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org.hl7.fhir.core
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Merge branch 'master' of https://github.com/hapifhir/org.hl7.fhir.core into Branch_685ea98d

This commit is contained in:
Lloyd McKenzie 2022-03-11 11:21:55 -07:00
parent a6faece71b e4ce145a0b
commit 4c82c9c738
105 changed files with 2017 additions and 893 deletions
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2
RELEASE_NOTES.md
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@ -4,4 +4,4 @@
## Other code changes
* fix various rendering issues from core spec
* no changes

2
org.hl7.fhir.convertors/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.6.35</version>
<version>5.6.38-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

189
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/JsonProcessor.java Normal file
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@ -0,0 +1,189 @@
package org.hl7.fhir.convertors.misc;
import java.io.File;
import java.io.IOException;
import org.hl7.fhir.utilities.json.JsonTrackingParser;
import com.google.gson.JsonObject;
public class JsonProcessor {
public static void main(String[] args) throws Exception {
new JsonProcessor().process(args[0]);
}
private void process(String source) throws IOException {
JsonObject json = JsonTrackingParser.parseJsonFile(source);
process(json);
JsonTrackingParser.write(json, new File(source), true);
}
private void process(JsonObject json) {
process(json, "ActivityDefinition.status");
process(json, "CapabilityStatement.status");
process(json, "CodeSystem.status");
process(json, "CompartmentDefinition.status");
process(json, "ConceptMap.status");
process(json, "DataElement.status");
process(json, "ExpansionProfile.status");
process(json, "GraphDefinition.status");
process(json, "ImplementationGuide.status");
process(json, "Library.status");
process(json, "Measure.status");
process(json, "MessageDefinition.status");
process(json, "OperationDefinition.status");
process(json, "PlanDefinition.status");
process(json, "Questionnaire.status");
process(json, "SearchParameter.status");
process(json, "ServiceDefinition.status");
process(json, "StructureDefinition.status");
process(json, "StructureMap.status");
process(json, "TestScript.status");
process(json, "ValueSet.status");
process(json, "ActivityDefinition.experimental");
process(json, "CapabilityStatement.experimental");
process(json, "CodeSystem.experimental");
process(json, "CompartmentDefinition.experimental");
process(json, "ConceptMap.experimental");
process(json, "DataElement.experimental");
process(json, "ExpansionProfile.experimental");
process(json, "GraphDefinition.experimental");
process(json, "ImplementationGuide.experimental");
process(json, "Library.experimental");
process(json, "Measure.experimental");
process(json, "MessageDefinition.experimental");
process(json, "OperationDefinition.experimental");
process(json, "PlanDefinition.experimental");
process(json, "Questionnaire.experimental");
process(json, "SearchParameter.experimental");
process(json, "ServiceDefinition.experimental");
process(json, "StructureDefinition.experimental");
process(json, "StructureMap.experimental");
process(json, "TestScript.experimental");
process(json, "ValueSet.experimental");
process(json, "Identifier.use");
process(json, "Quantity.comparator");
process(json, "Address.use");
process(json, "ContactPoint.use");
process(json, "HumanName.use");
process(json, "BackboneElement.modifierExtension");
process(json, "DomainResource.modifierExtension");
process(json, "Resource.implicitRules");
process(json, "Account.status");
process(json, "AllergyIntolerance.clinicalStatus");
process(json, "AllergyIntolerance.verificationStatus");
process(json, "Appointment.status");
process(json, "AppointmentResponse.participantStatus");
process(json, "Basic.code");
process(json, "BodySite.active");
process(json, "CarePlan.status");
process(json, "CarePlan.intent");
process(json, "CarePlan.activity.detail.status");
