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source: trunk/www/biomaterials/extracts/edit_extract.jsp @ 5767

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Last change on this file since 5767 was 5767, checked in by Nicklas Nordborg, 11 years ago
Fixes #1626: Center-align text on buttons
Property svn:eol-style set to `native` Property svn:keywords set to `Date Id`
File size: 31.3 KB

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1	<%-- $Id: edit_extract.jsp 5767 2011-09-28 07:31:39Z nicklas $
2	------------------------------------------------------------------
3	Copyright (C) 2005 Nicklas Nordborg
4	Copyright (C) 2006 Johan Enell, Jari Häkkinen, Nicklas Nordborg, Martin Svensson
5
6	This file is part of BASE - BioArray Software Environment.
7	Available at http://base.thep.lu.se/
8
9	BASE is free software; you can redistribute it and/or
10	modify it under the terms of the GNU General Public License
11	as published by the Free Software Foundation; either version 3
12	of the License, or (at your option) any later version.
13
14	BASE is distributed in the hope that it will be useful,
15	but WITHOUT ANY WARRANTY; without even the implied warranty of
16	MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17	GNU General Public License for more details.
18
19	You should have received a copy of the GNU General Public License
20	along with BASE. If not, see <http://www.gnu.org/licenses/>.
21	------------------------------------------------------------------
22
23
24	@author Nicklas
25	@version 2.0
26	--%>
27	<%@ page pageEncoding="UTF-8" session="false"
28	import="net.sf.basedb.core.SessionControl"
29	import="net.sf.basedb.core.DbControl"
30	import="net.sf.basedb.core.Item"
31	import="net.sf.basedb.core.Type"
32	import="net.sf.basedb.core.ItemContext"
33	import="net.sf.basedb.core.SystemItems"
34	import="net.sf.basedb.core.Permission"
35	import="net.sf.basedb.core.Sample"
36	import="net.sf.basedb.core.Extract"
37	import="net.sf.basedb.core.ItemSubtype"
38	import="net.sf.basedb.core.Tag"
39	import="net.sf.basedb.core.BioMaterialEvent"
40	import="net.sf.basedb.core.BioPlate"
41	import="net.sf.basedb.core.BioWell"
42	import="net.sf.basedb.core.Protocol"
43	import="net.sf.basedb.core.Project"
44	import="net.sf.basedb.core.PermissionDeniedException"
45	import="net.sf.basedb.core.BaseException"
46	import="net.sf.basedb.core.ItemQuery"
47	import="net.sf.basedb.core.ItemResultList"
48	import="net.sf.basedb.core.Include"
49	import="net.sf.basedb.core.query.Orders"
50	import="net.sf.basedb.core.query.Hql"
51	import="net.sf.basedb.core.query.Expressions"
52	import="net.sf.basedb.core.query.Restrictions"
53	import="net.sf.basedb.clients.web.Base"
54	import="net.sf.basedb.clients.web.util.HTML"
55	import="net.sf.basedb.util.Values"
56	import="net.sf.basedb.util.ListUtil"
57	import="net.sf.basedb.util.formatter.Formatter"
58	import="net.sf.basedb.util.formatter.WellCoordinateFormatter"
59	import="net.sf.basedb.clients.web.formatter.FormatterFactory"
60	import="net.sf.basedb.clients.web.formatter.FormatterSettings"
61	import="net.sf.basedb.core.plugin.GuiContext"
62	import="net.sf.basedb.clients.web.extensions.ExtensionsControl"
63	import="net.sf.basedb.clients.web.extensions.JspContext"
64	import="net.sf.basedb.clients.web.extensions.edit.EditUtil"
65	import="net.sf.basedb.util.extensions.ExtensionsInvoker"
66	import="java.util.List"
67	import="java.util.Set"
68	import="java.util.HashSet"
69	import="java.util.Date"
70	import="java.util.Collections"
71	%>
72	<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
73	<%@ taglib prefix="t" uri="/WEB-INF/tab.tld" %>
74	<%
75	final Item itemType = Item.EXTRACT;
76	final SessionControl sc = Base.getExistingSessionControl(pageContext, true);
77	final ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, null, null);
78	final int itemId = cc.getId();
79	final String ID = sc.getId();
80	final float scale = Base.getScale(sc);
81	final DbControl dc = sc.newDbControl();
82	try
83	{
84	String title = null;
85	Extract extract = null;
86	BioMaterialEvent creationEvent = null;
87	Date eventDate = null;
88	Item parentType = null;
89	boolean lockEventProperties = false;
