Merge branch 'HL7:master' into master

Author: brynrhodes

Dockerfile

@@ -1,4 +1,4 @@
-FROM maven:3.9.9-eclipse-temurin-11 AS build
+FROM maven:3.9.9-eclipse-temurin-17 AS build
 WORKDIR /build
 COPY lib ./lib
 COPY pom.xml ./pom.xml
@@ -8,7 +8,7 @@ RUN mvn dependency:go-offline
 COPY . .
 RUN mvn install -Dmaven.test.skip=true
 
-FROM eclipse-temurin:11
+FROM eclipse-temurin:17
 WORKDIR /app
 
 USER root

master-branch-pipeline.yml

@@ -66,7 +66,7 @@ jobs:
           mavenOptions: '-Xmx3072m'
           options: '--settings $(System.DefaultWorkingDirectory)/settings.xml'
           javaHomeOption: 'JDKVersion'
-          jdkVersionOption: '1.11'
+          jdkVersionOption: '1.17'
           jdkArchitectureOption: 'x64'
           publishJUnitResults: true
           testResultsFiles: '**/surefire-reports/TEST-*.xml'

nightly-xig-pipeline.yml

@@ -22,8 +22,8 @@ variables:
   value: xig.db
 
 jobs:
-- job: xig_step_1
-  timeoutInMinutes: 70
+- job: xig_step_0
+  timeoutInMinutes: 150
   steps:
   - task: Bash@3
     displayName: 'Download latest publisher'
@@ -44,99 +44,24 @@ jobs:
       script: 'mkdir $(XIG_CACHE_FOLDER)'
 
   - task: Bash@3
-    displayName: 'Run publisher with xig param step 1'
+    displayName: 'Run publisher with xig param step 0 (all steps)'
     inputs:
       targetType: 'inline'
-      script: 'java -Xmx7168m -jar ./publisher.jar -xig $(XIG_DB_FOLDER)/$(XIG_DB_FILE) -xig-cache $(XIG_CACHE_FOLDER) -xig-step 1'
+      script: 'java -Xmx7168m -jar ./publisher.jar -xig $(XIG_DB_FOLDER)/$(XIG_DB_FILE) -xig-cache $(XIG_CACHE_FOLDER) -xig-step 0'
 
   - task: PublishPipelineArtifact@1
     inputs:
       targetPath: $(XIG_DB_FOLDER)
-      artifactName: xig_step_1_db
-  - task: PublishPipelineArtifact@1
-    inputs:
-      targetPath: $(XIG_CACHE_FOLDER)
-      artifactName: xig_step_1_cache
-
-- job: xig_step_2
-  dependsOn: xig_step_1
-  steps:
-  - task: Bash@3
-    displayName: 'Download latest publisher'
-    inputs:
-      targetType: 'inline'
-      script: 'wget https://github.com/HL7/fhir-ig-publisher/releases/latest/download/publisher.jar'
-
-  - task: DownloadPipelineArtifact@2
-    inputs:
-      buildType: 'current'
-      artifactName: xig_step_1_cache
-      targetPath: $(XIG_CACHE_FOLDER)
-  - task: DownloadPipelineArtifact@2
-    inputs:
-      buildType: 'current'
-      artifactName: xig_step_1_db
-      targetPath: $(XIG_DB_FOLDER)
-
-  - task: Bash@3
-    displayName: 'Run publisher with xig param step 2'
-    inputs:
-      targetType: 'inline'
-      script: 'java -Xmx7168m -jar ./publisher.jar -xig $(XIG_DB_FOLDER)/$(XIG_DB_FILE) -xig-cache $(XIG_CACHE_FOLDER) -xig-step 2'
-
-  - task: PublishPipelineArtifact@1
-    inputs:
-      targetPath: $(XIG_DB_FOLDER)
-      artifactName: xig_step_2_db
-  - task: PublishPipelineArtifact@1
-    inputs:
-      targetPath: $(XIG_CACHE_FOLDER)
-      artifactName: xig_step_2_cache
-
-- job: xig_step_3
-  dependsOn: xig_step_2
-  pool:
-    vmImage: 'macOS-latest'
-  timeoutInMinutes: 360
-  steps:
-    - task: Bash@3
-      displayName: 'Download latest publisher'
-      inputs:
-        targetType: 'inline'
-        script: 'wget https://github.com/HL7/fhir-ig-publisher/releases/latest/download/publisher.jar'
-
-    - task: DownloadPipelineArtifact@2
-      inputs:
-        buildType: 'current'
-        artifactName: xig_step_2_cache
-        targetPath: $(XIG_CACHE_FOLDER)
-    - task: DownloadPipelineArtifact@2
-      inputs:
-        buildType: 'current'
-        artifactName: xig_step_2_db
-        targetPath: $(XIG_DB_FOLDER)
-
-    - task: Bash@3
-      displayName: 'Run publisher with xig param step 3'
-      inputs:
-        targetType: 'inline'
-        script: 'java -Xmx13G -jar ./publisher.jar -xig $(XIG_DB_FOLDER)/$(XIG_DB_FILE) -xig-cache $(XIG_CACHE_FOLDER) -xig-step 3'
-
-    - task: PublishPipelineArtifact@1
-      inputs:
-        targetPath: $(XIG_DB_FOLDER)
-        artifactName: xig_step_3_db
+      artifactName: xig_step_0_db
 
