Merge pull request #491 from hapifhir/gg-202105-bugfixes-2

* Validator: Load code systems from known packages on the fly

RELEASE_NOTES.md

@@ -3,6 +3,12 @@
 * Snapshot generator: fix problem checking types on logical models
 * Do not flag internal references as suspicious
 * XMLParser allows passing a schema location
+* XMLParser allows passing a schema location
 * Issue 484 https://github.com/hapifhir/org.hl7.fhir.core/issues/484
 * Adding Kotlin to the build process
 * random cleaning up in convertors
+* Validator: Load code systems from known packages on the fly
+* Validator: better handle invalid v3 dates
+* Renderer: Render OperationDefinition.InputProfile and OutputProfile
+* Important: Allow more valid schemas for Utilities.isAbsoluteUrl
+* Validator: remove notes about extensible bindings if profile extensible binding is valid

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/conv30_50/StructureMap30_50.java

@@ -267,7 +267,7 @@ public class StructureMap30_50 {
         VersionConvertor_30_50.copyElement(src, tgt);
         if (src.hasContext())
             tgt.setContextElement(VersionConvertor_30_50.convertId(src.getContextElement()));
-        if (src.hasContextType() && src.getContextType() == org.hl7.fhir.dstu3.model.StructureMap.StructureMapContextType.VARIABLE)
+        if (src.hasContextType() && src.getContextType() != org.hl7.fhir.dstu3.model.StructureMap.StructureMapContextType.VARIABLE)
           throw new Error("This conversion is not supported. Consult code maintainers"); // this should never happens - no one knows what the intent was here.
         if (src.hasElement())
             tgt.setElementElement(VersionConvertor_30_50.convertString(src.getElementElement()));

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/BaseWorkerContext.java

@@ -205,6 +205,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
   protected TerminologyCache txCache;
   protected TimeTracker clock;
   private boolean tlogging = true;
+  private ICanonicalResourceLocator locator;
   
   public BaseWorkerContext() throws FileNotFoundException, IOException, FHIRException {
     txCache = new TerminologyCache(lock, null);
@@ -498,9 +499,17 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
 
   @Override
   public CodeSystem fetchCodeSystem(String system) {
+    CodeSystem cs;
     synchronized (lock) {
-      return codeSystems.get(system);
+      cs = codeSystems.get(system);
     }
+    if (cs == null && locator != null) {
+      locator.findResource(system);
+      synchronized (lock) {
+        cs = codeSystems.get(system);
+      }
+    }
+    return cs;
   } 
 
   @Override
@@ -2002,4 +2011,12 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
     }
   }
 
+  public ICanonicalResourceLocator getLocator() {
+    return locator;
+  }
+
+  public void setLocator(ICanonicalResourceLocator locator) {
+    this.locator = locator;
+  }
+
 }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/IWorkerContext.java

@@ -170,6 +170,10 @@ public interface IWorkerContext {
     }
   }
 
+  public interface ICanonicalResourceLocator {
+    void findResource(String url); // if it can be found, put it in the context
+  }
+  
   public interface IContextResourceLoader {
     /** 
      * @return List of the resource types that shoud be loaded

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/XmlParser.java

@@ -468,8 +468,12 @@ public class XmlParser extends ParserBase {
 
 	private String convertForDateFormatFromExternal(String fmt, String av) throws FHIRException {
   	if ("v3".equals(fmt)) {
+  	  try {
     		DateTimeType d = DateTimeType.parseV3(av);
     		return d.asStringValue();
+  	  } catch (Exception e) {
+  	    return av; // not at all clear what to do in this case.
+  	  }
   	} else
       throw new FHIRException(context.formatMessage(I18nConstants.UNKNOWN_DATA_FORMAT_, fmt));
 	}

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/OperationDefinitionRenderer.java

@@ -50,6 +50,26 @@ public class OperationDefinitionRenderer extends TerminologyRenderer {
         x.para().tx("URL: [base]/"+c.getValue()+"/[id]/$"+opd.getCode());
     }
 
