Fix some issues with 'mvn test' on windows (#4223)

* fix handling of Windows line ends

* some tests need to wait a little longer for things to get done

* Windows path separator fix

* simpler lineend fix

* more timeouts and another path separator issue

* redo some timeout issues

* Issue in Windows: URI is not hierarchical

* another timeout issue

hapi-fhir-checkstyle/src/test/java/ca/uhn/fhir/checks/HapiErrorCodeCheckTest.java

@@ -42,7 +42,7 @@ class HapiErrorCodeCheckTest {
 		checker.process(files);
 
 		// validate
-		String[] errorLines = errors.toString().split("\n");
+		String[] errorLines = errors.toString().split("\r?\n");
 		Arrays.stream(errorLines).forEach(ourLog::info);
 		assertEquals(2, errorLines.length);
 		assertThat(errorLines[0], startsWith("[ERROR] "));

hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/UploadTerminologyCommandTest.java

@@ -331,7 +331,7 @@ public class UploadTerminologyCommandTest {
 			));
 			fail();
 		} catch (Error e) {
-			assertThat(e.toString(), Matchers.containsString("FileNotFoundException: target/concepts.csv/foo.csv"));
+			assertThat(e.toString().replace('\\', '/'), Matchers.containsString("FileNotFoundException: target/concepts.csv/foo.csv"));
 		}
 	}
 

hapi-fhir-jpaserver-test-dstu2/src/test/java/ca/uhn/fhir/jpa/subscription/email/EmailSubscriptionDstu2Test.java

@@ -128,7 +128,7 @@ public class EmailSubscriptionDstu2Test extends BaseResourceProviderDstu2Test {
 
 		Observation observation1 = sendObservation(code, "SNOMED-CT");
 
-		assertTrue(ourGreenMail.waitForIncomingEmail(1000, 1));
+		assertTrue(ourGreenMail.waitForIncomingEmail(10000, 1));
 
 		MimeMessage[] messages = ourGreenMail.getReceivedMessages();
 		assertEquals(2, messages.length);

hapi-fhir-jpaserver-test-dstu3/src/test/java/ca/uhn/fhir/jpa/subscription/email/EmailSenderImplTest.java

@@ -46,7 +46,7 @@ public class EmailSenderImplTest {
 		details.setBodyTemplate("foo");
 		fixture.send(details);
 
-		assertTrue(ourGreenMail.waitForIncomingEmail(1000, 1));
+		assertTrue(ourGreenMail.waitForIncomingEmail(10000, 1));
 
 		MimeMessage[] messages = ourGreenMail.getReceivedMessages();
 		assertEquals(2, messages.length);

hapi-fhir-jpaserver-test-dstu3/src/test/java/ca/uhn/fhir/jpa/subscription/email/EmailSubscriptionDstu3Test.java

@@ -151,7 +151,7 @@ public class EmailSubscriptionDstu3Test extends BaseResourceProviderDstu3Test {
 		sendObservation(code, "SNOMED-CT");
 		waitForQueueToDrain();
 
-		assertTrue(ourGreenMail.waitForIncomingEmail(1000, 1));
+		assertTrue(ourGreenMail.waitForIncomingEmail(10000, 1));
 
 		List<MimeMessage> received = Arrays.asList(ourGreenMail.getReceivedMessages());
 		assertEquals(1, received.get(0).getFrom().length);
@@ -196,7 +196,7 @@ public class EmailSubscriptionDstu3Test extends BaseResourceProviderDstu3Test {
 		sendObservation(code, "SNOMED-CT");
 		waitForQueueToDrain();
 
-		assertTrue(ourGreenMail.waitForIncomingEmail(1000, 1));
+		assertTrue(ourGreenMail.waitForIncomingEmail(10000, 1));
 
 		List<MimeMessage> received = Arrays.asList(ourGreenMail.getReceivedMessages());
 		assertEquals(1, received.size());

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/bulk/BulkExportUseCaseTest.java

@@ -52,6 +52,7 @@ import java.util.Map;
 import java.util.Optional;
 import java.util.Set;
 import java.util.stream.Collectors;
+import java.util.concurrent.TimeUnit;
 
 import static org.awaitility.Awaitility.await;
 import static org.hamcrest.CoreMatchers.is;
@@ -1061,9 +1062,9 @@ public class BulkExportUseCaseTest extends BaseResourceProviderR4Test {
 
 		assertNotNull(startResponse);
 
