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org.hl7.fhir.core
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Merge branch 'master' of https://github.com/hapifhir/org.hl7.fhir.core

This commit is contained in:
Grahame Grieve 2023-12-13 13:03:56 -05:00
parent 8ecf5a1790 0afea8dc1d
commit 93d5adc9da
49 changed files with 316 additions and 217 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/ExtensionDefinitionGenerator.java
View File

@ -387,7 +387,7 @@ public class ExtensionDefinitionGenerator {
private List<StructureDefinition> loadSource() throws IOException, FHIRException {
List<StructureDefinition> list = new ArrayList<>();
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER);
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager.Builder().build();
NpmPackage npm = pcm.loadPackage("hl7.fhir.core", sourceVersion.toCode());
if (sourceVersion == FHIRVersion._4_0_0)
context = SimpleWorkerContext.fromPackage(npm);

27
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/analytics/PackageVisitor.java
View File

@ -1,6 +1,5 @@
package org.hl7.fhir.convertors.analytics;
import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
@ -34,6 +33,16 @@ import org.xml.sax.SAXException;
public class PackageVisitor {
private PackageServer clientPackageServer = null;
public void setClientPackageServer(PackageServer packageServer) {
this.clientPackageServer = packageServer;
}
private List<PackageServer> cachePackageServers = null;
public void setCachePackageServers(List<PackageServer> packageServers) {
this.cachePackageServers = packageServers;
}
public static class PackageContext {
private String pid;
private NpmPackage npm;
@ -145,8 +154,13 @@ public class PackageVisitor {
public void visitPackages() throws IOException, ParserConfigurationException, SAXException, FHIRException, EOperationOutcome {
System.out.println("Finding packages");
pc = new PackageClient(PackageServer.primaryServer());
pcm = new FilesystemPackageCacheManager(org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER);
pc = clientPackageServer == null
? new PackageClient(PackageServer.primaryServer())
: new PackageClient(clientPackageServer);
pcm = cachePackageServers == null
? new FilesystemPackageCacheManager.Builder().build()
: new FilesystemPackageCacheManager.Builder().withPackageServers(cachePackageServers).build();
Set<String> pidList = getAllPackages();
@ -338,9 +352,14 @@ public class PackageVisitor {
String fv = null;
try {
npm = pcm.loadPackage(pid, v);
} catch (Throwable e) {
System.out.println("Unable to load package: "+pid+"#"+v+": "+e.getMessage());
}
try {
fv = npm.fhirVersion();
} catch (Throwable e) {
System.out.println("Unable to process: "+pid+"#"+v+": "+e.getMessage());
System.out.println("Unable to identify package FHIR version:: "+pid+"#"+v+": "+e.getMessage());
}
if (corePackages || !corePackage(npm)) {
PackageContext ctxt = new PackageContext(pid+"#"+v, npm, fv);

2
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/ExtensionExtractor.java
View File

@ -37,7 +37,7 @@ public class ExtensionExtractor {
private void process(String dst) throws IOException {
Set<String> ids = new HashSet<>();
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(true);
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager.Builder().build();
NpmPackage r5 = pcm.loadPackage("hl7.fhir.r5.core", "current");
CanonicalResourceManager<CodeSystem> cslist = new CanonicalResourceManager<CodeSystem>(true, false);
for (String r : r5.listResources("CodeSystem")) {

2
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/ExtensionStatusUpgrader.java
View File

@ -25,7 +25,7 @@ public class ExtensionStatusUpgrader implements IResourceObserver {
Map<String, CanonicalResource> r5 = new HashMap<>();
private void execute(String folder) throws IOException {
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(true);
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager.Builder().build();
// load R4
NpmPackage npm = pcm.loadPackage("hl7.fhir.r4.core");

2
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/OIDBasedValueSetImporter.java
View File

@ -15,7 +15,7 @@ public class OIDBasedValueSetImporter {
protected IWorkerContext context;
protected void init() throws FHIRException, IOException {
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER);
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager.Builder().build();
NpmPackage npm = pcm.loadPackage("hl7.fhir.r5.core", "5.0.0");
SimpleWorkerContext context = new SimpleWorkerContext.SimpleWorkerContextBuilder().withAllowLoadingDuplicates(true).fromPackage(npm);
context.loadFromPackage(pcm.loadPackage("hl7.terminology"), null);

2
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/PackageMinifier.java
View File

@ -18,7 +18,7 @@ public class PackageMinifier {
}
private void process(String source, String target) throws FileNotFoundException, IOException {
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(true);
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager.Builder().build();
NpmPackage src = pcm.loadPackage(source);
NpmPackage tgt = NpmPackage.empty();
tgt.setNpm(src.getNpm().deepCopy());

2
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/ResourceDependencyPackageBuilder.java
View File

@ -35,7 +35,7 @@ public class ResourceDependencyPackageBuilder {
public static void main(String[] args) throws IOException {
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(true);
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager.Builder().build();
System.out.println("Load Core");
NpmPackage src = pcm.loadPackage(VersionUtilities.packageForVersion(args[0]));
SimpleWorkerContext ctxt = new SimpleWorkerContextBuilder().withAllowLoadingDuplicates(true).fromPackage(src);

6
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/utg/UTGVersionSorter.java
View File

@ -89,7 +89,7 @@ public class UTGVersionSorter {
private Map<String, CanonicalResource> loadPackageR2(String id) throws IOException {
Map<String, CanonicalResource> res = new HashMap<>();
if (pcm == null) {
pcm = new FilesystemPackageCacheManager(org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER);
pcm = new FilesystemPackageCacheManager.Builder().build();
}
System.out.println("Load " + id);
NpmPackage npm = pcm.loadPackage(id);
@ -103,7 +103,7 @@ public class UTGVersionSorter {
private Map<String, CanonicalResource> loadPackageR3(String id) throws IOException {
Map<String, CanonicalResource> res = new HashMap<>();
if (pcm == null) {
pcm = new FilesystemPackageCacheManager(org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER);
pcm = new FilesystemPackageCacheManager.Builder().build();
}
System.out.println("Load " + id);
NpmPackage npm = pcm.loadPackage(id);
@ -117,7 +117,7 @@ public class UTGVersionSorter {
private Map<String, CanonicalResource> loadPackageR4(String id) throws IOException {
Map<String, CanonicalResource> res = new HashMap<>();
if (pcm == null) {
pcm = new FilesystemPackageCacheManager(org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER);
pcm = new FilesystemPackageCacheManager.Builder().build();
}
System.out.println("Load " + id);
NpmPackage npm = pcm.loadPackage(id);

2
org.hl7.fhir.convertors/src/test/java/org/hl7/fhir/convertors/Convertor_Factory_40_50Test.java
View File

