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org.hl7.fhir.core
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Merge branch 'master' of https://github.com/hapifhir/org.hl7.fhir.core

This commit is contained in:
Grahame Grieve 2020-04-17 10:58:54 +10:00
parent 4d30314a3d b4a9765aa0
commit ec517834b0
18 changed files with 366 additions and 26 deletions
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8
org.hl7.fhir.dstu2/pom.xml
View File

@ -95,7 +95,13 @@
<artifactId>Saxon-HE</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter</artifactId>
<version>RELEASE</version>
<scope>test</scope>
</dependency>
</dependencies>
</dependencies>
</project>

22
org.hl7.fhir.dstu2/src/main/java/org/hl7/fhir/dstu2/model/Base64BinaryType.java
View File

@ -49,6 +49,7 @@ package org.hl7.fhir.dstu2.model;
*/
import ca.uhn.fhir.parser.DataFormatException;
import org.apache.commons.codec.binary.Base64;
import ca.uhn.fhir.model.api.annotation.DatatypeDef;
@ -74,11 +75,17 @@ public class Base64BinaryType extends PrimitiveType<byte[]> {
public Base64BinaryType(String theValue) {
super();
// Null values still result in non-null instance being created
if (theValue != null) checkValidBase64(theValue);
setValueAsString(theValue);
}
protected byte[] parse(String theValue) {
return Base64.decodeBase64(theValue.getBytes(ca.uhn.fhir.rest.api.Constants.CHARSET_UTF8));
if (theValue != null) {
return Base64.decodeBase64(theValue.getBytes(ca.uhn.fhir.rest.api.Constants.CHARSET_UTF8));
} else {
return null;
}
}
protected String encode(byte[] theValue) {
@ -96,4 +103,17 @@ public class Base64BinaryType extends PrimitiveType<byte[]> {
public String fhirType() {
return "base64Binary";
}
/**
* Checks if the passed in String is a valid {@link Base64} encoded String. Will throw a {@link DataFormatException} if not
* formatted correctly.
*
* @param toCheck {@link String} to check if valid {@link Base64}
* @throws DataFormatException
*/
public void checkValidBase64(String toCheck) throws DataFormatException {
if (!Base64.isBase64(toCheck.getBytes())) {
throw new DataFormatException("");
}
}
}

38
org.hl7.fhir.dstu2/src/test/java/org/hl7/fhir/dstu2/model/Base64BinaryTypeTest.java Normal file
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@ -0,0 +1,38 @@
package org.hl7.fhir.dstu2.model;
import ca.uhn.fhir.parser.DataFormatException;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;
import static org.junit.jupiter.api.Assertions.*;
class Base64BinaryTypeTest {
@Test
@DisplayName("Passing a non Base64 encoded String to constructor causes exception.")
public void testNonBase64String() {
String nonBase64 = "Picard was the best starship captain.";
assertThrows(DataFormatException.class, () -> new Base64BinaryType(nonBase64));
}
@Test
@DisplayName("Null String value creates non-null instance with null value.")
public void testNullInstance() throws DataFormatException {
String v = null;
Base64BinaryType b64 = new Base64BinaryType(v);
Assertions.assertNotNull(b64);
Assertions.assertNull(b64.getValue());
Assertions.assertNull(b64.getValueAsString());
}
@Test
@DisplayName("Valid Base64 String creates non-null instance with non-null values.")
public void testValid() {
String v = "dGhpcyBpcyB2YWxpZCBiYXNlNjQ=";
Base64BinaryType b64 = new Base64BinaryType(v);
Assertions.assertNotNull(b64);
Assertions.assertNotNull(b64.getValue());
Assertions.assertEquals(v, b64.asStringValue());
}
}

8
org.hl7.fhir.dstu2016may/pom.xml
View File

@ -109,7 +109,13 @@
<artifactId>Saxon-HE</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter</artifactId>
<version>RELEASE</version>
<scope>test</scope>
</dependency>
</dependencies>
</dependencies>
</project>

22
org.hl7.fhir.dstu2016may/src/main/java/org/hl7/fhir/dstu2016may/model/Base64BinaryType.java
View File

