source: trunk/www/biomaterials/extracts/edit_extract.jsp @ 5687

<%-- $Id: edit_extract.jsp 5687 2011-08-09 11:39:40Z nicklas $
  ------------------------------------------------------------------
  Copyright (C) 2005 Nicklas Nordborg
  Copyright (C) 2006 Johan Enell, Jari Häkkinen, Nicklas Nordborg, Martin Svensson

  This file is part of BASE - BioArray Software Environment.
  Available at http://base.thep.lu.se/

  BASE is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License
  as published by the Free Software Foundation; either version 3
  of the License, or (at your option) any later version.

  BASE is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  GNU General Public License for more details.

  You should have received a copy of the GNU General Public License
  along with BASE. If not, see <http://www.gnu.org/licenses/>.
  ------------------------------------------------------------------


  @author Nicklas
  @version 2.0
--%>
<%@ page pageEncoding="UTF-8" session="false"
  import="net.sf.basedb.core.SessionControl"
  import="net.sf.basedb.core.DbControl"
  import="net.sf.basedb.core.Item"
  import="net.sf.basedb.core.Type"
  import="net.sf.basedb.core.ItemContext"
  import="net.sf.basedb.core.SystemItems"
  import="net.sf.basedb.core.Permission"
  import="net.sf.basedb.core.Sample"
  import="net.sf.basedb.core.Extract"
  import="net.sf.basedb.core.ItemSubtype"
  import="net.sf.basedb.core.Tag"
  import="net.sf.basedb.core.BioMaterialEvent"
  import="net.sf.basedb.core.BioPlate"
  import="net.sf.basedb.core.BioWell"
  import="net.sf.basedb.core.Protocol"
  import="net.sf.basedb.core.Project"
  import="net.sf.basedb.core.PermissionDeniedException"
  import="net.sf.basedb.core.BaseException"
  import="net.sf.basedb.core.ItemQuery"
  import="net.sf.basedb.core.ItemResultList"
  import="net.sf.basedb.core.Include"
  import="net.sf.basedb.core.query.Orders"
  import="net.sf.basedb.core.query.Hql"
  import="net.sf.basedb.core.query.Expressions"
  import="net.sf.basedb.core.query.Restrictions"
  import="net.sf.basedb.clients.web.Base"
  import="net.sf.basedb.clients.web.util.HTML"
  import="net.sf.basedb.util.Values"
  import="net.sf.basedb.util.ListUtil"
  import="net.sf.basedb.util.formatter.Formatter"
  import="net.sf.basedb.util.formatter.WellCoordinateFormatter"
  import="net.sf.basedb.clients.web.formatter.FormatterFactory"
  import="net.sf.basedb.clients.web.formatter.FormatterSettings"  
  import="net.sf.basedb.core.plugin.GuiContext"
  import="net.sf.basedb.clients.web.extensions.ExtensionsControl"
  import="net.sf.basedb.clients.web.extensions.JspContext"
  import="net.sf.basedb.clients.web.extensions.edit.EditUtil"
  import="net.sf.basedb.util.extensions.ExtensionsInvoker"
  import="java.util.List"
  import="java.util.Set"
  import="java.util.HashSet"
  import="java.util.Date"
  import="java.util.Collections"
%>
<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
<%@ taglib prefix="t" uri="/WEB-INF/tab.tld" %>
<%
final Item itemType = Item.EXTRACT;
final SessionControl sc = Base.getExistingSessionControl(pageContext, true);
final ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, null, null);
final int itemId = cc.getId();
final String ID = sc.getId();
final float scale = Base.getScale(sc);
final DbControl dc = sc.newDbControl();
try
{
  String title = null;
  Extract extract = null;
  BioMaterialEvent creationEvent = null;
  Date eventDate = null;
  Item parentType = null;
  boolean lockEventProperties = false;
  
  WellCoordinateFormatter rowFormatter = new WellCoordinateFormatter(true);
  WellCoordinateFormatter columnFormatter = new WellCoordinateFormatter(false);

  boolean readCurrentSubtype = true;
  ItemSubtype currentSubtype = null;
  boolean readCurrentProtocol = true;
  Protocol currentProtocol = null;
  boolean readCurrentTag = true;
  Tag currentTag = null;
  boolean readCurrentSample = true;
  Sample currentSample = null;
  Float usedFromSample = null;
  String name = null;
  ItemQuery<Extract> extractsQuery = null;
  boolean readCurrentBioWell = true;
  BioWell currentBioWell = null;  
  boolean lockedWell = false;
  boolean readCurrentBioPlate = true;
  BioPlate currentBioPlate = null;
  
