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org.hl7.fhir.core
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Merge branch 'master' into 2024-04-gg-lookup

This commit is contained in:
Grahame Grieve 2024-04-16 16:15:37 +10:00 committed by GitHub
parent 7796c93066 59a749a842
commit 0d7c837b85
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GPG Key ID: B5690EEEBB952194
6 changed files with 323 additions and 233 deletions
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13
org.hl7.fhir.utilities/pom.xml
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@ -89,7 +89,6 @@
<optional>true</optional> <optional>true</optional>
</dependency> </dependency>
<dependency> <dependency>
<groupId>com.ibm.icu</groupId> <groupId>com.ibm.icu</groupId>
<artifactId>icu4j</artifactId> <artifactId>icu4j</artifactId>
@ -107,18 +106,21 @@
<groupId>org.junit.jupiter</groupId> <groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-api</artifactId> <artifactId>junit-jupiter-api</artifactId>
<scope>provided</scope> <scope>provided</scope>
<optional>true</optional>
</dependency> </dependency>
<dependency> <dependency>
<groupId>net.bytebuddy</groupId> <groupId>net.bytebuddy</groupId>
<artifactId>byte-buddy</artifactId> <artifactId>byte-buddy</artifactId>
<scope>provided</scope> <scope>provided</scope>
<optional>true</optional>
</dependency> </dependency>
<dependency> <dependency>
<groupId>org.junit.jupiter</groupId> <groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-engine</artifactId> <artifactId>junit-jupiter-engine</artifactId>
<scope>provided</scope> <scope>provided</scope>
<optional>true</optional>
</dependency> </dependency>
<dependency> <dependency>
@ -126,12 +128,14 @@
<artifactId>junit-vintage-engine</artifactId> <artifactId>junit-vintage-engine</artifactId>
<version>${junit_jupiter_version}</version> <version>${junit_jupiter_version}</version>
<scope>provided</scope> <scope>provided</scope>
<optional>true</optional>
</dependency> </dependency>
<dependency> <dependency>
<groupId>org.junit.jupiter</groupId> <groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-params</artifactId> <artifactId>junit-jupiter-params</artifactId>
<scope>provided</scope> <scope>provided</scope>
<optional>true</optional>
</dependency> </dependency>
<dependency> <dependency>
@ -139,6 +143,7 @@
<artifactId>junit-platform-launcher</artifactId> <artifactId>junit-platform-launcher</artifactId>
<version>${junit_platform_launcher_version}</version> <version>${junit_platform_launcher_version}</version>
<scope>provided</scope> <scope>provided</scope>
<optional>true</optional>
</dependency> </dependency>
<dependency> <dependency>
@ -146,13 +151,14 @@
<artifactId>fhir-test-cases</artifactId> <artifactId>fhir-test-cases</artifactId>
<version>${validator_test_case_version}</version> <version>${validator_test_case_version}</version>
<scope>provided</scope> <scope>provided</scope>
<optional>true</optional>
</dependency> </dependency>
<dependency> <dependency>
<groupId>junit</groupId> <groupId>junit</groupId>
<artifactId>junit</artifactId> <artifactId>junit</artifactId>
<version>4.13.2</version>
<scope>provided</scope> <scope>provided</scope>
<optional>true</optional>
</dependency> </dependency>
<dependency> <dependency>
@ -161,14 +167,13 @@
<version>3.1.0</version> <version>3.1.0</version>
<scope>test</scope> <scope>test</scope>
</dependency> </dependency>
<dependency> <dependency>
<groupId>com.squareup.okhttp3</groupId> <groupId>com.squareup.okhttp3</groupId>
<artifactId>mockwebserver</artifactId> <artifactId>mockwebserver</artifactId>
<version>4.11.0</version>
<scope>test</scope> <scope>test</scope>
</dependency> </dependency>
<!-- <!--
<dependency> <dependency>
<groupId>com.squareup.okhttp3</groupId> <groupId>com.squareup.okhttp3</groupId>

2
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java
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@ -7499,7 +7499,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
// first case: the type value set is wrong for primitive special types // first case: the type value set is wrong for primitive special types
