/*
* 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.
*/
package org.broad.igv.gs;
import org.apache.log4j.Logger;
import org.broad.igv.Globals;
import org.broad.igv.prefs.Constants;
import org.broad.igv.prefs.PreferencesManager;
import java.io.*;
import java.net.MalformedURLException;
import java.net.URL;
/**
* @author jrobinso
* @date Jun 9, 2011
*/
public class GSUtils {
static final Logger log = Logger.getLogger(GSUtils.class);
/*
* Directory and filenames to save the token and username to facilitate SSO
*/
private static String tokenSaveDir = ".gs";
private static String tokenSaveFileName = ".gstoken";
private static String usernameSaveFileName = ".gsusername";
public static String gsUser = null;
public static String gsToken = null;
private static File getTokenSaveDir() {
String userDir = System.getProperty("user.home");
File gsDir = new File(userDir, tokenSaveDir);
if (!gsDir.exists()) {
gsDir.mkdir();
}
return gsDir;
}
private static File getTokenFile() {
File gsDir = getTokenSaveDir();
return (gsDir != null && gsDir.exists()) ? new File(gsDir, tokenSaveFileName) : null;
}
private static File getUsernameFile() {
File gsDir = getTokenSaveDir();
return (gsDir != null && gsDir.exists()) ? new File(gsDir, usernameSaveFileName) : null;
}
public static void setGSToken(String newToken) {
if (gsToken == null || !gsToken.equals(newToken)) {
gsToken = newToken;
if (Globals.isTesting()) {
return;
}
BufferedWriter bw = null;
File gsDir = getTokenSaveDir();
if (!gsDir.isDirectory()) {
log.error("Could not store token for SSO. File " + gsDir.getAbsolutePath() + "exists and is not a directory.");
return; // someone made a file with this name...
}
File tokenFile = getTokenFile();
if (tokenFile.exists()) tokenFile.delete();
writeToFile(gsToken, tokenFile);
}
}
public static String getGSToken() {
if (gsToken == null && !Globals.isTesting()) {
File file = GSUtils.getTokenFile();
if (file.exists()) {
BufferedReader br = null;
try {
br = new BufferedReader(new FileReader(file));
gsToken = br.readLine();
} catch (IOException e) {
log.error("Error reading GS cookie", e);
} finally {
if (br != null) try {
br.close();
} catch (IOException e) {
// Ignore
}
}
}
}
return gsToken;
}
public static void setGSUser(String newUser) {
if (gsUser == null || !gsUser.equals(newUser)) {
gsUser = newUser;
if (Globals.isTesting()) {
return;
}
File gsDir = getTokenSaveDir();
if (!gsDir.isDirectory()) {
log.error("Could not store token for SSO. File " + gsDir.getAbsolutePath() + "exists and is not a directory.");
return; // someone made a file with this name...
}
File userFile = getUsernameFile();
if (userFile.exists()) userFile.delete();
writeToFile(gsUser, userFile);
}
}
public static String getGSUser() throws IOException {
if (gsUser == null && !Globals.isTesting()) {
BufferedReader br = null;
try {
File tokenFile = getUsernameFile();
if (tokenFile.exists()) {
br = new BufferedReader(new FileReader(tokenFile));
gsUser = br.readLine().trim();
}
} finally {
try {
if (br != null) br.close();
} catch (Exception e) {
}
}
}
return gsUser;
}
public static void logout() {
gsToken = null;
gsUser = null;
gsToken = null;
File userfile = getUsernameFile();
if (userfile.exists()) {
userfile.delete();
}
File tokenFile = getTokenFile();
if (tokenFile.exists()) {
tokenFile.delete();
}
}
private static void writeToFile(String line, File aFile) {
BufferedWriter bw = null;
try {
bw = new BufferedWriter(new FileWriter(aFile));
bw.write(line);
bw.close();
} catch (Exception e) {
log.error("Failed to save the token for later Single Sign on", e);
} finally {
try {
if (bw != null) bw.close();
} catch (Exception e) {
}
}
}
public static boolean isGenomeSpace(URL url) {
//String dmServer = getDMHost();
//String atmServer = getATMHost();
return url.getHost().contains("genomespace.org");
}
private synchronized static String getDMHost() {
try {
return (new URL(PreferencesManager.getPreferences().get(Constants.GENOME_SPACE_DM_SERVER))).getHost();
} catch (MalformedURLException e) {
log.error(e);
return null;
}
}
private synchronized static String getATMHost() {
try {
return (new URL(PreferencesManager.getPreferences().get(Constants.GENOME_SPACE_ATM_SERVER))).getHost();
} catch (MalformedURLException e) {
log.error(e);
return null;
}
}
/**
* Convert GenomeSpace format string to igv format type (extension)
* Example: https://dmtest.genomespace.org:8444/datamanager/files/users/SAGDemo/Step1/TF.data.tab
* ?dataformat=http://www.genomespace.org/datamanager/dataformat/gct/0.0.0
*
* @param format
* @return
*/
public static String parseDataFormatString(String format) {
int versionIdx = format.lastIndexOf("/");
String tmp = format.substring(0, versionIdx);
int extIdx = tmp.lastIndexOf("/") + 1;
return "." + tmp.substring(extIdx);
}
}