// If there is a <title> element on the start page, use that as our AU
// name.
String recomputeRegName() {
if (!isStarted()) {
// This can get invoked (seveeral times, mostly from logging) before
// enough mechanism has started to make it possible to resolve the CuUrl
// below.
return null;
}
try {
CachedUrl cu = makeCachedUrl(m_registryUrl);
if (cu == null) return null;
URL cuUrl = CuUrl.fromCu(cu);
Parser parser = new Parser(cuUrl.toString());
NodeList nodelst = parser.extractAllNodesThatMatch(new NodeClassFilter(TitleTag.class));
Node nodes[] = nodelst.toNodeArray();
recomputeRegName = false;
if (nodes.length < 1) return null;
// Get the first title found
TitleTag tag = (TitleTag) nodes[0];
if (tag == null) return null;
return tag.getTitle();
} catch (MalformedURLException e) {
log.warning("recomputeRegName", e);
return null;
} catch (ParserException e) {
if (e.getThrowable() instanceof FileNotFoundException) {
log.warning("recomputeRegName: " + e.getThrowable().toString());
} else {
log.warning("recomputeRegName", e);
}
return null;
}
}
/** Create LockssKeystores from config subtree below {@link #PARAM_KEYSTORE} */
void configureKeyStores(Configuration config) {
Configuration allKs = config.getConfigTree(PARAM_KEYSTORE);
for (Iterator iter = allKs.nodeIterator(); iter.hasNext(); ) {
String id = (String) iter.next();
Configuration oneKs = allKs.getConfigTree(id);
try {
LockssKeyStore lk = createLockssKeyStore(oneKs);
String name = lk.getName();
if (name == null) {
log.error("KeyStore definition missing name: " + oneKs);
continue;
}
LockssKeyStore old = keystoreMap.get(name);
if (old != null && !lk.equals(old)) {
log.warning(
"Keystore "
+ name
+ " redefined. "
+ "New definition may not take effect until daemon restart");
}
log.debug("Adding keystore " + name);
keystoreMap.put(name, lk);
} catch (Exception e) {
log.error("Couldn't create keystore: " + oneKs, e);
}
}
}
LibManager(String[] libs, String[] versions) {
if (versions == null || libs == null) {
throw new RuntimeException("Neither libs nor versions can be null");
}
if (versions.length != libs.length) {
throw new RuntimeException("Invalid library versions: must match number of libraries");
}
checkSystemProperties();
locations = generateLocations();
for (int i = 0; i < libs.length; ++i) {
libraryVersions.put(libs[i], versions[i]);
}
properties = new LMProperties(detectJVM().intString(), libraryVersions);
if (AUTO_DOWNLOAD) {
downloadManager = new DownloadManager(properties);
}
if (!JUST_DO_SIMPLE_LOAD_LIBRARY && System.getProperty("vdb.deleteLibraries") != null) {
/* make sure we have the latest version of ngs-sdk & ncbi-vdb dll-s */
for (String libname : libs) {
Logger.warning("Deleting all JNI libraries...");
LibPathIterator.deleteLibraries(this, libname);
}
}
}
public boolean isMatch(Alert alert) {
try {
Object attr = alert.getAttribute(attribute);
switch (relation) {
case EQ:
return equalObjects(attr, value);
case NE:
return !equalObjects(attr, value);
case CONTAINS:
{
if (value instanceof Collection) {
return ((Collection) value).contains(attr);
}
return false;
}
default:
int cmp = ((Comparable) attr).compareTo(value);
switch (relation) {
case GT:
return cmp > 0;
case GE:
return cmp >= 0;
case LT:
return cmp < 0;
case LE:
return cmp <= 0;
default:
return false;
}
}
} catch (Exception e) {
log.warning("AlertPredicate.isMatch", e);
return false;
}
}
void setConfig(Configuration config) {
log.debug("config: " + config);
proxyHost = config.get(PARAM_PROXY_HOST);
proxyPort = config.getInt(PARAM_PROXY_PORT, DEFAULT_PROXY_PORT);
if (StringUtil.isNullString(proxyHost) || proxyPort <= 0) {
String http_proxy = System.getenv("http_proxy");
if (!StringUtil.isNullString(http_proxy)) {
try {
HostPortParser hpp = new HostPortParser(http_proxy);
proxyHost = hpp.getHost();
proxyPort = hpp.getPort();
} catch (HostPortParser.InvalidSpec e) {
log.warning("Can't parse http_proxy environment var, ignoring: " + http_proxy + ": " + e);
}
}
}
if (StringUtil.isNullString(proxyHost) || proxyPort <= 0) {
proxyHost = null;
} else {
log.info("Proxying through " + proxyHost + ":" + proxyPort);
}
userAgent = config.get(PARAM_USER_AGENT);
if (StringUtil.isNullString(userAgent)) {
userAgent = null;
} else {
log.debug("Setting User-Agent to " + userAgent);
}
}
protected void initFeatureVersions() throws PluginException.InvalidDefinition {
if (definitionMap.containsKey(KEY_PLUGIN_FEATURE_VERSION_MAP)) {
Map<Plugin.Feature, String> map = new HashMap<Plugin.Feature, String>();
Map<String, String> spec =
(Map<String, String>) definitionMap.getMap(KEY_PLUGIN_FEATURE_VERSION_MAP);
log.debug2("features: " + spec);
for (Map.Entry<String, String> ent : spec.entrySet()) {
try {
// Prefix version string with feature name to create separate
// namespace for each feature
String key = ent.getKey();
map.put(Plugin.Feature.valueOf(key), key + "_" + ent.getValue());
} catch (RuntimeException e) {
log.warning(
getPluginName()
+ " set unknown feature: "
+ ent.getKey()
+ " to version "
+ ent.getValue(),
e);
throw new PluginException.InvalidDefinition("Unknown feature: " + ent.getKey(), e);
}
}
featureVersion = map;
} else {
featureVersion = null;
}
}
/**
* Handles a message. Knows type "collectiveUpdate-"+name only. It is the responsibility of the
* owner to propagate messages of this type using this method.
