2024 11 gg custom resources 2

RELEASE_NOTES.md

@@ -0,0 +1,15 @@
+* Security: Enforce that XML can't load XML entity declarations
+* Loader: Fix missing isModifierReason on modifier extensions
+* Version Convertor: fix bug converting NamingSystem.url between versions
+* Version Convertor: Fix IG dependsOn.reason conversion
+* Validator: fix value set validation on import validation to find external value sets
+* Validator: Fix terminology tester for change to language header
+* Validator: Adjust wording of R5 slicing check
+* Validator: Sort entries in error message about profiles to make the order reproducible
+* Validator: support resolving /_history/ URLs in IG publisher
+* Renderer: make HTA messages translatable
+* Renderer: new release - pubpack
+* Renderer: suppress Json resourceType property in some logical models
+* Renderer: more support for canonical logical models
+* SQL: Fix NPE building package.db
+* Go-Publish: Fix bug in publication checker - space in sequence blows logic up

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

@@ -25,10 +25,12 @@
 import java.util.HashSet;
 import java.util.List;
 
+import org.hl7.fhir.r5.context.IWorkerContext;
 import org.hl7.fhir.r5.elementmodel.Element;
 import org.hl7.fhir.r5.model.ImplementationGuide.ImplementationGuideDefinitionResourceComponent;
 import org.hl7.fhir.r5.utils.UserDataNames;
 import org.hl7.fhir.r5.model.Resource;
+import org.hl7.fhir.r5.model.StructureDefinition;
 import org.hl7.fhir.utilities.json.model.JsonObject;
 import org.hl7.fhir.utilities.validation.ValidationMessage;
 
@@ -370,6 +372,17 @@ public boolean isCustomResource() {
       return getElement().getProperty().getStructure().hasUserData(UserDataNames.loader_custom_resource);
     }
   }
+
+  public boolean isCanonical(IWorkerContext context) {
+    StructureDefinition sd = getElement().getProperty().getStructure();
+    while (sd != null) {
+      if ("CanonicalResource".equals(sd.getType())) {
+        return true;
+      }
+      sd = context.fetchResource(StructureDefinition.class, sd.getBaseDefinition());
+    }
+    return false;
+  }
 
 
 }

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

@@ -399,7 +399,18 @@ public String getSourceFor(String ref) {
   public void findConfiguration(FetchedFile f, FetchedResource r) {
     if (template != null) {
       JsonObject cfg = null;
-      if (r.isExample()) {
+      if (r.isCanonical(context)) {
+        if (r.isExample()) {
+          cfg = defaultConfig.getJsonObject("example:canonical");
+        }
+        if (cfg == null) {
+          cfg = defaultConfig.getJsonObject(r.fhirType()+":canonical");
+        }
+        if (cfg == null) {
+          cfg = defaultConfig.getJsonObject("Any:canonical");
+        }
+      }
+      if (cfg == null && r.isExample()) {
         cfg = defaultConfig.getJsonObject("example");
       }        
       if (cfg == null && r.fhirType().equals("StructureDefinition")) {

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

@@ -9212,6 +9212,8 @@ private void generateSummaryOutputs(DBBuilder db) throws Exception {
         }
         if (r.getResource() != null) {
           populateResourceEntry(r, item, null);
+        } else if (r.isCustomResource()) {
+          populateCustomResourceEntry(r, item, null);          
         }
         JsonArray contained = null;
         // contained resources get added twice - once as sub-entries under the resource that contains them, and once as an entry in their own right, for their own rendering 
@@ -9272,7 +9274,233 @@ private void generateSummaryOutputs(DBBuilder db) throws Exception {
 