for (OperationOutcomeIssueComponent iss : vr.getIssues()) { for (OperationOutcomeIssueComponent iss : vr.getIssues()) {
if (iss.getDetails().getText().startsWith("Unable to resolve system - value set expansion has no matches for code 'http://hl7.org/fhirpath/System")) { if (iss.hasDetails() && iss.getDetails().getText().startsWith("Unable to resolve system - value set expansion has no matches for code 'http://hl7.org/fhirpath/System")) {
return new ValidationResult("http://hl7.org/fhirpath/System", null, null, null); return new ValidationResult("http://hl7.org/fhirpath/System", null, null, null);
} }
} }

215
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/special/TxServiceTestHelper.java Normal file
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@ -0,0 +1,215 @@
package org.hl7.fhir.validation.special;
import com.google.gson.JsonSyntaxException;
import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.formats.IParser;
import org.hl7.fhir.r5.model.*;
import org.hl7.fhir.r5.terminologies.utilities.TerminologyServiceErrorClass;
import org.hl7.fhir.r5.terminologies.utilities.ValidationResult;
import org.hl7.fhir.r5.test.utils.CompareUtilities;
import org.hl7.fhir.utilities.FhirPublication;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.i18n.I18nConstants;
import org.hl7.fhir.utilities.json.model.JsonObject;
import org.hl7.fhir.utilities.validation.ValidationOptions;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
public class TxServiceTestHelper {
public static String getDiffForValidation(String id, IWorkerContext context, String name, Resource requestParameters, String expectedResponse, String lang, String fp, JsonObject externals, boolean isCodeSystem) throws JsonSyntaxException, FileNotFoundException, IOException {
org.hl7.fhir.r5.model.Parameters p = (org.hl7.fhir.r5.model.Parameters) requestParameters;
ValueSet valueSet = null;
String valueSetUrl = null;
if (!isCodeSystem) {
if (p.hasParameter("valueSetVersion")) {
valueSetUrl = p.getParameterValue("url").primitiveValue()+"|"+p.getParameterValue("valueSetVersion").primitiveValue();
valueSet = context.fetchResource(ValueSet.class, p.getParameterValue("url").primitiveValue(), p.getParameterValue("valueSetVersion").primitiveValue());
} else {
valueSetUrl = p.getParameterValue("url").primitiveValue();
valueSet = context.fetchResource(ValueSet.class, p.getParameterValue("url").primitiveValue());
}
}
ValidationResult validationResult = null;
String code = null;
String system = null;
String version = null;
String display = null;
CodeableConcept codeableConcept = null;
org.hl7.fhir.r5.model.Parameters parameters = null;
OperationOutcome operationOutcome = null;
if (valueSet == null && valueSetUrl != null) {
String msg = context.formatMessage(I18nConstants.UNABLE_TO_RESOLVE_VALUE_SET_, valueSetUrl);
operationOutcome = new OperationOutcome();
CodeableConcept codeableConceptWhenNullValueSet = operationOutcome.addIssue().setSeverity(OperationOutcome.IssueSeverity.ERROR).setCode(OperationOutcome.IssueType.NOTFOUND).getDetails();
codeableConceptWhenNullValueSet.addCoding("http://hl7.org/fhir/tools/CodeSystem/tx-issue-type", "not-found", null);
codeableConceptWhenNullValueSet.setText(msg);
} else {
ValidationOptions options = new ValidationOptions(FhirPublication.R5);
if (p.hasParameter("displayLanguage")) {
options = options.withLanguage(p.getParameterString("displayLanguage"));
} else if (lang != null ) {
options = options.withLanguage(lang);
}
if (p.hasParameter("valueset-membership-only") && "true".equals(p.getParameterString("valueset-membership-only"))) {
options = options.withCheckValueSetOnly();
}
if (p.hasParameter("lenient-display-validation") && "true".equals(p.getParameterString("lenient-display-validation"))) {
options = options.setDisplayWarningMode(true);
}
if (p.hasParameter("activeOnly") && "true".equals(p.getParameterString("activeOnly"))) {
options = options.setActiveOnly(true);
}
context.getExpansionParameters().clearParameters("includeAlternateCodes");
for (Parameters.ParametersParameterComponent pp : p.getParameter()) {
if ("includeAlternateCodes".equals(pp.getName())) {
context.getExpansionParameters().addParameter(pp.copy());
}
