enable -extension parameter for validator

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/FHIRPathEngine.java

@@ -5497,7 +5497,6 @@ public class FHIRPathEngine {
     return list.size() != 1 ? true : Utilities.existsInList(list.get(0).getCode(), "Element", "BackboneElement", "Resource", "DomainResource");
   }
 
-
   private boolean hasType(ElementDefinition ed, String s) {
     for (TypeRefComponent t : ed.getType()) {
       if (s.equalsIgnoreCase(t.getCode())) {

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

@@ -95,6 +95,7 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
   private boolean buildLoaded = false;
   private Map<String, String> ciList = new HashMap<String, String>();
   private JsonArray buildInfo;
+  private boolean suppressErrors;
 
   /**
    * Constructor
@@ -354,7 +355,7 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
       System.out.print("  Installing: ");
     }
     
-    if (npm.name() == null || id == null || !id.equalsIgnoreCase(npm.name())) {
+    if (!suppressErrors && npm.name() == null || id == null || !id.equalsIgnoreCase(npm.name())) {
       if (!id.equals("hl7.fhir.r5.core") && !id.equals("hl7.fhir.us.immds")) {// temporary work around
         throw new IOException("Attempt to import a mis-identified package. Expected " + id + ", got " + npm.name());
       }
@@ -939,4 +940,13 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
       return false;
   }
 
+  public boolean isSuppressErrors() {
+    return suppressErrors;
+  }
+
+  public void setSuppressErrors(boolean suppressErrors) {
+    this.suppressErrors = suppressErrors;
+  }
+
+  
 }

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

@@ -159,6 +159,8 @@ public class ValidationEngine implements IValidatorResourceFetcher, IValidationP
   @Getter @Setter private boolean showMessagesFromReferences;
   @Getter @Setter private Locale locale;
   @Getter @Setter private List<ImplementationGuide> igs = new ArrayList<>();
+  @Getter @Setter private List<String> extensionDomains = new ArrayList<>();
+
   @Getter @Setter private boolean showTimes;
   @Getter @Setter private List<BundleValidationRule> bundleValidationRules = new ArrayList<>();
   @Getter @Setter private QuestionnaireMode questionnaireMode;
@@ -596,6 +598,8 @@ public class ValidationEngine implements IValidatorResourceFetcher, IValidationP
     InstanceValidator validator = new InstanceValidator(context, null, null);
     validator.setHintAboutNonMustSupport(hintAboutNonMustSupport);
     validator.setAnyExtensionsAllowed(anyExtensionsAllowed);
+    validator.getExtensionDomains().clear();
+    validator.getExtensionDomains().addAll(extensionDomains);
     validator.setNoInvariantChecks(isNoInvariantChecks());
     validator.setWantInvariantInMessage(isWantInvariantInMessage());
     validator.setValidationLanguage(language);

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/model/CliContext.java

@@ -22,8 +22,6 @@ public class CliContext {
 
   @JsonProperty("doNative")
   private boolean doNative = false;
-  @JsonProperty("anyExtensionsAllowed")
-  private boolean anyExtensionsAllowed = true;
   @JsonProperty("hintAboutNonMustSupport")
   private boolean hintAboutNonMustSupport = false;
   @JsonProperty("recursive")
@@ -72,6 +70,8 @@ public class CliContext {
   @JsonProperty("targetVer")
   private String targetVer = null;
 
+  @JsonProperty("extensions")
+  private List<String> extensions = new ArrayList<String>();
   @JsonProperty("igs")
   private List<String> igs = new ArrayList<String>();
   @JsonProperty("questionnaire")
@@ -191,15 +191,9 @@ public class CliContext {
     return this;
   }
 
-  @JsonProperty("anyExtensionsAllowed")
+  @JsonProperty("extensions")
-  public boolean isAnyExtensionsAllowed() {
+  public List<String> getExtensions() {
-    return anyExtensionsAllowed;
+    return extensions;
-  }
-
-  @JsonProperty("anyExtensionsAllowed")
-  public CliContext setAnyExtensionsAllowed(boolean anyExtensionsAllowed) {
-    this.anyExtensionsAllowed = anyExtensionsAllowed;
-    return this;
   }
 