     json = org.hl7.fhir.utilities.json.parser.JsonParser.compose(data, true);
     TextFile.stringToFile(json, Utilities.path(tempDir, "_data", "languages.json"));
-
+  }
+
+  private void populateCustomResourceEntry(FetchedResource r, JsonObject item, Object object) {
+    Element e = r.getElement();
+//      item.add("layout-type", "canonical");
+    if (e.getChildren("url").size() == 1) {
+      item.add("url", e.getNamedChildValue("url"));
+    }
+      if (e.hasChildren("identifier")) {
+        List<String> ids = new ArrayList<String>();
+        for (Element id : e.getChildren("identifier")) {
+          if (id.hasChild("value")) {
+            ids.add(dr.displayDataType(ResourceWrapper.forType(cu, id)));
+          }
+        }
+        if (!ids.isEmpty()) {
+          item.add("identifiers", String.join(", ", ids));
+        }
+      }
+      if (e.getChildren("version").size() == 1) {
+        item.add("version", e.getNamedChildValue("version"));
+      }
+      if (e.getChildren("name").size() == 1) {
+        item.add("name", e.getNamedChildValue("name"));
+      }
+      if (e.getChildren("title").size() == 1) {
+        item.add("title", e.getNamedChildValue("title"));
+//        addTranslationsToJson(item, "title", e.getNamedChild("title"), false);
+      }
+      if (e.getChildren("experimental").size() == 1) {
+        item.add("experimental", e.getNamedChildValue("experimental"));
+      }
+      if (e.getChildren("date").size() == 1) {
+        item.add("date", e.getNamedChildValue("date"));
+      }
+      if (e.getChildren("description").size() == 1) {
+        item.add("description", ProfileUtilities.processRelativeUrls(e.getNamedChildValue("description"), "", igpkp.specPath(), context.getResourceNames(), specMaps.get(0).listTargets(), pageTargets(), false));
+//        addTranslationsToJson(item, "description", e.getNamedChild("description"), false);
+      }
+
+//      if (cr.hasUseContext() && !containedCr) {
+//        List<String> contexts = new ArrayList<String>();
+//        for (UsageContext uc : cr.getUseContext()) {
+//          String label = dr.displayDataType(uc.getCode());
+//          if (uc.hasValueCodeableConcept()) {
+//            String value = dr.displayDataType(uc.getValueCodeableConcept());
+//            if (value!=null) {
+//              contexts.add(label + ":\u00A0" + value);
+//            }
+//          } else if (uc.hasValueQuantity()) {
+//            String value = dr.displayDataType(uc.getValueQuantity());
+//            if (value!=null)
+//              contexts.add(label + ":\u00A0" + value);
+//          } else if (uc.hasValueRange()) {
+//            String value = dr.displayDataType(uc.getValueRange());
+//            if (!value.isEmpty())
+//              contexts.add(label + ":\u00A0" + value);
+//
+//          } else if (uc.hasValueReference()) {
+//            String value = null;
+//            String reference = null;
+//            if (uc.getValueReference().hasReference()) {
+//              reference = uc.getValueReference().getReference().contains(":") ? "" : igpkp.getCanonical() + "/";
+//              reference += uc.getValueReference().getReference();
+//            }
+//            if (uc.getValueReference().hasDisplay()) {
+//              if (reference != null)
+//                value = "[" + uc.getValueReference().getDisplay() + "](" + reference + ")";
+//              else
+//                value = uc.getValueReference().getDisplay();
+//            } else if (reference!=null)
+//              value = "[" + uc.getValueReference().getReference() + "](" + reference + ")";
+//            else if (uc.getValueReference().hasIdentifier()) {
+//              String idLabel = dr.displayDataType(uc.getValueReference().getIdentifier().getType());
+//              value = idLabel!=null ? label + ":\u00A0" + uc.getValueReference().getIdentifier().getValue() : uc.getValueReference().getIdentifier().getValue();
+//            }
+//            if (value != null)
+//              contexts.add(value);
+//          } else if (uc.hasValue()) {
+//            throw new FHIRException("Unsupported type for UsageContext.value - " + uc.getValue().fhirType());
+//          }
+//        }
+//        if (!contexts.isEmpty())
+//          item.add("contexts", String.join(", ", contexts));              
+//      }
+//      if (cr.hasJurisdiction() && !containedCr) {
+//        File flagDir = new File(tempDir + "/assets/images");
+//        if (!flagDir.exists())
+//          flagDir.mkdirs();
+//        JsonArray jNodes = new JsonArray();
+//        item.add("jurisdictions", jNodes);
+//        ValueSet jvs = context.fetchResource(ValueSet.class, "http://hl7.org/fhir/ValueSet/jurisdiction");
+//        for (CodeableConcept cc : cr.getJurisdiction()) {
+//          JsonObject jNode = new JsonObject();
+//          jNodes.add(jNode);
+//          ValidationResult vr = jvs==null ? null : context.validateCode(new ValidationOptions(FhirPublication.R5, "en-US"),  cc, jvs);
+//          if (vr != null && vr.asCoding()!=null) {
+//            Coding cd = vr.asCoding();
+//            jNode.add("code", cd.getCode());
+//            if (cd.getSystem().equals("http://unstats.un.org/unsd/methods/m49/m49.htm") && cd.getCode().equals("001")) {
+//              jNode.add("name", "International");
+//              jNode.add("flag", "001");
+//            } else if (cd.getSystem().equals("urn:iso:std:iso:3166")) {
+//              String code = translateCountryCode(cd.getCode()).toLowerCase();
+//              jNode.add("name", displayForCountryCode(cd.getCode()));
+//              File flagFile = new File(vsCache + "/" + code + ".svg");
+//              if (!flagFile.exists() && !ignoreFlags.contains(code)) {
