fix bug loading R5 extensions with imported value sets

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/R5ExtensionsLoader.java

@@ -190,7 +190,10 @@ public class R5ExtensionsLoader {
       context.cacheResourceFromPackage(vs, vs.getSourcePackage());
       for (ConceptSetComponent inc : vs.getCompose().getInclude()) {
         for (CanonicalType t : inc.getValueSet()) {
-          loadValueSet(t.asStringValue(), context, valueSets, codeSystems);
+          ValueSet vsi = context.fetchResource(ValueSet.class, t.getValue());
+          if (vsi == null) {
+            loadValueSet(t.asStringValue(), context, valueSets, codeSystems);
+          }
         }
         if (inc.hasSystem()) {
           if (!inc.hasVersion()) {

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/ElementDefinition.java

@@ -4605,6 +4605,11 @@ public boolean hasTarget() {
 
   }
 
+  @Override
+  public String toString() {
+    return key + ":" + expression + (severity == null ? "("+severity.asStringValue()+")" : "");
+  }
+
   }
 
     @Block()
@@ -13093,6 +13098,10 @@ If a pattern[x] is declared on a repeating element, the pattern applies to all r
     return t;
   }
 
+  public boolean repeats() {
+    return !Utilities.existsInList(getMax(), "0", "1");
+  }
+
 // end addition
 
 }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/StructureDefinition.java

@@ -1499,6 +1499,34 @@ public class StructureDefinition extends CanonicalResource {
 
   }
 
+//added from java-adornments.txt:
+
+ public ElementDefinition getElementByPath(String path) {
+   if (path == null) {
+     return null;
+   }
+   for (ElementDefinition ed : getElement()) {
+     if (path.equals(ed.getPath()) || (path+"[x]").equals(ed.getPath())) {
+       return ed;
+     }
+   }
+   return null;
+ }
+
+
+ public ElementDefinition getElementById(String id) {
+   if (id == null) {
+     return null;
+   }
+   for (ElementDefinition ed : getElement()) {
+     if (id.equals(ed.getId())) {
+       return ed;
+     }
+   }
+   return null;
+ }
+
+//end addition
   }
 
     /**

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

@@ -161,4 +161,14 @@ public class CommaSeparatedStringBuilder {
     }
     return res;
   }
+
+  public static String joinWrapped(String sep, String leftWrap, String rightWrap, Collection<String> list) {
+    CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder(sep);
+    for (String s : list) {
+      if (s != null) {
+        b.append(leftWrap+s+rightWrap);
+      }
+    }
+    return b.toString();
+  }
 }

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

@@ -85,7 +85,7 @@ import org.hl7.fhir.validation.instance.utils.NodeStack;
 
 public class BaseValidator implements IValidationContextResourceLoader {
 
-  public class BooleanHolder {
+  public static class BooleanHolder {
     private boolean value = true;
 
     public BooleanHolder() {

org.hl7.fhir.validation/src/test/resources/txCache/org.hl7.fhir.validation/4.0.1/loinc.cache

@@ -6562,7 +6562,6 @@ v: {
   "error" : "The provided code 'http://loinc.org#5792-7' was not found in the value set 'http://hl7.org/fhir/ValueSet/birthDate'",
   "class" : "UNKNOWN",
   "server" : "http://tx-dev.fhir.org/r4",
-  "unknown-systems" : "",
   "issues" : {
   "resourceType" : "OperationOutcome",
   "issue" : [{
@@ -6586,3 +6585,68 @@ v: {
 
