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org.hl7.fhir.core
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Merge remote-tracking branch 'origin/master'

This commit is contained in:
Grahame Grieve 2024-09-17 16:18:15 +08:00
parent 11efed6635 dd01e008ca
commit fbfd81532d
17 changed files with 155 additions and 58 deletions
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2
org.hl7.fhir.convertors/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>6.3.25-SNAPSHOT</version>
<version>6.3.26-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.dstu2/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>6.3.25-SNAPSHOT</version>
<version>6.3.26-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.dstu2016may/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>6.3.25-SNAPSHOT</version>
<version>6.3.26-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.dstu3/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>6.3.25-SNAPSHOT</version>
<version>6.3.26-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.r4/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>6.3.25-SNAPSHOT</version>
<version>6.3.26-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.r4b/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>6.3.25-SNAPSHOT</version>
<version>6.3.26-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.r5/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>6.3.25-SNAPSHOT</version>
<version>6.3.26-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.report/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>6.3.25-SNAPSHOT</version>
<version>6.3.26-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.utilities/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>6.3.25-SNAPSHOT</version>
<version>6.3.26-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

22
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/FilesystemPackageCacheManager.java
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@ -210,26 +210,30 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
Utilities.createDirectory(cacheFolder.getAbsolutePath());
createIniFile();
} else {
if (!isCacheFolderValid()) {
if (!iniFileExists()) {
createIniFile();
}
if (!isIniFileCurrentVersion()) {
clearCache();
createIniFile();
} else {
deleteOldTempDirectories();
}
deleteOldTempDirectories();
}
return null;
});
}
private boolean isCacheFolderValid() throws IOException {
private boolean iniFileExists() throws IOException {
String iniPath = getPackagesIniPath();
File iniFile = ManagedFileAccess.file(iniPath);
if (!(iniFile.exists())) {
return false;
}
return iniFile.exists();
}
private boolean isIniFileCurrentVersion() throws IOException {
String iniPath = getPackagesIniPath();
IniFile ini = new IniFile(iniPath);
String v = ini.getStringProperty("cache", "version");
return CACHE_VERSION.equals(v);
String version = ini.getStringProperty("cache", "version");
return CACHE_VERSION.equals(version);
}
private void deleteOldTempDirectories() throws IOException {

12
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/NpmPackage.java
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@ -650,7 +650,17 @@ public class NpmPackage {
}
/**
* Create a package .index.json file for a package folder.
* <p>
* 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 folder
* @throws FileNotFoundException
* @throws IOException
*/
public void indexFolder(String desc, NpmPackageFolder folder) throws FileNotFoundException, IOException {
List<String> remove = new ArrayList<>();
NpmPackageIndexBuilder indexer = new NpmPackageIndexBuilder();

118
org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/npm/FilesystemPackageManagerTests.java
View File