  if (itemId == 0)
  {
    title = "Create extract";
    cc.removeObject("item");
    if (cc.getPropertyFilter("creationEvent.protocol.name") != null)
    {
      currentProtocol = Base.getFirstMatching(dc, Protocol.getQuery(), "name", cc.getPropertyFilter("creationEvent.protocol.name"));
    }
    if (cc.getPropertyFilter("tag.name") != null)
    {
      currentTag = Base.getFirstMatching(dc, Tag.getQuery(), "name", cc.getPropertyFilter("tag.name"));
    }
    int currentSubtypeId = Values.getInt(request.getParameter("subtype_id"));
    List<ItemSubtype> relatedToParent = Collections.emptyList();
    int sampleId = Values.getInt(request.getParameter("sample_id"));
    int extractId = Values.getInt(request.getParameter("extract_id"));

    if (sampleId != 0)
    {
      currentSample  = Sample.getById(dc, sampleId);
      parentType = Item.SAMPLE;
      name = currentSample.getName() + ".e" + (currentSample.countExtracts() + 1);      
      if (currentSubtypeId == 0)
      {
        relatedToParent = ItemSubtype.getParentSubtypes(dc, currentSample, Item.EXTRACT);
      }
    }
    else if (extractId != 0)
    {
      parentType = Item.EXTRACT;
      Extract e = Extract.getById(dc, extractId);
      name = e.getName() + ".e" + (e.countExtracts()+1);
      extractsQuery = Extract.getQuery();
      extractsQuery.restrict(Restrictions.eq(Hql.property("id"), Expressions.integer(extractId)));
      if (currentSubtypeId == 0)
      {
        relatedToParent = ItemSubtype.getParentSubtypes(dc, e, Item.EXTRACT);
      }
    }
    else if (Values.getBoolean(request.getParameter("pooled")))
    {
      parentType = Item.EXTRACT;
      name = Values.getString(cc.getPropertyValue("name"), "New pooled extract");
      extractsQuery = Extract.getQuery();
      extractsQuery.restrict(Restrictions.in(Hql.property("id"), Expressions.parameter("selected")));
      extractsQuery.setParameter("selected", cc.getSelected(), Type.INT);
    }
    else
    {
      name = Values.getString(cc.getPropertyValue("name"), "New extract");
    }
    if (currentSubtypeId == 0) 
    {
      if (relatedToParent.size() > 0)
      {
        // Find most recently used related subtype
        List<ItemSubtype> recentSubtypes = (List<ItemSubtype>)cc.getRecent(dc, Item.ITEMSUBTYPE);
        currentSubtype = ListUtil.findFirstCommon(recentSubtypes, relatedToParent, relatedToParent.get(0));
      }
      else
      {
        int recentSubtypeId = Values.getInt(cc.getRecent(Item.ITEMSUBTYPE.name(), 0));
        currentSubtypeId = Values.getInt(cc.getPropertyValue("itemSubtype"), recentSubtypeId);
        if (currentSubtypeId > 0) currentSubtype = ItemSubtype.getById(dc, currentSubtypeId);
      }
    }
    eventDate = (Date)cc.getPropertyObject("creationEvent.eventDate");    
  }
  else
  {
    extract = Extract.getById(dc, itemId);
    extract.checkPermission(Permission.WRITE);
    parentType = extract.getParentType();
    cc.setObject("item", extract);
    title = "Edit extract -- " + HTML.encodeTags(extract.getName());
  
    creationEvent = extract.getCreationEvent();
    eventDate = creationEvent.getEventDate();
    name = extract.getName();
    lockEventProperties = !creationEvent.hasPermission(Permission.WRITE);
    
    try
    {
      currentSubtype = extract.getItemSubtype();
    }
    catch (PermissionDeniedException ex)
    {
      readCurrentSubtype = false;
    }

    try
    {
      currentProtocol = creationEvent.getProtocol();
    }
    catch (PermissionDeniedException ex)
    {
      readCurrentProtocol = false;
    }
  
    try
    {
      currentTag = extract.getTag();
    }
    catch (PermissionDeniedException ex)
    {
      readCurrentTag = false;
    }

    try
    {
      if (parentType == Item.SAMPLE)
      {
        currentSample = (Sample)extract.getParent();
        if (currentSample != null) 
        {
          usedFromSample = creationEvent.getUsedQuantity(currentSample);
        }
      }
    }
    catch (PermissionDeniedException ex)
    {
      readCurrentSample = false;
    }
    try
    {
      currentBioWell = extract.getBioWell();
      lockedWell = extract.isLockedInWell();
      if (currentBioWell != null)
      {
        currentBioPlate = currentBioWell.getPlate();
      }
    }
    catch (PermissionDeniedException ex)
    {
      readCurrentBioWell = false;
      readCurrentBioPlate = false;
    }
  