 }
 -------------------------------------------------------------------------------------
+{"code" : {
+  "system" : "http://loinc.org",
+  "code" : "76534-7",
+  "display" : "Systolic blood pressure by Noninvasive"
+}, "valueSet" :null, "langs":"", "useServer":"true", "useClient":"false", "guessSystem":"false", "activeOnly":"false", "membershipOnly":"false", "displayWarningMode":"false", "versionFlexible":"false", "profile": {
+  "resourceType" : "Parameters",
+  "parameter" : [{
+    "name" : "profile-url",
+    "valueString" : "http://hl7.org/fhir/ExpansionProfile/dc8fd4bc-091a-424a-8a3b-6198ef146891"
+  }]
+}}####
+v: {
+  "display" : "Systolic blood pressure by Noninvasive",
+  "code" : "76534-7",
+  "system" : "http://loinc.org",
+  "version" : "2.74",
+  "server" : "http://tx-dev.fhir.org/r4",
+  "unknown-systems" : "",
+  "issues" : {
+  "resourceType" : "OperationOutcome"
+}
+
+}
+-------------------------------------------------------------------------------------
+{"code" : {
+  "system" : "http://loinc.org",
+  "code" : "76534-7"
+}, "url": "http://hl7.org/fhir/ValueSet/observation-vitalsignresult--0", "version": "4.0.1", "langs":"", "useServer":"true", "useClient":"false", "guessSystem":"false", "activeOnly":"false", "membershipOnly":"false", "displayWarningMode":"false", "versionFlexible":"false", "profile": {
+  "resourceType" : "Parameters",
+  "parameter" : [{
+    "name" : "profile-url",
+    "valueString" : "http://hl7.org/fhir/ExpansionProfile/dc8fd4bc-091a-424a-8a3b-6198ef146891"
+  }]
+}}####
+v: {
+  "display" : "Systolic blood pressure by Noninvasive",
+  "code" : "76534-7",
+  "severity" : "error",
+  "error" : "The provided code 'http://loinc.org#76534-7' was not found in the value set 'http://hl7.org/fhir/ValueSet/observation-vitalsignresult--0|4.0.1'",
+  "class" : "UNKNOWN",
+  "server" : "http://tx-dev.fhir.org/r4",
+  "unknown-systems" : "",
+  "issues" : {
+  "resourceType" : "OperationOutcome",
+  "issue" : [{
+    "extension" : [{
+      "url" : "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-server",
+      "valueUrl" : "http://tx-dev.fhir.org/r4"
+    }],
+    "severity" : "error",
+    "code" : "code-invalid",
+    "details" : {
+      "coding" : [{
+        "system" : "http://hl7.org/fhir/tools/CodeSystem/tx-issue-type",
+        "code" : "not-in-vs"
+      }],
+      "text" : "The provided code 'http://loinc.org#76534-7' was not found in the value set 'http://hl7.org/fhir/ValueSet/observation-vitalsignresult--0|4.0.1'"
+    },
+    "location" : ["Coding.code"],
+    "expression" : ["Coding.code"]
+  }]
+}
+
+}
+-------------------------------------------------------------------------------------

org.hl7.fhir.validation/src/test/resources/txCache/org.hl7.fhir.validation/4.0.1/smart-app-launchCodeSystemuser-access-category.cache

@@ -0,0 +1,42 @@
+-------------------------------------------------------------------------------------
+{"code" : {
+  "system" : "http://hl7.org/fhir/smart-app-launch/CodeSystem/user-access-category",
+  "code" : "laboratory",
+  "display" : "Laboratory"
+}, "valueSet" :null, "langs":"", "useServer":"true", "useClient":"false", "guessSystem":"false", "activeOnly":"false", "membershipOnly":"false", "displayWarningMode":"false", "versionFlexible":"false", "profile": {
+  "resourceType" : "Parameters",
+  "parameter" : [{
+    "name" : "profile-url",
+    "valueString" : "http://hl7.org/fhir/ExpansionProfile/dc8fd4bc-091a-424a-8a3b-6198ef146891"
+  }]
+}}####
+v: {
+  "code" : "laboratory",
+  "severity" : "error",
+  "error" : "A definition for CodeSystem 'http://hl7.org/fhir/smart-app-launch/CodeSystem/user-access-category' could not be found, so the code cannot be validated",
+  "class" : "CODESYSTEM_UNSUPPORTED",
+  "server" : "http://tx-dev.fhir.org/r4",
+  "unknown-systems" : "http://hl7.org/fhir/smart-app-launch/CodeSystem/user-access-category",
+  "issues" : {
+  "resourceType" : "OperationOutcome",
+  "issue" : [{
+    "extension" : [{
+      "url" : "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-server",
+      "valueUrl" : "http://tx-dev.fhir.org/r4"
+    }],
+    "severity" : "error",
+    "code" : "not-found",
+    "details" : {
+      "coding" : [{
+        "system" : "http://hl7.org/fhir/tools/CodeSystem/tx-issue-type",
+        "code" : "not-found"
+      }],
+      "text" : "A definition for CodeSystem 'http://hl7.org/fhir/smart-app-launch/CodeSystem/user-access-category' could not be found, so the code cannot be validated"
+    },
+    "location" : ["Coding.system"],
+    "expression" : ["Coding.system"]
+  }]
+}
+
+}
+-------------------------------------------------------------------------------------

org.hl7.fhir.validation/src/test/resources/txCache/org.hl7.fhir.validation/4.0.1/vs-externals.json