+//                URL url2 = new URL("https://flagcdn.com/" + shortCountryCode.get(code.toUpperCase()).toLowerCase() + ".svg");
+//                try {
+//                  InputStream in = url2.openStream();
+//                  Files.copy(in, Paths.get(flagFile.getAbsolutePath()));
+//                } catch (Exception e2) {
+//                  ignoreFlags.add(code);
+//                  System.out.println("Unable to access " + url2 + " or " + url2+" ("+e2.getMessage()+")");
+//                }
+//              }
+//              if (flagFile.exists()) {
+//                FileUtils.copyFileToDirectory(flagFile, flagDir);
+//                jNode.add("flag", code);
+//              }
+//            } else if (cd.getSystem().equals("urn:iso:std:iso:3166:-2")) {
+//              String code = cd.getCode();
+//              String[] codeParts = cd.getCode().split("-");
+//              jNode.add("name", displayForStateCode(cd.getCode()) + " (" + displayForCountryCode(codeParts[0]) + ")");
+//              File flagFile = new File(vsCache + "/" + code + ".svg");
+//              if (!flagFile.exists()) {
+//                URL url = new URL("http://flags.ox3.in/svg/" + codeParts[0].toLowerCase() + "/" + codeParts[1].toLowerCase() + ".svg");
+//                try (InputStream in = url.openStream()) {
+//                  Files.copy(in, Paths.get(flagFile.getAbsolutePath()));
+//                } catch (Exception e) {
+//                  // If we can't find the file, that's ok.
+//                }
+//              }
+//              if (flagFile.exists()) {
+//                FileUtils.copyFileToDirectory(flagFile, flagDir);
+//                jNode.add("flag", code);
+//              }
+//            }
+//          } else {
+//            jNode.add("name", dr.displayDataType(cc));
+//          }
+//        }
+//      }
+
+      if (e.getChildren("purpose").size() == 1) {
+        item.add("purpose", ProfileUtilities.processRelativeUrls(e.getNamedChildValue("purpose"), "", igpkp.specPath(), context.getResourceNames(), specMaps.get(0).listTargets(), pageTargets(), false));
+//        addTranslationsToJson(item, "purpose", e.getNamedChild("purpose"), false);
+      }
+      if (e.getChildren("status").size() == 1) {
+        item.add("status", e.getNamedChildValue("status"));
+      }
+      if (e.getChildren("copyright").size() == 1) {
+        item.add("copyright", ProfileUtilities.processRelativeUrls(e.getNamedChildValue("copyright"), "", igpkp.specPath(), context.getResourceNames(), specMaps.get(0).listTargets(), pageTargets(), false));
+//        addTranslationsToJson(item, "description", e.getNamedChild("description"), false);
+      }
+
+//      if (pcr!=null && pcr.hasExtension(ToolingExtensions.EXT_FMM_LEVEL)) {
+//        IntegerType fmm = pcr.getExtensionByUrl(ToolingExtensions.EXT_FMM_LEVEL).getValueIntegerType();
+//        item.add("fmm", fmm.asStringValue());
+//        if (fmm.hasExtension(ToolingExtensions.EXT_FMM_DERIVED)) {
+//          String derivedFrom = "FMM derived from: ";
+//          for (Extension ext: fmm.getExtensionsByUrl(ToolingExtensions.EXT_FMM_DERIVED)) {
+//            derivedFrom += "\r\n" + ext.getValueCanonicalType().asStringValue();                  
+//          }
+//          item.add("fmmSource", derivedFrom);
+//        }
+//      }
+//      List<String> keywords = new ArrayList<String>();
+//      if (r.getResource() instanceof StructureDefinition) {
+//        StructureDefinition sd = (StructureDefinition)r.getResource();
+//        if (sd.hasKeyword()) {
+//          for (Coding coding : sd.getKeyword()) {
+//            String value = dr.displayDataType(coding);
+//            if (value != null)
+//              keywords.add(value);
+//          }
+//        }
+//      } else if (r.getResource() instanceof CodeSystem) {
+//        CodeSystem cs = (CodeSystem)r.getResource();
+//        for (Extension e : cs.getExtensionsByUrl(ToolingExtensions.EXT_CS_KEYWORD)) {
+//          keywords.add(e.getValueStringType().asStringValue());
+//        }
+//      } else if (r.getResource() instanceof ValueSet) {
+//        ValueSet vs = (ValueSet)r.getResource();
+//        for (Extension e : vs.getExtensionsByUrl(ToolingExtensions.EXT_VS_KEYWORD)) {
+//          keywords.add(e.getValueStringType().asStringValue());
+//        }
+//      }
+//      if (!keywords.isEmpty())
+//        item.add("keywords", String.join(", ", keywords));              
+//    
+//
+      org.hl7.fhir.igtools.renderers.StatusRenderer.ResourceStatusInformation info = StatusRenderer.analyse(e);
+      JsonObject jo = new JsonObject();
+      if (info.getColorClass() != null) {
+        jo.add("class", info.getColorClass());
+      }
+      if (info.getOwner() != null) {
+        jo.add("owner", info.getOwner());
+      }
+      if (info.getOwnerLink() != null) {
+        jo.add("link", info.getOwnerLink());
+      }
+      if (info.getSstatus() != null) {
+        jo.add("standards-status", info.getSstatus());
+      } else if (sourceIg.hasExtension(ToolingExtensions.EXT_STANDARDS_STATUS)) {
+        jo.add("standards-status","informative");
+      }
+      if (info.getSstatusSupport() != null) {
+        jo.add("standards-status-support", info.getSstatusSupport());
+      }
+      if (info.getNormVersion() != null) {
+        item.add("normativeVersion", info.getNormVersion());
+      }
+      if (info.getFmm() != null) {
+        jo.add("fmm", info.getFmm());
+      }
+      if (info.getSstatusSupport() != null) {
+        jo.add("fmm-support", info.getFmmSupport());
+      }
+      if (info.getStatus() != null && !jo.has("status")) {
+        jo.add("status", info.getStatus());
+      }
+      if (!jo.getProperties().isEmpty()) {
+        item.set("status", jo);
+      }
+
   }
 
