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Merge pull request #1617 from hapifhir/2024-05-gg-misc2 

2024 05 gg misc2
This commit is contained in:
Grahame Grieve 2024-05-09 23:06:24 +00:00 committed by GitHub
parent ee5987a301 e57ef59ee9
commit ffec50c71b
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GPG Key ID: B5690EEEBB952194
8 changed files with 155 additions and 135 deletions
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12
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/BaseWorkerContext.java
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@ -1483,9 +1483,11 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
protected Parameters constructParameters(ValidationOptions options, Coding coding) {
Parameters pIn = new Parameters();
pIn.addParameter().setName("coding").setValue(coding);
if (options.isGuessSystem()) {
pIn.addParameter().setName("inferSystem").setValue(new BooleanType(true));
pIn.addParameter().setName("code").setValue(coding.getCodeElement());
} else {
pIn.addParameter().setName("coding").setValue(coding);
}
setTerminologyOptions(options, pIn);
return pIn;
@ -1500,9 +1502,11 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
protected Parameters constructParameters(ValidationOptions options, CodingValidationRequest codingValidationRequest, ValueSet valueSet) {
Parameters pIn = new Parameters();
pIn.addParameter().setName("coding").setValue(codingValidationRequest.getCoding());
if (options.isGuessSystem()) {
pIn.addParameter().setName("inferSystem").setValue(new BooleanType(true));
pIn.addParameter().setName("code").setValue(codingValidationRequest.getCoding().getCodeElement());
} else {
pIn.addParameter().setName("coding").setValue(codingValidationRequest.getCoding());
}
if (valueSet != null) {
pIn.addParameter().setName("valueSet").setResource(valueSet);
@ -1514,9 +1518,11 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
protected Parameters constructParameters(ValidationOptions options, CodingValidationRequest codingValidationRequest, String vsUrl) {
Parameters pIn = new Parameters();
pIn.addParameter().setName("coding").setValue(codingValidationRequest.getCoding());
if (options.isGuessSystem()) {
pIn.addParameter().setName("inferSystem").setValue(new BooleanType(true));
pIn.addParameter().setName("code").setValue(codingValidationRequest.getCoding().getCodeElement());
} else {
pIn.addParameter().setName("coding").setValue(codingValidationRequest.getCoding());
}
if (vsUrl != null) {
pIn.addParameter().setName("url").setValue(new CanonicalType(vsUrl));

14
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/StructureDefinitionRenderer.java
View File

@ -2237,8 +2237,9 @@ public class StructureDefinitionRenderer extends ResourceRenderer {
StructureDefinition sd = context.getWorker().fetchTypeDefinition(value.fhirType());
for (org.hl7.fhir.r5.model.Property t : value.children()) {
ElementDefinition ed = findElementDefinitionOrNull(sd, t.getName());
if (ed != null) { // might be null because of added properties across versions
if (t.getValues().size() > 0 || snapshot) {
ElementDefinition ed = findElementDefinition(sd, t.getName());
if (t.getValues().size() == 0 || (t.getValues().size() == 1 && t.getValues().get(0).isEmpty())) {
if (!skipnoValue) {
Row row = gen.new Row();
@ -2349,6 +2350,7 @@ public class StructureDefinitionRenderer extends ResourceRenderer {
}
}
}
}
private ElementDefinition findElementDefinition(StructureDefinition sd, String name) {
@ -2361,6 +2363,16 @@ public class StructureDefinitionRenderer extends ResourceRenderer {
}
private ElementDefinition findElementDefinitionOrNull(StructureDefinition sd, String name) {
String path = sd.getTypeName()+"."+name;
for (ElementDefinition ed : sd.getSnapshot().getElement()) {
if (ed.getPath().equals(path))
return ed;
}
return null;
}
private String getFixedUrl(StructureDefinition sd) {
for (ElementDefinition ed : sd.getSnapshot().getElement()) {
if (ed.getPath().equals("Extension.url")) {

4
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/ValueSetRenderer.java
View File

