fix extension status and extension generator

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/ExtensionStatusUpgrader.java

@@ -0,0 +1,118 @@
+package org.hl7.fhir.convertors.misc;
+
+import java.io.IOException;
+import java.util.HashMap;
+import java.util.Map;
+
+import org.hl7.fhir.convertors.conv40_50.VersionConvertor_40_50;
+import org.hl7.fhir.convertors.factory.VersionConvertorFactory_40_50;
+import org.hl7.fhir.r5.model.CanonicalResource;
+import org.hl7.fhir.r5.model.Enumerations.PublicationStatus;
+import org.hl7.fhir.r5.model.Resource;
+import org.hl7.fhir.r5.utils.ToolingExtensions;
+import org.hl7.fhir.r5.utils.formats.ResourceFolderVisitor;
+import org.hl7.fhir.r5.utils.formats.ResourceFolderVisitor.IResourceObserver;
+import org.hl7.fhir.utilities.StandardsStatus;
+import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
+import org.hl7.fhir.utilities.npm.NpmPackage;
+
+public class ExtensionStatusUpgrader implements IResourceObserver {
+
+  public static void main(String[] args) throws IOException {
+    new ExtensionStatusUpgrader().execute(args[0]);
+
+  }
+  Map<String, CanonicalResource> r4b = new HashMap<>();
+  Map<String, CanonicalResource> r5 = new HashMap<>();
+
+  private void execute(String folder) throws IOException {
+    FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(true);
+    
+    // load R4
+    NpmPackage npm = pcm.loadPackage("hl7.fhir.r4.core");
+    for (String n : npm.listResources("StructureDefinition", "ValueSet", "CodeSystem", "SearchParameter")) {
+      CanonicalResource cr = (CanonicalResource) VersionConvertorFactory_40_50.convertResource(new org.hl7.fhir.r4.formats.JsonParser().parse(npm.load(n)));
+      r4b.put(cr.getUrl(), cr);
+    }
+    // load R5-ballot3 
+    npm = pcm.loadPackage("hl7.fhir.r5.core#5.0.0-ballot");
+    for (String n : npm.listResources("StructureDefinition", "ValueSet", "CodeSystem", "SearchParameter")) {
+      CanonicalResource cr = (CanonicalResource) new org.hl7.fhir.r5.formats.JsonParser().parse(npm.load(n));
+      r5.put(cr.getUrl(), cr);
+    }
+    
+    new ResourceFolderVisitor(this, "StructureDefinition", "ValueSet", "CodeSystem", "SearchParameter").visit(folder);
+  }
+
+  @Override
+  public boolean visitResource(String filename, Resource resource) {
+    boolean changed = false;
+    CanonicalResource cr = (CanonicalResource) resource;
+    if (r4b.containsKey(cr.getUrl())) {
+      CanonicalResource ocr = r4b.get(cr.getUrl());
+      if (cr.getStatus() != PublicationStatus.ACTIVE) {
+        cr.setStatus(PublicationStatus.ACTIVE);
+        changed = true;
+      }
+      if (ocr.getStandardsStatus() == StandardsStatus.NORMATIVE) {
+        if (cr.getStandardsStatus() != StandardsStatus.NORMATIVE) {
+          cr.setStandardsStatus(StandardsStatus.NORMATIVE);
+          changed = true;
+        }
+      } else {
+        if (cr.getStandardsStatus() != StandardsStatus.TRIAL_USE) {
+          cr.setStandardsStatus(StandardsStatus.TRIAL_USE);
+          changed = true;
+        }
+      }
+      if (cr.getExperimental()) {
+        cr.setExperimental(false);
+        changed = true;        
+      }
+      if (!"3".equals(ToolingExtensions.readStringExtension(cr, ToolingExtensions.EXT_FMM_LEVEL))) {
+        ToolingExtensions.setIntegerExtension(cr, ToolingExtensions.EXT_FMM_LEVEL, 3);
+        changed = true;        
+      }
+    } else if (r5.containsKey(cr.getUrl())) {
+      CanonicalResource ocr = r5.get(cr.getUrl());
+      if (cr.getStatus() != PublicationStatus.DRAFT) {
+        cr.setStatus(PublicationStatus.DRAFT);
+        changed = true;
+      }
+      if (ocr.getStandardsStatus() == StandardsStatus.NORMATIVE) {
+        if (cr.getStandardsStatus() != StandardsStatus.NORMATIVE) {
+          cr.setStandardsStatus(StandardsStatus.NORMATIVE);
+          changed = true;
+        }
+      } else {
+        if (cr.getStandardsStatus() != StandardsStatus.TRIAL_USE) {
+          cr.setStandardsStatus(StandardsStatus.TRIAL_USE);
+          changed = true;
+        }
+      }
+      if (cr.getExperimental()) {
+        cr.setExperimental(false);
+        changed = true;        
+      }
+      if (!"2".equals(ToolingExtensions.readStringExtension(cr, ToolingExtensions.EXT_FMM_LEVEL))) {
+        ToolingExtensions.setIntegerExtension(cr, ToolingExtensions.EXT_FMM_LEVEL, 2);
+        changed = true;        
+      }
+    } else {
+      if (cr.getStatus() != PublicationStatus.DRAFT) {
+        cr.setStatus(PublicationStatus.DRAFT);
+        changed = true;
+      }
+      if (cr.getStandardsStatus() != StandardsStatus.DRAFT) {
+        cr.setStandardsStatus(StandardsStatus.DRAFT);
+        changed = true;
+      }
+      if (!cr.getExperimental()) {
+        cr.setExperimental(true);
+        changed = true;        
+      }
+    }
+    return changed;
+  }
+
+}