 - job: transfer_db_to_remote
   dependsOn:
-  - xig_step_1
-  - xig_step_2
-  - xig_step_3
+  - xig_step_0
   steps:
   - task: DownloadPipelineArtifact@2
     inputs:
       buildType: 'current'
-      artifactName: xig_step_3_db
+      artifactName: xig_step_0_db
       targetPath: $(XIG_DB_FOLDER)
 
   - task: DownloadSecureFile@1

org.hl7.fhir.publisher.cli/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <artifactId>org.hl7.fhir.publisher</artifactId>
         <groupId>org.hl7.fhir.publisher</groupId>
-        <version>2.0.10-SNAPSHOT</version>
+        <version>2.0.13-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
     <modelVersion>4.0.0</modelVersion>

org.hl7.fhir.publisher.core/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.hl7.fhir.publisher</groupId>
         <artifactId>org.hl7.fhir.publisher</artifactId>
-        <version>2.0.10-SNAPSHOT</version>
+        <version>2.0.13-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
     <modelVersion>4.0.0</modelVersion>

org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/openehr/ArchetypeImporter.java

@@ -13,6 +13,7 @@
 
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.r5.context.IWorkerContext;
+import org.hl7.fhir.r5.extensions.ExtensionDefinitions;
 import org.hl7.fhir.r5.model.Bundle;
 import org.hl7.fhir.r5.model.Bundle.BundleType;
 import org.hl7.fhir.r5.model.CanonicalResource;
@@ -36,7 +37,6 @@
 import org.hl7.fhir.r5.model.StructureDefinition.TypeDerivationRule;
 import org.hl7.fhir.r5.model.ValueSet;
 import org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent;
-import org.hl7.fhir.r5.utils.ToolingExtensions;
 import org.hl7.fhir.utilities.FileUtilities;
 import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.xml.XMLUtil;
@@ -352,7 +352,7 @@ private void processDefinition(List<ElementDefinition> defns, ElementDefinition
           at = at.substring(at.indexOf("[")+1).replace("]", "");
           var ct = ed.addType().setCode(c.getRmTypeName()).addProfileElement();
           ct.setValue(sd.getUrl());
-          ct.addExtension(ToolingExtensions.EXT_PROFILE_ELEMENT, new StringType(atMap.get(at)));
+          ct.addExtension(ExtensionDefinitions.EXT_PROFILE_ELEMENT, new StringType(atMap.get(at)));
         } else {
           System.out.println("not done yet: "+path+"."+name+": "+o.getClass().getName());
         }

