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Merge branch 'master' into do-20230815-bump-okhttp-dependencies
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@dotasek
dotasek committed Aug 15, 2023
2 parents dacc73a + 0087a77 commit 976915f
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Showing 19 changed files with 1,937 additions and 135 deletions.
4 changes: 4 additions & 0 deletions org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/comparison/CanonicalResourceComparer.java
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Expand Up @@ -232,6 +232,10 @@ public String getMetadataFieldsAsText() {
}
return b.toString();
}

public boolean noUpdates() {
return !(changedMetadata.noteable() || changedDefinitions.noteable() || !changedContent.noteable() || !changedContentInterpretation.noteable());
}
}

public CanonicalResourceComparer(ComparisonSession session) {
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4 changes: 2 additions & 2 deletions org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/comparison/CodeSystemComparer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -33,8 +33,8 @@ public class CodeSystemComparer extends CanonicalResourceComparer {

public class CodeSystemComparison extends CanonicalResourceComparison<CodeSystem> {

private StructuralMatch<PropertyComponent> properties;
private StructuralMatch<CodeSystemFilterComponent> filters;
private StructuralMatch<PropertyComponent> properties = new StructuralMatch<PropertyComponent>();
private StructuralMatch<CodeSystemFilterComponent> filters = new StructuralMatch<CodeSystemFilterComponent>();
private StructuralMatch<ConceptDefinitionComponent> combined;
private Map<String, String> propMap = new HashMap<>(); // right to left; left retains it's name
public CodeSystemComparison(CodeSystem left, CodeSystem right) {
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2 changes: 2 additions & 0 deletions org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/comparison/ComparisonSession.java
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Original file line number Diff line number Diff line change
Expand Up @@ -115,6 +115,7 @@ public ResourceComparison compare(CanonicalResource left, CanonicalResource righ
return csc;
}
} else if (left != null) {
VersionComparisonAnnotation.markDeleted(null, forVersion, left.fhirType(), left); // todo: waht?
String key = key(left.getUrl(), left.getVersion(), left.getUrl(), left.getVersion());
if (compares.containsKey(key)) {
return compares.get(key);
Expand All @@ -123,6 +124,7 @@ public ResourceComparison compare(CanonicalResource left, CanonicalResource righ
compares.put(key, csc);
return csc;
} else {
VersionComparisonAnnotation.markAdded(right, forVersion);
String key = key(right.getUrl(), right.getVersion(), right.getUrl(), right.getVersion());
if (compares.containsKey(key)) {
return compares.get(key);
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25 changes: 10 additions & 15 deletions org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/comparison/ProfileComparer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -173,7 +173,7 @@ public ProfileComparison compare(StructureDefinition left, StructureDefinition r
res.combined = sm;
ln = new DefinitionNavigator(session.getContextLeft(), left, true);
rn = new DefinitionNavigator(session.getContextRight(), right, true);
ch = compareDiff(ln.path(), null, ln, rn) || ch;
ch = compareDiff(ln.path(), null, ln, rn, res) || ch;
// we don't preserve the differences - we only want the annotations
}
res.updateDefinitionsState(ch);
Expand Down Expand Up @@ -389,7 +389,7 @@ private boolean compareChildren(ProfileComparison comp, StructuralMatch<ElementD
}


private boolean compareDiff(String path, String sliceName, DefinitionNavigator left, DefinitionNavigator right) throws DefinitionException, FHIRFormatError, IOException {
private boolean compareDiff(String path, String sliceName, DefinitionNavigator left, DefinitionNavigator right, ProfileComparison res) throws DefinitionException, FHIRFormatError, IOException {
assert(path != null);
assert(left != null);
assert(right != null);
Expand All @@ -414,7 +414,7 @@ private boolean compareDiff(String path, String sliceName, DefinitionNavigator l
def = comparePrimitivesWithTracking("max", left.current().getMaxElement(), right.current().getMaxElement(), null, IssueSeverity.INFORMATION, null, right.current(), session.getForVersion()) || def;

// add the children
def = compareDiffChildren(path, left, right) || def;
def = compareDiffChildren(path, left, right, right.current(), res) || def;
//
// // now process the slices
// if (left.current().hasSlicing() || right.current().hasSlicing()) {
Expand Down Expand Up @@ -478,31 +478,26 @@ private boolean compareDiff(String path, String sliceName, DefinitionNavigator l
}


private boolean compareDiffChildren(String path, DefinitionNavigator left, DefinitionNavigator right) throws DefinitionException, IOException, FHIRFormatError {
private boolean compareDiffChildren(String path, DefinitionNavigator left, DefinitionNavigator right, Base parent, ProfileComparison res) throws DefinitionException, IOException, FHIRFormatError {
boolean def = false;