@ -25,7 +25,7 @@ class Convertor_Factory_40_50Test {
@BeforeAll
static public void setUp() throws Exception {
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER);
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager.Builder().build();
context = TestingUtilities.getWorkerContext(pcm.loadPackage("hl7.fhir.r4.core", "4.0.1"));
}

2
org.hl7.fhir.core.generator/src/org/hl7/fhir/core/generator/engine/JavaCoreGenerator.java
View File

@ -73,7 +73,7 @@ public class JavaCoreGenerator {
Date ddate = new Date();
String date = config.DATE_FORMAT().format(ddate);
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER);
FilesystemPackageCacheManager pcm = new org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheManagerBuilder().build();
System.out.println("Cache: "+pcm.getFolder());
System.out.println("Load hl7.fhir."+pid+".core");
NpmPackage npm = pcm.loadPackage("hl7.fhir."+pid+".core", version);

3
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/test/utils/TestingUtilities.java
View File

@ -79,8 +79,7 @@ public class TestingUtilities {
if (fcontext == null) {
FilesystemPackageCacheManager pcm;
try {
pcm = new FilesystemPackageCacheManager(
org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER);
pcm = new FilesystemPackageCacheManager.Builder().build();
fcontext = SimpleWorkerContext.fromPackage(pcm.loadPackage("hl7.fhir.r4.core", "4.0.1"));
fcontext
.setUcumService(new UcumEssenceService(TestingUtilities.resourceNameToFile("ucum", "ucum-essence.xml")));

5
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/utils/CmdLineApp.java
View File

@ -11,7 +11,6 @@ import org.hl7.fhir.r4.context.SimpleWorkerContext;
import org.hl7.fhir.r4.fhirpath.FHIRPathEngine;
import org.hl7.fhir.r4.formats.IParser.OutputStyle;
import org.hl7.fhir.r4.formats.JsonParser;
import org.hl7.fhir.r4.formats.XmlParser;
import org.hl7.fhir.r4.model.Base;
import org.hl7.fhir.r4.model.BooleanType;
import org.hl7.fhir.r4.model.Bundle;
@ -27,8 +26,6 @@ import org.hl7.fhir.r4.model.HumanName;
import org.hl7.fhir.r4.model.Immunization;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent;
import org.hl7.fhir.r4.model.HumanName;
import org.hl7.fhir.r4.model.Immunization;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Period;
import org.hl7.fhir.r4.model.Procedure;
@ -55,7 +52,7 @@ public class CmdLineApp {
private void execute() throws IOException {
System.out.print("Loading...");
NpmPackage npm = new FilesystemPackageCacheManager(true).loadPackage("hl7.fhir.r4.core");
NpmPackage npm = new FilesystemPackageCacheManager.Builder().build().loadPackage("hl7.fhir.r4.core");
context = SimpleWorkerContext.fromPackage(npm);
fpe = new FHIRPathEngine(context);
System.out.println(" Done");

3
org.hl7.fhir.r4/src/test/java/org/hl7/fhir/r4/test/CDARoundTripTests.java
View File

@ -29,8 +29,7 @@ public class CDARoundTripTests {
@BeforeAll
public void setUp() throws Exception {
context = new SimpleWorkerContext();
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(
org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER);
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager.Builder().build();
context.loadFromPackage(pcm.loadPackage("hl7.fhir.core", "current"), null, "StructureDefinition");
context.loadFromPackage(pcm.loadPackage("hl7.fhir.cda", "current"), null, "StructureDefinition");
}

6
org.hl7.fhir.r4b/src/main/java/org/hl7/fhir/r4b/test/utils/TestingUtilities.java
View File

@ -20,8 +20,7 @@ import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode;
import org.hl7.fhir.utilities.npm.ToolsVersion;
import org.hl7.fhir.utilities.tests.BaseTestingUtilities;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
@ -85,8 +84,7 @@ public class TestingUtilities extends BaseTestingUtilities {
if (!fcontexts.containsKey(v)) {
FilesystemPackageCacheManager pcm;
try {
pcm = new FilesystemPackageCacheManager(
org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER);
pcm = new FilesystemPackageCacheManager.Builder().build();
IWorkerContext fcontext = SimpleWorkerContext
.fromPackage(pcm.loadPackage(VersionUtilities.packageForVersion(version), version));
fcontext.setUcumService(

5
org.hl7.fhir.r4b/src/test/java/org/hl7/fhir/r4b/test/ParsingTests.java
View File

@ -1,7 +1,6 @@
package org.hl7.fhir.r4b.test;
import java.io.IOException;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.List;
import java.util.stream.Stream;
@ -18,7 +17,6 @@ import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.utilities.npm.ToolsVersion;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.params.ParameterizedTest;
@ -36,8 +34,7 @@ public class ParsingTests {
public static Stream<Arguments> data()
throws ParserConfigurationException, IOException, FHIRFormatError, SAXException {
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(
org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER);
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager.Builder().build();
npm = pcm.loadPackage("hl7.fhir.r4b.examples", "4.3.0");
List<Arguments> objects = new ArrayList<>();
List<String> names = npm.list("package");

4
org.hl7.fhir.r4b/src/test/java/org/hl7/fhir/r4b/test/SnapShotGenerationTests.java
View File

@ -46,7 +46,6 @@ import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.npm.CommonPackages;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.utilities.npm.ToolsVersion;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.hl7.fhir.utilities.xml.XMLUtil;
@ -581,8 +580,7 @@ public class SnapShotGenerationTests {
pu.setDebug(test.isDebug());
pu.setIds(test.getSource(), false);
if (!TestingUtilities.context().hasPackage(CommonPackages.ID_XVER, CommonPackages.VER_XVER)) {
NpmPackage npm = new FilesystemPackageCacheManager(
org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER)
NpmPackage npm = new FilesystemPackageCacheManager.Builder().build()
.loadPackage(CommonPackages.ID_XVER, CommonPackages.VER_XVER);
TestingUtilities.context().loadFromPackage(npm, new TestLoader(new String[] { "StructureDefinition" }),
new String[] { "StructureDefinition" });

4
org.hl7.fhir.r4b/src/test/java/org/hl7/fhir/r4b/test/StructureMapUtilitiesTest.java
View File

@ -10,7 +10,6 @@ import org.hl7.fhir.r4b.test.utils.TestingUtilities;
import org.hl7.fhir.r4b.utils.structuremap.StructureMapUtilities;
import org.hl7.fhir.r4b.utils.structuremap.ITransformerServices;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.ToolsVersion;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
@ -24,8 +23,7 @@ public class StructureMapUtilitiesTest implements ITransformerServices {
@BeforeAll
static public void setUp() throws Exception {
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(
org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER);
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager.Builder().build();
context = SimpleWorkerContext.fromPackage(pcm.loadPackage("hl7.fhir.r4.core", "4.0.1"));
}

