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Merge pull request #1105 from hapifhir/gg-202302-more-extensions 

Fix R5 loading problem
This commit is contained in:
Grahame Grieve 2023-02-07 13:41:30 +11:00 committed by GitHub
parent eec7c33e63 ba731b0051
commit afc54c5b55
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GPG Key ID: 4AEE18F83AFDEB23
1 changed files with 39 additions and 27 deletions
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66
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/R5ExtensionsLoader.java
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@ -42,15 +42,17 @@ public class R5ExtensionsLoader {
}
public class Loadable<T extends CanonicalResource> {
public Loadable(PackageResourceInformation info) {
public Loadable(PackageResourceInformation info, NpmPackage source) {
this.info = info;
this.source = source;
}
private T resource;
private NpmPackage source;
private PackageResourceInformation info;
public T getResource() throws FHIRFormatError, FileNotFoundException, IOException {
if (resource == null) {
CanonicalResource r = (CanonicalResource) json.parse(pck.load(info));
r.setUserData("path", Utilities.pathURL(pck.getWebLocation(), r.fhirType().toLowerCase()+ "-"+r.getId().toLowerCase()+".html"));
CanonicalResource r = (CanonicalResource) json.parse(source.load(info));
r.setUserData("path", Utilities.pathURL(source.getWebLocation(), r.fhirType().toLowerCase()+ "-"+r.getId().toLowerCase()+".html"));
resource = (T) r;
}
return resource;
@ -59,12 +61,12 @@ public class R5ExtensionsLoader {
private BasePackageCacheManager pcm;
private int count;
private NpmPackage pck;
private NpmPackage pckCore;
private NpmPackage pckExt;
private Map<String, Loadable<ValueSet>> valueSets;
private Map<String, Loadable<CodeSystem>> codeSystems;
private List<Loadable<StructureDefinition>> structures;
private IWorkerContext context;
private PackageInformation pd;
private JsonParser json;
public R5ExtensionsLoader(BasePackageCacheManager pcm, IWorkerContext context) {
@ -78,22 +80,27 @@ public class R5ExtensionsLoader {
}
public void load() throws FHIRException, IOException {
pck = pcm.loadPackage("hl7.fhir.r5.core", "current");
pd = new PackageInformation(pck);
pckCore = pcm.loadPackage("hl7.fhir.r5.core", "current");
loadDetails(pckCore);
pckExt = pcm.loadPackage("hl7.fhir.uv.extensions", "current");
loadDetails(pckExt);
}
private void loadDetails(NpmPackage pck) throws IOException {
json = new JsonParser();
String[] types = new String[] { "StructureDefinition", "ValueSet", "CodeSystem" };
json = new JsonParser();
for (PackageResourceInformation pri : pck.listIndexedResources(types)) {
if (pri.getResourceType().equals("CodeSystem")) {
codeSystems.put(pri.getUrl(), new Loadable<CodeSystem>(pri));
codeSystems.put(pri.getUrl()+"|"+pri.getVersion(), new Loadable<CodeSystem>(pri));
codeSystems.put(pri.getUrl(), new Loadable<CodeSystem>(pri, pck));
codeSystems.put(pri.getUrl()+"|"+pri.getVersion(), new Loadable<CodeSystem>(pri, pck));
} else if (pri.getResourceType().equals("ValueSet")) {
valueSets.put(pri.getUrl(), new Loadable<ValueSet>(pri));
valueSets.put(pri.getUrl()+"|"+pri.getVersion(), new Loadable<ValueSet>(pri));
valueSets.put(pri.getUrl(), new Loadable<ValueSet>(pri, pck));
valueSets.put(pri.getUrl()+"|"+pri.getVersion(), new Loadable<ValueSet>(pri, pck));
} else if (pri.getResourceType().equals("StructureDefinition")) {
structures.add(new Loadable<StructureDefinition>(pri));
structures.add(new Loadable<StructureDefinition>(pri, pck));
}
}
}
}
