source: trunk/www/views/rawbioassays/edit_rawbioassay.jsp @ 3523

<%-- $Id: edit_rawbioassay.jsp 3523 2007-06-20 12:32:41Z nicklas $
  ------------------------------------------------------------------
  Copyright (C) Authors contributing to this file.

  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 2
  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 this program; if not, write to the Free Software
  Foundation, Inc., 59 Temple Place - Suite 330,
  Boston, MA  02111-1307, USA.
  ------------------------------------------------------------------


  @author Nicklas
  @version 2.0
--%>
<%@ page 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.Affymetrix"
  import="net.sf.basedb.core.Scan"
  import="net.sf.basedb.core.Protocol"
  import="net.sf.basedb.core.ProtocolType"
  import="net.sf.basedb.core.Project"
  import="net.sf.basedb.core.Software"
  import="net.sf.basedb.core.SoftwareType"
  import="net.sf.basedb.core.ArrayDesign"
  import="net.sf.basedb.core.File"
  import="net.sf.basedb.core.FileType"
  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.clients.web.Base"
  import="net.sf.basedb.clients.web.util.HTML"
  import="net.sf.basedb.util.Values"
  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 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 readCurrentCelFile = true;
  File currentCelFile = null; 
  boolean readCurrentScan = true;
  Scan currentScan = null;
  boolean readCurrentProtocol = true;
  Protocol currentProtocol = null;
  Protocol defaultProtocol = null;
  boolean readCurrentSoftware = true;
  Software currentSoftware = null;
  Software defaultSoftware = null;
  boolean readCurrentArrayDesign = true;
  ArrayDesign currentArrayDesign = null;
  ArrayDesign defaultArrayDesign = null;
  RawDataType currentRawDataType = null;
  RawDataType defaultRawDataType = null;

  // Load recently used items
  List<Protocol> recentProtocols = (List<Protocol>)cc.getRecent(dc, Item.PROTOCOL);
  List<Scan> recentScans = (List<Scan>)cc.getRecent(dc, Item.SCAN);
  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);
  
  int activeProjectId = sc.getActiveProjectId();
  if (activeProjectId > 0)
  {
    Project activeProject = Project.getById(dc, activeProjectId);
    try
    {
      defaultProtocol = (Protocol)activeProject.getDefaultItem(dc, Project.Default.FEATURE_EXTRACTION_PROTOCOL);      
    }
    catch (PermissionDeniedException pdex)
    {
      defaultProtocol = null;
    }
    try
    {
      defaultSoftware = (Software)activeProject.getDefaultItem(dc, Project.Default.SOFTWARE);     
    }
    catch (PermissionDeniedException pdex)
    {
      defaultSoftware = null;
    }
    try
    {
      defaultArrayDesign = (ArrayDesign)activeProject.getDefaultItem(dc, Project.Default.ARRAYDESIGN);      
    }
    catch (PermissionDeniedException pdex)
    {
      defaultArrayDesign = null;
    }
    defaultRawDataType = activeProject.getDefaultRawDataType();
  }
  if (itemId == 0)
  {
    title = "Create raw bioassay";
    cc.removeObject("item");
    currentRawDataType = RawDataTypes.getRawDataType(cc.getPropertyValue("rawDataType"));
    if (currentRawDataType == null)
    {
      currentRawDataType = RawDataTypes.getRawDataType(cc.getRecent("RawDataType", 0));
    }

    int scanId = Values.getInt(request.getParameter("scan_id"));
    if (scanId != 0)
    {
      currentScan = Scan.getById(dc, scanId);
    }
    else if (cc.getPropertyFilter("scan.name") != null)
    {
      currentScan = Base.getFirstMatching(dc, Scan.getQuery(), "name", cc.getPropertyFilter("scan.name"));
    }