13
org.hl7.fhir.r4b/src/test/java/org/hl7/fhir/r4b/test/XmlParserTests.java
View File

@ -1,21 +1,11 @@
package org.hl7.fhir.r4b.test;
import java.io.ByteArrayOutputStream;
import java.io.IOException;
import org.hl7.fhir.r4b.context.SimpleWorkerContext;
import org.hl7.fhir.r4b.elementmodel.Element;
import org.hl7.fhir.r4b.elementmodel.Manager;
import org.hl7.fhir.r4b.elementmodel.Manager.FhirFormat;
import org.hl7.fhir.r4b.fhirpath.FHIRPathEngine;
import org.hl7.fhir.r4b.formats.IParser.OutputStyle;
import org.hl7.fhir.r4b.model.StructureDefinition;
import org.hl7.fhir.r4b.test.utils.TestingUtilities;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.ToolsVersion;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
public class XmlParserTests {
@ -24,8 +14,7 @@ public class XmlParserTests {
@BeforeAll
public static void setUp() throws Exception {
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(
org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER);
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager.Builder().build();
context = SimpleWorkerContext.fromPackage(pcm.loadPackage("hl7.fhir.r4.core", "4.0.1"));
fp = new FHIRPathEngine(context);

5
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/test/utils/TestingUtilities.java
View File

@ -13,15 +13,12 @@ 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.utilities.TerminologyCache;
import org.hl7.fhir.r5.utils.R5Hacker;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.npm.BasePackageCacheManager.InputStreamWithSrc;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.IPackageProvider;
import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.utilities.npm.ToolsVersion;
import org.hl7.fhir.utilities.tests.BaseTestingUtilities;
import org.hl7.fhir.utilities.tests.TestConfig;
@ -80,7 +77,7 @@ public class TestingUtilities extends BaseTestingUtilities {
FilesystemPackageCacheManager pcm;
try {
pcm = new FilesystemPackageCacheManager(org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER);
pcm = new FilesystemPackageCacheManager.Builder().build();
IWorkerContext fcontext = null;
if (VersionUtilities.isR5Ver(version)) {
// for purposes of stability, the R5 core package comes from the test case repository

12
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/profiles/GeneratedPEModelTest.java
View File

@ -3,23 +3,13 @@ package org.hl7.fhir.r5.profiles;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
import java.util.TimeZone;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.model.CodeableConcept;
import org.hl7.fhir.r5.model.Identifier;
import org.hl7.fhir.r5.model.Observation;
import org.hl7.fhir.r5.model.Patient;
import org.hl7.fhir.r5.model.Reference;
import org.hl7.fhir.r5.context.SimpleWorkerContext;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.formats.XmlParser;
import org.hl7.fhir.r5.profilemodel.PEBuilder;
import org.hl7.fhir.r5.test.utils.CompareUtilities;
import org.hl7.fhir.r5.test.utils.TestPackageLoader;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
@ -36,7 +26,7 @@ public class GeneratedPEModelTest {
public void load() throws Exception {
if (ctxt == null) {
ctxt = TestingUtilities.getSharedWorkerContext();
FilesystemPackageCacheManager pc = new FilesystemPackageCacheManager(true);
FilesystemPackageCacheManager pc = new FilesystemPackageCacheManager.Builder().build();
NpmPackage npm = pc.loadPackage("hl7.fhir.us.core", "5.0.0");
ctxt.loadFromPackage(npm, new TestPackageLoader(Utilities.strings("StructureDefinition" )));

3
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/profiles/PEModelTest1343.java
View File

@ -1,7 +1,6 @@
package org.hl7.fhir.r5.profiles;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.model.Patient;
import org.hl7.fhir.r5.context.SimpleWorkerContext;
@ -22,7 +21,7 @@ public class PEModelTest1343 {
public void Load() throws Exception {
if (ctxt == null) {
ctxt = TestingUtilities.getSharedWorkerContext("4.0.1");
FilesystemPackageCacheManager pc = new FilesystemPackageCacheManager(true);
FilesystemPackageCacheManager pc = new FilesystemPackageCacheManager.Builder().build();
NpmPackage npm = pc.loadPackage("hl7.fhir.fr.core", "1.1.0");
ctxt.loadFromPackage(npm, new TestPackageLoader(Utilities.strings(SimpleWorkerContext.defaultTypesToLoad().stream().toArray(String[]::new))));
}

8
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/profiles/PETests.java
View File

@ -28,20 +28,14 @@ package org.hl7.fhir.r5.profiles;
POSSIBILITY OF SUCH DAMAGE.
*/
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.Date;
import java.util.List;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.Comparison;
import org.hl7.fhir.r5.model.Enumerations.ObservationStatus;
import org.hl7.fhir.r5.model.Observation;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.profilemodel.PEDefinition;
@ -71,7 +65,7 @@ public class PETests {
public void load() throws IOException {
if (ctxt == null) {
ctxt = TestingUtilities.getSharedWorkerContext();
FilesystemPackageCacheManager pc = new FilesystemPackageCacheManager(true);
FilesystemPackageCacheManager pc = new FilesystemPackageCacheManager.Builder().build();
NpmPackage npm = pc.loadPackage("hl7.fhir.us.core", "5.0.0");
ctxt.loadFromPackage(npm, new TestPackageLoader(Utilities.strings("StructureDefinition" )));

9
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/CDARoundTripTests.java
View File

@ -5,20 +5,15 @@ import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.util.List;
import org.hl7.fhir.r5.context.ContextUtilities;
import org.hl7.fhir.r5.context.SimpleWorkerContext;
import org.hl7.fhir.r5.elementmodel.Element;
import org.hl7.fhir.r5.elementmodel.Manager;
import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
import org.hl7.fhir.r5.fhirpath.FHIRPathEngine;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode;
import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.utilities.npm.ToolsVersion;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
@ -30,11 +25,11 @@ public class CDARoundTripTests {
@BeforeAll
public static void setUp() throws Exception {
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER);
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager.Builder().build();
context = TestingUtilities.getWorkerContext(pcm.loadPackage("hl7.fhir.r4.core", "4.0.1"));
fp = new FHIRPathEngine(context);
NpmPackage npm = new FilesystemPackageCacheManager(true).loadPackage("hl7.cda.uv.core", "current");
NpmPackage npm = new FilesystemPackageCacheManager.Builder().build().loadPackage("hl7.cda.uv.core", "current");
context.loadFromPackage(npm, null);
}

3
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/FHIRPathTests.java
View File