    // Query to retrieve pooled extracts
    if (parentType == Item.EXTRACT)
    {
      extractsQuery = (ItemQuery<Extract>)creationEvent.getSources();
    }
  }
  
  // Default items 
  int activeProjectId = sc.getActiveProjectId();
  List<Protocol> defaultProtocols = null;
  if (activeProjectId > 0)
  {
    Project activeProject = Project.getById(dc, activeProjectId);
    ItemSubtype protocolSubtype = currentSubtype == null ? null : currentSubtype.getRelatedSubtype(Item.PROTOCOL);
    if (protocolSubtype == null) protocolSubtype = ItemSubtype.getById(dc, SystemItems.getId(Protocol.EXTRACTION));
    defaultProtocols = (List<Protocol>)activeProject.findDefaultItems(dc, protocolSubtype, false);
  }

  // Load recently used items
  List<Protocol> recentProtocols = (List<Protocol>)cc.getRecent(dc, Item.PROTOCOL, currentSubtype);
  List<Sample> recentSamples = (List<Sample>)cc.getRecent(dc, Item.SAMPLE);
  List<BioPlate> recentBioPlates = (List<BioPlate>)cc.getRecent(dc, Item.BIOPLATE, currentSubtype);
  List<Tag> recentTags = (List<Tag>)cc.getRecent(dc, Item.TAG, currentSubtype);
  
  // Query to retrieve item types
  final ItemQuery<ItemSubtype> subtypesQuery = Base.getSubtypesQuery(itemType);
  subtypesQuery.include(Include.ALL);

  final String clazz = "class=\"text\"";
  final String requiredClazz = "class=\"text required\"";
  Formatter<Date> dateFormatter = FormatterFactory.getDateFormatter(sc);
  String dateFormat = FormatterSettings.getDateFormat(sc);
  String jsDateFormat = HTML.javaScriptEncode(dateFormat);
  String htmlDateFormat = HTML.encodeTags(dateFormat);
  JspContext jspContext = ExtensionsControl.createContext(dc, pageContext, GuiContext.item(itemType), extract);
  ExtensionsInvoker invoker = EditUtil.useEditExtensions(jspContext);
  %>
  <base:page type="popup" title="<%=title%>">
  <base:head scripts="tabcontrol.js,annotations.js,linkitems.js,subtypes.js,ajax.js,json2.js" styles="tabcontrol.css">
    <ext:scripts context="<%=jspContext%>" />
    <ext:stylesheets context="<%=jspContext%>" />
    <script language="JavaScript">
    // Validate the "Extract" tab
    function validateExtract()
    {
      var frm = document.forms['extract'];
      if (Main.trimString(frm.name.value) == '')
      {
        alert("You must enter a name");
        frm.name.focus();
        return false;
      }
      if (Main.trimString(frm.bioplate_id.value) != 0 && Main.trimString(frm.biowell_id.value) == 0)
      {
        alert("You must choose a biowell from the bioplate");
        return false;
      }
      return true;
    }

    // Submit the form
    function saveSettings()
    {
      var frm = document.forms['extract'];
      if (TabControl.validateActiveTab('settings'))
      {
        if (annotationsLoaded) 
        {
          Annotations.addModifiedAnnotationsToForm(frames.annotations, frm);
        }
        if (inheritedAnnotationsLoaded)
        {
          Annotations.addInheritedAnnotationsToForm(frames.inheritedAnnotations, frm);
        }
        frm.modifiedExtracts.value = Link.exportModified(frm, 'E', true).join(',');
        frm.removedExtracts.value = Link.getActionIds(-1, 'E').join(',');
        frm.submit();
      }
    }
    
    var annotationsLoaded = false;
    var inheritedAnnotationsLoaded = false;
    var parentsChanged = false;
    var protocolChanged = false;
    function switchTab(tabControlId, tabId)
    {
      if (TabControl.setActiveTab(tabControlId, tabId))
      {
        if (tabId == 'annotations' && (protocolChanged || !annotationsLoaded))
        {
          Annotations.loadAnnotateFrame(frames.annotations, '<%=ID%>', '<%=itemType.name()%>', <%=itemId%>, getProtocolId());
          annotationsLoaded = true;
          protocolChanged = false;
        }
        else if (tabId == 'inheritedAnnotations' && 
          (parentsChanged || !inheritedAnnotationsLoaded))
        {
          Annotations.loadInheritFrame(frames.inheritedAnnotations, '<%=ID%>', '<%=itemType.name()%>', <%=itemId%>, getParents());
          inheritedAnnotationsLoaded = true;
          parentsChanged = false;
        }
      }
    }