    if (currentScan != null)
    {
      name = currentScan.getName() + ".r" + (currentScan.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 (currentScan != null)
    {
      try
      {
        currentArrayDesign = currentScan.getArrayDesign();
      }
      catch (PermissionDeniedException ex)
      {}
    }
    if (currentArrayDesign == null && cc.getPropertyFilter("arrayDesign.name") != null)
    {
      currentArrayDesign = Base.getFirstMatching(dc, ArrayDesign.getQuery(), "name", cc.getPropertyFilter("arrayDesign.name"));
    } 
    currentRawDataType = currentRawDataType != null ? currentRawDataType : defaultRawDataType;
  }
  else
  {
    rawBioAssay = RawBioAssay.getById(dc, itemId);
    cc.setObject("item", rawBioAssay);
    name = rawBioAssay.getName();
    currentRawDataType = rawBioAssay.getRawDataType();
    title = "Edit raw bioassay -- " + HTML.encodeTags(rawBioAssay.getName());
    
    if (currentRawDataType.isAffymetrix())
    {
      try
      {
        currentCelFile = Affymetrix.getCelFile(rawBioAssay);
      }
      catch (PermissionDeniedException ex)
      {
        readCurrentCelFile = false;
      }
    }
    
    try
    {
      currentScan = rawBioAssay.getScan();
    }
    catch (PermissionDeniedException ex)
    {
      readCurrentScan = 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;
    }
  }
  if (rawBioAssay != null) rawBioAssay.checkPermission(Permission.WRITE);
  final String clazz = "class=\"text\"";
  final String requiredClazz = "class=\"text required\"";
  %>

  <base:page type="popup" title="<%=title%>">
  <base:head scripts="tabcontrol.js,annotations.js" styles="tabcontrol.css">
    <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;
      }
      if (frm.rawdatatype)
      {
        var rawDataType = frm.rawdatatype[frm.rawdatatype.selectedIndex].value;
        if (isAffymetrix[rawDataType])
        {
          var celFileId = frm.celfile_id[frm.celfile_id.selectedIndex].value;
          var arrayDesignId = frm.arraydesign_id[frm.arraydesign_id.selectedIndex].value;
          if (celFileId != 0 && arrayDesignId == 0)
          {
            alert('You must select an array design if a CEL file is specified');
            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);
        }
        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()%>', <%=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;
        }
      }
    }
    
    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 scanId = Math.abs(parseInt(frm.scan_id[frm.scan_id.selectedIndex].value));
      if (scanId > 0) parents[parents.length] = 'SCAN:'+scanId;
      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 += '&filter:INT:protocolType=<%=SystemItems.getId(ProtocolType.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 scanOnChange()
    {
      parentsChanged = true;
    }
    function selectScanOnClick()
    {
      var frm = document.forms['rawbioassay'];
      var url = '../scans/index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectone&callback=setScanCallback';
      if (frm.scan_id.length > 1) 
      {
        var id = Math.abs(parseInt(frm.scan_id[1].value));
        url += '&item_id='+id;
      }
      Main.openPopup(url, 'SelectScan', 1000, 700);
    }
    function setScanCallback(id, name)
    {
      var frm = document.forms['rawbioassay'];
      var list = frm.scan_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;
    }
    
    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 += '&filter:INT:softwareType=<%=SystemItems.getId(SoftwareType.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;
    }
    function selectArrayDesignOnClick()
    {
      var frm = document.forms['rawbioassay'];
      var url = '../../lims/arraydesigns/index.jsp?ID=<%=ID%>&mode=selectone&callback=setArrayDesignCallback';
      if (frm.arraydesign_id.length > 1) 
      {
        var id = Math.abs(parseInt(frm.arraydesign_id[1].value));       
        url += '&item_id='+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;
    }
    
    var isAffymetrix = new Array();
    <%
    for (RawDataType rdt : RawDataTypes.getRawDataTypes())
    {
      %>
      isAffymetrix['<%=rdt.getId()%>'] = <%=rdt.isAffymetrix() ? "true" : "false" %>;
      <%
    }
    %>
    
    function selectCelFileOnClick()
    {
      var frm = document.forms['rawbioassay'];
      
      if (frm.rawdatatype)
      {
        var rawDataType = frm.rawdatatype[frm.rawdatatype.selectedIndex].value;
        if (!isAffymetrix[rawDataType])
        {
          alert('CEL-files are only used for Affymetrix data types.');
          return;
        }
      }

