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org.hl7.fhir.core
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This commit is contained in:
markiantorno 2020-04-23 17:02:54 -04:00
parent 0ef4b01e90
commit 29d101fa09
4 changed files with 48 additions and 72 deletions
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1
org.hl7.fhir.validation/pom.xml
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@ -138,6 +138,7 @@
<version>${validator_test_case_version}</version> <version>${validator_test_case_version}</version>
<scope>test</scope> <scope>test</scope>
</dependency> </dependency>
</dependencies> </dependencies>
<build> <build>

111
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/conversion/tests/R3R4ConversionTests.java
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@ -1,21 +1,6 @@
package org.hl7.fhir.conversion.tests; package org.hl7.fhir.conversion.tests;
import java.io.ByteArrayInputStream; import com.google.gson.*;
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 org.hl7.fhir.convertors.R3ToR4Loader; import org.hl7.fhir.convertors.R3ToR4Loader;
import org.hl7.fhir.exceptions.DefinitionException; import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException; 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.Element;
import org.hl7.fhir.r4.elementmodel.Manager; import org.hl7.fhir.r4.elementmodel.Manager;
import org.hl7.fhir.r4.formats.IParser.OutputStyle; import org.hl7.fhir.r4.formats.IParser.OutputStyle;
import org.hl7.fhir.r4.model.Base; import org.hl7.fhir.r4.model.*;
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.StructureDefinition.StructureDefinitionKind; 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.test.utils.TestingUtilities;
import org.hl7.fhir.r4.utils.IResourceValidator; import org.hl7.fhir.r4.utils.IResourceValidator;
import org.hl7.fhir.r4.utils.IResourceValidator.IValidatorResourceFetcher; 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.cache.ToolsVersion;
import org.hl7.fhir.utilities.validation.ValidationMessage; import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity; import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.junit.Test; import org.junit.jupiter.api.Disabled;
import org.junit.runner.RunWith; import org.junit.jupiter.params.ParameterizedTest;
import org.junit.runners.Parameterized; import org.junit.jupiter.params.provider.Arguments;
import org.junit.runners.Parameterized.Parameters; import org.junit.jupiter.params.provider.MethodSource;
import org.xml.sax.SAXException; import org.xml.sax.SAXException;
import com.google.gson.Gson; import javax.xml.parsers.ParserConfigurationException;
import com.google.gson.GsonBuilder; import java.io.*;
import com.google.gson.JsonArray; import java.util.*;
import com.google.gson.JsonObject; import java.util.stream.Stream;
import com.google.gson.JsonPrimitive; import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream;
@RunWith(Parameterized.class) @Disabled
public class R3R4ConversionTests implements ITransformerServices, IValidatorResourceFetcher { public class R3R4ConversionTests implements ITransformerServices, IValidatorResourceFetcher {
private static final boolean SAVING = true; private static final boolean SAVING = true;
private PackageCacheManager pcm = null; private PackageCacheManager pcm = null;
@Parameters(name = "{index}: id {0}") public static Stream<Arguments> data() throws ParserConfigurationException, SAXException, IOException {
public static Iterable<Object[]> data() throws ParserConfigurationException, SAXException, IOException {
if (!(new File(Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "outcomes.json")).exists())) 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"); 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( 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")); rules = new IniFile(Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "test-rules.ini"));
String srcFile = Utilities.path(TestingUtilities.home(), "source", "release3", "examples.zip"); String srcFile = Utilities.path(TestingUtilities.home(), "source", "release3", "examples.zip");
@ -97,13 +74,13 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
names.addAll(examples.keySet()); names.addAll(examples.keySet());
Collections.sort(names); Collections.sort(names);
List<Object[]> objects = new ArrayList<Object[]>(examples.size()); List<Arguments> objects = new ArrayList<>();
for (String id : names) { 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; private static SimpleWorkerContext contextR3;
@ -111,20 +88,14 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
private static JsonObject r3r4Outcomes; private static JsonObject r3r4Outcomes;
private static IniFile rules; private static IniFile rules;
private List<Resource> extras; private List<Resource> extras;
private final byte[] content;
private final String name;
