use of org.hl7.fhir.r4b.model.UriType in project org.hl7.fhir.core by hapifhir.
the class XLSXWriter method itemList.
private String itemList(List l) {
StringBuilder s = new StringBuilder();
for (int i = 0; i < l.size(); i++) {
Object o = l.get(i);
String val = "";
if (o instanceof StringType) {
val = ((StringType) o).getValue();
} else if (o instanceof UriType) {
val = ((UriType) o).getValue();
} else if (o instanceof IdType) {
val = ((IdType) o).getValue();
} else if (o instanceof Enumeration<?>) {
val = o.toString();
} else if (o instanceof TypeRefComponent) {
TypeRefComponent t = (TypeRefComponent) o;
val = t.getWorkingCode();
if (val == null)
val = "";
if (val.startsWith("http://hl7.org/fhir/StructureDefinition/"))
val = val.substring(40);
if (t.hasTargetProfile())
val = val + "(" + canonicalList(t.getTargetProfile()) + ")";
if (t.hasProfile())
val = val + " {" + canonicalList(t.getProfile()) + "}";
if (t.hasAggregation())
val = val + " <<" + aggList(t.getAggregation()) + ">>";
} else if (o instanceof Coding) {
Coding t = (Coding) o;
val = (t.getSystem() == null ? "" : t.getSystem()) + (t.getCode() == null ? "" : "#" + t.getCode()) + (t.getDisplay() == null ? "" : " (" + t.getDisplay() + ")");
} else if (o instanceof ElementDefinitionConstraintComponent) {
ElementDefinitionConstraintComponent c = (ElementDefinitionConstraintComponent) o;
val = c.getKey() + ":" + c.getHuman() + " {" + c.getExpression() + "}";
} else if (o instanceof ElementDefinitionSlicingDiscriminatorComponent) {
ElementDefinitionSlicingDiscriminatorComponent c = (ElementDefinitionSlicingDiscriminatorComponent) o;
val = c.getType().toCode() + ":" + c.getPath() + "}";
} else {
val = o.toString();
val = val.substring(val.indexOf("[") + 1);
val = val.substring(0, val.indexOf("]"));
}
s = s.append(val);
if (i == 0)
s.append("\n");
}
return s.toString();
}
use of org.hl7.fhir.r4b.model.UriType in project org.hl7.fhir.core by hapifhir.
the class QuestionnaireBuilder method selectTypes.
private void selectTypes(StructureDefinition profile, QuestionnaireItemComponent sub, TypeRefComponent t, List<QuestionnaireResponse.QuestionnaireResponseItemComponent> source, List<QuestionnaireResponse.QuestionnaireResponseItemComponent> dest) throws FHIRFormatError {
List<QuestionnaireResponse.QuestionnaireResponseItemComponent> temp = new ArrayList<QuestionnaireResponse.QuestionnaireResponseItemComponent>();
for (QuestionnaireResponse.QuestionnaireResponseItemComponent g : source) if (instanceOf(t, (Element) g.getUserData("object")))
temp.add(g);
for (QuestionnaireResponse.QuestionnaireResponseItemComponent g : temp) source.remove(g);
for (QuestionnaireResponse.QuestionnaireResponseItemComponent g : temp) {
// it should be empty
assert (g.getItem().size() == 0);
QuestionnaireResponse.QuestionnaireResponseItemComponent q = g.addItem();
q.setLinkId(g.getLinkId() + "._type");
q.setText("type");
QuestionnaireResponseItemAnswerComponent a = q.addAnswer();
if (t.hasTarget()) {
for (UriType u : t.getTargetProfile()) {
if (u.getValue().startsWith("http://hl7.org/fhir/StructureDefinition/")) {
Coding cc = new Coding();
a.setValue(cc);
cc.setCode(u.getValue().substring(40));
cc.setSystem("http://hl7.org/fhir/resource-types");
}
}
} else {
Coding cc = new Coding();
a.setValue(cc);
ProfileUtilities pu = new ProfileUtilities(context, null, null);
StructureDefinition ps = null;
if (t.hasProfile())
ps = pu.getProfile(profile, t.getProfile().get(0).getValue());
if (ps != null) {
cc.setCode(t.getProfile().get(0).getValue());
cc.setSystem("http://hl7.org/fhir/resource-types");
} else {
cc.setCode(t.getWorkingCode());
cc.setSystem("http://hl7.org/fhir/data-types");
}
}
// 1st: create the subgroup
QuestionnaireResponse.QuestionnaireResponseItemComponent subg = a.addItem();
dest.add(subg);
subg.setLinkId(sub.getLinkId());
subg.setText(sub.getText());
subg.setUserData("object", g.getUserData("object"));
}
}
use of org.hl7.fhir.r4b.model.UriType in project org.hl7.fhir.core by hapifhir.
