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

This commit is contained in:
Oliver Egger 2020-06-04 10:29:48 +02:00
parent 429774afb9 fcc18a0e39
commit bc4f99bed8
32 changed files with 944 additions and 782 deletions
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17
module-snapshot-publishing.yml
View File

@ -21,7 +21,9 @@ strategy:
module: "org.hl7.fhir.r5"
validator:
module: "org.hl7.fhir.validation"
maxParallel: 3
validator_cli:
module: "org.hl7.fhir.validation.cli"
maxParallel: 8
pool:
vmImage: "ubuntu-16.04"
@ -105,6 +107,15 @@ steps:
displayName: 'Deploy $(module) to Sonatype staging'
inputs:
mavenPomFile: '$(System.DefaultWorkingDirectory)/$(module)/pom.xml'
goals: deploy
options: '--settings $(System.DefaultWorkingDirectory)/settings.xml '
goals: clean deploy
options: '--settings $(System.DefaultWorkingDirectory)/settings.xml'
publishJUnitResults: false
# Clean any existing deployment artifacts
- task: Maven@3
displayName: 'Clean any existing deploy artifacts.'
inputs:
mavenPomFile: '$(System.DefaultWorkingDirectory)/$(module)/pom.xml'
goals: clean
options: '--settings $(System.DefaultWorkingDirectory)/settings.xml'
publishJUnitResults: false

4
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/ExtensionDefinitionGenerator.java
View File

@ -62,7 +62,7 @@ import org.hl7.fhir.r4.utils.NPMPackageGenerator;
import org.hl7.fhir.r4.utils.NPMPackageGenerator.Category;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.cache.NpmPackage;
import org.hl7.fhir.utilities.cache.PackageCacheManager;
import org.hl7.fhir.utilities.cache.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.cache.PackageGenerator.PackageType;
import org.hl7.fhir.utilities.cache.ToolsVersion;
@ -392,7 +392,7 @@ public class ExtensionDefinitionGenerator {
private List<StructureDefinition> loadSource() throws IOException, FHIRException {
List<StructureDefinition> list = new ArrayList<>();
PackageCacheManager pcm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
NpmPackage npm = pcm.loadPackage("hl7.fhir.core", sourceVersion.toCode());
if (sourceVersion == FHIRVersion._4_0_0)
context = SimpleWorkerContext.fromPackage(npm);

8
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/test/utils/TestingUtilities.java
View File

@ -44,15 +44,13 @@ import javax.xml.parsers.DocumentBuilderFactory;
import org.apache.commons.codec.binary.Base64;
import org.fhir.ucum.UcumEssenceService;
import org.fhir.ucum.UcumException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r4.context.IWorkerContext;
import org.hl7.fhir.r4.context.SimpleWorkerContext;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.utilities.CSFile;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.cache.PackageCacheManager;
import org.hl7.fhir.utilities.cache.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.cache.ToolsVersion;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
@ -73,9 +71,9 @@ public class TestingUtilities {
public static IWorkerContext context() {
if (fcontext == null) {
PackageCacheManager pcm;
FilesystemPackageCacheManager pcm;
try {
pcm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
fcontext = SimpleWorkerContext.fromPackage(pcm.loadPackage("hl7.fhir.core", "4.0.0"));
fcontext.setUcumService(new UcumEssenceService(TestingUtilities.resourceNameToFile("ucum", "ucum-essence.xml")));
fcontext.setExpansionProfile(new Parameters());

4
org.hl7.fhir.r4/src/test/java/org/hl7/fhir/r4/test/CDARoundTripTests.java
View File

@ -8,7 +8,7 @@ import org.hl7.fhir.r4.elementmodel.Element;
import org.hl7.fhir.r4.elementmodel.Manager;
import org.hl7.fhir.r4.elementmodel.Manager.FhirFormat;
import org.hl7.fhir.r4.formats.IParser.OutputStyle;
import org.hl7.fhir.utilities.cache.PackageCacheManager;
import org.hl7.fhir.utilities.cache.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.cache.ToolsVersion;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Disabled;
@ -29,7 +29,7 @@ public class CDARoundTripTests {
@BeforeAll
public void setUp() throws Exception {
context = new SimpleWorkerContext();
PackageCacheManager pcm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
context.loadFromPackage(pcm.loadPackage("hl7.fhir.core", "current"), null, "StructureDefinition");
context.loadFromPackage(pcm.loadPackage("hl7.fhir.cda", "current"), null, "StructureDefinition");
}

4
org.hl7.fhir.r4/src/test/java/org/hl7/fhir/r4/test/FHIRMappingLanguageTests.java
View File

@ -14,7 +14,7 @@ import org.hl7.fhir.r4.utils.StructureMapUtilities;
import org.hl7.fhir.r4.utils.StructureMapUtilities.ITransformerServices;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.cache.PackageCacheManager;
import org.hl7.fhir.utilities.cache.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.cache.ToolsVersion;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.junit.jupiter.api.BeforeAll;
@ -61,7 +61,7 @@ public class FHIRMappingLanguageTests implements ITransformerServices {
@BeforeAll
static public void setUp() throws Exception {
if (context == null) {
PackageCacheManager pcm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
context = SimpleWorkerContext.fromPackage(pcm.loadPackage("hl7.fhir.core", "4.0.0"));
jsonParser = new JsonParser();
jsonParser.setOutputStyle(OutputStyle.PRETTY);

3
org.hl7.fhir.r5/pom.xml
View File

@ -13,12 +13,13 @@
<packaging>bundle</packaging>
<dependencies>
<!-- HAPI Dependencies -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.utilities</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-base</artifactId>

7
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/test/utils/TestingUtilities.java
View File

@ -18,12 +18,11 @@ import org.fhir.ucum.UcumEssenceService;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.context.SimpleWorkerContext;
import org.hl7.fhir.r5.model.Parameters;
import org.hl7.fhir.r5.terminologies.TerminologyClientR5;
import org.hl7.fhir.utilities.CSFile;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.cache.PackageCacheManager;
import org.hl7.fhir.utilities.cache.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.cache.ToolsVersion;
import org.hl7.fhir.utilities.tests.BaseTestingUtilities;
import org.w3c.dom.Document;
@ -83,9 +82,9 @@ public class TestingUtilities extends BaseTestingUtilities {
fcontexts = new HashMap<>();
}
if (!fcontexts.containsKey(v)) {
PackageCacheManager pcm;
FilesystemPackageCacheManager pcm;
try {
pcm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
IWorkerContext fcontext = SimpleWorkerContext.fromPackage(pcm.loadPackage(VersionUtilities.packageForVersion(version), version));
fcontext.setUcumService(new UcumEssenceService(TestingUtilities.loadTestResourceStream("ucum", "ucum-essence.xml")));
fcontext.setExpansionProfile(new Parameters());

4
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/CDARoundTripTests.java
View File

@ -9,7 +9,7 @@ import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.r5.utils.FHIRPathEngine;
import org.hl7.fhir.utilities.cache.PackageCacheManager;
import org.hl7.fhir.utilities.cache.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.cache.ToolsVersion;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
@ -175,7 +175,7 @@ public class CDARoundTripTests {
@Test
public void testSimple() throws IOException {
PackageCacheManager pcm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
SimpleWorkerContext context = SimpleWorkerContext.fromPackage(pcm.loadPackage("hl7.fhir.r4.core", "4.0.1"));
context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "any.xml"), "any.xml", null);
context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "ii.xml"), "ii.xml", null);

4
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/FHIRMappingLanguageTests.java
View File

@ -33,7 +33,7 @@ import org.hl7.fhir.r5.utils.StructureMapUtilities;
import org.hl7.fhir.r5.utils.StructureMapUtilities.ITransformerServices;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.cache.PackageCacheManager;
import org.hl7.fhir.utilities.cache.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.cache.ToolsVersion;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.junit.jupiter.api.BeforeAll;
@ -67,7 +67,7 @@ public class FHIRMappingLanguageTests implements ITransformerServices {
@BeforeAll
public static void setUp() throws Exception {
PackageCacheManager pcm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
context = SimpleWorkerContext.fromPackage(pcm.loadPackage("hl7.fhir.core", "4.0.1"));
jsonParser = new JsonParser();
jsonParser.setOutputStyle(OutputStyle.PRETTY);

4
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/SnapShotGenerationTests.java
View File

@ -43,7 +43,7 @@ import org.hl7.fhir.r5.utils.IResourceValidator;
import org.hl7.fhir.r5.utils.XVerExtensionManager;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.cache.NpmPackage;
import org.hl7.fhir.utilities.cache.PackageCacheManager;
import org.hl7.fhir.utilities.cache.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.cache.ToolsVersion;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
@ -522,7 +522,7 @@ public class SnapShotGenerationTests {
pu.setDebug(test.isDebug());
pu.setIds(test.getSource(), false);
if (!TestingUtilities.context().hasPackage("hl7.fhir.xver-extensions", "0.0.4")) {
NpmPackage npm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION).loadPackage("hl7.fhir.xver-extensions", "0.0.4");
NpmPackage npm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION).loadPackage("hl7.fhir.xver-extensions", "0.0.4");
TestingUtilities.context().loadFromPackage(npm, new TestLoader(new String[]{"StructureDefinition"}), new String[]{"StructureDefinition"});
}
pu.setXver(new XVerExtensionManager(TestingUtilities.context()));

