Merge branch 'master' of github.com:jamesagnew/hapi-fhir

hapi-fhir-base/.settings/org.eclipse.jdt.core.prefs

@@ -380,12 +380,12 @@ org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_enum_constan
 org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_method_declaration=do not insert
 org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_method_invocation=do not insert
 org.eclipse.jdt.core.formatter.join_lines_in_comments=false
-org.eclipse.jdt.core.formatter.join_wrapped_lines=true
+org.eclipse.jdt.core.formatter.join_wrapped_lines=false
 org.eclipse.jdt.core.formatter.keep_else_statement_on_same_line=false
 org.eclipse.jdt.core.formatter.keep_empty_array_initializer_on_one_line=false
 org.eclipse.jdt.core.formatter.keep_imple_if_on_one_line=false
 org.eclipse.jdt.core.formatter.keep_then_statement_on_same_line=false
-org.eclipse.jdt.core.formatter.lineSplit=200
+org.eclipse.jdt.core.formatter.lineSplit=250
 org.eclipse.jdt.core.formatter.never_indent_block_comments_on_first_column=false
 org.eclipse.jdt.core.formatter.never_indent_line_comments_on_first_column=false
 org.eclipse.jdt.core.formatter.number_of_blank_lines_at_beginning_of_method_body=0

hapi-fhir-cli/.settings/org.eclipse.jdt.core.prefs

@@ -5,6 +5,7 @@ org.eclipse.jdt.core.compiler.compliance=1.6
 org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
 org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
 org.eclipse.jdt.core.compiler.source=1.6
+org.eclipse.jdt.core.formatter.align_fields_grouping_blank_lines=2147483647
 org.eclipse.jdt.core.formatter.align_type_members_on_columns=false
 org.eclipse.jdt.core.formatter.alignment_for_arguments_in_allocation_expression=16
 org.eclipse.jdt.core.formatter.alignment_for_arguments_in_annotation=0
@@ -18,8 +19,10 @@ org.eclipse.jdt.core.formatter.alignment_for_compact_if=16
 org.eclipse.jdt.core.formatter.alignment_for_conditional_expression=80
 org.eclipse.jdt.core.formatter.alignment_for_enum_constants=0
 org.eclipse.jdt.core.formatter.alignment_for_expressions_in_array_initializer=16
+org.eclipse.jdt.core.formatter.alignment_for_expressions_in_for_loop_header=0
 org.eclipse.jdt.core.formatter.alignment_for_method_declaration=0
 org.eclipse.jdt.core.formatter.alignment_for_multiple_fields=16
+org.eclipse.jdt.core.formatter.alignment_for_parameterized_type_references=0
 org.eclipse.jdt.core.formatter.alignment_for_parameters_in_constructor_declaration=16
 org.eclipse.jdt.core.formatter.alignment_for_parameters_in_method_declaration=16
 org.eclipse.jdt.core.formatter.alignment_for_resources_in_try=80
@@ -29,6 +32,8 @@ org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_enum_declaration
 org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_type_declaration=16
 org.eclipse.jdt.core.formatter.alignment_for_throws_clause_in_constructor_declaration=16
 org.eclipse.jdt.core.formatter.alignment_for_throws_clause_in_method_declaration=16
+org.eclipse.jdt.core.formatter.alignment_for_type_arguments=0
+org.eclipse.jdt.core.formatter.alignment_for_type_parameters=0
 org.eclipse.jdt.core.formatter.alignment_for_union_type_in_multicatch=16
 org.eclipse.jdt.core.formatter.blank_lines_after_imports=1
 org.eclipse.jdt.core.formatter.blank_lines_after_package=1
@@ -56,16 +61,16 @@ org.eclipse.jdt.core.formatter.brace_position_for_type_declaration=end_of_line
 org.eclipse.jdt.core.formatter.comment.clear_blank_lines_in_block_comment=false
 org.eclipse.jdt.core.formatter.comment.clear_blank_lines_in_javadoc_comment=false
 org.eclipse.jdt.core.formatter.comment.format_block_comments=true
-org.eclipse.jdt.core.formatter.comment.format_header=false
+org.eclipse.jdt.core.formatter.comment.format_header=true
-org.eclipse.jdt.core.formatter.comment.format_html=false
+org.eclipse.jdt.core.formatter.comment.format_html=true
 org.eclipse.jdt.core.formatter.comment.format_javadoc_comments=true
-org.eclipse.jdt.core.formatter.comment.format_line_comments=false
+org.eclipse.jdt.core.formatter.comment.format_line_comments=true
 org.eclipse.jdt.core.formatter.comment.format_source_code=true