90
91	WellCoordinateFormatter rowFormatter = new WellCoordinateFormatter(true);
92	WellCoordinateFormatter columnFormatter = new WellCoordinateFormatter(false);
93
94	boolean readCurrentSubtype = true;
95	ItemSubtype currentSubtype = null;
96	boolean readCurrentProtocol = true;
97	Protocol currentProtocol = null;
98	boolean readCurrentTag = true;
99	Tag currentTag = null;
100	boolean readCurrentSample = true;
101	Sample currentSample = null;
102	Float usedFromSample = null;
103	String name = null;
104	ItemQuery<Extract> extractsQuery = null;
105	boolean readCurrentBioWell = true;
106	BioWell currentBioWell = null;
107	boolean lockedWell = false;
108	boolean readCurrentBioPlate = true;
109	BioPlate currentBioPlate = null;
110
111	if (itemId == 0)
112	{
113	title = "Create extract";
114	cc.removeObject("item");
115	if (cc.getPropertyFilter("creationEvent.protocol.name") != null)
116	{
117	currentProtocol = Base.getFirstMatching(dc, Protocol.getQuery(), "name", cc.getPropertyFilter("creationEvent.protocol.name"));
118	}
119	if (cc.getPropertyFilter("tag.name") != null)
120	{
121	currentTag = Base.getFirstMatching(dc, Tag.getQuery(), "name", cc.getPropertyFilter("tag.name"));
122	}
123	int currentSubtypeId = Values.getInt(request.getParameter("subtype_id"));
124	List<ItemSubtype> relatedToParent = Collections.emptyList();
125	int sampleId = Values.getInt(request.getParameter("sample_id"));
126	int extractId = Values.getInt(request.getParameter("extract_id"));
127
128	if (sampleId != 0)
129	{
130	currentSample = Sample.getById(dc, sampleId);
131	parentType = Item.SAMPLE;
132	name = currentSample.getName() + ".e" + (currentSample.countExtracts() + 1);
133	if (currentSubtypeId == 0)
134	{
135	relatedToParent = ItemSubtype.getParentSubtypes(dc, currentSample, Item.EXTRACT);
136	}
137	}
138	else if (extractId != 0)
139	{
140	parentType = Item.EXTRACT;
141	Extract e = Extract.getById(dc, extractId);
142	name = e.getName() + ".e" + (e.countExtracts()+1);
143	extractsQuery = Extract.getQuery();
144	extractsQuery.restrict(Restrictions.eq(Hql.property("id"), Expressions.integer(extractId)));
145	if (currentSubtypeId == 0)
146	{
147	relatedToParent = ItemSubtype.getParentSubtypes(dc, e, Item.EXTRACT);
148	}
149	}
150	else if (Values.getBoolean(request.getParameter("pooled")))
151	{
152	parentType = Item.EXTRACT;
153	name = Values.getString(cc.getPropertyValue("name"), "New pooled extract");
154	extractsQuery = Extract.getQuery();
155	extractsQuery.restrict(Restrictions.in(Hql.property("id"), Expressions.parameter("selected")));
156	extractsQuery.setParameter("selected", cc.getSelected(), Type.INT);
157	}
158	else
159	{
160	name = Values.getString(cc.getPropertyValue("name"), "New extract");
161	}
162	if (currentSubtypeId == 0)
163	{
164	if (relatedToParent.size() > 0)
165	{
166	// Find most recently used related subtype
167	List<ItemSubtype> recentSubtypes = (List<ItemSubtype>)cc.getRecent(dc, Item.ITEMSUBTYPE);
168	currentSubtype = ListUtil.findFirstCommon(recentSubtypes, relatedToParent, relatedToParent.get(0));
169	}
170	else
171	{
172	int recentSubtypeId = Values.getInt(cc.getRecent(Item.ITEMSUBTYPE.name(), 0));
173	currentSubtypeId = Values.getInt(cc.getPropertyValue("itemSubtype"), recentSubtypeId);
174	if (currentSubtypeId > 0) currentSubtype = ItemSubtype.getById(dc, currentSubtypeId);
175	}
176	}
177	eventDate = (Date)cc.getPropertyObject("creationEvent.eventDate");
178	}
179	else
180	{
181	extract = Extract.getById(dc, itemId);
182	extract.checkPermission(Permission.WRITE);
183	parentType = extract.getParentType();
184	cc.setObject("item", extract);
185	title = "Edit extract -- " + HTML.encodeTags(extract.getName());
186
187	creationEvent = extract.getCreationEvent();
188	eventDate = creationEvent.getEventDate();
189	name = extract.getName();
190	lockEventProperties = !creationEvent.hasPermission(Permission.WRITE);
191
192	try
193	{
194	currentSubtype = extract.getItemSubtype();
195	}
196	catch (PermissionDeniedException ex)
197	{
198	readCurrentSubtype = false;
199	}
200
201	try
202	{
203	currentProtocol = creationEvent.getProtocol();
204	}
205	catch (PermissionDeniedException ex)
