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org.hl7.fhir.core
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Merge 8d780e0784 into d0d30570f8

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Michael Rebsamen 2024-11-23 17:28:45 -05:00 committed by GitHub
parent d0d30570f8 8d780e0784
commit 960fd9e4a5
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GPG Key ID: B5690EEEBB952194
7 changed files with 77 additions and 21 deletions
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9
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/Element.java
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@ -476,7 +476,7 @@ public class Element extends Base implements NamedItem {
} else {
Element ne = new Element(child).setFormat(format);
children.add(ne);
numberChildren();
ne.index = children.getSizeByName(ne.getListName()) - 1;
childForValue = ne;
break;
}
@ -564,7 +564,7 @@ public class Element extends Base implements NamedItem {
} else {
Element ne = new Element(child).setFormat(format);
children.add(ne);
numberChildren();
ne.index = children.getSizeByName(ne.getListName()) - 1;
return ne;
}
}
@ -574,6 +574,7 @@ public class Element extends Base implements NamedItem {
if (p.getName().equals(name)) {
Element ne = new Element(name, p).setFormat(format);
children.add(ne);
ne.index = children.getSizeByName(ne.getListName()) - 1;
return ne;
} else if (p.getDefinition().isChoice() && name.startsWith(p.getName().replace("[x]", ""))) {
String type = name.substring(p.getName().length()-3);
@ -583,6 +584,7 @@ public class Element extends Base implements NamedItem {
Element ne = new Element(name, p).setFormat(format);
ne.setType(type);
children.add(ne);
ne.index = children.getSizeByName(ne.getListName()) - 1;
return ne;
}
@ -606,6 +608,7 @@ public class Element extends Base implements NamedItem {
if (p.getName().equals(name)) {
Element ne = new Element(name, p).setFormat(format);
children.add(ne);
ne.index = children.getSizeByName(ne.getListName()) - 1;
return ne;
}
}
@ -1664,4 +1667,4 @@ public class Element extends Base implements NamedItem {
return this.elided;
}
}
}

9
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/Manager.java
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@ -39,8 +39,9 @@ import java.util.List;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.context.ContextUtilities;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.model.StructureDefinition;
@ -144,7 +145,11 @@ public class Manager {
}
public static Element build(IWorkerContext context, StructureDefinition sd) {
Property p = new Property(context, sd.getSnapshot().getElementFirstRep(), sd);
return build(context, sd, new ProfileUtilities(context, null, null));
}
public static Element build(IWorkerContext context, StructureDefinition sd, ProfileUtilities profileUtilities) {
Property p = new Property(context, sd.getSnapshot().getElementFirstRep(), sd, profileUtilities, new ContextUtilities(context));
Element e = new Element(p.getName(), p);
e.setPath(sd.getType());
return e;

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

@ -1,6 +1,7 @@
package org.hl7.fhir.r5.utils.structuremap;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.Coding;
@ -10,7 +11,7 @@ public interface ITransformerServices {
// public boolean validateByValueSet(Coding code, String valuesetId);
public void log(String message); // log internal progress
public Base createType(Object appInfo, String name) throws FHIRException;
public Base createType(Object appInfo, String name, ProfileUtilities profileUtilities) throws FHIRException;
public Base createResource(Object appInfo, Base res, boolean atRootofTransform); // an already created resource is provided; this is to identify/store it

4
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/structuremap/StructureMapUtilities.java
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@ -1788,7 +1788,7 @@ public class StructureMapUtilities {
}
}
}
Base res = services != null ? services.createType(context.getAppInfo(), tn) : typeFactory(tn);
Base res = services != null ? services.createType(context.getAppInfo(), tn, profileUtilities) : typeFactory(tn);
if (res.isResource() && !res.fhirType().equals("Parameters")) {
// res.setIdBase(tgt.getParameter().size() > 1 ? getParamString(vars, tgt.getParameter().get(0)) : UUID.randomUUID().toString().toLowerCase());
if (services != null)
@ -1929,7 +1929,7 @@ public class StructureMapUtilities {
if (sd == null) {
throw new FHIRException("Unable to create type "+tn);
} else {
return Manager.build(worker, sd);
return Manager.build(worker, sd, profileUtilities);
}
} else {
return ResourceFactory.createResourceOrType(tn);

30
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/StructureMapUtilitiesTest.java
View File

