2025 01 gg misc

RELEASE_NOTES.md

@@ -0,0 +1,22 @@
+* Loader: Lazy load binaries for reduced memory usage
+* Loader: Support for Archetype processing in IG publisher
+* Loader: Process Archetypes properly as both IG input and output + remove ig-r4.json
+* Validator: Do not create issue about draft dependency for example bindings
+* Validator: Beef up validation of CodeSystem properties that are codes
+* Validator: Make sure all validation messages have a message id
+* Validator: enforce version-set-specific value for Extension and Extension context
+* Validator: Specific Error when ValueSet.compose.include.system refers to a ValueSet
+* Renderer: improved version specific extension rendering
+* Renderer: Add element view to generated fragments
+* Renderer: improve Extension context of use presentation - generate a fragment for that 
+* Renderer: resolve issues with references between IGs to example resources
+* Renderer: add use-context fragment for version contest restrictions
+* Renderer: Lookup compliesWithProfile target from link-only dependencies
+* Renderer: Accessibility - role=presentation on appropriate tables
+* Renderer: Add archetype processing, and also path-other support
+* Renderer: resolve issues with references between IGs to example resources
+* Renderer: Lookup compliesWithProfile target from link-only dependencies
+* Renderer: Update SNOMED editions related routines (add more editions)
+* Renderer: Accessibility - role=presentation on appropriate tables
+* Packages: Add support for ADL in packages
+* Terminology Tests: Report count of tests in output from TxTester

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

@@ -40,6 +40,7 @@
 
 import org.hl7.fhir.exceptions.FHIRFormatError;
 import org.hl7.fhir.igtools.publisher.Publisher.FragmentUseRecord;
+import org.hl7.fhir.igtools.publisher.Publisher.LinkedSpecification;
 import org.hl7.fhir.igtools.publisher.SpecMapManager.SpecialPackageType;
 import org.hl7.fhir.igtools.publisher.modules.IPublisherModule;
 import org.hl7.fhir.r5.context.ILoggingService;
@@ -199,7 +200,7 @@ public String getNextId() {
   private String rootFolder;
   private String altRootFolder;
   private List<SpecMapManager> specs;
-  private List<SpecMapManager> linkSpecs;
+  private List<LinkedSpecification> linkSpecs;
   private Map<String, LoadedFile> cache = new HashMap<String, LoadedFile>();
   private int iteration = 0;
   private List<StringPair> otherlinks = new ArrayList<StringPair>();
@@ -226,7 +227,7 @@ public String getNextId() {
   private Map<String, ValidationMessage> jsmsgs = new HashMap<>();
   private Map<String, FragmentUseRecord> fragmentUses = new HashMap<>();
 
-  public HTMLInspector(String rootFolder, List<SpecMapManager> specs, List<SpecMapManager> linkSpecs, ILoggingService log, String canonical, String packageId, Map<String, List<String>> trackedFragments, List<FetchedFile> sources, IPublisherModule module, boolean isCIBuild, Map<String, FragmentUseRecord> fragmentUses) {
+  public HTMLInspector(String rootFolder, List<SpecMapManager> specs, List<LinkedSpecification> linkSpecs, ILoggingService log, String canonical, String packageId, Map<String, List<String>> trackedFragments, List<FetchedFile> sources, IPublisherModule module, boolean isCIBuild, Map<String, FragmentUseRecord> fragmentUses) {
     this.rootFolder = rootFolder.replace("/", File.separator);
     this.specs = specs;
     this.linkSpecs = linkSpecs;
@@ -805,12 +806,12 @@ private boolean checkTarget(String filename, String ref, String rref, StringBuil
       }
     }
     if (!resolved && linkSpecs != null){
-      for (SpecMapManager spec : linkSpecs) {
-        if (!resolved && spec.getBase() != null) {
-          resolved = resolved || spec.getBase().equals(rref) || (spec.getBase()).equals(rref+"/") || (spec.getBase()+"/").equals(rref)|| spec.hasTarget(rref) || Utilities.existsInList(rref, Utilities.pathURL(spec.getBase(), "history.html"));
+      for (LinkedSpecification spec : linkSpecs) {
+        if (!resolved && spec.getSpm().getBase() != null) {
+          resolved = resolved || spec.getSpm().getBase().equals(rref) || (spec.getSpm().getBase()).equals(rref+"/") || (spec.getSpm().getBase()+"/").equals(rref)|| spec.getSpm().hasTarget(rref) || Utilities.existsInList(rref, Utilities.pathURL(spec.getSpm().getBase(), "history.html"));
         }
-        if (!resolved && spec.getBase2() != null) {
-          resolved = spec.getBase2().equals(rref) || (spec.getBase2()).equals(rref+"/"); 
+        if (!resolved && spec.getSpm().getBase2() != null) {
+          resolved = spec.getSpm().getBase2().equals(rref) || (spec.getSpm().getBase2()).equals(rref+"/"); 
         }
       }
     }

