source: trunk/www/views/physicalbioassays/edit_bioassay.jsp @ 5662

<%-- $Id: edit_bioassay.jsp 5662 2011-06-20 11:55:13Z nicklas $
  ------------------------------------------------------------------
  Copyright (C) 2005 Nicklas Nordborg, Gregory Vincic
  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.ItemContext"
  import="net.sf.basedb.core.SystemItems"
  import="net.sf.basedb.core.Permission"
  import="net.sf.basedb.core.Include"
  import="net.sf.basedb.core.Hardware"
  import="net.sf.basedb.core.PhysicalBioAssay"
  import="net.sf.basedb.core.BioMaterialEvent"
  import="net.sf.basedb.core.BioMaterialEventSource"
  import="net.sf.basedb.core.ItemSubtype"
  import="net.sf.basedb.core.ArraySlide"
  import="net.sf.basedb.core.Protocol"
  import="net.sf.basedb.core.Project"
  import="net.sf.basedb.core.Extract"
  import="net.sf.basedb.core.ItemQuery"
  import="net.sf.basedb.core.ItemResultList"
  import="net.sf.basedb.core.PermissionDeniedException"
  import="net.sf.basedb.core.BaseException"
  import="net.sf.basedb.core.Type"
  import="net.sf.basedb.core.query.Restrictions"
  import="net.sf.basedb.core.query.Expressions"
  import="net.sf.basedb.core.query.Orders"
  import="net.sf.basedb.core.query.Hql"
  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.formatter.Formatter"
  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"
%>
<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
<%@ taglib prefix="t" uri="/WEB-INF/tab.tld" %>
<%
final Item itemType = Item.PHYSICALBIOASSAY;
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;
  String name = null;
  PhysicalBioAssay pba = null;
  BioMaterialEvent creationEvent = null;
  Date eventDate = null;
  ItemQuery<Extract> extractsQuery = null;
  
  boolean readCurrentSubtype = true;
  int currentSubtypeId = 0;
  boolean readCurrentArraySlide = true;
  ArraySlide currentArraySlide = null;
  
  boolean readCurrentProtocol = true;
  Protocol currentProtocol = null;
  Protocol defaultProtocol = null;
  
  boolean readCurrentHardware = true;
  Hardware currentHardware = null;
  Hardware defaultHardware = null;

  // Load recently used items
  List<Protocol> recentProtocols = (List<Protocol>)cc.getRecent(dc, Item.PROTOCOL);
  List<Hardware> recentHardware = (List<Hardware>)cc.getRecent(dc, Item.HARDWARE);
  
  int activeProjectId = sc.getActiveProjectId();
  if (activeProjectId > 0)
  {
    Project activeProject = Project.getById(dc, activeProjectId);
    try
    {
      defaultProtocol = (Protocol)activeProject.findDefaultItem(dc, 
          ItemSubtype.getById(dc, SystemItems.getId(Protocol.HYBRIDIZATION)), false);
    }
    catch (PermissionDeniedException pdex)
    {
      defaultProtocol = null;
    }
    try
    {
      defaultHardware = (Hardware)activeProject.findDefaultItem(dc, 
          ItemSubtype.getById(dc, SystemItems.getId(Hardware.HYBRIDIZATION_STATION)), false);
    }
    catch (PermissionDeniedException pdex)
    {
      defaultHardware = null;
    }
  }
  if (itemId == 0)
  {
    title = "Create physical bioassay";
    cc.removeObject("item");
    currentSubtypeId = Values.getInt(request.getParameter("subtype_id"));
    if (currentSubtypeId == 0) 
    {
      int recentSubtypeId = Values.getInt(cc.getRecent(Item.ITEMSUBTYPE.name(), 0));
      currentSubtypeId = Values.getInt(cc.getPropertyValue("itemSubtype"), recentSubtypeId);
    }
    if (cc.getPropertyFilter("creationEvent.protocol.name") != null)
    {
      currentProtocol = Base.getFirstMatching(dc, Protocol.getQuery(), "name", cc.getPropertyFilter("creationEvent.protocol.name"));
    }
    if (cc.getPropertyFilter("creationEvent.hardware.name") != null)
    {
      currentHardware = Base.getFirstMatching(dc, Hardware.getQuery(), "name", cc.getPropertyFilter("creationEvent.hardware.name"));
    }
    if (cc.getPropertyFilter("arraySlide.name") != null)
    {
      currentArraySlide = Base.getFirstMatching(dc, ArraySlide.getQuery(), "name", cc.getPropertyFilter("arraySlide.name"));
    }
    name = Values.getString(cc.getPropertyValue("name"), "New physical bioassay");
    eventDate = (Date)cc.getPropertyObject("creationEvent.eventDate");
    
