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Merge pull request #756 from hapifhir/dotasek-fix-narrative-generation-test 

Fix intermittent failures in NarrativeGenerationTests
This commit is contained in:
Grahame Grieve 2022-03-08 07:08:17 +11:00 committed by GitHub
parent 38e84a46f2 8df7938f3e
commit 89d43b7ce8
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
19 changed files with 104 additions and 86 deletions
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2
RELEASE_NOTES.md
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@ -4,4 +4,4 @@
## Other code changes
* no changes
* Fix to r5 TestingUtilities to allow NarrativeGenerationTests to pass.

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/SimpleWorkerContext.java
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@ -239,7 +239,7 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
public SimpleWorkerContext fromPackage(NpmPackage pi, IContextResourceLoader loader) throws IOException, FHIRException {
SimpleWorkerContext context = getSimpleWorkerContextInstance();
context.setAllowLoadingDuplicates(true);
context.setAllowLoadingDuplicates(allowLoadingDuplicates);
context.version = pi.getNpm().get("version").getAsString();
context.loadFromPackage(pi, loader);
context.finishLoading();

50
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/test/utils/TestingUtilities.java
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@ -75,11 +75,23 @@ public class TestingUtilities extends BaseTestingUtilities {
static public Map<String, IWorkerContext> fcontexts;
public static IWorkerContext context() {
return context("4.0.1");
final static public String DEFAULT_CONTEXT_VERSION = "4.0.1";
/** Get an existing instantiation of a WorkerContext if available
*
* This uses the DEFAULT_CONTEXT_VERSION
* */
public static IWorkerContext getSharedWorkerContext() {
return getSharedWorkerContext(DEFAULT_CONTEXT_VERSION);
}
public static IWorkerContext context(String version) {
/**
* Get an existing instantiation of a WorkerContext if available
*
* @param version FHIR Version to get context for
* @return
*/
public static IWorkerContext getSharedWorkerContext(String version) {
if ("4.5.0".equals(version)) {
version = "4.4.0"; // temporary work around
}
@ -89,33 +101,35 @@ public class TestingUtilities extends BaseTestingUtilities {
fcontexts = new HashMap<>();
}
if (!fcontexts.containsKey(v)) {
FilesystemPackageCacheManager pcm;
try {
pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
IWorkerContext fcontext = getWorkerContext(pcm.loadPackage(VersionUtilities.packageForVersion(version), version));
fcontext.setUcumService(new UcumEssenceService(TestingUtilities.loadTestResourceStream("ucum", "ucum-essence.xml")));
fcontext.setExpansionProfile(new Parameters());
// ((SimpleWorkerContext) fcontext).connectToTSServer(new TerminologyClientR5("http://tx.fhir.org/r4"), null);
IWorkerContext fcontext = getWorkerContext(version);
fcontexts.put(v, fcontext);
} catch (Exception e) {
e.printStackTrace();
throw new Error(e);
}
}
return fcontexts.get(v);
}
public static IWorkerContext getWorkerContext(String version) {
FilesystemPackageCacheManager pcm;
try {
pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
IWorkerContext fcontext = getWorkerContext(pcm.loadPackage(VersionUtilities.packageForVersion(version), version));
fcontext.setUcumService(new UcumEssenceService(TestingUtilities.loadTestResourceStream("ucum", "ucum-essence.xml")));
fcontext.setExpansionProfile(new Parameters());
return fcontext;
} catch (Exception e) {
e.printStackTrace();
throw new Error(e);
}
}
public static SimpleWorkerContext getWorkerContext(NpmPackage npmPackage) throws Exception {
SimpleWorkerContext swc = new SimpleWorkerContext.SimpleWorkerContextBuilder().withUserAgent(TestConstants.USER_AGENT).withTerminologyCachePath(TestConstants.TX_CACHE).fromPackage(npmPackage);
SimpleWorkerContext swc = new SimpleWorkerContext.SimpleWorkerContextBuilder().withAllowLoadingDuplicates(true).withUserAgent(TestConstants.USER_AGENT).withTerminologyCachePath(TestConstants.TX_CACHE).fromPackage(npmPackage);
TerminologyCache.setCacheErrors(true);
swc.setAllowLoadingDuplicates(true);
return swc;
}
public static SimpleWorkerContext getWorkerContext(NpmPackage npmPackage, IWorkerContext.IContextResourceLoader loader) throws Exception {
SimpleWorkerContext swc = new SimpleWorkerContext.SimpleWorkerContextBuilder().withUserAgent(TestConstants.USER_AGENT).withTerminologyCachePath(TestConstants.TX_CACHE).fromPackage(npmPackage, loader);
SimpleWorkerContext swc = new SimpleWorkerContext.SimpleWorkerContextBuilder().withAllowLoadingDuplicates(true).withUserAgent(TestConstants.USER_AGENT).withTerminologyCachePath(TestConstants.TX_CACHE).fromPackage(npmPackage, loader);
TerminologyCache.setCacheErrors(true);
swc.setAllowLoadingDuplicates(true);
return swc;
}

