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2023 08 gg extension paths (#1380)
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* fix problem with whitespace in terminology caching

* Support for x-version extensions when generating snapshots

* Fix problem with evaluating extension contexts

* Produce useful error message when whitespace is wrong in display name

* Resolve URL for x-version extensions

* render inactive property in expansions

* fix tests

* ping build

* Point to correct test-cases version

---------

Co-authored-by: Grahame Grieve <[email protected]>
Co-authored-by: dotasek <[email protected]>
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@grahamegrieve @dotasek
3 people authored Aug 3, 2023
1 parent 011167a commit 6d08834
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Showing 19 changed files with 693 additions and 35 deletions.
32 changes: 28 additions & 4 deletions org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/profile/ProfileUtilities.java
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Original file line number Diff line number Diff line change
Expand Up @@ -846,7 +846,7 @@ public void generateSnapshot(StructureDefinition base, StructureDefinition deriv
for (UriType u : t.getProfile()) {
StructureDefinition sd = context.fetchResource(StructureDefinition.class, u.getValue(), derived);
if (sd == null) {
if (xver != null && xver.matchingUrl(u.getValue()) && xver.status(u.getValue()) == XVerExtensionStatus.Valid) {
if (makeXVer().matchingUrl(u.getValue()) && xver.status(u.getValue()) == XVerExtensionStatus.Valid) {
sd = xver.makeDefinition(u.getValue());
}
}
Expand Down Expand Up @@ -891,6 +891,13 @@ public void generateSnapshot(StructureDefinition base, StructureDefinition deriv
}
}

private XVerExtensionManager makeXVer() {
if (xver == null) {
xver = new XVerExtensionManager(context);
}
return xver;
}

private ElementDefinition getElementInCurrentContext(String path, List<ElementDefinition> list) {
for (int i = list.size() -1; i >= 0; i--) {
ElementDefinition t = list.get(i);
Expand Down Expand Up @@ -1759,7 +1766,7 @@ protected StructureDefinition getProfileForDataType(TypeRefComponent type, Strin
if (type.hasProfile()) {
sd = context.fetchResource(StructureDefinition.class, type.getProfile().get(0).getValue(), src);
if (sd == null) {
if (xver != null && xver.matchingUrl(type.getProfile().get(0).getValue()) && xver.status(type.getProfile().get(0).getValue()) == XVerExtensionStatus.Valid) {
if (makeXVer().matchingUrl(type.getProfile().get(0).getValue()) && xver.status(type.getProfile().get(0).getValue()) == XVerExtensionStatus.Valid) {
sd = xver.makeDefinition(type.getProfile().get(0).getValue());
generateSnapshot(context.fetchTypeDefinition("Extension"), sd, sd.getUrl(), webUrl, sd.getName());
}
Expand Down Expand Up @@ -2297,8 +2304,25 @@ protected void updateFromDefinition(ElementDefinition dest, ElementDefinition so
if (base.hasSliceName()) {
profile = base.getType().size() == 1 && base.getTypeFirstRep().hasProfile() ? context.fetchResource(StructureDefinition.class, base.getTypeFirstRep().getProfile().get(0).getValue(), srcSD) : null;
}
if (profile==null) {
profile = source.getType().size() == 1 && source.getTypeFirstRep().hasProfile() ? context.fetchResource(StructureDefinition.class, source.getTypeFirstRep().getProfile().get(0).getValue(), derivedSrc) : null;
if (profile == null && source.getTypeFirstRep().hasProfile()) {
String pu = source.getTypeFirstRep().getProfile().get(0).getValue();
profile = context.fetchResource(StructureDefinition.class, pu, derivedSrc);
if (profile == null) {
if (makeXVer().matchingUrl(pu)) {
switch (xver.status(pu)) {
case BadVersion:
throw new FHIRException("Reference to invalid version in extension url " + pu);
case Invalid:
throw new FHIRException("Reference to invalid extension " + pu);
case Unknown:
throw new FHIRException("Reference to unknown extension " + pu);
case Valid:
profile = xver.makeDefinition(pu);
generateSnapshot(context.fetchTypeDefinition("Extension"), profile, profile.getUrl(), context.getSpecUrl(), profile.getName());
}
}

