source: trunk/www/views/rawbioassays/index.jsp @ 3524

<%-- $Id: index.jsp 3524 2007-06-20 13:01:51Z 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.Application"
  import="net.sf.basedb.core.SessionControl"
  import="net.sf.basedb.core.DbControl"
  import="net.sf.basedb.core.Item"
  import="net.sf.basedb.core.Include"
  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.Software"
  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.User"
  import="net.sf.basedb.core.Path"
  import="net.sf.basedb.core.ItemQuery"
  import="net.sf.basedb.core.ItemResultIterator"
  import="net.sf.basedb.core.Permission"
  import="net.sf.basedb.core.ItemContext"
  import="net.sf.basedb.core.MultiPermissions"
  import="net.sf.basedb.core.PermissionDeniedException"
  import="net.sf.basedb.core.ItemAlreadyExistsException"
  import="net.sf.basedb.core.PluginDefinition"
  import="net.sf.basedb.core.Job"
  import="net.sf.basedb.core.ProgressReporter"
  import="net.sf.basedb.core.IntegerParameterType"
  import="net.sf.basedb.core.FloatParameterType"
  import="net.sf.basedb.core.StringParameterType"
  import="net.sf.basedb.core.FileParameterType"
  import="net.sf.basedb.core.ItemParameterType"
  import="net.sf.basedb.core.BooleanParameterType"
  import="net.sf.basedb.util.RemovableUtil"
  import="net.sf.basedb.util.ShareableUtil"
  import="net.sf.basedb.util.OwnableUtil"
  import="net.sf.basedb.clients.web.Base"
  import="net.sf.basedb.clients.web.WebException"
  import="net.sf.basedb.util.Values"
  import="net.sf.basedb.clients.web.util.HTML"
  import="java.util.Enumeration"
  import="java.util.Set"
  import="java.util.HashSet"
  import="java.util.List"
  import="java.util.ArrayList"
  import="java.util.Arrays"
  import="java.util.Collections"
%>
<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
<%!
  private static final ItemContext defaultContext = Base.createDefaultContext("name", "name,rawDataType,spots,description");
  private static final Item itemType = Item.RAWBIOASSAY;
  
  private static class UpdateArrayDesign
    implements Runnable
  {
    private final int jobId;
    private final int rawBioAssayId;
    private final int arrayDesignId;
    private final SessionControl sc;
    
    private UpdateArrayDesign(Job job, RawBioAssay rba, ArrayDesign design)
    {
      this.jobId = job.getId();
      this.rawBioAssayId = rba.getId();
      this.arrayDesignId = design.getId();
      this.sc = job.getSessionControl();
    }
    
    public void run()
    {
      DbControl dc = sc.newDbControl();
      try
      {
        Job j = Job.getById(dc, jobId);
        j.start("Initialising...", Application.getHostName());
        ProgressReporter progress = j.getProgressReporter(null);
        dc.commit();
        dc = sc.newDbControl();
        RawBioAssay rba = RawBioAssay.getById(dc, rawBioAssayId);
        ArrayDesign design = ArrayDesign.getById(dc, arrayDesignId);
        try
        {
          rba.updateArrayDesign(design, progress);
          progress.display(99, "Committing changes to database...");
          dc.commit();
          dc = sc.newDbControl();
          j = Job.getById(dc, jobId);
          j.doneOk("Array design updated successfully");
          j.setRemoved(true);
          dc.commit();
        }
        catch (Throwable t)
        {
          dc = sc.newDbControl();
          j = Job.getById(dc, jobId);
          j.doneError(t.getMessage(), Arrays.asList(t));
          j.setRemoved(true);
          dc.commit();
        }
      }
      finally
      {
        if (dc != null) dc.close();
      }
    }
  }
%>
<%
final SessionControl sc = Base.getExistingSessionControl(pageContext, true);
final String ID = sc.getId();
final String cmd = request.getParameter("cmd");
final String root = request.getContextPath()+"/";
final String mode = request.getParameter("mode");
final String callback = request.getParameter("callback");
final String itemId = request.getParameter("item_id");
final String listPage = "list_rawbioassays.jsp?ID="+ID
  +(mode == null ? "" : "&mode="+mode)
  +(callback == null ? "" : "&callback="+callback)
  +(itemId == null ? "" : "&item_id="+itemId);
final String viewPage = "view_rawbioassay.jsp?ID="+ID;
final String editPage = "edit_rawbioassay.jsp?ID="+ID;

