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Merge pull request #872 from hapifhir/gg-202207-bug-fixes 

Gg 202207 bug fixes
This commit is contained in:
Grahame Grieve 2022-07-22 13:19:50 +10:00 committed by GitHub
parent 6f3c297c35 4800d8a498
commit 78c372961e
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GPG Key ID: 4AEE18F83AFDEB23
15 changed files with 94 additions and 47 deletions
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20
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/ProfileUtilities.java
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@ -4229,14 +4229,16 @@ public class ProfileUtilities extends TranslatingUtilities {
Row currRow = row;
List<ElementChoiceGroup> groups = readChoices(element, children);
boolean isExtension = Utilities.existsInList(tail(element.getPath()), "extension", "modifierExtension");
for (ElementDefinition child : children) {
if (!child.hasSliceName()) {
currRow = row;
}
Row childRow = chooseChildRowByGroup(gen, currRow, groups, child, element, isConstraintMode);
if (logicalModel || !child.getPath().endsWith(".id") || (child.getPath().endsWith(".id") && (profile != null) && (profile.getDerivation() == TypeDerivationRule.CONSTRAINT))) {
currRow = genElement(defPath, gen, childRow.getSubRows(), child, all, profiles, showMissing, profileBaseFileName, isExtension, snapshot, corePath, imagePath, false, logicalModel, isConstraintMode, allInvariants, currRow, mustSupport, rc);
if (!element.prohibited()) {
for (ElementDefinition child : children) {
if (!child.hasSliceName()) {
currRow = row;
}
Row childRow = chooseChildRowByGroup(gen, currRow, groups, child, element, isConstraintMode);
if (logicalModel || !child.getPath().endsWith(".id") || (child.getPath().endsWith(".id") && (profile != null) && (profile.getDerivation() == TypeDerivationRule.CONSTRAINT))) {
currRow = genElement(defPath, gen, childRow.getSubRows(), child, all, profiles, showMissing, profileBaseFileName, isExtension, snapshot, corePath, imagePath, false, logicalModel, isConstraintMode, allInvariants, currRow, mustSupport, rc);
}
}
}
// if (!snapshot && (extensions == null || !extensions))
@ -4349,7 +4351,7 @@ public class ProfileUtilities extends TranslatingUtilities {
res.add(addCell(row, gen.new Cell(null, null, "?gen-e1? "+element.getType().get(0).getProfile(), null, null)));
res.add(generateDescription(gen, row, element, (ElementDefinition) element.getUserData(DERIVATION_POINTER), used.used, profile == null ? "" : profile.getUrl(), eurl, profile, corePath, imagePath, root, logicalModel, allInvariants, snapshot, mustSupport, allowSubRows, rc));
} else {
String name = urltail(eurl);
String name = element.hasSliceName() ? element.getSliceName() : urltail(eurl);
nameCell.getPieces().get(0).setText(name);
// left.getPieces().get(0).setReference((String) extDefn.getExtensionStructure().getTag("filename"));
nameCell.getPieces().get(0).setHint(translate("sd.table", "Extension URL")+" = "+extDefn.getUrl());

5
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/R5ExtensionsLoader.java
View File

@ -45,6 +45,7 @@ public class R5ExtensionsLoader {
JsonParser json = new JsonParser();
for (PackageResourceInformation pri : pck.listIndexedResources(types)) {
CanonicalResource r = (CanonicalResource) json.parse(pck.load(pri));
r.setUserData("path", Utilities.pathURL(pck.getWebLocation(), r.fhirType().toLowerCase()+ "-"+r.getId().toLowerCase()+".html"));
if (r instanceof CodeSystem) {
codeSystems.put(r.getUrl(), (CodeSystem) r);
} else if (r instanceof ValueSet) {
@ -75,7 +76,7 @@ public class R5ExtensionsLoader {
for (ElementDefinition ed : sd.getSnapshot().getElement()) {
if (ed.hasBinding() && ed.getBinding().hasValueSet()) {
String vs = ed.getBinding().getValueSet();
if (!context.hasResource(StructureDefinition.class, vs)) {
if (!context.hasResource(ValueSet.class, vs)) {
loadValueSet(vs, context, valueSets, codeSystems, pd);
}
}
@ -85,7 +86,7 @@ public class R5ExtensionsLoader {
private void loadValueSet(String url, IWorkerContext context, Map<String, ValueSet> valueSets, Map<String, CodeSystem> codeSystems, PackageVersion pd) {
if (valueSets.containsKey(url)) {
ValueSet vs = valueSets.get(url);
ValueSet vs = valueSets.get(url);
context.cacheResourceFromPackage(vs, pd);
for (ConceptSetComponent inc : vs.getCompose().getInclude()) {
for (CanonicalType t : inc.getValueSet()) {

