Merge pull request #480 from hapifhir/gg-202104-bugfixes

Gg 202104 bugfixes

RELEASE_NOTES.md

@@ -0,0 +1,5 @@
+* Breaking Change: Fix issue where primitive elements with required bindings must have a value, but this wasn't be checked
+* Fix bug with value set imports not working
+* Fix bug with base definitions not working properly for logical models
+* Better memory tracking for validator
+* Get code generator compiling

org.hl7.fhir.core.generator/src/org/hl7/fhir/core/generator/codegen/JavaResourceGenerator.java

@@ -996,7 +996,7 @@ private void generatePropertyMaker(Analysis analysis, TypeInfo ti, String indent
   private List<TypeRefComponent> getTypes(List<TypeRefComponent> types) {
     if (types.size() == 1 && types.get(0).getName().equals("*")) {
       List<TypeRefComponent> t = new ArrayList<TypeRefComponent>();
-      for (String s : TypesUtilities.wildcardTypes()) {
+      for (String s : TypesUtilities.wildcardTypes("5.0")) {
         t.add(new TypeRefComponent(s));
       }
       return t;

org.hl7.fhir.core.generator/src/org/hl7/fhir/core/generator/engine/DefinitionsLoader.java

@@ -13,8 +13,8 @@ import org.hl7.fhir.r5.model.Resource;
 import org.hl7.fhir.r5.model.SearchParameter;
 import org.hl7.fhir.r5.model.StructureDefinition;
 import org.hl7.fhir.r5.model.ValueSet;
-import org.hl7.fhir.utilities.cache.NpmPackage;
+import org.hl7.fhir.utilities.npm.NpmPackage;
-import org.hl7.fhir.utilities.cache.ToolsVersion;
+import org.hl7.fhir.utilities.npm.ToolsVersion;
 
 public class DefinitionsLoader {
 

org.hl7.fhir.core.generator/src/org/hl7/fhir/core/generator/engine/JavaCoreGenerator.java

@@ -30,9 +30,9 @@ import org.hl7.fhir.r5.model.SearchParameter;
 import org.hl7.fhir.r5.model.StructureDefinition;
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;
-import org.hl7.fhir.utilities.cache.FilesystemPackageCacheManager;
+import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
-import org.hl7.fhir.utilities.cache.NpmPackage;
+import org.hl7.fhir.utilities.npm.NpmPackage;
-import org.hl7.fhir.utilities.cache.ToolsVersion;
+import org.hl7.fhir.utilities.npm.ToolsVersion;
 
 public class JavaCoreGenerator {
 

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

@@ -2989,7 +2989,7 @@ public class ProfileUtilities extends TranslatingUtilities {
       }
       if (!ok) {
         StructureDefinition sdt = context.fetchTypeDefinition(tt);
-        if (sdt != null && sdt.getAbstract()) {
+        if (sdt != null && (sdt.getAbstract() || sdt.getKind() == StructureDefinitionKind.LOGICAL)) {
           StructureDefinition sdb = context.fetchTypeDefinition(t);
           while (sdb != null && !ok) {
             ok = sdb.getType().equals(sdt.getType());

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

@@ -923,13 +923,21 @@ public class ValueSetRenderer extends TerminologyRenderer {
       }
     } else {
       li.tx("Import all the codes that are contained in ");
-      boolean first = true;
+      if (inc.getValueSet().size() < 4) {
-      for (UriType vs : inc.getValueSet()) {
+        boolean first = true;
-        if (first)
+        for (UriType vs : inc.getValueSet()) {
-          first = false;
+          if (first)
-        else
+            first = false;
-          li.tx(", ");
+          else
-        AddVsRef(vs.asStringValue(), li);
+            li.tx(", ");
+          AddVsRef(vs.asStringValue(), li);
+        }
+      } else {
+        XhtmlNode xul = li.ul();
+        for (UriType vs : inc.getValueSet()) {
+          AddVsRef(vs.asStringValue(), xul.li());
+        }
+        
       }
     }
     return hasExtensions;

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/ValueSetExpanderSimple.java

@@ -510,10 +510,31 @@ public class ValueSetExpanderSimple implements ValueSetExpander {
       if (!existsInParams(exp.getParameter(), p.getName(), p.getValue()))
         exp.getParameter().add(p);
     }
+    copyExpansion(vso.getValueset().getExpansion().getContains());
     canBeHeirarchy = false; // if we're importing a value set, we have to be combining, so we won't try for a heirarchy
     return vso.getValueset();
   }
 