process(json, "CarePlan.activity.detail.prohibited");
process(json, "CareTeam.status");
process(json, "ChargeItem.status");
process(json, "Claim.status");
process(json, "ClaimResponse.status");
process(json, "ClinicalImpression.status");
process(json, "Communication.status");
process(json, "Communication.notDone");
process(json, "CommunicationRequest.status");
process(json, "Composition.status");
process(json, "Composition.confidentiality");
process(json, "Composition.section.mode");
process(json, "ConceptMap.group.element.target.equivalence");
process(json, "Condition.clinicalStatus");
process(json, "Condition.verificationStatus");
process(json, "Consent.status");
process(json, "Contract.status");
process(json, "Coverage.status");
process(json, "DetectedIssue.status");
process(json, "Device.status");
process(json, "DeviceRequest.status");
process(json, "DeviceRequest.intent");
process(json, "DeviceUseStatement.status");
process(json, "DiagnosticReport.status");
process(json, "DocumentManifest.status");
process(json, "DocumentReference.status");
process(json, "DocumentReference.relatesTo");
process(json, "EligibilityRequest.status");
process(json, "EligibilityResponse.status");
process(json, "Encounter.status");
process(json, "Endpoint.status");
process(json, "EnrollmentRequest.status");
process(json, "EnrollmentResponse.status");
process(json, "EpisodeOfCare.status");
process(json, "ExplanationOfBenefit.status");
process(json, "FamilyMemberHistory.status");
process(json, "FamilyMemberHistory.notDone");
process(json, "FamilyMemberHistory.estimatedAge");
process(json, "Flag.status");
process(json, "Goal.status");
process(json, "Group.characteristic.exclude");
process(json, "GuidanceResponse.status");
process(json, "HealthcareService.active");
process(json, "Immunization.status");
process(json, "Immunization.notGiven");
process(json, "List.status");
process(json, "List.mode");
process(json, "List.entry.deleted");
process(json, "Location.status");
process(json, "Location.mode");
process(json, "MeasureReport.status");
process(json, "MedicationAdministration.status");
process(json, "MedicationAdministration.notGiven");
process(json, "MedicationDispense.status");
process(json, "MedicationRequest.status");
process(json, "MedicationRequest.intent");
process(json, "MedicationRequest.substitution.allowed");
process(json, "MedicationStatement.status");
process(json, "MedicationStatement.taken");
process(json, "NamingSystem.status");
process(json, "NutritionOrder.status");
process(json, "Observation.status");
process(json, "OperationOutcome.issue.severity");
process(json, "Organization.active");
process(json, "Patient.active");
process(json, "Patient.deceased[x]");
process(json, "Patient.animal");
process(json, "Patient.link");
process(json, "PaymentNotice.status");
process(json, "PaymentReconciliation.status");
process(json, "Person.active");
process(json, "Procedure.status");
process(json, "Procedure.notDone");
process(json, "ProcedureRequest.status");
process(json, "ProcedureRequest.intent");
process(json, "ProcedureRequest.doNotPerform");
process(json, "ProcessRequest.status");
process(json, "ProcessResponse.status");
process(json, "Questionnaire.item.enableWhen");
process(json, "QuestionnaireResponse.status");
process(json, "ReferralRequest.status");
process(json, "ReferralRequest.intent");
process(json, "RelatedPerson.active");
process(json, "RequestGroup.status");
process(json, "RequestGroup.intent");
process(json, "ResearchStudy.status");
process(json, "ResearchSubject.status");
process(json, "Schedule.active");
process(json, "Specimen.status");
process(json, "Subscription.status");
process(json, "SupplyDelivery.status");
process(json, "SupplyRequest.status");
process(json, "TestReport.status");
process(json, "ValueSet.compose.include.filter");
process(json, "VisionPrescription.status");
}
private void process(JsonObject json, String name) {
JsonObject j = json.getAsJsonObject(name);
if (j == null) {
System.out.println("Can't find "+name);
} else {
j.addProperty("modifier", true);
}
}
}

