use of org.hl7.fhir.definitions.model.Invariant in project kindling by HL7.
the class OldSpreadsheetParser method parseCommonTypeColumns.
private ResourceDefn parseCommonTypeColumns(boolean isResource, boolean isTemplate) throws Exception {
ResourceDefn resource = new ResourceDefn();
resource.setInterface(isTemplate);
Sheet sheet = loadSheet("Bindings");
if (sheet != null)
readBindings(sheet);
sheet = loadSheet("Invariants");
Map<String, Invariant> invariants = null;
if (sheet != null)
invariants = readInvariants(sheet, title, "Invariants");
sheet = loadSheet("Data Elements");
if (sheet == null)
throw new Exception("No Sheet found for Data Elements");
for (int row = 0; row < sheet.rows.size(); row++) {
processLine(resource, sheet, row, invariants, false, null, row == 0);
}
// default...
StandardsStatus ss = StandardsStatus.TRIAL_USE;
String s = ini.getStringProperty("normative", resource.getName());
if (!Utilities.noString(s))
ss = StandardsStatus.NORMATIVE;
resource.setStatus(ss);
resource.setRequirements(resource.getRoot().getRequirements());
resource.addHints(checkIgnoredColumns(sheet));
if (template != null) {
resource.setTemplate(template.getRoot());
copySearchParameters(resource);
copyInvariants(resource);
template = null;
}
parseMetadata(resource);
if (invariants != null) {
for (Invariant inv : invariants.values()) {
if (Utilities.noString(inv.getContext()))
throw new Exception("Type " + resource.getRoot().getName() + " Invariant " + inv.getId() + " has no context");
else {
ElementDefn ed = findContext(resource.getRoot(), inv.getContext(), "Type " + resource.getRoot().getName() + " Invariant " + inv.getId() + " Context");
if (ed.getName().endsWith("[x]") && !inv.getContext().endsWith("[x]"))
inv.setFixedName(inv.getContext().substring(inv.getContext().lastIndexOf(".") + 1));
ed.getInvariants().put(inv.getId(), inv);
if (Utilities.noString(inv.getXpath())) {
throw new Exception("Type " + resource.getRoot().getName() + " Invariant " + inv.getId() + " (" + inv.getEnglish() + ") has no XPath statement");
} else if (inv.getXpath().contains("\""))
throw new Exception("Type " + resource.getRoot().getName() + " Invariant " + inv.getId() + " (" + inv.getEnglish() + ") contains a \" character");
if (Utilities.noString(inv.getExpression())) {
// This has been disabled for now, per Lloyd McKenzie's request via Skype - jamesagnew
// throw new Exception("Type "+resource.getRoot().getName()+" Invariant "+inv.getId()+" ("+inv.getEnglish()+") has no Expression statement (in FHIRPath format)");
} else {
fpUsages.add(new FHIRPathUsage(inv.getContext(), isResource ? resource.getName() : "DomainResource", inv.getContext(), null, inv.getExpression(), inv.getXpath()));
}
}
}
}
// EK: Future types. But those won't get there.
if (bindings != null)
resource.getRoot().getNestedBindings().putAll(bindings);
scanNestedTypes(resource, resource.getRoot(), resource.getName());
resolveElementReferences(resource, resource.getRoot());
resource.getRoot().setAbstractType(isAbstract);
return resource;
}
use of org.hl7.fhir.definitions.model.Invariant in project kindling by HL7.
the class SourceParser method loadCompositeType.