+    if (opd.hasInputProfile()) {
+      XhtmlNode p = x.para();
+      p.tx("Input parameters Profile: ");
+      StructureDefinition sd = context.getContext().fetchResource(StructureDefinition.class, opd.getInputProfile());
+      if (sd == null) {
+        p.pre().tx(opd.getInputProfile());        
+      } else {
+        p.ah(sd.getUserString("path")).tx(sd.present());                 
+      }      
+    }
+    if (opd.hasOutputProfile()) {
+      XhtmlNode p = x.para();
+      p.tx("Output parameters Profile: ");
+      StructureDefinition sd = context.getContext().fetchResource(StructureDefinition.class, opd.getOutputProfile());
+      if (sd == null) {
+        p.pre().tx(opd.getOutputProfile());        
+      } else {
+        p.ah(sd.getUserString("path")).tx(sd.present());                 
+      }      
+    }
     x.para().tx("Parameters");
     XhtmlNode tbl = x.table( "grid");
     XhtmlNode tr = tbl.tr();

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/Utilities.java

@@ -1093,10 +1093,12 @@ public class Utilities {
 
 
   public static boolean isAbsoluteUrl(String ref) {
-    return ref != null && (ref.startsWith("http:") || ref.startsWith("https:") || ref.startsWith("urn:uuid:") || ref.startsWith("urn:oid:") || 
+    if (ref != null && ref.contains(":")) {
-        Utilities.startsWithInList(ref, "urn:iso:", "urn:iso-iec:", "urn:iso-cie:", "urn:iso-astm:", "urn:iso-ieee:", "urn:iec:")); // rfc5141
+      String scheme = ref.substring(0, ref.indexOf(":"));
+      return existsInList(scheme, "http", "https", "urn") || isToken(scheme) || Utilities.startsWithInList(ref, "urn:iso:", "urn:iso-iec:", "urn:iso-cie:", "urn:iso-astm:", "urn:iso-ieee:", "urn:iec:"); // rfc5141
+    }
+    return false; 
   }
-
 
   public static boolean equivalent(String l, String r) {
     if (Utilities.noString(l) && Utilities.noString(r))

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/NpmPackage.java

@@ -814,7 +814,7 @@ public class NpmPackage {
   //  }
 
   public String getWebLocation() {
-    if (npm.has("url")) {
+    if (npm.has("url") && npm.get("url").isJsonPrimitive()) {
       return PackageHacker.fixPackageUrl(npm.get("url").getAsString());
     } else {
       return JSONUtil.str(npm, "canonical");

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/BaseValidator.java

@@ -833,7 +833,7 @@ public class BaseValidator {
     String targetUrl = null;
     String version = "";
     String resourceType = null;
-    if (ref.startsWith("http") || ref.startsWith("urn")) {
+    if (ref.startsWith("http:") || ref.startsWith("urn:") || Utilities.isAbsoluteUrl(ref)) {
       // We've got an absolute reference, no need to calculate
       if (ref.contains("/_history/")) {
         targetUrl = ref.substring(0, ref.indexOf("/_history/") - 1);

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/ValidationEngine.java

@@ -9,6 +9,7 @@ import org.hl7.fhir.convertors.txClient.TerminologyClientFactory;
 import org.hl7.fhir.exceptions.DefinitionException;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.r5.conformance.ProfileUtilities;
+import org.hl7.fhir.r5.context.IWorkerContext.ICanonicalResourceLocator;
 import org.hl7.fhir.r5.context.IWorkerContext.PackageVersion;
 import org.hl7.fhir.r5.context.SimpleWorkerContext;
 import org.hl7.fhir.r5.elementmodel.Element;
@@ -134,6 +135,7 @@ public class ValidationEngine implements IValidatorResourceFetcher, IPackageInst
   @Getter @Setter private PrintWriter mapLog;
   @Getter @Setter private boolean debug = false;
   @Getter @Setter private IValidatorResourceFetcher fetcher;
+  @Getter @Setter private ICanonicalResourceLocator locator;
   @Getter @Setter private boolean assumeValidRestReferences;
   @Getter @Setter private boolean noExtensibleBindingMessages;
   @Getter @Setter private boolean securityChecks;

