protected ElementDefn getRootDefinition() {
ElementDefn el = null;
ResourceDefn resource = definitions.getResources().get(name);
resource = (resource == null) ? definitions.getBaseResources().get(name) : resource;
if (resource != null) {
el = resource.getRoot();
} else {
el = definitions.getInfrastructure().get(name);
el = (el == null) ? definitions.getTypes().get(name) : el;
el = (el == null) ? definitions.getStructures().get(name) : el;
}
return el;
}
private ResourceDefn loadResource(String n, Map<String, ResourceDefn> map, boolean sandbox)
throws Exception {
String src = sandbox ? sndBoxDir : srcDir;
File spreadsheet =
new CSFile(
(sandbox ? sndBoxDir : srcDir) + n + File.separatorChar + n + "-spreadsheet.xml");
if (!spreadsheet.exists())
spreadsheet =
new CSFile((sandbox ? sndBoxDir : srcDir) + n + File.separatorChar + n + "-def.xml");
SpreadsheetParser sparser =
new SpreadsheetParser(
new CSFileInputStream(spreadsheet),
spreadsheet.getName(),
definitions,
src,
logger,
registry);
ResourceDefn root;
try {
root = sparser.parseResource();
} catch (Exception e) {
throw new Exception("Error Parsing Resource " + n + ": " + e.getMessage(), e);
}
root.setSandbox(sandbox);
for (EventDefn e : sparser.getEvents()) processEvent(e, root.getRoot());
// EK: Commented this out, seems double with next statement, since
// loadResource()
// is always called with definitions.getResources in its map argument.
// definitions.getResources().put(root.getName(), root);
if (map != null) {
map.put(root.getName(), root);
definitions
.getKnownResources()
.put(root.getName(), new DefinedCode(root.getName(), root.getRoot().getDefinition(), n));
}
root.setStatus(ini.getStringProperty("status", n));
return root;
}
private void gen(ResourceDefn rd) throws Exception {
Section section = section(rd.getName());
ElementDefn t = rd.getRoot();
if (t.getTypes().isEmpty()) section.triple("fhir:" + t.getName(), "a", "rdfs:Class");
else section.triple("fhir:" + t.getName(), "rdfs:subClassOf", processType(t.typeCode()));
section.comment("fhir:" + t.getName(), rd.getDefinition());
if (!Utilities.noString(t.getW5()))
section.triple(
"fhir:" + t.getName(), "fhir:w5", complex().predicate("a", "fhir:w5\\#" + t.getW5()));
processMappings(section, "fhir:" + rd.getName(), rd.getRoot());
for (ElementDefn e : t.getElements()) {
if (e.getName().endsWith("[x]")) {
String cn = e.getName().substring(0, e.getName().length() - 3);
section.triple("fhir:" + t.getName() + "." + cn, "a", "rdf:Property");
section.comment("fhir:" + t.getName() + "." + cn, e.getDefinition());
processMappings(section, "fhir:" + t.getName() + "." + cn, e);
for (TypeRef tr : e.typeCode().equals("*") ? getAnyTypes() : e.getTypes()) {
String en = cn + Utilities.capitalize(tr.getName());
section.triple(
"fhir:" + t.getName() + "." + en,
"rdfs:subPropertyOf",
"fhir:" + t.getName() + "." + cn);
section.triple("fhir:" + t.getName() + "." + en, "rdfs:domain", "fhir:" + rd.getName());
genRange(section, t.getName(), en, e, tr, false);
}
} else {
section.triple("fhir:" + t.getName() + "." + e.getName(), "a", "rdf:Property");
section.comment("fhir:" + t.getName() + "." + e.getName(), e.getDefinition());
section.triple(
"fhir:" + t.getName() + "." + e.getName(), "rdfs:domain", "fhir:" + rd.getName());
processMappings(section, "fhir:" + t.getName() + "." + e.getName(), e);
genRange(
section,
t.getName(),
e.getName(),
e,
e.getTypes().isEmpty() ? null : e.getTypes().get(0),
false);
}
}
processAnonTypes();
}
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));
}
}
}
