From 7b19236173ca67c6a1d51074741c889ec155955b Mon Sep 17 00:00:00 2001
From: Tim Prudhomme <tmprdh@gmail.com>
Date: Thu, 18 Apr 2024 22:38:37 -0400
Subject: [PATCH] Fix TTL resource serialization with TurtleParser

---
 .../hl7/fhir/tools/publisher/Publisher.java   | 23 ++++++++++++-------
 1 file changed, 15 insertions(+), 8 deletions(-)

diff --git a/src/main/java/org/hl7/fhir/tools/publisher/Publisher.java b/src/main/java/org/hl7/fhir/tools/publisher/Publisher.java
index 0f8d3ba..784be4d 100644
--- a/src/main/java/org/hl7/fhir/tools/publisher/Publisher.java
+++ b/src/main/java/org/hl7/fhir/tools/publisher/Publisher.java
@@ -151,6 +151,7 @@ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWIS
 import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
 import org.hl7.fhir.r5.elementmodel.ParserBase;
 import org.hl7.fhir.r5.elementmodel.ParserBase.ValidationPolicy;
+import org.hl7.fhir.r5.elementmodel.ResourceParser;
 import org.hl7.fhir.r5.fhirpath.FHIRPathEngine;
 import org.hl7.fhir.r5.fhirpath.TypeDetails;
 import org.hl7.fhir.r5.formats.FormatUtilities;
@@ -2116,14 +2117,16 @@ void serializeResource(Resource r, String baseFileName, String description, Stri
         json.compose(new FileOutputStream(Utilities.path(page.getFolders().dstDir, baseFileName + ".canonical.json")), r);
       }
       if (showTtl) {
-        resource2Ttl(r);
+        org.hl7.fhir.r5.elementmodel.Element resourceElement = parseR5ElementFromResource(r);
+        ParserBase tp = Manager.makeParser(page.getWorkerContext(), FhirFormat.TURTLE);
+        tp.compose(resourceElement, new FileOutputStream(Utilities.path(page.getFolders().dstDir, baseFileName + ".ttl")), OutputStyle.PRETTY, null);
       }
     }
     if (description!=null) {
       cloneToXhtml(baseFileName, description, false, pageType, crumbTitle, null, wg, r.fhirType()+"/"+r.getId());
       jsonToXhtml(baseFileName, description, resource2Json(r), pageType, crumbTitle, null, wg, r.fhirType()+"/"+r.getId());
       if (showTtl)
-        ttlToXhtml(baseFileName, description, resource2Ttl(r), pageType, crumbTitle, null, wg, r.fhirType()+"/"+r.getId());
+        ttlToXhtml(baseFileName, description, convertResourceToTtl(r), pageType, crumbTitle, null, wg, r.fhirType()+"/"+r.getId());
     }
   };
     
@@ -4493,18 +4496,22 @@ private String resource2Json(Resource r) throws Exception {
     return new String(bytes.toByteArray());
   }
 
-  private String resource2Ttl(Resource r) throws Exception {
+  private org.hl7.fhir.r5.elementmodel.Element parseR5ElementFromResource(Resource resource) {
+    // Some R5+ serializations rely on r5.elementmodel.Element, so transform Resource directly into Element for this purpose (instead of getting Element by re-parsing another serialization)
+      ResourceParser resourceParser = new org.hl7.fhir.r5.elementmodel.ResourceParser(page.getWorkerContext());
+      return resourceParser.parse(resource);
+  }
+
+  private String convertResourceToTtl(Resource r) throws Exception {
     ByteArrayOutputStream bytes = new ByteArrayOutputStream();
     if (VersionUtilities.isR4BVer(page.getVersion().toCode())) {
       org.hl7.fhir.r4.formats.IParser rdf = new org.hl7.fhir.r4.formats.RdfParser().setOutputStyle(org.hl7.fhir.r4.formats.IParser.OutputStyle.PRETTY);
 //      rdf.setSuppressXhtml("Snipped for Brevity");
       rdf.compose(bytes, VersionConvertorFactory_40_50.convertResource(r));
     } else {
-        // R5+ serialization relies on r5.elementmodel.Element, so transform Resource directly into it (instead of getting Element by re-parsing another serialization)
-        org.hl7.fhir.r5.elementmodel.ResourceParser resourceParser = new org.hl7.fhir.r5.elementmodel.ResourceParser(page.getWorkerContext());
-        org.hl7.fhir.r5.elementmodel.Element exe = resourceParser.parse(r);
+        org.hl7.fhir.r5.elementmodel.Element resourceElement = parseR5ElementFromResource(r);
         ParserBase tp = Manager.makeParser(page.getWorkerContext(), FhirFormat.TURTLE);
-        tp.compose(exe, bytes, OutputStyle.PRETTY, null);
+        tp.compose(resourceElement, bytes, OutputStyle.PRETTY, null);
     }
     bytes.close();
     return new String(bytes.toByteArray());
@@ -5584,7 +5591,7 @@ private StructureDefinition generateProfile(ResourceDefn root, String n, String
       saveAsPureHtml(rp, new FileOutputStream(page.getFolders().dstDir + "html" + File.separator + n + ".html"));
       cloneToXhtml(n + ".profile", "StructureDefinition for " + n, true, "profile-instance:resource:" + root.getName(), "Profile", root, root.getWg(), rp.fhirType()+"/"+rp.getId());
       jsonToXhtml(n + ".profile", "StructureDefinition for " + n, resource2Json(rp), "profile-instance:resource:" + root.getName(), "Profile", root, root.getWg(), rp.fhirType()+"/"+rp.getId());
-      ttlToXhtml(n + ".profile", "StructureDefinition for " + n, resource2Ttl(rp), "profile-instance:resource:" + root.getName(), "Profile", root, root.getWg(), rp.fhirType()+"/"+rp.getId());
+      ttlToXhtml(n + ".profile", "StructureDefinition for " + n, convertResourceToTtl(rp), "profile-instance:resource:" + root.getName(), "Profile", root, root.getWg(), rp.fhirType()+"/"+rp.getId());
       String shex = new ShExGenerator(page.getWorkerContext()).generate(HTMLLinkPolicy.NONE, rp);
       TextFile.stringToFile(shex, page.getFolders().dstDir + n+".shex");
       shexToXhtml(n, "ShEx statement for " + n, shex, "profile-instance:type:" + root.getName(), "Type", root, root.getWg(), rp.fhirType()+"/"+rp.getId());