Merge pull request #1033 from HL7/2025-02-gg-compiles-fixes

2025 02 gg compiles fixes

org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/openehr/ArchetypeImporter.java

@@ -37,7 +37,7 @@
 import org.hl7.fhir.r5.model.ValueSet;
 import org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent;
 import org.hl7.fhir.r5.utils.ToolingExtensions;
-import org.hl7.fhir.utilities.TextFile;
+import org.hl7.fhir.utilities.FileUtilities;
 import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.xml.XMLUtil;
 import org.openehr.referencemodels.BuiltinReferenceModels;
@@ -115,7 +115,7 @@ public ArchetypeImporter(IWorkerContext context, String canonicalBase) throws Pa
     byte[] tf = context.getBinaryForKey("openehr_terminology.xml");
     if (tf == null) {
       // hack temp workaround
-      tf = TextFile.fileToBytes("/Users/grahamegrieve/Downloads/openehr_terminology.xml");
+      tf = FileUtilities.fileToBytes("/Users/grahamegrieve/Downloads/openehr_terminology.xml");
     }
     terminology = XMLUtil.parseToDom(tf).getDocumentElement();
   }
@@ -126,7 +126,7 @@ public void checkArchetype(byte[] content, String name) throws ParserConfigurati
   }
 
   public void checkArchetype(InputStream stream, String name) throws ParserConfigurationException, SAXException, IOException, ADLParseException {
-    byte[] cnt = TextFile.streamToBytes(stream);
+    byte[] cnt = FileUtilities.streamToBytes(stream);
     try {
       archetype = load20(new ByteArrayInputStream(cnt));
     } catch (Exception e20) {
@@ -149,7 +149,7 @@ public ProcessedArchetype importArchetype(byte[] content, String name) throws Pa
   public ProcessedArchetype importArchetype(InputStream stream, String name) throws ParserConfigurationException, SAXException, IOException, ADLParseException {
     atMap.clear();
 
-    byte[] cnt = TextFile.streamToBytes(stream);
+    byte[] cnt = FileUtilities.streamToBytes(stream);
     try {
       archetype = load20(new ByteArrayInputStream(cnt));
     } catch (Exception e20) {

org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/openehr/OpenEHRTest.java

@@ -10,7 +10,7 @@
 import org.hl7.fhir.r5.formats.IParser.OutputStyle;
 import org.hl7.fhir.r5.formats.JsonParser;
 import org.hl7.fhir.r5.model.Bundle;
-import org.hl7.fhir.utilities.TextFile;
+import org.hl7.fhir.utilities.FileUtilities;
 import org.xml.sax.SAXException;
 
 import com.nedap.archie.adlparser.ADLParseException;
@@ -26,7 +26,7 @@ public void test() throws FileNotFoundException, ADLParseException, IOException,
     ProcessedArchetype pa = ai.importArchetype(new FileInputStream("/Users/grahamegrieve/Downloads/openEHR-EHR-OBSERVATION.blood_pressure.v2.adl"), "openEHR-EHR-OBSERVATION.blood_pressure.v2.adl");
     System.out.println();
     String json = new JsonParser().setOutputStyle(OutputStyle.PRETTY).composeString(pa.getBnd());
-    TextFile.stringToFile(json, "/Users/grahamegrieve/temp/igs/FHIR-sample-ig#master/input/resources/Bundle-openEHR-EHR-OBSERVATION.blood-pressure.v2.json");
+    FileUtilities.stringToFile(json, "/Users/grahamegrieve/temp/igs/FHIR-sample-ig#master/input/resources/Bundle-openEHR-EHR-OBSERVATION.blood-pressure.v2.json");
     System.out.println("Done");
   }
 

org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/ConfigFileConverter.java