}
if (profile != null && !"Extension".equals(profile.getType()) && profile.getKind() != StructureDefinitionKind.RESOURCE && profile.getKind() != StructureDefinitionKind.LOGICAL) {
// this is a problem - we're kind of hacking things here. The problem is that we sometimes want the details from the profile to override the
// inherited attributes, and sometimes not
Expand Down
2 changes: 1 addition & 1 deletion org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/TerminologyCache.java
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Original file line number Diff line number Diff line change
Expand Up @@ -695,7 +695,7 @@ private String loadJS(JsonElement e) {
}

protected String hashJson(String s) {
s = StringUtils.remove(s, ' ');
// s = StringUtils.remove(s, ' ');
s = StringUtils.remove(s, '\n');
s = StringUtils.remove(s, '\r');
return String.valueOf(s.hashCode());
Expand Down
9 changes: 9 additions & 0 deletions org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/ElementDefinition.java
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Original file line number Diff line number Diff line change
Expand Up @@ -12748,6 +12748,15 @@ public String typeSummary() {
}
return b.toString();
}

public List<String> typeList() {
List<String> res = new ArrayList<>();
for (TypeRefComponent tr : getType()) {
if (tr.hasCode())
res.add(tr.getWorkingCode());
}
return res;
}

public String typeSummaryVB() {
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder("|");
Expand Down
40 changes: 28 additions & 12 deletions org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/ValueSetRenderer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -198,16 +198,16 @@ private boolean generateExpansion(XhtmlNode x, ValueSet vs, boolean header, List
generateContentModeNotices(x, vs.getExpansion(), vs);
generateVersionNotice(x, vs.getExpansion(), vs);

CodeSystem allCS = null;
boolean doLevel = false;
for (ValueSetExpansionContainsComponent cc : vs.getExpansion().getContains()) {
if (cc.hasContains()) {
doLevel = true;
break;
}
}

boolean doInactive = checkDoInactive(vs.getExpansion().getContains());
boolean doDefinition = checkDoDefinition(vs.getExpansion().getContains());

XhtmlNode t = x.table( "codes");
XhtmlNode tr = t.tr();
if (doLevel)
Expand All @@ -221,6 +221,9 @@ private boolean generateExpansion(XhtmlNode x, ValueSet vs, boolean header, List
scanForDesignations(c, langs, designations);
}
scanForProperties(vs.getExpansion(), langs, properties);
if (doInactive) {
tr.td().b().tx("Inactive");
}
if (doDefinition) {
tr.td().b().tx("Definition");
doDesignations = false;
Expand Down Expand Up @@ -250,7 +253,7 @@ private boolean generateExpansion(XhtmlNode x, ValueSet vs, boolean header, List

addMapHeaders(tr, maps);
for (ValueSetExpansionContainsComponent c : vs.getExpansion().getContains()) {
addExpansionRowToTable(t, vs, c, 1, doLevel, true, doDefinition, maps, allCS, langs, designations, doDesignations, properties);
addExpansionRowToTable(t, vs, c, 1, doLevel, doDefinition, doInactive, maps, langs, designations, doDesignations, properties);
}

// now, build observed languages
Expand Down Expand Up @@ -673,6 +676,17 @@ private boolean checkDoDefinition(List<ValueSetExpansionContainsComponent> conta
return false;
}

private boolean checkDoInactive(List<ValueSetExpansionContainsComponent> contains) {
for (ValueSetExpansionContainsComponent c : contains) {
if (c.hasInactive()) {
return true;
}
if (checkDoInactive(c.getContains()))
return true;
}
return false;
}


private boolean allFromOneSystem(ValueSet vs) {
if (vs.getExpansion().getContains().isEmpty())
Expand Down Expand Up @@ -754,7 +768,7 @@ private void scanForLangs(ValueSetExpansionContainsComponent c, List<String> lan
}
}

