Example 21 with StructureDefinitionSnapshotComponent
use of org.hl7.fhir.r4b.model.StructureDefinition.StructureDefinitionSnapshotComponent 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
* @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 profileName) throws DefinitionException, FHIRException {
if (base == null)
throw new DefinitionException("no base profile provided");
if (derived == null)
throw new DefinitionException("no derived structure provided");
if (snapshotStack.contains(derived.getUrl()))
throw new DefinitionException("Circular snapshot references detected; cannot generate snapshot (stack = " + snapshotStack.toString() + ")");
snapshotStack.add(derived.getUrl());
derived.setSnapshot(new StructureDefinitionSnapshotComponent());
// 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;
if (derived.hasDifferential() && !derived.getDifferential().getElementFirstRep().getPath().contains(".") && !derived.getDifferential().getElementFirstRep().getType().isEmpty())
throw new Error("type on first differential element!");
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
processPaths("", derived.getSnapshot(), base.getSnapshot(), derived.getDifferential(), baseCursor, diffCursor, base.getSnapshot().getElement().size() - 1, derived.getDifferential().hasElement() ? derived.getDifferential().getElement().size() - 1 : -1, url, derived.getId(), null, null, false, base.getUrl(), null, false);
if (!derived.getSnapshot().getElementFirstRep().getType().isEmpty())
throw new Error("type on first snapshot element for " + derived.getSnapshot().getElementFirstRep().getPath() + " in " + derived.getUrl() + " from " + base.getUrl());
updateMaps(base, derived);
setIds(derived, false);
// Check that all differential elements have a corresponding snapshot element
for (ElementDefinition e : derived.getDifferential().getElement()) {
if (!e.hasUserData(GENERATED_IN_SNAPSHOT)) {
System.out.println("Error in snapshot generation: Snapshot for " + derived.getUrl() + " does not contain differential element with id: " + e.getId());
System.out.println("Differential: ");
for (ElementDefinition ed : derived.getDifferential().getElement()) System.out.println(" " + ed.getPath() + " : " + typeSummary(ed) + "[" + ed.getMin() + ".." + ed.getMax() + "]" + sliceSummary(ed) + " id = " + ed.getId());
System.out.println("Snapshot: ");
for (ElementDefinition ed : derived.getSnapshot().getElement()) System.out.println(" " + ed.getPath() + " : " + typeSummary(ed) + "[" + ed.getMin() + ".." + ed.getMax() + "]" + sliceSummary(ed) + " id = " + ed.getId());
throw new DefinitionException("Snapshot for " + derived.getUrl() + " does not contain differential element with id: " + e.getId());
// System.out.println("**BAD Differential element: " + profileName + ":" + e.getId());
}
}
}
Also used :
StructureDefinitionSnapshotComponent(org.hl7.fhir.dstu3.model.StructureDefinition.StructureDefinitionSnapshotComponent)
FHIRFormatError(org.hl7.fhir.exceptions.FHIRFormatError)
DefinitionException(org.hl7.fhir.exceptions.DefinitionException)
ElementDefinition(org.hl7.fhir.dstu3.model.ElementDefinition)
Example 22 with StructureDefinitionSnapshotComponent
use of org.hl7.fhir.r4b.model.StructureDefinition.StructureDefinitionSnapshotComponent in project org.hl7.fhir.core by hapifhir.
the class StructureDefinition method setProperty.
@Override
public Base setProperty(String name, Base value) throws FHIRException {
if (name.equals("url")) {
// UriType
this.url = castToUri(value);
} else if (name.equals("identifier")) {
this.getIdentifier().add(castToIdentifier(value));
} else if (name.equals("version")) {
// StringType
this.version = castToString(value);
} else if (name.equals("name")) {
// StringType
this.name = castToString(value);
} else if (name.equals("title")) {
// StringType
this.title = castToString(value);
} else if (name.equals("status")) {
value = new PublicationStatusEnumFactory().fromType(castToCode(value));
// Enumeration<PublicationStatus>
this.status = (Enumeration) value;
} else if (name.equals("experimental")) {
// BooleanType
this.experimental = castToBoolean(value);
} else if (name.equals("date")) {
// DateTimeType
this.date = castToDateTime(value);
} else if (name.equals("publisher")) {
// StringType
this.publisher = castToString(value);
} else if (name.equals("contact")) {
this.getContact().add(castToContactDetail(value));
} else if (name.equals("description")) {
// MarkdownType
this.description = castToMarkdown(value);
} else if (name.equals("useContext")) {
this.getUseContext().add(castToUsageContext(value));
} else if (name.equals("jurisdiction")) {
this.getJurisdiction().add(castToCodeableConcept(value));
} else if (name.equals("purpose")) {
// MarkdownType
this.purpose = castToMarkdown(value);
} else if (name.equals("copyright")) {
// MarkdownType
this.copyright = castToMarkdown(value);
} else if (name.equals("keyword")) {
this.getKeyword().add(castToCoding(value));
} else if (name.equals("fhirVersion")) {
// IdType
this.fhirVersion = castToId(value);
} else if (name.equals("mapping")) {
this.getMapping().add((StructureDefinitionMappingComponent) value);
} else if (name.equals("kind")) {
value = new StructureDefinitionKindEnumFactory().fromType(castToCode(value));
// Enumeration<StructureDefinitionKind>
this.kind = (Enumeration) value;
} else if (name.equals("abstract")) {
// BooleanType
this.abstract_ = castToBoolean(value);
} else if (name.equals("contextType")) {
value = new ExtensionContextEnumFactory().fromType(castToCode(value));
// Enumeration<ExtensionContext>
this.contextType = (Enumeration) value;
} else if (name.equals("context")) {
this.getContext().add(castToString(value));
} else if (name.equals("contextInvariant")) {
this.getContextInvariant().add(castToString(value));
} else if (name.equals("type")) {
// CodeType
this.type = castToCode(value);
} else if (name.equals("baseDefinition")) {
// UriType
this.baseDefinition = castToUri(value);
} else if (name.equals("derivation")) {
value = new TypeDerivationRuleEnumFactory().fromType(castToCode(value));
// Enumeration<TypeDerivationRule>
this.derivation = (Enumeration) value;
} else if (name.equals("snapshot")) {
// StructureDefinitionSnapshotComponent
this.snapshot = (StructureDefinitionSnapshotComponent) value;
} else if (name.equals("differential")) {
// StructureDefinitionDifferentialComponent
this.differential = (StructureDefinitionDifferentialComponent) value;
} else
return super.setProperty(name, value);
return value;
}
Also used :
PublicationStatusEnumFactory(org.hl7.fhir.dstu3.model.Enumerations.PublicationStatusEnumFactory)
Example 23 with StructureDefinitionSnapshotComponent
use of org.hl7.fhir.r4b.model.StructureDefinition.StructureDefinitionSnapshotComponent in project org.hl7.fhir.core by hapifhir.
the class ProfileUtilities method processPaths.
/**
* @param trimDifferential
* @throws DefinitionException, FHIRException
* @throws Exception
*/
private void processPaths(StructureDefinitionSnapshotComponent result, StructureDefinitionSnapshotComponent base, StructureDefinitionDifferentialComponent differential, int baseCursor, int diffCursor, int baseLimit, int diffLimit, String url, String profileName, String contextPath, boolean trimDifferential, String contextName, String resultPathBase, boolean slicingDone) throws DefinitionException, FHIRException {
// just repeat processing entries until we run out of our allowed scope (1st entry, the allowed scope is all the entries)
while (baseCursor <= baseLimit) {
// get the current focus of the base, and decide what to do
ElementDefinition currentBase = base.getElement().get(baseCursor);
String cpath = fixedPath(contextPath, currentBase.getPath());
// get a list of matching elements in scope
List<ElementDefinition> diffMatches = getDiffMatches(differential, cpath, diffCursor, diffLimit, profileName);
// in the simple case, source is not sliced.
