WIP refactor terminology service tests for reuse outside core
This commit is contained in:
dotasek.dev
parent
b2e3c261e4
commit
82c36de65d
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@ -0,0 +1,239 @@
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package org.hl7.fhir.validation.special;
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import com.google.gson.JsonSyntaxException;
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import lombok.Getter;
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import org.hl7.fhir.r5.formats.JsonParser;
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import org.hl7.fhir.r5.context.IWorkerContext;
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import org.hl7.fhir.r5.formats.IParser;
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import org.hl7.fhir.r5.model.*;
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import org.hl7.fhir.r5.terminologies.utilities.TerminologyServiceErrorClass;
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import org.hl7.fhir.r5.terminologies.utilities.ValidationResult;
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import org.hl7.fhir.r5.test.utils.CompareUtilities;
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import org.hl7.fhir.r5.test.utils.TestingUtilities;
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import org.hl7.fhir.utilities.FhirPublication;
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import org.hl7.fhir.utilities.TextFile;
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import org.hl7.fhir.utilities.Utilities;
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import org.hl7.fhir.utilities.i18n.I18nConstants;
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import org.hl7.fhir.utilities.json.model.JsonObject;
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import org.hl7.fhir.utilities.validation.ValidationOptions;
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import java.io.FileNotFoundException;
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import java.io.IOException;
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import java.util.*;
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public class TxServiceTestHelper {
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public static class TestSetup {
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public TestSetup(JsonObject suite, JsonObject test) {
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this.suite = suite;
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this.test = test;
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}
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@Getter
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private JsonObject suite;
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@Getter
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private JsonObject test;
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}
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public static class TestData {
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@Getter
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private final JsonObject manifest;
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@Getter
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private final JsonObject externals;
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@Getter
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private final List<Object[]> testData;
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public TestData() throws IOException {
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String contents = TestingUtilities.loadTestResource("tx", "test-cases.json");
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String externalSource = TestingUtilities.loadTestResource("tx", "messages-tx.fhir.org.json");
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externals = org.hl7.fhir.utilities.json.parser.JsonParser.parseObject(externalSource);
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Map<String, TestSetup> examples = new HashMap<String, TestSetup>();
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manifest = org.hl7.fhir.utilities.json.parser.JsonParser.parseObject(contents);
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for (org.hl7.fhir.utilities.json.model.JsonObject suite : manifest.getJsonObjects("suites")) {
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if (!"tx.fhir.org".equals(suite.asString("mode"))) {
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String sn = suite.asString("name");
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for (org.hl7.fhir.utilities.json.model.JsonObject test : suite.getJsonObjects("tests")) {
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String tn = test.asString("name");
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examples.put(sn+"."+tn, new TestSetup(suite, test));
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}
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}
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}
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List<String> names = new ArrayList<String>(examples.size());
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names.addAll(examples.keySet());
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Collections.sort(names);
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testData = new ArrayList<Object[]>(examples.size());
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for (String id : names) {
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testData.add(new Object[]{id, examples.get(id)});
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}
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}
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}
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public static String getDiffForValidation(IWorkerContext context, String name, Resource req, String resp, String lang, String fp, JsonObject ext, boolean isCS) throws JsonSyntaxException, FileNotFoundException, IOException {
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org.hl7.fhir.r5.model.Parameters p = (org.hl7.fhir.r5.model.Parameters) req;
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ValueSet vs = null;
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String vsurl = null;
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if (!isCS) {
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if (p.hasParameter("valueSetVersion")) {
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vsurl = p.getParameterValue("url").primitiveValue()+"|"+p.getParameterValue("valueSetVersion").primitiveValue();
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vs = context.fetchResource(ValueSet.class, p.getParameterValue("url").primitiveValue(), p.getParameterValue("valueSetVersion").primitiveValue());
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} else {
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vsurl = p.getParameterValue("url").primitiveValue();
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vs = context.fetchResource(ValueSet.class, p.getParameterValue("url").primitiveValue());
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}
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}
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ValidationResult vm = null;
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String code = null;
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String system = null;
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String version = null;
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String display = null;
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CodeableConcept cc = null;
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org.hl7.fhir.r5.model.Parameters res = null;
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OperationOutcome oo = null;
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if (vs == null && vsurl != null) {
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String msg = context.formatMessage(I18nConstants.UNABLE_TO_RESOLVE_VALUE_SET_, vsurl);
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oo = new OperationOutcome();
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CodeableConcept cct = oo.addIssue().setSeverity(OperationOutcome.IssueSeverity.ERROR).setCode(OperationOutcome.IssueType.NOTFOUND).getDetails();
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cct.addCoding("http://hl7.org/fhir/tools/CodeSystem/tx-issue-type", "not-found", null);
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cct.setText(msg);
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} else {