*/
public boolean handleMessage(Message m, Object o) {
if (!shouldLive || !m.getType().equals("collectiveUpdate-" + name)) return false;
final String logSender = observer + "#collectiveUpdate";
Logger.debug(logSender, "Update from " + m.getSender());
/**/
if (!m.getRecipient().name.equals(contributor.getName()))
Logger.warning(
logSender,
"Recipient and my contributor are not the same:\n"
+ "Recipient: "
+ m.getRecipient().name
+ "\n"
+ "Contributor: "
+ contributor.getName(),
null);
/**/
Collective c = (Collective) o;
// --- reset array representations
cacheCollection = null;
commandCollection = null;
// --- remove possible garbage
cache.remove(m.getRecipient().name);
c.cache.remove(m.getRecipient().name);
cache.remove(m.getSender().name);
c.cache.remove(m.getSender().name);
// --- sending our contributions
if (contributor == null)
Logger.warning(logSender, "Non-contributor observer is known by " + m.getSender(), null);
updateLocalInfo();
m.setReply(this);
// --- update containers
repairSenderAddress(c, m.getSender());
merge(c);
observer.collectiveUpdated((ContributionBox) cache.get(m.getSender().name));
return true;
}
/**
* Lookup the CU's archive file type in its AU's ArchiveFileTypes
*
* @return the file extension (including dot), or null if none found
*/
public static String getArchiveExtension(CachedUrl cu) {
ArchiveFileTypes aft = cu.getArchivalUnit().getArchiveFileTypes();
if (aft == null) {
return null;
}
try {
return aft.getFromCu(cu);
} catch (MalformedURLException e) {
log.warning("isArchive(" + cu + ")", e);
return null;
}
}
/**
* Gibt den Jahrgang der Klasse zurück.
*
* @return int-Wert, der den Jahrgang der Klasse angibt oder "0" bei Fehler
*/
public int getJahrgang() {
int jahrgang = 0;
if (isValid()) {
try {
jahrgang = Integer.parseInt(name.substring(0, 1));
} catch (Exception e) {
Logger.warning(this, "Konnte den Jahrgang nicht bestimmen für " + this);
}
}
return jahrgang;
}
private void checkSystemProperties() {
String loadLibraryProperty = System.getProperty("vdb.System.loadLibrary");
if (loadLibraryProperty != null && loadLibraryProperty.equals("1")) {
Logger.warning("Smart DLL search and library download was disabled");
JUST_DO_SIMPLE_LOAD_LIBRARY = true;
AUTO_DOWNLOAD = false;
SEARCH_FOR_LIBRARY = false;
return;
}
String noLibraryDownload = System.getProperty("vdb.System.noLibraryDownload");
if (noLibraryDownload != null && noLibraryDownload.equals("1")) {
Logger.warning("DLL download was disabled");
AUTO_DOWNLOAD = false;
}
String noLibrarySearch = System.getProperty("vdb.System.noLibrarySearch");
if (noLibrarySearch != null && noLibrarySearch.equals("1")) {
Logger.warning("Search of installed DLL was disabled");
SEARCH_FOR_LIBRARY = false;
}
}
protected String getHostName() {
String res = ConfigManager.getPlatformHostname();
if (res == null) {
try {
InetAddress inet = InetAddress.getLocalHost();
return inet.getHostName();
} catch (UnknownHostException e) {
log.warning("Can't get hostname", e);
return "unknown";
}
}
return res;
}
static Properties getAuIdProperties(String location) {
File propFile = new File(location + File.separator + AU_ID_FILE);
try {
InputStream is = new BufferedInputStream(new FileInputStream(propFile));
Properties idProps = new Properties();
idProps.load(is);
is.close();
return idProps;
} catch (Exception e) {
logger.warning("Error loading au id from " + propFile.getPath() + ".");
return null;
}
}
static String canonRoot(String root) {
synchronized (canonicalRoots) {
String canon = (String) canonicalRoots.get(root);
if (canon == null) {
try {
canon = new File(root).getCanonicalPath();
canonicalRoots.put(root, canon);
} catch (IOException e) {
logger.warning("Can't canonicalize: " + root, e);
return root;
}
}
return canon;
}
}
/**
* Repairing address of sender (might contain only name). This sets the right address of
* myContribution in c, and puts the contribution into c.cache. sender is the address of the peer
* to our best knowledge. However the atual address of the contributor might be different due to
* forwarding and other nuances. The authoritive name is in c.myContribution. The authoritive host
* and port are in sender.