List<DefinitionNavigator> lc = left.children();
List<DefinitionNavigator> rc = right.children();
// it's possible that one of these profiles walks into a data type and the other doesn't
// if it does, we have to load the children for that data into the profile that doesn't
// walk into it
if (lc.isEmpty() && !rc.isEmpty() && right.current().getType().size() == 1 && left.hasTypeChildren(right.current().getType().get(0), left.getStructure()))
lc = left.childrenFromType(right.current().getType().get(0), right.getStructure());
if (rc.isEmpty() && !lc.isEmpty() && left.current().getType().size() == 1 && right.hasTypeChildren(left.current().getType().get(0), right.getStructure()))
rc = right.childrenFromType(left.current().getType().get(0), left.getStructure());


List<DefinitionNavigator> matchR = new ArrayList<>();
for (DefinitionNavigator l : lc) {
DefinitionNavigator r = findInList(rc, l);
if (r == null) {
// todo
VersionComparisonAnnotation.markDeleted(parent, session.getForVersion(), "element", l.current());
res.updateContentState(true);
} else {
def = compareDiff(l.path(), null, l, r) || def;
def = compareDiff(l.path(), null, l, r, res) || def;
}
}
for (DefinitionNavigator r : rc) {
if (!matchR.contains(r)) {
// todo
VersionComparisonAnnotation.markAdded(r.current(), session.getForVersion());
res.updateContentState(true);
}
}
return def;
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42 changes: 26 additions & 16 deletions org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/comparison/ValueSetComparer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -142,7 +142,7 @@ public ValueSetComparison compare(ValueSet left, ValueSet right) {

def = compareCompose(left.getCompose(), right.getCompose(), res, res.getUnion().getCompose(), res.getIntersection().getCompose()) || def;
res.updateDefinitionsState(def);
compareExpansions(left, right, res);
// compareExpansions(left, right, res);
VersionComparisonAnnotation.annotate(right, session.getForVersion(), res);
return res;
}
Expand All @@ -166,7 +166,7 @@ private boolean compareCompose(ValueSetComposeComponent left, ValueSetComposeCom
intersection.getInclude().add(csI);
StructuralMatch<Element> sm = new StructuralMatch<Element>(l, r);
res.getIncludes().getChildren().add(sm);
def = compareDefinitions(l, r, sm, csM, csI, res) || def;
def = compareDefinitions("ValueSet.compose.exclude["+right.getInclude().indexOf(r)+"]", l, r, sm, csM, csI, res) || def;
}
}
for (ConceptSetComponent r : right.getInclude()) {
Expand Down Expand Up @@ -194,7 +194,7 @@ private boolean compareCompose(ValueSetComposeComponent left, ValueSetComposeCom
intersection.getExclude().add(csI);
StructuralMatch<Element> sm = new StructuralMatch<Element>(l, r);
res.getExcludes().getChildren().add(sm);
def = compareDefinitions(l, r, sm, csM, csI, res) || def;
def = compareDefinitions("ValueSet.compose.exclude["+right.getExclude().indexOf(r)+"]", l, r, sm, csM, csI, res) || def;
}
}
for (ConceptSetComponent r : right.getExclude()) {
Expand Down Expand Up @@ -241,7 +241,7 @@ private int countMatchesBySystem(List<ConceptSetComponent> list, ConceptSetCompo
}