private String loadCompositeType(String n, Map<String, org.hl7.fhir.definitions.model.TypeDefn> map, String fmm, boolean isAbstract) throws Exception {
TypeParser tp = new TypeParser(version.toString());
List<TypeRef> ts = tp.parse(n, false, null, context, true);
definitions.getKnownTypes().addAll(ts);
StandardsStatus status = loadStatus(n);
String nv = loadNormativeVersion(n);
try {
TypeRef t = ts.get(0);
File csv = new CSFile(dtDir + t.getName().toLowerCase() + ".xml");
if (csv.exists()) {
OldSpreadsheetParser p = new OldSpreadsheetParser("core", new CSFileInputStream(csv), csv.getName(), csv.getAbsolutePath(), definitions, srcDir, logger, registry, version, context, genDate, isAbstract, page, true, ini, wg("fhir"), definitions.getProfileIds(), fpUsages, page.getConceptMaps(), exceptionIfExcelNotNormalised, page.packageInfo(), page.getRc());
org.hl7.fhir.definitions.model.TypeDefn el = p.parseCompositeType();
el.setFmmLevel(fmm);
el.setStandardsStatus(status);
el.setNormativeVersion(nv);
map.put(t.getName(), el);
genTypeProfile(el);
errors.addAll(p.getErrors());
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());
new XLSXmlNormaliser(csv.getAbsolutePath(), exceptionIfExcelNotNormalised).go();
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"));
inv.setExpression(sheet.getColumn(i, "Expression"));
inv.setExplanation(sheet.getColumn(i, "Explanation"));
inv.setTurtle(sheet.getColumn(i, "RDF"));
ProfiledType pt = new ProfiledType();
pt.setDefinition(sheet.getColumn(i, "Definition"));
pt.setDescription(sheet.getColumn(i, "Rules"));
String structure = sheet.getColumn(i, "Structure");
if (!Utilities.noString(structure)) {
String[] parts = structure.split("\\;");
for (String pp : parts) {
String[] words = pp.split("\\=");
pt.getRules().put(words[0], words[1]);
}
}
pt.setName(n);
pt.setBaseType(p);
pt.setInvariant(inv);
definitions.getConstraints().put(n, pt);
}
}
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);
}
}
use of org.hl7.fhir.definitions.model.Invariant in project kindling by HL7.
the class ResourceParser method parseED.
private void parseED(ProfileUtilities pu, ElementDefn ed, ElementDefinition focus, StructureDefinition sd, String parentName) throws IOException {
ed.setMinCardinality(focus.getMin());
ed.setMaxCardinality("*".equals(focus.getMax()) ? Integer.MAX_VALUE : Integer.parseInt(focus.getMax()));
ed.setIsModifier(focus.getIsModifier());
ed.setModifierReason(focus.getIsModifierReason());
ed.setMustSupport(focus.getMustSupport());
ed.setSummaryItem(focus.getIsSummary());
ed.setRegex(ToolingExtensions.readStringExtension(focus, ToolingExtensions.EXT_REGEX));
ed.setXmlAttribute(focus.hasRepresentation(PropertyRepresentation.XMLATTR));
if (ToolingExtensions.hasExtension(focus, BuildExtensions.EXT_UML_DIR)) {
ed.setUmlDir(ToolingExtensions.readStringExtension(focus, BuildExtensions.EXT_UML_DIR));
}
if (ToolingExtensions.hasExtension(focus, BuildExtensions.EXT_UML_BREAK)) {
ed.setUmlBreak(ToolingExtensions.readBoolExtension(focus, BuildExtensions.EXT_UML_BREAK));
}
if (BuildExtensions.hasExtension(focus, BuildExtensions.EXT_SVG)) {
String svg = BuildExtensions.readStringExtension(focus, BuildExtensions.EXT_SVG);
if (svg.contains("w=")) {
ed.setSvgWidth(Integer.parseInt(svg.substring(svg.indexOf("w=") + 2)));
svg = svg.substring(0, svg.indexOf(";"));