    if (Values.getBoolean(request.getParameter("useParents")))
    {
      ItemContext lc = sc.getCurrentContext(Item.EXTRACT);
      if (lc.getSelected().size() > 0)
      {
        extractsQuery = Extract.getQuery();
        extractsQuery.include(Include.ALL);
        extractsQuery.order(Orders.asc(Hql.property("name")));
        extractsQuery.restrict(Restrictions.in(Hql.property("id"), 
          Expressions.parameter("selected", lc.getSelected(), Type.INT)));
      }
    }
    else if (request.getParameter("extract_id") != null)
    {
      int leId = Values.getInt(request.getParameter("extract_id"));
      extractsQuery = Extract.getQuery();
      extractsQuery.include(Include.ALL);
      extractsQuery.restrict(Restrictions.eq(Hql.property("id"), 
        Expressions.integer(leId)));
    }
  }
  else
  {
    pba = PhysicalBioAssay.getById(dc, itemId);
    pba.checkPermission(Permission.WRITE);
    creationEvent = pba.getCreationEvent();
    eventDate = creationEvent.getEventDate();
    cc.setObject("item", pba);
    title = "Edit physical bioassay -- " + HTML.encodeTags(pba.getName());
    name = pba.getName();
    
    try
    {
      ItemSubtype subtype = pba.getItemSubtype();
      if (subtype != null) currentSubtypeId = subtype.getId();
    }
    catch (PermissionDeniedException ex)
    {
      readCurrentSubtype = false;
    }

    try
    {
      currentArraySlide = pba.getArraySlide();
    }
    catch (PermissionDeniedException ex)
    {
      readCurrentArraySlide = false;
    }
    try
    {
      currentProtocol = creationEvent.getProtocol();
    }
    catch (PermissionDeniedException ex)
    {
      readCurrentProtocol = false;
    }
    try
    {
      currentHardware = creationEvent.getHardware();
    }
    catch (PermissionDeniedException ex)
    {
      readCurrentHardware = false;
    }
    
    // Query to retrieve source extracts
    extractsQuery = (ItemQuery<Extract>)creationEvent.getSources();
    extractsQuery.include(Include.ALL);
    extractsQuery.order(Orders.asc(Hql.property("name")));
    
  }
  // 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), pba);
  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 "Physical bioassay" tab
    function validatePhysicalBioAssay()
    {
      var frm = document.forms['bioassay'];
      if (Main.trimString(frm.name.value) == '')
      {
        alert("You must enter a name");
        frm.name.focus();
        return false;
      }
      else if (!Numbers.isInteger(frm.size.value))
      {
        alert("'" + frm.size.value + "' is not a valid number");
        frm.size.focus();
        return false;
      }
      else if (parseInt(frm.size.value) <= 0)
      {
        alert("Size must be > 0");
        frm.size.focus();
        return false;
      }
      return true;
    }