+  public void copyExpansion(List<ValueSetExpansionContainsComponent> list) {
+    for (ValueSetExpansionContainsComponent cc : list) {
+       ValueSetExpansionContainsComponent n = new ValueSet.ValueSetExpansionContainsComponent();
+       n.setSystem(cc.getSystem());
+       n.setCode(cc.getCode());
+       n.setAbstract(cc.getAbstract());
+       n.setInactive(cc.getInactive());
+       n.setDisplay(cc.getDisplay());
+       n.getDesignation().addAll(cc.getDesignation());
+
+       String s = key(n);
+       if (!map.containsKey(s) && !excludeKeys.contains(s)) {
+         codes.add(n);
+         map.put(s, n);
+         total++;
+       }
+       copyExpansion(cc.getContains());
+    }
+  }
+
   private void addErrors(List<String> errs) {
     for (String s : errs) {
       if (!allErrors.contains(s)) {

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

@@ -54,9 +54,9 @@ public class OperationOutcomeUtilities {
       issue.addExpression(message.getLocation());
     }
     // pass through line/col if they're present
-    if (message.getLine() != 0)
+    if (message.getLine() >= 0)
       issue.addExtension().setUrl(ToolingExtensions.EXT_ISSUE_LINE).setValue(new IntegerType(message.getLine()));
-    if (message.getCol() != 0)
+    if (message.getCol() >= 0)
       issue.addExtension().setUrl(ToolingExtensions.EXT_ISSUE_COL).setValue(new IntegerType(message.getCol()));
     issue.setSeverity(convert(message.getLevel()));
     CodeableConcept c = new CodeableConcept();

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

@@ -1346,6 +1346,21 @@ public class Utilities {
     return length + BT;
   }
 
+  public static String describeSize(long length) {
+    if (length < 0) throw new IllegalArgumentException("File length of < 0  passed in...");
+
+    if (length > Math.pow(ONE_MB, 3)) {
+      return length / ((long) Math.pow(ONE_MB, 3)) + GB;
+    }
+    if (length > Math.pow(ONE_MB, 2)) {
+      return length / ((long) Math.pow(ONE_MB, 2)) + MB;
+    }
+    if (length > ONE_MB) {
+      return length / (ONE_MB) + KB;
+    }
+    return length + BT;
+  }
+
   public static List<byte[]> splitBytes(byte[] array, byte[] delimiter) {
     List<byte[]> byteArrays = new LinkedList<byte[]>();
     if (delimiter.length == 0)

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/i18n/I18nConstants.java

@@ -386,6 +386,7 @@ public class I18nConstants {
   public static final String TERMINOLOGY_TX_CODE_NOTVALID = "Terminology_TX_Code_NotValid";
   public static final String TERMINOLOGY_TX_CODE_UNKNOWN = "Terminology_TX_Code_Unknown";
   public static final String TERMINOLOGY_TX_CODE_VALUESET = "Terminology_TX_Code_ValueSet";
+  public static final String Terminology_TX_Code_ValueSet_MISSING = "Terminology_TX_Code_ValueSet_MISSING";
   public static final String TERMINOLOGY_TX_CODE_VALUESETMAX = "Terminology_TX_Code_ValueSetMax";
   public static final String TERMINOLOGY_TX_CODE_VALUESET_EXT = "Terminology_TX_Code_ValueSet_Ext";
   public static final String TERMINOLOGY_TX_CODING_COUNT = "Terminology_TX_Coding_Count";

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/validation/ValidationMessage.java

@@ -164,6 +164,9 @@ public class ValidationMessage implements Comparator<ValidationMessage>, Compara
     public boolean isError() {
       return this == FATAL || this == ERROR;
     }
+    public boolean isHint() {
+      return this == INFORMATION;
+    }
   }
 
   public enum IssueType {

org.hl7.fhir.utilities/src/main/resources/Messages.properties

@@ -130,6 +130,7 @@ Terminology_TX_Binding_NoSource2 = Binding has no source, so can''t be checked
 Terminology_TX_Code_NotValid = Code {0} is not a valid code in code system {1}
 Terminology_TX_Code_Unknown = Unknown Code ({0}#{1})
 Terminology_TX_Code_ValueSet = No code provided, and a code is required from the value set {0} ({1})
+Terminology_TX_Code_ValueSet_MISSING = No code provided, and a code is required from the value set
 Terminology_TX_Code_ValueSetMax = No code provided, and a code must be provided from the value set {0} (max value set {1})
 Terminology_TX_Code_ValueSet_Ext = No code provided, and a code should be provided from the value set {0} ({1})
 Terminology_TX_Coding_Count = Expected {0} but found {1} coding elements