    function getProtocolId()
    {
      var frm = document.forms['extract'];
      var protocolId = 0;
      if (frm.protocol_id.length > 0 && !frm.protocol_id.disabled) 
      {
        protocolId = Math.abs(parseInt(frm.protocol_id[frm.protocol_id.selectedIndex].value));        
      }
      return protocolId;
    }

    function getParents()
    {
      var frm = document.forms['extract'];
      var parents = new Array();
      if (frm.parentType[0].checked)
      {
        var sampleId = Math.abs(parseInt(frm.sample_id[frm.sample_id.selectedIndex].value));
        if (sampleId > 0) parents[parents.length] = 'SAMPLE:'+sampleId;
      }
      else
      {
        var ids = Link.getListIds(frm.extracts, 'E');
        if (ids.length > 0)
        {
          parents[parents.length] = 'EXTRACT:'+ids.join(':');
        }
      }
      return parents;
    }
    
    function subtypeOnChange()
    {
      var frm = document.forms['extract'];
      var subtypeId = ItemSubtype.getSubtypeId('extract');
      var recentInfo = ItemSubtype.getRecentAndRelatedInfo(subtypeId, 'EXTRACT', ['PROTOCOL', 'BIOPLATE', 'TAG', 'SAMPLE', 'EXTRACT']);
      protocolChanged = ItemSubtype.updateRecentItemsInList(frm.protocol_id, recentInfo.PROTOCOL['recent']);
      ItemSubtype.updateDefaultItemsInList(frm.protocol_id, recentInfo.PROTOCOL['default']);
      ItemSubtype.updateRecentItemsInList(frm.tag_id, recentInfo.TAG['recent']);
      ItemSubtype.updateRecentItemsInList(frm.bioplate_id, recentInfo.BIOPLATE['recent']);
    }
    
    function selectProtocolOnClick()
    {
      var frm = document.forms['extract'];
      var url = '../../admin/protocols/index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectone';
      url += '&callback=setProtocolCallback&resetTemporary=1';
      url += ItemSubtype.createRelatedFilter('extract', 'PROTOCOL', <%=SystemItems.getId(Protocol.EXTRACTION)%>);
      if (frm.protocol_id.length > 1) 
      {
        var id = Math.abs(parseInt(frm.protocol_id[1].value));        
        url += '&item_id='+id;
      }
      Main.openPopup(url, 'SelectProtocol', 1000, 700);
    }
    function setProtocolCallback(id, name)
    {
      var frm = document.forms['extract'];
      var list = frm.protocol_id;
      if (list.length < 2 || list[1].value == '0') // >
      {
        Forms.addListOption(list, 1, new Option());
      }
      list[1].value = id;
      list[1].text = name;
      list.selectedIndex = 1;
      protocolChanged = true;
    }
    function protocolOnChange()
    {
      protocolChanged = true;
    }
    function selectTagOnClick()
    {
      var frm = document.forms['extract'];
      var url = '../tags/index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectone';
      url += '&callback=setTagCallback&resetTemporary=1';
      url += ItemSubtype.createRelatedFilter('extract', 'TAG');
      if (frm.tag_id.length > 1) 
      {
        var id = Math.abs(parseInt(frm.tag_id[1].value));       
        url += '&item_id='+id;
      }
      Main.openPopup(url, 'SelectTag', 1000, 700);
    }
    function setTagCallback(id, name)
    {
      var frm = document.forms['extract'];
      var list = frm.tag_id;
      if (list.length < 2 || list[1].value == '0') // >
      {
        Forms.addListOption(list, 1, new Option());
      }
      list[1].value = id;
      list[1].text = name;
      list.selectedIndex = 1;
    }
    function selectBioPlateOnClick()
    {
      var frm = document.forms['extract'];
      var url = '../bioplates/index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectone&callback=setBioPlateCallback';
      if (frm.bioplate_id.length > 1)
      {
        var id = Math.abs(parseInt(frm.bioplate_id[1].value));        
        url += '&item_id='+id;
      }
      url += '&resetTemporary=1&tmpfilter:INT:bioPlateType.lockMode=<><%=BioWell.LockMode.LOCKED_AFTER_CREATE.getValue()%>';
      url += '&tmpfilter:BOOLEAN:destroyed=false';
      Main.openPopup(url, 'SelectBioplate', 1000, 700);
    } 
    function setBioPlateCallback(id, name)
    {
      var frm = document.forms['extract'];
      var list = frm.bioplate_id;
      if (list.length < 2 || list[1].value == '0') // >
      {
        Forms.addListOption(list, 1, new Option());
      }
      list[1].value = id;
      list[1].text = name;
      list.selectedIndex = 1;
      frm.biowell_id.remove(1);
      frm.biowell_id.disabled = false;
    }
    function bioPlateOnChange()
    {
      var frm = document.forms['extract'];
      var list = frm.bioplate_id;
      frm.biowell_id.selectedIndex=0;
      frm.biowell_id.remove(1);     
    }