private String workingid; private String workingid;
private static Map<String, Exception> loadErrors = new HashMap<String, Exception>(); private static Map<String, Exception> loadErrors = new HashMap<String, Exception>();
private static String filter; private static String filter;
public R3R4ConversionTests(String name, byte[] content) {
this.name = name;
this.content = content;
}
@SuppressWarnings("deprecation") @SuppressWarnings("deprecation")
@Test @ParameterizedTest(name = "{index}: id {0}")
public void test() throws Exception { @MethodSource("data")
public void test(String name, byte[] content) throws Exception {
checkLoad(); checkLoad();
StructureMapUtilities smu4 = new StructureMapUtilities(contextR4, this); StructureMapUtilities smu4 = new StructureMapUtilities(contextR4, this);
StructureMapUtilities smu3 = new StructureMapUtilities(contextR3, this); StructureMapUtilities smu3 = new StructureMapUtilities(contextR3, this);
@ -141,7 +112,7 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
// load the example (r3) // load the example (r3)
org.hl7.fhir.r4.elementmodel.Element r3 = new org.hl7.fhir.r4.elementmodel.XmlParser(contextR3) 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(); tn = r3.fhirType();
workingid = r3.getChildValue("id"); workingid = r3.getChildValue("id");
if (SAVING) { if (SAVING) {
@ -150,10 +121,10 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
cnt = bso.toByteArray(); cnt = bso.toByteArray();
Utilities.createDirectory(Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "test-output")); Utilities.createDirectory(Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "test-output"));
TextFile.bytesToFile(cnt, 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()) { if (new File(mapFile).exists()) {
StructureMap sm = smu4.parse(TextFile.fileToString(mapFile), mapFile); 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); new org.hl7.fhir.r4.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(bs, r4);
if (SAVING) { if (SAVING) {
TextFile.bytesToFile(bs.toByteArray(), Utilities.path(TestingUtilities.home(), "implementations", "r3maps", 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) { for (Resource r : extras) {
bs = new ByteArrayOutputStream(); bs = new ByteArrayOutputStream();
new org.hl7.fhir.r4.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(bs, r); new org.hl7.fhir.r4.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(bs, r);
TextFile.bytesToFile(bs.toByteArray(), Utilities.path(TestingUtilities.home(), "implementations", "r3maps", 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); validator.validate(null, r4validationErrors, r4);
// load the R4 to R3 map // 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); sm = smu3.parse(TextFile.fileToString(mapFile), mapFile);
// convert to R3 // 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); new org.hl7.fhir.r4.elementmodel.JsonParser(contextR3).compose(ro3, bs, OutputStyle.PRETTY, null);
if (SAVING) if (SAVING)
TextFile.bytesToFile(bs.toByteArray(), Utilities.path(TestingUtilities.home(), "implementations", "r3maps", 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); // check(errors, tn, workingid);
roundTripError = TestingUtilities.checkJsonSrcIsSame(new String(cnt), new String(bs.toByteArray()), roundTripError = TestingUtilities.checkJsonSrcIsSame(new String(cnt), new String(bs.toByteArray()),
filter != null); filter != null);
if (roundTripError != null && roundTripError.equals(rules.getStringProperty(tn + "/" + workingid, "roundtrip"))) if (roundTripError != null && roundTripError.equals(rules.getStringProperty(tn + "/" + workingid, "roundtrip")))
roundTripError = null; roundTripError = null;
} else { } else {
@ -227,7 +198,7 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
} }
private void updateOutcomes(String tn, String id, Exception executionError, 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); JsonObject r = r3r4Outcomes.getAsJsonObject(tn);
if (r == null) { if (r == null) {
r = new JsonObject(); r = new JsonObject();
@ -264,7 +235,7 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
Gson gson = new GsonBuilder().setPrettyPrinting().create(); Gson gson = new GsonBuilder().setPrettyPrinting().create();
String json = gson.toJson(r3r4Outcomes); String json = gson.toJson(r3r4Outcomes);
TextFile.stringToFile(json, 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 * 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 * 2 contexts: - an R3 context which is used to read/write R3 instances - an R4
* context which is used to perform the transforms * context which is used to perform the transforms
* *
* R3 structure definitions are cloned into R3 context with a modified URL (as * R3 structure definitions are cloned into R3 context with a modified URL (as
* 3.0/) * 3.0/)
* *
*/ */
