From 8b338cd168c6da14f86b6b4f8684bb007b3502d6 Mon Sep 17 00:00:00 2001 From: Eric Prud'hommeaux Date: Sun, 17 Jan 2021 01:15:39 +0100 Subject: [PATCH] rework r4 RDF tests to skip fewer examples (#2159) + relative URL resolution in RDFParser + test non-DomainResources in RDFParserTest ~ factor/organize RDFParserTest ~ avoid EXTERNAL shapes (for now) in shex-java - disable the bundle-response.json example as it is apparently malformed + added urn:-guard to PreResourceStateHl7Org.wereBack ID update --- .../java/ca/uhn/fhir/parser/ParserState.java | 10 +- .../java/ca/uhn/fhir/parser/RDFParser.java | 9 +- .../ca/uhn/fhir/parser/RDFParserTest.java | 192 ++++++++++++------ .../rdf-test-input/DISABLED/README.md | 5 + .../{ => DISABLED}/bundle-response.json | 0 .../resources/rdf-validation/fhir-r4.shex | 2 +- 6 files changed, 152 insertions(+), 66 deletions(-) create mode 100644 hapi-fhir-structures-r4/src/test/resources/rdf-test-input/DISABLED/README.md rename hapi-fhir-structures-r4/src/test/resources/rdf-test-input/{ => DISABLED}/bundle-response.json (100%) diff --git a/hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/ParserState.java b/hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/ParserState.java index 392f57f5cc3..650b23365e9 100644 --- a/hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/ParserState.java +++ b/hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/ParserState.java @@ -1260,10 +1260,12 @@ class ParserState { String versionId = elem.getMeta().getVersionId(); if (StringUtils.isBlank(elem.getIdElement().getIdPart())) { // Resource has no ID - } else if (StringUtils.isNotBlank(versionId)) { - elem.getIdElement().setValue(resourceName + "/" + elem.getIdElement().getIdPart() + "/_history/" + versionId); - } else { - elem.getIdElement().setValue(resourceName + "/" + elem.getIdElement().getIdPart()); + } else if (!elem.getIdElement().getIdPart().startsWith("urn:")) { + if (StringUtils.isNotBlank(versionId)) { + elem.getIdElement().setValue(resourceName + "/" + elem.getIdElement().getIdPart() + "/_history/" + versionId); + } else { + elem.getIdElement().setValue(resourceName + "/" + elem.getIdElement().getIdPart()); + } } } } diff --git a/hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/RDFParser.java b/hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/RDFParser.java index 3105339a50d..324e8eb32e5 100644 --- a/hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/RDFParser.java +++ b/hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/RDFParser.java @@ -29,6 +29,7 @@ import org.apache.commons.lang3.StringUtils; import org.apache.jena.datatypes.xsd.XSDDatatype; import org.apache.jena.rdf.model.*; import org.apache.jena.riot.Lang; +import org.apache.jena.riot.system.IRIResolver; import org.apache.jena.vocabulary.RDF; import org.hl7.fhir.instance.model.api.*; @@ -171,10 +172,14 @@ public class RDFParser extends BaseParser { if (!uriBase.endsWith("/")) { uriBase = uriBase + "/"; } - String resourceUri = uriBase + resource.getIdElement().toUnqualified(); if (parentResource == null) { - parentResource = rdfModel.getResource(resourceUri); + if (!resource.getIdElement().toUnqualified().hasIdPart()) { + parentResource = rdfModel.getResource(null); + } else { + String resourceUri = IRIResolver.resolve(resource.getIdElement().toUnqualified().toString(), uriBase).toString(); + parentResource = rdfModel.getResource(resourceUri); + } // If the resource already exists and has statements, return that existing resource. if (parentResource != null && parentResource.listProperties().toList().size() > 0) { return parentResource; diff --git a/hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/RDFParserTest.java b/hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/RDFParserTest.java index 60c32608290..32d6ab8b196 100644 --- a/hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/RDFParserTest.java +++ b/hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/RDFParserTest.java @@ -9,15 +9,14 @@ import fr.inria.lille.shexjava.schema.parsing.GenParser; import