Improve performance of base64 validation

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/BaseAndListParam.java

@@ -20,25 +20,32 @@ package ca.uhn.fhir.rest.param;
  * #L%
  */
 
-import java.util.ArrayList;
-import java.util.List;
-
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.model.api.IQueryParameterAnd;
 import ca.uhn.fhir.model.api.IQueryParameterOr;
 import ca.uhn.fhir.rest.api.QualifiedParamList;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 
+import java.util.ArrayList;
+import java.util.List;
+
 public abstract class BaseAndListParam<T extends IQueryParameterOr<?>> implements IQueryParameterAnd<T> {
 
-	private List<T> myValues=new ArrayList<T>(); 
+	private List<T> myValues = new ArrayList<>();
+
+	public abstract BaseAndListParam<T> addAnd(T theValue);
 
 	public BaseAndListParam<T> addValue(T theValue) {
 		myValues.add(theValue);
 		return this;
 	}
 
-	public abstract BaseAndListParam<T> addAnd(T theValue);
+	@Override
+	public List<T> getValuesAsQueryTokens() {
+		return myValues;
+	}
+
+	abstract T newInstance();
 
 	@Override
 	public void setValuesAsQueryTokens(FhirContext theContext, String theParamName, List<QualifiedParamList> theParameters) throws InvalidRequestException {
@@ -50,11 +57,9 @@ public abstract class BaseAndListParam<T extends IQueryParameterOr<?>> implement
 		}
 	}
 
-	abstract T newInstance();
-
 	@Override
-	public List<T> getValuesAsQueryTokens() {
+	public String toString() {
-		return myValues;
+		return myValues.toString();
 	}
 
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/BaseOrListParam.java

@@ -20,22 +20,34 @@ package ca.uhn.fhir.rest.param;
  * #L%
  */
 
-import java.util.ArrayList;
-import java.util.List;
-
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.model.api.IQueryParameterOr;
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.rest.api.QualifiedParamList;
 
+import java.util.ArrayList;
+import java.util.List;
+
 abstract class BaseOrListParam<MT extends BaseOrListParam<?, ?>, PT extends IQueryParameterType> implements IQueryParameterOr<PT> {
 
-	private List<PT> myList=new ArrayList<PT>();
+	private List<PT> myList = new ArrayList<>();
 
-//	public void addToken(T theParam) {
+	@SuppressWarnings("unchecked")
-//		Validate.notNull(theParam,"Param can not be null");
+	public MT add(PT theParameter) {
-//		myList.add(theParam);
+		if (theParameter != null) {
-//	}
+			myList.add(theParameter);
+		}
+		return (MT) this;
+	}
+
+	public abstract MT addOr(PT theParameter);
+
+	@Override
+	public List<PT> getValuesAsQueryTokens() {
+		return myList;
+	}
+
+	abstract PT newInstance();
 
 	@Override
 	public void setValuesAsQueryTokens(FhirContext theContext, String theParamName, QualifiedParamList theParameters) {
@@ -47,21 +59,9 @@ abstract class BaseOrListParam<MT extends BaseOrListParam<?, ?>, PT extends IQue
 		}
 	}
 
-	abstract PT newInstance();
-
-	public abstract MT addOr(PT theParameter);
-	
-	@SuppressWarnings("unchecked")
-	public MT add(PT theParameter) {
-		if (theParameter != null) {
-			myList.add(theParameter);
-		}
-		return (MT) this;
-	}
-	
 	@Override
-	public List<PT> getValuesAsQueryTokens() {
+	public String toString() {
-		return myList;
+		return myList.toString();
 	}
 
 }

hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/api/server/RequestDetails.java

