Merge pull request #745 from hapifhir/gg-202202-broken-links

Gg 202202 broken links

RELEASE_NOTES.md

@@ -1,7 +1,10 @@
 ## Validator Changes
 
-* no changes
+* Improve code validation error when value set can't be supported on tx.fhir.org
+* Hide error about regex in core package
 
 ## Other code changes
 
-* no changes
+* Fix wrong URL links in processed markdown 
+* Don't let txCache errors stop the process
+* Fix broken links in questionnaire + 

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

@@ -48,7 +48,7 @@ import java.io.FileOutputStream;
 
 public class Test {
   public final static String DEF_TS_SERVER = "http://fhir-dev.healthintersections.com.au/open";
-  public final static String DEV_TS_SERVER = "http://local.fhir.org:960/open";
+  public final static String DEV_TS_SERVER = "http://local.fhir.org:8080/open";
 
 
   public static final String DEF_PATH = "c:\\work\\org.hl7.fhir\\build\\implementations\\java\\org.hl7.fhir.convertors\\samples\\";

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/argonaut/ArgonautConverter.java

@@ -78,7 +78,7 @@ import java.util.*;
 
 public class ArgonautConverter extends ConverterBase {
   //  public final static String DEF_TS_SERVER = "http://fhir-dev.healthintersections.com.au/open";
-  public final static String DEV_TS_SERVER = "http://local.fhir.org:960/open";
+  public final static String DEV_TS_SERVER = "http://local.fhir.org:8080/open";
   public static final String UCUM_PATH = "c:\\work\\org.hl7.fhir\\build\\implementations\\java\\org.hl7.fhir.convertors\\samples\\ucum-essence.xml";
   public static final String SRC_PATH = "c:\\work\\org.hl7.fhir\\build\\publish\\";
   private static final String DEFAULT_ID_SPACE = "urn:uuid:e8e06b15-0f74-4b8e-b5e2-609dae7119dc";

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/txClient/TerminologyClientFactory.java

@@ -92,7 +92,7 @@ public class TerminologyClientFactory {
       return url;
     if (url.startsWith("http://tx.fhir.org"))
       return Utilities.pathURL(url, term);
-    if (url.equals("http://local.fhir.org:960"))
+    if (url.equals("http://local.fhir.org:8080"))
       return Utilities.pathURL(url, term);
     return url;
   }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/ProfileUtilities.java

@@ -2523,7 +2523,8 @@ public class ProfileUtilities extends TranslatingUtilities {
               // disabled 7-Dec 2021 GDG - we don't want to fool with relative URLs at all? 
               // re-enabled 11-Feb 2022 GDG - we do want to do this. At least, $assemble in davinci-dtr, where the markdown comes from the SDC IG, and an SDC local reference must be changed to point to SDC. in this case, it's called when generating snapshots
               // added processRelatives parameter to deal with this (well, to try)
-              if (processRelatives) {
+              if (processRelatives && webUrl != null) {
+                System.out.println("Making "+url+" relative to '"+webUrl+"'");
                 b.append(webUrl);
               } else {
                 System.out.println("Not making "+url+" relative to '"+webUrl+"'");
@@ -4785,10 +4786,10 @@ public class ProfileUtilities extends TranslatingUtilities {
 
   private void renderAdditionalBinding(HierarchicalTableGenerator gen, Cell c, Extension ext) {
     // <nsbp>2 <sp> purpose <sp> value-set-link ([context]) {documentation}
-//    String purpose = ext.getExtensionString("purpose");
+    String purpose = ext.getExtensionString("purpose");
-//    String valueSet = ext.getExtensionString("valueSet");
+    String valueSet = ext.getExtensionString("valueSet");
-//    String doco = ext.getExtensionString("documentation");
+    String doco = ext.getExtensionString("documentation");
-//    UsageContext usage = (ext.hasExtension("usage")) ? ext.getExtensionByUrl("usage").getValueUsageContext() : null;
+    UsageContext usage = (ext.hasExtension("usage")) ? ext.getExtensionByUrl("usage").getValueUsageContext() : null;
 //    
 //    purpose: code - defines how the binding is used
 //    usage : UsageContext - defines the contexts in which this binding is used for it's purpose

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

@@ -813,7 +813,7 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
       pu.setDebug(false);
       for (String err : errors)
         msgs.add(new ValidationMessage(Source.ProfileValidator, IssueType.EXCEPTION, p.getUserString("path"), "Error sorting Differential: "+err, ValidationMessage.IssueSeverity.ERROR));
-      pu.generateSnapshot(sd, p, p.getUrl(), Utilities.extractBaseUrl(sd.getUserString("path")), p.getName());
+      pu.generateSnapshot(sd, p, p.getUrl(), sd.getUserString("webroot"), p.getName());
       for (ValidationMessage msg : msgs) {
         if ((!ignoreProfileErrors && msg.getLevel() == ValidationMessage.IssueSeverity.ERROR) || msg.getLevel() == ValidationMessage.IssueSeverity.FATAL)
           throw new DefinitionException(formatMessage(I18nConstants.PROFILE___ELEMENT__ERROR_GENERATING_SNAPSHOT_, p.getName(), p.getUrl(), msg.getLocation(), msg.getMessage()));