private void checkLoad() throws IOException, FHIRException, Exception { private void checkLoad() throws IOException, FHIRException, Exception {
if (contextR3 != null) if (contextR3 != null)
@ -321,7 +292,7 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
contextR3 = new SimpleWorkerContext(); contextR3 = new SimpleWorkerContext();
contextR3.setAllowLoadingDuplicates(true); contextR3.setAllowLoadingDuplicates(true);
contextR3.setOverrideVersionNs("http://hl7.org/fhir/3.0/StructureDefinition"); 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"); System.out.println("loading R4");
contextR4 = new SimpleWorkerContext(); contextR4 = new SimpleWorkerContext();
@ -341,7 +312,7 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
StructureDefinition sdn = sd.copy(); StructureDefinition sdn = sd.copy();
sdn.setUrl(sdn.getUrl().replace("http://hl7.org/fhir/", "http://hl7.org/fhir/3.0/")); 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") 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); contextR3.cacheResource(sdn);
contextR4.cacheResource(sdn); contextR4.cacheResource(sdn);
} }
@ -352,7 +323,7 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
contextR3.setName("R3"); contextR3.setName("R3");
contextR4.setName("R4"); contextR4.setName("R4");
// contextR4.setValidatorFactory(new InstanceValidatorFactory()); // contextR4.setValidatorFactory(new InstanceValidatorFactory());
// TODO: this has to be R% now... contextR4.setValidatorFactory(new InstanceValidatorFactory()); // TODO: this has to be R% now... contextR4.setValidatorFactory(new InstanceValidatorFactory());
System.out.println("loading Maps"); System.out.println("loading Maps");
@ -389,13 +360,13 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
@Override @Override
public void log(String message) { public void log(String message) {
System.out.println(message); System.out.println(message);
} }
@Override @Override
public Base createResource(Object appInfo, Base res, boolean atRootofTransform) { public Base createResource(Object appInfo, Base res, boolean atRootofTransform) {
if (res instanceof Resource && (res.fhirType().equals("CodeSystem") || res.fhirType().equals("CareTeam") if (res instanceof Resource && (res.fhirType().equals("CodeSystem") || res.fhirType().equals("CareTeam")
|| res.fhirType().equals("PractitionerRole"))) { || res.fhirType().equals("PractitionerRole"))) {
Resource r = (Resource) res; Resource r = (Resource) res;
extras.add(r); extras.add(r);
r.setId(workingid + "-" + extras.size()); r.setId(workingid + "-" + extras.size());
@ -413,7 +384,7 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
BaseWorkerContext context = (BaseWorkerContext) appInfo; BaseWorkerContext context = (BaseWorkerContext) appInfo;
if (context == contextR3) { if (context == contextR3) {
StructureDefinition sd = context.fetchResource(StructureDefinition.class, 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) if (sd == null)
throw new FHIRException("Type not found: '" + name + "'"); throw new FHIRException("Type not found: '" + name + "'");
return Manager.build(context, sd); return Manager.build(context, sd);
@ -445,7 +416,7 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
if (vals.length == 2 && vals[0].equals("practitioner")) if (vals.length == 2 && vals[0].equals("practitioner"))
for (Resource r : extras) { for (Resource r : extras) {
if (r instanceof PractitionerRole if (r instanceof PractitionerRole
&& ((PractitionerRole) r).getPractitioner().getReference().equals("Practitioner/" + vals[1])) { && ((PractitionerRole) r).getPractitioner().getReference().equals("Practitioner/" + vals[1])) {
results.add(r); results.add(r);
} }
} }
@ -455,7 +426,7 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
@Override @Override
public Element fetch(Object appContext, String url) public Element fetch(Object appContext, String url)
throws FHIRFormatError, DefinitionException, IOException, FHIRException { throws FHIRFormatError, DefinitionException, IOException, FHIRException {
return null; 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.r4.context.SimpleWorkerContext;
import org.hl7.fhir.r5.test.utils.TestingUtilities; import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.validation.Validator; 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 { public class CDAValidationTestCase {
private SimpleWorkerContext context; private SimpleWorkerContext context;

4
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/TransformationTests.java
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@ -5,8 +5,10 @@ import java.io.File;
import org.hl7.fhir.r4.test.utils.TestingUtilities; import org.hl7.fhir.r4.test.utils.TestingUtilities;
import org.hl7.fhir.validation.Validator; import org.hl7.fhir.validation.Validator;
import org.hl7.fhir.utilities.Utilities; 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 { public class TransformationTests {
@Test @Test