source: trunk/www/views/derivedbioassays/edit_bioassay.jsp @ 5687

<%-- $Id $
  ------------------------------------------------------------------
  Copyright (C) 2011 Nicklas Nordborg

  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/>.
  ------------------------------------------------------------------
--%>
<%@ page pageEncoding="UTF-8" session="false"
  import="net.sf.basedb.core.SessionControl"
  import="net.sf.basedb.core.DbControl"
  import="net.sf.basedb.core.DerivedBioAssay"
  import="net.sf.basedb.core.PhysicalBioAssay"
  import="net.sf.basedb.core.Extract"
  import="net.sf.basedb.core.ItemSubtype"
  import="net.sf.basedb.core.Protocol"
  import="net.sf.basedb.core.Hardware"
  import="net.sf.basedb.core.Software"
  import="net.sf.basedb.core.Project"
  import="net.sf.basedb.core.Item"
  import="net.sf.basedb.core.ItemContext"
  import="net.sf.basedb.core.Permission"
  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.PermissionDeniedException"
  import="net.sf.basedb.core.BaseException"
  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.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.Date"
  import="java.util.List"
  import="java.util.Collections"
%>
<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
<%@ taglib prefix="t" uri="/WEB-INF/tab.tld" %>
<%
final Item itemType = Item.DERIVEDBIOASSAY;
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
{
  DerivedBioAssay bioAssay = null;
  String title = null;
  
  boolean readCurrentSubtype = true;
  ItemSubtype currentSubtype = null;

  boolean readCurrentPhysicalBioAssay = true;
  PhysicalBioAssay currentPhysicalBioAssay = null;
  
  boolean readCurrentParentBioAssay = true;
  DerivedBioAssay currentParentBioAssay = null;
  
  boolean readCurrentExtract = true;
  Extract currentExtract = null;

  boolean readCurrentProtocol = true;
  Protocol currentProtocol = null;
  
  boolean readCurrentHardware = true;
  Hardware currentHardware = null;
  
  boolean readCurrentSoftware = true;
  Software currentSoftware = null;

  if (itemId == 0)
  {
    title = "New derived bioassay";
    cc.removeObject("item");
    int currentSubtypeId = Values.getInt(request.getParameter("subtype_id"));
    List<ItemSubtype> relatedToParent = Collections.emptyList();
    int parentId = Values.getInt(request.getParameter("parent_id"));
    if (parentId != 0)
    {
      currentParentBioAssay = DerivedBioAssay.getById(dc, parentId);
      if (currentSubtypeId == 0)
      {
        relatedToParent = ItemSubtype.getParentSubtypes(dc, currentParentBioAssay, Item.DERIVEDBIOASSAY);
      }
      try
      {
        currentPhysicalBioAssay = currentParentBioAssay.getPhysicalBioAssay();
      }
      catch (PermissionDeniedException ex)
      {
        readCurrentPhysicalBioAssay = false;
      }
      try
      {
        currentExtract = currentParentBioAssay.getExtract();
      }
      catch (PermissionDeniedException ex)
      {}
    }
    else
    {
      int physicalBioAssayId = Values.getInt(request.getParameter("physicalbioassay_id"));
      if (physicalBioAssayId != 0)
      {
        currentPhysicalBioAssay = PhysicalBioAssay.getById(dc, physicalBioAssayId);
        if (currentSubtypeId == 0)
        {
          relatedToParent = ItemSubtype.getParentSubtypes(dc, currentPhysicalBioAssay, Item.DERIVEDBIOASSAY);
        }
      }
    }
    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);
      }
    }
  }
  else
  {
    bioAssay = DerivedBioAssay.getById(dc, itemId);
    bioAssay.checkPermission(Permission.WRITE);
    cc.setObject("item", bioAssay);
    title = "Edit bioassay -- " + HTML.encodeTags(bioAssay.getName());
    