if (!currentBase.hasSlicing()) {
if (diffMatches.isEmpty()) {
// the differential doesn't say anything about this item
// so we just copy it in
ElementDefinition outcome = updateURLs(url, currentBase.copy());
outcome.setPath(fixedPath(contextPath, outcome.getPath()));
updateFromBase(outcome, currentBase);
markDerived(outcome);
if (resultPathBase == null)
resultPathBase = outcome.getPath();
else if (!outcome.getPath().startsWith(resultPathBase))
throw new DefinitionException("Adding wrong path");
result.getElement().add(outcome);
baseCursor++;
} else if (diffMatches.size() == 1 && (!diffMatches.get(0).hasSlicing() || slicingDone)) {
// one matching element in the differential
ElementDefinition template = null;
if (diffMatches.get(0).hasType() && diffMatches.get(0).getType().size() == 1 && diffMatches.get(0).getType().get(0).hasProfile() && !diffMatches.get(0).getType().get(0).getCode().equals("Reference")) {
String p = diffMatches.get(0).getType().get(0).getProfile().get(0).asStringValue();
StructureDefinition sd = context.fetchResource(StructureDefinition.class, p);
if (sd != null) {
if (!sd.hasSnapshot()) {
StructureDefinition sdb = context.fetchResource(StructureDefinition.class, sd.getBase());
if (sdb == null)
throw new DefinitionException("no base for " + sd.getBase());
generateSnapshot(sdb, sd, sd.getUrl(), sd.getName());
}
template = sd.getSnapshot().getElement().get(0).copy().setPath(currentBase.getPath());
// temporary work around
if (!diffMatches.get(0).getType().get(0).getCode().equals("Extension")) {
template.setMin(currentBase.getMin());
template.setMax(currentBase.getMax());
}
}
}
if (template == null)
template = currentBase.copy();
else
// some of what's in currentBase overrides template
template = overWriteWithCurrent(template, currentBase);
ElementDefinition outcome = updateURLs(url, template);
outcome.setPath(fixedPath(contextPath, outcome.getPath()));
updateFromBase(outcome, currentBase);
if (diffMatches.get(0).hasName())
outcome.setName(diffMatches.get(0).getName());
outcome.setSlicing(null);
updateFromDefinition(outcome, diffMatches.get(0), profileName, trimDifferential, url);
if (// if the base profile allows multiple types, but the profile only allows one, rename it
outcome.getPath().endsWith("[x]") && outcome.getType().size() == 1 && !outcome.getType().get(0).getCode().equals("*"))
outcome.setPath(outcome.getPath().substring(0, outcome.getPath().length() - 3) + Utilities.capitalize(outcome.getType().get(0).getCode()));
if (resultPathBase == null)
resultPathBase = outcome.getPath();
else if (!outcome.getPath().startsWith(resultPathBase))
throw new DefinitionException("Adding wrong path");
result.getElement().add(outcome);
baseCursor++;
diffCursor = differential.getElement().indexOf(diffMatches.get(0)) + 1;
if (differential.getElement().size() > diffCursor && outcome.getPath().contains(".") && isDataType(outcome.getType())) {
// don't want to do this for the root, since that's base, and we're already processing it
if (pathStartsWith(differential.getElement().get(diffCursor).getPath(), diffMatches.get(0).getPath() + ".")) {
if (outcome.getType().size() > 1)
throw new DefinitionException(diffMatches.get(0).getPath() + " has children (" + differential.getElement().get(diffCursor).getPath() + ") and multiple types (" + typeCode(outcome.getType()) + ") in profile " + profileName);
StructureDefinition dt = getProfileForDataType(outcome.getType().get(0));
if (dt == null)
throw new DefinitionException(diffMatches.get(0).getPath() + " has children (" + differential.getElement().get(diffCursor).getPath() + ") for type " + typeCode(outcome.getType()) + " in profile " + profileName + ", but can't find type");
contextName = dt.getUrl();
int start = diffCursor;
while (differential.getElement().size() > diffCursor && pathStartsWith(differential.getElement().get(diffCursor).getPath(), diffMatches.get(0).getPath() + ".")) diffCursor++;
processPaths(result, dt.getSnapshot(), differential, 1, /* starting again on the data type, but skip the root */
start - 1, dt.getSnapshot().getElement().size() - 1, diffCursor - 1, url, profileName + pathTail(diffMatches, 0), diffMatches.get(0).getPath(), trimDifferential, contextName, resultPathBase, false);
}
}
} else {
// ok, the differential slices the item. Let's check our pre-conditions to ensure that this is correct
if (!unbounded(currentBase) && !isSlicedToOneOnly(diffMatches.get(0)))
// (but you might do that in order to split up constraints by type)
throw new DefinitionException("Attempt to a slice an element that does not repeat: " + currentBase.getPath() + "/" + currentBase.getName() + " from " + contextName);
if (// well, the diff has set up a slice, but hasn't defined it. this is an error
!diffMatches.get(0).hasSlicing() && !isExtension(currentBase))
throw new DefinitionException("differential does not have a slice: " + currentBase.getPath());
// well, if it passed those preconditions then we slice the dest.
// we're just going to accept the differential slicing at face value
ElementDefinition outcome = updateURLs(url, currentBase.copy());
outcome.setPath(fixedPath(contextPath, outcome.getPath()));
updateFromBase(outcome, currentBase);
if (!diffMatches.get(0).hasSlicing())
outcome.setSlicing(makeExtensionSlicing());
else
outcome.setSlicing(diffMatches.get(0).getSlicing().copy());
if (!outcome.getPath().startsWith(resultPathBase))
throw new DefinitionException("Adding wrong path");
result.getElement().add(outcome);
// differential - if the first one in the list has a name, we'll process it. Else we'll treat it as the base definition of the slice.
int start = 0;
if (!diffMatches.get(0).hasName()) {
updateFromDefinition(outcome, diffMatches.get(0), profileName, trimDifferential, url);
if (!outcome.hasType()) {
throw new DefinitionException("not done yet");
}
start = 1;
} else
checkExtensionDoco(outcome);
// now, for each entry in the diff matches, we're going to process the base item
// our processing scope for base is all the children of the current path
int nbl = findEndOfElement(base, baseCursor);
int ndc = diffCursor;
int ndl = diffCursor;
for (int i = start; i < diffMatches.size(); i++) {
// our processing scope for the differential is the item in the list, and all the items before the next one in the list
ndc = differential.getElement().indexOf(diffMatches.get(i));
ndl = findEndOfElement(differential, ndc);
// now we process the base scope repeatedly for each instance of the item in the differential list
processPaths(result, base, differential, baseCursor, ndc, nbl, ndl, url, profileName + pathTail(diffMatches, i), contextPath, trimDifferential, contextName, resultPathBase, true);
}
// ok, done with that - next in the base list
baseCursor = nbl + 1;
diffCursor = ndl + 1;
}
} else {
// the item is already sliced in the base profile.
// here's the rules
// 1. irrespective of whether the slicing is ordered or not, the definition order must be maintained
// 2. slice element names have to match.
// 3. new slices must be introduced at the end
// corallory: you can't re-slice existing slices. is that ok?
// we're going to need this:
String path = currentBase.getPath();
ElementDefinition original = currentBase;
if (diffMatches.isEmpty()) {
// copy across the currentbase, and all of it's children and siblings
while (baseCursor < base.getElement().size() && base.getElement().get(baseCursor).getPath().startsWith(path)) {
ElementDefinition outcome = updateURLs(url, base.getElement().get(baseCursor).copy());
if (!outcome.getPath().startsWith(resultPathBase))
throw new DefinitionException("Adding wrong path");
// so we just copy it in
result.getElement().add(outcome);
baseCursor++;
}
} else {
// first - check that the slicing is ok
boolean closed = currentBase.getSlicing().getRules() == SlicingRules.CLOSED;
int diffpos = 0;
boolean isExtension = cpath.endsWith(".extension") || cpath.endsWith(".modifierExtension");
if (diffMatches.get(0).hasSlicing()) {
// it might be null if the differential doesn't want to say anything about slicing
if (!isExtension)
// if there's a slice on the first, we'll ignore any content it has
diffpos++;
ElementDefinitionSlicingComponent dSlice = diffMatches.get(0).getSlicing();
ElementDefinitionSlicingComponent bSlice = currentBase.getSlicing();
if (!orderMatches(dSlice.getOrderedElement(), bSlice.getOrderedElement()))
throw new DefinitionException("Slicing rules on differential (" + summariseSlicing(dSlice) + ") do not match those on base (" + summariseSlicing(bSlice) + ") - order @ " + path + " (" + contextName + ")");
if (!discriiminatorMatches(dSlice.getDiscriminator(), bSlice.getDiscriminator()))
throw new DefinitionException("Slicing rules on differential (" + summariseSlicing(dSlice) + ") do not match those on base (" + summariseSlicing(bSlice) + ") - disciminator @ " + path + " (" + contextName + ")");
if (!ruleMatches(dSlice.getRules(), bSlice.getRules()))
throw new DefinitionException("Slicing rules on differential (" + summariseSlicing(dSlice) + ") do not match those on base (" + summariseSlicing(bSlice) + ") - rule @ " + path + " (" + contextName + ")");
}
ElementDefinition outcome = updateURLs(url, currentBase.copy());
outcome.setPath(fixedPath(contextPath, outcome.getPath()));
updateFromBase(outcome, currentBase);
if (diffMatches.get(0).hasSlicing() && !isExtension) {
updateFromSlicing(outcome.getSlicing(), diffMatches.get(0).getSlicing());
// if there's no slice, we don't want to update the unsliced description
updateFromDefinition(outcome, diffMatches.get(0), profileName, closed, url);
}
if (diffMatches.get(0).hasSlicing() && !diffMatches.get(0).hasName())
diffpos++;
result.getElement().add(outcome);
// now, we have two lists, base and diff. we're going to work through base, looking for matches in diff.
List<ElementDefinition> baseMatches = getSiblings(base.getElement(), currentBase);
for (ElementDefinition baseItem : baseMatches) {
baseCursor = base.getElement().indexOf(baseItem);
outcome = updateURLs(url, baseItem.copy());
updateFromBase(outcome, currentBase);
outcome.setPath(fixedPath(contextPath, outcome.getPath()));
outcome.setSlicing(null);
if (!outcome.getPath().startsWith(resultPathBase))
throw new DefinitionException("Adding wrong path");
if (diffpos < diffMatches.size() && diffMatches.get(diffpos).getName().equals(outcome.getName())) {
// if there's a diff, we update the outcome with diff
// no? updateFromDefinition(outcome, diffMatches.get(diffpos), profileName, closed, url);
// then process any children
int nbl = findEndOfElement(base, baseCursor);
int ndc = differential.getElement().indexOf(diffMatches.get(diffpos));
int ndl = findEndOfElement(differential, ndc);
// now we process the base scope repeatedly for each instance of the item in the differential list
processPaths(result, base, differential, baseCursor, ndc, nbl, ndl, url, profileName + pathTail(diffMatches, diffpos), contextPath, closed, contextName, resultPathBase, true);
// ok, done with that - now set the cursors for if this is the end
baseCursor = nbl + 1;
diffCursor = ndl + 1;
diffpos++;
} else {
result.getElement().add(outcome);
baseCursor++;
// just copy any children on the base
while (baseCursor < base.getElement().size() && base.getElement().get(baseCursor).getPath().startsWith(path) && !base.getElement().get(baseCursor).getPath().equals(path)) {
outcome = updateURLs(url, currentBase.copy());
outcome.setPath(fixedPath(contextPath, outcome.getPath()));
if (!outcome.getPath().startsWith(resultPathBase))
throw new DefinitionException("Adding wrong path");
result.getElement().add(outcome);
baseCursor++;
}
}
}
// finally, we process any remaining entries in diff, which are new (and which are only allowed if the base wasn't closed
if (closed && diffpos < diffMatches.size())
throw new DefinitionException("The base snapshot marks a slicing as closed, but the differential tries to extend it in " + profileName + " at " + path + " (" + cpath + ")");
while (diffpos < diffMatches.size()) {
ElementDefinition diffItem = diffMatches.get(diffpos);
for (ElementDefinition baseItem : baseMatches) if (baseItem.getName().equals(diffItem.getName()))
throw new DefinitionException("Named items are out of order in the slice");
outcome = updateURLs(url, original.copy());
outcome.setPath(fixedPath(contextPath, outcome.getPath()));
updateFromBase(outcome, currentBase);
outcome.setSlicing(null);
if (!outcome.getPath().startsWith(resultPathBase))
throw new DefinitionException("Adding wrong path");
result.getElement().add(outcome);
updateFromDefinition(outcome, diffItem, profileName, trimDifferential, url);
diffpos++;
}
}
}
}
}
Also used :
StructureDefinition(org.hl7.fhir.dstu2.model.StructureDefinition)
ElementDefinitionSlicingComponent(org.hl7.fhir.dstu2.model.ElementDefinition.ElementDefinitionSlicingComponent)
ElementDefinition(org.hl7.fhir.dstu2.model.ElementDefinition)
DefinitionException(org.hl7.fhir.exceptions.DefinitionException)
Example 24 with StructureDefinitionSnapshotComponent
use of org.hl7.fhir.r4b.model.StructureDefinition.StructureDefinitionSnapshotComponent in project org.hl7.fhir.core by hapifhir.
the class ProfileUtilities method processPaths.