    function initBioWell()
    {
      var frm = document.forms['extract'];
      <%
      if (currentBioWell != null)
      {
        %>
        var list = frm.biowell_id;
        var wellId = <%=currentBioWell.getId()%>;
        Forms.addListOption(list, 1, new Option());
        list[1].value = '<%=currentBioWell.getId()*(extract == null ? 1 : -1)%>';
        list[1].text = '[<%=rowFormatter.format(currentBioWell.getRow())%>,<%=columnFormatter.format(currentBioWell.getColumn())%>]';
        list.selectedIndex = 1;
      <%
      }
      %>
    }         
    function selectBioWellOnClick()
    {
      var frm = document.forms['extract'];
      var bioplate_list = frm.bioplate_id;      
      var bioplateId = Math.abs(parseInt(bioplate_list[bioplate_list.selectedIndex].value))
      if (Main.trimString(frm.bioplate_id.value) == 0)
      {
        alert("You must first select the bioplate where the biowell is located");
        return;
      }     
        
      var url = '../bioplates/wells/index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectone&callback=setBioWellCallback';
      if (frm.biowell_id.length > 1)
      {
        var id = Math.abs(parseInt(frm.biowell_id[1].value));       
        url += '&item_id='+id;
      }
      url += '&bioplate_id='+bioplateId;
      url += '&resetTemporary=1&tmpfilter:STRING:$mbm.name='+escape('=');
      url += '&tmpfilter:STRING:originalBioMaterial.name='+escape('=');
      url += '&columns=row,column';
      Main.openPopup(url, 'SelectBiowell', 700, 700);
    }
    function setBioWellCallback(id, name)
    {
      var frm = document.forms['extract'];
      var list = frm.biowell_id;
      if (list.length < 2 || list[1].value == '0') // >
      {
        Forms.addListOption(list, 1, new Option());
      }
      list[1].value = id;
      list[1].text = name;
      list.selectedIndex = 1;
    }
    
    function parentTypeOnClick()
    {
      var frm = document.forms['extract'];
      var useExtracts = frm.parentType[1].checked;
      frm.sample_id.disabled = useExtracts;
      frm.used_from_sample.disabled = useExtracts;
      frm.extracts.disabled = !useExtracts;
      frm.used_quantity.disabled = !useExtracts;
      parentsChanged = true;
    }
    function sampleOnChange()
    {
      parentsChanged = true;
    }
    
    function selectSampleOnClick()
    {
      var frm = document.forms['extract'];
      var url = '../samples/index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectone';
      url += '&callback=setSampleCallback&resetTemporary=1';
      url += ItemSubtype.createRelatedFilter('extract', 'SAMPLE');
      if (frm.sample_id.length > 1) 
      {
        var id = Math.abs(parseInt(frm.sample_id[1].value));        
        url += '&item_id='+id;
      }
      Main.openPopup(url, 'SelectSample', 1000, 700);
    }
    function setSampleCallback(id, name)
    {
      var frm = document.forms['extract'];
      var list = frm.sample_id;
      if (list.length < 2 || list[1].value == '0') // >
      {
        Forms.addListOption(list, 1, new Option());
      }
      list[1].value = id;
      list[1].text = name;
      list.selectedIndex = 1;
      frm.parentType[0].checked = true;
      frm.parentType[1].checked = false;
      parentTypeOnClick();
      parentsChanged = true;
    }
    
    function addExtractsOnClick()
    {
      var frm = document.forms['extract'];
      var url = 'index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectmultiple';
      url += '&callback=addExtractCallback&resetTemporary=1';
      url += ItemSubtype.createRelatedFilter('extract', 'EXTRACT');
      Main.openPopup(url, 'AddExtracts', 1000, 700);
    }
    