@@ -279,21 +279,23 @@ public abstract class RequestDetails {
 	}
 
 	public Map<String, List<String>> getUnqualifiedToQualifiedNames() {
-		for (String next : myParameters.keySet()) {
+		if (myUnqualifiedToQualifiedNames == null) {
-			for (int i = 0; i < next.length(); i++) {
+			for (String next : myParameters.keySet()) {
-				char nextChar = next.charAt(i);
+				for (int i = 0; i < next.length(); i++) {
-				if (nextChar == ':' || nextChar == '.') {
+					char nextChar = next.charAt(i);
-					if (myUnqualifiedToQualifiedNames == null) {
+					if (nextChar == ':' || nextChar == '.') {
-						myUnqualifiedToQualifiedNames = new HashMap<>();
+						if (myUnqualifiedToQualifiedNames == null) {
+							myUnqualifiedToQualifiedNames = new HashMap<>();
+						}
+						String unqualified = next.substring(0, i);
+						List<String> list = myUnqualifiedToQualifiedNames.get(unqualified);
+						if (list == null) {
+							list = new ArrayList<>(4);
+							myUnqualifiedToQualifiedNames.put(unqualified, list);
+						}
+						list.add(next);
+						break;
 					}
-					String unqualified = next.substring(0, i);
-					List<String> list = myUnqualifiedToQualifiedNames.get(unqualified);
-					if (list == null) {
-						list = new ArrayList<>(4);
-						myUnqualifiedToQualifiedNames.put(unqualified, list);
-					}
-					list.add(next);
-					break;
 				}
 			}
 		}

hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/BaseQueryParameter.java

@@ -96,7 +96,7 @@ public abstract class BaseQueryParameter implements IParameter {
 	@Override
 	public Object translateQueryParametersIntoServerArgument(RequestDetails theRequest, BaseMethodBinding<?> theMethodBinding) throws InternalErrorException, InvalidRequestException {
 
-		List<QualifiedParamList> paramList = new ArrayList<QualifiedParamList>();
+		List<QualifiedParamList> paramList = new ArrayList<>();
 		String name = getName();
 		parseParams(theRequest, paramList, name, null);
 

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/rest/server/SearchDefaultMethodDstu3Test.java

@@ -165,7 +165,7 @@ public class SearchDefaultMethodDstu3Test {
 			assertThat(ourLastParam1.getValuesAsQueryTokens().get(0).getValuesAsQueryTokens(), hasSize(1));
 			assertEquals("val1", ourLastParam1.getValuesAsQueryTokens().get(0).getValuesAsQueryTokens().get(0).getValue());
 
-			assertThat(ourLastParam2.getValuesAsQueryTokens(), hasSize(2));
+			assertThat(ourLastParam2.toString(), ourLastParam2.getValuesAsQueryTokens(), hasSize(2));
 			assertThat(ourLastParam2.getValuesAsQueryTokens().get(0).getValuesAsQueryTokens(), hasSize(1));
 			assertEquals("val2", ourLastParam2.getValuesAsQueryTokens().get(0).getValuesAsQueryTokens().get(0).getValue());
 			assertEquals("val2e", ourLastParam2.getValuesAsQueryTokens().get(1).getValuesAsQueryTokens().get(0).getValue());

hapi-fhir-structures-r4/pom.xml

@@ -182,11 +182,21 @@
 			<scope>test</scope>
 		</dependency>
 
+		<dependency>
+			<groupId>org.springframework</groupId>
+			<artifactId>spring-context</artifactId>
+			<scope>test</scope>
+		</dependency>
 		<dependency>
 			<groupId>org.springframework</groupId>
 			<artifactId>spring-web</artifactId>
 			<scope>test</scope>
 		</dependency>
+		<dependency>
+			<groupId>org.springframework</groupId>
+			<artifactId>spring-context</artifactId>
+			<scope>test</scope>
+		</dependency>
 	</dependencies>
 
 	<reporting>

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/server/exceptions/ExceptionPropertiesTest.java

@@ -15,6 +15,12 @@ import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.rest.client.exceptions.FhirClientConnectionException;
 import ca.uhn.fhir.rest.client.exceptions.FhirClientInappropriateForServerException;
 import ca.uhn.fhir.util.TestUtil;
+import org.springframework.beans.factory.config.BeanDefinition;
+import org.springframework.context.annotation.ClassPathScanningCandidateComponentProvider;
+import org.springframework.core.type.filter.AssignableTypeFilter;
+import org.springframework.core.type.filter.TypeFilter;
+
+import java.util.Set;
 
 public class ExceptionPropertiesTest {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExceptionPropertiesTest.class);
@@ -37,13 +43,15 @@ public class ExceptionPropertiesTest {
 	@SuppressWarnings("deprecation")
 	@Test
 	public void testExceptionsAreGood() throws Exception {
-		ImmutableSet<ClassInfo> classes = ClassPath.from(Thread.currentThread().getContextClassLoader()).getTopLevelClasses(BaseServerResponseException.class.getPackage().getName());
+		ClassPathScanningCandidateComponentProvider scanner = new ClassPathScanningCandidateComponentProvider(false);
-		assertTrue(classes.size() > 5);
+		scanner.addIncludeFilter(new AssignableTypeFilter(BaseServerResponseException.class));
+		Set<BeanDefinition> classes = scanner.findCandidateComponents(BaseServerResponseException.class.getPackage().getName());
+		assertTrue(classes.toString(), classes.size() > 5);
 
