/**
* Return a string suitable for determining file type based on extension May or may not be a full,
* readable path. txt and gz extensions are stripped
*
* @return
*/
public String getTypeString() {
if (type != null) {
return type;
} else {
String typeString = path.toLowerCase();
if (path.startsWith("http://") || path.startsWith("https://")) {
try {
URL url = new URL(path);
typeString = url.getPath().toLowerCase();
String query = url.getQuery();
if (query != null) {
Map<String, String> queryMap = HttpUtils.parseQueryString(query);
// If type is set explicitly use it
if (queryMap.containsKey("dataformat")) {
String format = queryMap.get("dataformat");
if (format.contains("genomespace")) {
typeString = GSUtils.parseDataFormatString(format);
} else {
typeString = format;
}
} else if (queryMap.containsKey("file")) {
typeString = queryMap.get("file");
}
}
} catch (MalformedURLException e) {
log.error("Error interpreting url: " + path, e);
typeString = path;
}
}
// Strip .txt, .gz, and .xls extensions. (So foo.cn.gz => a .cn file)
if ((typeString.endsWith(".txt")
|| typeString.endsWith(".xls")
|| typeString.endsWith(".gz")
|| typeString.endsWith(".bgz"))) {
typeString = typeString.substring(0, typeString.lastIndexOf(".")).trim();
}
return typeString;
}
}
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;
}