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

@@ -61,6 +61,7 @@ POSSIBILITY OF SUCH DAMAGE.
 import org.hl7.fhir.r5.model.ImplementationGuide;
 import org.hl7.fhir.r5.model.StructureDefinition;
 import org.hl7.fhir.utilities.TimeTracker;
+import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.VersionUtilities;
 import org.hl7.fhir.validation.cli.model.CliContext;
 import org.hl7.fhir.validation.cli.services.ComparisonService;
@@ -238,6 +239,6 @@ public class ValidatorCli {
         }
         break;
     }
-    System.out.println("Done. " + tt.report());
+    System.out.println("Done. " + tt.report()+". Max Memory = "+Utilities.describeSize(Runtime.getRuntime().maxMemory()));
   }
 }

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

@@ -24,6 +24,8 @@ import org.hl7.fhir.validation.cli.utils.EngineMode;
 import org.hl7.fhir.validation.cli.utils.VersionSourceInformation;
 
 import java.io.FileOutputStream;
+import java.lang.management.ManagementFactory;
+import java.lang.management.MemoryMXBean;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -66,6 +68,7 @@ public class ValidationService {
       messages.forEach(outcome::addMessage);
       response.addOutcome(outcome);
     }
+    System.out.println("  Max Memory: "+Runtime.getRuntime().maxMemory());
     return response;
   }
 
@@ -87,7 +90,8 @@ public class ValidationService {
     List<ValidationRecord> records = new ArrayList<>();
     Resource r = validator.validate(cliContext.getSources(), cliContext.getProfiles(), records);
     int ec = 0;
-    System.out.println("Done. " + validator.getContext().clock().report());
+    MemoryMXBean mbean = ManagementFactory.getMemoryMXBean();
+    System.out.println("Done. " + validator.getContext().clock().report()+". Memory = "+Utilities.describeSize(mbean.getHeapMemoryUsage().getUsed()+mbean.getNonHeapMemoryUsage().getUsed()));
     System.out.println();
 
     if (cliContext.getOutput() == null) {
@@ -211,7 +215,9 @@ public class ValidationService {
   public String initializeValidator(CliContext cliContext, String definitions, TimeTracker tt, String sessionId) throws Exception {
     tt.milestone();
     if (!sessionCache.sessionExists(sessionId)) {
-      System.out.println("No such cached session exists for session id " + sessionId + ", re-instantiating validator.");
+      if (sessionId != null) {
+        System.out.println("No such cached session exists for session id " + sessionId + ", re-instantiating validator.");
+      }
       System.out.print("  Load FHIR v" + cliContext.getSv() + " from " + definitions);
       ValidationEngine validator = new ValidationEngine(definitions, cliContext.getSv(), tt);
       sessionId = sessionCache.cacheSession(validator);

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

@@ -1907,6 +1907,9 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
         rule(errors, IssueType.INVALID, e.line(), e.col(), path, e.hasChildren(), I18nConstants.TYPE_SPECIFIC_CHECKS_DT_PRIMITIVE_NOTEMPTY);
       else if (StringUtils.isWhitespace(e.primitiveValue()))
         warning(errors, IssueType.INVALID, e.line(), e.col(), path, e.hasChildren(), I18nConstants.TYPE_SPECIFIC_CHECKS_DT_PRIMITIVE_WS);
+      if (context.hasBinding()) {
+        rule(errors, IssueType.CODEINVALID, e.line(), e.col(), path, context.getBinding().getStrength() != BindingStrength.REQUIRED, I18nConstants.Terminology_TX_Code_ValueSet_MISSING);
+      }
       return;
     }
     String regex = context.getExtensionString(ToolingExtensions.EXT_REGEX);

pom.xml

@@ -19,7 +19,7 @@
 
     <properties>
         <hapi_fhir_version>5.1.0</hapi_fhir_version>
-        <validator_test_case_version>1.1.59</validator_test_case_version>
+        <validator_test_case_version>1.1.60-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>