   @JsonProperty("hintAboutNonMustSupport")
@@ -576,7 +570,6 @@ public class CliContext {
     if (o == null || getClass() != o.getClass()) return false;
     CliContext that = (CliContext) o;
     return doNative == that.doNative &&
-      anyExtensionsAllowed == that.anyExtensionsAllowed &&
       hintAboutNonMustSupport == that.hintAboutNonMustSupport &&
       recursive == that.recursive &&
       doDebug == that.doDebug &&
@@ -587,6 +580,7 @@ public class CliContext {
       noUnicodeBiDiControlChars == that.noUnicodeBiDiControlChars &&
       noInvariants == that.noInvariants &&
       wantInvariantsInMessages == that.wantInvariantsInMessages &&
+      Objects.equals(extensions, that.extensions) &&
       Objects.equals(map, that.map) &&
       Objects.equals(output, that.output) &&
       Objects.equals(htmlOutput, that.htmlOutput) &&
@@ -615,7 +609,7 @@ public class CliContext {
 
   @Override
   public int hashCode() {
-    return Objects.hash(doNative, anyExtensionsAllowed, hintAboutNonMustSupport, recursive, doDebug, assumeValidRestReferences, canDoNative, noInternalCaching, 
+    return Objects.hash(doNative, extensions, hintAboutNonMustSupport, recursive, doDebug, assumeValidRestReferences, canDoNative, noInternalCaching, 
             noExtensibleBindingMessages, noInvariants, wantInvariantsInMessages, map, output, htmlOutput, txServer, sv, txLog, txCache, mapLog, lang, fhirpath, snomedCT,
             targetVer, igs, questionnaireMode, level, profiles, sources, mode, locale, locations, crumbTrails, showTimes, allowExampleUrls, outputStyle, noUnicodeBiDiControlChars);
   }
@@ -624,7 +618,7 @@ public class CliContext {
   public String toString() {
     return "CliContext{" +
       "doNative=" + doNative +
-      ", anyExtensionsAllowed=" + anyExtensionsAllowed +
+      ", extensions=" + extensions +
       ", hintAboutNonMustSupport=" + hintAboutNonMustSupport +
       ", recursive=" + recursive +
       ", doDebug=" + doDebug +

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

@@ -340,7 +340,13 @@ public class ValidationService {
       validator.setLevel(cliContext.getLevel());
       validator.setDoNative(cliContext.isDoNative());
       validator.setHintAboutNonMustSupport(cliContext.isHintAboutNonMustSupport());
-      validator.setAnyExtensionsAllowed(cliContext.isAnyExtensionsAllowed());
+      for (String s : cliContext.getExtensions()) {
+        if ("*".equals(s)) {
+          validator.setAnyExtensionsAllowed(true);
+        } else {          
+          validator.getExtensionDomains().add(s);
+        }
+      }
       validator.setLanguage(cliContext.getLang());
       validator.setLocale(cliContext.getLocale());
       validator.setSnomedExtension(cliContext.getSnomedCTCode());

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/utils/Params.java

@@ -26,7 +26,7 @@ public class Params {
   public static final String RECURSE = "-recurse";
   public static final String SHOW_MESSAGES_FROM_REFERENCES = "-showReferenceMessages";
   public static final String LOCALE = "-locale";
-  public static final String STRICT_EXTENSIONS = "-strictExtensions";
+  public static final String EXTENSIONS = "-extensions";
   public static final String HINT_ABOUT_NON_MUST_SUPPORT = "-hintAboutNonMustSupport";
   public static final String TO_VERSION = "-to-version";
   public static final String DO_NATIVE = "-do-native";
@@ -169,8 +169,8 @@ public class Params {
         } else {
           cliContext.setLocale(new Locale(args[++i]));
         }
-      } else if (args[i].equals(STRICT_EXTENSIONS)) {
+      } else if (args[i].equals(EXTENSIONS)) {
-        cliContext.setAnyExtensionsAllowed(false);
+        cliContext.getExtensions().add(args[++i]);
       } else if (args[i].equals(NO_INTERNAL_CACHING)) {
         cliContext.setNoInternalCaching(true);
       } else if (args[i].equals(NO_EXTENSIBLE_BINDING_WARNINGS)) {

