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Merge pull request #179 from hapifhir/testing_updates 

Testing updates
This commit is contained in:
Grahame Grieve 2020-04-24 07:20:44 +10:00 committed by GitHub
parent 5d0fd426be c829de2f86
commit 83ea7fefa5
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GPG Key ID: 4AEE18F83AFDEB23
79 changed files with 3014 additions and 2362 deletions
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173
org.hl7.fhir.dstu2/pom.xml
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@ -1,6 +1,6 @@
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
@ -9,99 +9,92 @@
<relativePath>../pom.xml</relativePath>
</parent>
<artifactId>org.hl7.fhir.dstu2</artifactId>
<packaging>bundle</packaging>
<artifactId>org.hl7.fhir.dstu2</artifactId>
<packaging>bundle</packaging>
<dependencies>
<dependencies>
<!-- HAPI Dependencies -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-base</artifactId>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.utilities</artifactId>
</dependency>
<!-- UCUM -->
<dependency>
<groupId>org.fhir</groupId>
<artifactId>ucum</artifactId>
<version>1.0.2</version>
<optional>true</optional>
</dependency>
<!-- XML Parsers -->
<dependency>
<groupId>xpp3</groupId>
<artifactId>xpp3</artifactId>
<optional>true</optional>
</dependency>
<dependency>
<groupId>xpp3</groupId>
<artifactId>xpp3_xpath</artifactId>
<optional>true</optional>
</dependency>
<!-- Apache POI -->
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi</artifactId>
<version>4.0.1</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi-ooxml</artifactId>
<version>4.0.1</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi-ooxml-schemas</artifactId>
<version>4.0.1</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>ooxml-schemas</artifactId>
<version>1.4</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.antlr</groupId>
<artifactId>ST4</artifactId>
<version>4.1</version>
<optional>true</optional>
</dependency>
<!-- HTTP Client -->
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
<optional>true</optional>
</dependency>
<!-- Test dependencies -->
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>net.sf.saxon</groupId>
<artifactId>Saxon-HE</artifactId>
<scope>test</scope>
</dependency>
<!-- HAPI Dependencies -->
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter</artifactId>
<version>RELEASE</version>
<scope>test</scope>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-base</artifactId>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.utilities</artifactId>
</dependency>
<!-- UCUM -->
<dependency>
<groupId>org.fhir</groupId>
<artifactId>ucum</artifactId>
<version>1.0.2</version>
<optional>true</optional>
</dependency>
<!-- XML Parsers -->
<dependency>
<groupId>xpp3</groupId>
<artifactId>xpp3</artifactId>
<optional>true</optional>
</dependency>
<dependency>
<groupId>xpp3</groupId>
<artifactId>xpp3_xpath</artifactId>
<optional>true</optional>
</dependency>
<!-- Apache POI -->
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi</artifactId>
<version>4.0.1</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi-ooxml</artifactId>
<version>4.0.1</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi-ooxml-schemas</artifactId>
<version>4.0.1</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>ooxml-schemas</artifactId>
<version>1.4</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.antlr</groupId>
<artifactId>ST4</artifactId>
<version>4.1</version>
<optional>true</optional>
</dependency>
<!-- HTTP Client -->
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
<optional>true</optional>
</dependency>
<!-- Test dependencies -->
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>net.sf.saxon</groupId>
<artifactId>Saxon-HE</artifactId>
<scope>test</scope>
</dependency>
</dependencies>
</project>

25
org.hl7.fhir.dstu2/src/test/java/org/hl7/fhir/dstu2/test/ClientUtilsTest.java
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@ -1,25 +0,0 @@
package org.hl7.fhir.dstu2.test;
import org.junit.After;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.BeforeClass;
public class ClientUtilsTest {
@BeforeClass
public static void setUpBeforeClass() {
}
@AfterClass
public static void tearDownAfterClass() {
}
@Before
public void setUp() {
}
@After
public void tearDown() {
}
}

165
org.hl7.fhir.dstu2/src/test/java/org/hl7/fhir/dstu2/test/FluentPathTests.java
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@ -1,102 +1,51 @@
package org.hl7.fhir.dstu2.test;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import javax.xml.parsers.ParserConfigurationException;
import org.hl7.fhir.dstu2.formats.XmlParser;
import org.hl7.fhir.dstu2.model.Base;
import org.hl7.fhir.dstu2.model.BooleanType;
import org.hl7.fhir.dstu2.model.ElementDefinition;
import org.hl7.fhir.dstu2.model.*;
import org.hl7.fhir.dstu2.model.ElementDefinition.ElementDefinitionConstraintComponent;
import org.hl7.fhir.dstu2.model.ExpressionNode;
import org.hl7.fhir.dstu2.model.PrimitiveType;
import org.hl7.fhir.dstu2.model.Resource;
import org.hl7.fhir.dstu2.model.StructureDefinition;
import org.hl7.fhir.dstu2.utils.FHIRPathEngine;
import org.hl7.fhir.dstu2.utils.SimpleWorkerContext;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.PathEngineException;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.junit.runners.Parameterized;
import org.junit.runners.Parameterized.Parameters;
import org.junit.jupiter.api.*;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.Arguments;
import org.junit.jupiter.params.provider.MethodSource;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
import org.xml.sax.SAXException;
import junit.framework.Assert;
import javax.xml.parsers.ParserConfigurationException;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.stream.Stream;
@RunWith(Parameterized.class)
@TestInstance(TestInstance.Lifecycle.PER_CLASS)
@Disabled // TODO Need to find and fix files referenced here
public class FluentPathTests {
private static FHIRPathEngine fp;
private FHIRPathEngine fp;
@Parameters(name = "{index}: file {0}")
public static Iterable<Object[]> data() throws ParserConfigurationException, SAXException, IOException {
Document dom = XMLUtil.parseFileToDom("C:\\work\\fluentpath\\tests\\dstu2\\tests-fhir-r2.xml");
List<Element> list = new ArrayList<Element>();
List<Element> groups = new ArrayList<Element>();
XMLUtil.getNamedChildren(dom.getDocumentElement(), "group", groups);
for (Element g : groups) {
XMLUtil.getNamedChildren(g, "test", list);
}
List<Object[]> objects = new ArrayList<Object[]>(list.size());
for (Element e : list) {
objects.add(new Object[] { getName(e), e });
}
return objects;
}
private static Object getName(Element e) {
String s = e.getAttribute("name");
if (Utilities.noString(s)) {
Element p = (Element) e.getParentNode();
int ndx = 0;
for (int i = 0; i < p.getChildNodes().getLength(); i++) {
Node c = p.getChildNodes().item(i);
if (c == e)
break;
else if (c instanceof Element)
ndx++;
}
s = p.getAttribute("name")+" - "+Integer.toString(ndx+1);
}
return s;
}
private final Element test;
private final String name;
public FluentPathTests(String name, Element e) {
this.name = name;
this.test = e;
@BeforeAll
public void setup() throws IOException {
TestingUtilities.context = SimpleWorkerContext.fromPack("C:\\work\\org.hl7.fhir.dstu2\\build\\publish\\validation-min.xml.zip");
this.fp = new FHIRPathEngine(TestingUtilities.context);
}
@SuppressWarnings("deprecation")
@Test
public void test() throws FileNotFoundException, IOException, FHIRException, PathEngineException, DefinitionException {
if (TestingUtilities.context == null)
TestingUtilities.context = SimpleWorkerContext.fromPack("C:\\work\\org.hl7.fhir.dstu2\\build\\publish\\validation-min.xml.zip");
if (fp == null)
fp = new FHIRPathEngine(TestingUtilities.context);
String input = test.getAttribute("inputfile");
String expression = XMLUtil.getNamedChild(test, "expression").getTextContent();
boolean fail = "true".equals(XMLUtil.getNamedChild(test, "expression").getAttribute("invalid"));
@ParameterizedTest(name = "{index}: file {0}")
@MethodSource("data")
public void test(String name, Element element) throws IOException, FHIRException {
String input = element.getAttribute("inputfile");
String expression = XMLUtil.getNamedChild(element, "expression").getTextContent();
boolean fail = "true".equals(XMLUtil.getNamedChild(element, "expression").getAttribute("invalid"));
Resource res = null;
List<Base> outcome = new ArrayList<Base>();
ExpressionNode node = fp.parse(expression);
@ -108,12 +57,12 @@ public class FluentPathTests {
fp.check(res, res.getResourceType().toString(), res.getResourceType().toString(), node);
}
outcome = fp.evaluate(res, node);
Assert.assertTrue(String.format("Expected exception parsing %s", expression), !fail);
Assertions.assertTrue(!fail, String.format("Expected exception parsing %s", expression));
} catch (Exception e) {
Assert.assertTrue(String.format("Unexpected exception parsing %s: "+e.getMessage(), expression), fail);
Assertions.assertTrue(fail, String.format("Unexpected exception parsing %s: " + e.getMessage(), expression));
}
if ("true".equals(test.getAttribute("predicate"))) {
if ("true".equals(element.getAttribute("predicate"))) {
boolean ok = fp.convertToBoolean(outcome);
outcome.clear();
outcome.add(new BooleanType(ok));
@ -122,18 +71,18 @@ public class FluentPathTests {
System.out.println(fp.takeLog());
List<Element> expected = new ArrayList<Element>();
XMLUtil.getNamedChildren(test, "output", expected);
Assert.assertTrue(String.format("Expected %d objects but found %d", expected.size(), outcome.size()), outcome.size() == expected.size());
XMLUtil.getNamedChildren(element, "output", expected);
Assertions.assertTrue(outcome.size() == expected.size(), String.format("Expected %d objects but found %d", expected.size(), outcome.size()));
for (int i = 0; i < Math.min(outcome.size(), expected.size()); i++) {
String tn = expected.get(i).getAttribute("type");
if (!Utilities.noString(tn)) {
Assert.assertTrue(String.format("Outcome %d: Type should be %s but was %s", i, tn, outcome.get(i).fhirType()), tn.equals(outcome.get(i).fhirType()));
Assertions.assertTrue(tn.equals(outcome.get(i).fhirType()), String.format("Outcome %d: Type should be %s but was %s", i, tn, outcome.get(i).fhirType()));
}
String v = expected.get(i).getTextContent();
if (!Utilities.noString(v)) {
Assert.assertTrue(String.format("Outcome %d: Value should be a primitive type but was %s", i, outcome.get(i).fhirType()), outcome.get(i) instanceof PrimitiveType);
Assert.assertTrue(String.format("Outcome %d: Value should be %s but was %s", i, v, outcome.get(i).toString()), v.equals(((PrimitiveType)outcome.get(i)).asStringValue()));
}
Assertions.assertTrue(outcome.get(i) instanceof PrimitiveType, String.format("Outcome %d: Value should be a primitive type but was %s", i, outcome.get(i).fhirType()));
Assertions.assertTrue(v.equals(((PrimitiveType) outcome.get(i)).asStringValue()), String.format("Outcome %d: Value should be %s but was %s", i, v, outcome.get(i).toString()));
}
}
}
@ -152,7 +101,43 @@ public class FluentPathTests {
}
}
}
Assert.assertTrue(false);
Assertions.assertTrue(false);
}
public static Stream<Arguments> data() throws ParserConfigurationException, SAXException, IOException {
Document dom = XMLUtil.parseFileToDom("C:\\work\\fluentpath\\tests\\dstu2\\tests-fhir-r2.xml");
List<Element> list = new ArrayList<Element>();
List<Element> groups = new ArrayList<Element>();
XMLUtil.getNamedChildren(dom.getDocumentElement(), "group", groups);
for (Element g : groups) {
XMLUtil.getNamedChildren(g, "test", list);
}
List<Arguments> objects = new ArrayList<>();
for (Element e : list) {
objects.add(Arguments.of(getName(e), e));
}
return objects.stream();
}
private static Object getName(Element e) {
String s = e.getAttribute("name");
if (Utilities.noString(s)) {
Element p = (Element) e.getParentNode();
int ndx = 0;
for (int i = 0; i < p.getChildNodes().getLength(); i++) {
Node c = p.getChildNodes().item(i);
if (c == e)
break;
else if (c instanceof Element)
ndx++;
}
s = p.getAttribute("name") + " - " + Integer.toString(ndx + 1);
}
return s;
}
private void testExpression(StructureDefinition sd, ElementDefinition ed, ElementDefinitionConstraintComponent inv) throws FHIRException {
@ -163,9 +148,9 @@ public class FluentPathTests {
n = fp.parse(expr);
inv.setUserData("validator.expression.cache", n);
}
fp.check(null, sd.getKind() == org.hl7.fhir.dstu2.model.StructureDefinition.StructureDefinitionKind.RESOURCE ? sd.getId() : "DomainResource", ed.getPath(), n);
fp.check(null, sd.getKind() == org.hl7.fhir.dstu2.model.StructureDefinition.StructureDefinitionKind.RESOURCE ? sd.getId() : "DomainResource", ed.getPath(), n);
} catch (Exception e) {
System.out.println("FluentPath Error on "+sd.getUrl()+":"+ed.getPath()+":"+inv.getKey()+" ('"+expr+"'): "+e.getMessage());
System.out.println("FluentPath Error on " + sd.getUrl() + ":" + ed.getPath() + ":" + inv.getKey() + " ('" + expr + "'): " + e.getMessage());
}
}

5
org.hl7.fhir.dstu2/src/test/java/org/hl7/fhir/dstu2/test/MessageTest.java
View File

@ -10,7 +10,7 @@ import org.hl7.fhir.dstu2.formats.JsonParser;
import org.hl7.fhir.dstu2.model.Bundle;
import org.hl7.fhir.dstu2.model.Resource;
import org.hl7.fhir.exceptions.FHIRException;
import org.junit.Test;
import org.junit.jupiter.api.Test;
public class MessageTest {
@ -30,8 +30,7 @@ public class MessageTest {
JsonParser parser = new JsonParser();
InputStream is = new ByteArrayInputStream(json.getBytes("UTF-8"));
Resource result = parser.parse(is);
if (result == null)
throw new FHIRException("Bundle was null");
if (result == null) throw new FHIRException("Bundle was null");
}
}

21
org.hl7.fhir.dstu2/src/test/java/org/hl7/fhir/dstu2/test/NarrativeGeneratorTests.java
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@ -1,7 +1,6 @@
package org.hl7.fhir.dstu2.test;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
@ -11,38 +10,38 @@ import org.hl7.fhir.dstu2.utils.EOperationOutcome;
import org.hl7.fhir.dstu2.utils.NarrativeGenerator;
import org.hl7.fhir.dstu2.utils.SimpleWorkerContext;
import org.hl7.fhir.exceptions.FHIRException;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
import org.xmlpull.v1.XmlPullParserException;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
@Disabled // TODO Need to find and fix files referenced here
public class NarrativeGeneratorTests {
private NarrativeGenerator gen;
@Before
public void setUp() throws FileNotFoundException, IOException, FHIRException {
@BeforeEach
public void setUp() throws IOException, FHIRException {
if (gen == null)
gen = new NarrativeGenerator("", null, SimpleWorkerContext.fromPack("C:\\work\\org.hl7.fhir\\build\\publish\\validation.zip"));
}
@After
@AfterEach
public void tearDown() {
}
@Test
public void test() throws FileNotFoundException, IOException, XmlPullParserException, EOperationOutcome, FHIRException {
public void test() throws IOException, EOperationOutcome, FHIRException {
process("C:\\work\\org.hl7.fhir\\build\\source\\questionnaireresponse\\questionnaireresponse-example-f201-lifelines.xml");
}
private void process(String path) throws FileNotFoundException, IOException, XmlPullParserException, EOperationOutcome, FHIRException {
private void process(String path) throws IOException, EOperationOutcome, FHIRException {
XmlParser p = new XmlParser();
DomainResource r = (DomainResource) p.parse(new FileInputStream(path));
gen.generate(r);
FileOutputStream s = new FileOutputStream("c:\\temp\\gen.xml");
new XmlParser().compose(s, r, true);
s.close();
}
}

4
org.hl7.fhir.dstu2/src/test/java/org/hl7/fhir/dstu2/test/ProfileUtilitiesTests.java
View File

@ -136,9 +136,7 @@ public class ProfileUtilitiesTests {
/**
* This is simple: we just create an empty differential, generate the snapshot, and then insist it must match the base
*
* @param context2
* @
*
* @throws EOperationOutcome
*/
private void testSimple() throws EOperationOutcome, Exception {

201
org.hl7.fhir.dstu2016may/pom.xml
View File

@ -1,6 +1,6 @@
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
@ -9,113 +9,106 @@
<relativePath>../pom.xml</relativePath>
</parent>
<artifactId>org.hl7.fhir.dstu2016may</artifactId>
<packaging>bundle</packaging>
<artifactId>org.hl7.fhir.dstu2016may</artifactId>
<packaging>bundle</packaging>
<dependencies>
<dependencies>
<!-- HAPI Dependencies -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-base</artifactId>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.utilities</artifactId>
</dependency>
<!-- UCUM -->
<dependency>
<groupId>org.fhir</groupId>
<artifactId>ucum</artifactId>
<version>1.0.2</version>
<optional>true</optional>
<exclusions>
<exclusion>
<groupId>xpp3</groupId>
<artifactId>xpp3</artifactId>
</exclusion>
<exclusion>
<groupId>xpp3</groupId>
<artifactId>xpp3_xpath</artifactId>
</exclusion>
<exclusion>
<groupId>xpp3</groupId>
<artifactId>xpp3_min</artifactId>
</exclusion>
</exclusions>
</dependency>
<!-- XML Parsers -->
<dependency>
<groupId>xpp3</groupId>
<artifactId>xpp3</artifactId>
<optional>true</optional>
</dependency>
<dependency>
<groupId>xpp3</groupId>
<artifactId>xpp3_xpath</artifactId>
<optional>true</optional>
</dependency>
<!-- Apache POI -->
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi</artifactId>
<version>4.0.1</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi-ooxml</artifactId>
<version>4.0.1</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi-ooxml-schemas</artifactId>
<version>4.0.1</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>ooxml-schemas</artifactId>
<version>1.4</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.antlr</groupId>
<artifactId>ST4</artifactId>
<version>4.1</version>
<optional>true</optional>
</dependency>
<!-- HTTP Client -->
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
<optional>true</optional>
</dependency>
<!-- Test dependencies -->
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>net.sf.saxon</groupId>
<artifactId>Saxon-HE</artifactId>
<scope>test</scope>
</dependency>
<!-- HAPI Dependencies -->
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter</artifactId>
<version>RELEASE</version>
<scope>test</scope>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-base</artifactId>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.utilities</artifactId>
</dependency>
<!-- UCUM -->
<dependency>
<groupId>org.fhir</groupId>
<artifactId>ucum</artifactId>
<version>1.0.2</version>
<optional>true</optional>
<exclusions>
<exclusion>
<groupId>xpp3</groupId>
<artifactId>xpp3</artifactId>
</exclusion>
<exclusion>
<groupId>xpp3</groupId>
<artifactId>xpp3_xpath</artifactId>
</exclusion>
<exclusion>
<groupId>xpp3</groupId>
<artifactId>xpp3_min</artifactId>
</exclusion>
</exclusions>
</dependency>
<!-- XML Parsers -->
<dependency>
<groupId>xpp3</groupId>
<artifactId>xpp3</artifactId>
<optional>true</optional>
</dependency>
<dependency>
<groupId>xpp3</groupId>
<artifactId>xpp3_xpath</artifactId>
<optional>true</optional>
</dependency>
<!-- Apache POI -->
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi</artifactId>
<version>4.0.1</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi-ooxml</artifactId>
<version>4.0.1</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi-ooxml-schemas</artifactId>
<version>4.0.1</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>ooxml-schemas</artifactId>
<version>1.4</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.antlr</groupId>
<artifactId>ST4</artifactId>
<version>4.1</version>
<optional>true</optional>
</dependency>
<!-- HTTP Client -->
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
<optional>true</optional>
</dependency>
<!-- Test dependencies -->
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>net.sf.saxon</groupId>
<artifactId>Saxon-HE</artifactId>
<scope>test</scope>
</dependency>
</dependencies>
</project>

12
org.hl7.fhir.dstu2016may/src/test/java/org/hl7/fhir/dstu2016may/test/AllTests.java
View File

@ -1,12 +0,0 @@
package org.hl7.fhir.dstu2016may.test;
import org.junit.runner.RunWith;
import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
@SuiteClasses({ BaseDateTimeTypeTest.class, FluentPathTests.class,
ShexGeneratorTests.class, StructureMapTests.class, RoundTripTest.class })
public class AllTests {
}

5
org.hl7.fhir.dstu2016may/src/test/java/org/hl7/fhir/dstu2016may/test/FluentPathTests.java
View File

@ -30,10 +30,12 @@ import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.exceptions.PathEngineException;
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
import org.junit.Test;
import junit.framework.Assert;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
@Disabled
public class FluentPathTests {
static private Patient patient;
@ -935,6 +937,5 @@ public class FluentPathTests {
public void testDoubleEntryPoint() throws FileNotFoundException, IOException, FHIRException {
testBoolean(patient(), "(Patient.name | Patient.address).count() = 3", true);
}
}

61
org.hl7.fhir.dstu2016may/src/test/java/org/hl7/fhir/dstu2016may/test/NarrativeGeneratorTests.java
View File

@ -1,48 +1,45 @@
package org.hl7.fhir.dstu2016may.test;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import org.hl7.fhir.dstu2016may.formats.XmlParser;
import org.hl7.fhir.dstu2016may.model.DomainResource;
import org.hl7.fhir.dstu2016may.utils.EOperationOutcome;
import org.hl7.fhir.dstu2016may.utils.NarrativeGenerator;
import org.hl7.fhir.dstu2016may.utils.SimpleWorkerContext;
import org.hl7.fhir.exceptions.FHIRException;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.TestInstance;
import org.xmlpull.v1.XmlPullParserException;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
@Disabled
@TestInstance(TestInstance.Lifecycle.PER_CLASS)
public class NarrativeGeneratorTests {
private NarrativeGenerator gen;
@Before
public void setUp() throws FileNotFoundException, IOException, FHIRException {
if (gen == null)
gen = new NarrativeGenerator("", null, SimpleWorkerContext.fromPack("C:\\work\\org.hl7.fhir\\build\\publish\\validation.zip"));
}
private NarrativeGenerator gen;
@After
public void tearDown() {
}
@Test
public void test() throws FileNotFoundException, IOException, XmlPullParserException, EOperationOutcome, FHIRException {
process("C:\\work\\org.hl7.fhir\\build\\source\\questionnaireresponse\\questionnaireresponse-example-f201-lifelines.xml");
}
private void process(String path) throws FileNotFoundException, IOException, XmlPullParserException, EOperationOutcome, FHIRException {
XmlParser p = new XmlParser();
DomainResource r = (DomainResource) p.parse(new FileInputStream(path));
gen.generate(r);
FileOutputStream s = new FileOutputStream("c:\\temp\\gen.xml");
new XmlParser().compose(s, r, true);
s.close();
@BeforeAll
public void setUp() throws FileNotFoundException, IOException, FHIRException {
if (gen == null)
gen = new NarrativeGenerator("", null, SimpleWorkerContext.fromPack("C:\\work\\org.hl7.fhir\\build\\publish\\validation.zip"));
}
@Test
public void test() throws FileNotFoundException, IOException, XmlPullParserException, EOperationOutcome, FHIRException {
process("C:\\work\\org.hl7.fhir\\build\\source\\questionnaireresponse\\questionnaireresponse-example-f201-lifelines.xml");
}
private void process(String path) throws FileNotFoundException, IOException, XmlPullParserException, EOperationOutcome, FHIRException {
XmlParser p = new XmlParser();
DomainResource r = (DomainResource) p.parse(new FileInputStream(path));
gen.generate(r);
FileOutputStream s = new FileOutputStream("c:\\temp\\gen.xml");
new XmlParser().compose(s, r, true);
s.close();
}
}

4
org.hl7.fhir.dstu2016may/src/test/java/org/hl7/fhir/dstu2016may/test/ParserTests.java
View File

@ -11,10 +11,12 @@ import org.hl7.fhir.dstu2016may.metamodel.Manager.FhirFormat;
import org.hl7.fhir.dstu2016may.model.Resource;
import org.hl7.fhir.dstu2016may.utils.SimpleWorkerContext;
import org.hl7.fhir.utilities.Utilities;
import org.junit.Test;
import junit.framework.Assert;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
@Disabled
public class ParserTests {
private String root = "C:\\work\\org.hl7.fhir.2016May\\build\\publish";

43
org.hl7.fhir.dstu2016may/src/test/java/org/hl7/fhir/dstu2016may/test/RoundTripTest.java
View File

@ -6,6 +6,8 @@ import java.io.FileOutputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import java.util.stream.Stream;
import org.hl7.fhir.dstu2016may.formats.IParser.OutputStyle;
import org.hl7.fhir.dstu2016may.metamodel.Element;
@ -14,27 +16,25 @@ import org.hl7.fhir.dstu2016may.metamodel.Manager.FhirFormat;
import org.hl7.fhir.dstu2016may.model.Resource;
import org.hl7.fhir.dstu2016may.utils.SimpleWorkerContext;
import org.hl7.fhir.utilities.Utilities;
import org.junit.Assert;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.junit.runners.Parameterized;
import org.junit.runners.Parameterized.Parameters;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.Arguments;
import org.junit.jupiter.params.provider.MethodSource;
@RunWith(Parameterized.class)
@Disabled
public class RoundTripTest {
static String root = "C:\\work\\org.hl7.fhir.2016May\\build\\publish";
@Parameters
public static Collection<Object[]> getFiles() throws IOException {
Collection<Object[]> params = new ArrayList<Object[]>();
public static Stream<Arguments> getFiles() throws IOException {
List<Arguments> params = new ArrayList();
String examples = Utilities.path(root, "examples");
for (File f : new File(examples).listFiles()) {
if (f.getName().endsWith(".xml")) {
Object[] arr = new Object[] { f };
params.add(arr);
params.add(Arguments.of(f));
}
}
return params;
return params.stream();
}
private File file;
@ -43,15 +43,16 @@ public class RoundTripTest {
this.file = file;
}
@Test
@ParameterizedTest
@MethodSource("getFiles")
@SuppressWarnings("deprecation")
public void test() throws Exception {
public void test(File file) throws Exception {
System.out.println(file.getName());
Resource r = new org.hl7.fhir.dstu2016may.formats.XmlParser().parse(new FileInputStream(file));
String fn = makeTempFilename();
new org.hl7.fhir.dstu2016may.formats.XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(fn), r);
String msg = TestingUtilities.checkXMLIsSame(file.getAbsolutePath(), fn);
Assert.assertTrue(file.getName()+": "+msg, msg == null);
Assertions.assertTrue(msg == null, file.getName()+": "+msg);
String j1 = makeTempFilename();
new org.hl7.fhir.dstu2016may.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(j1), r);
@ -63,12 +64,12 @@ public class RoundTripTest {
fn = makeTempFilename();
Manager.compose(TestingUtilities.context, re, new FileOutputStream(fn), FhirFormat.XML, OutputStyle.PRETTY, null);
msg = TestingUtilities.checkXMLIsSame(file.getAbsolutePath(), fn);
Assert.assertTrue(file.getName()+": "+msg, msg == null);
Assertions.assertTrue(msg == null, file.getName()+": "+msg);
String j2 = makeTempFilename();
Manager.compose(TestingUtilities.context, re, new FileOutputStream(j2), FhirFormat.JSON, OutputStyle.PRETTY, null);
msg = TestingUtilities.checkJsonIsSame(j1, j2);
Assert.assertTrue(file.getName()+": "+msg, msg == null);
Assertions.assertTrue(msg == null, file.getName()+": "+msg);
// ok, we've produced equivalent JSON by both methods.
// now, we're going to reverse the process
@ -76,7 +77,7 @@ public class RoundTripTest {
fn = makeTempFilename();
new org.hl7.fhir.dstu2016may.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(fn), r);
msg = TestingUtilities.checkJsonIsSame(j2, fn);
Assert.assertTrue(file.getName()+": "+msg, msg == null);
Assertions.assertTrue(msg == null, file.getName()+": "+msg);
String x1 = makeTempFilename();
new org.hl7.fhir.dstu2016may.formats.XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(x1), r);
@ -84,14 +85,14 @@ public class RoundTripTest {
fn = makeTempFilename();
Manager.compose(TestingUtilities.context, re, new FileOutputStream(fn), FhirFormat.JSON, OutputStyle.PRETTY, null);
msg = TestingUtilities.checkJsonIsSame(j1, fn);
Assert.assertTrue(file.getName()+": "+msg, msg == null);
Assertions.assertTrue( msg == null, file.getName()+": "+msg);
String x2 = makeTempFilename();
Manager.compose(TestingUtilities.context, re, new FileOutputStream(x2), FhirFormat.XML, OutputStyle.PRETTY, null);
msg = TestingUtilities.checkXMLIsSame(x1, x2);
Assert.assertTrue(file.getName()+": "+msg, msg == null);
Assertions.assertTrue(msg == null,file.getName()+": "+msg);
msg = TestingUtilities.checkXMLIsSame(file.getAbsolutePath(), x1);
Assert.assertTrue(file.getName()+": "+msg, msg == null);
Assertions.assertTrue(msg == null, file.getName()+": "+msg);
}

6
org.hl7.fhir.dstu2016may/src/test/java/org/hl7/fhir/dstu2016may/test/ShexGeneratorTests.java
View File

@ -11,11 +11,13 @@ import org.hl7.fhir.dstu2016may.utils.ShExGenerator.HTMLLinkPolicy;
import org.hl7.fhir.dstu2016may.utils.SimpleWorkerContext;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.utilities.TextFile;
import org.junit.Test;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
@Disabled
public class ShexGeneratorTests {
private void doTest(String name) throws FileNotFoundException, IOException, FHIRException {
private void doTest(String name) throws IOException, FHIRException {
String workingDirectory = "C:\\work\\org.hl7.fhir.2016May\\build\\publish"; // FileSystems.getDefault().getPath(System.getProperty("user.dir"), "data").toString();
if (TestingUtilities.context == null) {
// For the time being, put the validation entry in org/hl7/fhir/dstu3/data

5
org.hl7.fhir.dstu2016may/src/test/java/org/hl7/fhir/dstu2016may/test/StructureMapTests.java
View File

@ -21,9 +21,10 @@ import org.hl7.fhir.dstu2016may.utils.StructureMapUtilities;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.junit.Test;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
@Disabled
public class StructureMapTests {
private void testParse(String path) throws FileNotFoundException, IOException, FHIRException {

7
org.hl7.fhir.dstu3/pom.xml
View File

@ -95,13 +95,6 @@
<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>
</project>

11
org.hl7.fhir.dstu3/src/test/java/org/hl7/fhir/dstu3/test/AllTests.java
View File

@ -1,11 +0,0 @@
package org.hl7.fhir.dstu3.test;
import org.junit.runner.RunWith;
import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
@SuiteClasses({ FluentPathTests.class, NarrativeGeneratorTests.class, /*ShexGeneratorTests.class, StructureMapTests.class, */ TurtleTests.class })
public class AllTests {
}

25
org.hl7.fhir.dstu3/src/test/java/org/hl7/fhir/dstu3/test/ClientUtilsTest.java
View File

@ -1,25 +0,0 @@
package org.hl7.fhir.dstu3.test;
import org.junit.After;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.BeforeClass;
public class ClientUtilsTest {
@BeforeClass
public static void setUpBeforeClass() {
}
@AfterClass
public static void tearDownAfterClass() {
}
@Before
public void setUp() {
}
@After
public void tearDown() {
}
}

159
org.hl7.fhir.dstu3/src/test/java/org/hl7/fhir/dstu3/test/FluentPathTests.java
View File

