Finalizing 1.2 release

hapi-fhir-cli/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>1.2-SNAPSHOT</version>
+		<version>1.2</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 
@@ -22,33 +22,33 @@
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-base</artifactId>
-			<version>1.2-SNAPSHOT</version>
+			<version>1.2</version>
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-jpaserver-example</artifactId>
-			<version>1.2-SNAPSHOT</version>
+			<version>1.2</version>
 			<type>war</type>
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-structures-dstu</artifactId>
-			<version>1.2-SNAPSHOT</version>
+			<version>1.2</version>
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-structures-dstu2</artifactId>
-			<version>1.2-SNAPSHOT</version>
+			<version>1.2</version>
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-structures-hl7org-dstu2</artifactId>
-			<version>1.2-SNAPSHOT</version>
+			<version>1.2</version>
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
-			<artifactId>hapi-fhir-validation-resources</artifactId>
-			<version>1.2-SNAPSHOT</version>
+			<artifactId>hapi-fhir-validation-resources-dstu2</artifactId>
+			<version>1.2</version>
 		</dependency>
 
 		<dependency>
@@ -143,7 +143,7 @@
 								<artifactItem>
 									<groupId>ca.uhn.hapi.fhir</groupId>
 									<artifactId>hapi-fhir-jpaserver-example</artifactId>
-									<version>1.2-SNAPSHOT</version>
+									<version>1.2</version>
 									<type>war</type>
 									<overWrite>true</overWrite>
 									<outputDirectory>target/classes</outputDirectory>

hapi-fhir-cli/src/main/java/ca/uhn/fhir/cli/App.java

@@ -28,10 +28,13 @@ public class App {
 	private static List<BaseCommand> ourCommands;
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(App.class);
 
+	public static final String LINESEP = System.getProperty("line.separator");
+	
 	static {
 		ourCommands = new ArrayList<BaseCommand>();
 		ourCommands.add(new RunServerCommand());
 		ourCommands.add(new ExampleDataUploader());
+		ourCommands.add(new ValidateCommand());
 
 		Collections.sort(ourCommands);
 	}
@@ -79,16 +82,22 @@ public class App {
 		System.out.println("  hapi-fhir-cli {command} [options]");
 		System.out.println();
 		System.out.println("Commands:");
+
+		int longestCommandLength = 0;
 		for (BaseCommand next : ourCommands) {
-			String left = "  " + next.getCommandName() + " - ";
-			String[] rightParts = WordUtils.wrap(next.getCommandDescription(), 80 - left.length()).split("\\n");
-			for (int i = 1; i < rightParts.length; i++) {
-				rightParts[i] = StringUtils.leftPad("", left.length()) + rightParts[i];
+			longestCommandLength = Math.max(longestCommandLength, next.getCommandName().length());
 		}
-			System.out.println(left + StringUtils.join(rightParts, '\n'));
+		
+		for (BaseCommand next : ourCommands) {
+			String left = "  " + StringUtils.rightPad(next.getCommandName(), longestCommandLength);
+			String[] rightParts = WordUtils.wrap(next.getCommandDescription(), 80 - (left.length() + 3)).split("\\n");
+			for (int i = 1; i < rightParts.length; i++) {
+				rightParts[i] = StringUtils.leftPad("", left.length() + 3) + rightParts[i];
+			}
+			System.out.println(ansi().bold().fg(Color.GREEN) + left + ansi().boldOff().fg(Color.WHITE) + " - " + ansi().bold() + StringUtils.join(rightParts, LINESEP));
 		}
 		System.out.println();
-		System.out.println("See what options are available:");
+		System.out.println(ansi().boldOff().fg(Color.WHITE) + "See what options are available:");
 		System.out.println("  hapi-fhir-cli help {command}");
 		System.out.println();
 	}
@@ -143,12 +152,14 @@ public class App {
 		Options options = command.getOptions();
 		DefaultParser parser = new DefaultParser();
 		CommandLine parsedOptions;
+		
+		logAppHeader();
+		loggingConfigOn();
+		
 		try {
 			String[] args = Arrays.asList(theArgs).subList(1, theArgs.length).toArray(new String[theArgs.length - 1]);
 			parsedOptions = parser.parse(options, args, true);
 