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/services/StandAloneValidatorFetcher.java

@@ -4,6 +4,7 @@ import com.google.gson.JsonObject;
 import org.hl7.fhir.convertors.txClient.TerminologyClientFactory;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.r5.context.IWorkerContext;
+import org.hl7.fhir.r5.context.IWorkerContext.ICanonicalResourceLocator;
 import org.hl7.fhir.r5.elementmodel.Element;
 import org.hl7.fhir.r5.model.CanonicalResource;
 import org.hl7.fhir.r5.terminologies.TerminologyClient;
@@ -26,7 +27,7 @@ import java.util.List;
 import java.util.Locale;
 import java.util.Map;
 
-public class StandAloneValidatorFetcher implements IValidatorResourceFetcher {
+public class StandAloneValidatorFetcher implements IValidatorResourceFetcher, ICanonicalResourceLocator {
 
   List<String> mappingsUris = new ArrayList<>();
   private FilesystemPackageCacheManager pcm;
@@ -63,7 +64,7 @@ public class StandAloneValidatorFetcher implements IValidatorResourceFetcher {
       url = url.substring(0, url.lastIndexOf("|"));
     }
 
-    if (type.equals("uri") && isMappingUri(url)) {
+    if (type != null && type.equals("uri") && isMappingUri(url)) {
       return true;
     }
 
@@ -128,6 +129,7 @@ public class StandAloneValidatorFetcher implements IValidatorResourceFetcher {
         pidMap.put(pid+"|"+ver, null);
       }
       if (pi != null) {
+        context.loadFromPackage(pi, null);
         return pi.hasCanonical(url);
       }
     }
@@ -249,4 +251,12 @@ public class StandAloneValidatorFetcher implements IValidatorResourceFetcher {
     return true;
   }
 
+  @Override
+  public void findResource(String url) {
+    try {
+      resolveURL(null, null, url, null);
+    } catch (Exception e) {
+    }
+  }
+
 }

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/services/ValidationService.java

@@ -246,7 +246,9 @@ public class ValidationService {
       validator.setSecurityChecks(cliContext.isSecurityChecks());
       validator.setCrumbTrails(cliContext.isCrumbTrails());
       validator.setShowTimes(cliContext.isShowTimes());
-      validator.setFetcher(new StandAloneValidatorFetcher(validator.getPcm(), validator.getContext(), validator));
+      StandAloneValidatorFetcher fetcher = new StandAloneValidatorFetcher(validator.getPcm(), validator.getContext(), validator);
+      validator.setFetcher(fetcher);
+      validator.getContext().setLocator(fetcher);
       validator.getBundleValidationRules().addAll(cliContext.getBundleValidationRules());
       TerminologyCache.setNoCaching(cliContext.isNoInternalCaching());
       validator.prepare(); // generate any missing snapshots

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java

@@ -1052,6 +1052,9 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
                       res = false;
                       txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, vr.getMessage());
                     } else {
+                      if (binding.getStrength() == BindingStrength.EXTENSIBLE) {
+                        removeTrackedMessagesForLocation(errors, element, path);
+                      }
                       res = false;
                     }
                   }

pom.xml

@@ -19,7 +19,7 @@
 
     <properties>
         <hapi_fhir_version>5.1.0</hapi_fhir_version>
-        <validator_test_case_version>1.1.62</validator_test_case_version>
+        <validator_test_case_version>1.1.63-SNAPSHOT</validator_test_case_version>
         <junit_jupiter_version>5.7.1</junit_jupiter_version>
         <junit_platform_launcher_version>1.7.1</junit_platform_launcher_version>
         <maven_surefire_version>3.0.0-M4</maven_surefire_version>