9
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/Element.java
View File

@ -55,8 +55,8 @@ import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionContainsComponent;
import org.hl7.fhir.r5.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
import org.hl7.fhir.utilities.ElementDecoration;
import org.hl7.fhir.utilities.ElementDecoration.DecorationType;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.xhtml.XhtmlNode;
/**
@ -360,9 +360,12 @@ public class Element extends Base {
if (childMap == null) {
childMap = new HashMap<>();
for (Element child : children) {
String n = child.getName();
if (n.endsWith("[x]")) {
String n;
if (child.getProperty().getName().endsWith("[x]")) {
n = child.getProperty().getName();
n = n.substring(0, n.length()-3);
} else {
n = child.getName();
}
List<Element> l = childMap.get(n);
if (l == null) {

19
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/JsonParser.java
View File

@ -54,8 +54,8 @@ import org.hl7.fhir.r5.formats.JsonCreator;
import org.hl7.fhir.r5.formats.JsonCreatorCanonical;
import org.hl7.fhir.r5.formats.JsonCreatorGson;
import org.hl7.fhir.r5.model.ElementDefinition.TypeRefComponent;
import org.hl7.fhir.r5.utils.FHIRPathEngine;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.utils.FHIRPathEngine;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.i18n.I18nConstants;
@ -477,16 +477,19 @@ public class JsonParser extends ParserBase {
}
private void compose(String path, Element e, Set<String> done, Element child) throws IOException {
boolean isList = child.hasElementProperty() ? child.getElementProperty().isList() : child.getProperty().isList();
if (!isList) {// for specials, ignore the cardinality of the stated type
compose(path, child);
} else if (!done.contains(child.getName())) {
done.add(child.getName());
List<Element> list = e.getChildrenByName(child.getName());
composeList(path, list);
if (wantCompose(path, child)) {
boolean isList = child.hasElementProperty() ? child.getElementProperty().isList() : child.getProperty().isList();
if (!isList) {// for specials, ignore the cardinality of the stated type
compose(path, child);
} else if (!done.contains(child.getName())) {
done.add(child.getName());
List<Element> list = e.getChildrenByName(child.getName());
composeList(path, list);
}
}
}
private void composeList(String path, List<Element> list) throws IOException {
// there will be at least one element
String name = list.get(0).getName();

33
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/ParserBase.java
View File

@ -40,7 +40,6 @@ import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.elementmodel.ParserBase.NamedElement;
import org.hl7.fhir.r5.formats.FormatUtilities;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.model.StructureDefinition;
@ -55,6 +54,18 @@ import org.hl7.fhir.utilities.validation.ValidationMessage.Source;
public abstract class ParserBase {
public enum IdRenderingPolicy {
All, None, RootOnly, NotRoot;
boolean forRoot() {
return this == All || this == RootOnly;
}
boolean forInner() {
return this == All || this == NotRoot;
}
}
public class NamedElement {
private String name;
private Element element;
@ -92,6 +103,7 @@ public abstract class ParserBase {
protected List<ValidationMessage> errors;
protected ILinkResolver linkResolver;
protected boolean showDecorations;
protected IdRenderingPolicy idPolicy = IdRenderingPolicy.All;
public ParserBase(IWorkerContext context) {
super();
@ -194,4 +206,23 @@ public abstract class ParserBase {
}
public IdRenderingPolicy getIdPolicy() {
return idPolicy;
}
public void setIdPolicy(IdRenderingPolicy idPolicy) {
this.idPolicy = idPolicy;
}
protected boolean wantCompose(String path, Element e) {
if (!"id".equals(e.getName())) {
return true;
}
if (path.contains(".")) {
return idPolicy.forInner();
} else {
return idPolicy.forRoot();
}
}
}