-			logAppHeader();
-			loggingConfigOn();
 			
 			// Actually execute the command
 			command.run(parsedOptions);

hapi-fhir-cli/src/main/java/ca/uhn/fhir/cli/BaseCommand.java

@@ -9,6 +9,8 @@ import ca.uhn.fhir.rest.client.IGenericClient;
 
 public abstract class BaseCommand implements Comparable<BaseCommand> {
 
+	private FhirContext myFhirCtx;
+
 	public BaseCommand() {
 		super();
 	}
@@ -32,4 +34,11 @@ public abstract class BaseCommand implements Comparable<BaseCommand> {
 
 	public abstract void run(CommandLine theCommandLine) throws ParseException, Exception;
 
+	public FhirContext getFhirCtx() {
+		if (myFhirCtx == null) {
+			myFhirCtx = FhirContext.forDstu2();
+		}
+		return myFhirCtx;
+	}
+
 }

hapi-fhir-cli/src/main/java/ca/uhn/fhir/cli/ValidateCommand.java

@@ -0,0 +1,116 @@
+package ca.uhn.fhir.cli;
+
+import static org.apache.commons.lang3.StringUtils.defaultString;
+import static org.apache.commons.lang3.StringUtils.isBlank;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+
+import static org.fusesource.jansi.Ansi.*;
+
+import java.io.FileInputStream;
+import java.io.InputStreamReader;
+
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.OptionGroup;
+import org.apache.commons.cli.Options;
+import org.apache.commons.cli.ParseException;
+import org.apache.commons.io.IOUtils;
+import org.fusesource.jansi.Ansi;
+
+import com.phloc.commons.io.file.FileUtils;
+
+import ca.uhn.fhir.rest.method.MethodUtil;
+import ca.uhn.fhir.rest.server.EncodingEnum;
+import ca.uhn.fhir.validation.FhirInstanceValidator;
+import ca.uhn.fhir.validation.FhirValidator;
+import ca.uhn.fhir.validation.SingleValidationMessage;
+import ca.uhn.fhir.validation.ValidationResult;
+
+public class ValidateCommand extends BaseCommand {
+
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ValidateCommand.class);
+
+	@Override
+	public String getCommandDescription() {
+		return "Validate a resource using the FHIR validation tools";
+	}
+
+	@Override
+	public String getCommandName() {
+		return "validate";
+	}
+
+	@Override
+	public Options getOptions() {
+		Options retVal = new Options();
+
+		OptionGroup source = new OptionGroup();
+		source.addOption(new Option("f", "file", true, "The name of the file to validate"));
+		source.addOption(new Option("d", "data", true, "The text to validate"));
+		retVal.addOptionGroup(source);
+
+		retVal.addOption("x", "xsd", false, "Validate using Schemas");
+		retVal.addOption("s", "sch", false, "Validate using Schematrons");
+		retVal.addOption("p", "profile", false, "Validate using Profiles (StructureDefinition / ValueSet)");
+
+		retVal.addOption("e", "encoding", false, "File encoding (default is UTF-8)");
+
+		return retVal;
+	}
+
+	@Override
+	public void run(CommandLine theCommandLine) throws ParseException, Exception {
+		String fileName = theCommandLine.getOptionValue("f");
+		String contents = theCommandLine.getOptionValue("c");
+		if (isNotBlank(fileName) && isNotBlank(contents)) {
+			throw new ParseException("Can not supply both a file (-f) and data (-d)");
+		}
+		if (isBlank(fileName) && isBlank(contents)) {
+			throw new ParseException("Must supply either a file (-f) or data (-d)");
+		}
+
+		if (isNotBlank(fileName)) {
+			String encoding = theCommandLine.getOptionValue("e", "UTF-8");
+			ourLog.info("Reading file '{}' using encoding {}", fileName, encoding);
+
+			contents = IOUtils.toString(new InputStreamReader(new FileInputStream(fileName), encoding));
+			ourLog.info("Fully read - Size is {}", FileUtils.getFileSizeDisplay(contents.length()));
+		}
+
+		EncodingEnum enc = MethodUtil.detectEncodingNoDefault(defaultString(contents));
+		if (enc == null) {
+			throw new ParseException("Could not detect encoding (json/xml) of contents");
+		}
+
+		FhirValidator val = getFhirCtx().newValidator();
+		if (theCommandLine.hasOption("p")) {
+			val.registerValidatorModule(new FhirInstanceValidator());
+		}
+
+		val.setValidateAgainstStandardSchema(theCommandLine.hasOption("x"));
+		val.setValidateAgainstStandardSchematron(theCommandLine.hasOption("s"));
+
+		ValidationResult results = val.validateWithResult(contents);
+		
+		StringBuilder b = new StringBuilder("Validation results:" + ansi().boldOff());
+		int count = 0;
+		for (SingleValidationMessage next : results.getMessages()) {
+			count++;
+			b.append(App.LINESEP);
+			b.append("Issue ").append(count).append(": ");
+			b.append(next.getSeverity()).append(" - ").append(next.getLocationString());
+			b.append(App.LINESEP);
+			b.append("        ").append(next.getMessage());
+		}
+		
+		if (count > 0) {
+			ourLog.info(b.toString());
+		}
+		
+		if (results.isSuccessful()) {
+			ourLog.info("Validation successful!");
+		} else {
+			ourLog.warn("Validation FAILED");
+		}
+	}
+}

