Merge pull request #191 from hapifhir/azure_pipelines_setup

Azure pipelines setup

azure-pipelines.yml

@@ -0,0 +1,62 @@
+trigger:
+  branches:
+    include:
+      - '*'
+
+strategy:
+  matrix:
+    linux:
+      imageName: "ubuntu-16.04"
+#     mac:
+#       imageName: "macos-10.14"
+#     windows:
+#       imageName: "vs2017-win2016"
+  maxParallel: 3
+
+pool:
+  vmImage: $(imageName)
+
+variables:
+  currentImage: $(imageName)
+  codecov: $(CODECOV_TOKEN)
+
+steps:
+  - task: PowerShell@2
+    inputs:
+      targetType: 'inline'
+      script: |
+        [xml]$pomXml = Get-Content .\pom.xml
+        # version
+        Write-Host $pomXml.project.version
+        $version=$pomXml.project.version
+        Write-Host "##vso[task.setvariable variable=version]$version"
+
+  - task: Maven@3
+    inputs:
+      mavenPomFile: 'pom.xml'
+      mavenOptions: '-Xmx3072m'
+      javaHomeOption: 'JDKVersion'
+      jdkVersionOption: '1.8'
+      jdkArchitectureOption: 'x64'
+      publishJUnitResults: true
+      testResultsFiles: '**/surefire-reports/TEST-*.xml'
+      goals: 'clean package'
+      
+  - bash: echo Current version => $(version)
+    displayName: 'version'
+
+  - script: bash <(curl https://codecov.io/bash) -t $(codecov)
+    displayName: 'codecov'
+  - task: PublishCodeCoverageResults@1
+    inputs:
+      codeCoverageTool: 'JaCoCo'
+      summaryFileLocation: '$(System.DefaultWorkingDirectory)/org.hl7.fhir.report/target/site/jacoco-aggregate/jacoco.xml'
+      reportDirectory: '$(System.DefaultWorkingDirectory)/org.hl7.fhir.report/target/site/jacoco-aggregate/'
+
+  - task: PublishPipelineArtifact@1
+    condition: eq(variables.currentImage, 'ubuntu-16.04')
+    inputs:
+      targetPath: "$(System.DefaultWorkingDirectory)/org.hl7.fhir.validation/target/org.hl7.fhir.validation-$(version).jar"
+      artifactName: Validator
+
+

org.hl7.fhir.report/pom.xml

@@ -0,0 +1,90 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<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">
+    <parent>
+        <groupId>ca.uhn.hapi.fhir</groupId>
+        <artifactId>org.hl7.fhir.core</artifactId>
+        <version>4.2.26-SNAPSHOT</version>
+        <relativePath>../pom.xml</relativePath>
+    </parent>
+
+    <modelVersion>4.0.0</modelVersion>
+
+    <artifactId>org.hl7.fhir.report</artifactId>
+
+    <packaging>bundle</packaging>
+
+    <properties>
+        <maven.deploy.skip>true</maven.deploy.skip>
+        <jacoco_version>0.8.5</jacoco_version>
+    </properties>
+
+    <dependencies>
+        <dependency>
+            <groupId>ca.uhn.hapi.fhir</groupId>
+            <artifactId>org.hl7.fhir.convertors</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>ca.uhn.hapi.fhir</groupId>
+            <artifactId>org.hl7.fhir.r5</artifactId>
+            <version>${project.version}</version>
+            <exclusions>
+                <exclusion>
+                    <groupId>org.antlr</groupId>
+                    <artifactId>ST4</artifactId>
+                </exclusion>
+            </exclusions>
+        </dependency>
+        <dependency>
+            <groupId>ca.uhn.hapi.fhir</groupId>
+            <artifactId>org.hl7.fhir.utilities</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>ca.uhn.hapi.fhir</groupId>
+            <artifactId>org.hl7.fhir.validation</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+    </dependencies>
+
+    <build>
+        <plugins>
+            <plugin>
+                <groupId>org.jacoco</groupId>
+                <artifactId>jacoco-maven-plugin</artifactId>
+                <version>${jacoco_version}</version>
+                <executions>
+                    <execution>
+                        <id>report-aggregate</id>
+                        <phase>prepare-package</phase>
+                        <goals>
+                            <goal>report-aggregate</goal>
+                        </goals>
+                        <configuration>
+                            <title>JaCoCo</title>
+                            <footer>Code Coverage Report for FHIR core libs ${project.version}</footer>
+                            <includes>
+                                <!-- Analyze class files only to exclude shaded agent JAR from report -->
+                                <include>**/*.class</include>
+                            </includes>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>org.basepom.maven</groupId>
+                <artifactId>duplicate-finder-maven-plugin</artifactId>
+                <version>1.4.0</version>
+                <configuration>
+                    <!-- The report project pulls in resources from all the other packages, which results in some duplicate
+                     classes being pulled in. This will need to be fixed eventually, but for now, we can just disable the
+                     check on this package. It's only purpose is to aggregate the reports.-->
+                    <skip>true</skip>
+                </configuration>
+            </plugin>
+        </plugins>
+    </build>
+
+</project>

org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/tests/XhtmlNodeTest.java

