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fix issue generation snapshot and content reference, and work around old erroneous binding description in R4

This commit is contained in:
Grahame Grieve 2021-09-29 16:16:30 +10:00
parent 23a5f47978
commit a6644ae49e
1 changed files with 60 additions and 21 deletions
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67
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/ProfileUtilities.java
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@ -109,6 +109,7 @@ import org.hl7.fhir.r5.renderers.spreadsheets.SpreadsheetGenerator;
import org.hl7.fhir.r5.terminologies.ValueSetExpander.ValueSetExpansionOutcome; import org.hl7.fhir.r5.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
import org.hl7.fhir.r5.utils.FHIRLexer; import org.hl7.fhir.r5.utils.FHIRLexer;
import org.hl7.fhir.r5.utils.FHIRPathEngine; import org.hl7.fhir.r5.utils.FHIRPathEngine;
import org.hl7.fhir.r5.utils.PublicationHacker;
import org.hl7.fhir.r5.utils.ToolingExtensions; import org.hl7.fhir.r5.utils.ToolingExtensions;
import org.hl7.fhir.r5.utils.TranslatingUtilities; import org.hl7.fhir.r5.utils.TranslatingUtilities;
import org.hl7.fhir.r5.utils.XVerExtensionManager; import org.hl7.fhir.r5.utils.XVerExtensionManager;
@ -666,6 +667,7 @@ public class ProfileUtilities extends TranslatingUtilities {
throw new Error(context.formatMessage(I18nConstants.TYPE_ON_FIRST_SNAPSHOT_ELEMENT_FOR__IN__FROM_, derived.getSnapshot().getElementFirstRep().getPath(), derived.getUrl(), base.getUrl())); throw new Error(context.formatMessage(I18nConstants.TYPE_ON_FIRST_SNAPSHOT_ELEMENT_FOR__IN__FROM_, derived.getSnapshot().getElementFirstRep().getPath(), derived.getUrl(), base.getUrl()));
updateMaps(base, derived); updateMaps(base, derived);
setIds(derived, false);
if (debug) { if (debug) {
System.out.println("Differential: "); System.out.println("Differential: ");
for (ElementDefinition ed : derived.getDifferential().getElement()) for (ElementDefinition ed : derived.getDifferential().getElement())
@ -674,7 +676,6 @@ public class ProfileUtilities extends TranslatingUtilities {
for (ElementDefinition ed : derived.getSnapshot().getElement()) for (ElementDefinition ed : derived.getSnapshot().getElement())
System.out.println(" "+ed.getId()+" : "+typeSummaryWithProfile(ed)+"["+ed.getMin()+".."+ed.getMax()+"]"+sliceSummary(ed)+" "+constraintSummary(ed)); System.out.println(" "+ed.getId()+" : "+typeSummaryWithProfile(ed)+"["+ed.getMin()+".."+ed.getMax()+"]"+sliceSummary(ed)+" "+constraintSummary(ed));
} }
setIds(derived, false);
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder(); CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
//Check that all differential elements have a corresponding snapshot element //Check that all differential elements have a corresponding snapshot element
int ce = 0; int ce = 0;
@ -702,10 +703,10 @@ public class ProfileUtilities extends TranslatingUtilities {
if (!debug) { if (!debug) {
System.out.println("Differential: "); System.out.println("Differential: ");
for (ElementDefinition ed : derived.getDifferential().getElement()) for (ElementDefinition ed : derived.getDifferential().getElement())
System.out.println(" "+ed.getId()+" : "+typeSummaryWithProfile(ed)+"["+ed.getMin()+".."+ed.getMax()+"]"+sliceSummary(ed)+" "+constraintSummary(ed)); System.out.println(" "+ed.getId()+" = "+ed.getPath()+" : "+typeSummaryWithProfile(ed)+"["+ed.getMin()+".."+ed.getMax()+"]"+sliceSummary(ed)+" "+constraintSummary(ed));
System.out.println("Snapshot: "); System.out.println("Snapshot: ");
for (ElementDefinition ed : derived.getSnapshot().getElement()) for (ElementDefinition ed : derived.getSnapshot().getElement())
System.out.println(" "+ed.getId()+" : "+typeSummaryWithProfile(ed)+"["+ed.getMin()+".."+ed.getMax()+"]"+sliceSummary(ed)+" "+constraintSummary(ed)); System.out.println(" "+ed.getId()+" = "+ed.getPath()+" : "+typeSummaryWithProfile(ed)+"["+ed.getMin()+".."+ed.getMax()+"]"+sliceSummary(ed)+" "+constraintSummary(ed));
