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Merge pull request #375 from hapifhir/gg-v5121 

Gg v5121
This commit is contained in:
Grahame Grieve 2020-11-11 10:37:49 +11:00 committed by GitHub
parent 1db9a028bf ef3e34ae01
commit 28eac1a7d5
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GPG Key ID: 4AEE18F83AFDEB23
11 changed files with 200 additions and 69 deletions
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11
RELEASE_NOTES.md
View File

@ -0,0 +1,11 @@
Validator:
* fix problem with min getting set to 1 on slices.
* fix problem with element definition resolution in profiles for contentReference
* don't apply warning about reference content when it's used as a pattern
Other code changes:
* fix problem with rendering unchanged terminology bindings in profiles
* fix problem rendering canonical URLs with | in them
* fix problem rendering multiple manifestations for an allergy reaction
* fix for NPE in version string comparison
* add styling when adding markdown to table

157
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/ProfileUtilities.java
View File

@ -590,7 +590,7 @@ public class ProfileUtilities extends TranslatingUtilities {
baseSnapshot = cloneSnapshot(baseSnapshot, base.getType(), derivedType);
}
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, new ArrayList<ElementRedirection>(), base);
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()) {
@ -968,7 +968,7 @@ public class ProfileUtilities extends TranslatingUtilities {
* @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, String typeSlicingPath, List<ElementRedirection> redirector, StructureDefinition srcSD) throws DefinitionException, FHIRException {
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+", redirector = "+(redirector == null ? "null" : redirector.toString())+")");
}
@ -1002,7 +1002,7 @@ public class ProfileUtilities extends TranslatingUtilities {
// well, the profile walks into this, so we need to as well
// 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, redirector, srcSD);
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) {
@ -1032,7 +1032,7 @@ public class ProfileUtilities extends TranslatingUtilities {
while (differential.getElement().size() > diffCursor && pathStartsWith(differential.getElement().get(diffCursor).getPath(), cpath+"."))
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-1, url, getWebUrl(dt, webUrl, indent), profileName, cpath, outcome.getPath(), trimDifferential, contextName, resultPathBase, false, null, redirector, srcSD);
diffCursor-1, url, getWebUrl(dt, webUrl, indent), profileName, cpath, outcome.getPath(), trimDifferential, contextName, resultPathBase, false, null, null, redirector, srcSD);
}
}
baseCursor++;
@ -1103,8 +1103,14 @@ public class ProfileUtilities extends TranslatingUtilities {
if (res == null)
res = outcome;
updateFromBase(outcome, currentBase);
if (diffMatches.get(0).hasSliceName())
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
@ -1148,7 +1154,7 @@ public class ProfileUtilities extends TranslatingUtilities {
while (diffCursor <= diffLimit && differential.getElement().size() > diffCursor && pathStartsWith(differential.getElement().get(diffCursor).getPath(), diffMatches.get(0).getPath()+"."))
diffCursor++;
if (outcome.hasContentReference()) {
ElementDefinition tgt = getElementById(base.getElement(), outcome.getContentReference());
ElementDefinition 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);
@ -1156,14 +1162,14 @@ public class ProfileUtilities extends TranslatingUtilities {
int nbl = nbc;
while (nbl < base.getElement().size() && base.getElement().get(nbl).getPath().startsWith(tgt.getPath()+"."))
nbl++;
processPaths(indent+" ", result, base, differential, nbc, start - 1, nbl-1, diffCursor - 1, url, webUrl, profileName, tgt.getPath(), diffMatches.get(0).getPath(), trimDifferential, contextName, resultPathBase, false, null, redirectorStack(redirector, outcome, cpath), srcSD);
