source: trunk/www/views/rawbioassays/edit_rawbioassay.jsp @ 5687

<%-- $Id: edit_rawbioassay.jsp 5687 2011-08-09 11:39:40Z nicklas $
  ------------------------------------------------------------------
  Copyright (C) 2005 Nicklas Nordborg
  Copyright (C) 2006 Jari Häkkinen, Nicklas Nordborg, Martin Svensson
  Copyright (C) 2007 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/>.
  ------------------------------------------------------------------


  @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.RawBioAssay"
  import="net.sf.basedb.core.Platform"
  import="net.sf.basedb.core.PlatformVariant"
  import="net.sf.basedb.core.Protocol"
  import="net.sf.basedb.core.Project"
  import="net.sf.basedb.core.Software"
  import="net.sf.basedb.core.ArrayDesign"
  import="net.sf.basedb.core.Extract"
  import="net.sf.basedb.core.DerivedBioAssay"
  import="net.sf.basedb.core.ItemSubtype"
  import="net.sf.basedb.core.File"
  import="net.sf.basedb.core.RawDataType"
  import="net.sf.basedb.core.RawDataTypes"
  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.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.core.Include"
  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"
%>
<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
<%@ taglib prefix="t" uri="/WEB-INF/tab.tld" %>
<%
final Item itemType = Item.RAWBIOASSAY;
final SessionControl sc = Base.getExistingSessionControl(pageContext, true);
final ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, null, null);
final String tabId = Values.getString(request.getParameter("tab"), 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;
  RawBioAssay rawBioAssay = null;
  String name = null;
  boolean hasDbSpots = false;

  boolean deniedPlatform = false;
  Platform currentPlatform = null;
  List<Platform> defaultPlatforms = null;
  PlatformVariant currentVariant = null;
  List<PlatformVariant> defaultVariants = null;
  
  boolean readCurrentBioAssay = true;
  DerivedBioAssay currentBioAssay = null;
  boolean readCurrentExtract = true;
  Extract currentExtract = null;
  boolean readCurrentProtocol = true;
  Protocol currentProtocol = null;
  List<Protocol> defaultProtocols = null;
  boolean readCurrentSoftware = true;
  Software currentSoftware = null;
  List<Software> defaultSoftware = null;
  boolean readCurrentArrayDesign = true;
  ArrayDesign currentArrayDesign = null;
  List<ArrayDesign> defaultArrayDesigns = null;
  RawDataType currentRawDataType = null;
  RawDataType defaultRawDataType = null;

  // Load recently used items
  List<Protocol> recentProtocols = (List<Protocol>)cc.getRecent(dc, Item.PROTOCOL);
  List<Software> recentSoftware = (List<Software>)cc.getRecent(dc, Item.SOFTWARE);
  List<ArrayDesign> recentArrayDesigns = (List<ArrayDesign>)cc.getRecent(dc, Item.ARRAYDESIGN);
  List<File> recentFiles = (List<File>)cc.getRecent(dc, Item.FILE);
  List<DerivedBioAssay> recentBioAssays = (List<DerivedBioAssay>)cc.getRecent(dc, Item.DERIVEDBIOASSAY);
  List<Extract> recentExtracts = (List<Extract>)cc.getRecent(dc, Item.EXTRACT);
  
  int activeProjectId = sc.getActiveProjectId();
  if (activeProjectId > 0)
  {
    Project activeProject = Project.getById(dc, activeProjectId);
    try
    {
      defaultProtocols = (List<Protocol>)activeProject.findDefaultItems(dc, 
          ItemSubtype.getById(dc, SystemItems.getId(Protocol.FEATURE_EXTRACTION)), false);
    }
    catch (PermissionDeniedException pdex)
    {}
    try
    {
      defaultSoftware = (List<Software>)activeProject.findDefaultItems(dc, 
          ItemSubtype.getById(dc, SystemItems.getId(Software.FEATURE_EXTRACTION)), false);
    }
    catch (PermissionDeniedException pdex)
    {}
    try
    {
      defaultArrayDesigns = (List<ArrayDesign>)activeProject.findDefaultItems(dc, Item.ARRAYDESIGN, true);
    }
    catch (PermissionDeniedException pdex)
    {}
    try
    {
      defaultPlatforms = (List<Platform>)activeProject.findDefaultItems(dc, Item.PLATFORM, true);
    }
    catch (PermissionDeniedException pdex)
    {}
    try
    {
      defaultVariants = (List<PlatformVariant>)activeProject.findDefaultItems(dc, Item.PLATFORMVARIANT, true);
    }
    catch (PermissionDeniedException pdex)
    {}
    defaultRawDataType = activeProject.getDefaultRawDataType();
  }
  if (itemId == 0)
  {
    title = "Create raw bioassay";
    cc.removeObject("item");
    