} }
if (exception) if (exception)
throw new DefinitionException(msg); throw new DefinitionException(msg);
@ -1053,7 +1054,7 @@ public class ProfileUtilities extends TranslatingUtilities {
private ElementDefinition processPaths(String indent, StructureDefinitionSnapshotComponent result, StructureDefinitionSnapshotComponent base, StructureDefinitionDifferentialComponent differential, int baseCursor, int diffCursor, int baseLimit, 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 { 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) { 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())+")"); 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; ElementDefinition res = null;
List<TypeSlice> typeList = new ArrayList<>(); List<TypeSlice> typeList = new ArrayList<>();
@ -1088,7 +1089,7 @@ public class ProfileUtilities extends TranslatingUtilities {
processPaths(indent+" ", result, base, differential, baseCursor+1, diffCursor, baseLimit, diffLimit, url, webUrl, profileName, contextPathSrc, contextPathDst, trimDifferential, contextName, resultPathBase, false, null, 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); baseCursor = indexOfFirstNonChild(base, currentBase, baseCursor+1, baseLimit);
} else { } else {
if (outcome.getType().size() == 0) { 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)); throw new DefinitionException(context.formatMessage(I18nConstants._HAS_NO_CHILDREN__AND_NO_TYPES_IN_PROFILE_, cpath, differential.getElement().get(diffCursor).getPath(), profileName));
} }
boolean nonExtension = false; boolean nonExtension = false;
@ -1103,19 +1104,46 @@ public class ProfileUtilities extends TranslatingUtilities {
} }
} }
} }
int start = diffCursor;
while (differential.getElement().size() > diffCursor && pathStartsWith(differential.getElement().get(diffCursor).getPath(), cpath+"."))
diffCursor++;
if (nonExtension) { 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)); 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)); StructureDefinition dt = outcome.getType().size() > 1 ? context.fetchTypeDefinition("Element") : getProfileForDataType(outcome.getType().get(0));
if (dt == null) { if (dt == null) {
throw new DefinitionException(context.formatMessage(I18nConstants.UNKNOWN_TYPE__AT_, outcome.getType().get(0), cpath)); throw new DefinitionException(context.formatMessage(I18nConstants.UNKNOWN_TYPE__AT_, outcome.getType().get(0), cpath));
} }
contextName = dt.getUrl(); contextName = dt.getUrl();
int start = diffCursor; if (redirector.isEmpty()) {
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, 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); 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++; baseCursor++;
@ -1716,8 +1744,9 @@ public class ProfileUtilities extends TranslatingUtilities {
updateFromSlicing(outcome.getSlicing(), diffMatches.get(0).getSlicing()); updateFromSlicing(outcome.getSlicing(), diffMatches.get(0).getSlicing());
updateFromDefinition(outcome, diffMatches.get(0), profileName, closed, url, srcSD); // if there's no slice, we don't want to update the unsliced description updateFromDefinition(outcome, diffMatches.get(0), profileName, closed, url, srcSD); // if there's no slice, we don't want to update the unsliced description
removeStatusExtensions(outcome); removeStatusExtensions(outcome);
} else if (!diffMatches.get(0).hasSliceName()) } else if (!diffMatches.get(0).hasSliceName()) {
diffMatches.get(0).setUserData(GENERATED_IN_SNAPSHOT, outcome); // because of updateFromDefinition isn't called diffMatches.get(0).setUserData(GENERATED_IN_SNAPSHOT, outcome); // because of updateFromDefinition isn't called
}
result.getElement().add(outcome); result.getElement().add(outcome);
@ -2314,7 +2343,12 @@ public class ProfileUtilities extends TranslatingUtilities {
