public String getBamIndexPath() {
if (indexPath != null) return indexPath;
if (path.toLowerCase().startsWith("http://") || path.toLowerCase().startsWith("https://")) {
// See if bam file is specified by parameter
try {
URL url = new URL(path);
String queryString = url.getQuery();
if (queryString != null) {
Map<String, String> parameters = HttpUtils.parseQueryString(queryString);
if (parameters.containsKey("index")) {
return parameters.get("index");
} else if (parameters.containsKey("file")) {
String bamFile = parameters.get("file");
String bamIndexFile = bamFile + ".bai";
String newQueryString = queryString.replace(bamFile, bamIndexFile);
return path.replace(queryString, newQueryString);
} else {
String ip = path.replace(url.getPath(), url.getPath() + ".bai");
return ip;
}
}
} catch (MalformedURLException e) {
log.error(e.getMessage(), e);
}
}
return path + ".bai";
}
/**
* Upload files to pre-configured url.
*
* @param uploadLocation the location we are uploading to.
* @param fileName the filename we use for the resulting filename we upload.
* @param params the optional parameter names.
* @param values the optional parameter values.
*/
static void uploadLogs(String uploadLocation, String fileName, String[] params, String[] values) {
try {
File tempDir = LoggingUtilsActivator.getFileAccessService().getTemporaryDirectory();
File newDest = new File(tempDir, fileName);
File optionalFile = null;
// if we have some description params
// save them to file and add it to archive
if (params != null) {
optionalFile =
new File(
LoggingUtilsActivator.getFileAccessService().getTemporaryDirectory(),
"description.txt");
OutputStream out = new FileOutputStream(optionalFile);
for (int i = 0; i < params.length; i++) {
out.write((params[i] + " : " + values[i] + "\r\n").getBytes("UTF-8"));
}
out.flush();
out.close();
}
newDest = LogsCollector.collectLogs(newDest, optionalFile);
// don't leave any unneeded information
if (optionalFile != null) optionalFile.delete();
if (uploadLocation == null) return;
if (HttpUtils.postFile(uploadLocation, "logs", newDest) != null) {
NotificationService notificationService = LoggingUtilsActivator.getNotificationService();
if (notificationService != null) {
ResourceManagementService resources = LoggingUtilsActivator.getResourceService();
String bodyMsgKey = "plugin.loggingutils.ARCHIVE_MESSAGE_OK";
notificationService.fireNotification(
LOGFILES_ARCHIVED,
resources.getI18NString("plugin.loggingutils.ARCHIVE_BUTTON"),
resources.getI18NString(bodyMsgKey, new String[] {uploadLocation}),
null);
}
}
} catch (Throwable e) {
logger.error("Cannot upload file", e);
}
}
/**
* 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;
}
}
