Merge branch 'release/0.3.0' into main

Author: hhund

pom.xml

@@ -6,7 +6,7 @@
 
 	<groupId>dev.dsf</groupId>
 	<artifactId>dsf-fhir-validator</artifactId>
-	<version>0.2.0</version>
+	<version>0.3.0</version>
 
 	<properties>
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>

src/main/java/dev/dsf/fhir/validator/client/TerminologyServerClient.java

@@ -1,8 +1,10 @@
 package dev.dsf.fhir.validator.client;
 
+import java.util.List;
 import java.util.Objects;
 
 import org.hl7.fhir.r4.model.CapabilityStatement;
+import org.hl7.fhir.r4.model.CodeSystem;
 import org.hl7.fhir.r4.model.Coding;
 import org.hl7.fhir.r4.model.OperationOutcome;
 import org.hl7.fhir.r4.model.ValueSet;
@@ -15,6 +17,14 @@ record ValidationResult(boolean result, String message, OperationOutcome outome)
 	{
 	}
 
+	record UrlAndVersion(String url, String version)
+	{
+		public static UrlAndVersion fromCodeSystem(CodeSystem cs)
+		{
+			return new UrlAndVersion(cs.getUrl(), cs.getVersion());
+		}
+	}
+
 	/**
 	 * @param valueSet
 	 *            not <code>null</code>
@@ -55,4 +65,12 @@ default ValidationResult validate(String system, String code, String display, St
 
 		return validate(new Coding(system, code, display).setVersion(version));
 	}
+
+	/**
+	 * @param url
+	 *            not <code>null</code>
+	 * @return
+	 * @throws WebApplicationException
+	 */
+	List<UrlAndVersion> getSupportedCodeSystemVersion(String url) throws WebApplicationException;
 }

src/main/java/dev/dsf/fhir/validator/client/TerminologyServerClientJersey.java

@@ -1,6 +1,7 @@
 package dev.dsf.fhir.validator.client;
 
 import java.security.KeyStore;
+import java.util.List;
 import java.util.Objects;
 import java.util.concurrent.TimeUnit;
 import java.util.logging.Level;
@@ -15,7 +16,10 @@
 import org.glassfish.jersey.jackson.internal.jackson.jaxrs.json.JacksonJsonProvider;
 import org.glassfish.jersey.logging.LoggingFeature;
 import org.glassfish.jersey.logging.LoggingFeature.Verbosity;
+import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
 import org.hl7.fhir.r4.model.CapabilityStatement;
+import org.hl7.fhir.r4.model.CodeSystem;
 import org.hl7.fhir.r4.model.Coding;
 import org.hl7.fhir.r4.model.OperationOutcome;
 import org.hl7.fhir.r4.model.Parameters;
@@ -143,4 +147,16 @@ public CapabilityStatement getMetadata() throws WebApplicationException
 	{
 		return getResource().path("metadata").request(Constants.CT_FHIR_JSON_NEW).get(CapabilityStatement.class);
 	}
+
+	@Override
+	public List<UrlAndVersion> getSupportedCodeSystemVersion(String url) throws WebApplicationException
+	{
+		Bundle resultBundle = getResource().path("CodeSystem").queryParam("url", url).queryParam("_summary", "true")
+				.request(Constants.CT_FHIR_JSON_NEW).get(Bundle.class);
+
+		return resultBundle.getEntry().stream().filter(BundleEntryComponent::hasResource)
+				.map(BundleEntryComponent::getResource).filter(r -> r instanceof CodeSystem).map(r -> (CodeSystem) r)
+				.filter(cs -> cs.hasVersionElement() && cs.getVersionElement().hasValue())
+				.map(UrlAndVersion::fromCodeSystem).distinct().toList();
+	}
 }

src/main/java/dev/dsf/fhir/validator/implementation_guide/ValidationPackage.java

@@ -151,9 +151,9 @@ private Consumer<ValidationPackageEntry> doParseResources(FhirContext context, L
 	{
 		return entry ->
 		{
-			if ("package/package.json".equals(entry.getFileName())
-					|| (entry.getFileName() != null && (entry.getFileName().startsWith("package/example")
-							|| entry.getFileName().endsWith(".index.json") || !entry.getFileName().endsWith(".json"))))
+			if ("package/package.json".equals(entry.getFileName()) || (entry.getFileName() != null
+					&& (entry.getFileName().startsWith("package/example") || entry.getFileName().endsWith(".index.json")
+							|| entry.getFileName().endsWith(".schema.json") || !entry.getFileName().endsWith(".json"))))
 			{
 				logger.debug("Ignoring {}", entry.getFileName());
 				return;
@@ -169,26 +169,26 @@ private Consumer<ValidationPackageEntry> doParseResources(FhirContext context, L
 				resourceString = resourceString.replaceAll("<h2>[\\s\\w\\[\\]]*</tt>", "");
 				IBaseResource resource = context.newJsonParser().parseResource(resourceString);
 