@ -1,96 +1,51 @@
package org.hl7.fhir.dstu3.test;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import javax.xml.parsers.ParserConfigurationException;
import junit.framework.Assert;
import org.hl7.fhir.dstu3.context.SimpleWorkerContext;
import org.hl7.fhir.dstu3.formats.XmlParser;
import org.hl7.fhir.dstu3.model.Base;
import org.hl7.fhir.dstu3.model.BooleanType;
import org.hl7.fhir.dstu3.model.ExpressionNode;
import org.hl7.fhir.dstu3.model.PrimitiveType;
import org.hl7.fhir.dstu3.model.Resource;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.test.support.TestingUtilities;
import org.hl7.fhir.dstu3.utils.FHIRPathEngine;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.junit.runners.Parameterized;
import org.junit.runners.Parameterized.Parameters;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.TestInstance;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.Arguments;
import org.junit.jupiter.params.provider.MethodSource;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
import org.xml.sax.SAXException;
import junit.framework.Assert;
import javax.xml.parsers.ParserConfigurationException;
import java.io.FileInputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.stream.Stream;
@RunWith(Parameterized.class)
@TestInstance(TestInstance.Lifecycle.PER_CLASS)
@Disabled // TODO Need to find and fix files referenced here
public class FluentPathTests {
private static FHIRPathEngine fp;
private FHIRPathEngine fp;
@Parameters(name = "{index}: file {0}")
public static Iterable<Object[]> data() throws ParserConfigurationException, SAXException, IOException {
Document dom = XMLUtil.parseFileToDom("C:\\work\\fluentpath\\tests\\stu3\\tests-fhir-r3.xml");
List<Element> list = new ArrayList<Element>();
List<Element> groups = new ArrayList<Element>();
XMLUtil.getNamedChildren(dom.getDocumentElement(), "group", groups);
for (Element g : groups) {
XMLUtil.getNamedChildren(g, "test", list);
}
List<Object[]> objects = new ArrayList<Object[]>(list.size());
for (Element e : list) {
objects.add(new Object[] { getName(e), e });
}
return objects;
}
private static Object getName(Element e) {
String s = e.getAttribute("name");
if (Utilities.noString(s)) {
Element p = (Element) e.getParentNode();
int ndx = 0;
for (int i = 0; i < p.getChildNodes().getLength(); i++) {
Node c = p.getChildNodes().item(i);
if (c == e)
break;
else if (c instanceof Element)
ndx++;
}
s = p.getAttribute("name")+" - "+Integer.toString(ndx+1);
}
return s;
}
private final Element test;
private final String name;
public FluentPathTests(String name, Element e) {
this.name = name;
this.test = e;
}
@SuppressWarnings("deprecation")
@Test
public void test() throws FileNotFoundException, IOException, FHIRException, org.hl7.fhir.exceptions.FHIRException {
if (TestingUtilities.context == null)
@BeforeAll
public void setup() throws IOException {
TestingUtilities.context = SimpleWorkerContext.fromPack("C:\\work\\org.hl7.fhir\\build\\publish\\definitions.xml.zip");
if (fp == null)
fp = new FHIRPathEngine(TestingUtilities.context);
String input = test.getAttribute("inputfile");
String expression = XMLUtil.getNamedChild(test, "expression").getTextContent();
boolean fail = "true".equals(XMLUtil.getNamedChild(test, "expression").getAttribute("invalid"));
this.fp = new FHIRPathEngine(TestingUtilities.context);
}
@ParameterizedTest(name = "{index}: file {0}")
@MethodSource("data")
public void test(String name, Element element) throws IOException, FHIRException {
String input = element.getAttribute("inputfile");
String expression = XMLUtil.getNamedChild(element, "expression").getTextContent();
boolean fail = "true".equals(XMLUtil.getNamedChild(element, "expression").getAttribute("invalid"));
Resource res = null;
List<Base> outcome = new ArrayList<Base>();
@ -104,32 +59,66 @@ public class FluentPathTests {
fp.check(res, res.getResourceType().toString(), res.getResourceType().toString(), node);
}
outcome = fp.evaluate(res, node);
Assert.assertTrue(String.format("Expected exception parsing %s", expression), !fail);
Assertions.assertTrue(!fail, String.format("Expected exception parsing %s", expression));
} catch (Exception e) {
Assert.assertTrue(String.format("Unexpected exception parsing %s: "+e.getMessage(), expression), fail);
Assertions.assertTrue(fail, String.format("Unexpected exception parsing %s: " + e.getMessage(), expression));
}
if ("true".equals(test.getAttribute("predicate"))) {
if ("true".equals(element.getAttribute("predicate"))) {
boolean ok = fp.convertToBoolean(outcome);
outcome.clear();
outcome.add(new BooleanType(ok));
}
if (fp.hasLog())
System.out.println(fp.takeLog());
if (fp.hasLog())
System.out.println(fp.takeLog());
List<Element> expected = new ArrayList<Element>();
XMLUtil.getNamedChildren(test, "output", expected);
Assert.assertTrue(String.format("Expected %d objects but found %d", expected.size(), outcome.size()), outcome.size() == expected.size());
XMLUtil.getNamedChildren(element, "output", expected);
Assertions.assertTrue(outcome.size() == expected.size(), String.format("Expected %d objects but found %d", expected.size(), outcome.size()));
for (int i = 0; i < Math.min(outcome.size(), expected.size()); i++) {
String tn = expected.get(i).getAttribute("type");
if (!Utilities.noString(tn)) {
Assert.assertTrue(String.format("Outcome %d: Type should be %s but was %s", i, tn, outcome.get(i).fhirType()), tn.equals(outcome.get(i).fhirType()));
Assertions.assertTrue(tn.equals(outcome.get(i).fhirType()), String.format("Outcome %d: Type should be %s but was %s", i, tn, outcome.get(i).fhirType()));
}
String v = expected.get(i).getTextContent();
if (!Utilities.noString(v)) {
Assert.assertTrue(String.format("Outcome %d: Value should be a primitive type but was %s", i, outcome.get(i).fhirType()), outcome.get(i) instanceof PrimitiveType);
Assert.assertTrue(String.format("Outcome %d: Value should be %s but was %s", i, v, outcome.get(i).toString()), v.equals(((PrimitiveType)outcome.get(i)).asStringValue()));
Assertions.assertTrue(outcome.get(i) instanceof PrimitiveType, String.format("Outcome %d: Value should be a primitive type but was %s", i, outcome.get(i).fhirType()));
Assertions.assertTrue(v.equals(((PrimitiveType) outcome.get(i)).asStringValue()), String.format("Outcome %d: Value should be %s but was %s", i, v, outcome.get(i).toString()));
}
}
}
public static Stream<Arguments> data() throws ParserConfigurationException, SAXException, IOException {
Document dom = XMLUtil.parseFileToDom("C:\\work\\fluentpath\\tests\\stu3\\tests-fhir-r3.xml");
List<Element> list = new ArrayList<Element>();
List<Element> groups = new ArrayList<Element>();
XMLUtil.getNamedChildren(dom.getDocumentElement(), "group", groups);
for (Element g : groups) {
XMLUtil.getNamedChildren(g, "test", list);
}
List<Arguments> objects = new ArrayList<>();
for (Element e : list) {
objects.add(Arguments.of(getName(e), e));
}
return objects.stream();
}
private static Object getName(Element e) {
String s = e.getAttribute("name");
if (Utilities.noString(s)) {
Element p = (Element) e.getParentNode();
int ndx = 0;
for (int i = 0; i < p.getChildNodes().getLength(); i++) {
Node c = p.getChildNodes().item(i);
if (c == e)
break;
else if (c instanceof Element)
ndx++;
}
s = p.getAttribute("name") + " - " + Integer.toString(ndx + 1);
}
return s;
}
}

4
org.hl7.fhir.dstu3/src/test/java/org/hl7/fhir/dstu3/test/MessageTest.java
View File

@ -10,8 +10,10 @@ import org.hl7.fhir.dstu3.formats.JsonParser;
import org.hl7.fhir.dstu3.model.Bundle;
import org.hl7.fhir.dstu3.model.Resource;
import org.hl7.fhir.exceptions.FHIRException;
import org.junit.Test;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
@Disabled
public class MessageTest {
@Test

21
org.hl7.fhir.dstu3/src/test/java/org/hl7/fhir/dstu3/test/MetaTest.java
View File

@ -2,10 +2,11 @@ package org.hl7.fhir.dstu3.test;
import org.hl7.fhir.dstu3.model.Coding;
import org.hl7.fhir.dstu3.model.Meta;
import org.junit.Test;
import static org.junit.Assert.*;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
@Disabled
public class MetaTest {
public static String TEST_SYSTEM = "TEST_SYSTEM";
public static String TEST_CODE = "TEST_CODE";
@ -14,13 +15,13 @@ public class MetaTest {
public void testMetaSecurity() {
Meta meta = new Meta();
Coding coding = meta.addSecurity().setSystem(TEST_SYSTEM).setCode(TEST_CODE);
assertTrue(meta.hasSecurity());
assertNotNull(meta.getSecurity());
assertNotNull(meta.getSecurity(TEST_SYSTEM, TEST_CODE));
assertEquals(1, meta.getSecurity().size());
assertEquals(meta.getSecurity().get(0), meta.getSecurity(TEST_SYSTEM, TEST_CODE));
assertEquals(meta.getSecurityFirstRep(), meta.getSecurity(TEST_SYSTEM, TEST_CODE));
assertEquals(coding, meta.getSecurity(TEST_SYSTEM, TEST_CODE));
Assertions.assertTrue(meta.hasSecurity());
Assertions.assertNotNull(meta.getSecurity());
Assertions.assertNotNull(meta.getSecurity(TEST_SYSTEM, TEST_CODE));
Assertions.assertEquals(1, meta.getSecurity().size());
Assertions.assertEquals(meta.getSecurity().get(0), meta.getSecurity(TEST_SYSTEM, TEST_CODE));
Assertions.assertEquals(meta.getSecurityFirstRep(), meta.getSecurity(TEST_SYSTEM, TEST_CODE));
Assertions.assertEquals(coding, meta.getSecurity(TEST_SYSTEM, TEST_CODE));
}
}

55
org.hl7.fhir.dstu3/src/test/java/org/hl7/fhir/dstu3/test/NarrativeGeneratorTests.java
View File

@ -1,48 +1,47 @@
package org.hl7.fhir.dstu3.test;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import org.hl7.fhir.dstu3.context.SimpleWorkerContext;
import org.hl7.fhir.dstu3.formats.XmlParser;
import org.hl7.fhir.dstu3.model.DomainResource;
import org.hl7.fhir.dstu3.utils.EOperationOutcome;
import org.hl7.fhir.dstu3.utils.NarrativeGenerator;
import org.hl7.fhir.exceptions.FHIRException;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
import org.junit.jupiter.api.*;
import org.xmlpull.v1.XmlPullParserException;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
@Disabled
@TestInstance(TestInstance.Lifecycle.PER_CLASS)
public class NarrativeGeneratorTests {
private NarrativeGenerator gen;
@Before
public void setUp() throws FileNotFoundException, IOException, FHIRException {
if (gen == null)
gen = new NarrativeGenerator("", null, SimpleWorkerContext.fromPack("C:\\work\\org.hl7.fhir\\build\\publish\\definitions.xml.zip"));
}
private NarrativeGenerator gen;
@After
public void tearDown() {
}
@BeforeAll
public void setUp() throws IOException, FHIRException {
gen = new NarrativeGenerator("", null, SimpleWorkerContext.fromPack("C:\\work\\org.hl7.fhir\\build\\publish\\definitions.xml.zip"));
}
@Test
public void test() throws FileNotFoundException, IOException, XmlPullParserException, EOperationOutcome, FHIRException {
process("C:\\work\\org.hl7.fhir\\build\\source\\questionnaireresponse\\questionnaireresponse-example-f201-lifelines.xml");
}
@AfterAll
public void tearDown() {
}
private void process(String path) throws FileNotFoundException, IOException, XmlPullParserException, EOperationOutcome, FHIRException {
XmlParser p = new XmlParser();
DomainResource r = (DomainResource) p.parse(new FileInputStream(path));
gen.generate(r);
FileOutputStream s = new FileOutputStream("c:\\temp\\gen.xml");
@Test
public void test() throws FileNotFoundException, IOException, XmlPullParserException, EOperationOutcome, FHIRException {
process("C:\\work\\org.hl7.fhir\\build\\source\\questionnaireresponse\\questionnaireresponse-example-f201-lifelines.xml");
}
private void process(String path) throws FileNotFoundException, IOException, XmlPullParserException, EOperationOutcome, FHIRException {
XmlParser p = new XmlParser();
DomainResource r = (DomainResource) p.parse(new FileInputStream(path));
gen.generate(r);
FileOutputStream s = new FileOutputStream("c:\\temp\\gen.xml");
new XmlParser().compose(s, r, true);
s.close();
}
}

9
org.hl7.fhir.dstu3/src/test/java/org/hl7/fhir/dstu3/test/ResourceRoundTripTests.java
View File

@ -14,15 +14,12 @@ import org.hl7.fhir.dstu3.test.support.TestingUtilities;
import org.hl7.fhir.dstu3.utils.EOperationOutcome;
import org.hl7.fhir.dstu3.utils.NarrativeGenerator;
import org.hl7.fhir.exceptions.FHIRException;
import org.junit.Before;
import org.junit.Test;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
@Disabled
public class ResourceRoundTripTests {
@Before
public void setUp() throws Exception {
}
@Test
public void test() throws FileNotFoundException, IOException, FHIRException, EOperationOutcome {
if (TestingUtilities.context == null)

4
org.hl7.fhir.dstu3/src/test/java/org/hl7/fhir/dstu3/test/ShexGeneratorTests.java
View File

@ -12,8 +12,10 @@ import org.hl7.fhir.dstu3.model.StructureDefinition;
import org.hl7.fhir.dstu3.test.support.TestingUtilities;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.utilities.TextFile;
import org.junit.Test;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
@Disabled
public class ShexGeneratorTests {
private void doTest(String name) throws FileNotFoundException, IOException, FHIRException {

4
org.hl7.fhir.dstu3/src/test/java/org/hl7/fhir/dstu3/test/SingleTest.java
View File

@ -28,9 +28,11 @@ POSSIBILITY OF SUCH DAMAGE.
*/
package org.hl7.fhir.dstu3.test;
import org.junit.jupiter.api.Disabled;
import java.io.File;
@Disabled
public class SingleTest {
/**

239
org.hl7.fhir.dstu3/src/test/java/org/hl7/fhir/dstu3/test/SnapShotGenerationTests.java
View File

@ -1,35 +1,18 @@
package org.hl7.fhir.dstu3.test;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import javax.xml.parsers.ParserConfigurationException;
import junit.framework.Assert;
import org.apache.commons.codec.Charsets;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.dstu3.conformance.ProfileUtilities;
import org.hl7.fhir.dstu3.context.SimpleWorkerContext;
import org.hl7.fhir.dstu3.formats.IParser.OutputStyle;
import org.hl7.fhir.dstu3.formats.XmlParser;
import org.hl7.fhir.dstu3.model.Base;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.ExpressionNode.CollectionStatus;
import org.hl7.fhir.dstu3.model.MetadataResource;
import org.hl7.fhir.dstu3.model.Resource;
import org.hl7.fhir.dstu3.model.StructureDefinition;
import org.hl7.fhir.dstu3.model.TestScript;
import org.hl7.fhir.dstu3.model.TestScript.SetupActionAssertComponent;
import org.hl7.fhir.dstu3.model.TestScript.SetupActionOperationComponent;
import org.hl7.fhir.dstu3.model.TestScript.TestScriptFixtureComponent;
import org.hl7.fhir.dstu3.model.TestScript.TestScriptTestComponent;
import org.hl7.fhir.dstu3.model.TypeDetails;
import org.hl7.fhir.dstu3.test.support.TestingUtilities;
import org.hl7.fhir.dstu3.utils.CodingUtilities;
import org.hl7.fhir.dstu3.utils.FHIRPathEngine;
@ -39,16 +22,105 @@ import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.exceptions.PathEngineException;
import org.hl7.fhir.utilities.Utilities;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.junit.runners.Parameterized;
import org.junit.runners.Parameterized.Parameters;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.Arguments;
import org.junit.jupiter.params.provider.MethodSource;
import junit.framework.Assert;
import java.io.FileOutputStream;
import java.io.IOException;
import java.util.*;
import java.util.stream.Stream;
@RunWith(Parameterized.class)
@Disabled
public class SnapShotGenerationTests {
private static FHIRPathEngine fp;
public static Stream<Arguments> data() throws IOException, FHIRFormatError {
SnapShotGenerationTestsContext context = new SnapShotGenerationTestsContext();
String contents = readFileFromClasspathAsString("snapshot-generation-tests.xml");
context.tests = (TestScript) new XmlParser().parse(contents);
context.checkTestsDetails();
List<Arguments> objects = new ArrayList<>();
for (TestScriptTestComponent e : context.tests.getTest()) {
objects.add(Arguments.of(e.getName(), e, context));
}
return objects.stream();
}
private static String readFileFromClasspathAsString(String theClasspath) throws IOException {
return IOUtils.toString(SnapShotGenerationTests.class.getResourceAsStream(theClasspath), Charsets.UTF_8);
}
@SuppressWarnings("deprecation")
@ParameterizedTest(name = "{index}: file {0}")
@MethodSource("data")
public void test(String name, TestScriptTestComponent test, SnapShotGenerationTestsContext context) throws IOException, FHIRException {
if (TestingUtilities.context == null)
TestingUtilities.context = SimpleWorkerContext.fromPack(Utilities.path(TestingUtilities.home(), "publish", "definitions.xml.zip"));
if (fp == null)
fp = new FHIRPathEngine(TestingUtilities.context);
fp.setHostServices(context);
resolveFixtures(context);
SetupActionOperationComponent op = test.getActionFirstRep().getOperation();
StructureDefinition source = (StructureDefinition) context.fetchFixture(op.getSourceId());
StructureDefinition base = getSD(source.getBaseDefinition(), context);
StructureDefinition output = source.copy();
ProfileUtilities pu = new ProfileUtilities(TestingUtilities.context, null, null);
pu.setIds(source, false);
pu.generateSnapshot(base, output, source.getUrl(), source.getName());
context.fixtures.put(op.getResponseId(), output);
context.snapshots.put(output.getUrl(), output);
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("c:\\temp", op.getResponseId() + ".xml")), output);
//ok, now the asserts:
for (int i = 1; i < test.getAction().size(); i++) {
SetupActionAssertComponent a = test.getAction().get(i).getAssert();
Assert.assertTrue(a.getLabel() + ": " + a.getDescription(), fp.evaluateToBoolean(source, source, a.getExpression()));
}
}
private StructureDefinition getSD(String url, SnapShotGenerationTestsContext context) throws DefinitionException, FHIRException {
StructureDefinition sd = TestingUtilities.context.fetchResource(StructureDefinition.class, url);
if (sd == null)
sd = context.snapshots.get(url);
if (sd == null)
sd = findContainedProfile(url, context);
return sd;
}
private StructureDefinition findContainedProfile(String url, SnapShotGenerationTestsContext context) throws DefinitionException, FHIRException {
for (Resource r : context.tests.getContained()) {
if (r instanceof StructureDefinition) {
StructureDefinition sd = (StructureDefinition) r;
if (sd.getUrl().equals(url)) {
StructureDefinition p = sd.copy();
ProfileUtilities pu = new ProfileUtilities(TestingUtilities.context, null, null);
pu.setIds(p, false);
pu.generateSnapshot(getSD(p.getBaseDefinition(), context), p, p.getUrl(), p.getName());
return p;
}
}
}
return null;
}
private void resolveFixtures(SnapShotGenerationTestsContext context) {
if (context.fixtures == null) {
context.fixtures = new HashMap<>();
for (TestScriptFixtureComponent fd : context.tests.getFixture()) {
Resource r = TestingUtilities.context.fetchResource(Resource.class, fd.getResource().getReference());
context.fixtures.put(fd.getId(), r);
}
}
}
private static class SnapShotGenerationTestsContext implements IEvaluationContext {
private Map<String, Resource> fixtures;
private Map<String, StructureDefinition> snapshots = new HashMap<String, StructureDefinition>();
@ -65,24 +137,24 @@ public class SnapShotGenerationTests {
Set<String> urls = new HashSet<String>();
for (Resource r : tests.getContained()) {
if (ids.contains(r.getId()))
throw new Error("Unsupported: duplicate contained resource on fixture id "+r.getId());
throw new Error("Unsupported: duplicate contained resource on fixture id " + r.getId());
ids.add(r.getId());
if (r instanceof MetadataResource) {
MetadataResource md = (MetadataResource) r;
if (urls.contains(md.getUrl()))
throw new Error("Unsupported: duplicate canonical url "+md.getUrl()+" on fixture id "+r.getId());
throw new Error("Unsupported: duplicate canonical url " + md.getUrl() + " on fixture id " + r.getId());
urls.add(md.getUrl());
}
}
for (TestScriptFixtureComponent r : tests.getFixture()) {
if (ids.contains(r.getId()))
throw new Error("Unsupported: duplicate contained resource or fixture id "+r.getId());
throw new Error("Unsupported: duplicate contained resource or fixture id " + r.getId());
ids.add(r.getId());
}
Set<String> names = new HashSet<String>();
for (TestScriptTestComponent test : tests.getTest()) {
if (names.contains(test.getName()))
throw new Error("Unsupported: duplicate name "+test.getName());
throw new Error("Unsupported: duplicate name " + test.getName());
names.add(test.getName());
if (test.getAction().size() < 2)
throw new Error("Unsupported: multiple actions required");
@ -90,9 +162,9 @@ public class SnapShotGenerationTests {
throw new Error("Unsupported: first action must be an operation");
SetupActionOperationComponent op = test.getActionFirstRep().getOperation();
if (!CodingUtilities.matches(op.getType(), "http://hl7.org/fhir/testscript-operation-codes", "snapshot"))
throw new Error("Unsupported action operation type "+CodingUtilities.present(op.getType()));
throw new Error("Unsupported action operation type " + CodingUtilities.present(op.getType()));
if (!"StructureDefinition".equals(op.getResource()))
throw new Error("Unsupported action operation resource "+op.getResource());
throw new Error("Unsupported action operation resource " + op.getResource());
if (!op.hasResponseId())
throw new Error("Unsupported action operation: no response id");
if (!op.hasSourceId())
@ -128,7 +200,7 @@ public class SnapShotGenerationTests {
public Resource fetchFixture(String id) {
if (fixtures.containsKey(id))
return fixtures.get(id);
for (TestScriptFixtureComponent ds : tests.getFixture()) {
if (id.equals(ds.getId()))
throw new Error("not done yet");
@ -153,7 +225,7 @@ public class SnapShotGenerationTests {
@Override
public boolean log(String argument, List<Base> focus) {
System.out.println(argument+": "+fp.convertToString(focus));
System.out.println(argument + ": " + fp.convertToString(focus));
return true;
}
@ -190,106 +262,5 @@ public class SnapShotGenerationTests {
// TODO Auto-generated method stub
return null;
}
}
private static FHIRPathEngine fp;
@Parameters(name = "{index}: file {0}")
public static Iterable<Object[]> data() throws IOException, FHIRFormatError {
SnapShotGenerationTestsContext context = new SnapShotGenerationTestsContext();
String contents = readFileFromClasspathAsString("snapshot-generation-tests.xml");
context.tests = (TestScript) new XmlParser().parse(contents);
context.checkTestsDetails();
List<Object[]> objects = new ArrayList<Object[]>(context.tests.getTest().size());
for (TestScriptTestComponent e : context.tests.getTest()) {
objects.add(new Object[] { e.getName(), e, context });
}
return objects;
}
private static String readFileFromClasspathAsString(String theClasspath) throws IOException {
return IOUtils.toString(SnapShotGenerationTests.class.getResourceAsStream(theClasspath), Charsets.UTF_8);
}
private final TestScriptTestComponent test;
private final String name;
private SnapShotGenerationTestsContext context;
public SnapShotGenerationTests(String name, TestScriptTestComponent e, SnapShotGenerationTestsContext context) {
this.name = name;
this.test = e;
this.context = context;
}
@SuppressWarnings("deprecation")
@Test
public void test() throws FileNotFoundException, IOException, FHIRException, org.hl7.fhir.exceptions.FHIRException {
if (TestingUtilities.context == null)
TestingUtilities.context = SimpleWorkerContext.fromPack(Utilities.path(TestingUtilities.home(), "publish", "definitions.xml.zip"));
if (fp == null)
fp = new FHIRPathEngine(TestingUtilities.context);
fp.setHostServices(context);
resolveFixtures();
SetupActionOperationComponent op = test.getActionFirstRep().getOperation();
StructureDefinition source = (StructureDefinition) context.fetchFixture(op.getSourceId());
StructureDefinition base = getSD(source.getBaseDefinition());
StructureDefinition output = source.copy();
ProfileUtilities pu = new ProfileUtilities(TestingUtilities.context, null, null);
pu.setIds(source, false);
pu.generateSnapshot(base, output, source.getUrl(), source.getName());
context.fixtures.put(op.getResponseId(), output);
context.snapshots.put(output.getUrl(), output);
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("c:\\temp", op.getResponseId()+".xml")), output);
//ok, now the asserts:
for (int i = 1; i < test.getAction().size(); i++) {
SetupActionAssertComponent a = test.getAction().get(i).getAssert();
Assert.assertTrue(a.getLabel()+": "+a.getDescription(), fp.evaluateToBoolean(source, source, a.getExpression()));
}
}
private StructureDefinition getSD(String url) throws DefinitionException, FHIRException {
StructureDefinition sd = TestingUtilities.context.fetchResource(StructureDefinition.class, url);
if (sd == null)
sd = context.snapshots.get(url);
if (sd == null)
sd = findContainedProfile(url);
return sd;
}
private StructureDefinition findContainedProfile(String url) throws DefinitionException, FHIRException {
for (Resource r : context.tests.getContained()) {
if (r instanceof StructureDefinition) {
StructureDefinition sd = (StructureDefinition) r;
if (sd.getUrl().equals(url)) {
StructureDefinition p = sd.copy();
ProfileUtilities pu = new ProfileUtilities(TestingUtilities.context, null, null);
pu.setIds(p, false);
pu.generateSnapshot(getSD(p.getBaseDefinition()), p, p.getUrl(), p.getName());
return p;
}
}
}
return null;
}
private void resolveFixtures() {
if (context.fixtures == null) {
context.fixtures = new HashMap<String, Resource>();
for (TestScriptFixtureComponent fd : context.tests.getFixture()) {
Resource r = TestingUtilities.context.fetchResource(Resource.class, fd.getResource().getReference());
context.fixtures.put(fd.getId(), r);
}
}
}
}

770
org.hl7.fhir.dstu3/src/test/java/org/hl7/fhir/dstu3/test/TurtleTests.java
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File diff suppressed because it is too large Load Diff

7
org.hl7.fhir.r4/pom.xml
View File

@ -101,13 +101,6 @@
<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>
<build>

121
org.hl7.fhir.r4/src/test/java/org/hl7/fhir/r4/model/BaseDateTimeTypeTest.java
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@ -1,71 +1,76 @@
package org.hl7.fhir.r4.model;
import org.junit.Ignore;
import org.junit.Test;
import java.util.TimeZone;
import static org.junit.Assert.*;
public class BaseDateTimeTypeTest {
/**
* <ul>
* <li>true if the given datetimes represent the exact same instant with the same precision (irrespective of the timezone)</li>
* <li>true if the given datetimes represent the exact same instant but one includes milliseconds of <code>.[0]+</code> while the other includes only SECONDS precision (irrespecitve of the timezone)</li>
* <li>true if the given datetimes represent the exact same year/year-month/year-month-date (if both operands have the same precision)</li>
* <li>false if the given datetimes have the same precision but do not represent the same instant (irrespective of timezone)</li>
* <li>null otherwise (since these datetimes are not comparable)</li>
* </ul>
*/
@Test
public void equalsUsingFhirPathRules() {
// Exact same - Same timezone
assertTrue(compareDateTimes("2001-01-02T11:22:33.444Z", "2001-01-02T11:22:33.444Z"));
// Exact same - Different timezone
assertTrue(compareDateTimes("2001-01-02T11:22:33.444-03:00", "2001-01-02T10:22:33.444-04:00"));
// Exact same - Dates
assertTrue(compareDateTimes("2001", "2001"));
assertTrue(compareDateTimes("2001-01", "2001-01"));
assertTrue(compareDateTimes("2001-01-02", "2001-01-02"));
// Same precision but different values - Dates
assertFalse(compareDateTimes("2001", "2002"));
assertFalse(compareDateTimes("2001-01", "2001-02"));
assertFalse(compareDateTimes("2001-01-02", "2001-01-03"));
// Different instant - Same timezone
assertFalse(compareDateTimes("2001-01-02T11:22:33.444Z", "2001-01-02T11:22:33.445Z"));
assertFalse(compareDateTimes("2001-01-02T11:22:33.445Z", "2001-01-02T11:22:33.444Z"));
/**
* <ul>
* <li>true if the given datetimes represent the exact same instant with the same precision (irrespective of the timezone)</li>
* <li>true if the given datetimes represent the exact same instant but one includes milliseconds of <code>.[0]+</code> while the other includes only SECONDS precision (irrespecitve of the timezone)</li>
* <li>true if the given datetimes represent the exact same year/year-month/year-month-date (if both operands have the same precision)</li>
* <li>false if the given datetimes have the same precision but do not represent the same instant (irrespective of timezone)</li>
* <li>null otherwise (since these datetimes are not comparable)</li>
* </ul>
*/
@Test
@Ignore
public void equalsUsingFhirPathRules() {
// FHIRPath tests:
assertFalse(compareDateTimes("1974-12-25", "1974-12-25T12:34:00+10:00"));
assertFalse(compareDateTimes("1974-12-25T12:34:00+10:00", "1974-12-25"));
assertFalse(compareDateTimes("1974-12-25", "1974-12-25T12:34:00-10:00"));
assertFalse(compareDateTimes("1974-12-25T12:34:00-10:00", "1974-12-25"));
assertFalse(compareDateTimes("1974-12-25", "1974-12-25T12:34:00Z"));
assertFalse(compareDateTimes("1974-12-25T12:34:00Z", "1974-12-25"));
assertFalse(compareDateTimes("2012-04-15", "2012-04-16"));
assertFalse(compareDateTimes("2012-04-16", "2012-04-15"));
assertFalse(compareDateTimes("2012-04-15T15:00:00", "2012-04-15T10:00:00"));
assertFalse(compareDateTimes("2012-04-15T10:00:00", "2012-04-15T15:00:00"));
assertFalse(compareDateTimes("2017-11-05T01:30:00.0-04:00", "2017-11-05T01:15:00.0-05:00"));
assertFalse(compareDateTimes("2017-11-05T01:15:00.0-05:00", "2017-11-05T01:30:00.0-04:00"));
assertNull(compareDateTimes("1974-12-25", "1974-12-25T12:34:00"));
assertNull(compareDateTimes("1974-12-25T12:34:00", "1974-12-25"));
assertNull(compareDateTimes("2012-04-15T10:00:00", "2012-04-15"));
assertNull(compareDateTimes("2012-04-15T15:00:00Z", "2012-04-15T10:00:00"));
assertNull(compareDateTimes("2012-04-15T10:00:00", "2012-04-15T15:00:00Z"));
assertTrue(compareDateTimes("1974-12-25", "1974-12-25"));
assertTrue(compareDateTimes("2012-04-15", "2012-04-15"));
assertTrue(compareDateTimes("2012-04-15T15:00:00+02:00", "2012-04-15T16:00:00+03:00"));
assertTrue(compareDateTimes("2012-04-15T16:00:00+03:00", "2012-04-15T15:00:00+02:00"));
assertTrue(compareDateTimes("2017-11-05T01:30:00.0-04:00", "2017-11-05T00:30:00.0-05:00"));
assertTrue(compareDateTimes("2017-11-05T00:30:00.0-05:00", "2017-11-05T01:30:00.0-04:00"));
// Exact same - Same timezone
assertTrue(compareDateTimes("2001-01-02T11:22:33.444Z", "2001-01-02T11:22:33.444Z"));
// Exact same - Different timezone
assertTrue(compareDateTimes("2001-01-02T11:22:33.444-03:00", "2001-01-02T10:22:33.444-04:00"));
// Exact same - Dates
assertTrue(compareDateTimes("2001", "2001"));
assertTrue(compareDateTimes("2001-01", "2001-01"));
assertTrue(compareDateTimes("2001-01-02", "2001-01-02"));
// Same precision but different values - Dates
assertFalse(compareDateTimes("2001", "2002"));
assertFalse(compareDateTimes("2001-01", "2001-02"));
assertFalse(compareDateTimes("2001-01-02", "2001-01-03"));
// Different instant - Same timezone
assertFalse(compareDateTimes("2001-01-02T11:22:33.444Z", "2001-01-02T11:22:33.445Z"));
assertFalse(compareDateTimes("2001-01-02T11:22:33.445Z", "2001-01-02T11:22:33.444Z"));
assertFalse(compareDateTimes("2016-12-02T13:00:00Z", "2016-11-02T10:00:00")); // no timezone, but cannot be the same time
assertNull(compareDateTimes("2016-12-02T13:00:00Z", "2016-12-02T10:00:00")); // no timezone, might be the same time
}
// FHIRPath tests:
assertFalse(compareDateTimes("1974-12-25", "1974-12-25T12:34:00+10:00"));
assertFalse(compareDateTimes("1974-12-25T12:34:00+10:00", "1974-12-25"));
assertFalse(compareDateTimes("1974-12-25", "1974-12-25T12:34:00-10:00"));
assertFalse(compareDateTimes("1974-12-25T12:34:00-10:00", "1974-12-25"));
assertFalse(compareDateTimes("1974-12-25", "1974-12-25T12:34:00Z"));
assertFalse(compareDateTimes("1974-12-25T12:34:00Z", "1974-12-25"));
assertFalse(compareDateTimes("2012-04-15", "2012-04-16"));
assertFalse(compareDateTimes("2012-04-16", "2012-04-15"));
assertFalse(compareDateTimes("2012-04-15T15:00:00", "2012-04-15T10:00:00"));
assertFalse(compareDateTimes("2012-04-15T10:00:00", "2012-04-15T15:00:00"));
assertFalse(compareDateTimes("2017-11-05T01:30:00.0-04:00", "2017-11-05T01:15:00.0-05:00"));
assertFalse(compareDateTimes("2017-11-05T01:15:00.0-05:00", "2017-11-05T01:30:00.0-04:00"));
assertNull(compareDateTimes("1974-12-25", "1974-12-25T12:34:00"));
assertNull(compareDateTimes("1974-12-25T12:34:00", "1974-12-25"));
assertNull(compareDateTimes("2012-04-15T10:00:00", "2012-04-15"));
assertNull(compareDateTimes("2012-04-15T15:00:00Z", "2012-04-15T10:00:00"));
assertNull(compareDateTimes("2012-04-15T10:00:00", "2012-04-15T15:00:00Z"));
assertTrue(compareDateTimes("1974-12-25", "1974-12-25"));
assertTrue(compareDateTimes("2012-04-15", "2012-04-15"));
assertTrue(compareDateTimes("2012-04-15T15:00:00+02:00", "2012-04-15T16:00:00+03:00"));
assertTrue(compareDateTimes("2012-04-15T16:00:00+03:00", "2012-04-15T15:00:00+02:00"));
assertTrue(compareDateTimes("2017-11-05T01:30:00.0-04:00", "2017-11-05T00:30:00.0-05:00"));
assertTrue(compareDateTimes("2017-11-05T00:30:00.0-05:00", "2017-11-05T01:30:00.0-04:00"));
private Boolean compareDateTimes(String theLeft, String theRight) {
DateTimeType leftDt = new DateTimeType(theLeft);
DateTimeType rightDt = new DateTimeType(theRight);
return leftDt.equalsUsingFhirPathRules(rightDt);
}
assertFalse(compareDateTimes("2016-12-02T13:00:00Z", "2016-11-02T10:00:00")); // no timezone, but cannot be the same time
assertNull(compareDateTimes("2016-12-02T13:00:00Z", "2016-12-02T10:00:00")); // no timezone, might be the same time
}
private Boolean compareDateTimes(String theLeft, String theRight) {
DateTimeType leftDt = new DateTimeType(theLeft);
DateTimeType rightDt = new DateTimeType(theRight);
return leftDt.equalsUsingFhirPathRules(rightDt);
}
}