 org.eclipse.jdt.core.formatter.comment.indent_parameter_description=true
 org.eclipse.jdt.core.formatter.comment.indent_root_tags=true
 org.eclipse.jdt.core.formatter.comment.insert_new_line_before_root_tags=insert
 org.eclipse.jdt.core.formatter.comment.insert_new_line_for_parameter=insert
-org.eclipse.jdt.core.formatter.comment.line_length=120
+org.eclipse.jdt.core.formatter.comment.line_length=200
 org.eclipse.jdt.core.formatter.comment.new_lines_at_block_boundaries=true
 org.eclipse.jdt.core.formatter.comment.new_lines_at_javadoc_boundaries=true
 org.eclipse.jdt.core.formatter.comment.preserve_white_space_between_code_and_line_comments=false
@@ -87,6 +92,7 @@ org.eclipse.jdt.core.formatter.indent_statements_compare_to_body=true
 org.eclipse.jdt.core.formatter.indent_switchstatements_compare_to_cases=true
 org.eclipse.jdt.core.formatter.indent_switchstatements_compare_to_switch=false
 org.eclipse.jdt.core.formatter.indentation.size=3
+org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_enum_constant=insert
 org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_field=insert
 org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_local_variable=insert
 org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_method=insert
@@ -271,21 +277,33 @@ org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_enum_constan
 org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_method_declaration=do not insert
 org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_method_invocation=do not insert
 org.eclipse.jdt.core.formatter.join_lines_in_comments=false
-org.eclipse.jdt.core.formatter.join_wrapped_lines=true
+org.eclipse.jdt.core.formatter.join_wrapped_lines=false
 org.eclipse.jdt.core.formatter.keep_else_statement_on_same_line=false
 org.eclipse.jdt.core.formatter.keep_empty_array_initializer_on_one_line=false
 org.eclipse.jdt.core.formatter.keep_imple_if_on_one_line=false
 org.eclipse.jdt.core.formatter.keep_then_statement_on_same_line=false
-org.eclipse.jdt.core.formatter.lineSplit=300
+org.eclipse.jdt.core.formatter.lineSplit=250
 org.eclipse.jdt.core.formatter.never_indent_block_comments_on_first_column=false
 org.eclipse.jdt.core.formatter.never_indent_line_comments_on_first_column=false
 org.eclipse.jdt.core.formatter.number_of_blank_lines_at_beginning_of_method_body=0
 org.eclipse.jdt.core.formatter.number_of_empty_lines_to_preserve=1
+org.eclipse.jdt.core.formatter.parentheses_positions_in_annotation=common_lines
+org.eclipse.jdt.core.formatter.parentheses_positions_in_catch_clause=common_lines
+org.eclipse.jdt.core.formatter.parentheses_positions_in_enum_constant_declaration=common_lines
+org.eclipse.jdt.core.formatter.parentheses_positions_in_for_statment=common_lines
+org.eclipse.jdt.core.formatter.parentheses_positions_in_if_while_statement=common_lines
+org.eclipse.jdt.core.formatter.parentheses_positions_in_lambda_declaration=common_lines
+org.eclipse.jdt.core.formatter.parentheses_positions_in_method_delcaration=common_lines
+org.eclipse.jdt.core.formatter.parentheses_positions_in_method_invocation=common_lines
+org.eclipse.jdt.core.formatter.parentheses_positions_in_switch_statement=common_lines
+org.eclipse.jdt.core.formatter.parentheses_positions_in_try_clause=common_lines
 org.eclipse.jdt.core.formatter.put_empty_statement_on_new_line=true
 org.eclipse.jdt.core.formatter.tabulation.char=tab
 org.eclipse.jdt.core.formatter.tabulation.size=3
 org.eclipse.jdt.core.formatter.use_on_off_tags=true
 org.eclipse.jdt.core.formatter.use_tabs_only_for_leading_indentations=false
+org.eclipse.jdt.core.formatter.wrap_before_assignment_operator=false
 org.eclipse.jdt.core.formatter.wrap_before_binary_operator=true
+org.eclipse.jdt.core.formatter.wrap_before_conditional_operator=true
 org.eclipse.jdt.core.formatter.wrap_before_or_operator_multicatch=true
 org.eclipse.jdt.core.formatter.wrap_outer_expressions_when_nested=true

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/StopWatch.java

@@ -1,5 +1,7 @@
 package ca.uhn.fhir.jpa.util;
 
