Update SPDX implementation

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/ExtensionDefinitionGenerator.java

@@ -361,7 +361,7 @@ public class ExtensionDefinitionGenerator {
     npm.addProperty("version", targetVersion.toCode().substring(0, 3));
     npm.addProperty("tools-version", ToolsVersion.TOOLS_VERSION);
     npm.addProperty("type", PackageType.IG.getCode());
-    npm.addProperty("license", SPDXLicense.CC01_0.toCode());
+    npm.addProperty("license", SPDXLicense.CC0_1_0.toCode());
     npm.addProperty("canonical", "http://hl7.org/fhir/" + sourceVersion.toCode().substring(0, 3) + "/extensions/" + targetVersion.toCode().substring(0, 3));
     npm.addProperty("url", "http://hl7.org/fhir/" + sourceVersion.toCode().substring(0, 3) + "/extensions/" + targetVersion.toCode().substring(0, 3));
     npm.addProperty("title", "Extension Definitions for representing elements from " + sourceVersion.toCode() + " in " + targetVersion.toCode());

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

@@ -200,6 +200,8 @@ public abstract class BaseLoaderR5 implements IContextResourceLoader {
       } else {
         return pi.isCore() && Utilities.tail(pri.getUrl()).equals(pri.getStatedType());
       }
+    } else if (pi.isCore() && "spdx-license".equals(pri.getId())) {
+      return false;
     } else {
       return true;
     }