processPaths(indent+" ", result, base, differential, nbc, start - 1, nbl-1, diffCursor - 1, url, webUrl, profileName, tgt.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)) : 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, new ArrayList<ElementRedirection>(), srcSD);
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);
}
}
}
@ -1249,7 +1255,7 @@ public class ProfileUtilities extends TranslatingUtilities {
// 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, redirector, srcSD);
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.
@ -1257,6 +1263,17 @@ public class ProfileUtilities extends TranslatingUtilities {
e.getSlicing().addDiscriminator().setType(DiscriminatorType.TYPE).setPath("$this");
e.getSlicing().setRules(SlicingRules.CLOSED); // 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().setOrdered(false);
// check that there's a slice for each allowed types
Set<String> allowedTypes = getListOfTypes(e);
for (TypeSlice t : typeList) {
allowedTypes.remove(t.type);
}
// GG - work in progress..
// if (!allowedTypes.isEmpty()) {
// System.out.println("!!: Error at "+cpath+": Allowed Types not sliced = "+allowedTypes);
// throw new Error("Error at "+cpath+": Allowed Types not sliced = "+allowedTypes);
// }
start++;
String fixedType = null;
@ -1274,7 +1291,7 @@ public class ProfileUtilities extends TranslatingUtilities {
}
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, null, redirector, srcSD);
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);
@ -1306,14 +1323,16 @@ public class ProfileUtilities extends TranslatingUtilities {
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, redirector, srcSD);
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
@ -1328,6 +1347,7 @@ public class ProfileUtilities extends TranslatingUtilities {
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()) {
@ -1348,7 +1368,7 @@ public class ProfileUtilities extends TranslatingUtilities {
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, redirector, srcSD);
diffCursor, url, getWebUrl(dt, webUrl, indent), profileName, cpath, outcome.getPath(), trimDifferential, contextName, resultPathBase, false, null, null, redirector, srcSD);
}
}
start++;
@ -1370,7 +1390,7 @@ public class ProfileUtilities extends TranslatingUtilities {
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, null, redirector, srcSD);
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;
@ -1403,7 +1423,7 @@ public class ProfileUtilities extends TranslatingUtilities {
// the profile walks into this, so we need to as well
// 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, redirector, srcSD);
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);
@ -1412,7 +1432,7 @@ public class ProfileUtilities extends TranslatingUtilities {
while (differential.getElement().size() > diffCursor && pathStartsWith(differential.getElement().get(diffCursor).getPath(), cpath+"."))
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-1, url, getWebUrl(dt, webUrl, indent), profileName, cpath, outcome.getPath(), trimDifferential, contextName, resultPathBase, false, null, redirector, srcSD);
diffCursor-1, url, getWebUrl(dt, webUrl, indent), profileName, cpath, outcome.getPath(), trimDifferential, contextName, resultPathBase, false, null, null, redirector, srcSD);
}
baseCursor++;
} else {
@ -1505,7 +1525,7 @@ public class ProfileUtilities extends TranslatingUtilities {
// 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, cpath, redirector, srcSD);
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.
@ -1538,7 +1558,7 @@ public class ProfileUtilities extends TranslatingUtilities {
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, cpath, redirector, srcSD);
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);
@ -1557,7 +1577,7 @@ public class ProfileUtilities extends TranslatingUtilities {
// 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, cpath, redirector, srcSD);
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);
}
}
@ -1614,10 +1634,10 @@ public class ProfileUtilities extends TranslatingUtilities {
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, redirector, srcSD);
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, srcSD);
