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Get validator CLI working

This commit is contained in:
James Agnew 2019-01-31 15:51:34 -05:00
parent 6194add99f
commit caf7cea4c6
10 changed files with 297 additions and 23 deletions
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44
org.hl7.fhir.utilities/pom.xml
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@ -62,4 +62,48 @@
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>buildnumber-maven-plugin</artifactId>
<inherited>true</inherited>
<executions>
<execution>
<id>standard</id>
<phase>validate</phase>
<goals>
<goal>create</goal>
</goals>
</execution>
<execution>
<id>downstream</id>
<phase>validate</phase>
<goals>
<goal>create-metadata</goal>
</goals>
<configuration>
<outputDirectory>${project.build.directory}/generated-sources/properties</outputDirectory>
<outputName>fhir-build.properties</outputName>
<revisionPropertyName>orgfhir.buildnumber</revisionPropertyName>
<timestampPropertyName>orgfhir.timestamp</timestampPropertyName>
<timestampFormat>yyyy-MM-dd'T'HH:mm:ss.SXXX</timestampFormat>
<versionPropertyName>orgfhir.version</versionPropertyName>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
<resources>
<resource>
<directory>src/main/resources</directory>
<filtering>true</filtering>
</resource>
<resource>
<directory>${project.build.directory}/generated-sources/properties</directory>
<filtering>false</filtering>
</resource>
</resources>
</build>
</project>

79
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/VersionUtil.java Normal file
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@ -0,0 +1,79 @@
package org.hl7.fhir.utilities;
/*
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2019 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import java.io.InputStream;
import java.util.Properties;
import static org.apache.commons.lang3.StringUtils.defaultIfBlank;
import static org.apache.commons.lang3.StringUtils.left;
/**
* Used internally by HAPI to log the version of the HAPI FHIR framework
* once, when the framework is first loaded by the classloader.
*/
public class VersionUtil {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ca.uhn.fhir.util.VersionUtil.class);
private static String ourVersion;
private static String ourBuildNumber;
private static String ourBuildTime;
static {
initialize();
}
public static String getBuildNumber() {
return ourBuildNumber;
}
public static String getBuildTime() {
return ourBuildTime;
}
public static String getVersion() {
return ourVersion;
}
private static void initialize() {
try (InputStream is = ca.uhn.fhir.util.VersionUtil.class.getResourceAsStream("/fhir-build.properties")) {
Properties p = new Properties();
if (is != null) {
p.load(is);
}
ourVersion = p.getProperty("orgfhir.version");
ourVersion = defaultIfBlank(ourVersion, "(unknown)");
ourBuildNumber = p.getProperty("orgfhir.buildnumber");
ourBuildTime = p.getProperty("orgfhir.timestamp");
} catch (Exception e) {
ourLog.warn("Unable to determine version information", e);
}
}
public static String getVersionString() {
return "Version " + getVersion() + " - Built " + getBuildTime() + " - Git " + left(getBuildNumber(), 12);
}
}