4
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/SHCParser.java
View File

@ -13,7 +13,6 @@ import java.util.Map.Entry;
import java.util.zip.DataFormatException;
import java.util.zip.Inflater;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
@ -22,15 +21,14 @@ import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.json.JsonUtilities;
import org.hl7.fhir.utilities.json.JsonTrackingParser;
import org.hl7.fhir.utilities.json.JsonTrackingParser.LocationData;
import org.hl7.fhir.utilities.json.JsonUtilities;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
import com.google.gson.JsonArray;
import com.google.gson.JsonElement;
import com.google.gson.JsonNull;
import com.google.gson.JsonObject;
import com.google.gson.JsonPrimitive;

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/Tester.java
View File

@ -34,13 +34,11 @@ package org.hl7.fhir.r5.elementmodel;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.util.List;
import java.util.Map.Entry;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.context.SimpleWorkerContext;
import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
import org.hl7.fhir.r5.elementmodel.ParserBase.NamedElement;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;

5
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/TurtleParser.java
View File

@ -43,7 +43,6 @@ import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.elementmodel.Element.SpecialElement;
import org.hl7.fhir.r5.elementmodel.ParserBase.NamedElement;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.model.ElementDefinition.TypeRefComponent;
import org.hl7.fhir.r5.model.StructureDefinition;
@ -395,6 +394,10 @@ public class TurtleParser extends ParserBase {
// (element.getProperty().getDefinition().getIsModifier()? "modifierExtension" : "extension") ;
String en = getFormalName(element);
if (!wantCompose(parent == null ? "" : parent.getPath(), element)) {
return;
}
Complex t;
if (element.getSpecial() == SpecialElement.BUNDLE_ENTRY && parent != null && parent.getNamedChildValue("fullUrl") != null) {
String url = "<"+parent.getNamedChildValue("fullUrl")+">";

1
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/VerticalBarParser.java
View File

@ -43,7 +43,6 @@ import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.elementmodel.ParserBase.NamedElement;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.model.StructureDefinition;

17
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/XmlParser.java
View File

@ -53,7 +53,6 @@ import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.elementmodel.Element.SpecialElement;
import org.hl7.fhir.r5.elementmodel.ParserBase.NamedElement;
import org.hl7.fhir.r5.formats.FormatUtilities;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.model.DateTimeType;
@ -702,7 +701,7 @@ public class XmlParser extends ParserBase {
} else {
setXsiTypeIfIsTypeAttr(xml, element);
for (Element child : element.getChildren()) {
if (isAttr(child.getProperty())) {
if (isAttr(child.getProperty()) && wantCompose(element.getPath(), child)) {
if (linkResolver != null)
xml.link(linkResolver.resolveType(child.getType()));
String av = child.getValue();
@ -720,12 +719,14 @@ public class XmlParser extends ParserBase {
xml.enter(element.getProperty().getXmlNamespace(),element.getType());
}
for (Element child : element.getChildren()) {
if (isText(child.getProperty())) {
if (linkResolver != null)
xml.link(linkResolver.resolveProperty(element.getProperty()));
xml.text(child.getValue());
} else if (!isAttr(child.getProperty()))
composeElement(xml, child, child.getName(), false);
if (wantCompose(element.getPath(), child)) {
if (isText(child.getProperty())) {
if (linkResolver != null)
xml.link(linkResolver.resolveProperty(element.getProperty()));
xml.text(child.getValue());
} else if (!isAttr(child.getProperty()))
composeElement(xml, child, child.getName(), false);
}
}
if (!root && element.getSpecial() != null)
xml.exit(element.getProperty().getXmlNamespace(),element.getType());

5
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/BundleRenderer.java
View File

@ -167,6 +167,9 @@ public class BundleRenderer extends ResourceRenderer {
}
private ResourceWrapper resolveReference(List<BaseWrapper> entries, Base base) throws UnsupportedEncodingException, FHIRException, IOException {
if (base == null) {
return null;
}
Property prop = base.getChildByName("reference");
if (prop.hasValues()) {
String ref = prop.getValues().get(0).primitiveValue();
@ -195,7 +198,7 @@ public class BundleRenderer extends ResourceRenderer {
Resource subject = resolveReference(b, comp.getSubject());
if (subject != null) {
XhtmlNode nx = (subject instanceof DomainResource) ? ((DomainResource) subject).getText().getDiv() : null;
if (nx != null) {
if (nx != null && !nx.isEmpty()) {
x.addChildren(nx);
} else {
RendererFactory.factory(subject, context).render(x, subject);

10
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/ConceptMapRenderer.java
View File