    // Submit the form
    function saveSettings()
    {
      var frm = document.forms['bioassay'];
      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()%>', <%=pba == null ? 0 : pba.getId()%>, 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['bioassay'];
      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['bioassay'];
      var parents = new Array();

      var arraySlideId = Math.abs(parseInt(frm.arrayslide_id[frm.arrayslide_id.selectedIndex].value));
      if (arraySlideId > 0) parents[parents.length] = 'ARRAYSLIDE:'+arraySlideId;

      var ids = Link.getListIds(frm.extracts, 'L');
      if (ids.length > 0)
      {
        parents[parents.length] = 'EXTRACT:'+ids.join(':');
      }
      return parents;
    }

    function selectProtocolOnClick()
    {
      var frm = document.forms['bioassay'];
      var url = '../../admin/protocols/index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectone';
      url += '&callback=setProtocolCallback&resetTemporary=1';
      url += ItemSubtype.createRelatedFilter('bioassay', 'PROTOCOL');
      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['bioassay'];
      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 selectHardwareOnClick()
    {
      var frm = document.forms['bioassay'];
      var url = '../../admin/hardware/index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectone';
      url += '&callback=setHardwareCallback&resetTemporary=1';
      url += ItemSubtype.createRelatedFilter('bioassay', 'HARDWARE');
      if (frm.hardware_id.length > 1)
      {
        var id = Math.abs(parseInt(frm.hardware_id[1].value));        
        url += '&item_id='+id;
      }
      Main.openPopup(url, 'SelectHardware', 1000, 700);
    }
    function setHardwareCallback(id, name)
    {
      var frm = document.forms['bioassay'];
      var list = frm.hardware_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 arraySlideOnChange()
    {
      var frm = document.forms['bioassay'];
      var selectedIndex = frm.arrayslide_id.selectedIndex
      var arraySlideId = frm.arrayslide_id[selectedIndex].value;
      if (arraySlideId > 0) updateSize(arraySlideId);
      parentsChanged = true;
    }
    function selectArraySlideOnClick()
    {
      var frm = document.forms['bioassay'];
      var url = '../../lims/arrayslides/index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectone&callback=setArraySlideCallback';
      if (frm.arrayslide_id.length > 1) 
      {
        var id = Math.abs(parseInt(frm.arrayslide_id[1].value));        
        url += '&item_id='+id;
      }
      url += '&resetTemporary=1&tmpfilter:STRING:physicalBioAssay.name==';
      url += '&tmpfilter:BOOLEAN:destroyed=false';
      Main.openPopup(url, 'SelectArraySlide', 1000, 700);
    }
    function setArraySlideCallback(arraySlideId, name)
    {
      var frm = document.forms['bioassay'];
      if (frm.arrayslide_id.length < 2) // >
      {
        frm.arrayslide_id[frm.arrayslide_id.length] = new Option();
      }
      frm.arrayslide_id[1].value = arraySlideId;
      frm.arrayslide_id[1].text = name;
      frm.arrayslide_id.selectedIndex = 1;
      updateSize(arraySlideId);
      parentsChanged = true;
    }
    function updateSize(arraySlideId)
    {
      var request = Ajax.getXmlHttpRequest();
      if (request != null)
      {
        var url = '../../lims/arrayslides/ajax.jsp?ID=<%=ID%>&cmd=GetArrayDesign&item_id=' + arraySlideId;
        request.open("GET", url, true);
        Ajax.setReadyStateHandler(request, updateSizeCallback);
        request.send(null);
      }
      return request != null;
    }
    function updateSizeCallback(request)
    {
      var frm = document.forms['bioassay'];
      var response = Ajax.parseJsonResponse(request.responseText);
      if (response.status != 'ok')
      {
        alert(response.message);
        return false;
      }

      if (response.numArrays)
      {
        frm.size.value = response.numArrays;
      }
    }
    
    function addExtractsOnClick()
    {
      var frm = document.forms['bioassay'];
      var ids = Link.getListIds(frm.extracts, 'L');
      var excludes = ids.join(',');
      
