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org.hl7.fhir.core
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Merge 9514aea5a3 into d0d30570f8

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dotasek 2024-11-23 17:28:45 -05:00 committed by GitHub
parent d0d30570f8 9514aea5a3
commit b250ca7610
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5 changed files with 146 additions and 115 deletions
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38
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/Utilities.java
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@ -67,7 +67,6 @@ import javax.annotation.Nullable;
import org.apache.commons.io.FileUtils;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.utilities.FileNotifier.FileNotifier2;
import org.hl7.fhir.utilities.Utilities.CaseInsensitiveSorter;
import org.hl7.fhir.utilities.filesystem.CSFile;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.settings.FhirSettings;
@ -449,6 +448,28 @@ public class Utilities {
return s.toString();
}
/**
* Delete a directory atomically by first renaming it to a temp directory in
* its parent, and then deleting its contents.
*
* @param path The directory to delete.
*/
public static void atomicDeleteDirectory(String path) throws IOException {
File directory = ManagedFileAccess.file(path);
String tempDirectoryPath = generateUniqueRandomUUIDPath(directory.getParent());
File tempDirectory = ManagedFileAccess.file(tempDirectoryPath);
if (!directory.renameTo(tempDirectory)) {
throw new IOException("Unable to rename directory " + path + " to " + tempDirectory +" for atomic delete");
}
clearDirectory(tempDirectory.getAbsolutePath());
if (!tempDirectory.delete()) {
throw new IOException("Unable to delete temp directory " + tempDirectory + " when atomically deleting " + path);
}
}
public static void clearDirectory(String folder, String... exemptions) throws IOException {
File dir = ManagedFileAccess.file(folder);
if (dir.exists()) {
@ -470,6 +491,21 @@ public class Utilities {
}
}
public static String generateUniqueRandomUUIDPath(String path) throws IOException {
String randomUUIDPath = null;
while (randomUUIDPath == null) {
final String uuid = UUID.randomUUID().toString().toLowerCase();
final String pathCandidate = Utilities.path(path, uuid);
if (!ManagedFileAccess.file(pathCandidate).exists()) {
randomUUIDPath = pathCandidate;
}
}
return randomUUIDPath;
}
public static File createDirectory(String path) throws IOException {
ManagedFileAccess.csfile(path).mkdirs();
return ManagedFileAccess.file(path);

