Merge branch 'master' of https://github.com/HL7/fhir-ig-publisher

RELEASE_NOTES.md

@@ -1,21 +0,0 @@
-* Loader: Fix problems setting owning committee consistently
-* Loader: Fix bug loading packages with partially specified version that doesn't exist
-* Loader: Fix problem with profiled resources being called examples in IG publisher
-* Package Manager: Write locking on FilesystemPackageCacheManager
-* Version Conversion: Fix StringType element properties not being copied in various Address, HumanName convertors
-* Validator: Fix narrative link validation and add id/idref validation (for IPS)
-* Validator: Fix to CDA xsi:type validation per SD decision 
-* Validator: Apply regex pattern to literal format if defined
-* Validator: Improvements to vital signs related messages
-* Validator: Fix R4 con-3 FHIRPath expression
-* Validator: Fix for occasional missing warnings around bundle link validation
-* Validator: Fix NPE in validator processing CCDA examples
-* Validator: Fix for SearchParameter validation using custom resource types
-* Validator: Fix stated path for error when code not in value set
-* Renderer: Fix rendering of trigger definition using tables inside paragraphs
-* Renderer: Fix problem with profiled resources being called examples in IG publisher
-* Renderer: Fix bug where version specific references to profiles not picked up
-* Renderer: Add more data to qa.json
-* Renderer: Fix rendering of trigger definition using tables inside paragraphs
-* Renderer: Handle all initial value types when rendering Questionnaires
-* US Realm: Add link to US Core derivation process

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>1.5.6-SNAPSHOT</version>
+        <version>1.5.9-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>1.5.6-SNAPSHOT</version>
+        <version>1.5.9-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
     <modelVersion>4.0.0</modelVersion>

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

@@ -20,7 +20,7 @@
 import org.hl7.fhir.utilities.json.model.JsonObject;
 import org.hl7.fhir.utilities.json.parser.JsonParser;
 import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
-import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode;
+
 import org.hl7.fhir.utilities.npm.NpmPackage;
 import org.hl7.fhir.utilities.npm.PackageClient;
 import org.hl7.fhir.utilities.npm.PackageList;
@@ -113,7 +113,7 @@ public DepInfo(String pid, String path) {
   public DependentIGFinder(String id) throws IOException {
     super();
     this.id = id;
-    pcm = new  FilesystemPackageCacheManager(FilesystemPackageCacheMode.USER);
+    pcm = new FilesystemPackageCacheManager.Builder().build();
     pcm.setSilent(true);
     outcome = "Finding Dependent IGs not done yet";
   }

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

@@ -39,6 +39,7 @@ public class FetchedResource {
   private String path; // where published
   private Resource resource;
   private Element element;
+  private Element logicalElement;
   private JsonObject config;
   private boolean validated;
   private boolean validateAsResource;
@@ -291,5 +292,13 @@ public String getNameForErrors() {
   public void setNameForErrors(String nameForErrors) {
     this.nameForErrors = nameForErrors;
   }
+
+  public Element getLogicalElement() {
+    return logicalElement;
+  }
+
+  public void setLogicalElement(Element logicalElement) {
+    this.logicalElement = logicalElement;
+  }
 
 }

org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/IGPack2NpmConvertor.java

@@ -164,7 +164,7 @@ public void execute() throws IOException {
   }
 
   private void init() throws IOException {
-    pcm = new FilesystemPackageCacheManager(org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER);
+    pcm = new FilesystemPackageCacheManager.Builder().build();
     scanner = new Scanner(System. in);
     paths = new ArrayList<String>();
   }

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

@@ -2417,9 +2417,12 @@ public void initialize() throws Exception {
   @Nonnull
   private FilesystemPackageCacheManager getFilesystemPackageCacheManager() throws IOException {
     if (getPackageCacheFolder() != null) {
-      return new FilesystemPackageCacheManager(getPackageCacheFolder());
+      return new FilesystemPackageCacheManager.Builder().withCacheFolder(getPackageCacheFolder()).build();
     }
-    return new FilesystemPackageCacheManager(mode == null || mode == IGBuildMode.MANUAL || mode == IGBuildMode.PUBLICATION);
+    return mode == null || mode == IGBuildMode.MANUAL || mode == IGBuildMode.PUBLICATION ?
+            new FilesystemPackageCacheManager.Builder().build()
+            : new FilesystemPackageCacheManager.Builder().withSystemCacheFolder().build();
+
   }
 
   private Coding checkForJurisdiction() {
@@ -3949,7 +3952,7 @@ private void copyDefaultTemplate() throws IOException, FHIRException {
       Utilities.createDirectory(adHocTmpDir);
     Utilities.clearDirectory(adHocTmpDir);
 
-    FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER);
+    FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager.Builder().build();
 