    int currentPlatformId = Values.getInt(cc.getPropertyValue("platform"), 0);
    if (currentPlatformId == 0)
    {
      currentPlatformId = Values.getInt(cc.getRecent(Item.PLATFORM.name(), 0), 0);
    }
    int currentVariantId = Values.getInt(cc.getRecent(Item.PLATFORMVARIANT.name(), 0), 0);
    
    try
    {
      if (currentVariantId != 0) currentVariant = PlatformVariant.getById(dc, currentVariantId);
      if (currentPlatformId != 0) currentPlatform = Platform.getById(dc, currentPlatformId);
    }
    catch (Throwable t)
    {}
    if (currentPlatform == null && defaultPlatforms.size() > 0) 
    {
      currentPlatform = defaultPlatforms.get(0);
    }
    if (currentVariant == null && defaultVariants.size() > 0)
    {
      currentVariant = defaultVariants.get(0);
    }
    
    currentRawDataType = RawDataTypes.getRawDataType(cc.getPropertyValue("rawDataType"));
    if (currentRawDataType == null)
    {
      currentRawDataType = RawDataTypes.getRawDataType(cc.getRecent("RawDataType", 0));
    }
    if (currentRawDataType == null) currentRawDataType = defaultRawDataType;

    
    int bioAssayId = Values.getInt(request.getParameter("bioassay_id"));
    if (bioAssayId != 0)
    {
      currentBioAssay = DerivedBioAssay.getById(dc, bioAssayId);
    }
    else if (cc.getPropertyFilter("derivedBioAssay.name") != null)
    {
      currentBioAssay = Base.getFirstMatching(dc, DerivedBioAssay.getQuery(), "name", cc.getPropertyFilter("derivedBioAssay.name"));
    }

    if (currentBioAssay != null)
    {
      name = currentBioAssay.getName() + ".r" + (currentBioAssay.countRawBioAssays() + 1);
    }
    else
    {
      name = Values.getString(cc.getPropertyValue("name"), "New raw bioassay");
    }

    if (cc.getPropertyFilter("protocol.name") != null)
    {
      currentProtocol = Base.getFirstMatching(dc, Protocol.getQuery(), "name", cc.getPropertyFilter("protocol.name"));
    }
    
    if (cc.getPropertyFilter("software.name") != null)
    {
      currentSoftware = Base.getFirstMatching(dc, Software.getQuery(), "name", cc.getPropertyFilter("software.name"));
    }

    if (currentBioAssay != null)
    {
      try
      {
        currentArrayDesign = currentBioAssay.getArrayDesign();
      }
      catch (PermissionDeniedException ex)
      {}
      try
      {
        currentExtract = currentBioAssay.getExtract();
      }
      catch (PermissionDeniedException ex)
      {}
    }
    if (currentArrayDesign == null && cc.getPropertyFilter("arrayDesign.name") != null)
    {
      currentArrayDesign = Base.getFirstMatching(dc, ArrayDesign.getQuery(), "name", cc.getPropertyFilter("arrayDesign.name"));
    }
  }
  else
  {
    rawBioAssay = RawBioAssay.getById(dc, itemId);
    rawBioAssay.checkPermission(Permission.WRITE);
    hasDbSpots = rawBioAssay.getNumDbSpots() > 0;
    cc.setObject("item", rawBioAssay);
    name = rawBioAssay.getName();
    try
    {
      currentRawDataType = rawBioAssay.getRawDataType();
    }
    catch (Throwable t)
    {}
    title = "Edit raw bioassay -- " + HTML.encodeTags(rawBioAssay.getName());
    
