public ElementDefn getElementByProfileName(String name) {
for (int i = elements.size() - 1; i >= 0; i--) {
ElementDefn e = elements.get(i);
if (e.getProfileName().equalsIgnoreCase(name)) return e;
}
return null;
}
public void generate() throws Exception {
outputFile.createNewFile();
GenBlock fileBlock = new GenBlock();
generateMainHeader(fileBlock);
ElementDefn root = getRootDefinition();
generateResourceHeader(fileBlock, root);
// first loop through and generate all of the embedded types from this
// schema
for (Iterator<ElementDefn> iterator = root.getElements().iterator(); iterator.hasNext(); ) {
ElementDefn elementDefinition = iterator.next();
generateEmbeddedType(outputFile.getParentFile(), fileBlock, elementDefinition);
}
generatePostEmbedded(fileBlock, root);
// next loop through and generate the filed elements
for (Iterator<ElementDefn> iterator = root.getElements().iterator(); iterator.hasNext(); ) {
ElementDefn elementDefinition = iterator.next();
if (!elementDefinition.isXmlAttribute() || xmlAttributeAsField)
generateElement(fileBlock, elementDefinition);
}
generateResourceFooter(fileBlock);
generateMainFooter(fileBlock);
Writer modelFile = new BufferedWriter(new FileWriter(outputFile));
modelFile.write(fileBlock.toString());
modelFile.flush();
modelFile.close();
}
private boolean nameMatches(String n, ElementDefn e, boolean throughChoice) {
if (e.getName().equals(n)) return true;
else if (!throughChoice || !e.getName().endsWith("[x]")) return false;
else {
String b = e.getName().substring(0, e.getName().indexOf("["));
if (!n.startsWith(b)) return false;
String tn = n.substring(b.length());
for (TypeRef t : e.getTypes()) if (t.getName().equalsIgnoreCase(tn)) return true;
return false;
}
}
public ElementDefn getElementByName(String name, boolean throughChoice) {
String n = name.contains(".") ? name.substring(0, name.indexOf(".")) : name;
String t = name.contains(".") ? name.substring(name.indexOf(".") + 1) : null;
if (n.equals(this.name) && t != null) return getElementByName(t);
for (int i = elements.size() - 1; i >= 0; i--) {
ElementDefn e = elements.get(i);
if (nameMatches(n, e, throughChoice)) return t == null ? e : e.getElementByName(t);
}
return null;
}
private ElementDefn getElementForPath(String pathname) throws Exception {
String[] path = pathname.split("\\.");
ElementDefn res = definitions.getElementDefn(path[0]);
for (int i = 1; i < path.length; i++) {
String en = path[i];
if (en.length() == 0) throw new Exception("Improper path " + pathname);
ElementDefn t = res.getElementByName(definitions, en, true, false);
if (t == null) {
throw new Exception("unable to resolve " + pathname);
}
res = t;
}
return res;
}
private void scan(ElementDefn e, String path) throws Exception {
if (e.hasBinding()) {
BindingSpecification cd = e.getBinding();
if (!txusages.containsKey(cd)) {
txusages.put(cd, new ArrayList<CDUsage>());
c++;
txusages.get(cd).add(new CDUsage(String.valueOf(c), null));
}
txusages.get(cd).add(new CDUsage(path, e));
}
for (ElementDefn c : e.getElements()) {
scan(c, path + "." + c.getName());
}
}
public ElementDefn getElementForPath(String pathname, Definitions definitions, String purpose)
throws Exception {
String[] path = pathname.split("\\.");
if (!path[0].equals(getName()))
throw new Exception(
"Element Path '" + pathname + "' is not legal in this context (" + purpose + ")");
ElementDefn res = this;
for (int i = 1; i < path.length; i++) {
String en = path[i];
if (en.length() == 0) throw new Exception("Improper path " + pathname);
ElementDefn t = null;
if (res.typeCode().startsWith("@")) {
res = this.getElementForPath(res.typeCode().substring(1), definitions, purpose);
} else if (definitions.dataTypeIsSharedInfo(res.typeCode())) {
res = definitions.getElementDefn(res.typeCode());
} else if (definitions.hasType(res.typeCode())) {
res = definitions.getElementDefn(res.typeCode());