/**
* @param trimDifferential
* @param srcSD
* @throws DefinitionException, FHIRException
* @throws Exception
*/
private ElementDefinition processPaths(String indent, StructureDefinitionSnapshotComponent result, StructureDefinitionSnapshotComponent base, StructureDefinitionDifferentialComponent differential, int baseCursor, int diffCursor, int baseLimit, int diffLimit, String url, String webUrl, String profileName, String contextPathSrc, String contextPathDst, boolean trimDifferential, String contextName, String resultPathBase, boolean slicingDone, ElementDefinition slicer, String typeSlicingPath, List<ElementRedirection> redirector, StructureDefinition srcSD) throws DefinitionException, FHIRException {
if (debug) {
System.out.println(indent + "PP @ " + resultPathBase + " / " + contextPathSrc + " : base = " + baseCursor + " to " + baseLimit + ", diff = " + diffCursor + " to " + diffLimit + " (slicing = " + slicingDone + ", k " + (redirector == null ? "null" : redirector.toString()) + ")");
}
ElementDefinition res = null;
List<TypeSlice> typeList = new ArrayList<>();
// just repeat processing entries until we run out of our allowed scope (1st entry, the allowed scope is all the entries)
while (baseCursor <= baseLimit) {
// get the current focus of the base, and decide what to do
ElementDefinition currentBase = base.getElement().get(baseCursor);
String cpath = fixedPathSource(contextPathSrc, currentBase.getPath(), redirector);
if (debug) {
System.out.println(indent + " - " + cpath + ": base = " + baseCursor + " (" + descED(base.getElement(), baseCursor) + ") to " + baseLimit + " (" + descED(base.getElement(), baseLimit) + "), diff = " + diffCursor + " (" + descED(differential.getElement(), diffCursor) + ") to " + diffLimit + " (" + descED(differential.getElement(), diffLimit) + ") " + "(slicingDone = " + slicingDone + ") (diffpath= " + (differential.getElement().size() > diffCursor ? differential.getElement().get(diffCursor).getPath() : "n/a") + ")");
}
// get a list of matching elements in scope
List<ElementDefinition> diffMatches = getDiffMatches(differential, cpath, diffCursor, diffLimit, profileName);
// in the simple case, source is not sliced.
if (!currentBase.hasSlicing() || cpath.equals(typeSlicingPath)) {
if (diffMatches.isEmpty()) {
// the differential doesn't say anything about this item
// so we just copy it in
ElementDefinition outcome = updateURLs(url, webUrl, currentBase.copy());
outcome.setPath(fixedPathDest(contextPathDst, outcome.getPath(), redirector, contextPathSrc));
updateFromBase(outcome, currentBase);
updateConstraintSources(outcome, srcSD.getUrl());
markDerived(outcome);
if (resultPathBase == null)
resultPathBase = outcome.getPath();
else if (!outcome.getPath().startsWith(resultPathBase))
throw new DefinitionException(context.formatMessage(I18nConstants.ADDING_WRONG_PATH__OUTCOMEGETPATH___RESULTPATHBASE__, outcome.getPath(), resultPathBase));
result.getElement().add(outcome);
if (hasInnerDiffMatches(differential, cpath, diffCursor, diffLimit, base.getElement(), true)) {
// did we implicitly step into a new type?
if (baseHasChildren(base, currentBase)) {
// not a new type here
processPaths(indent + " ", result, base, differential, baseCursor + 1, diffCursor, baseLimit, diffLimit, url, webUrl, profileName, contextPathSrc, contextPathDst, trimDifferential, contextName, resultPathBase, false, null, null, redirector, srcSD);
baseCursor = indexOfFirstNonChild(base, currentBase, baseCursor + 1, baseLimit);
} else {
if (outcome.getType().size() == 0 && !outcome.hasContentReference()) {
throw new DefinitionException(context.formatMessage(I18nConstants._HAS_NO_CHILDREN__AND_NO_TYPES_IN_PROFILE_, cpath, differential.getElement().get(diffCursor).getPath(), profileName));
}
boolean nonExtension = false;
if (outcome.getType().size() > 1) {
for (TypeRefComponent t : outcome.getType()) {
if (!t.getWorkingCode().equals("Reference")) {
for (ElementDefinition ed : diffMatches) {
if (ed != diffMatches.get(0) && !ed.getPath().endsWith(".extension")) {
nonExtension = true;
}
}
}
}
}
int start = diffCursor;
while (differential.getElement().size() > diffCursor && pathStartsWith(differential.getElement().get(diffCursor).getPath(), cpath + ".")) diffCursor++;
if (nonExtension) {
throw new DefinitionException(context.formatMessage(I18nConstants._HAS_CHILDREN__AND_MULTIPLE_TYPES__IN_PROFILE_, cpath, differential.getElement().get(diffCursor).getPath(), typeCode(outcome.getType()), profileName));
}
if (outcome.hasContentReference()) {
ElementDefinitionResolution tgt = getElementById(srcSD, base.getElement(), outcome.getContentReference());
if (tgt == null)
throw new DefinitionException(context.formatMessage(I18nConstants.UNABLE_TO_RESOLVE_REFERENCE_TO_, outcome.getContentReference()));
replaceFromContentReference(outcome, tgt.getElement());
if (tgt.getSource() != srcSD) {
base = tgt.getSource().getSnapshot();
int nbc = base.getElement().indexOf(tgt.getElement()) + 1;
int nbl = nbc;
while (nbl < base.getElement().size() && base.getElement().get(nbl).getPath().startsWith(tgt.getElement().getPath() + ".")) nbl++;
processPaths(indent + " ", result, base, differential, nbc, start - 1, nbl - 1, diffCursor - 1, url, webUrl, profileName, tgt.getElement().getPath(), diffMatches.get(0).getPath(), trimDifferential, contextName, resultPathBase, false, null, null, redirectorStack(redirector, outcome, cpath), tgt.getSource());
} else {
int nbc = base.getElement().indexOf(tgt.getElement()) + 1;
int nbl = nbc;
while (nbl < base.getElement().size() && base.getElement().get(nbl).getPath().startsWith(tgt.getElement().getPath() + ".")) nbl++;
System.out.println("Test!");
processPaths(indent + " ", result, base, differential, nbc, start, nbl - 1, diffCursor - 1, url, webUrl, profileName, tgt.getElement().getPath(), outcome.getPath(), trimDifferential, contextName, resultPathBase, false, null, null, redirectorStack(redirector, outcome, cpath), srcSD);
}
} else {
StructureDefinition dt = outcome.getType().size() > 1 ? context.fetchTypeDefinition("Element") : getProfileForDataType(outcome.getType().get(0), webUrl);
if (dt == null) {
throw new DefinitionException(context.formatMessage(I18nConstants.UNKNOWN_TYPE__AT_, outcome.getType().get(0), cpath));
}
contextName = dt.getUrl();
if (redirector.isEmpty()) {
processPaths(indent + " ", result, dt.getSnapshot(), differential, 1, /* starting again on the data type, but skip the root */
start, dt.getSnapshot().getElement().size() - 1, diffCursor - 1, url, getWebUrl(dt, webUrl, indent), profileName, cpath, outcome.getPath(), trimDifferential, contextName, resultPathBase, false, null, null, redirector, srcSD);
} else {
processPaths(indent + " ", result, dt.getSnapshot(), differential, 1, /* starting again on the data type, but skip the root */
start, dt.getSnapshot().getElement().size() - 1, diffCursor - 1, url, getWebUrl(dt, webUrl, indent), profileName, cpath, outcome.getPath(), trimDifferential, contextName, resultPathBase, false, null, null, redirectorStack(redirector, currentBase, cpath), srcSD);
}
}
}
}
baseCursor++;
} else if (diffMatches.size() == 1 && (slicingDone || (!isImplicitSlicing(diffMatches.get(0), cpath) && !(diffMatches.get(0).hasSlicing() || (isExtension(diffMatches.get(0)) && diffMatches.get(0).hasSliceName()))))) {
// one matching element in the differential
ElementDefinition template = null;
if (diffMatches.get(0).hasType() && "Reference".equals(diffMatches.get(0).getType().get(0).getWorkingCode()) && !isValidType(diffMatches.get(0).getType().get(0), currentBase)) {
throw new DefinitionException(context.formatMessage(I18nConstants.VALIDATION_VAL_ILLEGAL_TYPE_CONSTRAINT, url, diffMatches.get(0).getPath(), diffMatches.get(0).getType().get(0), currentBase.typeSummary()));
}
String id = diffMatches.get(0).getId();
String lid = tail(id);
if (lid.contains("/")) {
// the template comes from the snapshot of the base
generateIds(result.getElement(), url, srcSD.getType());
// this is wrong if there's more than one reslice (todo: one thing at a time)
String baseId = id.substring(0, id.length() - lid.length()) + lid.substring(0, lid.indexOf("/"));
template = getById(result.getElement(), baseId);
} else if (diffMatches.get(0).hasType() && diffMatches.get(0).getType().size() == 1 && diffMatches.get(0).getType().get(0).hasProfile() && !"Reference".equals(diffMatches.get(0).getType().get(0).getWorkingCode())) {
CanonicalType p = diffMatches.get(0).getType().get(0).getProfile().get(0);
StructureDefinition sd = context.fetchResource(StructureDefinition.class, p.getValue());
if (sd == null && xver != null && xver.matchingUrl(p.getValue())) {
switch(xver.status(p.getValue())) {
case BadVersion:
throw new FHIRException("Reference to invalid version in extension url " + p.getValue());
case Invalid:
throw new FHIRException("Reference to invalid extension " + p.getValue());
case Unknown:
throw new FHIRException("Reference to unknown extension " + p.getValue());
case Valid:
sd = xver.makeDefinition(p.getValue());