}
ed.setSvgLeft(Integer.parseInt(svg.substring(0, svg.indexOf(","))));
ed.setSvgTop(Integer.parseInt(svg.substring(svg.indexOf(",") + 1)));
}
ed.setName(tail(focus.getPath()));
ed.setShortDefn(focus.getShort());
ed.setDefinition(focus.getDefinition());
ed.setRequirements(focus.getRequirements());
ed.setComments(focus.getComment());
if (BuildExtensions.hasExtension(focus, BuildExtensions.EXT_TODO)) {
ed.setTodo(BuildExtensions.readStringExtension(focus, BuildExtensions.EXT_TODO));
}
if (BuildExtensions.hasExtension(focus, BuildExtensions.EXT_COMMITTEE_NOTES)) {
ed.setCommitteeNotes(BuildExtensions.readStringExtension(focus, BuildExtensions.EXT_COMMITTEE_NOTES));
}
if (BuildExtensions.hasExtension(focus, BuildExtensions.EXT_HINT)) {
ed.setDisplayHint(BuildExtensions.readStringExtension(focus, BuildExtensions.EXT_HINT));
}
if (focus.hasExtension(BuildExtensions.EXT_NO_BINDING)) {
ed.setNoBindingAllowed(focus.getExtensionString(BuildExtensions.EXT_NO_BINDING).equals("true"));
}
for (StringType t : focus.getAlias()) {
ed.getAliases().add(t.getValue());
}
if (focus.hasMaxLength()) {
ed.setMaxLength(Integer.toString(focus.getMaxLength()));
}
ed.setExample(focus.getExampleFirstRep().getValue());
ed.setMeaningWhenMissing(focus.getMeaningWhenMissing());
if (ToolingExtensions.hasExtension(focus, BuildExtensions.EXT_TRANSLATABLE)) {
ed.setTranslatable(ToolingExtensions.readBoolExtension(focus, BuildExtensions.EXT_TRANSLATABLE));
}
ed.setOrderMeaning(focus.getOrderMeaning());
if (BuildExtensions.hasExtension(focus, BuildExtensions.EXT_STANDARDS_STATUS)) {
ed.setStandardsStatus(StandardsStatus.fromCode(BuildExtensions.readStringExtension(focus, BuildExtensions.EXT_STANDARDS_STATUS)));
}
if (BuildExtensions.hasExtension(focus, BuildExtensions.EXT_NORMATIVE_VERSION)) {
ed.setNormativeVersion(BuildExtensions.readStringExtension(focus, BuildExtensions.EXT_NORMATIVE_VERSION));
}
for (ElementDefinitionConstraintComponent cst : focus.getConstraint()) {
Invariant inv = new Invariant();
inv.setContext(focus.getPath());
inv.setEnglish(cst.getHuman());
if (cst.hasExtension(BuildExtensions.EXT_OCL)) {
inv.setOcl(cst.getExtensionString(BuildExtensions.EXT_OCL));
}
inv.setXpath(cst.getXpath());
inv.setId(cst.getKey());
if (cst.hasExtension(BuildExtensions.EXT_FIXED_NAME)) {
inv.setFixedName(cst.getExtensionString(BuildExtensions.EXT_FIXED_NAME));
}
inv.setSeverity(cst.getSeverity().toCode());
if (cst.hasExtension(BuildExtensions.EXT_BEST_PRACTICE)) {
inv.setSeverity("best-practice");
}
if (cst.hasExtension(BuildExtensions.EXT_TURTLE)) {
inv.setTurtle(cst.getExtensionString(BuildExtensions.EXT_TURTLE));
}
inv.setRequirements(cst.getRequirements());
inv.setExpression(cst.getExpression());
if (cst.hasExtension(BuildExtensions.EXT_BEST_PRACTICE_EXPLANATION)) {
inv.setExplanation(cst.getExtensionString(BuildExtensions.EXT_BEST_PRACTICE_EXPLANATION));
}
ed.getInvariants().put(inv.getId(), inv);
invariants.put(inv.getId(), inv);
}
for (IdType cnd : focus.getCondition()) {
Invariant inv = invariants.get(cnd.primitiveValue());
if (inv == null) {
System.out.println("Unable to find invariant " + cnd.primitiveValue());
} else {
ed.getStatedInvariants().add(inv);
}
}
for (ElementDefinitionMappingComponent map : focus.getMapping()) {
String uri = getMappingUri(sd, map.getIdentity());