190
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/XVerPackegeFixer.java
View File

@ -6,13 +6,19 @@ import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
import javax.naming.ldap.StartTlsRequest;
import javax.xml.parsers.ParserConfigurationException;
import org.hl7.fhir.convertors.misc.XVerPackegeFixer.References;
import org.hl7.fhir.dstu2.model.ElementDefinition;
import org.hl7.fhir.dstu2.model.StructureDefinition;
import org.hl7.fhir.dstu2.model.StructureDefinition.StructureDefinitionSnapshotComponent;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.json.JsonTrackingParser;
@ -24,12 +30,35 @@ import com.google.gson.JsonObject;
public class XVerPackegeFixer {
private static final String R5_FOLDER = "C:\\work\\org.hl7.fhir\\packages\\hl7.fhir.rX\\hl7.fhir.r5.core\\package";
private static final String R4_FOLDER = "C:\\work\\org.hl7.fhir\\packages\\hl7.fhir.rX\\hl7.fhir.r4.core\\package";
private static final String R3_FOLDER = "C:\\work\\org.hl7.fhir\\packages\\hl7.fhir.rX\\hl7.fhir.r3.core\\package";
private static final String R2B_FOLDER = "C:\\work\\org.hl7.fhir\\packages\\hl7.fhir.rX\\hl7.fhir.r2b.core\\package";
private static final String R2_FOLDER = "C:\\work\\org.hl7.fhir\\packages\\hl7.fhir.rX\\hl7.fhir.r2.core\\package";
private static int mod;
public static class References {
private boolean modifier;
private boolean inherited;
public boolean getModifier() {
return modifier;
}
public void setModifier(boolean value) {
this.modifier = value;
}
public boolean getInherited() {
return inherited;
}
public void setInherited(boolean inherited) {
this.inherited = inherited;
}
}
private static final String R5_FOLDER = "/Users/grahamegrieve/work/packages/hl7.fhir.rX/hl7.fhir.r5.core/package";
private static final String R4_FOLDER = "/Users/grahamegrieve/work/packages/hl7.fhir.rX/hl7.fhir.r4.core/package";
private static final String R3_FOLDER = "/Users/grahamegrieve/work/packages/hl7.fhir.rX/hl7.fhir.r3.core/package";
private static final String R2B_FOLDER = "/Users/grahamegrieve/work/packages/hl7.fhir.rX/hl7.fhir.r2b.core/package";
private static final String R2_FOLDER = "/Users/grahamegrieve/work/packages/hl7.fhir.rX/hl7.fhir.r2.core/package";
private static int modCount;
private static Map<String, org.hl7.fhir.r5.model.StructureDefinition> map5 = new HashMap<>();
private static Map<String, org.hl7.fhir.r4.model.StructureDefinition> map4 = new HashMap<>();
@ -38,21 +67,23 @@ public class XVerPackegeFixer {
private static Map<String, org.hl7.fhir.dstu2016may.model.StructureDefinition> map2b = new HashMap<>();
public static void main(String[] args) throws FileNotFoundException, ParserConfigurationException, SAXException, IOException {
mod = 0;
modCount = 0;
for (File f : new File(args[0]).listFiles()) {
if (f.getName().startsWith("xver-")) {
if (f.getName().startsWith("xver-") && f.getName().contains("1.0")) {
JsonObject j = JsonTrackingParser.parseJson(f);
fixUp(j, f.getName());
JsonTrackingParser.write(j, f, true);
}
}
System.out.println("all done: "+mod+" modifiers");
System.out.println("all done: "+modCount+" modifiers");
}
private static void fixUp(JsonObject j, String name) throws FHIRFormatError, FileNotFoundException, IOException {
name = name.replace(".json", "");
System.out.println("Process "+name);
String version = name.substring(name.lastIndexOf("-")+1);
Set<String> pr = new HashSet<>();
int i = 0;
for (Entry<String, JsonElement> e : j.entrySet()) {
if (i == 50) {
@ -62,18 +93,31 @@ public class XVerPackegeFixer {
i++;
String n = e.getKey();
JsonObject o = ((JsonObject) e.getValue());
boolean ok = (o.has("types") && o.getAsJsonArray("types").size() > 0) || (o.has("elements") && o.getAsJsonArray("elements").size() > 0);
if (!ok) {
// boolean ok = (o.has("types") && o.getAsJsonArray("types").size() > 0) || (o.has("elements") && o.getAsJsonArray("elements").size() > 0);
// if (!ok) {
if (o.has("types")) {
o.remove("types");
}
if (o.has("elements")) {
o.remove("elements");
}
if (o.has("modifier")) {
o.remove("modifier");
}
List<String> types = new ArrayList<>();
List<String> elements = new ArrayList<>();
getElementInfo(version, n, types, elements);
References mod = new References();
getElementInfo(version, n, types, elements, mod);
if (mod.getInherited()) {
pr.add(n);
}
if (elements.size() > 0) {
JsonArray arr = o.getAsJsonArray("elements");
if (arr == null) {
arr = new JsonArray();
o.add("elements", arr);
}
for (String s : types) {
for (String s : elements) {