@@ -33,6 +33,7 @@
 import org.hl7.fhir.r5.utils.IGHelper;
 import org.hl7.fhir.r5.utils.ToolingExtensions;
 import org.hl7.fhir.utilities.FhirPublication;
+import org.hl7.fhir.utilities.FileUtilities;
 import org.hl7.fhir.utilities.IniFile;
 import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.json.model.JsonArray;
@@ -77,14 +78,14 @@ public class ConfigFileConverter {
   public void convert(String configFile, IWorkerContext context, FilesystemPackageCacheManager pcm) throws Exception {
     JsonObject configuration = org.hl7.fhir.utilities.json.parser.JsonParser.parseObjectFromFile(configFile);
     if (configuration.has("redirect")) { // redirect to support auto-build for complex projects with IG folder in subdirectory
-      String redirectFile = Utilities.path(Utilities.getDirectoryForFile(configFile), configuration.asString("redirect"));
+      String redirectFile = Utilities.path(FileUtilities.getDirectoryForFile(configFile), configuration.asString("redirect"));
       configFile = redirectFile;
       configuration = org.hl7.fhir.utilities.json.parser.JsonParser.parseObjectFromFile(redirectFile);
     }
     String version = ostr(configuration, "version");
     if (Utilities.noString(version))
       version = Constants.VERSION;
-    String rootDir = Utilities.getDirectoryForFile(configFile);
+    String rootDir = FileUtilities.getDirectoryForFile(configFile);
     if (Utilities.noString(rootDir))
       rootDir = getCurentDirectory();
     // We need the root to be expressed as a full path.  getDirectoryForFile will do that in general, but not in Eclipse
@@ -147,7 +148,7 @@ public void convert(String configFile, IWorkerContext context, FilesystemPackage
     String sct = str(configuration, "sct-edition", "http://snomed.info/sct/900000000000207008");
     p.addParameter("system-version", "http://snomed.info/sct|" + sct);
     p.addParameter("activeOnly", "true".equals(ostr(configuration, "no-inactive-codes")));
-    new JsonParser().compose(new FileOutputStream(Utilities.path(Utilities.getDirectoryForFile(igName), "ig-expansion-parameters.json")), ig);
+    new JsonParser().compose(new FileOutputStream(Utilities.path(FileUtilities.getDirectoryForFile(igName), "ig-expansion-parameters.json")), ig);
     p = new Parameters();
     p.addParameter("broken-links", "true".equals(ostr(configuration, "broken-links")));
     p.addParameter("check-aggregation", "true".equals(ostr(configuration, "check-aggregation")));
@@ -163,7 +164,7 @@ public void convert(String configFile, IWorkerContext context, FilesystemPackage
       for (JsonElement e : (JsonArray) paths.get("special-urls"))
         p.addParameter("special-url", e.asJsonPrimitive().asString());
     }
-    new JsonParser().compose(new FileOutputStream(Utilities.path(Utilities.getDirectoryForFile(igName), "ig-validation-parameters.json")), ig);
+    new JsonParser().compose(new FileOutputStream(Utilities.path(FileUtilities.getDirectoryForFile(igName), "ig-validation-parameters.json")), ig);
     if (paths.get("spreadsheets") instanceof JsonArray) {
       for (JsonElement e : (JsonArray) paths.get("spreadsheets"))
         ig.addExtension(ToolingExtensions.EXT_IGP_SPREADSHEET, new StringType(e.asJsonPrimitive().asString()));
@@ -238,9 +239,9 @@ public void convert(String configFile, IWorkerContext context, FilesystemPackage
       }
     }
 
-    String newfile = Utilities.path(Utilities.getDirectoryForFile(igName), "ig-new.json");
+    String newfile = Utilities.path(FileUtilities.getDirectoryForFile(igName), "ig-new.json");
     new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(newfile), ig);
-    newfile = Utilities.path(Utilities.getDirectoryForFile(igName), "ig-new.xml");
+    newfile = Utilities.path(FileUtilities.getDirectoryForFile(igName), "ig-new.xml");
     new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(newfile), ig);
     IniFile ini = new IniFile(Utilities.path(rootDir, "ig.ini"));
     ini.setStringProperty("IG", "ig", newfile.substring(rootDir.length() + 1), null);

org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/DependentIGFinder.java

@@ -14,7 +14,7 @@
 import org.hl7.fhir.exceptions.FHIRFormatError;
 import org.hl7.fhir.r4.model.CanonicalType;
 import org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent;
-import org.hl7.fhir.utilities.TextFile;
+import org.hl7.fhir.utilities.FileUtilities;
 import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.VersionUtilities;
 import org.hl7.fhir.utilities.json.model.JsonObject;
@@ -535,7 +535,7 @@ public void finish(String path, String title) throws IOException {
     t.add("details2", details2);
     t.add("errors", String.join("\r\n", errors));
 
-    TextFile.stringToFile(t.render(), Utilities.path(path, "qa-dep.html"));
+    FileUtilities.stringToFile(t.render(), Utilities.path(path, "qa-dep.html"));
   }
 
   public void addCodeSystem(String url, String title, String link) {

org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/ExtensionTracker.java

@@ -21,7 +21,7 @@
 import org.hl7.fhir.r5.model.ImplementationGuide;
 import org.hl7.fhir.r5.model.StructureDefinition;
 import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionKind;
-import org.hl7.fhir.utilities.TextFile;
+import org.hl7.fhir.utilities.FileUtilities;
 import org.hl7.fhir.utilities.Utilities;
 
 import com.google.gson.Gson;
@@ -208,7 +208,7 @@ public  byte[] generate() throws IOException {
     }
     Gson gson = new GsonBuilder().setPrettyPrinting().create();
     String json = gson.toJson(data);
-    return TextFile.stringToBytes(json);
+    return FileUtilities.stringToBytes(json);
   }
 