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()) {
@ -1648,7 +1668,7 @@ public class ProfileUtilities extends TranslatingUtilities {
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, redirector, srcSD);
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;
@ -1693,7 +1713,7 @@ public class ProfileUtilities extends TranslatingUtilities {
outcome.setPath(fixedPathDest(contextPathDst, outcome.getPath(), redirector, contextPathSrc));
updateFromBase(outcome, currentBase);
outcome.setSlicing(null);
outcome.setMin(0); // were in a slice, so it's only a mandatory if it's explicitly marked so
outcome.setMin(0); // we're in a slice, so it's only a mandatory if it's explicitly marked so
if (!outcome.getPath().startsWith(resultPathBase))
throw new DefinitionException(context.formatMessage(I18nConstants.ADDING_WRONG_PATH));
result.getElement().add(outcome);
@ -1719,7 +1739,7 @@ public class ProfileUtilities extends TranslatingUtilities {
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, redirector, srcSD);
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));
@ -1733,7 +1753,7 @@ public class ProfileUtilities extends TranslatingUtilities {
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, redirector, srcSD);
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);
}
}
}
@ -1756,6 +1776,14 @@ public class ProfileUtilities extends TranslatingUtilities {
return res;
}
private Set<String> getListOfTypes(ElementDefinition e) {
Set<String> result = new HashSet<>();
for (TypeRefComponent t : e.getType()) {
result.add(t.getCode());
}
return result;
}
public StructureDefinition getTypeForElement(StructureDefinitionDifferentialComponent differential, int diffCursor, String profileName,
List<ElementDefinition> diffMatches, ElementDefinition outcome) {
if (outcome.getType().size() == 0) {
@ -3457,7 +3485,18 @@ public class ProfileUtilities extends TranslatingUtilities {
// return null;
}
private ElementDefinition getElementById(List<ElementDefinition> elements, String contentReference) {
private ElementDefinition getElementById(StructureDefinition source, List<ElementDefinition> elements, String contentReference) {
if (!contentReference.startsWith("#") && contentReference.contains("#")) {
String url = contentReference.substring(0, contentReference.indexOf("#"));
contentReference = contentReference.substring(contentReference.indexOf("#"));
if (!url.equals(source.getUrl())){
source = context.fetchResource(StructureDefinition.class, url);
if (source == null) {
return null;
}
elements = source.getSnapshot().getElement();
}
}
for (ElementDefinition ed : elements)
if (ed.hasId() && ("#"+ed.getId()).equals(contentReference))
return ed;
@ -3549,6 +3588,25 @@ public class ProfileUtilities extends TranslatingUtilities {
return piece;
}
private String checkForNoChange(Element source) {
if (source.hasUserData(DERIVATION_EQUALS)) {
return "opacity: 0.5";
} else {
return null;
}
}
private Piece applyAsUnchanged(Piece piece) {
piece.addStyle("opacity: 0.5");
return piece;
}
private String applyAsUnchanged() {
return "opacity: 0.5";
}
private Piece checkForNoChange(Element src1, Element src2, Piece piece) {
if (src1.hasUserData(DERIVATION_EQUALS) && src2.hasUserData(DERIVATION_EQUALS)) {
piece.addStyle("opacity: 0.5");
@ -4314,20 +4372,19 @@ public class ProfileUtilities extends TranslatingUtilities {
if (definition != null) {
ElementDefinitionBindingComponent binding = null;
if (valueDefn != null && valueDefn.hasBinding() && !valueDefn.getBinding().isEmpty())
binding = valueDefn.getBinding();
binding = makeUnifiedBinding(valueDefn.getBinding(), valueDefn);
else if (definition.hasBinding())
binding = definition.getBinding();
binding = makeUnifiedBinding(definition.getBinding(), definition);
if (binding!=null && !binding.isEmpty()) {
if (!c.getPieces().isEmpty())
c.addPiece(gen.new Piece("br"));
BindingResolution br = pkp.resolveBinding(profile, binding, definition.getPath());
c.getPieces().add(checkForNoChange(binding, gen.new Piece(null, translate("sd.table", "Binding")+": ", null).addStyle("font-weight:bold")));