arr.add(s);
}
} else if (types.size() > 0) {
@ -86,30 +130,37 @@ public class XVerPackegeFixer {
arr.add(s);
}
}
}
if (mod.getModifier()) {
o.addProperty("modifier", true);
modCount++;
}
// }
}
for (String s : pr) {
j.remove(s);
}
System.out.println("done");
}
private static boolean getElementInfo(String version, String n, List<String> types, List<String> elements) throws FHIRFormatError, FileNotFoundException, IOException {
if ("contained".equals(n.substring(n.indexOf(".")+1))) {
return false;
}
private static boolean getElementInfo(String version, String n, List<String> types, List<String> elements, References mod) throws FHIRFormatError, FileNotFoundException, IOException {
// if ("contained".equals(n.substring(n.indexOf(".")+1))) {
// return false;
// }
switch (version) {
case "4.6": return getElementInfoR5(n, types, elements);
case "4.0": return getElementInfoR4(n, types, elements);
case "3.0": return getElementInfoR3(n, types, elements);
case "1.4": return getElementInfoR2B(n, types, elements);
case "1.0": return getElementInfoR2(n, types, elements);
case "4.6": return getElementInfoR5(n, types, elements, mod);
case "4.0": return getElementInfoR4(n, types, elements, mod);
case "3.0": return getElementInfoR3(n, types, elements, mod);
case "1.4": return getElementInfoR2B(n, types, elements, mod);
case "1.0": return getElementInfoR2(n, types, elements, mod);
}
return false;
}
private static Object tail(String value) {
private static String tail(String value) {
return value.contains("/") ? value.substring(value.lastIndexOf("/")+1) : value;
}
private static boolean getElementInfoR5(String n, List<String> types, List<String> elements) throws FHIRFormatError, FileNotFoundException, IOException {
private static boolean getElementInfoR5(String n, List<String> types, List<String> elements, References mod) throws FHIRFormatError, FileNotFoundException, IOException {
String tn = n.substring(0, n.indexOf("."));
org.hl7.fhir.r5.model.StructureDefinition sd = null;
if (map5.containsKey(tn)) {
@ -120,7 +171,8 @@ public class XVerPackegeFixer {
}
for (org.hl7.fhir.r5.model.ElementDefinition ed : sd.getSnapshot().getElement()) {
if (ed.getPath().equals(n)) {
List<org.hl7.fhir.r5.model.ElementDefinition> children = listChildrenR5(sd.getSnapshot().getElement(), ed);
mod.setModifier(ed.getIsModifier());
List<org.hl7.fhir.r5.model.ElementDefinition> children = listChildrenR5(sd.getSnapshot().getElement(), ed);
if (children.size() > 0) {
for (org.hl7.fhir.r5.model.ElementDefinition c : children) {
String en = c.getPath().substring(ed.getPath().length()+1);
@ -164,7 +216,7 @@ public class XVerPackegeFixer {
return res;
}
private static boolean getElementInfoR4(String n, List<String> types, List<String> elements) throws FHIRFormatError, FileNotFoundException, IOException {
private static boolean getElementInfoR4(String n, List<String> types, List<String> elements, References mod) throws FHIRFormatError, FileNotFoundException, IOException {
String tn = n.substring(0, n.indexOf("."));
org.hl7.fhir.r4.model.StructureDefinition sd = null;
if (map4.containsKey(tn)) {
@ -175,6 +227,7 @@ public class XVerPackegeFixer {
}
for (org.hl7.fhir.r4.model.ElementDefinition ed : sd.getSnapshot().getElement()) {
if (ed.getPath().equals(n)) {
mod.setModifier(ed.getIsModifier());
List<org.hl7.fhir.r4.model.ElementDefinition> children = listChildrenR4(sd.getSnapshot().getElement(), ed);
if (children.size() > 0) {
for (org.hl7.fhir.r4.model.ElementDefinition c : children) {
@ -220,7 +273,7 @@ public class XVerPackegeFixer {
}
private static boolean getElementInfoR3(String n, List<String> types, List<String> elements) throws FHIRFormatError, FileNotFoundException, IOException {
private static boolean getElementInfoR3(String n, List<String> types, List<String> elements, References mod) throws FHIRFormatError, FileNotFoundException, IOException {
String tn = n.substring(0, n.indexOf("."));
org.hl7.fhir.dstu3.model.StructureDefinition sd = null;
if (map3.containsKey(tn)) {
@ -231,6 +284,7 @@ public class XVerPackegeFixer {
}
for (org.hl7.fhir.dstu3.model.ElementDefinition ed : sd.getSnapshot().getElement()) {
if (ed.getPath().equals(n)) {
mod.setModifier(ed.getIsModifier());
List<org.hl7.fhir.dstu3.model.ElementDefinition> children = listChildrenR3(sd.getSnapshot().getElement(), ed);
if (children.size() > 0) {
for (org.hl7.fhir.dstu3.model.ElementDefinition c : children) {
@ -272,17 +326,14 @@ public class XVerPackegeFixer {
