Merge pull request #1179 from hapifhir/gg-202303-various-fixes

Gg 202303 various fixes

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/loaders/loaderR5/BaseLoaderR5.java

@@ -24,6 +24,7 @@ import org.hl7.fhir.r5.model.ElementDefinition.TypeRefComponent;
 import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.VersionUtilities;
 import org.hl7.fhir.utilities.npm.NpmPackage;
+import org.hl7.fhir.utilities.npm.NpmPackage.PackageResourceInformation;
 
 import com.google.gson.JsonSyntaxException;
 
@@ -40,6 +41,7 @@ public abstract class BaseLoaderR5 implements IContextResourceLoader {
   @Getter @Setter protected boolean killPrimitives;
   @Getter protected List<String> types = new ArrayList<>();
   protected ILoaderKnowledgeProviderR5 lkp;
+  private boolean loadProfiles = true;
 
   public BaseLoaderR5(List<String> types, ILoaderKnowledgeProviderR5 lkp) {
     super();
@@ -169,6 +171,12 @@ public abstract class BaseLoaderR5 implements IContextResourceLoader {
         String url = URL_BASE+versionString()+"/StructureDefinition/"+code;
         ToolingExtensions.setUrlExtension(tr, ToolingExtensions.EXT_FHIR_TYPE, url);
       }
+      for (CanonicalType c : tr.getProfile()) {
+        c.setValue(patchUrl(c.getValue(), "StructureDefinition"));
+      }
+      for (CanonicalType c : tr.getTargetProfile()) {
+        c.setValue(patchUrl(c.getValue(), "StructureDefinition"));
+      }
     }
     if (ed.hasBinding()) {
       ed.getBinding().setValueSet(patchUrl(ed.getBinding().getValueSet(), "ValueSet"));
@@ -178,4 +186,20 @@ public abstract class BaseLoaderR5 implements IContextResourceLoader {
     }
   }
 
+  public IContextResourceLoader setLoadProfiles(boolean value) {
+    loadProfiles = value;
+    return this;
+  }
+  
+  public boolean wantLoad(NpmPackage pi, PackageResourceInformation pri) {
+    if (pri.getResourceType().equals("StructureDefinition")) {
+      if (loadProfiles) {
+        return true;
+      } else {
+        return pi.isCore() && Utilities.tail(pri.getUrl()).equals(pri.getStatedType());
+      }
+    } else {
+      return true;
+    }
+  }
 }

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

@@ -661,10 +661,7 @@ public class ProfileUtilities extends TranslatingUtilities {
                 System.out.println("  "+ed.getId()+" = "+ed.getPath()+" : "+typeSummaryWithProfile(ed)+"["+ed.getMin()+".."+ed.getMax()+"]"+sliceSummary(ed)+"  "+constraintSummary(ed));
             }
           }
-          if (exception)
+          handleError(url, msg);
-            throw new DefinitionException(msg);
-          else
-            messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url, msg, ValidationMessage.IssueSeverity.ERROR));
         }
         // hack around a problem in R4 definitions (somewhere?)
         for (ElementDefinition ed : derived.getSnapshot().getElement()) {
@@ -712,14 +709,20 @@ public class ProfileUtilities extends TranslatingUtilities {
                 if (ed.getPath().equals("Bundle.entry.response.outcome")) {
                   wt = "OperationOutcome";
                 }
-                if (!sd.getType().equals(wt)) {
+                String tt = sd.getType();
-                  boolean ok = isCompatibleType(wt, sd);
+                boolean elementProfile = u.hasExtension(ToolingExtensions.EXT_PROFILE_ELEMENT);
+                if (elementProfile) {
+                  ElementDefinition edt = sd.getSnapshot().getElementById(u.getExtensionString(ToolingExtensions.EXT_PROFILE_ELEMENT));
+                  if (edt == null) {
+                    handleError(url, "The profile "+u.getValue()+" has type "+sd.getType()+" which is not consistent with the stated type "+wt);
+                  } else {
+                    tt = edt.typeSummary();
+                  }
+                }
+                if (!tt.equals(wt)) {
+                  boolean ok = !elementProfile && isCompatibleType(wt, sd);
                   if (!ok) {
-                    String smsg = "The profile "+u.getValue()+" has type "+sd.getType()+" which is not consistent with the stated type "+wt;
+                    handleError(url, "The profile "+u.getValue()+" has type "+sd.getType()+" which is not consistent with the stated type "+wt);
-                    if (exception)
-                      throw new DefinitionException(smsg);
-                    else
-                      messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url+"#"+ed.getId(), smsg, IssueSeverity.ERROR));
                   }
                 }
               }
@@ -738,6 +741,13 @@ public class ProfileUtilities extends TranslatingUtilities {
     }
   }
 