@ -41,7 +41,6 @@ import org.xml.sax.SAXException;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.when;
public class FHIRPathTests {
@ -111,7 +110,7 @@ public class FHIRPathTests {
@BeforeAll
public static void setUp() throws FileNotFoundException, FHIRException, IOException {
if (!TestingUtilities.getSharedWorkerContext().hasPackage("hl7.cda.us.ccda", null)) {
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(true);
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager.Builder().build();
NpmPackage npm = pcm.loadPackage("hl7.cda.uv.core", "2.0.0");
TestingUtilities.getSharedWorkerContext().loadFromPackage(npm, null);
npm = pcm.loadPackage("hl7.cda.us.ccda", "current");

2
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/NarrativeGenerationTests.java
View File

@ -213,7 +213,7 @@ public class NarrativeGenerationTests {
@BeforeAll
public static void setUp() throws IOException {
context = TestingUtilities.getSharedWorkerContext("5.0.0");
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(true);
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager.Builder().build();
NpmPackage ips = pcm.loadPackage("hl7.fhir.uv.ips#1.1.0");
context.loadFromPackage(ips, new TestPackageLoader(Utilities.strings("StructureDefinition", "ValueSet" )));
}

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

@ -17,8 +17,6 @@ import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.utilities.npm.ToolsVersion;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.params.ParameterizedTest;
@ -35,7 +33,7 @@ public class ParsingTests {
}
public static Stream<Arguments> data() throws ParserConfigurationException, IOException, FHIRFormatError, SAXException {
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER);
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager.Builder().build();
// npm = pcm.loadPackage("hl7.fhir.r5.examples", "5.0.0");
npm = NpmPackage.fromPackage(TestingUtilities.loadTestResourceStream("r5", "packages", "hl7.fhir.r5.examples.tgz"));
List<Arguments> objects = new ArrayList<>();

2
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/SnapShotGenerationTests.java
View File

@ -540,7 +540,7 @@ public class SnapShotGenerationTests {
pu.setIds(test.getSource(), false);
pu.setAllowUnknownProfile(test.allow);
if (!TestingUtilities.getSharedWorkerContext().hasPackage(CommonPackages.ID_XVER, CommonPackages.VER_XVER)) {
NpmPackage npm = new FilesystemPackageCacheManager(org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER).loadPackage(CommonPackages.ID_XVER, CommonPackages.VER_XVER);
NpmPackage npm = new FilesystemPackageCacheManager.Builder().build().loadPackage(CommonPackages.ID_XVER, CommonPackages.VER_XVER);
TestingUtilities.getSharedWorkerContext().loadFromPackage(npm, new TestPackageLoader(Utilities.strings("StructureDefinition")), Utilities.strings("StructureDefinition"));
}
pu.setXver(new XVerExtensionManager(TestingUtilities.getSharedWorkerContext()));

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

@ -17,8 +17,6 @@ import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.r5.utils.structuremap.ITransformerServices;
import org.hl7.fhir.r5.utils.structuremap.StructureMapUtilities;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.ToolsVersion;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
@ -29,7 +27,7 @@ public class StructureMapUtilitiesTest implements ITransformerServices {
@BeforeAll
static public void setUp() throws Exception {
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER);
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager.Builder().build();
context = TestingUtilities.getWorkerContext(pcm.loadPackage("hl7.fhir.r4.core", "4.0.1"));
}

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

@ -13,8 +13,6 @@ import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.ToolsVersion;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
@ -26,7 +24,7 @@ public class XmlParserTests {
@BeforeAll
public static void setUp() throws Exception {
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER);
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager.Builder().build();
context = TestingUtilities.getWorkerContext(pcm.loadPackage("hl7.fhir.r4.core", "4.0.1"));
fp = new FHIRPathEngine(context);

2
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/utils/structuremap/FHIRPathHostServicesTest.java
View File

@ -16,7 +16,7 @@ class FHIRPathHostServicesTest {
@BeforeAll
static public void setUp() throws Exception {
FilesystemPackageCacheManager pcm = new org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager(true);
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager.Builder().build();
context = TestingUtilities.getWorkerContext(pcm.loadPackage("hl7.fhir.r4.core", "4.0.1"));
}

29
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/SimpleHTTPClient.java
View File

@ -44,6 +44,29 @@ public class SimpleHTTPClient {
private static final int MAX_REDIRECTS = 5;
private static int counter = 1;
public static class HTTPResultException extends Exception{
public final int httpCode;
public final String message;
public final String url;
public final String logPath;
public HTTPResultException(int httpCode, String message, String url, String logPath) {
this.httpCode = httpCode;
this.message = message;
this.url = url;
this.logPath = logPath;
}
public String getMessage() {
return "Invalid HTTP response "+httpCode+" from "+url+" ("+message+") (" + (
logPath != null ? "Response in " + logPath : "No response content")
+ ")";
}
}
public static class HTTPResult {
private int code;
private String contentType;
@ -79,11 +102,13 @@ public class SimpleHTTPClient {
if (code >= 300) {
String filename = Utilities.path("[tmp]", "http-log", "fhir-http-"+(++counter)+".log");
if (content == null || content.length == 0) {
throw new IOException("Invalid HTTP response "+code+" from "+source+" ("+message+") (no content)");
HTTPResultException exception = new HTTPResultException(code, message, source, null);
throw new IOException(exception.message, exception);
} else {
Utilities.createDirectory(Utilities.path("[tmp]", "http-log"));
TextFile.bytesToFile(content, filename);
throw new IOException("Invalid HTTP response "+code+" from "+source+" ("+message+") (content in "+filename+")");
HTTPResultException exception = new HTTPResultException(code, message, source, filename);
throw new IOException(exception.message, exception);
}
}
}

119
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/FilesystemPackageCacheManager.java
View File