      var url = '../../biomaterials/extracts/index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectmultiple';
      url += '&callback=addExtractCallback&resetTemporary=1';
      url += ItemSubtype.createRelatedFilter('bioassay', 'EXTRACT');
      url += '&exclude='+excludes;
      Main.openPopup(url, 'AddExtracts', 1000, 700);
    }
    function addExtractCallback(extractId, name)
    {
      var item = Link.getItem('E', extractId);
      if (!item) item = new Item('E', extractId, '1: '+name+' [-]', '', '');
      Link.addItem(document.forms['bioassay'].extracts, item);
      parentsChanged = true;
      extractsOnChange();
    }
    function extractsOnChange()
    {
      var frm = document.forms['bioassay'];
      var item = frm.extracts[frm.extracts.selectedIndex].item;
      if (item && item.id)
      {
        var i = item.value ? item.value.indexOf(':') : -1;
        frm.used_quantity.value = i >= 0 ? item.value.substring(0, i) : item.value;
        frm.position.value = i >= 0 ? item.value.substring(i+1) : '1';
        frm.used_quantity.focus();
      }
      else
      {
        frm.used_quantity.value = '';
        frm.position.value = '1';
      }
    }
    function usedQuantityOnBlur()
    {
      var frm = document.forms['bioassay'];
      var usedQuantity = frm.used_quantity.value;
      var position = frm.position.value;
      var size = parseInt(frm.size.value);
      if (position != '' && (position > size || position <= 0))
      {
        alert('Position must be between 1 and ' + size);
        return;
      }
      if (position == '') position = 1;
      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 + ':' + position;
          var text = option.text.replace(/\[.*\]/, '['+displayQuantity+']');
          text = text.replace(/\d*\:/, position + ':');
          option.text = text; 
        }
      }
    }
    function positionOnBlur()
    {
      usedQuantityOnBlur();
    }

