Merge pull request #1517 from hapifhir/2023-12-gg-package-version-loading-fix

fix problem with version dependencies when loading npm packages direc…

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

@@ -64,6 +64,7 @@ import org.hl7.fhir.r5.model.IntegerType;
 import org.hl7.fhir.r5.model.Meta;
 import org.hl7.fhir.r5.model.StringType;
 import org.hl7.fhir.r5.model.UriType;
+import org.hl7.fhir.r5.utils.CanonicalResourceUtilities;
 import org.hl7.fhir.r5.utils.ToolingExtensions;
 import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
 import org.hl7.fhir.utilities.MarkDownProcessor;
@@ -504,7 +505,7 @@ public class CodeSystemUtilities extends TerminologyUtilities {
     if (wg != null) {
       if (!ToolingExtensions.hasExtension(cs, ToolingExtensions.EXT_WORKGROUP) || 
           (Utilities.existsInList(ToolingExtensions.readStringExtension(cs, ToolingExtensions.EXT_WORKGROUP), "fhir", "vocab") && !Utilities.existsInList(wg, "fhir", "vocab"))) {
-        ToolingExtensions.setCodeExtension(cs, ToolingExtensions.EXT_WORKGROUP, wg);
+        CanonicalResourceUtilities.setHl7WG(cs, wg);
       }
     }
     if (status != null) {

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

@@ -64,6 +64,7 @@ import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionContainsComponent;
 import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionPropertyComponent;
 import org.hl7.fhir.r5.terminologies.CodeSystemUtilities.ConceptDefinitionComponentSorter;
 import org.hl7.fhir.r5.terminologies.CodeSystemUtilities.ConceptStatus;
+import org.hl7.fhir.r5.utils.CanonicalResourceUtilities;
 import org.hl7.fhir.r5.utils.ToolingExtensions;
 import org.hl7.fhir.utilities.StandardsStatus;
 import org.hl7.fhir.utilities.Utilities;
@@ -139,7 +140,7 @@ public class ValueSetUtilities extends TerminologyUtilities {
     if (wg != null) {
       if (!ToolingExtensions.hasExtension(vs, ToolingExtensions.EXT_WORKGROUP) || 
           (!Utilities.existsInList(ToolingExtensions.readStringExtension(vs, ToolingExtensions.EXT_WORKGROUP), "fhir", "vocab") && Utilities.existsInList(wg, "fhir", "vocab"))) {
-        ToolingExtensions.setCodeExtension(vs, ToolingExtensions.EXT_WORKGROUP, wg);
+        CanonicalResourceUtilities.setHl7WG(vs, wg);
       }
     }
     if (status != null) {

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

@@ -6,6 +6,8 @@ import org.hl7.fhir.r5.elementmodel.Element;
 import org.hl7.fhir.r5.model.CanonicalResource;
 import org.hl7.fhir.r5.model.CompartmentDefinition;
 import org.hl7.fhir.r5.model.Constants;
+import org.hl7.fhir.r5.model.ContactDetail;
+import org.hl7.fhir.r5.model.ContactPoint;
 import org.hl7.fhir.r5.model.ContactPoint.ContactPointSystem;
 import org.hl7.fhir.utilities.HL7WorkGroups;
 import org.hl7.fhir.utilities.VersionUtilities;
@@ -14,17 +16,33 @@ import org.hl7.fhir.utilities.xml.XMLUtil;
 public class CanonicalResourceUtilities {
 
   public static void setHl7WG(CanonicalResource cr, String wgc) {
+    if ("http://hl7.org/fhir/days-of-week".equals(cr.getUrl())) {
+      System.out.println("!");
+    }
     var wg = HL7WorkGroups.find(wgc);
     if (wg == null) {
       throw new Error("Unknown WG "+wgc);
     }
     ToolingExtensions.setCodeExtension(cr, ToolingExtensions.EXT_WORKGROUP, wg.getCode());
     cr.setPublisher("HL7 International / "+wg.getName());
-    cr.getContact().clear();
+    boolean found = false;
-    cr.addContact().addTelecom().setSystem(ContactPointSystem.URL).setValue(wg.getLink());
+    for (ContactDetail c : cr.getContact()) {
+      for (ContactPoint t : c.getTelecom()) {
+        if ((t.getSystem() == ContactPointSystem.URL) && wg.getLink().equals(t.getValue())) {
+          found = true;
+        }
+      }
+    }
+    if (!found) {
+      cr.addContact().addTelecom().setSystem(ContactPointSystem.URL).setValue(wg.getLink());
+    }
   }
 
