Refactor package cache + more concurrency improvements
Make deletes atomic Apply indexing and renaming code operations to temporary package install before rename Track last update for CI build server (refresh every 24 hours)
This commit is contained in:
dotasek
parent
a1fbd674d6
commit
90b810e7ba
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@ -67,7 +67,6 @@ import javax.annotation.Nullable;
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import org.apache.commons.io.FileUtils;
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import org.hl7.fhir.exceptions.FHIRException;
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import org.hl7.fhir.utilities.FileNotifier.FileNotifier2;
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import org.hl7.fhir.utilities.Utilities.CaseInsensitiveSorter;
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import org.hl7.fhir.utilities.filesystem.CSFile;
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import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
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import org.hl7.fhir.utilities.settings.FhirSettings;
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@ -449,6 +448,28 @@ public class Utilities {
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return s.toString();
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}
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/**
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* Delete a directory atomically by first renaming it to a temp directory in
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* its parent, and then deleting its contents.
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*
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* @param path The directory to delete.
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*/
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public static void atomicDeleteDirectory(String path) throws IOException {
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File directory = ManagedFileAccess.file(path);
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String tempDirectoryPath = generateUniqueRandomUUIDPath(directory.getParent());
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File tempDirectory = ManagedFileAccess.file(tempDirectoryPath);
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if (!directory.renameTo(tempDirectory)) {
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throw new IOException("Unable to rename directory " + path + " to " + tempDirectory +" for atomic delete");
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}
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clearDirectory(tempDirectory.getAbsolutePath());
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if (!tempDirectory.delete()) {
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throw new IOException("Unable to delete temp directory " + tempDirectory + " when atomically deleting " + path);
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}
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}
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public static void clearDirectory(String folder, String... exemptions) throws IOException {
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File dir = ManagedFileAccess.file(folder);
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if (dir.exists()) {
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@ -470,6 +491,21 @@ public class Utilities {
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}
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}
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public static String generateUniqueRandomUUIDPath(String path) throws IOException {
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String randomUUIDPath = null;
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while (randomUUIDPath == null) {
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final String uuid = UUID.randomUUID().toString().toLowerCase();
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final String pathCandidate = Utilities.path(path, uuid);
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if (!ManagedFileAccess.file(pathCandidate).exists()) {
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randomUUIDPath = pathCandidate;
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}
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}
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return randomUUIDPath;
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}
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public static File createDirectory(String path) throws IOException {
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ManagedFileAccess.csfile(path).mkdirs();
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return ManagedFileAccess.file(path);
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@ -99,9 +99,14 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
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private final File cacheFolder;
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private final List<NpmPackage> temporaryPackages = new ArrayList<>();
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private boolean buildLoaded = false;
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private final Map<String, String> ciList = new HashMap<>();
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private JsonArray buildInfo;
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private long ciQueryTimeStamp = 0;
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private final long ciQueryInterval;
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private static final long DEFAULT_CI_QUERY_INTERVAL = 1000 * 60 * 60 * 24;
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/** key = packageId
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* value = url of built package on https://build.fhir.org/ig/ */
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private final Map<String, String> ciPackageList = new HashMap<>();
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private JsonArray ciBuildInfo;
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private boolean suppressErrors;
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@Setter
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@ -117,6 +122,10 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
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@Getter
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private final List<PackageServer> packageServers;
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@With
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@Getter
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private final long ciQueryInterval;
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@With
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@Getter
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private final FilesystemPackageCacheManagerLocks.LockParameters lockParameters;
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@ -125,11 +134,13 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
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this.cacheFolder = getUserCacheFolder();
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this.packageServers = getPackageServersFromFHIRSettings();
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this.lockParameters = null;
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this.ciQueryInterval = FilesystemPackageCacheManager.DEFAULT_CI_QUERY_INTERVAL;