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

@@ -12,6 +12,7 @@
 import org.hl7.fhir.convertors.factory.VersionConvertorFactory_30_50;
 import org.hl7.fhir.convertors.factory.VersionConvertorFactory_40_50;
 import org.hl7.fhir.r5.context.IWorkerContext;
+import org.hl7.fhir.r5.extensions.ExtensionDefinitions;
 import org.hl7.fhir.r5.formats.IParser.OutputStyle;
 import org.hl7.fhir.r5.formats.JsonParser;
 import org.hl7.fhir.r5.formats.XmlParser;
@@ -31,7 +32,6 @@
 import org.hl7.fhir.r5.terminologies.utilities.ValidationResult;
 import org.hl7.fhir.r5.utils.GuideParameterCode;
 import org.hl7.fhir.r5.utils.IGHelper;
-import org.hl7.fhir.r5.utils.ToolingExtensions;
 import org.hl7.fhir.utilities.FhirPublication;
 import org.hl7.fhir.utilities.FileUtilities;
 import org.hl7.fhir.utilities.IniFile;
@@ -121,9 +121,9 @@ public void convert(String configFile, IWorkerContext context, FilesystemPackage
     if (configuration.has("html-template"))
       IGHelper.setParameter(ig.getDefinition(), GuideParameterCode.HTMLTEMPLATE.toCode(), configuration.asString("html-template"));
     for (String s : resourceDirs)
-      ig.addExtension(ToolingExtensions.EXT_IGP_RESOURCES, new StringType(s));
+      ig.addExtension(ExtensionDefinitions.EXT_IGP_RESOURCES, new StringType(s));
     for (String s : pagesDirs)
-      ig.addExtension(ToolingExtensions.EXT_IGP_PAGES, new StringType(s));
+      ig.addExtension(ExtensionDefinitions.EXT_IGP_PAGES, new StringType(s));
     ig.setPackageId(configuration.asString("npm-name"));
     if (configuration.has("jurisdiction")) {
       ig.getJurisdiction().clear();
@@ -167,11 +167,11 @@ public void convert(String configFile, IWorkerContext context, FilesystemPackage
     new JsonParser().compose(new FileOutputStream(Utilities.path(FileUtilities.getDirectoryForFile(igName), "ig-validation-parameters.json")), ig);
     if (paths.get("spreadsheets") instanceof JsonArray) {
       for (JsonElement e : (JsonArray) paths.get("spreadsheets"))
-        ig.addExtension(ToolingExtensions.EXT_IGP_SPREADSHEET, new StringType(e.asJsonPrimitive().asString()));
+        ig.addExtension(ExtensionDefinitions.EXT_IGP_SPREADSHEET, new StringType(e.asJsonPrimitive().asString()));
     }
     if (paths.get("bundles") instanceof JsonArray) {
       for (JsonElement e : (JsonArray) paths.get("bundles"))
-        ig.addExtension(ToolingExtensions.EXT_IGP_BUNDLE, new StringType(e.asJsonPrimitive().asString()));
+        ig.addExtension(ExtensionDefinitions.EXT_IGP_BUNDLE, new StringType(e.asJsonPrimitive().asString()));
     }
     JsonObject defaults = configuration.getJsonObject("defaults");
     if (defaults != null) {
@@ -229,10 +229,10 @@ public void convert(String configFile, IWorkerContext context, FilesystemPackage
                 res = ig.getDefinition().addResource();
                 res.setReference(new Reference(s));
               }
-              res.addExtension(ToolingExtensions.EXT_IGP_BASE, new StringType(vb.asJsonPrimitive().asString()));
-              res.addExtension(ToolingExtensions.EXT_IGP_DEFNS, new StringType(vd.asJsonPrimitive().asString()));
-              res.addExtension(ToolingExtensions.EXT_IGP_FORMAT, new StringType(vf.asJsonPrimitive().asString()));
-              res.addExtension(ToolingExtensions.EXT_IGP_SOURCE, new StringType(vs.asJsonPrimitive().asString()));
+              res.addExtension(ExtensionDefinitions.EXT_IGP_BASE, new StringType(vb.asJsonPrimitive().asString()));
+              res.addExtension(ExtensionDefinitions.EXT_IGP_DEFNS, new StringType(vd.asJsonPrimitive().asString()));
+              res.addExtension(ExtensionDefinitions.EXT_IGP_FORMAT, new StringType(vf.asJsonPrimitive().asString()));
+              res.addExtension(ExtensionDefinitions.EXT_IGP_SOURCE, new StringType(vs.asJsonPrimitive().asString()));
             }
           }
         }

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

@@ -21,10 +21,7 @@
  */
 
 
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
+import java.util.*;
 
 import org.hl7.fhir.convertors.VersionConvertorConstants;
 import org.hl7.fhir.exceptions.FHIRException;
@@ -81,6 +78,7 @@ public class IGKnowledgeProvider implements ProfileKnowledgeProvider, ParserBase
   private XVerExtensionManager xver;
   private List<FetchedFile> files;
   private IPublisherModule module;
+  private Map<String, List<ExtensionUsage>> coreExtensionMap;
 
   public IGKnowledgeProvider(IWorkerContext context, String pathToSpec, String canonical, JsonObject igs, List<ValidationMessage> errors, boolean noXhtml, Template template, List<String> listedURLExemptions, String altCanonical, List<FetchedFile> files, IPublisherModule module) throws Exception {
     super();
@@ -844,7 +842,28 @@ public String getCanonicalForDefaultContext() {
     return canonical;
   }
 
-  
+  public Map<String, List<ExtensionUsage>> getCoreExtensionMap() {
+    if (coreExtensionMap == null) {
+      coreExtensionMap = new HashMap<>();
+    }
+    return coreExtensionMap;
+  }
 
-  
+  public static class ExtensionUsage {
+    private String name;
+    private String url;
+
+    public ExtensionUsage(String name, String url) {
+      this.name = name;
+      this.url = url;
+    }
+
+    public String getName() {
+      return name;
+    }
+
+    public String getUrl() {
+      return url;
+    }
+  }
 }