@ -49,6 +49,7 @@ package org.hl7.fhir.dstu2016may.model;
*/
import ca.uhn.fhir.parser.DataFormatException;
import org.apache.commons.codec.binary.Base64;
import ca.uhn.fhir.model.api.annotation.DatatypeDef;
@ -75,11 +76,17 @@ public class Base64BinaryType extends PrimitiveType<byte[]> {
public Base64BinaryType(String theValue) {
super();
// Null values still result in non-null instance being created
if (theValue != null) checkValidBase64(theValue);
setValueAsString(theValue);
}
protected byte[] parse(String theValue) {
return Base64.decodeBase64(theValue.getBytes(ca.uhn.fhir.rest.api.Constants.CHARSET_UTF8));
if (theValue != null) {
return Base64.decodeBase64(theValue.getBytes(ca.uhn.fhir.rest.api.Constants.CHARSET_UTF8));
} else {
return null;
}
}
protected String encode(byte[] theValue) {
@ -97,4 +104,17 @@ public class Base64BinaryType extends PrimitiveType<byte[]> {
public String fhirType() {
return "base64Binary";
}
/**
* Checks if the passed in String is a valid {@link Base64} encoded String. Will throw a {@link DataFormatException} if not
* formatted correctly.
*
* @param toCheck {@link String} to check if valid {@link Base64}
* @throws DataFormatException
*/
public void checkValidBase64(String toCheck) throws DataFormatException {
if (!Base64.isBase64(toCheck.getBytes())) {
throw new DataFormatException("");
}
}
}

38
org.hl7.fhir.dstu2016may/src/test/java/org/hl7/fhir/dstu2016may/model/Base64BinaryTypeTest.java Normal file
View File

@ -0,0 +1,38 @@
package org.hl7.fhir.dstu2016may.model;
import ca.uhn.fhir.parser.DataFormatException;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;
import static org.junit.jupiter.api.Assertions.*;
class Base64BinaryTypeTest {
@Test
@DisplayName("Passing a non Base64 encoded String to constructor causes exception.")
public void testNonBase64String() {
String nonBase64 = "Picard was the best starship captain.";
assertThrows(DataFormatException.class, () -> new Base64BinaryType(nonBase64));
}
@Test
@DisplayName("Null String value creates non-null instance with null value.")
public void testNullInstance() throws DataFormatException {
String v = null;
Base64BinaryType b64 = new Base64BinaryType(v);
Assertions.assertNotNull(b64);
Assertions.assertNull(b64.getValue());
Assertions.assertNull(b64.getValueAsString());
}
@Test
@DisplayName("Valid Base64 String creates non-null instance with non-null values.")
public void testValid() {
String v = "dGhpcyBpcyB2YWxpZCBiYXNlNjQ=";
Base64BinaryType b64 = new Base64BinaryType(v);
Assertions.assertNotNull(b64);
Assertions.assertNotNull(b64.getValue());
Assertions.assertEquals(v, b64.asStringValue());
}
}

6
org.hl7.fhir.dstu3/pom.xml
View File

@ -95,6 +95,12 @@
<artifactId>Saxon-HE</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter</artifactId>
<version>RELEASE</version>
<scope>test</scope>
</dependency>
</dependencies>

23
org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/model/Base64BinaryType.java
View File

@ -51,6 +51,7 @@ package org.hl7.fhir.dstu3.model;
import ca.uhn.fhir.model.api.IElement;
import ca.uhn.fhir.model.api.annotation.DatatypeDef;
import ca.uhn.fhir.parser.DataFormatException;
import org.apache.commons.codec.binary.Base64;
import org.hl7.fhir.instance.model.api.IBaseHasExtensions;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
@ -83,11 +84,17 @@ public class Base64BinaryType extends PrimitiveType<byte[]> implements IPrimitiv
public Base64BinaryType(String theValue) {
super();
// Null values still result in non-null instance being created
if (theValue != null) checkValidBase64(theValue);
setValueAsString(theValue);
}
protected byte[] parse(String theValue) {
return Base64.decodeBase64(theValue.getBytes(ca.uhn.fhir.rest.api.Constants.CHARSET_UTF8));
if (theValue != null) {
return Base64.decodeBase64(theValue.getBytes(ca.uhn.fhir.rest.api.Constants.CHARSET_UTF8));
} else {
return null;
}
}
protected String encode(byte[] theValue) {
@ -128,6 +135,7 @@ public class Base64BinaryType extends PrimitiveType<byte[]> implements IPrimitiv
@Override
public void setValueAsString(String theValue) throws IllegalArgumentException {
fromStringValue(theValue);
setValue(parse(theValue));
}
@ -153,5 +161,16 @@ public class Base64BinaryType extends PrimitiveType<byte[]> implements IPrimitiv
return ca.uhn.fhir.util.ElementUtil.isEmpty(id, extension) && !hasValue();
}
/**
* Checks if the passed in String is a valid {@link Base64} encoded String. Will throw a {@link DataFormatException} if not
* formatted correctly.
*
* @param toCheck {@link String} to check if valid {@link Base64}
* @throws DataFormatException
*/
public void checkValidBase64(String toCheck) throws DataFormatException {
if (!Base64.isBase64(toCheck.getBytes())) {
throw new DataFormatException("");
}
}
}

