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Fix R5 loading problem

This commit is contained in:
Grahame Grieve 2023-02-07 09:53:51 +10:00
parent eec7c33e63
commit ba731b0051
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 class Loadable<T extends CanonicalResource> {
public Loadable(PackageResourceInformation info) { public Loadable(PackageResourceInformation info, NpmPackage source) {
this.info = info; this.info = info;
this.source = source;
} }
private T resource; private T resource;
private NpmPackage source;
private PackageResourceInformation info; private PackageResourceInformation info;
public T getResource() throws FHIRFormatError, FileNotFoundException, IOException { public T getResource() throws FHIRFormatError, FileNotFoundException, IOException {
if (resource == null) { if (resource == null) {
CanonicalResource r = (CanonicalResource) json.parse(pck.load(info)); CanonicalResource r = (CanonicalResource) json.parse(source.load(info));
r.setUserData("path", Utilities.pathURL(pck.getWebLocation(), r.fhirType().toLowerCase()+ "-"+r.getId().toLowerCase()+".html")); r.setUserData("path", Utilities.pathURL(source.getWebLocation(), r.fhirType().toLowerCase()+ "-"+r.getId().toLowerCase()+".html"));
resource = (T) r; resource = (T) r;
} }
return resource; return resource;
@ -59,12 +61,12 @@ public class R5ExtensionsLoader {
private BasePackageCacheManager pcm; private BasePackageCacheManager pcm;
private int count; private int count;
private NpmPackage pck; private NpmPackage pckCore;
private NpmPackage pckExt;
private Map<String, Loadable<ValueSet>> valueSets; private Map<String, Loadable<ValueSet>> valueSets;
private Map<String, Loadable<CodeSystem>> codeSystems; private Map<String, Loadable<CodeSystem>> codeSystems;
private List<Loadable<StructureDefinition>> structures; private List<Loadable<StructureDefinition>> structures;
private IWorkerContext context; private IWorkerContext context;
private PackageInformation pd;
private JsonParser json; private JsonParser json;
public R5ExtensionsLoader(BasePackageCacheManager pcm, IWorkerContext context) { public R5ExtensionsLoader(BasePackageCacheManager pcm, IWorkerContext context) {
@ -78,22 +80,27 @@ public class R5ExtensionsLoader {
} }
public void load() throws FHIRException, IOException { public void load() throws FHIRException, IOException {
pck = pcm.loadPackage("hl7.fhir.r5.core", "current"); pckCore = pcm.loadPackage("hl7.fhir.r5.core", "current");
pd = new PackageInformation(pck); 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" }; String[] types = new String[] { "StructureDefinition", "ValueSet", "CodeSystem" };
json = new JsonParser();
for (PackageResourceInformation pri : pck.listIndexedResources(types)) { for (PackageResourceInformation pri : pck.listIndexedResources(types)) {
if (pri.getResourceType().equals("CodeSystem")) { if (pri.getResourceType().equals("CodeSystem")) {
codeSystems.put(pri.getUrl(), new Loadable<CodeSystem>(pri)); codeSystems.put(pri.getUrl(), new Loadable<CodeSystem>(pri, pck));
codeSystems.put(pri.getUrl()+"|"+pri.getVersion(), new Loadable<CodeSystem>(pri)); codeSystems.put(pri.getUrl()+"|"+pri.getVersion(), new Loadable<CodeSystem>(pri, pck));
} else if (pri.getResourceType().equals("ValueSet")) { } else if (pri.getResourceType().equals("ValueSet")) {
valueSets.put(pri.getUrl(), new Loadable<ValueSet>(pri)); valueSets.put(pri.getUrl(), new Loadable<ValueSet>(pri, pck));
valueSets.put(pri.getUrl()+"|"+pri.getVersion(), new Loadable<ValueSet>(pri)); valueSets.put(pri.getUrl()+"|"+pri.getVersion(), new Loadable<ValueSet>(pri, pck));
} else if (pri.getResourceType().equals("StructureDefinition")) { } 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 { public void loadR5Extensions() throws FHIRException, IOException {
@ -105,9 +112,9 @@ public class R5ExtensionsLoader {
if (sd.getDerivation() == TypeDerivationRule.CONSTRAINT) { if (sd.getDerivation() == TypeDerivationRule.CONSTRAINT) {
if (survivesStrippingTypes(sd, context, typeNames)) { if (survivesStrippingTypes(sd, context, typeNames)) {
count++; 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); registerTerminologies(sd);
context.cacheResourceFromPackage(sd, pd); context.cacheResourceFromPackage(sd, new PackageInformation(lsd.source));
} }
} }
} }
@ -119,9 +126,9 @@ public class R5ExtensionsLoader {
StructureDefinition sd = lsd.getResource(); StructureDefinition sd = lsd.getResource();
if (Utilities.existsInList(sd.getType(), types)) { if (Utilities.existsInList(sd.getType(), types)) {
count++; 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); 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(); String vsu = ed.getBinding().getValueSet();
ValueSet vs = context.fetchResource(ValueSet.class, vsu); ValueSet vs = context.fetchResource(ValueSet.class, vsu);
if (vs == null) { if (vs == null) {
loadValueSet(vsu, context, valueSets, codeSystems, pd); loadValueSet(vsu, context, valueSets, codeSystems);
} else if (vs.hasVersion()) { } else if (vs.hasVersion()) {
ed.getBinding().setValueSet(vs.getUrl()+"|"+vs.getVersion()); 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)) { if (valueSets.containsKey(url)) {
ValueSet vs = valueSets.get(url).getResource(); ValueSet vs = valueSets.get(url).getResource();
context.cacheResourceFromPackage(vs, pd); context.cacheResourceFromPackage(vs, vs.getSourcePackage());
for (ConceptSetComponent inc : vs.getCompose().getInclude()) { for (ConceptSetComponent inc : vs.getCompose().getInclude()) {
for (CanonicalType t : inc.getValueSet()) { for (CanonicalType t : inc.getValueSet()) {
loadValueSet(t.asStringValue(), context, valueSets, codeSystems, pd); loadValueSet(t.asStringValue(), context, valueSets, codeSystems);
} }
if (inc.hasSystem() && !inc.hasVersion()) { if (inc.hasSystem() && !inc.hasVersion()) {
if (codeSystems.containsKey(inc.getSystem())) { if (codeSystems.containsKey(inc.getSystem())) {
CodeSystem cs = codeSystems.get(inc.getSystem()).getResource(); CodeSystem cs = codeSystems.get(inc.getSystem()).getResource();
inc.setVersion(cs.getVersion()); 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())) { } 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 { 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() { public NpmPackage getPckCore() {
return pck; return pckCore;
}
public NpmPackage getPckExt() {
return pckExt;
} }