@@ -1,6 +1,7 @@
 package org.hl7.fhir.utilities.tests;
 
 import org.hl7.fhir.utilities.xhtml.XhtmlNode;
+import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.Test;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -9,8 +10,6 @@ import java.io.ByteArrayOutputStream;
 import java.io.IOException;
 import java.io.ObjectOutputStream;
 
-import static org.junit.Assert.assertEquals;
-
 public class XhtmlNodeTest {
 
   private static final Logger ourLog = LoggerFactory.getLogger(XhtmlNodeTest.class);
@@ -24,12 +23,12 @@ public class XhtmlNodeTest {
     // Entity that appears in XHTML not not in XML
     XhtmlNode node = new XhtmlNode();
     node.setValueAsString("<div>&reg;</div>");
-    assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\">®</div>", node.getValueAsString());
+    Assertions.assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\">®</div>", node.getValueAsString());
 
     // Entity that appears in both
     node = new XhtmlNode();
     node.setValueAsString("<div>&lt;</div>");
-    assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\">&lt;</div>", node.getValueAsString());
+    Assertions.assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\">&lt;</div>", node.getValueAsString());
   }
 
   /**
@@ -39,24 +38,24 @@ public class XhtmlNodeTest {
   public void testLangAttributePreserved() {
     XhtmlNode dt = new XhtmlNode();
     dt.setValueAsString("<div xmlns=\"http://www.w3.org/1999/xhtml\" lang=\"en-US\">help i'm a bug</div>");
-    assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\" lang=\"en-US\">help i'm a bug</div>", dt.getValueAsString());
+    Assertions.assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\" lang=\"en-US\">help i'm a bug</div>", dt.getValueAsString());
-    assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\" lang=\"en-US\">help i'm a bug</div>", new XhtmlNode().setValue(dt.getValue()).getValueAsString());
+    Assertions.assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\" lang=\"en-US\">help i'm a bug</div>", new XhtmlNode().setValue(dt.getValue()).getValueAsString());
   }
 
   @Test
   public void testParseRsquo() {
     XhtmlNode dt = new XhtmlNode();
     dt.setValueAsString("It&rsquo;s January again");
-    assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\">It’s January again</div>", dt.getValueAsString());
+    Assertions.assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\">It’s January again</div>", dt.getValueAsString());
-    assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\">It’s January again</div>", new XhtmlNode().setValue(dt.getValue()).getValueAsString());
+    Assertions.assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\">It’s January again</div>", new XhtmlNode().setValue(dt.getValue()).getValueAsString());
   }
 
   @Test
   public void testProcessingInstructionNotPreserved() {
     XhtmlNode dt = new XhtmlNode();
     dt.setValueAsString("<?xml version=\"1.0\" encoding=\"UTF-8\"?><div xmlns=\"http://www.w3.org/1999/xhtml\">help i'm a bug</div>");
-    assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\">help i'm a bug</div>", dt.getValueAsString());
+    Assertions.assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\">help i'm a bug</div>", dt.getValueAsString());
-    assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\">help i'm a bug</div>", new XhtmlNode().setValue(dt.getValue()).getValueAsString());
+    Assertions.assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\">help i'm a bug</div>", new XhtmlNode().setValue(dt.getValue()).getValueAsString());
   }
 
   @Test
@@ -71,7 +70,7 @@ public class XhtmlNodeTest {
     String output = node.getValueAsString();
     ourLog.info(output);
 
-    assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\"><img src=\"http://pbs.twimg.com/profile_images/544507893991485440/r_vo3uj2_bigger.png\" alt=\"Twitter Avatar\"/>@fhirabend</div>", output);
+    Assertions.assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\"><img src=\"http://pbs.twimg.com/profile_images/544507893991485440/r_vo3uj2_bigger.png\" alt=\"Twitter Avatar\"/>@fhirabend</div>", output);
   }
 
   @Test

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/ValidatorGui.java

@@ -13,7 +13,7 @@ import java.net.URISyntaxException;
 
 public class ValidatorGui {
 
-  private static final int GUI_FRONTEND_PORT = 8080;
+  private static final int GUI_FRONTEND_PORT = 8081;
   private static final String PAGE_ADDRESS = "http://localhost:" + GUI_FRONTEND_PORT + "/home";
   private static final String WEB_APP_FILE_LOCATION = "/public";
   private static Javalin app;
@@ -32,6 +32,10 @@ public class ValidatorGui {
     start(new CliContext(), validationEngine, false);
   }
 
