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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

60
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/ExtensionDefinitionGenerator.java
View File

@ -1,33 +1,33 @@
package org.hl7.fhir.convertors;
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific
prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific
prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
import java.io.IOException;
@ -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);

64
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/test/utils/TestingUtilities.java
View File

@ -1,33 +1,33 @@
package org.hl7.fhir.r4.test.utils;
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific
prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific
prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
import java.io.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);

27
org.hl7.fhir.r5/pom.xml
View File

@ -1,5 +1,5 @@
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
@ -13,14 +13,15 @@
<packaging>bundle</packaging>
<dependencies>
<!-- HAPI Dependencies -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.utilities</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-base</artifactId>
<exclusions>
<exclusion>
@ -133,16 +134,16 @@
<version>${junit_jupiter_version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.atlassian.commonmark</groupId>
<artifactId>commonmark</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.atlassian.commonmark</groupId>
<artifactId>commonmark-ext-gfm-tables</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.atlassian.commonmark</groupId>
<artifactId>commonmark</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.atlassian.commonmark</groupId>
<artifactId>commonmark-ext-gfm-tables</artifactId>
<scope>test</scope>
</dependency>
</dependencies>

63
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;
@ -31,34 +30,34 @@ import org.w3c.dom.Element;
import org.w3c.dom.NamedNodeMap;
import org.w3c.dom.Node;
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific
prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific
prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
import com.google.gson.JsonArray;
@ -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
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@ -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;
}
}

752
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
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File diff suppressed because it is too large Load Diff

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;
}

109
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/cache/NpmPackage.java vendored
View File

@ -1,33 +1,33 @@
package org.hl7.fhir.utilities.cache;
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific
prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific
prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
@ -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))

38
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 {
@ -34,7 +31,7 @@ public class PackageClient {
private String description;
private String url;
private String canonical;
public PackageInfo(String id, String version, String fhirVersion, String description, String url, String canonical) {
super();
this.id = id;
@ -62,16 +59,16 @@ public class PackageClient {
public String getUrl() {
return url;
}
public String getCanonical() {
return canonical;
}
@Override
public String toString() {
return id+"#"+(version == null ? "?pc-pi?" : version)+(fhirVersion == null ? "": " ("+canonical+") for FHIR "+fhirVersion)+(url == null ? "" : " @"+url)+(description == null ? "" : " '"+description+"'");
}
}
}
private String address;
private String cacheFolder;
@ -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";
}

70
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/cache/PackageGenerator.java vendored
View File

@ -1,33 +1,33 @@
package org.hl7.fhir.utilities.cache;
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific
prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific
prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
@ -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;
@ -79,7 +84,11 @@ public class PackageGenerator {
object = parser.parse(TextFile.streamToString(template)).getAsJsonObject();
}
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 -->

76
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;
@ -55,34 +51,34 @@ import java.util.Map.Entry;
import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream;
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific
prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific
prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
/*
Copyright (c) 2011+, HL7, Inc
@ -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");

62
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/conversion/tests/TestingUtilitiesX.java
View File

@ -1,33 +1,33 @@
package org.hl7.fhir.conversion.tests;
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific
prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific
prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
import java.io.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>