Merge remote-tracking branch 'remotes/origin/master' into ks-20200120-near-search

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_2_0/1676-allow-schemalocation-when-validating.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 1676
+title: "When validating an XML resource, the validatin failed if the resource contained an
+   `xsi:schemaLocation` declaration. This has been corrected. Thanks to Brian Kaney for reporting!"

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

@@ -187,7 +187,6 @@ public class ArbitrarySqlTask extends BaseTask<ArbitrarySqlTask> {
 	public int hashCode() {
 		return new HashCodeBuilder(17, 37)
 			.append(myTableName)
-			.append(myExecuteOnlyIfTableExists)
 			.toHashCode();
 	}
 }

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

@@ -159,8 +159,6 @@ public class RenameColumnTask extends BaseTableTask<RenameColumnTask> {
 			.appendSuper(super.hashCode())
 			.append(myOldName)
 			.append(myNewName)
-			.append(myIsOkayIfNeitherColumnExists)
-			.append(myDeleteTargetColumnFirstIfBothExist)
 			.toHashCode();
 	}
 }

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/api/Builder.java

@@ -50,9 +50,10 @@ public class Builder {
 		return new BuilderAddTableRawSql(theVersion, theTableName);
 	}
 
-	public Builder executeRawSql(String theVersion, @Language("SQL") String theSql) {
+	public BuilderCompleteTask executeRawSql(String theVersion, @Language("SQL") String theSql) {
-		mySink.addTask(new ExecuteRawSqlTask(myRelease, theVersion).addSql(theSql));
+		ExecuteRawSqlTask task = new ExecuteRawSqlTask(myRelease, theVersion).addSql(theSql);
-		return this;
+		mySink.addTask(task);
+		return new BuilderCompleteTask(task);
 	}
 
 	public Builder initializeSchema(String theVersion, ISchemaInitializationProvider theSchemaInitializationProvider) {
@@ -72,6 +73,7 @@ public class Builder {
 		return this;
 	}
 
+
 	// Flyway doesn't support these kinds of migrations
 	@Deprecated
 	public Builder startSectionWithMessage(String theMessage) {
@@ -395,7 +397,7 @@ public class Builder {
 			}
 		}
 
-		public static class BuilderAddColumnWithName {
+		public class BuilderAddColumnWithName {
 			private final String myRelease;
 			private final String myVersion;
 			private final String myColumnName;
@@ -427,11 +429,11 @@ public class Builder {
 					myNullable = theNullable;
 				}
 
-				public BuilderAddColumnComplete type(AddColumnTask.ColumnTypeEnum theColumnType) {
+				public BuilderCompleteTask type(AddColumnTask.ColumnTypeEnum theColumnType) {
 					return type(theColumnType, null);
 				}
 
-				public BuilderAddColumnComplete type(AddColumnTask.ColumnTypeEnum theColumnType, Integer theLength) {
+				public BuilderCompleteTask type(AddColumnTask.ColumnTypeEnum theColumnType, Integer theLength) {
 					AddColumnTask task = new AddColumnTask(myRelease, myVersion);
 					task.setColumnName(myColumnName);
 					task.setNullable(myNullable);
@@ -441,24 +443,26 @@ public class Builder {
 					}
 					myTaskSink.addTask(task);
 
-					return new BuilderAddColumnComplete(task);
+					return new BuilderCompleteTask(task);
 				}
 
-				public class BuilderAddColumnComplete {
-
-					private final AddColumnTask myTask;
-
-					public BuilderAddColumnComplete(AddColumnTask theTask) {
-						myTask = theTask;
-					}
-
-					public BuilderAddColumnComplete failureAllowed() {
-						myTask.setFailureAllowed(true);
-						return this;
-					}
-				}
 			}
 		}
 	}
 
+
+	public static class BuilderCompleteTask {
+
+		private final BaseTask<?> myTask;
+
+		public BuilderCompleteTask(BaseTask<?> theTask) {
+			myTask = theTask;
+		}
+
+		public BuilderCompleteTask failureAllowed() {
+			myTask.setFailureAllowed(true);
+			return this;
+		}
+	}
+
 }

hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/ExecuteRawSqlTaskTest.java