+import java.util.Date;
+
 /*
  * #%L
  * HAPI FHIR JPA Server
@@ -25,6 +27,20 @@ public class StopWatch {
 
 	private long myStarted = System.currentTimeMillis();
 	
+	/**
+	 * Constructor
+	 */
+	public StopWatch() {
+		super();
+	}
+	
+	/**
+	 * Constructor
+	 */
+	public StopWatch(Date theNow) {
+		myStarted = theNow.getTime();
+	}
+
 	public long getMillisAndRestart() {
 		long now = System.currentTimeMillis();
 		long retVal = now - myStarted;
@@ -38,6 +54,15 @@ public class StopWatch {
 		return retVal;
 	}
 	
+	public long getMillis(Date theNow) {
+		long retVal = theNow.getTime() - myStarted;
+		return retVal;
+	}
+
+	public Date getStartedDate() {
+		return new Date(myStarted);
+	}
+	
 	public double getMillisPerOperation(int theNumOperations) {
 		return ((double)getMillis()) / Math.max(1.0, theNumOperations);
 	}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3Test.java

@@ -50,6 +50,7 @@ import org.hl7.fhir.dstu3.model.Encounter.EncounterLocationComponent;
 import org.hl7.fhir.dstu3.model.Encounter.EncounterStatus;
 import org.hl7.fhir.dstu3.model.Enumerations.AdministrativeGender;
 import org.hl7.fhir.dstu3.model.Narrative.NarrativeStatus;
+import org.hl7.fhir.dstu3.model.Observation.ObservationStatus;
 import org.hl7.fhir.dstu3.model.Questionnaire.QuestionnaireItemType;
 import org.hl7.fhir.dstu3.model.Subscription.SubscriptionChannelType;
 import org.hl7.fhir.dstu3.model.Subscription.SubscriptionStatus;
@@ -92,6 +93,33 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 		TestUtil.clearAllStaticFieldsForUnitTest();
 	}
 
+	@Test
+	public void testFullTextSearch() throws RuntimeException, Exception {
+		Observation obs1 = new Observation();
+		obs1.getCode().setText("Systolic Blood Pressure");
+		obs1.setStatus(ObservationStatus.FINAL);
+		obs1.setValue(new Quantity(123));
+		obs1.setComment("obs1");
+		IIdType id1 = myObservationDao.create(obs1, mySrd).getId().toUnqualifiedVersionless();
+		
+		Observation obs2 = new Observation();
+		obs2.getCode().setText("Diastolic Blood Pressure");
+		obs2.setStatus(ObservationStatus.FINAL);
+		obs2.setValue(new Quantity(81));
+		IIdType id2 = myObservationDao.create(obs2, mySrd).getId().toUnqualifiedVersionless();
+			
+		HttpGet get = new HttpGet(ourServerBase + "/Observation?_content=systolic&_pretty=true");
+		CloseableHttpResponse response = ourHttpClient.execute(get);
+		try {
+			assertEquals(200, response.getStatusLine().getStatusCode());
+			String responseString = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
+			ourLog.info(responseString);
+			assertThat(responseString, containsString(id1.getIdPart()));
+		} finally {
+			response.close();
+		}
+	}
+	
 	/**
 	 * See #441
 	 */
@@ -110,6 +138,7 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 		try {
 			assertEquals(200, response.getStatusLine().getStatusCode());
 			String responseString = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
+			ourLog.info(responseString);
 			assertThat(responseString, containsString(moId.getIdPart()));
 		} finally {
 			response.close();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/util/StopWatchTest.java

@@ -0,0 +1,35 @@
+package ca.uhn.fhir.jpa.util;
+
+import static org.hamcrest.Matchers.greaterThan;
+import static org.hamcrest.Matchers.lessThan;
+import static org.junit.Assert.assertThat;
+
+import java.util.Date;
+
+import org.junit.Test;
+
+public class StopWatchTest {
+
+	@Test
+	public void testStopwatch() throws Exception {
+		StopWatch sw = new StopWatch();
+		
+		Thread.sleep(100);
+		
+		assertThat(sw.getMillis(new Date()), greaterThan(10L));
+		assertThat(sw.getMillis(), greaterThan(10L));
+		assertThat(sw.getStartedDate().getTime(), lessThan(System.currentTimeMillis()));
+	}
+	
+	@Test
+	public void testStopwatchWithDate() throws Exception {
+		StopWatch sw = new StopWatch(new Date());
+		
+		Thread.sleep(100);
+		
+		assertThat(sw.getMillis(new Date()), greaterThan(10L));
+		assertThat(sw.getMillis(), greaterThan(10L));
+		assertThat(sw.getStartedDate().getTime(), lessThan(System.currentTimeMillis()));
+	}
+
+}