@ -159,9 +159,9 @@ public class ConceptMapRenderer extends TerminologyRenderer {
else {
if (ccm.getRelationshipElement().hasExtension(ToolingExtensions.EXT_OLD_CONCEPTMAP_EQUIVALENCE)) {
String code = ToolingExtensions.readStringExtension(ccm.getRelationshipElement(), ToolingExtensions.EXT_OLD_CONCEPTMAP_EQUIVALENCE);
tr.td().ah(eqpath+"#"+code).tx(presentEquivalenceCode(code));
tr.td().ah(eqpath+"#"+code, code).tx(presentEquivalenceCode(code));
} else {
tr.td().ah(eqpath+"#"+ccm.getRelationship().toCode()).tx(presentRelationshipCode(ccm.getRelationship().toCode()));
tr.td().ah(eqpath+"#"+ccm.getRelationship().toCode(), ccm.getRelationship().toCode()).tx(presentRelationshipCode(ccm.getRelationship().toCode()));
}
}
td = tr.td();
@ -192,7 +192,7 @@ public class ConceptMapRenderer extends TerminologyRenderer {
if (hasRelationships) {
tr.td().b().tx("Relationship");
}
tr.td().colspan(Integer.toString(1+targets.size())).b().tx("Destination Concept Details");
tr.td().colspan(Integer.toString(1+targets.size())).b().tx("Target Concept Details");
if (comment) {
tr.td().b().tx("Comment");
}
@ -299,9 +299,9 @@ public class ConceptMapRenderer extends TerminologyRenderer {
else {
if (ccm.getRelationshipElement().hasExtension(ToolingExtensions.EXT_OLD_CONCEPTMAP_EQUIVALENCE)) {
String code = ToolingExtensions.readStringExtension(ccm.getRelationshipElement(), ToolingExtensions.EXT_OLD_CONCEPTMAP_EQUIVALENCE);
tr.td().ah(eqpath+"#"+code).tx(presentEquivalenceCode(code));
tr.td().ah(eqpath+"#"+code, code).tx(presentEquivalenceCode(code));
} else {
tr.td().ah(eqpath+"#"+ccm.getRelationship().toCode()).tx(presentRelationshipCode(ccm.getRelationship().toCode()));
tr.td().ah(eqpath+"#"+ccm.getRelationship().toCode(), ccm.getRelationship().toCode()).tx(presentRelationshipCode(ccm.getRelationship().toCode()));
}
}
}

3
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/FHIRPathEngine.java
View File

@ -5094,6 +5094,9 @@ public class FHIRPathEngine {
int i2 = -1;
if (exp.parameterCount() == 2) {
List<Base> n2 = execute(context, focus, exp.getParameters().get(1), true);
if (n2.isEmpty()|| !n2.get(0).isPrimitive() || !Utilities.isInteger(n2.get(0).primitiveValue())) {
return new ArrayList<Base>();
}
i2 = Integer.parseInt(n2.get(0).primitiveValue());
}

3
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/services/StandAloneValidatorFetcher.java
View File

@ -8,6 +8,7 @@ import org.hl7.fhir.r5.context.IWorkerContext.ICanonicalResourceLocator;
import org.hl7.fhir.r5.elementmodel.Element;
import org.hl7.fhir.r5.model.CanonicalResource;
import org.hl7.fhir.r5.model.ElementDefinition;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.terminologies.TerminologyClient;
@ -152,7 +153,7 @@ public class StandAloneValidatorFetcher implements IValidatorResourceFetcher, IV
}
if (pi != null) {
context.loadFromPackage(pi, null);
return pi.hasCanonical(url);
return pi.hasCanonical(url) || context.fetchResource(Resource.class, url) != null;
}
}

5
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java
View File

@ -2402,7 +2402,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
r = loadContainedResource(errors, path, hostContext.getRootResource(), url.substring(1), Resource.class);
}
if (r == null) {
fetcher.fetchCanonicalResource(this, url);
r = fetcher.fetchCanonicalResource(this, url);
}
if (r == null) {
r = this.context.fetchResource(Resource.class, url);
@ -5660,7 +5660,8 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
msg = fpe.forLog();
} catch (Exception ex) {
ok = false;
msg = ex.getMessage();
msg = ex.getClass().getName()+": "+ex.getMessage();
ex.printStackTrace();
}
if (!ok) {
if (!Utilities.noString(msg)) {