38
org.hl7.fhir.dstu3/src/test/java/org/hl7/fhir/dstu3/model/Base64BinaryTypeTest.java Normal file
View File

@ -0,0 +1,38 @@
package org.hl7.fhir.dstu3.model;
import ca.uhn.fhir.parser.DataFormatException;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;
import static org.junit.jupiter.api.Assertions.*;
class Base64BinaryTypeTest {
@Test
@DisplayName("Passing a non Base64 encoded String to constructor causes exception.")
public void testNonBase64String() {
String nonBase64 = "Picard was the best starship captain.";
assertThrows(DataFormatException.class, () -> new Base64BinaryType(nonBase64));
}
@Test
@DisplayName("Null String value creates non-null instance with null value.")
public void testNullInstance() throws DataFormatException {
String v = null;
Base64BinaryType b64 = new Base64BinaryType(v);
Assertions.assertNotNull(b64);
Assertions.assertNull(b64.getValue());
Assertions.assertNull(b64.getValueAsString());
}
@Test
@DisplayName("Valid Base64 String creates non-null instance with non-null values.")
public void testValid() {
String v = "dGhpcyBpcyB2YWxpZCBiYXNlNjQ=";
Base64BinaryType b64 = new Base64BinaryType(v);
Assertions.assertNotNull(b64);
Assertions.assertNotNull(b64.getValue());
Assertions.assertEquals(v, b64.asStringValue());
}
}

6
org.hl7.fhir.r4/pom.xml
View File

@ -101,6 +101,12 @@
<artifactId>Saxon-HE</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter</artifactId>
<version>RELEASE</version>
<scope>test</scope>
</dependency>
</dependencies>

22
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/model/Base64BinaryType.java
View File

@ -50,6 +50,7 @@ package org.hl7.fhir.r4.model;
import ca.uhn.fhir.model.api.IElement;
import ca.uhn.fhir.parser.DataFormatException;
import org.apache.commons.codec.binary.Base64;
import ca.uhn.fhir.model.api.annotation.DatatypeDef;
@ -84,11 +85,17 @@ public class Base64BinaryType extends PrimitiveType<byte[]> implements IPrimitiv
public Base64BinaryType(String theValue) {
super();
// Null values still result in non-null instance being created
if (theValue != null) checkValidBase64(theValue);
setValueAsString(theValue);
}
protected byte[] parse(String theValue) {
return Base64.decodeBase64(theValue.getBytes(ca.uhn.fhir.rest.api.Constants.CHARSET_UTF8));
if (theValue != null) {
return Base64.decodeBase64(theValue.getBytes(ca.uhn.fhir.rest.api.Constants.CHARSET_UTF8));
} else {
return null;
}
}
protected String encode(byte[] theValue) {
@ -129,6 +136,7 @@ public class Base64BinaryType extends PrimitiveType<byte[]> implements IPrimitiv
@Override
public void setValueAsString(String theValue) throws IllegalArgumentException {
fromStringValue(theValue);
setValue(parse(theValue));
}
@ -154,4 +162,16 @@ public class Base64BinaryType extends PrimitiveType<byte[]> implements IPrimitiv
return ca.uhn.fhir.util.ElementUtil.isEmpty(id, extension) && !hasValue();
}
/**
* Checks if the passed in String is a valid {@link Base64} encoded String. Will throw a {@link DataFormatException} if not
* formatted correctly.
*
* @param toCheck {@link String} to check if valid {@link Base64}
* @throws DataFormatException
*/
public void checkValidBase64(String toCheck) throws DataFormatException {
if (!Base64.isBase64(toCheck.getBytes())) {
throw new DataFormatException("");
}
}
}

38
org.hl7.fhir.r4/src/test/java/org/hl7/fhir/r4/model/Base64BinaryTypeTest.java Normal file
View File