    try
    {
      currentSubtype = bioAssay.getItemSubtype();
    }
    catch (PermissionDeniedException ex)
    {
      readCurrentSubtype = false;
    }
    try
    {
      currentParentBioAssay = bioAssay.getParent();
    }
    catch (PermissionDeniedException ex)
    {
      readCurrentParentBioAssay = false;
    }
    try
    {
      currentPhysicalBioAssay = bioAssay.getPhysicalBioAssay();
    }
    catch (PermissionDeniedException ex)
    {
      readCurrentPhysicalBioAssay = false;
    }
    try
    {
      currentExtract = bioAssay.getExtract();
    }
    catch (PermissionDeniedException ex)
    {
      readCurrentExtract = false;
    }
    try
    {
      currentProtocol = bioAssay.getProtocol();
    }
    catch (PermissionDeniedException ex)
    {
      readCurrentProtocol = false;
    }
    try
    {
      currentHardware = bioAssay.getHardware();
    }
    catch (PermissionDeniedException ex)
    {
      readCurrentHardware = false;
    }
    try
    {
      currentSoftware = bioAssay.getSoftware();
    }
    catch (PermissionDeniedException ex)
    {
      readCurrentSoftware = false;
    }
  }

  // Default items 
  int activeProjectId = sc.getActiveProjectId();
  List<Protocol> defaultProtocols = null;
  List<Hardware> defaultHardware = null;
  List<Software> defaultSoftware = null;
  if (activeProjectId > 0)
  {
    Project activeProject = Project.getById(dc, activeProjectId);
    defaultProtocols = (List<Protocol>)activeProject.findDefaultItemsOfRelatedSubtype(dc, currentSubtype, Item.PROTOCOL);
    defaultHardware = (List<Hardware>)activeProject.findDefaultItemsOfRelatedSubtype(dc, currentSubtype, Item.HARDWARE);
    defaultSoftware = (List<Software>)activeProject.findDefaultItemsOfRelatedSubtype(dc, currentSubtype, Item.SOFTWARE);
  }

  // Load recently used items
  List<PhysicalBioAssay> recentPhysicalBioAssays = (List<PhysicalBioAssay>)cc.getRecent(dc, Item.PHYSICALBIOASSAY);
  List<DerivedBioAssay> recentParentBioAssays = (List<DerivedBioAssay>)cc.getRecent(dc, Item.DERIVEDBIOASSAY);
  List<Protocol> recentProtocols = (List<Protocol>)cc.getRecent(dc, Item.PROTOCOL, currentSubtype);
  List<Hardware> recentHardware = (List<Hardware>)cc.getRecent(dc, Item.HARDWARE, currentSubtype);
  List<Software> recentSoftware = (List<Software>)cc.getRecent(dc, Item.SOFTWARE, 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\"";
  JspContext jspContext = ExtensionsControl.createContext(dc, pageContext, GuiContext.item(itemType), bioAssay);
  ExtensionsInvoker invoker = EditUtil.useEditExtensions(jspContext);
  %>
  <base:page type="popup" title="<%=title%>">
  <base:head scripts="tabcontrol.js,annotations.js,platforms.js,subtypes.js,ajax.js,json2.js" styles="tabcontrol.css">
    <ext:scripts context="<%=jspContext%>" />
    <ext:stylesheets context="<%=jspContext%>" />
    <script language="JavaScript">
    // Validate the "BioAssay" tab
    function validateBioAssay()
    {
      var frm = document.forms['bioAssay'];
      if (Main.trimString(frm.name.value) == '')
      {
        alert("You must enter a name");
        frm.name.focus();
        return false;
      }
      if (frm.isRoot)
      {
        if (frm.isRoot[0].checked)
        {
          if (frm.physicalbioassay_id.selectedIndex < 0)
          {
            alert("You must select a parent bioassay");
            frm.physicalbioassay_id.focus();
            return false;
          }
        }
        else
        {
          if (frm.parent_id.selectedIndex < 0)
          {
            alert("You must select a parent bioassay");
            frm.parent_id.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);
        }
        if (dataFilesLoaded)
        {
          Platforms.addDataFilesToForm(frames.datafiles, frm);
        }
        if (frm.isRoot)
        {
          if (frm.isRoot[0].checked)
          {
            frm.parent_id.selectedIndex = -1; 
          }
          else
          {
            frm.physicalbioassay_id.selectedIndex = -1;
          }
        }
        frm.submit();
      }
    }
    
    var annotationsLoaded = false;
    var inheritedAnnotationsLoaded = false;
    var parentsChanged = false;
    var protocolChanged = false;
    var dataFilesLoaded = 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;
        }
        else if (tabId == 'datafiles' && (!dataFilesLoaded))
        {
          //var platform = Platforms.getSelectedPlatform(frm.platform);
          //var variant = Platforms.getSelectedVariant(frm.platform);
          Platforms.loadDataFilesFrame(frames.datafiles, '<%=ID%>', '<%=itemType.name()%>', <%=itemId%>, 0, 0);
          dataFilesLoaded = true;
        }
      }
    }
    
