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Snapshot generation: handle profiles on Bundle.entry.resource properly

This commit is contained in:
Grahame Grieve 2020-02-07 10:27:52 +11:00
parent 2732ef3dd5
commit 139cd561df
1 changed files with 93 additions and 60 deletions
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153
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/ProfileUtilities.java
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@ -905,7 +905,7 @@ public class ProfileUtilities extends TranslatingUtilities {
result.getElement().add(outcome); result.getElement().add(outcome);
baseCursor++; baseCursor++;
diffCursor = differential.getElement().indexOf(diffMatches.get(0))+1; diffCursor = differential.getElement().indexOf(diffMatches.get(0))+1;
if (diffLimit >= diffCursor && outcome.getPath().contains(".") && (isDataType(outcome.getType()) || outcome.hasContentReference())) { // don't want to do this for the root, since that's base, and we're already processing it 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 (pathStartsWith(differential.getElement().get(diffCursor).getPath(), diffMatches.get(0).getPath()+".") && !baseWalksInto(base.getElement(), baseCursor)) {
if (outcome.getType().size() > 1) { if (outcome.getType().size() > 1) {
if (outcome.getPath().endsWith("[x]") && !diffMatches.get(0).getPath().endsWith("[x]")) { if (outcome.getPath().endsWith("[x]") && !diffMatches.get(0).getPath().endsWith("[x]")) {
@ -1540,6 +1540,18 @@ public class ProfileUtilities extends TranslatingUtilities {
} }
private boolean isBaseResource(List<TypeRefComponent> types) {
if (types.isEmpty())
return false;
for (TypeRefComponent type : types) {
String t = type.getWorkingCode();
if ("Resource".equals(t))
return false;
}
return true;
}
public String determineFixedType(List<ElementDefinition> diffMatches, String fixedType, int i) { public String determineFixedType(List<ElementDefinition> diffMatches, String fixedType, int i) {
if (diffMatches.get(i).getType().size() == 0 && diffMatches.get(i).hasSliceName()) { if (diffMatches.get(i).getType().size() == 0 && diffMatches.get(i).hasSliceName()) {
String n = tail(diffMatches.get(i).getPath()).replace("[x]", ""); String n = tail(diffMatches.get(i).getPath()).replace("[x]", "");
@ -2441,62 +2453,7 @@ public class ProfileUtilities extends TranslatingUtilities {
if (!Base.compareDeep(derived.getType(), base.getType(), false)) { if (!Base.compareDeep(derived.getType(), base.getType(), false)) {
if (base.hasType()) { if (base.hasType()) {
for (TypeRefComponent ts : derived.getType()) { for (TypeRefComponent ts : derived.getType()) {
boolean ok = false; checkTypeDerivation(purl, srcSD, base, derived, ts);
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
String t = ts.getWorkingCode();
for (TypeRefComponent td : base.getType()) {;
String tt = td.getWorkingCode();
b.append(tt);
if (td.hasCode() && (tt.equals(t))) {
ok = true;
}
if (!ok) {
StructureDefinition sdt = context.fetchTypeDefinition(tt);
if (sdt != null && sdt.getAbstract()) {
StructureDefinition sdb = context.fetchTypeDefinition(t);
while (sdb != null && !ok) {
ok = sdb.getType().equals(sdt.getUrl());
sdb = context.fetchResource(StructureDefinition.class, sdb.getBaseDefinition());
}
}
}
// work around for old badly generated SDs
if (DONT_DO_THIS && Utilities.existsInList(tt, "Extension", "uri", "string", "Element")) {
ok = true;
}
if (DONT_DO_THIS && Utilities.existsInList(tt, "Resource","DomainResource") && pkp.isResource(t)) {
ok = true;
}
if (ok && ts.hasTargetProfile()) {
// check that any derived target has a reference chain back to one of the base target profiles
for (UriType u : ts.getTargetProfile()) {
String url = u.getValue();
boolean tgtOk = !td.hasTargetProfile() || td.hasTargetProfile(url);
while (url != null && !tgtOk) {
StructureDefinition sd = context.fetchResource(StructureDefinition.class, url);
if (sd == null) {
if (messages != null) {
messages.add(new ValidationMessage(Source.InstanceValidator, IssueType.BUSINESSRULE, purl+"#"+derived.getPath(), "Connect check whether the target profile "+url+" is valid constraint on the base because it is not known", IssueSeverity.WARNING));
}
url = null;
tgtOk = true; // suppress error message
} else {
url = sd.getBaseDefinition();
tgtOk = td.hasTargetProfile(url);
}
}
if (!tgtOk) {
if (messages == null) {
throw new FHIRException("Error at "+purl+"#"+derived.getPath()+": The target profile "+url+" is not valid constraint on the base ("+td.getTargetProfile()+")");
} else {
messages.add(new ValidationMessage(Source.InstanceValidator, IssueType.BUSINESSRULE, derived.getPath(), "The target profile "+u.getValue()+" is not a valid constraint on the base ("+td.getTargetProfile()+") at "+derived.getPath(), IssueSeverity.ERROR));
}
}
}
}
}
if (!ok)
throw new DefinitionException("StructureDefinition "+purl+" at "+derived.getPath()+": illegal constrained type "+t+" from "+b.toString()+" in "+srcSD.getUrl());
} }
} }
base.getType().clear(); base.getType().clear();
@ -2576,6 +2533,66 @@ public class ProfileUtilities extends TranslatingUtilities {
} }
} }
public void checkTypeDerivation(String purl, StructureDefinition srcSD, ElementDefinition base, ElementDefinition derived, TypeRefComponent ts) {
boolean ok = false;