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

@@ -288,6 +288,7 @@
 import org.hl7.fhir.r5.renderers.utils.RenderingContext.ExampleScenarioRendererMode;
 import org.hl7.fhir.r5.renderers.utils.RenderingContext.FixedValueFormat;
 import org.hl7.fhir.r5.renderers.utils.RenderingContext.GenerationRules;
+import org.hl7.fhir.r5.renderers.utils.RenderingContext.IResourceLinkResolver;
 import org.hl7.fhir.r5.renderers.utils.RenderingContext.ITypeParser;
 import org.hl7.fhir.r5.renderers.utils.RenderingContext.KnownLinkType;
 import org.hl7.fhir.r5.renderers.utils.RenderingContext.QuestionnaireRendererMode;
@@ -360,6 +361,7 @@
 import org.hl7.fhir.utilities.npm.CommonPackages;
 import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
 import org.hl7.fhir.utilities.npm.NpmPackage;
+import org.hl7.fhir.utilities.npm.NpmPackage.PackageResourceInformation;
 import org.hl7.fhir.utilities.npm.PackageGenerator.PackageType;
 import org.hl7.fhir.utilities.npm.PackageHacker;
 import org.hl7.fhir.utilities.npm.PackageList;
@@ -447,7 +449,7 @@
 * ToC is generated by java, needs to be translated
  */
 
-public class Publisher implements ILoggingService, IReferenceResolver, IValidationProfileUsageTracker {
+public class Publisher implements ILoggingService, IReferenceResolver, IValidationProfileUsageTracker, IResourceLinkResolver {
 
   public class FragmentUseRecord {
 
@@ -654,6 +656,21 @@ public enum LinkTargetType {
 
   }
 
+  public static class LinkedSpecification {
+    private SpecMapManager spm;
+    private NpmPackage npm;
+    public LinkedSpecification(SpecMapManager spm, NpmPackage npm) {
+      super();
+      this.spm = spm;
+      this.npm = npm;
+    }
+    public SpecMapManager getSpm() {
+      return spm;
+    }
+    public NpmPackage getNpm() {
+      return npm;
+    }  
+  }
 
   public enum CacheOption {
     LEAVE, CLEAR_ERRORS, CLEAR_ALL;
@@ -732,7 +749,7 @@ public enum CacheOption {
   private IGKnowledgeProvider igpkp;
   private List<SpecMapManager> specMaps = new ArrayList<SpecMapManager>();
   private List<NpmPackage> npms = new ArrayList<NpmPackage>();
-  private List<SpecMapManager> linkSpecMaps = new ArrayList<SpecMapManager>();
+  private List<LinkedSpecification> linkSpecMaps = new ArrayList<>();
   private List<String> suppressedIds = new ArrayList<>();
 
   private Map<String, MappingSpace> mappingSpaces = new HashMap<String, MappingSpace>();
@@ -1582,7 +1599,7 @@ public void setCacheOption(CacheOption cacheOption) {
 
 
   @Override
-  public ResourceWithReference resolve(RenderingContext context, String url, String version) {
+  public ResourceWithReference resolve(RenderingContext context, String url, String version) throws IOException {
     if (url == null) {
       return null;
     }
@@ -1650,9 +1667,24 @@ public ResourceWithReference resolve(RenderingContext context, String url, Strin
         path = null;
       }
 