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

@@ -0,0 +1,260 @@
+package org.hl7.fhir.convertors.misc;
+
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+
+import org.hl7.fhir.r4.model.CodeSystem;
+import org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent;
+import org.hl7.fhir.r4.model.CodeSystem.PropertyType;
+import org.hl7.fhir.r4.model.StringType;
+import org.hl7.fhir.r4.terminologies.CodeSystemUtilities;
+import org.hl7.fhir.r5.model.ValueSet;
+import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionContainsComponent;
+import org.hl7.fhir.r4.formats.IParser.OutputStyle;
+import org.hl7.fhir.r4.model.BooleanType;
+import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
+import org.hl7.fhir.utilities.TextFile;
+import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.json.model.JsonObject;
+import org.hl7.fhir.utilities.json.parser.JsonParser;
+
+public class SPDXImporter {
+
+  private StringBuilder b;
+
+
+  public static void main(String[] args) throws Exception {
+    new SPDXImporter().generate(args);
+  }
+  
+  public void generate(String[] args) throws Exception {
+    JsonObject json = JsonParser.parseObjectFromUrl("https://raw.githubusercontent.com/spdx/license-list-data/main/json/licenses.json");
+    CodeSystem cs = (CodeSystem) new org.hl7.fhir.r4.formats.JsonParser().parse(new FileInputStream(args[0]));
+    cs.getConcept().clear();
+    cs.getProperty().clear();
+    cs.addProperty().setCode("reference").setType(PropertyType.STRING);
+    cs.addProperty().setCode("isOsiApproved").setType(PropertyType.BOOLEAN);
+    cs.addProperty().setCode("status").setType(PropertyType.CODE).setUri("http://hl7.org/fhir/concept-properties#status");
+    cs.addProperty().setCode("seeAlso").setType(PropertyType.STRING);
+    cs.setVersion(json.asString("licenseListVersion"));
+    for (JsonObject l : json.getJsonObjects("licenses")) {
+      ConceptDefinitionComponent cc = cs.addConcept();
+      cc.setCode(l.asString("licenseId"));
+      cc.setDisplay(l.asString("name"));
+      cc.setDefinition(l.asString("name"));
+      if (l.has("reference")) {
+        cc.addProperty().setCode("reference").setValue(new StringType(l.asString("reference")));
+      }
+      if (l.has("isOsiApproved")) {
+        cc.addProperty().setCode("isOsiApproved").setValue(new BooleanType(l.asBoolean("isOsiApproved")));
+      }
+      if (l.asBoolean("isDeprecatedLicenseId")) {
+        cc.addProperty().setCode("status").setValue(new BooleanType(l.asBoolean("deprecated")));
+      }
+      for (String s : l.getStrings("seeAlso")) {        
+        cc.addProperty().setCode("seeAlso").setValue(new StringType(s));
+      }
+    }
+    CodeSystemUtilities.sortAllCodes(cs);
+    new org.hl7.fhir.r4.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(args[1]), cs);
+    b = new StringBuilder();
+    generateEnum("SPDXLicense", cs);
+    TextFile.stringToFile(b.toString(), Utilities.changeFileExt(args[1], ".java"));
+  }
+
+  private void write(String s) {
+    b.append(s);
+  }
+  
+  private boolean allPlusMinus(String cc) {
+    for (char c : cc.toCharArray())
+      if (!(c == '-' || c == '+'))
+        return false;
+    return true;
+  }
+  
+  protected String makeConst(String cc) {
+    if (cc.equals("*"))
+      cc = "ASTERISK";
+    if (Utilities.isOid(cc) && Utilities.charCount(cc, '.') > 2)
+      cc = "OID_"+cc;
+    if (cc.equals("%"))
+      cc = "pct";
+    else if (cc.equals("<"))
+      cc = "less_Than";
+    else if (cc.equals("<="))
+      cc = "less_Or_Equal";
+    else if (cc.equals(">"))
+      cc = "greater_Than";
+    else if (cc.equals(">="))
+      cc = "greater_Or_Equal";
+    else if (cc.equals("="))
+      cc = "equal";
+    else if (cc.equals("!="))
+      cc = "not_equal";
+    else if (allPlusMinus(cc))
+      cc = cc.replace("-", "Minus").replace("+", "Plus");
+    else
+      cc = cc.replace("-", "_").replace("+", "PLUS");
+    cc = cc.replace("(", "_").replace(")", "_");
+    cc = cc.replace("{", "_").replace("}", "_");
+    cc = cc.replace("<", "_").replace(">", "_");
+    cc = cc.replace(".", "_").replace("/", "_");
+    cc = cc.replace(":", "_");
+    cc = cc.replace("%", "pct");
+    if (Utilities.isInteger(cc.substring(0, 1)))
+      cc = "_"+cc;
+    cc = cc.toUpperCase();
+    return cc;
+  }
+
+  
+  private void generateEnum(String name, CodeSystem cs) throws Exception {
+    String url = cs.getUrl();
+    CommaSeparatedStringBuilder el = new CommaSeparatedStringBuilder();
+
+    write("    public enum "+name+" {\r\n");
+    int l = cs.getConcept().size();
+    int i = 0;
+    for (ConceptDefinitionComponent c : cs.getConcept()) {
+        i++;
+        String cc = Utilities.camelCase(c.getCode());
+        cc = makeConst(cc);
+        el.append(cc);
+
+        write("        /**\r\n");
+        write("         * "+c.getDefinition()+"\r\n");
+        write("         */\r\n");      
+        write("        "+cc.toUpperCase()+", \r\n");
+      }
+    write("        /**\r\n");
+    write("         * added to help the parsers\r\n");
+    write("         */\r\n");      
+    write("        NULL;\r\n");
+    el.append("NULL");
+
+
+    write("        public static "+name+" fromCode(String codeString) throws FHIRException {\r\n");
+    write("            if (codeString == null || \"\".equals(codeString))\r\n");
+    write("                return null;\r\n");
+    for (ConceptDefinitionComponent c : cs.getConcept()) {