+  private void handleError(String url, String msg) {
+    if (exception)
+      throw new DefinitionException(msg);
+    else
+      messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url, msg, ValidationMessage.IssueSeverity.ERROR));
+  }
+
 
 
 

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

@@ -77,6 +77,7 @@ import org.hl7.fhir.utilities.TimeTracker;
 import org.hl7.fhir.utilities.TranslationServices;
 import org.hl7.fhir.utilities.npm.BasePackageCacheManager;
 import org.hl7.fhir.utilities.npm.NpmPackage;
+import org.hl7.fhir.utilities.npm.NpmPackage.PackageResourceInformation;
 import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
 import org.hl7.fhir.utilities.validation.ValidationMessage;
 import org.hl7.fhir.utilities.validation.ValidationOptions;
@@ -338,6 +339,23 @@ public interface IWorkerContext {
      * @return
      */
     String patchUrl(String url, String resourceType);
+    
+    /** 
+     * set this to false (default is true) if you don't want profiles loaded
+     * @param value
+     * @return
+     */
+    IContextResourceLoader setLoadProfiles(boolean value);
+    
+    /**
+     * Called during the loading process - the loader can decide which resources to load. 
+     * At this point, only the .index.json is being read 
+     *  
+     * @param pi
+     * @param pri
+     * @return
+     */
+    boolean wantLoad(NpmPackage pi, PackageResourceInformation pri);
   }
 
   /**

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

@@ -492,7 +492,7 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
         types = Utilities.strings("StructureDefinition", "ValueSet", "CodeSystem", "SearchParameter", "OperationDefinition", "Questionnaire", "ConceptMap", "StructureMap", "NamingSystem", "Measures" );
       }
       for (PackageResourceInformation pri : pi.listIndexedResources(types)) {
-        if (!pri.getFilename().contains("ig-r4")) {
+        if (!pri.getFilename().contains("ig-r4") && (loader == null || loader.wantLoad(pi, pri))) {
           try {
             registerResourceFromPackage(new PackageResourceLoader(pri, loader), new PackageInformation(pi));
             t++;

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

@@ -394,7 +394,7 @@ public class FmlParser extends ParserBase {
         if (rule.getChildrenByName("source").size() != 1 || !rule.getChildrenByName("source").get(0).hasChild("element"))
           throw lexer.error("Complex rules must have an explicit name");
         if (rule.getChildrenByName("source").get(0).hasChild("type"))
-          rule.makeElement("name").setValue(rule.getChildrenByName("source").get(0).getNamedChildValue("element") + rule.getChildrenByName("source").get(0).getNamedChildValue("type"));
+          rule.makeElement("name").setValue(rule.getChildrenByName("source").get(0).getNamedChildValue("element") + Utilities.capitalize(rule.getChildrenByName("source").get(0).getNamedChildValue("type")));
         else
           rule.makeElement("name").setValue(rule.getChildrenByName("source").get(0).getNamedChildValue("element"));
       }

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

@@ -1245,6 +1245,20 @@ public class StructureDefinition extends CanonicalResource {
     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.r5/src/main/java/org/hl7/fhir/r5/renderers/StructureMapRenderer.java

@@ -461,7 +461,7 @@ public class StructureMapRenderer extends TerminologyRenderer {
     if (n.equals(s) || n.equals("\"" + s + "\""))
       return true;
     if (source.get(0).hasType()) {
-      s = source.get(0).getElement() + "-" + source.get(0).getType();
+      s = source.get(0).getElement() + Utilities.capitalize(source.get(0).getType());
       return n.equals(s) || n.equals("\"" + s + "\"");
     }
     return false;

