Package org.gvt.action

Source Code of org.gvt.action.QueryPathwaysAction

package org.gvt.action;

import org.biopax.paxtools.io.SimpleIOHandler;
import org.biopax.paxtools.io.pathwayCommons.PathwayCommonsIOHandler;
import org.biopax.paxtools.model.Model;
import org.eclipse.jface.action.Action;
import org.eclipse.jface.dialogs.MessageDialog;
import org.eclipse.jface.resource.ImageDescriptor;
import org.gvt.ChisioMain;
import org.gvt.gui.ItemSelectionDialog;
import org.gvt.gui.StringInputDialog;
import org.gvt.model.biopaxl2.Actor;
import org.gvt.model.biopaxl2.Complex;
import org.patika.mada.util.XRef;

import java.io.IOException;
import java.util.*;

/**
* @author Ozgun Babur
*
* Copyright: Bilkent Center for Bioinformatics, 2007 - present
*/
public class QueryPathwaysAction extends Action
{
  private ChisioMain main;

  /**
   * Reference set to search. Only the first one that matches the db will be searched.
   */
  private Set<XRef> refs;

  /**
   * Flag for not asking the user reference to query but to use xref of the selected nodes.
   */
  private boolean useSelectedNodes;

  public QueryPathwaysAction(ChisioMain main, boolean useSelectedNodes)
  {
    super("Query Pathways");
    setImageDescriptor(ImageDescriptor.createFromFile(ChisioMain.class, "icon/query-pathways.png"));
    setToolTipText(getText());
    this.main = main;
    this.useSelectedNodes = useSelectedNodes;
  }

  public QueryPathwaysAction(ChisioMain main, Collection<XRef> refs)
  {
    this(main, false);
    this.refs = new HashSet<XRef>(refs);
  }

  public boolean isUseSelectedNodes()
  {
    return useSelectedNodes;
  }

  public void setUseSelectedNodes(boolean useSelectedNodes)
  {
    this.useSelectedNodes = useSelectedNodes;
  }

  public void run()
  {
    if (refs == null)
    {
      refs = new HashSet<XRef>();

      if (useSelectedNodes && main.getViewer() != null)
      {
        for (Object o : main.getSelectedModel())
        {
          if (o instanceof Actor)
          {
            refs.addAll(((Actor) o).getReferences());
          }
          else if (o instanceof Complex)
          {
            refs.addAll(((Complex) o).getReferences());
          }
        }
      }
    }

    if (refs.isEmpty() && !useSelectedNodes)
    {
      StringInputDialog dialog = new StringInputDialog(main.getShell(), "Query Pathways",
        "Enter UniProt or Entrez Gene ID", null);

      String ids = dialog.open();

      if (ids != null && ids.trim().length() > 0)
      {
        for (String id : ids.split(" "))
        {
          if (id.length() < 1) continue;
         
          String dbtext = Character.isDigit(id.charAt(0)) ?
            XRef.ENTREZ_GENE : XRef.UNIPROT;

          refs.add(new XRef(dbtext + ":" + id));
        }
      }
    }

    if (!refs.isEmpty())
    {
      try
      {
        main.lockWithMessage("Querying Pathway Commons Database ...");

        PathwayCommonsIOHandler ioHandler = new PathwayCommonsIOHandler(new SimpleIOHandler());
        Map<String, String> pathToID = new HashMap<String, String>();
        List<String> resultPathways = new ArrayList<String>();