    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'];
      if (!frm.physicalbioassay_id) return;
      
      var parents = new Array();
      if (frm.isRoot[0].checked)
      {
        var bioAssayId = Math.abs(parseInt(frm.physicalbioassay_id[frm.physicalbioassay_id.selectedIndex].value));
        if (bioAssayId > 0) parents[parents.length] = 'PHYSICALBIOASSAY:'+bioAssayId;
      }
      else
      {
        var bioAssayId = Math.abs(parseInt(frm.parent_id[frm.parent_id.selectedIndex].value));
        if (bioAssayId > 0) parents[parents.length] = 'DERIVEDBIOASSAY:'+bioAssayId;
      }
      return parents;
    }
    
    function subtypeOnChange()
    {
      var frm = document.forms['bioAssay'];
      var subtypeId = ItemSubtype.getSubtypeId('bioAssay');
      var recentInfo = ItemSubtype.getRecentAndRelatedInfo(subtypeId, 'BIOASSAY', ['PROTOCOL', 'HARDWARE', 'SOFTWARE']);
      protocolChanged = ItemSubtype.updateRecentItemsInList(frm.protocol_id, recentInfo.PROTOCOL['recent']);
      ItemSubtype.updateDefaultItemsInList(frm.protocol_id, recentInfo.PROTOCOL['default']);
      ItemSubtype.updateRecentItemsInList(frm.hardware_id, recentInfo.HARDWARE['recent']);
      ItemSubtype.updateDefaultItemsInList(frm.hardware_id, recentInfo.HARDWARE['default']);
      ItemSubtype.updateRecentItemsInList(frm.software_id, recentInfo.SOFTWARE['recent']);
      ItemSubtype.updateDefaultItemsInList(frm.software_id, recentInfo.SOFTWARE['default']);
    }

    
    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 selectPhysicalBioAssayOnClick()
    {
      var frm = document.forms['bioAssay'];
      var url = '../physicalbioassays/index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectone';
      url += '&callback=setPhysicalBioAssayCallback&resetTemporary=1';
      url += ItemSubtype.createRelatedFilter('bioAssay', 'PHYSICALBIOASSAY');
      if (frm.physicalbioassay_id.selectedIndex >= 0) 
      {
        var id = Math.abs(parseInt(frm.physicalbioassay_id[frm.physicalbioassay_id.selectedIndex].value));        
        url += '&item_id='+id;
      }
      Main.openPopup(url, 'SelectPhysicalBioAssay', 1000, 700);
    }
    function setPhysicalBioAssayCallback(id, name)
    {
      var frm = document.forms['bioAssay'];
      var list = frm.physicalbioassay_id;
      if (list.length < 1 || list[0].value == '0') // >
      {
        Forms.addListOption(list, 0, new Option());
      }
      list[0].value = id;
      list[0].text = name;
      list.selectedIndex = 0;
      physicalBioAssayOnChange();
    }
    function physicalBioAssayOnChange()
    {
      parentsChanged = true;
      var frm = document.forms['bioAssay'];
      initExtracts();
    }
    