    try
    {
      currentPlatform = rawBioAssay.getPlatform();
      currentVariant = rawBioAssay.getVariant();
    }
    catch (PermissionDeniedException ex)
    {
      deniedPlatform = true;
    }
    
    try
    {
      currentBioAssay = rawBioAssay.getParentBioAssay();
    }
    catch (PermissionDeniedException ex)
    {
      readCurrentBioAssay = false;
    }
    try
    {
      currentExtract = rawBioAssay.getParentExtract();
    }
    catch (PermissionDeniedException ex)
    {
      readCurrentExtract = false;
    }
    try
    {
      currentProtocol = rawBioAssay.getProtocol();
    }
    catch (PermissionDeniedException ex)
    {
      readCurrentProtocol = false;
    }
    try
    {
      currentSoftware = rawBioAssay.getSoftware();
    }
    catch (PermissionDeniedException ex)
    {
      readCurrentSoftware = false;
    }
    try
    {
      currentArrayDesign = rawBioAssay.getArrayDesign();
    }
    catch (PermissionDeniedException ex)
    {
      readCurrentArrayDesign = false;
    }
  }
  
  ItemQuery<Platform> platformQuery = Platform.getQuery();
  platformQuery.include(Include.REMOVED, Include.NOT_REMOVED);
  platformQuery.order(Orders.asc(Hql.property("name")));
  platformQuery.setCacheResult(true);
  ItemResultList<Platform> platforms = platformQuery.list(dc);

  ItemQuery<PlatformVariant> variantQuery = PlatformVariant.getQuery();
  variantQuery.include(Include.REMOVED, Include.NOT_REMOVED);
  variantQuery.order(Orders.asc(Hql.property("name")));
  variantQuery.setCacheResult(true);
  ItemResultList<PlatformVariant> variants = variantQuery.list(dc);
  
  final String clazz = "class=\"text\"";
  final String requiredClazz = "class=\"text required\"";
  JspContext jspContext = ExtensionsControl.createContext(dc, pageContext, GuiContext.item(itemType), rawBioAssay);
  ExtensionsInvoker invoker = EditUtil.useEditExtensions(jspContext);
  %>
  <base:page type="popup" title="<%=title%>">
  <base:head scripts="tabcontrol.js,annotations.js,platforms.js,ajax.js,json2.js" styles="tabcontrol.css">
    <ext:scripts context="<%=jspContext%>" />
    <ext:stylesheets context="<%=jspContext%>" />
    <script language="JavaScript">
    // Validate the "RawBioAssay" tab
    function validateRawBioAssay()
    {
      var frm = document.forms['rawbioassay'];
      if (Main.trimString(frm.name.value) == '')
      {
        alert("You must enter a name");
        frm.name.focus();
        return false;
      }
      return true;
    }

    // Submit the form
    function saveSettings()
    {
      var frm = document.forms['rawbioassay'];
      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);
        }
        frm.submit();
      }
    }
    
    var annotationsLoaded = false;
    var inheritedAnnotationsLoaded = false;
    var parentsChanged = false;
    var protocolChanged = false;
    var dataFilesLoaded = false;
    var platformChanged = false;
    function switchTab(tabControlId, tabId)
    {
      var frm = document.forms['rawbioassay'];
      if (TabControl.setActiveTab(tabControlId, tabId))
      {
        if (tabId == 'annotations' && (protocolChanged || !annotationsLoaded))
        {
          Annotations.loadAnnotateFrame(frames.annotations, '<%=ID%>', '<%=itemType.name()%>', <%=rawBioAssay == null ? 0 : rawBioAssay.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;
        }
        else if (tabId == 'datafiles' && (platformChanged || !dataFilesLoaded))
        {
          var platform = Platforms.getSelectedPlatform(frm.platform);
          var variant = Platforms.getSelectedVariant(frm.platform);
          Platforms.loadDataFilesFrame(frames.datafiles, '<%=ID%>', '<%=itemType.name()%>', <%=rawBioAssay == null ? 0 : rawBioAssay.getId()%>, platform == null ? 0 : platform.id, variant == null ? 0 : variant.id);
          dataFilesLoaded = true;
          platformChanged = false;
        }
      }
    }