String forward = null;
String redirect = null;
String message = null;
DbControl dc = null;

try
{
  if (cmd == null || "List".equals(cmd))
  {
    // Display the list page without updatinging the current context
    Base.getAndSetCurrentContext(sc, itemType, null, defaultContext, true);
    redirect = listPage;
  }
  else if ("UpdateContext".equals(cmd))
  {
    // Display the list page after updating the current context from the request parameters
    Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    redirect = listPage;
  }
  else if ("LoadContext".equals(cmd))
  {
    // Display the list page after loading a saved context
    int contextId = Values.getInt(request.getParameter("context"));
    Base.loadContext(sc, contextId, defaultContext);
    redirect = listPage;
  }

  else if ("ViewItem".equals(cmd))
  {
    // Display the view page for a single item 
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    forward = viewPage;
  }
  else if ("EditItem".equals(cmd))
  {
    // Display the edit page for a single item (should be opened in a popup)
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    redirect = editPage;
  }
  else if ("EditSpotImages".equals(cmd))
  {
    // Display the spot images edit page for a single item (should be opened in a popup)
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    redirect = "edit_spotimages.jsp?ID="+ID;
  }
  else if ("NewItem".equals(cmd))
  {
    // Display the edit page for a new item (should be opened in a popup)
    if (!sc.hasPermission(Permission.CREATE, itemType))
    {
      throw new PermissionDeniedException(Permission.CREATE, itemType.toString());
    }
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    cc.setId(0);
    forward = editPage;
  }
  else if ("UpdateItem".equals(cmd))
  {
    // Update the properties on an item (will close the popup)
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, null, defaultContext);
    final int maxRecent = Base.getMaxRecent(sc);
    dc = sc.newDbControl();
    RawBioAssay rba = (RawBioAssay)cc.getObject("item");
    RawDataType rdt = RawDataTypes.getRawDataType(Values.getStringOrNull(request.getParameter("rawdatatype")));
    if (rdt != null) cc.setRecent("RawDataType", rdt.getId(), maxRecent);

    if (rba == null)
    {
      rba = RawBioAssay.getNew(dc, rdt);
      message = "Raw bioassay created";
      dc.saveItem(rba);
    }
    else
    {
      if (rdt != null) rba.setRawDataType(rdt);
      dc.reattachItem(rba);
      message = "Raw bioassay updated";
    }
    rba.setName(Values.getStringOrNull(request.getParameter("name")));
    rba.setDescription(Values.getStringOrNull(request.getParameter("description")));
    int protocolId = Values.getInt(request.getParameter("protocol_id"), -1);
    if (protocolId >= 0)  // < 0 = denied or unchanged
    {
      Protocol pt = protocolId == 0 ? null : Protocol.getById(dc, protocolId);
      rba.setProtocol(pt);
      if (pt != null) cc.setRecent(pt, maxRecent);
    }
    int softwareId = Values.getInt(request.getParameter("software_id"), -1);
    if (softwareId >= 0) // < 0 = denied or unchanged
    {
      Software sw = softwareId == 0 ? null : Software.getById(dc, softwareId);
      rba.setSoftware(sw);
      if (sw != null) cc.setRecent(sw, maxRecent);
    }
    int scanId = Values.getInt(request.getParameter("scan_id"), -1);
    if (scanId >= 0) // < 0 = denied or unchanged
    {
      Scan scan = scanId == 0 ? null : Scan.getById(dc, scanId);
      rba.setScan(scan);
      if (scan != null) cc.setRecent(scan, maxRecent);
    }
    Job job = null;
    ArrayDesign ad = null;
    int arrayDesignId = Values.getInt(request.getParameter("arraydesign_id"), -1);
    if (arrayDesignId >= 0) // < 0 = denied or unchanged
    {
      ad = arrayDesignId == 0 ? null : ArrayDesign.getById(dc, arrayDesignId);
      if (rba.getSpots() > 0)
      {
        if (rba.getRawDataType().isStoredInDb() && ad != null && ad.hasFeatures())
        {
          // Create job and assign it to another thread
          job = Job.getNew(dc, null, null);
          job.setName("Validating array design on " + rba.getName());
          job.setPrepared(Application.getHostName());
          job.setSendMessage(Values.getBoolean(sc.getUserClientSetting("plugins.sendmessage"), false));
          dc.saveItem(job);
        }
        else
        {
          rba.updateArrayDesign(ad, null);
        }
      }
      else
      {
        rba.setArrayDesign(ad);
      }
      if (ad != null) cc.setRecent(ad, maxRecent);
    }
    rdt = rba.getRawDataType();
    if (rdt.isAffymetrix())
    {
      int celFileId = Values.getInt(request.getParameter("celfile_id"), -1);
      if (celFileId >= 0) // < 0 = denied or unchanged
      {
        File celFile = celFileId == 0 ? null : File.getById(dc, celFileId);
        Affymetrix.setCelFile(rba, celFile);
      }
    }