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/test/utils/TestPackageLoader.java

@@ -13,6 +13,7 @@ import org.hl7.fhir.r5.model.Bundle;
 import org.hl7.fhir.r5.model.CodeSystem;
 import org.hl7.fhir.r5.model.Resource;
 import org.hl7.fhir.utilities.npm.NpmPackage;
+import org.hl7.fhir.utilities.npm.NpmPackage.PackageResourceInformation;
 
 public class TestPackageLoader implements IContextResourceLoader {
 
@@ -62,4 +63,14 @@ public class TestPackageLoader implements IContextResourceLoader {
     return url;
   }
 
+  @Override
+  public IContextResourceLoader setLoadProfiles(boolean value) {
+    return this;
+  }
+
+  @Override
+  public boolean wantLoad(NpmPackage pi, PackageResourceInformation pri) {
+    return true;
+  }
+
 }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/structuremap/StructureMapUtilities.java

@@ -1000,7 +1000,7 @@ public class StructureMapUtilities {
         if (rule.getSource().size() != 1 || !rule.getSourceFirstRep().hasElement() && exceptionsForChecks )
           throw lexer.error("Complex rules must have an explicit name");
         if (rule.getSourceFirstRep().hasType())
-          rule.setName(rule.getSourceFirstRep().getElement() + "-" + rule.getSourceFirstRep().getType());
+          rule.setName(rule.getSourceFirstRep().getElement() + Utilities.capitalize(rule.getSourceFirstRep().getType()));
         else
           rule.setName(rule.getSourceFirstRep().getElement());
       }

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

@@ -1543,10 +1543,13 @@ public class Utilities {
       ZipEntry zipEntry = zis.getNextEntry();
       while (zipEntry != null) {
         boolean isDirectory = false;
-        if (zipEntry.getName().endsWith("/") || zipEntry.getName().endsWith("\\")) {
+        
+        String n = makeOSSafe(zipEntry.getName());
+      
+        if (n.endsWith(File.separator)) {
           isDirectory = true;
         }
-        Path newPath = zipSlipProtect(zipEntry, target);
+        Path newPath = zipSlipProtect(n, target);
         if (isDirectory) {
           Files.createDirectories(newPath);
         } else {
@@ -1563,19 +1566,23 @@ public class Utilities {
     }
   }
 
-  public static Path zipSlipProtect(ZipEntry zipEntry, Path targetDir)
+  public static String makeOSSafe(String name) {
+    return name.replace("\\", File.separator).replace("/", File.separator);
+  }
+
+  public static Path zipSlipProtect(String zipName, Path targetDir)
       throws IOException {
 
     // test zip slip vulnerability
     // Path targetDirResolved = targetDir.resolve("../../" + zipEntry.getName());
 
-    Path targetDirResolved = targetDir.resolve(zipEntry.getName());
+    Path targetDirResolved = targetDir.resolve(zipName);
 
     // make sure normalized file still has targetDir as its prefix
     // else throws exception
     Path normalizePath = targetDirResolved.normalize();
     if (!normalizePath.startsWith(targetDir)) {
-      throw new IOException("Bad zip entry: " + zipEntry.getName());
+      throw new IOException("Bad zip entry: " + zipName);
     }
 
     return normalizePath;
@@ -1920,7 +1927,7 @@ public class Utilities {
       if (ignoreList == null || !ignoreList.contains(f.getAbsolutePath())) {
         if (f.isDirectory()) {
           addAllFiles(res, root, f, ignoreList);
-        } else {
+        } else if (!f.getName().equals(".DS_Store")) {
           res.add(getRelativePath(root, f.getAbsolutePath()));
         }
       }