-		myBatch2JobHelper.awaitJobCompletion(startResponse.getJobId());
+		myBatch2JobHelper.awaitJobCompletion(startResponse.getJobId(), 60);
 
-		await().until(() -> myJobRunner.getJobInfo(startResponse.getJobId()).getReport() != null);
+		await().atMost(300, TimeUnit.SECONDS).until(() -> myJobRunner.getJobInfo(startResponse.getJobId()).getReport() != null);
 
 		String report = myJobRunner.getJobInfo(startResponse.getJobId()).getReport();
 		BulkExportJobResults results = JsonUtil.deserialize(report, BulkExportJobResults.class);

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/bulk/imprt/svc/BulkDataImportR4Test.java

@@ -169,7 +169,7 @@ public class BulkDataImportR4Test extends BaseJpaR4Test implements ITestDataBuil
 		ActivateJobResult activateJobOutcome = mySvc.activateNextReadyJob();
 		assertTrue(activateJobOutcome.isActivated);
 
-		JobInstance instance = myBatch2JobHelper.awaitJobCompletion(activateJobOutcome.jobId);
+		JobInstance instance = myBatch2JobHelper.awaitJobCompletion(activateJobOutcome.jobId, 60);
 		assertNotNull(instance);
 		assertEquals(StatusEnum.COMPLETED, instance.getStatus());
 

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/bulk/imprt2/BulkImportR4Test.java

@@ -34,6 +34,7 @@ import org.springframework.data.domain.Pageable;
 
 import java.util.ArrayList;
 import java.util.List;
+import java.util.concurrent.TimeUnit;
 import java.util.stream.Collectors;
 
 import static org.awaitility.Awaitility.await;
@@ -101,7 +102,7 @@ public class BulkImportR4Test extends BaseJpaR4Test {
 
 		// Verify
 
-		await().until(() -> {
+		await().atMost(120, TimeUnit.SECONDS).until(() -> {
 			myJobCleanerService.runMaintenancePass();
 			JobInstance instance = myJobCoordinator.getInstance(instanceId);
 			return instance.getStatus();
@@ -185,7 +186,7 @@ public class BulkImportR4Test extends BaseJpaR4Test {
 				return storage;
 			});
 
-			await().until(() -> {
+			await().atMost(120, TimeUnit.SECONDS).until(() -> {
 				myJobCleanerService.runMaintenancePass();
 				JobInstance instance = myJobCoordinator.getInstance(instanceId);
 				return instance.getErrorCount();

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/packages/NpmR4Test.java

@@ -936,7 +936,10 @@ public class NpmR4Test extends BaseJpaR4Test {
 	public void testInstallR4PackageFromFile() {
 
 		Path currentRelativePath = Paths.get("");
-		String s = currentRelativePath.toAbsolutePath().toString();
+		String s = currentRelativePath.toAbsolutePath().toString().replace('\\', '/');
+		if (s.charAt(0) != '/' && s.charAt(1) == ':') { // is Windows..
+			s = s.substring(2); // .. get rid of the "C:" part (not perfect but...
+		}
 		System.out.println("Current absolute path is: " + s);
 
 		String fileUrl = "file:" + s + "/src/test/resources/packages/de.basisprofil.r4-1.2.0.tgz";

hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/util/MemoryCacheServiceTest.java

@@ -214,7 +214,7 @@ class MemoryCacheServiceTest {
 
 			public Integer getOrTimeout(String theMessage) throws InterruptedException, ExecutionException {
 				try {
-					return future.get(1, TimeUnit.SECONDS);
+					return future.get(60, TimeUnit.SECONDS);
 				} catch (TimeoutException e) {
 					fail(theMessage);
 					return null;

hapi-fhir-server-openapi/src/test/java/ca/uhn/fhir/rest/openapi/OpenApiInterceptorTest.java