hapi-fhir-dist/src/assembly/hapi-fhir-android-distribution.xml

@@ -5,7 +5,7 @@
 
 	<formats>
 		<format>zip</format>
-		<!--<format>tar.bz2</format>-->
+		<format>tar.bz2</format>
 	</formats>
 
 	<includeBaseDirectory>false</includeBaseDirectory>

hapi-fhir-dist/src/assembly/hapi-fhir-jpaserver-example.xml

@@ -5,7 +5,7 @@
 
 	<formats>
 		<format>zip</format>
-		<!--<format>tar.bz2</format>-->
+		<format>tar.bz2</format>
 	</formats>
 
 	<includeBaseDirectory>false</includeBaseDirectory>

hapi-fhir-dist/src/assembly/hapi-fhir-standard-distribution.xml

@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="ISO-8859-1"?>
 <assembly xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2 http://maven.apache.org/xsd/assembly-1.1.2.xsd">
 
-	<id>hapi-fhir-standard-distribution</id>
+	<id>standard-distribution</id>
 
 	<formats>
 		<format>zip</format>
-		<!--<format>tar.bz2</format>-->
+		<format>tar.bz2</format>
 	</formats>
 
 	<includeBaseDirectory>false</includeBaseDirectory>

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/JpaValidationSupportDstu2.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.dao;
 
+/*
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2015 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 org.hl7.fhir.instance.model.ValueSet;
 import org.hl7.fhir.instance.model.ValueSet.ConceptSetComponent;
 import org.hl7.fhir.instance.model.ValueSet.ValueSetExpansionComponent;

pom.xml

@@ -1287,6 +1287,7 @@
 				<module>hapi-fhir-testpage-overlay</module>
 				<module>hapi-fhir-jpaserver-uhnfhirtest</module>
 				<module>hapi-fhir-android</module>
+				<module>hapi-fhir-cli</module>
 				<module>hapi-fhir-dist</module>
 				<module>examples</module>
 				<!--<module>hapi-fhir-osgi-core</module>-->