    function platformOnChange()
    {
      var frm = document.forms['rawbioassay'];
      platformChanged = true;
      var platform = Platforms.getSelectedPlatform(frm.platform);
      var variant = Platforms.getSelectedVariant(frm.platform);
      var fileOnly = (variant != null && variant.fileOnly) || 
        (variant == null && platform.fileOnly);
      var rawDataType = variant == null ? platform.rawDataType : variant.rawDataType;
      if (frm.rawdatatype[frm.rawdatatype.length - 1].value == '')
      {
        frm.rawdatatype[frm.rawdatatype.length - 1] = null;
      }
      if (fileOnly)
      {
        frm.rawdatatype.disabled = true;
        Main.removeClass(frm.rawdatatype, 'required');
        frm.rawdatatype[frm.rawdatatype.length] = new Option('- file only -', '');
        frm.rawdatatype.selectedIndex = frm.rawdatatype.length - 1;
      }
      else if (rawDataType)
      {
        frm.rawdatatype.disabled = true;
        Main.removeClass(frm.rawdatatype, 'required');
        Forms.selectListOption(frm.rawdatatype, rawDataType);
      }
      else
      {
        frm.rawdatatype.disabled = <%=hasDbSpots ? "true" : "false"%>;
        Main.addClass(frm.rawdatatype, 'required');
      }
    }

    function getProtocolId()
    {
      var frm = document.forms['rawbioassay'];
      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['rawbioassay'];
      var parents = new Array();

      var bioAssayId = Math.abs(parseInt(frm.bioassay_id[frm.bioassay_id.selectedIndex].value));
      if (bioAssayId > 0) parents[parents.length] = 'DERIVEDBIOASSAY:'+bioAssayId;
      var extractId = Math.abs(parseInt(frm.bioassay_id[frm.extract_id.selectedIndex].value));
      if (extractId > 0) parents[parents.length] = 'EXTRACT:'+extractId;
      if (frm.arraydesign_id)
      {
        var arrayDesignId = Math.abs(parseInt(frm.arraydesign_id[frm.arraydesign_id.selectedIndex].value));
        if (arrayDesignId > 0) parents[parents.length] = 'ARRAYDESIGN:'+arrayDesignId;
      }
      return parents;
    }

    function selectProtocolOnClick()
    {
      var frm = document.forms['rawbioassay'];
      var url = '../../admin/protocols/index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectone&callback=setProtocolCallback';
      if (frm.protocol_id.length > 1) 
      {
        var id = Math.abs(parseInt(frm.protocol_id[1].value));
        url += '&item_id='+id;
      }
      url += '&resetTemporary=1&tmpfilter:INT:itemSubtype=<%=SystemItems.getId(Protocol.FEATURE_EXTRACTION)%>';
      Main.openPopup(url, 'SelectProtocol', 1000, 700);
    }
    function setProtocolCallback(id, name)
    {
      var frm = document.forms['rawbioassay'];
      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 bioAssayOnChange()
    {
      var frm = document.forms['rawbioassay'];
      var selectedIndex = frm.bioassay_id.selectedIndex
      var bioAssayId = frm.bioassay_id[selectedIndex].value;
      if (bioAssayId > 0) updateArrayDesign(bioAssayId);
      parentsChanged = true;
    }
    function selectBioAssayOnClick()
    {
      var frm = document.forms['rawbioassay'];
      var url = '../derivedbioassays/index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectone&callback=setBioAssayCallback';
      if (frm.bioassay_id.length > 1) 
      {
        var id = Math.abs(parseInt(frm.bioassay_id[1].value));
        url += '&item_id='+id;
      }
      Main.openPopup(url, 'SelectDerivedBioAssay', 1000, 700);
    }
    function setBioAssayCallback(id, name)
    {
      var frm = document.forms['rawbioassay'];
      var list = frm.bioassay_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;
      updateArrayDesign(id)
      parentsChanged = true;
    }