   public boolean isoptIn() {

org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/FetchedFile.java

@@ -74,6 +74,7 @@ public enum FetchedBundleType {
   private String statedPath;  
   private String logical;
   private List<ProcessingReport> processes = new ArrayList<>();
+  private boolean loaded;
 
   public FetchedFile(String statedPath) {
     super();
@@ -288,5 +289,11 @@ public void appendReport(StringBuilder b) {
   public long getSize() {
     return size;
   }
+  public boolean isLoaded() {
+    return loaded;
+  }
+  public void setLoaded(boolean loaded) {
+    this.loaded = loaded;
+  }
 
 }

org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/HTMLInspector.java

@@ -49,7 +49,7 @@
 import org.hl7.fhir.r5.model.CanonicalResource;
 import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
 import org.hl7.fhir.utilities.PathBuilder;
-import org.hl7.fhir.utilities.TextFile;
+import org.hl7.fhir.utilities.FileUtilities;
 import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
 import org.hl7.fhir.utilities.npm.NpmPackage;
@@ -313,11 +313,11 @@ public List<ValidationMessage> check(String statusText) throws IOException {
           first = false;
         }
       }
-      checkFragmentIds(TextFile.fileToString(lf.filename));
+      checkFragmentIds(FileUtilities.fileToString(lf.filename));
 
       if (lf.isHasXhtml()) {
         if (fragmentUses != null) {
-          checkFragmentMarkers(TextFile.fileToString(lf.getFilename()));
+          checkFragmentMarkers(FileUtilities.fileToString(lf.getFilename()));
         }
         XhtmlNode x = new XhtmlParser().setMustBeWellFormed(strict).parse(new FileInputStream(lf.filename), null);
         referencesValidatorPack = false;
@@ -518,11 +518,11 @@ private void loadFile(String s, String base, List<ValidationMessage> messages) {
     if (x != null) {
       String src;
       try {
-        src = TextFile.fileToString(f);
+        src = FileUtilities.fileToString(f);
         hl7State = src.contains(RELEASE_HTML_MARKER);
         if (hl7State) {
           src = src.replace(RELEASE_HTML_MARKER, START_HTML_MARKER + statusText+END_HTML_MARKER);
-          TextFile.stringToFile(src, f);
+          FileUtilities.stringToFile(src, f);
         }
         x = new XhtmlParser().setMustBeWellFormed(strict).parse(new FileInputStream(f), null);
       } catch (Exception e1) {
@@ -746,7 +746,7 @@ private boolean checkResolveLink(String filename, Location loc, String path, Str
     links++;
     String rref = Utilities.URLDecode(ref);
     if ((rref.startsWith("http:") || rref.startsWith("https:") ) && (rref.endsWith(".sch") || rref.endsWith(".xsd") || rref.endsWith(".shex"))) { // work around for the fact that spec.internals does not track all these minor things 
-      rref = Utilities.changeFileExt(ref, ".html");
+      rref = FileUtilities.changeFileExt(ref, ".html");
     }
     if (rref.contains("validator.pack")) {
       referencesValidatorPack = true;
@@ -824,7 +824,7 @@ private boolean checkTarget(String filename, String ref, String rref, StringBuil
           resolved = true;
         }
       } else if (!resolved && !Utilities.isAbsoluteUrl(ref) && !rref.startsWith("#") && filename != null) {
-        String fref =  buildRef(Utilities.getDirectoryForFile(filename), ref);
+        String fref =  buildRef(FileUtilities.getDirectoryForFile(filename), ref);
         if (fref.equals(Utilities.path(rootFolder, "qa.html"))) {
           resolved = true;
         }
@@ -908,7 +908,7 @@ private boolean checkTarget(String filename, String ref, String rref, StringBuil
           }
         } else {
           try {
-            String folder = Utilities.getDirectoryForFile(filename);
+            String folder = FileUtilities.getDirectoryForFile(filename);
             String f = folder == null ? (altRootFolder != null && filename.startsWith(altRootFolder) ? altRootFolder : rootFolder) : folder;
             page = PathBuilder.getPathBuilder().withRequiredTarget(rootFolder).buildPath(f, page.replace("/", File.separator));
           } catch (java.nio.file.InvalidPathException e) {
@@ -1019,7 +1019,7 @@ private boolean checkImgSourceExists(String filename, String ref) throws IOExcep
           }
         }
       } else if (!ref.contains("#")) { 
-        String page = Utilities.path(filename == null ? rootFolder : Utilities.getDirectoryForFile(filename), ref.replace("/", File.separator));
+        String page = Utilities.path(filename == null ? rootFolder : FileUtilities.getDirectoryForFile(filename), ref.replace("/", File.separator));
         LoadedFile f = cache.get(page);
         resolved = f != null;
       }

org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/IGPack2NpmConvertor.java