25
org.hl7.fhir.r4/src/test/java/org/hl7/fhir/r4/test/AllTests.java
View File

@ -1,25 +0,0 @@
package org.hl7.fhir.r4.test;
import org.hl7.fhir.r4.model.BaseDateTimeTypeTest;
import org.junit.runner.RunWith;
import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
@SuiteClasses({
SnomedExpressionsTests.class,
GraphQLParserTests.class,
TurtleTests.class,
ProfileUtilitiesTests.class,
ResourceRoundTripTests.class,
GraphQLEngineTests.class,
LiquidEngineTests.class,
FHIRPathTests.class,
NarrativeGeneratorTests.class,
ShexGeneratorTests.class,
BaseDateTimeTypeTest.class,
SnapShotGenerationTests.class,
FHIRMappingLanguageTests.class})
public class AllTests {
}

24
org.hl7.fhir.r4/src/test/java/org/hl7/fhir/r4/test/CDARoundTripTests.java
View File

@ -1,10 +1,5 @@
package org.hl7.fhir.r4.test;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
@ -15,14 +10,23 @@ import org.hl7.fhir.r4.elementmodel.Manager.FhirFormat;
import org.hl7.fhir.r4.formats.IParser.OutputStyle;
import org.hl7.fhir.utilities.cache.PackageCacheManager;
import org.hl7.fhir.utilities.cache.ToolsVersion;
import org.junit.Before;
import org.junit.Test;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.TestInstance;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
@Disabled
@TestInstance(TestInstance.Lifecycle.PER_CLASS)
public class CDARoundTripTests {
private SimpleWorkerContext context;
@Before
@BeforeAll
public void setUp() throws Exception {
context = new SimpleWorkerContext();
PackageCacheManager pcm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
@ -33,8 +37,8 @@ public class CDARoundTripTests {
@Test
public void testDCI() throws FHIRFormatError, DefinitionException, FileNotFoundException, IOException, FHIRException {
try {
Element e = Manager.parse(context, new FileInputStream("C:\\work\\org.hl7.fhir.us\\ccda-to-fhir-maps\\cda\\IAT2-Discharge_Summary-DCI.xml"), FhirFormat.XML);
Manager.compose(context, e, new FileOutputStream("C:\\temp\\ccda.xml"), FhirFormat.XML, OutputStyle.PRETTY, null);
Element e = Manager.parse(context, new FileInputStream("C:\\work\\org.hl7.fhir.us\\ccda-to-fhir-maps\\cda\\IAT2-Discharge_Summary-DCI.xml"), FhirFormat.XML);
Manager.compose(context, e, new FileOutputStream("C:\\temp\\ccda.xml"), FhirFormat.XML, OutputStyle.PRETTY, null);
// Manager.compose(context, e, new FileOutputStream("C:\\work\\org.hl7.fhir.test\\ccda-to-fhir-maps\\testdocuments\\IAT2-Discharge_Summary-DCI.out.json"), FhirFormat.JSON, OutputStyle.PRETTY, null);
// Manager.compose(context, e, new FileOutputStream("C:\\work\\org.hl7.fhir.test\\ccda-to-fhir-maps\\testdocuments\\IAT2-Discharge_Summary-DCI.out.ttl"), FhirFormat.TURTLE, OutputStyle.PRETTY, null);
} catch (Exception e) {

234
org.hl7.fhir.r4/src/test/java/org/hl7/fhir/r4/test/FHIRMappingLanguageTests.java
View File

@ -1,29 +1,13 @@
package org.hl7.fhir.r4.test;
import static org.junit.Assert.assertTrue;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import javax.xml.parsers.ParserConfigurationException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r4.context.SimpleWorkerContext;
import org.hl7.fhir.r4.elementmodel.Manager;
import org.hl7.fhir.r4.elementmodel.Manager.FhirFormat;
import org.hl7.fhir.r4.formats.IParser.OutputStyle;
import org.hl7.fhir.r4.formats.JsonParser;
import org.hl7.fhir.r4.model.Base;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.Resource;
import org.hl7.fhir.r4.model.ResourceFactory;
import org.hl7.fhir.r4.model.StructureDefinition;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.StructureDefinition.StructureDefinitionKind;
import org.hl7.fhir.r4.model.StructureMap;
import org.hl7.fhir.r4.terminologies.ConceptMapEngine;
import org.hl7.fhir.r4.test.utils.TestingUtilities;
import org.hl7.fhir.r4.utils.StructureMapUtilities;
@ -33,135 +17,133 @@ import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.cache.PackageCacheManager;
import org.hl7.fhir.utilities.cache.ToolsVersion;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.junit.BeforeClass;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.junit.runners.Parameterized;
import org.junit.runners.Parameterized.Parameters;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.Arguments;
import org.junit.jupiter.params.provider.MethodSource;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.xml.sax.SAXException;
@RunWith(Parameterized.class)
import javax.xml.parsers.ParserConfigurationException;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.stream.Stream;
import static org.junit.Assert.assertTrue;
@Disabled
public class FHIRMappingLanguageTests implements ITransformerServices {
private List<Resource> outputs = new ArrayList<Resource>();
private List<Resource> outputs = new ArrayList<Resource>();
static private SimpleWorkerContext context;
static private JsonParser jsonParser;
static private SimpleWorkerContext context;
static private JsonParser jsonParser;
@Parameters(name = "{index}: {0}")
public static Iterable<Object[]> data()
throws FileNotFoundException, IOException, ParserConfigurationException, SAXException {
Document tests = XMLUtil.parseFileToDom(TestingUtilities.resourceNameToFile("fml", "manifest.xml"));
Element test = XMLUtil.getFirstChild(tests.getDocumentElement());
List<Object[]> objects = new ArrayList<Object[]>();
while (test != null && test.getNodeName().equals("test")) {
objects.add(new Object[] { test.getAttribute("name"), test.getAttribute("source"), test.getAttribute("map"),
test.getAttribute("output") });
test = XMLUtil.getNextSibling(test);
}
return objects;
}
public static Stream<Arguments> data()
throws FileNotFoundException, IOException, ParserConfigurationException, SAXException {
Document tests = XMLUtil.parseFileToDom(TestingUtilities.resourceNameToFile("fml", "manifest.xml"));
Element test = XMLUtil.getFirstChild(tests.getDocumentElement());
List<Arguments> objects = new ArrayList();
while (test != null && test.getNodeName().equals("test")) {
objects.add(Arguments.of(test.getAttribute("name"), test.getAttribute("source"), test.getAttribute("map"),
test.getAttribute("output")));
test = XMLUtil.getNextSibling(test);
}
return objects.stream();
}
private final String name;
private String source;
private String output;
private String map;
public FHIRMappingLanguageTests(String name, String source, String map, String output) {
this.name = name;
this.source = source;
this.output = output;
this.map = map;
}
@BeforeClass
static public void setUp() throws Exception {
if (context == null) {
PackageCacheManager pcm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
@BeforeAll
static public void setUp() throws Exception {
if (context == null) {
PackageCacheManager pcm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
context = SimpleWorkerContext.fromPackage(pcm.loadPackage("hl7.fhir.core", "4.0.0"));
jsonParser = new JsonParser();
jsonParser.setOutputStyle(OutputStyle.PRETTY);
}
}
jsonParser = new JsonParser();
jsonParser.setOutputStyle(OutputStyle.PRETTY);
}
}
@Test
public void test() throws Exception {
@ParameterizedTest(name = "{index}: {0}")
@MethodSource("data")
public void test(String name, String source, String map, String output) throws Exception {
String fileSource = TestingUtilities.resourceNameToFile("fml", source);
String fileMap = TestingUtilities.resourceNameToFile("fml", map);
String fileOutput = TestingUtilities.resourceNameToFile("fml", output);
String fileOutputRes = TestingUtilities.resourceNameToFile("fml", output)+".out";
String fileSource = TestingUtilities.resourceNameToFile("fml", source);
String fileMap = TestingUtilities.resourceNameToFile("fml", map);
String fileOutput = TestingUtilities.resourceNameToFile("fml", output);
String fileOutputRes = TestingUtilities.resourceNameToFile("fml", output) + ".out";
outputs.clear();
outputs.clear();
boolean ok = false;
String msg = null;
Resource resource = null;
try {
StructureMapUtilities scu = new StructureMapUtilities(context, this);
org.hl7.fhir.r4.elementmodel.Element src = Manager.parse(context,
new ByteArrayInputStream(TextFile.fileToBytes(fileSource)), FhirFormat.JSON);
StructureMap structureMap = scu.parse(TextFile.fileToString(fileMap), name);
String typeName = scu.getTargetType(structureMap).getType();
resource = ResourceFactory.createResource(typeName);
scu.transform(null, src, structureMap, resource);
ok = true;
} catch (Exception e) {
ok = false;
msg = e.getMessage();
}
if (ok) {
ByteArrayOutputStream boas = new ByteArrayOutputStream();
jsonParser.compose(boas, resource);
log(boas.toString());
TextFile.bytesToFile(boas.toByteArray(), fileOutputRes);
msg = TestingUtilities.checkJsonIsSame(fileOutputRes,fileOutput);
assertTrue(msg, Utilities.noString(msg));
} else
assertTrue("Error, but proper output was expected (" + msg + ")", output.equals("$error"));
}
boolean ok = false;
String msg = null;
Resource resource = null;
try {
StructureMapUtilities scu = new StructureMapUtilities(context, this);
org.hl7.fhir.r4.elementmodel.Element src = Manager.parse(context,
new ByteArrayInputStream(TextFile.fileToBytes(fileSource)), FhirFormat.JSON);
StructureMap structureMap = scu.parse(TextFile.fileToString(fileMap), name);
String typeName = scu.getTargetType(structureMap).getType();
resource = ResourceFactory.createResource(typeName);
scu.transform(null, src, structureMap, resource);
ok = true;
} catch (Exception e) {
ok = false;
msg = e.getMessage();
}
if (ok) {
ByteArrayOutputStream boas = new ByteArrayOutputStream();
jsonParser.compose(boas, resource);
log(boas.toString());
TextFile.bytesToFile(boas.toByteArray(), fileOutputRes);
msg = TestingUtilities.checkJsonIsSame(fileOutputRes, fileOutput);
assertTrue(msg, Utilities.noString(msg));
} else
assertTrue("Error, but proper output was expected (" + msg + ")", output.equals("$error"));
}
@Override
public void log(String message) {
System.out.println(message);
}
@Override
public void log(String message) {
System.out.println(message);
}
@Override
public Base createType(Object appInfo, String name) throws FHIRException {
StructureDefinition sd = context.fetchResource(StructureDefinition.class, name);
if (sd != null && sd.getKind() == StructureDefinitionKind.LOGICAL) {
return Manager.build(context, sd);
} else {
if (name.startsWith("http://hl7.org/fhir/StructureDefinition/"))
name = name.substring("http://hl7.org/fhir/StructureDefinition/".length());
return ResourceFactory.createResourceOrType(name);
}
}
@Override
public Base createType(Object appInfo, String name) throws FHIRException {
StructureDefinition sd = context.fetchResource(StructureDefinition.class, name);
if (sd != null && sd.getKind() == StructureDefinitionKind.LOGICAL) {
return Manager.build(context, sd);
} else {
if (name.startsWith("http://hl7.org/fhir/StructureDefinition/"))
name = name.substring("http://hl7.org/fhir/StructureDefinition/".length());
return ResourceFactory.createResourceOrType(name);
}
}
@Override
public Base createResource(Object appInfo, Base res, boolean atRootofTransform) {
if (atRootofTransform)
outputs.add((Resource) res);
return res;
}
@Override
public Base createResource(Object appInfo, Base res, boolean atRootofTransform) {
if (atRootofTransform)
outputs.add((Resource) res);
return res;
}
@Override
public Coding translate(Object appInfo, Coding source, String conceptMapUrl) throws FHIRException {
ConceptMapEngine cme = new ConceptMapEngine(context);
return cme.translate(source, conceptMapUrl);
}
@Override
public Coding translate(Object appInfo, Coding source, String conceptMapUrl) throws FHIRException {
ConceptMapEngine cme = new ConceptMapEngine(context);
return cme.translate(source, conceptMapUrl);
}
@Override
public Base resolveReference(Object appContext, String url) throws FHIRException {
throw new FHIRException("resolveReference is not supported yet");
}
@Override
public Base resolveReference(Object appContext, String url) throws FHIRException {
throw new FHIRException("resolveReference is not supported yet");
}
@Override
public List<Base> performSearch(Object appContext, String url) throws FHIRException {
throw new FHIRException("performSearch is not supported yet");
}
@Override
public List<Base> performSearch(Object appContext, String url) throws FHIRException {
throw new FHIRException("performSearch is not supported yet");
}
}

111
org.hl7.fhir.r4/src/test/java/org/hl7/fhir/r4/test/FHIRPathTests.java
View File

@ -1,5 +1,29 @@
package org.hl7.fhir.r4.test;
import junit.framework.Assert;
import org.apache.commons.lang3.NotImplementedException;
import org.fhir.ucum.UcumException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.PathEngineException;
import org.hl7.fhir.r4.formats.XmlParser;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.test.utils.TestingUtilities;
import org.hl7.fhir.r4.utils.FHIRPathEngine;
import org.hl7.fhir.r4.utils.FHIRPathEngine.IEvaluationContext;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.TestInstance;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.Arguments;
import org.junit.jupiter.params.provider.MethodSource;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
import org.xml.sax.SAXException;
import javax.xml.parsers.ParserConfigurationException;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
@ -7,41 +31,10 @@ import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.stream.Stream;
import javax.xml.parsers.ParserConfigurationException;
import org.apache.commons.lang3.NotImplementedException;
import org.fhir.ucum.UcumEssenceService;
import org.fhir.ucum.UcumException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.PathEngineException;
import org.hl7.fhir.r4.context.SimpleWorkerContext;
import org.hl7.fhir.r4.formats.XmlParser;
import org.hl7.fhir.r4.model.Base;
import org.hl7.fhir.r4.model.BooleanType;
import org.hl7.fhir.r4.model.ExpressionNode;
import org.hl7.fhir.r4.model.PrimitiveType;
import org.hl7.fhir.r4.model.Quantity;
import org.hl7.fhir.r4.model.Resource;
import org.hl7.fhir.r4.model.TypeDetails;
import org.hl7.fhir.r4.model.ValueSet;
import org.hl7.fhir.r4.test.utils.TestingUtilities;
import org.hl7.fhir.r4.utils.FHIRPathEngine;
import org.hl7.fhir.r4.utils.FHIRPathEngine.IEvaluationContext;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.junit.runners.Parameterized;
import org.junit.runners.Parameterized.Parameters;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
import org.xml.sax.SAXException;
import junit.framework.Assert;
@RunWith(Parameterized.class)
@Disabled
@TestInstance(TestInstance.Lifecycle.PER_CLASS)
public class FHIRPathTests {
public class FHIRPathTestEvaluationServices implements IEvaluationContext {
@ -63,7 +56,7 @@ public class FHIRPathTests {
@Override
public FunctionDetails resolveFunction(String functionName) {
throw new NotImplementedException("Not done yet (FHIRPathTestEvaluationServices.resolveFunction), when item is element (for "+functionName+")");
throw new NotImplementedException("Not done yet (FHIRPathTestEvaluationServices.resolveFunction), when item is element (for " + functionName + ")");
}
@Override
@ -87,8 +80,8 @@ public class FHIRPathTests {
return true;
if (url.equals("http://hl7.org/fhir/StructureDefinition/Person"))
return false;
throw new FHIRException("unknown profile "+url);
throw new FHIRException("unknown profile " + url);
}
@Override
@ -99,24 +92,26 @@ public class FHIRPathTests {
private static FHIRPathEngine fp;
@Parameters(name = "{index}: file {0}")
public static Iterable<Object[]> data() throws ParserConfigurationException, SAXException, IOException {
@BeforeAll
public void setup() {
fp = new FHIRPathEngine(TestingUtilities.context());
}
public static Stream<Arguments> data() throws ParserConfigurationException, SAXException, IOException {
Document dom = XMLUtil.parseFileToDom(TestingUtilities.resourceNameToFile("fhirpath", "tests-fhir-r4.xml"));
List<Element> list = new ArrayList<Element>();
List<Element> groups = new ArrayList<Element>();
XMLUtil.getNamedChildren(dom.getDocumentElement(), "group", groups);
for (Element g : groups) {
XMLUtil.getNamedChildren(g, "test", list);
XMLUtil.getNamedChildren(g, "test", list);
}
List<Object[]> objects = new ArrayList<Object[]>(list.size());
List<Arguments> objects = new ArrayList();
for (Element e : list) {
objects.add(new Object[] { getName(e), e });
objects.add(Arguments.of(getName(e), e));
}
return objects;
return objects.stream();
}
private static Object getName(Element e) {
@ -130,27 +125,21 @@ public class FHIRPathTests {
else if (c instanceof Element)
ndx++;
}
if (Utilities.noString(s))
s = "?? - G "+p.getAttribute("name")+"["+Integer.toString(ndx+1)+"]";
if (Utilities.noString(s))
s = "?? - G " + p.getAttribute("name") + "[" + Integer.toString(ndx + 1) + "]";
else
s = s + " - G "+p.getAttribute("name")+"["+Integer.toString(ndx+1)+"]";
s = s + " - G " + p.getAttribute("name") + "[" + Integer.toString(ndx + 1) + "]";
return s;
}
private final Element test;
private final String name;
private Map<String, Resource> resources = new HashMap<String, Resource>();
public FHIRPathTests(String name, Element e) {
this.name = name;
this.test = e;
}
@SuppressWarnings("deprecation")
@Test
public void test() throws FileNotFoundException, IOException, FHIRException, org.hl7.fhir.exceptions.FHIRException, UcumException {
if (fp == null)
fp = new FHIRPathEngine(TestingUtilities.context());
@ParameterizedTest(name = "{index}: file {0}")
@MethodSource("data")
public void test(String name, Element test) throws FileNotFoundException, IOException, FHIRException, org.hl7.fhir.exceptions.FHIRException, UcumException {
fp.setHostServices(new FHIRPathTestEvaluationServices());
String input = test.getAttribute("inputfile");
String expression = XMLUtil.getNamedChild(test, "expression").getTextContent();
@ -174,7 +163,7 @@ public class FHIRPathTests {
outcome = fp.evaluate(res, node);
Assert.assertTrue(String.format("Expected exception parsing %s", expression), !fail);
} catch (Exception e) {
Assert.assertTrue(String.format("Unexpected exception parsing %s: "+e.getMessage(), expression), fail);
Assert.assertTrue(String.format("Unexpected exception parsing %s: " + e.getMessage(), expression), fail);
}
if ("true".equals(test.getAttribute("predicate"))) {
@ -199,7 +188,7 @@ public class FHIRPathTests {
boolean found = false;
for (Element e : expected) {
if ((Utilities.noString(e.getAttribute("type")) || e.getAttribute("type").equals(tn)) &&
(Utilities.noString(e.getTextContent()) || e.getTextContent().equals(s)))
(Utilities.noString(e.getTextContent()) || e.getTextContent().equals(s)))
found = true;
}
Assert.assertTrue(String.format("Outcome %d: Value %s of type %s not expected for %s", i, s, tn, expression), found);
@ -217,7 +206,7 @@ public class FHIRPathTests {
Assert.assertTrue(String.format("Outcome %d: Value should be %s but was %s", i, v, outcome.get(i).toString()), outcome.get(i).equalsDeep(q));
} else {
Assert.assertTrue(String.format("Outcome %d: Value should be a primitive type but was %s", i, outcome.get(i).fhirType()), outcome.get(i) instanceof PrimitiveType);
Assert.assertTrue(String.format("Outcome %d: Value should be %s but was %s for expression %s", i, v, outcome.get(i).toString(), expression), v.equals(((PrimitiveType)outcome.get(i)).asStringValue()));
Assert.assertTrue(String.format("Outcome %d: Value should be %s but was %s for expression %s", i, v, outcome.get(i).toString(), expression), v.equals(((PrimitiveType) outcome.get(i)).asStringValue()));
}
}
}

100
org.hl7.fhir.r4/src/test/java/org/hl7/fhir/r4/test/GeneratorTestFragments.java
View File

@ -1,68 +1,62 @@
package org.hl7.fhir.r4.test;
import java.io.IOException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.DateTimeType;
import org.hl7.fhir.r4.model.Narrative;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.Narrative.NarrativeStatus;
import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.r4.model.Observation.ObservationStatus;
import org.hl7.fhir.r4.model.Quantity;
import org.hl7.fhir.r4.model.Reference;
import org.hl7.fhir.utilities.xhtml.XhtmlParser;
import java.io.IOException;
public class GeneratorTestFragments {
private void test() throws FHIRFormatError, IOException {
Observation res = new Observation();
res.setId("example");
Narrative n = new Narrative();
res.setText(n);
n.setStatus(NarrativeStatus.GENERATED);
n.setDiv(new XhtmlParser().parse("<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: example</p><p><b>status</b>: final</p><p><b>category</b>: Vital Signs <span>(Details : {http://hl7.org/fhir/observation-category code &#39;vital-signs&#39; = &#39;Vital Signs&#39;, given as &#39;Vital Signs&#39;})</span></p><p><b>code</b>: Body Weight <span>(Details : {LOINC code &#39;29463-7&#39; = &#39;Body weight&#39;, given as &#39;Body Weight&#39;}; {LOINC code &#39;3141-9&#39; = &#39;Body weight Measured&#39;, given as &#39;Body weight Measured&#39;}; {SNOMED CT code &#39;27113001&#39; = &#39;Body weight&#39;, given as &#39;Body weight&#39;}; {http://acme.org/devices/clinical-codes code &#39;body-weight&#39; = &#39;body-weight&#39;, given as &#39;Body Weight&#39;})</span></p><p><b>subject</b>: <a>Patient/example</a></p><p><b>context</b>: <a>Encounter/example</a></p><p><b>effective</b>: 28/03/2016</p><p><b>value</b>: 185 lbs<span> (Details: UCUM code [lb_av] = &#39;lb_av&#39;)</span></p></div>", "div"));
res.setStatus(ObservationStatus.FINAL);
CodeableConcept cc = res.addCategory();
Coding c = cc.addCoding();
c.setSystem("http://hl7.org/fhir/observation-category");
c.setCode("vital-signs");
c.setDisplay("Vital Signs");
cc = new CodeableConcept();
res.setCode(cc);
c = cc.addCoding();
c.setSystem("http://loinc.org");
c.setCode("29463-7");
c.setDisplay("Body Weight");
c = cc.addCoding();
c.setSystem("http://loinc.org");
c.setCode("3141-9");
c.setDisplay("Body weight Measured");
c = cc.addCoding();
c.setSystem("http://snomed.info/sct");
c.setCode("27113001");
c.setDisplay("Body weight");
c = cc.addCoding();
c.setSystem("http://acme.org/devices/clinical-codes");
c.setCode("body-weight");
c.setDisplay("Body Weight");
Reference r = new Reference();
res.setSubject(r);
r.setReference("Patient/example");
r = new Reference();
res.setEncounter(r);
r.setReference("Encounter/example");
res.setEffective(new DateTimeType("2016-03-28"));
Quantity q = new Quantity();
res.setValue(q);
q.setValue(185);
q.setUnit("lbs");
q.setSystem("http://unitsofmeasure.org");
q.setCode("[lb_av]");
Observation res = new Observation();
res.setId("example");
Narrative n = new Narrative();
res.setText(n);
n.setStatus(NarrativeStatus.GENERATED);
n.setDiv(new XhtmlParser().parse("<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: example</p><p><b>status</b>: final</p><p><b>category</b>: Vital Signs <span>(Details : {http://hl7.org/fhir/observation-category code &#39;vital-signs&#39; = &#39;Vital Signs&#39;, given as &#39;Vital Signs&#39;})</span></p><p><b>code</b>: Body Weight <span>(Details : {LOINC code &#39;29463-7&#39; = &#39;Body weight&#39;, given as &#39;Body Weight&#39;}; {LOINC code &#39;3141-9&#39; = &#39;Body weight Measured&#39;, given as &#39;Body weight Measured&#39;}; {SNOMED CT code &#39;27113001&#39; = &#39;Body weight&#39;, given as &#39;Body weight&#39;}; {http://acme.org/devices/clinical-codes code &#39;body-weight&#39; = &#39;body-weight&#39;, given as &#39;Body Weight&#39;})</span></p><p><b>subject</b>: <a>Patient/example</a></p><p><b>context</b>: <a>Encounter/example</a></p><p><b>effective</b>: 28/03/2016</p><p><b>value</b>: 185 lbs<span> (Details: UCUM code [lb_av] = &#39;lb_av&#39;)</span></p></div>", "div"));
res.setStatus(ObservationStatus.FINAL);
CodeableConcept cc = res.addCategory();
Coding c = cc.addCoding();
c.setSystem("http://hl7.org/fhir/observation-category");
c.setCode("vital-signs");
c.setDisplay("Vital Signs");
cc = new CodeableConcept();
res.setCode(cc);
c = cc.addCoding();
c.setSystem("http://loinc.org");
c.setCode("29463-7");
c.setDisplay("Body Weight");
c = cc.addCoding();
c.setSystem("http://loinc.org");
c.setCode("3141-9");
c.setDisplay("Body weight Measured");
c = cc.addCoding();
c.setSystem("http://snomed.info/sct");
c.setCode("27113001");
c.setDisplay("Body weight");
c = cc.addCoding();
c.setSystem("http://acme.org/devices/clinical-codes");
c.setCode("body-weight");
c.setDisplay("Body Weight");
Reference r = new Reference();
res.setSubject(r);
r.setReference("Patient/example");
r = new Reference();
res.setEncounter(r);
r.setReference("Encounter/example");
res.setEffective(new DateTimeType("2016-03-28"));
Quantity q = new Quantity();
res.setValue(q);
q.setValue(185);
q.setUnit("lbs");
q.setSystem("http://unitsofmeasure.org");
q.setCode("[lb_av]");
}
}

73
org.hl7.fhir.r4/src/test/java/org/hl7/fhir/r4/test/GraphQLEngineTests.java
View File

