Fixes for changes to core - BOM handling and terminology stack rework

src/main/java/org/hl7/fhir/definitions/generators/specification/json/SchemaGenerator.java

@@ -187,7 +187,7 @@ private void addAllResourcesChoice(Definitions definitions, JsonObject schema, L
   private void save(JsonObject s, String filename) throws IOException {
     Gson gson = new GsonBuilder().setPrettyPrinting().create();
     String json = gson.toJson(s);
-    TextFile.stringToFile(json, filename, false); // remove BOM, see https://chat.fhir.org/#narrow/stream/implementers/subject/Removal.20of.20byte.20order.20mark.20in.20json.20schemas
+    TextFile.stringToFile(json, filename); // remove BOM, see https://chat.fhir.org/#narrow/stream/implementers/subject/Removal.20of.20byte.20order.20mark.20in.20json.20schemas
   }
 
   private void produceCombinedSchema(Definitions definitions, String xsdDir, String dstDir, String srcDir) throws Exception {

src/main/java/org/hl7/fhir/tools/publisher/BuildWorkerContext.java

@@ -26,7 +26,6 @@
 import org.fhir.ucum.UcumEssenceService;
 import org.fhir.ucum.UcumException;
 import org.fhir.ucum.UcumService;
-import org.hl7.fhir.convertors.txClient.TerminologyClientR5;
 import org.hl7.fhir.definitions.model.Definitions;
 import org.hl7.fhir.exceptions.DefinitionException;
 import org.hl7.fhir.exceptions.FHIRException;
@@ -62,6 +61,7 @@
 import org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent;
 import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionContainsComponent;
 import org.hl7.fhir.r5.terminologies.client.ITerminologyClient;
+import org.hl7.fhir.r5.terminologies.client.TerminologyClientR5;
 import org.hl7.fhir.r5.terminologies.utilities.ValidationResult;
 import org.hl7.fhir.r5.utils.client.EFhirClientException;
 import org.hl7.fhir.r5.utils.validation.IResourceValidator;
@@ -129,11 +129,12 @@ public class BuildWorkerContext extends BaseWorkerContext implements IWorkerCont
 
   public BuildWorkerContext(Definitions definitions, String terminologyCachePath, ITerminologyClient client, CanonicalResourceManager<CodeSystem> codeSystems, CanonicalResourceManager<ValueSet> valueSets, CanonicalResourceManager<ConceptMap> maps, CanonicalResourceManager<StructureDefinition> profiles, CanonicalResourceManager<ImplementationGuide> guides, String folder) throws UcumException, ParserConfigurationException, SAXException, IOException, FHIRException {
     super(codeSystems, valueSets, maps, profiles, guides);
-    initTS(terminologyCachePath);
+    initTxCache(terminologyCachePath);
     this.definitions = definitions;
-    this.tcc.setClient(client);
+    this.terminologyClientManager.setMasterClient(client);
+    this.terminologyClientManager.setUsage("publication");
     this.txLog = new HTMLClientLogger(null);
-    setExpansionProfile(buildExpansionProfile());
+    setExpansionParameters(buildExpansionProfile());
     this.setTranslator(new TranslatorXml(Utilities.path(folder, "implementations", "translations.xml")));
     setWarnAboutMissingMessages(false);
   }
@@ -149,11 +150,11 @@ private Parameters buildExpansionProfile() {
   }
 
   public boolean hasClient() {
-    return tcc.getClient() != null;
+    return terminologyClientManager.hasClient();
   }
 
   public ITerminologyClient getClient() {
-    return tcc.getClient();
+    return terminologyClientManager.getMasterClient();
   }
 