generateSnapshot(context.fetchTypeDefinition("Extension"), sd, sd.getUrl(), webUrl, sd.getName());
}
}
if (sd != null) {
if (!isMatchingType(sd, diffMatches.get(0).getType(), p.getExtensionString(ToolingExtensions.EXT_PROFILE_ELEMENT))) {
throw new DefinitionException(context.formatMessage(I18nConstants.VALIDATION_VAL_PROFILE_WRONGTYPE2, sd.getUrl(), diffMatches.get(0).getPath(), sd.getType(), p.getValue(), diffMatches.get(0).getType().get(0).getWorkingCode()));
}
if (isGenerating(sd)) {
// but we check anyway
if (sd.getSnapshot().getElementFirstRep().isEmpty()) {
throw new FHIRException(context.formatMessage(I18nConstants.ATTEMPT_TO_USE_A_SNAPSHOT_ON_PROFILE__AS__BEFORE_IT_IS_GENERATED, sd.getUrl(), "Source for first element"));
}
} else if (!sd.hasSnapshot()) {
StructureDefinition sdb = context.fetchResource(StructureDefinition.class, sd.getBaseDefinition());
if (sdb == null)
throw new DefinitionException(context.formatMessage(I18nConstants.UNABLE_TO_FIND_BASE__FOR_, sd.getBaseDefinition(), sd.getUrl()));
checkNotGenerating(sdb, "an extension base");
generateSnapshot(sdb, sd, sd.getUrl(), (sdb.hasUserData("path")) ? Utilities.extractBaseUrl(sdb.getUserString("path")) : webUrl, sd.getName());
}
ElementDefinition src;
if (p.hasExtension(ToolingExtensions.EXT_PROFILE_ELEMENT)) {
src = null;
String eid = p.getExtensionString(ToolingExtensions.EXT_PROFILE_ELEMENT);
for (ElementDefinition t : sd.getSnapshot().getElement()) {
if (eid.equals(t.getId()))
src = t;
}
if (src == null)
throw new DefinitionException(context.formatMessage(I18nConstants.UNABLE_TO_FIND_ELEMENT__IN_, eid, p.getValue()));
} else
src = sd.getSnapshot().getElement().get(0);
template = src.copy().setPath(currentBase.getPath());
template.setSliceName(null);
// temporary work around
if (!"Extension".equals(diffMatches.get(0).getType().get(0).getCode())) {
template.setMin(currentBase.getMin());
template.setMax(currentBase.getMax());
}
}
}
if (template == null)
template = currentBase.copy();
else
// some of what's in currentBase overrides template
template = fillOutFromBase(template, currentBase);
ElementDefinition outcome = updateURLs(url, webUrl, template);
outcome.setPath(fixedPathDest(contextPathDst, outcome.getPath(), redirector, contextPathSrc));
if (res == null)
res = outcome;
updateFromBase(outcome, currentBase);
if (diffMatches.get(0).hasSliceName()) {
outcome.setSliceName(diffMatches.get(0).getSliceName());
if (!diffMatches.get(0).hasMin() && (diffMatches.size() > 1 || slicer == null || slicer.getSlicing().getRules() != SlicingRules.CLOSED) && !currentBase.hasSliceName()) {
if (!cpath.endsWith("xtension.value[x]")) {
// hack work around for problems with snapshots in official releases
outcome.setMin(0);
}
}
}
updateFromDefinition(outcome, diffMatches.get(0), profileName, trimDifferential, url, srcSD);
removeStatusExtensions(outcome);
// if (outcome.getPath().endsWith("[x]") && outcome.getType().size() == 1 && !outcome.getType().get(0).getCode().equals("*") && !diffMatches.get(0).hasSlicing()) // if the base profile allows multiple types, but the profile only allows one, rename it
// outcome.setPath(outcome.getPath().substring(0, outcome.getPath().length()-3)+Utilities.capitalize(outcome.getType().get(0).getCode()));
outcome.setSlicing(null);
if (resultPathBase == null)
resultPathBase = outcome.getPath();
else if (!outcome.getPath().startsWith(resultPathBase))
throw new DefinitionException(context.formatMessage(I18nConstants.ADDING_WRONG_PATH));
result.getElement().add(outcome);
baseCursor++;
diffCursor = differential.getElement().indexOf(diffMatches.get(0)) + 1;
if (diffLimit >= diffCursor && outcome.getPath().contains(".") && (isDataType(outcome.getType()) || isBaseResource(outcome.getType()) || outcome.hasContentReference())) {
// don't want to do this for the root, since that's base, and we're already processing it
if (pathStartsWith(differential.getElement().get(diffCursor).getPath(), diffMatches.get(0).getPath() + ".") && !baseWalksInto(base.getElement(), baseCursor)) {
if (outcome.getType().size() > 1) {
if (outcome.getPath().endsWith("[x]") && !diffMatches.get(0).getPath().endsWith("[x]")) {
String en = tail(outcome.getPath());
String tn = tail(diffMatches.get(0).getPath());
String t = tn.substring(en.length() - 3);
if (isPrimitive(Utilities.uncapitalize(t)))
t = Utilities.uncapitalize(t);
// keep any additional information
List<TypeRefComponent> ntr = getByTypeName(outcome.getType(), t);
if (ntr.isEmpty())
ntr.add(new TypeRefComponent().setCode(t));
outcome.getType().clear();
outcome.getType().addAll(ntr);
}
if (outcome.getType().size() > 1)
for (TypeRefComponent t : outcome.getType()) {
if (!t.getCode().equals("Reference")) {
boolean nonExtension = false;
for (ElementDefinition ed : diffMatches) if (ed != diffMatches.get(0) && !ed.getPath().endsWith(".extension"))
nonExtension = true;
if (nonExtension)
throw new DefinitionException(context.formatMessage(I18nConstants._HAS_CHILDREN__AND_MULTIPLE_TYPES__IN_PROFILE_, diffMatches.get(0).getPath(), differential.getElement().get(diffCursor).getPath(), typeCode(outcome.getType()), profileName));
}
}
}
int start = diffCursor;
while (diffCursor <= diffLimit && differential.getElement().size() > diffCursor && pathStartsWith(differential.getElement().get(diffCursor).getPath(), diffMatches.get(0).getPath() + ".")) diffCursor++;
if (outcome.hasContentReference()) {
ElementDefinitionResolution tgt = getElementById(srcSD, base.getElement(), outcome.getContentReference());
if (tgt == null)
throw new DefinitionException(context.formatMessage(I18nConstants.UNABLE_TO_RESOLVE_REFERENCE_TO_, outcome.getContentReference()));
replaceFromContentReference(outcome, tgt.getElement());
if (tgt.getSource() != srcSD) {
base = tgt.getSource().getSnapshot();
int nbc = base.getElement().indexOf(tgt.getElement()) + 1;
int nbl = nbc;
while (nbl < base.getElement().size() && base.getElement().get(nbl).getPath().startsWith(tgt.getElement().getPath() + ".")) nbl++;
processPaths(indent + " ", result, base, differential, nbc, start - 1, nbl - 1, diffCursor - 1, url, webUrl, profileName, tgt.getElement().getPath(), diffMatches.get(0).getPath(), trimDifferential, contextName, resultPathBase, false, null, null, redirectorStack(redirector, outcome, cpath), tgt.getSource());
} else {
int nbc = base.getElement().indexOf(tgt.getElement()) + 1;
int nbl = nbc;
while (nbl < base.getElement().size() && base.getElement().get(nbl).getPath().startsWith(tgt.getElement().getPath() + ".")) nbl++;
processPaths(indent + " ", result, base, differential, nbc, start - 1, nbl - 1, diffCursor - 1, url, webUrl, profileName, tgt.getElement().getPath(), diffMatches.get(0).getPath(), trimDifferential, contextName, resultPathBase, false, null, null, redirectorStack(redirector, outcome, cpath), srcSD);
}
} else {
StructureDefinition dt = outcome.getType().size() == 1 ? getProfileForDataType(outcome.getType().get(0), webUrl) : getProfileForDataType("Element");
if (dt == null)
throw new DefinitionException(context.formatMessage(I18nConstants._HAS_CHILDREN__FOR_TYPE__IN_PROFILE__BUT_CANT_FIND_TYPE, diffMatches.get(0).getPath(), differential.getElement().get(diffCursor).getPath(), typeCode(outcome.getType()), profileName));
contextName = dt.getUrl();
processPaths(indent + " ", result, dt.getSnapshot(), differential, 1, /* starting again on the data type, but skip the root */
start, dt.getSnapshot().getElement().size() - 1, diffCursor - 1, url, getWebUrl(dt, webUrl, indent), profileName + pathTail(diffMatches, 0), diffMatches.get(0).getPath(), outcome.getPath(), trimDifferential, contextName, resultPathBase, false, null, null, new ArrayList<ElementRedirection>(), srcSD);
}
}
}
} else if (diffsConstrainTypes(diffMatches, cpath, typeList)) {
int start = 0;
int nbl = findEndOfElement(base, baseCursor);
int ndc = differential.getElement().indexOf(diffMatches.get(0));
ElementDefinition elementToRemove = null;
boolean shortCut = !typeList.isEmpty() && typeList.get(0).type != null;
// we come here whether they are sliced in the diff, or whether the short cut is used.
if (shortCut) {
// in R3 (and unpatched R4, as a workaround right now...
if (!FHIRVersion.isR4Plus(context.getVersion()) || !newSlicingProcessing) {
// newSlicingProcessing is a work around for editorial loop dependency
// we insert a cloned element with the right types at the start of the diffMatches
ElementDefinition ed = new ElementDefinition();
ed.setPath(determineTypeSlicePath(diffMatches.get(0).getPath(), cpath));
for (TypeSlice ts : typeList) ed.addType().setCode(ts.type);
ed.setSlicing(new ElementDefinitionSlicingComponent());
ed.getSlicing().addDiscriminator().setType(DiscriminatorType.TYPE).setPath("$this");
ed.getSlicing().setRules(SlicingRules.CLOSED);
ed.getSlicing().setOrdered(false);
diffMatches.add(0, ed);
differential.getElement().add(ndc, ed);
elementToRemove = ed;
} else {
// as of R4, this changed; if there's no slice, there's no constraint on the slice types, only one the type.