@ -207,7 +207,7 @@ public class ValueSetRenderer extends TerminologyRenderer {
// }
String msg = null;
if (vs.getExpansion().getContains().isEmpty()) {
msg = context.formatMessage(RenderingContext.VALUE_SET_INF); // not sure that's true?
msg = context.formatMessage(RenderingContext.VALUE_SET_TOO_COSTLY);
} else {
msg = /*!#*/"This value set cannot be fully expanded, but a selection ("+countMembership(vs)+" codes) of the whole set of codes is shown here.";
}
@ -487,7 +487,7 @@ public class ValueSetRenderer extends TerminologyRenderer {
if (versions.size() == 1 && versions.get(s).size() == 1) {
for (String v : versions.get(s)) { // though there'll only be one
XhtmlNode p = x.para().style("border: black 1px dotted; background-color: #EEEEEE; padding: 8px; margin-bottom: 8px");
p.tx(context.formatMessage(RenderingContext.VALUE_SET_EXPANSION));
p.tx(context.formatMessage(RenderingContext.VALUE_SET_EXPANSION)+" ");
expRef(p, s, v, vs);
}
} else {

12
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/expansion/ValueSetExpander.java
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@ -987,14 +987,19 @@ public class ValueSetExpander extends ValueSetProcessBase {
}
}
private void copyImportContains(List<ValueSetExpansionContainsComponent> list, ValueSetExpansionContainsComponent parent, Parameters expParams, List<ValueSet> filter, boolean noInactive, List<ValueSetExpansionPropertyComponent> vsProps, ValueSet vsSrc, ValueSetExpansionComponent exp) throws FHIRException, ETooCostly {
private int copyImportContains(List<ValueSetExpansionContainsComponent> list, ValueSetExpansionContainsComponent parent, Parameters expParams, List<ValueSet> filter, boolean noInactive, List<ValueSetExpansionPropertyComponent> vsProps, ValueSet vsSrc, ValueSetExpansionComponent exp) throws FHIRException, ETooCostly {
int count = 0;
opContext.deadCheck();
for (ValueSetExpansionContainsComponent c : list) {
c.checkNoModifiers("Imported Expansion in Code System", "expanding");
ValueSetExpansionContainsComponent np = addCode(dwc, c.getSystem(), c.getCode(), c.getDisplay(), vsSrc.getLanguage(), parent, null, expParams, c.getAbstract(), c.getInactive(),
filter, noInactive, false, vsProps, makeCSProps(c.getExtensionString(ToolingExtensions.EXT_DEFINITION), null), null, c.getProperty(), null, c.getExtension(), exp, false);
copyImportContains(c.getContains(), np, expParams, filter, noInactive, vsProps, vsSrc, exp);
if (np != null) {
count++;
}
count = count + copyImportContains(c.getContains(), np, expParams, filter, noInactive, vsProps, vsSrc, exp);
}
return count;
}
private void includeCodes(ConceptSetComponent inc, ValueSetExpansionComponent exp, Parameters expParams, boolean heirarchical, boolean noInactive, List<Extension> extensions, ValueSet valueSet) throws ETooCostly, FileNotFoundException, IOException, FHIRException, CodeSystemProviderExtension {
@ -1008,11 +1013,12 @@ public class ValueSetExpander extends ValueSetProcessBase {
if (!inc.hasSystem()) {
if (imports.isEmpty()) // though this is not supposed to be the case
return;
dwc.resetTotal();
ValueSet base = imports.get(0);
checkCanonical(exp, base, focus);
imports.remove(0);
base.checkNoModifiers("Imported ValueSet", "expanding");
copyImportContains(base.getExpansion().getContains(), null, expParams, imports, noInactive, base.getExpansion().getProperty(), base, exp);
dwc.incTotal(copyImportContains(base.getExpansion().getContains(), null, expParams, imports, noInactive, base.getExpansion().getProperty(), base, exp));
} else {
CodeSystem cs = context.fetchSupplementedCodeSystem(inc.getSystem());
if (ValueSetUtilities.isServerSide(inc.getSystem()) || (cs == null || (cs.getContent() != CodeSystemContentMode.COMPLETE && cs.getContent() != CodeSystemContentMode.FRAGMENT))) {

4
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/expansion/WorkingContext.java
View File

@ -100,4 +100,8 @@ class WorkingContext {
this.noTotal = noTotal;
}
public void resetTotal() {
total = 0;
}
}

1
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/i18n/RenderingI18nContext.java
View File

@ -575,6 +575,7 @@ public class RenderingI18nContext extends I18nBase {
public static final String VALUE_SET_CONT = "VALUE_SET_CONT";
public static final String VALUE_SET_INF = "VALUE_SET_INF";
public static final String VALUE_SET_SEL = "VALUE_SET_SEL";
public static final String VALUE_SET_TOO_COSTLY = "VALUE_SET_TOO_COSTLY";
public static final String VALUE_SET_LEVEL = "VALUE_SET_LEVEL";
public static final String VALUE_SET_CODE = "VALUE_SET_CODE";
public static final String VALUE_SET_SYSTEM = "VALUE_SET_SYSTEM";