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ValidationOptions options = new ValidationOptions(FhirPublication.R5);
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if (p.hasParameter("displayLanguage")) {
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options = options.withLanguage(p.getParameterString("displayLanguage"));
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} else if (lang != null ) {
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options = options.withLanguage(lang);
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}
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if (p.hasParameter("valueset-membership-only") && "true".equals(p.getParameterString("valueset-membership-only"))) {
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options = options.withCheckValueSetOnly();
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}
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if (p.hasParameter("lenient-display-validation") && "true".equals(p.getParameterString("lenient-display-validation"))) {
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options = options.setDisplayWarningMode(true);
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}
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if (p.hasParameter("activeOnly") && "true".equals(p.getParameterString("activeOnly"))) {
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options = options.setActiveOnly(true);
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}
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context.getExpansionParameters().clearParameters("includeAlternateCodes");
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for (Parameters.ParametersParameterComponent pp : p.getParameter()) {
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if ("includeAlternateCodes".equals(pp.getName())) {
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context.getExpansionParameters().addParameter(pp.copy());
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}
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}
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if (p.hasParameter("code")) {
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code = p.getParameterString("code");
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system = p.getParameterString(isCS ? "url" : "system");
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version = p.getParameterString(isCS ? "version" : "systemVersion");
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display = p.getParameterString("display");
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vm = context.validateCode(options.withGuessSystem(),
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p.getParameterString(isCS ? "url" : "system"), p.getParameterString(isCS ? "version" : "systemVersion"),
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p.getParameterString("code"), p.getParameterString("display"), vs);
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} else if (p.hasParameter("coding")) {
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Coding coding = (Coding) p.getParameterValue("coding");
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code = coding.getCode();
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system = coding.getSystem();
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version = coding.getVersion();
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display = coding.getDisplay();
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vm = context.validateCode(options, coding, vs);
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} else if (p.hasParameter("codeableConcept")) {
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cc = (CodeableConcept) p.getParameterValue("codeableConcept");
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vm = context.validateCode(options, cc, vs);
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} else {
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throw new Error("validate not done yet for this steup");
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}
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}
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if (oo == null && vm != null && vm.getSeverity() == org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity.FATAL) {
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oo = new OperationOutcome();
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oo.getIssue().addAll(vm.getIssues());
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}
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if (oo != null) {
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TxTesterSorters.sortOperationOutcome(oo);
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TxTesterScrubbers.scrubOO(oo, false);
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String pj = new JsonParser().setOutputStyle(IParser.OutputStyle.PRETTY).composeString(oo);
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String diff = CompareUtilities.checkJsonSrcIsSame(resp, pj, ext);
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if (diff != null) {
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Utilities.createDirectory(Utilities.getDirectoryForFile(fp));
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TextFile.stringToFile(pj, fp);
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System.out.println("Test "+name+"failed: "+diff);
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}
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return diff;
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} else {
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if (res == null) {
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res = new org.hl7.fhir.r5.model.Parameters();
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if (vm.getSystem() != null) {
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res.addParameter("system", new UriType(vm.getSystem()));
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} else if (system != null) {
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res.addParameter("system", new UriType(system));
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}
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if (vm.getCode() != null) {
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if (code != null && !code.equals(vm.getCode())) {
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res.addParameter("code", new CodeType(code));
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res.addParameter("normalized-code", new CodeType(vm.getCode()));
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} else {
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res.addParameter("code", new CodeType(vm.getCode()));
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}
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} else if (code != null) {
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res.addParameter("code", new CodeType(code));
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}
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if (vm.getSeverity() == org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity.ERROR) {
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res.addParameter("result", false);
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} else {
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res.addParameter("result", true);
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}
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if (vm.getMessage() != null) {
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res.addParameter("message", vm.getMessage());
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}
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if (vm.getVersion() != null) {
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res.addParameter("version", vm.getVersion());
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} else if (version != null) {
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res.addParameter("version", new StringType(version));
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}
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if (vm.getDisplay() != null) {
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res.addParameter("display", vm.getDisplay());
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} else if (display != null) {
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res.addParameter("display", new StringType(display));
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}