206	{
207	readCurrentProtocol = false;
208	}
209
210	try
211	{
212	currentTag = extract.getTag();
213	}
214	catch (PermissionDeniedException ex)
215	{
216	readCurrentTag = false;
217	}
218
219	try
220	{
221	if (parentType == Item.SAMPLE)
222	{
223	currentSample = (Sample)extract.getParent();
224	if (currentSample != null)
225	{
226	usedFromSample = creationEvent.getUsedQuantity(currentSample);
227	}
228	}
229	}
230	catch (PermissionDeniedException ex)
231	{
232	readCurrentSample = false;
233	}
234	try
235	{
236	currentBioWell = extract.getBioWell();
237	lockedWell = extract.isLockedInWell();
238	if (currentBioWell != null)
239	{
240	currentBioPlate = currentBioWell.getPlate();
241	}
242	}
243	catch (PermissionDeniedException ex)
244	{
245	readCurrentBioWell = false;
246	readCurrentBioPlate = false;
247	}
248
249	// Query to retrieve pooled extracts
250	if (parentType == Item.EXTRACT)
251	{
252	extractsQuery = (ItemQuery<Extract>)creationEvent.getSources();
253	}
254	}
255
256	// Default items
257	int activeProjectId = sc.getActiveProjectId();
258	List<Protocol> defaultProtocols = null;
259	if (activeProjectId > 0)
260	{
261	Project activeProject = Project.getById(dc, activeProjectId);
262	ItemSubtype protocolSubtype = currentSubtype == null ? null : currentSubtype.getRelatedSubtype(Item.PROTOCOL);
263	if (protocolSubtype == null) protocolSubtype = ItemSubtype.getById(dc, SystemItems.getId(Protocol.EXTRACTION));
264	defaultProtocols = (List<Protocol>)activeProject.findDefaultItems(dc, protocolSubtype, false);
265	}
266
267	// Load recently used items
268	List<Protocol> recentProtocols = (List<Protocol>)cc.getRecent(dc, Item.PROTOCOL, currentSubtype);
269	List<Sample> recentSamples = (List<Sample>)cc.getRecent(dc, Item.SAMPLE);
270	List<BioPlate> recentBioPlates = (List<BioPlate>)cc.getRecent(dc, Item.BIOPLATE, currentSubtype);
271	List<Tag> recentTags = (List<Tag>)cc.getRecent(dc, Item.TAG, currentSubtype);
272
273	// Query to retrieve item types
274	final ItemQuery<ItemSubtype> subtypesQuery = Base.getSubtypesQuery(itemType);
275	subtypesQuery.include(Include.ALL);
276
277	final String clazz = "class=\"text\"";
278	final String requiredClazz = "class=\"text required\"";
279	Formatter<Date> dateFormatter = FormatterFactory.getDateFormatter(sc);
280	String dateFormat = FormatterSettings.getDateFormat(sc);
281	String jsDateFormat = HTML.javaScriptEncode(dateFormat);
282	String htmlDateFormat = HTML.encodeTags(dateFormat);
283	JspContext jspContext = ExtensionsControl.createContext(dc, pageContext, GuiContext.item(itemType), extract);
284	ExtensionsInvoker invoker = EditUtil.useEditExtensions(jspContext);
285	%>
286	<base:page type="popup" title="<%=title%>">
287	<base:head scripts="tabcontrol.js,annotations.js,linkitems.js,subtypes.js,ajax.js,json2.js" styles="tabcontrol.css">
288	<ext:scripts context="<%=jspContext%>" />
289	<ext:stylesheets context="<%=jspContext%>" />
290	<script language="JavaScript">
291	// Validate the "Extract" tab
292	function validateExtract()
293	{
294	var frm = document.forms['extract'];
295	if (Main.trimString(frm.name.value) == '')
296	{
297	alert("You must enter a name");
298	frm.name.focus();
299	return false;
300	}
301	if (Main.trimString(frm.bioplate_id.value) != 0 && Main.trimString(frm.biowell_id.value) == 0)
302	{
303	alert("You must choose a biowell from the bioplate");
304	return false;
305	}
306	return true;
307	}
308
309	// Submit the form
310	function saveSettings()
311	{
312	var frm = document.forms['extract'];
313	if (TabControl.validateActiveTab('settings'))
314	{
315	if (annotationsLoaded)
316	{
317	Annotations.addModifiedAnnotationsToForm(frames.annotations, frm);
318	}
319	if (inheritedAnnotationsLoaded)
320	{
321	Annotations.addInheritedAnnotationsToForm(frames.inheritedAnnotations, frm);
322	}
323	frm.modifiedExtracts.value = Link.exportModified(frm, 'E', true).join(',');
324	frm.removedExtracts.value = Link.getActionIds(-1, 'E').join(',');
325	frm.submit();
326	}
327	}
328
329	var annotationsLoaded = false;
330	var inheritedAnnotationsLoaded = false;
331	var parentsChanged = false;
332	var protocolChanged = false;