}
if (p.hasParameter("code")) {
code = p.getParameterString("code");
system = p.getParameterString(isCodeSystem ? "url" : "system");
version = p.getParameterString(isCodeSystem ? "version" : "systemVersion");
display = p.getParameterString("display");
validationResult = context.validateCode(options.withGuessSystem(),
p.getParameterString(isCodeSystem ? "url" : "system"), p.getParameterString(isCodeSystem ? "version" : "systemVersion"),
p.getParameterString("code"), p.getParameterString("display"), valueSet);
} else if (p.hasParameter("coding")) {
Coding coding = (Coding) p.getParameterValue("coding");
code = coding.getCode();
system = coding.getSystem();
version = coding.getVersion();
display = coding.getDisplay();
validationResult = context.validateCode(options, coding, valueSet);
} else if (p.hasParameter("codeableConcept")) {
codeableConcept = (CodeableConcept) p.getParameterValue("codeableConcept");
validationResult = context.validateCode(options, codeableConcept, valueSet);
} else {
throw new Error("validate not done yet for this steup");
}
}
if (operationOutcome == null && validationResult != null && validationResult.getSeverity() == org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity.FATAL) {
operationOutcome = new OperationOutcome();
operationOutcome.getIssue().addAll(validationResult.getIssues());
}
if (operationOutcome != null) {
TxTesterSorters.sortOperationOutcome(operationOutcome);
TxTesterScrubbers.scrubOO(operationOutcome, false);
String actualResponse = new JsonParser().setOutputStyle(IParser.OutputStyle.PRETTY).composeString(operationOutcome);
writeDiffToFileSystem( name, expectedResponse, actualResponse);
String diff = CompareUtilities.checkJsonSrcIsSame(id, expectedResponse, actualResponse, externals);
if (diff != null) {
Utilities.createDirectory(Utilities.getDirectoryForFile(fp));
TextFile.stringToFile(actualResponse, fp);
System.out.println("Test "+name+"failed: "+diff);
}
return diff;
} else {
if (parameters == null) {
parameters = new org.hl7.fhir.r5.model.Parameters();
if (validationResult.getSystem() != null) {
parameters.addParameter("system", new UriType(validationResult.getSystem()));
} else if (system != null) {
parameters.addParameter("system", new UriType(system));
}
if (validationResult.getCode() != null) {
if (code != null && !code.equals(validationResult.getCode())) {
parameters.addParameter("code", new CodeType(code));
parameters.addParameter("normalized-code", new CodeType(validationResult.getCode()));
} else {
parameters.addParameter("code", new CodeType(validationResult.getCode()));
}
} else if (code != null) {
parameters.addParameter("code", new CodeType(code));
}
if (validationResult.getSeverity() == org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity.ERROR) {
parameters.addParameter("result", false);
} else {
parameters.addParameter("result", true);
}
if (validationResult.getMessage() != null) {
parameters.addParameter("message", validationResult.getMessage());
}
if (validationResult.getVersion() != null) {
parameters.addParameter("version", validationResult.getVersion());
} else if (version != null) {
parameters.addParameter("version", new StringType(version));
}
if (validationResult.getDisplay() != null) {
parameters.addParameter("display", validationResult.getDisplay());
} else if (display != null) {
parameters.addParameter("display", new StringType(display));
}
// if (vm.getCodeableConcept() != null) {
// res.addParameter("codeableConcept", vm.getCodeableConcept());
// } else
if (codeableConcept != null) {
parameters.addParameter("codeableConcept", codeableConcept);
}
if (validationResult.isInactive()) {
parameters.addParameter("inactive", true);
}
if (validationResult.getStatus() != null) {
parameters.addParameter("status", validationResult.getStatus());
}
if (validationResult.getUnknownSystems() != null) {
for (String s : validationResult.getUnknownSystems()) {
parameters.addParameter(validationResult.getErrorClass() == TerminologyServiceErrorClass.CODESYSTEM_UNSUPPORTED ? "x-caused-by-unknown-system" : "x-unknown-system", new CanonicalType(s));
}
}
if (validationResult.getIssues().size() > 0) {