   public StructureDefinition getExtensionStructure(StructureDefinition context, String url) throws Exception {
@@ -559,14 +560,14 @@ private String lookupLoinc(String code) throws Exception {
       try {
         triedServer = true;
         // for this, we use the FHIR client
-        if (tcc.getClient() == null) {
-          tcc.setClient(new TerminologyClientR5("tx.fhir.org", tcc.getServer(), "fhir/main-build"));
+        if (terminologyClientManager.getMasterClient() == null) {
+          terminologyClientManager.setMasterClient(new TerminologyClientR5("tx-dev.fhir.org", "?", "fhir/main-build"));
           this.txLog = new HTMLClientLogger(null);
         }
         Map<String, String> params = new HashMap<String, String>();
         params.put("code", code);
         params.put("system", "http://loinc.org");
-        Parameters result = tcc.getClient().lookupCode(params);
+        Parameters result = terminologyClientManager.getMasterClient().lookupCode(params);
 
         for (ParametersParameterComponent p : result.getParameter()) {
           if (p.getName().equals("display"))

src/main/java/org/hl7/fhir/tools/publisher/ExampleInspector.java

@@ -8,6 +8,7 @@
 import java.net.MalformedURLException;
 import java.net.URISyntaxException;
 import java.util.ArrayList;
+import java.util.EnumSet;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Locale;
@@ -53,6 +54,10 @@
 import org.hl7.fhir.r5.utils.validation.IResourceValidator;
 import org.hl7.fhir.r5.utils.validation.IValidationPolicyAdvisor;
 import org.hl7.fhir.r5.utils.validation.IValidatorResourceFetcher;
+import org.hl7.fhir.r5.utils.validation.IValidationPolicyAdvisor.AdditionalBindingPurpose;
+import org.hl7.fhir.r5.utils.validation.IValidationPolicyAdvisor.CodedContentValidationAction;
+import org.hl7.fhir.r5.utils.validation.IValidationPolicyAdvisor.ElementValidationAction;
+import org.hl7.fhir.r5.utils.validation.IValidationPolicyAdvisor.ResourceValidationAction;
 import org.hl7.fhir.r5.utils.validation.constants.BestPracticeWarningLevel;
 import org.hl7.fhir.r5.utils.validation.constants.BindingKind;
 import org.hl7.fhir.r5.utils.validation.constants.CodedContentValidationPolicy;
@@ -696,18 +701,44 @@ public ReferenceValidationPolicy policyForReference(IResourceValidator validator
 
 
   @Override
-  public ContainedReferenceValidationPolicy policyForContained(IResourceValidator validator, Object appContext, String containerType, String containerId, SpecialElement containingResourceType, String path, String url) {
+  public ContainedReferenceValidationPolicy policyForContained(IResourceValidator validator,
+      Object appContext,
+      StructureDefinition structure,
+      ElementDefinition element,
+      String containerType,
+      String containerId,
+      Element.SpecialElement containingResourceType,
+      String path,
+      String url) {
     return ContainedReferenceValidationPolicy.CHECK_VALID;
   }
 
 
   @Override
-  public CodedContentValidationPolicy policyForCodedContent(IResourceValidator validator, Object appContext, String stackPath, ElementDefinition definition,
-      StructureDefinition structure, BindingKind kind, ValueSet valueSet, List<String> systems) {
-    return CodedContentValidationPolicy.VALUESET;
+  public EnumSet<CodedContentValidationAction> policyForCodedContent(IResourceValidator validator,
+      Object appContext,
+      String stackPath,
+      ElementDefinition definition,
+      StructureDefinition structure,
+      BindingKind kind,
+      AdditionalBindingPurpose purpose,
+      ValueSet valueSet,
+      List<String> systems) {
+    return EnumSet.allOf(CodedContentValidationAction.class);
   }
 