@@ -58,6 +58,7 @@
 import org.hl7.fhir.r5.model.Reference;
 import org.hl7.fhir.r5.utils.NPMPackageGenerator;
 import org.hl7.fhir.r5.utils.NPMPackageGenerator.Category;
+import org.hl7.fhir.utilities.FileUtilities;
 import org.hl7.fhir.utilities.IniFile;
 import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
@@ -213,7 +214,7 @@ private void processValidatorPack(File f) throws IOException {
 
         if (files.containsKey("spec.internals"))
           loadSpecInternals(ig,  files.get("spec.internals"), "??", version, canonical, files);
-        String destFile = dest != null ? dest : Utilities.path(Utilities.getDirectoryForFile(f.getAbsolutePath()), "package.tgz");
+        String destFile = dest != null ? dest : Utilities.path(FileUtilities.getDirectoryForFile(f.getAbsolutePath()), "package.tgz");
         String url = Utilities.noString(website) ? canonical : website;
         NPMPackageGenerator npm = new NPMPackageGenerator(destFile, canonical, url, PackageType.IG, ig, new Date(), false);
 

org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/IGPublisherLiquidTemplateServices.java

@@ -30,7 +30,7 @@
 import org.hl7.fhir.r5.model.DomainResource;
 import org.hl7.fhir.r5.renderers.utils.RenderingContext;
 import org.hl7.fhir.r5.renderers.utils.RenderingContext.ILiquidTemplateProvider;
-import org.hl7.fhir.utilities.TextFile;
+import org.hl7.fhir.utilities.FileUtilities;
 
 public class IGPublisherLiquidTemplateServices implements ILiquidTemplateProvider {
 
@@ -48,10 +48,10 @@ public void load(String path) throws FileNotFoundException, IOException {
       if (f.getName().endsWith(".liquid")) {
         String fn = f.getName();
         fn = fn.substring(0, fn.indexOf("."));
-        templates.put(fn.toLowerCase(), TextFile.fileToString(f));
+        templates.put(fn.toLowerCase(), FileUtilities.fileToString(f));
       } else if (f.getName().endsWith(".html")) {
         String fn = f.getName();
-        templates.put(fn, TextFile.fileToString(f));
+        templates.put(fn, FileUtilities.fileToString(f));
       } 
     }
   }

org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/PageFactory.java

@@ -15,7 +15,7 @@
 import org.hl7.fhir.r5.model.ImplementationGuide.GuidePageGeneration;
 import org.hl7.fhir.r5.model.ImplementationGuide.ImplementationGuideDefinitionPageComponent;
 import org.hl7.fhir.r5.model.UrlType;
-import org.hl7.fhir.utilities.TextFile;
+import org.hl7.fhir.utilities.FileUtilities;
 import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.json.JsonException;
 import org.hl7.fhir.utilities.json.model.JsonObject;
@@ -162,15 +162,15 @@ public static List<String> sorted(Collection<String> set) {
   }
 
   private void execute(String item, String repoSource, ImplementationGuide ig) throws FileNotFoundException, IOException {
-    String source = TextFile.fileToString(Utilities.path(repoSource, sourceFile()));
+    String source = FileUtilities.fileToString(Utilities.path(repoSource, sourceFile()));
     for (String n : variables()) {
       String v = variableValue(n, item);
       doDebug("   "+n+" --> "+v);
       source = source.replace(n, v);
     }
     String fn = generatedFileName(item);
     doDebug("  save to "+fn);
-    TextFile.stringToFile(source, Utilities.path(dir, "_includes", fn));
+    FileUtilities.stringToFile(source, Utilities.path(dir, "_includes", fn));
     ImplementationGuideDefinitionPageComponent page = getParentPage(ig.getDefinition().getPage());
     ImplementationGuideDefinitionPageComponent subPage = page.addPage();
     subPage.setSource(new UrlType(statedFileName(item)));
@@ -208,8 +208,8 @@ private String statedFileName(String item) {
   private void checks(String repoSource, ImplementationGuide ig) throws IOException {
     checkFileExists("source-file", Utilities.path(repoSource, sourceFile()));
     checkFileExists("page folder", dir);
-    Utilities.clearDirectory(dir);
-    Utilities.createDirectory(Utilities.path(dir, "_includes"));
+    FileUtilities.clearDirectory(dir);
+    FileUtilities.createDirectory(Utilities.path(dir, "_includes"));
   }
 
   private void checkFileExists(String purpose, String path) {