}
t = res.getElementByName(en);
if (t == null) {
throw new Exception("unable to resolve " + pathname);
}
res = t;
}
return res;
}
protected String getEmbeddedClassName(ElementDefn elementDefinition, TypeRef typeRef) {
if (typeRef != null) return typeRef.getResolvedTypeName();
String typeName = generateTypeName(elementDefinition, null);
String cname = elementDefinition.getDeclaredTypeName();
cname = (cname == null) ? typeName : cname;
return Character.toUpperCase(cname.charAt(0)) + cname.substring(1);
}
public ElementDefn(ElementDefn pattern) {
super();
types.addAll(pattern.types);
for (ElementDefn c : pattern.getElements()) elements.add(new ElementDefn(c));
minCardinality = pattern.minCardinality;
maxCardinality = pattern.maxCardinality;
statedInvariants.addAll(pattern.statedInvariants);
modifier = pattern.modifier;
mustSupport = pattern.mustSupport;
binding = pattern.binding;
name = pattern.name;
shortDefn = pattern.shortDefn;
definition = pattern.definition;
requirements = pattern.requirements;
mappings.putAll(pattern.mappings);
comments = pattern.comments;
todo = pattern.todo;
committeeNotes = pattern.committeeNotes;
condition = pattern.condition;
example = pattern.example;
profileName = pattern.profileName;
fixed = pattern.fixed;
inherited = pattern.inherited;
}
public ElementDefn getElementByName(String name) {
String n = name.contains(".") ? name.substring(0, name.indexOf(".")) : name;
String t = name.contains(".") ? name.substring(name.indexOf(".") + 1) : null;
if (n.equals(this.name) && t != null) return getElementByName(t);
for (int i = elements.size() - 1; i >= 0; i--) {
ElementDefn e = elements.get(i);
if (nameMatches(n, e, false, null)) return t == null ? e : e.getElementByName(t);
// if (e.getName().length() > name.length()
// && e.getName().substring(0, name.length())
// .equalsIgnoreCase(name)
// && e.getElements().size() == 1
// && e.getElements().get(0).getName().equalsIgnoreCase(name))
// return e.getElements().get(0);
}
return null;
}
private void processMappings(Section section, String subject, ElementDefn e) throws Exception {
for (String m : e.getMappings().keySet()) {
if (m.equals("http://hl7.org/orim")) section.importTtl(e.getMappings().get(m));
if (m.equals("http://snomed.info")) {
System.out.println("sct = " + e.getMappings().get(m));
throw new Error(
"Snomed CT mappings are not done for RDF"); // reminder to actually do this //
// http://snomed.info/id/{sctid}
}
if (m.equals("http://loinc.org")) {
String[] sl = e.getMappings().get(m).split("\\,");
for (String sp : sl) {
String s = sp.contains("(") ? sp.substring(0, sp.indexOf("(")).trim() : sp.trim();
if (!s.contains(" ") && !s.contains("/"))
section.triple(subject, "fhir:loinc", "loinc:" + s);
}
}
}
}
private String loadCompositeType(String n, Map<String, ElementDefn> map) throws Exception {
TypeParser tp = new TypeParser();
List<TypeRef> ts = tp.parse(n);
definitions.getKnownTypes().addAll(ts);
try {
TypeRef t = ts.get(0);
File csv = new CSFile(dtDir + t.getName().toLowerCase() + ".xml");
if (csv.exists()) {
SpreadsheetParser p =
new SpreadsheetParser(
new CSFileInputStream(csv), csv.getName(), definitions, srcDir, logger, registry);
ElementDefn el = p.parseCompositeType();
map.put(t.getName(), el);
el.getAcceptableGenericTypes().addAll(ts.get(0).getParams());
return el.getName();
} else {
String p = ini.getStringProperty("types", n);
csv = new CSFile(dtDir + p.toLowerCase() + ".xml");
if (!csv.exists()) throw new Exception("unable to find a definition for " + n + " in " + p);
XLSXmlParser xls = new XLSXmlParser(new CSFileInputStream(csv), csv.getAbsolutePath());
Sheet sheet = xls.getSheets().get("Restrictions");
boolean found = false;
for (int i = 0; i < sheet.rows.size(); i++) {
if (sheet.getColumn(i, "Name").equals(n)) {
found = true;
Invariant inv = new Invariant();
inv.setId(n);