@@ -0,0 +1,48 @@
+package ca.uhn.fhir.jpa.migrate.taskdef;
+
+import ca.uhn.fhir.jpa.migrate.tasks.api.BaseMigrationTasks;
+import ca.uhn.fhir.util.VersionEnum;
+import org.junit.Test;
+
+import java.util.List;
+import java.util.Map;
+
+import static org.junit.Assert.assertEquals;
+
+public class ExecuteRawSqlTaskTest extends BaseTest {
+
+	@Test
+	public void testExecuteSql() {
+		executeSql("create table SOMETABLE (PID bigint not null, TEXTCOL varchar(255))");
+
+		BaseMigrationTasks<VersionEnum> tasks = new BaseMigrationTasks<>();
+		tasks
+			.forVersion(VersionEnum.V4_0_0)
+			.executeRawSql("2001.01", "INSERT INTO SOMETABLE (PID, TEXTCOL) VALUES (123, 'abc')");
+
+		getMigrator().addTasks(tasks.getTasks(VersionEnum.V0_1, VersionEnum.V4_0_0));
+		getMigrator().migrate();
+
+		List<Map<String, Object>> output = executeQuery("SELECT PID FROM SOMETABLE");
+		assertEquals(1, output.size());
+		assertEquals(123L, output.get(0).get("PID"));
+	}
+
+	@Test
+	public void testExecuteSql_AllowedToFail() {
+		executeSql("create table SOMETABLE (PID bigint not null, TEXTCOL varchar(255))");
+
+		BaseMigrationTasks<VersionEnum> tasks = new BaseMigrationTasks<>();
+		tasks
+			.forVersion(VersionEnum.V4_0_0)
+			.executeRawSql("2001.01", "INSERT INTO SOMETABLE (PID_BAD_COLUMN, TEXTCOL) VALUES (123, 'abc')")
+			.failureAllowed();
+
+		getMigrator().addTasks(tasks.getTasks(VersionEnum.V0_1, VersionEnum.V4_0_0));
+		getMigrator().migrate();
+
+		List<Map<String, Object>> output = executeQuery("SELECT PID FROM SOMETABLE");
+		assertEquals(0, output.size());
+	}
+
+}

hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/ValidatorWrapper.java

@@ -82,6 +82,7 @@ public class ValidatorWrapper {
 		v.setNoTerminologyChecks(myNoTerminologyChecks);
 		v.setErrorForUnknownProfiles(myErrorForUnknownProfiles);
 		v.getExtensionDomains().addAll(myExtensionDomains);
+		v.setAllowXsiLocation(true);
 
 		List<ValidationMessage> messages = new ArrayList<>();
 

hapi-fhir-validation/src/test/java/org/hl7/fhir/r4/validation/FhirInstanceValidatorR4Test.java

@@ -12,7 +12,6 @@ import ca.uhn.fhir.validation.ValidationResult;
 import com.google.common.base.Charsets;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.Validate;
-import org.hl7.fhir.dstu3.hapi.validation.ResourceValidatorDstu3Test;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r4.conformance.ProfileUtilities;
@@ -36,7 +35,11 @@ import org.hl7.fhir.r4.utils.FHIRPathEngine;
 import org.hl7.fhir.r5.utils.IResourceValidator;
 import org.hl7.fhir.utilities.validation.ValidationMessage;
 import org.hl7.fhir.utilities.xhtml.XhtmlNode;
-import org.junit.*;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Ignore;
+import org.junit.Rule;
+import org.junit.Test;
 import org.junit.rules.TestRule;
 import org.junit.rules.TestWatcher;
 import org.junit.runner.Description;
@@ -44,13 +47,25 @@ import org.mockito.invocation.InvocationOnMock;
 import org.mockito.stubbing.Answer;
 
 import java.io.IOException;
-import java.io.InputStream;
+import java.util.ArrayList;
-import java.util.*;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeSet;
 import java.util.stream.Collectors;
-import java.util.zip.GZIPInputStream;
 