}
private static boolean getElementInfoR2(String n, List<String> types, List<String> elements) throws FHIRFormatError, FileNotFoundException, IOException {
private static boolean getElementInfoR2(String n, List<String> types, List<String> elements, References mod) throws FHIRFormatError, FileNotFoundException, IOException {
String tn = n.substring(0, n.indexOf("."));
org.hl7.fhir.dstu2.model.StructureDefinition sd = null;
if (map2.containsKey(tn)) {
sd = map2.get(tn);
} else {
sd = (org.hl7.fhir.dstu2.model.StructureDefinition) new org.hl7.fhir.dstu2.formats.JsonParser().parse(new FileInputStream(Utilities.path(R2_FOLDER, "StructureDefinition-"+tn+".json")));
map2.put(tn, sd);
}
sd = loadType(tn);
mod.setInherited(isInherited(n, sd));
for (org.hl7.fhir.dstu2.model.ElementDefinition ed : sd.getSnapshot().getElement()) {
if (ed.getPath().equals(n)) {
mod.setModifier(ed.getIsModifier());
List<org.hl7.fhir.dstu2.model.ElementDefinition> children = listChildrenR2(sd.getSnapshot().getElement(), ed);
if (children.size() > 0) {
for (org.hl7.fhir.dstu2.model.ElementDefinition c : children) {
@ -290,28 +341,76 @@ public class XVerPackegeFixer {
elements.add(en);
}
} else {
boolean isReference = false;
StringBuilder r = new StringBuilder();
r.append("Reference(");
for (org.hl7.fhir.dstu2.model.ElementDefinition.TypeRefComponent t : ed.getType()) {
if (t.hasProfile()) {
StringBuilder b = new StringBuilder();
b.append(t.getCode());
b.append("(");
boolean first = true;
for (org.hl7.fhir.dstu2.model.UriType u : t.getProfile()) {
if (first) first = false; else b.append("|");
b.append(tail(u.getValue()));
if ("Reference".equals(t.getCode())) {
for (org.hl7.fhir.dstu2.model.UriType u : t.getProfile()) {
if (isReference)
r.append("|");
r.append(tail(u.getValue()));
isReference = true;
}
} else {
StringBuilder b = new StringBuilder();
b.append(t.getCode());
b.append("(");
boolean first = true;
for (org.hl7.fhir.dstu2.model.UriType u : t.getProfile()) {
if (first) first = false; else b.append("|");
b.append(tail(u.getValue()));
}
b.append(")");
types.add(b.toString());
}
b.append(")");
types.add(b.toString());
} else {
types.add(t.getCode());
}
}
if (isReference) {
r.append(")");
types.add(r.toString());
}
}
}
}
return false;
}
private static org.hl7.fhir.dstu2.model.StructureDefinition loadType(String tn)
throws IOException, FileNotFoundException {
org.hl7.fhir.dstu2.model.StructureDefinition sd;
if (map2.containsKey(tn)) {
sd = map2.get(tn);
} else {
sd = (org.hl7.fhir.dstu2.model.StructureDefinition) new org.hl7.fhir.dstu2.formats.JsonParser().parse(new FileInputStream(Utilities.path(R2_FOLDER, "StructureDefinition-"+tn+".json")));
map2.put(tn, sd);
}
return sd;
}
private static boolean isInherited(String n, StructureDefinition sd) throws FileNotFoundException, IOException {
String tail = n.substring(n.indexOf(".")+1);
while (sd != null) {
sd = sd.hasBase() ? loadType(tail(sd.getBase())) : null;
if (sd != null && hasPath(sd.getSnapshot(), sd.getName()+"."+tail)) {
return true;
}
}
return false;
}
private static boolean hasPath(StructureDefinitionSnapshotComponent snapshot, String path) {
for (ElementDefinition ed : snapshot.getElement()) {
if (ed.getPath().equals(path)) {
return true;
}
}
return false;
}
private static List<org.hl7.fhir.dstu2.model.ElementDefinition> listChildrenR2(List<org.hl7.fhir.dstu2.model.ElementDefinition> list, org.hl7.fhir.dstu2.model.ElementDefinition ed) {
List<org.hl7.fhir.dstu2.model.ElementDefinition> res = new ArrayList<>();
@ -328,7 +427,7 @@ public class XVerPackegeFixer {
}
private static boolean getElementInfoR2B(String n, List<String> types, List<String> elements) throws FHIRFormatError, FileNotFoundException, IOException {
private static boolean getElementInfoR2B(String n, List<String> types, List<String> elements, References mod) throws FHIRFormatError, FileNotFoundException, IOException {
String tn = n.substring(0, n.indexOf("."));
org.hl7.fhir.dstu2016may.model.StructureDefinition sd = null;
if (map2b.containsKey(tn)) {
@ -339,6 +438,7 @@ public class XVerPackegeFixer {
}
for (org.hl7.fhir.dstu2016may.model.ElementDefinition ed : sd.getSnapshot().getElement()) {
if (ed.getPath().equals(n)) {
mod.setModifier(ed.getIsModifier());
List<org.hl7.fhir.dstu2016may.model.ElementDefinition> children = listChildrenR2B(sd.getSnapshot().getElement(), ed);
if (children.size() > 0) {
for (org.hl7.fhir.dstu2016may.model.ElementDefinition c : children) {