4
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/StructureMapUtilitiesTest.java
View File

@ -13,7 +13,7 @@ import org.hl7.fhir.r5.model.StructureMap;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.r5.utils.StructureMapUtilities;
import org.hl7.fhir.r5.utils.StructureMapUtilities.ITransformerServices;
import org.hl7.fhir.utilities.cache.PackageCacheManager;
import org.hl7.fhir.utilities.cache.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.cache.ToolsVersion;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
@ -25,7 +25,7 @@ public class StructureMapUtilitiesTest implements ITransformerServices {
// @BeforeAll
static public void setUp() throws Exception {
PackageCacheManager pcm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
context = SimpleWorkerContext.fromPackage(pcm.loadPackage("hl7.fhir.core", "4.0.0"));
}

1
org.hl7.fhir.report/pom.xml
View File

@ -12,7 +12,6 @@
<modelVersion>4.0.0</modelVersion>
<artifactId>org.hl7.fhir.report</artifactId>
<packaging>bundle</packaging>
<properties>

1
org.hl7.fhir.utilities/pom.xml
View File

@ -13,7 +13,6 @@
<packaging>bundle</packaging>
<dependencies>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-base</artifactId>

158
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/cache/BasePackageCacheManager.java vendored Normal file
View File

@ -0,0 +1,158 @@
package org.hl7.fhir.utilities.cache;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.utilities.Utilities;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.List;
import java.util.function.Function;
public abstract class BasePackageCacheManager implements IPackageCacheManager {
private static final Logger ourLog = LoggerFactory.getLogger(BasePackageCacheManager.class);
private List<String> myPackageServers = new ArrayList<>();
private Function<String, PackageClient> myClientFactory = address -> new CachingPackageClient(address);
/**
* Constructor
*/
public BasePackageCacheManager() {
super();
}
/**
* Provide a new client factory implementation
*/
public void setClientFactory(Function<String, PackageClient> theClientFactory) {
Validate.notNull(theClientFactory, "theClientFactory must not be null");
myClientFactory = theClientFactory;
}
public List<String> getPackageServers() {
return myPackageServers;
}
/**
* Add a package server that can be used to fetch remote packages
*/
public void addPackageServer(@Nonnull String thePackageServer) {
Validate.notBlank(thePackageServer, "thePackageServer must not be null or empty");
if (!myPackageServers.contains(thePackageServer)) {
myPackageServers.add(thePackageServer);
}
}
/**
* Load the latest version of the identified package from the cache - it it exists
*/
public NpmPackage loadPackageFromCacheOnly(String id) throws IOException {
return loadPackageFromCacheOnly(id, null);
}
/**
* Try to load a package from all registered package servers, and return <code>null</code>
* if it can not be found at any of them.
*/
@Nullable
protected InputStreamWithSrc loadFromPackageServer(String id, String version) {
for (String nextPackageServer : getPackageServers()) {
PackageClient packageClient = myClientFactory.apply(nextPackageServer);
try {
if (Utilities.noString(version)) {
version = packageClient.getLatestVersion(id);
}
InputStream stream = packageClient.fetch(id, version);
String url = packageClient.url(id, version);
return new InputStreamWithSrc(stream, url, version);
} catch (IOException e) {
ourLog.info("Failed to resolve package {}#{} from server: {}", id, version, nextPackageServer);
}
}
return null;
}
public abstract NpmPackage loadPackageFromCacheOnly(String id, @Nullable String version) throws IOException;
@Override
public String getPackageUrl(String packageId) throws IOException {
String result = null;
NpmPackage npm = loadPackageFromCacheOnly(packageId);
if (npm != null) {
return npm.canonical();
}
for (String nextPackageServer : getPackageServers()) {
result = getPackageUrl(packageId, nextPackageServer);
if (result != null) {
return result;
}
}
return result;
}
private String getPackageUrl(String packageId, String server) throws IOException {
PackageClient pc = myClientFactory.apply(server);
List<PackageClient.PackageInfo> res = pc.search(packageId, null, null, false);
if (res.size() == 0) {
return null;
} else {
return res.get(0).getUrl();
}
}
@Override
public String getPackageId(String canonicalUrl) throws IOException {
String result = null;
for (String nextPackageServer : getPackageServers()) {
result = getPackageId(canonicalUrl, nextPackageServer);
if (result != null) {
break;
}
}
return result;
}
private String getPackageId(String canonical, String server) throws IOException {
PackageClient pc = myClientFactory.apply(server);
List<PackageClient.PackageInfo> res = pc.search(null, canonical, null, false);
if (res.size() == 0) {
return null;
} else {
// this is driven by HL7 Australia (http://hl7.org.au/fhir/ is the canonical url for the base package, and the root for all the others)
for (PackageClient.PackageInfo pi : res) {
if (canonical.equals(pi.getCanonical())) {
return pi.getId();
}
}
return res.get(0).getId();
}
}
public class InputStreamWithSrc {
public InputStream stream;
public String url;
public String version;
public InputStreamWithSrc(InputStream stream, String url, String version) {
this.stream = stream;
this.url = url;
this.version = version;
}
}
}

58
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/cache/CachingPackageClient.java vendored Normal file
View File

@ -0,0 +1,58 @@
package org.hl7.fhir.utilities.cache;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.util.Date;
import java.util.List;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
/**
* Implementation of a package client that keeps a local disk cache of downloaded artifacts
* in order to avoid re-downloading things
*/
public class CachingPackageClient extends PackageClient {
private String cacheFolder;
public CachingPackageClient(String address) {
super(address);
try {
cacheFolder = Utilities.path(System.getProperty("user.home"), ".fhir", "package-client");
Utilities.createDirectory(cacheFolder);
} catch (IOException e) {
}
}
public boolean exists(String id, String ver) throws IOException {
List<PackageInfo> vl = getVersions(id);
for (PackageInfo pi : vl) {
if (ver.equals(pi.getVersion())) {
return true;
}
}
return false;
}
public InputStream fetchCached(String url) throws IOException {
File cacheFile = new File(Utilities.path(cacheFolder, fn(url)));
if (cacheFile.exists()) {
return new FileInputStream(cacheFile);
}
InputStream fetchedPackage = super.fetchCached(url);
TextFile.bytesToFile(TextFile.streamToBytes(fetchedPackage), cacheFile);
return new FileInputStream(cacheFile);
}
public Date getNewPackages(Date lastCalled, List<PackageInfo> updates) {
return null;
}
}

614
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/cache/PackageCacheManager.java → org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/cache/FilesystemPackageCacheManager.java vendored
View File

