FI-3387: Bump dependencies (#77)

build.gradle.kts

@@ -15,16 +15,19 @@ repositories {
 }
 
 dependencies {
-    implementation("ca.uhn.hapi.fhir", "org.hl7.fhir.validation", "6.2.8")
+    implementation("ca.uhn.hapi.fhir", "org.hl7.fhir.validation", "6.4.0")
 
     // validator dependency needed for terminology (why can't it get this automatically?)
-    implementation("com.squareup.okhttp3", "okhttp", "4.9.0")
+    implementation("com.squareup.okhttp3", "okhttp", "4.12.0")
+
+    // validator dependency needed to prevent a ClassNotFoundException
+    implementation("org.fhir:ucum:1.0.8")
 
     // GSON for our JSON needs
-    implementation("com.google.code.gson", "gson", "2.10.1")
+    implementation("com.google.code.gson", "gson", "2.11.0")
 
     // Basic logging. Reload4J is a security-focused fork of Log4J 1.x
-    implementation("org.slf4j", "slf4j-reload4j", "2.0.7")
+    implementation("org.slf4j", "slf4j-reload4j", "2.0.16")
 
     // Web Server
     implementation("com.sparkjava", "spark-core", "2.9.4")

src/main/java/org/mitre/inferno/Validator.java

@@ -27,6 +27,9 @@
 import org.hl7.fhir.utilities.VersionUtilities;
 import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
 import org.hl7.fhir.utilities.npm.NpmPackage;
+import org.hl7.fhir.utilities.npm.PackageClient;
+import org.hl7.fhir.utilities.npm.PackageInfo;
+import org.hl7.fhir.utilities.npm.PackageServer;
 import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
 import org.hl7.fhir.validation.BaseValidator;
 import org.hl7.fhir.validation.BaseValidator.ValidationControl;
@@ -68,12 +71,14 @@ public Validator(String igDir, boolean displayIssuesAreWarnings) throws Exceptio
     final String txServer = getTxServerUrl();
     final String txLog = null;
     final String fhirVersion = "4.0.1";
+    final boolean useEcosystem = true;
 
     ValidationEngineBuilder engineBuilder =
         new ValidationEngineBuilder().withTxServer(
                                                    txServer,
                                                    txLog,
-                                                   FhirPublication.fromCode(fhirVersion)
+                                                   FhirPublication.fromCode(fhirVersion),
+                                                   useEcosystem
                                                    );
     hl7Validator = engineBuilder.fromSource(definitions);
 
@@ -103,7 +108,8 @@ public Validator(String igDir, boolean displayIssuesAreWarnings) throws Exceptio
       }
     }
 
-    hl7Validator.connectToTSServer(txServer, txLog, FhirPublication.fromCode(fhirVersion));
+    hl7Validator.connectToTSServer(
+        txServer, txLog, FhirPublication.fromCode(fhirVersion), useEcosystem);
     hl7Validator.setDoNative(false);
     hl7Validator.setAnyExtensionsAllowed(true);
     hl7Validator.setDisplayWarnings(displayIssuesAreWarnings);
@@ -210,11 +216,27 @@ public Map<String, String> getKnownIGs() throws IOException {
       String canonical = e.getValue().canonical();
       igs.put(id, canonical);
     }
-    // Add IGs known to the package manager, replacing any conflicting package IDs
-    packageManager.listAllIds(igs);
+    // Add IGs known to the package manager
+    for (PackageServer next : packageManager.getPackageServers()) {
+      // https://github.com/hapifhir/org.hl7.fhir.core/blob/6.2.8/org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/FilesystemPackageCacheManager.java#L585
+      listSpecs(igs, next);
+    }
+
     return igs;
   }
 
+  // copied from
+  // https://github.com/hapifhir/org.hl7.fhir.core/blob/6.2.8/org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/FilesystemPackageCacheManager.java#L318
+  private void listSpecs(Map<String, String> specList, PackageServer server) throws IOException {
+    PackageClient pc = new PackageClient(server);
+    List<PackageInfo> matches = pc.search(null, null, null, false);
+    for (PackageInfo m : matches) {
+      if (!specList.containsKey(m.getId())) {
+        specList.put(m.getId(), m.getUrl());
+      }
+    }
+  }
+
   /**
    * Load a profile into the validator.
    *
@@ -229,7 +251,7 @@ public void loadProfile(byte[] profile) throws IOException {
       LOGGER.info("Loaded profile from file, url: " + sd.getUrl() + " version: " + sd.getVersion());
     } else if (resource != null) {
       LOGGER.info("Loaded resource from file but it wasn't a StructureDefinition, it was a "
-        + resource.fhirType());
+          + resource.fhirType());
     }
   }
 

src/test/java/org/mitre/inferno/ValidatorTest.java

@@ -160,19 +160,19 @@ void getKnownIGs() throws IOException {
 
   @Test
   void loadIg() throws Exception {
-    // A small subset of the profiles in mCODE 3.0.0
+    // A small subset of the profiles in mCODE 4.0.0
     List<String> profilesToLoad = Arrays.asList(
         "http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-cancer-disease-status",
         "http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-cancer-patient",
         "http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-cancer-related-medication-request",
         "http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-cancer-related-surgical-procedure",
-        "http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-cancer-stage-group"
+        "http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-cancer-stage"
     );
     assertTrue(profilesToLoad.stream().noneMatch(this::isProfileLoaded));
 
     // Because the version isn't given, this should load the "current" version of hl7.fhir.us.mcode
     // Note this means that if a new version is published that changes the profile names
-    // (as has happened in updates 1->2 and 2->3) this test may fail
+    // (as has happened in updates 1->2, 2->3, and 3->4) this test may fail
     IgResponse ig = validator.loadIg("hl7.fhir.us.mcode", null);
     assertEquals("hl7.fhir.us.mcode", ig.id);
     assertTrue(ig.profiles.containsAll(profilesToLoad));