c.getPieces().add(checkForNoChange(binding, gen.new Piece(br.url == null ? null : Utilities.isAbsoluteUrl(br.url) || !pkp.prependLinks() ? br.url : corePath+br.url, br.display, null)));
c.getPieces().add(checkForNoChange(binding.getValueSetElement(), gen.new Piece(br.url == null ? null : Utilities.isAbsoluteUrl(br.url) || !pkp.prependLinks() ? br.url : corePath+br.url, br.display, null)));
if (binding.hasStrength()) {
c.getPieces().add(checkForNoChange(binding, gen.new Piece(null, " (", null)));
c.getPieces().add(checkForNoChange(binding, gen.new Piece(corePath+"terminologies.html#"+binding.getStrength().toCode(), egt(binding.getStrengthElement()), binding.getStrength().getDefinition())));
c.getPieces().add(gen.new Piece(null, ")", null));
c.getPieces().add(checkForNoChange(binding.getStrengthElement(), gen.new Piece(null, " (", null)));
c.getPieces().add(checkForNoChange(binding.getStrengthElement(), gen.new Piece(corePath+"terminologies.html#"+binding.getStrength().toCode(), egt(binding.getStrengthElement()), binding.getStrength().getDefinition())));
c.getPieces().add(checkForNoChange(binding.getStrengthElement(), gen.new Piece(null, ")", null)));
}
if (binding.hasExtension(ToolingExtensions.EXT_MAX_VALUESET)) {
br = pkp.resolveBinding(profile, ToolingExtensions.readStringExtension(binding, ToolingExtensions.EXT_MAX_VALUESET), definition.getPath());
@ -4343,7 +4400,7 @@ public class ProfileUtilities extends TranslatingUtilities {
}
if (binding.hasDescription() && MarkDownProcessor.isSimpleMarkdown(binding.getDescription())) {
c.getPieces().add(gen.new Piece(null, ": ", null));
c.addMarkdownNoPara(binding.getDescription());
c.addMarkdownNoPara(binding.getDescription(), checkForNoChange(binding.getDescriptionElement()));
}
}
for (ElementDefinitionConstraintComponent inv : definition.getConstraint()) {
@ -4424,6 +4481,38 @@ public class ProfileUtilities extends TranslatingUtilities {
return c;
}
private ElementDefinitionBindingComponent makeUnifiedBinding(ElementDefinitionBindingComponent binding, ElementDefinition element) {
if (!element.hasUserData(DERIVATION_POINTER)) {
return binding;
}
ElementDefinition base = (ElementDefinition) element.getUserData(DERIVATION_POINTER);
if (!base.hasBinding()) {
return binding;
}
ElementDefinitionBindingComponent o = base.getBinding();
ElementDefinitionBindingComponent b = new ElementDefinitionBindingComponent();
b.setUserData(DERIVATION_POINTER, o);
if (binding.hasValueSet()) {
b.setValueSet(binding.getValueSet());
} else if (o.hasValueSet()) {
b.setValueSet(o.getValueSet());
b.getValueSetElement().setUserData(DERIVATION_EQUALS, o.getValueSetElement());
}
if (binding.hasStrength()) {
b.setStrength(binding.getStrength());
} else if (o.hasStrength()) {
b.setStrength(o.getStrength());
b.getStrengthElement().setUserData(DERIVATION_EQUALS, o.getStrengthElement());
}
if (binding.hasDescription()) {
b.setDescription(binding.getDescription());
} else if (o.hasDescription()) {
b.setDescription(o.getDescription());
b.getDescriptionElement().setUserData(DERIVATION_EQUALS, o.getDescriptionElement());
}
return b;
}
private void genFixedValue(HierarchicalTableGenerator gen, Row erow, DataType value, boolean snapshot, boolean pattern, String corePath, boolean skipnoValue) {
String ref = pkp.getLinkFor(corePath, value.fhirType());
if (ref != null) {
@ -6016,7 +6105,7 @@ public class ProfileUtilities extends TranslatingUtilities {
TableModel model = gen.new TableModel(id, true);
model.setDocoImg(prefix+"help16.png");
model.setDocoRef(prefix+"formats.html#table"); // todo: change to graph definition
model.setDocoRef(Utilities.pathURL(prefix, "formats.html#table")); // todo: change to graph definition
model.getTitles().add(gen.new Title(null, model.getDocoRef(), "Property", "A profiled resource", null, 0));
model.getTitles().add(gen.new Title(null, model.getDocoRef(), "Card.", "Minimum and Maximum # of times the the element can appear in the instance", null, 0));
model.getTitles().add(gen.new Title(null, model.getDocoRef(), "Content", "What goes here", null, 0));