-      if (path != null)
-
-        return new ResourceWithReference(ResourceReferenceKind.EXTERNAL, url, path, null);
+      if (path != null) {
+        InputStream s = null;
+        if (sp.getNpm() != null && fp.contains("/") && sp.getLoader() != null) {
+          String[] pl = fp.split("\\/");
+          String rt = pl[pl.length-2];
+          String id = pl[pl.length-1]; 
+          s = sp.getNpm().loadExampleResource(rt, id);
+        }
+        if (s == null) {
+          return new ResourceWithReference(ResourceReferenceKind.EXTERNAL, url, path, null);
+        } else {
+          IContextResourceLoader loader = sp.getLoader();
+          Resource res = loader.loadResource(s, true);
+          res.setWebPath(path);
+          return new ResourceWithReference(ResourceReferenceKind.EXTERNAL, url, path, ResourceWrapper.forResource(context, res));
+
+        }
+      }
     }
 
     for (FetchedFile f : fileList) {
@@ -4132,7 +4164,7 @@ private void loadLinkIg(String packageId) throws Exception {
       igm.setName(pi.title());
       igm.setBase(pi.canonical());
       igm.setBase2(PackageHacker.fixPackageUrl(pi.url()));
-      linkSpecMaps.add(igm);
+      linkSpecMaps.add(new LinkedSpecification(igm, pi));
     }
   }
 
@@ -4218,6 +4250,7 @@ private void loadIGPackage(String name, String canonical, String packageId, Stri
     igm.setName(name);
     igm.setBase(canonical);
     igm.setBase2(PackageHacker.fixPackageUrl(pi.url()));
+    igm.setNpm(pi);
     specMaps.add(igm);
     if (!VersionUtilities.versionsCompatible(version, pi.fhirVersion())) {
       if (!pi.isWarned()) {
@@ -4227,7 +4260,7 @@ private void loadIGPackage(String name, String canonical, String packageId, Stri
       }
     }
 
-    loadFromPackage(name, canonical, pi, webref, igm, loadDeps);
+    igm.setLoader(loadFromPackage(name, canonical, pi, webref, igm, loadDeps));
   }
 
   private boolean isValidIGToken(String tail) {
@@ -4264,7 +4297,7 @@ private String getIgUri(NpmPackage pi) throws IOException {
 
 
 
-  public void loadFromPackage(String name, String canonical, NpmPackage pi, String webref, SpecMapManager igm, boolean loadDeps) throws IOException {
+  public IContextResourceLoader loadFromPackage(String name, String canonical, NpmPackage pi, String webref, SpecMapManager igm, boolean loadDeps) throws IOException {
     if (loadDeps) { // we do not load dependencies for packages the tooling loads on it's own initiative
       for (String dep : pi.dependencies()) {
         if (!context.hasPackage(dep)) {
@@ -4291,6 +4324,7 @@ public void loadFromPackage(String name, String canonical, NpmPackage pi, String
                 smm.setName(dpi.name()+"_"+dpi.version());
                 smm.setBase(dpi.canonical());
                 smm.setBase2(PackageHacker.fixPackageUrl(dpi.url()));
+                smm.setNpm(pi);
                 specMaps.add(smm);
               } catch (Exception e) {
                 if (!"hl7.fhir.core".equals(dpi.name())) {
@@ -4299,7 +4333,7 @@ public void loadFromPackage(String name, String canonical, NpmPackage pi, String
               }
 
               try {
-                loadFromPackage(dpi.title(), dpi.canonical(), dpi, PackageHacker.fixPackageUrl(dpi.getWebLocation()), smm, true);
+                smm.setLoader(loadFromPackage(dpi.title(), dpi.canonical(), dpi, PackageHacker.fixPackageUrl(dpi.getWebLocation()), smm, true));
               } catch (Exception e) {
                 throw new IOException("Error loading "+dpi.name()+"#"+dpi.version()+": "+e.getMessage(), e);                
               }
@@ -4310,6 +4344,7 @@ public void loadFromPackage(String name, String canonical, NpmPackage pi, String
     }    
     IContextResourceLoader loader = new PublisherLoader(pi, igm, webref, igpkp).makeLoader();
     context.loadFromPackage(pi, loader);
+    return loader;
   }
 