@ -9,7 +9,6 @@ import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.r4.model.Bundle.BundleLinkComponent;
import org.hl7.fhir.r4.model.Bundle.SearchEntryMode;
import org.hl7.fhir.r4.model.DomainResource;
import org.hl7.fhir.r4.model.Reference;
import org.hl7.fhir.r4.model.Resource;
import org.hl7.fhir.r4.test.utils.TestingUtilities;
import org.hl7.fhir.r4.utils.GraphQLEngine;
@ -20,10 +19,10 @@ import org.hl7.fhir.utilities.graphql.IGraphQLStorageServices;
import org.hl7.fhir.utilities.graphql.NameValue;
import org.hl7.fhir.utilities.graphql.Parser;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.junit.runners.Parameterized;
import org.junit.runners.Parameterized.Parameters;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.Arguments;
import org.junit.jupiter.params.provider.MethodSource;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.xml.sax.SAXException;
@ -35,52 +34,37 @@ import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.stream.Stream;
import static org.junit.Assert.assertTrue;
@RunWith(Parameterized.class)
@Disabled
public class GraphQLEngineTests implements IGraphQLStorageServices {
@Parameters(name = "{index}: {0}")
public static Iterable<Object[]> data() throws FileNotFoundException, IOException, ParserConfigurationException, SAXException {
public static Stream<Arguments> data() throws FileNotFoundException, IOException, ParserConfigurationException, SAXException {
Document tests = XMLUtil.parseFileToDom(TestingUtilities.resourceNameToFile("graphql", "manifest.xml"));
Element test = XMLUtil.getFirstChild(tests.getDocumentElement());
List<Object[]> objects = new ArrayList<Object[]>();
List<Arguments> objects = new ArrayList<>();
while (test != null && test.getNodeName().equals("test")) {
objects.add(new Object[] { test.getAttribute("name"), test.getAttribute("source"), test.getAttribute("output"),
test.getAttribute("context"), test.getAttribute("resource"), test.getAttribute("operation")} );
objects.add(Arguments.of(new Object[]{test.getAttribute("name"), test.getAttribute("source"), test.getAttribute("output"),
test.getAttribute("context"), test.getAttribute("resource"), test.getAttribute("operation")}));
test = XMLUtil.getNextSibling(test);
}
return objects;
return objects.stream();
}
private final String name;
private String source;
private String output;
private String context;
private String resource;
private String operation;
public GraphQLEngineTests(String name, String source, String output, String context, String resource, String operation) {
this.name = name;
this.source = source;
this.output = output;
this.context = context;
this.resource = resource;
this.operation = operation;
}
@Test
public void test() throws Exception {
@ParameterizedTest(name = "{index}: {0}")
@MethodSource("data")
public void test(String name, String source, String output, String context, String resource, String operation) throws Exception {
String filename = null;
if (!Utilities.noString(context)) {
String[] parts = context.split("/");
if (parts.length != 3)
throw new Exception("not done yet "+source+" "+output+" "+context);
if (!Utilities.noString(resource))
filename = TestingUtilities.resourceNameToFile(resource+".xml");
throw new Exception("not done yet " + source + " " + output + " " + context);
if (!Utilities.noString(resource))
filename = TestingUtilities.resourceNameToFile(resource + ".xml");
else
filename = TestingUtilities.resourceNameToFile(parts[0].toLowerCase()+"-"+parts[1].toLowerCase()+".xml");
filename = TestingUtilities.resourceNameToFile(parts[0].toLowerCase() + "-" + parts[1].toLowerCase() + ".xml");
}
GraphQLEngine gql = new GraphQLEngine(TestingUtilities.context());
@ -106,18 +90,17 @@ public class GraphQLEngineTests implements IGraphQLStorageServices {
StringBuilder str = new StringBuilder();
gql.getOutput().setWriteWrapper(false);
gql.getOutput().write(str, 0);
TextFile.stringToFile(str.toString(), TestingUtilities.resourceNameToFile("graphql", output+".out"));
msg = TestingUtilities.checkJsonIsSame(TestingUtilities.resourceNameToFile("graphql", output+".out"), TestingUtilities.resourceNameToFile("graphql", output));
TextFile.stringToFile(str.toString(), TestingUtilities.resourceNameToFile("graphql", output + ".out"));
msg = TestingUtilities.checkJsonIsSame(TestingUtilities.resourceNameToFile("graphql", output + ".out"), TestingUtilities.resourceNameToFile("graphql", output));
assertTrue(msg, Utilities.noString(msg));
}
else
assertTrue("Error, but proper output was expected ("+msg+")", output.equals("$error"));
} else
assertTrue("Error, but proper output was expected (" + msg + ")", output.equals("$error"));
}
@Override
public Resource lookup(Object appInfo, String type, String id) throws FHIRException {
public Resource lookup(Object appInfo, String type, String id) throws FHIRException {
try {
String filename = TestingUtilities.resourceNameToFile(type.toLowerCase()+'-'+id.toLowerCase()+".xml");
String filename = TestingUtilities.resourceNameToFile(type.toLowerCase() + '-' + id.toLowerCase() + ".xml");
if (new File(filename).exists())
return new XmlParser().parse(new FileInputStream(filename));
else
@ -133,14 +116,14 @@ public class GraphQLEngineTests implements IGraphQLStorageServices {
if (reference.getReferenceElement().isLocal()) {
if (!(context instanceof DomainResource))
return null;
for (Resource r : ((DomainResource)context).getContained()) {
if (('#'+r.getId()).equals(reference.getReferenceElement().getValue())) {
for (Resource r : ((DomainResource) context).getContained()) {
if (('#' + r.getId()).equals(reference.getReferenceElement().getValue())) {
return new ReferenceResolution(context, r);
}
}
} else {
String[] parts = reference.getReferenceElement().getValue().split("/");
String filename = TestingUtilities.resourceNameToFile(parts[0].toLowerCase()+'-'+parts[1].toLowerCase()+".xml");
String filename = TestingUtilities.resourceNameToFile(parts[0].toLowerCase() + '-' + parts[1].toLowerCase() + ".xml");
if (new File(filename).exists())
return new ReferenceResolution(null, new XmlParser().parse(new FileInputStream(filename)));
}
@ -153,7 +136,7 @@ public class GraphQLEngineTests implements IGraphQLStorageServices {
@Override
public void listResources(Object appInfo, String type, List<Argument> searchParams, List<IBaseResource> matches) throws FHIRException {
try {
if (type.equals("Condition"))
if (type.equals("Condition"))
matches.add(new XmlParser().parse(new FileInputStream(TestingUtilities.resourceNameToFile("condition-example.xml"))));
else if (type.equals("Patient")) {
matches.add(new XmlParser().parse(new FileInputStream(TestingUtilities.resourceNameToFile("patient-example.xml"))));

54
org.hl7.fhir.r4/src/test/java/org/hl7/fhir/r4/test/GraphQLParserTests.java
View File

@ -1,12 +1,5 @@
package org.hl7.fhir.r4.test;
import static org.junit.Assert.assertTrue;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import org.hl7.fhir.r4.test.utils.TestingUtilities;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
@ -14,43 +7,38 @@ import org.hl7.fhir.utilities.graphql.EGraphEngine;
import org.hl7.fhir.utilities.graphql.EGraphQLException;
import org.hl7.fhir.utilities.graphql.Package;
import org.hl7.fhir.utilities.graphql.Parser;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.junit.runners.Parameterized;
import org.junit.runners.Parameterized.Parameters;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.Arguments;
import org.junit.jupiter.params.provider.MethodSource;
@RunWith(Parameterized.class)
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.stream.Stream;
import static org.junit.Assert.assertTrue;
@Disabled
public class GraphQLParserTests {
@Parameters(name = "{index}: {0}")
public static Iterable<Object[]> data() throws FileNotFoundException, IOException {
public static Stream<Arguments> data() throws FileNotFoundException, IOException {
String src = TextFile.fileToString(TestingUtilities.resourceNameToFile("graphql", "parser-tests.gql"));
String[] tests = src.split("###");
int i = 0;
for (String s : tests)
if (!Utilities.noString(s.trim()))
i++;
List<Object[]> objects = new ArrayList<Object[]>(i);
i = 0;
List<Arguments> objects = new ArrayList<>();
for (String s : tests) {
if (!Utilities.noString(s.trim())) {
int l = s.indexOf('\r');
objects.add(new Object[] { s.substring(0, l), s.substring(l+2).trim()});
int l = s.indexOf('\r');
objects.add(Arguments.of(s.substring(0, l), s.substring(l + 2).trim()));
}
}
return objects;
return objects.stream();
}
private final String test;
private final String name;
public GraphQLParserTests(String name, String test) {
this.name = name;
this.test = test;
}
@Test
public void test() throws IOException, EGraphQLException, EGraphEngine {
@ParameterizedTest(name = "{index}: {0}")
@MethodSource("data")
public void test(String name, String test) throws IOException, EGraphQLException, EGraphEngine {
Package doc = Parser.parse(test);
assertTrue(doc != null);
}

17
org.hl7.fhir.r4/src/test/java/org/hl7/fhir/r4/test/JsonDirectTests.java
View File

@ -1,11 +1,5 @@
package org.hl7.fhir.r4.test;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import org.apache.commons.io.FileUtils;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r4.formats.IParser.OutputStyle;
@ -13,15 +7,14 @@ import org.hl7.fhir.r4.formats.JsonParser;
import org.hl7.fhir.r4.formats.XmlParser;
import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.utilities.Utilities;
import org.junit.Before;
import org.junit.Test;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
import java.io.*;
@Disabled
public class JsonDirectTests {
@Before
public void setUp() throws Exception {
}
@Test
public void test() throws FHIRFormatError, FileNotFoundException, IOException {
File src = new File(Utilities.path("[tmp]", "obs.xml"));

38
org.hl7.fhir.r4/src/test/java/org/hl7/fhir/r4/test/LiquidEngineTests.java
View File

@ -1,17 +1,11 @@
package org.hl7.fhir.r4.test;
import java.io.FileInputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import javax.xml.parsers.ParserConfigurationException;
import com.google.gson.JsonArray;
import com.google.gson.JsonElement;
import com.google.gson.JsonObject;
import junit.framework.Assert;
import org.apache.commons.collections4.map.HashedMap;
import org.fhir.ucum.UcumEssenceService;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r4.context.SimpleWorkerContext;
import org.hl7.fhir.r4.formats.XmlParser;
import org.hl7.fhir.r4.model.Resource;
import org.hl7.fhir.r4.test.utils.TestingUtilities;
@ -19,36 +13,37 @@ import org.hl7.fhir.r4.utils.LiquidEngine;
import org.hl7.fhir.r4.utils.LiquidEngine.ILiquidEngineIcludeResolver;
import org.hl7.fhir.r4.utils.LiquidEngine.LiquidDocument;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.junit.Before;
import org.junit.Ignore;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.junit.runners.Parameterized;
import org.junit.runners.Parameterized.Parameters;
import org.xml.sax.SAXException;
import com.google.gson.JsonArray;
import com.google.gson.JsonElement;
import com.google.gson.JsonObject;
import junit.framework.Assert;
import javax.xml.parsers.ParserConfigurationException;
import java.io.FileInputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
@RunWith(Parameterized.class)
public class LiquidEngineTests implements ILiquidEngineIcludeResolver {
private static Map<String, Resource> resources = new HashedMap<>();
private static JsonObject testdoc = null;
private JsonObject test;
private LiquidEngine engine;
@Parameters(name = "{index}: file{0}")
public static Iterable<Object[]> data() throws ParserConfigurationException, SAXException, IOException {
testdoc = (JsonObject) new com.google.gson.JsonParser().parse(TextFile.fileToString(TestingUtilities.resourceNameToFile("liquid", "liquid-tests.json")));
JsonArray tests = testdoc.getAsJsonArray("tests");
List<Object[]> objects = new ArrayList<Object[]>(tests.size());
for (JsonElement n : tests) {
objects.add(new Object[] {n});
objects.add(new Object[]{n});
}
return objects;
}
@ -76,14 +71,15 @@ public class LiquidEngineTests implements ILiquidEngineIcludeResolver {
private Resource loadResource() throws IOException, FHIRFormatError {
String name = test.get("focus").getAsString();
if (!resources.containsKey(name)) {
String fn = TestingUtilities.resourceNameToFile(name.replace("/", "-")+".xml");
String fn = TestingUtilities.resourceNameToFile(name.replace("/", "-") + ".xml");
resources.put(name, new XmlParser().parse(new FileInputStream(fn)));
}
return resources.get(test.get("focus").getAsString());
}
@Test
@Ignore
public void test() throws Exception {
LiquidDocument doc = engine.parse(test.get("template").getAsString(), "test-script");
String output = engine.evaluate(doc, loadResource(), null);

21
org.hl7.fhir.r4/src/test/java/org/hl7/fhir/r4/test/MetaTest.java
View File

@ -2,12 +2,11 @@ package org.hl7.fhir.r4.test;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.Meta;
import org.junit.Test;
import static org.junit.Assert.*;
import static org.junit.Assert.assertEquals;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
public class MetaTest {
public static String TEST_SYSTEM = "TEST_SYSTEM";
public static String TEST_CODE = "TEST_CODE";
@ -15,12 +14,12 @@ public class MetaTest {
public void testMetaSecurity() {
Meta meta = new Meta();
Coding coding = meta.addSecurity().setSystem(TEST_SYSTEM).setCode(TEST_CODE);
assertTrue(meta.hasSecurity());
assertNotNull(meta.getSecurity());
assertNotNull(meta.getSecurity(TEST_SYSTEM, TEST_CODE));
assertEquals(1, meta.getSecurity().size());
assertEquals(meta.getSecurity().get(0), meta.getSecurity(TEST_SYSTEM, TEST_CODE));
assertEquals(meta.getSecurityFirstRep(), meta.getSecurity(TEST_SYSTEM, TEST_CODE));
assertEquals(coding, meta.getSecurity(TEST_SYSTEM, TEST_CODE));
Assertions.assertTrue(meta.hasSecurity());
Assertions.assertNotNull(meta.getSecurity());
Assertions.assertNotNull(meta.getSecurity(TEST_SYSTEM, TEST_CODE));
Assertions.assertEquals(1, meta.getSecurity().size());
Assertions.assertEquals(meta.getSecurity().get(0), meta.getSecurity(TEST_SYSTEM, TEST_CODE));
Assertions.assertEquals(meta.getSecurityFirstRep(), meta.getSecurity(TEST_SYSTEM, TEST_CODE));
Assertions.assertEquals(coding, meta.getSecurity(TEST_SYSTEM, TEST_CODE));
}
}

64
org.hl7.fhir.r4/src/test/java/org/hl7/fhir/r4/test/NarrativeGeneratorTests.java
View File

@ -1,51 +1,47 @@
package org.hl7.fhir.r4.test;
import org.fhir.ucum.UcumException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r4.formats.XmlParser;
import org.hl7.fhir.r4.model.DomainResource;
import org.hl7.fhir.r4.test.utils.TestingUtilities;
import org.hl7.fhir.r4.utils.EOperationOutcome;
import org.hl7.fhir.r4.utils.NarrativeGenerator;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.TestInstance;
import org.xmlpull.v1.XmlPullParserException;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import org.fhir.ucum.UcumException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r4.context.SimpleWorkerContext;
import org.hl7.fhir.r4.formats.XmlParser;
import org.hl7.fhir.r4.model.DomainResource;
import org.hl7.fhir.r4.test.utils.TestingUtilities;
import org.hl7.fhir.r4.utils.EOperationOutcome;
import org.hl7.fhir.r4.utils.NarrativeGenerator;
import org.hl7.fhir.utilities.Utilities;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
import org.xmlpull.v1.XmlPullParserException;
@Disabled
@TestInstance(TestInstance.Lifecycle.PER_CLASS)
public class NarrativeGeneratorTests {
private NarrativeGenerator gen;
@Before
public void setUp() throws FileNotFoundException, IOException, FHIRException, UcumException {
if (gen == null)
gen = new NarrativeGenerator("", null, TestingUtilities.context());
}
private NarrativeGenerator gen;
@After
public void tearDown() {
}
@BeforeAll
public void setUp() throws FHIRException {
gen = new NarrativeGenerator("", null, TestingUtilities.context());
}
@Test
public void test() throws FileNotFoundException, IOException, XmlPullParserException, EOperationOutcome, FHIRException {
process(TestingUtilities.resourceNameToFile("questionnaireresponse-example-f201-lifelines.xml"));
}
@Test
public void test() throws FileNotFoundException, IOException, XmlPullParserException, EOperationOutcome, FHIRException {
process(TestingUtilities.resourceNameToFile("questionnaireresponse-example-f201-lifelines.xml"));
}
private void process(String path) throws FileNotFoundException, IOException, XmlPullParserException, EOperationOutcome, FHIRException {
XmlParser p = new XmlParser();
DomainResource r = (DomainResource) p.parse(new FileInputStream(path));
gen.generate(r, null);
FileOutputStream s = new FileOutputStream(TestingUtilities.resourceNameToFile("gen", "gen.xml"));
private void process(String path) throws FileNotFoundException, IOException, XmlPullParserException, EOperationOutcome, FHIRException {
XmlParser p = new XmlParser();
DomainResource r = (DomainResource) p.parse(new FileInputStream(path));
gen.generate(r, null);
FileOutputStream s = new FileOutputStream(TestingUtilities.resourceNameToFile("gen", "gen.xml"));
new XmlParser().compose(s, r, true);
s.close();
}
}

47
org.hl7.fhir.r4/src/test/java/org/hl7/fhir/r4/test/ProfileUtilitiesTests.java
View File

@ -1,15 +1,8 @@
package org.hl7.fhir.r4.test;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import org.fhir.ucum.UcumException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r4.conformance.ProfileUtilities;
import org.hl7.fhir.r4.context.SimpleWorkerContext;
import org.hl7.fhir.r4.formats.IParser.OutputStyle;
import org.hl7.fhir.r4.formats.XmlParser;
import org.hl7.fhir.r4.model.Base;
@ -21,12 +14,19 @@ import org.hl7.fhir.r4.utils.EOperationOutcome;
import org.hl7.fhir.utilities.CSFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.junit.Test;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
@Disabled
public class ProfileUtilitiesTests {
// /**
// /**
// * This is simple: we just create an empty differential, generate the snapshot, and then insist it must match the base
// *
// * @param context2
@ -50,9 +50,9 @@ public class ProfileUtilitiesTests {
ElementDefinition b = base.getSnapshot().getElement().get(i);
ElementDefinition f = focus.getSnapshot().getElement().get(i);
if (ok) {
if (!f.hasBase())
if (!f.hasBase())
ok = false;
else if (!b.getPath().equals(f.getPath()))
else if (!b.getPath().equals(f.getPath()))
ok = false;
else {
b.setBase(null);
@ -65,12 +65,12 @@ public class ProfileUtilitiesTests {
if (!ok) {
compareXml(base, focus);
throw new FHIRException("Snap shot generation simple test failed");
} else
} else
System.out.println("Snap shot generation simple test passed");
}
//
//
// /**
// * This is simple: we just create an empty differential, generate the snapshot, and then insist it must match the base. for a different resource with recursion
// *
@ -86,14 +86,14 @@ public class ProfileUtilitiesTests {
focus.setSnapshot(null);
focus.setDifferential(null);
List<ValidationMessage> messages = new ArrayList<ValidationMessage>();
new ProfileUtilities(TestingUtilities.context(), messages, null).generateSnapshot(base, focus, focus.getUrl(), "http://hl7.org/fhir/R4", "Simple Test" );
new ProfileUtilities(TestingUtilities.context(), messages, null).generateSnapshot(base, focus, focus.getUrl(), "http://hl7.org/fhir/R4", "Simple Test");
boolean ok = base.getSnapshot().getElement().size() == focus.getSnapshot().getElement().size();
for (int i = 0; i < base.getSnapshot().getElement().size(); i++) {
if (ok) {
ElementDefinition b = base.getSnapshot().getElement().get(i);
ElementDefinition f = focus.getSnapshot().getElement().get(i);
if (!f.hasBase() || !b.getPath().equals(f.getPath()))
if (!f.hasBase() || !b.getPath().equals(f.getPath()))
ok = false;
else {
f.setBase(null);
@ -102,12 +102,12 @@ public class ProfileUtilitiesTests {
}
}
}
if (!ok) {
compareXml(base, focus);
System.out.println("Snap shot generation simple test failed");
throw new FHIRException("Snap shot generation simple test failed");
} else
} else
System.out.println("Snap shot generation simple test passed");
}
@ -793,8 +793,10 @@ public class ProfileUtilitiesTests {
// focus.setDifferential(null);
String f1 = Utilities.path("c:", "temp", "base.xml");
String f2 = Utilities.path("c:", "temp", "derived.xml");
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(f1), base);;
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(f2), focus);;
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(f1), base);
;
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(f2), focus);
;
String diff = Utilities.path(System.getenv("ProgramFiles(X86)"), "WinMerge", "WinMergeU.exe");
List<String> command = new ArrayList<String>();
command.add("\"" + diff + "\" \"" + f1 + "\" \"" + f2 + "\"");
@ -803,7 +805,6 @@ public class ProfileUtilitiesTests {
builder.directory(new CSFile("c:\\temp"));
builder.start();
}
}

34
org.hl7.fhir.r4/src/test/java/org/hl7/fhir/r4/test/QuestionnaireBuilderTester.java
View File

@ -1,33 +1,33 @@
package org.hl7.fhir.r4.test;
import java.io.File;
import java.io.FileInputStream;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r4.formats.XmlParser;
import org.hl7.fhir.r4.model.StructureDefinition;
import org.hl7.fhir.r4.utils.QuestionnaireBuilder;
import java.io.File;
import java.io.FileInputStream;
public class QuestionnaireBuilderTester {
private static final String TEST_PROFILE_DIR = "C:\\work\\org.hl7.fhir\\build\\publish";
private static final String TEST_DEST = "c:\\temp\\questionnaires\\";
private static final String TEST_PROFILE_DIR = "C:\\work\\org.hl7.fhir\\build\\publish";
private static final String TEST_DEST = "c:\\temp\\questionnaires\\";
public static void main(String[] args) {
QuestionnaireBuilder b = new QuestionnaireBuilder(null);
for (String f : new File(TEST_PROFILE_DIR).list()) {
if (f.endsWith(".profile.xml") && !f.contains("type-")) {
System.out.println("process "+f);
try {
StructureDefinition p = (StructureDefinition) new XmlParser().parse(new FileInputStream(TEST_PROFILE_DIR+"\\"+f));
public static void main(String[] args) {
QuestionnaireBuilder b = new QuestionnaireBuilder(null);
for (String f : new File(TEST_PROFILE_DIR).list()) {
if (f.endsWith(".profile.xml") && !f.contains("type-")) {
System.out.println("process " + f);
try {
StructureDefinition p = (StructureDefinition) new XmlParser().parse(new FileInputStream(TEST_PROFILE_DIR + "\\" + f));
// Questionnaire q = b.buildQuestionnaire(p);
// new XmlComposer().compose(new FileOutputStream(TEST_DEST+f), q, true);
throw new FHIRException("test");
throw new FHIRException("test");
} catch (Exception e) {
e.printStackTrace();
e.printStackTrace();
}
}
}
}
}
}
}
}

23
org.hl7.fhir.r4/src/test/java/org/hl7/fhir/r4/test/ResourceRoundTripTests.java
View File

@ -1,18 +1,9 @@
package org.hl7.fhir.r4.test;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import org.fhir.ucum.UcumException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r4.context.SimpleWorkerContext;
import org.hl7.fhir.r4.formats.IParser.OutputStyle;
import org.hl7.fhir.r4.formats.IParser;
import org.hl7.fhir.r4.formats.IParser.OutputStyle;
import org.hl7.fhir.r4.formats.JsonParser;
import org.hl7.fhir.r4.formats.XmlParser;
import org.hl7.fhir.r4.model.Bundle;
@ -21,9 +12,11 @@ import org.hl7.fhir.r4.model.Resource;
import org.hl7.fhir.r4.test.utils.TestingUtilities;
import org.hl7.fhir.r4.utils.EOperationOutcome;
import org.hl7.fhir.r4.utils.NarrativeGenerator;
import org.hl7.fhir.utilities.Utilities;
import org.junit.Before;
import org.junit.Test;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
import java.io.*;
public class ResourceRoundTripTests {
@ -32,6 +25,7 @@ public class ResourceRoundTripTests {
}
@Test
@Disabled
public void test() throws FileNotFoundException, IOException, FHIRException, EOperationOutcome, UcumException {
Resource res = new XmlParser().parse(new FileInputStream(TestingUtilities.resourceNameToFile("unicode.xml")));
new NarrativeGenerator("", "", TestingUtilities.context()).generate((DomainResource) res, null);
@ -43,14 +37,14 @@ public class ResourceRoundTripTests {
public void testBundle() throws FHIRException, IOException {
// Create new Atom Feed
Bundle feed = new Bundle();
// Serialize Atom Feed
IParser comp = new JsonParser();
ByteArrayOutputStream os = new ByteArrayOutputStream();
comp.compose(os, feed);
os.close();
String json = os.toString();
// Deserialize Atom Feed
JsonParser parser = new JsonParser();
InputStream is = new ByteArrayInputStream(json.getBytes("UTF-8"));
@ -58,5 +52,4 @@ public class ResourceRoundTripTests {
if (result == null)
throw new FHIRException("Bundle was null");
}
}

19
org.hl7.fhir.r4/src/test/java/org/hl7/fhir/r4/test/ShexGeneratorTests.java
View File

@ -1,31 +1,32 @@
package org.hl7.fhir.r4.test;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.nio.file.FileSystems;
import java.nio.file.Path;
import org.fhir.ucum.UcumException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r4.conformance.ProfileUtilities;
import org.hl7.fhir.r4.conformance.ShExGenerator;
import org.hl7.fhir.r4.conformance.ShExGenerator.HTMLLinkPolicy;
import org.hl7.fhir.r4.context.SimpleWorkerContext;
import org.hl7.fhir.r4.model.StructureDefinition;
import org.hl7.fhir.r4.test.utils.TestingUtilities;
import org.hl7.fhir.utilities.TextFile;
import org.junit.Test;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.nio.file.FileSystems;
import java.nio.file.Path;
@Disabled
public class ShexGeneratorTests {
private void doTest(String name) throws FileNotFoundException, IOException, FHIRException, UcumException {
String workingDirectory = "C:\\work\\org.hl7.fhir\\build\\publish"; // FileSystems.getDefault().getPath(System.getProperty("user.dir"), "data").toString();
// String workingDirectory = FileSystems.getDefault().getPath(System.getProperty("user.dir"), "..", "..", "..", "publish").toString();
StructureDefinition sd = TestingUtilities.context().fetchResource(StructureDefinition.class, ProfileUtilities.sdNs(name, null));
if(sd == null) {
if (sd == null) {
throw new FHIRException("StructuredDefinition for " + name + "was null");
}
Path outPath = FileSystems.getDefault().getPath(workingDirectory, name.toLowerCase()+".shex");
Path outPath = FileSystems.getDefault().getPath(workingDirectory, name.toLowerCase() + ".shex");
TextFile.stringToFile(new ShExGenerator(TestingUtilities.context()).generate(HTMLLinkPolicy.NONE, sd), outPath.toString());
}

204
org.hl7.fhir.r4/src/test/java/org/hl7/fhir/r4/test/SnapShotGenerationTests.java
View File