@ -30,9 +30,20 @@ package org.hl7.fhir.utilities.cache;
*/
import com.google.gson.GsonBuilder;
import com.google.gson.JsonArray;
import com.google.gson.JsonElement;
import com.google.gson.JsonObject;
import org.apache.commons.io.FileUtils;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.utilities.IniFile;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.cache.NpmPackage.NpmPackageFolder;
import org.hl7.fhir.utilities.json.JSONUtil;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.BufferedOutputStream;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
@ -58,31 +69,12 @@ import java.util.Locale;
import java.util.Map;
import java.util.Map.Entry;
import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
import org.apache.commons.compress.archivers.tar.TarArchiveInputStream;
import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream;
import org.apache.commons.io.FileUtils;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.utilities.IniFile;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.cache.NpmPackage.NpmPackageFolder;
import org.hl7.fhir.utilities.cache.PackageCacheManager.BuildRecord;
import org.hl7.fhir.utilities.cache.PackageCacheManager.BuildRecordSorter;
import org.hl7.fhir.utilities.cache.PackageCacheManager.InputStreamWithSrc;
import org.hl7.fhir.utilities.cache.PackageClient.PackageInfo;
import org.hl7.fhir.utilities.json.JSONUtil;
import com.google.gson.GsonBuilder;
import com.google.gson.JsonArray;
import com.google.gson.JsonElement;
import com.google.gson.JsonObject;
/**
* Package cache manager
* This is a package cache manager implementation that uses a local disk cache
*
* <p>
* API:
*
* <p>
* constructor
* getPackageUrl
* getPackageId
@ -90,153 +82,30 @@ import com.google.gson.JsonObject;
* addPackageToCache
*
* @author Grahame Grieve
*
*/
public class PackageCacheManager {
public class InputStreamWithSrc {
public InputStream stream;
public String url;
public String version;
public InputStreamWithSrc(InputStream stream, String url, String version) {
this.stream = stream;
this.url = url;
this.version = version;
}
}
public class BuildRecordSorter implements Comparator<BuildRecord> {
@Override
public int compare(BuildRecord arg0, BuildRecord arg1) {
return arg1.date.compareTo(arg0.date);
}
}
public class BuildRecord {
private String url;
private String packageId;
private String repo;
private Date date;
public BuildRecord(String url, String packageId, String repo, Date date) {
super();
this.url = url;
this.packageId = packageId;
this.repo = repo;
this.date = date;
}
public String getUrl() {
return url;
}
public String getPackageId() {
return packageId;
}
public String getRepo() {
return repo;
}
public Date getDate() {
return date;
}
}
/** if you don't provide and implementation of this interface, the PackageCacheManager will use the web directly.
*
* You can use this interface to
* @author graha
*
*/
public interface INetworkServices {
InputStream resolvePackage(String packageId, String version);
}
public class VersionHistory {
private String id;
private String canonical;
private String current;
private Map<String, String> versions = new HashMap<>();
public String getCanonical() {
return canonical;
}
public String getCurrent() {
return current;
}
public Map<String, String> getVersions() {
return versions;
}
public String getId() {
return id;
}
}
public class PackageEntry {
private byte[] bytes;
private String name;
public PackageEntry(String name) {
this.name = name;
}
public PackageEntry(String name, byte[] bytes) {
this.name = name;
this.bytes = bytes;
}
}
public interface CacheLockFunction<T> {
T get() throws IOException;
}
public class CacheLock {
private final File lockFile;
public CacheLock(String name) throws IOException {
this.lockFile = new File(cacheFolder, name + ".lock");
if (!lockFile.isFile()) {
TextFile.stringToFile("", lockFile);
}
}
public <T> T doWithLock(CacheLockFunction<T> f) throws FileNotFoundException, IOException {
try (FileChannel channel = new RandomAccessFile(lockFile, "rw").getChannel()) {
final FileLock fileLock = channel.lock();
T result = null;
try {
result = f.get();
} finally {
fileLock.release();
}
if (!lockFile.delete()) {
lockFile.deleteOnExit();
}
return result;
}
}
}
public class FilesystemPackageCacheManager extends BasePackageCacheManager implements IPackageCacheManager {
public static final String PRIMARY_SERVER = "http://packages.fhir.org";
public static final String SECONDARY_SERVER = "http://packages2.fhir.org/packages";
// private static final String SECONDARY_SERVER = "http://local.fhir.org:960/packages";
// private static final String SECONDARY_SERVER = "http://local.fhir.org:960/packages";
public static final String PACKAGE_REGEX = "^[a-z][a-z0-9\\_\\-]*(\\.[a-z0-9\\_\\-]+)+$";
public static final String PACKAGE_VERSION_REGEX = "^[a-z][a-z0-9\\_\\-]*(\\.[a-z0-9\\_\\-]+)+\\#[a-z0-9\\-\\_]+(\\.[a-z0-9\\-\\_]+)*$";
private static final Logger ourLog = LoggerFactory.getLogger(FilesystemPackageCacheManager.class);
private static final String CACHE_VERSION = "3"; // second version - see wiki page
private String cacheFolder;
private boolean progress = true;
private List<NpmPackage> temporaryPackages = new ArrayList<NpmPackage>();
private List<NpmPackage> temporaryPackages = new ArrayList<>();
private boolean buildLoaded = false;
private Map<String, String> ciList = new HashMap<String, String>();
private JsonArray buildInfo;
// private List<String> allUrls;
// private Map<String, VersionHistory> historyCache = new HashMap<>();
/**
* Constructor
*/
public FilesystemPackageCacheManager(boolean userMode, int toolsVersion) throws IOException {
addPackageServer(PRIMARY_SERVER);
addPackageServer(SECONDARY_SERVER);
// ========================= Initialization ============================================================================
public PackageCacheManager(boolean userMode, int toolsVersion) throws IOException {
if (userMode)
cacheFolder = Utilities.path(System.getProperty("user.home"), ".fhir", "packages");
else
@ -244,7 +113,7 @@ public class PackageCacheManager {
if (!(new File(cacheFolder).exists()))
Utilities.createDirectory(cacheFolder);
if (!(new File(Utilities.path(cacheFolder, "packages.ini")).exists()))
TextFile.stringToFile("[cache]\r\nversion="+CACHE_VERSION+"\r\n\r\n[urls]\r\n\r\n[local]\r\n\r\n", Utilities.path(cacheFolder, "packages.ini"), false);
TextFile.stringToFile("[cache]\r\nversion=" + CACHE_VERSION + "\r\n\r\n[urls]\r\n\r\n[local]\r\n\r\n", Utilities.path(cacheFolder, "packages.ini"), false);
createIniFile();
}
@ -259,16 +128,10 @@ public class PackageCacheManager {
}
}
// ========================= Utilities ============================================================================
public String getFolder() {
return cacheFolder;
}
private static String userDir() throws IOException {
return Utilities.path(System.getProperty("user.home"), ".fhir", "packages");
}
private List<String> sorted(String[] keys) {
List<String> names = new ArrayList<String>();
for (String s : keys)
@ -304,8 +167,7 @@ public class PackageCacheManager {
}
return null; // must return something
});
}
else if (!f.getName().equals("packages.ini"))
} else if (!f.getName().equals("packages.ini"))
FileUtils.forceDelete(f);
}
IniFile ini = new IniFile(Utilities.path(cacheFolder, "packages.ini"));
@ -326,114 +188,66 @@ public class PackageCacheManager {
private void checkValidVersionString(String version, String id) {
if (Utilities.noString(version)) {
throw new FHIRException("Cannot add package "+id+" to the package cache - a version must be provided");
throw new FHIRException("Cannot add package " + id + " to the package cache - a version must be provided");
}
if (version.startsWith("file:")) {
throw new FHIRException("Cannot add package "+id+" to the package cache - the version '"+version+"' is illegal in this context");
throw new FHIRException("Cannot add package " + id + " to the package cache - the version '" + version + "' is illegal in this context");
}
for (char ch : version.toCharArray()) {
if (!Character.isAlphabetic(ch) && !Character.isDigit(ch) && !Utilities.existsInList(ch, '.', '-')) {
throw new FHIRException("Cannot add package "+id+" to the package cache - the version '"+version+"' is illegal (ch '"+ch+"'");
throw new FHIRException("Cannot add package " + id + " to the package cache - the version '" + version + "' is illegal (ch '" + ch + "'");
}
}
}
private String getPackageId(String canonical, String server) throws IOException {
PackageClient pc = new PackageClient(server);
List<PackageInfo> res = pc.search(null, canonical, null, false);
if (res.size() == 0) {
return null;
} else {
// this is driven by HL7 Australia (http://hl7.org.au/fhir/ is the canonical url for the base package, and the root for all the others)
for (PackageInfo pi : res) {
if (canonical.equals(pi.getCanonical())) {
return pi.getId();
}
}
return res.get(0).getId();
}
}
private String getPackageUrl(String packageId, String server) throws IOException {
PackageClient pc = new PackageClient(server);
List<PackageInfo> res = pc.search(packageId, null, null, false);
if (res.size() == 0) {
return null;
} else {
return res.get(0).getUrl();
}
}
private void listSpecs(Map<String, String> specList, String server) throws IOException {
PackageClient pc = new PackageClient(server);
List<PackageInfo> matches = pc.search(null, null, null, false);
for (PackageInfo m : matches) {
CachingPackageClient pc = new CachingPackageClient(server);
List<PackageClient.PackageInfo> matches = pc.search(null, null, null, false);
for (PackageClient.PackageInfo m : matches) {
if (!specList.containsKey(m.getId())) {
specList.put(m.getId(), m.getUrl());
}
}
}
private InputStreamWithSrc loadFromPackageServer(String id, String v) {