*/
private static void repairSenderAddress(Collective c, Address sender) {
if (c.myContribution != null) {
c.cache.put(
c.myContribution.contributor.name,
new ContributionBox(
new Address(sender.getHost(), sender.port, c.myContribution.contributor.name),
c.myContribution.timeStamp,
c.myContribution.contribution));
} else
Logger.warning(
"Collective#repairSenderAddress()",
"Update doesn't contain contribution of sender " + sender,
null);
}
public static boolean isForwardingEnabled() {
boolean forwarding = false;
BufferedReader reader;
String line;
try {
reader = new BufferedReader(new FileReader(IPV4_FORWARD_FILEPATH));
line = reader.readLine().trim();
forwarding = line.equals("1");
reader.close();
} catch (IOException e) {
Logger.warning(e.toString());
}
return forwarding;
}
void checkParamAgreement(String key, PrintfContext context) {
List<String> printfList = getElementList(key);
if (printfList == null) {
return;
}
for (String printf : printfList) {
if (StringUtil.isNullString(printf)) {
log.warning("Null printf string in " + key);
continue;
}
PrintfUtil.PrintfData p_data = PrintfUtil.stringToPrintf(printf);
Collection<String> p_args = p_data.getArguments();
for (String arg : p_args) {
ConfigParamDescr descr = findAuConfigDescr(arg);
if (descr == null) {
throw new PluginException.InvalidDefinition(
"Not a declared parameter: " + arg + " in " + printf + " in " + getPluginName());
}
// ensure range and set params used only in legal context
switch (context) {
case Regexp:
case Display:
// everything is legal in a regexp or a display string
break;
case URL:
// NUM_RANGE and SET legal because can enumerate. Can't
// enumerate RANGE
switch (descr.getType()) {
case ConfigParamDescr.TYPE_RANGE:
throw new PluginException.InvalidDefinition(
"Range parameter ("
+ arg
+ ") used in illegal context in "
+ getPluginName()
+ ": "
+ key
+ ": "
+ printf);
default:
}
}
}
}
}
/*
* This is comlicated. MOST AUs have articles that live below and issue level TOC
* that is,
* <blah>/<journal_id>/vol#/iss#/ is a toc with no relevant metadata
* <blah>/<journal_id>/vol#/iss#/xxx is an article with metadata
* (eg Economist Voice V1)
* BUT
* in some AUs there are issues with only 1 article, in which case
* <blah>/<journal_id>/vol#/iss#/ is an abstract with metadata
* (eg Rhodes Cook V4)
* and a few AUs with a mixture
* (eg Forum for Health Economics V5)
* So to identify ALL articles, we'll also have to capture issue level items and then look
* at the html and if it has article metadata in it, count it as an article.
*
*/
@Override
protected ArticleFiles createArticleFiles(CachedUrl cu) {
String url = cu.getUrl();
Matcher mat = pattern.matcher(url);
if (mat.find()) {
// we matched, but could this pattern potentially be a toc?
