source: extensions/net.sf.basedb.mev/trunk/resources/launch_mev.jsp @ 1395

<%-- $Id: launch_mev.jsp 1395 2011-09-15 12:58:04Z nicklas $
  ------------------------------------------------------------------
  Copyright (C) 2009 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 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 Jari, Nicklas
--%>
<%@ page 
  pageEncoding="UTF-8"
  session="false"
  import="net.sf.basedb.core.Application"
  import="net.sf.basedb.core.BioAssaySet"
  import="net.sf.basedb.core.Experiment"
  import="net.sf.basedb.core.Directory"
  import="net.sf.basedb.core.File"
  import="net.sf.basedb.core.User"
  import="net.sf.basedb.core.DbControl"
  import="net.sf.basedb.core.SessionControl"
  import="net.sf.basedb.core.ItemContext"
  import="net.sf.basedb.core.Item"
  import="net.sf.basedb.core.Include"
  import="net.sf.basedb.core.Permission"
  import="net.sf.basedb.core.Path"
  import="net.sf.basedb.core.FileStoreUtil"
  import="net.sf.basedb.core.ItemQuery"
  import="net.sf.basedb.core.PluginConfiguration"
  import="net.sf.basedb.core.query.Restrictions"
  import="net.sf.basedb.core.query.Expressions"
  import="net.sf.basedb.core.query.Hql"
  import="net.sf.basedb.core.query.Orders"
  import="net.sf.basedb.clients.web.Base"
  import="net.sf.basedb.clients.web.util.HTML"
  import="net.sf.basedb.clients.web.extensions.ExtensionsControl"
  import="net.sf.basedb.util.Values"
  import="java.util.List"
%>
<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
<%!
// Get an attached file or null in case there is some kind of error
private File safeGetFile(DbControl dc, BioAssaySet bas, String fileType)
{
  File file = null;
  try
  {
    file = FileStoreUtil.getDataFile(dc, bas, fileType, false);
  }
  catch (Throwable t)
  {}
  return file;
}
%>
<%
final SessionControl sc = Base.getExistingSessionControl(request, true);
final String ID = sc.getId();
final int bioAssaySetId = Values.getInt(request.getParameter("bioassayset_id"));
final String title = "Launch MeV";
final String homeUrl = ExtensionsControl.getHomeUrl("net.sf.basedb.mev.launchmev");
final String root = request.getContextPath()+"/";

DbControl dc = null;
String defaultPath = "/";

try
{
  dc = sc.newDbControl();
  BioAssaySet bas = BioAssaySet.getById(dc, bioAssaySetId);
  ItemContext cc = sc.getCurrentContext(Item.BIOASSAYSET);
  cc.setId(bioAssaySetId);

  // Get the current files
  File tdmsFile = safeGetFile(dc, bas, "mev.tdms");
  File cghFile = safeGetFile(dc, bas, "mev.cgh");
  File anlFile = safeGetFile(dc, bas, "mev.anl");
  boolean allowCreateFile = bas.hasPermission(Permission.WRITE)
    && sc.hasPermission(Permission.CREATE, Item.FILE);
  
  // Get the avilable CGH export configurations
  ItemQuery<PluginConfiguration> cghQuery = PluginConfiguration.getQuery();
  cghQuery.restrict(Restrictions.eq(
      Hql.property("pluginDefinition.className"),
      Expressions.string("net.sf.basedb.mev.plugin.CghExporterPlugin")));
  cghQuery.order(Orders.asc(Hql.property("name")));
  cghQuery.include(Include.MINE, Include.IN_PROJECT, Include.SHARED, Include.OTHERS);
  List<PluginConfiguration> cghConfigurations = cghQuery.list(dc);
  boolean canCreateCGHFile = cghConfigurations.size() > 0;
  
  // Default names of export files and export jobs
  String defaultTdmsFileName = Path.makeSafeFilename(bas.getName() + "-" + bas.getId() + ".tdms.txt", "");
  String defaultCghFileName = Path.makeSafeFilename(bas.getName() + "-" + bas.getId() + ".cgh.txt", "");
  String tdmsJobName = "Create TDMS file for " + bas.getName();
  String cghJobName = "Create CGH file for " + bas.getName();
  
  // Default home directory of either experiment or user
  try
  {
    Experiment exp = bas.getExperiment();
    Directory dir = exp.getDirectory();
    if (dir == null)
    {
      User user = User.getById(dc, sc.getLoggedInUserId());
      dir = user.getHomeDirectory();
    }
    if (dir != null)
    {
      defaultPath = dir.getPath().toString() + "/";
    }
  }
  catch (Throwable t)
  {}
%>
<base:page type="popup" title="<%=title%>">
<base:head>
  <script language="JavaScript">
  function launchMev(fileType)
  {
    var url = 'mev_jnlp.jsp?ID=<%=ID%>&bioassayset_id=<%=bioAssaySetId%>';
    url += '&filetype=' + fileType;
    window.opener.location.href = url;
    setTimeout('window.close()', 500);
  }
  function exportTdms()
  {
    var url = getRoot()+'common/plugin/index.jsp?ID='+getSessionId();
    url += '&cmd=NewJob&plugin_class=net.sf.basedb.mev.plugin.TdmsExporterPlugin';
    url += '&item_type=BIOASSAYSET&context_type=ITEM';
    url += '&job_name=' + encodeURIComponent('<%=HTML.javaScriptEncode(tdmsJobName)%>');
    url += '&parameter:saveAs='+encodeURIComponent('<%=HTML.javaScriptEncode(defaultPath+defaultTdmsFileName)%>');
    url += '&parameter:attachToBioAssaySet=true';
    Main.openPopup(url, 'CreateTDMSFile', 740, 540);
    window.close();
  }
  function exportCgh()
  {
    var frm = document.forms['mev'];
    var url = getRoot()+'common/plugin/index.jsp?ID='+getSessionId();
    url += '&cmd=NewJob&plugin_class=net.sf.basedb.mev.plugin.CghExporterPlugin';
    url += '&pluginconfiguration_id=' + frm.cgh_configuration[frm.cgh_configuration.selectedIndex].value;
    url += '&item_type=BIOASSAYSET&context_type=ITEM';
    url += '&job_name=' + encodeURIComponent('<%=HTML.javaScriptEncode(cghJobName)%>');
    url += '&parameter:saveAs='+encodeURIComponent('<%=HTML.javaScriptEncode(defaultPath+defaultCghFileName)%>');
    url += '&parameter:attachToBioAssaySet=true';
    Main.openPopup(url, 'CreateCGHFile', 740, 540);
    window.close();
  }
  </script>
</base:head>
<base:body>