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

    
    function init()
    {
      var frm = document.forms['bioassay'];
      var extracts = frm.extracts;
      <%
      if (pba == null)
      {
        %>
        frm.name.focus();
        frm.name.select();
        <%
      }
      if (extractsQuery != null)
      {
        ItemResultList<Extract> extracts = extractsQuery.list(dc);
        for (Extract extract : extracts)
        {
          if (pba == null)
          {
            %>
            Link.addItem(extracts, new Item('E', <%=extract.getId()%>, '1: <%=HTML.javaScriptEncode(extract.getName())%> [-]', ':1'));
            <%
          }
          else
          {
            BioMaterialEventSource evtSrc = creationEvent.getEventSource(extract);
            Float used = evtSrc.getUsedQuantity();
            String usedQuantity = Values.formatNumber(used, -1);
            String usedWithUnit = used == null ? "-" : usedQuantity + " µg";
            int position = evtSrc.getPosition();
            %>
            Link.addNewItem(extracts, new Item('E', <%=extract.getId()%>, '<%=position + ": " + HTML.javaScriptEncode(extract.getName())%> [<%=usedWithUnit%>]', '<%=usedQuantity%>:<%=position%>'));
            <%
          }
        }
      }
      %>
    }
    </script>
  </base:head>
  <base:body onload="init()">
    <p>
    <form action="index.jsp?ID=<%=ID%>" method="post" name="bioassay" 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="<%=pba != null%>" switch="switchTab"
      extensions="<%=invoker%>">
    <t:tab id="info" title="Physical bioassay" validate="validatePhysicalBioAssay()" helpid="physicalbioassay.edit">
      <table class="form" cellspacing=0>
      <tr>
        <td class="prompt">Name</td>
        <td><input <%=requiredClazz%> type="text" name="name" 
          value="<%=name%>" 
          size="40" maxlength="<%=PhysicalBioAssay.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\""%>>
          <%
          if (!readCurrentSubtype)
          {
            %>
            <option value="-1">- denied -
            <%
          }
          else
          {
            %>
            <option value="0">-none-
            <%
            for (ItemSubtype subtype : subtypesQuery.list(dc))
            {
              int id = subtype.getId();
              if (id != currentSubtypeId && subtype.isRemoved()) continue;
              %>
              <option value="<%=id == currentSubtypeId && pba != null ? -id : id%>" 
                <%=id == currentSubtypeId ? "selected" : ""%>
                title="<%=HTML.encodeTags(subtype.getDescription()) %>"
                ><%=HTML.encodeTags(subtype.getName())%>
              <%
            }
          }
          %>
          </select>
        </td>
      </tr>
      <tr>
        <td class="prompt">Size</td>
        <td><input <%=requiredClazz%> type="text" name="size" 
          value="<%=pba == null ? Values.getString(cc.getPropertyValue("size"), "1") : pba.getSize()%>" 
          size="12" maxlength="10" onkeypress="return Numbers.integerOnly(event)"></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" 
              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', 'bioassay', 'event_date', null, '"+jsDateFormat+"')"%>"
            image="calendar.png"
            title="Calendar&hellip;" 
            tooltip="Select a date from a calendar" 
          />
          </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%>"
            defaultitem="<%=defaultProtocol%>"
            newitem="<%=pba == null%>"
            onselect="selectProtocolOnClick()"
            onchange="protocolOnChange()"
          />
        </td>
      </tr>
      <tr>
        <td class="prompt">Hardware</td>
        <td>
          <base:select 
            id="hardware_id"
            clazz="selectionlist"
            required="false"
            current="<%=currentHardware%>"
            denied="<%=!readCurrentHardware%>"
            recent="<%=recentHardware%>"
            defaultitem="<%=defaultHardware%>"
            newitem="<%=pba == null%>"
            onselect="selectHardwareOnClick()"
          />
        </td>
      </tr>
      <tr>
        <td class="prompt">Array slide</td>
        <td>
          <base:select 
            id="arrayslide_id"
            clazz="selectionlist"
            required="false"
            current="<%=currentArraySlide%>"
            denied="<%=!readCurrentArraySlide%>"
            newitem="<%=pba == null%>"
            onselect="selectArraySlideOnClick()"
            onchange="arraySlideOnChange()"
          />
        </td>
      </tr>
      <tr valign=top>
        <td class="prompt">Description</td>
        <td nowrap>
          <textarea <%=clazz%> rows="4" cols="40" name="description" wrap="virtual"
            ><%=HTML.encodeTags(pba == null ? cc.getPropertyValue("description") : pba.getDescription())%></textarea>
          <a href="javascript:Main.zoom('Description', 'bioassay', '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="extracts" title="Extracts" helpid="physicalbioassay.extracts">
      <input type="hidden" name="modifiedExtracts" value="">
      <input type="hidden" name="removedExtracts" value="">
    
      <table class="form" cellspacing=0>
      <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 style="width: 20em;" 
              onchange="extractsOnChange()">
            </select>&nbsp;<br>
          </td>
          <td>
            <table border="0">
            <tr><td width="150"><base:button 
              onclick="addExtractsOnClick()" 
              title="Add&nbsp;extracts&hellip;" 
              tooltip="Add extracts"
              /></td></tr>
            <tr><td width="150"><base:button 
              onclick="removeOnClick()" 
              title="Remove" 
              tooltip="Remove the selected extracts"
            /></td></tr>
            </table>
          </td>
          </tr>
          </table>
        </td>
      </tr>
      
      <tr>
        <td style="text-align: right; padding-right: 5px;">- used quantity</td>
        <td>
            <input <%=clazz%> type="text" name="used_quantity" value=""
              size="12" maxlength="10" onkeypress="return Numbers.numberOnly(event)"
              onkeyup="usedQuantityOnBlur()"
            > (µg)
        </td>
      </tr>

      <tr>
        <td style="text-align: right; padding-right: 5px;">- position</td>
        <td>
            <input <%=clazz%> type="text" name="position" value=""
              size="12" maxlength="10" onkeypress="return Numbers.numberOnly(event)"
              onkeyup="positionOnBlur()"
            > (1 -- size of bioassay)
        </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();
}
%>