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

@ -257,7 +257,7 @@ public class CDARoundTripTests {
value.setValue("öé");
ByteArrayOutputStream baosXml = new ByteArrayOutputStream();
Manager.compose(TestingUtilities.context(), xml, baosXml, FhirFormat.XML, OutputStyle.PRETTY, null);
Manager.compose(TestingUtilities.getSharedWorkerContext(), xml, baosXml, FhirFormat.XML, OutputStyle.PRETTY, null);
String cdaSerialised = baosXml.toString("UTF-8");
Assertions.assertTrue(cdaSerialised.indexOf("öé") > 0);
}

4
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/FHIRPathTests.java
View File

@ -93,7 +93,7 @@ public class FHIRPathTests {
@Override
public ValueSet resolveValueSet(Object appContext, String url) {
return TestingUtilities.context().fetchResource(ValueSet.class, url);
return TestingUtilities.getSharedWorkerContext().fetchResource(ValueSet.class, url);
}
}
@ -103,7 +103,7 @@ public class FHIRPathTests {
@BeforeAll
public static void setUp() {
fp = new FHIRPathEngine(TestingUtilities.context());
fp = new FHIRPathEngine(TestingUtilities.getSharedWorkerContext());
}
public static Stream<Arguments> data() throws ParserConfigurationException, SAXException, IOException {

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

@ -65,7 +65,7 @@ public class GraphQLEngineTests implements IGraphQLStorageServices {
stream = TestingUtilities.loadTestResourceStream("r5", parts[0].toLowerCase()+"-"+parts[1].toLowerCase()+".xml");
}
GraphQLEngine gql = new GraphQLEngine(TestingUtilities.context());
GraphQLEngine gql = new GraphQLEngine(TestingUtilities.getSharedWorkerContext());
gql.setServices(this);
if (stream != null)
gql.setFocus(new XmlParser().parse(stream));

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

@ -37,7 +37,7 @@ public class LiquidEngineTests implements ILiquidEngineIncludeResolver {
@BeforeEach
public void setUp() throws Exception {
engine = new LiquidEngine(TestingUtilities.context(), null);
engine = new LiquidEngine(TestingUtilities.getSharedWorkerContext(), null);
engine.setIncludeResolver(this);
}

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

@ -103,7 +103,7 @@ public class NarrativeGenerationTests {
@BeforeAll
public static void setUp() {
context = TestingUtilities.context();
context = TestingUtilities.getSharedWorkerContext();
}
@ParameterizedTest(name = "{index}: file {0}")

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

@ -34,7 +34,7 @@ public class NarrativeGeneratorTests {
@BeforeAll
public static void setUp() throws FHIRException {
rc = new RenderingContext(TestingUtilities.context(), null, null, "http://hl7.org/fhir", "", null, ResourceRendererMode.END_USER);
rc = new RenderingContext(TestingUtilities.getSharedWorkerContext(), null, null, "http://hl7.org/fhir", "", null, ResourceRendererMode.END_USER);
}
@Test

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

@ -32,7 +32,7 @@ public class OpenApiGeneratorTest {
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));
OpenApiGenerator gen = new OpenApiGenerator(TestingUtilities.context(), cs, oa);
OpenApiGenerator gen = new OpenApiGenerator(TestingUtilities.getSharedWorkerContext(), cs, oa);
gen.generate("test-lic", "http://spdx.org/licenses/test-lic.html");
oa.commit();
}

20
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/ProfileUtilitiesTests.java
View File