operationOutcome = new OperationOutcome();
operationOutcome.getIssue().addAll(validationResult.getIssues());
parameters.addParameter().setName("issues").setResource(operationOutcome);
}
}
TxTesterSorters.sortParameters(parameters);
TxTesterScrubbers.scrubParams(parameters);
String actualResponse = new JsonParser().setOutputStyle(IParser.OutputStyle.PRETTY).composeString(parameters);
writeDiffToFileSystem(name, expectedResponse, actualResponse);
String diff = CompareUtilities.checkJsonSrcIsSame(id, expectedResponse, actualResponse, externals);
if (diff != null) {
Utilities.createDirectory(Utilities.getDirectoryForFile(fp));
TextFile.stringToFile(actualResponse, fp);
System.out.println("Test "+name+"failed: "+diff);
}
return diff;
}
}
public static void writeDiffToFileSystem(String testName, String expected, String actual) throws IOException {
String rootDirectory = System.getenv("TX_SERVICE_TEST_DIFF_TARGET");
if (rootDirectory == null || rootDirectory.isEmpty()) {
return;
}
String fullExpected = rootDirectory + "/expected/";
String fullActual = rootDirectory + "/actual/";
File expectedDirectory = new File(fullExpected);
if (!expectedDirectory.exists()) {
expectedDirectory.mkdirs();
}
File actualDirectory = new File(fullActual);
if (!actualDirectory.exists()) {
actualDirectory.mkdirs();
}
TextFile.stringToFile(expected, fullExpected + testName + ".json");
TextFile.stringToFile(actual, fullActual + testName + ".json");
}
}

55
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/special/TxTestData.java Normal file
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@ -0,0 +1,55 @@
package org.hl7.fhir.validation.special;
import lombok.Getter;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.utilities.json.model.JsonObject;
import java.io.IOException;
import java.util.*;
public class TxTestData {
@Getter
private final JsonObject manifest;
@Getter
private final JsonObject externals;
@Getter
private final List<Object[]> testData;
private TxTestData(List<Object[]> testData, JsonObject manifest, JsonObject externals) throws IOException {
this.testData = testData;
this.manifest = manifest;
this.externals = externals;
}
public static TxTestData loadTestDataFromDefaultClassPath() throws IOException {
String contents = TestingUtilities.loadTestResource("tx", "test-cases.json");
String externalSource = TestingUtilities.loadTestResource("tx", "messages-tx.fhir.org.json");
JsonObject externals = org.hl7.fhir.utilities.json.parser.JsonParser.parseObject(externalSource);
Map<String, TxTestSetup> examples = new HashMap<String, TxTestSetup>();
JsonObject manifest = org.hl7.fhir.utilities.json.parser.JsonParser.parseObject(contents);
for (JsonObject suite : manifest.getJsonObjects("suites")) {
if (!"tx.fhir.org".equals(suite.asString("mode"))) {
String sn = suite.asString("name");
for (JsonObject test : suite.getJsonObjects("tests")) {
String tn = test.asString("name");
examples.put(sn + "." + tn, new TxTestSetup(suite, test));
}
}
}
List<String> names = new ArrayList<String>(examples.size());
names.addAll(examples.keySet());
Collections.sort(names);
List<Object[]> testData = new ArrayList<Object[]>(examples.size());
for (String id : names) {
testData.add(new Object[]{id, examples.get(id)});
}
return new TxTestData(testData, manifest, externals);
}
}

17
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/special/TxTestSetup.java Normal file
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@ -0,0 +1,17 @@
package org.hl7.fhir.validation.special;
import lombok.Getter;
import org.hl7.fhir.utilities.json.model.JsonObject;
public class TxTestSetup {
public TxTestSetup(JsonObject suite, JsonObject test) {
this.suite = suite;
this.test = test;
}
@Getter
private JsonObject suite;
@Getter
private JsonObject test;
}

254
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/terminology/tests/TerminologyServiceTests.java
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@ -4,11 +4,6 @@ import java.io.File;
import java.io.FileNotFoundException; import java.io.FileNotFoundException;
import java.io.IOException; import java.io.IOException;