@ -22,6 +22,8 @@ import java.util.UUID;
import javax.annotation.Nonnull;
import lombok.Getter;
import lombok.With;
import org.apache.commons.io.FileUtils;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.utilities.IniFile;
@ -84,13 +86,8 @@ import org.slf4j.LoggerFactory;
*/
public class FilesystemPackageCacheManager extends BasePackageCacheManager implements IPackageCacheManager {
public static final String INI_TIMESTAMP_FORMAT = "yyyyMMddHHmmss";
public enum FilesystemPackageCacheMode {
USER, SYSTEM, TESTING, CUSTOM
}
// When running in testing mode, some packages are provided from the test case repository rather than by the normal means
// the PackageProvider is responsible for this. if no package provider is defined, or it declines to handle the package,
// then the normal means will be used
@ -99,8 +96,6 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
InputStreamWithSrc provide(String id, String version) throws IOException;
}
private static IPackageProvider packageProvider;
// private static final String SECONDARY_SERVER = "http://local.fhir.org:8080/packages";
public static final String PACKAGE_REGEX = "^[a-zA-Z][A-Za-z0-9\\_\\-]*(\\.[A-Za-z0-9\\_\\-]+)+$";
public static final String PACKAGE_VERSION_REGEX = "^[A-Za-z][A-Za-z0-9\\_\\-]*(\\.[A-Za-z0-9\\_\\-]+)+\\#[A-Za-z0-9\\-\\_\\$]+(\\.[A-Za-z0-9\\-\\_\\$]+)*$";
public static final String PACKAGE_VERSION_REGEX_OPT = "^[A-Za-z][A-Za-z0-9\\_\\-]*(\\.[A-Za-z0-9\\_\\-]+)+(\\#[A-Za-z0-9\\-\\_]+(\\.[A-Za-z0-9\\-\\_]+)*)?$";
@ -115,52 +110,78 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
private boolean suppressErrors;
private boolean minimalMemory;
public FilesystemPackageCacheManager(boolean userMode) throws IOException {
init(userMode ? FilesystemPackageCacheMode.USER : FilesystemPackageCacheMode.SYSTEM);
public static class Builder {
@Getter
private final File cacheFolder;
@With @Getter
private final List<PackageServer> packageServers;
public Builder() throws IOException {
this.cacheFolder = getUserCacheFolder();
this.packageServers = getPackageServersFromFHIRSettings();
}
public FilesystemPackageCacheManager(FilesystemPackageCacheMode mode) throws IOException {
init(mode);
}
/**
* Defined for use on Android
*
* @param customFolder
* @throws IOException
*/
public FilesystemPackageCacheManager(String customFolder) throws IOException {
this.cacheFolder = new File(customFolder);
init(FilesystemPackageCacheMode.CUSTOM);
}
protected void init(FilesystemPackageCacheMode mode) throws IOException {
initPackageServers();
if (mode == FilesystemPackageCacheMode.CUSTOM) {
if (!this.cacheFolder.exists()) {
throw new FHIRException("The folder ''"+cacheFolder+"' could not be found");
}
} else {
this.cacheFolder = getCacheFolder(mode);
}
initCacheFolder();
}
public static File getCacheFolder(FilesystemPackageCacheMode mode) throws IOException {
switch (mode) {
case SYSTEM:
if (Utilities.isWindows()) {
return new File(Utilities.path(System.getenv("ProgramData"), ".fhir", "packages"));
} else {
return new File(Utilities.path("/var", "lib", ".fhir", "packages"));
}
case USER:
private File getUserCacheFolder() throws IOException {
return new File(Utilities.path(System.getProperty("user.home"), ".fhir", "packages"));
case TESTING:
return new File(Utilities.path("[tmp]", ".fhir", "packages"));
}
return null;
private List<PackageServer> getPackageServersFromFHIRSettings() {
List<PackageServer> packageServers = new ArrayList<>(getConfiguredServers());
if (!isIgnoreDefaultPackageServers()) {
packageServers.addAll(getDefaultServers());
}
return packageServers;
}
protected boolean isIgnoreDefaultPackageServers() {
return FhirSettings.isIgnoreDefaultPackageServers();
}
@Nonnull
protected List<PackageServer> getDefaultServers() {
return PackageServer.defaultServers();
}
protected List<PackageServer> getConfiguredServers() {
return PackageServer.getConfiguredServers();
}
private Builder(File cacheFolder, List<PackageServer> packageServers) {
this.cacheFolder = cacheFolder;
this.packageServers = packageServers;
}
public Builder withCacheFolder (String cacheFolderPath) throws IOException {
File cacheFolder = new File(cacheFolderPath);
if (!cacheFolder.exists()) {
throw new FHIRException("The folder '"+cacheFolder+"' could not be found");
}
return new Builder(cacheFolder, this.packageServers);
}
public Builder withSystemCacheFolder() throws IOException {
final File systemCacheFolder;
if (Utilities.isWindows()) {
systemCacheFolder = new File(Utilities.path(System.getenv("ProgramData"), ".fhir", "packages"));
} else {
systemCacheFolder = new File(Utilities.path("/var", "lib", ".fhir", "packages"));
}
return new Builder(systemCacheFolder, this.packageServers);
}
public Builder withTestingCacheFolder() throws IOException {
return new Builder(new File(Utilities.path("[tmp]", ".fhir", "packages")), this.packageServers);
}
public FilesystemPackageCacheManager build() throws IOException {
return new FilesystemPackageCacheManager(cacheFolder, packageServers);
}
}
private FilesystemPackageCacheManager(File cacheFolder, List<PackageServer> packageServers) throws IOException {
this.cacheFolder = cacheFolder;
this.myPackageServers = packageServers;
initCacheFolder();
}
protected void initCacheFolder() throws IOException {

28
org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/npm/FilesystemPackageManagerTests.java
View File

@ -56,7 +56,8 @@ public class FilesystemPackageManagerTests {
@Nonnull
private FilesystemPackageCacheManager getFilesystemPackageCacheManager(final boolean ignoreDefaultPackageServers) throws IOException {
return new FilesystemPackageCacheManager(FilesystemPackageCacheManager.FilesystemPackageCacheMode.TESTING) {
FilesystemPackageCacheManager.Builder builder = new FilesystemPackageCacheManager.Builder() {
protected boolean isIgnoreDefaultPackageServers() {
return ignoreDefaultPackageServers;
}
@ -70,14 +71,14 @@ public class FilesystemPackageManagerTests {
return dummyPrivateServers;
}
};
return builder.build();
}
@Test
public void testUserCacheDirectory() throws IOException {
FilesystemPackageCacheManager filesystemPackageCacheManager = new FilesystemPackageCacheManager(true) {
protected void initCacheFolder() throws IOException {
}
};
FilesystemPackageCacheManager filesystemPackageCacheManager = new FilesystemPackageCacheManager.Builder().build();
assertEquals(System.getProperty("user.home") + File.separator + ".fhir" + File.separator + "packages", filesystemPackageCacheManager.getFolder());
}
@ -87,27 +88,22 @@ public class FilesystemPackageManagerTests {
@Test
@DisabledOnOs(OS.WINDOWS)
public void testSystemCacheDirectory() throws IOException {
FilesystemPackageCacheManager filesystemPackageCacheManager = new FilesystemPackageCacheManager(false) {
protected void initCacheFolder() throws IOException {
}
};
assertEquals( "/var/lib/.fhir/packages", filesystemPackageCacheManager.getFolder());
File folder = new FilesystemPackageCacheManager.Builder().withSystemCacheFolder().getCacheFolder();
assertEquals( "/var/lib/.fhir/packages", folder.getAbsolutePath());
}
@Test
@EnabledOnOs(OS.WINDOWS)
public void testSystemCacheDirectoryWin() throws IOException {
FilesystemPackageCacheManager filesystemPackageCacheManager = new FilesystemPackageCacheManager(false) {
protected void initCacheFolder() throws IOException {
}
};
assertEquals( System.getenv("ProgramData") + "\\.fhir\\packages", filesystemPackageCacheManager.getFolder());
File folder = new FilesystemPackageCacheManager.Builder().withSystemCacheFolder().getCacheFolder();
assertEquals( System.getenv("ProgramData") + "\\.fhir\\packages", folder.getAbsolutePath());
}
@Test
public void multithreadingTest() throws IOException {
String pcmPath = Files.createTempDirectory("fpcm-multithreadingTest").toFile().getAbsolutePath();
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(pcmPath);
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager.Builder().withCacheFolder(pcmPath).build();
final AtomicInteger totalSuccessful = new AtomicInteger();