+  public static int getPort() {
+    return GUI_FRONTEND_PORT;
+  }
+
   public static void start(CliContext currentContext, ValidationEngine validationEngine, boolean bootBrowser) {
     app = Javalin.create();
     new RestEndpoints().initRestEndpoints(app, currentContext, validationEngine);

org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/cli/ValidatorGuiTest.java

@@ -24,7 +24,7 @@ class ValidatorGuiTest {
     options.addArguments("--headless");
     options.addArguments("--disable-gpu");
     WebDriver driver = new ChromeDriver(options);
-    driver.get("http://localhost:8080/home");
+    driver.get("http://localhost:" + ValidatorGui.getPort() + "/home");
 
     Assertions.assertTrue(driver.getPageSource().contains(HTML_TITLE_TAG));
     driver.quit();

org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/cli/controller/HttpGetContextTest.java

@@ -7,6 +7,7 @@ import org.apache.http.client.methods.HttpUriRequest;
 import org.apache.http.entity.ContentType;
 import org.apache.http.impl.client.HttpClientBuilder;
 import org.hl7.fhir.validation.cli.BaseRestTest;
+import org.hl7.fhir.validation.cli.ValidatorGui;
 import org.hl7.fhir.validation.cli.model.CliContext;
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.DisplayName;
@@ -16,7 +17,7 @@ import java.io.IOException;
 
 class HttpGetContextTest extends BaseRestTest {
 
-  private final String GET_CONTEXT_URL = "http://localhost:8080/context";
+  private final String GET_CONTEXT_URL = "http://localhost:" + ValidatorGui.getPort() + "/context";
 
   @Test
   @DisplayName("Testing status code on get context endpoint.")

pom.xml

@@ -20,6 +20,7 @@
         <validator_test_case_version>1.1.13-SNAPSHOT</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>
     </properties>
 
     <artifactId>org.hl7.fhir.core</artifactId>
@@ -119,7 +120,6 @@
                 <version>0.13</version>
             </dependency>
         </dependencies>
-
     </dependencyManagement>
 
     <modules>
@@ -129,10 +129,11 @@
         <module>org.hl7.fhir.dstu3</module>
         <module>org.hl7.fhir.r4</module>
         <module>org.hl7.fhir.r5</module>
-        <!--<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>
+        <!-- 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>
@@ -160,8 +161,13 @@
                 <configuration>
                     <trimStackTrace>false</trimStackTrace>
                     <testFailureIgnore>false</testFailureIgnore>
-                    <argLine>-Xmx4096m</argLine>
+                    <!-- We need to include the ${argLine} here so the Jacoco test arguments are included in the
+                     Surefire testing run. This may appear as an error in some IDEs, but it will run regardless. -->
+                    <argLine>${argLine} -Xmx4096m</argLine>
                     <redirectTestOutputToFile>false</redirectTestOutputToFile>
+                    <excludes>
+                        <exclude>org/hl7/fhir/validation/cli/**</exclude>
+                    </excludes>
                 </configuration>
             </plugin>
             <plugin>
@@ -272,7 +278,40 @@
                     <skipUpdateLicense>true</skipUpdateLicense>
                 </configuration>
             </plugin>
+            <plugin>
+                <groupId>org.jacoco</groupId>
+                <artifactId>jacoco-maven-plugin</artifactId>
+                <version>${jacoco_version}</version>
+                <configuration>
+                    <excludes>
+                        <!-- These files blow away the JVM limit on file size. Until we refactor, we need to ignore or
+                             Jacoco complains and won't run the validator tests. -->
+                        <exclude>org/hl7/fhir/r5/formats/JsonParser</exclude>
+                        <exclude>org/hl7/fhir/r5/formats/XmlParser</exclude>
+                        <exclude>org/hl7/fhir/r4/formats/JsonParser</exclude>
+                        <exclude>org/hl7/fhir/r4/formats/XmlParser</exclude>
+                        <exclude>org/hl7/fhir/r4/**/*</exclude>
+                        <exclude>org/hl7/fhir/dstu3/**/*</exclude>
+                        <exclude>org/hl7/fhir/dstu2/**/*</exclude>
+                        <exclude>org/hl7/fhir/dstu2016may/**/*</exclude>
+                    </excludes>
+                </configuration>
+                <executions>
+                    <execution>
+                        <id>jacoco-initialize</id>
+                        <goals>
+                            <goal>prepare-agent</goal>
+                        </goals>
+                    </execution>
+                    <execution>
+                        <id>report</id>
+                        <phase>package</phase>
+                        <goals>
+                            <goal>report</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
         </plugins>
     </build>
-
 </project>