     NpmPackage npm = null; 
     if (specifiedVersion == null) {
@@ -7103,7 +7106,7 @@ private void validate() throws Exception {
 
   private void validate(FetchedFile f, FetchedResource r, Binary bin, List<ValidationMessage> errs, FhirFormat fmt, List<StructureDefinition> profiles) {
     long ts = System.currentTimeMillis();
-    validator.validate(r.getElement(), errs, new ByteArrayInputStream(bin.getContent()), fmt, profiles);
+    r.setLogicalElement(validator.validate(r.getElement(), errs, new ByteArrayInputStream(bin.getContent()), fmt, profiles));
     long tf = System.currentTimeMillis();
     if (tf-ts > validationLogTime && validationLogTime > 0) {
       reportLongValidation(f, r, tf-ts);
@@ -12137,7 +12140,9 @@ public static void main(String[] args) throws Exception {
         s = s + " "+removePassword(args, i);
       }      
       System.out.println(s);
-      FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(!CliParams.hasNamedParam(args, "system"));
+      FilesystemPackageCacheManager pcm = CliParams.hasNamedParam(args, "system")
+              ? new FilesystemPackageCacheManager.Builder().withSystemCacheFolder().build()
+              : new FilesystemPackageCacheManager.Builder().build();
       System.out.println("Cache = "+pcm.getFolder());
       for (String p : CliParams.getNamedParam(args, "-package").split("\\;")) {
         NpmPackage npm = pcm.loadPackage(p);

org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/R4ToR4BAnalyser.java

@@ -677,7 +677,7 @@ private void processPackage(String filename) throws FileNotFoundException, IOExc
     String pid = VersionUtilities.packageForVersion(version);
     String specPath = VersionUtilities.getSpecUrl(version);
     System.out.println("Loaded. Version = "+version);
-    FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER);
+    FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager.Builder().build();
     System.out.println("Preparing using "+pid);
     NpmPackage pi = pcm.loadPackage(pid);
 

org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/comparators/ImposesComparator.java

@@ -167,7 +167,7 @@ public void startChecks(ImplementationGuide ig) {
         String filename = "";
         try {
           vi.resources = new ArrayList<>();
-          BasePackageCacheManager pcm = new FilesystemPackageCacheManager(org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER);
+          BasePackageCacheManager pcm = new FilesystemPackageCacheManager.Builder().build();
           NpmPackage current = pcm.loadPackage(pid, vi.version);
           for (String id : current.listResources("StructureDefinition", "ValueSet", "CodeSystem", "CapabilityStatement")) {
             filename = id;

org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/comparators/IpaComparator.java

@@ -167,7 +167,7 @@ public void startChecks(ImplementationGuide ig) {
         String filename = "";
         try {
           vi.resources = new ArrayList<>();
-          BasePackageCacheManager pcm = new FilesystemPackageCacheManager(org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER);
+          BasePackageCacheManager pcm = new FilesystemPackageCacheManager.Builder().build();
           NpmPackage current = pcm.loadPackage(pid, vi.version);
           for (String id : current.listResources("StructureDefinition", "ValueSet", "CodeSystem", "CapabilityStatement")) {
             filename = id;

org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/comparators/IpsComparator.java

@@ -167,7 +167,7 @@ public void startChecks(ImplementationGuide ig) {
         String filename = "";
         try {
           vi.resources = new ArrayList<>();
-          BasePackageCacheManager pcm = new FilesystemPackageCacheManager(org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER);
+          BasePackageCacheManager pcm = new FilesystemPackageCacheManager.Builder().build();
           NpmPackage current = pcm.loadPackage(pid, vi.version);
           for (String id : current.listResources("StructureDefinition", "ValueSet", "CodeSystem", "CapabilityStatement")) {
             filename = id;

org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/comparators/PreviousVersionComparator.java

@@ -188,7 +188,7 @@ public void startChecks(ImplementationGuide ig) {
         String filename = "";
         try {
           vi.resources = new ArrayList<>();
-          BasePackageCacheManager pcm = new FilesystemPackageCacheManager(org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER);
+          BasePackageCacheManager pcm = new FilesystemPackageCacheManager.Builder().build();
           NpmPackage current = pcm.loadPackage(pid, vi.version);
           for (String id : current.listResources("StructureDefinition", "ValueSet", "CodeSystem")) {
             filename = id;

org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/realm/USRealmBusinessRules.java

@@ -172,18 +172,18 @@ private NpmPackage fetchLatestUSCore() throws IOException {
       PackageList pl = PackageList.fromUrl("https://hl7.org/fhir/us/core/package-list.json");
       for (PackageListEntry v : pl.versions()) {
         if (VersionUtilities.versionsCompatible(version, v.fhirVersion())) {
-          return new FilesystemPackageCacheManager(org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER).loadPackage("hl7.fhir.us.core", v.version());
+          return new FilesystemPackageCacheManager.Builder().build().loadPackage("hl7.fhir.us.core", v.version());
         }
       }
       // we didn't find a compatible version, we'll just take the last version
       for (PackageListEntry v : pl.versions()) {
-        return new FilesystemPackageCacheManager(org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER).loadPackage("hl7.fhir.us.core", v.version());
+        return new FilesystemPackageCacheManager.Builder().build().loadPackage("hl7.fhir.us.core", v.version());
       }
       return null;
     } catch (Exception e) {
       System.out.println("Error checking US Core: "+e.getMessage());
     }
-    FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(true);
+    FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager.Builder().build();
     return pcm.loadPackage("hl7.fhir.us.core");
   }
 

org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/utils/CrossVersionOIDScanner.java

