/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
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package org.broad.igv.ui.action;
import org.apache.log4j.Logger;
import org.broad.igv.exceptions.HttpResponseException;
import org.broad.igv.feature.genome.GenomeManager;
import org.broad.igv.ga4gh.GoogleUtils;
import org.broad.igv.ga4gh.OAuthUtils;
import org.broad.igv.prefs.Constants;
import org.broad.igv.prefs.PreferencesManager;
import org.broad.igv.ui.IGV;
import org.broad.igv.ui.IGVMenuBar;
import org.broad.igv.ui.util.LoadFromURLDialog;
import org.broad.igv.ui.util.MessageUtils;
import org.broad.igv.util.HttpUtils;
import org.broad.igv.util.ResourceLocator;
import javax.swing.*;
import java.awt.*;
import java.awt.event.ActionEvent;
import java.io.IOException;
import java.io.InputStream;
import java.net.URL;
import java.util.Arrays;
import java.util.HashMap;
import java.util.Map;
/**
* @author jrobinso
*/
public class LoadFromURLMenuAction extends MenuAction {
static Logger log = Logger.getLogger(LoadFilesMenuAction.class);
public static final String LOAD_FROM_DAS = "Load from DAS...";
public static final String LOAD_FROM_URL = "Load from URL...";
public static final String LOAD_FILE_AND_INDEX_FROM_URLS = "Load file and index from URLs...";
public static final String LOAD_GENOME_FROM_URL = "Load Genome from URL...";
private IGV igv;
public LoadFromURLMenuAction(String label, int mnemonic, IGV igv) {
super(label, null, mnemonic);
this.igv = igv;
}
@Override
public void actionPerformed(ActionEvent e) {
JPanel ta = new JPanel();
ta.setPreferredSize(new Dimension(600, 20));
if (e.getActionCommand().equalsIgnoreCase(LOAD_FROM_URL)) {
LoadFromURLDialog dlg = new LoadFromURLDialog(IGV.getMainFrame());
dlg.setVisible(true);
if (!dlg.isCanceled()) {
String url = dlg.getFileURL();
if (url != null && url.trim().length() > 0) {
url = url.trim();
if (url.startsWith("gs://")) {
enableGoogleMenu();
url = GoogleUtils.translateGoogleCloudURL(url);
}
if (OAuthUtils.isGoogleCloud(url)) {
// if user is not currently logged in, attempt to
// log in user if not logged in dwm08
if (!OAuthUtils.getInstance().isLoggedIn()) {
try {
OAuthUtils.getInstance().openAuthorizationPage();
} catch (Exception ex) {
MessageUtils.showErrorMessage("Error fetching oAuth tokens. See log for details", ex);
log.error("Error fetching oAuth tokens", ex);
}
}
// wait until authentication successful or 1 minute - dwm08
int i = 0;
while (!OAuthUtils.getInstance().isLoggedIn() && i<600) {
++i;
try {
Thread.sleep(100);
} catch (InterruptedException e1) {
e1.printStackTrace();
}
}
// Access a few bytes as a means to check authorization
if (!ping(url)) return;
if (url.indexOf("alt=media") < 0) {
url = url + (url.indexOf('?') > 0 ? "&" : "?") + "alt=media";
}
}
if (url.endsWith(".xml") || url.endsWith(".session")) {
try {
boolean merge = false;
String locus = null;
igv.doRestoreSession(url, locus, merge);
} catch (Exception ex) {
MessageUtils.showMessage("Error loading url: " + url + " (" + ex.toString() + ")");
}
} else {
ResourceLocator rl = new ResourceLocator(url.trim());
if(dlg.getIndexURL() != null) {
String indexUrl = dlg.getIndexURL().trim();
if (indexUrl.startsWith("gs://")) {
enableGoogleMenu();
indexUrl = GoogleUtils.translateGoogleCloudURL(indexUrl);
}
if (OAuthUtils.isGoogleCloud(indexUrl)) {
if (indexUrl.indexOf("alt=media") < 0) {
indexUrl = indexUrl + (indexUrl.indexOf('?') > 0 ? "&" : "?") + "alt=media";
}
}
rl.setIndexPath(indexUrl);
}
igv.loadTracks(Arrays.asList(rl));
}
}
}
} else if ((e.getActionCommand().equalsIgnoreCase(LOAD_FROM_DAS))) {
String url = JOptionPane.showInputDialog(IGV.getMainFrame(), ta, "Enter DAS feature source URL",
JOptionPane.QUESTION_MESSAGE);
if (url != null && url.trim().length() > 0) {
ResourceLocator rl = new ResourceLocator(url.trim());
rl.setType("das");
igv.loadTracks(Arrays.asList(rl));
}
} else if ((e.getActionCommand().equalsIgnoreCase(LOAD_GENOME_FROM_URL))) {
String url = JOptionPane.showInputDialog(IGV.getMainFrame(), ta, "Enter URL to .genome or FASTA file",
JOptionPane.QUESTION_MESSAGE);
if (url != null && url.trim().length() > 0) {
try {
GenomeManager.getInstance().loadGenome(url.trim(), null);
} catch (Exception e1) {
MessageUtils.showMessage("Error loading genome: " + e1.getMessage());
}
}
}
}
private void enableGoogleMenu() {
if (!PreferencesManager.getPreferences().getAsBoolean(Constants.ENABLE_GOOGLE_MENU)) {
PreferencesManager.getPreferences().put(Constants.ENABLE_GOOGLE_MENU, true);
IGVMenuBar.getInstance().enableGoogleMenu(true);
}
}
private boolean ping(String url) {
InputStream is = null;
try {
Map<String, String> params = new HashMap();
params.put("Range", "bytes=0-10");
byte[] buffer = new byte[10];
is = HttpUtils.getInstance().openConnectionStream(new URL(url), params);
is.read(buffer);
is.close();
} catch (HttpResponseException e1) {
MessageUtils.showMessage(e1.getMessage());
return false;
} catch (IOException e) {
log.error(e);
} finally {
if (is != null) try {
is.close();
} catch (IOException e) {
e.printStackTrace();
}
}
return true;
}
}