inv.setEnglish(sheet.getColumn(i, "Rules"));
inv.setOcl(sheet.getColumn(i, "OCL"));
inv.setXpath(sheet.getColumn(i, "XPath"));
definitions.getConstraints().put(n, new DefinedCode(n, sheet.getColumn(i, "Rules"), p));
definitions.getConstraintInvariants().put(n, inv);
}
}
if (!found) throw new Exception("Unable to find definition for " + n);
return n;
}
} catch (Exception e) {
throw new Exception("Unable to load " + n + ": " + e.getMessage(), e);
}
}
public ElementDefn getElementByName(
String name, boolean throughChoice, Definitions definitions, String purpose)
throws Exception {
String n = name.contains(".") ? name.substring(0, name.indexOf(".")) : name;
String t = name.contains(".") ? name.substring(name.indexOf(".") + 1) : null;
if (n.equals(this.name) && t != null) return getElementByName(t);
ElementDefn focus = this;
if (typeCode().startsWith("@")) {
String s = typeCode().substring(1);
focus = definitions.getElementDefn(s.substring(0, s.indexOf(".")));
focus = focus.getElementForPath(s, definitions, purpose, throughChoice);
}
for (int i = focus.elements.size() - 1; i >= 0; i--) {
ElementDefn e = focus.elements.get(i);
if (nameMatches(n, e, throughChoice, definitions))
return t == null ? e : e.getElementByName(t);
}
return null;
}
protected void generateElement(GenBlock block, ElementDefn elementDefinition) {
List<TypeRef> types = elementDefinition.getTypes();
boolean multipleCardinality =
elementDefinition.getMaxCardinality() == null || elementDefinition.getMaxCardinality() > 1;
if (types.size() > 0) {
for (TypeRef typeRef : types) {
String elementType = typeRef.getName();
if (elementType.startsWith("@")) {
handleField(block, FieldType.EMBEDDED, multipleCardinality, elementDefinition, typeRef);
} else {
handleField(
block,
FieldType.getFieldType(elementType),
multipleCardinality,
elementDefinition,
typeRef);
dataTypes.add(elementType);
}
}
} else if (types.size() == 0) {
handleField(block, FieldType.EMBEDDED, multipleCardinality, elementDefinition, null);
}
}
protected String generateTypeName(ElementDefn elementDefinition, TypeRef type, boolean fixTypes) {
String elementName = elementDefinition.getName().replace("[x]", "");
if (elementDefinition.getTypes().size() > 1) {
String typeName = type.getName();
typeName = Character.toUpperCase(typeName.charAt(0)) + typeName.substring(1);
if (FieldType.QUANTITY == FieldType.getFieldType(typeName)) {
elementName += "Quantity";
} else {
elementName += typeName;
}
}
if (!fixTypes) {
return elementName;
} else if (elementName.equals("type")) {
elementName = "fhirType";
} else if (elementName.equals("collection")) {
elementName = "fhirCollection";
} else if (elementName.equals("deleted")) {
elementName = "fhirDeleted";
} else if (elementName.equals("version")) {
elementName = "versionNum";
} else if (elementName.equals("class")) {
elementName = "fhirClass";
} else if (elementName.equals("hash")) {
elementName = "fhirHash";
} else if (elementName.equals("identity")) {
elementName = "fhirIdentity";
} else if (elementName.equals("modifier")) {
elementName = "fhirModifier";
} else if (elementName.equals("validated")) {
elementName = "fhirValidated";
}
return elementName;
}
private boolean nameMatches(
String n, ElementDefn e, boolean throughChoice, Definitions definitions) {
if (e.getName().equals(n)) return true;
else if (!throughChoice || !e.getName().endsWith("[x]")) return false;
else {
String b = e.getName().substring(0, e.getName().indexOf("["));
if (!n.startsWith(b)) return false;
String tn = n.substring(b.length());
if (e.typeCode().equals("*") && definitions != null) {
for (TypeRef t : definitions.getKnownTypes()) {
if (!definitions.getInfrastructure().containsKey(t.getName())
&& !definitions.getConstraints().containsKey(t.getName())) {
if (t.getName().equalsIgnoreCase(tn)) return true;
}
}
} else for (TypeRef t : e.getTypes()) if (t.getName().equalsIgnoreCase(tn)) return true;