private void addExpansionRowToTable(XhtmlNode t, ValueSet vs, ValueSetExpansionContainsComponent c, int i, boolean doLevel, boolean doSystem, boolean doDefinition, List<UsedConceptMap> maps, CodeSystem allCS, List<String> langs, Map<String, String> designations, boolean doDesignations, Map<String, String> properties) throws FHIRFormatError, DefinitionException, IOException {
private void addExpansionRowToTable(XhtmlNode t, ValueSet vs, ValueSetExpansionContainsComponent c, int i, boolean doLevel, boolean doDefinition, boolean doInactive, List<UsedConceptMap> maps, List<String> langs, Map<String, String> designations, boolean doDesignations, Map<String, String> properties) throws FHIRFormatError, DefinitionException, IOException {
XhtmlNode tr = t.tr();
if (ValueSetUtilities.isDeprecated(vs, c)) {
tr.setAttribute("style", "background-color: #ffeeee");
Expand All @@ -772,19 +786,21 @@ private void addExpansionRowToTable(XhtmlNode t, ValueSet vs, ValueSetExpansionC
String s = Utilities.padLeft("", '\u00A0', i*2);
td.attribute("style", "white-space:nowrap").addText(s);
addCodeToTable(c.getAbstract(), c.getSystem(), c.getCode(), c.getDisplay(), td);
if (doSystem) {
td = tr.td();
td.addText(c.getSystem());
}
td = tr.td();
td.addText(c.getSystem());
td = tr.td();
if (c.hasDisplayElement())
td.addText(c.getDisplay());

if (doInactive) {
td = tr.td();
if (c.getInactive()) {
td.tx("inactive");
}
}
if (doDefinition) {
CodeSystem cs = allCS;
if (cs == null)
cs = getContext().getWorker().fetchCodeSystem(c.getSystem());
td = tr.td();
CodeSystem cs = getContext().getWorker().fetchCodeSystem(c.getSystem());
if (cs != null) {
String defn = CodeSystemUtilities.getCodeDefinition(cs, c.getCode());
addMarkdown(td, defn, cs.getWebPath());
Expand Down Expand Up @@ -817,7 +833,7 @@ private void addExpansionRowToTable(XhtmlNode t, ValueSet vs, ValueSetExpansionC
addLangaugesToRow(c, langs, tr);
}
for (ValueSetExpansionContainsComponent cc : c.getContains()) {
addExpansionRowToTable(t, vs, cc, i+1, doLevel, doSystem, doDefinition, maps, allCS, langs, designations, doDesignations, properties);
addExpansionRowToTable(t, vs, cc, i+1, doLevel, doDefinition, doInactive, maps, langs, designations, doDesignations, properties);
}
}

Expand Down
9 changes: 8 additions & 1 deletion ...hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/validation/ValueSetValidator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -648,6 +648,7 @@ private ValidationResult validateCode(String path, Coding code, CodeSystem cs, C
if (vcc != null) {
vcc.addCoding(vc);
}
boolean ws = false;
if (code.getDisplay() == null) {
return new ValidationResult(code.getSystem(), cs.getVersion(), cc, vc.getDisplay());
}
Expand All @@ -656,14 +657,20 @@ private ValidationResult validateCode(String path, Coding code, CodeSystem cs, C
b.append("'"+cc.getDisplay()+"'");
if (code.getDisplay().equalsIgnoreCase(cc.getDisplay())) {
return new ValidationResult(code.getSystem(), cs.getVersion(), cc, getPreferredDisplay(cc, cs));
} else if (Utilities.normalize(code.getDisplay()).equals(Utilities.normalize(cc.getDisplay()))) {
ws = true;
}
}