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
String t = ts.getWorkingCode();
for (TypeRefComponent td : base.getType()) {;
String tt = td.getWorkingCode();
b.append(tt);
if (td.hasCode() && (tt.equals(t))) {
ok = true;
}
if (!ok) {
StructureDefinition sdt = context.fetchTypeDefinition(tt);
if (sdt != null && sdt.getAbstract()) {
StructureDefinition sdb = context.fetchTypeDefinition(t);
while (sdb != null && !ok) {
ok = sdb.getType().equals(sdt.getType());
sdb = context.fetchResource(StructureDefinition.class, sdb.getBaseDefinition());
}
}
}
// work around for old badly generated SDs
if (DONT_DO_THIS && Utilities.existsInList(tt, "Extension", "uri", "string", "Element")) {
ok = true;
}
if (DONT_DO_THIS && Utilities.existsInList(tt, "Resource","DomainResource") && pkp.isResource(t)) {
ok = true;
}
if (ok && ts.hasTargetProfile()) {
// check that any derived target has a reference chain back to one of the base target profiles
for (UriType u : ts.getTargetProfile()) {
String url = u.getValue();
boolean tgtOk = !td.hasTargetProfile() || td.hasTargetProfile(url);
while (url != null && !tgtOk) {
StructureDefinition sd = context.fetchResource(StructureDefinition.class, url);
if (sd == null) {
if (messages != null) {
messages.add(new ValidationMessage(Source.InstanceValidator, IssueType.BUSINESSRULE, purl+"#"+derived.getPath(), "Connect check whether the target profile "+url+" is valid constraint on the base because it is not known", IssueSeverity.WARNING));
}
url = null;
tgtOk = true; // suppress error message
} else {
url = sd.getBaseDefinition();
tgtOk = td.hasTargetProfile(url);
}
}
if (!tgtOk) {
if (messages == null) {
throw new FHIRException("Error at "+purl+"#"+derived.getPath()+": The target profile "+url+" is not valid constraint on the base ("+td.getTargetProfile()+")");
} else {
messages.add(new ValidationMessage(Source.InstanceValidator, IssueType.BUSINESSRULE, derived.getPath(), "The target profile "+u.getValue()+" is not a valid constraint on the base ("+td.getTargetProfile()+") at "+derived.getPath(), IssueSeverity.ERROR));
}
}
}
}
}
if (!ok) {
throw new DefinitionException("StructureDefinition "+purl+" at "+derived.getPath()+": illegal constrained type "+t+" from "+b.toString()+" in "+srcSD.getUrl());
}
}
public void checkTypeOk(ElementDefinition dest, String ft) { public void checkTypeOk(ElementDefinition dest, String ft) {
boolean ok = false; boolean ok = false;
@ -4518,8 +4535,9 @@ public class ProfileUtilities extends TranslatingUtilities {
for (ElementDefinitionHolder child : edh.getChildren()) { for (ElementDefinitionHolder child : edh.getChildren()) {
if (child.getChildren().size() > 0) { if (child.getChildren().size() > 0) {
ElementDefinitionComparer ccmp = getComparer(cmp, child); ElementDefinitionComparer ccmp = getComparer(cmp, child);
if (ccmp != null) if (ccmp != null) {
sortElements(child, ccmp, errors); sortElements(child, ccmp, errors);
}
} }
} }
} }
@ -4530,7 +4548,22 @@ public class ProfileUtilities extends TranslatingUtilities {
ElementDefinition ed = cmp.snapshot.get(child.getBaseIndex()); ElementDefinition ed = cmp.snapshot.get(child.getBaseIndex());
ElementDefinitionComparer ccmp; ElementDefinitionComparer ccmp;
if (ed.getType().isEmpty() || isAbstract(ed.getType().get(0).getWorkingCode()) || ed.getType().get(0).getWorkingCode().equals(ed.getPath())) { if (ed.getType().isEmpty() || isAbstract(ed.getType().get(0).getWorkingCode()) || ed.getType().get(0).getWorkingCode().equals(ed.getPath())) {
ccmp = new ElementDefinitionComparer(true, cmp.snapshot, cmp.base, cmp.prefixLength, cmp.name); if (ed.hasType() && "Resource".equals(ed.getType().get(0).getWorkingCode()) && child.getSelf().getType().get(0).hasProfile()) {
if (child.getSelf().getType().get(0).getProfile().size() > 1) {
throw new FHIRException("Unhandled situation: resource is profiled to more than one option - cannot sort profile");
}
StructureDefinition profile = context.fetchResource(StructureDefinition.class, child.getSelf().getType().get(0).getProfile().get(0).getValue());
while (profile != null && profile.getDerivation() == TypeDerivationRule.CONSTRAINT) {
profile = context.fetchResource(StructureDefinition.class, profile.getBaseDefinition());
}
if (profile==null) {
ccmp = null; // this might happen before everything is loaded. And we don't so much care about sot order in this case
} else {
ccmp = new ElementDefinitionComparer(true, profile.getSnapshot().getElement(), profile.getType(), child.getSelf().getPath().length(), cmp.name);
}
} else {
ccmp = new ElementDefinitionComparer(true, cmp.snapshot, cmp.base, cmp.prefixLength, cmp.name);
}
} else if (ed.getType().get(0).getWorkingCode().equals("Extension") && child.getSelf().getType().size() == 1 && child.getSelf().getType().get(0).hasProfile()) { } else if (ed.getType().get(0).getWorkingCode().equals("Extension") && child.getSelf().getType().size() == 1 && child.getSelf().getType().get(0).hasProfile()) {
StructureDefinition profile = context.fetchResource(StructureDefinition.class, child.getSelf().getType().get(0).getProfile().get(0).getValue()); StructureDefinition profile = context.fetchResource(StructureDefinition.class, child.getSelf().getType().get(0).getProfile().get(0).getValue());
if (profile==null) if (profile==null)