-				if (resource instanceof CodeSystem)
-					codeSystems.add((CodeSystem) resource);
-				else if (resource instanceof NamingSystem)
-					namingSystems.add((NamingSystem) resource);
-				else if (resource instanceof StructureDefinition)
+				if (resource instanceof CodeSystem c)
+					codeSystems.add(c);
+				else if (resource instanceof NamingSystem n)
+					namingSystems.add(n);
+				else if (resource instanceof StructureDefinition s)
 				{
-					if (!StructureDefinitionKind.LOGICAL.equals(((StructureDefinition) resource).getKind()))
-						structureDefinitions.add((StructureDefinition) resource);
+					if (!StructureDefinitionKind.LOGICAL.equals(s.getKind()))
+						structureDefinitions.add(s);
 					else
 						logger.debug("Ignoring StructureDefinition with kind = logical");
 				}
-				else if (resource instanceof ValueSet)
-					valueSets.add((ValueSet) resource);
+				else if (resource instanceof ValueSet v)
+					valueSets.add(v);
 				else
 					logger.debug("Ignoring resource of type {}", resource.getClass().getName());
 			}
 			catch (Exception e)
 			{
-				logger.warn("Ignoring resource with error while parsing, {}: {}", e.getClass().getName(),
-						e.getMessage());
+				logger.warn("Ignoring resource with error while parsing {}, {}: {}", entry.getFileName(),
+						e.getClass().getName(), e.getMessage());
 			}
 		};
 	}

src/main/java/dev/dsf/fhir/validator/implementation_guide/ValidationPackageClientJersey.java

@@ -97,10 +97,10 @@ public ValidationPackage download(ValidationPackageIdentifier identifier)
 	{
 		Objects.requireNonNull(identifier, "identifier");
 
-		try (InputStream in = getResource().path(identifier.getName()).path(identifier.getVersion())
+		try (InputStream in = getResource().path(identifier.name()).path(identifier.version())
 				.request("application/tar+gzip").get(InputStream.class))
 		{
-			return ValidationPackage.from(identifier.getName(), identifier.getVersion(), in);
+			return ValidationPackage.from(identifier.name(), identifier.version(), in);
 		}
 	}
 

src/main/java/dev/dsf/fhir/validator/implementation_guide/ValidationPackageIdentifier.java

@@ -1,8 +1,6 @@
 package dev.dsf.fhir.validator.implementation_guide;
 
-import java.util.Objects;
-
-public class ValidationPackageIdentifier
+public record ValidationPackageIdentifier(String name, String version)
 {
 	public static ValidationPackageIdentifier fromString(String nameAndVersion)
 	{
@@ -14,65 +12,9 @@ public static ValidationPackageIdentifier fromString(String nameAndVersion)
 		return new ValidationPackageIdentifier(split[0], split[1]);
 	}
 
-	private final String name;
-	private final String version;
-
-	public ValidationPackageIdentifier(String name, String version)
-	{
-		this.name = Objects.requireNonNull(name, "name");
-		this.version = Objects.requireNonNull(version, "version");
-	}
-
-	public String getName()
-	{
-		return name;
-	}
-
-	public String getVersion()
-	{
-		return version;
-	}
-
 	@Override
 	public String toString()
 	{
 		return name + "|" + version;
 	}
-
-	@Override
-	public int hashCode()
-	{
-		final int prime = 31;
-		int result = 1;
-		result = prime * result + ((name == null) ? 0 : name.hashCode());
-		result = prime * result + ((version == null) ? 0 : version.hashCode());
-		return result;
-	}
-
-	@Override
-	public boolean equals(Object obj)
-	{
-		if (this == obj)
-			return true;
-		if (obj == null)
-			return false;
-		if (getClass() != obj.getClass())
-			return false;
-		ValidationPackageIdentifier other = (ValidationPackageIdentifier) obj;
-		if (name == null)
-		{
-			if (other.name != null)
-				return false;
-		}
-		else if (!name.equals(other.name))
-			return false;
-		if (version == null)
-		{
-			if (other.version != null)
-				return false;
-		}
-		else if (!version.equals(other.version))
-			return false;
-		return true;
-	}
 }

src/main/java/dev/dsf/fhir/validator/implementation_guide/ValidationPackageManager.java

@@ -26,7 +26,10 @@ default ValidationPackageWithDepedencies downloadPackageWithDependencies(String
 	 * @param identifier
 	 * @return validation package with dependencies
 	 */
-	ValidationPackageWithDepedencies downloadPackageWithDependencies(ValidationPackageIdentifier identifier);
+	default ValidationPackageWithDepedencies downloadPackageWithDependencies(ValidationPackageIdentifier identifier)
+	{
+		return downloadPackagesWithDependencies(identifier).get(0);
+	}
 