    // Annotations tab
    Base.updateAnnotations(dc, rba, rba, request);
    dc.commit();
    cc.removeObject("item");
    if (job != null) 
    {
      redirect = "../jobs/index.jsp?ID="+ID+"&cmd=ViewItem&item_id="+job.getId();
      Thread updateThread = new Thread(new UpdateArrayDesign(job, rba, ad));
      updateThread.setPriority(Thread.currentThread().getPriority() - 1);
      updateThread.start();
    }
  }
  else if ("DeleteItem".equals(cmd))
  {
    // Delete a single item and then return to the view page
    dc = sc.newDbControl();
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    RemovableUtil.setRemoved(dc, itemType, Collections.singleton(cc.getId()), true);
    dc.commit();
    redirect = viewPage;
  }
  else if ("DeleteItems".equals(cmd))
  {
    // Delete all selected items on the list page
    dc = sc.newDbControl();
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    int numTotal = cc.getSelected().size();
    int numRemoved = RemovableUtil.setRemoved(dc, itemType, cc.getSelected(), true);
    dc.commit();
    if (numTotal != numRemoved)
    {
      message = (numRemoved == 0 ? "No" : "Only "+numRemoved+" of "+numTotal) + " items could be deleted, because you have no DELETE permission";
    }
    redirect = listPage+(message != null ? "&popmessage="+HTML.urlEncode(message) : "");
  }
  else if ("RestoreItem".equals(cmd))
  {
    // Restore a single item and then return to the view page
    dc = sc.newDbControl();
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    RemovableUtil.setRemoved(dc, itemType, Collections.singleton(cc.getId()), false);
    dc.commit();
    redirect = viewPage;
  }
  else if ("RestoreItems".equals(cmd))
  {
    // Restore all selected items on the list page
    dc = sc.newDbControl();
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    int numTotal = cc.getSelected().size();
    int numRemoved = RemovableUtil.setRemoved(dc, itemType, cc.getSelected(), false);
    dc.commit();
    if (numTotal != numRemoved)
    {
      message = (numRemoved == 0 ? "No" : "Only "+numRemoved+" of "+numTotal) + " items could be restored, because you have no WRITE permission";
    }
    redirect = listPage+(message != null ? "&popmessage="+HTML.urlEncode(message) : "");
  }
  else if ("ShareItem".equals(cmd))
  {
    // Display a popup window for sharing a single item
    dc = sc.newDbControl();
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    MultiPermissions permissions = ShareableUtil.getMultiPermissions(dc, itemType, Collections.singleton(cc.getId()));
    dc.close();
    cc.setObject("MultiPermissions", permissions);
    redirect = "../../common/share/share.jsp?ID="+ID+"&item_type="+itemType.name();
  }
  else if ("ShareItems".equals(cmd))
  {
    // Display a popup window for sharing all selected items on the list page
    dc = sc.newDbControl();
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    MultiPermissions permissions = ShareableUtil.getMultiPermissions(dc, itemType, cc.getSelected());
    dc.close();
    cc.setObject("MultiPermissions", permissions);
    redirect = "../../common/share/share.jsp?ID="+ID+"&item_type="+itemType.name();
  }
  else if ("TakeOwnershipOfItem".equals(cmd))
  {