return pathSimple; return pathSimple;
// String ptail = pathSimple.substring(contextPath.length() + 1); // String ptail = pathSimple.substring(contextPath.length() + 1);
if (redirector.size() > 0) { if (redirector.size() > 0) {
String ptail = pathSimple.substring(contextPath.length()+1); String ptail = null;
if (contextPath.length() >= pathSimple.length()) {
ptail = pathSimple.substring(pathSimple.indexOf(".")+1);
} else {
ptail = pathSimple.substring(contextPath.length()+1);
}
return redirector.get(redirector.size()-1).getPath()+"."+ptail; return redirector.get(redirector.size()-1).getPath()+"."+ptail;
// return contextPath+"."+tail(redirector.getPath())+"."+ptail.substring(ptail.indexOf(".")+1); // return contextPath+"."+tail(redirector.getPath())+"."+ptail.substring(ptail.indexOf(".")+1);
} else { } else {
@ -2329,7 +2363,12 @@ public class ProfileUtilities extends TranslatingUtilities {
s = pathSimple; s = pathSimple;
else { else {
if (redirector.size() > 0) { if (redirector.size() > 0) {
String ptail = pathSimple.substring(redirectSource.length() + 1); String ptail = null;
if (redirectSource.length() >= pathSimple.length()) {
ptail = pathSimple.substring(pathSimple.indexOf(".")+1);
} else {
ptail = pathSimple.substring(redirectSource.length()+1);
}
// ptail = ptail.substring(ptail.indexOf(".")+1); // ptail = ptail.substring(ptail.indexOf(".")+1);
s = contextPath+"."+/*tail(redirector.getPath())+"."+*/ptail; s = contextPath+"."+/*tail(redirector.getPath())+"."+*/ptail;
} else { } else {
@ -3346,7 +3385,7 @@ public class ProfileUtilities extends TranslatingUtilities {
} }
if (ved.getBinding().hasDescription() && MarkDownProcessor.isSimpleMarkdown(ved.getBinding().getDescription())) { if (ved.getBinding().hasDescription() && MarkDownProcessor.isSimpleMarkdown(ved.getBinding().getDescription())) {
c.getPieces().add(gen.new Piece(null, ": ", null)); c.getPieces().add(gen.new Piece(null, ": ", null));
c.addMarkdownNoPara(ved.getBinding().getDescription()); c.addMarkdownNoPara(PublicationHacker.fixBindingDescriptions(context, ved.getBinding().getDescriptionElement()).asStringValue());
} }
} }
c.addPiece(gen.new Piece("br")).addPiece(gen.new Piece(null, describeExtensionContext(ed), null)); c.addPiece(gen.new Piece("br")).addPiece(gen.new Piece(null, describeExtensionContext(ed), null));
@ -4584,7 +4623,7 @@ public class ProfileUtilities extends TranslatingUtilities {
} }
if (binding.hasDescription() && MarkDownProcessor.isSimpleMarkdown(binding.getDescription())) { if (binding.hasDescription() && MarkDownProcessor.isSimpleMarkdown(binding.getDescription())) {
c.getPieces().add(gen.new Piece(null, ": ", null)); c.getPieces().add(gen.new Piece(null, ": ", null));
c.addMarkdownNoPara(binding.getDescription(), checkForNoChange(binding.getDescriptionElement())); c.addMarkdownNoPara(PublicationHacker.fixBindingDescriptions(context, binding.getDescriptionElement()).asStringValue(), checkForNoChange(PublicationHacker.fixBindingDescriptions(context, binding.getDescriptionElement())));
} }
} }
for (ElementDefinitionConstraintComponent inv : definition.getConstraint()) { for (ElementDefinitionConstraintComponent inv : definition.getConstraint()) {
@ -4937,7 +4976,7 @@ public class ProfileUtilities extends TranslatingUtilities {
} }
if (binding.hasDescription() && MarkDownProcessor.isSimpleMarkdown(binding.getDescription())) { if (binding.hasDescription() && MarkDownProcessor.isSimpleMarkdown(binding.getDescription())) {
c.getPieces().add(gen.new Piece(null, ": ", null)); c.getPieces().add(gen.new Piece(null, ": ", null));
c.addMarkdownNoPara(binding.getDescription()); c.addMarkdownNoPara(PublicationHacker.fixBindingDescriptions(context, binding.getDescriptionElement()).asStringValue());
} }
} }
for (ElementDefinitionConstraintComponent inv : definition.getConstraint()) { for (ElementDefinitionConstraintComponent inv : definition.getConstraint()) {