PackageClient pc = new PackageClient(PRIMARY_SERVER);
String u = null;
InputStream stream;
try {
if (Utilities.noString(v)) {
v = pc.getLatestVersion(id);
protected InputStreamWithSrc loadFromPackageServer(String id, String version) {
InputStreamWithSrc retVal = super.loadFromPackageServer(id, version);
if (retVal != null) {
return retVal;
}
stream = pc.fetch(id, v);
u = pc.url(id, v);
} catch (IOException e) {
pc = new PackageClient(SECONDARY_SERVER);
try {
if (Utilities.noString(v)) {
v = pc.getLatestVersion(id);
}
stream = pc.fetch(id, v);
u = pc.url(id, v);
} catch (IOException e1) {
// ok, well, we'll try the old way
return fetchTheOldWay(id, v);
}
}
return new InputStreamWithSrc(stream, pc.url(id, v), v);
return fetchTheOldWay(id, version);
}
public String getLatestVersion(String id) throws IOException {
PackageClient pc = new PackageClient(PRIMARY_SERVER);
for (String nextPackageServer : getPackageServers()) {
CachingPackageClient pc = new CachingPackageClient(nextPackageServer);
try {
return pc.getLatestVersion(id);
} catch (IOException e) {
pc = new PackageClient(SECONDARY_SERVER);
try {
return pc.getLatestVersion(id);
} catch (IOException e1) {
ourLog.info("Failed to determine latest version of package {} from server: {}", id, nextPackageServer);
}
}
return fetchVersionTheOldWay(id);
}
}
}
private NpmPackage loadPackageFromFile(String id, String folder) throws IOException {
File f = new File(Utilities.path(folder, id));
if (!f.exists()) {
throw new FHIRException("Package '"+id+" not found in folder "+folder);
throw new FHIRException("Package '" + id + " not found in folder " + folder);
}
if (!f.isDirectory()) {
throw new FHIRException("File for '"+id+" found in folder "+folder+", not a folder");
throw new FHIRException("File for '" + id + " found in folder " + folder + ", not a folder");
}
File fp = new File(Utilities.path(folder, id, "package", "package.json"));
if (!fp.exists()) {
throw new FHIRException("Package '"+id+" found in folder "+folder+", but does not contain a package.json file in /package");
throw new FHIRException("Package '" + id + " found in folder " + folder + ", but does not contain a package.json file in /package");
}
return NpmPackage.fromFolder(f.getAbsolutePath());
}
// ========================= Package Mgmt API =======================================================================
/**
* Clear the cache
*
@ -443,6 +257,8 @@ public class PackageCacheManager {
clearCache();
}
// ========================= Utilities ============================================================================
/**
* Remove a particular package from the cache
*
@ -451,13 +267,13 @@ public class PackageCacheManager {
* @throws IOException
*/
public void removePackage(String id, String ver) throws IOException {
new CacheLock(id+"#"+ver).doWithLock(() -> {
String f = Utilities.path(cacheFolder, id+"#"+ver);
new CacheLock(id + "#" + ver).doWithLock(() -> {
String f = Utilities.path(cacheFolder, id + "#" + ver);
File ff = new File(f);
if (ff.exists()) {
Utilities.clearDirectory(f);
IniFile ini = new IniFile(Utilities.path(cacheFolder, "packages.ini"));
ini.removeProperty("packages", id+"#"+ver);
ini.removeProperty("packages", id + "#" + ver);
ini.save();
ff.delete();
}
@ -465,20 +281,9 @@ public class PackageCacheManager {
});
}
/**
* Load the latest version of the identified package from the cache - it it exists
*
* @param id
* @return
* @throws IOException
*/
public NpmPackage loadPackageFromCacheOnly(String id) throws IOException {
return loadPackageFromCacheOnly(id, null);
}
/**
* Load the identified package from the cache - it it exists
*
* <p>
* This is for special purpose only (testing, control over speed of loading).
* Generally, use the loadPackage method
*
@ -487,6 +292,7 @@ public class PackageCacheManager {
* @return
* @throws IOException
*/
@Override
public NpmPackage loadPackageFromCacheOnly(String id, String version) throws IOException {
if (!Utilities.noString(version) && version.startsWith("file:")) {
return loadPackageFromFile(id, version.substring(5));
@ -501,7 +307,7 @@ public class PackageCacheManager {
}
}
for (String f : sorted(new File(cacheFolder).list())) {
if (f.equals(id+"#"+version) || (Utilities.noString(version) && f.startsWith(id+"#"))) {
if (f.equals(id + "#" + version) || (Utilities.noString(version) && f.startsWith(id + "#"))) {
return loadPackageInfo(Utilities.path(cacheFolder, f));
}
}
@ -514,31 +320,32 @@ public class PackageCacheManager {
/**
* Add an already fetched package to the cache
*/
public NpmPackage addPackageToCache(String id, String version, InputStream tgz, String sourceDesc) throws IOException {
@Override
public NpmPackage addPackageToCache(String id, String version, InputStream packageTgzInputStream, String sourceDesc) throws IOException {
checkValidVersionString(version, id);
if (progress ) {
System.out.println("Installing "+id+"#"+(version == null ? "?" : version)+" to the package cache");
if (progress) {
System.out.println("Installing " + id + "#" + (version == null ? "?" : version) + " to the package cache");
System.out.print(" Fetching:");
}
NpmPackage npm = NpmPackage.fromPackage(tgz, sourceDesc, true);
NpmPackage npm = NpmPackage.fromPackage(packageTgzInputStream, sourceDesc, true);
if (progress ) {
if (progress) {
System.out.println();
System.out.print(" Installing: ");
}
if (npm.name() == null || id == null || !id.equals(npm.name())) {
if (!id.equals("hl7.fhir.r5.core")) {// 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 " + npm.name());
}
}
if (version == null)
version = npm.version();
String v = version;
return new CacheLock(id+"#"+version).doWithLock(() -> {
return new CacheLock(id + "#" + version).doWithLock(() -> {
NpmPackage pck = null;
String packRoot = Utilities.path(cacheFolder, id+"#"+v);
String packRoot = Utilities.path(cacheFolder, id + "#" + v);
try {
// ok, now we have a lock on it... check if something created it while we were waiting
if (!new File(packRoot).exists()) {
@ -549,7 +356,7 @@ public class PackageCacheManager {
int c = 0;
int size = 0;
for (Entry<String, NpmPackageFolder> e : npm.getFolders().entrySet()) {
String dir = e.getKey().equals("package") ? Utilities.path(packRoot, "package") : Utilities.path(packRoot, "package", e.getKey());;
String dir = e.getKey().equals("package") ? Utilities.path(packRoot, "package") : Utilities.path(packRoot, "package", e.getKey());
if (!(new File(dir).exists()))
Utilities.createDirectory(dir);
for (Entry<String, byte[]> fe : e.getValue().getContent().entrySet()) {
@ -573,8 +380,8 @@ public class PackageCacheManager {
IniFile ini = new IniFile(Utilities.path(cacheFolder, "packages.ini"));
ini.setTimeStampFormat("yyyyMMddhhmmss");
ini.setTimestampProperty("packages", id+"#"+v, Timestamp.from(Instant.now()), null);
ini.setIntegerProperty("package-sizes", id+"#"+v, size, null);
ini.setTimestampProperty("packages", id + "#" + v, Timestamp.from(Instant.now()), null);
ini.setIntegerProperty("package-sizes", id + "#" + v, size, null);
ini.save();
if (progress)
System.out.println(" done.");
@ -591,12 +398,12 @@ public class PackageCacheManager {
npm.getNpm().remove("version");
npm.getNpm().addProperty("version", v);
}
TextFile.stringToFile(new GsonBuilder().setPrettyPrinting().create().toJson(npm.getNpm()), Utilities.path(cacheFolder, id+"#"+v, "package", "package.json"), false);
TextFile.stringToFile(new GsonBuilder().setPrettyPrinting().create().toJson(npm.getNpm()), Utilities.path(cacheFolder, id + "#" + v, "package", "package.json"), false);
}
} catch (Exception e) {
try {
// don't leave a half extracted package behind
System.out.println("Clean up package "+packRoot+" because installation failed: "+e.getMessage());
System.out.println("Clean up package " + packRoot + " because installation failed: " + e.getMessage());
e.printStackTrace();
Utilities.clearDirectory(packRoot);
new File(packRoot).delete();
@ -609,35 +416,13 @@ public class PackageCacheManager {
});
}
public String getPackageId(String canonical) throws IOException {
String result = null;
if (result == null) {
result = getPackageId(canonical, PRIMARY_SERVER);
}
if (result == null) {
result = getPackageId(canonical, SECONDARY_SERVER);
}
if (result == null) {
result = getPackageIdFromBuildList(canonical);
}
return result;
}
@Override
public String getPackageUrl(String packageId) throws IOException {
String result = null;
NpmPackage npm = loadPackageFromCacheOnly(packageId);
if (npm != null) {
return npm.canonical();
}
if (result == null) {
getPackageUrl(packageId, PRIMARY_SERVER);
}
if (result == null) {
result = getPackageUrl(packageId, SECONDARY_SERVER);
}
String result = super.getPackageUrl(packageId);
if (result == null) {
result = getPackageUrlFromBuildList(packageId);
}
return result;
}
@ -645,51 +430,47 @@ public class PackageCacheManager {
for (NpmPackage p : temporaryPackages) {
specList.put(p.name(), p.canonical());
}
listSpecs(specList, PRIMARY_SERVER);
listSpecs(specList, SECONDARY_SERVER);
for (String next : getPackageServers()) {
listSpecs(specList, next);
}
addCIBuildSpecs(specList);
}
public NpmPackage loadPackage(String id, String v) throws FHIRException, IOException {
@Override
public NpmPackage loadPackage(String id, String version) throws FHIRException, IOException {
//ok, try to resolve locally
if (!Utilities.noString(v) && v.startsWith("file:")) {
return loadPackageFromFile(id, v.substring(5));
if (!Utilities.noString(version) && version.startsWith("file:")) {
return loadPackageFromFile(id, version.substring(5));
}
NpmPackage p = loadPackageFromCacheOnly(id, v);
NpmPackage p = loadPackageFromCacheOnly(id, version);
if (p != null) {
if ("current".equals(v)) {
if ("current".equals(version)) {