@ -29,13 +29,13 @@ public class ProfileUtilitiesTests {
public void testSimple() throws FHIRException {
StructureDefinition focus = new StructureDefinition();
StructureDefinition base = TestingUtilities.context().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Patient").copy();
StructureDefinition base = TestingUtilities.getSharedWorkerContext().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Patient").copy();
focus.setUrl(Utilities.makeUuidUrn());
focus.setBaseDefinition(base.getUrl());
focus.setType("Patient");
focus.setDerivation(TypeDerivationRule.CONSTRAINT);
List<ValidationMessage> messages = new ArrayList<>();
new ProfileUtilities(TestingUtilities.context(), messages, null).generateSnapshot(base, focus, focus.getUrl(), "http://test.org/test", "Simple Test");
new ProfileUtilities(TestingUtilities.getSharedWorkerContext(), messages, null).generateSnapshot(base, focus, focus.getUrl(), "http://test.org/test", "Simple Test");
boolean ok = base.getSnapshot().getElement().size() == focus.getSnapshot().getElement().size();
for (int i = 0; i < base.getSnapshot().getElement().size(); i++) {
@ -70,13 +70,13 @@ public class ProfileUtilitiesTests {
// */
@Test
public void testSimple2() {
StructureDefinition base = TestingUtilities.context().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/ValueSet").copy();
StructureDefinition base = TestingUtilities.getSharedWorkerContext().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/ValueSet").copy();
StructureDefinition focus = base.copy();
focus.setUrl(Utilities.makeUuidUrn());
focus.setSnapshot(null);
focus.setDifferential(null);
List<ValidationMessage> messages = new ArrayList<>();
new ProfileUtilities(TestingUtilities.context(), messages, null).generateSnapshot(base, focus, focus.getUrl(), "http://test.org", "Simple Test");
new ProfileUtilities(TestingUtilities.getSharedWorkerContext(), messages, null).generateSnapshot(base, focus, focus.getUrl(), "http://test.org", "Simple Test");
boolean ok = base.getSnapshot().getElement().size() == focus.getSnapshot().getElement().size();
for (int i = 0; i < base.getSnapshot().getElement().size(); i++) {
@ -110,7 +110,7 @@ public class ProfileUtilitiesTests {
@Test
void testCardinalityChange() {
StructureDefinition focus = new StructureDefinition();
StructureDefinition base = TestingUtilities.context().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Patient").copy();
StructureDefinition base = TestingUtilities.getSharedWorkerContext().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Patient").copy();
focus.setUrl(Utilities.makeUuidUrn());
focus.setBaseDefinition(base.getUrl());
focus.setType(base.getType());
@ -119,7 +119,7 @@ public class ProfileUtilitiesTests {
id.setPath("Patient.identifier");
id.setMin(1);
List<ValidationMessage> messages = new ArrayList<>();
new ProfileUtilities(TestingUtilities.context(), messages, null).generateSnapshot(base, focus, focus.getUrl(), "http://test.org", "Simple Test");
new ProfileUtilities(TestingUtilities.getSharedWorkerContext(), messages, null).generateSnapshot(base, focus, focus.getUrl(), "http://test.org", "Simple Test");
boolean ok = base.getSnapshot().getElement().size() == focus.getSnapshot().getElement().size();
for (int i = 0; i < base.getSnapshot().getElement().size(); i++) {
@ -155,7 +155,7 @@ public class ProfileUtilitiesTests {
void testMinValueChange() {
// Given
StructureDefinition focus = new StructureDefinition();
StructureDefinition base = TestingUtilities.context().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Appointment").copy();
StructureDefinition base = TestingUtilities.getSharedWorkerContext().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Appointment").copy();
focus.setUrl(Utilities.makeUuidUrn());
focus.setBaseDefinition(base.getUrl());
focus.setType(base.getType());
@ -165,7 +165,7 @@ public class ProfileUtilitiesTests {
id.setMinValue(new IntegerType(1));
List<ValidationMessage> messages = new ArrayList<>();
// When
new ProfileUtilities(TestingUtilities.context(), messages, null).generateSnapshot(base, focus, focus.getUrl(), "http://test.org", "Simple Test");
new ProfileUtilities(TestingUtilities.getSharedWorkerContext(), messages, null).generateSnapshot(base, focus, focus.getUrl(), "http://test.org", "Simple Test");
// Then
boolean ok = base.getSnapshot().getElement().size() == focus.getSnapshot().getElement().size();
for (int i = 0; i < base.getSnapshot().getElement().size(); i++) {
@ -202,7 +202,7 @@ public class ProfileUtilitiesTests {
void testMaxValueChange() {
// Given
StructureDefinition focus = new StructureDefinition();
StructureDefinition base = TestingUtilities.context().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Appointment").copy();
StructureDefinition base = TestingUtilities.getSharedWorkerContext().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Appointment").copy();
focus.setUrl(Utilities.makeUuidUrn());
focus.setBaseDefinition(base.getUrl());
focus.setType(base.getType());
@ -212,7 +212,7 @@ public class ProfileUtilitiesTests {
id.setMaxValue(new IntegerType(1));
List<ValidationMessage> messages = new ArrayList<>();
// When
new ProfileUtilities(TestingUtilities.context(), messages, null).generateSnapshot(base, focus, focus.getUrl(), "http://test.org", "Simple Test");
new ProfileUtilities(TestingUtilities.getSharedWorkerContext(), messages, null).generateSnapshot(base, focus, focus.getUrl(), "http://test.org", "Simple Test");
// Then
boolean ok = base.getSnapshot().getElement().size() == focus.getSnapshot().getElement().size();
for (int i = 0; i < base.getSnapshot().getElement().size(); i++) {