202
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/FilesystemPackageCacheManager.java
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@ -99,9 +99,14 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
private final File cacheFolder;
private final List<NpmPackage> temporaryPackages = new ArrayList<>();
private boolean buildLoaded = false;
private final Map<String, String> ciList = new HashMap<>();
private JsonArray buildInfo;
private long ciQueryTimeStamp = 0;
private final long ciQueryInterval;
private static final long DEFAULT_CI_QUERY_INTERVAL = 1000 * 60 * 60 * 24;
/** key = packageId
* value = url of built package on https://build.fhir.org/ig/ */
private final Map<String, String> ciPackageList = new HashMap<>();
private JsonArray ciBuildInfo;
private boolean suppressErrors;
@Setter
@ -117,6 +122,10 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
@Getter
private final List<PackageServer> packageServers;
@With
@Getter
private final long ciQueryInterval;
@With
@Getter
private final FilesystemPackageCacheManagerLocks.LockParameters lockParameters;
@ -125,11 +134,13 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
this.cacheFolder = getUserCacheFolder();
this.packageServers = getPackageServersFromFHIRSettings();
this.lockParameters = null;
this.ciQueryInterval = FilesystemPackageCacheManager.DEFAULT_CI_QUERY_INTERVAL;
}
private Builder(File cacheFolder, List<PackageServer> packageServers, FilesystemPackageCacheManagerLocks.LockParameters lockParameters) {
private Builder(File cacheFolder, List<PackageServer> packageServers, long ciQueryInterval, FilesystemPackageCacheManagerLocks.LockParameters lockParameters) {
this.cacheFolder = cacheFolder;
this.packageServers = packageServers;
this.ciQueryInterval = ciQueryInterval;
this.lockParameters = lockParameters;
}
@ -163,7 +174,7 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
if (!cacheFolder.exists()) {
throw new FHIRException("The folder '" + cacheFolder + "' could not be found");
}
return new Builder(cacheFolder, this.packageServers, this.lockParameters);
return new Builder(cacheFolder, this.packageServers, this.ciQueryInterval, this.lockParameters);
}
public Builder withSystemCacheFolder() throws IOException {
@ -173,11 +184,11 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
} else {
systemCacheFolder = ManagedFileAccess.file(Utilities.path("/var", "lib", ".fhir", "packages"));
}
return new Builder(systemCacheFolder, this.packageServers, this.lockParameters);
return new Builder(systemCacheFolder, this.packageServers, this.ciQueryInterval, this.lockParameters);
}
public Builder withTestingCacheFolder() throws IOException {
return new Builder(ManagedFileAccess.file(Utilities.path("[tmp]", ".fhir", "packages")), this.packageServers, this.lockParameters);
return new Builder(ManagedFileAccess.file(Utilities.path("[tmp]", ".fhir", "packages")), this.packageServers, this.ciQueryInterval, this.lockParameters);
}
public FilesystemPackageCacheManager build() throws IOException {
@ -191,13 +202,14 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
throw e;
}
}
return new FilesystemPackageCacheManager(cacheFolder, packageServers, locks, lockParameters);
return new FilesystemPackageCacheManager(cacheFolder, packageServers, ciQueryInterval, locks, lockParameters);
}
}
private FilesystemPackageCacheManager(@Nonnull File cacheFolder, @Nonnull List<PackageServer> packageServers, @Nonnull FilesystemPackageCacheManagerLocks locks, @Nullable FilesystemPackageCacheManagerLocks.LockParameters lockParameters) throws IOException {
private FilesystemPackageCacheManager(@Nonnull File cacheFolder, @Nonnull List<PackageServer> packageServers, long ciQueryInterval,@Nonnull FilesystemPackageCacheManagerLocks locks, @Nullable FilesystemPackageCacheManagerLocks.LockParameters lockParameters) throws IOException {
super(packageServers);
this.cacheFolder = cacheFolder;
this.ciQueryInterval = ciQueryInterval;
this.locks = locks;
this.lockParameters = lockParameters;
prepareCacheFolder();
@ -280,27 +292,6 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
}
}
private void initPackageServers() {
myPackageServers.addAll(getConfiguredServers());
if (!isIgnoreDefaultPackageServers()) {
myPackageServers.addAll(getDefaultServers());
}
}
protected boolean isIgnoreDefaultPackageServers() {
return FhirSettings.isIgnoreDefaultPackageServers();
}
@Nonnull
protected List<PackageServer> getDefaultServers() {
return PackageServer.defaultServers();
}
protected List<PackageServer> getConfiguredServers() {
return PackageServer.getConfiguredServers();
}
public String getFolder() {
return cacheFolder.getAbsolutePath();
}
@ -312,16 +303,7 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
private void clearCache() throws IOException {
for (File f : Objects.requireNonNull(cacheFolder.listFiles())) {
if (f.isDirectory()) {
