Merge pull request #1826 from hapifhir/2024-11-gg-clean0up

2024 11 gg clean0up

Author: grahamegrieve

RELEASE_NOTES.md

@@ -1,7 +1,11 @@
 ## Validator Changes
 
 * fix pattern discriminator validation rule
+* fix issue with FHIRPath engine throwing exception for an invalid path
 
 ## Other code changes
 
-* no changes
+* fix NPE rendering reference
+* fix NPE processing issue from template
+* Add FeatureDefinition renderer
+* Support for Custom resources in publisher

org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/utils/ToolingExtensions.java

@@ -874,6 +874,9 @@ private static IssueType mapType(org.hl7.fhir.r4.model.OperationOutcome.IssueTyp
   }
 
   private static IssueSeverity mapSeverity(org.hl7.fhir.r4.model.OperationOutcome.IssueSeverity severity) {
+    if (severity == null) {
+      return null;
+    }
     switch (severity) {
     case ERROR:
       return IssueSeverity.ERROR;

org.hl7.fhir.r4b/src/main/java/org/hl7/fhir/r4b/utils/ToolingExtensions.java

@@ -903,6 +903,9 @@ private static IssueType mapType(org.hl7.fhir.r4b.model.OperationOutcome.IssueTy
   }
 
   private static IssueSeverity mapSeverity(org.hl7.fhir.r4b.model.OperationOutcome.IssueSeverity severity) {
+    if (severity == null) {
+      return null;
+    }
     switch (severity) {
     case ERROR:
       return IssueSeverity.ERROR;

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

@@ -846,22 +846,26 @@ protected XhtmlNode renderResourceTechDetails(ResourceWrapper r, XhtmlNode x, St
     if (!Utilities.noString(r.getId())) {
       if (!context.isSecondaryLang()) {
         String sid = r.getScopedId();
-        if (!context.hasAnchor(sid)) {
-          context.addAnchor(sid);
-          x.an(context.prefixAnchor(sid));
-        }
-        sid = "hc"+sid;
-        if (!context.hasAnchor(sid)) {
-          context.addAnchor(sid);
-          x.an(context.prefixAnchor(sid));
+        if (sid != null) {
+          if (!context.hasAnchor(sid)) {
+            context.addAnchor(sid);
+            x.an(context.prefixAnchor(sid));
+          }
+          sid = "hc"+sid;
+          if (!context.hasAnchor(sid)) {
+            context.addAnchor(sid);
+            x.an(context.prefixAnchor(sid));
+          }
         }
       }
       if (context.getLocale() != null) {
         String langSuffix = "-"+context.getLocale().toLanguageTag();
-        String sid = r.getScopedId()+langSuffix;
-        if (!context.hasAnchor(sid)) {
-          context.addAnchor(sid);
-          x.an(context.prefixAnchor(sid));
+        if (r.getScopedId() != null) {
+          String sid = r.getScopedId()+langSuffix;
+          if (!context.hasAnchor(sid)) {
+            context.addAnchor(sid);
+            x.an(context.prefixAnchor(sid));
+          }
         }
       }
     }

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

@@ -1071,6 +1071,9 @@ private static IssueType mapType(org.hl7.fhir.r5.model.OperationOutcome.IssueTyp
   }
 
   private static IssueSeverity mapSeverity(org.hl7.fhir.r5.model.OperationOutcome.IssueSeverity severity) {
+    if (severity == null) {
+      return null;
+    }
     switch (severity) {
     case ERROR: return IssueSeverity.ERROR;
     case FATAL: return IssueSeverity.FATAL;

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

@@ -331,6 +331,7 @@ public JsonObject oidIndex() throws IOException {
 
   }
 
+
   private String path;
   private JsonObject npm;
   private Map<String, NpmPackageFolder> folders = new HashMap<>();
@@ -339,6 +340,7 @@ public JsonObject oidIndex() throws IOException {
   private boolean minimalMemory;
   private int size;
   private boolean warned = false;
+  private static boolean loadCustomResources;
 
   /**
    * Constructor
@@ -406,7 +408,7 @@ public Map<String, Object> getUserData() {
   public void loadFiles(String path, File source, String... exemptions) throws FileNotFoundException, IOException {
     this.npm = JsonParser.parseObject(TextFile.fileToString(Utilities.path(path, "package", "package.json")));
     this.path = path;
-    
+
     File dir = ManagedFileAccess.file(path);
     for (File f : dir.listFiles()) {
       if (!isInternalExemptFile(f) && !Utilities.existsInList(f.getName(), exemptions)) {
@@ -431,6 +433,7 @@ public void loadFiles(String path, File source, String... exemptions) throws Fil
             }
           }
           loadSubFolders(dir.getAbsolutePath(), f);
+
         } else {
           NpmPackageFolder folder = this.new NpmPackageFolder(Utilities.path("package", "$root"));
           folder.folder = dir;
@@ -448,24 +451,26 @@ public static boolean isInternalExemptFile(File f) {
   private void loadSubFolders(String rootPath, File dir) throws IOException {
     for (File f : dir.listFiles()) {
       if (f.isDirectory()) {
-        String d = f.getAbsolutePath().substring(rootPath.length()+1);
-        if (!d.startsWith("package")) {
-          d = Utilities.path("package", d);
-        }
-        NpmPackageFolder folder = this.new NpmPackageFolder(d);
-        folder.folder = f;
-        this.folders.put(d, folder);
-        File ij = ManagedFileAccess.file(Utilities.path(f.getAbsolutePath(), ".index.json"));
-        if (ij.exists() || !minimalMemory) {
-          try {
-            if (!ij.exists() || !folder.readIndex(JsonParser.parseObject(ij), folder.getTypes())) {
-              indexFolder(folder.getFolderName(), folder);
+        if (!"custom".equals(f.getName()) || loadCustomResources) {
+          String d = f.getAbsolutePath().substring(rootPath.length()+1);
+          if (!d.startsWith("package")) {
+            d = Utilities.path("package", d);
+          }
+          NpmPackageFolder folder = this.new NpmPackageFolder(d);
+          folder.folder = f;
+          this.folders.put(d, folder);
+          File ij = ManagedFileAccess.file(Utilities.path(f.getAbsolutePath(), ".index.json"));
+          if (ij.exists() || !minimalMemory) {
+            try {
+              if (!ij.exists() || !folder.readIndex(JsonParser.parseObject(ij), folder.getTypes())) {
+                indexFolder(folder.getFolderName(), folder);
+              }
+            } catch (Exception e) {
+              throw new IOException("Error parsing "+ij.getAbsolutePath()+": "+e.getMessage(), e);
             }
-          } catch (Exception e) {
-            throw new IOException("Error parsing "+ij.getAbsolutePath()+": "+e.getMessage(), e);
           }
+          loadSubFolders(rootPath, f); 
         }
-        loadSubFolders(rootPath, f);        
       }
     }    
   }
@@ -1510,5 +1515,12 @@ public String vid() {
     return id()+"#"+version();
   }
 
-  
+  public static boolean isLoadCustomResources() {
+    return loadCustomResources;
+  }
+
+  public static void setLoadCustomResources(boolean loadCustomResources) {
+    NpmPackage.loadCustomResources = loadCustomResources;
+  }
+
 }