  <form name="mev">
  <h3><%=title%></h3>
  <div class="boxedbottom">
  <table class="form">
  <tr>
    <td class="prompt" colspan="2">MeV analysis file</td>
  </tr>
  <tr>
    <td><base:button title="Start MeV" 
      onclick="launchMev('mev.anl')" 
      image="<%=anlFile == null ? homeUrl + "/images/tm4_disabled.png" : homeUrl + "/images/tm4.png" %>" 
      disabled="<%=anlFile == null%>"/></td>
    <td>
    <%
    if (anlFile == null)
    {
      %>
      There is currently no MeV analysis file associated with the bioassay set.
      <%
    }
    else
    {
      %>
      Start MeV with the current analysis file:<br>
      <%=HTML.encodeTags(anlFile.getName())%> <%=Base.getFileLinks(ID, anlFile, root) %>
      <%
    }
    %>
    </td>
  </tr>
  <tr>
    <td class="prompt" colspan="2">TDMS - Tab-delimited multiple sample</td>
  </tr>
  <tr>
    <td><base:button title="Start MeV" 
      onclick="launchMev('mev.tdms')" 
      image="<%=tdmsFile == null ? homeUrl + "/images/tm4_disabled.png" : homeUrl + "/images/tm4.png" %>" 
      disabled="<%=tdmsFile == null%>"/></td>
    <td>
    <%
    if (tdmsFile == null)
    {
      %>
      There is currently no TDMS file associated with the bioassay set.
      <%
    }
    else
    {
      %>
      Start MeV with the current TDMS file:<br>
      <%=HTML.encodeTags(tdmsFile.getName())%> <%=Base.getFileLinks(ID, tdmsFile, root) %>
      <%
    }
    %>
    </td>
  </tr>
  <tr>
    <td><base:button title="Export" 
      onclick="exportTdms()"
      disabled="<%=!allowCreateFile%>" 
      image="<%=allowCreateFile ? "export.gif" : homeUrl + "/images/export_disabled.gif"%>" /></td>
    <td>
    <%
    if (allowCreateFile)
    {
      %>
      Export the spot data to a MeV TDMS file that can be opened with MeV.
      <%
    }
    else
    {
      %>
      You don't have enough permissions to create a MeV TDSM file.
      <%
    }
    %>
    </td>
  </tr>
  <tr>
    <td class="prompt" colspan="2">CGH - Comparative genomics hybridization</td>
  </tr>
  <tr>
    <td><base:button title="Start MeV" 
      onclick="launchMev('mev.cgh')" 
      image="<%=cghFile == null ? homeUrl + "/images/tm4_disabled.png" : homeUrl + "/images/tm4.png" %>" 
      disabled="<%=cghFile == null%>"/></td>
    <td>
    <%
    if (cghFile == null)
    {
      %>
      There is currently no CGH file associated with the bioassay set.
      <%
    }
    else
    {
      %>
      Start MeV with the current CGH file:<br>
      <%=HTML.encodeTags(cghFile.getName())%> <%=Base.getFileLinks(ID, cghFile, root) %>
      <%
    }
    %>
    </td>
  </tr>
  <tr>
    <td><base:button title="Export" 
      onclick="exportCgh()" 
      disabled="<%=!canCreateCGHFile%>" 
      image="<%=canCreateCGHFile ? "export.gif" : homeUrl + "/images/export_disabled.gif"%>" /></td>
    <td>
    <%
    if (canCreateCGHFile)
    {
      %>
      Export the spot data to a MeV CGH file that can be opened with MeV.
      <%
    }
    else
    {
      %>
      You don't have enough permissions to create a MeV CGH file.
      <%
    }
    %>
    </td>
  </tr>
  <%
  if (canCreateCGHFile)
  {
    %>
    <tr>
      <td style="text-align: right;">-configuration</td>
      <td>
        <select name="cgh_configuration">
        <%
        for (PluginConfiguration cfg : cghConfigurations)
        {
          %>
          <option value="<%=cfg.getId()%>"><%=HTML.encodeTags(cfg.getName())%>
          <%
        }
        %>
        </select>
      </td>
    </tr>
    <%
  }
  %>
  </table>
  </div>
  </form>

  <table align="center">
  <tr>
    <td><base:button onclick="window.close();" title="Close" /></td>
  </tr>
  </table>

</base:body>
</base:page>
  <%
}
finally
{
  if (dc != null) dc.close();
}
%>