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

@ -33,7 +33,7 @@ public class ResourceRoundTripTests {
@Test
public void test() throws IOException, FHIRException, EOperationOutcome {
DomainResource res = (DomainResource) new XmlParser().parse(TestingUtilities.loadTestResourceStream("r5", "unicode.xml"));
RenderingContext rc = new RenderingContext(TestingUtilities.context(), null, null, "http://hl7.org/fhir", "", null, ResourceRendererMode.END_USER);
RenderingContext rc = new RenderingContext(TestingUtilities.getSharedWorkerContext(), null, null, "http://hl7.org/fhir", "", null, ResourceRendererMode.END_USER);
RendererFactory.factory(res, rc).render(res);
IOUtils.copy(TestingUtilities.loadTestResourceStream("r5", "unicode.xml"), new FileOutputStream(TestingUtilities.tempFile("gen", "unicode.xml")));
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(TestingUtilities.tempFile("gen", "unicode.out.xml")), res);
@ -64,7 +64,7 @@ public class ResourceRoundTripTests {
* verify that umlaut like äö etc are not encoded in UTF-8 in attributes
*/
public void testSerializeUmlaut() throws IOException {
Element xml = Manager.parseSingle(TestingUtilities.context(), TestingUtilities.loadTestResourceStream("r5", "unicode.xml"),
Element xml = Manager.parseSingle(TestingUtilities.getSharedWorkerContext(), TestingUtilities.loadTestResourceStream("r5", "unicode.xml"),
FhirFormat.XML);
List<Element> concept = xml.getChildrenByName("concept");
assertTrue(concept!=null && concept.size()==1);
@ -72,7 +72,7 @@ public class ResourceRoundTripTests {
assertTrue(code!=null && code.size()==1);
code.get(0).setValue("ö");
ByteArrayOutputStream baosXml = new ByteArrayOutputStream();
Manager.compose(TestingUtilities.context(), xml, baosXml, FhirFormat.XML, OutputStyle.PRETTY, null);
Manager.compose(TestingUtilities.getSharedWorkerContext(), xml, baosXml, FhirFormat.XML, OutputStyle.PRETTY, null);
String cdaSerialised = baosXml.toString("UTF-8");
assertTrue(cdaSerialised.indexOf("ö")>0);
}

4
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/ShexGeneratorTests.java
View File

@ -18,12 +18,12 @@ import org.junit.jupiter.api.Test;
public class ShexGeneratorTests {
private void doTest(String name) throws FileNotFoundException, IOException, FHIRException, UcumException {
StructureDefinition sd = TestingUtilities.context().fetchResource(StructureDefinition.class, ProfileUtilities.sdNs(name, null));
StructureDefinition sd = TestingUtilities.getSharedWorkerContext().fetchResource(StructureDefinition.class, ProfileUtilities.sdNs(name, null));
if (sd == null) {
throw new FHIRException("StructuredDefinition for " + name + "was null");
}
Path outPath = FileSystems.getDefault().getPath(System.getProperty("java.io.tmpdir"), name.toLowerCase() + ".shex");
TextFile.stringToFile(new ShExGenerator(TestingUtilities.context()).generate(HTMLLinkPolicy.NONE, sd), outPath.toString());
TextFile.stringToFile(new ShExGenerator(TestingUtilities.getSharedWorkerContext()).generate(HTMLLinkPolicy.NONE, sd), outPath.toString());
}
@Test

50
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/SnapShotGenerationTests.java
View File