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}
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private Builder(File cacheFolder, List<PackageServer> packageServers, FilesystemPackageCacheManagerLocks.LockParameters lockParameters) {
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private Builder(File cacheFolder, List<PackageServer> packageServers, long ciQueryInterval, FilesystemPackageCacheManagerLocks.LockParameters lockParameters) {
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this.cacheFolder = cacheFolder;
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this.packageServers = packageServers;
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this.ciQueryInterval = ciQueryInterval;
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this.lockParameters = lockParameters;
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}
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@ -163,7 +174,7 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
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if (!cacheFolder.exists()) {
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throw new FHIRException("The folder '" + cacheFolder + "' could not be found");
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}
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return new Builder(cacheFolder, this.packageServers, this.lockParameters);
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return new Builder(cacheFolder, this.packageServers, this.ciQueryInterval, this.lockParameters);
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}
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public Builder withSystemCacheFolder() throws IOException {
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@ -173,11 +184,11 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
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} else {
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systemCacheFolder = ManagedFileAccess.file(Utilities.path("/var", "lib", ".fhir", "packages"));
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}
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return new Builder(systemCacheFolder, this.packageServers, this.lockParameters);
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return new Builder(systemCacheFolder, this.packageServers, this.ciQueryInterval, this.lockParameters);
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}
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public Builder withTestingCacheFolder() throws IOException {
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return new Builder(ManagedFileAccess.file(Utilities.path("[tmp]", ".fhir", "packages")), this.packageServers, this.lockParameters);
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return new Builder(ManagedFileAccess.file(Utilities.path("[tmp]", ".fhir", "packages")), this.packageServers, this.ciQueryInterval, this.lockParameters);
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}
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public FilesystemPackageCacheManager build() throws IOException {
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@ -191,13 +202,14 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
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throw e;
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}
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}
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return new FilesystemPackageCacheManager(cacheFolder, packageServers, locks, lockParameters);
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return new FilesystemPackageCacheManager(cacheFolder, packageServers, ciQueryInterval, locks, lockParameters);
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}
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}
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private FilesystemPackageCacheManager(@Nonnull File cacheFolder, @Nonnull List<PackageServer> packageServers, @Nonnull FilesystemPackageCacheManagerLocks locks, @Nullable FilesystemPackageCacheManagerLocks.LockParameters lockParameters) throws IOException {
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private FilesystemPackageCacheManager(@Nonnull File cacheFolder, @Nonnull List<PackageServer> packageServers, long ciQueryInterval,@Nonnull FilesystemPackageCacheManagerLocks locks, @Nullable FilesystemPackageCacheManagerLocks.LockParameters lockParameters) throws IOException {
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super(packageServers);
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this.cacheFolder = cacheFolder;
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this.ciQueryInterval = ciQueryInterval;
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this.locks = locks;
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this.lockParameters = lockParameters;
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prepareCacheFolder();
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@ -280,27 +292,6 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
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}
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}
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private void initPackageServers() {
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myPackageServers.addAll(getConfiguredServers());
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if (!isIgnoreDefaultPackageServers()) {
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myPackageServers.addAll(getDefaultServers());
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}
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}
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protected boolean isIgnoreDefaultPackageServers() {
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return FhirSettings.isIgnoreDefaultPackageServers();
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}
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@Nonnull
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protected List<PackageServer> getDefaultServers() {
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return PackageServer.defaultServers();
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}
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protected List<PackageServer> getConfiguredServers() {
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return PackageServer.getConfiguredServers();
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}
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public String getFolder() {
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return cacheFolder.getAbsolutePath();
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}
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@ -312,16 +303,7 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
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private void clearCache() throws IOException {
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for (File f : Objects.requireNonNull(cacheFolder.listFiles())) {
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if (f.isDirectory()) {
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Utilities.clearDirectory(f.getAbsolutePath());
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try {
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FileUtils.deleteDirectory(f);
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} catch (Exception e1) {
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try {
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FileUtils.deleteDirectory(f);