org.hl7.fhir.validation/src/test/resources/txCache/iso4217.cache

@@ -0,0 +1,19 @@
+-------------------------------------------------------------------------------------
+{"hierarchical" : false, "valueSet" :{
+  "resourceType" : "ValueSet",
+  "compose" : {
+    "inactive" : true,
+    "include" : [{
+      "system" : "urn:iso:std:iso:4217"
+    }]
+  }
+}}####
+e: {
+  "error" : "java.lang.NullPointerException"
+}
+-------------------------------------------------------------------------------------
+{"hierarchical" : false, "url": "http://hl7.org/fhir/ValueSet/currencies", "version": "4.0.1"}####
+e: {
+  "error" : "java.lang.NullPointerException"
+}
+-------------------------------------------------------------------------------------

org.hl7.fhir.validation/src/test/resources/txCache/lang.cache

@@ -0,0 +1,11 @@
+-------------------------------------------------------------------------------------
+{"code" : {
+  "system" : "urn:ietf:bcp:47",
+  "code" : "fr-CA"
+}, "valueSet" :null, "lang":"en-US", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "versionFlexible":"true"}####
+v: {
+  "severity" : "error",
+  "error" : "Attempt to use Terminology server when no Terminology server is available",
+  "class" : "SERVER_ERROR"
+}
+-------------------------------------------------------------------------------------

org.hl7.fhir.validation/src/test/resources/txCache/loinc.cache

@@ -0,0 +1,90 @@
+-------------------------------------------------------------------------------------
+{"hierarchical" : false, "valueSet" :{
+  "resourceType" : "ValueSet",
+  "compose" : {
+    "inactive" : true,
+    "include" : [{
+      "system" : "http://loinc.org",
+      "concept" : [{
+        "extension" : [{
+          "url" : "http://hl7.org/fhir/StructureDefinition/valueset-label",
+          "valueString" : "A."
+        }],
+        "code" : "LA20752-4",
+        "display" : "Within 24 hours"
+      },
+      {
+        "extension" : [{
+          "url" : "http://hl7.org/fhir/StructureDefinition/valueset-label",
+          "valueString" : "B."
+        }],
+        "code" : "LA20753-2",
+        "display" : "After 24 hours but before 3 days"
+      },
+      {
+        "extension" : [{
+          "url" : "http://hl7.org/fhir/StructureDefinition/valueset-label",
+          "valueString" : "C."
+        }],
+        "code" : "LA20754-0",
+        "display" : "Three days or later"
+      },
+      {
+        "extension" : [{
+          "url" : "http://hl7.org/fhir/StructureDefinition/valueset-label",
+          "valueString" : "D."
+        }],
+        "code" : "LA4489-6",
+        "display" : "Unknown"
+      }]
+    }]
+  }
+}}####
+e: {
+  "error" : "java.lang.NullPointerException"
+}
+-------------------------------------------------------------------------------------
+{"hierarchical" : false, "valueSet" :{
+  "resourceType" : "ValueSet",
+  "compose" : {
+    "include" : [{
+      "system" : "http://loinc.org",
+      "concept" : [{
+        "extension" : [{
+          "url" : "http://hl7.org/fhir/StructureDefinition/valueset-label",
+          "valueString" : "A."
+        }],
+        "code" : "LA20752-4",
+        "display" : "Within 24 hours"
+      },
+      {
+        "extension" : [{
+          "url" : "http://hl7.org/fhir/StructureDefinition/valueset-label",
+          "valueString" : "B."
+        }],
+        "code" : "LA20753-2",
+        "display" : "After 24 hours but before 3 days"
+      },
+      {
+        "extension" : [{
+          "url" : "http://hl7.org/fhir/StructureDefinition/valueset-label",
+          "valueString" : "C."
+        }],
+        "code" : "LA20754-0",
+        "display" : "Three days or later"
+      },
+      {
+        "extension" : [{
+          "url" : "http://hl7.org/fhir/StructureDefinition/valueset-label",
+          "valueString" : "D."
+        }],
+        "code" : "LA4489-6",
+        "display" : "Unknown"
+      }]
+    }]
+  }
+}}####
+e: {
+  "error" : "java.lang.NullPointerException"
+}
+-------------------------------------------------------------------------------------