Matcher tocmat = TOC_pattern.matcher(url);
// if we could be a TOC then we must have metadata to be considered an article
if (tocmat.find()) {
if (hasArticleMetadata(cu)) {
return processUrl(cu, mat);
}
} else {
// we're not a potential TOC, so treat this as an article without checking
return processUrl(cu, mat);
}
return null; // this was a TOC, not an article
}
log.warning("Mismatch between article iterator factory and article iterator: " + url);
return null;
}
public boolean needed() {
Logger.debug("Checking version file " + mVersionFile);
File file = new File(mVersionFile);
BufferedReader reader;
String line;
boolean needed = true;
try {
if (file.exists()) {
reader = new BufferedReader(new FileReader(file));
line = reader.readLine().trim();
needed = !line.equals(mAppVersion);
reader.close();
}
} catch (IOException e) {
Logger.warning(e.toString());
}
return needed;
}
/** check timeout site */
private void check() {
int size = mapTime.size();
if (size == 0) return;
ArrayList<SiteHost> dels = new ArrayList<SiteHost>(size);
ArrayList<SiteHost> notifys = new ArrayList<SiteHost>(size);
super.lockSingle();
try {
long nowTime = System.currentTimeMillis();
for (SiteHost host : mapTime.keySet()) {
Long value = mapTime.get(host);
if (value == null) {
dels.add(host);
continue;
}
long time = value.longValue();
if (nowTime - time >= deleteTime) {
dels.add(host);
} else if (nowTime - time >= refreshTimeout) {
notifys.add(host);
}
}
} catch (Throwable exp) {
exp.printStackTrace();
} finally {
super.unlockSingle();
}
// remove timeout site
for (SiteHost host : dels) {
Logger.error("WorkPool.check, delete timeout site:%s", host);
remove(host);
}
// notify site
SiteHost listen = Launcher.getInstance().getLocalHost();
for (SiteHost host : notifys) {
Logger.warning("WorkPool.check, notify timeout site:%s", host);
this.sendTimeout(host, listen, 2);
}
}
protected CIProperties makeCIProperties(ArchiveRecordHeader elementHeader) throws IOException {
CIProperties ret = new CIProperties();
Set elementHeaderFieldKeys = elementHeader.getHeaderFieldKeys();
for (Iterator i = elementHeaderFieldKeys.iterator(); i.hasNext(); ) {
String key = (String) i.next();
try {
Object valueObject = elementHeader.getHeaderValue(key);
if (valueObject == null) {
logger.warning("Ignoring null value for key '" + key + "'.");
} else {
String value = valueObject.toString();
logger.debug3(key + ": " + value);
ret.put(key, value);
}
} catch (ClassCastException ex) {
logger.error("makeCIProperties: " + key + " threw ", ex);
throw new CacheException.ExploderException(ex);
}
}
return (ret);
}
public void warning(String message, Throwable t) {
logger.warning(message, t);
}
/**
* Get or create TdbTitle for the specified properties and TdbAu.
*
* @param props the properties
* @param au the TdbAu
* @return the corresponding TdbTitle
*/
private TdbTitle getTdbTitle(Properties props, TdbAu au) {
TdbTitle title = null;
// get publisher name
String publisherNameFromProps = getTdbPublisherName(props, au);
// get the title name
String titleNameFromProps = getTdbTitleName(props, au);
// get the title ID
String titleIdFromProps = getTdbTitleId(props, au);
String titleId = titleIdFromProps;
if (titleId == null) {
// generate a titleId if one not specified, using the
// hash code of the combined title name and publisher names
int hash = (titleNameFromProps + publisherNameFromProps).hashCode();
titleId = (hash < 0) ? ("id:1" + (-hash)) : ("id:0" + hash);
}
// get publisher specified by property name
TdbPublisher publisher = tdbPublisherMap.get(publisherNameFromProps);
if (publisher != null) {
// find title from publisher
title = publisher.getTdbTitleById(titleId);
if (title != null) {
// warn that title name is different
if (!title.getName().equals(titleNameFromProps)) {
logger.warning(
"Title for au \""
+ au.getName()
+ "\": \""
+ titleNameFromProps
+ "\" is different than existing title \""
+ title.getName()
+ "\" for id "
+ titleId
+ " -- using existing title.");
}
return title;
}
}
if (publisher == null) {
// warn of missing publisher name
if (publisherNameFromProps.startsWith(UNKNOWN_PUBLISHER_PREFIX)) {
logger.warning(
"Publisher missing for au \""
+ au.getName()
+ "\" -- using \""
+ publisherNameFromProps
+ "\"");
}
// create new publisher for specified publisher name
publisher = new TdbPublisher(publisherNameFromProps);
tdbPublisherMap.put(publisherNameFromProps, publisher);
}
// warn of missing title name and/or id
if (titleNameFromProps.startsWith(UNKNOWN_TITLE_PREFIX)) {
logger.warning(
"Title missing for au \"" + au.getName() + "\" -- using \"" + titleNameFromProps + "\"");
}
if (titleIdFromProps == null) {
logger.debug2("Title ID missing for au \"" + au.getName() + "\" -- using " + titleId);
}
// create title and add to publisher
title = new TdbTitle(titleNameFromProps, titleId);
try {
publisher.addTdbTitle(title);
} catch (TdbException ex) {
// shouldn't happen: title already exists in publisher
logger.error(ex.getMessage(), ex);
}
return title;
}
public void warning(String message) {
logger.warning(message);
}
/** Clean up all resources used by this poll. Removes the poll directory. */
public void closePoll() {
if (pollDir != null && pollDir.isDirectory() && !FileUtil.delTree(pollDir))
log.warning("Unable to delete poll state directory: " + pollDir);
}
/** Query the daemon for information required to set up this command */
private boolean commandSetup() {
Configuration configuration = null;
Collection noEditKeys = null;
String key;
String value;
/*
* Configure a well known publication?
