Set up CI with Azure Pipelines (#1502)

* Set up CI with Azure Pipelines

[skip ci]

* Update azure-pipelines.yml for Azure Pipelines

* Skip tests for a build

* Work on pipeline

* Update azure-pipelines.yml for Azure Pipelines

* Interceptors docs

* Test fix

* Disable releases from snapshot repo

* Try disabling jitpack

* Fix dependency issue

* A couple of test fixes

* Change to trigger a build

* Force a change to trigger a build

* Force a build

* FIx test

README.md

@@ -17,3 +17,5 @@ http://hapi.fhir.org/
 This project is Open Source, licensed under the Apache Software License 2.0.
 
 Please see [this wiki page](https://github.com/jamesagnew/hapi-fhir/wiki/Getting-Help) for information on where to get help with HAPI FHIR. Please see [Smile CDR](https://smilecdr.com) for information on commercial support.
+
+---

appveyor.yml

@@ -1,9 +0,0 @@
-version: 1.0.{build}
-image: Visual Studio 2017
-cache:
-  - C:\maven\
-  - C:\Users\appveyor\.m2\repository
-build_script:
-  - SET JAVA_HOME=C:\Program Files\Java\jdk10
-  - SET PATH=C:\Program Files\Java\jdk10\bin;%PATH%
-  - cmd: mvn -P MINPARALLEL,ALLMODULES,REDUCED_JPA_TESTS clean install

azure-pipelines.yml

@@ -0,0 +1,60 @@
+# Starter pipeline
+# Start with a minimal pipeline that you can customize to build and deploy your code.
+# Add steps that build, run tests, deploy, and more:
+# https://aka.ms/yaml
+
+variables:
+  MAVEN_CACHE_FOLDER: $(Pipeline.Workspace)/.m2/repository
+  MAVEN_OPTS: '-Dmaven.repo.local=$(MAVEN_CACHE_FOLDER)'
+
+trigger:
+- master
+
+pool:
+  vmImage: 'ubuntu-latest'
+
+
+jobs:
+  - job: Build
+    timeoutInMinutes: 360
+    steps:
+      - task: CacheBeta@0
+        inputs:
+          key: maven
+          path: $(MAVEN_CACHE_FOLDER)
+          displayName: Cache Maven local repo
+
+      - task: Maven@3
+        inputs:
+          goals: 'validate'
+
+      - task: Maven@3
+        inputs:
+          #mavenPomFile: 'pom.xml' 
+          goals: 'clean install' # Optional
+          options: ''
+          #publishJUnitResults: true 
+          #testResultsFiles: '**/surefire-reports/TEST-*.xml' # Required when publishJUnitResults == True
+          #testRunTitle: # Optional
+          #codeCoverageToolOption: 'None' # Optional. Options: none, cobertura, jaCoCo. Enabling code coverage inserts the `clean` goal into the Maven goals list when Maven runs.
+          #codeCoverageClassFilter: # Optional. Comma-separated list of filters to include or exclude classes from collecting code coverage. For example: +:com.*,+:org.*,-:my.app*.*
+          #codeCoverageClassFilesDirectories: # Optional
+          #codeCoverageSourceDirectories: # Optional
+          #codeCoverageFailIfEmpty: false # Optional
+          #javaHomeOption: 'JDKVersion' # Options: jDKVersion, path
+          #jdkVersionOption: 'default' # Optional. Options: default, 1.11, 1.10, 1.9, 1.8, 1.7, 1.6
+          #jdkDirectory: # Required when javaHomeOption == Path
+          #jdkArchitectureOption: 'x64' # Optional. Options: x86, x64
+          #mavenVersionOption: 'Default' # Options: default, path
+          #mavenDirectory: # Required when mavenVersionOption == Path
+          #mavenSetM2Home: false # Required when mavenVersionOption == Path
+          mavenOptions: '-Xmx2048m $(MAVEN_OPTS)' # Optional
+          #mavenAuthenticateFeed: false 
+          #effectivePomSkip: false 
+          #sonarQubeRunAnalysis: false 
+          #sqMavenPluginVersionChoice: 'latest' # Required when sonarQubeRunAnalysis == True# Options: latest, pom
+          #checkStyleRunAnalysis: false # Optional
+          #pmdRunAnalysis: false # Optional
+          #findBugsRunAnalysis: false # Optional
+
+

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/interceptors/interceptors.md

@@ -7,3 +7,4 @@ Interceptor classes may "hook into" various points in the processing chain in bo
 ```java
 {{snippet:classpath:/ca/uhn/hapi/fhir/docs/MyInterceptor.java|sampleClass}}
 ```
+

hapi-fhir-jaxrsserver-base/pom.xml

@@ -50,31 +50,26 @@
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-structures-dstu2</artifactId>
 			<version>${project.version}</version>
-			<optional>true</optional>
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-structures-hl7org-dstu2</artifactId>
 			<version>${project.version}</version>
-			<optional>true</optional>
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-structures-dstu2.1</artifactId>
 			<version>${project.version}</version>
-			<optional>true</optional>
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-structures-dstu3</artifactId>
 			<version>${project.version}</version>
-			<optional>true</optional>
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-structures-r4</artifactId>
 			<version>${project.version}</version>
-			<optional>true</optional>
 		</dependency>
 
 		<dependency>

hapi-fhir-jpaserver-base/pom.xml

@@ -212,7 +212,6 @@
 		<dependency>
 			<groupId>com.github.dnault</groupId>
 			<artifactId>xml-patch</artifactId>
-			<version>0.3.0</version>
 		</dependency>
 
 		<!-- FHIR RI is pulled in for UCUM support, but we don't want any of its dependencies. -->