11
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/DataRenderer.java
View File

@ -392,13 +392,18 @@ public class DataRenderer extends Renderer {
} else if (!getContext().isCanonicalUrlsAsLinks())
url = null;
}
if (url == null)
if (url == null) {
x.b().tx(uri.getValue());
else if (uri.getValue().startsWith("mailto:"))
} else if (uri.getValue().startsWith("mailto:")) {
x.ah(uri.getValue()).addText(uri.getValue().substring(7));
else
} else {
if (uri.getValue().contains("|")) {
x.ah(uri.getValue().substring(0, uri.getValue().indexOf("|"))).addText(uri.getValue());
} else {
x.ah(uri.getValue()).addText(uri.getValue());
}
}
}
protected void renderAnnotation(XhtmlNode x, Annotation annot) {
renderAnnotation(x, annot, false);

5
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/ProfileDrivenRenderer.java
View File

@ -824,7 +824,10 @@ public class ProfileDrivenRenderer extends ResourceRenderer {
if (p == null || p.getValues().size() == 0 || p.getValues().get(0) == null)
td.tx(" ");
else {
renderLeaf(res, p.getValues().get(0), e, td, td, false, showCodeDetails, displayHints, path, indent);
for (BaseWrapper vv : p.getValues()) {
td.sep(", ");
renderLeaf(res, vv, e, td, td, false, showCodeDetails, displayHints, path, indent);
}
}
}
}

1
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/SnapShotGenerationTests.java
View File

@ -465,6 +465,7 @@ public class SnapShotGenerationTests {
fp.setHostServices(context);
messages = new ArrayList<ValidationMessage>();
System.out.println("---- "+id+" -----------------------------------------");
if (test.isFail()) {
boolean failed = true;
try {

6
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/VersionUtilities.java
View File

@ -229,8 +229,14 @@ public class VersionUtilities {
* @return Is {@literal current} later or equal to {@literal test}? For example, if <code>this = 0.5</code> and <code>current = 0.6</code> this method will return true
*/
public static boolean isThisOrLater(String test, String current) {
if (test == null || current == null) {
return false;
}
String t = getMajMin(test);
String c = getMajMin(current);
if (t == null || c == null) {
return false;
}
if (c.compareTo(t) == 0) {
return isMajMinOrLaterPatch(test, current);
}

2
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/FilesystemPackageCacheManager.java
View File

@ -352,7 +352,7 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
System.out.print(" Installing: ");
}
if (npm.name() == null || id == null || !id.equals(npm.name())) {
if (npm.name() == null || id == null || !id.equalsIgnoreCase(npm.name())) {
if (!id.equals("hl7.fhir.r5.core")) {// temporary work around
throw new IOException("Attempt to import a mis-identified package. Expected " + id + ", got " + npm.name());
}

56
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/xhtml/HierarchicalTableGenerator.java
View File