import java.io.InputStream; import java.io.InputStream;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_10_50; import org.hl7.fhir.convertors.factory.VersionConvertorFactory_10_50;
@ -21,34 +16,27 @@ import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.formats.IParser.OutputStyle; import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.formats.JsonParser; import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.formats.XmlParser; import org.hl7.fhir.r5.formats.XmlParser;
import org.hl7.fhir.r5.model.CanonicalType;
import org.hl7.fhir.r5.model.CodeType; import org.hl7.fhir.r5.model.CodeType;
import org.hl7.fhir.r5.model.StringType;
import org.hl7.fhir.r5.model.CodeableConcept;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.Constants; import org.hl7.fhir.r5.model.Constants;
import org.hl7.fhir.r5.model.OperationOutcome; import org.hl7.fhir.r5.model.OperationOutcome;
import org.hl7.fhir.r5.model.OperationOutcome.IssueSeverity; import org.hl7.fhir.r5.model.OperationOutcome.IssueSeverity;
import org.hl7.fhir.r5.model.OperationOutcome.IssueType; import org.hl7.fhir.r5.model.OperationOutcome.IssueType;
import org.hl7.fhir.r5.model.OperationOutcome.OperationOutcomeIssueComponent; import org.hl7.fhir.r5.model.OperationOutcome.OperationOutcomeIssueComponent;
import org.hl7.fhir.r5.model.Parameters.ParametersParameterComponent;
import org.hl7.fhir.r5.model.Resource; import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.UriType;
import org.hl7.fhir.r5.model.ValueSet; import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionParameterComponent; import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionParameterComponent;
import org.hl7.fhir.r5.terminologies.expansion.ValueSetExpansionOutcome; import org.hl7.fhir.r5.terminologies.expansion.ValueSetExpansionOutcome;
import org.hl7.fhir.r5.terminologies.utilities.TerminologyServiceErrorClass;
import org.hl7.fhir.r5.terminologies.utilities.ValidationResult;
import org.hl7.fhir.r5.test.utils.CompareUtilities; import org.hl7.fhir.r5.test.utils.CompareUtilities;
import org.hl7.fhir.r5.test.utils.TestingUtilities; import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.utilities.FhirPublication; import org.hl7.fhir.utilities.FhirPublication;
import org.hl7.fhir.utilities.TextFile; import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities; import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess; import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.i18n.I18nConstants;
import org.hl7.fhir.utilities.json.model.JsonObject; import org.hl7.fhir.utilities.json.model.JsonObject;
import org.hl7.fhir.utilities.validation.ValidationOptions;
import org.hl7.fhir.validation.ValidationEngine; import org.hl7.fhir.validation.ValidationEngine;
import org.hl7.fhir.validation.special.TxServiceTestHelper;
import org.hl7.fhir.validation.special.TxTestSetup;
import org.hl7.fhir.validation.special.TxTestData;
import org.hl7.fhir.validation.special.TxTesterScrubbers; import org.hl7.fhir.validation.special.TxTesterScrubbers;
import org.hl7.fhir.validation.special.TxTesterSorters; import org.hl7.fhir.validation.special.TxTesterSorters;
import org.hl7.fhir.validation.tests.utilities.TestUtilities; import org.hl7.fhir.validation.tests.utilities.TestUtilities;
@ -60,62 +48,30 @@ import org.junit.runners.Parameterized;
import org.junit.runners.Parameterized.Parameters; import org.junit.runners.Parameterized.Parameters;
import com.google.common.base.Charsets; import com.google.common.base.Charsets;
import com.google.gson.JsonSyntaxException;
import static org.junit.Assert.assertNull;
@RunWith(Parameterized.class) @RunWith(Parameterized.class)
public class TerminologyServiceTests { public class TerminologyServiceTests {
public static class JsonObjectPair {
public JsonObjectPair(JsonObject suite, JsonObject test) { private static TxTestData testData;
this.suite = suite;
this.test = test;
}
private JsonObject suite;
private JsonObject test;
}
@Parameters(name = "{index}: id {0}") @Parameters(name = "{index}: id {0}")
public static Iterable<Object[]> data() throws IOException { public static Iterable<Object[]> data() throws IOException {
testData = TxTestData.loadTestDataFromDefaultClassPath();