p = checkCurrency(id, p);
}
if (p != null)
return p;
}
if ("dev".equals(v)) {
if ("dev".equals(version)) {
p = loadPackageFromCacheOnly(id, "current");
p = checkCurrency(id, p);
if (p != null)
return p;
v = "current";
version = "current";
}
// nup, don't have it locally (or it's expired)
InputStreamWithSrc source;
if ("current".equals(v)) {
FilesystemPackageCacheManager.InputStreamWithSrc source;
if ("current".equals(version)) {
// special case - fetch from ci-build server
source = loadFromCIBuild(id);
} else {
source = loadFromPackageServer(id, v);
source = loadFromPackageServer(id, version);
}
return addPackageToCache(id, v == null ? source.version : v, source.stream, source.url);
return addPackageToCache(id, version == null ? source.version : version, source.stream, source.url);
}
// ---------- Current Build SubSystem --------------------------------------------------------------------------------------
private boolean buildLoaded = false;
private Map<String, String> ciList = new HashMap<String, String>();
private JsonArray buildInfo;
private InputStream fetchFromUrlSpecific(String source, boolean optional) throws FHIRException {
try {
URL url = new URL(source);
@ -709,32 +490,13 @@ public class PackageCacheManager {
InputStream stream = fetchFromUrlSpecific(Utilities.pathURL(ciList.get(id), "package.tgz"), false);
return new InputStreamWithSrc(stream, Utilities.pathURL(ciList.get(id), "package.tgz"), "current");
} else if (id.startsWith("hl7.fhir.r5")) {
InputStream stream = fetchFromUrlSpecific(Utilities.pathURL("http://build.fhir.org", id+".tgz"), false);
return new InputStreamWithSrc(stream, Utilities.pathURL("http://build.fhir.org", id+".tgz"), "current");
InputStream stream = fetchFromUrlSpecific(Utilities.pathURL("http://build.fhir.org", id + ".tgz"), false);
return new InputStreamWithSrc(stream, Utilities.pathURL("http://build.fhir.org", id + ".tgz"), "current");
} else {
throw new FHIRException("The package '"+id+"' has not entry on the current build server");
throw new FHIRException("The package '" + id + "' has not entry on the current build server");
}
}
private String getPackageIdFromBuildList(String canonical) throws IOException {
checkBuildLoaded();
if (buildInfo != null) {
for (JsonElement n : buildInfo) {
JsonObject o = (JsonObject) n;
if (canonical.equals(JSONUtil.str(o, "url"))) {
return JSONUtil.str(o, "package-id");
}
}
for (JsonElement n : buildInfo) {
JsonObject o = (JsonObject) n;
if (JSONUtil.str(o, "url").startsWith(canonical+"/ImplementationGuide/")) {
return JSONUtil.str(o, "package-id");
}
}
}
return null;
}
private String getPackageUrlFromBuildList(String packageId) throws IOException {
checkBuildLoaded();
for (JsonElement n : buildInfo) {
@ -746,7 +508,6 @@ public class PackageCacheManager {
return null;
}
private void addCIBuildSpecs(Map<String, String> specList) throws IOException {
checkBuildLoaded();
for (JsonElement n : buildInfo) {
@ -757,6 +518,38 @@ public class PackageCacheManager {
}
}
@Override
public String getPackageId(String canonicalUrl) throws IOException {
String retVal = super.getPackageId(canonicalUrl);
if (retVal == null) {
retVal = getPackageIdFromBuildList(canonicalUrl);
}
return retVal;
}
// ========================= Package Mgmt API =======================================================================
private String getPackageIdFromBuildList(String canonical) throws IOException {
checkBuildLoaded();
if (buildInfo != null) {
for (JsonElement n : buildInfo) {
JsonObject o = (JsonObject) n;
if (canonical.equals(JSONUtil.str(o, "url"))) {
return JSONUtil.str(o, "package-id");
}
}
for (JsonElement n : buildInfo) {
JsonObject o = (JsonObject) n;
if (JSONUtil.str(o, "url").startsWith(canonical + "/ImplementationGuide/")) {
return JSONUtil.str(o, "package-id");
}
}
}
return null;
}
private NpmPackage checkCurrency(String id, NpmPackage p) throws IOException {
checkBuildLoaded();
@ -780,12 +573,11 @@ public class PackageCacheManager {
try {
loadFromBuildServer();
} catch (Exception e) {
System.out.println("Error connecting to build server - running without build ("+e.getMessage()+")");
System.out.println("Error connecting to build server - running without build (" + e.getMessage() + ")");
}
return false;
}
private void loadFromBuildServer() throws IOException {
URL url = new URL("https://build.fhir.org/ig/qas.json?nocache=" + System.currentTimeMillis());
HttpURLConnection connection = (HttpURLConnection) url.openConnection();
@ -807,13 +599,13 @@ public class PackageCacheManager {
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());
ciList.put(bld.getPackageId(), "https://build.fhir.org/ig/" + bld.getRepo());
}
}
buildLoaded = true; // whether it succeeds or not
}
// private String buildPath(String url) {
// private String buildPath(String url) {
// for (JsonElement e : buildInfo) {
// JsonObject j = (JsonObject) e;
// if (j.has("url") && (url.equals(j.get("url").getAsString()) || j.get("url").getAsString().startsWith(url+"/ImplementationGuide"))) {
@ -825,7 +617,7 @@ public class PackageCacheManager {
//
private String getRepo(String path) {
String[] p = path.split("\\/");
return p[0]+"/"+p[1];
return p[0] + "/" + p[1];
}
private Date readDate(String s) {
@ -849,7 +641,7 @@ public class PackageCacheManager {
}
}
if (url == null) {
throw new FHIRException("Unable to resolve package id "+id+"#"+v);
throw new FHIRException("Unable to resolve package id " + id + "#" + v);
}
if (url.contains("/ImplementationGuide/")) {
url = url.substring(0, url.indexOf("/ImplementationGuide/"));
@ -866,11 +658,11 @@ public class PackageCacheManager {
InputStreamWithSrc src = new InputStreamWithSrc(fetchFromUrlSpecific(pv, true), pv, v);
return src;
} catch (Exception e1) {
throw new FHIRException("Error fetching package directly ("+pv+"), or fetching package list for "+id+" from "+pu+": "+e1.getMessage(), e1);
throw new FHIRException("Error fetching package directly (" + pv + "), or fetching package list for " + id + " from " + pu + ": " + e1.getMessage(), e1);
}
}
if (!id.equals(JSONUtil.str(json, "package-id")))
throw new FHIRException("Package ids do not match in "+pu+": "+id+" vs "+JSONUtil.str(json, "package-id"));
throw new FHIRException("Package ids do not match in " + pu + ": " + id + " vs " + JSONUtil.str(json, "package-id"));
for (JsonElement e : json.getAsJsonArray("list")) {
JsonObject vo = (JsonObject) e;
if (v.equals(JSONUtil.str(vo, "version"))) {
@ -883,6 +675,9 @@ public class PackageCacheManager {
return null;
}
// ---------- Current Build SubSystem --------------------------------------------------------------------------------------
private String fetchVersionTheOldWay(String id) throws IOException {
String url = getUrlForPackage(id);
if (url == null) {
@ -893,12 +688,12 @@ public class PackageCacheManager {
}
}
if (url == null) {
throw new FHIRException("Unable to resolve package id "+id);
throw new FHIRException("Unable to resolve package id " + id);
}
String pu = Utilities.pathURL(url, "package-list.json");
JsonObject json = fetchJson(pu);
if (!id.equals(JSONUtil.str(json, "package-id")))
throw new FHIRException("Package ids do not match in "+pu+": "+id+" vs "+JSONUtil.str(json, "package-id"));
throw new FHIRException("Package ids do not match in " + pu + ": " + id + " vs " + JSONUtil.str(json, "package-id"));
for (JsonElement e : json.getAsJsonArray("list")) {
JsonObject vo = (JsonObject) e;
if (JSONUtil.bool(vo, "current")) {
@ -926,6 +721,135 @@ public class PackageCacheManager {
return res;
}
/**
* if you don't provide and implementation of this interface, the PackageCacheManager will use the web directly.
* <p>
* You can use this interface to
*
* @author graha
*/
public interface INetworkServices {
InputStream resolvePackage(String packageId, String version);
}
public interface CacheLockFunction<T> {
T get() throws IOException;
}
public class BuildRecordSorter implements Comparator<BuildRecord> {
@Override
public int compare(BuildRecord arg0, BuildRecord arg1) {
return arg1.date.compareTo(arg0.date);
}
}
public class BuildRecord {
private String url;
private String packageId;
private String repo;
private Date date;
public BuildRecord(String url, String packageId, String repo, Date date) {
super();
this.url = url;
this.packageId = packageId;
this.repo = repo;
this.date = date;
}
public String getUrl() {
return url;
}
public String getPackageId() {
return packageId;
}
public String getRepo() {
return repo;
}
public Date getDate() {
return date;
}
}
public class VersionHistory {
private String id;
private String canonical;
private String current;
private Map<String, String> versions = new HashMap<>();
public String getCanonical() {
return canonical;
}
public String getCurrent() {
return current;
}
public Map<String, String> getVersions() {
return versions;
}
public String getId() {
return id;
}
}
public class PackageEntry {
private byte[] bytes;
private String name;
public PackageEntry(String name) {
this.name = name;
}
public PackageEntry(String name, byte[] bytes) {
this.name = name;
this.bytes = bytes;
}
}
public class CacheLock {
private final File lockFile;
public CacheLock(String name) throws IOException {
this.lockFile = new File(cacheFolder, name + ".lock");
if (!lockFile.isFile()) {
TextFile.stringToFile("", lockFile);
}
}
public <T> T doWithLock(CacheLockFunction<T> f) throws FileNotFoundException, IOException {
try (FileChannel channel = new RandomAccessFile(lockFile, "rw").getChannel()) {
final FileLock fileLock = channel.lock();
T result = null;
try {
result = f.get();
} finally {
fileLock.release();
}
if (!lockFile.delete()) {
lockFile.deleteOnExit();
}
return result;
}
}
}
//public List<String> getUrls() throws IOException {