      var url = '../../filemanager/index.jsp?ID=<%=ID%>&cmd=SelectOne&callback=setCelFileCallback';
      if (frm.celfile_id.length > 1) 
      {
        var id = Math.abs(parseInt(frm.celfile_id[1].value));       
        url += '&item_id='+id;
      }
      url += '&filter:STRING:name=%25.cel';
      Main.openPopup(url, 'SelectFile', 1000, 700);
    }
    function setCelFileCallback(id, name)
    {
      var frm = document.forms['rawbioassay'];
      var list = frm.celfile_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 rawDataTypeOnChange()
    {
      var frm = document.forms['rawbioassay'];
      if (frm.rawdatatype)
      {
        var rawDataType = frm.rawdatatype[frm.rawdatatype.selectedIndex].value;
        if (isAffymetrix[rawDataType])
        {
          frm.celfile_id.disabled = false;
        }
        else
        {
          frm.celfile_id.disabled = true;
        }
      }
    }

    function init()
    {
      <%
      if (rawBioAssay == null)
      {
        %>
        var frm = document.forms['rawbioassay'];
        frm.name.focus();
        frm.name.select();
        <%
      }
      %>
      rawDataTypeOnChange();
    }
    </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"  remember="<%=rawBioAssay != null%>" switch="switchTab">
    <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">Raw data type</td>
        <td>
          <%
          if (rawBioAssay == null || !rawBioAssay.hasData())
          {
            %>
            <select name="rawdatatype" class="required" onchange="rawDataTypeOnChange()">
            <%
            for (RawDataType rdt : RawDataTypes.getRawDataTypes())
            {
              String selected = rdt.equals(currentRawDataType) ? "selected" : "";
              %>
              <option value="<%=rdt.getId()%>" <%=selected%>><%=HTML.encodeTags(rdt.getName())%>
              <%
            }
            %>
            </select>
            <%
          }
          else
          {
            %>
            <%=HTML.encodeTags(currentRawDataType.getName())%>
            <%
          }
          %>
        
        </td>
      </tr>
      
      <tr>
        <td class="prompt">Array design</td>
        <td>
          <%
          //if (rawBioAssay == null || !rawBioAssay.hasData())
          {
            %>
            <base:select 
              id="arraydesign_id"
              clazz="selectionlist"
              required="false"
              current="<%=currentArrayDesign%>"
              denied="<%=!readCurrentArrayDesign%>"
              recent="<%=recentArrayDesigns%>"
              defaultitem="<%=defaultArrayDesign%>"
              newitem="<%=rawBioAssay == null%>"
              onselect="selectArrayDesignOnClick()"
              onchange="arrayDesignOnChange()"
            />
            <%
          }
          /*
          else
          {
            %>
            <%=readCurrentArrayDesign ? 
              (currentArrayDesign != null ? HTML.encodeTags(currentArrayDesign.getName()) : "<i>- none -</i>") 
              : "<i>- denied - </i>"%>
            <%
          }
          */
          %>
        </td>
      </tr>
      <% 
      if (rawBioAssay == null || !rawBioAssay.hasData() || rawBioAssay.getRawDataType().isAffymetrix())
      {
        %>
        <tr id="celFile">
          <td class="prompt">CEL file</td>
          <td>
            <base:select 
              id="celfile_id"
              clazz="selectionlist"
              required="false"
              current="<%=currentCelFile%>"
              denied="<%=!readCurrentCelFile%>"
              recent="<%=recentFiles%>"
              newitem="<%=rawBioAssay == null%>"
              onselect="selectCelFileOnClick()"
            />
          </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="<%=rawBioAssay == null%>"
            onselect="selectProtocolOnClick()"
            onchange="protocolOnChange()"
          />
        </td>
      </tr>
      <tr>
        <td class="prompt">Scan</td>
        <td>
          <base:select 
            id="scan_id"
            clazz="selectionlist"
            required="false"
            current="<%=currentScan%>"
            denied="<%=!readCurrentScan%>"
            recent="<%=recentScans%>"
            newitem="<%=rawBioAssay == null%>"
            onselect="selectScanOnClick()"
          />
        </td>
      </tr>
      <tr>
        <td class="prompt">Software</td>
        <td>
          <base:select 
            id="software_id"
            clazz="selectionlist"
            required="false"
            current="<%=currentSoftware%>"
            denied="<%=!readCurrentSoftware%>"
            recent="<%=recentSoftware%>"
            defaultitem="<%=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="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();
}
%>