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

@ -17,7 +17,7 @@ public class MinimalMemoryTests {
} else {
Utilities.createDirectory(folder.getAbsolutePath());
}
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(folder.getAbsolutePath());
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager.Builder().withCacheFolder(folder.getAbsolutePath()).build();
pcm.setMinimalMemory(true);
NpmPackage npm = pcm.loadPackage("hl7.fhir.us.core", "5.0.0");
Assertions.assertTrue(npm.isMinimalMemory());

11
org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/tests/PackageCacheTests.java
View File

@ -8,7 +8,6 @@ import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.npm.CommonPackages;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode;
import org.hl7.fhir.utilities.npm.NpmPackage;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
@ -17,7 +16,7 @@ public class PackageCacheTests {
@Test
public void testPath() throws IOException {
FilesystemPackageCacheManager cache = new FilesystemPackageCacheManager(FilesystemPackageCacheMode.TESTING);
FilesystemPackageCacheManager cache = new FilesystemPackageCacheManager.Builder().withTestingCacheFolder().build();
NpmPackage npm = cache.loadPackage(CommonPackages.ID_PUBPACK, CommonPackages.VER_PUBPACK);
cache.clear();
List<String> list = cache.listPackages();
@ -43,7 +42,7 @@ public class PackageCacheTests {
@Test
public void testPatchWildCard() throws IOException {
FilesystemPackageCacheManager cache = new FilesystemPackageCacheManager(FilesystemPackageCacheMode.TESTING);
FilesystemPackageCacheManager cache = new FilesystemPackageCacheManager.Builder().withTestingCacheFolder().build();
cache.clear();
Assertions.assertEquals(cache.loadPackage("hl7.fhir.us.core", "3.1.0").version(), "3.1.0");
Assertions.assertEquals(cache.loadPackage("hl7.fhir.us.core", "3.1.1").version(), "3.1.1");
@ -53,7 +52,7 @@ public class PackageCacheTests {
@Test
public void testNotCaseSensitive() throws IOException {
FilesystemPackageCacheManager cache = new FilesystemPackageCacheManager(FilesystemPackageCacheMode.TESTING);
FilesystemPackageCacheManager cache = new FilesystemPackageCacheManager.Builder().withTestingCacheFolder().build();
cache.clear();
Assertions.assertEquals(cache.loadPackage("KBV.Basis", "1.1.3").version(), "1.1.3");
Assertions.assertEquals(cache.loadPackage("kbv.basis", "1.1.3").version(), "1.1.3");
@ -61,7 +60,7 @@ public class PackageCacheTests {
@Test
public void testLastReleasedVersion() throws IOException {
FilesystemPackageCacheManager cache = new FilesystemPackageCacheManager(FilesystemPackageCacheMode.TESTING);
FilesystemPackageCacheManager cache = new FilesystemPackageCacheManager.Builder().withTestingCacheFolder().build();
cache.clear();
Assertions.assertEquals("0.0.8", cache.loadPackage(CommonPackages.ID_PUBPACK, "0.0.8").version());
Assertions.assertEquals(CommonPackages.VER_PUBPACK, cache.loadPackage(CommonPackages.ID_PUBPACK).version());
@ -69,7 +68,7 @@ public class PackageCacheTests {
@Test
public void testMinimal() throws IOException {
FilesystemPackageCacheManager cache = new FilesystemPackageCacheManager(FilesystemPackageCacheMode.TESTING);
FilesystemPackageCacheManager cache = new FilesystemPackageCacheManager.Builder().withTestingCacheFolder().build();
cache.clear();
NpmPackage uscore = cache.loadPackage("hl7.fhir.us.core", "3.1.0");
cache.setMinimalMemory(true);

3
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/ValidationEngine.java
View File

@ -29,7 +29,6 @@ import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.context.ContextUtilities;
import org.hl7.fhir.r5.context.ILoggingService;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.context.IWorkerContextManager;
import org.hl7.fhir.r5.context.SimpleWorkerContext;
import org.hl7.fhir.r5.context.SystemOutLoggingService;
@ -1055,7 +1054,7 @@ public class ValidationEngine implements IValidatorResourceFetcher, IValidationP
public FilesystemPackageCacheManager getPcm() throws IOException {
if (pcm == null) {
//System.out.println("Creating Package manager?");
pcm = new FilesystemPackageCacheManager(org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER);
pcm = new FilesystemPackageCacheManager.Builder().build();
}
return pcm;
}

21
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/ValidatorCli.java
View File

@ -74,25 +74,7 @@ import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.settings.FhirSettings;
import org.hl7.fhir.validation.cli.model.CliContext;
import org.hl7.fhir.validation.cli.services.ValidationService;
import org.hl7.fhir.validation.cli.tasks.CliTask;
import org.hl7.fhir.validation.cli.tasks.CompareTask;
import org.hl7.fhir.validation.cli.tasks.CompileTask;
import org.hl7.fhir.validation.cli.tasks.ConvertTask;
import org.hl7.fhir.validation.cli.tasks.FhirpathTask;
import org.hl7.fhir.validation.cli.tasks.InstallTask;
import org.hl7.fhir.validation.cli.tasks.LangTransformTask;
import org.hl7.fhir.validation.cli.tasks.NarrativeTask;
import org.hl7.fhir.validation.cli.tasks.ScanTask;
import org.hl7.fhir.validation.cli.tasks.SnapshotTask;
import org.hl7.fhir.validation.cli.tasks.SpecialTask;
import org.hl7.fhir.validation.cli.tasks.SpreadsheetTask;
import org.hl7.fhir.validation.cli.tasks.StandaloneTask;
import org.hl7.fhir.validation.cli.tasks.TestsTask;
import org.hl7.fhir.validation.cli.tasks.TransformTask;
import org.hl7.fhir.validation.cli.tasks.TxTestsTask;
import org.hl7.fhir.validation.cli.tasks.ValidateTask;
import org.hl7.fhir.validation.cli.tasks.ValidationEngineTask;
import org.hl7.fhir.validation.cli.tasks.VersionTask;
import org.hl7.fhir.validation.cli.tasks.*;
import org.hl7.fhir.validation.cli.utils.Display;
import org.hl7.fhir.validation.cli.utils.Params;
@ -144,6 +126,7 @@ public class ValidatorCli {
new InstallTask(),
new LangTransformTask(),
new NarrativeTask(),
new PreloadCacheTask(),
new ScanTask(),
new SnapshotTask(),
new SpecialTask(),