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

@@ -600,7 +600,8 @@ public class TerminologyCache {
         caches.put(nc.name, nc);
           }        
         } catch (Exception e) {
-          throw new FHIRException("Error loading "+fn+": "+e.getMessage()+" entry "+c, e);
+          System.out.println("Error loading "+fn+": "+e.getMessage()+" entry "+c+" - ignoring it");
+          e.printStackTrace();
         }
       }
 

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

@@ -202,13 +202,13 @@ public class QuestionnaireRenderer extends TerminologyRenderer {
 
     r.setIcon("icon_q_root.gif", "QuestionnaireRoot");
     r.getCells().add(gen.new Cell(null, null, q.getName(), null, null));
-    r.getCells().add(gen.new Cell(null, null, "", null, null));
+    r.getCells().add(gen.new Cell(null, null, q.getDescription(), null, null));
     r.getCells().add(gen.new Cell(null, null, "", null, null));
     r.getCells().add(gen.new Cell(null, null, "Questionnaire", null, null));
     if (hasFlags) {
       r.getCells().add(gen.new Cell(null, null, "", null, null));
     }
-    r.getCells().add(gen.new Cell(null, null, q.getDescription(), null, null));
+    r.getCells().add(gen.new Cell(null, null, q.hasUrl() ? q.hasVersion() ? q.getUrl()+"#"+q.getVersion() : q.getUrl() : "", null, null));
     return r;    
   }
   
@@ -226,7 +226,9 @@ public class QuestionnaireRenderer extends TerminologyRenderer {
     boolean hasExt = false;
 
     r.setIcon("icon-q-"+i.getType().toCode().toLowerCase()+".png", i.getType().getDisplay());
-    r.getCells().add(gen.new Cell(null, context.getDefinitionsTarget() == null ? "" : context.getDefinitionsTarget()+"#item."+i.getLinkId(), i.getLinkId(), null, null));
+    Cell c1 = gen.new Cell(null, context.getDefinitionsTarget() == null ? "" : context.getDefinitionsTarget()+"#item."+i.getLinkId(), i.getLinkId(), null, null);
+    c1.setId("item."+i.getLinkId());
+    r.getCells().add(c1);
     String txt = (i.hasPrefix() ? i.getPrefix() + ". " : "") + i.getText();
     r.getCells().add(gen.new Cell(null, null, txt, null, null));
     r.getCells().add(gen.new Cell(null, null, (i.getRequired() ? "1" : "0")+".."+(i.getRepeats() ? "*" : "1"), null, null));
@@ -282,7 +284,7 @@ public class QuestionnaireRenderer extends TerminologyRenderer {
       if (!defn.getPieces().isEmpty()) defn.addPiece(gen.new Piece("br"));
       Piece p = gen.new Piece(null, "Enable When: ", null);
       defn.getPieces().add(p);
-      if (i.getEnableWhen().size() == 0) {
+      if (i.getEnableWhen().size() == 1) {
         XhtmlNode x = new XhtmlNode(NodeType.Element, "span");
         p.getChildren().add(x);
         renderEnableWhen(x, i.getEnableWhenFirstRep());        

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/ValueSetCheckerSimple.java

@@ -255,7 +255,11 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
             res = new ValidationResult((IssueSeverity) null, null);
           }
           if (!inExpansion && !inInclude) {
+            if (warnings != null) {
+              res.setMessage("Not in value set "+valueset.getUrl()+" ("+warnings+")").setSeverity(IssueSeverity.ERROR);              
+            } else {
               res.setMessage("Not in value set "+valueset.getUrl()).setSeverity(IssueSeverity.ERROR);
+            }
           } else if (warningMessage!=null) {
             res = new ValidationResult(IssueSeverity.WARNING, context.formatMessage(I18nConstants.CODE_FOUND_IN_EXPANSION_HOWEVER_, warningMessage));
           } else if (inExpansion) {

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

@@ -83,7 +83,7 @@ import java.util.Map.Entry;
  */
 public class FilesystemPackageCacheManager extends BasePackageCacheManager implements IPackageCacheManager {
 
-  //  private static final String SECONDARY_SERVER = "http://local.fhir.org:960/packages";
+  //  private static final String SECONDARY_SERVER = "http://local.fhir.org:8080/packages";
   public static final String PACKAGE_REGEX = "^[a-zA-Z][A-Za-z0-9\\_\\-]*(\\.[A-Za-z0-9\\_\\-]+)+$";
   public static final String PACKAGE_VERSION_REGEX = "^[A-Za-z][A-Za-z0-9\\_\\-]*(\\.[A-Za-z0-9\\_\\-]+)+\\#[A-Za-z0-9\\-\\_\\$]+(\\.[A-Za-z0-9\\-\\_\\$]+)*$";
   public static final String PACKAGE_VERSION_REGEX_OPT = "^[A-Za-z][A-Za-z0-9\\_\\-]*(\\.[A-Za-z0-9\\_\\-]+)+(\\#[A-Za-z0-9\\-\\_]+(\\.[A-Za-z0-9\\-\\_]+)*)?$";