    
    function selectSoftwareOnClick()
    {
      var frm = document.forms['rawbioassay'];
      var url = '../../admin/software/index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectone&callback=setSoftwareCallback';
      if (frm.software_id.length > 1)
      {
        var id = Math.abs(parseInt(frm.software_id[1].value));        
        url += '&item_id='+id;
      }
      url += '&resetTemporary=1&tmpfilter:INT:itemSubtype=<%=SystemItems.getId(Software.FEATURE_EXTRACTION)%>';
      Main.openPopup(url, 'SelectSoftware', 1000, 700);
    }
    function setSoftwareCallback(id, name)
    {
      var frm = document.forms['rawbioassay'];
      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 arrayDesignOnChange()
    {
      parentsChanged = true;
      <%
      if (rawBioAssay != null && rawBioAssay.getNumDbSpots() > 0)
      {
        %>
        var frm = document.forms['rawbioassay'];
        var selectedId = frm.arraydesign_id[frm.arraydesign_id.selectedIndex].value;
        var showFiMethod = (selectedId > 0 && selectedId != <%=currentArrayDesign == null ? 0 : currentArrayDesign.getId()%>);
        if (showFiMethod)
        {
          Main.show('fiMethod');
        }
        else
        {
          Main.hide('fiMethod');
        }
        <%
      }
      %>
    }
    function selectArrayDesignOnClick()
    {
      var frm = document.forms['rawbioassay'];
      var url = '../../lims/arraydesigns/index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectone&callback=setArrayDesignCallback';
      if (frm.arraydesign_id.length > 1) 
      {
        var id = Math.abs(parseInt(frm.arraydesign_id[1].value));       
        url += '&item_id='+id;
      }
      var platform = Platforms.getSelectedPlatform(frm.platform);
      url += '&resetTemporary=1&tmpfilter:INT:platform='+platform.id;
      Main.openPopup(url, 'SelectArrayDesign', 1000, 700);
    }
    function setArrayDesignCallback(id, name)
    {
      var frm = document.forms['rawbioassay'];
      var list = frm.arraydesign_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;
      parentsChanged = true;
      arrayDesignOnChange();
    }
    
    function updateArrayDesign(bioAssayId)
    {
      var request = Ajax.getXmlHttpRequest();
      if (request != null)
      {
        var url = '../derivedbioassays/ajax.jsp?ID=<%=ID%>&cmd=GetArrayDesign&item_id=' + bioAssayId;
        request.open("GET", url, true);
        Ajax.setReadyStateHandler(request, updateArrayDesignCallback);
        request.send(null);
      }
      return request != null;
    }
    function updateArrayDesignCallback(request)
    {
      var frm = document.forms['rawbioassay'];
      var response = Ajax.parseJsonResponse(request.responseText);
      if (response.status != 'ok')
      {
        alert(response.message);
        return false;
      }
      
      if (response.id)
      {
        var designList = frm.arraydesign_id;
        if (designList.length < 2 || designList[1].value == '0') // >
        {
          Forms.addListOption(designList, 1, new Option());
        }
        designList[1].value = response.id;
        designList[1].text = response.name;
        designList.selectedIndex = 1;
      }
    }

    function init()
    {
      <%
      if (rawBioAssay == null)
      {
        %>
        var frm = document.forms['rawbioassay'];
        frm.name.focus();
        frm.name.select();
        <%
      }
      %>
      initPlatforms(<%=currentPlatform == null ? 0 : currentPlatform.getId()%>, <%=currentVariant == null ? 0 : currentVariant.getId()%>);
      platformOnChange();
    }
    