 	/**
 	 * Downloads the given FHIR packages and all its dependencies.

src/main/java/dev/dsf/fhir/validator/implementation_guide/ValidationPackageManagerImpl.java

@@ -8,6 +8,7 @@
 import java.util.Map;
 import java.util.Objects;
 import java.util.Optional;
+import java.util.stream.Collectors;
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -72,18 +73,13 @@ public List<ValidationPackageWithDepedencies> downloadPackagesWithDependencies(
 			packages.add(ValidationPackageWithDepedencies.from(packagesByNameAndVersion, identifier));
 		}
 
-		return packages;
-	}
-
-	@Override
-	public ValidationPackageWithDepedencies downloadPackageWithDependencies(ValidationPackageIdentifier identifier)
-	{
-		Objects.requireNonNull(identifier, "identifier");
+		logger.info("Validating with packages {}",
+				packages.stream().map(p -> p.getIdentifier().toString() + " {dependencies: "
+						+ p.getDependencies().stream().map(ValidationPackage::getIdentifier)
+								.map(ValidationPackageIdentifier::toString).sorted().collect(Collectors.joining(", "))
+						+ "}").collect(Collectors.joining(", ", "[", "]")));
 
-		Map<ValidationPackageIdentifier, ValidationPackage> packagesByNameAndVersion = new HashMap<>();
-		downloadPackageWithDependencies(identifier, packagesByNameAndVersion, new HashMap<>());
-
-		return ValidationPackageWithDepedencies.from(packagesByNameAndVersion, identifier);
+		return packages;
 	}
 
 	private void downloadPackageWithDependencies(ValidationPackageIdentifier identifier,
@@ -92,6 +88,9 @@ private void downloadPackageWithDependencies(ValidationPackageIdentifier identif
 	{
 		if (allPackagesByNameAndVersion.containsKey(identifier))
 		{
+			ValidationPackage dependency = allPackagesByNameAndVersion.get(identifier);
+			packagesByNameAndVersion.put(identifier, dependency);
+
 			// already downloaded
 			return;
 		}
@@ -102,6 +101,23 @@ else if (noDownloadPackages.contains(identifier))
 		}
 
 		ValidationPackage vPackage = downloadAndHandleException(identifier);
+		identifier = vPackage.getIdentifier();
+
+		// check again, as the identifier may have changed from a A.B.x wildcard
+		if (allPackagesByNameAndVersion.containsKey(identifier))
+		{
+			ValidationPackage dependency = allPackagesByNameAndVersion.get(identifier);
+			packagesByNameAndVersion.put(identifier, dependency);
+
+			// already downloaded
+			return;
+		}
+		else if (noDownloadPackages.contains(identifier))
+		{
+			logger.debug("Not using package {}", identifier.toString());
+			return;
+		}
+
 		packagesByNameAndVersion.put(identifier, vPackage);
 		allPackagesByNameAndVersion.put(identifier, vPackage);
 
@@ -112,15 +128,15 @@ else if (noDownloadPackages.contains(identifier))
 
 	private ValidationPackage downloadAndHandleException(ValidationPackageIdentifier identifier)
 	{
-		if (identifier.getVersion().matches("\\d+\\.\\d+\\.x"))
+		if (identifier.version().matches("\\d+\\.\\d+\\.x"))
 		{
-			String versoinPrefix = identifier.getVersion().substring(0, identifier.getVersion().length() - 1);
+			String versoinPrefix = identifier.version().substring(0, identifier.version().length() - 1);
 
-			PackageVersions versions = validationPackageClient.list(identifier.getName());
+			PackageVersions versions = validationPackageClient.list(identifier.name());
 			Optional<String> latest = versions.getLatest(versoinPrefix);
 
 			if (latest.isPresent())
-				identifier = new ValidationPackageIdentifier(identifier.getName(), latest.get());
+				identifier = new ValidationPackageIdentifier(identifier.name(), latest.get());
 		}
 
 		try

src/main/java/dev/dsf/fhir/validator/implementation_guide/ValidationPackageWithDepedencies.java

@@ -256,7 +256,7 @@ private void logMissingValueSets(Set<String> neededValueSets, List<ValueSet> fou
 		if (!missingValueSets.isEmpty())
 		{
 			logger.warn(
-					"The following ValueSet are required for validation but could not be found in validation package {}|{} or its dependencies, this may result in incomplete valdidation: [{}]",
+					"The following ValueSet are required for validation but could not be found in package (incl. dependencies) {}|{}, this may result in incomplete valdidation: [{}]",
 					getName(), getVersion(), missingValueSets);
 		}
 	}