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