Merge pull request #698 from lantanagroup/LNK-2065

LNK-2065: Using NPM packages to load resources for validation

api/src/main/java/com/lantanagroup/link/api/ApiApplication.java

@@ -5,6 +5,7 @@
 import com.fasterxml.jackson.databind.module.SimpleModule;
 import com.lantanagroup.link.FhirContextProvider;
 import com.lantanagroup.link.FhirHelper;
+import com.lantanagroup.link.config.api.ApiConfig;
 import com.lantanagroup.link.db.SharedService;
 import com.lantanagroup.link.validation.Validator;
 import org.springframework.beans.factory.InitializingBean;
@@ -73,8 +74,8 @@ public ApiInit apiInit() {
   }
 
   @Bean
-  public Validator validator(SharedService sharedService) {
-    return new Validator(sharedService);
+  public Validator validator(SharedService sharedService, ApiConfig apiConfig) {
+    return new Validator(sharedService, apiConfig);
   }
 
   /**

core/src/main/java/com/lantanagroup/link/config/api/ApiConfig.java

@@ -182,4 +182,9 @@ public class ApiConfig {
 
   private List<ApiInfoGroup> infoGroups = new ArrayList<>();
 
+  /**
+   * <strong>api.validation-packages-path</strong><br>The path to the validation packages
+   */
+  private String validationPackagesPath = "classpath:/packages/**";
+
 }

core/src/main/java/com/lantanagroup/link/validation/Validator.java

@@ -1,10 +1,12 @@
 package com.lantanagroup.link.validation;
 
 import ca.uhn.fhir.context.support.DefaultProfileValidationSupport;
+import ca.uhn.fhir.parser.DataFormatException;
 import ca.uhn.fhir.parser.IParser;
 import ca.uhn.fhir.validation.*;
 import com.lantanagroup.link.Constants;
 import com.lantanagroup.link.FhirContextProvider;
+import com.lantanagroup.link.config.api.ApiConfig;
 import com.lantanagroup.link.db.SharedService;
 import lombok.Setter;
 import org.apache.commons.lang3.StringUtils;
@@ -15,18 +17,23 @@
 import org.hl7.fhir.common.hapi.validation.validator.FhirInstanceValidator;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r4.model.*;
+import org.hl7.fhir.utilities.npm.NpmPackage;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.core.io.support.PathMatchingResourcePatternResolver;
 
 import java.io.IOException;
 import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
+import java.nio.file.Files;
+import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.Date;
 import java.util.List;
 import java.util.UUID;
 import java.util.concurrent.Executors;
 import java.util.concurrent.TimeUnit;
+import java.util.stream.Collectors;
 
 public class Validator {
   protected static final Logger logger = LoggerFactory.getLogger(Validator.class);
@@ -41,8 +48,14 @@ public class Validator {
   @Setter
   private SharedService sharedService;
 
-  public Validator(SharedService sharedService) {
+  private final List<String> allowsResourceTypes = List.of("StructureDefinition", "ValueSet", "CodeSystem", "ImplementationGuide", "Measure", "Library");
+
+  @Setter
+  private ApiConfig apiConfig;
+
+  public Validator(SharedService sharedService, ApiConfig apiConfig) {
     this.sharedService = sharedService;
+    this.apiConfig = apiConfig;
     this.prePopulatedValidationSupport = new PrePopulatedValidationSupport(FhirContextProvider.getFhirContext());
   }
 
@@ -93,32 +106,84 @@ private static OperationOutcome.IssueType getIssueCode(String messageId) {
     }
   }
 