// so the element we insert specifies no types (= all types) allowed in the base, not just the listed type.
// see also discussion here: https://chat.fhir.org/#narrow/stream/179177-conformance/topic/Slicing.20a.20non-repeating.20element
ElementDefinition ed = new ElementDefinition();
ed.setPath(determineTypeSlicePath(diffMatches.get(0).getPath(), cpath));
ed.setSlicing(new ElementDefinitionSlicingComponent());
ed.getSlicing().addDiscriminator().setType(DiscriminatorType.TYPE).setPath("$this");
ed.getSlicing().setRules(SlicingRules.CLOSED);
ed.getSlicing().setOrdered(false);
diffMatches.add(0, ed);
differential.getElement().add(ndc, ed);
elementToRemove = ed;
}
}
int ndl = findEndOfElement(differential, ndc);
if (diffMatches.get(0).getSlicing().hasOrdered()) {
if (diffMatches.get(0).getSlicing().getOrdered()) {
throw new FHIRException(context.formatMessage(I18nConstants.ERROR_AT_PATH__IN__TYPE_SLICING_WITH_SLICINGORDERED__TRUE, cpath, url));
}
}
if (diffMatches.get(0).getSlicing().hasDiscriminator()) {
if (diffMatches.get(0).getSlicing().getDiscriminator().size() != 1) {
throw new FHIRException(context.formatMessage(I18nConstants.ERROR_AT_PATH__IN__TYPE_SLICING_WITH_SLICINGDISCRIMINATORCOUNT__1, cpath, url));
}
if (diffMatches.get(0).getSlicing().getDiscriminatorFirstRep().getType() != DiscriminatorType.TYPE) {
throw new FHIRException(context.formatMessage(I18nConstants.ERROR_AT_PATH__IN__TYPE_SLICING_WITH_SLICINGDISCRIMINATORTYPE__TYPE, cpath, url));
}
if (!"$this".equals(diffMatches.get(0).getSlicing().getDiscriminatorFirstRep().getPath())) {
throw new FHIRException(context.formatMessage(I18nConstants.ERROR_AT_PATH__IN__TYPE_SLICING_WITH_SLICINGDISCRIMINATORPATH__THIS, cpath, url));
}
}
// check the slice names too while we're at it...
for (TypeSlice ts : typeList) {
if (ts.type != null) {
String tn = rootName(cpath) + Utilities.capitalize(ts.type);
if (!ts.defn.hasSliceName()) {
ts.defn.setSliceName(tn);
} else if (!ts.defn.getSliceName().equals(tn)) {
if (autoFixSliceNames) {
ts.defn.setSliceName(tn);
} else {
throw new FHIRException(context.formatMessage(I18nConstants.ERROR_AT_PATH__SLICE_NAME_MUST_BE__BUT_IS_, (!Utilities.noString(contextPathSrc) ? contextPathSrc : cpath), tn, ts.defn.getSliceName()));
}
}
if (!ts.defn.hasType()) {
ts.defn.addType().setCode(ts.type);
} else if (ts.defn.getType().size() > 1) {
throw new FHIRException(context.formatMessage(I18nConstants.ERROR_AT_PATH__SLICE_FOR_TYPE__HAS_MORE_THAN_ONE_TYPE_, (!Utilities.noString(contextPathSrc) ? contextPathSrc : cpath), tn, ts.defn.typeSummary()));
} else if (!ts.defn.getType().get(0).getCode().equals(ts.type)) {
throw new FHIRException(context.formatMessage(I18nConstants.ERROR_AT_PATH__SLICE_FOR_TYPE__HAS_WRONG_TYPE_, (!Utilities.noString(contextPathSrc) ? contextPathSrc : cpath), tn, ts.defn.typeSummary()));
}
}
}
// ok passed the checks.
// copy the root diff, and then process any children it has
ElementDefinition e = processPaths(indent + " ", result, base, differential, baseCursor, ndc, nbl, ndl, url, webUrl, profileName + pathTail(diffMatches, 0), contextPathSrc, contextPathDst, trimDifferential, contextName, resultPathBase, true, null, null, redirector, srcSD);
if (e == null)
throw new FHIRException(context.formatMessage(I18nConstants.DID_NOT_FIND_TYPE_ROOT_, diffMatches.get(0).getPath()));
// now set up slicing on the e (cause it was wiped by what we called.
e.setSlicing(new ElementDefinitionSlicingComponent());
e.getSlicing().addDiscriminator().setType(DiscriminatorType.TYPE).setPath("$this");
// type slicing is always closed; the differential might call it open, but that just means it's not constraining the slices it doesn't mention
e.getSlicing().setRules(SlicingRules.CLOSED);
e.getSlicing().setOrdered(false);
start++;
String fixedType = null;
// now we process the base scope repeatedly for each instance of the item in the differential list
for (int i = start; i < diffMatches.size(); i++) {
// our processing scope for the differential is the item in the list, and all the items before the next one in the list
if (diffMatches.get(i).getMin() > 0) {
if (diffMatches.size() > i + 1) {
throw new FHIRException(context.formatMessage(I18nConstants.INVALID_SLICING__THERE_IS_MORE_THAN_ONE_TYPE_SLICE_AT__BUT_ONE_OF_THEM__HAS_MIN__1_SO_THE_OTHER_SLICES_CANNOT_EXIST, diffMatches.get(i).getPath(), diffMatches.get(i).getSliceName()));
} else {
e.setMin(1);
}
fixedType = determineFixedType(diffMatches, fixedType, i);
}
ndc = differential.getElement().indexOf(diffMatches.get(i));
ndl = findEndOfElement(differential, ndc);
processPaths(indent + " ", result, base, differential, baseCursor, ndc, nbl, ndl, url, webUrl, profileName + pathTail(diffMatches, i), contextPathSrc, contextPathDst, trimDifferential, contextName, resultPathBase, true, e, null, redirector, srcSD);
}
if (elementToRemove != null) {
differential.getElement().remove(elementToRemove);
ndl--;
}
if (fixedType != null) {
for (Iterator<TypeRefComponent> iter = e.getType().iterator(); iter.hasNext(); ) {
TypeRefComponent tr = iter.next();
if (!tr.getCode().equals(fixedType)) {
iter.remove();
}
}
}
if (!"0".equals(e.getMax())) {
// check that there's a slice for each allowed types
Set<String> allowedTypes = getListOfTypes(e);
for (TypeSlice t : typeList) {
if (t.type != null) {
allowedTypes.remove(t.type);
} else if (t.getDefn().hasSliceName() && t.getDefn().getType().size() == 1) {
allowedTypes.remove(t.getDefn().getType().get(0).getCode());
}
}
if (!allowedTypes.isEmpty()) {
if (cpath.contains("xtension.value")) {
for (Iterator<TypeRefComponent> iter = e.getType().iterator(); iter.hasNext(); ) {
TypeRefComponent tr = iter.next();
if (allowedTypes.contains(tr.getCode())) {
iter.remove();
}
}
// System.out.println("!!: Extension Error at "+cpath+": Allowed Types not sliced = "+allowedTypes+". !Extension!!");
// throw new Error("Extension Error at "+cpath+": Allowed Types not sliced = "+allowedTypes+". !Extension!!");
} else {
e.getSlicing().setRules(SlicingRules.OPEN);
}
}
}
// ok, done with that - next in the base list
baseCursor = nbl + 1;
diffCursor = ndl + 1;
} else {
// ok, the differential slices the item. Let's check our pre-conditions to ensure that this is correct
if (!unbounded(currentBase) && !isSlicedToOneOnly(diffMatches.get(0)))
// (but you might do that in order to split up constraints by type)
throw new DefinitionException(context.formatMessage(I18nConstants.ATTEMPT_TO_A_SLICE_AN_ELEMENT_THAT_DOES_NOT_REPEAT__FROM__IN_, currentBase.getPath(), currentBase.getPath(), contextName, url, diffMatches.get(0).getId(), sliceNames(diffMatches)));
if (// well, the diff has set up a slice, but hasn't defined it. this is an error
!diffMatches.get(0).hasSlicing() && !isExtension(currentBase))
throw new DefinitionException(context.formatMessage(I18nConstants.DIFFERENTIAL_DOES_NOT_HAVE_A_SLICE__B_OF_____IN_PROFILE_, currentBase.getPath(), baseCursor, baseLimit, diffCursor, diffLimit, url, cpath));
// well, if it passed those preconditions then we slice the dest.
int start = 0;
int nbl = findEndOfElement(base, baseCursor);
// if (diffMatches.size() > 1 && diffMatches.get(0).hasSlicing() && differential.getElement().indexOf(diffMatches.get(1)) > differential.getElement().indexOf(diffMatches.get(0))+1) {
ElementDefinition slicerElement;
if (diffMatches.size() > 1 && diffMatches.get(0).hasSlicing() && (nbl > baseCursor || differential.getElement().indexOf(diffMatches.get(1)) > differential.getElement().indexOf(diffMatches.get(0)) + 1)) {
// there's a default set before the slices
int ndc = differential.getElement().indexOf(diffMatches.get(0));
int ndl = findEndOfElement(differential, ndc);
ElementDefinition e = processPaths(indent + " ", result, base, differential, baseCursor, ndc, nbl, ndl, url, webUrl, profileName + pathTail(diffMatches, 0), contextPathSrc, contextPathDst, trimDifferential, contextName, resultPathBase, true, null, null, redirector, srcSD);
if (e == null)
throw new FHIRException(context.formatMessage(I18nConstants.DID_NOT_FIND_SINGLE_SLICE_, diffMatches.get(0).getPath()));
e.setSlicing(diffMatches.get(0).getSlicing());
slicerElement = e;
start++;
} else {
// we're just going to accept the differential slicing at face value
ElementDefinition outcome = updateURLs(url, webUrl, currentBase.copy());
outcome.setPath(fixedPathDest(contextPathDst, outcome.getPath(), redirector, contextPathSrc));
updateFromBase(outcome, currentBase);
if (!diffMatches.get(0).hasSlicing())
outcome.setSlicing(makeExtensionSlicing());
else
outcome.setSlicing(diffMatches.get(0).getSlicing().copy());
if (!outcome.getPath().startsWith(resultPathBase))
throw new DefinitionException(context.formatMessage(I18nConstants.ADDING_WRONG_PATH));
result.getElement().add(outcome);
slicerElement = outcome;
// differential - if the first one in the list has a name, we'll process it. Else we'll treat it as the base definition of the slice.
