopup('"+root+"my_base/user/settings.jsp?ID="+ID+"&page=password', 'Settings', 500, 360);"%>"
453	tooltip="Set your password"
454	/>
455	<m:menuitem
456	title="Other information…"
457	onclick="<%="Main.openPopup('"+root+"my_base/user/settings.jsp?ID="+ID+"&page=other', 'Settings', 500, 360);"%>"
458	tooltip="Other user-related information"
459	/>
460	<m:menuseparator />
461	<m:menuitem
462	title="Preferences…"
463	onclick="<%="Main.openPopup('"+root+"my_base/user/preferences.jsp?ID="+ID+"', 'Preferences', 500, 400);"%>"
464	tooltip="Change font sizes, etc."
465	/>
466	<m:menuitem
467	title="Reload permissions"
468	onclick="<%="Main.openPopup('"+root+"my_base/user/submit_user.jsp?ID="+ID+"&cmd=ReloadPermissions', 'ReloadPermissions', 300, 200);"%>"
469	tooltip="Reload permissions"
470	/>
471	<m:menuseparator />
472	<m:menuitem
473	title="Logout…"
474	onclick="<%="Main.openPopup('"+root+"logout.jsp?ID="+ID+"', 'Logout', 360, 200);"%>"
475	tooltip="Exit from BASE"
476	/>
477	</m:menu>
478	<%
479	// Projects menu
480	int activeProjectId = sc.getActiveProjectId();
481	final ItemQuery<Project> projectQuery = Project.getQuery();
482	projectQuery.include(Include.MINE, Include.SHARED);
483	projectQuery.order(Orders.asc(Hql.property("name")));
484	projectQuery.setCacheResult(true);
485	%>
486	<m:menu
487	id="projects"
488	style="display: none"
489	>
490	<m:menuitem
491	title="<i>- no active project -</i>"
492	onclick="<%="Main.openPopup('"+root+"my_base/projects/set_active.jsp?ID="+ID+"', 'ActivateProject', 300, 140)"%>"
493	icon="<%=activeProjectId == 0 ? "checkedmenu.gif" : null%>"
494	enabled="<%=activeProjectId != 0%>"
495	tooltip="<%=activeProjectId == 0 ? "No project is active" : "Disable the currently active project"%>"
496	/>
497	<%
498	projects = projectQuery.list(dc);
499	for (Project p : projects)
500	{
501	int projectId = p.getId();
502	boolean active = activeProjectId == projectId;
503	%>
504	<m:menuitem
505	title="<%=HTML.encodeTags(p.getName())%>"
506	style="<%=active ? "color: #000000; font-weight: bold;" : null %>"
507	onclick="<%="Main.openPopup('"+root+"my_base/projects/set_active.jsp?ID="+ID+"&project_id="+p.getId()+"', 'ActivateProject', 300, 140)"%>"
508	icon="<%=active ? "checkedmenu.gif" : null%>"
509	enabled="<%=!active%>"
510	tooltip="<%=active ? "This is the active project" : "Set this project to the active project"%>"
511	/>
512	<%
513	}
514	%>
515	</m:menu>
516
517	<%
518	// Array LIMS - menu
519	final boolean hasPlateGeometries = sc.hasPermission(Permission.READ, Item.PLATEGEOMETRY);
520	final boolean hasPlateTypes = !sc.hasPermission(Permission.DENIED, Item.PLATETYPE);
521	final boolean hasPlates = !sc.hasPermission(Permission.DENIED, Item.PLATE);
522	final boolean hasPlateMappings = !sc.hasPermission(Permission.DENIED, Item.PLATEMAPPING);
523	final boolean hasArraySlides = !sc.hasPermission(Permission.DENIED, Item.ARRAYSLIDE);
524	final boolean hasArrayBatches = !sc.hasPermission(Permission.DENIED, Item.ARRAYBATCH);
525	final boolean hasArrayDesigns = !sc.hasPermission(Permission.DENIED, Item.ARRAYDESIGN);
526	final boolean hasLims = hasPlateGeometries \|\| hasPlateTypes \|\| hasPlates \|\| hasPlateMappings \|\|
527	hasArraySlides \|\| hasArrayBatches \|\| hasArrayDesigns;