return false;
}
}
protected boolean isResource(ElementDefn elementDefinition) {
for (TypeRef type : elementDefinition.getTypes()) {
if (type.getName().endsWith(RESOURCE_TYPE)) return true;
}
return false;
}
public void generate(String prefix, ElementDefn root) throws Exception {
scan(root, root.getName());
gen(prefix, txusages);
flush();
close();
}
private void genAnon(AnonTypeInfo at) throws Exception {
if (at.isType()) at.getSection().triple("fhir:" + at.getName(), "a", "fhir:Element");
else at.getSection().triple("fhir:" + at.getName(), "a", "fhir:BackboneElement");
at.getSection().comment("fhir:" + at.getName(), at.getDefn().getDefinition());
processMappings(at.getSection(), "fhir:" + at.getName(), at.getDefn());
for (ElementDefn e : at.getDefn().getElements()) {
if (e.getName().endsWith("[x]")) {
String cn = e.getName().substring(0, e.getName().length() - 3);
at.getSection().triple("fhir:" + at.getName() + "." + cn, "a", "rdf:Property");
at.getSection().comment("fhir:" + at.getName() + "." + cn, e.getDefinition());
processMappings(at.getSection(), "fhir:" + at.getName() + "." + cn, e);
for (TypeRef tr : e.typeCode().equals("*") ? getAnyTypes() : e.getTypes()) {
String en = cn + Utilities.capitalize(tr.getName());
at.getSection()
.triple(
"fhir:" + at.getName() + "." + en,
"rdfs:subPropertyOf",
"fhir:" + at.getName() + "." + cn);
at.getSection()
.triple("fhir:" + at.getName() + "." + en, "rdfs:domain", "fhir:" + at.getName());
genRange(at.getSection(), at.getName(), en, e, tr, at.isType());
}
} else {
at.getSection().triple("fhir:" + at.getName() + "." + e.getName(), "a", "rdf:Property");
at.getSection().comment("fhir:" + at.getName() + "." + e.getName(), e.getDefinition());
processMappings(at.getSection(), "fhir:" + at.getName() + "." + e.getName(), e);
at.getSection()
.triple(
"fhir:" + at.getName() + "." + e.getName(), "rdfs:domain", "fhir:" + at.getName());
genRange(
at.getSection(),
at.getName(),
e.getName(),
e,
e.getTypes().isEmpty() ? null : e.getTypes().get(0),
at.isType());
}
}
}
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();
}
private void genRange(
Section section, String tn, String en, ElementDefn e, TypeRef tr, boolean datatype)
throws Exception {
// metadata
if (e.isModifier())
section.triple(
"fhir:" + tn + "." + en, "fhir:hasFlag", complex().predicate("a", "fhir:isModifier"));
if (e.isXmlAttribute())
section.triple(
"fhir:" + tn + "." + en, "fhir:hasFlag", complex().predicate("a", "fhir:isXmlAtribute"));
if (e.hasMustSupport() && e.isMustSupport())
section.triple(
"fhir:" + tn + "." + en, "fhir:hasFlag", complex().predicate("a", "fhir:isMustSupport"));
if (e.hasSummaryItem() && e.isSummaryItem())
section.triple(
"fhir:" + tn + "." + en, "fhir:hasFlag", complex().predicate("a", "fhir:isSummaryItem"));
if (!Utilities.noString(e.getW5()))
section.triple(
"fhir:" + tn + "." + en, "fhir:w5", complex().predicate("a", "fhir:w5\\#" + e.getW5()));
if (e.hasMeaningWhenMissing())
section.triple(
"fhir:" + tn + "." + en, "fhir:missingMeaning", literal(e.getMeaningWhenMissing()));
// cardinality
cardinality(
section,
"fhir:" + tn + "." + en,
e.getMinCardinality().toString(),
e.getMaxCardinality() == Integer.MAX_VALUE ? "*" : e.getMaxCardinality().toString());
// section.triple("fhir:"+tn+"."+en, "fhir:minCardinality",
// literal(e.getMinCardinality().toString()));
// section.triple("fhir:"+tn+"."+en, "fhir:maxCardinality", literal(e.getMaxCardinality() ==
// Integer.MAX_VALUE ? "*" : e.getMaxCardinality().toString()));
// now in OWL:
if (e.getMinCardinality() > 0)
section.triple(
"fhir:" + tn,
"rdfs:subClassOf",
complex()
.predicate("a", "owl:Restriction")
.predicate("owl:onProperty", "fhir:" + tn + "." + en)
.predicate(
"owl:minCardinality",
literalTyped(e.getMinCardinality().toString(), "nonNegativeInteger")));
if (e.getMaxCardinality() < Integer.MAX_VALUE)