*/
if ((value = getParameter(AP_E_PUBLICATION)) != null) {
PluginProxy plugin = getTitlePlugin(value);
/*
* Set plugin and Title configuration information
*/
if (plugin == null) {
String message = "Unknown Publication:" + value;
log.warning(message);
return error(message);
}
setPlugin(plugin);
setTitleConfig(plugin.getTitleConfig(value));
configuration = getTitleConfig().getConfig();
noEditKeys = getNoEditKeys();
} else {
/*
* Lookup by Plugin or Class name - set the plugin
*
* NB: As of 23-Feb-04, this is not supported from AddAuPage.java. See
* AddAuWithCompleteFunctionalityPage.java for full support.
*/
if ((value = getParameter(AP_E_PLUGIN)) != null) {
key = RemoteApi.pluginKeyFromId(value);
} else if ((value = getParameter(AP_E_CLASSNAME)) != null) {
key = RemoteApi.pluginKeyFromId(value);
} else {
return error("Supply a Publication, Plugin, or Class name");
}
if (StringUtil.isNullString(key)) {
return error("Supply a valid Publication, Plugin, or Class name");
}
if (!pluginLoaded(key)) {
return error("Plugin is not loaded: " + key);
}
setPlugin(getPluginProxy(key));
}
/*
* Finally, return an XML rendition of the Plugin and AU key set up
*/
generateSetupXml(configuration, noEditKeys);
return true;
}
/**
* Creates a file by finding directory by iterating the location array and using libname to
* generate the file name
*/
public BufferedOutputStream create(String libname) {
createdFileName = null;
for (int i = 0; i < 2; ++i) {
Location location = null;
boolean model = true;
switch (i) {
case 0:
location = Location.NCBI_HOME;
model = false;
break;
case 1:
break;
}
LibPathIterator it =
new LibPathIterator(this, location, mapLibraryName(libname, model), true);
while (true) {
String pathname = it.nextName();
if (pathname == null) {
return null;
}
Logger.fine("Trying to create " + pathname + "...");
File file = new File(pathname);
try {
pathname = file.getAbsolutePath();
} catch (SecurityException e) {
Logger.warning(pathname + " : cannot getAbsolutePath " + e);
continue;
}
if (file.exists()) {
String dathname = pathname + ".bak";
File dest = new File(dathname);
{
String name = System.getProperty("os.name");
if (name != null && name.startsWith("Win")) {
/* On Windows delete the file we are going to rename to.
Otherwise renaming will fail. */
if (dest.exists()) {
Logger.fine("Trying to remove " + dathname + " ...");
dest.delete();
}
}
}
Logger.finest("Trying to rename " + pathname + " to " + dathname + " ...");
if (!file.renameTo(dest)) {
Logger.warning(pathname + ".renameTo(" + dathname + ") failed");
}
}
FileOutputStream s = null;
try {
s = new FileOutputStream(pathname);
} catch (FileNotFoundException e) {
/* e.message = pathname (Permission denied):
could be because pathname is not writable
or pathname not found and its directory is not writable */
Logger.warning("Cannot open " + pathname);
continue;
}
createdFileName = pathname;
Logger.fine("Opened " + pathname);
return new BufferedOutputStream(s, HttpManager.BUF_SZ);
}
}
return null;
}
/**
* Loads the system library by finding it by iterating the location array. Try to download it from
* NCBI if not found.
*
* <p>Will throw LibraryLoadError when failed.
*/
void loadLibrary(String libname) {
Version requiredVersion = getRequiredVersion(libname);
boolean updateCache = Arrays.asList(locations).contains(Location.CACHE);
Logger.fine("Searching for " + libname + " library...");
try {
LibSearchResult searchResult = searchLibrary(libname, requiredVersion);
if (searchResult.path == null) {
throw new LibraryNotFoundError(
libname, "No installed library was found", searchResult.failCause);
}
Logger.fine("Found " + libname + " library");
String libpath = searchResult.path;
Logger.info("Loading " + libname + "...");
try {
if (!mocksEnabled) {
if (libpath.startsWith(libname)) {
System.loadLibrary(libpath);
} else {
System.load(libpath);
}
} else if (mockLoadException != null) {
throw mockLoadException;
}
} catch (Throwable e) {
if (searchResult.location != Location.DOWNLOAD) {
throw new LibraryLoadError(
libname, "Failed to load found library " + libpath, new JvmErrorCause(e));
}
throw new LibraryLoadError(
libname,
"No installed library was found and downloaded library '"
+ libpath
+ "' cannot be loaded",
new JvmErrorCause(e),
"Please install ngs and ncbi-vdb manually:"
+ " https://github.com/ncbi/ngs/wiki/Downloads"
+ " or write to \"[email protected]\" if problems persist");
}
Logger.fine("Loaded " + libname + " library");
Logger.fine("Checking library " + libname + " version...");
String v;
if (!mocksEnabled) {
v = LibVersionChecker.getLoadedVersion(libname);
} else {
v = mockLoadedLibraryVersion;
}
if (v == null) {
throw new LibraryLoadError(
libname, "Failed to retrieve loaded library's version", new InvalidLibraryCause());
}
Version loadedVersion = new Version(v);
if (loadedVersion.compareTo(requiredVersion) < 0
|| !loadedVersion.isCompatible(requiredVersion)) {
Logger.fine(
"Library version is not compatible. Required: "
+ requiredVersion.toSimpleVersion()
+ " loaded: "
+ loadedVersion.toSimpleVersion());
LibraryLoadCause failCause = searchResult.failCause;
if (searchResult.location == Location.DOWNLOAD || failCause == null) {
failCause =
(loadedVersion.compareTo(requiredVersion) < 0)
? new PrereleaseReqLibCause()
: new OutdatedJarCause();
}
throw new LibraryIncompatibleVersionError(
libname, "Library is incompatible", libpath, failCause);
}
Logger.fine(
"Library "
+ libname
+ " was loaded successfully."