    function selectParentBioAssayOnClick()
    {
      var frm = document.forms['bioAssay'];
      var url = 'index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectone';
      url += '&callback=setParentBioAssayCallback&resetTemporary=1';
      url += ItemSubtype.createRelatedFilter('bioAssay', 'DERIVEDBIOASSAY');
      if (frm.parent_id.selectedIndex >= 0) 
      {
        var id = Math.abs(parseInt(frm.physicalbioassay_id[frm.parent_id.selectedIndex].value));        
        url += '&item_id='+id;
      }
      Main.openPopup(url, 'SelectParentBioAssay', 1000, 700);
    }
    function setParentBioAssayCallback(id, name)
    {
      var frm = document.forms['bioAssay'];
      var list = frm.parent_id;
      if (list.length < 1 || list[0].value == '0') // >
      {
        Forms.addListOption(list, 0, new Option());
      }
      list[0].value = id;
      list[0].text = name;
      list.selectedIndex = 0;
      parentsChanged = true;
    }
    function parentBioAssayOnChange()
    {
      parentsChanged = 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 selectSoftwareOnClick()
    {
      var frm = document.forms['bioAssay'];
      var url = '../../admin/software/index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectone';
      url += '&callback=setSoftwareCallback&resetTemporary=1';
      url += ItemSubtype.createRelatedFilter('bioAssay', 'SOFTWARE');
      if (frm.software_id.length > 1)
      {
        var id = Math.abs(parseInt(frm.software_id[1].value));        
        url += '&item_id='+id;
      }
      Main.openPopup(url, 'SelectSoftware', 1000, 700);
    }
    function setSoftwareCallback(id, name)
    {
      var frm = document.forms['bioAssay'];
      var list = frm.software_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 init()
    {
      var frm = document.forms['bioAssay'];
      <%
      if (bioAssay == null)
      {
        %>
        frm.name.focus();
        frm.name.select();
        <%
      }
      %>
      if (frm.isRoot) 
      {
        isRootOnChange();
      }
      else
      {
        initExtracts();
      }
    }
    
    function isRootOnChange()
    {
      var frm = document.forms['bioAssay'];
      var isRoot = frm.isRoot[0].checked;
      Main.showHide('physicalBioAssaySection', isRoot);
      Main.showHide('parentBioAssaySection', !isRoot);
      initExtracts();
    }
    
    function initExtracts()
    {
      var frm = document.forms['bioAssay'];
      frm.extract_id.length = 0;
      var extracts;
      <%
      if (bioAssay == null)
      {
        %>
        if (frm.isRoot[0].checked)
        {
          extracts = getExtractsFromPhysicalBioAssay(frm.physicalbioassay_id[frm.physicalbioassay_id.selectedIndex].value);
        }
        else
        {
          extracts = getExtractsFromParentBioassay(frm.parent_id[frm.parent_id.selectedIndex].value);
        }
        <%
      }
      else
      {
        if (currentParentBioAssay != null)
        {
          %>
          extracts = getExtractsFromParentBioassay(<%=currentParentBioAssay.getId()%>);
          <%
        }
        else if (currentPhysicalBioAssay != null)
        {
          %>
          extracts = getExtractsFromPhysicalBioAssay(<%=currentPhysicalBioAssay.getId()%>);
          <%
        }
      }
      %>

      var frm = document.forms['bioAssay'];
      frm.extract_id.length = 0;
      frm.extract_id[frm.extract_id.length] = new Option('- none -', 0);
      var currentExtractId = <%=currentExtract == null ? 0 : currentExtract.getId()%>;
      var currentWasFound = 0;
      for (var i = 0; i < extracts.length; i++)
      {
        var position = extracts[i].position;
        var prefix = position ? position + ': ' : '';
        frm.extract_id[frm.extract_id.length] = new Option(prefix + extracts[i].name, extracts[i].id);
        if (currentExtractId == extracts[i].id) 
        {
          frm.extract_id.selectedIndex = frm.extract_id.length - 1;
          currentWasFound = 1;
        }
      }
      <%
      if (currentExtract != null)
      {
        %>
        if (currentExtractId && !currentWasFound)
        {
          frm.extract_id[frm.extract_id.length] = new Option('<%=HTML.javaScriptEncode(currentExtract.getName())%>', currentExtractId);
          frm.extract_id.selectedIndex = frm.extract_id.length - 1;
        }
        <%
      }
      %>
    }
    
    function getExtractsFromPhysicalBioAssay(physicalBioAssayId)
    {
      var request = Ajax.getXmlHttpRequest();
      var url = '../physicalbioassays/ajax.jsp?ID=<%=ID%>&cmd=GetSources';
      url += '&item_id=' + physicalBioAssayId;
      request.open("GET", url, false); 
      request.send(null);
      
      var response = JSON.parse(request.responseText);
      if (response.status != 'ok')
      {
        alert(response.message);
        return;
      }
      return response.sources;
    }
  
    function getExtractsFromParentBioassay(bioAssayId)
    {
      var request = Ajax.getXmlHttpRequest();
      var url = 'ajax.jsp?ID=<%=ID%>&cmd=GetExtracts';
      url += '&item_id=' + bioAssayId;
      request.open("GET", url, false); 
      request.send(null);