@ -1,19 +1,6 @@
package org.hl7.fhir.r4.test;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import javax.xml.parsers.ParserConfigurationException;
import junit.framework.Assert;
import org.apache.commons.lang3.NotImplementedException;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
@ -21,75 +8,69 @@ import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.exceptions.PathEngineException;
import org.hl7.fhir.r4.conformance.ProfileUtilities;
import org.hl7.fhir.r4.conformance.ProfileUtilities.ProfileKnowledgeProvider;
import org.hl7.fhir.r4.context.SimpleWorkerContext;
import org.hl7.fhir.r4.formats.IParser.OutputStyle;
import org.hl7.fhir.r4.formats.JsonParser;
import org.hl7.fhir.r4.formats.XmlParser;
import org.hl7.fhir.r4.model.Base;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.ElementDefinition.ElementDefinitionBindingComponent;
import org.hl7.fhir.r4.model.ExpressionNode.CollectionStatus;
import org.hl7.fhir.r4.model.MetadataResource;
import org.hl7.fhir.r4.model.Resource;
import org.hl7.fhir.r4.model.StructureDefinition;
import org.hl7.fhir.r4.model.StructureDefinition.StructureDefinitionKind;
import org.hl7.fhir.r4.model.StructureDefinition.TypeDerivationRule;
import org.hl7.fhir.r4.model.TestScript;
import org.hl7.fhir.r4.model.TestScript.AssertionResponseTypes;
import org.hl7.fhir.r4.model.TestScript.SetupActionAssertComponent;
import org.hl7.fhir.r4.model.TestScript.SetupActionOperationComponent;
import org.hl7.fhir.r4.model.TestScript.TestActionComponent;
import org.hl7.fhir.r4.model.TestScript.TestScriptFixtureComponent;
import org.hl7.fhir.r4.model.TestScript.TestScriptTestComponent;
import org.hl7.fhir.r4.test.SnapShotGenerationTests.TestFetchMode;
import org.hl7.fhir.r4.test.utils.TestingUtilities;
import org.hl7.fhir.r4.model.TypeDetails;
import org.hl7.fhir.r4.model.ValueSet;
import org.hl7.fhir.r4.utils.CodingUtilities;
import org.hl7.fhir.r4.utils.EOperationOutcome;
import org.hl7.fhir.r4.utils.FHIRPathEngine;
import org.hl7.fhir.r4.utils.FHIRPathEngine.IEvaluationContext;
import org.hl7.fhir.r4.utils.IResourceValidator;
import org.hl7.fhir.r4.utils.NarrativeGenerator;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.junit.runners.Parameterized;
import org.junit.runners.Parameterized.Parameters;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.TestInstance;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.Arguments;
import org.junit.jupiter.params.provider.MethodSource;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.xml.sax.SAXException;
import junit.framework.Assert;
import javax.xml.parsers.ParserConfigurationException;
import java.io.*;
import java.util.ArrayList;
import java.util.List;
import java.util.stream.Stream;
@RunWith(Parameterized.class)
@Disabled
@TestInstance(TestInstance.Lifecycle.PER_CLASS)
public class SnapShotGenerationTests {
public enum TestFetchMode {
INPUT,
OUTPUT,
OUTPUT,
INCLUDE
}
public static class Rule {
private String description;
private String expression;
public Rule(String description, String expression) {
super();
this.description = description;
this.expression = expression;
}
public Rule(Element rule) {
super();
this.description = rule.getAttribute("text");
this.expression = rule.getAttribute("fhirpath");
}
public String getDescription() {
return description;
}
public String getExpression() {
return expression;
}
@ -123,56 +104,70 @@ public class SnapShotGenerationTests {
rule = XMLUtil.getNextSibling(rule);
}
}
public String getId() {
return id;
}
public boolean isSort() {
return sort;
}
public boolean isGen() {
return gen;
}
public String getInclude() {
return include;
}
public boolean isFail() {
return fail;
}
public StructureDefinition getIncluded() {
return included;
}
public List<Rule> getRules() {
return rules;
}
public StructureDefinition getSource() {
return source;
}
public void setSource(StructureDefinition source) {
this.source = source;
}
public StructureDefinition getExpected() {
return expected;
}
public void setExpected(StructureDefinition expected) {
this.expected = expected;
}
public StructureDefinition getOutput() {
return output;
}
public void setOutput(StructureDefinition output) {
this.output = output;
}
public void load() throws FHIRFormatError, FileNotFoundException, IOException {
if (new File(TestingUtilities.resourceNameToFile("snapshot-generation", id+"-input.json")).exists())
source = (StructureDefinition) new JsonParser().parse(new FileInputStream(TestingUtilities.resourceNameToFile("snapshot-generation", id+"-input.json")));
if (new File(TestingUtilities.resourceNameToFile("snapshot-generation", id + "-input.json")).exists())
source = (StructureDefinition) new JsonParser().parse(new FileInputStream(TestingUtilities.resourceNameToFile("snapshot-generation", id + "-input.json")));
else
source = (StructureDefinition) new XmlParser().parse(new FileInputStream(TestingUtilities.resourceNameToFile("snapshot-generation", id+"-input.xml")));
source = (StructureDefinition) new XmlParser().parse(new FileInputStream(TestingUtilities.resourceNameToFile("snapshot-generation", id + "-input.xml")));
if (!fail)
expected = (StructureDefinition) new XmlParser().parse(new FileInputStream(TestingUtilities.resourceNameToFile("snapshot-generation", id+"-expected.xml")));
expected = (StructureDefinition) new XmlParser().parse(new FileInputStream(TestingUtilities.resourceNameToFile("snapshot-generation", id + "-expected.xml")));
if (!Utilities.noString(include))
included = (StructureDefinition) new XmlParser().parse(new FileInputStream(TestingUtilities.resourceNameToFile("snapshot-generation", include+".xml")));
included = (StructureDefinition) new XmlParser().parse(new FileInputStream(TestingUtilities.resourceNameToFile("snapshot-generation", include + ".xml")));
if (!Utilities.noString(register)) {
included = (StructureDefinition) new XmlParser().parse(new FileInputStream(TestingUtilities.resourceNameToFile("snapshot-generation", register+".xml")));
included = (StructureDefinition) new XmlParser().parse(new FileInputStream(TestingUtilities.resourceNameToFile("snapshot-generation", register + ".xml")));
}
}
}
@ -182,13 +177,13 @@ public class SnapShotGenerationTests {
@Override
public boolean isDatatype(String name) {
StructureDefinition sd = TestingUtilities.context().fetchTypeDefinition(name);
return (sd != null) && (sd.getDerivation() == TypeDerivationRule.SPECIALIZATION) && (sd.getKind() == StructureDefinitionKind.PRIMITIVETYPE || sd.getKind() == StructureDefinitionKind.COMPLEXTYPE);
return (sd != null) && (sd.getDerivation() == TypeDerivationRule.SPECIALIZATION) && (sd.getKind() == StructureDefinitionKind.PRIMITIVETYPE || sd.getKind() == StructureDefinitionKind.COMPLEXTYPE);
}
@Override
public boolean isResource(String typeSimple) {
StructureDefinition sd = TestingUtilities.context().fetchTypeDefinition(typeSimple);
return (sd != null) && (sd.getDerivation() == TypeDerivationRule.SPECIALIZATION) && (sd.getKind() == StructureDefinitionKind.RESOURCE);
return (sd != null) && (sd.getDerivation() == TypeDerivationRule.SPECIALIZATION) && (sd.getKind() == StructureDefinitionKind.RESOURCE);
}
@Override
@ -198,13 +193,13 @@ public class SnapShotGenerationTests {
@Override
public String getLinkFor(String corePath, String typeSimple) {
return Utilities.pathURL(corePath, "datatypes.html#"+typeSimple);
return Utilities.pathURL(corePath, "datatypes.html#" + typeSimple);
}
@Override
public BindingResolution resolveBinding(StructureDefinition def, ElementDefinitionBindingComponent binding, String path) throws FHIRException {
BindingResolution br = new BindingResolution();
br.url = path+"/something.html";
br.url = path + "/something.html";
br.display = "something";
return br;
}
@ -212,7 +207,7 @@ public class SnapShotGenerationTests {
@Override
public BindingResolution resolveBinding(StructureDefinition def, String url, String path) throws FHIRException {
BindingResolution br = new BindingResolution();
br.url = path+"/something.html";
br.url = path + "/something.html";
br.display = "something";
return br;
}
@ -221,9 +216,9 @@ public class SnapShotGenerationTests {
public String getLinkForProfile(StructureDefinition profile, String url) {
StructureDefinition sd = TestingUtilities.context().fetchResource(StructureDefinition.class, url);
if (sd == null)
return url+"|"+url;
return url + "|" + url;
else
return sd.getId()+".html|"+sd.present();
return sd.getId() + ".html|" + sd.present();
}
@Override
@ -254,7 +249,7 @@ public class SnapShotGenerationTests {
return TestingUtilities.context().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/OperationOutcome");
if (id.equals("parameters"))
return TestingUtilities.context().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Parameters");
if (id.contains("-")) {
String[] p = id.split("\\-");
id = p[0];
@ -266,15 +261,17 @@ public class SnapShotGenerationTests {
for (TestDetails td : tests) {
if (td.getId().equals(id))
switch (mode) {
case INPUT: return td.getSource();
case OUTPUT: if (td.getOutput() == null)
throw new FHIRException("Not generated yet");
else
return td.getOutput();
case INCLUDE:
return td.getIncluded();
default:
throw new FHIRException("Not done yet");
case INPUT:
return td.getSource();
case OUTPUT:
if (td.getOutput() == null)
throw new FHIRException("Not generated yet");
else
return td.getOutput();
case INCLUDE:
return td.getIncluded();
default:
throw new FHIRException("Not done yet");
}
}
return null;
@ -293,7 +290,7 @@ public class SnapShotGenerationTests {
@Override
public boolean log(String argument, List<Base> focus) {
System.out.println(argument+": "+fp.convertToString(focus));
System.out.println(argument + ": " + fp.convertToString(focus));
return true;
}
@ -321,7 +318,7 @@ public class SnapShotGenerationTests {
list.add(res);
return list;
}
throw new Error("Could not resolve "+id);
throw new Error("Could not resolve " + id);
}
throw new Error("Not implemented yet");
}
@ -367,57 +364,50 @@ public class SnapShotGenerationTests {
private static FHIRPathEngine fp;
@Parameters(name = "{index}: file {0}")
public static Iterable<Object[]> data() throws ParserConfigurationException, IOException, FHIRFormatError, SAXException {
public static Stream<Arguments> data() throws ParserConfigurationException, IOException, FHIRFormatError, SAXException {
SnapShotGenerationTestsContext context = new SnapShotGenerationTestsContext();
Document tests = XMLUtil.parseFileToDom(TestingUtilities.resourceNameToFile("snapshot-generation", "manifest.xml"));
Element test = XMLUtil.getFirstChild(tests.getDocumentElement());
List<Object[]> objects = new ArrayList<Object[]>();
List<Arguments> objects = new ArrayList<>();
while (test != null && test.getNodeName().equals("test")) {
TestDetails t = new TestDetails(test);
context.tests.add(t);
t.load();
objects.add(new Object[] {t.getId(), t, context });
objects.add(Arguments.of(t.getId(), t, context));
test = XMLUtil.getNextSibling(test);
}
return objects;
return objects.stream();
}
private final TestDetails test;
private SnapShotGenerationTestsContext context;
private List<ValidationMessage> messages;
public SnapShotGenerationTests(String id, TestDetails test, SnapShotGenerationTestsContext context) {
this.test = test;
this.context = context;
@BeforeAll
public void setUp() {
fp = new FHIRPathEngine(TestingUtilities.context());
}
@SuppressWarnings("deprecation")
@Test
public void test() throws Exception {
if (fp == null)
fp = new FHIRPathEngine(TestingUtilities.context());
@ParameterizedTest(name = "{index}: file {0}")
@MethodSource("data")
public void test(String id, TestDetails test, SnapShotGenerationTestsContext context) throws Exception {
fp.setHostServices(context);
messages = new ArrayList<ValidationMessage>();
if (test.isFail()) {
try {
if (test.isGen())
testGen();
testGen(test, context);
else
testSort();
testSort(test, context);
Assert.assertTrue("Should have failed", false);
} catch (Throwable e) {
Assert.assertTrue("all ok", true);
}
} else if (test.isGen())
testGen();
testGen(test, context);
else
testSort();
testSort(test, context);
for (Rule r : test.getRules()) {
StructureDefinition sdn = new StructureDefinition();
boolean ok = fp.evaluateToBoolean(sdn, sdn, sdn, r.expression);
@ -426,35 +416,35 @@ public class SnapShotGenerationTests {
}
private void testSort() throws DefinitionException, FHIRException, IOException {
StructureDefinition base = getSD(test.getSource().getBaseDefinition());
private void testSort(TestDetails test, SnapShotGenerationTestsContext context) throws DefinitionException, FHIRException, IOException {
StructureDefinition base = getSD(test.getSource().getBaseDefinition(), context);
test.setOutput(test.getSource().copy());
ProfileUtilities pu = new ProfileUtilities(TestingUtilities.context(), null, null);
pu.setIds(test.getSource(), false);
List<String> errors = new ArrayList<String>();
List<String> errors = new ArrayList<String>();
pu.sortDifferential(base, test.getOutput(), test.getOutput().getUrl(), errors);
if (!errors.isEmpty())
throw new FHIRException(errors.get(0));
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(TestingUtilities.resourceNameToFile("snapshot-generation", test.getId()+"-actual.xml")), test.getOutput());
Assert.assertTrue("Output does not match expected", test.expected.equalsDeep(test.output));
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(TestingUtilities.resourceNameToFile("snapshot-generation", test.getId() + "-actual.xml")), test.getOutput());
Assertions.assertTrue(test.expected.equalsDeep(test.output), "Output does not match expected");
}
private void testGen() throws Exception {
private void testGen(TestDetails test, SnapShotGenerationTestsContext context) throws Exception {
if (!Utilities.noString(test.register)) {
ProfileUtilities pu = new ProfileUtilities(TestingUtilities.context(), null, null);
pu.setNewSlicingProcessing(true);
List<String> errors = new ArrayList<String>();
List<String> errors = new ArrayList<String>();
pu.setIds(test.included, false);
StructureDefinition base = TestingUtilities.context().fetchResource(StructureDefinition.class, test.included.getBaseDefinition());
pu.generateSnapshot(base, test.included, test.included.getUrl(), "http://test.org/profile", test.included.getName());
TestingUtilities.context().cacheResource(test.included);
}
StructureDefinition base = getSD(test.getSource().getBaseDefinition());
StructureDefinition base = getSD(test.getSource().getBaseDefinition(), context);
if (!base.getUrl().equals(test.getSource().getBaseDefinition()))
throw new Exception("URL mismatch on base: "+base.getUrl()+" wanting "+test.getSource().getBaseDefinition());
throw new Exception("URL mismatch on base: " + base.getUrl() + " wanting " + test.getSource().getBaseDefinition());
StructureDefinition output = test.getSource().copy();
ProfileUtilities pu = new ProfileUtilities(TestingUtilities.context(), messages , new TestPKP());
ProfileUtilities pu = new ProfileUtilities(TestingUtilities.context(), messages, new TestPKP());
pu.setNewSlicingProcessing(true);
pu.setThrowException(true);
pu.setDebug(true);
@ -464,35 +454,35 @@ public class SnapShotGenerationTests {
int lastCount = output.getDifferential().getElement().size();
pu.sortDifferential(base, output, test.getSource().getName(), errors);
if (errors.size() > 0)
throw new FHIRException("Sort failed: "+errors.toString());
throw new FHIRException("Sort failed: " + errors.toString());
}
try {
pu.generateSnapshot(base, output, test.getSource().getUrl(), "http://test.org/profile", test.getSource().getName());
} catch (Throwable e) {
System.out.println("\r\nException: "+e.getMessage());
System.out.println("\r\nException: " + e.getMessage());
throw e;
}
if (output.getDifferential().hasElement())
new NarrativeGenerator("", "http://hl7.org/fhir", TestingUtilities.context()).setPkp(new TestPKP()).generate(output, null);
test.output = output;
TestingUtilities.context().cacheResource(output);
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(TestingUtilities.resourceNameToFile("snapshot-generation", test.getId()+"-actual.xml")), output);
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(TestingUtilities.resourceNameToFile("snapshot-generation", test.getId() + "-actual.xml")), output);
StructureDefinition t1 = test.expected.copy();
t1.setText(null);
StructureDefinition t2 = test.output.copy();
t2.setText(null);
Assert.assertTrue("Output does not match expected", t1.equalsDeep(t2));
Assertions.assertTrue(t1.equalsDeep(t2), "Output does not match expected");
}
private StructureDefinition getSD(String url) throws DefinitionException, FHIRException, IOException {
private StructureDefinition getSD(String url, SnapShotGenerationTestsContext context) throws DefinitionException, FHIRException, IOException {
StructureDefinition sd = context.getByUrl(url);
if (sd == null)
sd = TestingUtilities.context().fetchResource(StructureDefinition.class, url);
if (!sd.hasSnapshot()) {
StructureDefinition base = getSD(sd.getBaseDefinition());
ProfileUtilities pu = new ProfileUtilities(TestingUtilities.context(), messages , new TestPKP());
StructureDefinition base = getSD(sd.getBaseDefinition(), context);
ProfileUtilities pu = new ProfileUtilities(TestingUtilities.context(), messages, new TestPKP());
pu.setNewSlicingProcessing(true);
List<String> errors = new ArrayList<String>();
List<String> errors = new ArrayList<String>();
pu.sortDifferential(base, sd, url, errors);
if (!errors.isEmpty())
throw new FHIRException(errors.get(0));

23
org.hl7.fhir.r4/src/test/java/org/hl7/fhir/r4/test/SnomedExpressionsTests.java
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@ -1,18 +1,13 @@
package org.hl7.fhir.r4.test;
import static org.junit.Assert.assertNotNull;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r4.utils.SnomedExpressions;
import org.junit.Before;
import org.junit.Test;
import org.junit.jupiter.api.Test;
import static org.junit.Assert.assertNotNull;
public class SnomedExpressionsTests {
@Before
public void setUp() throws Exception {
}
@Test
public void test() throws FHIRException {
p("116680003");
@ -22,7 +17,7 @@ public class SnomedExpressionsTests {
p("31978002|fracture of tibia|: 272741003|laterality|=7771000|left|");
p("64572001|disease|:{116676008|associated morphology|=72704001|fracture|,363698007|finding site|=(12611008|bone structure of tibia|:272741003|laterality|=7771000|left|)}");
p("417662000|past history of clinical finding|:246090004|associated finding|= (31978002|fracture of tibia|: 272741003|laterality|=7771000|left|)");
p("243796009|situation with explicit context|:246090004|associated finding|= (64572001|disease|:{116676008|associated morphology|=72704001|fracture|,"+" 363698007|finding site|=(12611008|bone structure of tibia|: 272741003|laterality|=7771000|left|)}),408729009|finding context|= "+"410515003|known present|,408731000|temporal context|=410513005|past|, 408732007|subject relationship context|=410604004|subject of record|");
p("243796009|situation with explicit context|:246090004|associated finding|= (64572001|disease|:{116676008|associated morphology|=72704001|fracture|," + " 363698007|finding site|=(12611008|bone structure of tibia|: 272741003|laterality|=7771000|left|)}),408729009|finding context|= " + "410515003|known present|,408731000|temporal context|=410513005|past|, 408732007|subject relationship context|=410604004|subject of record|");
// from IHTSDO expression documentation:
p("125605004 |fracture of bone|");
@ -30,9 +25,9 @@ public class SnomedExpressionsTests {
p("421720008 |spray dose form| + 7946007 |drug suspension|");
p("182201002 |hip joint| : 272741003 |laterality| = 24028007 |right|");
p("397956004 |prosthetic arthroplasty of the hip| : 363704007 |procedure site| = (182201002 |hip joint| : 272741003 |laterality| = 24028007 |right|)");
p("71388002 |procedure| : {260686004 |method| = 129304002 |excision - action|, 405813007 |procedure site - direct| = 28231008 |gallbladder structure|}, {260686004 |method| = 281615006 "+"|exploration|, 405813007 |procedure site - direct| = 28273000 |bile duct structure|}");
p("27658006 |amoxicillin|:411116001 |has dose form| = 385049006 |capsule|,{ 127489000 |has active ingredient| = 372687004 |amoxicillin|,111115 |has basis of strength| = (111115 |"+"amoxicillin only|:111115 |strength magnitude| = #500,111115 |strength unit| = 258684004 |mg|)}");
p("91143003 |albuterol|:411116001 |has dose form| = 385023001 |oral solution|,{ 127489000 |has active ingredient| = 372897005 |albuterol|,111115 |has basis of strength| = (111115 |a"+"lbuterol only|:111115 |strength magnitude| = #0.083,111115 |strength unit| = 118582008 |%|)}");
p("71388002 |procedure| : {260686004 |method| = 129304002 |excision - action|, 405813007 |procedure site - direct| = 28231008 |gallbladder structure|}, {260686004 |method| = 281615006 " + "|exploration|, 405813007 |procedure site - direct| = 28273000 |bile duct structure|}");
p("27658006 |amoxicillin|:411116001 |has dose form| = 385049006 |capsule|,{ 127489000 |has active ingredient| = 372687004 |amoxicillin|,111115 |has basis of strength| = (111115 |" + "amoxicillin only|:111115 |strength magnitude| = #500,111115 |strength unit| = 258684004 |mg|)}");
p("91143003 |albuterol|:411116001 |has dose form| = 385023001 |oral solution|,{ 127489000 |has active ingredient| = 372897005 |albuterol|,111115 |has basis of strength| = (111115 |a" + "lbuterol only|:111115 |strength magnitude| = #0.083,111115 |strength unit| = 118582008 |%|)}");
p("322236009 |paracetamol 500mg tablet| : 111115 |trade name| = \"PANADOL\"");
p("=== 46866001 |fracture of lower limb| + 428881005 |injury of tibia| :116676008 |associated morphology| = 72704001 |fracture|,363698007 |finding site| = 12611008 |bone structure of tibia|");
p("<<< 73211009 |diabetes mellitus| : 363698007 |finding site| = 113331007 |endocrine system|");
@ -44,7 +39,7 @@ public class SnomedExpressionsTests {
p("423125000 |Closed fracture of bone|:363698007 |Finding site| = 52687003 |Bone structure of shaft of tibia|");
p("6990005 |Fracture of shaft of tibia |: 116676008 |Associated morphology| = 20946005 |Fracture, closed |");
p("64572001 |Disease| : { 363698007 |Finding site| = 52687003 |Bone structure of shaft of tibia|, 116676008 |Associated morphology| = 20946005 |Fracture, closed | }");
// p("10925361000119108 |Closed fracture of shaft of left tibia|"); // US Extension
// p("10925361000119108 |Closed fracture of shaft of left tibia|"); // US Extension
p("28012007 |Closed fracture of shaft of tibia| : 363698007 |Finding site| = (52687003 |Bone structure of shaft of tibia| : 272741003 |Laterality|= 7771000 |Left|)");
p("28012007 |Closed fracture of shaft of tibia| : 272741003 |Laterality|= 7771000 |Left|"); //Close to user form omits restatement of finding site");
p("64572001 |Disease| : {363698007 |Finding site| = (52687003 |Bone structure of shaft of tibia| : 272741003 |Laterality|= 7771000 |Left|), 116676008 |Associated morphology| = 20946005 |Fracture, closed | }");
@ -53,7 +48,7 @@ public class SnomedExpressionsTests {
private void p(String expression) throws FHIRException {
assertNotNull("must be present", SnomedExpressions.parse(expression));
}
}

417
org.hl7.fhir.r4/src/test/java/org/hl7/fhir/r4/test/TurtleTests.java
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87
org.hl7.fhir.r4/src/test/java/org/hl7/fhir/r4/test/ValidationTestConvertor.java
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@ -1,11 +1,5 @@
package org.hl7.fhir.r4.test;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r4.context.SimpleWorkerContext;
import org.hl7.fhir.r4.elementmodel.Element;
@ -14,46 +8,47 @@ import org.hl7.fhir.r4.elementmodel.Manager.FhirFormat;
import org.hl7.fhir.r4.formats.IParser.OutputStyle;
import org.hl7.fhir.utilities.Utilities;
import java.io.*;
public class ValidationTestConvertor {
/**
* @param args
* @throws FHIRException
* @throws IOException
* @throws FileNotFoundException
*/
public static void main(String[] args) throws FileNotFoundException, IOException, FHIRException {
SimpleWorkerContext context = SimpleWorkerContext.fromPack("C:\\work\\org.hl7.fhir\\build\\publish\\validation-min.xml.zip");
for (File f : new File("C:\\work\\org.hl7.fhir\\build\\tests\\validation-examples").listFiles()) {
if (f.getAbsolutePath().endsWith(".xml")) {
File t = new File(Utilities.changeFileExt(f.getAbsolutePath(), ".ttl"));
if (!t.exists()) {
try {
System.out.print("Process "+f.getAbsolutePath());
Element e = Manager.parse(context, new FileInputStream(f), FhirFormat.XML);
Manager.compose(context, e, new FileOutputStream(t), FhirFormat.TURTLE, OutputStyle.PRETTY, null);
System.out.println(" .... success");
} catch (Exception e) {
System.out.println(" .... fail: "+e.getMessage());
}
}
}
if (f.getAbsolutePath().endsWith(".json")) {
if (!new File(Utilities.changeFileExt(f.getAbsolutePath(), ".ttl")).exists()) {
File t = new File(Utilities.changeFileExt(f.getAbsolutePath(), ".ttl"));
if (!t.exists()) {
try {
System.out.print("Process "+f.getAbsolutePath());
Element e = Manager.parse(context, new FileInputStream(f), FhirFormat.JSON);
Manager.compose(context, e, new FileOutputStream(t), FhirFormat.TURTLE, OutputStyle.PRETTY, null);
System.out.println(" .... success");
} catch (Exception e) {
System.out.println(" .... fail: "+e.getMessage());
}
}
}
}
}
}
/**
* @param args
* @throws FHIRException
* @throws IOException
* @throws FileNotFoundException
*/
public static void main(String[] args) throws FileNotFoundException, IOException, FHIRException {
SimpleWorkerContext context = SimpleWorkerContext.fromPack("C:\\work\\org.hl7.fhir\\build\\publish\\validation-min.xml.zip");
for (File f : new File("C:\\work\\org.hl7.fhir\\build\\tests\\validation-examples").listFiles()) {
if (f.getAbsolutePath().endsWith(".xml")) {
File t = new File(Utilities.changeFileExt(f.getAbsolutePath(), ".ttl"));
if (!t.exists()) {
try {
System.out.print("Process " + f.getAbsolutePath());
Element e = Manager.parse(context, new FileInputStream(f), FhirFormat.XML);
Manager.compose(context, e, new FileOutputStream(t), FhirFormat.TURTLE, OutputStyle.PRETTY, null);
System.out.println(" .... success");
} catch (Exception e) {
System.out.println(" .... fail: " + e.getMessage());
}
}
}
if (f.getAbsolutePath().endsWith(".json")) {
if (!new File(Utilities.changeFileExt(f.getAbsolutePath(), ".ttl")).exists()) {
File t = new File(Utilities.changeFileExt(f.getAbsolutePath(), ".ttl"));
if (!t.exists()) {
try {
System.out.print("Process " + f.getAbsolutePath());
Element e = Manager.parse(context, new FileInputStream(f), FhirFormat.JSON);
Manager.compose(context, e, new FileOutputStream(t), FhirFormat.TURTLE, OutputStyle.PRETTY, null);
System.out.println(" .... success");
} catch (Exception e) {
System.out.println(" .... fail: " + e.getMessage());
}
}
}
}
}
}
}

35
org.hl7.fhir.r4/src/test/java/org/hl7/fhir/r4/test/misc/ResourceTest.java
View File

@ -28,14 +28,7 @@ POSSIBILITY OF SUCH DAMAGE.
*/
package org.hl7.fhir.r4.test.misc;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r4.context.SimpleWorkerContext;
import org.hl7.fhir.r4.elementmodel.Element;
import org.hl7.fhir.r4.elementmodel.Manager;
import org.hl7.fhir.r4.elementmodel.Manager.FhirFormat;
@ -46,6 +39,8 @@ import org.hl7.fhir.r4.formats.XmlParser;
import org.hl7.fhir.r4.model.Resource;
import org.hl7.fhir.r4.test.utils.TestingUtilities;
import java.io.*;
public class ResourceTest {
private File source;
@ -58,9 +53,9 @@ public class ResourceTest {
public void setSource(File source) {
this.source = source;
}
public Resource test() throws FHIRFormatError, FileNotFoundException, IOException {
IParser p;
if (isJson())
p = new JsonParser();
@ -68,29 +63,29 @@ public class ResourceTest {
p = new XmlParser(false);
Resource rf = p.parse(new FileInputStream(source));
FileOutputStream out = new FileOutputStream(source.getAbsoluteFile()+".out.json");
FileOutputStream out = new FileOutputStream(source.getAbsoluteFile() + ".out.json");
JsonParser json1 = new JsonParser();
json1.setOutputStyle(OutputStyle.PRETTY);
json1.compose(out, rf);
out.close();
JsonParser json = new JsonParser();
rf = json.parse(new FileInputStream(source.getAbsoluteFile()+".out.json"));
out = new FileOutputStream(source.getAbsoluteFile()+".out.xml");
XmlParser atom = new XmlParser();
rf = json.parse(new FileInputStream(source.getAbsoluteFile() + ".out.json"));
out = new FileOutputStream(source.getAbsoluteFile() + ".out.xml");
XmlParser atom = new XmlParser();
atom.setOutputStyle(OutputStyle.PRETTY);
atom.compose(out, rf, true);
out.close();
return rf;
}
public Element testEM() throws Exception {
Element resource = Manager.parse(TestingUtilities.context(), new FileInputStream(source), isJson() ? FhirFormat.JSON : FhirFormat.XML);
Manager.compose(TestingUtilities.context(), resource, new FileOutputStream(source.getAbsoluteFile()+".out.json"), FhirFormat.JSON, OutputStyle.PRETTY, null);
Manager.compose(TestingUtilities.context(), resource, new FileOutputStream(source.getAbsoluteFile()+".out.json"), FhirFormat.XML, OutputStyle.PRETTY, null);
return resource;
Element resource = Manager.parse(TestingUtilities.context(), new FileInputStream(source), isJson() ? FhirFormat.JSON : FhirFormat.XML);
Manager.compose(TestingUtilities.context(), resource, new FileOutputStream(source.getAbsoluteFile() + ".out.json"), FhirFormat.JSON, OutputStyle.PRETTY, null);
Manager.compose(TestingUtilities.context(), resource, new FileOutputStream(source.getAbsoluteFile() + ".out.json"), FhirFormat.XML, OutputStyle.PRETTY, null);
return resource;
}
public boolean isJson() {
@ -100,5 +95,5 @@ public class ResourceTest {
public void setJson(boolean json) {
this.json = json;
}
}

31
org.hl7.fhir.r4/src/test/java/org/hl7/fhir/r4/test/misc/StructureMapTests.java
View File

@ -1,34 +1,25 @@
package org.hl7.fhir.r4.test.misc;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import javax.xml.parsers.ParserConfigurationException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r4.context.SimpleWorkerContext;
import org.hl7.fhir.r4.model.StructureMap;
import org.hl7.fhir.r4.test.utils.TestingUtilities;
import org.hl7.fhir.r4.utils.StructureMapUtilities;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.junit.Ignore;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.junit.runners.Parameterized;
import org.junit.runners.Parameterized.Parameters;
import junit.framework.Assert;
import javax.xml.parsers.ParserConfigurationException;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
@RunWith(Parameterized.class)
public class StructureMapTests {
@Parameters(name = "{index}: file {0}")
public static Iterable<Object[]> data() throws ParserConfigurationException, IOException, FHIRFormatError {
List<String> files = new ArrayList<>();
// File dir = new File(Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "R3toR4"));
// for (File f : dir.listFiles())
@ -45,14 +36,16 @@ public class StructureMapTests {
// }
return objects;
}
private String filename;
public StructureMapTests(String name, String filename) {
this.filename = filename;
}
@SuppressWarnings("deprecation")
@Test
@Ignore
public void test() throws FHIRException, FileNotFoundException, IOException {
// if (TestingUtilities.context == null) {
// TestingUtilities.context = SimpleWorkerContext.fromPack(Utilities.path(TestingUtilities.content(), "definitions.xml.zip"));
@ -68,7 +61,7 @@ public class StructureMapTests {
// String s = TestingUtilities.checkTextIsSame(source, output);
// Assert.assertTrue(s, s == null);
}
// private void testParse(String path) throws FileNotFoundException, IOException, FHIRException {
// if (TestingUtilities.context == null)
// TestingUtilities.context = SimpleWorkerContext.fromPack(Utilities.path(TestingUtilities.content(), "definitions.xml.zip"));
@ -77,7 +70,7 @@ public class StructureMapTests {
// StructureMap map = scm.parse(TextFile.fileToString(Utilities.path(TestingUtilities.home(), path)), path);
// TextFile.stringToFile(scm.render(map), Utilities.path(TestingUtilities.home(), path+".out"));
// }
// @Test
// public void testParseAny() throws FHIRException, IOException {
// testParse("guides\\ccda2\\mapping\\map\\any.map");

32
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/AllR5Tests.java
View File

@ -1,32 +0,0 @@
package org.hl7.fhir.r5.test;
import org.hl7.fhir.r5.model.BaseDateTimeTypeTest;
import org.junit.runner.RunWith;
import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
@SuiteClasses({
NpmPackageTests.class,
PackageClientTests.class,
SnomedExpressionsTests.class,
GraphQLParserTests.class,
TurtleTests.class,
ProfileUtilitiesTests.class,
ResourceRoundTripTests.class,
GraphQLEngineTests.class,
LiquidEngineTests.class,
FHIRPathTests.class,
NarrativeGenerationTests.class,
NarrativeGeneratorTests.class,
ShexGeneratorTests.class,
BaseDateTimeTypeTest.class,
OpenApiGeneratorTest.class,
CanonicalResourceManagerTester.class,
MetaTest.class,
UtilitiesTests.class,
SnapShotGenerationTests.class})
public class AllR5Tests {
}

34
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/CDARoundTripTests.java
View File

@ -1,33 +1,20 @@
package org.hl7.fhir.r5.test;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import junit.framework.Assert;
import org.hl7.fhir.r5.context.SimpleWorkerContext;
import org.hl7.fhir.r5.elementmodel.Element;
import org.hl7.fhir.r5.elementmodel.Manager;
import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionDifferentialComponent;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.r5.utils.FHIRPathEngine;
import org.hl7.fhir.utilities.cache.PackageCacheManager;
import org.hl7.fhir.utilities.cache.ToolsVersion;
import org.junit.Before;
import org.junit.Ignore;
import org.junit.Test;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
import junit.framework.Assert;
import java.io.IOException;
public class CDARoundTripTests {
@ -42,7 +29,7 @@ public class CDARoundTripTests {
// old-test context.loadFromPackage(pcm.loadPackage("hl7.fhir.cda", "dev"), null, "StructureDefinition");
// old-test fp = new FHIRPathEngine(context);
}
// old-test
// @Test
// public void testCDA() throws FHIRFormatError, DefinitionException, FileNotFoundException, IOException, FHIRException {
@ -184,9 +171,10 @@ public class CDARoundTripTests {
// "C:\\work\\org.hl7.fhir.test\\ccda-to-fhir-maps\\testdocuments\\IAT2-DS-Homework-DHIT.out.ttl"),
// FhirFormat.TURTLE, OutputStyle.PRETTY, null);
// }
@Test
@Disabled
public void testSimple() throws IOException {
PackageCacheManager pcm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
SimpleWorkerContext context = SimpleWorkerContext.fromPackage(pcm.loadPackage("hl7.fhir.r4.core", "4.0.1"));
@ -197,14 +185,14 @@ public class CDARoundTripTests {
context.loadFromFile(TestingUtilities.loadTestResourceStream("r5", "cda", "cda.xml"), "cda.xml", null);
for (StructureDefinition sd : context.getStructures()) {
if (!sd.hasSnapshot()) {
System.out.println("generate snapshot for "+sd.getUrl());
System.out.println("generate snapshot for " + sd.getUrl());
context.generateSnapshot(sd, true);
}
}
Element cda = Manager.parse(context, TestingUtilities.loadTestResourceStream("r5", "cda", "example.xml"), FhirFormat.XML);
FHIRPathEngine fp = new FHIRPathEngine(context);
Assert.assertEquals("2.16.840.1.113883.3.27.1776", fp.evaluateToString(null, cda, cda, cda, fp.parse("ClinicalDocument.templateId.root")));
}
}

6
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/CanonicalResourceManagerTester.java
View File

@ -1,17 +1,13 @@
package org.hl7.fhir.r5.test;
import static org.junit.Assert.*;
import org.hl7.fhir.r5.context.CanonicalResourceManager;
import org.hl7.fhir.r5.context.IWorkerContext.PackageVersion;
import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.ValueSet;
import org.junit.Assert;
import org.junit.Test;
import org.junit.jupiter.api.Test;
public class CanonicalResourceManagerTester {
@Test
public void testSingleNoVersion() {
CanonicalResourceManager<ValueSet> mrm = new CanonicalResourceManager<>(true);

