Compile fix (#728)

Co-authored-by: Grahame Grieve <[email protected]>

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

@@ -0,0 +1,82 @@
+package org.hl7.fhir.igtools.publisher;
+
+/*
+  Copyright (c) 2011+, HL7, Inc.
+  All rights reserved.
+  
+  Redistribution and use in source and binary forms, with or without modification, 
+  are permitted provided that the following conditions are met:
+    
+   * Redistributions of source code must retain the above copyright notice, this 
+     list of conditions and the following disclaimer.
+   * Redistributions in binary form must reproduce the above copyright notice, 
+     this list of conditions and the following disclaimer in the documentation 
+     and/or other materials provided with the distribution.
+   * Neither the name of HL7 nor the names of its contributors may be used to 
+     endorse or promote products derived from this software without specific 
+     prior written permission.
+  
+  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 
+  ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+  WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. 
+  IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, 
+  INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT 
+  NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 
+  PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, 
+  WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
+  ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
+  POSSIBILITY OF SUCH DAMAGE.
+  
+ */
+
+
+
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import org.hl7.fhir.r5.context.IWorkerContext;
+import org.hl7.fhir.r5.model.CodeSystem;
+import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent;
+import org.hl7.fhir.r5.utils.XVerExtensionManager;
+import org.hl7.fhir.utilities.validation.ValidationMessage;
+import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
+import org.hl7.fhir.validation.BaseValidator;
+
+/**
+ * This is defunct, I think? All this checking happens in the main code system validator?
+ * 
+ * @author grahamegrieve
+ *
+ */
+public class CodeSystemValidator extends BaseValidator {
+
+  public CodeSystemValidator(IWorkerContext context, XVerExtensionManager xverManager) {
+    super(context, xverManager, false);
+  }
+
+  public List<ValidationMessage> validate(CodeSystem cs, boolean forBuild) {
+    List<ValidationMessage> errors = new ArrayList<ValidationMessage>();
+
+    // this is an invariant on CodeSystem, but the invariant is wrong in R3, and doesn't work 
+    checkCodesUnique(cs, errors);
+    return errors;
+  }
+
+  private void checkCodesUnique(CodeSystem cs, List<ValidationMessage> errors) {
+    Set<String> codes = new HashSet<String>();
+    checkCodes(codes, cs.getConcept(), "CodeSystem.where(id = '"+cs.getId()+"')", errors);
+  }
+
+  private void checkCodes(Set<String> codes, List<ConceptDefinitionComponent> list, String path, List<ValidationMessage> errors) {
+    for (ConceptDefinitionComponent cc : list) {
+      String npath = path+".concept.where(code = '"+cc.getCode()+"')";
+      if (codes.contains(cc.getCode())) {
+        rule(errors, NO_RULE_DATE, IssueType.BUSINESSRULE, npath, false, "Duplicate Code "+cc.getCode());
+      }
+      codes.add(cc.getCode());
+      checkCodes(codes, cc.getConcept(), npath, errors);
+    }
+  }
+}