52
org.hl7.fhir.validation.cli/.classpath Normal file
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@ -0,0 +1,52 @@
<?xml version="1.0" encoding="UTF-8"?>
<classpath>
<classpathentry kind="src" path="src/test/java" output="target/test-classes" including="**/*.java"/>
<classpathentry kind="src" path="src/test/resources" output="target/test-classes" excluding="**/*.java"/>
<classpathentry kind="src" path="src/main/java" including="**/*.java"/>
<classpathentry kind="src" path="src/main/resources" excluding="**/*.java"/>
<classpathentry kind="output" path="target/classes"/>
<classpathentry kind="var" path="M2_REPO/javax/xml/bind/jaxb-api/2.3.1/jaxb-api-2.3.1.jar" sourcepath="M2_REPO/javax/xml/bind/jaxb-api/2.3.1/jaxb-api-2.3.1-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/javax/activation/javax.activation-api/1.2.0/javax.activation-api-1.2.0.jar" sourcepath="M2_REPO/javax/activation/javax.activation-api/1.2.0/javax.activation-api-1.2.0-sources.jar"/>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8"/>
<classpathentry kind="var" path="M2_REPO/ca/uhn/hapi/fhir/hapi-fhir-base/3.7.0-SNAPSHOT/hapi-fhir-base-3.7.0-SNAPSHOT.jar" sourcepath="M2_REPO/ca/uhn/hapi/fhir/hapi-fhir-base/3.7.0-SNAPSHOT/hapi-fhir-base-3.7.0-SNAPSHOT-sources.jar"/>
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<classpathentry kind="var" path="M2_REPO/org/apache/commons/commons-lang3/3.8.1/commons-lang3-3.8.1.jar" sourcepath="M2_REPO/org/apache/commons/commons-lang3/3.8.1/commons-lang3-3.8.1-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/org/apache/commons/commons-text/1.6/commons-text-1.6.jar" sourcepath="M2_REPO/org/apache/commons/commons-text/1.6/commons-text-1.6-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/commons-codec/commons-codec/1.11/commons-codec-1.11.jar" sourcepath="M2_REPO/commons-codec/commons-codec/1.11/commons-codec-1.11-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/commons-io/commons-io/2.6/commons-io-2.6.jar" sourcepath="M2_REPO/commons-io/commons-io/2.6/commons-io-2.6-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/com/google/guava/guava/25.0-jre/guava-25.0-jre.jar" sourcepath="M2_REPO/com/google/guava/guava/25.0-jre/guava-25.0-jre-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/com/google/code/findbugs/jsr305/1.3.9/jsr305-1.3.9.jar"/>
<classpathentry kind="var" path="M2_REPO/org/checkerframework/checker-compat-qual/2.0.0/checker-compat-qual-2.0.0.jar" sourcepath="M2_REPO/org/checkerframework/checker-compat-qual/2.0.0/checker-compat-qual-2.0.0-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/com/google/errorprone/error_prone_annotations/2.1.3/error_prone_annotations-2.1.3.jar" sourcepath="M2_REPO/com/google/errorprone/error_prone_annotations/2.1.3/error_prone_annotations-2.1.3-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/com/google/j2objc/j2objc-annotations/1.1/j2objc-annotations-1.1.jar" sourcepath="M2_REPO/com/google/j2objc/j2objc-annotations/1.1/j2objc-annotations-1.1-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/org/codehaus/mojo/animal-sniffer-annotations/1.14/animal-sniffer-annotations-1.14.jar" sourcepath="M2_REPO/org/codehaus/mojo/animal-sniffer-annotations/1.14/animal-sniffer-annotations-1.14-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/org/slf4j/slf4j-api/1.7.25/slf4j-api-1.7.25.jar" sourcepath="M2_REPO/org/slf4j/slf4j-api/1.7.25/slf4j-api-1.7.25-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/org/slf4j/jcl-over-slf4j/1.7.25/jcl-over-slf4j-1.7.25.jar" sourcepath="M2_REPO/org/slf4j/jcl-over-slf4j/1.7.25/jcl-over-slf4j-1.7.25-sources.jar"/>
<classpathentry kind="src" path="/org.hl7.fhir.utilities"/>
<classpathentry kind="src" path="/org.hl7.fhir.convertors"/>
<classpathentry kind="src" path="/org.hl7.fhir.dstu2"/>
<classpathentry kind="src" path="/org.hl7.fhir.dstu2016may"/>
<classpathentry kind="src" path="/org.hl7.fhir.dstu3"/>
<classpathentry kind="src" path="/org.hl7.fhir.r4"/>