@ -211,13 +211,13 @@ public class SnapShotGenerationTests {
@Override
public boolean isDatatype(String name) {
StructureDefinition sd = TestingUtilities.context().fetchTypeDefinition(name);
StructureDefinition sd = TestingUtilities.getSharedWorkerContext().fetchTypeDefinition(name);
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);
StructureDefinition sd = TestingUtilities.getSharedWorkerContext().fetchTypeDefinition(typeSimple);
return (sd != null) && (sd.getDerivation() == TypeDerivationRule.SPECIALIZATION) && (sd.getKind() == StructureDefinitionKind.RESOURCE);
}
@ -249,7 +249,7 @@ public class SnapShotGenerationTests {
@Override
public String getLinkForProfile(StructureDefinition profile, String url) {
StructureDefinition sd = TestingUtilities.context().fetchResource(StructureDefinition.class, url);
StructureDefinition sd = TestingUtilities.getSharedWorkerContext().fetchResource(StructureDefinition.class, url);
if (sd == null)
return url + "|" + url;
else
@ -275,15 +275,15 @@ public class SnapShotGenerationTests {
public Resource fetchFixture(String id) {
TestFetchMode mode = TestFetchMode.INPUT;
if (id.equals("patient"))
return TestingUtilities.context().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Patient");
return TestingUtilities.getSharedWorkerContext().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Patient");
if (id.equals("valueset"))
return TestingUtilities.context().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/ValueSet");
return TestingUtilities.getSharedWorkerContext().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/ValueSet");
if (id.equals("organization"))
return TestingUtilities.context().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Organization");
return TestingUtilities.getSharedWorkerContext().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Organization");
if (id.equals("operationoutcome"))
return TestingUtilities.context().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/OperationOutcome");
return TestingUtilities.getSharedWorkerContext().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");
return TestingUtilities.getSharedWorkerContext().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Parameters");
if (id.contains("-")) {
String[] p = id.split("\\-");
@ -339,7 +339,7 @@ public class SnapShotGenerationTests {
@Override
public TypeDetails checkFunction(Object appContext, String functionName, List<TypeDetails> parameters) throws PathEngineException {
if ("fixture".equals(functionName))
return new TypeDetails(CollectionStatus.SINGLETON, TestingUtilities.context().getResourceNamesAsSet());
return new TypeDetails(CollectionStatus.SINGLETON, TestingUtilities.getSharedWorkerContext().getResourceNamesAsSet());
return null;
}
@ -366,7 +366,7 @@ public class SnapShotGenerationTests {
@Override
public boolean conformsToProfile(Object appContext, Base item, String url) throws FHIRException {
IResourceValidator val = TestingUtilities.context().newValidator();
IResourceValidator val = TestingUtilities.getSharedWorkerContext().newValidator();
List<ValidationMessage> valerrors = new ArrayList<ValidationMessage>();
if (item instanceof Resource) {
val.validate(appContext, valerrors, (Resource) item, url);
@ -404,7 +404,7 @@ public class SnapShotGenerationTests {
@BeforeAll
public static void setUp() {
fp = new FHIRPathEngine(TestingUtilities.context());
fp = new FHIRPathEngine(TestingUtilities.getSharedWorkerContext());
}
public static Stream<Arguments> data() throws ParserConfigurationException, IOException, FHIRFormatError, SAXException {
@ -462,7 +462,7 @@ public class SnapShotGenerationTests {
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);
ProfileUtilities pu = new ProfileUtilities(TestingUtilities.getSharedWorkerContext(), null, null);
pu.setIds(test.getSource(), false);
List<String> errors = new ArrayList<String>();
pu.sortDifferential(base, test.getOutput(), test.getOutput().getUrl(), errors, false);
@ -476,17 +476,17 @@ public class SnapShotGenerationTests {
private void testGen(boolean fail, TestDetails test, SnapShotGenerationTestsContext context) throws Exception {
if (!Utilities.noString(test.register)) {