for (ConceptDefinitionDesignationComponent ds : cc.getDesignation()) {
if (isOkLanguage(ds.getLanguage())) {
b.append("'"+ds.getValue()+"'");
if (code.getDisplay().equalsIgnoreCase(ds.getValue())) {
return new ValidationResult(code.getSystem(),cs.getVersion(), cc, getPreferredDisplay(cc, cs));
}
if (Utilities.normalize(code.getDisplay()).equalsIgnoreCase(Utilities.normalize(ds.getValue()))) {
ws = true;
}
}
}
// also check to see if the value set has another display
Expand All @@ -690,7 +697,7 @@ private ValidationResult validateCode(String path, Coding code, CodeSystem cs, C
String msg = context.formatMessagePlural(options.getLanguages().size(), I18nConstants.NO_VALID_DISPLAY_FOUND, code.getSystem(), code.getCode(), code.getDisplay(), options.langSummary());
return new ValidationResult(IssueSeverity.WARNING, msg, code.getSystem(), cs.getVersion(), cc, getPreferredDisplay(cc, cs), makeIssue(IssueSeverity.WARNING, IssueType.INVALID, path+".display", msg));
} else {
String msg = context.formatMessagePlural(b.count(), I18nConstants.DISPLAY_NAME_FOR__SHOULD_BE_ONE_OF__INSTEAD_OF, code.getSystem(), code.getCode(), b.toString(), code.getDisplay(), options.langSummary());
String msg = context.formatMessagePlural(b.count(), ws ? I18nConstants.DISPLAY_NAME_WS_FOR__SHOULD_BE_ONE_OF__INSTEAD_OF : I18nConstants.DISPLAY_NAME_FOR__SHOULD_BE_ONE_OF__INSTEAD_OF, code.getSystem(), code.getCode(), b.toString(), code.getDisplay(), options.langSummary());
return new ValidationResult(dispWarningStatus(), msg, code.getSystem(), cs.getVersion(), cc, getPreferredDisplay(cc, cs), makeIssue(dispWarning(), IssueType.INVALID, path+".display", msg));
}
}
Expand Down
30 changes: 30 additions & 0 deletions org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/XVerExtensionManager.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -256,4 +256,34 @@ private boolean isVersionPattern(String v) {
return v.length() == 3 && Character.isDigit(v.charAt(0)) && v.charAt(1) == '.' && Character.isDigit(v.charAt(2));
}

public String getReference(String url) {
String version = getVersion(url);
String base = VersionUtilities.getSpecUrl(version);
if (base == null) {
return null;
} else {
String path = url.substring(url.indexOf("-")+1);
if (!path.contains(".")) {
return null;
}
String type = path.substring(0, path.indexOf("."));
if (Utilities.existsInList(type, "Annotation", "Attachment", "Identifier", "CodeableConcept", "Coding", "Quantity", "Duration", "Range", "Period", "Ratio", "RatioRange", "SampledData", "Signature", "HumanName", "Address", "ContactPoint", "Timing")) {
return Utilities.pathURL(base, "datatypes-definitions.html#"+path+"|"+VersionUtilities.getNameForVersion(version)+" "+path);
}
if (Utilities.existsInList(type, "Element", "BackboneElement", "BackboneType", "PrimitiveType", "DataType", "Base")) {
return Utilities.pathURL(base, "types-definitions.html#"+path+"|"+VersionUtilities.getNameForVersion(version)+" "+path);
}
if (Utilities.existsInList(type, "UsageContext", "RelatedArtifact", "DataRequirement", "ParameterDefinition", "TriggerDefinition", "Expression", "ContactDetail", "ExtendedContactDetail", "VirtualServiceDetail", "Availability", "MonetaryComponent", "Contributor")) {
return Utilities.pathURL(base, "metadatatypes-definitions.html#"+path+"|"+VersionUtilities.getNameForVersion(version)+" "+path);
}
if (Utilities.existsInList(type, "Reference", "CodeableReference")) {
return Utilities.pathURL(base, "references-definitions.html#"+path+"|"+VersionUtilities.getNameForVersion(version)+" "+path);
}
if (Utilities.existsInList(type, "Meta")) {
return Utilities.pathURL(base, "resource-definitions.html#"+path+"|"+VersionUtilities.getNameForVersion(version)+" "+path);
}
return Utilities.pathURL(base, type.toLowerCase()+"-definitions.html#"+path+"|"+VersionUtilities.getNameForVersion(version)+" "+path);
}
}