    function addExtractCallback(extractId, name)
    {
      var item = Link.getItem('E', extractId);
      if (!item) item = new Item('E', extractId, name+' [-]', '', '');
      Link.addItem(document.forms['extract'].extracts, item);
      frm.parentType[0].checked = false;
      frm.parentType[1].checked = true;
      parentTypeOnClick();
      parentsChanged = true;
    }
    function extractsOnChange()
    {
      var frm = document.forms['extract'];
      var item = frm.extracts[frm.extracts.selectedIndex].item;
      if (item && item.id)
      {
        frm.used_quantity.value = item.value;
        frm.used_quantity.focus();
      }
      else
      {
        frm.used_quantity.value = '';
      }
    }
    function usedQuantityOnBlur()
    {
      var frm = document.forms['extract'];
      var usedQuantity = frm.used_quantity.value;
      var displayQuantity = usedQuantity == '' ? '-' : usedQuantity+' µg';
      for (var i = 0; i < frm.extracts.length; i++) // >
      {
        var option = frm.extracts[i];
        if (option.selected && option.item.id)
        {
          option.item.value = usedQuantity;
          var text = option.text.replace(/\[.*\]/, '['+displayQuantity+']');
          option.text = text; 
        }
      }
    }
    function usedFromSampleOnBlur()
    {
      var frm = document.forms['extract'];
      
      var sampleId = parseInt(frm.sample_id[frm.sample_id.selectedIndex].value);
      if (sampleId < 0)
      {
        frm.sample_id[frm.sample_id.selectedIndex].value = -sampleId;
      }
    }
    

    function removeOnClick()
    {
      Link.removeSelected(document.forms['extract'].extracts);
      parentsChanged = true;
    }

    function init()
    {
      <%
      if (extract == null)
      {
        %>
        var frm = document.forms['extract'];
        frm.name.focus();
        frm.name.select();
        <%
      }
      %>
      initBioWell();      
      initExtracts();
      parentTypeOnClick();
    }
    function initExtracts()
    {
      var extracts = document.forms['extract'].extracts;
      <%
      if (extractsQuery != null)
      {
        extractsQuery.include(Include.ALL);
        extractsQuery.order(Orders.asc(Hql.property("name")));
        ItemResultList<Extract> extracts = extractsQuery.list(dc);
        for (Extract e : extracts)
        {
          if (extract != null)
          {
            String usedQuantity = Values.formatNumber(creationEvent.getUsedQuantity(e), -1);
            %>
            Link.addNewItem(extracts, new Item('E', <%=e.getId()%>, '<%=HTML.javaScriptEncode(e.getName())%> [<%=usedQuantity%> µg]', '<%=usedQuantity%>'));
            <%
          }
          else
          {
            %>
            Link.addItem(extracts, new Item('E', <%=e.getId()%>, '<%=HTML.javaScriptEncode(e.getName())%> [-]', '', ''));
            <%
            
          }
        }
      }
      %>
    }
    </script>
  </base:head>
  <base:body onload="init()">
    <p>
    <form action="index.jsp?ID=<%=ID%>" method="post" name="extract" onsubmit="return false;">
    <input type="hidden" name="cmd" value="UpdateItem">