@@ -291,7 +291,7 @@ private List<String> getOids(LoadedCanonicalResource lcr) {
 
   private void loadPackage(String pid, List<LoadedCanonicalResource> reslist) throws IOException {
     System.out.println("Load Package "+pid);
-    FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER);
+    FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager.Builder().build();
     NpmPackage npm = pcm.loadPackage(pid);
 //    SpecMapManager spm = new SpecMapManager(TextFile.streamToBytes(npm.load("other", "spec.internals")), npm.fhirVersion());
     IContextResourceLoader loader = new PublisherLoader(npm, null, npm.getWebLocation(), null).makeLoader();

org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/utils/IGCategorizer.java

@@ -19,7 +19,6 @@
 import org.hl7.fhir.utilities.json.model.JsonObject;
 import org.hl7.fhir.utilities.json.parser.JsonParser;
 import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
-import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode;
 import org.hl7.fhir.utilities.npm.NpmPackage;
 
 
@@ -36,7 +35,7 @@ public static void main(String[] args) throws IOException {
   private FilesystemPackageCacheManager pcm;
 
   public IGCategorizer() throws IOException {
-    pcm = new FilesystemPackageCacheManager(FilesystemPackageCacheMode.USER);
+    pcm = new FilesystemPackageCacheManager.Builder().build();
     pcm.setSuppressErrors(true);
   }
 

org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/utils/PackagCanonicalClashDetector.java

@@ -95,7 +95,7 @@ private void checkResources(String s, List<LoadedCanonicalResource> list) throws
 
   private void check(String pid) throws IOException {
     System.out.println("Load Package "+pid);
-    FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER);
+    FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager.Builder().build();
     NpmPackage npm = pcm.loadPackage(pid);
 //    SpecMapManager spm = new SpecMapManager(TextFile.streamToBytes(npm.load("other", "spec.internals")), npm.fhirVersion());
     IContextResourceLoader loader = new PublisherLoader(npm, null, npm.getWebLocation(), null).makeLoader();

org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/utils/PackageReleaser.java

@@ -210,7 +210,7 @@ private void packPackage(String path, String dst) throws IOException {
   }
 
   private void release(String source, String dest) throws Exception {
-    pcm = new FilesystemPackageCacheManager(org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER);
+    pcm = new FilesystemPackageCacheManager.Builder().build();
     System.out.println("Load hl7.fhir.r4.core");
     r4 = org.hl7.fhir.r4.context.SimpleWorkerContext.fromPackage(pcm.loadPackage("hl7.fhir.r4.core", "4.0.1"));
     System.out.println("Load hl7.fhir.r3.core");

org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/xig/XIGGenerator.java

@@ -50,7 +50,7 @@ public XIGGenerator(String target, String cache) throws FHIRException, IOExcepti
     this.target = target;
     this.cache = cache;
     Utilities.createDirectory(cache);
-    pcm = new FilesystemPackageCacheManager(org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER);
+    pcm = new FilesystemPackageCacheManager.Builder().build();
     String ds = new SimpleDateFormat("dd MMM yyyy", new Locale("en", "US")).format(Calendar.getInstance().getTime());
     String dl = new SimpleDateFormat("yyyy-MM-dd'T'hh:mm:ssZ", new Locale("en", "US")).format(Calendar.getInstance().getTime());
     date = "<span title=\""+dl+"\">"+ds+"</span>";    

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

@@ -2009,7 +2009,7 @@ public String references() throws FHIRFormatError, IOException {
     }
     if (VersionUtilities.isR5Plus(context.getVersion())) {
       if (usages == null) {
-        FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(true);
+        FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager.Builder().build();
         NpmPackage npm = pcm.loadPackage("hl7.fhir.r5.core");
         usages = org.hl7.fhir.utilities.json.parser.JsonParser.parseObject(npm.load("other", "sdmap.details"));
       }

org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/templates/TemplateManager.java

@@ -254,6 +254,7 @@ private void checkTemplateId(String template, String packageId, String reason) {
         "hl7.davinci.template",
         "openhie.fhir.template",
         "who.fhir.template",
+        "who.template.root",
         "ihe.fhir.template")) {
       canExecute = false;
       templateThatCantExecute = template;

pom.xml

@@ -21,10 +21,10 @@
 <!--        <version>5.3.14</version>-->
 <!--    </parent>-->
 
-    <version>1.5.6-SNAPSHOT</version> <!-- See the note above -->
+    <version>1.5.9-SNAPSHOT</version> <!-- See the note above -->
 
     <properties>
-        <core_version>6.2.6-SNAPSHOT</core_version>
+        <core_version>6.2.7-SNAPSHOT</core_version>
         <maven_surefire_version>3.0.0-M5</maven_surefire_version>
         <apache_poi_version>5.2.1</apache_poi_version>
         <okhttp.version>4.11.0</okhttp.version>