      var response = JSON.parse(request.responseText);
      if (response.status != 'ok')
      {
        alert(response.message);
        return;
      }
      
      return response.sources;
    }
    </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="<%=bioAssay != null%>" switch="switchTab"
      extensions="<%=invoker%>">
    <t:tab id="info" title="Bioassay" validate="validateBioAssay()" helpid="derivedbioassay.edit">
      <table class="form" cellspacing=0>
      <tr>
        <td class="prompt" width="120px">Name</td>
        <td><input <%=requiredClazz%> type="text" name="name" 
          value="<%=HTML.encodeTags(bioAssay == null ? Values.getString(cc.getPropertyValue("name"), "New derived bioassay") : bioAssay.getName())%>" 
          size="40" maxlength="<%=DerivedBioAssay.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 && bioAssay != null ? -id : id%>" 
                <%=id == currentSubtypeId ? "selected" : ""%>
                title="<%=HTML.encodeTags(subtype.getDescription()) %>"
                ><%=HTML.encodeTags(subtype.getName())%>
              <%
            }
          }
          %>
          </select>
        </td>
      </tr>
      <%
      if (bioAssay == null)
      {
        %>
        <tr>
          <td class="prompt">Parent type</td>
          <td>
            <input id="isRoot" type="radio" name="isRoot" value="1" 
              <%=currentParentBioAssay == null ? "checked" : "" %>
              onchange="isRootOnChange()"><label for="isRoot">Physical bioassay</label>
            <input id="isChild" type="radio" name="isRoot" value="0"
              <%=currentParentBioAssay == null ? "" : "checked" %>
              onchange="isRootOnChange()"><label for="isChild">Derived bioassay</label><br>
          </td>
        </tr>
        <tr id="physicalBioAssaySection" style="display: none;">
          <td class="subprompt">-physical bioassay</td>
          <td>
            <base:select 
              id="physicalbioassay_id"
              clazz="selectionlist unchangeable"
              required="true"
              current="<%=currentPhysicalBioAssay%>"
              recent="<%=recentPhysicalBioAssays%>"
              newitem="true"
              onselect="selectPhysicalBioAssayOnClick()"
              onchange="physicalBioAssayOnChange()"
            />
          </td>
        </tr>
        <tr id="parentBioAssaySection" style="display: none;">
          <td class="subprompt">-bioassay</td>
          <td>
            <base:select 
              id="parent_id"
              clazz="selectionlist unchangeable"
              required="true"
              current="<%=currentParentBioAssay%>"
              recent="<%=recentParentBioAssays%>"
              newitem="true"
              onselect="selectParentBioAssayOnClick()"
              onchange="parentBioAssayOnChange()"
            />
          </td>
        </tr>
        <%
      }
      %>
      <tr>
        <td class="prompt">Extract</td>
        <td>
          <select name="extract_id" class="selectionlist"></select>
        </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="<%=bioAssay == 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%>"
            defaultitems="<%=defaultHardware%>"
            newitem="<%=bioAssay == null%>"
            onselect="selectHardwareOnClick()"
          />
        </td>
      </tr>
      <tr>
        <td class="prompt">Software</td>
        <td>
          <base:select 
            id="software_id"
            clazz="selectionlist"
            required="false"
            current="<%=currentSoftware%>"
            denied="<%=!readCurrentSoftware%>"
            recent="<%=recentSoftware%>"
            defaultitems="<%=defaultSoftware%>"
            newitem="<%=bioAssay == null%>"
            onselect="selectSoftwareOnClick()"
          />
        </td>
      </tr>

      <tr valign=top>
        <td class="prompt">Description</td>
        <td nowrap>
          <textarea <%=clazz%> rows="4" cols="40" name="description" wrap="virtual"
            ><%=HTML.encodeTags(bioAssay == null ? cc.getPropertyValue("description") : bioAssay.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>
      <%if (bioAssay == null) {%><br>
        <i><base:icon image="unchangeable.gif" /> = can't be changed later</i>
      <%}%>
      </div>
    </t:tab>

    <t:tab id="datafiles" title="Data files" helpid="datafiles.edit">
      <iframe name="datafiles" id="idDatafiles" src="../../../common/datafiles/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="annotations" title="Annotations" 
      helpid="annotations.edit" tooltip="Enter values for annotations">
      <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();
}
%>