528	if (hasLims)
529	{
530	%>
531	<m:menu
532	id="lims"
533	style="display: none"
534	>
535	<m:menuitem
536	title="Plate geometries"
537	onclick="<%="Menu.openUrl('"+root+"lims/geometries/index.jsp?ID="+ID+"')"%>"
538	tooltip="<%=hasPlateGeometries ? "Manage plate geometries" : "You do not have permission to manage plate geometries"%>"
539	enabled="<%=hasPlateGeometries%>"
540	/>
541	<m:menuitem
542	title="Plate types"
543	onclick="<%="Menu.openUrl('"+root+"lims/platetypes/index.jsp?ID="+ID+"')"%>"
544	tooltip="<%=hasPlateTypes ? "Manage plate types" : "You do not have permission to manage plate types"%>"
545	enabled="<%=hasPlateTypes%>"
546	/>
547	<m:menuitem
548	title="Plates"
549	onclick="<%="Menu.openUrl('"+root+"lims/plates/index.jsp?ID="+ID+"')"%>"
550	tooltip="<%=hasPlates ? "Manage plates" : "You do not have permission to manage plates"%>"
551	enabled="<%=hasPlates%>"
552	/>
553	<m:menuitem
554	title="Plate mappings"
555	onclick="<%="Menu.openUrl('"+root+"lims/platemappings/index.jsp?ID="+ID+"')"%>"
556	tooltip="<%=hasPlateTypes ? "Manage plate mappings" : "You do not have permission to manage plate mappings"%>"
557	enabled="<%=hasPlateTypes%>"
558	/>
559	<m:menuseparator />
560	<m:menuitem
561	title="Array designs"
562	onclick="<%="Menu.openUrl('"+root+"lims/arraydesigns/index.jsp?ID="+ID+"')"%>"
563	tooltip="<%=hasArrayDesigns ? "Manage array designs" : "You do not have permission to manage array designs"%>"
564	enabled="<%=hasArrayDesigns%>"
565	/>
566	<m:menuitem
567	title="Array batches"
568	onclick="<%="Menu.openUrl('"+root+"lims/arraybatches/index.jsp?ID="+ID+"')"%>"
569	tooltip="<%=hasArrayBatches ? "Manage array batches" : "You do not have permission to manage array batches"%>"
570	enabled="<%=hasArrayBatches%>"
571	/>
572	<m:menuitem
573	title="Array slides"
574	onclick="<%="Menu.openUrl('"+root+"lims/arrayslides/index.jsp?ID="+ID+"')"%>"
575	tooltip="<%=hasArraySlides ? "Manage array slides" : "You do not have permission to manage array slides"%>"
576	enabled="<%=hasArraySlides%>"
577	/>
578	</m:menu>
579	<%
580	}
581	%>
582	<%
583	// Administrate -> Types menu
584	final boolean hasQuotaTypes = sc.hasPermission(Permission.READ, Item.QUOTATYPE);
585	final boolean hasProtocolTypes = sc.hasPermission(Permission.READ, Item.PROTOCOLTYPE);
586	final boolean hasFileTypes = sc.hasPermission(Permission.READ, Item.FILETYPE);
587	final boolean hasMimeTypes = sc.hasPermission(Permission.READ, Item.MIMETYPE);
588	final boolean hasHardwareTypes = sc.hasPermission(Permission.READ, Item.HARDWARETYPE);
589	final boolean hasSoftwareTypes = sc.hasPermission(Permission.READ, Item.SOFTWARETYPE);
590	final boolean hasAnnotationTypeCategories = !sc.hasPermission(Permission.DENIED, Item.ANNOTATIONTYPECATEGORY);
591	final boolean hasAnnotationTypes = !sc.hasPermission(Permission.DENIED, Item.ANNOTATIONTYPE);
592	final boolean hasReporterTypes = !sc.hasPermission(Permission.DENIED, Item.REPORTERTYPE);
593	final boolean hasExtraValueTypes = !sc.hasPermission(Permission.DENIED, Item.EXTRAVALUETYPE);
594	final boolean hasTypes = hasFileTypes \|\| hasProtocolTypes \|\| hasMimeTypes \|\| hasQuotaTypes \|\|
595	hasSoftwareTypes \|\| hasHardwareTypes \|\| hasAnnotationTypeCategories \|\| hasAnnotationTypes \|\|
