Merge remote-tracking branch 'origin/master' into ks-20191119-scheduler

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

@@ -146,6 +146,34 @@ public class HapiFlywayMigrateDatabaseCommandTest {
 		assertTrue(JdbcUtils.getTableNames(connectionProperties).contains("HFJ_BLK_EXPORT_JOB")); // Late table
 	}
 
+	@Test
+	public void testMigrateFromEmptySchema_NoFlyway() throws IOException, SQLException {
+
+		File location = getLocation("migrator_h2_test_empty_current_noflyway");
+
+		String url = "jdbc:h2:" + location.getAbsolutePath() + ";create=true";
+		DriverTypeEnum.ConnectionProperties connectionProperties = DriverTypeEnum.H2_EMBEDDED.newConnectionProperties(url, "", "");
+
+		ourLog.info("**********************************************");
+		ourLog.info("Starting Migration...");
+		ourLog.info("**********************************************");
+
+		String[] args = new String[]{
+			BaseFlywayMigrateDatabaseCommand.MIGRATE_DATABASE,
+			"-d", "H2_EMBEDDED",
+			"-u", url,
+			"-n", "",
+			"-p", "",
+			"--" + BaseFlywayMigrateDatabaseCommand.DONT_USE_FLYWAY
+		};
+
+		assertFalse(JdbcUtils.getTableNames(connectionProperties).contains("HFJ_RESOURCE"));
+		assertFalse(JdbcUtils.getTableNames(connectionProperties).contains("HFJ_BLK_EXPORT_JOB"));
+		App.main(args);
+		assertTrue(JdbcUtils.getTableNames(connectionProperties).contains("HFJ_RESOURCE")); // Early table
+		assertTrue(JdbcUtils.getTableNames(connectionProperties).contains("HFJ_BLK_EXPORT_JOB")); // Late table
+	}
+
 	@NotNull
 	private File getLocation(String theDatabaseName) throws IOException {
 		File directory = new File(DB_DIRECTORY);

hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/Parser.java

@@ -23,40 +23,57 @@ package ca.uhn.hapi.fhir.docs;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.parser.DataFormatException;
 import ca.uhn.fhir.parser.IParser;
+import org.hl7.fhir.r4.model.Patient;
 
 import java.io.IOException;
 
 public class Parser {
 
-public static void main(String[] args) throws DataFormatException, IOException {
+	public static void main(String[] args) throws DataFormatException, IOException {
 		{
-//START SNIPPET: disableStripVersions
+			//START SNIPPET: createParser
-FhirContext ctx = FhirContext.forDstu2();
+			// Create a FHIR context
-IParser parser = ctx.newJsonParser();
+			FhirContext ctx = FhirContext.forR4();
 
-// Disable the automatic stripping of versions from references on the parser
+			// Create a Patient resource to serialize
-parser.setStripVersionsFromReferences(false);
+			Patient patient = new Patient();
-//END SNIPPET: disableStripVersions
+			patient.addName().setFamily("Simpson").addGiven("James");
 
-//START SNIPPET: disableStripVersionsCtx
+			// Instantiate a new parser
-ctx.getParserOptions().setStripVersionsFromReferences(false);
+			IParser parser = ctx.newJsonParser();
-//END SNIPPET: disableStripVersionsCtx
 
+			// Serialize it
+			String serialized = parser.encodeResourceToString(patient);
+			System.out.println(serialized);
+			//END SNIPPET: createParser
+		}
+		{
+			//START SNIPPET: disableStripVersions
+			FhirContext ctx = FhirContext.forR4();
+			IParser parser = ctx.newJsonParser();
+
+			// Disable the automatic stripping of versions from references on the parser
+			parser.setStripVersionsFromReferences(false);
+			//END SNIPPET: disableStripVersions
+
+			//START SNIPPET: disableStripVersionsCtx
+			ctx.getParserOptions().setStripVersionsFromReferences(false);
+			//END SNIPPET: disableStripVersionsCtx
 		}
 
 		{
-//START SNIPPET: disableStripVersionsField
+			//START SNIPPET: disableStripVersionsField
-FhirContext ctx = FhirContext.forDstu2();
+			FhirContext ctx = FhirContext.forR4();
-IParser parser = ctx.newJsonParser();
+			IParser parser = ctx.newJsonParser();
 
-// Preserve versions only on these two fields (for the given parser)
+			// Preserve versions only on these two fields (for the given parser)
-parser.setDontStripVersionsFromReferencesAtPaths("AuditEvent.entity.reference", "Patient.managingOrganization");
+			parser.setDontStripVersionsFromReferencesAtPaths("AuditEvent.entity.reference", "Patient.managingOrganization");
 
-// You can also apply this setting to the context so that it will 
+			// You can also apply this setting to the context so that it will
-// flow to all parsers
+			// flow to all parsers
-ctx.getParserOptions().setDontStripVersionsFromReferencesAtPaths("AuditEvent.entity.reference", "Patient.managingOrganization");
+			ctx.getParserOptions().setDontStripVersionsFromReferencesAtPaths("AuditEvent.entity.reference", "Patient.managingOrganization");
-//END SNIPPET: disableStripVersionsField
+			//END SNIPPET: disableStripVersionsField
 
 		}
-}	
+	}
 }

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/files.properties

@@ -9,6 +9,7 @@ page.introduction.downloading_and_importing=Downloading and Importing
 
 section.model.title=Working With The FHIR Model
 page.model.working_with_resources=Working With Resources
+page.model.parsers=Parsing and Serializing
 page.model.references=Resource References
 page.model.profiles_and_extensions=Profiles and Extensions
 page.model.converter=Version Converters

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

@@ -0,0 +1,17 @@
+# Parsers and Serializers
+
+HAPI FHIR has built-in support for the FHIR [JSON](http://hl7.org/fhir/json.html) and [XML](http://hl7.org/fhir/json.html) encoding formats.
+
+A built in parser can be used to convert HAPI FHIR Java objects into a serialized form, and to parse serialized data into Java objects. Note that unlike some other frameworks, HAPI FHIR does not have separate parsers and serializers. Both of these functions are handled by a single object called the **Parser**.
+
+# Serializing
+
+As with many parts of the HAPI FHIR API, parsing beginis with a [FhirContext](/apidocs/hapi-fhr-base/ca/uhn/fhir/context/FhirContext.html) object. The FhirContext can be used to request an [IParser](/apidocs/hapi-fhir-base/ca/uhn/fhir/parser/IParser.html) for your chosen encodng style that is then used to serialize.   
+
+The following example shows a JSON Parser being used to serialize a FHIR resource. 
+
+```java
+{{snippet:classpath:/ca/uhn/hapi/fhir/docs/Parser.java|createParser}}
+``` 
+   
+HapiWorkerContext

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/BruteForceMigrator.java

@@ -42,11 +42,12 @@ public class BruteForceMigrator extends BaseMigrator {
 
 	@Override
 	public void migrate() {
+		DriverTypeEnum.ConnectionProperties connectionProperties = getDriverType().newConnectionProperties(getConnectionUrl(), getUsername(), getPassword());
+
 		for (BaseTask<?> next : myTasks) {
 			next.setDriverType(getDriverType());
 			next.setDryRun(isDryRun());
 			next.setNoColumnShrink(isNoColumnShrink());
-			DriverTypeEnum.ConnectionProperties connectionProperties = getDriverType().newConnectionProperties(getConnectionUrl(), getUsername(), getPassword());
 			next.setConnectionProperties(connectionProperties);
 
 			try {