if (!diffMatches.get(0).hasSliceName()) {
updateFromDefinition(outcome, diffMatches.get(0), profileName, trimDifferential, url, srcSD);
removeStatusExtensions(outcome);
if (!outcome.hasContentReference() && !outcome.hasType()) {
throw new DefinitionException(context.formatMessage(I18nConstants.NOT_DONE_YET));
}
if (hasInnerDiffMatches(differential, currentBase.getPath(), diffCursor, diffLimit, base.getElement(), false)) {
if (baseHasChildren(base, currentBase)) {
// not a new type here
throw new Error("This situation is not yet handled (constrain slicing to 1..1 and fix base slice for inline structure - please report issue to grahame@fhir.org along with a test case that reproduces this error (@ " + cpath + " | " + currentBase.getPath() + ")");
} else {
StructureDefinition dt = getTypeForElement(differential, diffCursor, profileName, diffMatches, outcome, webUrl);
contextName = dt.getUrl();
diffCursor++;
start = diffCursor;
while (differential.getElement().size() > diffCursor && pathStartsWith(differential.getElement().get(diffCursor).getPath(), cpath + ".")) diffCursor++;
diffCursor--;
processPaths(indent + " ", result, dt.getSnapshot(), differential, 1, /* starting again on the data type, but skip the root */
start, dt.getSnapshot().getElement().size() - 1, diffCursor, url, getWebUrl(dt, webUrl, indent), profileName, cpath, outcome.getPath(), trimDifferential, contextName, resultPathBase, false, null, null, redirector, srcSD);
}
}
start++;
// result.getElement().remove(result.getElement().size()-1);
} else
checkExtensionDoco(outcome);
}
// now, for each entry in the diff matches, we're going to process the base item
// our processing scope for base is all the children of the current path
int ndc = diffCursor;
int ndl = diffCursor;
for (int i = start; i < diffMatches.size(); i++) {
// our processing scope for the differential is the item in the list, and all the items before the next one in the list
ndc = differential.getElement().indexOf(diffMatches.get(i));
ndl = findEndOfElement(differential, ndc);
/* if (skipSlicingElement && i == 0) {
ndc = ndc + 1;
if (ndc > ndl)
continue;
}*/
// now we process the base scope repeatedly for each instance of the item in the differential list
processPaths(indent + " ", result, base, differential, baseCursor, ndc, nbl, ndl, url, webUrl, profileName + pathTail(diffMatches, i), contextPathSrc, contextPathDst, trimDifferential, contextName, resultPathBase, true, slicerElement, null, redirector, srcSD);
}
// ok, done with that - next in the base list
baseCursor = nbl + 1;
diffCursor = ndl + 1;
}
} else {
// the item is already sliced in the base profile.
// here's the rules
// 1. irrespective of whether the slicing is ordered or not, the definition order must be maintained
// 2. slice element names have to match.
// 3. new slices must be introduced at the end
// corallory: you can't re-slice existing slices. is that ok?
// we're going to need this:
String path = currentBase.getPath();
ElementDefinition original = currentBase;
if (diffMatches.isEmpty()) {
if (hasInnerDiffMatches(differential, path, diffCursor, diffLimit, base.getElement(), true)) {
// so we just copy it in
ElementDefinition outcome = updateURLs(url, webUrl, currentBase.copy());
outcome.setPath(fixedPathDest(contextPathDst, outcome.getPath(), redirector, contextPathSrc));
updateFromBase(outcome, currentBase);
markDerived(outcome);
if (resultPathBase == null)
resultPathBase = outcome.getPath();
else if (!outcome.getPath().startsWith(resultPathBase))
throw new DefinitionException(context.formatMessage(I18nConstants.ADDING_WRONG_PATH));
result.getElement().add(outcome);
// did we implicitly step into a new type?
if (baseHasChildren(base, currentBase)) {
// not a new type here
processPaths(indent + " ", result, base, differential, baseCursor + 1, diffCursor, baseLimit, diffLimit, url, webUrl, profileName, contextPathSrc, contextPathDst, trimDifferential, contextName, resultPathBase, false, null, null, redirector, srcSD);
baseCursor = indexOfFirstNonChild(base, currentBase, baseCursor, baseLimit);
} else {
StructureDefinition dt = getTypeForElement(differential, diffCursor, profileName, diffMatches, outcome, webUrl);
contextName = dt.getUrl();
int start = diffCursor;
if (differential.getElement().get(diffCursor).getPath().equals(cpath)) {
diffCursor++;
}
while (differential.getElement().size() > diffCursor && pathStartsWith(differential.getElement().get(diffCursor).getPath(), cpath + ".")) {
diffCursor++;
}
if (diffCursor > start) {
processPaths(indent + " ", result, dt.getSnapshot(), differential, 1, /* starting again on the data type, but skip the root */
start, dt.getSnapshot().getElement().size() - 1, diffCursor - 1, url, getWebUrl(dt, webUrl, indent), profileName, cpath, outcome.getPath(), trimDifferential, contextName, resultPathBase, false, null, null, redirector, srcSD);
}
}
baseCursor++;
} else {
// copy across the currentbase, and all of its children and siblings
while (baseCursor < base.getElement().size() && base.getElement().get(baseCursor).getPath().startsWith(path)) {
ElementDefinition outcome = updateURLs(url, webUrl, base.getElement().get(baseCursor).copy());
outcome.setPath(fixedPathDest(contextPathDst, outcome.getPath(), redirector, contextPathSrc));
if (!outcome.getPath().startsWith(resultPathBase))
throw new DefinitionException(context.formatMessage(I18nConstants.ADDING_WRONG_PATH_IN_PROFILE___VS_, profileName, outcome.getPath(), resultPathBase));
// so we just copy it in
result.getElement().add(outcome);
baseCursor++;
}
}
} else if (diffsConstrainTypes(diffMatches, cpath, typeList)) {
int start = 0;
int nbl = findEndOfElement(base, baseCursor);
int ndc = differential.getElement().indexOf(diffMatches.get(0));
ElementDefinition elementToRemove = null;
boolean shortCut = (!typeList.isEmpty() && typeList.get(0).type != null) || (diffMatches.get(0).hasSliceName() && !diffMatches.get(0).hasSlicing());
// we come here whether they are sliced in the diff, or whether the short cut is used.
if (shortCut) {
// in R3 (and unpatched R4, as a workaround right now...
if (!FHIRVersion.isR4Plus(context.getVersion()) || !newSlicingProcessing) {
// newSlicingProcessing is a work around for editorial loop dependency
// we insert a cloned element with the right types at the start of the diffMatches
ElementDefinition ed = new ElementDefinition();
ed.setPath(determineTypeSlicePath(diffMatches.get(0).getPath(), cpath));
for (TypeSlice ts : typeList) ed.addType().setCode(ts.type);
ed.setSlicing(new ElementDefinitionSlicingComponent());
ed.getSlicing().addDiscriminator().setType(DiscriminatorType.TYPE).setPath("$this");
ed.getSlicing().setRules(SlicingRules.CLOSED);
ed.getSlicing().setOrdered(false);
diffMatches.add(0, ed);
differential.getElement().add(ndc, ed);
elementToRemove = ed;
} else {
// as of R4, this changed; if there's no slice, there's no constraint on the slice types, only one the type.
// so the element we insert specifies no types (= all types) allowed in the base, not just the listed type.
// see also discussion here: https://chat.fhir.org/#narrow/stream/179177-conformance/topic/Slicing.20a.20non-repeating.20element
ElementDefinition ed = new ElementDefinition();
ed.setPath(determineTypeSlicePath(diffMatches.get(0).getPath(), cpath));
ed.setSlicing(new ElementDefinitionSlicingComponent());
ed.getSlicing().addDiscriminator().setType(DiscriminatorType.TYPE).setPath("$this");
ed.getSlicing().setRules(SlicingRules.CLOSED);
ed.getSlicing().setOrdered(false);
diffMatches.add(0, ed);
differential.getElement().add(ndc, ed);
elementToRemove = ed;
}
}
int ndl = findEndOfElement(differential, ndc);
if (diffMatches.get(0).getSlicing().hasOrdered()) {
if (diffMatches.get(0).getSlicing().getOrdered()) {
throw new FHIRException(context.formatMessage(I18nConstants.ERROR_AT_PATH__IN__TYPE_SLICING_WITH_SLICINGORDERED__TRUE, cpath, url));
}
}
if (diffMatches.get(0).getSlicing().hasDiscriminator()) {
if (diffMatches.get(0).getSlicing().getDiscriminator().size() != 1) {
throw new FHIRException(context.formatMessage(I18nConstants.ERROR_AT_PATH__IN__TYPE_SLICING_WITH_SLICINGDISCRIMINATORCOUNT__1, cpath, url));
}
if (diffMatches.get(0).getSlicing().getDiscriminatorFirstRep().getType() != DiscriminatorType.TYPE) {
throw new FHIRException(context.formatMessage(I18nConstants.ERROR_AT_PATH__IN__TYPE_SLICING_WITH_SLICINGDISCRIMINATORTYPE__TYPE, cpath, url));
}
if (!"$this".equals(diffMatches.get(0).getSlicing().getDiscriminatorFirstRep().getPath())) {
throw new FHIRException(context.formatMessage(I18nConstants.ERROR_AT_PATH__IN__TYPE_SLICING_WITH_SLICINGDISCRIMINATORPATH__THIS, cpath, url));
}
}
// check the slice names too while we're at it...
for (TypeSlice ts : typeList) {
if (ts.type != null) {
String tn = rootName(cpath) + Utilities.capitalize(ts.type);
if (!ts.defn.hasSliceName()) {
ts.defn.setSliceName(tn);
} else if (!ts.defn.getSliceName().equals(tn)) {
throw new FHIRException(context.formatMessage(I18nConstants.ERROR_AT_PATH__SLICE_NAME_MUST_BE__BUT_IS_, (!Utilities.noString(contextPathSrc) ? contextPathSrc : cpath), tn, ts.defn.getSliceName()));
}
if (!ts.defn.hasType()) {
ts.defn.addType().setCode(ts.type);
} else if (ts.defn.getType().size() > 1) {
throw new FHIRException(context.formatMessage(I18nConstants.ERROR_AT_PATH__SLICE_FOR_TYPE__HAS_MORE_THAN_ONE_TYPE_, (!Utilities.noString(contextPathSrc) ? contextPathSrc : cpath), tn, ts.defn.typeSummary()));
} else if (!ts.defn.getType().get(0).getCode().equals(ts.type)) {
throw new FHIRException(context.formatMessage(I18nConstants.ERROR_AT_PATH__SLICE_FOR_TYPE__HAS_WRONG_TYPE_, (!Utilities.noString(contextPathSrc) ? contextPathSrc : cpath), tn, ts.defn.typeSummary()));
}
}
}
// ok passed the checks.