+  /**
+   * Writes all conformance resources to a file for debugging purposes
+   */
+  private void writeConformanceResourcesToFile() {
+    String resources = this.prePopulatedValidationSupport.fetchAllConformanceResources().stream()
+            .map(Object::toString)
+            .collect(Collectors.joining("\n"));
+    try {
+      Files.writeString(Path.of("conformance-resources.txt"), resources);
+    } catch (IOException e) {
+      throw new RuntimeException(e);
+    }
+  }
+
   public void init() {
-    this.loadFiles();
-    this.updateMeasures();
+    this.loadPackages();
+    this.loadTerminology();
+
+    // When needed for debugging
+    //this.writeConformanceResourcesToFile();
 
     this.validator = FhirContextProvider.getFhirContext().newValidator();
     this.validator.setExecutorService(Executors.newWorkStealingPool());
-    IValidatorModule module = new FhirInstanceValidator(this.getCachingValidationSupport());
+    IValidatorModule module = new FhirInstanceValidator(this.getValidationSupportChain());
     this.validator.registerValidatorModule(module);
     this.validator.setConcurrentBundleValidation(true);
   }
 
-  private void loadFiles() {
+  /**
+   * Load allowed resources for all packages from the configured path into the pre-populated validation support
+   */
+  private void loadPackages() {
+    if (StringUtils.isEmpty(this.apiConfig.getValidationPackagesPath())) {
+      logger.info("No validation packages path configured");
+      return;
+    }
+
     try {
       PathMatchingResourcePatternResolver resolver = new PathMatchingResourcePatternResolver();
-      this.loadClassResources(resolver.getResources("terminology/**"));
-      this.loadClassResources(resolver.getResources("profiles/**"));
-    } catch (IOException ex) {
-      logger.error("Error loading resources for validation", ex);
+      org.springframework.core.io.Resource[] resources = resolver.getResources(this.apiConfig.getValidationPackagesPath());
+      for (org.springframework.core.io.Resource packageResource : resources) {
+        if (packageResource.getFile().isDirectory()) {
+          continue;
+        } else if (!packageResource.getFile().getName().endsWith(".tgz")) {
+          logger.warn("Unexpected package file name {}", packageResource.getFilename());
+          continue;
+        }
+
+        logger.info("Loading package {}", packageResource.getFilename());
+        NpmPackage npmPackage = NpmPackage.fromPackage(packageResource.getInputStream());
+
+        npmPackage.listResources(allowsResourceTypes).forEach(resource -> {
+          try {
+            String resourceJson = new String(npmPackage.getFolders().get("package").getContent().get(resource), StandardCharsets.UTF_8);
+            IBaseResource baseResource = this.jsonParser.parseResource(resourceJson);
+            this.prePopulatedValidationSupport.addResource(baseResource);
+          } catch (DataFormatException ex) {
+            logger.error("Error parsing package {} resource {}", packageResource, resource, ex);
+          }
+        });
+      }
+    } catch (IOException e) {
+      logger.error("Error loading packages for validation: {}", e.getMessage());
     }
   }
 
-  public void updateMeasures() {
-    // Add each measure canonical url to the resource fetcher
-    this.sharedService.getMeasureDefinitions().forEach(md -> {
-      // TODO
-    });
+  /**
+   * Load resources from the terminology classpath directory into the pre-populated validation support
+   */
+  private void loadTerminology() {
+    try {
+      PathMatchingResourcePatternResolver resolver = new PathMatchingResourcePatternResolver();
+      org.springframework.core.io.Resource[] resources = resolver.getResources("terminology/**");
+      this.loadClassResources(resources);
+    } catch (IOException e) {
+      logger.error("Error loading class resources for validation: {}", e.getMessage());
+    }
+
   }
 
   private void loadClassResources(org.springframework.core.io.Resource[] classResources) {
@@ -161,7 +226,7 @@ private void loadClassResources(org.springframework.core.io.Resource[] classReso
     }
   }
 
-  private CachingValidationSupport getCachingValidationSupport() {
+  private CachingValidationSupport getValidationSupportChain() {
     ValidationSupportChain validationSupportChain = new ValidationSupportChain(
             new DefaultProfileValidationSupport(FhirContextProvider.getFhirContext()),
             new InMemoryTerminologyServerValidationSupport(FhirContextProvider.getFhirContext()),