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/xhtml/HierarchicalTableGenerator.java

@@ -221,6 +221,7 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
     private String cellStyle;
     protected int span = 1;
     private TextAlignment alignment = TextAlignment.LEFT;
+    private String id;
  
     public Cell() {
       
@@ -241,6 +242,8 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
       return this;
     }
 
+
+    
     public Cell addMarkdown(String md) {
       if (!Utilities.noString(md)) {
         try {
@@ -428,6 +431,12 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
       return this;
     }
     
+    public String getId() {
+      return id;
+    }
+    public void setId(String id) {
+      this.id = id;
+    }
 
   }
 
@@ -725,6 +734,10 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
     if (c.span > 1) {
       tc.colspan(Integer.toString(c.span));
     }
+    if (c.getId() != null) {
+      tc.setAttribute("id", c.getId());
+    }
+
     if (indents != null) {
       tc.addTag("img").setAttribute("src", srcFor(imagePath, "tbl_spacer.png")).setAttribute("style", "background-color: inherit").setAttribute("class", "hierarchy").setAttribute("alt", ".");
       tc.setAttribute("style", "vertical-align: top; text-align : left; "+(c.cellStyle != null  && c.cellStyle.contains("background-color") ? "" : "background-color: "+color+"; ")+"border: "+ border +"px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url("+imagePath+checkExists(indents, hasChildren, lineColor, outputTracker)+")"+(c.cellStyle != null ? ";"+c.cellStyle : ""));
@@ -795,8 +808,9 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
         if (p.getHint() != null)
           tag.setAttribute("title", p.getHint());
         addStyle(tag, p);
-        if (p.hasChildren())
+        if (p.hasChildren()) {
           tag.getChildNodes().addAll(p.getChildren());
+        }
       } else if (!Utilities.noString(p.getReference())) {
         XhtmlNode a = addStyle(tc.addTag("a"), p);
         a.setAttribute("href", p.getReference());
@@ -818,6 +832,9 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
           s.addText(p.getText());
         } else
           tc.addText(p.getText());
+        if (p.hasChildren()) {
+          tc.getChildNodes().addAll(p.getChildren());
+        }
       }
     }
     if (makeTargets && !Utilities.noString(anchor))

org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/tests/CachingPackageClientTests.java

@@ -13,7 +13,7 @@ public class CachingPackageClientTests {
 
   private static final String SERVER1 = "http://packages.fhir.org";
   private static final String SERVER2 = "https://packages2.fhir.org/packages";
-//  private static final String SERVER2 = "http://local.fhir.org:960/packages";
+//  private static final String SERVER2 = "http://local.fhir.org:8080/packages";
 
   @Test
   public void testExists() throws IOException {

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java

@@ -1876,9 +1876,13 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     }
     // the history of this is a mess - see https://jira.hl7.org/browse/FHIR-13328
     // we in practice we will support it in either place, but the specification says on ElementDefinition, not on ElementDefinition.type
-//    if ("http://hl7.org/fhir/StructureDefinition/regex".equals(extUrl)) {
+    // but this creates validation errors people can't fix all over the place if we don't do this.
-//      list.get(1).setExpression("ElementDefinition.type");
+    if ("http://hl7.org/fhir/StructureDefinition/regex".equals(extUrl)) {
-//    }
+      StructureDefinitionContextComponent e = new StructureDefinitionContextComponent();
+      e.setExpression("ElementDefinition.type");
+      e.setType(ExtensionContextType.ELEMENT);
+      list.add(e);
+    }
     if ("http://hl7.org/fhir/StructureDefinition/structuredefinition-normative-version".equals(extUrl)) {
       list.get(0).setExpression("Element"); // well, it can't be used anywhere but the list of places it can be used is quite long
     }

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/StructureDefinitionValidator.java

@@ -77,7 +77,7 @@ public class StructureDefinitionValidator extends BaseValidator {
             List<ValidationMessage> msgs = new ArrayList<>();
             ProfileUtilities pu = new ProfileUtilities(context, msgs, null);
             pu.setXver(xverManager);
-            pu.generateSnapshot(base, sd, sd.getUrl(), "http://hl7.org/fhir", sd.getName());
+            pu.generateSnapshot(base, sd, sd.getUrl(), "http://hl7.org/fhir/R4/", sd.getName());
             if (msgs.size() > 0) {
               for (ValidationMessage msg : msgs) {
                 // we need to set the location for the context 

org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/ValidationEngineTests.java

@@ -22,7 +22,7 @@ import static org.junit.jupiter.api.Assertions.assertTrue;
 public class ValidationEngineTests {
 
   public static final String DEF_TX = "http://tx.fhir.org";
-//  public static final String DEF_TX = "http://local.fhir.org:960";
+//  public static final String DEF_TX = "http://local.fhir.org:8080";
 
   public static boolean inbuild;