Utilities.clearDirectory(f.getAbsolutePath());
try {
FileUtils.deleteDirectory(f);
} catch (Exception e1) {
try {
FileUtils.deleteDirectory(f);
} catch (Exception e2) {
// just give up
}
}
Utilities.atomicDeleteDirectory(f.getAbsolutePath());
} else if (!f.getName().equals("packages.ini")) {
FileUtils.forceDelete(f);
@ -449,12 +431,10 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
locks.getPackageLock(id + "#" + version).doWriteWithLock(() -> {
String f = Utilities.path(cacheFolder, id + "#" + version);
File ff = ManagedFileAccess.file(f);
if (ff.exists()) {
Utilities.clearDirectory(f);
ff.delete();
}
File ff = ManagedFileAccess.file(f);
if (ff.exists()) {
Utilities.atomicDeleteDirectory(f);
}
return null;
}, lockParameters);
}
@ -561,25 +541,42 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
public NpmPackage addPackageToCache(final String id, final String version, final InputStream packageTgzInputStream, final String sourceDesc) throws IOException {
checkValidVersionString(version, id);
return locks.getPackageLock(id + "#" + version).doWriteWithLock(() -> {
String uuid = UUID.randomUUID().toString().toLowerCase();
String tempDir = Utilities.path(cacheFolder, uuid);
NpmPackage npm = NpmPackage.extractFromTgz(packageTgzInputStream, sourceDesc, tempDir, minimalMemory);
String tempDir = Utilities.generateUniqueRandomUUIDPath(cacheFolder.getAbsolutePath());
NpmPackage extractedNpm = NpmPackage.extractFromTgz(packageTgzInputStream, sourceDesc, tempDir, minimalMemory);
log("");
log("Installing " + id + "#" + version);
if ((npm.name() != null && id != null && !id.equalsIgnoreCase(npm.name()))) {
if ((extractedNpm.name() != null && id != null && !id.equalsIgnoreCase(extractedNpm.name()))) {
if (!suppressErrors && (!id.equals("hl7.fhir.r5.core") && !id.equals("hl7.fhir.us.immds"))) {// temporary work around
throw new IOException("Attempt to import a mis-identified package. Expected " + id + ", got " + npm.name());
throw new IOException("Attempt to import a mis-identified package. Expected " + id + ", got " + extractedNpm.name());
}
}
NpmPackage npmPackage = null;
String packageRoot = Utilities.path(cacheFolder, id + "#" + version);
try {
// ok, now we have a lock on it... check if something created it while we were waiting
if (!id.equals(extractedNpm.getNpm().asString("name")) || !version.equals(extractedNpm.getNpm().asString("version"))) {
if (!id.equals(extractedNpm.getNpm().asString("name"))) {
extractedNpm.getNpm().add("original-name", extractedNpm.getNpm().asString("name"));
extractedNpm.getNpm().remove("name");
extractedNpm.getNpm().add("name", id);
}
if (!version.equals(extractedNpm.getNpm().asString("version"))) {
extractedNpm.getNpm().add("original-version", extractedNpm.getNpm().asString("version"));
extractedNpm.getNpm().remove("version");
extractedNpm.getNpm().add("version", version);
}
TextFile.stringToFile(JsonParser.compose(extractedNpm.getNpm(), true), Utilities.path(tempDir, "package", "package.json"));
}
final NpmPackage tempPackage = loadPackageInfo(tempDir);
if (tempPackage != null && !tempPackage.isIndexed()) {
tempPackage.checkIndexed(packageRoot);
}
if (!ManagedFileAccess.file(packageRoot).exists() || Utilities.existsInList(version, "current", "dev")) {
Utilities.createDirectory(packageRoot);
try {
@ -587,30 +584,18 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
} catch (Throwable t) {
log("Unable to clear directory: " + packageRoot + ": " + t.getMessage() + " - this may cause problems later");
}
Utilities.renameDirectory(tempDir, packageRoot);
npmPackage = loadPackageInfo(packageRoot);
log(" done.");
} else {
Utilities.clearDirectory(tempDir);
ManagedFileAccess.file(tempDir).delete();
}
if (!id.equals(npm.getNpm().asString("name")) || !version.equals(npm.getNpm().asString("version"))) {
if (!id.equals(npm.getNpm().asString("name"))) {
npm.getNpm().add("original-name", npm.getNpm().asString("name"));
npm.getNpm().remove("name");
npm.getNpm().add("name", id);
}
if (!version.equals(npm.getNpm().asString("version"))) {
npm.getNpm().add("original-version", npm.getNpm().asString("version"));
npm.getNpm().remove("version");
npm.getNpm().add("version", version);
}
TextFile.stringToFile(JsonParser.compose(npm.getNpm(), true), Utilities.path(cacheFolder, id + "#" + version, "package", "package.json"));
}
npmPackage = loadPackageInfo(packageRoot);
if (npmPackage != null && !npmPackage.isIndexed()) {
npmPackage.checkIndexed(packageRoot);
}
} catch (Exception e) {
try {
// don't leave a half extracted package behind
@ -741,31 +726,31 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
}
private InputStreamWithSrc loadFromCIBuild(String id, String branch) throws IOException {
checkBuildLoaded();
if (ciList.containsKey(id)) {
checkCIServerQueried();
if (ciPackageList.containsKey(id)) {
if (branch == null) {
InputStream stream;
try {
