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Merged
merged 4 commits into from
Nov 29, 2024
Merged

Key elements enhancements #996

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c28cbab
Fix fragment problem with multi-word resource names. https://chat.fh…
lmckenzi Nov 15, 2024
2e21700
Merge branch 'master' of https://github.com/HL7/fhir-ig-publisher
lmckenzi Nov 19, 2024
d546685
Merge branch 'master' of https://github.com/HL7/fhir-ig-publisher
lmckenzi Nov 20, 2024
f5b65b5
Update logic for determining key elements to include elements where m…
lmckenzi Nov 21, 2024
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4 changes: 3 additions & 1 deletion org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/Publisher.java
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Original file line number Diff line number Diff line change
Expand Up @@ -11341,6 +11341,8 @@ private byte[] processCustomLiquid(DBBuilder db, byte[] content, FetchedFile f)
} catch (Exception e) {
if (debug) {
e.printStackTrace();
} else {
System.out.println("Error processing custom liquid: " + e.getMessage());
}
return content;
}
Expand Down Expand Up @@ -11423,7 +11425,7 @@ private String processFragment(String arguments, FetchedFile f) throws FHIRExcep
String format = (secondSpace == -1) ? arguments.substring(firstSpace) : arguments.substring(firstSpace, secondSpace);
format = format.trim().toLowerCase();
String filters = (secondSpace == -1) ? "" : arguments.substring(secondSpace).trim();
Pattern refPattern = Pattern.compile("^([A-Z][a-z]+)+\\/([A-Za-z0-9\\-\\.]{1,64})$");
Pattern refPattern = Pattern.compile("^([A-Za-z]+)\\/([A-Za-z0-9\\-\\.]{1,64})$");
Matcher refMatcher = refPattern.matcher(reference);
if (!refMatcher.find())
throw new FHIRException("Fragment syntax error: Referenced instance must be expressed as [ResourceType]/[id]. Found " + reference + " in file " + f.getName());
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104 changes: 101 additions & 3 deletions ...lisher.core/src/main/java/org/hl7/fhir/igtools/renderers/StructureDefinitionRenderer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@

import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashMap;
Expand Down Expand Up @@ -109,6 +110,16 @@ public BindingResolutionDetails(String vss, String vsn) {
public static final String ANCHOR_PREFIX_MS = "ms_";
public static final String ANCHOR_PREFIX_KEY = "key_";

private static List<String> SIGNIFICANT_EXTENSIONS = new ArrayList<String>(Arrays.asList(new String[]
{"http://hl7.org/fhir/StructureDefinition/elementdefinition-allowedUnits",
"http://hl7.org/fhir/StructureDefinition/elementdefinition-bestPractice",
"http://hl7.org/fhir/StructureDefinition/elementdefinition-graphConstraint",
"http://hl7.org/fhir/StructureDefinition/elementdefinition-maxDecimalPlaces",
"http://hl7.org/fhir/StructureDefinition/elementdefinition-maxSize",
"http://hl7.org/fhir/StructureDefinition/elementdefinition-mimeType",
"http://hl7.org/fhir/StructureDefinition/elementdefinition-minLength",
"http://hl7.org/fhir/StructureDefinition/elementdefinition-obligation"}
));
ProfileUtilities utils;
private StructureDefinition sd;
private String destDir;
Expand Down Expand Up @@ -624,12 +635,14 @@ private void scanForMustSupport(Map<String, ElementDefinition> mustSupport, List

protected List<ElementDefinition> getKeyElements() {
if (keyElements==null) {
boolean keyEligible = sd.getDerivation().equals(TypeDerivationRule.CONSTRAINT) && !sd.getKind().equals(StructureDefinitionKind.LOGICAL);
keyElements = new ArrayList<ElementDefinition>();
Map<String, ElementDefinition> mustSupport = getMustSupport();
Set<ElementDefinition> keyElementsSet = new HashSet<ElementDefinition>();
scanForKeyElements(keyElementsSet, mustSupport, sd.getSnapshot().getElement(), sd.getSnapshot().getElementFirstRep(), null);
if (keyEligible)
scanForKeyElements(keyElementsSet, mustSupport, sd.getSnapshot().getElement(), sd.getSnapshot().getElementFirstRep(), null);
for (ElementDefinition ed : sd.getSnapshot().getElement()) {
if (keyElementsSet.contains(ed)) {
if (!keyEligible || keyElementsSet.contains(ed)) {
ElementDefinition edCopy = ed.copy();
edCopy.copyUserData(ed);
keyElements.add(edCopy);
Expand All @@ -653,12 +666,97 @@ private void scanForKeyElements(Set<ElementDefinition> keyElements, Map<String,
// - it's a slice (which means it's a constraint on the core) or declares slicing not implicit in the core spec (i.e. extension/modifierExtension)
// - it appears in the differential
// - the max cardinality has been constrained from the base max cardinality
if (mustSupport.containsKey(child.getId()) || child.getMin()!=0 || (child.hasCondition() && child.getCondition().size()>1) || child.getIsModifier() || (child.hasSlicing() && !child.getPath().endsWith(".extension") && !child.getPath().endsWith(".modifierExtension")) || child.hasSliceName() || getDifferential().containsKey(child.getId()) || !child.getMax().equals(child.getBase().getMax())) {
// - the min cardinality has been constrained from the base min cardinality
// - it has a vocabulary binding or additional binding that is required, extensible, minimum, maximum, or current binding that differs from the base resource.
// - it has a fixed value, pattern value, minValue, maxValue, maxLength, mustHaveValue, valueAlternatives
// - it has any of the following extensions: allowedUnits, bestPractice, graphConstraint, maxDecimalPlaces, maxSize, mimeType, minLength, obligation,