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

@@ -354,7 +354,6 @@
 import org.hl7.fhir.utilities.xml.XMLUtil;
 import org.hl7.fhir.utilities.xml.XmlEscaper;
 import org.hl7.fhir.validation.ValidatorUtils;
-import org.hl7.fhir.validation.codesystem.CodeSystemValidator;
 import org.hl7.fhir.validation.instance.InstanceValidator;
 import org.hl7.fhir.validation.instance.utils.ValidatorHostContext;
 import org.hl7.fhir.validation.profile.ProfileValidator;
@@ -1059,6 +1058,16 @@ private void processTxLog(String path) throws FileNotFoundException, IOException
       PrintStream f = new PrintStream(new FileOutputStream(path));
       String title = "Terminology Server Log";
       f.println("<html><head><title>"+title+"</title></head><body><h2>"+title+"</h2><pre>");
+      for (String s : tx.split("\\r?\\n|\\r")) {
+        if (s.startsWith("---") && s.endsWith("---")) {
+          f.println("</pre><hr/>");
+          String id = s.replace("-", "").trim();
+          f.println("<a name=\"l"+id+"\"> </a><h3>"+id+"</h3>");
+          f.println("<pre>");
+        } else {
+          f.println(s);
+        }
+      }
       f.print(tx);
       f.println("</pre></head></html>");
       f.close();
@@ -11321,14 +11330,14 @@ public static void main(String[] args) throws Exception {
         NpmPackage npm = pcm.loadPackage(p);
         System.out.println("OK: "+npm.name()+"#"+npm.version()+" for FHIR version(s) "+npm.fhirVersionList()+" with canonical "+npm.canonical());
       }
-    } else if (hasNamedParam(args, "-dicom-gen")) {
-      DicomPackageBuilder pgen = new DicomPackageBuilder();
-      pgen.setSource(getNamedParam(args, "src"));
-      pgen.setDest(getNamedParam(args, "dst"));
-      if (hasNamedParam(args, "-pattern")) {
-        pgen.setPattern(getNamedParam(args, "-pattern"));
-      }
-      pgen.execute();
+//    } else if (hasNamedParam(args, "-dicom-gen")) {
+//      DicomPackageBuilder pgen = new DicomPackageBuilder();
+//      pgen.setSource(getNamedParam(args, "src"));
+//      pgen.setDest(getNamedParam(args, "dst"));
+//      if (hasNamedParam(args, "-pattern")) {
+//        pgen.setPattern(getNamedParam(args, "-pattern"));
+//      }
+//      pgen.execute();
     } else if (hasNamedParam(args, "-help") || hasNamedParam(args, "-?") || hasNamedParam(args, "/?") || hasNamedParam(args, "?") || args.length == 0) {
       System.out.println("");
       System.out.println("To use this publisher to publish a FHIR Implementation Guide, run ");
@@ -11372,16 +11381,16 @@ public static void main(String[] args) throws Exception {
       System.out.println("or you can configure the proxy using -Dhttp.proxyHost=<ip> -Dhttp.proxyPort=<port> -Dhttps.proxyHost=<ip> -Dhttps.proxyPort=<port>");
       System.out.println("");
       System.out.println("For additional information, see https://confluence.hl7.org/display/FHIR/IG+Publisher+Documentation");
-    } else if (hasNamedParam(args, "-convert")) {
-      // convert a igpack.zip to a package.tgz
-      IGPack2NpmConvertor conv = new IGPack2NpmConvertor();
-      conv.setSource(getNamedParam(args, "-source"));
-      conv.setDest(getNamedParam(args, "-dest"));
-      conv.setPackageId(getNamedParam(args, "-npm-name"));
-      conv.setVersionIg(getNamedParam(args, "-version"));
-      conv.setLicense(getNamedParam(args, "-license"));
-      conv.setWebsite(getNamedParam(args, "-website"));
-      conv.execute();
+//    } else if (hasNamedParam(args, "-convert")) {
+//      // convert a igpack.zip to a package.tgz
+//      IGPack2NpmConvertor conv = new IGPack2NpmConvertor();
+//      conv.setSource(getNamedParam(args, "-source"));
+//      conv.setDest(getNamedParam(args, "-dest"));
+//      conv.setPackageId(getNamedParam(args, "-npm-name"));
+//      conv.setVersionIg(getNamedParam(args, "-version"));
+//      conv.setLicense(getNamedParam(args, "-license"));
+//      conv.setWebsite(getNamedParam(args, "-website"));
+//      conv.execute();
     } else if (hasNamedParam(args, "-delete-current")) {
       if (!args[0].equals("-delete-current")) {
         throw new Error("-delete-current must have the format -delete-current {root}/{realm}/{code} -history {history} (first argument is not -delete-current)");
@@ -11549,7 +11558,7 @@ public static void main(String[] args) throws Exception {
         self.setSourceDir(getNamedParam(args, "-source"));
         self.setDestDir(getNamedParam(args, "-destination"));
         self.specifiedVersion = getNamedParam(args, "-version");
-      } else if(!hasNamedParam(args, "-ig") && args.length == 1 && new File(args[0]).exists()) {
+      } else if (!hasNamedParam(args, "-ig") && args.length == 1 && new File(args[0]).exists()) {
         self.setConfigFile(determineActualIG(args[0], IGBuildMode.MANUAL));
       } else if (hasNamedParam(args, "-prompt")) {
         IniFile ini = new IniFile("publisher.ini");

pom.xml

@@ -24,7 +24,7 @@
     <version>1.3.25-SNAPSHOT</version> <!-- See the note above -->
 
     <properties>
-        <core_version>6.0.22</core_version>
+        <core_version>6.0.23-SNAPSHOT</core_version>
         <maven_surefire_version>3.0.0-M5</maven_surefire_version>
         <apache_poi_version>5.2.1</apache_poi_version>
         <okhttp.version>4.10.0</okhttp.version>