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} catch (Exception e2) {
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// just give up
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}
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}
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Utilities.atomicDeleteDirectory(f.getAbsolutePath());
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} else if (!f.getName().equals("packages.ini")) {
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FileUtils.forceDelete(f);
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@ -449,12 +431,10 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
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locks.getPackageLock(id + "#" + version).doWriteWithLock(() -> {
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String f = Utilities.path(cacheFolder, id + "#" + version);
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File ff = ManagedFileAccess.file(f);
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if (ff.exists()) {
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Utilities.clearDirectory(f);
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ff.delete();
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}
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File ff = ManagedFileAccess.file(f);
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if (ff.exists()) {
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Utilities.atomicDeleteDirectory(f);
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}
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return null;
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}, lockParameters);
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}
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@ -561,25 +541,42 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
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public NpmPackage addPackageToCache(final String id, final String version, final InputStream packageTgzInputStream, final String sourceDesc) throws IOException {
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checkValidVersionString(version, id);
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return locks.getPackageLock(id + "#" + version).doWriteWithLock(() -> {
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String uuid = UUID.randomUUID().toString().toLowerCase();
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String tempDir = Utilities.path(cacheFolder, uuid);
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NpmPackage npm = NpmPackage.extractFromTgz(packageTgzInputStream, sourceDesc, tempDir, minimalMemory);
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String tempDir = Utilities.generateUniqueRandomUUIDPath(cacheFolder.getAbsolutePath());
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NpmPackage extractedNpm = NpmPackage.extractFromTgz(packageTgzInputStream, sourceDesc, tempDir, minimalMemory);
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log("");
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log("Installing " + id + "#" + version);
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if ((npm.name() != null && id != null && !id.equalsIgnoreCase(npm.name()))) {
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if ((extractedNpm.name() != null && id != null && !id.equalsIgnoreCase(extractedNpm.name()))) {
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if (!suppressErrors && (!id.equals("hl7.fhir.r5.core") && !id.equals("hl7.fhir.us.immds"))) {// temporary work around
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throw new IOException("Attempt to import a mis-identified package. Expected " + id + ", got " + npm.name());
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throw new IOException("Attempt to import a mis-identified package. Expected " + id + ", got " + extractedNpm.name());
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}
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}
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NpmPackage npmPackage = null;
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String packageRoot = Utilities.path(cacheFolder, id + "#" + version);
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try {
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// ok, now we have a lock on it... check if something created it while we were waiting
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if (!id.equals(extractedNpm.getNpm().asString("name")) || !version.equals(extractedNpm.getNpm().asString("version"))) {
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if (!id.equals(extractedNpm.getNpm().asString("name"))) {
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extractedNpm.getNpm().add("original-name", extractedNpm.getNpm().asString("name"));
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extractedNpm.getNpm().remove("name");
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extractedNpm.getNpm().add("name", id);
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}
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if (!version.equals(extractedNpm.getNpm().asString("version"))) {
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extractedNpm.getNpm().add("original-version", extractedNpm.getNpm().asString("version"));
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extractedNpm.getNpm().remove("version");
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extractedNpm.getNpm().add("version", version);
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}
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TextFile.stringToFile(JsonParser.compose(extractedNpm.getNpm(), true), Utilities.path(tempDir, "package", "package.json"));
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}
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final NpmPackage tempPackage = loadPackageInfo(tempDir);
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if (tempPackage != null && !tempPackage.isIndexed()) {
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tempPackage.checkIndexed(packageRoot);
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}
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if (!ManagedFileAccess.file(packageRoot).exists() || Utilities.existsInList(version, "current", "dev")) {
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Utilities.createDirectory(packageRoot);
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try {
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@ -587,30 +584,18 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
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} catch (Throwable t) {
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log("Unable to clear directory: " + packageRoot + ": " + t.getMessage() + " - this may cause problems later");
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}
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Utilities.renameDirectory(tempDir, packageRoot);
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npmPackage = loadPackageInfo(packageRoot);
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log(" done.");
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} else {
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Utilities.clearDirectory(tempDir);
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ManagedFileAccess.file(tempDir).delete();
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}
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if (!id.equals(npm.getNpm().asString("name")) || !version.equals(npm.getNpm().asString("version"))) {