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

@@ -2646,7 +2646,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     if (fetcher != null && !type.equals("uuid")) {
       boolean found;
       try {
-        found = isDefinitionURL(url) || (allowExamples && (url.contains("example.org") || url.contains("acme.com")) || url.contains("acme.org")) || (url.startsWith("http://hl7.org/fhir/tools")) || 
+        found = isDefinitionURL(url) || (allowExamples && (url.contains("example.org") || url.contains("acme.com")) || url.contains("acme.org")) /* || (url.startsWith("http://hl7.org/fhir/tools")) */ || 
             SpecialExtensions.isKnownExtension(url) || isXverUrl(url);
         if (!found) {
           found = fetcher.resolveURL(this, hostContext, path, url, type);

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

@@ -199,6 +199,11 @@ public class StructureMapValidator extends BaseValidator {
       return sd.getUrl().equals(other.sd.getUrl()) && ed.getPath().equals(other.ed.getPath()) && Utilities.stringsEqual(type, other.type);
     }
 
+    @Override
+    public String toString() {
+      return summary();
+    }
+
   }
 
   public class VariableSet {
@@ -623,10 +628,16 @@ public class StructureMapValidator extends BaseValidator {
           } else {
             ok = false;
           }
-        }
           // check condition
           // check check
         }
+      } else {
+        String variable = source.getChildValue("variable");
+        if (variable != null) {
+          variables.add(variable, v.getMode()); // may overwrite
+
+        }      
+      }
     } 
     return ok;
   }
@@ -873,7 +884,7 @@ public class StructureMapValidator extends BaseValidator {
     // under some special conditions, we can infer what the type will be:
     //  * there's a nominated default variable 
     //  * that variable has as single type
-    //  * there's a create with no param
+    //  * there's a create/copy with no param
     //  * there's a single dependent rule with name = StructureMapUtilities.DEF_GROUP_NAME
     //  * there's a default type group for the type of the source type 
     // otherwise, we can't know the target type. 
@@ -882,11 +893,25 @@ public class StructureMapValidator extends BaseValidator {
       VariableDefn v = variables.getVariable(ruleInfo.getDefVariable(), SOURCE);
       if (v != null && v.getEd() != null  && (v.getEd().getType().size() == 1 || v.getType() != null)) {
         List<Element> dependents = rule.getChildrenByName("dependent");
-        if (dependents.size() == 1 && StructureMapUtilities.DEF_GROUP_NAME.equals(dependents.get(0).getChildValue("name"))) {
         String type = v.getType() != null ? getTypeFromDefn(v.getEd(), v.getType()) : v.getEd().getTypeFirstRep().getWorkingCode();
+        if (dependents.size() == 1 && StructureMapUtilities.DEF_GROUP_NAME.equals(dependents.get(0).getChildValue("name"))) {
           // now, we look for a default group.
           // todo: look in this source
           // now look through the inputs
+          for (StructureMap map : imports) {
+            for (StructureMapGroupComponent grp : map.getGroup()) {
+              if (grp.getTypeMode() != StructureMapGroupTypeMode.NULL && grp.getInput().size() == 2) {
+                String grpType = getTypeForGroupInput(map, grp, grp.getInput().get(0));
+                if (sameTypes(type, grpType)) {
+                  String tgtType = getTypeForGroupInput(map, grp, grp.getInput().get(1));
+                  if (tgtType != null) {
+                    return tgtType;
+                  }
+                }
+              }
+            }
+          }
+        } else if (dependents.size() == 0) {
           for (StructureMap map : imports) {
             for (StructureMapGroupComponent grp : map.getGroup()) {
               if (grp.getTypeMode() == StructureMapGroupTypeMode.TYPEANDTYPES && grp.getInput().size() == 2) {
@@ -900,6 +925,7 @@ public class StructureMapValidator extends BaseValidator {
               }
             }
           }
+          
         }
       }
     }

pom.xml

@@ -19,7 +19,7 @@
 
     <properties>
         <hapi_fhir_version>6.2.1</hapi_fhir_version>
-        <validator_test_case_version>1.2.21</validator_test_case_version>
+        <validator_test_case_version>1.2.22-SNAPSHOT</validator_test_case_version>
         <junit_jupiter_version>5.7.1</junit_jupiter_version>
         <junit_platform_launcher_version>1.8.2</junit_platform_launcher_version>
         <maven_surefire_version>3.0.0-M5</maven_surefire_version>