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

<%-- $Id: launch_mev.jsp 2209 2014-02-03 07:36:18Z nicklas $
  ------------------------------------------------------------------
  Copyright (C) 2009 Nicklas Nordborg

  This file is part of the MeV Launcher extension for BASE.
  Available at http://baseplugins.thep.lu.se/
  BASE main site: http://base.thep.lu.se/
  -----------------------------------------------------------
  
  This 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.
  
  The software 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 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%>" id="mev-launch">
<base:head scripts="~scripts/mev.js" />
<base:body>
  <h1><%=title%></h1>
  
  <div id="page-data" class="datacontainer"
    data-bioassayset-id="<%=bioAssaySetId%>"
  ></div>

  <form name="mev">
  <div class="content bottomborder">

  <table class="fullform">
    <tbody class="sectionheader">
      <tr>
        <th colspan="2">MeV analysis file</th>
      </tr>
    </tbody>
    <tbody>
      <tr>
        <td style="padding-bottom: 1em;"><base:button 
          title="Start MeV" 
          subclass="auto-init"
          data-auto-init="start-mev"
          data-mev-file-type="mev.anl"
          image="<%=homeUrl + "/images/tm4.png" %>" 
          disabled="<%=anlFile == null%>"/></td>
        <td style="padding-bottom: 1em;">
        <%
        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>
    </tbody>
    <tbody class="sectionheader">
      <tr>
        <th colspan="2">TDMS - Tab-delimited multiple sample</th>
      </tr>
    </tbody>
    <tbody>
      <tr>
        <td><base:button 
          title="Start MeV" 
          subclass="auto-init"
          data-auto-init="start-mev"
          data-mev-file-type="mev.tdms"
          image="<%=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 style="padding-bottom: 1em;"><base:button 
          id="export-tdms"
          title="Export" 
          disabled="<%=!allowCreateFile%>" 
          data-job-name="<%=HTML.encodeTags(tdmsJobName) %>"
          data-save-as="<%=HTML.encodeTags(defaultPath+defaultTdmsFileName)%>"
          image="export.png" /></td>
        <td style="padding-bottom: 1em;">
        <%
        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>
    </tbody>
    <tbody class="sectionheader">
      <tr>
        <th colspan="2">CGH - Comparative genomics hybridization</th>
      </tr>
    </tbody>
    <tbody>
      <tr>
        <td><base:button 
          title="Start MeV" 
          subclass="auto-init"
          data-auto-init="start-mev"
          data-mev-file-type="mev.cgh"
          image="<%=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 
          id="export-cgh"
          title="Export" 
          disabled="<%=!canCreateCGHFile%>" 
          data-job-name="<%=HTML.encodeTags(cghJobName) %>"
          data-save-as="<%=HTML.encodeTags(defaultPath+defaultCghFileName)%>"
          image="export.png" /></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>
        <%
      }
      %>
    </tbody>
    <tr class="dynamic">
      <td></td>
      <td></td>
    </tr>
  </table>
  </div>
  </form>

  <base:buttongroup subclass="dialogbuttons">
    <base:button id="close" title="Close" />
  </base:buttongroup>

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