String contents = TestingUtilities.loadTestResource("tx", "test-cases.json"); return testData.getTestData();
String externalSource = TestingUtilities.loadTestResource("tx", "messages-tx.fhir.org.json");
externals = org.hl7.fhir.utilities.json.parser.JsonParser.parseObject(externalSource);
Map<String, JsonObjectPair> examples = new HashMap<String, JsonObjectPair>();
manifest = org.hl7.fhir.utilities.json.parser.JsonParser.parseObject(contents);
for (org.hl7.fhir.utilities.json.model.JsonObject suite : manifest.getJsonObjects("suites")) {
if (!"tx.fhir.org".equals(suite.asString("mode"))) {
String sn = suite.asString("name");
for (org.hl7.fhir.utilities.json.model.JsonObject test : suite.getJsonObjects("tests")) {
String tn = test.asString("name");
examples.put(sn+"."+tn, new JsonObjectPair(suite, test));
}
}
}
List<String> names = new ArrayList<String>(examples.size());
names.addAll(examples.keySet());
Collections.sort(names);
List<Object[]> objects = new ArrayList<Object[]>(examples.size());
for (String id : names) {
objects.add(new Object[]{id, examples.get(id)});
}
return objects;
} }
private static org.hl7.fhir.utilities.json.model.JsonObject manifest; private final TxTestSetup setup;
private static org.hl7.fhir.utilities.json.model.JsonObject externals; private final String version;
private JsonObjectPair setup; private final String name;
private String version;
private String name;
private static ValidationEngine baseEngine; private static ValidationEngine baseEngine;
public TerminologyServiceTests(String name, JsonObjectPair setup) { public TerminologyServiceTests(String name, TxTestSetup setup) {
this.name = name; this.name = name;
this.setup = setup; this.setup = setup;
version = "5.0.0"; version = "5.0.0";
@ -128,7 +84,7 @@ public class TerminologyServiceTests {
baseEngine = TestUtilities.getValidationEngineNoTxServer("hl7.fhir.r5.core#5.0.0", FhirPublication.R5, "5.0.0"); baseEngine = TestUtilities.getValidationEngineNoTxServer("hl7.fhir.r5.core#5.0.0", FhirPublication.R5, "5.0.0");
} }
ValidationEngine engine = new ValidationEngine(this.baseEngine); ValidationEngine engine = new ValidationEngine(this.baseEngine);
for (String s : setup.suite.forceArray("setup").asStrings()) { for (String s : setup.getSuite().forceArray("setup").asStrings()) {
// System.out.println(s); // System.out.println(s);
Resource res = loadResource(s); Resource res = loadResource(s);
engine.seeResource(res); engine.seeResource(res);
@ -137,27 +93,29 @@ public class TerminologyServiceTests {
return; return;
} }
Resource req = loadResource(setup.test.asString("request")); Resource req = loadResource(setup.test.asString("request"));
String fn = setup.test.has("response:tx.fhir.org") ? setup.test.asString("response:tx.fhir.org") : setup.test.asString("response"); String fn = setup.getTest().has("response:tx.fhir.org") ? setup.getTest().asString("response:tx.fhir.org") : setup.getTest().asString("response");
String resp = TestingUtilities.loadTestResource("tx", fn); String resp = TestingUtilities.loadTestResource("tx", fn);
String fp = Utilities.path("[tmp]", "tx", fn); String fp = Utilities.path("[tmp]", "tx", fn);
JsonObject ext = externals == null ? null : externals.getJsonObject(fn); JsonObject ext = testData.getExternals() == null ? null : testData.getExternals().getJsonObject(fn);
File fo = ManagedFileAccess.file(fp); File fo = ManagedFileAccess.file(fp);
if (fo.exists()) { if (fo.exists()) {
fo.delete(); fo.delete();
} }
if (setup.test.has("profile")) { if (setup.getTest().has("profile")) {
engine.getContext().setExpansionParameters((org.hl7.fhir.r5.model.Parameters) loadResource(setup.test.asString("profile"))); engine.getContext().setExpansionParameters((org.hl7.fhir.r5.model.Parameters) loadResource(setup.getTest().asString("profile")));
} else { } else {
engine.getContext().setExpansionParameters((org.hl7.fhir.r5.model.Parameters) loadResource("parameters-default.json")); engine.getContext().setExpansionParameters((org.hl7.fhir.r5.model.Parameters) loadResource("parameters-default.json"));
} }
if (setup.test.asString("operation").equals("expand")) { if (setup.getTest().asString("operation").equals("expand")) {