    // Take ownership a single item and then return to the view page
    dc = sc.newDbControl();
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    OwnableUtil.setOwner(dc, itemType, Collections.singleton(cc.getId()), null);
    dc.commit();
    redirect = viewPage;
  }
  else if ("TakeOwnershipOfItems".equals(cmd))
  {
    // Take ownership all selected items on the list page
    dc = sc.newDbControl();
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    int numTotal = cc.getSelected().size();
    int numOwned = OwnableUtil.setOwner(dc, itemType, cc.getSelected(), null);
    dc.commit();
    if (numTotal != numOwned)
    {
      message = (numOwned == 0 ? "No" : "Only "+numOwned+" of "+numTotal) + " items could be taken, because you have no SET_OWNER permission";
    }
    redirect = listPage+(message != null ? "&popmessage="+HTML.urlEncode(message) : "");
  }
  else if ("ExportItems".equals(cmd))
  {
    // Run an export plugin in a list context
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    final ItemQuery<RawBioAssay> query = RawBioAssay.getQuery();
    cc.configureQuery(query, true);
    cc.setQuery(query);
    redirect = "../../common/export/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=LIST&title=Export+raw+bioassays";
  }
  else if ("ExportItem".equals(cmd))
  {
    // Run an export plugin in single-item context
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    redirect = "../../common/export/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=ITEM&title=Export+raw+bioassay";
  }
  else if ("ImportItems".equals(cmd))
  {
    // Run an import plugin in a list context
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    final ItemQuery<RawBioAssay> query = RawBioAssay.getQuery();
    cc.configureQuery(query, true);
    cc.setQuery(query);
    redirect = "../../common/import/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=LIST&title=Import+raw+bioassays";
  }
  else if ("ImportItem".equals(cmd))
  {
    // Run an import plugin in single-item context
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    // Set file type filter
    ItemContext fileContext = sc.getCurrentContext(Item.FILE);
    fileContext.setPropertyFilter(FileType.getPropertyFilter(FileType.RAW_DATA));
    redirect = "../../common/import/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=ITEM&title=Import+raw+bioassay";
  }
  else if ("RunListPlugin".equals(cmd))
  {
    // Run another plugin in a list context
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    final ItemQuery<RawBioAssay> query = RawBioAssay.getQuery();
    cc.configureQuery(query, true);
    cc.setQuery(query);
    redirect = "../../common/plugin/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=LIST&main_type=OTHER&title=Run+plugin";
  }
  else if ("RunPlugin".equals(cmd))
  {
    // Run another plugin in single-item context
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    redirect = "../../common/plugin/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=ITEM&main_type=OTHER&title=Run+plugin";
  }
  else if ("CreateSpotImages".equals(cmd))
  {
    dc = sc.newDbControl();
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    RawBioAssay rba = RawBioAssay.getById(dc, cc.getId());
    