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// if (vm.getCodeableConcept() != null) {
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// res.addParameter("codeableConcept", vm.getCodeableConcept());
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// } else
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if (cc != null) {
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res.addParameter("codeableConcept", cc);
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}
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if (vm.isInactive()) {
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res.addParameter("inactive", true);
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}
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if (vm.getStatus() != null) {
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res.addParameter("status", vm.getStatus());
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}
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if (vm.getUnknownSystems() != null) {
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for (String s : vm.getUnknownSystems()) {
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res.addParameter(vm.getErrorClass() == TerminologyServiceErrorClass.CODESYSTEM_UNSUPPORTED ? "x-caused-by-unknown-system" : "x-unknown-system", new CanonicalType(s));
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}
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}
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if (vm.getIssues().size() > 0) {
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oo = new OperationOutcome();
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oo.getIssue().addAll(vm.getIssues());
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res.addParameter().setName("issues").setResource(oo);
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}
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}
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TxTesterSorters.sortParameters(res);
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TxTesterScrubbers.scrubParams(res);
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String pj = new JsonParser().setOutputStyle(IParser.OutputStyle.PRETTY).composeString(res);
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String diff = CompareUtilities.checkJsonSrcIsSame(resp, pj, ext);
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if (diff != null) {
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Utilities.createDirectory(Utilities.getDirectoryForFile(fp));
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TextFile.stringToFile(pj, fp);
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System.out.println("Test "+name+"failed: "+diff);
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}
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return diff;
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}
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}
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}
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@ -48,6 +48,8 @@ import org.hl7.fhir.utilities.i18n.I18nConstants;
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import org.hl7.fhir.utilities.json.model.JsonObject;
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import org.hl7.fhir.utilities.validation.ValidationOptions;
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import org.hl7.fhir.validation.ValidationEngine;
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import org.hl7.fhir.validation.special.TxServiceTestHelper;
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import org.hl7.fhir.validation.special.TxServiceTestHelper.TestSetup;
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import org.hl7.fhir.validation.special.TxTesterScrubbers;
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import org.hl7.fhir.validation.special.TxTesterSorters;
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import org.hl7.fhir.validation.tests.utilities.TestUtilities;
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@ -61,60 +63,31 @@ import org.junit.runners.Parameterized.Parameters;
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import com.google.common.base.Charsets;
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import com.google.gson.JsonSyntaxException;
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import org.hl7.fhir.r5.context.IWorkerContext;
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import static org.junit.Assert.assertNull;
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@RunWith(Parameterized.class)
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public class TerminologyServiceTests {
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public static class JsonObjectPair {
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public JsonObjectPair(JsonObject suite, JsonObject test) {
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this.suite = suite;
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this.test = test;
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}
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private JsonObject suite;
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private JsonObject test;
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}
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private static TxServiceTestHelper.TestData testData;
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@Parameters(name = "{index}: id {0}")
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public static Iterable<Object[]> data() throws IOException {
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String contents = TestingUtilities.loadTestResource("tx", "test-cases.json");
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String externalSource = TestingUtilities.loadTestResource("tx", "messages-tx.fhir.org.json");
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externals = org.hl7.fhir.utilities.json.parser.JsonParser.parseObject(externalSource);
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Map<String, JsonObjectPair> examples = new HashMap<String, JsonObjectPair>();
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manifest = org.hl7.fhir.utilities.json.parser.JsonParser.parseObject(contents);
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for (org.hl7.fhir.utilities.json.model.JsonObject suite : manifest.getJsonObjects("suites")) {
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if (!"tx.fhir.org".equals(suite.asString("mode"))) {
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String sn = suite.asString("name");
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for (org.hl7.fhir.utilities.json.model.JsonObject test : suite.getJsonObjects("tests")) {
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String tn = test.asString("name");
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examples.put(sn+"."+tn, new JsonObjectPair(suite, test));
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}
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}
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}
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List<String> names = new ArrayList<String>(examples.size());
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names.addAll(examples.keySet());
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Collections.sort(names);
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List<Object[]> objects = new ArrayList<Object[]>(examples.size());
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for (String id : names) {
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objects.add(new Object[]{id, examples.get(id)});
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}
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return objects;
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testData = new TxServiceTestHelper.TestData();
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return testData.getTestData();
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}
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private static org.hl7.fhir.utilities.json.model.JsonObject manifest;
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private static org.hl7.fhir.utilities.json.model.JsonObject externals;
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private JsonObjectPair setup;
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private String version;
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private String name;
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private final TestSetup setup;
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private final String version;