 private String fixPackageReference(String dep) {
@@ -4808,6 +4843,8 @@ private boolean load() throws Exception {
     rc.setParser(getTypeLoader(version));
     rc.addLink(KnownLinkType.SELF, targetOutput);
     rc.setFixedFormat(fixedFormat);
+    rc.setResolveLinkResolver(this);
+    rc.setDebug(debug);
     module.defineTypeMap(rc.getTypeMap());
     if (publishedIg.hasJurisdiction()) {
       Locale locale = null;
@@ -13412,6 +13449,10 @@ private void generateOutputsStructureDefinition(FetchedFile f, FetchedResource r
       long start = System.currentTimeMillis();
       fragment("StructureDefinition-"+prefixForContainer+sd.getId()+"-sd-xref"+langSfx, sdr.references(), f.getOutputNames(), r, vars, null, start, "xref", "StructureDefinition");
     }
+    if (igpkp.wantGen(r, "use-context")) {
+      long start = System.currentTimeMillis();
+      fragment("StructureDefinition-"+prefixForContainer+sd.getId()+"-sd-use-context"+langSfx, sdr.useContext(), f.getOutputNames(), r, vars, null, start, "use-context", "StructureDefinition");
+    }
     if (igpkp.wantGen(r, "changes")) {
       long start = System.currentTimeMillis();
       fragment("StructureDefinition-"+prefixForContainer+sd.getId()+"-sd-changes"+langSfx, sdr.changeSummary(), f.getOutputNames(), r, vars, null, start, "changes", "StructureDefinition");
@@ -14840,7 +14881,6 @@ public static void publishDirect(String path) throws Exception {
     if (self.countErrs(self.errors) > 0) {
       throw new Exception("Building IG '"+path+"' caused an error");
     }
-
   }
 
   public long getMaxMemory() {
@@ -14859,4 +14899,26 @@ public String resolveUri(RenderingContext context, String uri) {
     return null;
   }
 
+  @Override
+  public <T extends Resource> T findLinkableResource(Class<T> class_, String uri) throws IOException {
+    for (LinkedSpecification spec : linkSpecMaps) {
+      String name = class_.getSimpleName();
+      for (PackageResourceInformation pri : spec.getNpm().listIndexedResources(name)) {
+        boolean match = false;
+        if (uri.contains("|")) {
+          match = uri.equals(pri.getUrl()+"|"+pri.getVersion());
+        } else {
+          match = uri.equals(pri.getUrl());          
+        }
+        if (match) {
+          InputStream s = spec.getNpm().load(pri);
+          IContextResourceLoader pl = new PublisherLoader(spec.getNpm(), spec.getSpm(), PackageHacker.fixPackageUrl(spec.getNpm().getWebLocation()), igpkp).makeLoader();
+          Resource res = pl.loadResource(s, true);
+          return (T) res;
+        }
+      }
+    }
+    return null;
+  }
+
 }

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

@@ -33,6 +33,7 @@
 import java.util.Set;
 
 import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.r5.context.IContextResourceLoader;
 import org.hl7.fhir.r5.model.Constants;
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;
@@ -77,6 +78,7 @@ public enum SpecialPackageType {
   private String auth;
   private String realm;
   private String npmVId;
+  private IContextResourceLoader loader;
 
   private SpecMapManager() {
 
@@ -459,7 +461,7 @@ public static SpecMapManager createSpecialPackage(NpmPackage pi, BasePackageCach
       res.special = SpecialPackageType.DICOM;
     } else if (pi.name().startsWith("hl7.fhir.") && pi.name().endsWith(".examples") ) {
       res.special = SpecialPackageType.Examples;
-    } else {
+    } else if (!pi.name().startsWith("hl7.fhir.us.core.v")) {
       res.special = SpecialPackageType.Simplifier;  
     }
     res.pi = pi;
@@ -511,5 +513,21 @@ public boolean isCore() {
     return "hl7.fhir.core".equals(getNpmName());
   }
 