@@ -8,6 +8,7 @@
     "server" : "https://tx.ontoserver.csiro.au/fhir",
     "filename" : "vs-2a3253d9-d12e-45f3-877e-0dc2654b3904.json"
   },
+  "http://hl7.org/fhir/smart-app-launch/ValueSet/user-access-category" : null,
   "http://fhir.ch/ig/ch-ig/ValueSet/OrganizationType" : null,
   "http://loinc.org/vs/LL4048-6" : null,
   "https://fhir.kbv.de/ValueSet/KBV_VS_SFHIR_ICD_SEITENLOKALISATION" : null

org.hl7.fhir.validation/src/test/resources/txCache/org.hl7.fhir.validation/5.0.0/all-systems.cache

@@ -214,7 +214,6 @@ v: {
   "code" : "text/plain",
   "system" : "urn:ietf:bcp:13",
   "server" : "http://tx-dev.fhir.org/r4",
-  "unknown-systems" : "",
   "issues" : {
   "resourceType" : "OperationOutcome"
 }
@@ -239,7 +238,6 @@ v: {
   "error" : "The provided code 'http://snomed.info/sct#271649006 ('Systolic blood pressure')' was not found in the value set 'http://hl7.org/fhir/ValueSet/observation-vitalsignresult|5.0.0'",
   "class" : "UNKNOWN",
   "server" : "http://tx-dev.fhir.org/r4",
-  "unknown-systems" : "",
   "issues" : {
   "resourceType" : "OperationOutcome",
   "issue" : [{
@@ -277,7 +275,6 @@ v: {
   "code" : "json",
   "system" : "urn:ietf:bcp:13",
   "server" : "http://tx-dev.fhir.org/r4",
-  "unknown-systems" : "",
   "issues" : {
   "resourceType" : "OperationOutcome"
 }
@@ -299,7 +296,6 @@ v: {
   "code" : "001",
   "system" : "http://unstats.un.org/unsd/methods/m49/m49.htm",
   "server" : "http://tx-dev.fhir.org/r4",
-  "unknown-systems" : "",
   "issues" : {
   "resourceType" : "OperationOutcome",
   "issue" : [{
@@ -335,7 +331,6 @@ v: {
   "code" : "nl-NL",
   "system" : "urn:ietf:bcp:47",
   "server" : "http://tx-dev.fhir.org/r4",
-  "unknown-systems" : "",
   "issues" : {
   "resourceType" : "OperationOutcome"
 }
@@ -356,7 +351,6 @@ v: {
   "code" : "en-AU",
   "system" : "urn:ietf:bcp:47",
   "server" : "http://tx-dev.fhir.org/r4",
-  "unknown-systems" : "",
   "issues" : {
   "resourceType" : "OperationOutcome"
 }
@@ -377,7 +371,6 @@ v: {
   "code" : "en",
   "system" : "urn:ietf:bcp:47",
   "server" : "http://tx-dev.fhir.org/r4",
-  "unknown-systems" : "",
   "issues" : {
   "resourceType" : "OperationOutcome"
 }
@@ -400,7 +393,6 @@ v: {
   "code" : "001",
   "system" : "http://unstats.un.org/unsd/methods/m49/m49.htm",
   "server" : "http://tx-dev.fhir.org/r4",
-  "unknown-systems" : "",
   "issues" : {
   "resourceType" : "OperationOutcome",
   "issue" : [{
@@ -422,3 +414,24 @@ v: {
 
 }
 -------------------------------------------------------------------------------------
+{"code" : {
+  "code" : "image/gif"
+}, "url": "http://hl7.org/fhir/ValueSet/mimetypes", "version": "5.0.0", "langs":"", "useServer":"true", "useClient":"true", "guessSystem":"true", "activeOnly":"false", "membershipOnly":"false", "displayWarningMode":"false", "versionFlexible":"false", "profile": {
+  "resourceType" : "Parameters",
+  "parameter" : [{
+    "name" : "profile-url",
+    "valueString" : "http://hl7.org/fhir/ExpansionProfile/dc8fd4bc-091a-424a-8a3b-6198ef146891"
+  }]
+}}####
+v: {
+  "display" : "image/gif",
+  "code" : "image/gif",
+  "system" : "urn:ietf:bcp:13",
+  "server" : "http://tx-dev.fhir.org/r4",
+  "unknown-systems" : "",
+  "issues" : {
+  "resourceType" : "OperationOutcome"
+}
+
+}
+-------------------------------------------------------------------------------------