 
+  @Override
+  public EnumSet<ResourceValidationAction> policyForResource(IResourceValidator validator, Object appContext,
+      StructureDefinition type, String path) {
+    return EnumSet.allOf(ResourceValidationAction.class);
+  }
+
+  @Override
+  public EnumSet<ElementValidationAction> policyForElement(IResourceValidator validator, Object appContext,
+      StructureDefinition structure, ElementDefinition element, String path) {
+    return EnumSet.allOf(ElementValidationAction.class);
+  }
   public List<ValidationMessage> getErrors() {
     return errorsInt;
   }

src/main/java/org/hl7/fhir/tools/publisher/PageProcessor.java

@@ -75,7 +75,6 @@ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWIS
 import org.hl7.fhir.convertors.SpecDifferenceEvaluator;
 import org.hl7.fhir.convertors.TypeLinkProvider;
 import org.hl7.fhir.convertors.loaders.loaderR5.R4ToR5Loader;
-import org.hl7.fhir.convertors.txClient.TerminologyClientR5;
 import org.hl7.fhir.definitions.Config;
 import org.hl7.fhir.definitions.generators.specification.BaseGenerator;
 import org.hl7.fhir.definitions.generators.specification.DataTypeTableGenerator;
@@ -224,6 +223,7 @@ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWIS
 import org.hl7.fhir.r5.terminologies.TerminologyCacheManager;
 import org.hl7.fhir.r5.terminologies.ValueSetUtilities;
 import org.hl7.fhir.r5.terminologies.client.ITerminologyClient;
+import org.hl7.fhir.r5.terminologies.client.TerminologyClientR5;
 import org.hl7.fhir.r5.terminologies.expansion.ValueSetExpansionOutcome;
 import org.hl7.fhir.r5.utils.ToolingExtensions;
 import org.hl7.fhir.r5.utils.Translations;
@@ -532,8 +532,6 @@ public PageProcessor(String tsServer) throws URISyntaxException, UcumException {
   private static final String REASON_UNKNOWN = "Unknown";
   private static final String UNNOWN_DESCRIPTION =  "no reason provided";
   public static final String CODE_LIMIT_EXPANSION = "1000";
-  public static final String TOO_MANY_CODES_TEXT_NOT_EMPTY = "This value set has >1000 codes in it. In order to keep the publication size manageable, only a selection (1000 codes) of the whole set of codes is shown";
-  public static final String TOO_MANY_CODES_TEXT_EMPTY = "This value set cannot be expanded because of the way it is defined - it has an infinite number of members";
   private static final String NO_CODESYSTEM_TEXT = "This value set refers to code systems that the FHIR Publication Tooling does not support";
 
   private static final String VS_INC_START = ""; // "<div style=\"background-color: Floralwhite; border:1px solid maroon; padding: 5px;\">";
@@ -2316,7 +2314,7 @@ public void updateDiffEngineDefinitions() {
         if (vs.hasUserData("expansion"))
           evs = (ValueSet) vs.getUserData("expansion");
         else {
-          ValueSetExpansionOutcome vse = getWorkerContext().expandVS(vs, true, false);
+          ValueSetExpansionOutcome vse = getWorkerContext().expandVS(vs, true, false, true);
           if (vse.getValueset() != null) {
             evs = vse.getValueset();
             vs.setUserData("expansion", evs);
@@ -2730,7 +2728,7 @@ private String umlForDt(String dt, String id) throws Exception {
       String s = "\r\n[diagram]\r\n"+
           "classes="+dt+"\r\n"+
           "element-attributes=true\r\n";
-      TextFile.stringToFileNoPrefix(s, tmp.getAbsolutePath());
+      TextFile.stringToFile(s, tmp.getAbsolutePath());
       return new SvgGenerator(this, "", null, false, "", version).generate(tmp.getAbsolutePath(), id);
     } finally {
       tmp.delete();
@@ -5415,7 +5413,7 @@ private String expandValueSetIG(ValueSet vs, boolean heirarchy) throws Exception
       exp.setCompose(null);
       exp.setText(null);
       exp.setDescription("Value Set Contents (Expansion) for "+vs.present()+" at "+Config.DATE_FORMAT().format(new Date()));
-      RenderingContext lrc = rc.copy().setTooCostlyNoteEmpty(TOO_MANY_CODES_TEXT_EMPTY).setTooCostlyNoteNotEmpty(TOO_MANY_CODES_TEXT_NOT_EMPTY);
+      RenderingContext lrc = rc.copy();
       RendererFactory.factory(exp, lrc).render(exp);
       return "<hr/>\r\n"+VS_INC_START+""+new XhtmlComposer(XhtmlComposer.HTML).compose(exp.getText().getDiv())+VS_INC_END;
     } catch (Exception e) {
@@ -5425,7 +5423,7 @@ private String expandValueSetIG(ValueSet vs, boolean heirarchy) throws Exception
 