the class QuestionnaireBuilder method makeTypeList.
private ValueSet makeTypeList(StructureDefinition profile, List<TypeRefComponent> types, String path) {
ValueSet vs = new ValueSet();
vs.setName("Type options for " + path);
vs.setDescription(vs.present());
vs.setStatus(PublicationStatus.ACTIVE);
vs.setExpansion(new ValueSetExpansionComponent());
vs.getExpansion().setIdentifier(Factory.createUUID());
vs.getExpansion().setTimestampElement(DateTimeType.now());
for (TypeRefComponent t : types) {
if (t.hasTarget()) {
for (UriType u : t.getTargetProfile()) {
if (u.getValue().startsWith("http://hl7.org/fhir/StructureDefinition/")) {
ValueSetExpansionContainsComponent cc = vs.getExpansion().addContains();
cc.setCode(u.getValue().substring(40));
cc.setSystem("http://hl7.org/fhir/resource-types");
cc.setDisplay(cc.getCode());
}
}
} else if (!t.hasProfile()) {
ValueSetExpansionContainsComponent cc = vs.getExpansion().addContains();
cc.setCode(t.getWorkingCode());
cc.setDisplay(t.getWorkingCode());
cc.setSystem("http://hl7.org/fhir/data-types");
} else
for (UriType u : t.getProfile()) {
ProfileUtilities pu = new ProfileUtilities(context, null, null);
StructureDefinition ps = pu.getProfile(profile, u.getValue());
if (ps != null) {
ValueSetExpansionContainsComponent cc = vs.getExpansion().addContains();
cc.setCode(u.getValue());
cc.setDisplay(ps.getType());
cc.setSystem("http://hl7.org/fhir/resource-types");
}
}
}
return vs;
}
use of org.hl7.fhir.r4b.model.UriType in project org.hl7.fhir.core by hapifhir.
the class StructureMapUtilities method parseConceptMap.
private void parseConceptMap(StructureMap result, FHIRLexer lexer) throws FHIRLexerException {
lexer.token("conceptmap");
ConceptMap map = new ConceptMap();
String id = lexer.readConstant("map id");
if (id.startsWith("#")) {
throw lexer.error("Concept Map identifier must start with #");
}
map.setId(id);
// todo: how to add this to the text format
map.setStatus(PublicationStatus.DRAFT);
result.getContained().add(map);
lexer.token("{");
// lexer.token("source");
// map.setSource(new UriType(lexer.readConstant("source")));
// lexer.token("target");
// map.setSource(new UriType(lexer.readConstant("target")));
Map<String, String> prefixes = new HashMap<String, String>();
while (lexer.hasToken("prefix")) {
lexer.token("prefix");
String n = lexer.take();
lexer.token("=");
String v = lexer.readConstant("prefix url");
prefixes.put(n, v);
}
while (lexer.hasToken("unmapped")) {
lexer.token("unmapped");
lexer.token("for");
String n = readPrefix(prefixes, lexer);
ConceptMapGroupComponent g = getGroup(map, n, null);
lexer.token("=");
String v = lexer.take();
if (v.equals("provided")) {
g.getUnmapped().setMode(ConceptMapGroupUnmappedMode.PROVIDED);
} else {
throw lexer.error("Only unmapped mode PROVIDED is supported at this time");
}
}
while (!lexer.hasToken("}")) {
String srcs = readPrefix(prefixes, lexer);
lexer.token(":");
String sc = lexer.getCurrent().startsWith("\"") ? lexer.readConstant("code") : lexer.take();
ConceptMapEquivalence eq = readEquivalence(lexer);
String tgts = (eq != ConceptMapEquivalence.UNMATCHED) ? readPrefix(prefixes, lexer) : "";
ConceptMapGroupComponent g = getGroup(map, srcs, tgts);
SourceElementComponent e = g.addElement();
e.setCode(sc);
if (e.getCode().startsWith("\"")) {
e.setCode(lexer.processConstant(e.getCode()));
}
TargetElementComponent tgt = e.addTarget();
tgt.setEquivalence(eq);
if (tgt.getEquivalence() != ConceptMapEquivalence.UNMATCHED) {
lexer.token(":");
tgt.setCode(lexer.take());
if (tgt.getCode().startsWith("\"")) {
tgt.setCode(lexer.processConstant(tgt.getCode()));
}
}
tgt.setComment(lexer.getFirstComment());
}
lexer.token("}");
}
use of org.hl7.fhir.r4b.model.UriType in project org.hl7.fhir.core by hapifhir.