596	hasReporterTypes \|\| hasExtraValueTypes;
597	if (hasTypes)
598	{
599	%>
600	<m:menu
601	id="types"
602	style="display: none"
603	>
604	<m:menuitem
605	title="Quota types"
606	onclick="<%="Menu.openUrl('"+root+"admin/quotatypes/index.jsp?ID="+ID+"')"%>"
607	tooltip="<%=hasQuotaTypes ? "Administrate quota types" : "You do not have permission to administrate quota types"%>"
608	enabled="<%=hasQuotaTypes%>"
609	/>
610	<m:menuitem
611	title="Protocol types"
612	onclick="<%="Menu.openUrl('"+root+"admin/protocoltypes/index.jsp?ID="+ID+"')"%>"
613	tooltip="<%=hasProtocolTypes ? "Administrate protocol types" : "You do not have permission to administrate protocol types"%>"
614	enabled="<%=hasProtocolTypes%>"
615	/>
616	<m:menuitem
617	title="File types"
618	onclick="<%="Menu.openUrl('"+root+"admin/filetypes/index.jsp?ID="+ID+"')"%>"
619	tooltip="<%=hasFileTypes ? "Administrate file types" : "You do not have permission to administrate file types"%>"
620	enabled="<%=hasFileTypes%>"
621	/>
622	<m:menuitem
623	title="MIME types"
624	onclick="<%="Menu.openUrl('"+root+"admin/mimetypes/index.jsp?ID="+ID+"')"%>"
625	tooltip="<%=hasMimeTypes ? "Administrate MIME types" : "You do not have permission to administrate mime types"%>"
626	enabled="<%=hasMimeTypes%>"
627	/>
628	<m:menuitem
629	title="Software types"
630	onclick="<%="Menu.openUrl('"+root+"admin/softwaretypes/index.jsp?ID="+ID+"')"%>"
631	tooltip="<%=hasSoftwareTypes ? "Administrate software types" : "You do not have permission to administrate software types"%>"
632	enabled="<%=hasSoftwareTypes%>"
633	/>
634	<m:menuitem
635	title="Hardware types"
636	onclick="<%="Menu.openUrl('"+root+"admin/hardwaretypes/index.jsp?ID="+ID+"')"%>"
637	tooltip="<%=hasHardwareTypes ? "Administrate hardware types" : "You do not have permission to administrate hardware types"%>"
638	enabled="<%=hasHardwareTypes%>"
639	/>
640	<m:menuitem
641	title="Annotation type categories"
642	onclick="<%="Menu.openUrl('"+root+"admin/annotationtypecategories/index.jsp?ID="+ID+"')"%>"
643	tooltip="<%=hasAnnotationTypeCategories ? "Administrate annotation type categories" : "You do not have permission to administrate annotation types categories"%>"
644	enabled="<%=hasAnnotationTypeCategories%>"
645	/>
646	<m:menuitem
647	title="Annotation types"
648	onclick="<%="Menu.openUrl('"+root+"admin/annotationtypes/index.jsp?ID="+ID+"')"%>"
649	tooltip="<%=hasAnnotationTypes ? "Administrate annotation types" : "You do not have permission to administrate annotation types"%>"
650	enabled="<%=hasAnnotationTypes%>"
651	/>
652	<m:menuitem
653	title="Reporter types"
654	onclick="<%="Menu.openUrl('"+root+"admin/reportertypes/index.jsp?ID="+ID+"')"%>"
655	tooltip="<%=hasReporterTypes ? "Administrate reporter types" : "You do not have permission to administrate reporter types"%>"
656	enabled="<%=hasReporterTypes%>"
657	/>
658	<m:menuitem
659	title="Extra value types"
660	onclick="<%="Menu.openUrl('"+root+"admin/extravaluetypes/index.jsp?ID="+ID+"')"%>"
661	tooltip="<%=hasExtraValueTypes ? "Administrate extra value types" : "You do not have permission to administrate extra value types"%>"
662	enabled="<%=hasExtraValueTypes%>"
663	/>
664	</m:menu>
665	<%
666	}
667	%>
668
669	<%
670	// Plugins menu