    int redFileId = Values.getInt(request.getParameter("redfile_id"));
    File red = redFileId == 0 ? null : File.getById(dc, redFileId);
    int greenFileId = Values.getInt(request.getParameter("greenfile_id"));
    File green = greenFileId == 0 ? null : File.getById(dc, greenFileId);
    int blueFileId = Values.getInt(request.getParameter("bluefile_id"));
    File blue = blueFileId == 0 ? null : File.getById(dc, blueFileId);

    String path = Values.getStringOrNull(request.getParameter("path"));
    if (path.startsWith("~/"))
    {
      User user = User.getById(dc, sc.getLoggedInUserId());
      path = "~"+user.getLogin()+path.substring(1);
    }
    Path p = new Path(path, Path.Type.FILE);
    File saveAs = File.getByPath(dc, p, true);
    if (saveAs.isInDatabase() && !Values.getBoolean(request.getParameter("overwrite")))
    {
      throw new ItemAlreadyExistsException("File[path="+path+"]");
    }
    
    IntegerParameterType integerParameter = new IntegerParameterType();
    FloatParameterType floatParameter = new FloatParameterType();
    FileParameterType fileParameter = new FileParameterType();
    ItemParameterType<RawBioAssay> itemParameter = new ItemParameterType(RawBioAssay.class, null);
    StringParameterType stringParameter = new StringParameterType();
    BooleanParameterType booleanParameter = new BooleanParameterType();
    
    PluginDefinition plugin = PluginDefinition.getByClassName(dc, "net.sf.basedb.plugins.SpotImageCreator");
    Job job = Job.getNew(dc, plugin, null);
    job.setName("Create spot images for raw bioassay: " + rba.getName());
    job.setParameterValue("rawBioAssay", "Raw bioassay", 
      "The raw bioassay to create spot images for", itemParameter, rba);
    job.setParameterValue("xScale", "X scale factor", 
      "The raw data X value will be divided by this value to get the pixel coordinate", 
      integerParameter, Values.getInt(request.getParameter("x_scale")));
    job.setParameterValue("yScale", "Y scale factor", 
      "The raw data Y value will be divided by this value to get the pixel coordinate", 
      integerParameter, Values.getInt(request.getParameter("y_scale")));
    job.setParameterValue("xOffset", "X offset value",
      "The offset is subtracted from the raw data X value",
      integerParameter, Values.getInt(request.getParameter("x_offset")));
    job.setParameterValue("yOffset", "Y offset value",
      "The offset is subtracted from the raw data Y value",
      integerParameter, Values.getInt(request.getParameter("y_offset")));
    job.setParameterValue("spotsize", "Spot size", "The size of each spot in pixels",
      integerParameter, Values.getInt(request.getParameter("spotsize")));
    job.setParameterValue("gamma", "Gamma", "Gamma correction for display",
      floatParameter, Values.getFloat(request.getParameter("gamma")));
    job.setParameterValue("quality", "Quality", 
      "The quality is a number between 0.0 and 1.0, with 1.0 indicating highest quality.", 
      floatParameter, Values.getFloat(request.getParameter("quality")));
    job.setParameterValue("redFile", "Red image", 
      "The file containing the image to use for the red part", fileParameter, red);
    job.setParameterValue("greenFile", "Green image", 
      "The file containing the image to use for the green part", fileParameter, green);
    job.setParameterValue("blueFile", "Blue image",
      "The file containing the image to use for the red part", fileParameter, blue);
    job.setParameterValue("path", "Save as", 
      "The file name where the spot images should be saved", stringParameter, path);
    job.setParameterValue("overwrite", "Overwrite", 
      "If an existing file should be overwritten or not", booleanParameter, Values.getBoolean(request.getParameter("overwrite")));
    
    dc.saveItem(job);
    dc.commit();

    redirect = "../jobs/index.jsp?ID="+ID+"&cmd=ViewItem&item_id="+job.getId();
  }
  else
  {
    throw new WebException("popup", "Invalid command", "The command {1} is not recognised as a valid command.", cmd);
  }


  /*
  else if ("ImportRawData".equals(cmd))
  {
    RawBioAssay rba = (RawBioAssay)sc.getSessionSetting(itemType.name()+".item");
    ItemContext context = sc.getCurrentContext(itemType);
    context.setId(rba.getId());
    redirect = "../../common/import/configure.jsp?ID="+ID+"&item_type="+itemType.name()+"&context_type=ITEM&title=Import+raw+data+for+"+HTML.urlEncode(rba.getName());

  }
  */
}
finally
{
  if (dc != null) dc.close();
}

if (forward != null)
{
  pageContext.forward(forward);
}
else if (redirect != null)
{
  response.sendRedirect(redirect);
}
else if (message == null)
{
  response.sendRedirect(root + "common/close_popup.jsp?refresh_opener=1&wait=0");
}
else
{
  response.sendRedirect(root + "common/close_popup.jsp?refresh_opener=1&message="+HTML.urlEncode(message));
}
%>