   private void genBasePages() throws IOException, Exception {
@@ -9556,6 +9784,7 @@ private List<DependencyAnalyser.ArtifactDependency> makeDependencies() {
 
   public void populateResourceEntry(FetchedResource r, JsonObject item, ContainedResourceDetails crd) throws Exception {
     if (r.getResource() instanceof CanonicalResource || (crd!= null && crd.getCanonical() != null)) {
+//      item.add("layout-type", "canonical");
       boolean containedCr = crd != null && crd.getCanonical() != null;
       CanonicalResource cr = containedCr ? crd.getCanonical() : (CanonicalResource) r.getResource();
       CanonicalResource pcr = r.getResource() instanceof CanonicalResource ? (CanonicalResource) r.getResource() : null;

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

@@ -107,6 +107,9 @@ public ValidationServices(IWorkerContext context, IGKnowledgeProvider ipg, Imple
   public Element fetch(IResourceValidator validator, Object appContext, String url) throws FHIRException, IOException {
     if (url == null)
       return null;
+    if (url.contains("/_history/")) {
+      url = url.substring(0, url.indexOf("/_history"));
+    }
     String turl = (!Utilities.isAbsoluteUrl(url)) ? Utilities.pathURL(ipg.getCanonical(), url) : url;
     Resource res = context.fetchResource(getResourceType(turl), turl);
     if (res != null) {