671	final boolean hasPluginTypes = !sc.hasPermission(Permission.DENIED, Item.PLUGINTYPE);
672	final boolean hasPluginDefinitions = !sc.hasPermission(Permission.DENIED, Item.PLUGINDEFINITION);
673	final boolean hasPluginConfigurations = !sc.hasPermission(Permission.DENIED, Item.PLUGINCONFIGURATION);
674	final boolean hasJobAgents = sc.hasPermission(Permission.READ, Item.JOBAGENT);
675	final boolean hasPlugins = hasPluginTypes \|\| hasPluginDefinitions \|\|
676	hasPluginConfigurations \|\| hasJobAgents;
677
678	if (hasPlugins)
679	{
680	%>
681	<m:menu
682	id="plugins"
683	style="display: none"
684	>
685	<m:menuitem
686	title="Types"
687	onclick="<%="Menu.openUrl('"+root+"admin/plugintypes/index.jsp?ID="+ID+"')"%>"
688	tooltip="<%=hasPluginDefinitions ? "Administrate plugin types" : "You do not have permission to administrate plugin types"%>"
689	enabled="<%=hasPluginTypes%>"
690	/>
691	<m:menuitem
692	title="Definitions"
693	onclick="<%="Menu.openUrl('"+root+"admin/plugindefinitions/index.jsp?ID="+ID+"')"%>"
694	tooltip="<%=hasPluginDefinitions ? "Administrate plugin definitions" : "You do not have permission to administrate plugin definitions"%>"
695	enabled="<%=hasPluginDefinitions%>"
696	/>
697	<m:menuitem
698	title="Configurations"
699	onclick="<%="Menu.openUrl('"+root+"admin/pluginconfigurations/index.jsp?ID="+ID+"')"%>"
700	tooltip="<%=hasPluginConfigurations ? "Administrate plugin configurations" : "You do not have permission to administrate plugin configurations"%>"
701	enabled="<%=hasPluginConfigurations%>"
702	/>
703	<m:menuseparator />
704	<m:menuitem
705	title="Job agents"
706	onclick="<%="Menu.openUrl('"+root+"admin/jobagents/index.jsp?ID="+ID+"')"%>"
707	tooltip="<%=hasJobAgents ? "Administrate job agents" : "You do not have permission to administrate job agents"%>"
708	enabled="<%=hasJobAgents%>"
709	/>
710	</m:menu>
711	<%
712	}
713	%>
714
715	<%
716	// Administrate menu
717	final boolean hasUsers = sc.hasPermission(Permission.READ, Item.USER);
718	final boolean hasGroups = sc.hasPermission(Permission.READ, Item.GROUP);
719	final boolean hasRoles = sc.hasPermission(Permission.READ, Item.ROLE);
720	final boolean hasQuota = sc.hasPermission(Permission.READ, Item.QUOTA);
721	final boolean hasSoftware = !sc.hasPermission(Permission.DENIED, Item.SOFTWARE);
722	final boolean hasHardware = !sc.hasPermission(Permission.DENIED, Item.HARDWARE);
723	final boolean hasProtocols = !sc.hasPermission(Permission.DENIED, Item.PROTOCOL);
724	final boolean hasClients = sc.hasPermission(Permission.READ, Item.CLIENT);
725	final boolean hasNews = sc.hasPermission(Permission.READ, Item.NEWS);
726	final boolean hasDiskUsage = sc.hasPermission(Permission.READ, Item.DISKUSAGE);
727	final Client currentClient = Client.getById(dc, sc.getClientId());
728	final boolean hasServer = currentClient.hasPermission(Permission.WRITE);
729
730	final boolean hasAdministrate =
731	hasUsers \|\| hasGroups \|\| hasRoles \|\| hasQuota \|\| hasTypes \|\| hasPlugins \|\|
732	hasSoftware \|\| hasHardware \|\| hasProtocols \|\| hasClients \|\| hasNews \|\|
733	hasDiskUsage \|\| hasServer;
734
735	if (hasAdministrate)
736	{
737	%>
738	<m:menu
739	id="administrate"
740	style="display: none"
741	>
742	<m:menuitem
743	title="Users"