2
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/txClient/TerminologyClientR3.java
View File

@ -72,7 +72,7 @@ public class TerminologyClientR3 implements TerminologyClient {
@Override
public ValueSet expandValueset(ValueSet vs, Parameters p, Map<String, String> params) throws FHIRException {
org.hl7.fhir.dstu3.model.ValueSet vs2 = (org.hl7.fhir.dstu3.model.ValueSet) VersionConvertorFactory_30_50.convertResource(vs);
org.hl7.fhir.dstu3.model.ExpansionProfile p2 = (org.hl7.fhir.dstu3.model.ExpansionProfile) VersionConvertorFactory_30_50.convertResource(p);
org.hl7.fhir.dstu3.model.Parameters p2 = (org.hl7.fhir.dstu3.model.Parameters) VersionConvertorFactory_30_50.convertResource(p);
vs2 = client.expandValueset(vs2, p2, params); // todo: second parameter
return (ValueSet) VersionConvertorFactory_30_50.convertResource(vs2);
}

2
org.hl7.fhir.dstu2/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.6.35</version>
<version>5.6.38-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.dstu2016may/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.6.35</version>
<version>5.6.38-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.dstu3/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.6.35</version>
<version>5.6.38-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/utils/FHIRPathEngine.java
View File

@ -2219,7 +2219,7 @@ public class FHIRPathEngine {
if (!Utilities.noString(f)) {
if (exp.getParameters().size() != 2) {
if (exp.getParameters().size() == 2) {
String t = convertToString(execute(context, focus, exp.getParameters().get(0), true));
String r = convertToString(execute(context, focus, exp.getParameters().get(1), true));

61
org.hl7.fhir.dstu3/src/test/java/org/hl7/fhir/dstu3/utils/FhirPathTests.java Normal file
View File

@ -0,0 +1,61 @@
package org.hl7.fhir.dstu3.utils;
import org.hl7.fhir.dstu3.context.IWorkerContext;
import org.hl7.fhir.dstu3.model.Base;
import org.hl7.fhir.dstu3.model.ExpressionNode;
import org.hl7.fhir.dstu3.model.StringType;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.Mock;
import org.mockito.Mockito;
import org.mockito.junit.jupiter.MockitoExtension;
import java.util.List;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.Mockito.times;
@ExtendWith(MockitoExtension.class)
public class FhirPathTests {
@Mock
IWorkerContext iWorkerContext;
@Mock
Object appContext;
@Mock
Base resource;
@Mock
Base base;
@Test
public void testFuncReplaceParamSize() {
FHIRPathEngine engine = Mockito.spy(new FHIRPathEngine(iWorkerContext));
ExpressionNode expressionNode = new ExpressionNode(0);
expressionNode.setKind(ExpressionNode.Kind.Function);
expressionNode.setFunction(ExpressionNode.Function.Replace);
ExpressionNode expressionNodeB = new ExpressionNode(1);
expressionNodeB.setKind(ExpressionNode.Kind.Function);
expressionNodeB.setFunction(ExpressionNode.Function.Empty);
ExpressionNode expressionNodeC = new ExpressionNode(2);
expressionNodeC.setKind(ExpressionNode.Kind.Function);
expressionNodeC.setFunction(ExpressionNode.Function.Empty);
expressionNode.getParameters().add(expressionNodeB);
expressionNode.getParameters().add(expressionNodeC);
List<Base> result = engine.evaluate(appContext, resource, base, expressionNode);
assertEquals(1, result.size());
Base onlyResult = result.get(0);
assertTrue(onlyResult instanceof StringType);
assertEquals("base", ((StringType)result.get(0)).asStringValue());
Mockito.verify(engine, times(2)).convertToString(any());
}
}