hapi-tinder-plugin/.settings/org.eclipse.jdt.core.prefs

@@ -97,6 +97,7 @@ org.eclipse.jdt.core.compiler.problem.unusedTypeParameter=ignore
 org.eclipse.jdt.core.compiler.problem.unusedWarningToken=warning
 org.eclipse.jdt.core.compiler.problem.varargsArgumentNeedCast=warning
 org.eclipse.jdt.core.compiler.source=1.6
+org.eclipse.jdt.core.formatter.align_fields_grouping_blank_lines=2147483647
 org.eclipse.jdt.core.formatter.align_type_members_on_columns=false
 org.eclipse.jdt.core.formatter.alignment_for_arguments_in_allocation_expression=16
 org.eclipse.jdt.core.formatter.alignment_for_arguments_in_annotation=0
@@ -110,8 +111,10 @@ org.eclipse.jdt.core.formatter.alignment_for_compact_if=16
 org.eclipse.jdt.core.formatter.alignment_for_conditional_expression=80
 org.eclipse.jdt.core.formatter.alignment_for_enum_constants=0
 org.eclipse.jdt.core.formatter.alignment_for_expressions_in_array_initializer=16
+org.eclipse.jdt.core.formatter.alignment_for_expressions_in_for_loop_header=0
 org.eclipse.jdt.core.formatter.alignment_for_method_declaration=0
 org.eclipse.jdt.core.formatter.alignment_for_multiple_fields=16
+org.eclipse.jdt.core.formatter.alignment_for_parameterized_type_references=0
 org.eclipse.jdt.core.formatter.alignment_for_parameters_in_constructor_declaration=16
 org.eclipse.jdt.core.formatter.alignment_for_parameters_in_method_declaration=16
 org.eclipse.jdt.core.formatter.alignment_for_resources_in_try=80
@@ -121,6 +124,8 @@ org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_enum_declaration
 org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_type_declaration=16
 org.eclipse.jdt.core.formatter.alignment_for_throws_clause_in_constructor_declaration=16
 org.eclipse.jdt.core.formatter.alignment_for_throws_clause_in_method_declaration=16
+org.eclipse.jdt.core.formatter.alignment_for_type_arguments=0
+org.eclipse.jdt.core.formatter.alignment_for_type_parameters=0
 org.eclipse.jdt.core.formatter.alignment_for_union_type_in_multicatch=16
 org.eclipse.jdt.core.formatter.blank_lines_after_imports=1
 org.eclipse.jdt.core.formatter.blank_lines_after_package=1
@@ -148,16 +153,16 @@ org.eclipse.jdt.core.formatter.brace_position_for_type_declaration=end_of_line
 org.eclipse.jdt.core.formatter.comment.clear_blank_lines_in_block_comment=false
 org.eclipse.jdt.core.formatter.comment.clear_blank_lines_in_javadoc_comment=false
 org.eclipse.jdt.core.formatter.comment.format_block_comments=true
-org.eclipse.jdt.core.formatter.comment.format_header=false
+org.eclipse.jdt.core.formatter.comment.format_header=true
-org.eclipse.jdt.core.formatter.comment.format_html=false
+org.eclipse.jdt.core.formatter.comment.format_html=true
 org.eclipse.jdt.core.formatter.comment.format_javadoc_comments=true
-org.eclipse.jdt.core.formatter.comment.format_line_comments=false
+org.eclipse.jdt.core.formatter.comment.format_line_comments=true
 org.eclipse.jdt.core.formatter.comment.format_source_code=true
 org.eclipse.jdt.core.formatter.comment.indent_parameter_description=true
 org.eclipse.jdt.core.formatter.comment.indent_root_tags=true
 org.eclipse.jdt.core.formatter.comment.insert_new_line_before_root_tags=insert
 org.eclipse.jdt.core.formatter.comment.insert_new_line_for_parameter=insert
-org.eclipse.jdt.core.formatter.comment.line_length=120
+org.eclipse.jdt.core.formatter.comment.line_length=200
 org.eclipse.jdt.core.formatter.comment.new_lines_at_block_boundaries=true
 org.eclipse.jdt.core.formatter.comment.new_lines_at_javadoc_boundaries=true
 org.eclipse.jdt.core.formatter.comment.preserve_white_space_between_code_and_line_comments=false
@@ -179,6 +184,7 @@ org.eclipse.jdt.core.formatter.indent_statements_compare_to_body=true
 org.eclipse.jdt.core.formatter.indent_switchstatements_compare_to_cases=true
 org.eclipse.jdt.core.formatter.indent_switchstatements_compare_to_switch=false
