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;
}
/**
* 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();
}
}
}