section.triple(
"fhir:" + tn,
"rdfs:subClassOf",
complex()
.predicate("a", "owl:Restriction")
.predicate("owl:onProperty", "fhir:" + tn + "." + en)
.predicate(
"owl:maxCardinality",
literalTyped(e.getMaxCardinality().toString(), "nonNegativeInteger")));
// define
if (tr == null) {
section.triple("fhir:" + tn + "." + en, "rdfs:range", "fhir:" + e.getDeclaredTypeName());
anonTypes.push(new AnonTypeInfo(section, e.getDeclaredTypeName(), e, datatype));
} else if (tr.getName().startsWith("@")) {
ElementDefn r = getElementForPath(tr.getName().substring(1));
section.triple("fhir:" + tn + "." + en, "rdfs:range", "fhir:" + r.getDeclaredTypeName());
} else {
if (e.hasBinding()) {
BindingSpecification bs = e.getBinding();
if (bs.getValueSet() != null) {
String bn = getPNameForUri(bs.getValueSet().getUrl());
section.triple("fhir:" + tn + "." + en, "rdfs:range", processType(tr.getName()));
section.triple("fhir:" + tn + "." + en, "fhir:binding", bn);
if (!bn.startsWith("vs:")) // a v3 valueset
valuesets.put(bn, bs.getValueSet());
} else if (!Utilities.noString(bs.getReference())) {
section.triple("fhir:" + tn + "." + en, "rdfs:range", processType(tr.getName()));
section.triple("fhir:" + tn + "." + en, "fhir:binding", "<" + bs.getReference() + ">");
}
// if (bs.hasMax())
// need to figure out how this should be represented in Turtle
section.triple(
"fhir:" + tn + "." + en,
"fhir:bindingStrength",
complex().predicate("a", "fhir:binding-strength\\#" + bs.getStrength().toCode()));
} else section.triple("fhir:" + tn + "." + en, "rdfs:range", processType(tr.getName()));
}
if (e.getDefaultValue() != null) {
if (e.getDefaultValue() instanceof DecimalType)
section.triple(
"fhir:" + tn + "." + en,
"fhir:default",
complex()
.predicate("a", "fhir:decimal")
.predicate(
"fhir:value", literal(((DecimalType) e.getDefaultValue()).asStringValue())));
else if (e.getDefaultValue() instanceof BooleanType)
section.triple(
"fhir:" + tn + "." + en,
"fhir:default",
complex()
.predicate("a", "fhir:boolean")
.predicate(
"fhir:value", literal(((BooleanType) e.getDefaultValue()).asStringValue())));
else if (e.getDefaultValue() instanceof IntegerType)
section.triple(
"fhir:" + tn + "." + en,
"fhir:default",
complex()
.predicate("a", "fhir:integer")
.predicate(
"fhir:value", literal(((IntegerType) e.getDefaultValue()).asStringValue())));
else if (e.getDefaultValue() instanceof CodeType)
section.triple(
"fhir:" + tn + "." + en,
"fhir:default",
complex()
.predicate("a", "fhir:integer")
.predicate(
"fhir:value", literal(((CodeType) e.getDefaultValue()).asStringValue())));
else
throw new Error(
"default of type " + e.getDefaultValue().getClass().getName() + " not handled yet");
}
}
private void gen(TypeDefn t) throws Exception {
Section section = section(t.getName());
if (t.getTypes().isEmpty()) section.triple("fhir:" + t.getName(), "a", "rdfs:Class");
else section.triple("fhir:" + t.getName(), "rdfs:subClassOf", "fhir:Element");
section.label("fhir:" + t.getName(), t.getShortDefn());
section.comment("fhir:" + t.getName(), t.getDefinition());
if (t.getName().equals("Reference"))
section.triple(
"fhir:" + t.getName(),
"a",
"fhir:Resource"); // This is so that a reference can be replaced by a direct reference to
// it's target
nilInstance.predicate("a", "fhir:" + t.getName());
processMappings(section, "fhir:" + t.getName(), t);
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.label("fhir:" + t.getName() + "." + cn, e.getShortDefn());
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:" + t.getName());
genRange(section, t.getName(), en, e, tr, true);
}
} 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:" + t.getName());
processMappings(section, "fhir:" + t.getName() + "." + e.getName(), e);
genRange(
section,
t.getName(),
e.getName(),
e,
e.getTypes().isEmpty() ? null : e.getTypes().get(0),
true);
}
}
processAnonTypes();
}