    function initPlatforms(platformId, variantId)
    {
      <%
      for (Platform p : platforms)
      {
        if (!p.isRemoved() || p.equals(currentPlatform))
        {
          RawDataType rdt = p.isFileOnly() ? null : p.getRawDataType();
          %>
          var p<%=p.getId()%> = new Platform(<%=p.getId()%>, '<%=HTML.javaScriptEncode(p.getExternalId())%>', '<%=HTML.javaScriptEncode(p.getName())%>', <%=p.isFileOnly()%>, '<%=rdt == null ? "" : rdt.getId()%>');
          <%
        }
      }
      for (PlatformVariant v : variants)
      {
        Platform p = v.getPlatform();
        if ((!v.isRemoved() || v.equals(currentVariant)) && (!p.isRemoved() || p.equals(currentPlatform)))
        {
          RawDataType rdt = v.isFileOnly() ? null : v.getRawDataType();
          %>
          var v<%=v.getId()%> = new Variant(p<%=p.getId()%>, <%=v.getId()%>, '<%=HTML.javaScriptEncode(v.getExternalId())%>', '<%=HTML.javaScriptEncode(v.getName())%>', <%=v.isFileOnly()%>, '<%=rdt == null ? "" : rdt.getId()%>');
          <%
        }
      }
      %>
      var frm = document.forms['rawbioassay'];
      Platforms.populateList(frm.platform, platformId, variantId);
    }
    </script>
  </base:head>
  <base:body onload="init()">
    <p>
    <form action="index.jsp?ID=<%=ID%>" method="post" name="rawbioassay" 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" active="<%=tabId%>" remember="<%=tabId == null && rawBioAssay != null%>" switch="switchTab"
      extensions="<%=invoker%>">
    <t:tab id="info" title="Raw bioassay" validate="validateRawBioAssay()" helpid="rawbioassay.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="<%=RawBioAssay.MAX_NAME_LENGTH%>"></td>
      </tr>
      <tr>
        <td class="prompt">Platform</td>
        <td>
          <select name="platform" onchange="platformOnChange()" class="required"
            <%=deniedPlatform || hasDbSpots ? "disabled" : "" %>>
          <%
          if (deniedPlatform)
          {
            %>
            <option value="-1">- denied -
            <%
          }
          %>
          </select>
        </td>
      </tr>
      <tr>
        <td class="prompt">Raw data type</td>
        <td>
          <select name="rawdatatype" class="required"
            <%=hasDbSpots ? "disabled" : "" %>>
          <%
          for (RawDataType rdt : RawDataTypes.getSortedRawDataTypes(new RawDataTypes.NameComparator()))
          {
            if (rdt.isStoredInDb())
            {
              String selected = rdt.equals(currentRawDataType) ? "selected" : "";
              %>
              <option value="<%=rdt.getId()%>" <%=selected%>><%=HTML.encodeTags(rdt.getName())%>
              <%
            }
          }
          %>
          </select>
        </td>
      </tr>
      <tr>
        <td class="prompt">Parent bioassay</td>
        <td>
          <base:select 
            id="bioassay_id"
            clazz="selectionlist"
            required="false"
            current="<%=currentBioAssay%>"
            denied="<%=!readCurrentBioAssay%>"
            recent="<%=recentBioAssays%>"
            newitem="<%=rawBioAssay == null%>"
            onselect="selectBioAssayOnClick()"
            onchange="bioAssayOnChange()"
          />
        </td>
      </tr>
      <tr>
        <td class="prompt">Parent extract</td>
        <td>
          <base:select 
            id="extract_id"
            clazz="selectionlist"
            required="false"
            current="<%=currentExtract%>"
            denied="<%=!readCurrentExtract%>"
            recent="<%=recentExtracts%>"
            newitem="<%=rawBioAssay == null%>"
            onselect="selectExtractOnClick()"
            onchange="extractOnChange()"
          />
        </td>
      </tr>
      <tr>
        <td class="prompt">Array design</td>
        <td>
          <base:select 
            id="arraydesign_id"
            clazz="selectionlist"
            required="false"
            current="<%=currentArrayDesign%>"
            denied="<%=!readCurrentArrayDesign%>"
            recent="<%=recentArrayDesigns%>"
            defaultitems="<%=defaultArrayDesigns%>"
            newitem="<%=rawBioAssay == null%>"
            onselect="selectArrayDesignOnClick()"
            onchange="arrayDesignOnChange()"
          />
        </td>
      </tr>
      <tr id="fiMethod" style="display: none;">
        <td></td>
        <td>
        <select name="fiMethod">
        <option value="">-auto- (array design decides)
        <option value="COORDINATES">Coordinates
        <option value="POSITION">Position
        <option value="FEATURE_ID">Feature ID (*)
        </select>
        <br>
        Select a method for feature identification. <br>
        (*) The Feature ID method only works if the raw data is currently
        connected to an array design which has Feature ID values.
        </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="<%=rawBioAssay == null%>"
            onselect="selectProtocolOnClick()"
            onchange="protocolOnChange()"
          />
        </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="<%=rawBioAssay == 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(rawBioAssay == null ? cc.getPropertyValue("description") : rawBioAssay.getDescription())%></textarea>
          <a href="javascript:Main.zoom('Description', 'rawbioassay', '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="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 &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();
}
%>