+        String cc = Utilities.camelCase(c.getCode());
+        cc = makeConst(cc);
+        write("        if (\""+c.getCode()+"\".equals(codeString))\r\n");
+        write("          return "+cc+";\r\n");
+      }
+    write("        throw new FHIRException(\"Unknown "+name+" code '\"+codeString+\"'\");\r\n");
+    write("        }\r\n"); 
+
+    write("        public static boolean isValidCode(String codeString) {\r\n");
+    write("            if (codeString == null || \"\".equals(codeString))\r\n");
+    write("                return false;\r\n");
+    write("          return Utilities.existsInList(codeString");
+    for (ConceptDefinitionComponent c : cs.getConcept()) {
+        write(", \""+c.getCode()+"\"");
+    }
+    write(");\r\n");
+    write("        }\r\n"); 
+
+    write("        public String toCode() {\r\n");
+    write("          switch (this) {\r\n");
+    for (ConceptDefinitionComponent c : cs.getConcept()) {
+        String cc = Utilities.camelCase(c.getCode());
+        cc = makeConst(cc);
+        write("            case "+cc+": return \""+c.getCode()+"\";\r\n");
+      }
+    write("            case NULL: return null;\r\n");
+    write("            default: return \"?\";\r\n");
+    write("          }\r\n"); 
+    write("        }\r\n"); 
+
+    write("        public String getSystem() {\r\n");
+    write("          switch (this) {\r\n");
+    for (ConceptDefinitionComponent c : cs.getConcept()) {
+      String cc = Utilities.camelCase(c.getCode());
+      cc = makeConst(cc);
+      write("            case "+cc+": return \""+cs.getUrl()+"\";\r\n");
+    }
+    write("            case NULL: return null;\r\n");
+    write("            default: return \"?\";\r\n");
+    write("          }\r\n"); 
+    write("        }\r\n"); 
+
+    write("        public String getDefinition() {\r\n");
+    write("          switch (this) {\r\n");
+    for (ConceptDefinitionComponent c : cs.getConcept()) {
+        String cc = Utilities.camelCase(c.getCode());
+        cc = makeConst(cc);
+        write("            case "+cc+": return \""+Utilities.escapeJava(c.getDefinition())+"\";\r\n");
+      }
+    write("            case NULL: return null;\r\n");
+    write("            default: return \"?\";\r\n");
+    write("          }\r\n"); 
+    write("        }\r\n"); 
+
+    write("        public String getDisplay() {\r\n");
+    write("          switch (this) {\r\n");
+    for (ConceptDefinitionComponent c : cs.getConcept()) {
+        String cc = Utilities.camelCase(c.getCode());
+        cc = makeConst(cc);
+        write("            case "+cc+": return \""+Utilities.escapeJava(Utilities.noString(c.getDisplay()) ? c.getCode() : c.getDisplay())+"\";\r\n");
+      }
+    write("            case NULL: return null;\r\n");
+    write("            default: return \"?\";\r\n");
+    write("          }\r\n"); 
+    write("        }\r\n"); 
+
+    write("    }\r\n");
+    write("\r\n");
+
+    
+    write("  public static class "+name+"EnumFactory implements EnumFactory<"+name+"> {\r\n");
+    write("    public "+name+" fromCode(String codeString) throws IllegalArgumentException {\r\n");
+    
+    write("      if (codeString == null || \"\".equals(codeString))\r\n");
+    write("            if (codeString == null || \"\".equals(codeString))\r\n");
+    write("                return null;\r\n");
+    for (ConceptDefinitionComponent c : cs.getConcept()) {
+        String cc = Utilities.camelCase(c.getCode());
+        cc = makeConst(cc);
+        write("        if (\""+c.getCode()+"\".equals(codeString))\r\n");
+        write("          return "+name+"."+cc+";\r\n");
+      }
+    write("        throw new IllegalArgumentException(\"Unknown "+name+" code '\"+codeString+\"'\");\r\n");
+    write("        }\r\n"); 
+    write("\r\n");
+    write("        public Enumeration<"+name+"> fromType(PrimitiveType<?> code) throws FHIRException {\r\n");
+    write("          if (code == null)\r\n");
+    write("            return null;\r\n");
+    write("          if (code.isEmpty())\r\n");
+    write("            return new Enumeration<"+name+">(this, "+name+".NULL, code);\r\n");
+    write("          String codeString = ((PrimitiveType) code).asStringValue();\r\n");
+    write("          if (codeString == null || \"\".equals(codeString))\r\n");
+    write("            return new Enumeration<"+name+">(this, "+name+".NULL, code);\r\n");
+    for (ConceptDefinitionComponent c : cs.getConcept()) {
+      String cc = Utilities.camelCase(c.getCode());
+      cc = makeConst(cc);
+      write("        if (\""+c.getCode()+"\".equals(codeString))\r\n");
+      write("          return new Enumeration<"+name+">(this, "+name+"."+cc+", code);\r\n");
+    }   
+    write("        throw new FHIRException(\"Unknown "+name+" code '\"+codeString+\"'\");\r\n");
+    write("        }\r\n"); 
+    write("    public String toCode("+name+" code) {\r\n");
+    for (ConceptDefinitionComponent c : cs.getConcept()) {
+        String cc = Utilities.camelCase(c.getCode());
+        cc = makeConst(cc);
+        write("      if (code == "+name+"."+cc+")\r\n        return \""+c.getCode()+"\";\r\n");
+    }
+    write("      return \"?\";\r\n"); 
+    write("      }\r\n");
+    
+    write("    public String toSystem("+name+" code) {\r\n");
+    write("      return code.getSystem();\r\n");
+    write("      }\r\n"); 
+
+    write("    }\r\n"); 
+    write("\r\n");
+  }
+
+}
+