    <h3 class="docked"><%=title%> <base:help tabcontrol="settings" /></h3>
    <t:tabcontrol id="settings" contentstyle="<%="height: "+(int)(scale*370)+"px;"%>" 
      position="bottom"  remember="<%=extract != null%>" switch="switchTab"
      extensions="<%=invoker%>">
    <t:tab id="info" title="Extract" validate="validateExtract()" helpid="extract.edit">
      <table class="form" cellspacing=0>
      <tr>
        <td class="prompt">Name</td>
        <td><input <%=requiredClazz%> type="text" name="name" 
          value="<%=HTML.encodeTags(name)%>" 
          size="40" maxlength="<%=Extract.MAX_NAME_LENGTH%>"></td>
      </tr>
      <tr valign="top">
        <td class="prompt">Type</td>
        <td colspan="2">
          <select name="subtype_id"
            <%=!readCurrentSubtype ? "disabled readonly class=\"disabled selectionlist\"" : "class=\"selectionlist\""%>
            onchange="subtypeOnChange()"
            >
          <%
          if (!readCurrentSubtype)
          {
            %>
            <option value="-1">- denied -
            <%
          }
          else
          {
            %>
            <option value="0">-none-
            <%
            int currentSubtypeId = currentSubtype == null ? 0 : currentSubtype.getId();
            for (ItemSubtype subtype : subtypesQuery.list(dc))
            {
              int id = subtype.getId();
              if (id != currentSubtypeId && subtype.isRemoved()) continue;
              %>
              <option value="<%=id == currentSubtypeId && extract != null ? -id : id%>" 
                <%=id == currentSubtypeId ? "selected" : ""%>
                title="<%=HTML.encodeTags(subtype.getDescription()) %>"
                ><%=HTML.encodeTags(subtype.getName())%>
              <%
            }
          }
          %>
          </select>
        </td>
      </tr>
      <tr>
        <td class="prompt">Tag</td>
        <td>
          <base:select 
            id="tag_id"
            clazz="selectionlist"
            required="false"
            current="<%=currentTag%>"
            denied="<%=!readCurrentTag%>"
            recent="<%=recentTags%>"
            newitem="<%=extract == null%>"
            onselect="selectTagOnClick()"
          />
        </td>
      </tr>
      <tr>
        <td class="prompt">External ID</td>
        <td><input <%=clazz%> type="text" name="external_id" 
          value="<%=HTML.encodeTags(extract == null ? Values.getString(cc.getPropertyValue("externalId"), "") : extract.getExternalId())%>" 
          size="40" maxlength="<%=Extract.MAX_EXTERNAL_ID_LENGTH%>"></td>
      </tr>
      <tr>
        <td class="prompt">Original quantity</td>
        <td><input <%=clazz%> type="text" name="original_quantity" 
          value="<%=Values.formatNumber(extract == null ? Values.getFloat(cc.getPropertyValue("originalQuantity"), null): extract.getOriginalQuantity(), -1)%>" size="12" 
          maxlength="10" onkeypress="return Numbers.numberOnly(event)"> (µg)</td>
      </tr>
      <tr>
        <td class="prompt">Created</td>
        <td>
          <table border="0" cellspacing="0" cellpadding="0">
          <tr>
          <td>
            <input <%=clazz%> type="text" name="event_date" <%=lockEventProperties ? "disabled" : ""%>
              value="<%=HTML.encodeTags(dateFormatter.format(eventDate))%>" 
              size="20" maxlength="20" title="Enter date in format: <%=htmlDateFormat%>">
            &nbsp;
          </td>
          <td>
          <base:button 
            onclick="<%="Dates.selectDate('Created', 'extract', 'event_date', null, '"+jsDateFormat+"')"%>"
            image="calendar.png" 
            title="Calendar&hellip;" 
            tooltip="Select a date from a calendar" 
            disabled="<%=lockEventProperties%>"
          />
          </td>
          </tr>
          </table>
        </td>
      </tr>
      <tr>
        <td class="prompt">Registered</td>
        <td><%=dateFormatter.format(creationEvent == null ? new Date() : creationEvent.getEntryDate())%></td>
      </tr>
      <tr>
        <td class="prompt">Protocol</td>
        <td>
          <base:select 
            id="protocol_id"
            clazz="selectionlist"
            required="false"
            current="<%=currentProtocol%>"
            denied="<%=!readCurrentProtocol%>"
            recent="<%=recentProtocols%>"
            defaultitems="<%=defaultProtocols%>"
            newitem="<%=extract == null%>"
            onselect="selectProtocolOnClick()"
            onchange="protocolOnChange()"
            disabled="<%=lockEventProperties%>"
          />
        </td>
      </tr>
      <tr>
        <td class="prompt">Bioplate</td>
        <td>
          <base:select 
            id="bioplate_id"
            clazz="selectionlist"
            required="false"
            current="<%=currentBioPlate%>"
            denied="<%=!readCurrentBioPlate%>"
            recent="<%=recentBioPlates%>"
            newitem="<%=extract == null%>"
            onselect="selectBioPlateOnClick()"
            onchange="bioPlateOnChange()"
            disabled="<%=lockedWell%>"
          />
        </td>
      </tr>
      <tr>
        <td class="prompt">Biowell</td>
        <td>
          <base:select 
            id="biowell_id"
            clazz="selectionlist"
            required="false"            
            current="<%=null %>"
            denied="<%=!readCurrentBioWell%>"
            newitem="<%=extract == null%>"
            onselect="selectBioWellOnClick()"
            onchange="bioWellOnChange()"
            disabled="<%=lockedWell%>"
          />
        </td>
      </tr>
      <tr valign=top>
        <td class="prompt">Description</td>
        <td nowrap>
          <textarea <%=clazz%> rows="4" cols="40" name="description" wrap="virtual"
            ><%=HTML.encodeTags(extract == null ? cc.getPropertyValue("description") : extract.getDescription())%></textarea>
          <a href="javascript:Main.zoom('Description', 'extract', 'description')"
            title="Edit in larger window"><base:icon image="zoom.gif" /></a>
        </td>
      </tr>
      </table>
      <div align=right>&nbsp;<i><base:icon image="required.gif" /> = required information</i></div>
    </t:tab>
    