+ " Version = "
+ loadedVersion.toSimpleVersion());
if (updateCache) {
properties.loaded(libname, searchResult.version.toSimpleVersion(), libpath);
if (searchResult.location != Location.CACHE) {
properties.setLastSearch(libname);
}
}
} catch (LibraryLoadError e) {
if (updateCache) {
properties.notLoaded(libname);
}
Logger.warning("Loading of " + libname + " library failed");
throw e;
} finally {
if (updateCache) {
properties.store();
}
}
}
public static String getMyJarPath() {
if (myJarPath != null) {
return myJarPath;
}
myJarPath = System.getProperty(P_JARPATH);
if (myJarPath == null) {
try {
// Hack to obtain the name of this jar file.
String jarname = System.getProperty(P_JAVA_CLASS_PATH);
// Open each Jar file looking for this class name. This allows for
// JVM's that place more than the jar file on the classpath.
String jars[] = jarname.split(System.getProperty("path.separator"));
for (int i = 0; i < jars.length; i++) {
jarname = jars[i];
LOGGER.fine("Checking " + jarname + " as One-Jar file");
// Allow for URL based paths, as well as file-based paths. File
InputStream is = null;
try {
is = new URL(jarname).openStream();
} catch (MalformedURLException mux) {
// Try a local file.
try {
is = new FileInputStream(jarname);
} catch (IOException iox) {
// Ignore..., but it isn't good to have bad entries on the classpath.
continue;
}
}
ZipEntry entry =
findJarEntry(
new JarInputStream(is), Boot.class.getName().replace('.', '/') + ".class");
if (entry != null) {
myJarPath = jarname;
break;
} else {
// One more try as a Zip file: supports launch4j on Windows.
entry =
findZipEntry(
new ZipFile(jarname), Boot.class.getName().replace('.', '/') + ".class");
if (entry != null) {
myJarPath = jarname;
break;
}
}
}
} catch (Exception x) {
x.printStackTrace();
LOGGER.warning(
"jar="
+ myJarPath
+ " loaded from "
+ P_JAVA_CLASS_PATH
+ " ("
+ System.getProperty(P_JAVA_CLASS_PATH)
+ ")");
}
}
if (myJarPath == null) {
throw new IllegalArgumentException(
"Unable to locate "
+ Boot.class.getName()
+ " in the java.class.path: consider using -D"
+ P_JARPATH
+ " to specify the one-jar filename.");
}
// Normalize those annoying DOS backslashes.
myJarPath = myJarPath.replace('\\', '/');
return myJarPath;
}
public static void run(String args[]) throws Exception {
args = processArgs(args);
initializeLogging();
// Is the main class specified on the command line? If so, boot it.
// Otherwise, read the main class out of the manifest.
String mainClass = null;
initializeProperties();
// Reinitialze Logging (property file could have other loglevel set)
initializeLogging();
if (Boolean.valueOf(System.getProperty(P_SHOW_PROPERTIES, "false")).booleanValue()) {
// What are the system properties.
Properties props = System.getProperties();
String keys[] = props.keySet().toArray(new String[0]);
Arrays.sort(keys);
for (int i = 0; i < keys.length; i++) {
String key = keys[i];
System.out.println(key + "=" + props.get(key));
}
}
// Process developer properties:
if (mainClass == null) {
mainClass = System.getProperty(P_MAIN_CLASS);
}
if (mainJar == null) {
String app = System.getProperty(P_MAIN_APP);
if (app != null) {
mainJar = "main/" + app + ".jar";
} else {
mainJar = System.getProperty(P_MAIN_JAR, MAIN_JAR);
}
}
// Pick some things out of the top-level JAR file.