@ -247,7 +247,7 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
Node document = parser.parse(md);
HtmlRenderer renderer = HtmlRenderer.builder().escapeHtml(true).build();
String html = renderer.render(document);
pieces.addAll(htmlToParagraphPieces(html));
pieces.addAll(htmlToParagraphPieces(html, null));
} catch (Exception e) {
e.printStackTrace();
}
@ -255,19 +255,23 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
}
public Cell addMarkdownNoPara(String md) {
return addMarkdownNoPara(md, null);
}
public Cell addMarkdownNoPara(String md, String style) {
try {
Parser parser = Parser.builder().build();
Node document = parser.parse(md);
HtmlRenderer renderer = HtmlRenderer.builder().escapeHtml(true).build();
String html = renderer.render(document);
pieces.addAll(htmlToParagraphPieces(html));
pieces.addAll(htmlToParagraphPieces(html, style));
} catch (Exception e) {
e.printStackTrace();
}
return this;
}
private List<Piece> htmlToParagraphPieces(String html) {
private List<Piece> htmlToParagraphPieces(String html, String style) {
List<Piece> myPieces = new ArrayList<Piece>();
try {
XhtmlNode node = new XhtmlParser().parseFragment("<html>"+html+"</html>");
@ -281,14 +285,17 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
}
if (c.getNodeType() == NodeType.Text) {
if (!Utilities.isWhitespace(c.getContent()))
addNode(myPieces, c);
addNode(myPieces, c, style);
} else if ("p".equals(c.getName())) {
for (XhtmlNode g : c.getChildNodes()) {
addNode(myPieces, g);
addNode(myPieces, g, style);
}
} else {
Piece x = new Piece(c.getName());
x.getChildren().addAll(c.getChildNodes());
if (style != null) {
x.addStyle(style);
}
myPieces.add(x);
}
}
@ -314,49 +321,56 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
if (html.contains(("<"))) {
XhtmlNode node = new XhtmlParser().parseFragment("<p>"+html+"</p>");
for (XhtmlNode c : node.getChildNodes()) {
addNode(myPieces, c);
addNode(myPieces, c, null);
}
} else
myPieces.add(new Piece(null, html, null));
return myPieces;
}
private void addNode(List<Piece> list, XhtmlNode c) {
private void addNode(List<Piece> list, XhtmlNode c, String style) {
if (c.getNodeType() == NodeType.Text)
list.add(new Piece(null, c.getContent(), null));
list.add(styleIt(new Piece(null, c.getContent(), null), style));
else if (c.getNodeType() == NodeType.Element) {
if (c.getName().equals("a")) {
list.add(new Piece(c.getAttribute("href"), c.allText(), c.getAttribute("title")));
list.add(styleIt(new Piece(c.getAttribute("href"), c.allText(), c.getAttribute("title")), style));
} else if (c.getName().equals("b") || c.getName().equals("em") || c.getName().equals("strong")) {
list.add(new Piece(null, c.allText(), null).setStyle("font-face: bold"));
list.add(styleIt(new Piece(null, c.allText(), null).setStyle("font-face: bold"), style));
} else if (c.getName().equals("code")) {
list.add(new Piece(null, c.allText(), null).setStyle("padding: 2px 4px; color: #005c00; background-color: #f9f2f4; white-space: nowrap; border-radius: 4px"));
list.add(styleIt(new Piece(null, c.allText(), null).setStyle("padding: 2px 4px; color: #005c00; background-color: #f9f2f4; white-space: nowrap; border-radius: 4px"), style));
} else if (c.getName().equals("i")) {
list.add(new Piece(null, c.allText(), null).setStyle("font-style: italic"));
list.add(styleIt(new Piece(null, c.allText(), null).setStyle("font-style: italic"), style));
} else if (c.getName().equals("pre")) {
Piece p = new Piece(c.getName()).setStyle("white-space: pre; font-family: courier");
Piece p = styleIt(new Piece(c.getName()).setStyle("white-space: pre; font-family: courier"), style);
list.add(p);
p.getChildren().addAll(c.getChildNodes());
} else if (c.getName().equals("ul") || c.getName().equals("ol")) {
Piece p = new Piece(c.getName());
Piece p = styleIt(new Piece(c.getName()), style);
list.add(p);
p.getChildren().addAll(c.getChildNodes());
} else if (c.getName().equals("i")) {
list.add(new Piece(null, c.allText(), null).setStyle("font-style: italic"));
list.add(styleIt(new Piece(null, c.allText(), null).setStyle("font-style: italic"), style));
} else if (c.getName().equals("h1")||c.getName().equals("h2")||c.getName().equals("h3")||c.getName().equals("h4")) {
Piece p = new Piece(c.getName());
Piece p = styleIt(new Piece(c.getName()), style);
list.add(p);
p.getChildren().addAll(c.getChildNodes());
} else if (c.getName().equals("br")) {
list.add(new Piece(c.getName()));
list.add(styleIt(new Piece(c.getName()), style));
} else {
throw new Error("Not handled yet: "+c.getName());
}
} else
throw new Error("Unhandled type "+c.getNodeType().toString());
}
private Piece styleIt(Piece piece, String style) {
if (style != null) {
piece.addStyle(style);
}
return piece;
}
public Cell addStyle(String style) {
for (Piece p : pieces)
p.addStyle(style);
@ -583,7 +597,7 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
model.setAlternating(alternating);
model.setDocoImg(prefix+"help16.png");
model.setDocoRef(prefix+"formats.html#table");
model.setDocoRef(Utilities.pathURL(prefix, "formats.html#table"));
model.getTitles().add(new Title(null, model.getDocoRef(), translate("sd.head", "Name"), translate("sd.hint", "The logical name of the element"), null, 0));
model.getTitles().add(new Title(null, model.getDocoRef(), translate("sd.head", "Flags"), translate("sd.hint", "Information about the use of the element"), null, 0));
model.getTitles().add(new Title(null, model.getDocoRef(), translate("sd.head", "Card."), translate("sd.hint", "Minimum and Maximum # of times the the element can appear in the instance"), null, 0));
@ -600,7 +614,7 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
model.setAlternating(true);
model.setDocoImg(prefix+"help16.png");
model.setDocoRef(prefix+"formats.html#table");
model.setDocoRef(Utilities.pathURL(prefix, "formats.html#table"));
model.getTitles().add(new Title(null, model.getDocoRef(), translate("sd.head", "Name"), translate("sd.hint", "The logical name of the element"), null, 0));
model.getTitles().add(new Title(null, model.getDocoRef(), translate("sd.head", "L Flags"), translate("sd.hint", "Information about the use of the element - Left Structure"), null, 0).setStyle("border-left: 1px grey solid"));
model.getTitles().add(new Title(null, model.getDocoRef(), translate("sd.head", "L Card."), translate("sd.hint", "Minimum and Maximum # of times the the element can appear in the instance - Left Structure"), null, 0));