2
org.hl7.fhir.r4/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.6.35</version>
<version>5.6.38-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/model/FhirPublication.java
View File

@ -49,7 +49,7 @@ public enum FhirPublication {
R4;
public static FhirPublication fromCode(String v) {
if (VersionUtilities.isR4Ver(v))
if (VersionUtilities.isR2Ver(v))
return FhirPublication.DSTU2;
if ("1.0".equals(v))
return FhirPublication.DSTU2;

2
org.hl7.fhir.r4b/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.6.35</version>
<version>5.6.38-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

156
org.hl7.fhir.r4b/src/main/java/org/hl7/fhir/r4b/comparison/ProfileComparer.java
View File

@ -45,14 +45,14 @@ public class ProfileComparer extends CanonicalResourceComparer {
public class ProfileComparison extends CanonicalResourceComparison<StructureDefinition> {
private StructuralMatch<ElementDefinition> combined;
private StructuralMatch<ElementDefinitionNode> combined;
public ProfileComparison(StructureDefinition left, StructureDefinition right) {
super(left, right);
combined = new StructuralMatch<ElementDefinition>(); // base
combined = new StructuralMatch<ElementDefinitionNode>(); // base
}
public StructuralMatch<ElementDefinition> getCombined() {
public StructuralMatch<ElementDefinitionNode> getCombined() {
return combined;
}
@ -79,7 +79,21 @@ public class ProfileComparer extends CanonicalResourceComparer {
}
private class ElementDefinitionNode {
private ElementDefinition def;
private StructureDefinition src;
private ElementDefinitionNode(StructureDefinition src, ElementDefinition def) {
super();
this.src = src;
this.def = def;
}
public ElementDefinition getDef() {
return def;
}
public StructureDefinition getSrc() {
return src;
}
}
private ProfileUtilities utilsLeft;
private ProfileUtilities utilsRight;
@ -127,7 +141,7 @@ public class ProfileComparer extends CanonicalResourceComparer {
if (left.getType().equals(right.getType())) {
DefinitionNavigator ln = new DefinitionNavigator(session.getContextLeft(), left);
DefinitionNavigator rn = new DefinitionNavigator(session.getContextRight(), right);
StructuralMatch<ElementDefinition> sm = new StructuralMatch<ElementDefinition>(ln.current(), rn.current());
StructuralMatch<ElementDefinitionNode> sm = new StructuralMatch<ElementDefinitionNode>(new ElementDefinitionNode(left, ln.current()), new ElementDefinitionNode(right, rn.current()));
compareElements(res, sm, ln.path(), null, ln, rn);
res.combined = sm;
}
@ -147,7 +161,7 @@ public class ProfileComparer extends CanonicalResourceComparer {
throw new DefinitionException("StructureDefinition snapshot is empty ("+name+": "+sd.getName()+")");
}
private void compareElements(ProfileComparison comp, StructuralMatch<ElementDefinition> res, String path, String sliceName, DefinitionNavigator left, DefinitionNavigator right) throws DefinitionException, FHIRFormatError, IOException {
private void compareElements(ProfileComparison comp, StructuralMatch<ElementDefinitionNode> res, String path, String sliceName, DefinitionNavigator left, DefinitionNavigator right) throws DefinitionException, FHIRFormatError, IOException {
assert(path != null);
assert(left != null);
assert(right != null);
@ -190,7 +204,7 @@ public class ProfileComparer extends CanonicalResourceComparer {
subset.setExample(left.current().hasExample() ? left.current().getExample() : right.current().getExample());
if (left.current().getMustSupport() != right.current().getMustSupport()) {
vm(IssueSeverity.ERROR, "Elements differ in definition for mustSupport:\r\n \""+left.current().getMustSupport()+"\"\r\n \""+right.current().getMustSupport()+"\"", path, comp.getMessages(), res.getMessages());
vm(IssueSeverity.WARNING, "Elements differ in definition for mustSupport: '"+left.current().getMustSupport()+"' vs '"+right.current().getMustSupport()+"'", path, comp.getMessages(), res.getMessages());