// copy the root diff, and then process any children it has
ElementDefinition e = processPaths(indent + " ", result, base, differential, baseCursor, ndc, nbl, ndl, url, webUrl, profileName + pathTail(diffMatches, 0), contextPathSrc, contextPathDst, trimDifferential, contextName, resultPathBase, true, null, cpath, redirector, srcSD);
if (e == null)
throw new FHIRException(context.formatMessage(I18nConstants.DID_NOT_FIND_TYPE_ROOT_, diffMatches.get(0).getPath()));
// now set up slicing on the e (cause it was wiped by what we called.
e.setSlicing(new ElementDefinitionSlicingComponent());
e.getSlicing().addDiscriminator().setType(DiscriminatorType.TYPE).setPath("$this");
// type slicing is always closed; the differential might call it open, but that just means it's not constraining the slices it doesn't mention
e.getSlicing().setRules(SlicingRules.CLOSED);
e.getSlicing().setOrdered(false);
start++;
String fixedType = null;
List<BaseTypeSlice> baseSlices = findBaseSlices(base, nbl);
// now we process the base scope repeatedly for each instance of the item in the differential list
for (int i = start; i < diffMatches.size(); i++) {
String type = determineFixedType(diffMatches, fixedType, i);
// our processing scope for the differential is the item in the list, and all the items before the next one in the list
if (diffMatches.get(i).getMin() > 0) {
if (diffMatches.size() > i + 1) {
throw new FHIRException(context.formatMessage(I18nConstants.INVALID_SLICING__THERE_IS_MORE_THAN_ONE_TYPE_SLICE_AT__BUT_ONE_OF_THEM__HAS_MIN__1_SO_THE_OTHER_SLICES_CANNOT_EXIST, diffMatches.get(i).getPath(), diffMatches.get(i).getSliceName()));
}
fixedType = type;
}
ndc = differential.getElement().indexOf(diffMatches.get(i));
ndl = findEndOfElement(differential, ndc);
int sStart = baseCursor;
int sEnd = nbl;
BaseTypeSlice bs = chooseMatchingBaseSlice(baseSlices, type);
if (bs != null) {
sStart = bs.start;
sEnd = bs.end;
bs.handled = true;
}
processPaths(indent + " ", result, base, differential, sStart, ndc, sEnd, ndl, url, webUrl, profileName + pathTail(diffMatches, i), contextPathSrc, contextPathDst, trimDifferential, contextName, resultPathBase, true, e, cpath, redirector, srcSD);
}
if (elementToRemove != null) {
differential.getElement().remove(elementToRemove);
ndl--;
}
if (fixedType != null) {
for (Iterator<TypeRefComponent> iter = e.getType().iterator(); iter.hasNext(); ) {
TypeRefComponent tr = iter.next();
if (!tr.getCode().equals(fixedType)) {
iter.remove();
}
}
}
for (BaseTypeSlice bs : baseSlices) {
if (!bs.handled) {
// ok we gimme up a fake differential that says nothing, and run that against the slice.
StructureDefinitionDifferentialComponent fakeDiff = new StructureDefinitionDifferentialComponent();
fakeDiff.getElementFirstRep().setPath(bs.defn.getPath());
processPaths(indent + " ", result, base, fakeDiff, bs.start, 0, bs.end, 0, url, webUrl, profileName + tail(bs.defn.getPath()), contextPathSrc, contextPathDst, trimDifferential, contextName, resultPathBase, true, e, cpath, redirector, srcSD);
}
}
// ok, done with that - next in the base list
baseCursor = baseSlices.get(baseSlices.size() - 1).end + 1;
diffCursor = ndl + 1;
// throw new Error("not done yet - slicing / types @ "+cpath);
} else {
// first - check that the slicing is ok
boolean closed = currentBase.getSlicing().getRules() == SlicingRules.CLOSED;
int diffpos = 0;
boolean isExtension = cpath.endsWith(".extension") || cpath.endsWith(".modifierExtension");
if (diffMatches.get(0).hasSlicing()) {
// it might be null if the differential doesn't want to say anything about slicing
// if (!isExtension)
// diffpos++; // if there's a slice on the first, we'll ignore any content it has
ElementDefinitionSlicingComponent dSlice = diffMatches.get(0).getSlicing();
ElementDefinitionSlicingComponent bSlice = currentBase.getSlicing();
if (dSlice.hasOrderedElement() && bSlice.hasOrderedElement() && !orderMatches(dSlice.getOrderedElement(), bSlice.getOrderedElement()))
throw new DefinitionException(context.formatMessage(I18nConstants.SLICING_RULES_ON_DIFFERENTIAL__DO_NOT_MATCH_THOSE_ON_BASE___ORDER___, summarizeSlicing(dSlice), summarizeSlicing(bSlice), path, contextName));
if (!discriminatorMatches(dSlice.getDiscriminator(), bSlice.getDiscriminator()))
throw new DefinitionException(context.formatMessage(I18nConstants.SLICING_RULES_ON_DIFFERENTIAL__DO_NOT_MATCH_THOSE_ON_BASE___DISCIMINATOR___, summarizeSlicing(dSlice), summarizeSlicing(bSlice), path, contextName));
if (!currentBase.isChoice() && !ruleMatches(dSlice.getRules(), bSlice.getRules()))
throw new DefinitionException(context.formatMessage(I18nConstants.SLICING_RULES_ON_DIFFERENTIAL__DO_NOT_MATCH_THOSE_ON_BASE___RULE___, summarizeSlicing(dSlice), summarizeSlicing(bSlice), path, contextName));
}
ElementDefinition outcome = updateURLs(url, webUrl, currentBase.copy());
outcome.setPath(fixedPathDest(contextPathDst, outcome.getPath(), redirector, contextPathSrc));
updateFromBase(outcome, currentBase);
if (diffMatches.get(0).hasSlicing() || !diffMatches.get(0).hasSliceName()) {
updateFromSlicing(outcome.getSlicing(), diffMatches.get(0).getSlicing());
// if there's no slice, we don't want to update the unsliced description
updateFromDefinition(outcome, diffMatches.get(0), profileName, closed, url, srcSD);
removeStatusExtensions(outcome);
} else if (!diffMatches.get(0).hasSliceName()) {
// because of updateFromDefinition isn't called
diffMatches.get(0).setUserData(GENERATED_IN_SNAPSHOT, outcome);
}
result.getElement().add(outcome);
if (!diffMatches.get(0).hasSliceName()) {
// it's not real content, just the slice
diffpos++;
}
if (hasInnerDiffMatches(differential, cpath, diffCursor, diffLimit, base.getElement(), false)) {
int nbl = findEndOfElement(base, baseCursor);
int ndx = differential.getElement().indexOf(diffMatches.get(0));
int ndc = ndx + (diffMatches.get(0).hasSlicing() ? 1 : 0);
int ndl = findEndOfElement(differential, ndx);
if (nbl == baseCursor) {
if (base.getElement().get(baseCursor).getType().size() != 1) {
throw new Error(context.formatMessage(I18nConstants.DIFFERENTIAL_WALKS_INTO____BUT_THE_BASE_DOES_NOT_AND_THERE_IS_NOT_A_SINGLE_FIXED_TYPE_THE_TYPE_IS__THIS_IS_NOT_HANDLED_YET, cpath, diffMatches.get(0).toString(), base.getElement().get(baseCursor).typeSummary()));
}
StructureDefinition dt = getProfileForDataType(base.getElement().get(baseCursor).getType().get(0), webUrl);
if (dt == null) {
throw new DefinitionException(context.formatMessage(I18nConstants.UNKNOWN_TYPE__AT_, outcome.getType().get(0), diffMatches.get(0).getPath()));
}
contextName = dt.getUrl();
while (differential.getElement().size() > diffCursor && pathStartsWith(differential.getElement().get(diffCursor).getPath(), cpath + ".")) diffCursor++;
processPaths(indent + " ", result, dt.getSnapshot(), differential, 1, ndc, dt.getSnapshot().getElement().size() - 1, ndl, url, getWebUrl(dt, webUrl, indent), profileName, cpath, outcome.getPath(), trimDifferential, contextName, resultPathBase, false, null, null, redirector, srcSD);
} else {
processPaths(indent + " ", result, base, differential, baseCursor + 1, ndc, nbl, ndl, url, webUrl, profileName + pathTail(diffMatches, 0), contextPathSrc, contextPathDst, trimDifferential, contextName, resultPathBase, false, null, null, null, srcSD);
}
// throw new Error("Not done yet");
// } else if (currentBase.getType().get(0).getCode().equals("BackboneElement") && diffMatches.size() > 0 && diffMatches.get(0).hasSliceName()) {
} else if (currentBase.getType().get(0).getCode().equals("BackboneElement")) {
// We need to copy children of the backbone element before we start messing around with slices
int nbl = findEndOfElement(base, baseCursor);
for (int i = baseCursor + 1; i <= nbl; i++) {
outcome = updateURLs(url, webUrl, base.getElement().get(i).copy());
result.getElement().add(outcome);
}
}
// now, we have two lists, base and diff. we're going to work through base, looking for matches in diff.