333	function switchTab(tabControlId, tabId)
334	{
335	if (TabControl.setActiveTab(tabControlId, tabId))
336	{
337	if (tabId == 'annotations' && (protocolChanged \|\| !annotationsLoaded))
338	{
339	Annotations.loadAnnotateFrame(frames.annotations, '<%=ID%>', '<%=itemType.name()%>', <%=itemId%>, getProtocolId());
340	annotationsLoaded = true;
341	protocolChanged = false;
342	}
343	else if (tabId == 'inheritedAnnotations' &&
344	(parentsChanged \|\| !inheritedAnnotationsLoaded))
345	{
346	Annotations.loadInheritFrame(frames.inheritedAnnotations, '<%=ID%>', '<%=itemType.name()%>', <%=itemId%>, getParents());
347	inheritedAnnotationsLoaded = true;
348	parentsChanged = false;
349	}
350	}
351	}
352
353	function getProtocolId()
354	{
355	var frm = document.forms['extract'];
356	var protocolId = 0;
357	if (frm.protocol_id.length > 0 && !frm.protocol_id.disabled)
358	{
359	protocolId = Math.abs(parseInt(frm.protocol_id[frm.protocol_id.selectedIndex].value));
360	}
361	return protocolId;
362	}
363
364	function getParents()
365	{
366	var frm = document.forms['extract'];
367	var parents = new Array();
368	if (frm.parentType[0].checked)
369	{
370	var sampleId = Math.abs(parseInt(frm.sample_id[frm.sample_id.selectedIndex].value));
371	if (sampleId > 0) parents[parents.length] = 'SAMPLE:'+sampleId;
372	}
373	else
374	{
375	var ids = Link.getListIds(frm.extracts, 'E');
376	if (ids.length > 0)
377	{
378	parents[parents.length] = 'EXTRACT:'+ids.join(':');
379	}
380	}
381	return parents;
382	}
383
384	function subtypeOnChange()
385	{
386	var frm = document.forms['extract'];
387	var subtypeId = ItemSubtype.getSubtypeId('extract');
388	var recentInfo = ItemSubtype.getRecentAndRelatedInfo(subtypeId, 'EXTRACT', ['PROTOCOL', 'BIOPLATE', 'TAG', 'SAMPLE', 'EXTRACT']);
389	protocolChanged = ItemSubtype.updateSelectionList(frm.protocol_id, recentInfo.PROTOCOL['recent'], recentInfo.PROTOCOL['default']);
390	ItemSubtype.updateSelectionList(frm.tag_id, recentInfo.TAG['recent']);
391	ItemSubtype.updateSelectionList(frm.bioplate_id, recentInfo.BIOPLATE['recent']);
392	}
393
394	function selectProtocolOnClick()
395	{
396	var frm = document.forms['extract'];
397	var url = '../../admin/protocols/index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectone';
398	url += '&callback=setProtocolCallback&resetTemporary=1';
399	url += ItemSubtype.createRelatedFilter('extract', 'PROTOCOL', <%=SystemItems.getId(Protocol.EXTRACTION)%>);
400	if (frm.protocol_id.length > 1)
401	{
402	var id = Math.abs(parseInt(frm.protocol_id[1].value));
403	url += '&item_id='+id;
404	}
405	Main.openPopup(url, 'SelectProtocol', 1000, 700);
406	}
407	function setProtocolCallback(id, name)
408	{
409	var frm = document.forms['extract'];
410	var list = frm.protocol_id;
411	if (list.length < 2 \|\| list[1].value == '0') // >
412	{
413	Forms.addListOption(list, 1, new Option());
414	}
415	list[1].value = id;
416	list[1].text = name;
417	list.selectedIndex = 1;
418	protocolChanged = true;
419	}
420	function protocolOnChange()
421	{
422	protocolChanged = true;
423	}
424	function selectTagOnClick()
425	{
426	var frm = document.forms['extract'];
427	var url = '../tags/index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectone';
428	url += '&callback=setTagCallback&resetTemporary=1';
429	url += ItemSubtype.createRelatedFilter('extract', 'TAG');
430	if (frm.tag_id.length > 1)
431	{
432	var id = Math.abs(parseInt(frm.tag_id[1].value));
433	url += '&item_id='+id;
434	}
435	Main.openPopup(url, 'SelectTag', 1000, 700);
436	}
437	function setTagCallback(id, name)
438	{
439	var frm = document.forms['extract'];
440	var list = frm.tag_id;
441	if (list.length < 2 \|\| list[1].value == '0') // >
442	{
443	Forms.addListOption(list, 1, new Option());
444	}
445	list[1].value = id;
446	list[1].text = name;
447	list.selectedIndex = 1;
448	}
449	function selectBioPlateOnClick()
450	{
451	var frm = document.forms['extract'];
452	var url = '../bioplates/index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectone&callback=setBioPlateCallback';
453	if (frm.bioplate_id.length > 1)
454	{
455	var id = Math.abs(parseInt(frm.bioplate_id[1].value));
456	url += '&item_id='+id;
457	}