6
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/xhtml/XhtmlNode.java
View File

@ -843,11 +843,11 @@ public class XhtmlNode implements IBaseXhtml {
public XhtmlNode sep(String separator) {
// if there's already text, add the separator
if (seperated) {
// if there's already text, add the separator. otherwise, we'll add it next time
if (!seperated) {
seperated = true;
return this;
}
seperated = true;
return tx(separator);
}

2
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java
View File

@ -2419,9 +2419,11 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
String ref = reference.getReference();
if (Utilities.noString(ref)) {
if (!path.contains("element.pattern")) { // this business rule doesn't apply to patterns
if (Utilities.noString(reference.getIdentifier().getSystem()) && Utilities.noString(reference.getIdentifier().getValue())) {
warning(errors, IssueType.STRUCTURE, element.line(), element.col(), path, !Utilities.noString(element.getNamedChildValue("display")), I18nConstants.REFERENCE_REF_NODISPLAY);
}
}
return;
} else if (Utilities.existsInList(ref, "http://tools.ietf.org/html/bcp47")) {
// special known URLs that can't be validated but are known to be valid

2
pom.xml
View File

@ -19,7 +19,7 @@
<properties>
<hapi_fhir_version>5.1.0</hapi_fhir_version>
<validator_test_case_version>1.1.48-SNAPSHOT</validator_test_case_version>
<validator_test_case_version>1.1.49-SNAPSHOT</validator_test_case_version>
<junit_jupiter_version>5.6.2</junit_jupiter_version>
<maven_surefire_version>3.0.0-M4</maven_surefire_version>
<jacoco_version>0.8.5</jacoco_version>