@ -0,0 +1,38 @@
package org.hl7.fhir.r4.model;
import ca.uhn.fhir.parser.DataFormatException;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;
import static org.junit.jupiter.api.Assertions.*;
class Base64BinaryTypeTest {
@Test
@DisplayName("Passing a non Base64 encoded String to constructor causes exception.")
public void testNonBase64String() {
String nonBase64 = "Picard was the best starship captain.";
assertThrows(DataFormatException.class, () -> new Base64BinaryType(nonBase64));
}
@Test
@DisplayName("Null String value creates non-null instance with null value.")
public void testNullInstance() throws DataFormatException {
String v = null;
Base64BinaryType b64 = new Base64BinaryType(v);
Assertions.assertNotNull(b64);
Assertions.assertNull(b64.getValue());
Assertions.assertNull(b64.getValueAsString());
}
@Test
@DisplayName("Valid Base64 String creates non-null instance with non-null values.")
public void testValid() {
String v = "dGhpcyBpcyB2YWxpZCBiYXNlNjQ=";
Base64BinaryType b64 = new Base64BinaryType(v);
Assertions.assertNotNull(b64);
Assertions.assertNotNull(b64.getValue());
Assertions.assertEquals(v, b64.asStringValue());
}
}

4
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/formats/JsonParser.java
View File

@ -54,6 +54,7 @@ package org.hl7.fhir.r5.formats;
import ca.uhn.fhir.parser.DataFormatException;
import org.hl7.fhir.r5.model.*;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.xhtml.XhtmlNode;
@ -160,8 +161,7 @@ public class JsonParser extends JsonParserBase {
}
protected Base64BinaryType parseBase64Binary(String v) throws IOException, FHIRFormatError {
Base64BinaryType res = new Base64BinaryType(v);
return res;
return new Base64BinaryType(v);
}
protected UnsignedIntType parseUnsignedInt(String v) throws IOException, FHIRFormatError {

24
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/Base64BinaryType.java
View File

@ -51,8 +51,8 @@ package org.hl7.fhir.r5.model;
import ca.uhn.fhir.model.api.IElement;
import ca.uhn.fhir.model.api.annotation.DatatypeDef;
import ca.uhn.fhir.parser.DataFormatException;
import org.apache.commons.codec.binary.Base64;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.instance.model.api.IBaseHasExtensions;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
@ -84,11 +84,17 @@ public class Base64BinaryType extends PrimitiveType<byte[]> implements IPrimitiv
public Base64BinaryType(String theValue) {
super();
// Null values still result in non-null instance being created
if (theValue != null) checkValidBase64(theValue);
setValueAsString(theValue);
}
protected byte[] parse(String theValue) {
return Base64.decodeBase64(theValue.getBytes(ca.uhn.fhir.rest.api.Constants.CHARSET_UTF8));
if (theValue != null) {
return Base64.decodeBase64(theValue.getBytes(ca.uhn.fhir.rest.api.Constants.CHARSET_UTF8));
} else {
return null;
}
}
protected String encode(byte[] theValue) {
@ -129,6 +135,7 @@ public class Base64BinaryType extends PrimitiveType<byte[]> implements IPrimitiv
@Override
public void setValueAsString(String theValue) throws IllegalArgumentException {
fromStringValue(theValue);
setValue(parse(theValue));
}
@ -158,4 +165,17 @@ public class Base64BinaryType extends PrimitiveType<byte[]> implements IPrimitiv
public String primitiveValue() {
return encode(myValue);
}
/**
* Checks if the passed in String is a valid {@link Base64} encoded String. Will throw a {@link DataFormatException} if not
* formatted correctly.
*
* @param toCheck {@link String} to check if valid {@link Base64}
* @throws DataFormatException
*/
public void checkValidBase64(String toCheck) throws DataFormatException {
if (!Base64.isBase64(toCheck.getBytes())) {
throw new DataFormatException("");
}
}
}

40
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/NarrativeGenerator.java
View File