458	url += '&resetTemporary=1&tmpfilter:INT:bioPlateType.lockMode=<><%=BioWell.LockMode.LOCKED_AFTER_CREATE.getValue()%>';
459	// Restrict to plates that can holds extracts
460	url += '&tmpfilter:INT:bioPlateType.bioMaterialType=\|<%=itemType.getValue()%>';
461	var subtypeId = ItemSubtype.getSubtypeId('extract');
462	// Restrict to plates with the given subtype
463	url += '&tmpfilter:INT:bioPlateType.itemSubtype='+(subtypeId ? '\|' + subtypeId : '=');
464	url += '&tmpfilter:BOOLEAN:destroyed=false';
465	Main.openPopup(url, 'SelectBioplate', 1000, 700);
466	}
467	function setBioPlateCallback(id, name)
468	{
469	var frm = document.forms['extract'];
470	var list = frm.bioplate_id;
471	if (list.length < 2 \|\| list[1].value == '0') // >
472	{
473	Forms.addListOption(list, 1, new Option());
474	}
475	list[1].value = id;
476	list[1].text = name;
477	list.selectedIndex = 1;
478	frm.biowell_id.remove(1);
479	frm.biowell_id.disabled = false;
480	}
481	function bioPlateOnChange()
482	{
483	var frm = document.forms['extract'];
484	var list = frm.bioplate_id;
485	frm.biowell_id.selectedIndex=0;
486	frm.biowell_id.remove(1);
487	}
488
489	function initBioWell()
490	{
491	var frm = document.forms['extract'];
492	<%
493	if (currentBioWell != null)
494	{
495	%>
496	var list = frm.biowell_id;
497	var wellId = <%=currentBioWell.getId()%>;
498	Forms.addListOption(list, 1, new Option());
499	list[1].value = '<%=currentBioWell.getId()*(extract == null ? 1 : -1)%>';
500	list[1].text = '<%=rowFormatter.format(currentBioWell.getRow())%><%=columnFormatter.format(currentBioWell.getColumn())%>';
501	list.selectedIndex = 1;
502	<%
503	}
504	%>
505	}
506	function selectBioWellOnClick()
507	{
508	var frm = document.forms['extract'];
509	var bioplate_list = frm.bioplate_id;
510	var bioplateId = Math.abs(parseInt(bioplate_list[bioplate_list.selectedIndex].value))
511	if (Main.trimString(frm.bioplate_id.value) == 0)
512	{
513	alert("You must first select the bioplate where the biowell is located");
514	return;
515	}
516
517	var url = '../bioplates/wells/index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectone&callback=setBioWellCallback';
518	if (frm.biowell_id.length > 1)
519	{
520	var id = Math.abs(parseInt(frm.biowell_id[1].value));
521	url += '&item_id='+id;
522	}
523	url += '&bioplate_id='+bioplateId;
524	url += '&resetTemporary=1&tmpfilter:STRING:$mbm.name='+escape('=');
525	url += '&tmpfilter:STRING:originalBioMaterial.name='+escape('=');
526	url += '&columns=row,column';
527	Main.openPopup(url, 'SelectBiowell', 700, 700);
528	}
529	function setBioWellCallback(id, name)
530	{
531	var frm = document.forms['extract'];
532	var list = frm.biowell_id;
533	if (list.length < 2 \|\| list[1].value == '0') // >
534	{
535	Forms.addListOption(list, 1, new Option());
536	}
537	list[1].value = id;
538	list[1].text = name;
539	list.selectedIndex = 1;
540	}
541
542	function parentTypeOnClick()
543	{
544	var frm = document.forms['extract'];
545	var useExtracts = frm.parentType[1].checked;
546	frm.sample_id.disabled = useExtracts;
547	frm.used_from_sample.disabled = useExtracts;
548	frm.extracts.disabled = !useExtracts;
549	frm.used_quantity.disabled = !useExtracts;
550	parentsChanged = true;
551	}
552	function sampleOnChange()
553	{
554	parentsChanged = true;
555	}
556
557	function selectSampleOnClick()
558	{
559	var frm = document.forms['extract'];
560	var url = '../samples/index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectone';
561	url += '&callback=setSampleCallback&resetTemporary=1';
562	url += ItemSubtype.createRelatedFilter('extract', 'SAMPLE');
563	if (frm.sample_id.length > 1)
564	{
565	var id = Math.abs(parseInt(frm.sample_id[1].value));
566	url += '&item_id='+id;
567	}
568	Main.openPopup(url, 'SelectSample', 1000, 700);
569	}
570	function setSampleCallback(id, name)
571	{
572	var frm = document.forms['extract'];
573	var list = frm.sample_id;
574	if (list.length < 2 \|\| list[1].value == '0') // >
575	{
576	Forms.addListOption(list, 1, new Option());
577	}
578	list[1].value = id;
579	list[1].text = name;
580	list.selectedIndex = 1;
581	frm.parentType[0].checked = true;
582	frm.parentType[1].checked = false;