org.hl7.fhir.core.generator/src/org/hl7/fhir/core/generator/codegen/extensions/JavaExtensionsFactoryGenerator.java

@@ -101,23 +101,23 @@ public class JavaExtensionsFactoryGenerator extends JavaBaseGenerator {
     ElementDefinition edValue = sd.getSnapshot().getElementByPath("Extension.value[x]");
     List<TypeTuple> types = analyseTypes(edValue);
     if (types.size() > 5) {
-      src.append("  public Extension make"+name+"(DataType value) {\r\n");
+      src.append("  public static Extension make"+name+"(DataType value) {\r\n");
       src.append("    return new Extension(ExtensionConstants.EXT_"+constName+").setValue(value);\r\n");
       src.append("  }\r\n");
       src.append("\r\n");
       for (String ctxt : Utilities.sorted(contexts)) {
-        src.append("  public "+ctxt+" "+verb+name+"("+ctxt+" context, DataType value) {\r\n");
+        src.append("  public static "+ctxt+" "+verb+name+"("+ctxt+" context, DataType value) {\r\n");
         src.append("    ExtensionsUtils."+verb+"Extension(context, ExtensionConstants.EXT_"+constName+", value);\r\n");
         src.append("    return context;\r\n");
         src.append("  }\r\n");
         src.append("\r\n");
         if (repeats) {
-          src.append("  public List<DataType> get"+name+"List("+ctxt+" context) {\r\n");
+          src.append("  public static List<DataType> get"+name+"List("+ctxt+" context) {\r\n");
           src.append("    return ExtensionsUtils.getExtensionList(DataType.class, context, ExtensionConstants.EXT_"+constName+");\r\n");
           src.append("  }\r\n");
           src.append("\r\n");
         } else {
-          src.append("  public DataType get"+name+"("+ctxt+" context) {\r\n");
+          src.append("  public static DataType get"+name+"("+ctxt+" context) {\r\n");
           src.append("    return ExtensionsUtils.getExtension(DataType.class, context, ExtensionConstants.EXT_"+constName+");\r\n");
           src.append("  }\r\n");
           src.append("\r\n");
@@ -126,7 +126,7 @@ public class JavaExtensionsFactoryGenerator extends JavaBaseGenerator {
     } else {      
       for (TypeTuple t : types) {
         String sfx = typeCount(t.getJavaType(), types) > 1 ? Utilities.capitalize(t.getFhirType()) : "";
-        src.append("  public Extension make"+name+sfx+"("+t.getJavaType()+" value) {\r\n");
+        src.append("  public static Extension make"+name+sfx+"("+t.getJavaType()+" value) {\r\n");
         src.append("    return new Extension(ExtensionConstants.EXT_"+constName+").setValue("+(t.adapt("value"))+");\r\n");
         src.append("  }\r\n");
         src.append("\r\n");
@@ -135,7 +135,7 @@ public class JavaExtensionsFactoryGenerator extends JavaBaseGenerator {
         Set<String> td = new HashSet<>();
         for (TypeTuple t : types) {
           String sfx = typeCount(t.getJavaType(), types) > 1 ? Utilities.capitalize(t.getFhirType()) : "";
-          src.append("  public "+ctxt+" "+verb+name+sfx+"("+ctxt+" context, "+t.getJavaType()+" value) {\r\n");
+          src.append("  public static "+ctxt+" "+verb+name+sfx+"("+ctxt+" context, "+t.getJavaType()+" value) {\r\n");
           src.append("    ExtensionsUtils."+verb+"Extension(context, ExtensionConstants.EXT_"+constName+", "+(t.adapt("value"))+");\r\n");
           src.append("    return context;\r\n");
           src.append("  }\r\n");
@@ -144,7 +144,7 @@ public class JavaExtensionsFactoryGenerator extends JavaBaseGenerator {
           if (!td.contains(sfx)) {
             td.add(sfx);
             if (repeats) {
-              src.append("  public List<"+t.getJavaRType()+"> get"+name+sfx+"List("+ctxt+" context) {\r\n");
+              src.append("  public static List<"+t.getJavaRType()+"> get"+name+sfx+"List("+ctxt+" context) {\r\n");
               if (t.getFhirType() == null) {
                 src.append("    return ExtensionsUtils.getExtensionList("+t.getJavaType()+".class, context, ExtensionConstants.EXT_"+constName+");\r\n");                
               } else {
@@ -153,7 +153,7 @@ public class JavaExtensionsFactoryGenerator extends JavaBaseGenerator {
               src.append("  }\r\n");
               src.append("\r\n");
             } else {
-              src.append("  public "+t.getJavaRType()+" get"+name+sfx+"("+ctxt+" context) {\r\n");
+              src.append("  public static "+t.getJavaRType()+" get"+name+sfx+"("+ctxt+" context) {\r\n");
               if (t.getFhirType() == null) {
                 src.append("    return ExtensionsUtils.getExtension("+t.getJavaType()+".class, context, ExtensionConstants.EXT_"+constName+");\r\n");
               } else {