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

@@ -328,12 +328,12 @@ public void saveResource(FetchedFile f, FetchedResource r, byte[] json) {
         psql.setInt(3, r.getElement().getProperty().getStructure().hasUserData(UserDataNames.loader_custom_resource) ? 1 : 0);
         bindString(psql, 4, r.getId());
         bindString(psql, 5, r.getElement().getWebPath());
-        bindString(psql, 6, r.getElement().getNamedChildValue("url"));
-        bindString(psql, 7, r.getElement().getNamedChildValue("version"));
-        bindString(psql, 8, r.getElement().getNamedChildValue("status"));
-        bindString(psql, 9, r.getElement().getNamedChildValue("date"));
-        bindString(psql, 10, r.getElement().getChildren("name").size() == 1 && r.getElement().getNamedChild("name").isPrimitive() ? r.getElement().getNamedChildValue("name") : r.getResourceName());
-        bindString(psql, 11, r.getElement().getNamedChildValue("title"));
+        bindString(psql, 6, getSingleChildValue(r, "url", null));
+        bindString(psql, 7, getSingleChildValue(r, "version", null));
+        bindString(psql, 8, getSingleChildValue(r, "status", null));
+        bindString(psql, 9, getSingleChildValue(r, "date", null));
+        bindString(psql, 10, getSingleChildValue(r, "name", r.getResourceName()));
+        bindString(psql, 11, getSingleChildValue(r, "title", null));
         bindString(psql, 12, r.getResourceDescription());
         psql.setBytes(13, json);
         psql.executeUpdate();   
@@ -380,6 +380,10 @@ public void saveResource(FetchedFile f, FetchedResource r, byte[] json) {
     time(start);
   }
 
+  private String getSingleChildValue(FetchedResource r, String name, String defaultValue) {
+    return r.getElement().getChildren(name).size() == 1 && r.getElement().getNamedChild(name).isPrimitive() ? r.getElement().getNamedChildValue(name) : defaultValue;
+  }
+
   public void finishResources() {
     long start = System.currentTimeMillis();
     if (con == null) {

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

@@ -28,6 +28,7 @@
 import org.hl7.fhir.r5.renderers.utils.RenderingContext.RenderingContextLangs;
 import org.hl7.fhir.utilities.MarkDownProcessor;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.i18n.I18nConstants;
 import org.hl7.fhir.utilities.xhtml.XhtmlComposer;
 import org.hl7.fhir.utilities.xhtml.XhtmlNode;
 import org.hl7.fhir.utilities.xhtml.XhtmlParser;
@@ -216,14 +217,12 @@ private boolean isHL7Ig() {
 
   private String getCopyRightStatement(SystemUsage system) throws IOException {
     if ("http://snomed.info/sct".equals(system.system)) {
-      system.desc = "SNOMED Clinical Terms® (SNOMED CT®)";
-      return "This material contains content that is copyright of SNOMED International. Implementers of these specifications must have the appropriate SNOMED CT Affiliate license - "+
-       "for more information contact <a href=\"https://www.snomed.org/get-snomed\">https://www.snomed.org/get-snomed</a> or <a href=\"mailto:[email protected]\">[email protected]</a>.";
+      system.desc = ctxt.formatMessage(I18nConstants.HTA_SCT_DESC);
+      return ctxt.formatMessage(I18nConstants.HTA_SCT_MESSAGE);
     }
     if ("http://loinc.org".equals(system.system)) {
-      system.desc = "LOINC";
-      return "This material contains content from <a href=\"http://loinc.org\">LOINC</a>. LOINC is copyright © 1995-2020, Regenstrief Institute, Inc. and the Logical Observation Identifiers Names and Codes (LOINC) "+
-         "Committee and is available at no cost under the <a href=\"http://loinc.org/license\">license</a>. LOINC® is a registered United States trademark of Regenstrief Institute, Inc.";
+      system.desc = ctxt.formatMessage(I18nConstants.HTA_LOINC_DESC);
+      return ctxt.formatMessage(I18nConstants.HTA_LOINC_MESSAGE);
     }
     if (system.cs != null) {
       system.desc = system.cs.present();