UploadDisplay.java

package com.github.jmchilton.jgalaxy;

import com.github.jmchilton.blend4j.galaxy.ToolsClient.FileUploadRequest;
import com.github.jmchilton.blend4j.galaxy.ToolsClient.UploadFile;
import com.github.jmchilton.jgalaxy.mvp.DialogDisplay;
import com.google.common.collect.Lists;
import com.google.common.collect.Maps;
import java.io.File;
import java.util.List;
import java.util.Map;
import javax.swing.table.DefaultTableModel;

public class UploadDisplay extends DialogDisplay {
  private final HistoryContentsSelectionModel model;

  public UploadDisplay(final HistoryContentsSelectionModel model) {
    this.model = model;
    initComponents();
  }

  /**
   * This method is called from within the constructor to initialize the form.
   * WARNING: Do NOT modify this code. The content of this method is always
   * regenerated by the Form Editor.
   */
  @SuppressWarnings("unchecked")
  // <editor-fold defaultstate="collapsed" desc="Generated Code">//GEN-BEGIN:initComponents
  private void initComponents() {

    uploadFileChooser = new javax.swing.JFileChooser();
    uploadPane = new javax.swing.JScrollPane();
    uploadTable = new javax.swing.JTable();
    selectFilesButton = new javax.swing.JButton();
    jSeparator3 = new javax.swing.JSeparator();
    fileType = new javax.swing.JTextField();
    fileTypeLabel = new javax.swing.JLabel();
    jSeparator4 = new javax.swing.JSeparator();
    uploadButton = new javax.swing.JButton();
    jLabel3 = new javax.swing.JLabel();
    dbKeyTextField = new javax.swing.JTextField();
    jSeparator5 = new javax.swing.JSeparator();
    namePanel = new javax.swing.JPanel();
    jLabel1 = new javax.swing.JLabel();
    datasetName = new javax.swing.JTextField();

    uploadFileChooser.setMultiSelectionEnabled(true);
    uploadFileChooser.addActionListener(new java.awt.event.ActionListener() {
      public void actionPerformed(java.awt.event.ActionEvent evt) {
        uploadFileChooserActionPerformed(evt);
      }
    });

    setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);

    uploadTable.setModel(new javax.swing.table.DefaultTableModel(
      new Object [][] {

      },
      new String [] {
        "Dataset", "Filename", "Status"
      }
    ) {
      Class[] types = new Class [] {
        java.lang.String.class, java.lang.String.class, java.lang.Object.class
      };
      boolean[] canEdit = new boolean [] {
        true, true, false
      };

      public Class getColumnClass(int columnIndex) {
        return types [columnIndex];
      }

      public boolean isCellEditable(int rowIndex, int columnIndex) {
        return canEdit [columnIndex];
      }
    });
    uploadPane.setViewportView(uploadTable);
    uploadTable.getColumnModel().getColumn(2).setCellRenderer(   new ProgressRenderer());

    selectFilesButton.setText("Select Files");
    selectFilesButton.addActionListener(new java.awt.event.ActionListener() {
      public void actionPerformed(java.awt.event.ActionEvent evt) {
        selectFilesButtonActionPerformed(evt);
      }
    });

    jSeparator3.setOrientation(javax.swing.SwingConstants.VERTICAL);

    fileType.setHorizontalAlignment(javax.swing.JTextField.TRAILING);
    fileType.setText("auto");
    fileType.addActionListener(new java.awt.event.ActionListener() {
      public void actionPerformed(java.awt.event.ActionEvent evt) {
        fileTypeActionPerformed(evt);
      }
    });

    fileTypeLabel.setText("File Type");

    jSeparator4.setOrientation(javax.swing.SwingConstants.VERTICAL);

    uploadButton.setText("Upload");
    uploadButton.addActionListener(new java.awt.event.ActionListener() {
      public void actionPerformed(java.awt.event.ActionEvent evt) {
        uploadButtonActionPerformed(evt);
      }
    });

    jLabel3.setText("Genome");

    dbKeyTextField.setHorizontalAlignment(javax.swing.JTextField.TRAILING);
    dbKeyTextField.setText("?");

    jSeparator5.setOrientation(javax.swing.SwingConstants.VERTICAL);

    jLabel1.setText("Dataset Name");

    datasetName.addActionListener(new java.awt.event.ActionListener() {
      public void actionPerformed(java.awt.event.ActionEvent evt) {
        datasetNameActionPerformed(evt);
      }
    });

    javax.swing.GroupLayout namePanelLayout = new javax.swing.GroupLayout(namePanel);
    namePanel.setLayout(namePanelLayout);
    namePanelLayout.setHorizontalGroup(
      namePanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
      .addGroup(namePanelLayout.createSequentialGroup()
        .addComponent(jLabel1)
        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
        .addComponent(datasetName, javax.swing.GroupLayout.PREFERRED_SIZE, 227, javax.swing.GroupLayout.PREFERRED_SIZE)
        .addGap(0, 0, Short.MAX_VALUE))
    );
    namePanelLayout.setVerticalGroup(
      namePanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
      .addGroup(namePanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
        .addComponent(datasetName, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
        .addComponent(jLabel1))
    );