<classpathentry kind="var" path="M2_REPO/ca/uhn/hapi/fhir/hapi-fhir-structures-r4/3.7.0-SNAPSHOT/hapi-fhir-structures-r4-3.7.0-SNAPSHOT.jar" sourcepath="M2_REPO/ca/uhn/hapi/fhir/hapi-fhir-structures-r4/3.7.0-SNAPSHOT/hapi-fhir-structures-r4-3.7.0-SNAPSHOT-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/ca/uhn/hapi/fhir/hapi-fhir-utilities/3.7.0-SNAPSHOT/hapi-fhir-utilities-3.7.0-SNAPSHOT.jar" sourcepath="M2_REPO/ca/uhn/hapi/fhir/hapi-fhir-utilities/3.7.0-SNAPSHOT/hapi-fhir-utilities-3.7.0-SNAPSHOT-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/org/glassfish/jaxb/jaxb-runtime/2.3.1/jaxb-runtime-2.3.1.jar" sourcepath="M2_REPO/org/glassfish/jaxb/jaxb-runtime/2.3.1/jaxb-runtime-2.3.1-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/org/glassfish/jaxb/txw2/2.3.1/txw2-2.3.1.jar" sourcepath="M2_REPO/org/glassfish/jaxb/txw2/2.3.1/txw2-2.3.1-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/com/sun/istack/istack-commons-runtime/3.0.7/istack-commons-runtime-3.0.7.jar" sourcepath="M2_REPO/com/sun/istack/istack-commons-runtime/3.0.7/istack-commons-runtime-3.0.7-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/org/jvnet/staxex/stax-ex/1.8/stax-ex-1.8.jar" sourcepath="M2_REPO/org/jvnet/staxex/stax-ex/1.8/stax-ex-1.8-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/com/sun/xml/fastinfoset/FastInfoset/1.2.15/FastInfoset-1.2.15.jar" sourcepath="M2_REPO/com/sun/xml/fastinfoset/FastInfoset/1.2.15/FastInfoset-1.2.15-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/ca/uhn/hapi/fhir/hapi-fhir-validation-resources-r4/3.7.0-SNAPSHOT/hapi-fhir-validation-resources-r4-3.7.0-SNAPSHOT.jar" sourcepath="M2_REPO/ca/uhn/hapi/fhir/hapi-fhir-validation-resources-r4/3.7.0-SNAPSHOT/hapi-fhir-validation-resources-r4-3.7.0-SNAPSHOT-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/net/sf/saxon/Saxon-HE/9.5.1-5/Saxon-HE-9.5.1-5.jar" sourcepath="M2_REPO/net/sf/saxon/Saxon-HE/9.5.1-5/Saxon-HE-9.5.1-5-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/xpp3/xpp3/1.1.4c/xpp3-1.1.4c.jar" sourcepath="M2_REPO/xpp3/xpp3/1.1.4c/xpp3-1.1.4c-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/xpp3/xpp3_xpath/1.1.4c/xpp3_xpath-1.1.4c.jar" sourcepath="M2_REPO/xpp3/xpp3_xpath/1.1.4c/xpp3_xpath-1.1.4c-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/org/everit/json/org.everit.json.schema/1.1.0/org.everit.json.schema-1.1.0.jar"/>
<classpathentry kind="var" path="M2_REPO/org/everit/osgi/bundles/org.everit.osgi.bundles.org.json/1.0.0-v20140107/org.everit.osgi.bundles.org.json-1.0.0-v20140107.jar"/>
<classpathentry kind="var" path="M2_REPO/ch/qos/logback/logback-classic/1.2.3/logback-classic-1.2.3.jar" sourcepath="M2_REPO/ch/qos/logback/logback-classic/1.2.3/logback-classic-1.2.3-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/ch/qos/logback/logback-core/1.2.3/logback-core-1.2.3.jar" sourcepath="M2_REPO/ch/qos/logback/logback-core/1.2.3/logback-core-1.2.3-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/junit/junit/4.12/junit-4.12.jar" sourcepath="M2_REPO/junit/junit/4.12/junit-4.12-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/org/hamcrest/java-hamcrest/2.0.0.0/java-hamcrest-2.0.0.0.jar" sourcepath="M2_REPO/org/hamcrest/java-hamcrest/2.0.0.0/java-hamcrest-2.0.0.0-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/org/mockito/mockito-core/2.23.4/mockito-core-2.23.4.jar" sourcepath="M2_REPO/org/mockito/mockito-core/2.23.4/mockito-core-2.23.4-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/net/bytebuddy/byte-buddy/1.9.3/byte-buddy-1.9.3.jar" sourcepath="M2_REPO/net/bytebuddy/byte-buddy/1.9.3/byte-buddy-1.9.3-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/net/bytebuddy/byte-buddy-agent/1.9.3/byte-buddy-agent-1.9.3.jar" sourcepath="M2_REPO/net/bytebuddy/byte-buddy-agent/1.9.3/byte-buddy-agent-1.9.3-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/org/objenesis/objenesis/2.6/objenesis-2.6.jar" sourcepath="M2_REPO/org/objenesis/objenesis/2.6/objenesis-2.6-sources.jar"/>
</classpath>

