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Merge pull request #1614 from Boereck/fix/canonical_split_base_validator 

Fix/canonical split base validator
This commit is contained in:
Grahame Grieve 2024-05-09 22:48:30 +00:00 committed by GitHub
parent 743b2fb33f be0d718ac7
commit 4b32505953
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5 changed files with 184 additions and 26 deletions
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66
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/CanonicalPair.java
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@ -1,26 +1,82 @@
package org.hl7.fhir.utilities;
import org.apache.commons.lang3.StringUtils;
/**
* Abstraction that splits a canonical in form of {@code <url>|<version>} into a URL and a version part.
*/
public class CanonicalPair {
private String url;
private String version;
private final String url;
private final String version;
/**
* Static factory method, that invokes the {@link CanonicalPair#CanonicalPair(String) CanonicalPair constructor}
* with the given argument.
* @param target the canonical to be split. May be {@code null}.
* @return new instance of CanonicalPair
*/
public static CanonicalPair of(String target) {
return new CanonicalPair(target);
}
/**
* Wraps the given canonical and if needed splits off the version part.<p>
* The given parameter {@code target} is expected to be a canonical.
* @param target canonical to create a url, version pair from. May be {@code null}.
*/
public CanonicalPair(String target) {
if (target != null && target.contains("|")) {
this.url = target.substring(0, target.indexOf("|"));
this.version = target.substring(target.indexOf("|")+1);
int pipeIndex = target != null ? target.indexOf('|') : -1;
if (pipeIndex >= 0) {
this.url = target.substring(0, pipeIndex);
this.version = target.substring(pipeIndex+1);
} else {
this.url = target;
this.version = null;
}
}
/**
* Returns the URL part of the canonical (everything before the {@code "|"} character, or the complete
* canonical if the character is not present). If the source
* @return URL part of the source canonical. May be {@code null}, if source canonical was {@code null}
*/
public String getUrl() {
return url;
}
/**
* Returns the version part of the source canonical (everything after the {@code "|"} character.
* @return version part of the canonical, may be {@code null}, if canonical was {@code null}, or canonical contains no
* {@code "|"} character.
*/
public String getVersion() {
return version;
}
/**
* Determines if the version part of the canonical is not {@code null}
* @return {@code true} if version is not {@code null}, otherwise {@code false}
*/
public boolean hasVersion() {
return version != null;
}
/**
* Returns the version of this pair, or the parameter {@code alternative},
* if the version of this pair is {@code null}.
* @param alternative to be returned from this method if the encapsulated version is {@code null}.
* @return either the held version, or {@code alternative}, if version is {@code null}
*/
public String getVersionOr(String alternative) {
return hasVersion() ? version : alternative;
}
/**
* Determines if the encapsulated version of this pair is not {@code null} and not an empty string.
* @return {@code true} if the version of this pair is not {@code null} and not an empty string, {@code false} otherwise
*/
public boolean hasNonEmptyVersion() {
return StringUtils.isNotEmpty(version);
}
}

90
org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/CanonicalPairTest.java Normal file
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@ -0,0 +1,90 @@
package org.hl7.fhir.utilities;
import static org.junit.jupiter.api.Assertions.*;
import org.junit.jupiter.api.Test;
class CanonicalPairTest {
@Test
void testCanonicalNull() {
var canonical = new CanonicalPair(null);
assertNull(canonical.getUrl());
assertNull(canonical.getVersion());
assertFalse(canonical.hasVersion());
assertFalse(canonical.hasNonEmptyVersion());
String expectedVer = "1.0";
String actualVer = canonical.getVersionOr(expectedVer);
assertEquals(expectedVer, actualVer);
}
@Test
void testCanonicalEmpty() {
var url = "";
var canonical = new CanonicalPair(url);
assertEquals(url, canonical.getUrl());
assertFalse(canonical.hasVersion());
assertFalse(canonical.hasNonEmptyVersion());
String expectedVer = "1.0";
String actualVer = canonical.getVersionOr(expectedVer);
assertEquals(expectedVer, actualVer);
}
@Test
void testCanonicalWithoutVersion() {
var url = "https://www.test.org";
var canonical = new CanonicalPair(url);
assertEquals(url, canonical.getUrl());
assertNull(canonical.getVersion());
assertFalse(canonical.hasVersion());
assertFalse(canonical.hasNonEmptyVersion());
String expectedVer = "1.0";
String actualVer = canonical.getVersionOr(expectedVer);
assertEquals(expectedVer, actualVer);
}
@Test
void testCanonicalWithEmptyVersion() {
var expectedUrl = "https://www.test.org";
var url = expectedUrl + "|";
var canonical = new CanonicalPair(url);
assertEquals(expectedUrl, canonical.getUrl());
assertEquals("", canonical.getVersion());
assertTrue(canonical.hasVersion());
assertFalse(canonical.hasNonEmptyVersion());
String alternativeVer = "1.0";
String actualVer = canonical.getVersionOr(alternativeVer);
assertEquals("", actualVer);
}
@Test
void testCanonicalWithVersion() {
var expectedUrl = "https://www.test.org";
var expectedVersion = "2.6";
var url = expectedUrl + "|" + expectedVersion;
var canonical = new CanonicalPair(url);
assertEquals(expectedUrl, canonical.getUrl());
assertEquals(expectedVersion, canonical.getVersion());
assertTrue(canonical.hasVersion());
assertTrue(canonical.hasNonEmptyVersion());
String alternativeVer = "1.0";
String actualVer = canonical.getVersionOr(alternativeVer);
assertEquals(expectedVersion, actualVer);
}
@Test
void testCanonicalWithVersionIncludingPipe() {
var expectedUrl = "https://www.test.org";
var expectedVersion = "2024|05";
var url = expectedUrl + "|" + expectedVersion;
var canonical = new CanonicalPair(url);
assertEquals(expectedUrl, canonical.getUrl());
assertEquals(expectedVersion, canonical.getVersion());
assertTrue(canonical.hasVersion());
assertTrue(canonical.hasNonEmptyVersion());
String alternativeVer = "1.0";
String actualVer = canonical.getVersionOr(alternativeVer);
assertEquals(expectedVersion, actualVer);
}
}