    <t:tab id="parents" title="Parents" helpid="extract.parent">
      <table class="form" cellspacing=0>
      <tr>
        <td class="prompt">Parent type</td>
        <td>
          <input type="radio" name="parentType" id="parentType.sample" 
            value="SAMPLE" onclick="parentTypeOnClick()"
            <%=parentType != Item.EXTRACT ? "checked" : ""%>
            ><label for="parentType.sample">Sample</label>
          <input type="radio" name="parentType" id="parentType.extract" 
            value="EXTRACT" onclick="parentTypeOnClick()"
            <%=parentType == Item.EXTRACT ? "checked" : ""%>
            ><label for="parentType.extract">Extract</label>
        </td>
      </tr>
      <tr valign="top">
        <td class="prompt">Sample</td>
        <td>
          <base:select 
            id="sample_id"
            clazz="selectionlist"
            buttonstyle="width: 150px;"
            buttonicon="add.png"
            buttontitle="Select sample&hellip;"
            required="false"
            current="<%=currentSample%>"
            denied="<%=!readCurrentSample%>"
            recent="<%=recentSamples%>"
            selectrecent="false"
            newitem="<%=extract == null%>"
            onselect="selectSampleOnClick()"
            onchange="sampleOnChange()"
          />
        </td>
      </tr>
      <tr>
        <td class="subprompt">-</td>
        <td>
          used quantity
          <input <%=clazz%> type="text" name="used_from_sample" value="<%=Values.formatNumber(usedFromSample, -1)%>"
            size="12" maxlength="10" onkeypress="return Numbers.numberOnly(event)"
            onblur="usedFromSampleOnBlur()"> (µg)
        </td>
      </tr>
      <tr valign="top">
        <td class="prompt">Extracts</td>
        <td>
          <table border="0" cellspacing="0" cellpadding="0">
          <tr valign="top">
          <td>
            <select name="extracts" size="5" multiple class="selectionlist" 
              onchange="extractsOnChange()">
            </select>&nbsp;
            <input type="hidden" name="modifiedExtracts" value="">
            <input type="hidden" name="removedExtracts" value="">
          </td>
          <td>
            <table border="0" cellspacing="0" cellpadding="0">
            <tr><td style="padding: 1px 0px 4px 0px;"><base:button 
              style="width: 150px;"
              onclick="addExtractsOnClick()" 
              title="Add&nbsp;extracts&hellip;" 
              tooltip="Add extracts"
              /></td></tr>
            <tr><td width="150"><base:button 
              style="width: 150px;"
              onclick="removeOnClick()" 
              title="Remove" 
              tooltip="Remove the selected extracts"
            /></td></tr>
            </table>
          </td>
          </tr>
          </table>
        </td>
      </tr>
      <tr>
        <td class="subprompt">-</td>
        <td>used quantity
        <input <%=clazz%> type="text" name="used_quantity" value=""
              size="12" maxlength="10" onkeypress="return Numbers.numberOnly(event)"
              onkeyup="usedQuantityOnBlur();"
            > (µg)
        </td>
      </tr>         
      </table>
    </t:tab>

    <t:tab id="annotations" title="Annotations &amp; parameters" 
      helpid="annotations.edit" tooltip="Enter values for annotations and protocol parameters">
      <iframe name="annotations" id="idAnnotations" src="../../common/annotations/wait.jsp" 
        width="100%"  height="<%=(int)(scale*370)%>" frameborder=0 vspace=0 hspace=0
        marginwidth=0 marginheight=0 scrolling="auto" style="overflow: visible"></iframe>
    </t:tab>
    
    <t:tab id="inheritedAnnotations" title="Inherited annotations" helpid="annotations.edit.inherited">
    
      <iframe name="inheritedAnnotations" id="idInheritedAnnotations" src="../../common/annotations/wait.jsp" 
        width="100%"  height="<%=(int)(scale*370)%>" frameborder=0 vspace=0 hspace=0
        marginwidth=0 marginheight=0 scrolling="auto" style="overflow: visible"></iframe>
    </t:tab>
    </t:tabcontrol>

    <table align="center">
    <tr>
      <td width="50%"><base:button onclick="saveSettings()" title="Save" /></td>
      <td width="50%"><base:button onclick="window.close()" title="Cancel" /></td>
    </tr>
    </table>
    </form>
  </base:body>
  </base:page>
  <%
}
finally
{
  if (dc != null) dc.close();
}
%>