private boolean compareDefinitions(ConceptSetComponent left, ConceptSetComponent right, StructuralMatch<Element> combined, ConceptSetComponent union, ConceptSetComponent intersection, ValueSetComparison res) {
private boolean compareDefinitions(String path, ConceptSetComponent left, ConceptSetComponent right, StructuralMatch<Element> combined, ConceptSetComponent union, ConceptSetComponent intersection, ValueSetComparison res) {
boolean def = false;
// system must match, but the rest might not. we're going to do the full comparison whatever, so the outcome looks consistent to the user
List<CanonicalType> matchVSR = new ArrayList<>();
Expand All @@ -250,7 +250,7 @@ private boolean compareDefinitions(ConceptSetComponent left, ConceptSetComponent
if (r == null) {
union.getValueSet().add(l);
res.updateContentState(true);
combined.getChildren().add(new StructuralMatch<Element>(l, vmI(IssueSeverity.INFORMATION, "Removed ValueSet", "ValueSet.compose.include.valueSet")));
combined.getChildren().add(new StructuralMatch<Element>(l, vmI(IssueSeverity.ERROR, "Removed ValueSet", "ValueSet.compose.include.valueSet")));
if (session.isAnnotate()) {
VersionComparisonAnnotation.markDeleted(right, session.getForVersion(), "valueset", l);
}
Expand All @@ -266,7 +266,7 @@ private boolean compareDefinitions(ConceptSetComponent left, ConceptSetComponent
union.getValueSet().add(l);
union.getValueSet().add(r);
res.updateContentState(true);
StructuralMatch<Element> sm = new StructuralMatch<Element>(l, r, vmI(IssueSeverity.INFORMATION, "Values are different", "ValueSet.compose.include.valueSet"));
StructuralMatch<Element> sm = new StructuralMatch<Element>(l, r, vmI(IssueSeverity.WARNING, "Values are different", "ValueSet.compose.include.valueSet"));
combined.getChildren().add(sm);
if (session.isAnnotate()) {
VersionComparisonAnnotation.markChanged(r, session.getForVersion());
Expand All @@ -279,7 +279,7 @@ private boolean compareDefinitions(ConceptSetComponent left, ConceptSetComponent
if (!matchVSR.contains(r)) {
union.getValueSet().add(r);
res.updateContentState(true);
combined.getChildren().add(new StructuralMatch<Element>(vmI(IssueSeverity.INFORMATION, "Add ValueSet", "ValueSet.compose.include.valueSet"), r));
combined.getChildren().add(new StructuralMatch<Element>(vmI(IssueSeverity.ERROR, "Add ValueSet", "ValueSet.compose.include.valueSet"), r));
VersionComparisonAnnotation.markAdded(r, session.getForVersion());
}
}
Expand All @@ -290,7 +290,8 @@ private boolean compareDefinitions(ConceptSetComponent left, ConceptSetComponent
if (r == null) {
union.getConcept().add(l);
res.updateContentState(true);
combined.getChildren().add(new StructuralMatch<Element>(l, vmI(IssueSeverity.INFORMATION, "Removed this Concept", "ValueSet.compose.include.concept")));
combined.getChildren().add(new StructuralMatch<Element>(l, vmI(IssueSeverity.ERROR, "Removed this Concept", "ValueSet.compose.include.concept")));
res.getMessages().add(new ValidationMessage(Source.ProfileComparer, IssueType.INFORMATIONAL, path, "Code "+l.getCode()+" removed", IssueSeverity.ERROR));
VersionComparisonAnnotation.markDeleted(right, session.getForVersion(), "concept", l);
} else {
matchCR.add(r);
Expand All @@ -301,15 +302,15 @@ private boolean compareDefinitions(ConceptSetComponent left, ConceptSetComponent
intersection.getConcept().add(ci);
StructuralMatch<Element> sm = new StructuralMatch<Element>(l, r);
combined.getChildren().add(sm);
def = compareConcepts(l, r, sm, cu, ci) || def;
def = compareConcepts(path+".concept["+right.getConcept().indexOf(r)+"]", l, r, sm, cu, ci, res) || def;
} else {
// not that it's possible to get here?
union.getConcept().add(l);
union.getConcept().add(r);
StructuralMatch<Element> sm = new StructuralMatch<Element>(l, r, vmI(IssueSeverity.INFORMATION, "Concepts are different", "ValueSet.compose.include.concept"));
StructuralMatch<Element> sm = new StructuralMatch<Element>(l, r, vmI(IssueSeverity.WARNING, "Concepts are different", "ValueSet.compose.include.concept"));
combined.getChildren().add(sm);
res.updateContentState(true);
compareConcepts(l, r, sm, null, null);
compareConcepts(path+".concept["+right.getConcept().indexOf(r)+"]", l, r, sm, null, null, res);
VersionComparisonAnnotation.markChanged(r, session.getForVersion());
}
}
Expand All @@ -318,7 +319,8 @@ private boolean compareDefinitions(ConceptSetComponent left, ConceptSetComponent
if (!matchCR.contains(r)) {
union.getConcept().add(r);
res.updateContentState(true);
combined.getChildren().add(new StructuralMatch<Element>(vmI(IssueSeverity.INFORMATION, "Added this Concept", "ValueSet.compose.include.concept"), r));
combined.getChildren().add(new StructuralMatch<Element>(vmI(IssueSeverity.ERROR, "Added this Concept", "ValueSet.compose.include.concept"), r));
res.getMessages().add(new ValidationMessage(Source.ProfileComparer, IssueType.INFORMATIONAL, path, "Code "+r.getCode()+" added", IssueSeverity.ERROR));
VersionComparisonAnnotation.markAdded(r, session.getForVersion());
}
}
Expand All @@ -329,7 +331,7 @@ private boolean compareDefinitions(ConceptSetComponent left, ConceptSetComponent
if (r == null) {
union.getFilter().add(l);
res.updateContentState(true);
combined.getChildren().add(new StructuralMatch<Element>(l, vmI(IssueSeverity.INFORMATION, "Removed this item", "ValueSet.compose.include.filter")));
combined.getChildren().add(new StructuralMatch<Element>(l, vmI(IssueSeverity.ERROR, "Removed this item", "ValueSet.compose.include.filter")));
VersionComparisonAnnotation.markDeleted(right, session.getForVersion(), "filter", l);
} else {
matchFR.add(r);
Expand All @@ -347,7 +349,7 @@ private boolean compareDefinitions(ConceptSetComponent left, ConceptSetComponent
} else {
union.getFilter().add(l);
union.getFilter().add(r);
StructuralMatch<Element> sm = new StructuralMatch<Element>(l, r, vmI(IssueSeverity.INFORMATION, "Codes are different", "ValueSet.compose.include.filter"));
StructuralMatch<Element> sm = new StructuralMatch<Element>(l, r, vmI(IssueSeverity.WARNING, "Codes are different", "ValueSet.compose.include.filter"));
res.updateContentState(true);
combined.getChildren().add(sm);
compareFilters(l, r, sm, null, null);
Expand All @@ -358,14 +360,14 @@ private boolean compareDefinitions(ConceptSetComponent left, ConceptSetComponent
if (!matchFR.contains(r)) {
union.getFilter().add(r);
res.updateContentState(true);
combined.getChildren().add(new StructuralMatch<Element>(vmI(IssueSeverity.INFORMATION, "Added this item", "ValueSet.compose.include.filter"), r));
combined.getChildren().add(new StructuralMatch<Element>(vmI(IssueSeverity.ERROR, "Added this item", "ValueSet.compose.include.filter"), r));
VersionComparisonAnnotation.markAdded(r, session.getForVersion());
}
}
return def;
}