1
org.hl7.fhir.utilities/src/main/resources/rendering-phrases.properties
View File

@ -582,6 +582,7 @@ TEST_PLAN_RESULT = Result
VALUE_SET_CONT = Value Set Contents
VALUE_SET_INF = This value set cannot be expanded because of the way it is defined - it has an infinite number of members.
VALUE_SET_SEL = This value set has >1000 codes in it. In order to keep the publication size manageable, only a selection (1000 codes) of the whole set of codes is shown
VALUE_SET_TOO_COSTLY = This value set cannot be expanded because the terminology server(s) deemed it too costly to do so
VALUE_SET_LEVEL = Level
VALUE_SET_CODE = Code
VALUE_SET_SYSTEM = System

42
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java
View File

@ -4649,57 +4649,47 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
private ResolvedReference localResolve(String ref, NodeStack stack, List<ValidationMessage> errors, String path, Element rootResource, Element groupingResource, Element source, BooleanHolder bh) {
if (ref.startsWith("#")) {
// work back through the parent list.
// work back through the parent list, tracking the stack as we go
// really, there should only be one level for this (contained resources cannot contain
// contained resources), but we'll leave that to some other code to worry about
boolean wasContained = false;
Element focus = stack.getElement();
NodeStack nstack = stack;
while (nstack != null && nstack.getElement() != null) {
if (nstack.getElement().getProperty().isResource()) {
while (focus != null) {
if (focus.getProperty().isResource()) {
// ok, we'll try to find the contained reference
if (ref.equals("#") && nstack.getElement().getSpecial() != SpecialElement.CONTAINED && wasContained) {
if (ref.equals("#") && focus.getSpecial() != SpecialElement.CONTAINED && wasContained) {
ResolvedReference rr = new ResolvedReference();
rr.setResource(nstack.getElement());
rr.setFocus(nstack.getElement());
rr.setResource(focus);
rr.setFocus(focus);
rr.setExternal(false);
rr.setStack(nstack);
// rr.getStack().qualifyPath(".ofType("+nstack.getElement().fhirType()+")");
// System.out.println("-->"+nstack.getLiteralPath());
return rr;
}
if (nstack.getElement().getSpecial() == SpecialElement.CONTAINED) {
if (focus.getSpecial() == SpecialElement.CONTAINED) {
wasContained = true;
}
IndexedElement res = getContainedById(nstack.getElement(), ref.substring(1));
IndexedElement res = getContainedById(focus, ref.substring(1));
if (res != null) {
ResolvedReference rr = new ResolvedReference();
rr.setResource(nstack.getElement());
rr.setResource(focus);
rr.setFocus(res.getMatch());
rr.setExternal(false);
rr.setStack(nstack.push(res.getMatch(), res.getIndex(), res.getMatch().getProperty().getDefinition(), res.getMatch().getProperty().getDefinition()));
rr.getStack().pathComment(nstack.getElement().fhirType()+"/"+stack.getElement().getIdBase());
rr.getStack().pathComment(res.getMatch().fhirType()+"/"+res.getMatch().getIdBase());
return rr;
}
}
if (nstack.getElement().getSpecial() == SpecialElement.BUNDLE_ENTRY || nstack.getElement().getSpecial() == SpecialElement.PARAMETER) {
if (focus.getSpecial() == SpecialElement.BUNDLE_ENTRY || focus.getSpecial() == SpecialElement.PARAMETER) {
return null; // we don't try to resolve contained references across this boundary
}
focus = focus.getParentForValidator();
nstack = nstack.getParent();
}
// try again, and work up the element parent list
if (ref.equals("#")) {
Element e = stack.getElement();
while (e != null) {
if (e.getProperty().isResource() && (e.getSpecial() != SpecialElement.CONTAINED)) {
ResolvedReference rr = new ResolvedReference();
rr.setResource(e);
rr.setFocus(e);
rr.setExternal(false);
rr.setStack(stack.push(e, -1, e.getProperty().getDefinition(), e.getProperty().getDefinition()));
rr.getStack().pathComment(e.fhirType()+"/"+e.getIdBase());
return rr;
}
e = e.getParentForValidator();
if (focus != null && nstack == null) {
// we have run off the bottom of the stack, need to fake something
nstack = new NodeStack(context, focus, focus.fhirType(), validationLanguage);
}
}
return null;