source: trunk/www/views/rawbioassays/edit_spotimages.jsp @ 6217

<%-- $Id: edit_spotimages.jsp 6217 2012-12-14 13:05:00Z nicklas $
  ------------------------------------------------------------------
  Copyright (C) 2006 Jari Häkkinen, 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.SystemItems"
  import="net.sf.basedb.core.ItemContext"
  import="net.sf.basedb.core.Permission"
  import="net.sf.basedb.core.RawBioAssay"
  import="net.sf.basedb.core.SpotImages"
  import="net.sf.basedb.core.File"
  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 = "Create spot images";
  RawBioAssay rawBioAssay = RawBioAssay.getById(dc, itemId);
  SpotImages spi = rawBioAssay.getSpotImages();

  if (!rawBioAssay.hasPermission(Permission.WRITE))
  {
    throw new PermissionDeniedException(Permission.WRITE, itemType.toString());
  }
  boolean readRedImageFile = true;
  boolean readGreenImageFile = true;
  boolean readBlueImageFile = true;
  boolean readSpotImagesFile = true;
  File redImageFile = null;
  File greenImageFile = null;
  File blueImageFile = null;
  File spotImagesFile = null;
  try
  {
    redImageFile = spi.getRedImageFile();
  }
  catch (PermissionDeniedException ex)
  {
    readRedImageFile = false;
  }
  try
  {
    greenImageFile = spi.getGreenImageFile();
  }
  catch (PermissionDeniedException ex)
  {
    readGreenImageFile = false;
  }
  try
  {
    blueImageFile = spi.getBlueImageFile();
  }
  catch (PermissionDeniedException ex)
  {
    readBlueImageFile = false;
  }
  try
  {
    spotImagesFile = spi.getSpotImagesFile();
  }
  catch (PermissionDeniedException ex)
  {
    readSpotImagesFile = false;
  }
  
  
  
  %>

  <base:page type="popup" title="<%=title%>">
  <base:head scripts="tabcontrol.js,annotations.js" styles="tabcontrol.css">
    <script>
    // Validate the "RawBioAssay" tab
    function validateSpotImages()
    {
      var frm = document.forms['spotimages'];
      
      return true;
    }
    function selectRedFileOnClick()
    {
      var frm = document.forms['spotimages'];
      var url = '../../filemanager/index.jsp?ID=<%=ID%>&cmd=SelectOne&callback=setRedFileCallback';
      url += '&resetTemporary=1&tmpfilter:INT:itemSubtype=<%=SystemItems.getId(File.IMAGE)%>';
      if (frm.redfile_id.length > 1) url += '&item_id='+frm.redfile_id[1].value;
      Main.openPopup(url, 'SelectRedFile', 1050, 700);
    }
    function setRedFileCallback(fileId, name)
    {
      var frm = document.forms['spotimages'];
      if (frm.redfile_id.length < 2) // >
      {
        frm.redfile_id[frm.redfile_id.length] = new Option();
      }
      frm.redfile_id[1].value = fileId;
      frm.redfile_id[1].text = name;
      frm.redfile_id.selectedIndex = 1;
    }

    function selectGreenFileOnClick()
    {
      var frm = document.forms['spotimages'];
      var url = '../../filemanager/index.jsp?ID=<%=ID%>&cmd=SelectOne&callback=setGreenFileCallback';
      url += '&resetTemporary=1&tmpfilter:INT:itemSubtype=<%=SystemItems.getId(File.IMAGE)%>';
      if (frm.greenfile_id.length > 1) url += '&item_id='+frm.greenfile_id[1].value;
      Main.openPopup(url, 'SelectGreenFile', 1050, 700);
    }
    function setGreenFileCallback(fileId, name)
    {
      var frm = document.forms['spotimages'];
      if (frm.greenfile_id.length < 2) // >
      {
        frm.greenfile_id[frm.greenfile_id.length] = new Option();
      }
      frm.greenfile_id[1].value = fileId;
      frm.greenfile_id[1].text = name;
      frm.greenfile_id.selectedIndex = 1;
    }
    
    function selectBlueFileOnClick()
    {
      var frm = document.forms['spotimages'];
      var url = '../../filemanager/index.jsp?ID=<%=ID%>&cmd=SelectOne&callback=setBlueFileCallback';
      url += '&resetTemporary=1&tmpfilter:INT:itemSubtype=<%=SystemItems.getId(File.IMAGE)%>';
      if (frm.bluefile_id.length > 1) url += '&item_id='+frm.bluefile_id[1].value;
      Main.openPopup(url, 'SelectBlueFile', 1050, 700);
    }
    function setBlueFileCallback(fileId, name)
    {
      var frm = document.forms['spotimages'];
      if (frm.bluefile_id.length < 2) // >
      {
        frm.bluefile_id[frm.bluefile_id.length] = new Option();
      }
      frm.bluefile_id[1].value = fileId;
      frm.bluefile_id[1].text = name;
      frm.bluefile_id.selectedIndex = 1;
    }

    function browseOnClick()
    {
      Main.openPopup('../../filemanager/index.jsp?ID=<%=ID%>&cmd=SaveAs&callback=setSaveAsCallback', 'SaveAs', 1050, 700);
    }
    function setSaveAsCallback(path)
    {
      var frm = document.forms['spotimages'];
      frm.path.value = path;
    }