3
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/services/ValidationService.java
View File

@ -33,7 +33,6 @@ import org.hl7.fhir.r5.model.ConceptMap;
import org.hl7.fhir.r5.model.OperationOutcome;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionKind;
import org.hl7.fhir.r5.model.StructureMap;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.renderers.spreadsheets.CodeSystemSpreadsheetGenerator;
@ -154,7 +153,7 @@ public class ValidationService {
public VersionSourceInformation scanForVersions(CliContext cliContext) throws Exception {
VersionSourceInformation versions = new VersionSourceInformation();
IgLoader igLoader = new IgLoader(
new FilesystemPackageCacheManager(org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER),
new FilesystemPackageCacheManager.Builder().build(),
new SimpleWorkerContext.SimpleWorkerContextBuilder().fromNothing(),
null);
for (String src : cliContext.getIgs()) {

57
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/tasks/PreloadCacheTask.java Normal file
View File

@ -0,0 +1,57 @@
package org.hl7.fhir.validation.cli.tasks;
import org.hl7.fhir.convertors.analytics.PackageVisitor;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.utils.EOperationOutcome;
import org.hl7.fhir.utilities.SystemExitManager;
import org.hl7.fhir.utilities.TimeTracker;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.json.JsonException;
import org.hl7.fhir.utilities.json.model.JsonObject;
import org.hl7.fhir.utilities.json.parser.JsonParser;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.PackageServer;
import org.hl7.fhir.utilities.settings.FhirSettings;
import org.hl7.fhir.validation.cli.model.CliContext;
import org.hl7.fhir.validation.cli.utils.Params;
import org.hl7.fhir.validation.packages.PackageCacheDownloader;
import org.hl7.fhir.validation.special.TxTester;
import java.io.IOException;
import java.io.PrintStream;
import java.util.List;
public class PreloadCacheTask extends StandaloneTask {
@Override
public String getName() {
return "preloadCache";
}
@Override
public String getDisplayName() {
return "Pre-load Package Cache";
}
@Override
public boolean isHidden() {
return true;
}
@Override
public boolean shouldExecuteTask(CliContext cliContext, String[] args) {
return Params.hasParam(args, Params.PRELOAD_CACHE);
}
@Override
public void printHelp(PrintStream out) {
}
@Override
public void executeTask(CliContext cliContext, String[] args, TimeTracker tt, TimeTracker.Session tts) throws Exception {
PackageVisitor pv = new PackageCacheDownloader();
pv.visitPackages();
}
}

2
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/utils/Display.java
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@ -21,7 +21,7 @@ public class Display {
}
public static void printCliParamsAndInfo(String[] args) throws IOException {
System.out.println(" Paths: Current = " + System.getProperty("user.dir") + ", Package Cache = " + new FilesystemPackageCacheManager(org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER).getFolder());
System.out.println(" Paths: Current = " + System.getProperty("user.dir") + ", Package Cache = " + new FilesystemPackageCacheManager.Builder().build().getFolder());
System.out.print(" Params:");
for (String s : args) {
System.out.print(s.contains(" ") ? " \"" + s + "\"" : " " + s);

2
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/utils/Params.java
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@ -69,6 +69,8 @@ public class Params {
public static final String LEFT = "-left";
public static final String RIGHT = "-right";
public static final String NO_INTERNAL_CACHING = "-no-internal-caching";
public static final String PRELOAD_CACHE = "-preload-cache";
public static final String NO_EXTENSIBLE_BINDING_WARNINGS = "-no-extensible-binding-warnings";
public static final String NO_UNICODE_BIDI_CONTROL_CHARS = "-no_unicode_bidi_control_chars";
public static final String NO_INVARIANTS = "-no-invariants";

58
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/packages/PackageCacheDownloader.java Normal file
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@ -0,0 +1,58 @@
package org.hl7.fhir.validation.packages;
import org.hl7.fhir.convertors.analytics.PackageVisitor;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.utils.EOperationOutcome;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.npm.PackageServer;
import java.io.IOException;
import java.util.List;
/**
* A PackageVisitor that is intended to visit each available package from
* https://packages2.fhir.org/packages aka PackageServer.secondaryServer()
* <p/>
* A useful side effect of this is that it fills the package cache on the disk
* with all available packages. Aside from this, it does nothing but write to
* console out.
* <p/>
* It targets the secondary server to avoid loading the primary server.
*
*/
public class PackageCacheDownloader extends PackageVisitor implements PackageVisitor.IPackageVisitorProcessor{
public PackageCacheDownloader() throws IOException {
super();
setClientPackageServer(PackageServer.secondaryServer());
setCachePackageServers(List.of(PackageServer.secondaryServer()));
String taskCache = Utilities.path("[tmp]", "package-cache-task");
setProcessor(this);
setCache(taskCache);
setOldVersions(true);
setCorePackages(true);
}
@Override
public Object startPackage(PackageVisitor.PackageContext context) throws FHIRException {
System.out.println("Currently loading " + context.getPid());
return null;
}
@Override
public void processResource(PackageVisitor.PackageContext context, Object clientContext, String type, String id, byte[] content) throws FHIRException {
}
@Override
public void finishPackage(PackageVisitor.PackageContext context) throws FHIRException {
}
@Override
public void alreadyVisited(String pid) throws FHIRException {
}
}

2
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/packages/PackageValidator.java
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@ -20,7 +20,7 @@ public class PackageValidator {
}
private void execute() throws IOException {
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER);
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager.Builder().build();
PackageClient pc = new PackageClient(PackageServer.primaryServer());
for (PackageInfo t : pc.search(null, null, null, false)) {

2
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/special/R4R5MapTester.java
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@ -167,7 +167,7 @@ public class R4R5MapTester implements IValidatorResourceFetcher {
log("Load Test Outcomes");
JsonObject json = JsonParser.parseObjectFromFile(Utilities.path(src, "input", "_data", "conversions.json"));
log("Load R5");
pcm = new FilesystemPackageCacheManager(true);
pcm = new FilesystemPackageCacheManager.Builder().build();
context = new SimpleWorkerContextBuilder().withAllowLoadingDuplicates(true).fromPackage(pcm.loadPackage("hl7.fhir.r5.core#current"));
log("Load Maps");
// context.loadFromPackage(pcm.loadPackage(), null);