@ -1,22 +1,25 @@
package org.hl7.fhir.utilities.npm;
import static org.assertj.core.api.Assertions.assertThat;
import static org.junit.jupiter.api.Assertions.assertEquals;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.nio.file.Files;
import java.util.ArrayList;
import java.util.List;
import java.util.Random;
import java.util.UUID;
import java.util.concurrent.ConcurrentHashMap;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.stream.Stream;
import javax.annotation.Nonnull;
import org.hl7.fhir.utilities.IniFile;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.junit.jupiter.api.RepeatedTest;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.condition.DisabledOnOs;
import org.junit.jupiter.api.condition.EnabledOnOs;
@ -100,7 +103,6 @@ public class FilesystemPackageManagerTests {
@DisabledOnOs(OS.WINDOWS)
public void testSystemCacheDirectory() throws IOException {
File folder = new FilesystemPackageCacheManager.Builder().withSystemCacheFolder().getCacheFolder();
assertEquals( "/var/lib/.fhir/packages", folder.getAbsolutePath());
}
@ -124,6 +126,118 @@ public class FilesystemPackageManagerTests {
return params.stream();
}
private void createDummyTemp(File cacheDirectory, String lowerCase) throws IOException {
createDummyPackage(cacheDirectory, lowerCase);
}
private void createDummyPackage(File cacheDirectory, String packageName, String packageVersion) throws IOException {
String directoryName = packageName + "#" + packageVersion;
createDummyPackage(cacheDirectory, directoryName);
}
private static void createDummyPackage(File cacheDirectory, String directoryName) throws IOException {
File packageDirectory = ManagedFileAccess.file(cacheDirectory.getAbsolutePath(), directoryName);
packageDirectory.mkdirs();
File dummyContentFile = ManagedFileAccess.file(packageDirectory.getAbsolutePath(), "dummy.txt");
FileWriter wr = new FileWriter(dummyContentFile);
wr.write("Ain't nobody here but us chickens");
wr.flush();
wr.close();
}
private void assertThatDummyTempExists(File cacheDirectory, String dummyTempPackage) throws IOException {
File dummyTempDirectory = ManagedFileAccess.file(cacheDirectory.getAbsolutePath(), dummyTempPackage);
assertThat(dummyTempDirectory).exists();
File dummyContentFile = ManagedFileAccess.file(dummyTempDirectory.getAbsolutePath(), "dummy.txt");
assertThat(dummyContentFile).exists();
}
@Test
public void testCreatesIniIfDoesntExistAndCacheStaysIntact() throws IOException {
File cacheDirectory = ManagedFileAccess.fromPath(Files.createTempDirectory("fpcm-multithreadingTest"));
File cacheIni = ManagedFileAccess.file(cacheDirectory.getAbsolutePath(), "packages.ini");
createDummyPackage(cacheDirectory, "example.fhir.uv.myig", "1.2.3");
String dummyTempPackage = UUID.randomUUID().toString().toLowerCase();
createDummyTemp(cacheDirectory, dummyTempPackage);
assertThatDummyTempExists(cacheDirectory, dummyTempPackage);
assertThat(cacheIni).doesNotExist();
FilesystemPackageCacheManager filesystemPackageCacheManager = new FilesystemPackageCacheManager.Builder().withCacheFolder(cacheDirectory.getAbsolutePath()).build();
assertInitializedTestCacheIsValid(cacheDirectory, true);
}
@Test
public void testClearsCacheIfVersionIsWrong() throws IOException {
File cacheDirectory = ManagedFileAccess.fromPath(Files.createTempDirectory("fpcm-multithreadingTest"));
File cacheIni = ManagedFileAccess.file(cacheDirectory.getAbsolutePath(), "packages.ini");
createDummyPackage(cacheDirectory, "example.fhir.uv.myig", "1.2.3");
String dummyTempPackage = UUID.randomUUID().toString().toLowerCase();
createDummyTemp(cacheDirectory, dummyTempPackage);
assertThatDummyTempExists(cacheDirectory, dummyTempPackage);
IniFile ini = new IniFile(cacheIni.getAbsolutePath());
ini.setStringProperty("cache", "version", "2", null);
ini.save();
assertThat(cacheIni).exists();
FilesystemPackageCacheManager filesystemPackageCacheManager = new FilesystemPackageCacheManager.Builder().withCacheFolder(cacheDirectory.getAbsolutePath()).build();
assertInitializedTestCacheIsValid(cacheDirectory, false);
}
@Test
public void testCacheStaysIntactIfVersionIsTheSame() throws IOException {
File cacheDirectory = ManagedFileAccess.fromPath(Files.createTempDirectory("fpcm-multithreadingTest"));
File cacheIni = ManagedFileAccess.file(cacheDirectory.getAbsolutePath(), "packages.ini");
createDummyPackage(cacheDirectory, "example.fhir.uv.myig", "1.2.3");
String dummyTempPackage = UUID.randomUUID().toString().toLowerCase();
createDummyTemp(cacheDirectory, dummyTempPackage);
assertThatDummyTempExists(cacheDirectory, dummyTempPackage);
IniFile ini = new IniFile(cacheIni.getAbsolutePath());
ini.setStringProperty("cache", "version", "3", null);
ini.save();
assertThat(cacheIni).exists();
FilesystemPackageCacheManager filesystemPackageCacheManager = new FilesystemPackageCacheManager.Builder().withCacheFolder(cacheDirectory.getAbsolutePath()).build();
assertInitializedTestCacheIsValid(cacheDirectory, true);
}
private void assertInitializedTestCacheIsValid(File cacheDirectory, boolean dummyPackageShouldExist) throws IOException {
assertThat(cacheDirectory).exists();
File iniFile = ManagedFileAccess.file(cacheDirectory.getAbsolutePath(), "packages.ini");
assertThat(ManagedFileAccess.file(cacheDirectory.getAbsolutePath(), "packages.ini")).exists();
IniFile ini = new IniFile(iniFile.getAbsolutePath());
String version = ini.getStringProperty("cache", "version");
assertThat(version).isEqualTo("3");
File[] files = cacheDirectory.listFiles();
if (dummyPackageShouldExist) {
// Check that only packages.ini and our dummy package are in the cache. Our previous temp should be deleted.
assertThat(files).hasSize(2); // packages.ini and example.fhir.uv.myig#1.2.3 (directory)
File dummyPackage = ManagedFileAccess.file(cacheDirectory.getAbsolutePath(), "example.fhir.uv.myig#1.2.3");
assertThat(dummyPackage).exists();
File dummyContentFile = ManagedFileAccess.file(dummyPackage.getAbsolutePath(), "dummy.txt");
assertThat(dummyContentFile).exists();
} else {
// Check that only packages.ini is in the cache.
assertThat(files).hasSize(1);
}
}
@MethodSource("packageCacheMultiThreadTestParams")
@ParameterizedTest
public void packageCacheMultiThreadTest(final int threadTotal, final int packageCacheManagerTotal) throws IOException {