org.hl7.fhir.validation/src/test/resources/txCache/mimetypes.cache

@@ -0,0 +1,19 @@
+-------------------------------------------------------------------------------------
+{"hierarchical" : false, "valueSet" :{
+  "resourceType" : "ValueSet",
+  "compose" : {
+    "inactive" : true,
+    "include" : [{
+      "system" : "urn:ietf:bcp:13"
+    }]
+  }
+}}####
+e: {
+  "error" : "java.lang.NullPointerException"
+}
+-------------------------------------------------------------------------------------
+{"hierarchical" : false, "url": "http://hl7.org/fhir/ValueSet/mimetypes", "version": "4.0.1"}####
+e: {
+  "error" : "java.lang.NullPointerException"
+}
+-------------------------------------------------------------------------------------

org.hl7.fhir.validation/src/test/resources/txCache/ucum.cache

@@ -0,0 +1,103 @@
+-------------------------------------------------------------------------------------
+{"hierarchical" : false, "valueSet" :{
+  "resourceType" : "ValueSet",
+  "compose" : {
+    "inactive" : true,
+    "include" : [{
+      "system" : "http://unitsofmeasure.org",
+      "concept" : [{
+        "extension" : [{
+          "url" : "http://hl7.org/fhir/StructureDefinition/valueset-concept-definition",
+          "valueString" : "second"
+        }],
+        "code" : "s",
+        "display" : "second",
+        "designation" : [{
+          "language" : "zh",
+          "value" : "秒"
+        }]
+      },
+      {
+        "extension" : [{
+          "url" : "http://hl7.org/fhir/StructureDefinition/valueset-concept-definition",
+          "valueString" : "minute"
+        }],
+        "code" : "min",
+        "display" : "minute",
+        "designation" : [{
+          "language" : "zh",
+          "value" : "分钟"
+        }]
+      },
+      {
+        "extension" : [{
+          "url" : "http://hl7.org/fhir/StructureDefinition/valueset-concept-definition",
+          "valueString" : "hour"
+        }],
+        "code" : "h",
+        "display" : "hour",
+        "designation" : [{
+          "language" : "zh",
+          "value" : "小时"
+        }]
+      },
+      {
+        "extension" : [{
+          "url" : "http://hl7.org/fhir/StructureDefinition/valueset-concept-definition",
+          "valueString" : "day"
+        }],
+        "code" : "d",
+        "display" : "day",
+        "designation" : [{
+          "language" : "zh",
+          "value" : "天"
+        }]
+      },
+      {
+        "extension" : [{
+          "url" : "http://hl7.org/fhir/StructureDefinition/valueset-concept-definition",
+          "valueString" : "week"
+        }],
+        "code" : "wk",
+        "display" : "week",
+        "designation" : [{
+          "language" : "zh",
+          "value" : "星期"
+        }]
+      },
+      {
+        "extension" : [{
+          "url" : "http://hl7.org/fhir/StructureDefinition/valueset-concept-definition",
+          "valueString" : "month"
+        }],
+        "code" : "mo",
+        "display" : "month",
+        "designation" : [{
+          "language" : "zh",
+          "value" : "月"
+        }]
+      },
+      {
+        "extension" : [{
+          "url" : "http://hl7.org/fhir/StructureDefinition/valueset-concept-definition",
+          "valueString" : "year"
+        }],
+        "code" : "a",
+        "display" : "year",
+        "designation" : [{
+          "language" : "zh",
+          "value" : "年"
+        }]
+      }]
+    }]
+  }
+}}####
+e: {
+  "error" : "java.lang.NullPointerException"
+}
+-------------------------------------------------------------------------------------
+{"hierarchical" : false, "url": "http://hl7.org/fhir/ValueSet/units-of-time", "version": "4.0.1"}####
+e: {
+  "error" : "java.lang.NullPointerException"
+}
+-------------------------------------------------------------------------------------