5
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/comparison/tests/ComparisonTests.java
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@ -64,7 +64,6 @@ import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.json.model.*;
import org.hl7.fhir.utilities.json.parser.*;
import org.hl7.fhir.utilities.npm.CommonPackages;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.NpmPackage;
@ -127,7 +126,7 @@ public class ComparisonTests {
if (context == null) {
System.out.println("---- Load R5 ----------------------------------------------------------------");
context = TestingUtilities.getSharedWorkerContext();
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER);
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager.Builder().build();
NpmPackage npm = pcm.loadPackage("hl7.fhir.us.core#3.1.0");
BaseWorkerContext bc = (BaseWorkerContext) context;
boolean dupl = bc.isAllowLoadingDuplicates();
@ -140,7 +139,7 @@ public class ComparisonTests {
if (!new File(Utilities.path("[tmp]", "comparison")).exists()) {
System.out.println("---- Set up Output ----------------------------------------------------------");
Utilities.createDirectory(Utilities.path("[tmp]", "comparison"));
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER);
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager.Builder().build();
NpmPackage npm = pcm.loadPackage(CommonPackages.ID_PUBPACK, CommonPackages.VER_PUBPACK);
for (String f : npm.list("other")) {
TextFile.streamToFile(npm.load("other", f), Utilities.path("[tmp]", "comparison", f));

2
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/conversion/tests/R3R4ConversionTests.java
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@ -308,7 +308,7 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
if (contextR3 != null)
return;
pcm = new FilesystemPackageCacheManager(org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER);
pcm = new FilesystemPackageCacheManager.Builder().build();
R3ToR4Loader ldr = (R3ToR4Loader) new R3ToR4Loader().setPatchUrls(true).setKillPrimitives(true);
System.out.println("loading R3");

2
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/conversion/tests/UtilitiesXTests.java
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@ -87,7 +87,7 @@ public class UtilitiesXTests {
if (!fcontexts.containsKey(version)) {
FilesystemPackageCacheManager pcm;
try {
pcm = new FilesystemPackageCacheManager(org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER);
pcm = new FilesystemPackageCacheManager.Builder().build();
IWorkerContext fcontext = TestingUtilities.getWorkerContext(pcm.loadPackage(VersionUtilities.packageForVersion(version), version), loaderForVersion(version));
fcontext.setUcumService(new UcumEssenceService(UtilitiesXTests.loadTestResourceStream("ucum", "ucum-essence.xml")));
fcontext.setExpansionProfile(new Parameters());

35
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/ValidatorCliTests.java
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@ -16,23 +16,7 @@ import org.hl7.fhir.utilities.TimeTracker;
import org.hl7.fhir.validation.cli.model.CliContext;
import org.hl7.fhir.validation.cli.services.ValidationService;
import org.hl7.fhir.validation.cli.services.ValidatorWatchMode;
import org.hl7.fhir.validation.cli.tasks.CliTask;
import org.hl7.fhir.validation.cli.tasks.CompareTask;
import org.hl7.fhir.validation.cli.tasks.CompileTask;
import org.hl7.fhir.validation.cli.tasks.ConvertTask;
import org.hl7.fhir.validation.cli.tasks.FhirpathTask;
import org.hl7.fhir.validation.cli.tasks.InstallTask;
import org.hl7.fhir.validation.cli.tasks.LangTransformTask;
import org.hl7.fhir.validation.cli.tasks.NarrativeTask;
import org.hl7.fhir.validation.cli.tasks.ScanTask;
import org.hl7.fhir.validation.cli.tasks.SnapshotTask;
import org.hl7.fhir.validation.cli.tasks.SpecialTask;
import org.hl7.fhir.validation.cli.tasks.SpreadsheetTask;
import org.hl7.fhir.validation.cli.tasks.TestsTask;
import org.hl7.fhir.validation.cli.tasks.TransformTask;
import org.hl7.fhir.validation.cli.tasks.TxTestsTask;
import org.hl7.fhir.validation.cli.tasks.ValidateTask;
import org.hl7.fhir.validation.cli.tasks.VersionTask;
import org.hl7.fhir.validation.cli.tasks.*;
import org.hl7.fhir.validation.cli.utils.Params;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
@ -74,6 +58,12 @@ public class ValidatorCliTests {
@Spy
SpreadsheetTask spreadsheetTask;
@Spy
PreloadCacheTask preloadCacheTask = new PreloadCacheTask() {
@Override
public void executeTask(CliContext cliContext, String[] args, TimeTracker tt, TimeTracker.Session tts) {}
};
@Spy
TestsTask testsTask = new TestsTask() {
@Override
@ -119,6 +109,7 @@ public class ValidatorCliTests {
installTask,
langTransformTask,
narrativeTask,
preloadCacheTask,
scanTask,
snapshotTask,
specialTask,
@ -304,6 +295,16 @@ public class ValidatorCliTests {
Mockito.verify(compareTask).executeTask(same(validationService), same(validationEngine), same(cliContext), eq(args), any(TimeTracker.class), any(TimeTracker.Session.class));
}
@Test
public void preloadCacheTest() throws Exception {
final String[] args = new String[]{"-preload-cache"};
CliContext cliContext = Params.loadCliContext(args);
ValidatorCli cli = mockValidatorCli();
cli.readParamsAndExecuteTask(cliContext, args);
Mockito.verify(preloadCacheTask).executeTask(same(cliContext), eq(args), any(TimeTracker.class), any(TimeTracker.Session.class));
}
@Test
public void txTestsTest() throws Exception {
final String[] args = new String[]{"-txTests"};

4
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/ValidationTests.java
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@ -22,7 +22,6 @@ import org.hl7.fhir.convertors.factory.VersionConvertorFactory_10_50;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_14_50;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_30_50;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_40_50;
import org.hl7.fhir.convertors.loaders.loaderR5.R4ToR5Loader;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
@ -39,7 +38,6 @@ import org.hl7.fhir.r5.fhirpath.TypeDetails;
import org.hl7.fhir.r5.fhirpath.FHIRPathEngine.IEvaluationContext;
import org.hl7.fhir.r5.fhirpath.FHIRPathUtilityClasses.FunctionDetails;
import org.hl7.fhir.r5.elementmodel.ObjectConverter;
import org.hl7.fhir.r5.elementmodel.SHLParser;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.formats.XmlParser;
@ -445,7 +443,7 @@ public class ValidationTests implements IEvaluationContext, IValidatorResourceFe
private NpmPackage loadPackage(String idAndVer) throws IOException {
var pcm = new FilesystemPackageCacheManager(true);
var pcm = new FilesystemPackageCacheManager.Builder().build();
return pcm.loadPackage(idAndVer);
}