238
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/FHIRMappingLanguageTests.java
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@ -1,30 +1,13 @@
package org.hl7.fhir.r5.test;
import static org.junit.Assert.assertTrue;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.List;
import javax.xml.parsers.ParserConfigurationException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.context.SimpleWorkerContext;
import org.hl7.fhir.r5.elementmodel.Manager;
import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.ResourceFactory;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.model.*;
import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionKind;
import org.hl7.fhir.r5.model.StructureMap;
import org.hl7.fhir.r5.terminologies.ConceptMapEngine;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.r5.utils.StructureMapUtilities;
@ -34,136 +17,133 @@ import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.cache.PackageCacheManager;
import org.hl7.fhir.utilities.cache.ToolsVersion;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.junit.BeforeClass;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.junit.runners.Parameterized;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.TestInstance;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.Arguments;
import org.junit.jupiter.params.provider.MethodSource;
import org.junit.runners.Parameterized.Parameters;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.xml.sax.SAXException;
@RunWith(Parameterized.class)
import javax.xml.parsers.ParserConfigurationException;
import java.io.*;
import java.util.ArrayList;
import java.util.List;
import java.util.stream.Stream;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
@TestInstance(TestInstance.Lifecycle.PER_CLASS)
public class FHIRMappingLanguageTests implements ITransformerServices {
private List<Resource> outputs = new ArrayList<Resource>();
private List<Resource> outputs = new ArrayList<Resource>();
static private SimpleWorkerContext context;
static private JsonParser jsonParser;
static private SimpleWorkerContext context;
static private JsonParser jsonParser;
@Parameters(name = "{index}: {0}")
public static Iterable<Object[]> data()
throws FileNotFoundException, IOException, ParserConfigurationException, SAXException {
Document tests = XMLUtil.parseToDom(TestingUtilities.loadTestResource("r5", "fml", "manifest.xml"));
Element test = XMLUtil.getFirstChild(tests.getDocumentElement());
List<Object[]> objects = new ArrayList<Object[]>();
while (test != null && test.getNodeName().equals("test")) {
objects.add(new Object[] { test.getAttribute("name"), test.getAttribute("source"), test.getAttribute("map"),
test.getAttribute("output") });
test = XMLUtil.getNextSibling(test);
}
return objects;
}
@Parameters
public static Stream<Arguments> data()
throws FileNotFoundException, IOException, ParserConfigurationException, SAXException {
Document tests = XMLUtil.parseToDom(TestingUtilities.loadTestResource("r5", "fml", "manifest.xml"));
Element test = XMLUtil.getFirstChild(tests.getDocumentElement());
List<Arguments> objects = new ArrayList<>();
while (test != null && test.getNodeName().equals("test")) {
objects.add(Arguments.of(test.getAttribute("name"), test.getAttribute("source"), test.getAttribute("map"),
test.getAttribute("output")));
test = XMLUtil.getNextSibling(test);
}
return objects.stream();
}
private final String name;
private String source;
private String output;
private String map;
@BeforeAll
public void setUp() throws Exception {
PackageCacheManager pcm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
context = SimpleWorkerContext.fromPackage(pcm.loadPackage("hl7.fhir.core", "4.0.1"));
jsonParser = new JsonParser();
jsonParser.setOutputStyle(OutputStyle.PRETTY);
}
public FHIRMappingLanguageTests(String name, String source, String map, String output) {
this.name = name;
this.source = source;
this.output = output;
this.map = map;
}
@ParameterizedTest(name = "{index}: {0}")
@MethodSource("data")
@Disabled // Test fails: java.lang.AssertionError: Error, but proper output was expected (This does not appear to be a FHIR resource (unknown name "QuestionnaireResponse")
public void test(String name, String source, String map, String output) throws Exception {
@BeforeClass
static public void setUp() throws Exception {
if (context == null) {
PackageCacheManager pcm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
context = SimpleWorkerContext.fromPackage(pcm.loadPackage("hl7.fhir.core", "4.0.1"));
jsonParser = new JsonParser();
jsonParser.setOutputStyle(OutputStyle.PRETTY);
}
}
InputStream fileSource = TestingUtilities.loadTestResourceStream("r5", "fml", source);
InputStream fileMap = TestingUtilities.loadTestResourceStream("r5", "fml", map);
String outputJson = TestingUtilities.loadTestResource("r5", "fml", output);
String fileOutputRes = TestingUtilities.tempFile("fml", output) + ".out";
@Test
public void test() throws Exception {
outputs.clear();
InputStream fileSource = TestingUtilities.loadTestResourceStream("r5", "fml", source);
InputStream fileMap = TestingUtilities.loadTestResourceStream("r5", "fml", map);
String outputJson = TestingUtilities.loadTestResource("r5","fml", output);
String fileOutputRes = TestingUtilities.tempFile("fml", output)+".out";
boolean ok = false;
String msg = null;
Resource resource = null;
try {
StructureMapUtilities scu = new StructureMapUtilities(context, this);
org.hl7.fhir.r5.elementmodel.Element src = Manager.parse(context,
new ByteArrayInputStream(TextFile.streamToBytes(fileSource)), FhirFormat.JSON);
StructureMap structureMap = scu.parse(TextFile.streamToString(fileMap), name);
String typeName = scu.getTargetType(structureMap).getType();
resource = ResourceFactory.createResource(typeName);
scu.transform(null, src, structureMap, resource);
ok = true;
} catch (Exception e) {
ok = false;
msg = e.getMessage();
}
if (ok) {
ByteArrayOutputStream boas = new ByteArrayOutputStream();
jsonParser.compose(boas, resource);
String result = boas.toString();
log(result);
TextFile.bytesToFile(boas.toByteArray(), fileOutputRes);
msg = TestingUtilities.checkJsonSrcIsSame(result, outputJson);
assertTrue(msg, Utilities.noString(msg));
} else
assertEquals("Error, but proper output was expected (" + msg + ")", "$error", output);
}
outputs.clear();
@Override
public void log(String message) {
System.out.println(message);
}
boolean ok = false;
String msg = null;
Resource resource = null;
try {
StructureMapUtilities scu = new StructureMapUtilities(context, this);
org.hl7.fhir.r5.elementmodel.Element src = Manager.parse(context,
new ByteArrayInputStream(TextFile.streamToBytes(fileSource)), FhirFormat.JSON);
StructureMap structureMap = scu.parse(TextFile.streamToString(fileMap), name);
String typeName = scu.getTargetType(structureMap).getType();
resource = ResourceFactory.createResource(typeName);
scu.transform(null, src, structureMap, resource);
ok = true;
} catch (Exception e) {
ok = false;
msg = e.getMessage();
}
if (ok) {
ByteArrayOutputStream boas = new ByteArrayOutputStream();
jsonParser.compose(boas, resource);
String result = boas.toString();
log(result);
TextFile.bytesToFile(boas.toByteArray(), fileOutputRes);
msg = TestingUtilities.checkJsonSrcIsSame(result, outputJson);
assertTrue(msg, Utilities.noString(msg));
} else
assertTrue("Error, but proper output was expected (" + msg + ")", output.equals("$error"));
}
@Override
public Base createType(Object appInfo, String name) throws FHIRException {
StructureDefinition sd = context.fetchResource(StructureDefinition.class, name);
if (sd != null && sd.getKind() == StructureDefinitionKind.LOGICAL) {
return Manager.build(context, sd);
} else {
if (name.startsWith("http://hl7.org/fhir/StructureDefinition/"))
name = name.substring("http://hl7.org/fhir/StructureDefinition/".length());
return ResourceFactory.createResourceOrType(name);
}
}
@Override
public void log(String message) {
System.out.println(message);
}
@Override
public Base createResource(Object appInfo, Base res, boolean atRootofTransform) {
if (atRootofTransform)
outputs.add((Resource) res);
return res;
}
@Override
public Base createType(Object appInfo, String name) throws FHIRException {
StructureDefinition sd = context.fetchResource(StructureDefinition.class, name);
if (sd != null && sd.getKind() == StructureDefinitionKind.LOGICAL) {
return Manager.build(context, sd);
} else {
if (name.startsWith("http://hl7.org/fhir/StructureDefinition/"))
name = name.substring("http://hl7.org/fhir/StructureDefinition/".length());
return ResourceFactory.createResourceOrType(name);
}
}
@Override
public Coding translate(Object appInfo, Coding source, String conceptMapUrl) throws FHIRException {
ConceptMapEngine cme = new ConceptMapEngine(context);
return cme.translate(source, conceptMapUrl);
}
@Override
public Base createResource(Object appInfo, Base res, boolean atRootofTransform) {
if (atRootofTransform)
outputs.add((Resource) res);
return res;
}
@Override
public Coding translate(Object appInfo, Coding source, String conceptMapUrl) throws FHIRException {
ConceptMapEngine cme = new ConceptMapEngine(context);
return cme.translate(source, conceptMapUrl);
}
@Override
public Base resolveReference(Object appContext, String url) throws FHIRException {
throw new FHIRException("resolveReference is not supported yet");
}
@Override
public List<Base> performSearch(Object appContext, String url) throws FHIRException {
throw new FHIRException("performSearch is not supported yet");
}
@Override
public Base resolveReference(Object appContext, String url) throws FHIRException {
throw new FHIRException("resolveReference is not supported yet");
}
@Override
public List<Base> performSearch(Object appContext, String url) throws FHIRException {
throw new FHIRException("performSearch is not supported yet");
}
}

86
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/FHIRPathTests.java
View File

@ -1,44 +1,32 @@
package org.hl7.fhir.r5.test;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.*;
import javax.xml.parsers.ParserConfigurationException;
import junit.framework.Assert;
import org.apache.commons.lang3.NotImplementedException;
import org.fhir.ucum.UcumEssenceService;
import org.fhir.ucum.UcumException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.PathEngineException;
import org.hl7.fhir.r5.context.SimpleWorkerContext;
import org.hl7.fhir.r5.formats.XmlParser;
import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.BooleanType;
import org.hl7.fhir.r5.model.ExpressionNode;
import org.hl7.fhir.r5.model.PrimitiveType;
import org.hl7.fhir.r5.model.Quantity;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.TypeDetails;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.model.*;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.r5.utils.FHIRPathEngine;
import org.hl7.fhir.r5.utils.FHIRPathEngine.IEvaluationContext;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.junit.runners.Parameterized;
import org.junit.runners.Parameterized.Parameters;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.Arguments;
import org.junit.jupiter.params.provider.MethodSource;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
import org.xml.sax.SAXException;
import junit.framework.Assert;
import javax.xml.parsers.ParserConfigurationException;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.*;
import java.util.stream.Stream;
@RunWith(Parameterized.class)
public class FHIRPathTests {
public class FHIRPathTestEvaluationServices implements IEvaluationContext {
@ -60,7 +48,7 @@ public class FHIRPathTests {
@Override
public FunctionDetails resolveFunction(String functionName) {
throw new NotImplementedException("Not done yet (FHIRPathTestEvaluationServices.resolveFunction), when item is element (for "+functionName+")");
throw new NotImplementedException("Not done yet (FHIRPathTestEvaluationServices.resolveFunction), when item is element (for " + functionName + ")");
}
@Override
@ -84,8 +72,8 @@ public class FHIRPathTests {
return true;
if (url.equals("http://hl7.org/fhir/StructureDefinition/Person"))
return false;
throw new FHIRException("unknown profile "+url);
throw new FHIRException("unknown profile " + url);
}
@Override
@ -96,25 +84,29 @@ public class FHIRPathTests {
}
private static FHIRPathEngine fp;
private final Map<String, Resource> resources = new HashMap<String, Resource>();
@Parameters(name = "{index}: file {0}")
public static Iterable<Object[]> data() throws ParserConfigurationException, SAXException, IOException {
@BeforeAll
public static void setUp() {
fp = new FHIRPathEngine(TestingUtilities.context());
}
public static Stream<Arguments> data() throws ParserConfigurationException, SAXException, IOException {
Document dom = XMLUtil.parseToDom(TestingUtilities.loadTestResource("r5", "fhirpath", "tests-fhir-r5.xml"));
List<Element> list = new ArrayList<Element>();
List<Element> groups = new ArrayList<Element>();
XMLUtil.getNamedChildren(dom.getDocumentElement(), "group", groups);
for (Element g : groups) {
XMLUtil.getNamedChildren(g, "test", list);
XMLUtil.getNamedChildren(g, "test", list);
}
List<Object[]> objects = new ArrayList<Object[]>(list.size());
List<Arguments> objects = new ArrayList<>();
for (Element e : list) {
objects.add(new Object[] { getName(e), e });
objects.add(Arguments.of(getName(e), e));
}
return objects;
return objects.stream();
}
private static Object getName(Element e) {
@ -128,31 +120,21 @@ public class FHIRPathTests {
else if (c instanceof Element)
ndx++;
}
if (Utilities.noString(s))
s = "?? - G "+p.getAttribute("name")+"["+Integer.toString(ndx+1)+"]";
if (Utilities.noString(s))
s = "?? - G " + p.getAttribute("name") + "[" + Integer.toString(ndx + 1) + "]";
else
s = s + " - G "+p.getAttribute("name")+"["+Integer.toString(ndx+1)+"]";
s = s + " - G " + p.getAttribute("name") + "[" + Integer.toString(ndx + 1) + "]";
return s;
}
private final Element test;
private final String name;
private Map<String, Resource> resources = new HashMap<String, Resource>();
public FHIRPathTests(String name, Element e) {
this.name = name;
this.test = e;
}
@SuppressWarnings("deprecation")
@Test
public void test() throws FileNotFoundException, IOException, FHIRException, org.hl7.fhir.exceptions.FHIRException, UcumException {
@ParameterizedTest(name = "{index}: file {0}")
@MethodSource("data")
public void test(String name, Element test) throws FileNotFoundException, IOException, FHIRException, org.hl7.fhir.exceptions.FHIRException, UcumException {
// Setting timezone for this test. Grahame is in UTC+11, Travis is in GMT, and I'm here in Toronto, Canada with
// all my time based tests failing locally...
TimeZone.setDefault(TimeZone.getTimeZone("UTC+1100"));
if (fp == null)
fp = new FHIRPathEngine(TestingUtilities.context());
fp.setHostServices(new FHIRPathTestEvaluationServices());
String input = test.getAttribute("inputfile");
String expression = XMLUtil.getNamedChild(test, "expression").getTextContent();
@ -176,7 +158,7 @@ public class FHIRPathTests {
outcome = fp.evaluate(res, node);
Assert.assertTrue(String.format("Expected exception parsing %s", expression), !fail);
} catch (Exception e) {
Assert.assertTrue(String.format("Unexpected exception parsing %s: "+e.getMessage(), expression), fail);
Assert.assertTrue(String.format("Unexpected exception parsing %s: " + e.getMessage(), expression), fail);
}
if ("true".equals(test.getAttribute("predicate"))) {
@ -201,7 +183,7 @@ public class FHIRPathTests {
boolean found = false;
for (Element e : expected) {
if ((Utilities.noString(e.getAttribute("type")) || e.getAttribute("type").equals(tn)) &&
(Utilities.noString(e.getTextContent()) || e.getTextContent().equals(s)))
(Utilities.noString(e.getTextContent()) || e.getTextContent().equals(s)))
found = true;
}
Assert.assertTrue(String.format("Outcome %d: Value %s of type %s not expected for %s", i, s, tn, expression), found);
@ -219,7 +201,7 @@ public class FHIRPathTests {
Assert.assertTrue(String.format("Outcome %d: Value should be %s but was %s", i, v, outcome.get(i).toString()), outcome.get(i).equalsDeep(q));
} else {
Assert.assertTrue(String.format("Outcome %d: Value should be a primitive type but was %s", i, outcome.get(i).fhirType()), outcome.get(i) instanceof PrimitiveType);
Assert.assertTrue(String.format("Outcome %d: Value should be %s but was %s for expression %s", i, v, outcome.get(i).toString(), expression), v.equals(((PrimitiveType)outcome.get(i)).asStringValue()));
Assert.assertTrue(String.format("Outcome %d: Value should be %s but was %s for expression %s", i, v, outcome.get(i).toString(), expression), v.equals(((PrimitiveType) outcome.get(i)).asStringValue()));
}
}
}

37
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/GraphQLEngineTests.java
View File

@ -21,6 +21,9 @@ import org.hl7.fhir.utilities.graphql.NameValue;
import org.hl7.fhir.utilities.graphql.Parser;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.junit.Test;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.Arguments;
import org.junit.jupiter.params.provider.MethodSource;
import org.junit.runner.RunWith;
import org.junit.runners.Parameterized;
import org.junit.runners.Parameterized.Parameters;
@ -37,43 +40,27 @@ import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.List;
import java.util.stream.Stream;
import static org.junit.Assert.assertTrue;
@RunWith(Parameterized.class)
public class GraphQLEngineTests implements IGraphQLStorageServices {
@Parameters(name = "{index}: {0}")
public static Iterable<Object[]> data() throws FileNotFoundException, IOException, ParserConfigurationException, SAXException {
public static Stream<Arguments> data() throws IOException, ParserConfigurationException, SAXException {
Document tests = XMLUtil.parseToDom(TestingUtilities.loadTestResource("r5", "graphql", "manifest.xml"));
Element test = XMLUtil.getFirstChild(tests.getDocumentElement());
List<Object[]> objects = new ArrayList<Object[]>();
List<Arguments> objects = new ArrayList<>();
while (test != null && test.getNodeName().equals("test")) {
objects.add(new Object[] { test.getAttribute("name"), test.getAttribute("source"), test.getAttribute("output"),
test.getAttribute("context"), test.getAttribute("resource"), test.getAttribute("operation")} );
objects.add(Arguments.of(test.getAttribute("name"), test.getAttribute("source"), test.getAttribute("output"),
test.getAttribute("context"), test.getAttribute("resource"), test.getAttribute("operation")));
test = XMLUtil.getNextSibling(test);
}
return objects;
return objects.stream();
}
private final String name;
private String source;
private String output;
private String context;
private String resource;
private String operation;
public GraphQLEngineTests(String name, String source, String output, String context, String resource, String operation) {
this.name = name;
this.source = source;
this.output = output;
this.context = context;
this.resource = resource;
this.operation = operation;
}
@Test
public void test() throws Exception {
@ParameterizedTest(name = "{index}: {0}")
@MethodSource("data")
public void test(String name, String source, String output, String context, String resource, String operation) throws Exception {
InputStream stream = null;
if (!Utilities.noString(context)) {
String[] parts = context.split("/");

32
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/GraphQLParserTests.java
View File

@ -6,6 +6,7 @@ import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.stream.Stream;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.utilities.TextFile;
@ -15,42 +16,31 @@ import org.hl7.fhir.utilities.graphql.EGraphQLException;
import org.hl7.fhir.utilities.graphql.Package;
import org.hl7.fhir.utilities.graphql.Parser;
import org.junit.Test;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.Arguments;
import org.junit.jupiter.params.provider.MethodSource;
import org.junit.runner.RunWith;
import org.junit.runners.Parameterized;
import org.junit.runners.Parameterized.Parameters;
@RunWith(Parameterized.class)
public class GraphQLParserTests {
@Parameters(name = "{index}: {0}")
public static Iterable<Object[]> data() throws FileNotFoundException, IOException {
public static Stream<Arguments> data() throws FileNotFoundException, IOException {
String src = TestingUtilities.loadTestResource("r5", "graphql", "parser-tests.gql");
String[] tests = src.split("###");
int i = 0;
for (String s : tests)
if (!Utilities.noString(s.trim()))
i++;
List<Object[]> objects = new ArrayList<Object[]>(i);
i = 0;
List<Arguments> objects = new ArrayList<>();
for (String s : tests) {
if (!Utilities.noString(s.trim())) {
int l = s.indexOf('\r');
objects.add(new Object[] { s.substring(0, l), s.substring(l+2).trim()});
objects.add(Arguments.of(s.substring(0, l), s.substring(l+2).trim()));
}
}
return objects;
return objects.stream();
}
private final String test;
private final String name;
public GraphQLParserTests(String name, String test) {
this.name = name;
this.test = test;
}
@Test
public void test() throws IOException, EGraphQLException, EGraphEngine {
@ParameterizedTest(name = "{index}: {0}")
@MethodSource("data")
public void test(String name, String test) throws IOException, EGraphQLException, EGraphEngine {
Package doc = Parser.parse(test);
assertTrue(doc != null);
}

9
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/JsonDirectTests.java
View File

@ -13,16 +13,13 @@ import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.formats.XmlParser;
import org.hl7.fhir.r5.model.Observation;
import org.hl7.fhir.utilities.Utilities;
import org.junit.Before;
import org.junit.Test;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
public class JsonDirectTests {
@Before
public void setUp() throws Exception {
}
@Test
@Disabled // Hard coded path here
public void test() throws FHIRFormatError, FileNotFoundException, IOException {
File src = new File(Utilities.path("[tmp]", "obs.xml"));
File xml = new File(Utilities.path("[tmp]", "xml.xml"));

38
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/LiquidEngineTests.java
View File

@ -1,25 +1,17 @@
package org.hl7.fhir.r5.test;
import java.io.FileInputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import javax.xml.parsers.ParserConfigurationException;
import com.google.gson.JsonArray;
import com.google.gson.JsonElement;
import com.google.gson.JsonObject;
import junit.framework.Assert;
import org.apache.commons.collections4.map.HashedMap;
import org.fhir.ucum.UcumEssenceService;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.context.SimpleWorkerContext;
import org.hl7.fhir.r5.formats.XmlParser;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.r5.utils.LiquidEngine;
import org.hl7.fhir.r5.utils.LiquidEngine.ILiquidEngineIcludeResolver;
import org.hl7.fhir.r5.utils.LiquidEngine.LiquidDocument;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.junit.Before;
import org.junit.Test;
import org.junit.runner.RunWith;
@ -27,28 +19,30 @@ import org.junit.runners.Parameterized;
import org.junit.runners.Parameterized.Parameters;
import org.xml.sax.SAXException;
import com.google.gson.JsonArray;
import com.google.gson.JsonElement;
import com.google.gson.JsonObject;
import junit.framework.Assert;
import javax.xml.parsers.ParserConfigurationException;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
@RunWith(Parameterized.class)
public class LiquidEngineTests implements ILiquidEngineIcludeResolver {
//TODO Migrate this test to JUnit Jupiter. Need to refactor the base class ILiquidEngineIcludeResolver to do this properly.
private static Map<String, Resource> resources = new HashedMap<>();
private static JsonObject testdoc = null;
private JsonObject test;
private LiquidEngine engine;
@Parameters(name = "{index}: file{0}")
public static Iterable<Object[]> data() throws ParserConfigurationException, SAXException, IOException {
testdoc = (JsonObject) new com.google.gson.JsonParser().parse(TestingUtilities.loadTestResource("r5", "liquid", "liquid-tests.json"));
JsonArray tests = testdoc.getAsJsonArray("tests");
List<Object[]> objects = new ArrayList<Object[]>(tests.size());
for (JsonElement n : tests) {
objects.add(new Object[] {n});
objects.add(new Object[]{n});
}
return objects;
}
@ -58,7 +52,6 @@ public class LiquidEngineTests implements ILiquidEngineIcludeResolver {
this.test = test;
}
@Before
public void setUp() throws Exception {
engine = new LiquidEngine(TestingUtilities.context(), null);
@ -76,12 +69,11 @@ public class LiquidEngineTests implements ILiquidEngineIcludeResolver {
private Resource loadResource() throws IOException, FHIRFormatError {
String name = test.get("focus").getAsString();
if (!resources.containsKey(name)) {
resources.put(name, new XmlParser().parse(TestingUtilities.loadTestResourceStream("r5", (name.replace("/", "-")+".xml").toLowerCase())));
resources.put(name, new XmlParser().parse(TestingUtilities.loadTestResourceStream("r5", (name.replace("/", "-") + ".xml").toLowerCase())));
}
return resources.get(test.get("focus").getAsString());
}
@Test
public void test() throws Exception {
LiquidDocument doc = engine.parse(test.get("template").getAsString(), "test-script");

2
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/MetaTest.java
View File

@ -2,7 +2,7 @@ package org.hl7.fhir.r5.test;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.Meta;
import org.junit.Test;
import org.junit.jupiter.api.Test;
import static org.junit.Assert.*;
import static org.junit.Assert.assertEquals;

119
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/NarrativeGenerationTests.java
View File

@ -1,80 +1,39 @@
package org.hl7.fhir.r5.test;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import javax.xml.parsers.ParserConfigurationException;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.NotImplementedException;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.exceptions.PathEngineException;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.conformance.ProfileUtilities.ProfileKnowledgeProvider;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.context.SimpleWorkerContext;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.formats.XmlParser;
import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.DomainResource;
import org.hl7.fhir.r5.model.ElementDefinition.ElementDefinitionBindingComponent;
import org.hl7.fhir.r5.model.ExpressionNode.CollectionStatus;
import org.hl7.fhir.r5.model.CanonicalResource;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionKind;
import org.hl7.fhir.r5.model.StructureDefinition.TypeDerivationRule;
import org.hl7.fhir.r5.model.TestScript;
import org.hl7.fhir.r5.model.TestScript.AssertionResponseTypes;
import org.hl7.fhir.r5.model.TestScript.SetupActionAssertComponent;
import org.hl7.fhir.r5.model.TestScript.SetupActionOperationComponent;
import org.hl7.fhir.r5.model.TestScript.TestActionComponent;
import org.hl7.fhir.r5.model.TestScript.TestScriptFixtureComponent;
import org.hl7.fhir.r5.model.TestScript.TestScriptTestComponent;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.r5.model.TypeDetails;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.utils.CodingUtilities;
import org.hl7.fhir.r5.utils.EOperationOutcome;
import org.hl7.fhir.r5.utils.FHIRPathEngine;
import org.hl7.fhir.r5.utils.FHIRPathEngine.IEvaluationContext;
import org.hl7.fhir.r5.utils.IResourceValidator;
import org.hl7.fhir.r5.utils.NarrativeGenerator;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.cache.PackageCacheManager;
import org.hl7.fhir.utilities.cache.ToolsVersion;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.xhtml.XhtmlComposer;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.junit.runners.Parameterized;
import org.junit.runners.Parameterized.Parameters;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.TestInstance;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.Arguments;
import org.junit.jupiter.params.provider.MethodSource;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.xml.sax.SAXException;
import ca.uhn.fhir.rest.api.Constants;
import junit.framework.Assert;
import javax.xml.parsers.ParserConfigurationException;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.stream.Stream;
@RunWith(Parameterized.class)
@TestInstance(TestInstance.Lifecycle.PER_CLASS)
@Disabled //Test case 1 doesn't pass in r5 yet
public class NarrativeGenerationTests {
private IWorkerContext context;
public static class TestDetails {
private String id;
@ -82,49 +41,39 @@ public class NarrativeGenerationTests {
super();
id = test.getAttribute("id");
}
public String getId() {
return id;
}
}
private static FHIRPathEngine fp;
@Parameters(name = "{index}: file {0}")
public static Iterable<Object[]> data() throws ParserConfigurationException, IOException, FHIRFormatError, SAXException {
public static Stream<Arguments> data() throws ParserConfigurationException, IOException, FHIRFormatError, SAXException {
Document tests = XMLUtil.parseToDom(TestingUtilities.loadTestResource("r5", "narrative", "manifest.xml"));
Element test = XMLUtil.getFirstChild(tests.getDocumentElement());
List<Object[]> objects = new ArrayList<Object[]>();
List<Arguments> objects = new ArrayList<>();
while (test != null && test.getNodeName().equals("test")) {
TestDetails t = new TestDetails(test);
objects.add(new Object[] {t.getId(), t});
objects.add(Arguments.of(t.getId(), t));
test = XMLUtil.getNextSibling(test);
}
return objects;
return objects.stream();
}
private final TestDetails test;
private IWorkerContext context;
private List<ValidationMessage> messages;
public NarrativeGenerationTests(String id, TestDetails test) {
this.test = test;
@BeforeAll
public void setUp() {
this.context = TestingUtilities.context();
}
@SuppressWarnings("deprecation")
@Test
public void test() throws Exception {
@ParameterizedTest(name = "{index}: file {0}")
@MethodSource("data")
public void test(String id, TestDetails test) throws Exception {
NarrativeGenerator gen = new NarrativeGenerator("", "http://hl7.org/fhir", context);
IOUtils.copy(TestingUtilities.loadTestResourceStream("r5", "narrative", test.getId()+"-expected.xml"), new FileOutputStream(TestingUtilities.tempFile("narrative", test.getId()+"-expected.xml")));
DomainResource source = (DomainResource) new XmlParser().parse(TestingUtilities.loadTestResourceStream("r5", "narrative", test.getId()+"-input.xml"));
DomainResource target = (DomainResource) new XmlParser().parse(TestingUtilities.loadTestResourceStream("r5", "narrative", test.getId()+"-expected.xml"));
IOUtils.copy(TestingUtilities.loadTestResourceStream("r5", "narrative", test.getId() + "-expected.xml"), new FileOutputStream(TestingUtilities.tempFile("narrative", test.getId() + "-expected.xml")));
DomainResource source = (DomainResource) new XmlParser().parse(TestingUtilities.loadTestResourceStream("r5", "narrative", test.getId() + "-input.xml"));
DomainResource target = (DomainResource) new XmlParser().parse(TestingUtilities.loadTestResourceStream("r5", "narrative", test.getId() + "-expected.xml"));
gen.generate(source);
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(TestingUtilities.tempFile("narrative", test.getId()+"-actual.xml")), source);
source = (DomainResource) new XmlParser().parse(new FileInputStream(TestingUtilities.tempFile("narrative", test.getId()+"-actual.xml")));
Assert.assertTrue("Output does not match expected", source.equalsDeep(target));
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(TestingUtilities.tempFile("narrative", test.getId() + "-actual.xml")), source);
source = (DomainResource) new XmlParser().parse(new FileInputStream(TestingUtilities.tempFile("narrative", test.getId() + "-actual.xml")));
Assertions.assertTrue(source.equalsDeep(target), "Output does not match expected");
}
}

61
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/NarrativeGeneratorTests.java
View File

@ -1,52 +1,43 @@
package org.hl7.fhir.r5.test;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import org.fhir.ucum.UcumException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.context.SimpleWorkerContext;
import org.hl7.fhir.r5.formats.XmlParser;
import org.hl7.fhir.r5.model.DomainResource;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.r5.utils.EOperationOutcome;
import org.hl7.fhir.r5.utils.NarrativeGenerator;
import org.hl7.fhir.utilities.Utilities;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.TestInstance;
import org.xmlpull.v1.XmlPullParserException;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
@TestInstance(TestInstance.Lifecycle.PER_CLASS)
public class NarrativeGeneratorTests {
private NarrativeGenerator gen;
@Before
public void setUp() throws FileNotFoundException, IOException, FHIRException, UcumException {
if (gen == null)
gen = new NarrativeGenerator("", null, TestingUtilities.context());
}
private NarrativeGenerator gen;
@After
public void tearDown() {
}
@Test
public void test() throws FileNotFoundException, IOException, XmlPullParserException, EOperationOutcome, FHIRException {
process(TestingUtilities.loadTestResourceStream("r5", "questionnaireresponse-example-f201-lifelines.xml"));
}
private void process(InputStream stream) throws FileNotFoundException, IOException, XmlPullParserException, EOperationOutcome, FHIRException {
XmlParser p = new XmlParser();
DomainResource r = (DomainResource) p.parse(stream);
gen.generate(r, null);
FileOutputStream s = new FileOutputStream(TestingUtilities.tempFile("gen", "gen.xml"));
new XmlParser().compose(s, r, true);
s.close();
@BeforeAll
public void setUp() throws FileNotFoundException, IOException, FHIRException, UcumException {
gen = new NarrativeGenerator("", null, TestingUtilities.context());
}
@Test
public void test() throws FileNotFoundException, IOException, XmlPullParserException, EOperationOutcome, FHIRException {
process(TestingUtilities.loadTestResourceStream("r5", "questionnaireresponse-example-f201-lifelines.xml"));
}
private void process(InputStream stream) throws FileNotFoundException, IOException, XmlPullParserException, EOperationOutcome, FHIRException {
XmlParser p = new XmlParser();
DomainResource r = (DomainResource) p.parse(stream);
gen.generate(r, null);
FileOutputStream s = new FileOutputStream(TestingUtilities.tempFile("gen", "gen.xml"));
new XmlParser().compose(s, r, true);
s.close();
}
}