public void loadR5Extensions() throws FHIRException, IOException {
@ -105,9 +112,9 @@ public class R5ExtensionsLoader {
if (sd.getDerivation() == TypeDerivationRule.CONSTRAINT) {
if (survivesStrippingTypes(sd, context, typeNames)) {
count++;
sd.setUserData("path", Utilities.pathURL(pck.getWebLocation(), "extension-"+sd.getId().toLowerCase()+".html"));
sd.setUserData("path", Utilities.pathURL(pckExt.getWebLocation(), "extension-"+sd.getId().toLowerCase()+".html"));
registerTerminologies(sd);
context.cacheResourceFromPackage(sd, pd);
context.cacheResourceFromPackage(sd, new PackageInformation(lsd.source));
}
}
}
@ -119,9 +126,9 @@ public class R5ExtensionsLoader {
StructureDefinition sd = lsd.getResource();
if (Utilities.existsInList(sd.getType(), types)) {
count++;
sd.setUserData("path", Utilities.pathURL(pck.getWebLocation(), sd.getId().toLowerCase()+".html"));
sd.setUserData("path", Utilities.pathURL(lsd.source.getWebLocation(), sd.getId().toLowerCase()+".html"));
registerTerminologies(sd);
context.cacheResourceFromPackage(sd, pd);
context.cacheResourceFromPackage(sd, new PackageInformation(lsd.source));
}
}
}
@ -132,7 +139,7 @@ public class R5ExtensionsLoader {
String vsu = ed.getBinding().getValueSet();
ValueSet vs = context.fetchResource(ValueSet.class, vsu);
if (vs == null) {
loadValueSet(vsu, context, valueSets, codeSystems, pd);
loadValueSet(vsu, context, valueSets, codeSystems);
} else if (vs.hasVersion()) {
ed.getBinding().setValueSet(vs.getUrl()+"|"+vs.getVersion());
}
@ -140,21 +147,22 @@ public class R5ExtensionsLoader {
}
}
private void loadValueSet(String url, IWorkerContext context, Map<String, Loadable<ValueSet>> valueSets, Map<String, Loadable<CodeSystem>> codeSystems, PackageInformation pd) throws FHIRFormatError, FileNotFoundException, IOException {
private void loadValueSet(String url, IWorkerContext context, Map<String, Loadable<ValueSet>> valueSets, Map<String, Loadable<CodeSystem>> codeSystems) throws FHIRFormatError, FileNotFoundException, IOException {
if (valueSets.containsKey(url)) {
ValueSet vs = valueSets.get(url).getResource();
context.cacheResourceFromPackage(vs, pd);
context.cacheResourceFromPackage(vs, vs.getSourcePackage());
for (ConceptSetComponent inc : vs.getCompose().getInclude()) {
for (CanonicalType t : inc.getValueSet()) {
loadValueSet(t.asStringValue(), context, valueSets, codeSystems, pd);
loadValueSet(t.asStringValue(), context, valueSets, codeSystems);
}
if (inc.hasSystem() && !inc.hasVersion()) {
if (codeSystems.containsKey(inc.getSystem())) {
CodeSystem cs = codeSystems.get(inc.getSystem()).getResource();
inc.setVersion(cs.getVersion());
context.cacheResourceFromPackage(cs, pd);
context.cacheResourceFromPackage(cs, cs.getSourcePackage());
} else if (!context.hasResource(CodeSystem.class, inc.getSystem()) && codeSystems.containsKey(inc.getSystem())) {
context.cacheResourceFromPackage(codeSystems.get(inc.getSystem()).getResource(), pd);
CodeSystem cs1 = codeSystems.get(inc.getSystem()).getResource();
context.cacheResourceFromPackage(cs1, cs1.getSourcePackage());
}
}
}
@ -202,11 +210,15 @@ public class R5ExtensionsLoader {
}
public byte[] getMap() throws IOException {
return pck.hasFile("other", "spec.internals") ? TextFile.streamToBytes(pck.load("other", "spec.internals")) : null;
return pckCore.hasFile("other", "spec.internals") ? TextFile.streamToBytes(pckCore.load("other", "spec.internals")) : null;
}
public NpmPackage getPck() {
return pck;
public NpmPackage getPckCore() {
return pckCore;
}
public NpmPackage getPckExt() {
return pckExt;
}