List<String> urls = extensionUrls(child.getExtension());
urls.retainAll(SIGNIFICANT_EXTENSIONS);
boolean bindingChanged = false;
String basePath = child.getBase().getPath();
StructureDefinition baseType = context.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/" + basePath.substring(0, basePath.indexOf(".")));
ElementDefinition baseElement = null;
for (ElementDefinition e: baseType.getSnapshot().getElement()) {
if (e.getPath().equals(basePath)) {
baseElement = e;
break;
}
}
if (baseElement==null) {
baseElement = baseElement;
//This shouldn't have happened
} else {
if (!baseElement.hasBinding())
bindingChanged = true;
else {
ElementDefinitionBindingComponent baseBinding = baseElement.getBinding();
ElementDefinitionBindingComponent binding = child.getBinding();
if (binding.hasValueSet() && (binding.getStrength().equals(BindingStrength.REQUIRED) || binding.getStrength().equals(BindingStrength.EXTENSIBLE))) {
if (!baseBinding.hasStrength() || !binding.getStrength().toCode().equals(baseBinding.getStrength().toCode()))
bindingChanged = true;
else if (!baseBinding.hasValueSet() || !baseBinding.getValueSet().equals(binding.getValueSet()))
bindingChanged = true;
}
String additionalBindings = getAdditional(binding.getAdditional());
String baseAdditionalBindings = getAdditional(binding.getAdditional());
if (!additionalBindings.equals(baseAdditionalBindings))
bindingChanged = true;
}
}
if (child.hasBinding()) {
if (baseType.hasSnapshot()) {
for (ElementDefinition e : baseType.getSnapshot().getElement()) {
if (e.getPath().equals(basePath)) {
baseElement = e;
break;
}
}
}
}
boolean oldMS = mustSupport.containsKey(child.getId()) ||
child.getMin()!=0 ||
(child.hasCondition() && child.getCondition().size()>1) ||
child.getIsModifier() ||
(child.hasSlicing() && !child.getPath().endsWith(".extension") && !child.getPath().endsWith(".modifierExtension")) ||
child.hasSliceName() ||
getDifferential().containsKey(child.getId()) ||
!child.getMax().equals(child.getBase().getMax());
boolean newMS = child.getMin()!=child.getBase().getMin() ||
child.hasFixed() ||
child.hasPattern() ||
child.hasMinValue() && (baseElement==null || !baseElement.hasMinValue() || !child.getMinValue().toString().equals(baseElement.getMinValue().toString())) ||
child.hasMaxValue() && (baseElement==null || !baseElement.hasMaxValue() || !child.getMaxValue().toString().equals(baseElement.getMaxValue().toString())) ||
child.hasMaxLength() && (baseElement==null || !baseElement.hasMaxLength() || child.getMaxLength()!=baseElement.getMaxLength()) ||
child.hasMustHaveValue() ||
child.hasValueAlternatives() ||
!urls.isEmpty();
if ( oldMS || newMS) {
scanForKeyElements(keyElements ,mustSupport, elements, child, baseModelUrl);
}
}
}

private String getAdditional(List<ElementDefinition.ElementDefinitionBindingAdditionalComponent> additionalBindings) {
String bindings = "";
for (ElementDefinition.ElementDefinitionBindingAdditionalComponent additional: additionalBindings) {
if (additional.getPurpose().equals(ElementDefinition.AdditionalBindingPurposeVS.REQUIRED) ||
additional.getPurpose().equals(ElementDefinition.AdditionalBindingPurposeVS.EXTENSIBLE) ||
additional.getPurpose().equals(ElementDefinition.AdditionalBindingPurposeVS.REQUIRED))
bindings += additional.getPurpose().getDisplay()+":" + additional.getValueSet()+";";
}
return bindings;
}

private List<String> extensionUrls(List<Extension> extensions) {
List<String> urls = new ArrayList<String>();
for (Extension e: extensions) {
if (!urls.contains(e.getUrl()))
urls.add(e.getUrl());
}
return urls;
}

public String grid(String defnFile, Set<String> outputTracker) throws IOException, FHIRException, org.hl7.fhir.exceptions.FHIRException {
if (sd.getSnapshot().getElement().isEmpty())
return "";
Expand Down
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