        XRef xr = XRef.getFirstRef(refs,
          new String[]{XRef.CPATH, XRef.ENTREZ_GENE, XRef.UNIPROT});

        refs.clear();
        if (xr != null)
        {
          refs.add(xr);
        }
        else
        {
          MessageDialog.openError(main.getShell(), "No Reference ID",
            "No CPATH, Entrez Gene or UniProt ID found to query.");
        }

       
        for (XRef ref : refs)
        {
          if (ref.getDb().equalsIgnoreCase(XRef.CPATH))
          {
            ioHandler.setInputIdType(PathwayCommonsIOHandler.ID_TYPE.CPATH_ID);
          }
          else if (ref.getDb().equalsIgnoreCase(XRef.UNIPROT))
          {
            ioHandler.setInputIdType(PathwayCommonsIOHandler.ID_TYPE.UNIPROT);
          }
          else if (ref.getDb().equalsIgnoreCase(XRef.ENTREZ_GENE))
          {
            ioHandler.setInputIdType(PathwayCommonsIOHandler.ID_TYPE.ENTREZ_GENE);
          }
          else
          {
            continue;
          }

          System.out.println("Querying pathways for " + ref);

          List<List<String>> resultList = ioHandler.getPathways(ref.getRef());
          main.unlock();

          if (resultList.get(0).get(0).contains("xml"))
          {
            MessageDialog.openError(main.getShell(), "Error!", "Unexpected error!");
            resultList.clear();
          }
          else if (resultList.get(1).size() == 2)
          {
//            MessageDialog.openInformation(main.getShell(), "No results",
//              "No results found.");

            resultList.clear();
          }
          else
          {
            resultList.remove(0);
          }

          // Prepare the result as listable pathway items

          for (List<String> columns : resultList)
          {
            assert columns.size() == 4;

            String cpathid = columns.get(3);

            if (!pathToID.containsValue(cpathid))
            {
              String pathwayName = columns.get(1);
              String db = columns.get(2);

              String line = "[" + db + "] " + pathwayName;

              resultPathways.add(line);
              pathToID.put(line, cpathid);
            }
          }
        }
       
        if (!resultPathways.isEmpty())
        {
          ArrayList<String> selectedItems = new ArrayList<String>();

          ItemSelectionDialog dialog = new ItemSelectionDialog(main.getShell(),
            500,
            "Pathway Selection Dialog",
            "Select pathways to retrieve",
            resultPathways, selectedItems,
            true, true, null);

          dialog.setMinValidSelect(1);
          dialog.open();

          List<String> idList = new ArrayList<String>();

          if (!dialog.isCancelled())
          {
            for (String item : selectedItems)
            {
              idList.add(pathToID.get(item));
            }
          }

          if (!idList.isEmpty())
          {
            try
            {
              main.lockWithMessage("Querying Pathway Commons Database ...");
              queryIDs(ioHandler, idList);
            }
            catch (Exception e){e.printStackTrace();}
            finally { main.unlock(); }


            new UpdatePathwayAction(main, true).run();
            OpenPathwaysAction opa = new OpenPathwaysAction(main);
            opa.setRefsToHighlight(refs);
            opa.run();
          }
        }
        else if (!refs.isEmpty())
        {
          MessageDialog.openInformation(main.getShell(), "Not found!",
            "No pathway found.");
        }
      }
      catch (Exception e)
      {
        refs = null;
        e.printStackTrace();
        MessageDialog.openError(main.getShell(), "Error",
          "An error occured during querying:\n" + e.getMessage());
      }
      finally
      {
        main.unlock();
      }
    }
    refs = null;
  }

  private void queryIDs(PathwayCommonsIOHandler ioHandler, List<String> idList) throws IOException
  {
    for (String id : idList)
    {
      ioHandler.setInputIdType(PathwayCommonsIOHandler.ID_TYPE.CPATH_ID);
      Model resultModel = ioHandler.retrieveByID(id);

      if (resultModel != null && !resultModel.getObjects().isEmpty())
      {
        if (main.getOwlModel() != null)
        {
          MergeAction merge = new MergeAction(main, resultModel);
          merge.setOpenPathways(false);
          merge.setUpdatePathways(false);
          merge.run();
        }
        else
        {
          LoadBioPaxModelAction load = new LoadBioPaxModelAction(main, resultModel);
          load.setOpenPathways(false);
          load.run();
        }
      }
    }
  }
}
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