the class ProfileUtilities method generateSnapshot.
/**
* Given a base (snapshot) profile structure, and a differential profile, generate a new snapshot profile
*
* @param base - the base structure on which the differential will be applied
* @param differential - the differential to apply to the base
* @param url - where the base has relative urls for profile references, these need to be converted to absolutes by prepending this URL (e.g. the canonical URL)
* @param webUrl - where the base has relative urls in markdown, these need to be converted to absolutes by prepending this URL (this is not the same as the canonical URL)
* @param trimDifferential - if this is true, then the snap short generator will remove any material in the element definitions that is not different to the base
* @return
* @throws FHIRException
* @throws DefinitionException
* @throws Exception
*/
public void generateSnapshot(StructureDefinition base, StructureDefinition derived, String url, String webUrl, String profileName) throws DefinitionException, FHIRException {
if (base == null) {
throw new DefinitionException(context.formatMessage(I18nConstants.NO_BASE_PROFILE_PROVIDED));
}
if (derived == null) {
throw new DefinitionException(context.formatMessage(I18nConstants.NO_DERIVED_STRUCTURE_PROVIDED));
}
checkNotGenerating(base, "Base for generating a snapshot for the profile " + derived.getUrl());
checkNotGenerating(derived, "Focus for generating a snapshot");
if (!base.hasType()) {
throw new DefinitionException(context.formatMessage(I18nConstants.BASE_PROFILE__HAS_NO_TYPE, base.getUrl()));
}
if (!derived.hasType()) {
throw new DefinitionException(context.formatMessage(I18nConstants.DERIVED_PROFILE__HAS_NO_TYPE, derived.getUrl()));
}
if (!derived.hasDerivation()) {
throw new DefinitionException(context.formatMessage(I18nConstants.DERIVED_PROFILE__HAS_NO_DERIVATION_VALUE_AND_SO_CANT_BE_PROCESSED, derived.getUrl()));
}
if (!base.getType().equals(derived.getType()) && derived.getDerivation() == TypeDerivationRule.CONSTRAINT) {
throw new DefinitionException(context.formatMessage(I18nConstants.BASE__DERIVED_PROFILES_HAVE_DIFFERENT_TYPES____VS___, base.getUrl(), base.getType(), derived.getUrl(), derived.getType()));
}
if (snapshotStack.contains(derived.getUrl())) {
throw new DefinitionException(context.formatMessage(I18nConstants.CIRCULAR_SNAPSHOT_REFERENCES_DETECTED_CANNOT_GENERATE_SNAPSHOT_STACK__, snapshotStack.toString()));
}
derived.setUserData("profileutils.snapshot.generating", true);
snapshotStack.add(derived.getUrl());
try {
if (!Utilities.noString(webUrl) && !webUrl.endsWith("/"))
webUrl = webUrl + '/';
if (defWebRoot == null)
defWebRoot = webUrl;
derived.setSnapshot(new StructureDefinitionSnapshotComponent());
try {
checkDifferential(derived.getDifferential().getElement(), typeName(derived.getType()), derived.getUrl());
checkDifferentialBaseType(derived);
// so we have two lists - the base list, and the differential list
// the differential list is only allowed to include things that are in the base list, but
// is allowed to include them multiple times - thereby slicing them
// our approach is to walk through the base list, and see whether the differential
// says anything about them.