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

@@ -1,56 +1,47 @@
 package org.hl7.fhir.igtools.publisher;
 
 import java.util.ArrayList;
-import java.util.HashMap;
 import java.util.List;
-import java.util.Map;
 
 import org.apache.commons.lang3.NotImplementedException;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.exceptions.PathEngineException;
 import org.hl7.fhir.r5.context.SimpleWorkerContext;
+import org.hl7.fhir.r5.fhirpath.BaseHostServices;
 import org.hl7.fhir.r5.fhirpath.FHIRPathEngine;
 import org.hl7.fhir.r5.fhirpath.TypeDetails;
 import org.hl7.fhir.r5.liquid.GlobalObject;
 import org.hl7.fhir.r5.fhirpath.ExpressionNode.CollectionStatus;
-import org.hl7.fhir.r5.fhirpath.FHIRPathEngine.IEvaluationContext;
-import org.hl7.fhir.r5.fhirpath.FHIRPathUtilityClasses.FunctionDetails;
 import org.hl7.fhir.r5.model.Base;
 import org.hl7.fhir.r5.model.DateTimeType;
 import org.hl7.fhir.r5.model.Resource;
 import org.hl7.fhir.r5.model.StringType;
 import org.hl7.fhir.r5.model.ValueSet;
 import org.hl7.fhir.r5.utils.validation.IResourceValidator;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.fhirpath.FHIRPathConstantEvaluationMode;
 import org.hl7.fhir.utilities.validation.ValidationMessage;
 
-public class IGPublisherHostServices implements IEvaluationContext {
-
-
+public class IGPublisherHostServices extends BaseHostServices {
+  
   private IGKnowledgeProvider igpkp;
   private List<FetchedFile> fileList = new ArrayList<FetchedFile>();
   private SimpleWorkerContext context;
   private DateTimeType dt;
   private StringType pathToSpec;
-  private Map<String, FunctionDefinition> functions = new HashMap<>();
 
   public IGPublisherHostServices(IGKnowledgeProvider igpkp, List<FetchedFile> fileList,
       SimpleWorkerContext context, DateTimeType dt, StringType pathToSpec) {
-    super();
+    super(context);
     this.igpkp = igpkp;
     this.fileList = fileList;
     this.context = context;
     this.dt = dt;
     this.pathToSpec = pathToSpec;
   }
-
-  public IGPublisherHostServices registerFunction(FunctionDefinition function) {
-    functions.put(function.name(), function);
-    return this;
-  }
 
   @Override
-  public List<Base> resolveConstant(FHIRPathEngine engine, Object appContext, String name, boolean beforeContext, boolean explicitConstant) throws PathEngineException {
+  public List<Base> resolveConstant(FHIRPathEngine engine, Object appContext, String name, FHIRPathConstantEvaluationMode mode) throws PathEngineException {
     if ("Globals".equals(name)) {
       List<Base> list = new ArrayList<Base>();
       list.add(new GlobalObject(dt, pathToSpec));
@@ -61,7 +52,7 @@ public List<Base> resolveConstant(FHIRPathEngine engine, Object appContext, Stri
   }
 
   @Override
-  public TypeDetails resolveConstantType(FHIRPathEngine engine, Object appContext, String name, boolean explicitConstant) throws PathEngineException {
+  public TypeDetails resolveConstantType(FHIRPathEngine engine, Object appContext, String name, FHIRPathConstantEvaluationMode mode) throws PathEngineException {
     if ("Globals".equals(name)) {
       return new TypeDetails(CollectionStatus.SINGLETON, "GlobalObject");
     } else {
@@ -79,24 +70,6 @@ public boolean log(String argument, List<Base> focus) {
     return false;
   }
 
-  @Override
-  public FunctionDetails resolveFunction(FHIRPathEngine engine, String functionName) {
-    FunctionDefinition fd = functions.get(functionName);
-    return fd == null ? null : fd.details();
-  }
-
-  @Override
-  public TypeDetails checkFunction(FHIRPathEngine engine, Object appContext, String functionName, TypeDetails focus, List<TypeDetails> parameters) throws PathEngineException {
-    FunctionDefinition fd = functions.get(functionName);
-    return fd == null ? null : fd.check(engine, appContext, focus, parameters);
-  }
-
-  @Override
-  public List<Base> executeFunction(FHIRPathEngine engine, Object appContext, List<Base> focus, String functionName, List<List<Base>> parameters) {
-    FunctionDefinition fd = functions.get(functionName);
-    return fd == null ? null : fd.execute(engine, appContext, focus, parameters);
-  }
-
   @Override
   public Base resolveReference(FHIRPathEngine engine, Object appContext, String url, Base refContext) {
     if (Utilities.isAbsoluteUrl(url)) {