-import static org.hamcrest.Matchers.*;
+import static org.hamcrest.Matchers.containsString;
-import static org.junit.Assert.*;
+import static org.hamcrest.Matchers.empty;
+import static org.hamcrest.Matchers.greaterThan;
+import static org.hamcrest.Matchers.hasSize;
+import static org.hamcrest.Matchers.lessThan;
+import static org.hamcrest.Matchers.not;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertThat;
+import static org.junit.Assert.assertTrue;
 import static org.mockito.ArgumentMatchers.nullable;
 import static org.mockito.Mockito.mock;
 import static org.mockito.Mockito.when;
@@ -127,8 +142,8 @@ public class FhirInstanceValidatorR4Test extends BaseTest {
 		});
 		when(myMockSupport.isCodeSystemSupported(nullable(FhirContext.class), nullable(String.class))).thenAnswer(new Answer<Boolean>() {
 			@Override
-			public Boolean answer(InvocationOnMock theInvocation) throws Throwable {
+			public Boolean answer(InvocationOnMock theInvocation) {
-				boolean retVal = myValidSystems.contains(theInvocation.getArguments()[1]);
+				boolean retVal = myValidSystems.contains(theInvocation.getArgument(1, String.class));
 				ourLog.debug("isCodeSystemSupported({}) : {}", new Object[]{theInvocation.getArguments()[1], retVal});
 				return retVal;
 			}
@@ -139,7 +154,7 @@ public class FhirInstanceValidatorR4Test extends BaseTest {
 				IBaseResource retVal;
 				String id = (String) theInvocation.getArguments()[2];
 				if ("Questionnaire/q_jon".equals(id)) {
-					retVal = ourCtx.newJsonParser().parseResource(IOUtils.toString(FhirInstanceValidatorR4Test.class.getResourceAsStream("/q_jon.json")));
+					retVal = ourCtx.newJsonParser().parseResource(loadResource("/q_jon.json"));
 				} else {
 					retVal = myDefaultValidationSupport.fetchResource((FhirContext) theInvocation.getArguments()[0], (Class<IBaseResource>) theInvocation.getArguments()[1], id);
 				}
@@ -210,7 +225,7 @@ public class FhirInstanceValidatorR4Test extends BaseTest {
 	}
 
 	private List<SingleValidationMessage> logResultsAndReturnAll(ValidationResult theOutput) {
-		List<SingleValidationMessage> retVal = new ArrayList<SingleValidationMessage>();
+		List<SingleValidationMessage> retVal = new ArrayList<>();
 
 		int index = 0;
 		for (SingleValidationMessage next : theOutput.getMessages()) {
@@ -264,6 +279,27 @@ public class FhirInstanceValidatorR4Test extends BaseTest {
 		assertEquals("Primitive types must have a value that is not empty", all.get(0).getMessage());
 	}
 
+	/**
+	 * See #1676 - We should ignore schema location
+	 */
+	@Test
+	public void testValidateResourceWithSchemaLocation() {
+		String input = "<Patient xmlns=\"http://hl7.org/fhir\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation=\"http://hl7.org/fhir ../../schema/foo.xsd\">" +
+			"  <text>\n" +
+			"    <status value=\"generated\"/>\n" +
+			"    <div xmlns=\"http://www.w3.org/1999/xhtml\">AAA</div>\n" +
+			"  </text>" +
+			"  <active value=\"true\"/>" +
+			"</Patient>";
+
+		FhirValidator val = ourCtx.newValidator();
+		val.registerValidatorModule(new FhirInstanceValidator(myDefaultValidationSupport));
+
+		ValidationResult result = val.validateWithResult(input);
+		logResultsAndReturnAll(result);
+		assertTrue(result.isSuccessful());
+	}
+
 	/**
 	 * See #942
 	 */