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/formats/ResourceFolderVisitor.java

@@ -0,0 +1,72 @@
+package org.hl7.fhir.r5.utils.formats;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.sound.sampled.FloatControl.Type;
+
+import org.hl7.fhir.r5.formats.JsonParser;
+import org.hl7.fhir.r5.formats.XmlParser;
+import org.hl7.fhir.r5.formats.IParser.OutputStyle;
+import org.hl7.fhir.r5.model.Resource;
+
+public class ResourceFolderVisitor {
+
+  public interface IResourceObserver {
+    public boolean visitResource(String filename, Resource resource);
+  }
+  
+  private IResourceObserver observer;
+  private List<String> types = new ArrayList<>();
+
+  public ResourceFolderVisitor(IResourceObserver observer) {
+    super();
+    this.observer = observer;
+  }
+  
+  public ResourceFolderVisitor(IResourceObserver observer, String... types) {
+    super();
+    this.observer = observer;
+    for (String t : types) {
+      this.types.add(t);
+    }
+  }
+  
+
+  public void visit(String folder) {
+    visit(new File(folder));
+  }
+  
+  public void visit(File file) {
+    for (File f : file.listFiles()) {
+      if (f.isDirectory()) {
+        visit(f);
+      } else if (f.getName().endsWith(".xml")) {
+        try {
+          Resource res = new XmlParser().parse(new FileInputStream(f));
+          if (types.isEmpty() || types.contains(res.fhirType())) {
+            if (observer.visitResource(f.getAbsolutePath(), res)) {
+              new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(f), res); 
+            }
+          }
+        } catch (Exception e) {
+        }
+      } else if (f.getName().endsWith(".json")) {
+        try {
+          Resource res = new JsonParser().parse(new FileInputStream(f));
+          if (types.isEmpty() || types.contains(res.fhirType())) {
+            if (observer.visitResource(f.getAbsolutePath(), res)) {
+             new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(f), res);
+            }
+          }
+        } catch (Exception e) {
+        }
+      }
+    }    
+  }
+
+  
+}