@ -6,6 +6,7 @@ import java.io.IOException;
import java.util.List;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.context.SimpleWorkerContext;
import org.hl7.fhir.r5.elementmodel.Element;
import org.hl7.fhir.r5.elementmodel.Manager;
@ -52,6 +53,7 @@ public class StructureMapUtilitiesTest implements ITransformerServices {
StructureMap structureMap = scu.parse(fileMap, "cast");
Element target = Manager.build(context, scu.getTargetType(structureMap));
scu.transform(null, source, structureMap, target);
checkNumberChildren(target, "");
FHIRPathEngine fp = new FHIRPathEngine(context);
Assertions.assertEquals("implicit",fp.evaluateToString(target, "extension[0].value"));
Assertions.assertEquals("explicit",fp.evaluateToString(target, "extension[1].value"));
@ -67,6 +69,7 @@ public class StructureMapUtilitiesTest implements ITransformerServices {
StructureMap structureMap = scu.parse(fileMap, "qr2patfordates");
Element target = Manager.build(context, scu.getTargetType(structureMap));
scu.transform(null, source, structureMap, target);
checkNumberChildren(target, "");
FHIRPathEngine fp = new FHIRPathEngine(context);
assertEquals("2023-10-26", fp.evaluateToString(target, "birthDate"));
assertEquals("2023-09-20T13:19:13.502Z", fp.evaluateToString(target, "deceased"));
@ -81,6 +84,7 @@ public class StructureMapUtilitiesTest implements ITransformerServices {
StructureMap structureMap = scu.parse(fileMap, "whereclause");
Element target = Manager.build(context, scu.getTargetType(structureMap));
scu.transform(null, source, structureMap, target);
checkNumberChildren(target, "");
FHIRPathEngine fp = new FHIRPathEngine(context);
assertEquals("true", fp.evaluateToString(target, "rest.resource.interaction.where(code='create').exists()"));
}
@ -134,13 +138,37 @@ public class StructureMapUtilitiesTest implements ITransformerServices {
Assertions.assertEquals("-quote", structureMap.getGroup().get(0).getRule().get(1).getSourceFirstRep().getElement());
Assertions.assertEquals("-backtick", structureMap.getGroup().get(0).getRule().get(2).getSourceFirstRep().getElement());
}
// assert indices are equal to Element.numberChildren()
private void checkNumberChildren(Element e, String indent) {
System.out.println(indent + e + ", index: " + e.getIndex());
String last = "";
int index = 0;
for (Element child : e.getChildren()) {
if (child.getProperty().isList()) {
if (last.equals(child.getName())) {
index++;
} else {
last = child.getName();
index = 0;
}
// child.index = index;
Assertions.assertEquals(index, child.getIndex());
} else {
// child.index = -1;
Assertions.assertEquals(-1, child.getIndex());
}
checkNumberChildren(child, indent + " ");
}
}
@Override
public void log(String message) {
}
@Override
public Base createType(Object appInfo, String name) throws FHIRException {
public Base createType(Object appInfo, String name, ProfileUtilities profileUtilities) throws FHIRException {
return null;
}

38
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/NamedItemList.java
View File

@ -53,12 +53,12 @@ public class NamedItemList<T extends org.hl7.fhir.utilities.NamedItemList.NamedI
@Override
public boolean add(T e) {
map = null;
addToMap(e);
return list.add(e);
}
public void add(int index, T e) {
addToMap(e);
list.add(index, e);
map = null;
}
@Override
@ -74,7 +74,9 @@ public class NamedItemList<T extends org.hl7.fhir.utilities.NamedItemList.NamedI
@Override
public boolean addAll(Collection<? extends T> c) {
map = null;
for(T e : c) {
addToMap(e);
}
return list.addAll(c);
}
@ -115,6 +117,14 @@ public class NamedItemList<T extends org.hl7.fhir.utilities.NamedItemList.NamedI
}
return res;
}
public int getSizeByName(String name) {
if (map == null) {
buildMap();
}
List<T> l = map.get(name);
return l == null ? 0 : l.size();
}
public T get(int c) {
return list.get(c);
@ -123,15 +133,23 @@ public class NamedItemList<T extends org.hl7.fhir.utilities.NamedItemList.NamedI
private void buildMap() {
map = new HashMap<>();
for (T child : list) {
String n = child.getListName();
List<T> l = map.get(n);
if (l == null) {
l = new ArrayList<>();
map.put(n,l);
}
l.add(child);
addToMap(child);
}
}
private void addToMap(T child) {
if (map == null) {
// map will be re-built anyway in next call to getByName
return;
}
String n = child.getListName();
List<T> l = map.get(n);
if (l == null) {
l = new ArrayList<>();
map.put(n,l);
}
l.add(child);
}
public void sort(Comparator<? super T> sorter) {
Collections.sort(list, sorter);

5
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/TransformSupportServices.java
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@ -4,6 +4,7 @@ import java.io.PrintWriter;
import java.util.List;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.context.SimpleWorkerContext;
import org.hl7.fhir.r5.elementmodel.Manager;
import org.hl7.fhir.r5.model.Base;
@ -34,9 +35,9 @@ public class TransformSupportServices implements ITransformerServices {
}
@Override
public Base createType(Object appInfo, String name) throws FHIRException {
public Base createType(Object appInfo, String name, ProfileUtilities profileUtilities) throws FHIRException {
StructureDefinition sd = context.fetchResource(StructureDefinition.class, name);
return Manager.build(context, sd);
return Manager.build(context, sd, profileUtilities);
}
@Override