+  public NpmPackage getNpm() {
+    return pi;
+  }
+
+  public void setNpm(NpmPackage pi) {
+    this.pi = pi;
+  }
+
+  public IContextResourceLoader getLoader() {
+    return loader;
+  }
+
+  public void setLoader(IContextResourceLoader loader) {
+    this.loader = loader;
+  }
+
 
 }

org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/modules/CrossVersionModule.java

@@ -191,7 +191,7 @@ private void genExtensionPage(String path, StructureDefinition sd) throws IOExce
     }
     XhtmlNode body = new XhtmlNode(NodeType.Element, "div");  
     body.h1().tx(sd.getTitle());
-    var tbl = body.table("grid");
+    var tbl = body.table("grid", false);
     var tr = tbl.tr();
     tr.td().b().tx("URL");
     tr.td().tx(sd.getUrl());
@@ -336,7 +336,7 @@ private void genVersionType(String path, StructureDefinition sd, ImplementationG
     XhtmlNode body = new XhtmlNode(NodeType.Element, "div");  
     body.h1().tx(sd.getName());
     body.para().tx("FHIR Cross-version Mappings for "+sd.getType()+" based on the R5 structure");
-    XhtmlNode tbl = body.table("grid");
+    XhtmlNode tbl = body.table("grid", false);
     XhtmlNode tr = tbl.tr();
 
     // we're going to generate a table with a column for each target structure definition in the chains that terminate in the provided sd

org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/renderers/CrossViewRenderer.java

@@ -795,7 +795,7 @@ private String buildExtensionTable(String type, List<ExtensionDefinition> defini
     } else {
       kind = "data type";
     }
-    var tbl = x.table("list");
+    var tbl = x.table("list", false);
     var tr = tbl.tr();
     var td = tr.td();
     td.b().tx("Identity");
@@ -1318,7 +1318,7 @@ public String renderVSList(String versionToAnnotate, List<ValueSet> vslist, bool
 
     XhtmlNode x = new XhtmlNode(NodeType.Element, "div");
     Collections.sort(vslist, new CanonicalResourceSortByUrl());
-    var tbl = x.table("grid");
+    var tbl = x.table("grid", false);
     var tr = tbl.tr();
     tr.th().tx("URL");
     if (versions) {
@@ -1613,7 +1613,7 @@ private void resolveCS(List<CodeSystem> list, String url, Resource source) {
   public String renderCSList(String versionToAnnotate, List<CodeSystem> cslist, boolean versions, boolean used) throws IOException {
     XhtmlNode x = new XhtmlNode(NodeType.Element, "div");
     Collections.sort(cslist, new CanonicalResourceSortByUrl());
-    var tbl = x.table("grid");
+    var tbl = x.table("grid", false);
     var tr = tbl.tr();
     tr.th().tx("URL");
     if (versions) {

org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/renderers/HistoryGenerator.java

@@ -60,7 +60,7 @@ public XhtmlNode internalGenerate(List<ProvenanceDetails> entries, boolean showT
       XhtmlNode div = new XhtmlNode(NodeType.Element, "div");
       div.hr();
       div.para().b().tx("History");
-      XhtmlNode tbl = div.table("grid");
+      XhtmlNode tbl = div.table("grid", false);
 
       // headers
       XhtmlNode tr = tbl.tr();

org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/renderers/StatusRenderer.java

@@ -260,7 +260,7 @@ private static String readOwner(Element resource) {
 
   public static String render(String src, ResourceStatusInformation info, RenderingContext rc) {
     StringBuilder b = new StringBuilder();
-    b.append("<table class=\"");
+    b.append("<table role=\"presentation\" class=\"");
     b.append(info.getColorClass());
     b.append("\"><tr>");
     String pub = rc.formatPhrase(RenderingContext.MATURITY_PUBLISHER, Utilities.escapeXml(info.getOwner()));