org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/terminologies/CodeSystemUtilities.java

@@ -33,6 +33,8 @@ package org.hl7.fhir.r4.terminologies;
 
 import java.util.ArrayList;
 import java.util.Calendar;
+import java.util.Collections;
+import java.util.Comparator;
 import java.util.List;
 
 import org.hl7.fhir.exceptions.FHIRException;
@@ -52,6 +54,7 @@ import org.hl7.fhir.r4.model.Meta;
 import org.hl7.fhir.r4.model.Type;
 import org.hl7.fhir.r4.model.UriType;
 import org.hl7.fhir.r4.utils.ToolingExtensions;
+import org.hl7.fhir.r4.terminologies.CodeSystemUtilities.ConceptDefinitionComponentSorter;
 import org.hl7.fhir.utilities.StandardsStatus;
 import org.hl7.fhir.utilities.Utilities;
 
@@ -288,4 +291,27 @@ public class CodeSystemUtilities {
     owner.addProperty().setCode("child").setValue(new CodeType(code));
   }
 
+
+  public static class ConceptDefinitionComponentSorter implements Comparator<ConceptDefinitionComponent> {
+
+    @Override
+    public int compare(ConceptDefinitionComponent o1, ConceptDefinitionComponent o2) {
+      return o1.getCode().compareToIgnoreCase(o2.getCode());
+    }
+
+  }
+
+  public static void sortAllCodes(CodeSystem cs) {
+    sortAllCodes(cs.getConcept());
+  }
+
+  public static void sortAllCodes(List<ConceptDefinitionComponent> list) {
+    Collections.sort(list, new ConceptDefinitionComponentSorter());
+    for (ConceptDefinitionComponent cd : list) {
+      if (cd.hasConcept()) {
+        sortAllCodes(cd.getConcept());
+      }
+    }    
+  }
+
 }

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

@@ -72,6 +72,7 @@ import org.hl7.fhir.r5.utils.validation.IResourceValidator;
 import org.hl7.fhir.r5.utils.R5Hacker;
 import org.hl7.fhir.r5.utils.XVerExtensionManager;
 import org.hl7.fhir.utilities.CSFileInputStream;
+import org.hl7.fhir.utilities.MagicResources;
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.TimeTracker;
 import org.hl7.fhir.utilities.Utilities;
@@ -232,6 +233,7 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
       context.initTS(terminologyCachePath);
       context.setUserAgent(userAgent);
       context.setLogger(loggingService);
+      context.cacheResource(new org.hl7.fhir.r5.formats.JsonParser().parse(MagicResources.spdxCodesAsData()));
       return context;
     }
 

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

@@ -0,0 +1,15 @@
+package org.hl7.fhir.utilities;
+
+import java.io.IOException;
+import java.io.InputStream;
+
+public class MagicResources {
+
+  public static byte[] spdxCodesAsData() throws IOException {
+    ClassLoader classLoader = MagicResources.class.getClassLoader();
+    InputStream help = classLoader.getResourceAsStream("spdx.json");
+    return TextFile.streamToBytes(help);
+  }
+  
+  
+}