private boolean compareConcepts(ConceptReferenceComponent l, ConceptReferenceComponent r, StructuralMatch<Element> sm, ConceptReferenceComponent cu, ConceptReferenceComponent ci) {
private boolean compareConcepts(String path, ConceptReferenceComponent l, ConceptReferenceComponent r, StructuralMatch<Element> sm, ConceptReferenceComponent cu, ConceptReferenceComponent ci, ValueSetComparison res) {
boolean def = false;
sm.getChildren().add(new StructuralMatch<Element>(l.getCodeElement(), r.getCodeElement(), l.getCode().equals(r.getCode()) ? null : vmI(IssueSeverity.INFORMATION, "Codes do not match", "ValueSet.compose.include.concept")));
if (ci != null) {
Expand All @@ -379,14 +381,22 @@ private boolean compareConcepts(ConceptReferenceComponent l, ConceptReferenceCom
cu.setDisplay(r.getDisplay());
}
def = !l.getDisplay().equals(r.getDisplay());
if (def) {
res.getMessages().add(new ValidationMessage(Source.ProfileComparer, IssueType.INFORMATIONAL, path, "Code "+l.getCode()+" display changed from '"+l.getDisplay()+"' to '"+r.getDisplay()+"'", IssueSeverity.WARNING));
VersionComparisonAnnotation.markChanged(r.getDisplayElement(), session.getForVersion());
}
} else if (l.hasDisplay()) {
VersionComparisonAnnotation.markDeleted(r, session.getForVersion(), "display", l.getDisplayElement());
res.getMessages().add(new ValidationMessage(Source.ProfileComparer, IssueType.INFORMATIONAL, path, "Code "+l.getCode()+" display '"+l.getDisplay()+"' removed", IssueSeverity.WARNING));
sm.getChildren().add(new StructuralMatch<Element>(l.getDisplayElement(), null, vmI(IssueSeverity.INFORMATION, "Display Removed", "ValueSet.compose.include.concept")));
if (ci != null) {
ci.setDisplay(l.getDisplay());
cu.setDisplay(l.getDisplay());
}
def = true;
} else if (r.hasDisplay()) {
VersionComparisonAnnotation.markAdded(r.getDisplayElement(), session.getForVersion());
res.getMessages().add(new ValidationMessage(Source.ProfileComparer, IssueType.INFORMATIONAL, path, "Code "+l.getCode()+" display '"+r.getDisplay()+"' added", IssueSeverity.WARNING));
sm.getChildren().add(new StructuralMatch<Element>(null, r.getDisplayElement(), vmI(IssueSeverity.INFORMATION, "Display added", "ValueSet.compose.include.concept")));
if (ci != null) {
ci.setDisplay(r.getDisplay());
Expand Down
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