String jar = getMyJarPath();
JarFile jarFile = new JarFile(jar);
Manifest manifest = jarFile.getManifest();
Attributes attributes = manifest.getMainAttributes();
String bootLoaderName = attributes.getValue(ONE_JAR_CLASSLOADER);
if (mainJar == null) {
mainJar = attributes.getValue(ONE_JAR_DEFAULT_MAIN_JAR);
}
String mainargs = attributes.getValue(ONE_JAR_MAIN_ARGS);
if (mainargs != null && args.length == 0) {
// Replace the args with built-in. Support escaped whitespace.
args = mainargs.split("[^\\\\]\\s");
for (int i = 0; i < args.length; i++) {
args[i] = args[i].replaceAll("\\\\(\\s)", "$1");
}
}
// If no main-class specified, check the manifest of the main jar for
// a Boot-Class attribute.
if (mainClass == null) {
mainClass = attributes.getValue(ONE_JAR_MAIN_CLASS);
if (mainClass == null) {
mainClass = attributes.getValue(BOOT_CLASS);
if (mainClass != null) {
LOGGER.warning(
"The manifest attribute "
+ BOOT_CLASS
+ " is deprecated in favor of the attribute "
+ ONE_JAR_MAIN_CLASS);
}
}
}
if (mainClass == null) {
// Still don't have one (default). One final try: look for a jar file in a
// main directory. There should be only one, and it's manifest
// Main-Class attribute is the main class. The JarClassLoader will take
// care of finding it.
InputStream is = Boot.class.getResourceAsStream("/" + mainJar);
if (is != null) {
JarInputStream jis = new JarInputStream(is);
Manifest mainmanifest = jis.getManifest();
jis.close();
mainClass = mainmanifest.getMainAttributes().getValue(Attributes.Name.MAIN_CLASS);
} else {
// There is no main jar. Info unless mainJar is empty string.
// The load(mainClass) will scan for main jars anyway.
if (mainJar != null && !mainJar.isEmpty()) {
LOGGER.info(
"Unable to locate main jar '" + mainJar + "' in the JAR file " + getMyJarPath());
}
}
}
// Do we need to create a wrapping classloader? Check for the
// presence of a "wrap" directory at the top of the jar file.
URL url = Boot.class.getResource(WRAP_JAR);
if (url != null) {
// Wrap class loaders.
final JarClassLoader bootLoader = getBootLoader(bootLoaderName);
bootLoader.load(null);
// Read the "Wrap-Class-Loader" property from the wraploader jar file.
// This is the class to use as a wrapping class-loader.
InputStream is = Boot.class.getResourceAsStream(WRAP_JAR);
if (is != null) {
JarInputStream jis = new JarInputStream(is);
final String wrapLoader = jis.getManifest().getMainAttributes().getValue(WRAP_CLASS_LOADER);
jis.close();
if (wrapLoader == null) {
LOGGER.warning(
url
+ " did not contain a "
+ WRAP_CLASS_LOADER
+ " attribute, unable to load wrapping classloader");
} else {
LOGGER.info("using " + wrapLoader);
JarClassLoader wrapped = getWrapLoader(bootLoader, wrapLoader);
if (wrapped == null) {
LOGGER.warning(
"Unable to instantiate "
+ wrapLoader
+ " from "
+ WRAP_DIR
+ ": using default JarClassLoader");
wrapped = getBootLoader(null);
}
setClassLoader(wrapped);
}
}
} else {
setClassLoader(getBootLoader(bootLoaderName, Boot.class.getClassLoader()));
LOGGER.info("using JarClassLoader: " + getClassLoader().getClass().getName());
}
// Allow injection of the URL factory.
String urlfactory = attributes.getValue(ONE_JAR_URL_FACTORY);
if (urlfactory != null) {
loader.setURLFactory(urlfactory);
}
mainClass = loader.load(mainClass);
if (mainClass == null && !loader.isExpanded())
throw new Exception(
getMyJarName()
+ " main class was not found (fix: add main/main.jar with a Main-Class manifest attribute, or specify -D"
+ P_MAIN_CLASS
+ "=<your.class.name>), or use "
+ ONE_JAR_MAIN_CLASS
+ " in the manifest");
if (mainClass != null) {
// Guard against the main.jar pointing back to this
// class, and causing an infinite recursion.