@@ -27,6 +27,7 @@ import io.swagger.v3.core.util.Yaml;
 import io.swagger.v3.oas.models.OpenAPI;
 import io.swagger.v3.oas.models.PathItem;
 import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.http.client.methods.CloseableHttpResponse;
 import org.apache.http.client.methods.HttpGet;
 import org.apache.http.impl.client.CloseableHttpClient;
@@ -218,9 +219,17 @@ public class OpenApiInterceptorTest {
 			font-size: 1.1em;
 			}
 			""";
-		assertEquals(expected, resp);
+		assertEquals(removeCtrlR(expected), removeCtrlR(resp));
 	}
 
+	protected String removeCtrlR (String source) {
+		String result = source;
+		if (source != null) {
+			result = StringUtils.remove(source, '\r');
+		}
+		return result;
+	}
+	
 	@Test
 	public void testSwaggerUiNotPaged() throws IOException {
 		myServer.getRestfulServer().registerInterceptor(new AddResourceCountsInterceptor());

hapi-fhir-server/src/test/java/ca/uhn/fhir/rest/server/mail/MailSvcIT.java

@@ -42,7 +42,7 @@ public class MailSvcIT {
 		// execute
 		fixture.sendMail(email);
 		// validate
-		assertTrue(ourGreenMail.waitForIncomingEmail(1000, 1));
+		assertTrue(ourGreenMail.waitForIncomingEmail(5000, 1));
 		final MimeMessage[] receivedMessages = ourGreenMail.getReceivedMessages();
 		assertEquals(1, receivedMessages.length);
 		assertEquals(SUBJECT, receivedMessages[0].getSubject());
@@ -56,7 +56,7 @@ public class MailSvcIT {
 		// execute
 		fixture.sendMail(emails);
 		// validate
-		assertTrue(ourGreenMail.waitForIncomingEmail(1000, emails.size()));
+		assertTrue(ourGreenMail.waitForIncomingEmail(15000, emails.size()));
 		final MimeMessage[] receivedMessages = ourGreenMail.getReceivedMessages();
 		assertEquals(emails.size(), receivedMessages.length);
 		assertEquals(SUBJECT, receivedMessages[0].getSubject());
@@ -76,7 +76,7 @@ public class MailSvcIT {
 		fixture.sendMail(email);
 
 		// validate
-		assertTrue(ourGreenMail.waitForIncomingEmail(1000, 0));
+		assertTrue(ourGreenMail.waitForIncomingEmail(5000, 0));
 		final MimeMessage[] receivedMessages = ourGreenMail.getReceivedMessages();
 		assertEquals(0, receivedMessages.length);
 	}

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/ctx/FhirContextDstu2Test.java

@@ -110,7 +110,7 @@ public class FhirContextDstu2Test {
 				}
 			});
 		}
-		assertConcurrent("Unable to encode resources multithreaded", runnables, 1000);
+		assertConcurrent("Unable to encode resources multithreaded", runnables, 30000);
 	}
 
 	private void parseStringResourceMultipleTimesWithClass(IParser iParser, String medicationOrderResource) {
@@ -163,7 +163,7 @@ public class FhirContextDstu2Test {
 				});
 			}
 			// wait until all threads are ready
-			assertTrue(allExecutorThreadsReady.await(runnables.size() * 10L, TimeUnit.MILLISECONDS), "Timeout initializing threads! Perform long lasting initializations before passing runnables to assertConcurrent");
+			assertTrue(allExecutorThreadsReady.await(runnables.size() * 1000L, TimeUnit.MILLISECONDS), "Timeout initializing threads! Perform long lasting initializations before passing runnables to assertConcurrent");
 			// start all test runners
 			afterInitBlocker.countDown();
 			assertTrue(allDone.await(maxTimeoutSeconds, TimeUnit.SECONDS), message + " timeout! More than" + maxTimeoutSeconds + "seconds");

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/rest/server/BinaryDstu2Test.java

@@ -271,7 +271,7 @@ public class BinaryDstu2Test {
 		PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
 		HttpClientBuilder builder = HttpClientBuilder.create();
 
-		int timeout = 5;
+		int timeout = 60;
 		RequestConfig config = RequestConfig.custom()
 			.setConnectTimeout(timeout * 1000)
 			.setConnectionRequestTimeout(timeout * 1000)