583	parentTypeOnClick();
584	parentsChanged = true;
585	}
586
587	function addExtractsOnClick()
588	{
589	var frm = document.forms['extract'];
590	var url = 'index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectmultiple';
591	url += '&callback=addExtractCallback&resetTemporary=1';
592	url += ItemSubtype.createRelatedFilter('extract', 'EXTRACT');
593	Main.openPopup(url, 'AddExtracts', 1000, 700);
594	}
595
596	function addExtractCallback(extractId, name)
597	{
598	var item = Link.getItem('E', extractId);
599	if (!item) item = new Item('E', extractId, name+' [-]', '', '');
600	Link.addItem(document.forms['extract'].extracts, item);
601	frm.parentType[0].checked = false;
602	frm.parentType[1].checked = true;
603	parentTypeOnClick();
604	parentsChanged = true;
605	}
606	function extractsOnChange()
607	{
608	var frm = document.forms['extract'];
609	var item = frm.extracts[frm.extracts.selectedIndex].item;
610	if (item && item.id)
611	{
612	frm.used_quantity.value = item.value;
613	frm.used_quantity.focus();
614	}
615	else
616	{
617	frm.used_quantity.value = '';
618	}
619	}
620	function usedQuantityOnBlur()
621	{
622	var frm = document.forms['extract'];
623	var usedQuantity = frm.used_quantity.value;
624	var displayQuantity = usedQuantity == '' ? '-' : usedQuantity+' µg';
625	for (var i = 0; i < frm.extracts.length; i++) // >
626	{
627	var option = frm.extracts[i];
628	if (option.selected && option.item.id)
629	{
630	option.item.value = usedQuantity;
631	var text = option.text.replace(/\[.*\]/, '['+displayQuantity+']');
632	option.text = text;
633	}
634	}
635	}
636	function usedFromSampleOnBlur()
637	{
638	var frm = document.forms['extract'];
639
640	var sampleId = parseInt(frm.sample_id[frm.sample_id.selectedIndex].value);
641	if (sampleId < 0)
642	{
643	frm.sample_id[frm.sample_id.selectedIndex].value = -sampleId;
644	}
645	}
646
647
648	function removeOnClick()
649	{
650	Link.removeSelected(document.forms['extract'].extracts);
651	parentsChanged = true;
652	}
653
654	function init()
655	{
656	<%
657	if (extract == null)
658	{
659	%>
660	var frm = document.forms['extract'];
661	frm.name.focus();
662	frm.name.select();
663	<%
664	}
665	%>
666	initBioWell();
667	initExtracts();
668	parentTypeOnClick();
669	}
670	function initExtracts()
671	{
672	var extracts = document.forms['extract'].extracts;
673	<%
674	if (extractsQuery != null)
675	{
676	extractsQuery.include(Include.ALL);
677	extractsQuery.order(Orders.asc(Hql.property("name")));
678	ItemResultList<Extract> extracts = extractsQuery.list(dc);
679	for (Extract e : extracts)
680	{
681	if (extract != null)
682	{
683	String usedQuantity = Values.formatNumber(creationEvent.getUsedQuantity(e), -1);
684	%>
685	Link.addNewItem(extracts, new Item('E', <%=e.getId()%>, '<%=HTML.javaScriptEncode(e.getName())%> [<%=usedQuantity%> µg]', '<%=usedQuantity%>'));
686	<%
687	}
688	else
689	{
690	%>
691	Link.addItem(extracts, new Item('E', <%=e.getId()%>, '<%=HTML.javaScriptEncode(e.getName())%> [-]', '', ''));
692	<%
693
694	}
695	}
696	}
697	%>
698	}
699	</script>
700	</base:head>
701	<base:body onload="init()">
702	<p>
703	<form action="index.jsp?ID=<%=ID%>" method="post" name="extract" onsubmit="return false;">
704	<input type="hidden" name="cmd" value="UpdateItem">
705
706	<h3 class="docked"><%=title%> <base:help tabcontrol="settings" /></h3>
707	<t:tabcontrol id="settings" contentstyle="<%="height: "+(int)(scale*370)+"px;"%>"
708	position="bottom" remember="<%=extract != null%>" switch="switchTab"
709	extensions="<%=invoker%>">
710	<t:tab id="info" title="Extract" validate="validateExtract()" helpid="extract.edit">
711	<table class="form" cellspacing=0>
712	<tr>
713	<td class="prompt">Name</td>
714	<td><input <%=requiredClazz%> type="text" name="name"
715	value="<%=HTML.encodeTags(name)%>"
716	size="40" maxlength="<%=Extract.MAX_NAME_LENGTH%>"></td>
717	</tr>
718	<tr valign="top">
719	<td class="prompt">Type</td>
720	<td colspan="2">
721	<select name="subtype_id"
722	<%=!readCurrentSubtype ? "disabled readonly class=\"disabled selectionlist\"" : "class=\"selectionlist\""%>
723	onchange="subtypeOnChange()"
724	>
725	<%
726	if (!readCurrentSubtype)