17
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/cache/IPackageCacheManager.java vendored Normal file
View File

@ -0,0 +1,17 @@
package org.hl7.fhir.utilities.cache;
import org.hl7.fhir.exceptions.FHIRException;
import java.io.IOException;
import java.io.InputStream;
public interface IPackageCacheManager {
String getPackageId(String canonicalUrl) throws IOException;
NpmPackage addPackageToCache(String id, String version, InputStream packageTgzInputStream, String sourceDesc) throws IOException;
String getPackageUrl(String packageId) throws IOException;
NpmPackage loadPackage(String id, String version) throws FHIRException, IOException;
}

53
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/cache/NpmPackage.java vendored
View File

@ -35,12 +35,12 @@ import java.io.BufferedOutputStream;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.nio.charset.Charset;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
@ -57,20 +57,14 @@ import org.apache.commons.compress.archivers.tar.TarArchiveInputStream;
import org.apache.commons.compress.archivers.tar.TarArchiveOutputStream;
import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream;
import org.apache.commons.compress.compressors.gzip.GzipCompressorOutputStream;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
import org.hl7.fhir.utilities.IniFile;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.cache.NpmPackage.IndexVersionSorter;
import org.hl7.fhir.utilities.cache.PackageCacheManager.PackageEntry;
import org.hl7.fhir.utilities.cache.PackageGenerator.PackageType;
import org.hl7.fhir.utilities.json.JSONUtil;
import org.hl7.fhir.utilities.json.JsonTrackingParser;
import com.google.common.base.Charsets;
import com.google.gson.GsonBuilder;
import com.google.gson.JsonArray;
import com.google.gson.JsonElement;
@ -109,7 +103,7 @@ public class NpmPackage {
public class NpmPackageFolder {
private String name;
private Map<String, List<String>> types = new HashMap<>();
private Map<String, byte[]> content = new HashMap<String, byte[]>();
private Map<String, byte[]> content = new HashMap<>();
private JsonObject index;
private File folder;
@ -118,6 +112,10 @@ public class NpmPackage {
this.name = name;
}
public Map<String, List<String>> getTypes() {
return types;
}
public String getName() {
return name;
}
@ -198,17 +196,18 @@ public class NpmPackage {
private JsonObject npm;
private Map<String, NpmPackageFolder> folders = new HashMap<>();
private boolean changedByLoader; // internal qa only!
private Map<String, Object> userData = new HashMap<>();
/**
* Constructor
*/
private NpmPackage() {
super();
}
// public NpmPackage(JsonObject npm, Map<String, byte[]> content, List<String> folders) {
// this.path = null;
// this.content = content;
// this.npm = npm;
// this.folders = folders;
// }
/**
* Factory method that parses a package from an extracted folder
*/
public static NpmPackage fromFolder(String path) throws IOException {
NpmPackage res = new NpmPackage();
loadFiles(res, path, new File(path));
@ -216,6 +215,19 @@ public class NpmPackage {
return res;
}
/**
* Factory method that starts a new empty package using the given PackageGenerator to create the manifest
*/
public static NpmPackage empty(PackageGenerator thePackageGenerator) {
NpmPackage retVal = new NpmPackage();
retVal.npm = thePackageGenerator.getRootJsonObject();
return retVal;
}
public Map<String, Object> getUserData() {
return userData;
}
public static void loadFiles(NpmPackage res, String path, File source, String... exemptions) throws FileNotFoundException, IOException {
res.npm = (JsonObject) new com.google.gson.JsonParser().parse(TextFile.fileToString(Utilities.path(path, "package", "package.json")));
res.path = path;
@ -788,7 +800,7 @@ public class NpmPackage {
TextFile.bytesToFile(b, Utilities.path(dir.getAbsolutePath(), n, s));
}
}
byte[] cnt = indexer.build().getBytes(Charset.forName("UTF-8"));
byte[] cnt = indexer.build().getBytes(StandardCharsets.UTF_8);
TextFile.bytesToFile(cnt, Utilities.path(dir.getAbsolutePath(), n, ".index.json"));
}
byte[] cnt = TextFile.stringToBytes(new GsonBuilder().setPrettyPrinting().create().toJson(npm), false);
@ -826,7 +838,7 @@ public class NpmPackage {
tar.closeArchiveEntry();
}
}
byte[] cnt = indexer.build().getBytes(Charset.forName("UTF-8"));
byte[] cnt = indexer.build().getBytes(StandardCharsets.UTF_8);
TarArchiveEntry entry = new TarArchiveEntry(n+"/.index.json");
entry.setSize(cnt.length);
tar.putArchiveEntry(entry);
@ -849,7 +861,9 @@ public class NpmPackage {
stream.write(b);
}
/**
* Keys are resource type names, values are filenames
*/
public Map<String, List<String>> getTypes() {
return folders.get("package").types;
}
@ -941,6 +955,9 @@ public class NpmPackage {
}
public void addFile(String folderName, String name, byte[] cnt, String type) {
if (!folders.containsKey(folderName)) {
folders.put(folderName, new NpmPackageFolder(folderName));
}
NpmPackageFolder folder = folders.get(folderName);
folder.content.put(name, cnt);
if (!folder.types.containsKey(type))

30
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/cache/PackageClient.java vendored
View File

@ -1,5 +1,14 @@
package org.hl7.fhir.utilities.cache;
import com.google.gson.JsonArray;
import com.google.gson.JsonElement;
import com.google.gson.JsonObject;
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.json.JSONUtil;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
@ -13,18 +22,6 @@ import java.util.Date;
import java.util.List;
import java.util.Set;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.cache.PackageClient.PackageInfo;
import org.hl7.fhir.utilities.json.JSONUtil;
import com.google.gson.JsonArray;
import com.google.gson.JsonElement;
import com.google.gson.JsonObject;
public class PackageClient {
public class PackageInfo {
@ -109,15 +106,10 @@ public class PackageClient {
}
public InputStream fetchCached(String url) throws IOException, FileNotFoundException {
File cacheFile = new File(Utilities.path(cacheFolder, fn(url)));
if (cacheFile.exists()) {
return new FileInputStream(cacheFile);
}
TextFile.bytesToFile(TextFile.streamToBytes(fetchUrl(url, null)), cacheFile);
return new FileInputStream(cacheFile);
return fetchUrl(url, null);
}
private String fn(String url) {
protected String fn(String url) {
String[] p = url.split("\\/");
return p[2]+"-"+p[p.length-2]+"-"+p[p.length-1]+".tgz";
}

12
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/cache/PackageGenerator.java vendored
View File

@ -63,9 +63,14 @@ public class PackageGenerator {
throw new Error("Unknown Type");
}
}
private OutputStream stream;
private JsonObject object;
public PackageGenerator() {
object = new JsonObject();
}
public PackageGenerator(OutputStream stream) {
super();
this.stream = stream;
@ -80,6 +85,10 @@ public class PackageGenerator {
}
public JsonObject getRootJsonObject() {
return object;
}
public void commit() throws IOException {
Gson gson = new GsonBuilder().setPrettyPrinting().create();
String json = gson.toJson(object);
@ -91,7 +100,8 @@ public class PackageGenerator {
}
public PackageGenerator name(String value) {
object.addProperty("name", "@fhir/"+value);
// NOTE: I removed a prefix of "@fhir/" here. What was this for? -JA
object.addProperty("name", value);
return this;
}

25
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/tests/BaseTestingUtilities.java
View File

@ -22,8 +22,9 @@ public class BaseTestingUtilities {
* the name of the project directory to something other than 'fhir-test-cases', or move it to another location, not
* at the same directory level as the core project.
*/
if (new File("../../fhir-test-cases").exists() && isTryToLoadFromFileSystem()) {
String n = Utilities.path(System.getProperty("user.dir"), "..", "..", "fhir-test-cases", Utilities.path(paths));
String dir = System.getenv("FHIR-TEST-CASES");
if (dir != null && new File(dir).exists()) {
String n = Utilities.path(dir, Utilities.path(paths));
// ok, we'll resolve this locally
return TextFile.fileToString(new File(n));
} else {
@ -41,8 +42,9 @@ public class BaseTestingUtilities {
}
public static InputStream loadTestResourceStream(String... paths) throws IOException {
if (new File("../../fhir-test-cases").exists() && isTryToLoadFromFileSystem()) {
String n = Utilities.path(System.getProperty("user.dir"), "..", "..", "fhir-test-cases", Utilities.path(paths));
String dir = System.getenv("FHIR-TEST-CASES");
if (dir != null && new File(dir).exists()) {
String n = Utilities.path(dir, Utilities.path(paths));
return new FileInputStream(n);
} else {
String classpath = ("/org/hl7/fhir/testcases/" + Utilities.pathURL(paths));
@ -55,8 +57,9 @@ public class BaseTestingUtilities {
}
public static byte[] loadTestResourceBytes(String... paths) throws IOException {
if (new File("../../fhir-test-cases").exists() && isTryToLoadFromFileSystem()) {
String n = Utilities.path(System.getProperty("user.dir"), "..", "..", "fhir-test-cases", Utilities.path(paths));
String dir = System.getenv("FHIR-TEST-CASES");
if (dir != null && new File(dir).exists()) {
String n = Utilities.path(dir, Utilities.path(paths));
return TextFile.fileToBytes(n);
} else {
String classpath = ("/org/hl7/fhir/testcases/" + Utilities.pathURL(paths));
@ -69,8 +72,9 @@ public class BaseTestingUtilities {
}
public static boolean findTestResource(String... paths) throws IOException {
if (new File("../../fhir-test-cases").exists() && isTryToLoadFromFileSystem()) {
String n = Utilities.path(System.getProperty("user.dir"), "..", "..", "fhir-test-cases", Utilities.path(paths));
String dir = System.getenv("FHIR-TEST-CASES");
if (dir != null && new File(dir).exists()) {
String n = Utilities.path(dir, Utilities.path(paths));
return new File(n).exists();
} else {
String classpath = ("/org/hl7/fhir/testcases/" + Utilities.pathURL(paths));
@ -83,10 +87,5 @@ public class BaseTestingUtilities {
}
}
// TODO: JA need to figure out how to detect that we're running in maven
public static boolean isTryToLoadFromFileSystem() {
return !"true".equals(System.getProperty("dont_load_from_filesystem"));
}
}