expand(setup.test.str("name"), engine, req, resp, setup.test.asString("Content-Language"), fp, ext); expand(setup.getTest().str("name"), engine, req, resp, setup.getTest().asString("Content-Language"), fp, ext);
} else if (setup.test.asString("operation").equals("validate-code")) { } else if (setup.getTest().asString("operation").equals("validate-code")) {
validate(setup.test.str("name"), engine, setup.test.asString("name"), req, resp, setup.test.asString("Content-Language"), fp, ext, false); String diff = TxServiceTestHelper.getDiffForValidation(setup.getTest().str("name"), engine.getContext(), setup.getTest().asString("name"), req, resp, setup.getTest().asString("Content-Language"), fp, ext, false);
} else if (setup.test.asString("operation").equals("cs-validate-code")) { assertNull(diff, diff);
validate(setup.test.str("name"), engine, setup.test.asString("name"), req, resp, setup.test.asString("Content-Language"), fp, ext, true); } else if (setup.getTest().asString("operation").equals("cs-validate-code")) {
String diff = TxServiceTestHelper.getDiffForValidation(setup.getTest().str("name"), engine.getContext(), setup.getTest().asString("name"), req, resp, setup.getTest().asString("Content-Language"), fp, ext, true);
assertNull(diff, diff);
} else { } else {
Assertions.fail("Unknown Operation "+setup.test.asString("operation")); Assertions.fail("Unknown Operation "+ setup.getTest().asString("operation"));
} }
} }
@ -247,167 +205,7 @@ public class TerminologyServiceTests {
} }
} }
private void validate(String id, ValidationEngine engine, String name, Resource req, String resp, String lang, String fp, JsonObject ext, boolean isCS) throws JsonSyntaxException, FileNotFoundException, IOException {
org.hl7.fhir.r5.model.Parameters p = (org.hl7.fhir.r5.model.Parameters) req;
ValueSet vs = null;
String vsurl = null;
if (!isCS) {
if (p.hasParameter("valueSetVersion")) {
vsurl = p.getParameterValue("url").primitiveValue()+"|"+p.getParameterValue("valueSetVersion").primitiveValue();
vs = engine.getContext().fetchResource(ValueSet.class, p.getParameterValue("url").primitiveValue(), p.getParameterValue("valueSetVersion").primitiveValue());
} else {
vsurl = p.getParameterValue("url").primitiveValue();
vs = engine.getContext().fetchResource(ValueSet.class, p.getParameterValue("url").primitiveValue());
}
}
ValidationResult vm = null;
String code = null;
String system = null;
String version = null;
String display = null;
CodeableConcept cc = null;
org.hl7.fhir.r5.model.Parameters res = null;
OperationOutcome oo = null;
if (vs == null && vsurl != null) {
String msg = engine.getContext().formatMessage(I18nConstants.UNABLE_TO_RESOLVE_VALUE_SET_, vsurl);
oo = new OperationOutcome();
CodeableConcept cct = oo.addIssue().setSeverity(IssueSeverity.ERROR).setCode(IssueType.NOTFOUND).getDetails();
cct.addCoding("http://hl7.org/fhir/tools/CodeSystem/tx-issue-type", "not-found", null);
cct.setText(msg);
} else {
ValidationOptions options = new ValidationOptions(FhirPublication.R5);
if (p.hasParameter("displayLanguage")) {
options = options.withLanguage(p.getParameterString("displayLanguage"));
} else if (lang != null ) {
options = options.withLanguage(lang);
}
if (p.hasParameter("valueset-membership-only") && "true".equals(p.getParameterString("valueset-membership-only"))) {
options = options.withCheckValueSetOnly();
}
if (p.hasParameter("lenient-display-validation") && "true".equals(p.getParameterString("lenient-display-validation"))) {
options = options.setDisplayWarningMode(true);
}
if (p.hasParameter("activeOnly") && "true".equals(p.getParameterString("activeOnly"))) {
options = options.setActiveOnly(true);
}
engine.getContext().getExpansionParameters().clearParameters("includeAlternateCodes");
for (ParametersParameterComponent pp : p.getParameter()) {
if ("includeAlternateCodes".equals(pp.getName())) {
engine.getContext().getExpansionParameters().addParameter(pp.copy());
}
}
if (p.hasParameter("code")) {
code = p.getParameterString("code");
system = p.getParameterString(isCS ? "url" : "system");
version = p.getParameterString(isCS ? "version" : "systemVersion");