727	{
728	%>
729	<option value="-1">- denied -
730	<%
731	}
732	else
733	{
734	%>
735	<option value="0">-none-
736	<%
737	int currentSubtypeId = currentSubtype == null ? 0 : currentSubtype.getId();
738	for (ItemSubtype subtype : subtypesQuery.list(dc))
739	{
740	int id = subtype.getId();
741	if (id != currentSubtypeId && subtype.isRemoved()) continue;
742	%>
743	<option value="<%=id == currentSubtypeId && extract != null ? -id : id%>"
744	<%=id == currentSubtypeId ? "selected" : ""%>
745	title="<%=HTML.encodeTags(subtype.getDescription()) %>"
746	><%=HTML.encodeTags(subtype.getName())%>
747	<%
748	}
749	}
750	%>
751	</select>
752	</td>
753	</tr>
754	<tr>
755	<td class="prompt">Tag</td>
756	<td>
757	<base:select
758	id="tag_id"
759	clazz="selectionlist"
760	required="false"
761	current="<%=currentTag%>"
762	denied="<%=!readCurrentTag%>"
763	recent="<%=recentTags%>"
764	newitem="<%=extract == null%>"
765	onselect="selectTagOnClick()"
766	/>
767	</td>
768	</tr>
769	<tr>
770	<td class="prompt">External ID</td>
771	<td><input <%=clazz%> type="text" name="external_id"
772	value="<%=HTML.encodeTags(extract == null ? Values.getString(cc.getPropertyValue("externalId"), "") : extract.getExternalId())%>"
773	size="40" maxlength="<%=Extract.MAX_EXTERNAL_ID_LENGTH%>"></td>
774	</tr>
775	<tr>
776	<td class="prompt">Original quantity</td>
777	<td><input <%=clazz%> type="text" name="original_quantity"
778	value="<%=Values.formatNumber(extract == null ? Values.getFloat(cc.getPropertyValue("originalQuantity"), null): extract.getOriginalQuantity(), -1)%>" size="12"
779	maxlength="10" onkeypress="return Numbers.numberOnly(event)"> (µg)</td>
780	</tr>
781	<tr>
782	<td class="prompt">Created</td>
783	<td>
784	<table border="0" cellspacing="0" cellpadding="0">
785	<tr>
786	<td>
787	<input <%=clazz%> type="text" name="event_date" <%=lockEventProperties ? "disabled" : ""%>
788	value="<%=HTML.encodeTags(dateFormatter.format(eventDate))%>"
789	size="20" maxlength="20" title="Enter date in format: <%=htmlDateFormat%>">
790
791	</td>
792	<td>
793	<base:button
794	onclick="<%="Dates.selectDate('Created', 'extract', 'event_date', null, '"+jsDateFormat+"')"%>"
795	image="calendar.png"
796	title="Calendar…"
797	tooltip="Select a date from a calendar"
798	disabled="<%=lockEventProperties%>"
799	/>
800	</td>
801	</tr>
802	</table>
803	</td>
804	</tr>
805	<tr>
806	<td class="prompt">Registered</td>
807	<td><%=dateFormatter.format(creationEvent == null ? new Date() : creationEvent.getEntryDate())%></td>
808	</tr>
809	<tr>
810	<td class="prompt">Protocol</td>
811	<td>
812	<base:select
813	id="protocol_id"
814	clazz="selectionlist"
815	required="false"
816	current="<%=currentProtocol%>"
817	denied="<%=!readCurrentProtocol%>"
818	recent="<%=recentProtocols%>"
819	defaultitems="<%=defaultProtocols%>"
820	newitem="<%=extract == null%>"
821	onselect="selectProtocolOnClick()"
822	onchange="protocolOnChange()"
823	disabled="<%=lockEventProperties%>"
824	/>
825	</td>
826	</tr>
827	<tr>
828	<td class="prompt">Bioplate</td>
829	<td>
830	<base:select
831	id="bioplate_id"
832	clazz="selectionlist"
833	required="false"
834	current="<%=currentBioPlate%>"
835	denied="<%=!readCurrentBioPlate%>"
836	recent="<%=recentBioPlates%>"
837	newitem="<%=extract == null%>"
838	onselect="selectBioPlateOnClick()"
839	onchange="bioPlateOnChange()"
840	disabled="<%=lockedWell%>"
841	/>
842	</td>
843	</tr>
844	<tr>
845	<td class="prompt">Biowell</td>
846	<td>
847	<base:select
848	id="biowell_id"
849	clazz="selectionlist"
850	required="false"
851	current="<%=null %>"
852	denied="<%=!readCurrentBioWell%>"
853	newitem="<%=extract == null%>"
854	onselect="selectBioWellOnClick()"
855	onchange="bioWellOnChange()"
856	disabled="<%=lockedWell%>"
857	/>
858	</td>
859	</tr>
860	<tr valign=top>
861	<td class="prompt">Description</td>
862	<td nowrap>
863	<textarea <%=clazz%> rows="4" cols="40" name="description" wrap="virtual"
864	><%=HTML.encodeTags(extract == null ? cc.getPropertyValue("description") : extract.getDescription())%></textarea>
865	<a href="javascript:Main.zoom('Description', 'extract', 'description')"
