/**
* Downloads the library and default configuration from NCBI. Save them where it can be found by
* LibManager.loadLibrary()
*/
private LibDownloadResult download(String libname) {
if (!AUTO_DOWNLOAD) {
throw new RuntimeException("AUTO_DOWNLOAD is disabled. This method should not be called");
}
LibDownloadResult result = new LibDownloadResult();
Version latestVersion = getLatestVersion(libname);
if (latestVersion == null) {
result.status = DownloadManager.DownloadResult.FAILED;
return result;
}
result.status = downloadManager.downloadLib(this, libname, latestVersion);
if (result.status == DownloadManager.DownloadResult.SUCCESS) {
result.savedPath = createdFileName;
createdFileName = null;
properties.saved(libname, latestVersion.toSimpleVersion(), result.savedPath);
}
return result;
// return downloadKfg(knownLibPath[i + 1]);
}
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;
}