List<ValidationMessage> messages = new ArrayList<ValidationMessage>();
ProfileUtilities pu = new ProfileUtilities(TestingUtilities.context(), messages, null);
ProfileUtilities pu = new ProfileUtilities(TestingUtilities.getSharedWorkerContext(), messages, null);
pu.setNewSlicingProcessing(true);
for (StructureDefinition sd : test.included) {
pu.setIds(sd, false);
}
for (StructureDefinition sd : test.included) {
if (!TestingUtilities.context().hasResource(StructureDefinition.class, sd.getUrl())) {
TestingUtilities.context().cacheResource(sd);
if (!TestingUtilities.getSharedWorkerContext().hasResource(StructureDefinition.class, sd.getUrl())) {
TestingUtilities.getSharedWorkerContext().cacheResource(sd);
}
}
StructureDefinition base = TestingUtilities.context().fetchResource(StructureDefinition.class, test.included.get(0).getBaseDefinition());
StructureDefinition base = TestingUtilities.getSharedWorkerContext().fetchResource(StructureDefinition.class, test.included.get(0).getBaseDefinition());
if (base != null) {
pu.generateSnapshot(base, test.included.get(0), test.included.get(0).getUrl(), "http://test.org/profile", test.included.get(0).getName());
}
@ -505,16 +505,16 @@ public class SnapShotGenerationTests {
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.getSharedWorkerContext(), messages, new TestPKP());
pu.setNewSlicingProcessing(test.isNewSliceProcessing());
pu.setThrowException(false);
pu.setDebug(test.isDebug());
pu.setIds(test.getSource(), false);
if (!TestingUtilities.context().hasPackage(CommonPackages.ID_XVER, CommonPackages.VER_XVER)) {
if (!TestingUtilities.getSharedWorkerContext().hasPackage(CommonPackages.ID_XVER, CommonPackages.VER_XVER)) {
NpmPackage npm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION).loadPackage(CommonPackages.ID_XVER, CommonPackages.VER_XVER);
TestingUtilities.context().loadFromPackage(npm, new TestPackageLoader(new String[]{"StructureDefinition"}), new String[]{"StructureDefinition"});
TestingUtilities.getSharedWorkerContext().loadFromPackage(npm, new TestPackageLoader(new String[]{"StructureDefinition"}), new String[]{"StructureDefinition"});
}
pu.setXver(new XVerExtensionManager(TestingUtilities.context()));
pu.setXver(new XVerExtensionManager(TestingUtilities.getSharedWorkerContext()));
if (test.isSort()) {
List<String> errors = new ArrayList<String>();
int lastCount = output.getDifferential().getElement().size();
@ -539,14 +539,14 @@ public class SnapShotGenerationTests {
throw e;
}
if (output.getDifferential().hasElement()) {
RenderingContext rc = new RenderingContext(TestingUtilities.context(), null, null, "http://hl7.org/fhir", "", null, ResourceRendererMode.END_USER);
RenderingContext rc = new RenderingContext(TestingUtilities.getSharedWorkerContext(), null, null, "http://hl7.org/fhir", "", null, ResourceRendererMode.END_USER);
rc.setDestDir(Utilities.path("[tmp]", "snapshot"));
rc.setProfileUtilities(new ProfileUtilities(TestingUtilities.context(), null, new TestPKP()));
rc.setProfileUtilities(new ProfileUtilities(TestingUtilities.getSharedWorkerContext(), null, new TestPKP()));
RendererFactory.factory(output, rc).render(output);
}
if (!fail) {
test.output = output;
TestingUtilities.context().cacheResource(output);
TestingUtilities.getSharedWorkerContext().cacheResource(output);
File dst = new File(TestingUtilities.tempFile("snapshot", test.getId() + "-expected.xml"));
if (dst.exists())
dst.delete();
@ -563,14 +563,14 @@ public class SnapShotGenerationTests {
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);
sd = TestingUtilities.getSharedWorkerContext().fetchResource(StructureDefinition.class, url);
}
if (sd == null) {
throw new DefinitionException("Unable to find profile "+url);
}
if (!sd.hasSnapshot()) {
StructureDefinition base = getSD(sd.getBaseDefinition(), context);
ProfileUtilities pu = new ProfileUtilities(TestingUtilities.context(), messages, new TestPKP());
ProfileUtilities pu = new ProfileUtilities(TestingUtilities.getSharedWorkerContext(), messages, new TestPKP());
pu.setNewSlicingProcessing(true);
List<String> errors = new ArrayList<String>();
pu.sortDifferential(base, sd, url, errors, false);