2
org.hl7.fhir.validation.cli/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>6.3.25-SNAPSHOT</version>
<version>6.3.26-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

33
org.hl7.fhir.validation/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>6.3.25-SNAPSHOT</version>
<version>6.3.26-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
@ -119,37 +119,6 @@
<optional>true</optional>
</dependency>
<!-- CQL-to-ELM -->
<dependency>
<groupId>info.cqframework</groupId>
<artifactId>cql</artifactId>
<version>${info_cqframework_version}</version>
</dependency>
<dependency>
<groupId>info.cqframework</groupId>
<artifactId>model</artifactId>
<version>${info_cqframework_version}</version>
</dependency>
<dependency>
<groupId>info.cqframework</groupId>
<artifactId>elm</artifactId>
<version>${info_cqframework_version}</version>
</dependency>
<dependency>
<groupId>info.cqframework</groupId>
<artifactId>cql-to-elm</artifactId>
<version>${info_cqframework_version}</version>
</dependency>
<dependency>
<groupId>info.cqframework</groupId>
<artifactId>quick</artifactId>
<version>${info_cqframework_version}</version>
</dependency>
<dependency>
<groupId>info.cqframework</groupId>
<artifactId>qdm</artifactId>
<version>${info_cqframework_version}</version>
</dependency>
<!-- OkHttpDependency -->
<dependency>
<groupId>com.squareup.okhttp3</groupId>

2
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java
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@ -46,7 +46,7 @@ import javax.annotation.Nonnull;
import org.apache.commons.lang3.NotImplementedException;
import org.apache.commons.lang3.StringUtils;
import org.fhir.ucum.Decimal;
import org.hl7.elm.r1.Code;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.PathEngineException;

4
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/special/TxTesterSorters.java
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@ -8,10 +8,10 @@ import java.util.Collections;
import java.util.Comparator;
import java.util.List;
import org.hl7.fhir.ParametersParameter;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.Extension;
import org.hl7.fhir.r5.model.OperationOutcome;
import org.hl7.fhir.r5.model.OperationOutcome.OperationOutcomeIssueComponent;

2
pom.xml
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@ -14,7 +14,7 @@
HAPI FHIR
-->
<artifactId>org.hl7.fhir.core</artifactId>
<version>6.3.25-SNAPSHOT</version>
<version>6.3.26-SNAPSHOT</version>
<packaging>pom</packaging>
<properties>