18
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/BaseValidator.java
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@ -1428,25 +1428,7 @@ public class BaseValidator implements IValidationContextResourceLoader {
return null;
}
protected String versionFromCanonical(String system) {
if (system == null) {
return null;
} else if (system.contains("|")) {
return system.substring(0, system.indexOf("|"));
} else {
return system;
}
}
protected String systemFromCanonical(String system) {
if (system == null) {
return null;
} else if (system.contains("|")) {
return system.substring(system.indexOf("|")+1);
} else {
return system;
}
}
@Override
public Resource loadContainedResource(List<ValidationMessage> errors, String path, Element resource, String id, Class<? extends Resource> class1) throws FHIRException {

4
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/CodeSystemValidator.java
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@ -13,6 +13,7 @@ import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.terminologies.CodeSystemUtilities;
import org.hl7.fhir.utilities.CanonicalPair;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.i18n.I18nConstants;
@ -620,7 +621,8 @@ public class CodeSystemValidator extends BaseValidator {
private boolean validateSupplementConcept(List<ValidationMessage> errors, Element concept, NodeStack stack, String supp, ValidationOptions options) {
String code = concept.getChildValue("code");
if (!Utilities.noString(code)) {
org.hl7.fhir.r5.terminologies.utilities.ValidationResult res = context.validateCode(options, systemFromCanonical(supp), versionFromCanonical(supp), code, null);
var canonical = new CanonicalPair(supp);
org.hl7.fhir.r5.terminologies.utilities.ValidationResult res = context.validateCode(options, canonical.getUrl(), canonical.getVersion(), code, null);
return rule(errors, NO_RULE_DATE, IssueType.BUSINESSRULE, stack.getLiteralPath(), res.isOk(), I18nConstants.CODESYSTEM_CS_SUPP_INVALID_CODE, supp, code);
} else {
return true;

30
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/ResourceValidationTests.java
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@ -1,5 +1,9 @@
package org.hl7.fhir.validation;
import static org.hamcrest.Matchers.is;
import static org.hamcrest.Matchers.empty;
import static org.hamcrest.MatcherAssert.assertThat;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.ArrayList;
@ -10,6 +14,7 @@ import org.hl7.fhir.r5.formats.XmlParser;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.utilities.FhirPublication;
import org.hl7.fhir.utilities.i18n.I18nConstants;
import org.hl7.fhir.utilities.settings.FhirSettings;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.validation.instance.InstanceValidator;
@ -25,7 +30,7 @@ public class ResourceValidationTests {
private static InstanceValidator val;
private void runTest(String filename) throws IOException, FileNotFoundException, Exception {
private List<ValidationMessage> runTest(String filename) throws IOException, FileNotFoundException, Exception {
TestingUtilities.injectCorePackageLoader();
if (val == null) {
ctxt = TestingUtilities.getSharedWorkerContext();
@ -37,6 +42,7 @@ public class ResourceValidationTests {
Resource res = (Resource) new XmlParser().parse(TestingUtilities.loadTestResourceStream("r5", filename));
val.validate(val, errors, res);
Assertions.assertNotNull(errors);
return errors;
}
@ -123,4 +129,26 @@ public class ResourceValidationTests {
}
@Test
public void testCodesystemSupplementsVersion() throws Exception {
List<ValidationMessage> errors = runTest("codesystem-example-supplement-version.xml");
assertNoErrors(errors);
}
private void assertNoErrors(List<ValidationMessage> errors) {
List<String> errorMessages = new ArrayList<>();
for(ValidationMessage message : errors) {
// we will skip the message that WG citation is needed
if(I18nConstants.VALIDATION_HL7_WG_NEEDED.equals(message.getMessageId())) {
continue;
}
if(message.getLevel().isError()) {
errorMessages.add(message.getMessage());
}
}
assertThat("No error message expected in validation outcome.", errorMessages, is(empty()));
}
}