stream = fetchFromUrlSpecific(Utilities.pathURL(ciList.get(id), "package.tgz"), false);
stream = fetchFromUrlSpecific(Utilities.pathURL(ciPackageList.get(id), "package.tgz"), false);
} catch (Exception e) {
stream = fetchFromUrlSpecific(Utilities.pathURL(ciList.get(id), "branches", "main", "package.tgz"), false);
stream = fetchFromUrlSpecific(Utilities.pathURL(ciPackageList.get(id), "branches", "main", "package.tgz"), false);
}
return new InputStreamWithSrc(stream, Utilities.pathURL(ciList.get(id), "package.tgz"), "current");
return new InputStreamWithSrc(stream, Utilities.pathURL(ciPackageList.get(id), "package.tgz"), "current");
} else {
InputStream stream = fetchFromUrlSpecific(Utilities.pathURL(ciList.get(id), "branches", branch, "package.tgz"), false);
return new InputStreamWithSrc(stream, Utilities.pathURL(ciList.get(id), "branches", branch, "package.tgz"), "current$" + branch);
InputStream stream = fetchFromUrlSpecific(Utilities.pathURL(ciPackageList.get(id), "branches", branch, "package.tgz"), false);
return new InputStreamWithSrc(stream, Utilities.pathURL(ciPackageList.get(id), "branches", branch, "package.tgz"), "current$" + branch);
}
} else if (id.startsWith("hl7.fhir.r6")) {
InputStream stream = fetchFromUrlSpecific(Utilities.pathURL("https://build.fhir.org", id + ".tgz"), false);
return new InputStreamWithSrc(stream, Utilities.pathURL("https://build.fhir.org", id + ".tgz"), "current");
} else {
throw new FHIRException("The package '" + id + "' has no entry on the current build server (" + ciList + ")");
throw new FHIRException("The package '" + id + "' has no entry on the current build server (" + ciPackageList + ")");
}
}
private String getPackageUrlFromBuildList(String packageId) throws IOException {
checkBuildLoaded();
for (JsonObject o : buildInfo.asJsonObjects()) {
checkCIServerQueried();
for (JsonObject o : ciBuildInfo.asJsonObjects()) {
if (packageId.equals(o.asString("package-id"))) {
return o.asString("url");
}
@ -810,15 +795,15 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
if (canonical == null) {
return null;
}
checkBuildLoaded();
if (buildInfo != null) {
for (JsonElement n : buildInfo) {
checkCIServerQueried();
if (ciBuildInfo != null) {
for (JsonElement n : ciBuildInfo) {
JsonObject o = (JsonObject) n;
if (canonical.equals(o.asString("url"))) {
return o.asString("package-id");
}
}
for (JsonElement n : buildInfo) {
for (JsonElement n : ciBuildInfo) {
JsonObject o = (JsonObject) n;
if (o.asString("url").startsWith(canonical + "/ImplementationGuide/")) {
return o.asString("package-id");
@ -828,25 +813,32 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
return null;
}
private NpmPackage checkCurrency(String id, NpmPackage p) {
checkBuildLoaded();
/**
* Checks https://
*
* @param id
* @param npmPackage
* @return
*/
private NpmPackage checkCurrency(String id, NpmPackage npmPackage) {
checkCIServerQueried();
// special case: current versions roll over, and we have to check their currency
try {
String url = ciList.get(id);
JsonObject json = JsonParser.parseObjectFromUrl(Utilities.pathURL(url, "package.manifest.json"));
String currDate = json.asString("date");
String packDate = p.date();
if (!currDate.equals(packDate)) {
String packageManifestUrl = ciPackageList.get(id);
JsonObject packageManifestJson = JsonParser.parseObjectFromUrl(Utilities.pathURL(packageManifestUrl, "package.manifest.json"));
String currentDate = packageManifestJson.asString("date");
String packageDate = npmPackage.date();
if (!currentDate.equals(packageDate)) {
return null; // nup, we need a new copy
}
} catch (Exception e) {
log("Unable to check package currency: " + id + ": " + id);
}
return p;
return npmPackage;
}
private void checkBuildLoaded() {
if (!buildLoaded) {
private void checkCIServerQueried() {
if (System.currentTimeMillis() - ciQueryTimeStamp > ciQueryInterval) {
try {
loadFromBuildServer();
} catch (Exception e) {
@ -865,26 +857,26 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
HTTPResult res = ManagedWebAccess.get(Arrays.asList("web"), "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) {

16
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/NpmPackage.java
View File

@ -637,11 +637,11 @@ 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);
}
}
}
@ -653,18 +653,18 @@ 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) {
@ -681,7 +681,7 @@ 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);
}
}

3
org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/npm/FilesystemPackageManagerTests.java
View File

@ -50,7 +50,10 @@ public class FilesystemPackageManagerTests {
new PackageServer(DUMMY_URL_4)
);
@Test
public void testCheckCurrentPackage() {
}
@Test
public void testDefaultServers() throws IOException {

2
org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/npm/LockfileTestProcessUtility.java
View File

@ -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();