744	onclick="<%="Menu.openUrl('"+root+"admin/users/index.jsp?ID="+ID+"')"%>"
745	tooltip="<%=hasUsers ? "Administrate users" : "You do not have permission to administrate users"%>"
746	enabled="<%=hasUsers%>"
747	/>
748	<m:menuitem
749	title="Groups"
750	onclick="<%="Menu.openUrl('"+root+"admin/groups/index.jsp?ID="+ID+"')"%>"
751	tooltip="<%=hasGroups ? "Administrate groups" : "You do not have permission to administrate groups"%>"
752	enabled="<%=hasGroups%>"
753	/>
754	<m:menuitem
755	title="Roles"
756	onclick="<%="Menu.openUrl('"+root+"admin/roles/index.jsp?ID="+ID+"')"%>"
757	tooltip="<%=hasRoles ? "Administrate roles" : "You do not have permission to administrate roles"%>"
758	enabled="<%=hasRoles%>"
759	/>
760	<m:menuseparator />
761	<m:submenu
762	subid="plugins"
763	title="Plugins"
764	tooltip="Administrate plugin definitions and configurations"
765	enabled="<%=hasPlugins%>"
766	/>
767	<m:menuseparator />
768	<m:menuitem
769	title="Quota"
770	onclick="<%="Menu.openUrl('"+root+"admin/quota/index.jsp?ID="+ID+"')"%>"
771	tooltip="<%=hasQuota ? "Administrate quota" : "You do not have permission to administrate quota"%>"
772	enabled="<%=hasQuota%>"
773	/>
774	<m:menuitem
775	title="Software"
776	onclick="<%="Menu.openUrl('"+root+"admin/software/index.jsp?ID="+ID+"')"%>"
777	tooltip="<%=hasSoftware ? "Administrate software" : "You do not have permission to administrate software"%>"
778	enabled="<%=hasSoftware%>"
779	/>
780	<m:menuitem
781	title="Hardware"
782	onclick="<%="Menu.openUrl('"+root+"admin/hardware/index.jsp?ID="+ID+"')"%>"
783	tooltip="<%=hasHardware ? "Administrate hardware" : "You do not have permission to administrate hardware"%>"
784	enabled="<%=hasHardware%>"
785	/>
786	<m:menuitem
787	title="Protocols"
788	onclick="<%="Menu.openUrl('"+root+"admin/protocols/index.jsp?ID="+ID+"')"%>"
789	tooltip="<%=hasProtocols ? "Administrate protocols" : "You do not have permission to administrate protocols"%>"
790	enabled="<%=hasProtocols%>"
791	/>
792	<m:menuitem
793	title="Clients"
794	onclick="<%="Menu.openUrl('"+root+"admin/clients/index.jsp?ID="+ID+"')"%>"
795	tooltip="<%=hasClients ? "Administrate client applications" : "You do not have permission to administrate client applications"%>"
796	enabled="<%=hasClients%>"
797	/>
798	<m:menuitem
799	title="News"
800	onclick="<%="Menu.openUrl('"+root+"admin/news/index.jsp?ID="+ID+"')"%>"
801	tooltip="<%=hasNews ? "Administrate news" : "You do not have permission to administrate news"%>"
802	enabled="<%=hasNews%>"
803	/>
804	<m:menuseparator />
805	<m:submenu
806	subid="types"
807	title="Types"
808	tooltip="Administrate quota, file, hardware and software types"
809	enabled="<%=hasTypes%>"
810	/>
811	<m:menuseparator />
812	<m:menuitem
813	title="Disk usage"
814	onclick="<%="Menu.openUrl('"+root+"admin/diskusage/index.jsp?ID="+ID+"')"%>"
815	tooltip="<%=hasDiskUsage ? "Check disk usage" : "You do not have permission to check disk usage"%>"
816	enabled="<%=hasDiskUsage%>"
817	/>
818	<m:menuitem
819	title="Server settings…"
820	onclick="<%="Main.openPopup('"+root+"admin/server/configure.jsp?ID="+ID+"', 'ServerSettings', 500, 400);"%>"
821	tooltip="<%=hasServer ? "Configure the server" : "You do not have permission to configure the server"%>"