63
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/NpmPackageTests.java
View File

@ -1,24 +1,14 @@
package org.hl7.fhir.r5.test;
import static org.junit.Assert.*;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.cache.NpmPackage;
import org.junit.Test;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
import junit.framework.Assert;
import java.io.*;
import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream;
public class NpmPackageTests {
@ -67,46 +57,43 @@ public class NpmPackageTests {
private void checkNpm(NpmPackage npm) throws IOException {
Assert.assertEquals(1, npm.list("other").size());
Assert.assertEquals("help.png", npm.list("other").get(0));
Assert.assertEquals(1, npm.list("package").size());
Assert.assertEquals("StructureDefinition-Definition.json", npm.list("package").get(0));
Assertions.assertEquals(1, npm.list("other").size());
Assertions.assertEquals("help.png", npm.list("other").get(0));
Assertions.assertEquals(1, npm.list("package").size());
Assertions.assertEquals("StructureDefinition-Definition.json", npm.list("package").get(0));
}
private static void unzip(InputStream source, File destDir) throws IOException {
Utilities.createDirectory(destDir.getAbsolutePath());
byte[] buffer = new byte[1024];
ZipInputStream zis = new ZipInputStream(source);
ZipEntry zipEntry = zis.getNextEntry();
while (zipEntry != null) {
File newFile = newFile(destDir, zipEntry);
if (zipEntry.isDirectory()) {
Utilities.createDirectory(newFile.getAbsolutePath());
} else {
FileOutputStream fos = new FileOutputStream(newFile);
int len;
while ((len = zis.read(buffer)) > 0) {
fos.write(buffer, 0, len);
}
fos.close();
File newFile = newFile(destDir, zipEntry);
if (zipEntry.isDirectory()) {
Utilities.createDirectory(newFile.getAbsolutePath());
} else {
FileOutputStream fos = new FileOutputStream(newFile);
int len;
while ((len = zis.read(buffer)) > 0) {
fos.write(buffer, 0, len);
}
zipEntry = zis.getNextEntry();
fos.close();
}
zipEntry = zis.getNextEntry();
}
zis.closeEntry();
zis.close();
}
public static File newFile(File destinationDir, ZipEntry zipEntry) throws IOException {
File destFile = new File(destinationDir, zipEntry.getName());
String destDirPath = destinationDir.getCanonicalPath();
String destFilePath = destFile.getCanonicalPath();
if (!destFilePath.startsWith(destDirPath + File.separator)) {
throw new IOException("Entry is outside of the target dir: " + zipEntry.getName());
}
throw new IOException("Entry is outside of the target dir: " + zipEntry.getName());
}
return destFile;
}
}
}

24
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/OpenApiGeneratorTest.java
View File

@ -1,39 +1,34 @@
package org.hl7.fhir.r5.test;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.model.CapabilityStatement;
import org.hl7.fhir.r5.openapi.OpenApiGenerator;
import org.hl7.fhir.r5.openapi.Writer;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.junit.Test;
import org.w3c.dom.Document;
import org.junit.jupiter.api.Test;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
public class OpenApiGeneratorTest {
@Test
public void testBase1() throws IOException, FHIRFormatError {
public void testBase1() throws IOException, FHIRFormatError {
InputStream sfn = TestingUtilities.loadTestResourceStream("r5", "openapi", "cs-base.json");
String dfn = TestingUtilities.tempFile("openapi", "swagger-base.json");
run(sfn, dfn);
}
@Test
public void testBase2() throws FHIRFormatError, FileNotFoundException, IOException {
public void testBase2() throws FHIRFormatError, FileNotFoundException, IOException {
InputStream sfn = TestingUtilities.loadTestResourceStream("r5", "openapi", "cs-base2.json");
String dfn = TestingUtilities.tempFile("openapi", "swagger-base2.json");
run(sfn, dfn);
}
public void run(InputStream sfn, String dfn) throws IOException, FHIRFormatError, FileNotFoundException {
CapabilityStatement cs = (CapabilityStatement) new JsonParser().parse(sfn);
Writer oa = new Writer(new FileOutputStream(dfn));
@ -41,5 +36,4 @@ public class OpenApiGeneratorTest {
gen.generate("test-lic", "http://spdx.org/licenses/test-lic.html");
oa.commit();
}
}

15
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/PackageCacheTests.java
View File

@ -7,19 +7,21 @@ import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.cache.NpmPackage;
import org.hl7.fhir.utilities.cache.PackageCacheManager;
import org.hl7.fhir.utilities.cache.ToolsVersion;
import org.junit.Assert;
import org.junit.Test;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
public class PackageCacheTests {
@Test
@Disabled // This test is currently set to always fail.
public void testPath() throws IOException {
PackageCacheManager cache = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
cache.clear();
Assert.assertTrue(false);
Assertions.assertTrue(false);
NpmPackage npm = cache.loadPackage("hl7.fhir.pubpack", "0.0.3");
npm.loadAllFiles();
Assert.assertNotNull(npm);
Assertions.assertNotNull(npm);
File dir = new File(Utilities.path("[tmp]", "cache"));
if (dir.exists()) {
Utilities.clearDirectory(dir.getAbsolutePath());
@ -28,10 +30,7 @@ public class PackageCacheTests {
}
npm.save(dir);
NpmPackage npm2 = cache.loadPackage("hl7.fhir.pubpack", "file:"+dir.getAbsolutePath());
Assert.assertNotNull(npm2);
Assertions.assertNotNull(npm2);
}
}

51
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/PackageClientTests.java
View File

@ -1,21 +1,21 @@
package org.hl7.fhir.r5.test;
import java.io.IOException;
import java.util.List;
import org.hl7.fhir.utilities.cache.PackageClient;
import org.hl7.fhir.utilities.cache.PackageClient.PackageInfo;
import org.junit.Assert;
import org.junit.Test;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
import java.io.IOException;
import java.util.List;
public class PackageClientTests {
@Test
public void testExists() throws IOException {
PackageClient client = new PackageClient("http://packages.fhir.org");
Assert.assertTrue(client.exists("hl7.fhir.r4.core", "4.0.1"));
Assert.assertTrue(!client.exists("hl7.fhir.r4.core", "1.0.2"));
Assert.assertTrue(!client.exists("hl7.fhir.nothing", "1.0.1"));
Assertions.assertTrue(client.exists("hl7.fhir.r4.core", "4.0.1"));
Assertions.assertTrue(!client.exists("hl7.fhir.r4.core", "1.0.2"));
Assertions.assertTrue(!client.exists("hl7.fhir.nothing", "1.0.1"));
}
@Test
@ -25,15 +25,14 @@ public class PackageClientTests {
for (PackageInfo pi : matches) {
System.out.println(pi.toString());
}
Assert.assertTrue(matches.size() > 0);
Assertions.assertTrue(matches.size() > 0);
}
@Test
public void testSearchNoMatches() throws IOException {
PackageClient client = new PackageClient("http://packages.fhir.org");
List<PackageInfo> matches = client.search("corezxxx", null, null, false);
Assert.assertTrue(matches.size() == 0);
Assertions.assertTrue(matches.size() == 0);
}
@Test
@ -43,23 +42,23 @@ public class PackageClientTests {
for (PackageInfo pi : matches) {
System.out.println(pi.toString());
}
Assert.assertTrue(matches.size() > 0);
Assertions.assertTrue(matches.size() > 0);
}
@Test
public void testVersionsNone() throws IOException {
PackageClient client = new PackageClient("http://packages.fhir.org");
List<PackageInfo> matches = client.getVersions("Simplifier.Core.STU3X");
Assert.assertTrue(matches.size() == 0);
Assertions.assertTrue(matches.size() == 0);
}
@Test
public void testExists2() throws IOException {
PackageClient client = new PackageClient("http://test.fhir.org/packages");
Assert.assertTrue(client.exists("hl7.fhir.r4.core", "4.0.1"));
Assert.assertTrue(!client.exists("hl7.fhir.r4.core", "1.0.2"));
Assert.assertTrue(!client.exists("hl7.fhir.nothing", "1.0.1"));
Assertions.assertTrue(client.exists("hl7.fhir.r4.core", "4.0.1"));
Assertions.assertTrue(!client.exists("hl7.fhir.r4.core", "1.0.2"));
Assertions.assertTrue(!client.exists("hl7.fhir.nothing", "1.0.1"));
}
@Test
@ -69,14 +68,14 @@ public class PackageClientTests {
for (PackageInfo pi : matches) {
System.out.println(pi.toString());
}
Assert.assertTrue(matches.size() > 0);
Assertions.assertTrue(matches.size() > 0);
}
@Test
public void testSearchNoMatches2() throws IOException {
PackageClient client = new PackageClient("http://test.fhir.org/packages");
List<PackageInfo> matches = client.search("corezxxx", null, null, false);
Assert.assertTrue(matches.size() == 0);
Assertions.assertTrue(matches.size() == 0);
}
@Test
@ -86,9 +85,9 @@ public class PackageClientTests {
for (PackageInfo pi : matches) {
System.out.println(pi.toString());
}
Assert.assertTrue(matches.size() == 0);
Assertions.assertTrue(matches.size() == 0);
}
@Test
public void testVersions2A() throws IOException {
PackageClient client = new PackageClient("http://test.fhir.org/packages");
@ -96,15 +95,13 @@ public class PackageClientTests {
for (PackageInfo pi : matches) {
System.out.println(pi.toString());
}
Assert.assertTrue(matches.size() > 0);
Assertions.assertTrue(matches.size() > 0);
}
@Test
public void testVersionsNone2() throws IOException {
PackageClient client = new PackageClient("http://test.fhir.org/packages");
List<PackageInfo> matches = client.getVersions("Simplifier.Core.STU3X");
Assert.assertTrue(matches.size() == 0);
Assertions.assertTrue(matches.size() == 0);
}
}

7
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/ProfileUtilitiesTests.java
View File

@ -9,7 +9,6 @@ import java.util.List;
import org.fhir.ucum.UcumException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.context.SimpleWorkerContext;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.formats.XmlParser;
import org.hl7.fhir.r5.model.Base;
@ -21,8 +20,7 @@ import org.hl7.fhir.r5.utils.EOperationOutcome;
import org.hl7.fhir.utilities.CSFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.junit.Test;
import org.junit.jupiter.api.Test;
public class ProfileUtilitiesTests {
@ -811,7 +809,4 @@ public class ProfileUtilitiesTests {
builder.directory(new CSFile("c:\\temp"));
builder.start();
}
}

1
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/QuestionnaireBuilderTester.java
View File

@ -29,5 +29,4 @@ public class QuestionnaireBuilderTester {
}
}
}
}

27
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/ResourceRoundTripTests.java
View File

@ -1,19 +1,10 @@
package org.hl7.fhir.r5.test;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import org.apache.commons.io.IOUtils;
import org.fhir.ucum.UcumException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.context.SimpleWorkerContext;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.formats.IParser;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.formats.XmlParser;
import org.hl7.fhir.r5.model.Bundle;
@ -22,16 +13,12 @@ import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.r5.utils.EOperationOutcome;
import org.hl7.fhir.r5.utils.NarrativeGenerator;
import org.hl7.fhir.utilities.Utilities;
import org.junit.Before;
import org.junit.Test;
import org.junit.jupiter.api.Test;
import java.io.*;
public class ResourceRoundTripTests {
@Before
public void setUp() throws Exception {
}
@Test
public void test() throws FileNotFoundException, IOException, FHIRException, EOperationOutcome, UcumException {
Resource res = new XmlParser().parse(TestingUtilities.loadTestResourceStream("r5", "unicode.xml"));
@ -40,19 +27,18 @@ public class ResourceRoundTripTests {
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(TestingUtilities.tempFile("gen", "unicode.out.xml")), res);
}
@Test
public void testBundle() throws FHIRException, IOException {
// Create new Atom Feed
Bundle feed = new Bundle();
// Serialize Atom Feed
IParser comp = new JsonParser();
ByteArrayOutputStream os = new ByteArrayOutputStream();
comp.compose(os, feed);
os.close();
String json = os.toString();
// Deserialize Atom Feed
JsonParser parser = new JsonParser();
InputStream is = new ByteArrayInputStream(json.getBytes("UTF-8"));
@ -60,5 +46,4 @@ public class ResourceRoundTripTests {
if (result == null)
throw new FHIRException("Bundle was null");
}
}

3
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/ShexGeneratorTests.java
View File

@ -10,11 +10,10 @@ import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.conformance.ShExGenerator;
import org.hl7.fhir.r5.conformance.ShExGenerator.HTMLLinkPolicy;
import org.hl7.fhir.r5.context.SimpleWorkerContext;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.utilities.TextFile;
import org.junit.Test;
import org.junit.jupiter.api.Test;
public class ShexGeneratorTests {

240
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/SnapShotGenerationTests.java
View File

@ -1,20 +1,5 @@
package org.hl7.fhir.r5.test;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import javax.xml.parsers.ParserConfigurationException;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.NotImplementedException;
import org.hl7.fhir.exceptions.DefinitionException;
@ -24,40 +9,20 @@ import org.hl7.fhir.exceptions.PathEngineException;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.conformance.ProfileUtilities.ProfileKnowledgeProvider;
import org.hl7.fhir.r5.context.IWorkerContext.IContextResourceLoader;
import org.hl7.fhir.r5.context.SimpleWorkerContext;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.formats.XmlParser;
import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.Bundle;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.*;
import org.hl7.fhir.r5.model.ElementDefinition.ElementDefinitionBindingComponent;
import org.hl7.fhir.r5.model.ExpressionNode.CollectionStatus;
import org.hl7.fhir.r5.model.CanonicalResource;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionKind;
import org.hl7.fhir.r5.model.StructureDefinition.TypeDerivationRule;
import org.hl7.fhir.r5.model.TestScript;
import org.hl7.fhir.r5.model.TestScript.AssertionResponseTypes;
import org.hl7.fhir.r5.model.TestScript.SetupActionAssertComponent;
import org.hl7.fhir.r5.model.TestScript.SetupActionOperationComponent;
import org.hl7.fhir.r5.model.TestScript.TestActionComponent;
import org.hl7.fhir.r5.model.TestScript.TestScriptFixtureComponent;
import org.hl7.fhir.r5.model.TestScript.TestScriptTestComponent;
import org.hl7.fhir.r5.test.SnapShotGenerationTests.TestFetchMode;
import org.hl7.fhir.r5.test.SnapShotGenerationTests.TestLoader;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.r5.model.TypeDetails;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.utils.CodingUtilities;
import org.hl7.fhir.r5.utils.EOperationOutcome;
import org.hl7.fhir.r5.utils.FHIRPathEngine;
import org.hl7.fhir.r5.utils.FHIRPathEngine.IEvaluationContext;
import org.hl7.fhir.r5.utils.IResourceValidator;
import org.hl7.fhir.r5.utils.NarrativeGenerator;
import org.hl7.fhir.r5.utils.XVerExtensionManager;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.cache.NpmPackage;
import org.hl7.fhir.utilities.cache.PackageCacheManager;
@ -65,17 +30,21 @@ import org.hl7.fhir.utilities.cache.ToolsVersion;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.junit.runners.Parameterized;
import org.junit.runners.Parameterized.Parameters;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.Arguments;
import org.junit.jupiter.params.provider.MethodSource;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.xml.sax.SAXException;
import junit.framework.Assert;
import javax.xml.parsers.ParserConfigurationException;
import java.io.*;
import java.util.ArrayList;
import java.util.List;
import java.util.stream.Stream;
@RunWith(Parameterized.class)
public class SnapShotGenerationTests {
public class TestLoader implements IContextResourceLoader {
@ -100,26 +69,30 @@ public class SnapShotGenerationTests {
public enum TestFetchMode {
INPUT,
OUTPUT,
OUTPUT,
INCLUDE
}
public static class Rule {
private String description;
private String expression;
public Rule(String description, String expression) {
super();
this.description = description;
this.expression = expression;
}
public Rule(Element rule) {
super();
this.description = rule.getAttribute("text");
this.expression = rule.getAttribute("fhirpath");
}
public String getDescription() {
return description;
}
public String getExpression() {
return expression;
}
@ -136,7 +109,7 @@ public class SnapShotGenerationTests {
private boolean fail;
private boolean newSliceProcessing;
private boolean debug;
private List<Rule> rules = new ArrayList<>();
private StructureDefinition source;
private StructureDefinition included;
@ -150,7 +123,7 @@ public class SnapShotGenerationTests {
fail = "true".equals(test.getAttribute("fail"));
newSliceProcessing = !"false".equals(test.getAttribute("new-slice-processing"));
debug = "true".equals(test.getAttribute("debug"));
id = test.getAttribute("id");
include = test.getAttribute("include");
register = test.getAttribute("register");
@ -161,65 +134,81 @@ public class SnapShotGenerationTests {
rule = XMLUtil.getNextSibling(rule);
}
}
public String getId() {
return id;
}
public boolean isSort() {
return sort;
}
public boolean isGen() {
return gen;
}
public String getInclude() {
return include;
}
public boolean isFail() {
return fail;
}
public StructureDefinition getIncluded() {
return included;
}
public List<Rule> getRules() {
return rules;
}
public StructureDefinition getSource() {
return source;
}
public void setSource(StructureDefinition source) {
this.source = source;
}
public StructureDefinition getExpected() {
return expected;
}
public void setExpected(StructureDefinition expected) {
this.expected = expected;
}
public StructureDefinition getOutput() {
return output;
}
public void setOutput(StructureDefinition output) {
this.output = output;
}
public void load() throws FHIRFormatError, FileNotFoundException, IOException {
if (TestingUtilities.findTestResource("r5", "snapshot-generation", id+"-input.json"))
source = (StructureDefinition) new JsonParser().parse(TestingUtilities.loadTestResourceStream("r5", "snapshot-generation", id+"-input.json"));
if (TestingUtilities.findTestResource("r5", "snapshot-generation", id + "-input.json"))
source = (StructureDefinition) new JsonParser().parse(TestingUtilities.loadTestResourceStream("r5", "snapshot-generation", id + "-input.json"));
else
source = (StructureDefinition) new XmlParser().parse(TestingUtilities.loadTestResourceStream("r5", "snapshot-generation", id+"-input.xml"));
source = (StructureDefinition) new XmlParser().parse(TestingUtilities.loadTestResourceStream("r5", "snapshot-generation", id + "-input.xml"));
if (!fail)
expected = (StructureDefinition) new XmlParser().parse(TestingUtilities.loadTestResourceStream("r5", "snapshot-generation", id+"-expected.xml"));
expected = (StructureDefinition) new XmlParser().parse(TestingUtilities.loadTestResourceStream("r5", "snapshot-generation", id + "-expected.xml"));
if (!Utilities.noString(include))
included = (StructureDefinition) new XmlParser().parse(TestingUtilities.loadTestResourceStream("r5", "snapshot-generation", include+".xml"));
included = (StructureDefinition) new XmlParser().parse(TestingUtilities.loadTestResourceStream("r5", "snapshot-generation", include + ".xml"));
if (!Utilities.noString(register)) {
if (TestingUtilities.findTestResource("r5", "snapshot-generation", register+".xml")) {
included = (StructureDefinition) new XmlParser().parse(TestingUtilities.loadTestResourceStream("r5", "snapshot-generation", register+".xml"));
if (TestingUtilities.findTestResource("r5", "snapshot-generation", register + ".xml")) {
included = (StructureDefinition) new XmlParser().parse(TestingUtilities.loadTestResourceStream("r5", "snapshot-generation", register + ".xml"));
} else {
included = (StructureDefinition) new JsonParser().parse(TestingUtilities.loadTestResourceStream("r5", "snapshot-generation", register+".json"));
included = (StructureDefinition) new JsonParser().parse(TestingUtilities.loadTestResourceStream("r5", "snapshot-generation", register + ".json"));
}
}
}
public boolean isNewSliceProcessing() {
return newSliceProcessing;
}
public boolean isDebug() {
return debug;
}
@ -230,13 +219,13 @@ public class SnapShotGenerationTests {
@Override
public boolean isDatatype(String name) {
StructureDefinition sd = TestingUtilities.context().fetchTypeDefinition(name);
return (sd != null) && (sd.getDerivation() == TypeDerivationRule.SPECIALIZATION) && (sd.getKind() == StructureDefinitionKind.PRIMITIVETYPE || sd.getKind() == StructureDefinitionKind.COMPLEXTYPE);
return (sd != null) && (sd.getDerivation() == TypeDerivationRule.SPECIALIZATION) && (sd.getKind() == StructureDefinitionKind.PRIMITIVETYPE || sd.getKind() == StructureDefinitionKind.COMPLEXTYPE);
}
@Override
public boolean isResource(String typeSimple) {
StructureDefinition sd = TestingUtilities.context().fetchTypeDefinition(typeSimple);
return (sd != null) && (sd.getDerivation() == TypeDerivationRule.SPECIALIZATION) && (sd.getKind() == StructureDefinitionKind.RESOURCE);
return (sd != null) && (sd.getDerivation() == TypeDerivationRule.SPECIALIZATION) && (sd.getKind() == StructureDefinitionKind.RESOURCE);
}
@Override
@ -246,13 +235,13 @@ public class SnapShotGenerationTests {
@Override
public String getLinkFor(String corePath, String typeSimple) {
return Utilities.pathURL(corePath, "datatypes.html#"+typeSimple);
return Utilities.pathURL(corePath, "datatypes.html#" + typeSimple);
}
@Override
public BindingResolution resolveBinding(StructureDefinition def, ElementDefinitionBindingComponent binding, String path) throws FHIRException {
BindingResolution br = new BindingResolution();
br.url = path+"/something.html";
br.url = path + "/something.html";
br.display = "something";
return br;
}
@ -260,7 +249,7 @@ public class SnapShotGenerationTests {
@Override
public BindingResolution resolveBinding(StructureDefinition def, String url, String path) throws FHIRException {
BindingResolution br = new BindingResolution();
br.url = path+"/something.html";
br.url = path + "/something.html";
br.display = "something";
return br;
}
@ -269,9 +258,9 @@ public class SnapShotGenerationTests {
public String getLinkForProfile(StructureDefinition profile, String url) {
StructureDefinition sd = TestingUtilities.context().fetchResource(StructureDefinition.class, url);
if (sd == null)
return url+"|"+url;
return url + "|" + url;
else
return sd.getId()+".html|"+sd.present();
return sd.getId() + ".html|" + sd.present();
}
@Override
@ -302,7 +291,7 @@ public class SnapShotGenerationTests {
return TestingUtilities.context().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/OperationOutcome");
if (id.equals("parameters"))
return TestingUtilities.context().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Parameters");
if (id.contains("-")) {
String[] p = id.split("\\-");
id = p[0];
@ -314,15 +303,17 @@ public class SnapShotGenerationTests {
for (TestDetails td : tests) {
if (td.getId().equals(id))
switch (mode) {
case INPUT: return td.getSource();
case OUTPUT: if (td.getOutput() == null)
throw new FHIRException("Not generated yet");
else
return td.getOutput();
case INCLUDE:
return td.getIncluded();
default:
throw new FHIRException("Not done yet");
case INPUT:
return td.getSource();
case OUTPUT:
if (td.getOutput() == null)
throw new FHIRException("Not generated yet");
else
return td.getOutput();
case INCLUDE:
return td.getIncluded();
default:
throw new FHIRException("Not done yet");
}
}
return null;
@ -341,7 +332,7 @@ public class SnapShotGenerationTests {
@Override
public boolean log(String argument, List<Base> focus) {
System.out.println(argument+": "+fp.convertToString(focus));
System.out.println(argument + ": " + fp.convertToString(focus));
return true;
}
@ -369,7 +360,7 @@ public class SnapShotGenerationTests {
list.add(res);
return list;
}
throw new Error("Could not resolve "+id);
throw new Error("Could not resolve " + id);
}
throw new Error("Not implemented yet");
}
@ -414,90 +405,81 @@ public class SnapShotGenerationTests {
}
private static FHIRPathEngine fp;
private List<ValidationMessage> messages;
@Parameters(name = "{index}: file {0}")
public static Iterable<Object[]> data() throws ParserConfigurationException, IOException, FHIRFormatError, SAXException {
@BeforeAll
public static void setUp() {
fp = new FHIRPathEngine(TestingUtilities.context());
}
public static Stream<Arguments> data() throws ParserConfigurationException, IOException, FHIRFormatError, SAXException {
SnapShotGenerationTestsContext context = new SnapShotGenerationTestsContext();
Document tests = XMLUtil.parseToDom(TestingUtilities.loadTestResource("r5", "snapshot-generation", "manifest.xml"));
Element test = XMLUtil.getFirstChild(tests.getDocumentElement());
List<Object[]> objects = new ArrayList<Object[]>();
List<Arguments> objects = new ArrayList<>();
while (test != null && test.getNodeName().equals("test")) {
TestDetails t = new TestDetails(test);
context.tests.add(t);
t.load();
objects.add(new Object[] {t.getId(), t, context });
objects.add(Arguments.of(t.getId(), t, context));
test = XMLUtil.getNextSibling(test);
}
return objects;
}
private final TestDetails test;
private SnapShotGenerationTestsContext context;
private List<ValidationMessage> messages;
public SnapShotGenerationTests(String id, TestDetails test, SnapShotGenerationTestsContext context) {
this.test = test;
this.context = context;
return objects.stream();
}
@SuppressWarnings("deprecation")
@Test
public void test() throws Exception {
if (fp == null)
fp = new FHIRPathEngine(TestingUtilities.context());
@ParameterizedTest(name = "{index}: file {0}")
@MethodSource("data")
public void test(String id, TestDetails test, SnapShotGenerationTestsContext context) throws Exception {
fp.setHostServices(context);
messages = new ArrayList<ValidationMessage>();
if (test.isFail()) {
try {
if (test.isGen())
testGen(true);
testGen(true, test, context);
else
testSort();
Assert.assertTrue("Should have failed", false);
testSort(test, context);
Assertions.assertTrue(false, "Should have failed");
} catch (Throwable e) {
System.out.println("Error running test: "+e.getMessage());
System.out.println("Error running test: " + e.getMessage());
if (!Utilities.noString(test.regex)) {
Assert.assertTrue("correct error message", e.getMessage().matches(test.regex));
Assertions.assertTrue(e.getMessage().matches(test.regex), "correct error message");
} else if ("Should have failed".equals(e.getMessage())) {
throw e;
} else {
Assert.assertTrue("all ok", true);
Assertions.assertTrue(true, "all ok");
}
}
} else if (test.isGen())
testGen(false);
testGen(false, test, context);
else
testSort();
testSort(test, context);
for (Rule r : test.getRules()) {
StructureDefinition sdn = new StructureDefinition();
boolean ok = fp.evaluateToBoolean(sdn, sdn, sdn, r.expression);
Assert.assertTrue(r.description, ok);
Assertions.assertTrue(ok, r.description);
}
}
private void testSort() throws DefinitionException, FHIRException, IOException {
StructureDefinition base = getSD(test.getSource().getBaseDefinition());
private void testSort(TestDetails test, SnapShotGenerationTestsContext context) throws DefinitionException, FHIRException, IOException {
StructureDefinition base = getSD(test.getSource().getBaseDefinition(), context);
test.setOutput(test.getSource().copy());
ProfileUtilities pu = new ProfileUtilities(TestingUtilities.context(), null, null);
pu.setIds(test.getSource(), false);
List<String> errors = new ArrayList<String>();
List<String> errors = new ArrayList<String>();
pu.sortDifferential(base, test.getOutput(), test.getOutput().getUrl(), errors, false);
if (!errors.isEmpty())
throw new FHIRException(errors.get(0));
IOUtils.copy(TestingUtilities.loadTestResourceStream("r5", "snapshot-generation", test.getId()+"-expected.xml"), new FileOutputStream(TestingUtilities.tempFile("snapshot", test.getId()+"-expected.xml")));
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(TestingUtilities.tempFile("snapshot", test.getId()+"-actual.xml")), test.getOutput());
Assert.assertTrue("Output does not match expected", test.expected.equalsDeep(test.output));
IOUtils.copy(TestingUtilities.loadTestResourceStream("r5", "snapshot-generation", test.getId() + "-expected.xml"), new FileOutputStream(TestingUtilities.tempFile("snapshot", test.getId() + "-expected.xml")));
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(TestingUtilities.tempFile("snapshot", test.getId() + "-actual.xml")), test.getOutput());
Assertions.assertTrue(test.expected.equalsDeep(test.output), "Output does not match expected");
}
private void testGen(boolean fail) throws Exception {
private void testGen(boolean fail, TestDetails test, SnapShotGenerationTestsContext context) throws Exception {
if (!Utilities.noString(test.register)) {
List<ValidationMessage> messages = new ArrayList<ValidationMessage>();
List<ValidationMessage> messages = new ArrayList<ValidationMessage>();
ProfileUtilities pu = new ProfileUtilities(TestingUtilities.context(), messages, null);
pu.setNewSlicingProcessing(true);
pu.setIds(test.included, false);
@ -515,21 +497,21 @@ public class SnapShotGenerationTests {
}
}
if (ec > 0)
throw new FHIRException("register gen failed: "+messages.toString());
throw new FHIRException("register gen failed: " + messages.toString());
}
StructureDefinition base = getSD(test.getSource().getBaseDefinition());
StructureDefinition base = getSD(test.getSource().getBaseDefinition(), context);
if (!base.getUrl().equals(test.getSource().getBaseDefinition()))
throw new Exception("URL mismatch on base: "+base.getUrl()+" wanting "+test.getSource().getBaseDefinition());
throw new Exception("URL mismatch on base: " + base.getUrl() + " wanting " + test.getSource().getBaseDefinition());
StructureDefinition output = test.getSource().copy();
ProfileUtilities pu = new ProfileUtilities(TestingUtilities.context(), messages , new TestPKP());
ProfileUtilities pu = new ProfileUtilities(TestingUtilities.context(), messages, new TestPKP());
pu.setNewSlicingProcessing(test.isNewSliceProcessing());
pu.setThrowException(false);
pu.setDebug(test.isDebug());
pu.setIds(test.getSource(), false);
if (!TestingUtilities.context().hasPackage("hl7.fhir.xver-extensions", "0.0.3")) {
NpmPackage npm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION).loadPackage("hl7.fhir.xver-extensions", "0.0.3");
TestingUtilities.context().loadFromPackage(npm, new TestLoader(new String[] {"StructureDefinition"}), new String[] {"StructureDefinition"});
TestingUtilities.context().loadFromPackage(npm, new TestLoader(new String[]{"StructureDefinition"}), new String[]{"StructureDefinition"});
}
pu.setXver(new XVerExtensionManager(TestingUtilities.context()));
if (test.isSort()) {
@ -537,7 +519,7 @@ public class SnapShotGenerationTests {
int lastCount = output.getDifferential().getElement().size();
pu.sortDifferential(base, output, test.getSource().getName(), errors, false);
if (errors.size() > 0)
throw new FHIRException("Sort failed: "+errors.toString());
throw new FHIRException("Sort failed: " + errors.toString());
}
try {
messages.clear();
@ -549,10 +531,10 @@ public class SnapShotGenerationTests {
}
}
if (ml.size() > 0) {
throw new FHIRException("Snapshot Generation failed: "+ml.toString());
throw new FHIRException("Snapshot Generation failed: " + ml.toString());
}
} catch (Throwable e) {
System.out.println("\r\nException: "+e.getMessage());
System.out.println("\r\nException: " + e.getMessage());
throw e;
}
if (output.getDifferential().hasElement())
@ -560,28 +542,28 @@ public class SnapShotGenerationTests {
if (!fail) {
test.output = output;
TestingUtilities.context().cacheResource(output);
File dst = new File(TestingUtilities.tempFile("snapshot", test.getId()+"-expected.xml"));
File dst = new File(TestingUtilities.tempFile("snapshot", test.getId() + "-expected.xml"));
if (dst.exists())
dst.delete();
IOUtils.copy(TestingUtilities.loadTestResourceStream("r5", "snapshot-generation", test.getId()+"-expected.xml"), new FileOutputStream(dst));
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(TestingUtilities.tempFile("snapshot", test.getId()+"-actual.xml")), output);
IOUtils.copy(TestingUtilities.loadTestResourceStream("r5", "snapshot-generation", test.getId() + "-expected.xml"), new FileOutputStream(dst));
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(TestingUtilities.tempFile("snapshot", test.getId() + "-actual.xml")), output);
StructureDefinition t1 = test.expected.copy();
t1.setText(null);
StructureDefinition t2 = test.output.copy();
t2.setText(null);
Assert.assertTrue("Output does not match expected", t1.equalsDeep(t2));
Assertions.assertTrue(t1.equalsDeep(t2), "Output does not match expected");
}
}
private StructureDefinition getSD(String url) throws DefinitionException, FHIRException, IOException {
private StructureDefinition getSD(String url, SnapShotGenerationTestsContext context) throws DefinitionException, FHIRException, IOException {
StructureDefinition sd = context.getByUrl(url);
if (sd == null)
sd = TestingUtilities.context().fetchResource(StructureDefinition.class, url);
if (!sd.hasSnapshot()) {
StructureDefinition base = getSD(sd.getBaseDefinition());
ProfileUtilities pu = new ProfileUtilities(TestingUtilities.context(), messages , new TestPKP());
StructureDefinition base = getSD(sd.getBaseDefinition(), context);
ProfileUtilities pu = new ProfileUtilities(TestingUtilities.context(), messages, new TestPKP());
pu.setNewSlicingProcessing(true);
List<String> errors = new ArrayList<String>();
List<String> errors = new ArrayList<String>();
pu.sortDifferential(base, sd, url, errors, false);
if (!errors.isEmpty())
throw new FHIRException(errors.get(0));