866	title="Edit in larger window"><base:icon image="zoom.gif" /></a>
867	</td>
868	</tr>
869	</table>
870	<div align=right> <i><base:icon image="required.gif" /> = required information</i></div>
871	</t:tab>
872
873	<t:tab id="parents" title="Parents" helpid="extract.parent">
874	<table class="form" cellspacing=0>
875	<tr>
876	<td class="prompt">Parent type</td>
877	<td>
878	<input type="radio" name="parentType" id="parentType.sample"
879	value="SAMPLE" onclick="parentTypeOnClick()"
880	<%=parentType != Item.EXTRACT ? "checked" : ""%>
881	><label for="parentType.sample">Sample</label>
882	<input type="radio" name="parentType" id="parentType.extract"
883	value="EXTRACT" onclick="parentTypeOnClick()"
884	<%=parentType == Item.EXTRACT ? "checked" : ""%>
885	><label for="parentType.extract">Extract</label>
886	</td>
887	</tr>
888	<tr valign="top">
889	<td class="prompt">Sample</td>
890	<td>
891	<base:select
892	id="sample_id"
893	clazz="selectionlist"
894	buttonstyle="width: 150px;"
895	buttonicon="add.png"
896	buttontitle="Select sample…"
897	buttonclass="leftaligned buttonclass"
898	required="false"
899	current="<%=currentSample%>"
900	denied="<%=!readCurrentSample%>"
901	recent="<%=recentSamples%>"
902	selectrecent="false"
903	newitem="<%=extract == null%>"
904	onselect="selectSampleOnClick()"
905	onchange="sampleOnChange()"
906	/>
907	</td>
908	</tr>
909	<tr>
910	<td class="subprompt">-</td>
911	<td>
912	used quantity
913	<input <%=clazz%> type="text" name="used_from_sample" value="<%=Values.formatNumber(usedFromSample, -1)%>"
914	size="12" maxlength="10" onkeypress="return Numbers.numberOnly(event)"
915	onblur="usedFromSampleOnBlur()"> (µg)
916	</td>
917	</tr>
918	<tr valign="top">
919	<td class="prompt">Extracts</td>
920	<td>
921	<table border="0" cellspacing="0" cellpadding="0">
922	<tr valign="top">
923	<td>
924	<select name="extracts" size="12" multiple class="selectionlist"
925	onchange="extractsOnChange()">
926	</select>
927	<input type="hidden" name="modifiedExtracts" value="">
928	<input type="hidden" name="removedExtracts" value="">
929	</td>
930	<td>
931	<table border="0" cellspacing="0" cellpadding="0">
932	<tr><td style="padding: 1px 0px 4px 0px;"><base:button
933	clazz="leftaligned buttonclass"
934	style="width: 150px;"
935	onclick="addExtractsOnClick()"
936	title="Add extracts…"
937	tooltip="Add extracts"
938	/></td></tr>
939	<tr><td width="150"><base:button
940	clazz="leftaligned buttonclass"
941	style="width: 150px;"
942	onclick="removeOnClick()"
943	title="Remove"
944	tooltip="Remove the selected extracts"
945	/></td></tr>
946	</table>
947	</td>
948	</tr>
949	</table>
950	</td>
951	</tr>
952	<tr>
953	<td class="subprompt">-</td>
954	<td>used quantity
955	<input <%=clazz%> type="text" name="used_quantity" value=""
956	size="12" maxlength="10" onkeypress="return Numbers.numberOnly(event)"
957	onkeyup="usedQuantityOnBlur();"
958	> (µg)
959	</td>
960	</tr>
961	</table>
962	</t:tab>
963
964	<t:tab id="annotations" title="Annotations & parameters"
965	helpid="annotations.edit" tooltip="Enter values for annotations and protocol parameters">
966	<iframe name="annotations" id="idAnnotations" src="../../common/annotations/wait.jsp"
967	width="100%" height="<%=(int)(scale*370)%>" frameborder=0 vspace=0 hspace=0
968	marginwidth=0 marginheight=0 scrolling="auto" style="overflow: visible"></iframe>
969	</t:tab>
970
971	<t:tab id="inheritedAnnotations" title="Inherited annotations" helpid="annotations.edit.inherited">
972
973	<iframe name="inheritedAnnotations" id="idInheritedAnnotations" src="../../common/annotations/wait.jsp"
974	width="100%" height="<%=(int)(scale*370)%>" frameborder=0 vspace=0 hspace=0
975	marginwidth=0 marginheight=0 scrolling="auto" style="overflow: visible"></iframe>
976	</t:tab>
977	</t:tabcontrol>
978
979	<table align="center">
980	<tr>
981	<td width="50%"><base:button onclick="saveSettings()" title="Save" /></td>
982	<td width="50%"><base:button onclick="window.close()" title="Cancel" /></td>
983	</tr>
984	</table>
985	</form>
986	</base:body>
987	</base:page>
988	<%
989	}
990	finally
991	{
992	if (dc != null) dc.close();
993	}
994	%>

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