String bootClass = Boot.class.getName();
if (bootClass.equals(mainClass))
throw new Exception(
getMyJarName()
+ " main class ("
+ mainClass
+ ") would cause infinite recursion: check main.jar/META-INF/MANIFEST.MF/Main-Class attribute: "
+ mainClass);
Class cls = loader.loadClass(mainClass);
endTime = System.currentTimeMillis();
showTime();
Method main = cls.getMethod("main", new Class[] {String[].class});
main.invoke(null, new Object[] {args});
}
}
private LibSearchResult searchLibrary(String libname, Version requiredVersion) {
LibSearchResult searchResult = new LibSearchResult();
for (Location l : locations) {
Logger.info("Checking " + libname + " from " + l + "...");
List<String> pathsToCheck = new ArrayList<String>();
boolean useLoadLibrary = false;
boolean searchEvenAfterFound = !JUST_DO_SIMPLE_LOAD_LIBRARY;
switch (l) {
case LIBPATH:
{
pathsToCheck.add(libname);
String libnameWithDataModel = libnameWithDataModel(libname);
if (libnameWithDataModel != null) {
pathsToCheck.add(libnameWithDataModel);
}
useLoadLibrary = true;
break;
}
case CACHE:
{
String filename = properties.get(libname);
if (filename == null) {
continue;
}
// when search is enabled, we might skip it if cache has information about previously
// loaded library and last search was less than SEARCH_LIB_FREQUENCY_INTERVAL ago
Date lastSearchDate = properties.getLastSeach(libname);
searchEvenAfterFound =
lastSearchDate == null
|| (new Date().getTime() - lastSearchDate.getTime()
> SEARCH_LIB_FREQUENCY_INTERVAL);
pathsToCheck.add(filename);
// this is kind of hack, but it does not require different checks between win/unix
// we say that library was loaded from LIBPATH location when its path starts from
// library simple name
useLoadLibrary = filename.startsWith(libname);
break;
}
case DOWNLOAD:
{
Logger.info("Downloading " + libname + " from NCBI...");
LibDownloadResult downloadResult;
if (!mocksEnabled) {
downloadResult = download(libname);
} else if (mockDownloadStatus == null) {
throw new RuntimeException("mockDownloadStatus must be set when mocks enabled");
} else {
downloadResult = new LibDownloadResult();
downloadResult.status = mockDownloadStatus;
downloadResult.savedPath = "/some/path/" + libname;
}
if (downloadResult.status != DownloadManager.DownloadResult.SUCCESS) {
Logger.warning("Failed to download " + libname + " from NCBI");
if (downloadResult.status == DownloadManager.DownloadResult.UNSUPPORTED_OS) {
searchResult.failCause = new UnsupportedArchCause();
} else {
searchResult.failCause = new ConnectionProblemCause();
}
continue;
}
Logger.info("Downloaded " + libname + " from NCBI");
Logger.fine("Checking " + libname + " library...");
pathsToCheck.add(downloadResult.savedPath);
break;
}
default:
{
String name[] = mapLibraryName(libname);
Logger.finest("System.mapLibraryName(" + libname + ") = " + name[0]);
LibPathIterator it = new LibPathIterator(l, name);
while (true) {
String filename = it.nextName();
if (filename == null) {
break;
}
pathsToCheck.add(filename);
}
break;
}
}
boolean foundInLocation = false;
for (String path : pathsToCheck) {
Version v;
if (!mocksEnabled) {
v = checkLibraryVersion(libname, path, useLoadLibrary);
} else if (mockLocationVersions == null) {
throw new RuntimeException("mockLocationVersions must be set when mocks enabled");
} else {
v = mockLocationVersions.get(l);
}
if (v == null) {
continue;
}
foundInLocation = true;
boolean versionFits = v.isCompatible(requiredVersion) && v.compareTo(requiredVersion) >= 0;
// replace a found version if either:
// a) none was previously found
// b) found version which fits requirements and it is higher than previously found
// c) found version version which fits requirements while previously found one does not
if (searchResult.path == null
|| (versionFits && (v.compareTo(searchResult.version) > 0)
|| !searchResult.versionFits)) {
searchResult.versionFits = versionFits;
searchResult.location = l;
searchResult.version = v;
searchResult.path = path;
}
if (searchResult.versionFits && !searchEvenAfterFound) {
break;
}
}
if (l == Location.DOWNLOAD) {
// when we downloaded something that either can't be loaded or does not fit our requirements
// or we just overwrote our best found library and cannot load it
if (!searchResult.versionFits
|| (!foundInLocation && searchResult.path.equals(pathsToCheck.get(0)))) {
searchResult.versionFits = false;
searchResult.location = l;
searchResult.version = null;
searchResult.path = pathsToCheck.get(0);
}
}
if (searchResult.version != null && searchResult.version.isCompatible(requiredVersion)) {
Version latestVersion = getLatestVersion(libname);
// if we don't know the latest version, then we might stop the search if
// found version is okay and searchEvenAfterFound == false
if (latestVersion == null
&& searchResult.version.compareTo(requiredVersion) >= 0
&& !searchEvenAfterFound) {
break;
}
// if we know the latest version, then we should search until find it
if (latestVersion != null && searchResult.version.compareTo(requiredVersion) >= 0) {
break;
}
}
}
boolean downloadEnabled = Arrays.asList(locations).contains(Location.DOWNLOAD);
if (searchResult.failCause == null && !downloadEnabled) {
searchResult.failCause = new DownloadDisabledCause();
}
return searchResult;
}