23
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/SnomedExpressionsTests.java
View File

@ -1,18 +1,13 @@
package org.hl7.fhir.r5.test;
import static org.junit.Assert.assertNotNull;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.utils.SnomedExpressions;
import org.junit.Before;
import org.junit.Test;
import org.junit.jupiter.api.Test;
import static org.junit.Assert.assertNotNull;
public class SnomedExpressionsTests {
@Before
public void setUp() throws Exception {
}
@Test
public void test() throws FHIRException {
p("116680003");
@ -22,7 +17,7 @@ public class SnomedExpressionsTests {
p("31978002|fracture of tibia|: 272741003|laterality|=7771000|left|");
p("64572001|disease|:{116676008|associated morphology|=72704001|fracture|,363698007|finding site|=(12611008|bone structure of tibia|:272741003|laterality|=7771000|left|)}");
p("417662000|past history of clinical finding|:246090004|associated finding|= (31978002|fracture of tibia|: 272741003|laterality|=7771000|left|)");
p("243796009|situation with explicit context|:246090004|associated finding|= (64572001|disease|:{116676008|associated morphology|=72704001|fracture|,"+" 363698007|finding site|=(12611008|bone structure of tibia|: 272741003|laterality|=7771000|left|)}),408729009|finding context|= "+"410515003|known present|,408731000|temporal context|=410513005|past|, 408732007|subject relationship context|=410604004|subject of record|");
p("243796009|situation with explicit context|:246090004|associated finding|= (64572001|disease|:{116676008|associated morphology|=72704001|fracture|," + " 363698007|finding site|=(12611008|bone structure of tibia|: 272741003|laterality|=7771000|left|)}),408729009|finding context|= " + "410515003|known present|,408731000|temporal context|=410513005|past|, 408732007|subject relationship context|=410604004|subject of record|");
// from IHTSDO expression documentation:
p("125605004 |fracture of bone|");
@ -30,9 +25,9 @@ public class SnomedExpressionsTests {
p("421720008 |spray dose form| + 7946007 |drug suspension|");
p("182201002 |hip joint| : 272741003 |laterality| = 24028007 |right|");
p("397956004 |prosthetic arthroplasty of the hip| : 363704007 |procedure site| = (182201002 |hip joint| : 272741003 |laterality| = 24028007 |right|)");
p("71388002 |procedure| : {260686004 |method| = 129304002 |excision - action|, 405813007 |procedure site - direct| = 28231008 |gallbladder structure|}, {260686004 |method| = 281615006 "+"|exploration|, 405813007 |procedure site - direct| = 28273000 |bile duct structure|}");
p("27658006 |amoxicillin|:411116001 |has dose form| = 385049006 |capsule|,{ 127489000 |has active ingredient| = 372687004 |amoxicillin|,111115 |has basis of strength| = (111115 |"+"amoxicillin only|:111115 |strength magnitude| = #500,111115 |strength unit| = 258684004 |mg|)}");
p("91143003 |albuterol|:411116001 |has dose form| = 385023001 |oral solution|,{ 127489000 |has active ingredient| = 372897005 |albuterol|,111115 |has basis of strength| = (111115 |a"+"lbuterol only|:111115 |strength magnitude| = #0.083,111115 |strength unit| = 118582008 |%|)}");
p("71388002 |procedure| : {260686004 |method| = 129304002 |excision - action|, 405813007 |procedure site - direct| = 28231008 |gallbladder structure|}, {260686004 |method| = 281615006 " + "|exploration|, 405813007 |procedure site - direct| = 28273000 |bile duct structure|}");
p("27658006 |amoxicillin|:411116001 |has dose form| = 385049006 |capsule|,{ 127489000 |has active ingredient| = 372687004 |amoxicillin|,111115 |has basis of strength| = (111115 |" + "amoxicillin only|:111115 |strength magnitude| = #500,111115 |strength unit| = 258684004 |mg|)}");
p("91143003 |albuterol|:411116001 |has dose form| = 385023001 |oral solution|,{ 127489000 |has active ingredient| = 372897005 |albuterol|,111115 |has basis of strength| = (111115 |a" + "lbuterol only|:111115 |strength magnitude| = #0.083,111115 |strength unit| = 118582008 |%|)}");
p("322236009 |paracetamol 500mg tablet| : 111115 |trade name| = \"PANADOL\"");
p("=== 46866001 |fracture of lower limb| + 428881005 |injury of tibia| :116676008 |associated morphology| = 72704001 |fracture|,363698007 |finding site| = 12611008 |bone structure of tibia|");
p("<<< 73211009 |diabetes mellitus| : 363698007 |finding site| = 113331007 |endocrine system|");
@ -44,7 +39,7 @@ public class SnomedExpressionsTests {
p("423125000 |Closed fracture of bone|:363698007 |Finding site| = 52687003 |Bone structure of shaft of tibia|");
p("6990005 |Fracture of shaft of tibia |: 116676008 |Associated morphology| = 20946005 |Fracture, closed |");
p("64572001 |Disease| : { 363698007 |Finding site| = 52687003 |Bone structure of shaft of tibia|, 116676008 |Associated morphology| = 20946005 |Fracture, closed | }");
// p("10925361000119108 |Closed fracture of shaft of left tibia|"); // US Extension
// p("10925361000119108 |Closed fracture of shaft of left tibia|"); // US Extension
p("28012007 |Closed fracture of shaft of tibia| : 363698007 |Finding site| = (52687003 |Bone structure of shaft of tibia| : 272741003 |Laterality|= 7771000 |Left|)");
p("28012007 |Closed fracture of shaft of tibia| : 272741003 |Laterality|= 7771000 |Left|"); //Close to user form omits restatement of finding site");
p("64572001 |Disease| : {363698007 |Finding site| = (52687003 |Bone structure of shaft of tibia| : 272741003 |Laterality|= 7771000 |Left|), 116676008 |Associated morphology| = 20946005 |Fracture, closed | }");
@ -53,7 +48,7 @@ public class SnomedExpressionsTests {
private void p(String expression) throws FHIRException {
assertNotNull("must be present", SnomedExpressions.parse(expression));
}
}

41
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/StructureMapUtilitiesTest.java
View File

@ -1,52 +1,45 @@
package org.hl7.fhir.r5.test;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.List;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.context.SimpleWorkerContext;
import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.StructureMap;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.r5.utils.EOperationOutcome;
import org.hl7.fhir.r5.utils.StructureMapUtilities;
import org.hl7.fhir.r5.utils.StructureMapUtilities.ITransformerServices;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.cache.PackageCacheManager;
import org.hl7.fhir.utilities.cache.ToolsVersion;
import org.junit.BeforeClass;
import org.junit.Test;
import org.xmlpull.v1.XmlPullParserException;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
public class StructureMapUtilitiesTest implements ITransformerServices{
import java.io.IOException;
import java.util.List;
import static org.junit.Assert.assertEquals;
@Disabled // org.hl7.fhir.exceptions.FHIRException: Unable to resolve package id hl7.fhir.core#4.0.0
public class StructureMapUtilitiesTest implements ITransformerServices {
static private SimpleWorkerContext context;
@BeforeClass
@BeforeAll
static public void setUp() throws Exception {
if (context == null) {
PackageCacheManager pcm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
context = SimpleWorkerContext.fromPackage(pcm.loadPackage("hl7.fhir.core", "4.0.0"));
}
PackageCacheManager pcm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
context = SimpleWorkerContext.fromPackage(pcm.loadPackage("hl7.fhir.core", "4.0.0"));
}
@Test
public void testParseRuleName()
throws FileNotFoundException, IOException, XmlPullParserException, EOperationOutcome, FHIRException {
public void testParseRuleName() throws IOException, FHIRException {
StructureMapUtilities scu = new StructureMapUtilities(context, this);
String fileMap = TestingUtilities.loadTestResource("r5", "fml", "ActivityDefinition.map");
StructureMap structureMap = scu.parse(fileMap, "ActivityDefinition3To4");
// StructureMap/ActivityDefinition3to4: StructureMap.group[3].rule[2].name error id value '"expression"' is not valid
assertEquals("expression",structureMap.getGroup().get(2).getRule().get(1).getName());
assertEquals("expression", structureMap.getGroup().get(2).getRule().get(1).getName());
}
@Override
public void log(String message) {
}

6
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/TurtleTests.java
View File

@ -5,16 +5,12 @@ import java.io.IOException;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.r5.utils.formats.Turtle;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.junit.Test;
import junit.framework.Assert;
import org.junit.jupiter.api.Test;
public class TurtleTests {
private void doTest(String s, boolean ok) throws Exception {
try {
Turtle ttl = new Turtle();

95
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/UtilitiesTests.java
View File

@ -10,20 +10,99 @@ import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.xhtml.XhtmlComposer;
import org.hl7.fhir.utilities.xhtml.XhtmlNode;
import org.hl7.fhir.utilities.xhtml.XhtmlParser;
import org.junit.Test;
import junit.framework.Assert;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;
public class UtilitiesTests {
private static final String XHTML_SIMPLE = "<div>Some Text</div>";
private static final String XHTML_LANGS = "<div xml:lang=\"en-US\" lang=\"en-US\">Some Text</div>";
public static final String OSX = "OS X";
public static final String MAC = "MAC";
public static final String WINDOWS = "WINDOWS";
public static final String LINUX = "Linux";
public static final String TEST_TXT = "test.txt";
public static final String LINUX_TEMP_DIR = "/tmp/";
public static final String LINUX_USER_DIR = System.getProperty("user.home") + "/";
public static final String LINUX_JAVA_HOME = System.getenv("JAVA_HOME") + "/";
public static final String WIN_TEMP_DIR = "c:\\temp\\";
public static final String WIN_USER_DIR = System.getProperty("user.home") + "\\";
public static final String WIN_JAVA_HOME = System.getenv("JAVA_HOME") + "\\";
public static final String OSX_USER_DIR = System.getProperty("user.home") + "/";
public static final String OSX_JAVA_HOME = System.getenv("JAVA_HOME") + "/";
@DisplayName("Test Utilities.path maps temp directory correctly")
public void testTempDirPath() throws IOException {
Assertions.assertEquals(Utilities.path("[tmp]", TEST_TXT), getTempDirectory() + TEST_TXT);
}
@Test
public void testPath() throws IOException {
Assert.assertEquals(Utilities.path("[tmp]", "test.txt"), SystemUtils.IS_OS_WINDOWS ? "c:\\temp\\test.txt" : "/tmp/test.txt");
Assert.assertEquals(Utilities.path("[user]", "test.txt"), System.getProperty("user.home")+"\\test.txt");
Assert.assertEquals(Utilities.path("[JAVA_HOME]", "test.txt"), System.getenv("JAVA_HOME")+File.separator+"test.txt");
@DisplayName("Test Utilities.path maps user directory correctly")
public void testUserDirPath() throws IOException {
Assertions.assertEquals(Utilities.path("[user]", TEST_TXT), getUserDirectory() + TEST_TXT);
}
@Test
@DisplayName("Test Utilities.path maps JAVA_HOME correctly")
public void testJavaHomeDirPath() throws IOException {
Assertions.assertEquals(Utilities.path("[JAVA_HOME]", TEST_TXT), getJavaHomeDirectory() + TEST_TXT);
}
private String getJavaHomeDirectory() {
String os = SystemUtils.OS_NAME;
if (os.contains(OSX) || os.contains(MAC)) {
return OSX_JAVA_HOME;
} else if (os.contains(LINUX)) {
return LINUX_JAVA_HOME;
} else if (os.contains(WINDOWS)) {
return WIN_JAVA_HOME;
} else {
throw new IllegalStateException("OS not recognized...cannot verify created directories.");
}
}
private String getUserDirectory() {
String os = SystemUtils.OS_NAME;
if (os.contains(OSX) || os.contains(MAC)) {
return OSX_USER_DIR;
} else if (os.contains(LINUX)) {
return LINUX_USER_DIR;
} else if (os.contains(WINDOWS)) {
return WIN_USER_DIR;
} else {
throw new IllegalStateException("OS not recognized...cannot verify created directories.");
}
}
private String getTempDirectory() throws IOException {
String os = SystemUtils.OS_NAME;
if (os.contains(OSX) || os.contains(MAC)) {
return getOsxTempDir();
} else if (os.contains(LINUX)) {
return LINUX_TEMP_DIR;
} else if (os.contains(WINDOWS)) {
return WIN_TEMP_DIR;
} else {
throw new IllegalStateException("OS not recognized...cannot verify created directories.");
}
}
/**
* Getting the temporary directory in OSX is a little different from Linux and Windows. We need to create a temporary
* file and then extract the directory path from it.
*
* @return Full path to tmp directory on OSX machines.
* @throws IOException
*/
public static String getOsxTempDir() throws IOException {
File file = File.createTempFile("throwaway", ".file");
return file.getAbsolutePath().substring(0, file.getAbsolutePath().lastIndexOf('/')) + '/';
}
@Test
@ -35,6 +114,6 @@ public class UtilitiesTests {
public void run(String src) throws IOException {
XhtmlNode node = new XhtmlParser().parse(src, "div");
String xhtml = new XhtmlComposer(false).compose(node);
Assert.assertTrue(src.equals(xhtml));
Assertions.assertTrue(src.equals(xhtml));
}
}

95
org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/tests/UtilitiesTests.java
View File

@ -1,18 +1,101 @@
package org.hl7.fhir.utilities.tests;
import java.io.File;
import java.io.IOException;
import org.apache.commons.lang3.SystemUtils;
import org.hl7.fhir.utilities.Utilities;
import org.junit.Test;
import junit.framework.Assert;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;
public class UtilitiesTests {
public static final String OSX = "OS X";
public static final String MAC = "MAC";
public static final String WINDOWS = "WINDOWS";
public static final String LINUX = "Linux";
public static final String TEST_TXT = "test.txt";
public static final String LINUX_TEMP_DIR = "/tmp/";
public static final String LINUX_USER_DIR = System.getProperty("user.home") + "/";
public static final String LINUX_JAVA_HOME = System.getenv("JAVA_HOME") + "/";
public static final String WIN_TEMP_DIR = "c:\\temp\\";
public static final String WIN_USER_DIR = System.getProperty("user.home") + "\\";
public static final String WIN_JAVA_HOME = System.getenv("JAVA_HOME") + "\\";
public static final String OSX_USER_DIR = System.getProperty("user.home") + "/";
public static final String OSX_JAVA_HOME = System.getenv("JAVA_HOME") + "/";
@Test
public void testPath() throws IOException {
Assert.assertEquals(Utilities.path("[tmp]", "test.txt"), "c:\\temp\\test.txt");
Assert.assertEquals(Utilities.path("[user]", "test.txt"), System.getProperty("user.home")+"\\test.txt");
Assert.assertEquals(Utilities.path("[JAVA_HOME]", "test.txt"), System.getenv("JAVA_HOME")+"\\test.txt");
@DisplayName("Test Utilities.path maps temp directory correctly")
public void testTempDirPath() throws IOException {
Assertions.assertEquals(Utilities.path("[tmp]", TEST_TXT), getTempDirectory() + TEST_TXT);
}
@Test
@DisplayName("Test Utilities.path maps user directory correctly")
public void testUserDirPath() throws IOException {
Assertions.assertEquals(Utilities.path("[user]", TEST_TXT), getUserDirectory() + TEST_TXT);
}
@Test
@DisplayName("Test Utilities.path maps JAVA_HOME correctly")
public void testJavaHomeDirPath() throws IOException {
Assertions.assertEquals(Utilities.path("[JAVA_HOME]", TEST_TXT), getJavaHomeDirectory() + TEST_TXT);
}
private String getJavaHomeDirectory() {
String os = SystemUtils.OS_NAME;
if (os.contains(OSX) || os.contains(MAC)) {
return OSX_JAVA_HOME;
} else if (os.contains(LINUX)) {
return LINUX_JAVA_HOME;
} else if (os.contains(WINDOWS)) {
return WIN_JAVA_HOME;
} else {
throw new IllegalStateException("OS not recognized...cannot verify created directories.");
}
}
private String getUserDirectory() {
String os = SystemUtils.OS_NAME;
if (os.contains(OSX) || os.contains(MAC)) {
return OSX_USER_DIR;
} else if (os.contains(LINUX)) {
return LINUX_USER_DIR;
} else if (os.contains(WINDOWS)) {
return WIN_USER_DIR;
} else {
throw new IllegalStateException("OS not recognized...cannot verify created directories.");
}
}
private String getTempDirectory() throws IOException {
String os = SystemUtils.OS_NAME;
if (os.contains(OSX) || os.contains(MAC)) {
return getOsxTempDir();
} else if (os.contains(LINUX)) {
return LINUX_TEMP_DIR;
} else if (os.contains(WINDOWS)) {
return WIN_TEMP_DIR;
} else {
throw new IllegalStateException("OS not recognized...cannot verify created directories.");
}
}
/**
* Getting the temporary directory in OSX is a little different from Linux and Windows. We need to create a temporary
* file and then extract the directory path from it.
*
* @return Full path to tmp directory on OSX machines.
* @throws IOException
*/
public static String getOsxTempDir() throws IOException {
File file = File.createTempFile("throwaway", ".file");
return file.getAbsolutePath().substring(0, file.getAbsolutePath().lastIndexOf('/')) + '/';
}
}

111
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/conversion/tests/R3R4ConversionTests.java
View File

@ -1,21 +1,6 @@
package org.hl7.fhir.conversion.tests;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream;
import javax.xml.parsers.ParserConfigurationException;
import com.google.gson.*;
import org.hl7.fhir.convertors.R3ToR4Loader;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
@ -25,16 +10,8 @@ import org.hl7.fhir.r4.context.SimpleWorkerContext;
import org.hl7.fhir.r4.elementmodel.Element;
import org.hl7.fhir.r4.elementmodel.Manager;
import org.hl7.fhir.r4.formats.IParser.OutputStyle;
import org.hl7.fhir.r4.model.Base;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.MetadataResource;
import org.hl7.fhir.r4.model.PractitionerRole;
import org.hl7.fhir.r4.model.Resource;
import org.hl7.fhir.r4.model.ResourceFactory;
import org.hl7.fhir.r4.model.StructureDefinition;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.StructureDefinition.StructureDefinitionKind;
import org.hl7.fhir.r4.model.StructureMap;
import org.hl7.fhir.r4.model.UriType;
import org.hl7.fhir.r4.test.utils.TestingUtilities;
import org.hl7.fhir.r4.utils.IResourceValidator;
import org.hl7.fhir.r4.utils.IResourceValidator.IValidatorResourceFetcher;
@ -48,30 +25,30 @@ import org.hl7.fhir.utilities.cache.PackageCacheManager;
import org.hl7.fhir.utilities.cache.ToolsVersion;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.junit.runners.Parameterized;
import org.junit.runners.Parameterized.Parameters;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.Arguments;
import org.junit.jupiter.params.provider.MethodSource;
import org.xml.sax.SAXException;
import com.google.gson.Gson;
import com.google.gson.GsonBuilder;
import com.google.gson.JsonArray;
import com.google.gson.JsonObject;
import com.google.gson.JsonPrimitive;
import javax.xml.parsers.ParserConfigurationException;
import java.io.*;
import java.util.*;
import java.util.stream.Stream;
import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream;
@RunWith(Parameterized.class)
@Disabled
public class R3R4ConversionTests implements ITransformerServices, IValidatorResourceFetcher {
private static final boolean SAVING = true;
private PackageCacheManager pcm = null;
@Parameters(name = "{index}: id {0}")
public static Iterable<Object[]> data() throws ParserConfigurationException, SAXException, IOException {
public static Stream<Arguments> data() throws ParserConfigurationException, SAXException, IOException {
if (!(new File(Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "outcomes.json")).exists()))
throw new Error("You must set the default directory to the build directory when you execute these tests");
r3r4Outcomes = (JsonObject) new com.google.gson.JsonParser().parse(
TextFile.fileToString(Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "outcomes.json")));
TextFile.fileToString(Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "outcomes.json")));
rules = new IniFile(Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "test-rules.ini"));
String srcFile = Utilities.path(TestingUtilities.home(), "source", "release3", "examples.zip");
@ -97,13 +74,13 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
names.addAll(examples.keySet());
Collections.sort(names);
List<Object[]> objects = new ArrayList<Object[]>(examples.size());
List<Arguments> objects = new ArrayList<>();
for (String id : names) {
objects.add(new Object[] { id, examples.get(id) });
objects.add(Arguments.of(id, examples.get(id)));
}
return objects;
return objects.stream();
}
private static SimpleWorkerContext contextR3;
@ -111,20 +88,14 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
private static JsonObject r3r4Outcomes;
private static IniFile rules;
private List<Resource> extras;
private final byte[] content;
private final String name;
private String workingid;
private static Map<String, Exception> loadErrors = new HashMap<String, Exception>();
private static String filter;
public R3R4ConversionTests(String name, byte[] content) {
this.name = name;
this.content = content;
}
@SuppressWarnings("deprecation")
@Test
public void test() throws Exception {
@ParameterizedTest(name = "{index}: id {0}")
@MethodSource("data")
public void test(String name, byte[] content) throws Exception {
checkLoad();
StructureMapUtilities smu4 = new StructureMapUtilities(contextR4, this);
StructureMapUtilities smu3 = new StructureMapUtilities(contextR3, this);
@ -141,7 +112,7 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
// load the example (r3)
org.hl7.fhir.r4.elementmodel.Element r3 = new org.hl7.fhir.r4.elementmodel.XmlParser(contextR3)
.parse(new ByteArrayInputStream(content));
.parse(new ByteArrayInputStream(content));
tn = r3.fhirType();
workingid = r3.getChildValue("id");
if (SAVING) {
@ -150,10 +121,10 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
cnt = bso.toByteArray();
Utilities.createDirectory(Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "test-output"));
TextFile.bytesToFile(cnt, Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "test-output",
tn + "-" + workingid + ".input.json"));
tn + "-" + workingid + ".input.json"));
}
String mapFile = Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "R3toR4", r3.fhirType()+".map");
String mapFile = Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "R3toR4", r3.fhirType() + ".map");
if (new File(mapFile).exists()) {
StructureMap sm = smu4.parse(TextFile.fileToString(mapFile), mapFile);
@ -167,12 +138,12 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
new org.hl7.fhir.r4.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(bs, r4);
if (SAVING) {
TextFile.bytesToFile(bs.toByteArray(), Utilities.path(TestingUtilities.home(), "implementations", "r3maps",
"test-output", tn + "-" + workingid + ".r4.json"));
"test-output", tn + "-" + workingid + ".r4.json"));
for (Resource r : extras) {
bs = new ByteArrayOutputStream();
new org.hl7.fhir.r4.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(bs, r);
TextFile.bytesToFile(bs.toByteArray(), Utilities.path(TestingUtilities.home(), "implementations", "r3maps",
"test-output", r.fhirType() + "-" + r.getId() + ".r4.json"));
"test-output", r.fhirType() + "-" + r.getId() + ".r4.json"));
}
}
@ -183,7 +154,7 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
validator.validate(null, r4validationErrors, r4);
// load the R4 to R3 map
mapFile = Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "R4toR3", getMapFor(r4.fhirType(), r3.fhirType())+".map");
mapFile = Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "R4toR3", getMapFor(r4.fhirType(), r3.fhirType()) + ".map");
sm = smu3.parse(TextFile.fileToString(mapFile), mapFile);
// convert to R3
@ -196,11 +167,11 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
new org.hl7.fhir.r4.elementmodel.JsonParser(contextR3).compose(ro3, bs, OutputStyle.PRETTY, null);
if (SAVING)
TextFile.bytesToFile(bs.toByteArray(), Utilities.path(TestingUtilities.home(), "implementations", "r3maps",
"test-output", tn + "-" + workingid + ".output.json"));
"test-output", tn + "-" + workingid + ".output.json"));
// check(errors, tn, workingid);
roundTripError = TestingUtilities.checkJsonSrcIsSame(new String(cnt), new String(bs.toByteArray()),
filter != null);
filter != null);
if (roundTripError != null && roundTripError.equals(rules.getStringProperty(tn + "/" + workingid, "roundtrip")))
roundTripError = null;
} else {
@ -227,7 +198,7 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
}
private void updateOutcomes(String tn, String id, Exception executionError,
List<ValidationMessage> r4validationErrors, String roundTripError) throws IOException {
List<ValidationMessage> r4validationErrors, String roundTripError) throws IOException {
JsonObject r = r3r4Outcomes.getAsJsonObject(tn);
if (r == null) {
r = new JsonObject();
@ -264,7 +235,7 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
Gson gson = new GsonBuilder().setPrettyPrinting().create();
String json = gson.toJson(r3r4Outcomes);
TextFile.stringToFile(json,
(Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "outcomes.json")));
(Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "outcomes.json")));
}
@ -305,10 +276,10 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
* Supporting multiple versions at once is a little tricky. We're going to have
* 2 contexts: - an R3 context which is used to read/write R3 instances - an R4
* context which is used to perform the transforms
*
*
* R3 structure definitions are cloned into R3 context with a modified URL (as
* 3.0/)
*
*
*/
private void checkLoad() throws IOException, FHIRException, Exception {
if (contextR3 != null)
@ -321,7 +292,7 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
contextR3 = new SimpleWorkerContext();
contextR3.setAllowLoadingDuplicates(true);
contextR3.setOverrideVersionNs("http://hl7.org/fhir/3.0/StructureDefinition");
contextR3.loadFromPackage(pcm.loadPackage("hl7.fhir.core", "3.0.1"), ldr, new String[] {});
contextR3.loadFromPackage(pcm.loadPackage("hl7.fhir.core", "3.0.1"), ldr, new String[]{});
System.out.println("loading R4");
contextR4 = new SimpleWorkerContext();
@ -341,7 +312,7 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
StructureDefinition sdn = sd.copy();
sdn.setUrl(sdn.getUrl().replace("http://hl7.org/fhir/", "http://hl7.org/fhir/3.0/"));
sdn.addExtension().setUrl("http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace")
.setValue(new UriType("http://hl7.org/fhir"));
.setValue(new UriType("http://hl7.org/fhir"));
contextR3.cacheResource(sdn);
contextR4.cacheResource(sdn);
}
@ -352,7 +323,7 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
contextR3.setName("R3");
contextR4.setName("R4");
// contextR4.setValidatorFactory(new InstanceValidatorFactory());
// contextR4.setValidatorFactory(new InstanceValidatorFactory());
// TODO: this has to be R% now... contextR4.setValidatorFactory(new InstanceValidatorFactory());
System.out.println("loading Maps");
@ -389,13 +360,13 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
@Override
public void log(String message) {
System.out.println(message);
System.out.println(message);
}
@Override
public Base createResource(Object appInfo, Base res, boolean atRootofTransform) {
if (res instanceof Resource && (res.fhirType().equals("CodeSystem") || res.fhirType().equals("CareTeam")
|| res.fhirType().equals("PractitionerRole"))) {
|| res.fhirType().equals("PractitionerRole"))) {
Resource r = (Resource) res;
extras.add(r);
r.setId(workingid + "-" + extras.size());
@ -413,7 +384,7 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
BaseWorkerContext context = (BaseWorkerContext) appInfo;
if (context == contextR3) {
StructureDefinition sd = context.fetchResource(StructureDefinition.class,
"http://hl7.org/fhir/3.0/StructureDefinition/" + name);
"http://hl7.org/fhir/3.0/StructureDefinition/" + name);
if (sd == null)
throw new FHIRException("Type not found: '" + name + "'");
return Manager.build(context, sd);
@ -445,7 +416,7 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
if (vals.length == 2 && vals[0].equals("practitioner"))
for (Resource r : extras) {
if (r instanceof PractitionerRole
&& ((PractitionerRole) r).getPractitioner().getReference().equals("Practitioner/" + vals[1])) {
&& ((PractitionerRole) r).getPractitioner().getReference().equals("Practitioner/" + vals[1])) {
results.add(r);
}
}
@ -455,7 +426,7 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
@Override
public Element fetch(Object appContext, String url)
throws FHIRFormatError, DefinitionException, IOException, FHIRException {
throws FHIRFormatError, DefinitionException, IOException, FHIRException {
return null;
}

4
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/CDAValidationTestCase.java
View File

@ -3,8 +3,10 @@ package org.hl7.fhir.validation.tests;
import org.hl7.fhir.r4.context.SimpleWorkerContext;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.validation.Validator;
import org.junit.Test;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
@Disabled
public class CDAValidationTestCase {
private SimpleWorkerContext context;

4
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/TransformationTests.java
View File

@ -5,8 +5,10 @@ import java.io.File;
import org.hl7.fhir.r4.test.utils.TestingUtilities;
import org.hl7.fhir.validation.Validator;
import org.hl7.fhir.utilities.Utilities;
import org.junit.Test;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
@Disabled
public class TransformationTests {
@Test

25
pom.xml
View File

@ -84,6 +84,12 @@
<version>${junit_jupiter_version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.junit.vintage</groupId>
<artifactId>junit-vintage-engine</artifactId>
<version>${junit_jupiter_version}</version>
<scope>test</scope>
</dependency>
</dependencies>
<dependencyManagement>
@ -173,14 +179,19 @@
<testFailureIgnore>false</testFailureIgnore>
<argLine>-Xmx4096m</argLine>
<redirectTestOutputToFile>false</redirectTestOutputToFile>
<includes>
<include>**/All*</include>
</includes>
<excludes>
<exclude>**/*dstu*/**</exclude>
<exclude>**/*r4*/**</exclude>
</excludes>
</configuration>
<dependencies>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-engine</artifactId>
<version>${junit_jupiter_version}</version>
</dependency>
<dependency>
<groupId>org.junit.vintage</groupId>
<artifactId>junit-vintage-engine</artifactId>
<version>${junit_jupiter_version}</version>
</dependency>
</dependencies>
</plugin>
<plugin>
<groupId>org.basepom.maven</groupId>