fr.inria.lille.shexjava.validation.RecursiveValidation; import fr.inria.lille.shexjava.validation.ValidationAlgorithm; import org.apache.commons.rdf.api.Graph; -import org.apache.commons.rdf.api.IRI; +import org.apache.commons.rdf.api.RDFTerm; import org.apache.commons.rdf.rdf4j.RDF4J; import org.eclipse.rdf4j.model.Model; -import org.eclipse.rdf4j.model.impl.SimpleIRI; import org.eclipse.rdf4j.rio.RDFFormat; import org.eclipse.rdf4j.rio.Rio; import org.hl7.fhir.instance.model.api.IBaseResource; import org.hl7.fhir.r4.model.Base; -import org.hl7.fhir.r4.model.DomainResource; +import org.junit.jupiter.api.AfterAll; import org.junit.jupiter.api.BeforeAll; import org.junit.jupiter.params.ParameterizedTest; import org.junit.jupiter.params.provider.MethodSource; @@ -25,8 +24,10 @@ import org.springframework.core.io.Resource; import org.springframework.core.io.support.PathMatchingResourcePatternResolver; import org.springframework.core.io.support.ResourcePatternResolver; +import java.io.ByteArrayInputStream; import java.io.FileInputStream; import java.io.IOException; +import java.io.InputStream; import java.io.StringReader; import java.nio.file.Path; import java.nio.file.Paths; @@ -53,6 +54,15 @@ public class RDFParserTest extends BaseTest { fhirSchema = GenParser.parseSchema(schemaFile, Collections.emptyList()); } + // If we can't round-trip JSON, we skip the Turtle round-trip test. + private static ArrayList jsonRoundTripErrors = new ArrayList(); + @AfterAll + static void reportJsonRoundTripErrors() { + System.out.println(jsonRoundTripErrors.size() + " tests disqualified because of JSON round-trip errors"); + for (String e : jsonRoundTripErrors) + System.out.println(e); + } + /** * This test method has a method source for each JSON file in the resources/rdf-test-input directory (see #getInputFiles). * Each input file is expected to be a JSON representation of an R4 FHIR resource. @@ -62,71 +72,48 @@ public class RDFParserTest extends BaseTest { * 3. Perform a graph validation on the resulting RDF using ShEx and ShEx-java -- ensure validation passed * 4. Parse the RDF string into the HAPI object model -- ensure resource instance is not null * 5. Perform deep equals comparison of JSON-originated instance and RDF-originated instance -- ensure equality - * @param inputFile -- path to resource file to be tested + * @param referenceFilePath -- path to resource file to be tested * @throws IOException -- thrown when parsing RDF string into graph model */ @ParameterizedTest @MethodSource("getInputFiles") - public void testRDFRoundTrip(String inputFile) throws IOException { - FileInputStream inputStream = new FileInputStream(inputFile); - IBaseResource resource; - String resourceType; - // Parse JSON input as Resource - resource = ourCtx.newJsonParser().parseResource(inputStream); - assertNotNull(resource); - resourceType = resource.fhirType(); - - // Write the resource out to an RDF String - String rdfContent = ourCtx.newRDFParser().encodeResourceToString(resource); - assertNotNull(rdfContent); + public void testRDFRoundTrip(String referenceFilePath) throws IOException { + String referenceFileName = referenceFilePath.substring(referenceFilePath.lastIndexOf("/")+1); + IBaseResource referenceResource = parseJson(new FileInputStream(referenceFilePath)); + String referenceJson = serializeJson(ourCtx, referenceResource); // Perform ShEx validation on RDF - RDF4J factory = new RDF4J(); - GlobalFactory.RDFFactory = factory; //set the global factory used in shexjava + String turtleString = serializeRdf(ourCtx, referenceResource); + validateRdf(turtleString, referenceFileName, referenceResource); - // load the model - String baseIRI = "http://a.example.shex/"; - Model data = Rio.parse(new StringReader(rdfContent), baseIRI, RDFFormat.TURTLE); + // If we can round-trip JSON + IBaseResource viaJsonResource = parseJson(new ByteArrayInputStream(referenceJson.getBytes())); + if (((Base)viaJsonResource).equalsDeep((Base)referenceResource)) { - String rootSubjectIri = null; - for (org.eclipse.rdf4j.model.Resource resourceStream : data.subjects()) { - if (resourceStream instanceof SimpleIRI) { - Model filteredModel = data.filter(resourceStream, factory.getValueFactory().createIRI(NODE_ROLE_IRI), factory.getValueFactory().createIRI(TREE_ROOT_IRI), (org.eclipse.rdf4j.model.Resource)null); - if (filteredModel != null && filteredModel.subjects().size() == 1) { - Optional rootResource = filteredModel.subjects().stream().findFirst(); - if (rootResource.isPresent()) { - rootSubjectIri = rootResource.get().stringValue(); - break; - } + // Parse RDF content as resource + IBaseResource viaTurtleResource = parseRdf(ourCtx, new StringReader(turtleString)); + assertNotNull(viaTurtleResource); - } + // Compare original JSON-based resource against RDF-based resource + String viaTurtleJson = serializeJson(ourCtx, viaTurtleResource); + if (!((Base)viaTurtleResource).equalsDeep((Base)referenceResource)) { + String failMessage = referenceFileName + ": failed to round-trip Turtle "; + if (referenceJson.equals(viaTurtleJson)) + throw new Error(failMessage + + "\nttl: " + turtleString + + "\nexp: " + referenceJson); + else + assertEquals(referenceJson, viaTurtleJson, failMessage + "\nttl: " + turtleString); } - } - - // create the graph - Graph dataGraph = factory.asGraph(data); - - // choose focus node and shapelabel - IRI focusNode = factory.createIRI(rootSubjectIri); - Label shapeLabel = new Label(factory.createIRI(FHIR_SHAPE_PREFIX + resourceType)); - - ValidationAlgorithm validation = new RecursiveValidation(fhirSchema, dataGraph); - validation.validate(focusNode, shapeLabel); - boolean result = validation.getTyping().isConformant(focusNode, shapeLabel); - assertTrue(result); - - // Parse RDF content as resource - IBaseResource parsedResource = ourCtx.newRDFParser().parseResource(new StringReader(rdfContent)); - assertNotNull(parsedResource); - - // Compare original JSON-based resource against RDF-based resource - if (parsedResource instanceof DomainResource) { - // This is a hack because this initializes the collection if it is empty - ((DomainResource) parsedResource).getContained(); - boolean deepEquals = ((Base)parsedResource).equalsDeep((Base)resource); - assertTrue(deepEquals); } else { - ourLog.warn("Input JSON did not yield a DomainResource"); + String gotString = serializeJson(ourCtx, viaJsonResource); + String skipMessage = referenceFileName + ": failed to round-trip JSON" + + (referenceJson.equals(gotString) + ? "\ngot: " + gotString + "\nexp: " + referenceJson + : "\nsome inequality not visible in: " + referenceJson); + System.out.println(referenceFileName + " skipped"); + // Specific messages are printed at end of run. + jsonRoundTripErrors.add(skipMessage); } } @@ -135,11 +122,98 @@ public class RDFParserTest extends BaseTest { List resourceList = new ArrayList<>(); ResourcePatternResolver resolver = new PathMatchingResourcePatternResolver(cl); Resource[] resources = resolver.getResources("classpath:rdf-test-input/*.json") ; - for (Resource resource: resources){ + for (Resource resource: resources) resourceList.add(resource.getFile().getPath()); - } return resourceList.stream(); } + // JSON functions + public IBaseResource parseJson(InputStream inputStream) { + IParser refParser = ourCtx.newJsonParser(); + refParser.setStripVersionsFromReferences(false); + // parser.setDontStripVersionsFromReferencesAtPaths(); + IBaseResource ret = refParser.parseResource(inputStream); + assertNotNull(ret); + return ret; + } + + public String serializeJson(FhirContext ctx, IBaseResource resource) { + IParser jsonParser = ctx.newJsonParser(); + jsonParser.setStripVersionsFromReferences(false); + String ret = jsonParser.encodeResourceToString(resource); + assertNotNull(ret); + return ret; + } + + // Rdf (Turtle) functions + public IBaseResource parseRdf(FhirContext ctx, StringReader inputStream) { + IParser refParser = ctx.newRDFParser(); + IBaseResource ret = refParser.parseResource(inputStream); + assertNotNull(ret); + return ret; + } + + public String serializeRdf(FhirContext ctx, IBaseResource resource) { + IParser rdfParser = ourCtx.newRDFParser(); + rdfParser.setStripVersionsFromReferences(false); + rdfParser.setServerBaseUrl("http://a.example/fhir/"); + String ret = rdfParser.encodeResourceToString(resource); + assertNotNull(ret); + return ret; + } + + public void validateRdf(String rdfContent, String referenceFileName, IBaseResource referenceResource) throws IOException { + String baseIRI = "http://a.example/shex/"; + RDF4J factory = new RDF4J(); + GlobalFactory.RDFFactory = factory; //set the global factory used in shexjava + Model data = Rio.parse(new StringReader(rdfContent), baseIRI, RDFFormat.TURTLE); + FixedShapeMapEntry fixedMapEntry = new FixedShapeMapEntry(factory, data, referenceResource.fhirType(), baseIRI); + Graph dataGraph = factory.asGraph(data); // create the graph + ValidationAlgorithm validation = new RecursiveValidation(fhirSchema, dataGraph); + validation.validate(fixedMapEntry.node, fixedMapEntry.shape); + boolean result = validation.getTyping().isConformant(fixedMapEntry.node, fixedMapEntry.shape); + assertTrue(result, + referenceFileName + ": failed to validate " + fixedMapEntry + + "\n" + referenceFileName + + "\n" + rdfContent + ); + } + + // Shape Expressions functions + class FixedShapeMapEntry { + RDFTerm node; + Label shape; + + FixedShapeMapEntry(RDF4J factory, Model data, String resourceType, String baseIRI) { + String rootSubjectIri = null; + // StmtIterator i = data.listStatements(); + for (org.eclipse.rdf4j.model.Resource resourceStream : data.subjects()) { +// if (resourceStream instanceof SimpleIRI) { + Model filteredModel = data.filter(resourceStream, factory.getValueFactory().createIRI(NODE_ROLE_IRI), factory.getValueFactory().createIRI(TREE_ROOT_IRI), (org.eclipse.rdf4j.model.Resource)null); + if (filteredModel != null && filteredModel.subjects().size() == 1) { + Optional rootResource = filteredModel.subjects().stream().findFirst(); + if (rootResource.isPresent()) { + rootSubjectIri = rootResource.get().stringValue(); + break; + } + + } +// } + } + + // choose focus node and shapelabel + this.node = rootSubjectIri.indexOf(":") == -1 + ? factory.createBlankNode(rootSubjectIri) + : factory.createIRI(rootSubjectIri); + Label shapeLabel = new Label(factory.createIRI(FHIR_SHAPE_PREFIX + resourceType)); +// this.node = focusNode; + this.shape = shapeLabel; + } + + public String toString() { + return "<" + node.toString() + ">@" + shape.toPrettyString(); + } + } + } diff --git a/hapi-fhir-structures-r4/src/test/resources/rdf-test-input/DISABLED/README.md b/hapi-fhir-structures-r4/src/test/resources/rdf-test-input/DISABLED/README.md new file mode 100644 index 00000000000..43a69e1cb67 --- /dev/null +++ b/hapi-fhir-structures-r4/src/test/resources/rdf-test-input/DISABLED/README.md @@ -0,0 +1,5 @@ +# Why is this disabled? + +| file | reason | +| - | - | +| [bundle-response](bundle-response.json) | [entry\[0\].response.outcome.issue](bundle-response.json#L50-L61) is not in [R4 Resource](http://hl7.org/fhir/resource.html#Resource) | diff --git a/hapi-fhir-structures-r4/src/test/resources/rdf-test-input/bundle-response.json b/hapi-fhir-structures-r4/src/test/resources/rdf-test-input/DISABLED/bundle-response.json similarity index 100% rename from hapi-fhir-structures-r4/src/test/resources/rdf-test-input/bundle-response.json rename to hapi-fhir-structures-r4/src/test/resources/rdf-test-input/DISABLED/bundle-response.json diff --git a/hapi-fhir-structures-r4/src/test/resources/rdf-validation/fhir-r4.shex b/hapi-fhir-structures-r4/src/test/resources/rdf-validation/fhir-r4.shex index 040ca2b9c67..ec75815f9e1 100644 --- a/hapi-fhir-structures-r4/src/test/resources/rdf-validation/fhir-r4.shex +++ b/hapi-fhir-structures-r4/src/test/resources/rdf-validation/fhir-r4.shex @@ -13267,7 +13267,7 @@ fhirvs:contact-point-use ["home" "work" "temp" "old" "mobile"] fhirvs:immunization-status ["completed" "entered-in-error" "not-done"] # This value set includes all possible codes from BCP-13 (http://tools.ietf.org/html/bcp13) -fhirvs:mimetypes EXTERNAL +fhirvs:mimetypes . # The use of an address. fhirvs:address-use ["home" "work" "temp" "old" "billing"]