822	enabled="<%=hasServer%>"
823	/>
824	<m:menuitem
825	title="Restart BASE…"
826	onclick="<%="Main.openPopup('"+root+"admin/server/restart.jsp?ID="+ID+"', 'RestartServer', 360, 200);"%>"
827	tooltip="<%=hasServer ? "Restart the server" : "You do not have permission to restart the server"%>"
828	enabled="<%=hasServer%>"
829	/>
830	</m:menu>
831	<%
832	}
833	%>
834	<%
835	// Help menu
836	final String helplink = Values.getStringOrNull(sc.getClientDefaultSetting("server.links.help"));
837	final String faqlink = Values.getStringOrNull(sc.getClientDefaultSetting("server.links.faq"));
838	final String reportbuglink = Values.getStringOrNull(sc.getClientDefaultSetting("server.links.reportbug"));
839	%>
840	<m:menu id="help" style="display: none">
841	<m:menuitem
842	visible="<%=HTML.isValidUrl(helplink)%>"
843	title="Help&hellip"
844	onclick="<%="window.open('"+helplink+"','Help')"%>"
845	/>
846	<m:menuitem
847	visible="<%=HTML.isValidUrl(faqlink)%>"
848	title="FAQ&hellip"
849	onclick="<%="window.open('"+faqlink+"','FAQ')"%>"
850	/>
851	<m:menuseparator />
852
853	<m:menuitem
854	title="About…"
855	onclick="<%="Main.openPopup('"+root+"info/about.jsp?ID="+ID+"&page=about', 'About', 500, 350)"%>"
856	/>
857
858	<m:menuitem
859	title="License…"
860	onclick="<%="Main.openPopup('"+root+"info/about.jsp?ID="+ID+"&page=license', 'About', 500, 350)"%>"
861
862	/>
863	<m:menuitem
864	visible="<%=HTML.isValidUrl(reportbuglink)%>"
865	title="Report a bug&hellip"
866	onclick="<%="window.open('"+reportbuglink+"','Reportbug')"%>"
867	/>
868	<m:menuseparator />
869	<m:menuitem
870	title="Base project site" onclick="<%="Menu.openUrl('http://base.thep.lu.se', 'basesite')"%>"
871	/>
872	</m:menu>
873
874	<%
875	//Switch user/logout menu
876	final boolean hasImpersonate =
877	!sc.isImpersonated() && sc.hasSystemPermission(Permission.ACT_AS_ANOTHER_USER);
878	%>
879	<m:menu
880	id="switchuser"
881	style="display: none;"
882	>
883	<m:menuitem
884	title="Switch user…"
885	onclick="<%="Main.openPopup('"+root+"switch.jsp?ID="+ID+"', 'Switch', 360, 200);"%>"
886	tooltip="Login as another user"
887	/>
888	<m:menuitem
889	title="Impersonate…"
890	onclick="<%="Main.openPopup('"+root+"impersonate.jsp?ID="+ID+"', 'Impersonate', 480, 240);"%>"
891	tooltip="Login as another user without knowing the password"
892	visible="<%=hasImpersonate%>"
893	/>
894	<m:menuitem
895	title="Logout…"
896	onclick="<%="Main.openPopup('"+root+"logout.jsp?ID="+ID+"', 'Logout', 360, 200);"%>"
897	tooltip="Exit from BASE"
898	/>
899	</m:menu>
900	<%
901	// Main menu
902	%>
903	<m:menu
904	type="horizontal"
905	clazz="menu_horizontal"
906	id="menubar"
907	style="top: 10px; left: 8px; width: 98%"
908	open="click"
909	filltext="<%=fillText.toString()%>"
910	>
911
912	<m:submenu
913	subid="file"
914	title="File"
915	/>
916	<m:submenu
917	subid="view"
918	title="View"
919	/>
920	<m:submenu
921	subid="lims"
922	title="Array LIMS"
923	/>
924	<m:submenu
925	subid="administrate"
926	title="Administrate"
927	visible="<%=hasAdministrate%>"
928	/>
929	<m:submenu
930	subid="help"
931	title="Help"
932	/>
933	</m:menu>
934	<br><br>
935	<%
936	}
937	finally
938	{
939	if (dc != null) dc.close();
940	}
941
942	}
943	%>
944
945
946

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