@ -59,6 +59,8 @@ import java.util.ArrayList;
import java.util.Collections;
import java.util.Date;
import java.util.HashMap;
import com.google.common.collect.Multimap;
import com.google.common.collect.HashMultimap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
@ -3385,7 +3387,7 @@ public class NarrativeGenerator implements INarrativeGenerator {
@SuppressWarnings("rawtypes")
private void generateVersionNotice(XhtmlNode x, ValueSetExpansionComponent expansion) {
Map<String, String> versions = new HashMap<String, String>();
Multimap<String, String> versions = HashMultimap.create();
for (ValueSetExpansionParameterComponent p : expansion.getParameter()) {
if (p.getName().equals("version")) {
String[] parts = ((PrimitiveType) p.getValue()).asStringValue().split("\\|");
@ -3393,20 +3395,30 @@ public class NarrativeGenerator implements INarrativeGenerator {
versions.put(parts[0], parts[1]);
}
}
if (versions.size() > 1) {
XhtmlNode div = x.div().style("border: black 1px dotted; background-color: #EEEEEE; padding: 8px; margin-bottom: 8px");
div.para().tx("Expansion based on: ");
XhtmlNode ul = div.ul();
for (String s : versions.keySet()) { // though there'll only be one
expRef(ul.li(), s, versions.get(s));
if (versions.size() > 0) {
XhtmlNode div = null;
XhtmlNode ul = null;
boolean first = true;
for (String s : versions.keySet()) {
if (versions.size() == 1 && versions.get(s).size() == 1) {
for (String v : versions.get(s)) { // though there'll only be one
XhtmlNode p = x.para().style("border: black 1px dotted; background-color: #EEEEEE; padding: 8px; margin-bottom: 8px");
p.tx("Expansion based on ");
expRef(p, s, v);
}
} else {
for (String v : versions.get(s)) {
if (first) {
div = x.div().style("border: black 1px dotted; background-color: #EEEEEE; padding: 8px; margin-bottom: 8px");
div.para().tx("Expansion based on: ");
ul = div.ul();
first = false;
}
expRef(ul.li(), s, v);
}
}
}
} else if (versions.size() == 1) {
XhtmlNode p = x.para().style("border: black 1px dotted; background-color: #EEEEEE; padding: 8px; margin-bottom: 8px");
p.tx("Expansion based on ");
for (String s : versions.keySet()) { // though there'll only be one
expRef(p, s, versions.get(s));
}
}
}
}
private void expRef(XhtmlNode x, String u, String v) {

39
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/model/Base64BinaryTypeTest.java Normal file
View File

@ -0,0 +1,39 @@
package org.hl7.fhir.r5.model;
import ca.uhn.fhir.parser.DataFormatException;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;
import static org.junit.jupiter.api.Assertions.*;
class Base64BinaryTypeTest {
@Test
@DisplayName("Passing a non Base64 encoded String to constructor causes exception.")
public void testNonBase64String() {
String nonBase64 = "Picard was the best starship captain.";
assertThrows(DataFormatException.class, () -> new Base64BinaryType(nonBase64));
}
@Test
@DisplayName("Null String value creates non-null instance with null value.")
public void testNullInstance() throws DataFormatException {
String v = null;
Base64BinaryType b64 = new Base64BinaryType(v);
Assertions.assertNotNull(b64);
Assertions.assertNull(b64.getValue());
Assertions.assertNull(b64.getValueAsString());
}
@Test
@DisplayName("Valid Base64 String creates non-null instance with non-null values.")
public void testValid() {
String v = "dGhpcyBpcyB2YWxpZCBiYXNlNjQ=";
Base64BinaryType b64 = new Base64BinaryType(v);
Assertions.assertNotNull(b64);
Assertions.assertNotNull(b64.getValue());
Assertions.assertEquals(v, b64.asStringValue());
}
}

4
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/xhtml/XhtmlNode.java
View File

@ -50,6 +50,7 @@ package org.hl7.fhir.utilities.xhtml;
import java.io.IOException;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
@ -67,7 +68,8 @@ public class XhtmlNode implements IBaseXhtml {
private static final long serialVersionUID = -4362547161441436492L;
public static class Location {
public static class Location implements Serializable {
private static final long serialVersionUID = -4079302502900219721L;
private int line;
private int column;
public Location(int line, int column) {

12
org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/tests/XhtmlNodeTest.java
View File

@ -1,5 +1,8 @@
package org.hl7.fhir.utilities.tests;
import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.io.ObjectOutputStream;
import org.hl7.fhir.utilities.xhtml.XhtmlNode;
import org.junit.Test;
import org.slf4j.Logger;
@ -71,4 +74,13 @@ public class XhtmlNodeTest {
assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\"><img src=\"http://pbs.twimg.com/profile_images/544507893991485440/r_vo3uj2_bigger.png\" alt=\"Twitter Avatar\"/>@fhirabend</div>", output);
}
@Test
public void testSerializable() throws IOException {
XhtmlNode node = new XhtmlNode();
node.setValueAsString("<?xml version=\"1.0\" encoding=\"UTF-8\"?><div xmlns=\"http://www.w3.org/1999/xhtml\">Test</div>");
ByteArrayOutputStream bout = new ByteArrayOutputStream();
ObjectOutputStream oout = new ObjectOutputStream(bout);
oout.writeObject(node);
}
}