    // Submit the form
    function saveSettings()
    {
      var frm = document.forms['spotimages'];
      frm.submit();
    }
    </script>
  </base:head>
  <base:body>
    <h1><%=title%> <base:help helpid="rawbioassay.edit.spotimages" /></h1>
    <form action="index.jsp?ID=<%=ID%>" method="post" name="spotimages">
    <input type="hidden" name="item_id" value="<%=itemId%>">
    <input type="hidden" name="cmd" value="CreateSpotImages">

    <div class="content filled bottomborder">
      <table class="fullform input100">
      <tbody class="sectionheader">
        <tr>
          <th colspan="4">Scale, offset, etc. for the spots</th>
        </tr>
      </tbody>
      <tbody>
      <tr>
        <th>X scale</th>
        <td><input type="text" class="text required" name="x_scale" style="width: 8em;"
          value="<%=spi.getXScale()%>" maxlength="10" 
          onkeypress="return Numbers.integerOnly(event)"></td>

        <th class="leftborder">Y scale</th>
        <td><input type="text" class="text required" name="y_scale" style="width: 8em;"
          value="<%=spi.getYScale()%>" maxlength="10" 
          onkeypress="return Numbers.integerOnly(event)"></td>
      </tr>
      <tr>
        <th>X offset</th>
        <td><input type="text" class="text required" name="x_offset" style="width: 8em;"
          value="<%=spi.getXOffset()%>" maxlength="10" 
          onkeypress="return Numbers.integerOnly(event)"></td>

        <th class="leftborder">Y offset</th>
        <td><input type="text" class="text required" name="y_offset" style="width: 8em;"
          value="<%=spi.getYOffset()%>" maxlength="10" 
          onkeypress="return Numbers.integerOnly(event)"></td>
      </tr>
      <tr>
        <th>Spot size</th>
        <td><input type="text" class="text required" name="spotsize" style="width: 8em;"
          value="<%=spi.getSpotsize()%>" maxlength="10" 
          onkeypress="return Numbers.integerOnly(event)"></td>

        <th class="leftborder">Gamma correction</th>
        <td><input type="text" class="text required" name="gamma" style="width: 8em;"
          value="<%=spi.getGamma()%>" maxlength="10" 
          onkeypress="return Numbers.numberOnly(event)"></td>
      </tr>
      <tr>
        <th>Quality</th>
        <td><input type="text" class="text required" name="quality" style="width: 8em;"
          value="<%=spi.getQuality()%>" maxlength="10" 
          onkeypress="return Numbers.integerOnly(event)"></td>
        <th class="leftborder"></th>
        <td></td>
      </tr>
      </tbody>
      <tbody class="sectionheader">
        <tr>
          <th colspan="4">Raw image files</th>
        </tr>
      </tbody>
      <tbody>
      <tr>
        <th>Red image file</th>
        <td colspan="3">
          <table>
          <tr>
          <td>
            <select name="redfile_id" style="width: 25em;">
              <option value="0">- none -
              <%
              if (redImageFile != null)
              {
                %>
                <option value="<%=redImageFile.getId()%>" selected><%=HTML.encodeTags(redImageFile.getPath().toString())%>
                <%
              }
              %>
            </select>
          </td>
          <td><base:button onclick="selectRedFileOnClick()" title="Select&hellip;" /></td>
          </tr>
          </table>
        </td>
      </tr>

      <tr>
        <th>Green image file</th>
        <td colspan="3">
          <table>
          <tr>
          <td>
            <select name="greenfile_id" style="width: 25em;">
              <option value="0">- none -
              <%
              if (greenImageFile != null)
              {
                %>
                <option value="<%=greenImageFile.getId()%>" selected><%=HTML.encodeTags(greenImageFile.getPath().toString())%>
                <%
              }
              %>
            </select>
          </td>
          <td><base:button onclick="selectGreenFileOnClick()" title="Select&hellip;" /></td>
          </tr>
          </table>
        </td>
      </tr>

      <tr>
        <th>Blue image file</th>
        <td colspan="3">
          <table>
          <tr>
          <td>
            <select name="bluefile_id" style="width: 25em;">
              <option value="0">- none -
              <%
              if (blueImageFile != null)
              {
                %>
                <option value="<%=blueImageFile.getId()%>" selected><%=HTML.encodeTags(blueImageFile.getPath().toString())%>
                <%
              }
              %>
            </select>
          </td>
          <td><base:button onclick="selectBlueFileOnClick()" title="Select&hellip;" /></td>
          </tr>
          </table>
        </td>
      </tr>
      
      <tr >
        <th>Save as</th>
        <td colspan="3">
          <table style="width: 100%;">
          <tr>
          <td style="width: 98%;"><input type="text" class="text required" 
            name="path" 
            value="<%=spotImagesFile == null ? "" : HTML.encodeTags(spotImagesFile.getPath().toString())%>"></td>
          <td ><base:button 
              title="Browse..."
              onclick="browseOnClick()"
              />
          </td>
          </tr>
          </table>
        </td>
      </tr>
      <tr>
        <th class="subprompt"></th>
        <td colspan="3"><input type="checkbox" name="overwrite" id="overwrite" value="1"><label for="overwrite">Overwrite existing file</label></td>
      </tr>
      <tr class="dynamic">
        <th></th>
        <td colspan="3"></td>
      </tr>
      </tbody>
      </table>
    </div>
    </form>

    <div class="legend">
      <base:icon image="required.png" />= required information
    </div>

    <base:buttongroup subclass="dialogbuttons">
      <base:button onclick="saveSettings()" title="Create" image="ok.png"/>
      <base:button onclick="window.close()" title="Cancel" />
    </base:buttongroup>
  </base:body>
  </base:page>
  <%
}
finally
{
  if (dc != null) dc.close();
}
%>