   public static void setHl7WG(CanonicalResource cr) {
+    if ("http://hl7.org/fhir/days-of-week".equals(cr.getUrl())) {
+      System.out.println("!");
+    }
+
     String wgc = ToolingExtensions.readStringExtension(cr, ToolingExtensions.EXT_WORKGROUP);
     if (wgc == null) {
       wgc = "fhir";      
@@ -35,8 +53,17 @@ public class CanonicalResourceUtilities {
     }
     ToolingExtensions.setCodeExtension(cr, ToolingExtensions.EXT_WORKGROUP, wg.getCode());
     cr.setPublisher("HL7 International / "+wg.getName());
-    cr.getContact().clear();
+    boolean found = false;
-    cr.addContact().addTelecom().setSystem(ContactPointSystem.URL).setValue(wg.getLink());
+    for (ContactDetail c : cr.getContact()) {
+      for (ContactPoint t : c.getTelecom()) {
+        if ((t.getSystem() == ContactPointSystem.URL) && wg.getLink().equals(t.getValue())) {
+          found = true;
+        }
+      }
+    }
+    if (!found) {
+      cr.addContact().addTelecom().setSystem(ContactPointSystem.URL).setValue(wg.getLink());
+    }
   }
 
   public static void setHl7WG(Element res, String code) {

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

@@ -264,6 +264,7 @@ public class ToolingExtensions {
   public static final String EXT_ARTIFACT_NAME = "http://hl7.org/fhir/StructureDefinition/artifact-name";
   public static final String EXT_ARTIFACT_DESC = "http://hl7.org/fhir/StructureDefinition/artifact-description";  
   public static final String EXT_ED_SUPPRESS = "http://hl7.org/fhir/StructureDefinition/elementdefinition-suppress";
+  public static final String EXT_SEARCH_PARAMETER_BASE = "http://hl7.org/fhir/tools/StructureDefinition/searchparameter-base-type";;
   
   // specific extension helpers
 

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

@@ -105,6 +105,14 @@ public class IgLoader implements IValidationEngineLoader {
     }
 
     NpmPackage npm = srcPackage.matches(FilesystemPackageCacheManager.PACKAGE_VERSION_REGEX_OPT) && !new File(srcPackage).exists() ? getPackageCacheManager().loadPackage(srcPackage, null) : null;
+    if (npm == null && new File(srcPackage).exists()) {
+      // try treating the file as an npm
+      try {
+        npm = NpmPackage.fromPackage(new FileInputStream(srcPackage));
+      } catch (Exception e) {
+        // nothing - any errors will be properly handled later in the process
+      }
+    }
     if (npm != null) {
       for (String s : npm.dependencies()) {
         if (!getContext().getLoadedPackages().contains(s)) {

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/SearchParameterValidator.java

@@ -12,6 +12,7 @@ import org.hl7.fhir.r5.fhirpath.ExpressionNode.Kind;
 import org.hl7.fhir.r5.fhirpath.ExpressionNode.Operation;
 import org.hl7.fhir.r5.fhirpath.FHIRPathEngine.IssueMessage;
 import org.hl7.fhir.r5.model.SearchParameter;
+import org.hl7.fhir.r5.utils.ToolingExtensions;
 import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.i18n.I18nConstants;
 import org.hl7.fhir.utilities.validation.ValidationMessage;
@@ -45,9 +46,15 @@ public class SearchParameterValidator extends BaseValidator {
     if (cs.hasChild("expression", false)) {
       List<String> bases = new ArrayList<>();
       for (Element b : cs.getChildrenByName("base")) {
-        bases.add(b.primitiveValue());
+        if (b.hasExtension(ToolingExtensions.EXT_SEARCH_PARAMETER_BASE)) {
+          bases.add(b.getExtensionValue(ToolingExtensions.EXT_SEARCH_PARAMETER_BASE).primitiveValue());
+        } else {
+          bases.add(b.primitiveValue());
+        }
+      }
+      if (!bases.isEmpty()) { // that'd be an error somewhere else
+        ok = checkExpression(errors, stack.push(cs.getNamedChild("expression", false), -1, null, null), cs.getNamedChildValue("expression", false), bases) && ok;
       }
-      ok = checkExpression(errors, stack.push(cs.getNamedChild("expression", false), -1, null, null), cs.getNamedChildValue("expression", false), bases) && ok;
     }
     String master = cs.getNamedChildValue("derivedFrom", false);
     if (!Utilities.noString(master)) {