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if (!id.equals(npm.getNpm().asString("name"))) {
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npm.getNpm().add("original-name", npm.getNpm().asString("name"));
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npm.getNpm().remove("name");
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npm.getNpm().add("name", id);
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}
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if (!version.equals(npm.getNpm().asString("version"))) {
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npm.getNpm().add("original-version", npm.getNpm().asString("version"));
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npm.getNpm().remove("version");
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npm.getNpm().add("version", version);
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}
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TextFile.stringToFile(JsonParser.compose(npm.getNpm(), true), Utilities.path(cacheFolder, id + "#" + version, "package", "package.json"));
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}
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npmPackage = loadPackageInfo(packageRoot);
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if (npmPackage != null && !npmPackage.isIndexed()) {
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npmPackage.checkIndexed(packageRoot);
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}
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} catch (Exception e) {
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try {
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// don't leave a half extracted package behind
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@ -741,31 +726,31 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
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}
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private InputStreamWithSrc loadFromCIBuild(String id, String branch) throws IOException {
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checkBuildLoaded();
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if (ciList.containsKey(id)) {
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checkCIServerQueried();
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if (ciPackageList.containsKey(id)) {
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if (branch == null) {
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InputStream stream;
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try {
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stream = fetchFromUrlSpecific(Utilities.pathURL(ciList.get(id), "package.tgz"), false);
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stream = fetchFromUrlSpecific(Utilities.pathURL(ciPackageList.get(id), "package.tgz"), false);
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} catch (Exception e) {
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stream = fetchFromUrlSpecific(Utilities.pathURL(ciList.get(id), "branches", "main", "package.tgz"), false);
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stream = fetchFromUrlSpecific(Utilities.pathURL(ciPackageList.get(id), "branches", "main", "package.tgz"), false);
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}
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return new InputStreamWithSrc(stream, Utilities.pathURL(ciList.get(id), "package.tgz"), "current");
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return new InputStreamWithSrc(stream, Utilities.pathURL(ciPackageList.get(id), "package.tgz"), "current");
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} else {
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InputStream stream = fetchFromUrlSpecific(Utilities.pathURL(ciList.get(id), "branches", branch, "package.tgz"), false);
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return new InputStreamWithSrc(stream, Utilities.pathURL(ciList.get(id), "branches", branch, "package.tgz"), "current$" + branch);
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InputStream stream = fetchFromUrlSpecific(Utilities.pathURL(ciPackageList.get(id), "branches", branch, "package.tgz"), false);
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return new InputStreamWithSrc(stream, Utilities.pathURL(ciPackageList.get(id), "branches", branch, "package.tgz"), "current$" + branch);
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}
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} else if (id.startsWith("hl7.fhir.r6")) {
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InputStream stream = fetchFromUrlSpecific(Utilities.pathURL("https://build.fhir.org", id + ".tgz"), false);
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return new InputStreamWithSrc(stream, Utilities.pathURL("https://build.fhir.org", id + ".tgz"), "current");
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} else {
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throw new FHIRException("The package '" + id + "' has no entry on the current build server (" + ciList + ")");
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throw new FHIRException("The package '" + id + "' has no entry on the current build server (" + ciPackageList + ")");
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}
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}
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private String getPackageUrlFromBuildList(String packageId) throws IOException {
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checkBuildLoaded();
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for (JsonObject o : buildInfo.asJsonObjects()) {
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checkCIServerQueried();
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for (JsonObject o : ciBuildInfo.asJsonObjects()) {
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if (packageId.equals(o.asString("package-id"))) {
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return o.asString("url");
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}
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@ -810,15 +795,15 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
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if (canonical == null) {
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return null;
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}
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checkBuildLoaded();
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if (buildInfo != null) {
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for (JsonElement n : buildInfo) {
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checkCIServerQueried();
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if (ciBuildInfo != null) {
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for (JsonElement n : ciBuildInfo) {
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JsonObject o = (JsonObject) n;
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if (canonical.equals(o.asString("url"))) {
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return o.asString("package-id");
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}
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}
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for (JsonElement n : buildInfo) {
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for (JsonElement n : ciBuildInfo) {
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JsonObject o = (JsonObject) n;