8
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/VocabTests.java
View File

@ -24,6 +24,7 @@ import org.hl7.fhir.r5.renderers.utils.RenderingContext.ITypeParser;
import org.hl7.fhir.r5.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.utilities.npm.ToolsVersion;
@ -104,8 +105,11 @@ public class VocabTests {
}
@BeforeAll
public static void setUp() throws FileNotFoundException, FHIRException, IOException {
context = TestingUtilities.context();
public static void setUp() throws FHIRException, IOException {
/* Do NOT get a shared worker context from Testing Utilities or else the terminology package loaded below
will appear in tests where it causes failures.
*/
context = TestingUtilities.getWorkerContext(VersionUtilities.getMajMin(TestingUtilities.DEFAULT_CONTEXT_VERSION));
if (!context.hasPackage("hl7.terminology", null)) {
NpmPackage utg = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION).loadPackage("hl7.terminology");

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

@ -86,9 +86,9 @@ public class ResourceTest {
}
public Element testEM() throws Exception {
Element resource = Manager.parseSingle(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);
Element resource = Manager.parseSingle(TestingUtilities.getSharedWorkerContext(), new FileInputStream(source), isJson() ? FhirFormat.JSON : FhirFormat.XML);
Manager.compose(TestingUtilities.getSharedWorkerContext(), resource, new FileOutputStream(source.getAbsoluteFile()+".out.json"), FhirFormat.JSON, OutputStyle.PRETTY, null);
Manager.compose(TestingUtilities.getSharedWorkerContext(), resource, new FileOutputStream(source.getAbsoluteFile()+".out.json"), FhirFormat.XML, OutputStyle.PRETTY, null);
return resource;
}

2
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/comparison/tests/ComparisonTests.java
View File

@ -108,7 +108,7 @@ public class ComparisonTests {
if (context == null) {
System.out.println("---- Load R5 ----------------------------------------------------------------");
context = TestingUtilities.context();
context = TestingUtilities.getSharedWorkerContext();
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
NpmPackage npm = pcm.loadPackage("hl7.fhir.us.core#3.1.0");
BaseWorkerContext bc = (BaseWorkerContext) context;

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

@ -522,9 +522,9 @@ public class SnapShotGenerationXTests {
throw e;
}
if (output.getDifferential().hasElement()) {
RenderingContext rc = new RenderingContext(TestingUtilities.context(), null, null, "http://hl7.org/fhir", "", null, ResourceRendererMode.END_USER);
RenderingContext rc = new RenderingContext(TestingUtilities.getSharedWorkerContext(), null, null, "http://hl7.org/fhir", "", null, ResourceRendererMode.END_USER);
rc.setDestDir(makeTempDir());
rc.setProfileUtilities(new ProfileUtilities(TestingUtilities.context(), null, new TestPKP()));
rc.setProfileUtilities(new ProfileUtilities(TestingUtilities.getSharedWorkerContext(), null, new TestPKP()));
RendererFactory.factory(output, rc).render(output);
}
if (!fail) {

20
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/ValidationTests.java
View File