if ("http://hl7.org/fhir/fivews".equals(uri)) {
ed.setW5(reverseW5(map.getMap()));
} else {
ed.getMappings().put(uri, map.getMap());
}
}
if (focus.hasContentReference()) {
ed.getTypes().add(new TypeRef("@" + focus.getContentReference().substring(1)));
} else {
for (TypeRefComponent tr : focus.getType()) {
if (!Utilities.existsInList(tr.getCode(), "Element", "BackboneElement")) {
TypeRef t = new TypeRef();
ed.getTypes().add(t);
if (tr.hasExtension("http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type")) {
t.setName(tr.getExtensionString("http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type"));
} else {
t.setName(tr.getCode());
}
if (ToolingExtensions.hasExtension(tr, BuildExtensions.EXT_HIERARCHY)) {
ed.setHierarchy(ToolingExtensions.readBoolExtension(tr, BuildExtensions.EXT_HIERARCHY));
}
for (CanonicalType u : tr.getProfile()) {
t.setProfile(u.getValue().replace("http://hl7.org/fhir/StructureDefinition/", ""));
}
for (CanonicalType u : tr.getTargetProfile()) {
String s = u.getValue().replace("http://hl7.org/fhir/StructureDefinition/", "");
if ("Resource".equals(s)) {
t.getParams().add("Any");
} else {
t.getParams().add(s);
}
}
if (t.getName().equals("Quantity") && "SimpleQuantity".equals(t.getProfile())) {
t.setName("SimpleQuantity");
t.setProfile(null);
}
if ("Resource".equals(t.getProfile())) {
t.setProfile("Any");
}
if (t.getParams().toString().equals("[ActivityDefinition, EventDefinition, EvidenceVariable, Measure, OperationDefinition, PlanDefinition, Questionnaire, SubscriptionTopic]")) {
t.getParams().clear();
t.getParams().add("Definition");
}
}
}
if (ed.getTypes().size() == STAR_TYPES_COUNT) {
ed.getTypes().clear();
ed.getTypes().add(new TypeRef("*"));
}
}
String name = parentName + Utilities.capitalize(ed.getName());
if (focus.hasExtension("http://hl7.org/fhir/StructureDefinition/structuredefinition-explicit-type-name")) {
ed.setStatedType(focus.getExtensionString("http://hl7.org/fhir/StructureDefinition/structuredefinition-explicit-type-name"));
ed.setDeclaredTypeName(ed.getStatedType());
} else if (ed.getTypes().isEmpty() && !focus.hasContentReference()) {
ed.setDeclaredTypeName(name + "Component");
}
if (focus.hasBinding()) {
ed.setBinding(parseBinding(focus.getBinding()));
}
for (ElementDefinition child : pu.getChildList(sd, focus, true, false)) {
ElementDefn c = new ElementDefn();
ed.getElements().add(c);
parseED(pu, c, child, sd, name);
}
// todo:
// private ElementDefinition derivation;
}
use of org.hl7.fhir.definitions.model.Invariant in project kindling by HL7.
the class XmlSpecGenerator method getInvariants.
private String getInvariants(ElementDefn elem) {
StringBuilder b = new StringBuilder();
boolean first = true;
for (Invariant i : elem.getStatedInvariants()) {
if (!first)
b.append("; ");
first = false;
b.append(i.getId() + ": " + i.getEnglish());
}
return b.toString();
}
use of org.hl7.fhir.definitions.model.Invariant in project kindling by HL7.
the class JsonSpecGenerator method getInvariants.
private String getInvariants(ElementDefn elem) {
StringBuilder b = new StringBuilder();
boolean first = true;
for (Invariant i : elem.getStatedInvariants()) {
if (!first)
b.append("; ");
first = false;
b.append(i.getId() + ": " + i.getEnglish());
}
return b.toString();
}
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