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if (o.asString("url").startsWith(canonical + "/ImplementationGuide/")) {
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return o.asString("package-id");
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@ -828,32 +813,39 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
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return null;
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}
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private NpmPackage checkCurrency(String id, NpmPackage p) {
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checkBuildLoaded();
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/**
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* Checks https://
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*
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* @param id
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* @param npmPackage
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* @return
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*/
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private NpmPackage checkCurrency(String id, NpmPackage npmPackage) {
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checkCIServerQueried();
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// special case: current versions roll over, and we have to check their currency
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try {
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String url = ciList.get(id);
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JsonObject json = JsonParser.parseObjectFromUrl(Utilities.pathURL(url, "package.manifest.json"));
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String currDate = json.asString("date");
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String packDate = p.date();
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if (!currDate.equals(packDate)) {
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String packageManifestUrl = ciPackageList.get(id);
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JsonObject packageManifestJson = JsonParser.parseObjectFromUrl(Utilities.pathURL(packageManifestUrl, "package.manifest.json"));
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String currentDate = packageManifestJson.asString("date");
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String packageDate = npmPackage.date();
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if (!currentDate.equals(packageDate)) {
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return null; // nup, we need a new copy
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}
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} catch (Exception e) {
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log("Unable to check package currency: " + id + ": " + id);
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}
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return p;
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return npmPackage;
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}
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private void checkBuildLoaded() {
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if (!buildLoaded) {
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private void checkCIServerQueried() {
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if (System.currentTimeMillis() - ciQueryTimeStamp > ciQueryInterval) {
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try {
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loadFromBuildServer();
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queryCIServer();
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} catch (Exception e) {
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try {
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// we always pause a second and try again - the most common reason to be here is that the file was being changed on the server
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Thread.sleep(1000);
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loadFromBuildServer();
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queryCIServer();
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} catch (Exception e2) {
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log("Error connecting to build server - running without build (" + e2.getMessage() + ")");
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}
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@ -861,31 +853,31 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
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}
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}
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private void loadFromBuildServer() throws IOException {
|
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private void queryCIServer() throws IOException {
|
||||
|
||||
HTTPResult res = ManagedWebAccess.get("https://build.fhir.org/ig/qas.json?nocache=" + System.currentTimeMillis());
|
||||
res.checkThrowException();
|
||||
|
||||
buildInfo = (JsonArray) JsonParser.parse(TextFile.bytesToString(res.getContent()));
|
||||
ciBuildInfo = (JsonArray) JsonParser.parse(TextFile.bytesToString(res.getContent()));
|
||||
|
||||
List<BuildRecord> builds = new ArrayList<>();
|
||||
|
||||
for (JsonElement n : buildInfo) {
|
||||
JsonObject o = (JsonObject) n;
|
||||
if (o.has("url") && o.has("package-id") && o.asString("package-id").contains(".")) {
|
||||
String u = o.asString("url");
|
||||
if (u.contains("/ImplementationGuide/"))
|
||||
u = u.substring(0, u.indexOf("/ImplementationGuide/"));
|
||||
builds.add(new BuildRecord(u, o.asString("package-id"), getRepo(o.asString("repo")), readDate(o.asString("date"))));
|
||||
for (JsonElement n : ciBuildInfo) {
|
||||
JsonObject j = (JsonObject) n;
|
||||
if (j.has("url") && j.has("package-id") && j.asString("package-id").contains(".")) {
|
||||
String packageUrl = j.asString("url");
|
||||
if (packageUrl.contains("/ImplementationGuide/"))
|
||||
packageUrl = packageUrl.substring(0, packageUrl.indexOf("/ImplementationGuide/"));
|
||||
builds.add(new BuildRecord(packageUrl, j.asString("package-id"), getRepo(j.asString("repo")), readDate(j.asString("date"))));
|
||||
}
|
||||
}
|
||||
Collections.sort(builds, new BuildRecordSorter());
|
||||
for (BuildRecord bld : builds) {
|
||||
if (!ciList.containsKey(bld.getPackageId())) {
|
||||
ciList.put(bld.getPackageId(), "https://build.fhir.org/ig/" + bld.getRepo());
|
||||
for (BuildRecord build : builds) {
|
||||
if (!ciPackageList.containsKey(build.getPackageId())) {
|
||||
ciPackageList.put(build.getPackageId(), "https://build.fhir.org/ig/" + build.getRepo());
|
||||
}
|
||||
}
|
||||
buildLoaded = true;
|
||||
ciQueryTimeStamp = System.currentTimeMillis();
|
||||
}
|
||||
|
||||
private String getRepo(String path) {
|
||||
|
|
|
|||
|
|
@ -640,11 +640,11 @@ public class NpmPackage {
|
|||
}
|
||||
|
||||
|
||||
public void checkIndexed(String desc) throws IOException {
|
||||
public void checkIndexed(String path) throws IOException {
|
||||
for (NpmPackageFolder folder : folders.values()) {
|
||||
JsonObject index = folder.index();
|
||||
if (index == null || index.forceArray("files").size() == 0) {
|
||||
indexFolder(desc, folder);
|
||||
indexFolder(path, folder);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -656,18 +656,18 @@ public class NpmPackage {
|
|||
* See <a href="https://hl7.org/fhir/packages.html#2.1.10.4">the FHIR specification</a> for details on .index.json
|
||||
* format and usage.