 org.eclipse.jdt.core.formatter.indentation.size=3
+org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_enum_constant=insert
 org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_field=insert
 org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_local_variable=insert
 org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_method=insert
@@ -363,22 +369,34 @@ org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_enum_constan
 org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_method_declaration=do not insert
 org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_method_invocation=do not insert
 org.eclipse.jdt.core.formatter.join_lines_in_comments=false
-org.eclipse.jdt.core.formatter.join_wrapped_lines=true
+org.eclipse.jdt.core.formatter.join_wrapped_lines=false
 org.eclipse.jdt.core.formatter.keep_else_statement_on_same_line=false
 org.eclipse.jdt.core.formatter.keep_empty_array_initializer_on_one_line=false
 org.eclipse.jdt.core.formatter.keep_imple_if_on_one_line=false
 org.eclipse.jdt.core.formatter.keep_then_statement_on_same_line=false
-org.eclipse.jdt.core.formatter.lineSplit=300
+org.eclipse.jdt.core.formatter.lineSplit=250
 org.eclipse.jdt.core.formatter.never_indent_block_comments_on_first_column=false
 org.eclipse.jdt.core.formatter.never_indent_line_comments_on_first_column=false
 org.eclipse.jdt.core.formatter.number_of_blank_lines_at_beginning_of_method_body=0
 org.eclipse.jdt.core.formatter.number_of_empty_lines_to_preserve=1
+org.eclipse.jdt.core.formatter.parentheses_positions_in_annotation=common_lines
+org.eclipse.jdt.core.formatter.parentheses_positions_in_catch_clause=common_lines
+org.eclipse.jdt.core.formatter.parentheses_positions_in_enum_constant_declaration=common_lines
+org.eclipse.jdt.core.formatter.parentheses_positions_in_for_statment=common_lines
+org.eclipse.jdt.core.formatter.parentheses_positions_in_if_while_statement=common_lines
+org.eclipse.jdt.core.formatter.parentheses_positions_in_lambda_declaration=common_lines
+org.eclipse.jdt.core.formatter.parentheses_positions_in_method_delcaration=common_lines
+org.eclipse.jdt.core.formatter.parentheses_positions_in_method_invocation=common_lines
+org.eclipse.jdt.core.formatter.parentheses_positions_in_switch_statement=common_lines
+org.eclipse.jdt.core.formatter.parentheses_positions_in_try_clause=common_lines
 org.eclipse.jdt.core.formatter.put_empty_statement_on_new_line=true
 org.eclipse.jdt.core.formatter.tabulation.char=tab
 org.eclipse.jdt.core.formatter.tabulation.size=3
 org.eclipse.jdt.core.formatter.use_on_off_tags=true
 org.eclipse.jdt.core.formatter.use_tabs_only_for_leading_indentations=false
+org.eclipse.jdt.core.formatter.wrap_before_assignment_operator=false
 org.eclipse.jdt.core.formatter.wrap_before_binary_operator=true
+org.eclipse.jdt.core.formatter.wrap_before_conditional_operator=true
 org.eclipse.jdt.core.formatter.wrap_before_or_operator_multicatch=true
 org.eclipse.jdt.core.formatter.wrap_outer_expressions_when_nested=true
 org.eclipse.jdt.core.javaFormatter=org.eclipse.jdt.core.defaultJavaFormatter

pom.xml

@@ -678,7 +678,7 @@
 			<dependency>
 				<groupId>org.springframework.data</groupId>
 				<artifactId>spring-data-jpa</artifactId>
-				<version>1.10.2.RELEASE</version>
+				<version>1.10.4.RELEASE</version>
 			</dependency>
 			<dependency>
 				<groupId>org.springframework</groupId>

src/changes/changes.xml

@@ -7,6 +7,15 @@
 	</properties>
 	<body>
 		<release version="2.1" date="TBD">
+			<action type="add">
+				Bump the version of a few dependencies to the
+				latest versions (dependent HAPI modules listed in brackets):
+				<![CDATA[
+					<ul>
+						<li>spring-data-orm (JPA): 1.10.2 -&gt; 1.10.4</li>
+					</ul>
+				]]>
+			</action>
 			<action type="add">
 				Client, Server, and JPA server now support experimental support
 				for