26
org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/tests/PackageClientTests.java → org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/tests/CachingPackageClientTests.java
View File

@ -1,6 +1,6 @@
package org.hl7.fhir.utilities.tests;
import org.hl7.fhir.utilities.cache.PackageClient;
import org.hl7.fhir.utilities.cache.CachingPackageClient;
import org.hl7.fhir.utilities.cache.PackageClient.PackageInfo;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
@ -8,11 +8,11 @@ import org.junit.jupiter.api.Test;
import java.io.IOException;
import java.util.List;
public class PackageClientTests {
public class CachingPackageClientTests {
@Test
public void testExists() throws IOException {
PackageClient client = new PackageClient("http://packages.fhir.org");
CachingPackageClient client = new CachingPackageClient("http://packages.fhir.org");
Assertions.assertTrue(client.exists("hl7.fhir.r4.core", "4.0.1"));
Assertions.assertTrue(!client.exists("hl7.fhir.r4.core", "1.0.2"));
Assertions.assertTrue(!client.exists("hl7.fhir.nothing", "1.0.1"));
@ -20,7 +20,7 @@ public class PackageClientTests {
@Test
public void testSearch() throws IOException {
PackageClient client = new PackageClient("http://packages.fhir.org");
CachingPackageClient client = new CachingPackageClient("http://packages.fhir.org");
List<PackageInfo> matches = client.search("core", null, null, false);
for (PackageInfo pi : matches) {
System.out.println(pi.toString());
@ -30,14 +30,14 @@ public class PackageClientTests {
@Test
public void testSearchNoMatches() throws IOException {
PackageClient client = new PackageClient("http://packages.fhir.org");
CachingPackageClient client = new CachingPackageClient("http://packages.fhir.org");
List<PackageInfo> matches = client.search("corezxxx", null, null, false);
Assertions.assertTrue(matches.size() == 0);
}
@Test
public void testVersions() throws IOException {
PackageClient client = new PackageClient("http://packages.fhir.org");
CachingPackageClient client = new CachingPackageClient("http://packages.fhir.org");
List<PackageInfo> matches = client.getVersions("Simplifier.Core.STU3");
for (PackageInfo pi : matches) {
System.out.println(pi.toString());
@ -47,14 +47,14 @@ public class PackageClientTests {
@Test
public void testVersionsNone() throws IOException {
PackageClient client = new PackageClient("http://packages.fhir.org");
CachingPackageClient client = new CachingPackageClient("http://packages.fhir.org");
List<PackageInfo> matches = client.getVersions("Simplifier.Core.STU3X");
Assertions.assertTrue(matches.size() == 0);
}
@Test
public void testExists2() throws IOException {
PackageClient client = new PackageClient("http://packages2.fhir.org/packages");
CachingPackageClient client = new CachingPackageClient("http://packages2.fhir.org/packages");
Assertions.assertTrue(client.exists("hl7.fhir.r4.core", "4.0.1"));
Assertions.assertTrue(!client.exists("hl7.fhir.r4.core", "1.0.2"));
Assertions.assertTrue(!client.exists("hl7.fhir.nothing", "1.0.1"));
@ -62,7 +62,7 @@ public class PackageClientTests {
@Test
public void testSearch2() throws IOException {
PackageClient client = new PackageClient("http://packages2.fhir.org/packages");
CachingPackageClient client = new CachingPackageClient("http://packages2.fhir.org/packages");
List<PackageInfo> matches = client.search("core", null, null, false);
for (PackageInfo pi : matches) {
System.out.println(pi.toString());
@ -72,14 +72,14 @@ public class PackageClientTests {
@Test
public void testSearchNoMatches2() throws IOException {
PackageClient client = new PackageClient("http://packages2.fhir.org/packages");
CachingPackageClient client = new CachingPackageClient("http://packages2.fhir.org/packages");
List<PackageInfo> matches = client.search("corezxxx", null, null, false);
Assertions.assertTrue(matches.size() == 0);
}
@Test
public void testVersions2() throws IOException {
PackageClient client = new PackageClient("http://packages2.fhir.org/packages");
CachingPackageClient client = new CachingPackageClient("http://packages2.fhir.org/packages");
List<PackageInfo> matches = client.getVersions("Simplifier.Core.STU3");
for (PackageInfo pi : matches) {
System.out.println(pi.toString());
@ -89,7 +89,7 @@ public class PackageClientTests {
@Test
public void testVersions2A() throws IOException {
PackageClient client = new PackageClient("http://packages2.fhir.org/packages");
CachingPackageClient client = new CachingPackageClient("http://packages2.fhir.org/packages");
List<PackageInfo> matches = client.getVersions("hl7.fhir.us.core");
for (PackageInfo pi : matches) {
System.out.println(pi.toString());
@ -99,7 +99,7 @@ public class PackageClientTests {
@Test
public void testVersionsNone2() throws IOException {
PackageClient client = new PackageClient("http://packages2.fhir.org/packages");
CachingPackageClient client = new CachingPackageClient("http://packages2.fhir.org/packages");
List<PackageInfo> matches = client.getVersions("Simplifier.Core.STU3X");
Assertions.assertTrue(matches.size() == 0);
}

5
org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/tests/PackageCacheTests.java
View File

@ -2,10 +2,9 @@ package org.hl7.fhir.utilities.tests;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.cache.NpmPackage;
import org.hl7.fhir.utilities.cache.PackageCacheManager;
import org.hl7.fhir.utilities.cache.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.cache.ToolsVersion;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
import java.io.File;
@ -16,7 +15,7 @@ public class PackageCacheTests {
@Test
public void testPath() throws IOException {
PackageCacheManager cache = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
FilesystemPackageCacheManager cache = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
cache.clear();
List<String> list = cache.listPackages();
if (!list.isEmpty()) {

2
org.hl7.fhir.validation/pom.xml
View File

@ -23,9 +23,11 @@
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-base</artifactId>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.utilities</artifactId>
<version>${project.version}</version>
</dependency>
<!-- FHIR Versions -->

20
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/ValidationEngine.java
View File

@ -4,7 +4,6 @@ import org.apache.commons.io.IOUtils;
import org.hl7.fhir.convertors.*;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.context.IWorkerContext.IContextResourceLoader;
import org.hl7.fhir.r5.context.IWorkerContext.PackageVersion;
@ -33,7 +32,7 @@ import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.cache.NpmPackage;
import org.hl7.fhir.utilities.cache.PackageCacheManager;
import org.hl7.fhir.utilities.cache.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.cache.ToolsVersion;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
@ -42,11 +41,8 @@ import org.hl7.fhir.utilities.validation.ValidationMessage.Source;
import org.hl7.fhir.utilities.xhtml.XhtmlComposer;
import org.xml.sax.SAXException;
import com.google.gson.JsonObject;
import java.io.*;
import java.net.HttpURLConnection;
import java.net.MalformedURLException;
import java.net.URISyntaxException;
import java.net.URL;
import java.net.URLConnection;
@ -254,7 +250,7 @@ public class ValidationEngine implements IValidatorResourceFetcher {
private boolean anyExtensionsAllowed = false;
private String version;
private String language;
private PackageCacheManager pcm;
private FilesystemPackageCacheManager pcm;
private PrintWriter mapLog;
private boolean debug;
private Set<String> loadedIgs = new HashSet<>();
@ -301,7 +297,7 @@ public class ValidationEngine implements IValidatorResourceFetcher {
}
public ValidationEngine() throws IOException {
pcm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
}
public void setTerminologyServer(String src, String log, FhirPublication version) throws Exception {
@ -325,7 +321,7 @@ public class ValidationEngine implements IValidatorResourceFetcher {
}
public ValidationEngine(String src, String txsrvr, String txLog, FhirPublication version, boolean canRunWithoutTerminologyServer, String vString) throws Exception {
pcm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
loadCoreDefinitions(src, false);
context.setCanRunWithoutTerminology(canRunWithoutTerminologyServer);
setTerminologyServer(txsrvr, txLog, version);
@ -333,7 +329,7 @@ public class ValidationEngine implements IValidatorResourceFetcher {
}
public ValidationEngine(String src, String txsrvr, String txLog, FhirPublication version, String vString) throws Exception {
pcm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
loadCoreDefinitions(src, false);
setTerminologyServer(txsrvr, txLog, version);
this.version = vString;
@ -341,7 +337,7 @@ public class ValidationEngine implements IValidatorResourceFetcher {
public ValidationEngine(String src) throws Exception {
loadCoreDefinitions(src, false);
pcm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
}
public String getLanguage() {
@ -473,7 +469,7 @@ public class ValidationEngine implements IValidatorResourceFetcher {
res.put(Utilities.changeFileExt(src, "."+fmt.getExtension()), TextFile.fileToBytesNCS(src));
return res;
}
} else if ((src.matches(PackageCacheManager.PACKAGE_REGEX) || src.matches(PackageCacheManager.PACKAGE_VERSION_REGEX)) && !src.endsWith(".zip") && !src.endsWith(".tgz")) {
} else if ((src.matches(FilesystemPackageCacheManager.PACKAGE_REGEX) || src.matches(FilesystemPackageCacheManager.PACKAGE_VERSION_REGEX)) && !src.endsWith(".zip") && !src.endsWith(".tgz")) {
return fetchByPackage(src);
}
throw new Exception("Unable to find/resolve/read -ig "+src);
@ -627,7 +623,7 @@ public class ValidationEngine implements IValidatorResourceFetcher {
}
if (pcm == null) {
log("Creating Package manager?");
pcm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
}
if (version == null) {
version = pcm.getLatestVersion(id);