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private final String name;
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private static ValidationEngine baseEngine;
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public TerminologyServiceTests(String name, JsonObjectPair setup) {
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public TerminologyServiceTests(String name, TestSetup setup) {
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this.name = name;
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this.setup = setup;
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version = "5.0.0";
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@ -127,33 +100,35 @@ public class TerminologyServiceTests {
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baseEngine = TestUtilities.getValidationEngineNoTxServer("hl7.fhir.r5.core#5.0.0", FhirPublication.R5, "5.0.0");
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}
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ValidationEngine engine = new ValidationEngine(this.baseEngine);
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for (String s : setup.suite.forceArray("setup").asStrings()) {
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for (String s : setup.getSuite().forceArray("setup").asStrings()) {
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// System.out.println(s);
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Resource res = loadResource(s);
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engine.seeResource(res);
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}
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Resource req = loadResource(setup.test.asString("request"));
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String fn = setup.test.has("response:tx.fhir.org") ? setup.test.asString("response:tx.fhir.org") : setup.test.asString("response");
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Resource req = loadResource(setup.getTest().asString("request"));
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String fn = setup.getTest().has("response:tx.fhir.org") ? setup.getTest().asString("response:tx.fhir.org") : setup.getTest().asString("response");
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String resp = TestingUtilities.loadTestResource("tx", fn);
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String fp = Utilities.path("[tmp]", "tx", fn);
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JsonObject ext = externals == null ? null : externals.getJsonObject(fn);
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JsonObject ext = testData.getExternals() == null ? null : testData.getExternals().getJsonObject(fn);
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File fo = new File(fp);
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if (fo.exists()) {
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fo.delete();
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}
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if (setup.test.has("profile")) {
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engine.getContext().setExpansionParameters((org.hl7.fhir.r5.model.Parameters) loadResource(setup.test.asString("profile")));
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if (setup.getTest().has("profile")) {
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engine.getContext().setExpansionParameters((org.hl7.fhir.r5.model.Parameters) loadResource(setup.getTest().asString("profile")));
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} else {
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engine.getContext().setExpansionParameters((org.hl7.fhir.r5.model.Parameters) loadResource("parameters-default.json"));
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}
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if (setup.test.asString("operation").equals("expand")) {
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expand(engine, req, resp, setup.test.asString("Content-Language"), fp, ext);
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} else if (setup.test.asString("operation").equals("validate-code")) {
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validate(engine, setup.test.asString("name"), req, resp, setup.test.asString("Content-Language"), fp, ext, false);
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} else if (setup.test.asString("operation").equals("cs-validate-code")) {
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validate(engine, setup.test.asString("name"), req, resp, setup.test.asString("Content-Language"), fp, ext, true);
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if (setup.getTest().asString("operation").equals("expand")) {
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expand(engine, req, resp, setup.getTest().asString("Content-Language"), fp, ext);
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} else if (setup.getTest().asString("operation").equals("validate-code")) {
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String diff = TxServiceTestHelper.getDiffForValidation(engine.getContext(), setup.getTest().asString("name"), req, resp, setup.getTest().asString("Content-Language"), fp, ext, false);
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assertNull(diff, diff);
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} else if (setup.getTest().asString("operation").equals("cs-validate-code")) {
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String diff = TxServiceTestHelper.getDiffForValidation(engine.getContext(), setup.getTest().asString("name"), req, resp, setup.getTest().asString("Content-Language"), fp, ext, true);
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assertNull(diff, diff);
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} else {
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Assertions.fail("Unknown Operation "+setup.test.asString("operation"));
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Assertions.fail("Unknown Operation "+ setup.getTest().asString("operation"));
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}
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}
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@ -243,167 +218,7 @@ public class TerminologyServiceTests {
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}
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}
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private void validate(ValidationEngine engine, String name, Resource req, String resp, String lang, String fp, JsonObject ext, boolean isCS) throws JsonSyntaxException, FileNotFoundException, IOException {
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org.hl7.fhir.r5.model.Parameters p = (org.hl7.fhir.r5.model.Parameters) req;
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ValueSet vs = null;
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String vsurl = null;
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if (!isCS) {
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if (p.hasParameter("valueSetVersion")) {
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vsurl = p.getParameterValue("url").primitiveValue()+"|"+p.getParameterValue("valueSetVersion").primitiveValue();
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vs = engine.getContext().fetchResource(ValueSet.class, p.getParameterValue("url").primitiveValue(), p.getParameterValue("valueSetVersion").primitiveValue());
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} else {
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vsurl = p.getParameterValue("url").primitiveValue();
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vs = engine.getContext().fetchResource(ValueSet.class, p.getParameterValue("url").primitiveValue());
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}
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}
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ValidationResult vm = null;
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String code = null;
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String system = null;
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String version = null;
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String display = null;
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CodeableConcept cc = null;
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org.hl7.fhir.r5.model.Parameters res = null;
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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 {
|
||||
String contents = TestingUtilities.loadTestResource("tx", filename);
|
||||
|
|
|
|||
Loading…
Reference in New Issue