-		for (ClassInfo classInfo : classes) {
+		for (BeanDefinition classInfo : classes) {
-			ourLog.info("Scanning {}", classInfo.getName());
+			ourLog.info("Scanning {}", classInfo.getBeanClassName());
 
-			Class<?> next = Class.forName(classInfo.getName());
+			Class<?> next = Class.forName(classInfo.getBeanClassName());
 			assertNotNull(next);
 
 			if (next == getClass()) {
@@ -69,7 +77,7 @@ public class ExceptionPropertiesTest {
 			try {
 				next.getConstructor(String.class, IBaseOperationOutcome.class);
 			} catch (NoSuchMethodException e) {
-				fail(classInfo.getName() + " has no constructor with params: (String, IBaseOperationOutcome)");
+				fail(classInfo.getBeanClassName() + " has no constructor with params: (String, IBaseOperationOutcome)");
 			}
 		}
 

hapi-fhir-validation/src/main/java/org/hl7/fhir/r4/validation/InstanceValidator.java

@@ -1340,15 +1340,27 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
 		String encoded = e.primitiveValue();
 		if (isNotBlank(encoded)) {
 			/*
-			 * Note: Regex comes from: https://stackoverflow.com/questions/8571501/how-to-check-whether-the-string-is-base64-encoded-or-not
-			 *
 			 * Technically this is not bulletproof as some invalid base64 won't be caught,
 			 * but I think it's good enough. The original code used Java8 Base64 decoder
 			 * but I've replaced it with a regex for 2 reasons:
 			 * 1. This code will run on any version of Java
 			 * 2. This code doesn't actually decode, which is much easier on memory use for big payloads
 			 */
-			if (!encoded.matches("^([A-Za-z0-9+/]{4})*([A-Za-z0-9+/]{4}|[A-Za-z0-9+/]{3}=|[A-Za-z0-9+/]{2}==)$")) {
+			int charCount = 0;
+			for (int i = 0; i < encoded.length(); i++) {
+				char nextChar = encoded.charAt(i);
+				if (Character.isWhitespace(nextChar)) {
+					continue;
+				}
+				if (Character.isLetterOrDigit(nextChar)) {
+					charCount++;
+				}
+				if (nextChar == '/' || nextChar == '=' || nextChar == '+') {
+					charCount++;
+				}
+			}
+
+			if (charCount > 0 && charCount % 4 != 0) {
 				String value = encoded.length() < 100 ? encoded : "(snip)";
 				rule(errors, IssueType.INVALID, e.line(), e.col(), path, false, "The value \"{0}\" is not a valid Base64 value", value);
 			}

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

@@ -17,6 +17,7 @@ import java.io.InputStream;
 import java.util.*;
 import java.util.zip.GZIPInputStream;
 
+import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.validation.FhirValidator;
 import ca.uhn.fhir.validation.ResultSeverityEnum;
 import ca.uhn.fhir.validation.SingleValidationMessage;
@@ -247,6 +248,15 @@ public class FhirInstanceValidatorR4Test {
 
 	}
 
+	@Test
+	public void testLargeBase64() throws IOException {
+		String input = IOUtils.toString(FhirInstanceValidatorR4Test.class.getResourceAsStream("/r4/diagnosticreport-example-gingival-mass.json"), Constants.CHARSET_UTF8);
+		ValidationResult output = myVal.validateWithResult(input);
+		List<SingleValidationMessage> errors = logResultsAndReturnNonInformationalOnes(output);
+		assertEquals(0, errors.size());
+	}
+
+
 	@Test @Ignore
 	public void testValidateDocument() throws Exception {
 		String vsContents = IOUtils.toString(FhirInstanceValidatorR4Test.class.getResourceAsStream("/sample-document.xml"), "UTF-8");