@ -350,9 +350,9 @@ public class ValidationTests implements IEvaluationContext, IValidatorResourceFe
public StructureDefinition loadProfile(String filename, String contents, List<ValidationMessage> messages) throws IOException, FHIRFormatError, FileNotFoundException, FHIRException, DefinitionException {
StructureDefinition sd = (StructureDefinition) loadResource(filename, contents);
ProfileUtilities pu = new ProfileUtilities(TestingUtilities.context(version), messages, null);
ProfileUtilities pu = new ProfileUtilities(TestingUtilities.getSharedWorkerContext(version), messages, null);
if (!sd.hasSnapshot()) {
StructureDefinition base = TestingUtilities.context(version).fetchResource(StructureDefinition.class, sd.getBaseDefinition());
StructureDefinition base = TestingUtilities.getSharedWorkerContext(version).fetchResource(StructureDefinition.class, sd.getBaseDefinition());
pu.generateSnapshot(base, sd, sd.getUrl(), null, sd.getTitle());
// (debugging) new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", sd.getId()+".xml")), sd);
}
@ -360,7 +360,7 @@ public class ValidationTests implements IEvaluationContext, IValidatorResourceFe
if (r instanceof StructureDefinition) {
StructureDefinition childSd = (StructureDefinition) r;
if (!childSd.hasSnapshot()) {
StructureDefinition base = TestingUtilities.context(version).fetchResource(StructureDefinition.class, childSd.getBaseDefinition());
StructureDefinition base = TestingUtilities.getSharedWorkerContext(version).fetchResource(StructureDefinition.class, childSd.getBaseDefinition());
pu.generateSnapshot(base, childSd, childSd.getUrl(), null, childSd.getTitle());
}
}
@ -427,7 +427,7 @@ public class ValidationTests implements IEvaluationContext, IValidatorResourceFe
}
}
}
if (!TestingUtilities.context(version).isNoTerminologyServer() || !focus.has("tx-dependent")) {
if (!TestingUtilities.getSharedWorkerContext(version).isNoTerminologyServer() || !focus.has("tx-dependent")) {
Assert.assertEquals("Test " + name + (profile == null ? "" : " profile: "+ profile) + ": Expected " + Integer.toString(java.get("errorCount").getAsInt()) + " errors, but found " + Integer.toString(ec) + ".", java.get("errorCount").getAsInt(), ec);
if (java.has("warningCount")) {
Assert.assertEquals( "Test " + name + (profile == null ? "" : " profile: "+ profile) + ": Expected " + Integer.toString(java.get("warningCount").getAsInt()) + " warnings, but found " + Integer.toString(wc) + ".", java.get("warningCount").getAsInt(), wc);
@ -501,18 +501,18 @@ public class ValidationTests implements IEvaluationContext, IValidatorResourceFe
public Element fetch(IResourceValidator validator, Object appContext, String url) throws FHIRFormatError, DefinitionException, IOException, FHIRException {
Element res = null;
if (url.equals("Patient/test")) {
res = new ObjectConverter(TestingUtilities.context(version)).convert(new Patient());
res = new ObjectConverter(TestingUtilities.getSharedWorkerContext(version)).convert(new Patient());
} else if (TestingUtilities.findTestResource("validator", url.replace("/", "-").toLowerCase() + ".json")) {
res = Manager.makeParser(TestingUtilities.context(version), FhirFormat.JSON).parseSingle(TestingUtilities.loadTestResourceStream("validator", url.replace("/", "-").toLowerCase() + ".json"));
res = Manager.makeParser(TestingUtilities.getSharedWorkerContext(version), FhirFormat.JSON).parseSingle(TestingUtilities.loadTestResourceStream("validator", url.replace("/", "-").toLowerCase() + ".json"));
} else if (TestingUtilities.findTestResource("validator", url.replace("/", "-").toLowerCase() + ".xml")) {
res = Manager.makeParser(TestingUtilities.context(version), FhirFormat.XML).parseSingle(TestingUtilities.loadTestResourceStream("validator", url.replace("/", "-").toLowerCase() + ".xml"));
res = Manager.makeParser(TestingUtilities.getSharedWorkerContext(version), FhirFormat.XML).parseSingle(TestingUtilities.loadTestResourceStream("validator", url.replace("/", "-").toLowerCase() + ".xml"));
}
if (res == null && url.contains("/")) {
String tail = url.substring(url.indexOf("/") + 1);
if (TestingUtilities.findTestResource("validator", tail.replace("/", "-").toLowerCase() + ".json")) {
res = Manager.makeParser(TestingUtilities.context(version), FhirFormat.JSON).parseSingle(TestingUtilities.loadTestResourceStream("validator", tail.replace("/", "-").toLowerCase() + ".json"));
res = Manager.makeParser(TestingUtilities.getSharedWorkerContext(version), FhirFormat.JSON).parseSingle(TestingUtilities.loadTestResourceStream("validator", tail.replace("/", "-").toLowerCase() + ".json"));
} else if (TestingUtilities.findTestResource("validator", tail.replace("/", "-").toLowerCase() + ".xml")) {
res = Manager.makeParser(TestingUtilities.context(version), FhirFormat.XML).parseSingle(TestingUtilities.loadTestResourceStream("validator", tail.replace("/", "-").toLowerCase() + ".xml"));
res = Manager.makeParser(TestingUtilities.getSharedWorkerContext(version), FhirFormat.XML).parseSingle(TestingUtilities.loadTestResourceStream("validator", tail.replace("/", "-").toLowerCase() + ".xml"));
}
}
return res;
@ -558,7 +558,7 @@ public class ValidationTests implements IEvaluationContext, IValidatorResourceFe
@Override
public boolean conformsToProfile(Object appContext, Base item, String url) throws FHIRException {
IResourceValidator val = TestingUtilities.context(version).newValidator();
IResourceValidator val = TestingUtilities.getSharedWorkerContext(version).newValidator();
List<ValidationMessage> valerrors = new ArrayList<ValidationMessage>();
if (item instanceof Resource) {
val.validate(appContext, valerrors, (Resource) item, url);