List<ElementDefinition> baseMatches = getSiblings(base.getElement(), currentBase);
for (ElementDefinition baseItem : baseMatches) {
baseCursor = base.getElement().indexOf(baseItem);
outcome = updateURLs(url, webUrl, baseItem.copy());
updateFromBase(outcome, currentBase);
outcome.setPath(fixedPathDest(contextPathDst, outcome.getPath(), redirector, contextPathSrc));
outcome.setSlicing(null);
if (!outcome.getPath().startsWith(resultPathBase))
throw new DefinitionException(context.formatMessage(I18nConstants.ADDING_WRONG_PATH));
if (diffpos < diffMatches.size() && diffMatches.get(diffpos).hasSliceName() && diffMatches.get(diffpos).getSliceName().equals(outcome.getSliceName())) {
// if there's a diff, we update the outcome with diff
// no? updateFromDefinition(outcome, diffMatches.get(diffpos), profileName, closed, url);
// then process any children
int nbl = findEndOfElement(base, baseCursor);
int ndc = differential.getElement().indexOf(diffMatches.get(diffpos));
int ndl = findEndOfElement(differential, ndc);
// now we process the base scope repeatedly for each instance of the item in the differential list
processPaths(indent + " ", result, base, differential, baseCursor, ndc, nbl, ndl, url, webUrl, profileName + pathTail(diffMatches, diffpos), contextPathSrc, contextPathDst, closed, contextName, resultPathBase, true, null, null, redirector, srcSD);
// ok, done with that - now set the cursors for if this is the end
baseCursor = nbl;
diffCursor = ndl + 1;
diffpos++;
} else {
result.getElement().add(outcome);
baseCursor++;
// just copy any children on the base
while (baseCursor < base.getElement().size() && base.getElement().get(baseCursor).getPath().startsWith(path) && !base.getElement().get(baseCursor).getPath().equals(path)) {
outcome = updateURLs(url, webUrl, base.getElement().get(baseCursor).copy());
outcome.setPath(fixedPathDest(contextPathDst, outcome.getPath(), redirector, contextPathSrc));
if (!outcome.getPath().startsWith(resultPathBase))
throw new DefinitionException(context.formatMessage(I18nConstants.ADDING_WRONG_PATH));
result.getElement().add(outcome);
baseCursor++;
}
// Lloyd - add this for test T15
baseCursor--;
}
}
// finally, we process any remaining entries in diff, which are new (and which are only allowed if the base wasn't closed
boolean checkImplicitTypes = false;
if (closed && diffpos < diffMatches.size()) {
// this is a problem, unless we're on a polymorhpic type and we're going to constrain a slice that actually implicitly exists
if (currentBase.getPath().endsWith("[x]")) {
checkImplicitTypes = true;
} else {
throw new DefinitionException(context.formatMessage(I18nConstants.THE_BASE_SNAPSHOT_MARKS_A_SLICING_AS_CLOSED_BUT_THE_DIFFERENTIAL_TRIES_TO_EXTEND_IT_IN__AT__, profileName, path, cpath));
}
}
if (diffpos == diffMatches.size()) {
// Lloyd This was causing problems w/ Telus
// diffCursor++;
} else {
while (diffpos < diffMatches.size()) {
ElementDefinition diffItem = diffMatches.get(diffpos);
for (ElementDefinition baseItem : baseMatches) if (baseItem.getSliceName().equals(diffItem.getSliceName()))
throw new DefinitionException(context.formatMessage(I18nConstants.NAMED_ITEMS_ARE_OUT_OF_ORDER_IN_THE_SLICE));
outcome = updateURLs(url, webUrl, currentBase.copy());
// outcome = updateURLs(url, diffItem.copy());
outcome.setPath(fixedPathDest(contextPathDst, outcome.getPath(), redirector, contextPathSrc));
updateFromBase(outcome, currentBase);
outcome.setSlicing(null);
// we're in a slice, so it's only a mandatory if it's explicitly marked so
outcome.setMin(0);
if (!outcome.getPath().startsWith(resultPathBase))
throw new DefinitionException(context.formatMessage(I18nConstants.ADDING_WRONG_PATH));
result.getElement().add(outcome);
updateFromDefinition(outcome, diffItem, profileName, trimDifferential, url, srcSD);
removeStatusExtensions(outcome);
// --- LM Added this
diffCursor = differential.getElement().indexOf(diffItem) + 1;
if (!outcome.getType().isEmpty() && (/*outcome.getType().get(0).getCode().equals("Extension") || */
differential.getElement().size() > diffCursor) && outcome.getPath().contains(".")) /* && isDataType(outcome.getType())*/
{
// don't want to do this for the root, since that's base, and we're already processing it
if (!baseWalksInto(base.getElement(), baseCursor)) {
if (differential.getElement().size() > diffCursor && pathStartsWith(differential.getElement().get(diffCursor).getPath(), diffMatches.get(0).getPath() + ".")) {
if (outcome.getType().size() > 1)
for (TypeRefComponent t : outcome.getType()) {
if (!t.getCode().equals("Reference"))
throw new DefinitionException(context.formatMessage(I18nConstants._HAS_CHILDREN__AND_MULTIPLE_TYPES__IN_PROFILE_, diffMatches.get(0).getPath(), differential.getElement().get(diffCursor).getPath(), typeCode(outcome.getType()), profileName));
}
TypeRefComponent t = outcome.getType().get(0);
if (t.getCode().equals("BackboneElement")) {
int baseStart = base.getElement().indexOf(currentBase) + 1;
int baseMax = baseStart + 1;
while (baseMax < base.getElement().size() && base.getElement().get(baseMax).getPath().startsWith(currentBase.getPath() + ".")) baseMax++;
int start = diffCursor;
while (differential.getElement().size() > diffCursor && pathStartsWith(differential.getElement().get(diffCursor).getPath(), diffMatches.get(0).getPath() + ".")) diffCursor++;
processPaths(indent + " ", result, base, differential, baseStart, start - 1, baseMax - 1, diffCursor - 1, url, webUrl, profileName + pathTail(diffMatches, 0), base.getElement().get(0).getPath(), base.getElement().get(0).getPath(), trimDifferential, contextName, resultPathBase, false, null, null, redirector, srcSD);
} else {
StructureDefinition dt = getProfileForDataType(outcome.getType().get(0), webUrl);
// }
if (dt == null)
throw new DefinitionException(context.formatMessage(I18nConstants._HAS_CHILDREN__FOR_TYPE__IN_PROFILE__BUT_CANT_FIND_TYPE, diffMatches.get(0).getPath(), differential.getElement().get(diffCursor).getPath(), typeCode(outcome.getType()), profileName));
contextName = dt.getUrl();
int start = diffCursor;
while (differential.getElement().size() > diffCursor && pathStartsWith(differential.getElement().get(diffCursor).getPath(), diffMatches.get(0).getPath() + ".")) diffCursor++;
processPaths(indent + " ", result, dt.getSnapshot(), differential, 1, /* starting again on the data type, but skip the root */
start - 1, dt.getSnapshot().getElement().size() - 1, diffCursor - 1, url, getWebUrl(dt, webUrl, indent), profileName + pathTail(diffMatches, 0), diffMatches.get(0).getPath(), outcome.getPath(), trimDifferential, contextName, resultPathBase, false, null, null, redirector, srcSD);
}
}
}
}
// ---
diffpos++;
}
}
baseCursor++;
}
}
}
int i = 0;
for (ElementDefinition e : result.getElement()) {
i++;
if (e.hasMinElement() && e.getMinElement().getValue() == null)
throw new Error(context.formatMessage(I18nConstants.NULL_MIN));
}
return res;
}
Also used :
ArrayList(java.util.ArrayList)
FHIRFormatError(org.hl7.fhir.exceptions.FHIRFormatError)
CanonicalType(org.hl7.fhir.r5.model.CanonicalType)
FHIRException(org.hl7.fhir.exceptions.FHIRException)
StructureDefinition(org.hl7.fhir.r5.model.StructureDefinition)
TypeRefComponent(org.hl7.fhir.r5.model.ElementDefinition.TypeRefComponent)
Iterator(java.util.Iterator)
StructureDefinitionDifferentialComponent(org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionDifferentialComponent)
ElementDefinitionSlicingComponent(org.hl7.fhir.r5.model.ElementDefinition.ElementDefinitionSlicingComponent)
ArrayList(java.util.ArrayList)
List(java.util.List)
ElementDefinition(org.hl7.fhir.r5.model.ElementDefinition)
DefinitionException(org.hl7.fhir.exceptions.DefinitionException)
Aggregations
DefinitionException (org.hl7.fhir.exceptions.DefinitionException)12
ElementDefinition (org.hl7.fhir.r5.model.ElementDefinition)10
FHIRFormatError (org.hl7.fhir.exceptions.FHIRFormatError)8
StructureDefinition (org.hl7.fhir.r5.model.StructureDefinition)8
StructureDefinitionSnapshotComponent (org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionSnapshotComponent)8
StructureDefinitionDifferentialComponent (org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionDifferentialComponent)7
ArrayList (java.util.ArrayList)6
HashSet (java.util.HashSet)6
FHIRException (org.hl7.fhir.exceptions.FHIRException)6
Narrative (org.hl7.fhir.r5.model.Narrative)6
XhtmlNode (org.hl7.fhir.utilities.xhtml.XhtmlNode)6
TypeRefComponent (org.hl7.fhir.r5.model.ElementDefinition.TypeRefComponent)5
ElementDefinition (org.hl7.fhir.r4b.model.ElementDefinition)4
UriType (org.hl7.fhir.r5.model.UriType)4
IOException (java.io.IOException)3
List (java.util.List)3
FileNotFoundException (java.io.FileNotFoundException)2
Iterator (java.util.Iterator)2
ElementDefinition (org.hl7.fhir.dstu3.model.ElementDefinition)2
ElementDefinition (org.hl7.fhir.r4.model.ElementDefinition)2