   private String processExpansionError(String error) {
     if (error.contains("Too many codes"))
-      return TOO_MANY_CODES_TEXT_NOT_EMPTY;
+      return "This value set has >1000 codes in it. In order to keep the publication size manageable, only a selection (1000 codes) of the whole set of codes is shown";
     if (error.contains("unable to provide support"))
       return NO_CODESYSTEM_TEXT;
     return "This value set could not be expanded by the publication tooling: "+Utilities.escapeXml(error);
@@ -5477,7 +5475,7 @@ private String vsCLD(String fileTitle, ValueSet vs, String prefix) throws Except
     vs1.setExpansion(null);
     vs1.setText(null);
     ImplementationGuideDefn ig = (ImplementationGuideDefn) vs.getUserData(ToolResourceUtilities.NAME_RES_IG);
-    RenderingContext lrc = rc.copy().setLocalPrefix(prefix).setTooCostlyNoteNotEmpty(TOO_MANY_CODES_TEXT_NOT_EMPTY);
+    RenderingContext lrc = rc.copy().setLocalPrefix(prefix);
     RendererFactory.factory(vs1, lrc).render(vs1);
     return "<hr/>\r\n"+VS_INC_START+""+new XhtmlComposer(XhtmlComposer.HTML).compose(vs1.getText().getDiv())+VS_INC_END;
   }
@@ -11352,7 +11350,7 @@ private ElementDefn getElementDefn(String n) throws Exception {
   public String expandVS(ValueSet vs, String prefix, String base) {
     try {
 
-      ValueSetExpansionOutcome result = workerContext.expandVS(vs, true, true);
+      ValueSetExpansionOutcome result = workerContext.expandVS(vs, true, true, true);
       if (result.getError() != null)
         return "<hr/>\r\n"+VS_INC_START+"<!--3-->"+processExpansionError(result.getError())+VS_INC_END;
 
@@ -11369,11 +11367,12 @@ public String expandVS(ValueSet vs, String prefix, String base) {
       IniFile sini = new IniFile(Utilities.path(folders.rootDir, "temp", "stats.ini"));
       sini.setIntegerProperty("valuesets", vs.getId(), i, null);
       sini.save();
-      RenderingContext lrc = rc.copy().setLocalPrefix(prefix).setTooCostlyNoteEmpty(TOO_MANY_CODES_TEXT_EMPTY).setTooCostlyNoteNotEmpty(TOO_MANY_CODES_TEXT_NOT_EMPTY);
+      RenderingContext lrc = rc.copy().setLocalPrefix(prefix);
       RendererFactory.factory(exp, lrc).render(exp);
       return "<hr/>\r\n"+VS_INC_START+""+new XhtmlComposer(XhtmlComposer.HTML).compose(exp.getText().getDiv())+VS_INC_END;
     } catch (Exception e) {
-      e.printStackTrace();
+      // e.printStackTrace();
+      System.err.println(e.getMessage());
       return "<hr/>\r\n"+VS_INC_START+"<!--5-->"+processExpansionError(e instanceof NullPointerException ? "NullPointerException" : e.getMessage())+" "+Utilities.escapeXml(stack(e))+VS_INC_END;
     }
   }
@@ -12423,7 +12422,7 @@ public void setExtensionsLocation(String extensionsLocation) {
 
   @Override
   public boolean isDebugLogging() {
-    return true;
+    return false;
   }
 
   @Override