}
2 changes: 1 addition & 1 deletion org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/context/TerminologyCacheTests.java
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Original file line number Diff line number Diff line change
Expand Up @@ -149,7 +149,7 @@ public void testCachePersistence() throws IOException, URISyntaxException {
assertCanonicalResourceEquals(terminologyCapabilities, terminologyCacheB.getTerminologyCapabilities());
assertCanonicalResourceEquals(capabilityStatement, terminologyCacheB.getCapabilityStatement());

assertValidationResultEquals(codingResultA, terminologyCacheB.getValidation( terminologyCacheA.generateValidationToken(CacheTestUtils.validationOptions, coding, valueSet, new Parameters())));
assertValidationResultEquals(codingResultA, terminologyCacheB.getValidation(terminologyCacheA.generateValidationToken(CacheTestUtils.validationOptions, coding, valueSet, new Parameters())));
assertValidationResultEquals(codeableConceptResultA, terminologyCacheB.getValidation(terminologyCacheA.generateValidationToken(CacheTestUtils.validationOptions, concept, valueSet, new Parameters())));
assertExpansionOutcomeEquals(expansionOutcomeA,terminologyCacheB.getExpansion(terminologyCacheA.generateExpandToken(valueSet, true)));
}
Expand Down
39 changes: 39 additions & 0 deletions org.hl7.fhir.r5/src/test/resources/txCache/org.hl7.fhir.r5/lang.cache
View file
Original file line number Diff line number Diff line change
Expand Up @@ -12,3 +12,42 @@ e: {
"error" : "Cannot invoke \"org.hl7.fhir.r5.terminologies.client.ITerminologyClient.expandValueset(org.hl7.fhir.r5.model.ValueSet, org.hl7.fhir.r5.model.Parameters, java.util.Map)\" because the return value of \"org.hl7.fhir.r5.terminologies.client.TerminologyClientContext.getClient()\" is null"
}
-------------------------------------------------------------------------------------
{"hierarchical" : false, "valueSet" :{
"resourceType" : "ValueSet",
"compose" : {
"inactive" : true,
"include" : [{
"system" : "urn:ietf:bcp:47"
}]
}
}}####
e: {
"error" : "Cannot invoke \"org.hl7.fhir.r5.terminologies.client.ITerminologyClient.expandValueset(org.hl7.fhir.r5.model.ValueSet, org.hl7.fhir.r5.model.Parameters, java.util.Map)\" because the return value of \"org.hl7.fhir.r5.terminologies.client.TerminologyClientContext.getClient()\" is null"
}
-------------------------------------------------------------------------------------
{"hierarchical" : false, "valueSet" :{
"resourceType" : "ValueSet",
"compose" : {
"inactive" : true,
"include" : [{
"system" : "urn:ietf:bcp:47"
}]
}
}}####
e: {
"error" : "Cannot invoke \"org.hl7.fhir.r5.terminologies.client.ITerminologyClient.expandValueset(org.hl7.fhir.r5.model.ValueSet, org.hl7.fhir.r5.model.Parameters, java.util.Map)\" because the return value of \"org.hl7.fhir.r5.terminologies.client.TerminologyClientContext.getClient()\" is null"
}
-------------------------------------------------------------------------------------
{"hierarchical" : false, "valueSet" :{
"resourceType" : "ValueSet",
"compose" : {
"inactive" : true,
"include" : [{
"system" : "urn:ietf:bcp:47"
}]
}
}}####
e: {
"error" : "Cannot invoke \"org.hl7.fhir.r5.terminologies.client.ITerminologyClient.expandValueset(org.hl7.fhir.r5.model.ValueSet, org.hl7.fhir.r5.model.Parameters, java.util.Map)\" because the return value of \"org.hl7.fhir.r5.terminologies.client.TerminologyClientContext.getClient()\" is null"
}
-------------------------------------------------------------------------------------
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