private void loadGlobalConceptDomains() throws Exception {
logger.log("Load Concept Domains", LogMessageType.Process);
BindingsParser parser =
new BindingsParser(
new CSFileInputStream(new CSFile(termDir + "bindings.xml")),
termDir + "bindings.xml",
srcDir,
registry);
List<BindingSpecification> cds = parser.parse();
for (BindingSpecification cd : cds) {
definitions.getBindings().put(cd.getName(), cd);
definitions.getCommonBindings().add(cd);
}
for (BindingSpecification cd : definitions.getBindings().values()) {
if (cd.getBinding() == BindingSpecification.Binding.CodeList) {
if (!parser.loadCodes(cd)) {
File file = new CSFile(termDir + cd.getReference().substring(1) + ".csv");
if (!file.exists())
throw new Exception(
"code source file not found for " + cd.getName() + ": " + file.getAbsolutePath());
CodeListParser cparser = new CodeListParser(new CSFileInputStream(file));
cparser.parse(cd.getCodes());
cparser.close();
}
}
if (cd.getBinding() == Binding.ValueSet && !Utilities.noString(cd.getReference())) {
if (cd.getReference().startsWith("http://hl7.org/fhir")) {
// ok, it's a reference to a value set defined within this build. Since it's an absolute
// reference, it's into the base infrastructure. That's not loaded yet, so we will try
// to resolve it later
} else if (new File(Utilities.appendSlash(termDir) + cd.getReference() + ".xml").exists()) {
XmlParser p = new XmlParser();
FileInputStream input =
new FileInputStream(Utilities.appendSlash(termDir) + cd.getReference() + ".xml");
cd.setReferredValueSet((ValueSet) p.parse(input));
} else if (new File(Utilities.appendSlash(termDir) + cd.getReference() + ".json")
.exists()) {
JsonParser p = new JsonParser();
FileInputStream input =
new FileInputStream(Utilities.appendSlash(termDir) + cd.getReference() + ".json");
cd.setReferredValueSet((ValueSet) p.parse(input));
} else
throw new Exception(
"Unable to find source for "
+ cd.getReference()
+ " ("
+ Utilities.appendSlash(termDir)
+ cd.getReference()
+ ".xml/json)");
}
}
}
public void parse(Calendar genDate, String version) throws Exception {
logger.log("Loading", LogMessageType.Process);
eCoreParseResults = DefinitionsImpl.build(genDate.getTime(), version);
loadGlobalConceptDomains();
eCoreParseResults
.getBinding()
.addAll(
sortBindings(
BindingConverter.buildBindingsFromFhirModel(
definitions.getBindings().values(), null)));
loadPrimitives();
eCoreParseResults
.getPrimitive()
.addAll(
PrimitiveConverter.buildPrimitiveTypesFromFhirModel(
definitions.getPrimitives().values()));
for (String n : ini.getPropertyNames("removed-resources"))
definitions.getDeletedResources().add(n);
for (String n : ini.getPropertyNames("types")) loadCompositeType(n, definitions.getTypes());
for (String n : ini.getPropertyNames("structures"))
loadCompositeType(n, definitions.getStructures());
String[] shared = ini.getPropertyNames("shared");
if (shared != null)
for (String n : shared)
definitions.getShared().add(loadCompositeType(n, definitions.getStructures()));
for (String n : ini.getPropertyNames("infrastructure"))
loadCompositeType(n, definitions.getInfrastructure());
List<TypeDefn> allFhirComposites = new ArrayList<TypeDefn>();
allFhirComposites.add(CompositeTypeConverter.buildElementBaseType());
allFhirComposites.addAll(
PrimitiveConverter.buildCompositeTypesForPrimitives(eCoreParseResults.getPrimitive()));
allFhirComposites.addAll(
CompositeTypeConverter.buildCompositeTypesFromFhirModel(
definitions.getTypes().values(), null));
allFhirComposites.addAll(
CompositeTypeConverter.buildCompositeTypesFromFhirModel(
definitions.getStructures().values(), null));
List<CompositeTypeDefn> infra =
CompositeTypeConverter.buildCompositeTypesFromFhirModel(
definitions.getInfrastructure().values(), null);
for (CompositeTypeDefn composite : infra) composite.setInfrastructure(true);
allFhirComposites.addAll(infra);
allFhirComposites.addAll(
ConstrainedTypeConverter.buildConstrainedTypesFromFhirModel(
definitions.getConstraints().values(), definitions.getConstraintInvariants()));
eCoreParseResults.getType().addAll(sortTypes(allFhirComposites));
for (String n : ini.getPropertyNames("resources"))
loadResource(n, definitions.getResources(), false);
ResourceDefn baseResource = loadResource("resource", null, false);
baseResource.setAbstract(true);
definitions.setBaseResource(baseResource);
loadCompartments();
loadStatusCodes();
org.hl7.fhir.definitions.ecore.fhir.ResourceDefn eCoreBaseResource =
CompositeTypeConverter.buildResourceFromFhirModel(baseResource, null);
eCoreBaseResource.getElement().add(CompositeTypeConverter.buildInternalIdElement());
eCoreParseResults.getType().add(eCoreBaseResource);
eCoreParseResults
.getType()
.addAll(
sortTypes(
CompositeTypeConverter.buildResourcesFromFhirModel(
definitions.getResources().values())));
eCoreParseResults.getType().add(CompositeTypeConverter.buildBinaryResourceDefn());
for (String n : ini.getPropertyNames("svg"))
definitions.getDiagrams().put(n, ini.getStringProperty("svg", n));
if (ini.getPropertyNames("future-resources") != null)
for (String n : ini.getPropertyNames("future-resources")) {
DefinedCode cd =
new DefinedCode(ini.getStringProperty("future-resources", n), "Yet to be defined", n);
definitions.getKnownResources().put(n, cd);
ResourceDefn futureResource = new ResourceDefn();
futureResource.setName(cd.getCode());
futureResource.setDefinition("Future resource " + cd.getCode() + ". As yet undefined.");
futureResource.setForFutureUse(true);
definitions.getFutureResources().put(cd.getCode(), futureResource);
}
eCoreParseResults
.getType()
.addAll(
CompositeTypeConverter.buildResourcesFromFhirModel(
definitions.getFutureResources().values()));
eCoreParseResults
.getEvent()
.addAll(EventConverter.buildEventsFromFhirModel(definitions.getEvents().values()));
// As a second pass, resolve typerefs to the types
fixTypeRefs(eCoreParseResults);
eCoreParseResults
.getBinding()
.add(BindingConverter.buildResourceTypeBinding(eCoreParseResults));
for (String n : ini.getPropertyNames("special-resources"))
definitions.getAggregationEndpoints().add(n);
String[] pn = ini.getPropertyNames("valuesets");
if (pn != null)
for (String n : pn) {
loadValueSet(n);
}
for (String n : ini.getPropertyNames("profiles")) {
loadProfile(n, definitions.getProfiles());
}
for (ResourceDefn r : definitions.getResources().values()) {
for (RegisteredProfile p : r.getProfiles()) {
SpreadsheetParser sparser =
new SpreadsheetParser(
new CSFileInputStream(p.getFilepath()),
p.getName(),
definitions,
srcDir,
logger,
registry);
sparser.setFolder(Utilities.getDirectoryForFile(p.getFilepath()));
p.setProfile(sparser.parseProfile(definitions));
}
}
}