    javax.swing.GroupLayout layout = new javax.swing.GroupLayout(getContentPane());
    getContentPane().setLayout(layout);
    layout.setHorizontalGroup(
      layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
      .addGroup(layout.createSequentialGroup()
        .addContainerGap()
        .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
          .addComponent(namePanel, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
          .addGroup(layout.createSequentialGroup()
            .addComponent(selectFilesButton)
            .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
            .addComponent(jSeparator4, javax.swing.GroupLayout.PREFERRED_SIZE, 6, javax.swing.GroupLayout.PREFERRED_SIZE)
            .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
            .addComponent(fileTypeLabel)
            .addGap(6, 6, 6)
            .addComponent(fileType, javax.swing.GroupLayout.PREFERRED_SIZE, 71, javax.swing.GroupLayout.PREFERRED_SIZE)
            .addGap(18, 18, 18)
            .addComponent(jSeparator3, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
            .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
            .addComponent(jLabel3)
            .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
            .addComponent(dbKeyTextField, javax.swing.GroupLayout.PREFERRED_SIZE, 80, javax.swing.GroupLayout.PREFERRED_SIZE)
            .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
            .addComponent(jSeparator5, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
            .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, 60, Short.MAX_VALUE)
            .addComponent(uploadButton))
          .addComponent(uploadPane))
        .addContainerGap())
    );
    layout.setVerticalGroup(
      layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
      .addGroup(layout.createSequentialGroup()
        .addContainerGap()
        .addComponent(uploadPane, javax.swing.GroupLayout.DEFAULT_SIZE, 206, Short.MAX_VALUE)
        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
        .addComponent(namePanel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
        .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.TRAILING, false)
          .addComponent(jSeparator3)
          .addComponent(selectFilesButton, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
          .addComponent(jSeparator4)
          .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
            .addComponent(fileType, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
            .addComponent(fileTypeLabel))
          .addComponent(uploadButton, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
          .addGroup(javax.swing.GroupLayout.Alignment.LEADING, layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
            .addComponent(jLabel3)
            .addComponent(dbKeyTextField, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
          .addComponent(jSeparator5))
        .addContainerGap())
    );

    pack();
  }// </editor-fold>//GEN-END:initComponents

  private void selectFilesButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_selectFilesButtonActionPerformed
    uploadFileChooser.showOpenDialog(this);
  }//GEN-LAST:event_selectFilesButtonActionPerformed

  private void fileTypeActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_fileTypeActionPerformed
    // TODO add your handling code here:
  }//GEN-LAST:event_fileTypeActionPerformed

  private void uploadButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_uploadButtonActionPerformed
    final List<UploadFile> uploads = getUploads();
    final String historyId = model.getHistory().getId();
    final boolean multipleFile = this.namePanel.isVisible();
    final List<FileUploadRequest> uploadRequests = Lists.newArrayList();
    if(multipleFile) {
      final FileUploadRequest request = new FileUploadRequest(historyId, uploads);
      request.setToolId("multi_upload1");
      request.setDatasetName(this.datasetName.getText());
      request.getExtraParameters().put("raw_merge_type", fileType.getText());
      uploadRequests.add(request);
    } else {
      for(UploadFile file : uploads) {
        final FileUploadRequest request = new FileUploadRequest(historyId, file);
        request.setFileType(fileType.getText());
        uploadRequests.add(request);
      }
    }
    for(final FileUploadRequest request : uploadRequests) {
      request.setDbKey(dbKeyTextField.getText());
    }

    new UploadTask(uploadRequests, model.getGalaxyInstance().getToolsClient(), new IndexedProgressUpdater() {

      public void setProgress(int index, int percentComplete) {
        uploadTable.setValueAt(percentComplete, index, 2);
      }

    }).execute();
  }//GEN-LAST:event_uploadButtonActionPerformed

  private void uploadFileChooserActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_uploadFileChooserActionPerformed
    final File[] files = uploadFileChooser.getSelectedFiles();
    final DefaultTableModel model = getUploadModel();
    for(final File file : files) {
      model.addRow(new Object[] { file.getName(), file.getPath(), -1 });
    }
  }//GEN-LAST:event_uploadFileChooserActionPerformed

  private void datasetNameActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_datasetNameActionPerformed
  }//GEN-LAST:event_datasetNameActionPerformed
  
  public void displayDatasetName(final boolean visible) {
    namePanel.setVisible(visible);
  }
  
  private DefaultTableModel getUploadModel() {
    final DefaultTableModel model = (DefaultTableModel) uploadTable.getModel();
    return model;
  }  
  
  private List<UploadFile> getUploads() {
    final List<UploadFile> uploads = Lists.newArrayList();
    final DefaultTableModel tableModel = getUploadModel();
    final int rowCount = tableModel.getRowCount();
    for(int i = 0; i < rowCount; i++) {
      final String fileName = (String) tableModel.getValueAt(i, 0);
      final String filename = (String) tableModel.getValueAt(i, 1);
      final UploadFile file = new UploadFile(new File(filename), fileName);
      uploads.add(file);
    }
    return uploads;
  }  
  
  // Variables declaration - do not modify//GEN-BEGIN:variables
  private javax.swing.JTextField datasetName;
  private javax.swing.JTextField dbKeyTextField;
  private javax.swing.JTextField fileType;
  private javax.swing.JLabel fileTypeLabel;
  private javax.swing.JLabel jLabel1;
  private javax.swing.JLabel jLabel3;
  private javax.swing.JSeparator jSeparator3;
  private javax.swing.JSeparator jSeparator4;
  private javax.swing.JSeparator jSeparator5;
  private javax.swing.JPanel namePanel;
  private javax.swing.JButton selectFilesButton;
  private javax.swing.JButton uploadButton;
  private javax.swing.JFileChooser uploadFileChooser;
  private javax.swing.JScrollPane uploadPane;
  private javax.swing.JTable uploadTable;
  // End of variables declaration//GEN-END:variables
}