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

@@ -35,10 +35,10 @@ public interface ITermCodeSystemVersionDao extends JpaRepository<TermCodeSystemV
 	@Query("DELETE FROM TermCodeSystemVersion csv WHERE csv.myCodeSystem = :cs")
 	void deleteForCodeSystem(@Param("cs") TermCodeSystem theCodeSystem);
 
-	@Query("SELECT cs FROM TermCodeSystemVersion cs WHERE cs.myResourcePid = :resource_id")
+	@Query("SELECT cs FROM TermCodeSystemVersion cs WHERE cs.myCodeSystemPid = :codesystem_pid")
-	List<TermCodeSystemVersion> findByCodeSystemPid(@Param("resource_id") Long theCodeSystemResourcePid);
+	List<TermCodeSystemVersion> findByCodeSystemPid(@Param("codesystem_pid") Long theCodeSystemPid);
 
-	@Query("SELECT cs FROM TermCodeSystemVersion cs WHERE cs.myResource.myId = :resource_id")
+	@Query("SELECT cs FROM TermCodeSystemVersion cs WHERE cs.myResourcePid = :resource_id")
 	List<TermCodeSystemVersion> findByCodeSystemResourcePid(@Param("resource_id") Long theCodeSystemResourcePid);
 
 	@Query("SELECT cs FROM TermCodeSystemVersion cs WHERE cs.myCodeSystemHavingThisVersionAsCurrentVersionIfAny.myResource.myId = :resource_id")

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermCodeSystemVersion.java

@@ -58,6 +58,7 @@ public class TermCodeSystemVersion implements Serializable {
 
 	@Column(name = "CS_VERSION_ID", nullable = true, updatable = false, length = MAX_VERSION_LENGTH)
 	private String myCodeSystemVersionId;
+
 	/**
 	 * This was added in HAPI FHIR 3.3.0 and is nullable just to avoid migration
 	 * issued. It should be made non-nullable at some point.
@@ -65,8 +66,11 @@ public class TermCodeSystemVersion implements Serializable {
 	@ManyToOne
 	@JoinColumn(name = "CODESYSTEM_PID", referencedColumnName = "PID", nullable = true, foreignKey = @ForeignKey(name = "FK_CODESYSVER_CS_ID"))
 	private TermCodeSystem myCodeSystem;
-	@SuppressWarnings("unused")
 
+	@Column(name = "CODESYSTEM_PID", insertable = false, updatable = false)
+	private Long myCodeSystemPid;
+
+	@SuppressWarnings("unused")
 	@OneToOne(mappedBy = "myCurrentVersion", optional = true)
 	private TermCodeSystem myCodeSystemHavingThisVersionAsCurrentVersionIfAny;
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoFtTest.java

@@ -1368,11 +1368,14 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 			map.setLastUpdated(new DateRangeParam().setUpperBound(new DateParam(ParamPrefixEnum.LESSTHAN, "2022-01-01")));
 			IBundleProvider found = myPatientDao.search(map);
 			Set<String> dates = new HashSet<>();
+			String searchId = found.getUuid();
 			for (int i = 0; i < 9; i++) {
 				List<IBaseResource> resources = found.getResources(i, i + 1);
-				assertThat("Failed to load range " + i + " - " + (i + 1), resources, hasSize(1));
+				assertThat("Failed to load range " + i + " - " + (i + 1) + " - from provider of type: " + found.getClass(), resources, hasSize(1));
 				Patient nextResource = (Patient) resources.get(0);
 				dates.add(nextResource.getBirthDateElement().getValueAsString());
+
+				found = myPagingProvider.retrieveResultList(null, searchId);
 			}
 
 			assertThat(dates, hasItems(

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchOptimizedTest.java

@@ -120,7 +120,7 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
 
 		myDaoConfig.setSearchPreFetchThresholds(Arrays.asList(20, 50, 190));
 
-		// Seach with count only
+		// Search with count only
 		SearchParameterMap params = new SearchParameterMap();
 		params.add(Patient.SP_NAME, new StringParam("FAM"));
 		params.setSummaryMode((SummaryEnum.COUNT));
@@ -142,7 +142,9 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
 		assertEquals(201, results.size().intValue());
 		ids = toUnqualifiedVersionlessIdValues(results, 0, 10, true);
 		assertThat(ids, hasSize(10));
-		assertEquals(201, myDatabaseBackedPagingProvider.retrieveResultList(null, uuid).size().intValue());
+		IBundleProvider bundleProvider = myDatabaseBackedPagingProvider.retrieveResultList(null, uuid);
+		Integer bundleSize = bundleProvider.size();
+		assertEquals(201, bundleSize.intValue());
 
 		// Search with count only
 		params = new SearchParameterMap();

pom.xml

@@ -45,14 +45,7 @@
 	</scm>
 
 	<repositories>
-		<repository>
+		<!--
-			<snapshots>
-				<enabled>false</enabled>
-			</snapshots>
-			<id>bintray-dnault-maven</id>
-			<name>bintray</name>
-			<url>https://dl.bintray.com/dnault/maven</url>
-		</repository>
 		<repository>
 			<id>jitpack.io</id>
 			<url>https://jitpack.io</url>
@@ -60,12 +53,16 @@
 				<enabled>false</enabled>
 			</snapshots>
 		</repository>
+		-->
 		<repository>
 			<id>oss-snapshot</id>
 			<url>https://oss.sonatype.org/content/repositories/snapshots/</url>
 			<snapshots>
 				<enabled>true</enabled>
 			</snapshots>
+			<releases>
+				<enabled>false</enabled>
+			</releases>
 		</repository>
 	</repositories>