21
org.hl7.fhir.validation.cli/.project Normal file
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@ -0,0 +1,21 @@
<?xml version="1.0" encoding="UTF-8"?>
<projectDescription>
<name>org.hl7.fhir.validation</name>
<comment>An open-source implementation of the FHIR specification in Java. NO_M2ECLIPSE_SUPPORT: Project files created with the maven-eclipse-plugin are not supported in M2Eclipse.</comment>
<projects>
<project>org.hl7.fhir.utilities</project>
<project>org.hl7.fhir.convertors</project>
<project>org.hl7.fhir.dstu2</project>
<project>org.hl7.fhir.dstu2016may</project>
<project>org.hl7.fhir.dstu3</project>
<project>org.hl7.fhir.r4</project>
</projects>
<buildSpec>
<buildCommand>
<name>org.eclipse.jdt.core.javabuilder</name>
</buildCommand>
</buildSpec>
<natures>
<nature>org.eclipse.jdt.core.javanature</nature>
</natures>
</projectDescription>

82
org.hl7.fhir.validation.cli/pom.xml Normal file
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@ -0,0 +1,82 @@
<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">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>3.7.3-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
<artifactId>org.hl7.fhir.validation.cli</artifactId>
<packaging>jar</packaging>
<dependencies>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.validation</artifactId>
<version>${project.version}</version>
</dependency>
<!--
The following dependencies are all listed as optional dependencies in
org.hl7.fhir.utilities (and others) but are required for the CLI to work,
so we explicitly bring them in here.
-->
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-compress</artifactId>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
</dependency>
<dependency>
<groupId>org.fhir</groupId>
<artifactId>ucum</artifactId>
<version>1.0.2</version>
</dependency>
<dependency>
<groupId>xpp3</groupId>
<artifactId>xpp3</artifactId>
</dependency>
<dependency>
<groupId>xpp3</groupId>
<artifactId>xpp3_xpath</artifactId>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>3.2.1</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<mainClass>org.hl7.fhir.r4.validation.Validator</mainClass>
</transformer>
</transformers>
<shadedArtifactAttached>true</shadedArtifactAttached>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>

0
org.hl7.fhir.validation/src/main/resources/.keep.15 → org.hl7.fhir.validation.cli/src/main/java/.keep.16
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16
org.hl7.fhir.validation.cli/src/main/resources/logback.xml Normal file
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@ -0,0 +1,16 @@
<configuration scan="true" scanPeriod="30 seconds">
<appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
<filter class="ch.qos.logback.classic.filter.ThresholdFilter">
<level>INFO</level>
</filter>
<encoder>
<pattern>%d{yyyy-MM-dd HH:mm:ss.SSS} [%thread] %-5level %logger{36} [%file:%line] %msg%n</pattern>
</encoder>
</appender>
<root level="info">
<appender-ref ref="STDOUT" />
</root>
</configuration>

21
org.hl7.fhir.validation/pom.xml
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@ -89,27 +89,6 @@
<build>
<plugins>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<archive>
<manifest>
<mainClass>org.hl7.fhir.r4.validation.Validator</mainClass>
</manifest>
</archive>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>

4
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r4/validation/Validator.java
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@ -75,6 +75,7 @@ import org.hl7.fhir.r4.model.OperationOutcome.OperationOutcomeIssueComponent;
import org.hl7.fhir.r4.model.Resource;
import org.hl7.fhir.r4.model.StructureDefinition;
import org.hl7.fhir.r4.utils.ToolingExtensions;
import org.hl7.fhir.utilities.VersionUtil;
import org.hl7.fhir.utilities.cache.ToolsVersion;
import org.hl7.fhir.utilities.xhtml.XhtmlComposer;
@ -100,6 +101,7 @@ public class Validator {
public static void main(String[] args) throws Exception {
System.out.println("FHIR Validation tool " + VersionUtil.getVersionString());
if (hasParam(args, "-tests")) {
try {
Class<?> clazz = Class.forName("org.hl7.fhir.validation.r4.tests.ValidationEngineTests");
@ -108,7 +110,6 @@ public class Validator {
e.printStackTrace();
}
} else if (args.length == 0 || hasParam(args, "help") || hasParam(args, "?") || hasParam(args, "-?") || hasParam(args, "/?") ) {
System.out.println("FHIR Validation tool v"+Constants.VERSION+" ("+ToolsVersion.TOOLS_VERSION+")");
System.out.println("");
System.out.println("The FHIR validation tool validates a FHIR resource or bundle.");
System.out.println("The validation tool compares a resource against the base definitions and any");
@ -245,7 +246,6 @@ public class Validator {
}
}
} else {
System.out.println("FHIR Validator Build "+getGitBuild());
System.out.print("Arguments:");
for (String s : args)
System.out.print(s.contains(" ") ? " \""+s+"\"" : " "+s);

1
pom.xml
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@ -125,6 +125,7 @@
<!--<module>org.hl7.fhir.rdf</module>-->
<module>org.hl7.fhir.convertors</module>
<module>org.hl7.fhir.validation</module>
<module>org.hl7.fhir.validation.cli</module>
</modules>
<build>