|
||||
*
|
||||
* @param desc
|
||||
* @param path
|
||||
* @param folder
|
||||
* @throws FileNotFoundException
|
||||
* @throws IOException
|
||||
*/
|
||||
public void indexFolder(String desc, NpmPackageFolder folder) throws FileNotFoundException, IOException {
|
||||
public void indexFolder(String path, NpmPackageFolder folder) throws FileNotFoundException, IOException {
|
||||
List<String> remove = new ArrayList<>();
|
||||
NpmPackageIndexBuilder indexer = new NpmPackageIndexBuilder();
|
||||
indexer.start(folder.folder != null ? Utilities.path(folder.folder.getAbsolutePath(), ".index.db") : null);
|
||||
for (String n : folder.listFiles()) {
|
||||
if (!indexer.seeFile(n, folder.fetchFile(n))) {
|
||||
remove.add(n);
|
||||
for (String file : folder.listFiles()) {
|
||||
if (!indexer.seeFile(file, folder.fetchFile(file))) {
|
||||
remove.add(file);
|
||||
}
|
||||
}
|
||||
for (String n : remove) {
|
||||
|
|
@ -684,7 +684,7 @@ public class NpmPackage {
|
|||
}
|
||||
} catch (Exception e) {
|
||||
TextFile.stringToFile(json, Utilities.path("[tmp]", ".index.json"));
|
||||
throw new IOException("Error parsing "+(desc == null ? "" : desc+"#")+"package/"+folder.folderName+"/.index.json: "+e.getMessage(), e);
|
||||
throw new IOException("Error parsing "+(path == null ? "" : path+"#")+"package/"+folder.folderName+"/.index.json: "+e.getMessage(), e);
|
||||
}
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -50,7 +50,10 @@ public class FilesystemPackageManagerTests {
|
|||
new PackageServer(DUMMY_URL_4)
|
||||
);
|
||||
|
||||
@Test
|
||||
public void testCheckCurrentPackage() {
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testDefaultServers() throws IOException {
|
||||
|
|
|
|||
|
|
@ -105,7 +105,7 @@ public class LockfileTestProcessUtility {
|
|||
System.out.println("File "+lockFileName+" is locked. Waiting for " + seconds + " seconds to release. ");
|
||||
Thread.sleep(seconds * 1000L);
|
||||
|
||||
lockFile.renameTo(ManagedFileAccess.file(File.createTempFile(lockFile.getName(), ".lock-renamed").getAbsolutePath()));
|
||||
lockFile.renameTo(File.createTempFile(lockFile.getName(), ".lock-renamed"));
|
||||
|
||||
fileLock.release();
|
||||
channel.close();
|
||||
|
|
|
|||
2
pom.xml
2
pom.xml
|
|
@ -21,7 +21,7 @@
|
|||
<commons_compress_version>1.26.0</commons_compress_version>
|
||||
<guava_version>32.0.1-jre</guava_version>
|
||||
<hapi_fhir_version>6.4.1</hapi_fhir_version>
|
||||
<validator_test_case_version>1.5.24</validator_test_case_version>
|
||||
<validator_test_case_version>1.5.25-SNAPSHOT</validator_test_case_version>
|
||||
<jackson_version>2.17.0</jackson_version>
|
||||
<junit_jupiter_version>5.9.2</junit_jupiter_version>
|
||||
<junit_platform_launcher_version>1.8.2</junit_platform_launcher_version>
|
||||
|
|
|
|||
Loading…
Reference in New Issue