int baseCursor = 0;
// we need a diff cursor because we can only look ahead, in the bound scoped by longer paths
int diffCursor = 0;
for (ElementDefinition e : derived.getDifferential().getElement()) e.clearUserData(GENERATED_IN_SNAPSHOT);
// we actually delegate the work to a subroutine so we can re-enter it with a different cursors
// we make a copy here because we're sometimes going to hack the differential while processing it. Have to migrate user data back afterwards
StructureDefinitionDifferentialComponent diff = cloneDiff(derived.getDifferential());
StructureDefinitionSnapshotComponent baseSnapshot = base.getSnapshot();
if (derived.getDerivation() == TypeDerivationRule.SPECIALIZATION) {
String derivedType = derived.getType();
if (StructureDefinitionKind.LOGICAL.equals(derived.getKind()) && derived.getType().contains("/")) {
derivedType = derivedType.substring(derivedType.lastIndexOf("/") + 1);
}
baseSnapshot = cloneSnapshot(baseSnapshot, base.getType(), derivedType);
}
// if (derived.getId().equals("2.16.840.1.113883.10.20.22.2.1.1")) {
// debug = true;
// }
processPaths("", derived.getSnapshot(), baseSnapshot, diff, baseCursor, diffCursor, baseSnapshot.getElement().size() - 1, derived.getDifferential().hasElement() ? derived.getDifferential().getElement().size() - 1 : -1, url, webUrl, derived.present(), null, null, false, base.getUrl(), null, false, null, null, new ArrayList<ElementRedirection>(), base);
checkGroupConstraints(derived);
if (derived.getDerivation() == TypeDerivationRule.SPECIALIZATION) {
for (ElementDefinition e : diff.getElement()) {
if (!e.hasUserData(GENERATED_IN_SNAPSHOT)) {
ElementDefinition outcome = updateURLs(url, webUrl, e.copy());
e.setUserData(GENERATED_IN_SNAPSHOT, outcome);
derived.getSnapshot().addElement(outcome);
}
}
}
if (derived.getKind() != StructureDefinitionKind.LOGICAL && !derived.getSnapshot().getElementFirstRep().getType().isEmpty())
throw new Error(context.formatMessage(I18nConstants.TYPE_ON_FIRST_SNAPSHOT_ELEMENT_FOR__IN__FROM_, derived.getSnapshot().getElementFirstRep().getPath(), derived.getUrl(), base.getUrl()));
updateMaps(base, derived);
setIds(derived, false);
if (debug) {
System.out.println("Differential: ");
for (ElementDefinition ed : derived.getDifferential().getElement()) System.out.println(" " + ed.getId() + " : " + typeSummaryWithProfile(ed) + "[" + ed.getMin() + ".." + ed.getMax() + "]" + sliceSummary(ed) + " " + constraintSummary(ed));
System.out.println("Snapshot: ");
for (ElementDefinition ed : derived.getSnapshot().getElement()) System.out.println(" " + ed.getId() + " : " + typeSummaryWithProfile(ed) + "[" + ed.getMin() + ".." + ed.getMax() + "]" + sliceSummary(ed) + " " + constraintSummary(ed));
}
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
// Check that all differential elements have a corresponding snapshot element
int ce = 0;
for (ElementDefinition e : diff.getElement()) {
if (!e.hasUserData("diff-source"))
throw new Error(context.formatMessage(I18nConstants.UNXPECTED_INTERNAL_CONDITION__NO_SOURCE_ON_DIFF_ELEMENT));
else {
if (e.hasUserData(DERIVATION_EQUALS))
((Base) e.getUserData("diff-source")).setUserData(DERIVATION_EQUALS, e.getUserData(DERIVATION_EQUALS));
if (e.hasUserData(DERIVATION_POINTER))
((Base) e.getUserData("diff-source")).setUserData(DERIVATION_POINTER, e.getUserData(DERIVATION_POINTER));
}
if (!e.hasUserData(GENERATED_IN_SNAPSHOT)) {
b.append(e.hasId() ? "id: " + e.getId() : "path: " + e.getPath());
ce++;
if (e.hasId()) {
String msg = "No match found in the generated snapshot: check that the path and definitions are legal in the differential (including order)";
messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url + "#" + e.getId(), msg, ValidationMessage.IssueSeverity.ERROR));
}
}
}
if (!Utilities.noString(b.toString())) {
String msg = "The profile " + derived.getUrl() + " has " + ce + " " + Utilities.pluralize("element", ce) + " in the differential (" + b.toString() + ") that don't have a matching element in the snapshot: check that the path and definitions are legal in the differential (including order)";
System.out.println("Error in snapshot generation: " + msg);
if (!debug) {
System.out.println("Differential: ");
for (ElementDefinition ed : derived.getDifferential().getElement()) System.out.println(" " + ed.getId() + " = " + ed.getPath() + " : " + typeSummaryWithProfile(ed) + "[" + ed.getMin() + ".." + ed.getMax() + "]" + sliceSummary(ed) + " " + constraintSummary(ed));
System.out.println("Snapshot: ");
for (ElementDefinition ed : derived.getSnapshot().getElement()) System.out.println(" " + ed.getId() + " = " + ed.getPath() + " : " + typeSummaryWithProfile(ed) + "[" + ed.getMin() + ".." + ed.getMax() + "]" + sliceSummary(ed) + " " + constraintSummary(ed));
}
if (exception)
throw new DefinitionException(msg);
else
messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url, msg, ValidationMessage.IssueSeverity.ERROR));
}
// hack around a problem in R4 definitions (somewhere?)
for (ElementDefinition ed : derived.getSnapshot().getElement()) {
for (ElementDefinitionMappingComponent mm : ed.getMapping()) {
if (mm.hasMap()) {
mm.setMap(mm.getMap().trim());
}
}
for (ElementDefinitionConstraintComponent s : ed.getConstraint()) {
if (s.hasSource()) {
String ref = s.getSource();
if (!Utilities.isAbsoluteUrl(ref)) {
if (ref.contains(".")) {
s.setSource("http://hl7.org/fhir/StructureDefinition/" + ref.substring(0, ref.indexOf(".")) + "#" + ref);
} else {
s.setSource("http://hl7.org/fhir/StructureDefinition/" + ref);
}
}
}
}
}
if (derived.getDerivation() == TypeDerivationRule.SPECIALIZATION) {
for (ElementDefinition ed : derived.getSnapshot().getElement()) {
if (!ed.hasBase()) {
ed.getBase().setPath(ed.getPath()).setMin(ed.getMin()).setMax(ed.getMax());
}
}
}
// last, check for wrong profiles or target profiles
for (ElementDefinition ed : derived.getSnapshot().getElement()) {
for (TypeRefComponent t : ed.getType()) {
for (UriType u : t.getProfile()) {
StructureDefinition sd = context.fetchResource(StructureDefinition.class, u.getValue());
if (sd == null) {
if (xver != null && xver.matchingUrl(u.getValue()) && xver.status(u.getValue()) == XVerExtensionStatus.Valid) {
sd = xver.makeDefinition(u.getValue());
}
}
if (sd == null) {
if (messages != null) {
messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url + "#" + ed.getId(), "The type of profile " + u.getValue() + " cannot be checked as the profile is not known", IssueSeverity.WARNING));
}
} else {
String wt = t.getWorkingCode();
if (ed.getPath().equals("Bundle.entry.response.outcome")) {
wt = "OperationOutcome";
}
if (!sd.getType().equals(wt)) {
boolean ok = isCompatibleType(wt, sd);
if (!ok) {
String smsg = "The profile " + u.getValue() + " has type " + sd.getType() + " which is not consistent with the stated type " + wt;
if (exception)
throw new DefinitionException(smsg);
else
messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url + "#" + ed.getId(), smsg, IssueSeverity.ERROR));
}
}
}
}
}
}
} catch (Exception e) {
// if we had an exception generating the snapshot, make sure we don't leave any half generated snapshot behind
derived.setSnapshot(null);
derived.clearUserData("profileutils.snapshot.generating");
throw e;
}
} finally {
derived.clearUserData("profileutils.snapshot.generating");
snapshotStack.remove(derived.getUrl());
}
}
Aggregations