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WIP refactor terminology service tests for reuse outside core

This commit is contained in:
dotasek.dev 2024-03-19 17:53:45 -04:00
parent b2e3c261e4
commit 82c36de65d
2 changed files with 267 additions and 213 deletions
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239
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/special/TxServiceTestHelper.java Normal file
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@ -0,0 +1,239 @@
package org.hl7.fhir.validation.special;
import com.google.gson.JsonSyntaxException;
import lombok.Getter;
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.r5.test.utils.TestingUtilities;
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.FileNotFoundException;
import java.io.IOException;
import java.util.*;
public class TxServiceTestHelper {
public static class TestSetup {
public TestSetup(JsonObject suite, JsonObject test) {
this.suite = suite;
this.test = test;
}
@Getter
private JsonObject suite;
@Getter
private JsonObject test;
}
public static class TestData {
@Getter
private final JsonObject manifest;
@Getter
private final JsonObject externals;
@Getter
private final List<Object[]> testData;
public TestData() throws IOException {
String contents = TestingUtilities.loadTestResource("tx", "test-cases.json");
String externalSource = TestingUtilities.loadTestResource("tx", "messages-tx.fhir.org.json");
externals = org.hl7.fhir.utilities.json.parser.JsonParser.parseObject(externalSource);
Map<String, TestSetup> examples = new HashMap<String, TestSetup>();
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 TestSetup(suite, test));
}
}
}
List<String> names = new ArrayList<String>(examples.size());
names.addAll(examples.keySet());
Collections.sort(names);
testData = new ArrayList<Object[]>(examples.size());
for (String id : names) {
testData.add(new Object[]{id, examples.get(id)});
}
}
}
public static String getDiffForValidation(IWorkerContext context, 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 = context.fetchResource(ValueSet.class, p.getParameterValue("url").primitiveValue(), p.getParameterValue("valueSetVersion").primitiveValue());
} else {
vsurl = p.getParameterValue("url").primitiveValue();
vs = context.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 = context.formatMessage(I18nConstants.UNABLE_TO_RESOLVE_VALUE_SET_, vsurl);
oo = new OperationOutcome();
CodeableConcept cct = oo.addIssue().setSeverity(OperationOutcome.IssueSeverity.ERROR).setCode(OperationOutcome.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);
}
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(isCS ? "url" : "system");
version = p.getParameterString(isCS ? "version" : "systemVersion");
display = p.getParameterString("display");
vm = context.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 = context.validateCode(options, coding, vs);
} else if (p.hasParameter("codeableConcept")) {
cc = (CodeableConcept) p.getParameterValue("codeableConcept");
vm = context.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(IParser.OutputStyle.PRETTY).composeString(oo);
String diff = CompareUtilities.checkJsonSrcIsSame(resp, pj, ext);
if (diff != null) {
Utilities.createDirectory(Utilities.getDirectoryForFile(fp));
TextFile.stringToFile(pj, fp);
System.out.println("Test "+name+"failed: "+diff);
}
return 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(IParser.OutputStyle.PRETTY).composeString(res);
String diff = CompareUtilities.checkJsonSrcIsSame(resp, pj, ext);
if (diff != null) {
Utilities.createDirectory(Utilities.getDirectoryForFile(fp));
TextFile.stringToFile(pj, fp);
System.out.println("Test "+name+"failed: "+diff);
}
return diff;
}
}
}

241
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/terminology/tests/TerminologyServiceTests.java
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@ -48,6 +48,8 @@ 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.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.TxServiceTestHelper.TestSetup;
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;
@ -61,60 +63,31 @@ import org.junit.runners.Parameterized.Parameters;
import com.google.common.base.Charsets; import com.google.common.base.Charsets;
import com.google.gson.JsonSyntaxException; import com.google.gson.JsonSyntaxException;
import org.hl7.fhir.r5.context.IWorkerContext;
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 TxServiceTestHelper.TestData 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 = new TxServiceTestHelper.TestData();
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()); private final TestSetup setup;
names.addAll(examples.keySet()); private final String version;
Collections.sort(names); private final String name;
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 static org.hl7.fhir.utilities.json.model.JsonObject externals;
private JsonObjectPair setup;
private String version;
private String name;
private static ValidationEngine baseEngine; private static ValidationEngine baseEngine;
public TerminologyServiceTests(String name, JsonObjectPair setup) { public TerminologyServiceTests(String name, TestSetup setup) {
this.name = name; this.name = name;
this.setup = setup; this.setup = setup;
version = "5.0.0"; version = "5.0.0";
@ -127,33 +100,35 @@ 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);
} }
Resource req = loadResource(setup.test.asString("request")); Resource req = loadResource(setup.getTest().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 = new File(fp); File fo = new 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(engine, req, resp, setup.test.asString("Content-Language"), fp, ext); expand(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(engine, setup.test.asString("name"), req, resp, setup.test.asString("Content-Language"), fp, ext, false); String diff = TxServiceTestHelper.getDiffForValidation(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(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(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"));
} }
} }
@ -243,167 +218,7 @@ public class TerminologyServiceTests {
} }
} }
private void validate(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(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(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);