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Switch remaining R5 Turtle RDF generation to TurtleParser implementation #148

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merged 13 commits into from
Dec 17, 2024
Merged

Switch remaining R5 Turtle RDF generation to TurtleParser implementation #148

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9f461c5
Switch remaining (R5) RDF generation to TurtleParser implementation
tmprd Sep 7, 2023
0c396e0
Serialize turtle Element from Resource directly
tmprd Oct 4, 2023
deff42c
Merge branch 'main' into r5-rdf-generation-fix
tmprd Oct 4, 2023
22aa382
Merge branch 'main' into r5-rdf-generation-fix
tmprd Nov 10, 2023
9a471e0
Merge branch 'main' into r5-rdf-generation-fix
tmprd Dec 10, 2023
6f7311a
Merge branch 'main' into r5-rdf-generation-fix
tmprd Jan 28, 2024
e7120ec
Merge branch 'main' into r5-rdf-generation-fix
tmprd Feb 15, 2024
1b42123
Merge branch 'main' into r5-rdf-generation-fix
tmprd Apr 14, 2024
d12b093
Merge branch 'main' into r5-rdf-generation-fix
tmprd Apr 17, 2024
7b19236
Fix TTL resource serialization with TurtleParser
tmprd Apr 19, 2024
87fbc6c
Merge branch 'main' into r5-rdf-generation-fix
tmprd Apr 19, 2024
beebb48
Merge branch 'main' into r5-rdf-generation-fix
tmprd Sep 25, 2024
210d3ab
Merge branch 'main' into r5-rdf-generation-fix
tmprd Dec 16, 2024
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24 changes: 16 additions & 8 deletions src/main/java/org/hl7/fhir/tools/publisher/Publisher.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand Down Expand Up @@ -2116,15 +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) {
IParser rdf = new RdfParser().setOutputStyle(OutputStyle.PRETTY);
rdf.compose(new FileOutputStream(Utilities.path(page.getFolders().dstDir, baseFileName + ".ttl")), 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());
}
};

Expand Down Expand Up @@ -4494,16 +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 {
IParser rdf = new RdfParser().setOutputStyle(OutputStyle.PRETTY);
// rdf.setSuppressXhtml("Snipped for Brevity");
rdf.compose(bytes, r);
org.hl7.fhir.r5.elementmodel.Element resourceElement = parseR5ElementFromResource(r);
ParserBase tp = Manager.makeParser(page.getWorkerContext(), FhirFormat.TURTLE);
tp.compose(resourceElement, bytes, OutputStyle.PRETTY, null);
}
bytes.close();
return new String(bytes.toByteArray());
Expand Down Expand Up @@ -5583,7 +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());
Expand Down
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