4
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/utils/Display.java
View File

@ -2,7 +2,7 @@ package org.hl7.fhir.validation.cli.utils;
import org.hl7.fhir.r5.model.Constants;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.cache.PackageCacheManager;
import org.hl7.fhir.utilities.cache.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.cache.ToolsVersion;
import java.io.IOException;
@ -20,7 +20,7 @@ public class Display {
System.out.print(s.contains(" ") ? " \"" + s + "\"" : " " + s);
}
System.out.println();
System.out.println("Directories: Current = " + System.getProperty("user.dir") + ", Package Cache = " + new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION).getFolder());
System.out.println("Directories: Current = " + System.getProperty("user.dir") + ", Package Cache = " + new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION).getFolder());
}
public static void displayHelpDetails() {

11
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/packages/PackageValidator.java
View File

@ -6,14 +6,11 @@ import java.util.List;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.context.SimpleWorkerContext;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.cache.NpmPackage;
import org.hl7.fhir.utilities.cache.PackageCacheManager;
import org.hl7.fhir.utilities.cache.PackageClient;
import org.hl7.fhir.utilities.cache.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.cache.CachingPackageClient;
import org.hl7.fhir.utilities.cache.PackageClient.PackageInfo;
import org.xml.sax.InputSource;
import org.hl7.fhir.utilities.cache.ToolsVersion;
public class PackageValidator {
@ -23,9 +20,9 @@ public class PackageValidator {
}
private void execute() throws IOException {
PackageCacheManager pcm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
PackageClient pc = new PackageClient(PackageCacheManager.PRIMARY_SERVER);
CachingPackageClient pc = new CachingPackageClient(FilesystemPackageCacheManager.PRIMARY_SERVER);
for (PackageInfo t : pc.search(null, null, null, false)) {
System.out.println("Check Package "+t.getId());
List<PackageInfo> vl = pc.getVersions(t.getId());

4
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/comparison/tests/ComparisonTests.java
View File

@ -30,7 +30,7 @@ import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.cache.NpmPackage;
import org.hl7.fhir.utilities.cache.PackageCacheManager;
import org.hl7.fhir.utilities.cache.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.cache.ToolsVersion;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
@ -102,7 +102,7 @@ public class ComparisonTests {
if (!new File(Utilities.path("[tmp]", "comparison")).exists()) {
System.out.println("---- Set up Output ----------------------------------------------------------");
Utilities.createDirectory(Utilities.path("[tmp]", "comparison"));
PackageCacheManager pcm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
NpmPackage npm = pcm.loadPackage("hl7.fhir.pubpack", "0.0.5");
for (String f : npm.list("other")) {
TextFile.streamToFile(npm.load("other", f), Utilities.path("[tmp]", "comparison", f));

6
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/conversion/tests/R3R4ConversionTests.java
View File

@ -21,7 +21,7 @@ import org.hl7.fhir.r4.utils.StructureMapUtilities.ITransformerServices;
import org.hl7.fhir.utilities.IniFile;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.cache.PackageCacheManager;
import org.hl7.fhir.utilities.cache.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.cache.ToolsVersion;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
@ -42,7 +42,7 @@ import java.util.zip.ZipInputStream;
public class R3R4ConversionTests implements ITransformerServices, IValidatorResourceFetcher {
private static final boolean SAVING = true;
private PackageCacheManager pcm = null;
private FilesystemPackageCacheManager pcm = null;
public static Stream<Arguments> data() throws ParserConfigurationException, SAXException, IOException {
if (!(new File(Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "outcomes.json")).exists()))
@ -285,7 +285,7 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
if (contextR3 != null)
return;
pcm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
R3ToR4Loader ldr = new R3ToR4Loader().setPatchUrls(true).setKillPrimitives(true);
System.out.println("loading R3");

6
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/conversion/tests/TestingUtilitiesX.java
View File

@ -58,7 +58,7 @@ import org.hl7.fhir.utilities.CSFile;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.cache.PackageCacheManager;
import org.hl7.fhir.utilities.cache.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.cache.ToolsVersion;
import org.w3c.dom.Document;
@ -83,9 +83,9 @@ public class TestingUtilitiesX {
fcontexts = new HashMap<>();
}
if (!fcontexts.containsKey(version)) {
PackageCacheManager pcm;
FilesystemPackageCacheManager pcm;
try {
pcm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
IWorkerContext fcontext = SimpleWorkerContext.fromPackage(pcm.loadPackage(VersionUtilities.packageForVersion(version), version), loaderForVersion(version));
fcontext.setUcumService(new UcumEssenceService(TestingUtilitiesX.loadTestResourceStream("ucum", "ucum-essence.xml")));
fcontext.setExpansionProfile(new Parameters());

13
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/ProfileComparisonTests.java
View File

@ -1,18 +1,5 @@
package org.hl7.fhir.validation.tests;
import java.io.File;
import java.util.UUID;
import org.hl7.fhir.convertors.R5ToR5Loader;
import org.hl7.fhir.r5.conformance.ProfileComparer;
import org.hl7.fhir.r5.model.FhirPublication;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.utils.KeyGenerator;
import org.hl7.fhir.utilities.cache.PackageCacheManager;
import org.hl7.fhir.utilities.cache.ToolsVersion;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.validation.ValidationEngine;
import org.hl7.fhir.validation.tests.utilities.TestUtilities;
import org.junit.jupiter.api.Test;
public class ProfileComparisonTests {

33
pom.xml
View File

@ -17,7 +17,7 @@
<properties>
<hapi_fhir_version>5.0.0</hapi_fhir_version>
<validator_test_case_version>1.1.18-SNAPSHOT</validator_test_case_version>
<validator_test_case_version>1.1.18</validator_test_case_version>
<junit_jupiter_version>5.6.2</junit_jupiter_version>
<maven_surefire_version>3.0.0-M4</maven_surefire_version>
<jacoco_version>0.8.5</jacoco_version>
@ -33,6 +33,20 @@
<url>http://hl7.org</url>
</organization>
<modules>
<module>org.hl7.fhir.utilities</module>
<module>org.hl7.fhir.dstu2</module>
<module>org.hl7.fhir.dstu2016may</module>
<module>org.hl7.fhir.dstu3</module>
<module>org.hl7.fhir.r4</module>
<module>org.hl7.fhir.r5</module>
<module>org.hl7.fhir.convertors</module>
<module>org.hl7.fhir.validation</module>
<module>org.hl7.fhir.validation.cli</module>
<!-- The report project exists only to aggregate the test results from the other projects into a central report. -->
<module>org.hl7.fhir.report</module>
</modules>
<repositories>
<repository>
<snapshots>
@ -122,21 +136,6 @@
</dependencies>
</dependencyManagement>
<modules>
<module>org.hl7.fhir.utilities</module>
<module>org.hl7.fhir.dstu2</module>
<module>org.hl7.fhir.dstu2016may</module>
<module>org.hl7.fhir.dstu3</module>
<module>org.hl7.fhir.r4</module>
<module>org.hl7.fhir.r5</module>
<module>org.hl7.fhir.convertors</module>
<module>org.hl7.fhir.validation</module>
<module>org.hl7.fhir.validation.cli</module>
<!-- The report project exists only to aggregate the test results from the other projects into a central report. -->
<module>org.hl7.fhir.report</module>
</modules>
<build>
<plugins>
<plugin>
@ -148,7 +147,7 @@
<target>1.8</target>
<forceJavacCompilerUse>false</forceJavacCompilerUse>
<encoding>UTF-8</encoding>
<fork>true</fork>
<fork>false</fork>
<meminitial>512m</meminitial>
<maxmem>4000m</maxmem>
<debug>true</debug>