display = p.getParameterString("display");
vm = engine.getContext().validateCode(options.withGuessSystem(),
p.getParameterString(isCS ? "url" : "system"), p.getParameterString(isCS ? "version" : "systemVersion"),
p.getParameterString("code"), p.getParameterString("display"), vs);
} else if (p.hasParameter("coding")) {
Coding coding = (Coding) p.getParameterValue("coding");
code = coding.getCode();
system = coding.getSystem();
version = coding.getVersion();
display = coding.getDisplay();
vm = engine.getContext().validateCode(options, coding, vs);
} else if (p.hasParameter("codeableConcept")) {
cc = (CodeableConcept) p.getParameterValue("codeableConcept");
vm = engine.getContext().validateCode(options, cc, vs);
} else {
throw new Error("validate not done yet for this steup");
}
}
if (oo == null && vm != null && vm.getSeverity() == org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity.FATAL) {
oo = new OperationOutcome();
oo.getIssue().addAll(vm.getIssues());
}
if (oo != null) {
TxTesterSorters.sortOperationOutcome(oo);
TxTesterScrubbers.scrubOO(oo, false);
String pj = new JsonParser().setOutputStyle(OutputStyle.PRETTY).composeString(oo);
String diff = CompareUtilities.checkJsonSrcIsSame(id, resp, pj, ext);
if (diff != null) {
Utilities.createDirectory(Utilities.getDirectoryForFile(fp));
TextFile.stringToFile(pj, fp);
System.out.println("Test "+name+"failed: "+diff);
}
Assertions.assertTrue(diff == null, diff);
} else {
if (res == null) {
res = new org.hl7.fhir.r5.model.Parameters();
if (vm.getSystem() != null) {
res.addParameter("system", new UriType(vm.getSystem()));
} else if (system != null) {
res.addParameter("system", new UriType(system));
}
if (vm.getCode() != null) {
if (code != null && !code.equals(vm.getCode())) {
res.addParameter("code", new CodeType(code));
res.addParameter("normalized-code", new CodeType(vm.getCode()));
} else {
res.addParameter("code", new CodeType(vm.getCode()));
}
} else if (code != null) {
res.addParameter("code", new CodeType(code));
}
if (vm.getSeverity() == org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity.ERROR) {
res.addParameter("result", false);
} else {
res.addParameter("result", true);
}
if (vm.getMessage() != null) {
res.addParameter("message", vm.getMessage());
}
if (vm.getVersion() != null) {
res.addParameter("version", vm.getVersion());
} else if (version != null) {
res.addParameter("version", new StringType(version));
}
if (vm.getDisplay() != null) {
res.addParameter("display", vm.getDisplay());
} else if (display != null) {
res.addParameter("display", new StringType(display));
}
// if (vm.getCodeableConcept() != null) {
// res.addParameter("codeableConcept", vm.getCodeableConcept());
// } else
if (cc != null) {
res.addParameter("codeableConcept", cc);
}
if (vm.isInactive()) {
res.addParameter("inactive", true);
}
if (vm.getStatus() != null) {
res.addParameter("status", vm.getStatus());
}
if (vm.getUnknownSystems() != null) {
for (String s : vm.getUnknownSystems()) {
res.addParameter(vm.getErrorClass() == TerminologyServiceErrorClass.CODESYSTEM_UNSUPPORTED ? "x-caused-by-unknown-system" : "x-unknown-system", new CanonicalType(s));
}
}
if (vm.getIssues().size() > 0) {
oo = new OperationOutcome();
oo.getIssue().addAll(vm.getIssues());
res.addParameter().setName("issues").setResource(oo);
}
}
TxTesterSorters.sortParameters(res);
TxTesterScrubbers.scrubParams(res);
String pj = new JsonParser().setOutputStyle(OutputStyle.PRETTY).composeString(res);
String diff = CompareUtilities.checkJsonSrcIsSame(id, resp, pj, ext);
if (diff != null) {
Utilities.createDirectory(Utilities.getDirectoryForFile(fp));
TextFile.stringToFile(pj, fp);
System.out.println("Test "+name+"failed: "+diff);
}
Assertions.assertTrue(diff == null, diff);
}
}
public Resource loadResource(String filename) throws IOException, FHIRFormatError, FileNotFoundException, FHIRException, DefinitionException { public Resource loadResource(String filename) throws IOException, FHIRFormatError, FileNotFoundException, FHIRException, DefinitionException {
String contents = TestingUtilities.loadTestResource("tx", filename); String contents = TestingUtilities.loadTestResource("tx", filename);