}
subset.setMustSupport(left.current().getMustSupport() || right.current().getMustSupport());
@ -198,15 +212,20 @@ public class ProfileComparer extends CanonicalResourceComparer {
// compare and intersect
superset.setMin(unionMin(left.current().getMin(), right.current().getMin()));
superset.setMax(unionMax(left.current().getMax(), right.current().getMax()));
subset.setMin(intersectMin(left.current().getMin(), right.current().getMin()));
subset.setMax(intersectMax(left.current().getMax(), right.current().getMax()));
rule(comp, res, subset.getMax().equals("*") || Integer.parseInt(subset.getMax()) >= subset.getMin(), path, "Cardinality Mismatch: "+card(left)+"/"+card(right));
int leftMin = left.current().getMin();
int rightMin = right.current().getMin();
int leftMax = "*".equals(left.current().getMax()) ? Integer.MAX_VALUE : Integer.parseInt(left.current().getMax());
int rightMax = "*".equals(right.current().getMax()) ? Integer.MAX_VALUE : Integer.parseInt(right.current().getMax());
checkMinMax(comp, res, path, leftMin, rightMin, leftMax, rightMax);
superset.setMin(unionMin(leftMin, rightMin));
superset.setMax(unionMax(leftMax, rightMax, left.current().getMax(), right.current().getMax()));
subset.setMin(intersectMin(leftMin, rightMin));
subset.setMax(intersectMax(leftMax, rightMax, left.current().getMax(), right.current().getMax()));
superset.getType().addAll(unionTypes(comp, res, path, left.current().getType(), right.current().getType()));
subset.getType().addAll(intersectTypes(comp, res, subset, path, left.current().getType(), right.current().getType()));
rule(comp, res, !subset.getType().isEmpty() || (!left.current().hasType() && !right.current().hasType()), path, "Type Mismatch:\r\n "+typeCode(left)+"\r\n "+typeCode(right));
rule(comp, res, !subset.getType().isEmpty() || (!left.current().hasType() && !right.current().hasType()), path, "Type Mismatch: "+typeCode(left)+" vs "+typeCode(right));
// <fixed[x]><!-- ?? 0..1 * Value must be exactly this --></fixed[x]>
// <pattern[x]><!-- ?? 0..1 * Value must have at least these property values --></pattern[x]>
superset.setMaxLengthElement(unionMaxLength(left.current().getMaxLength(), right.current().getMaxLength()));
@ -283,7 +302,8 @@ public class ProfileComparer extends CanonicalResourceComparer {
// return null;
}
private void compareChildren(ProfileComparison comp, StructuralMatch<ElementDefinition> res, String path, DefinitionNavigator left, DefinitionNavigator right) throws DefinitionException, IOException, FHIRFormatError {
private void compareChildren(ProfileComparison comp, StructuralMatch<ElementDefinitionNode> res, String path, DefinitionNavigator left, DefinitionNavigator right) throws DefinitionException, IOException, FHIRFormatError {
List<DefinitionNavigator> lc = left.children();
List<DefinitionNavigator> rc = right.children();
// it's possible that one of these profiles walks into a data type and the other doesn't
@ -299,10 +319,10 @@ public class ProfileComparer extends CanonicalResourceComparer {
DefinitionNavigator r = findInList(rc, l);
if (r == null) {
comp.getUnion().getSnapshot().getElement().add(l.current().copy());
res.getChildren().add(new StructuralMatch<ElementDefinition>(l.current(), vmI(IssueSeverity.INFORMATION, "Removed this element", path)));
res.getChildren().add(new StructuralMatch<ElementDefinitionNode>(new ElementDefinitionNode(l.getStructure(), l.current()), vmI(IssueSeverity.INFORMATION, "Removed this element", path)));
} else {
matchR.add(r);
StructuralMatch<ElementDefinition> sm = new StructuralMatch<ElementDefinition>(l.current(), r.current());
StructuralMatch<ElementDefinitionNode> sm = new StructuralMatch<ElementDefinitionNode>(new ElementDefinitionNode(l.getStructure(), l.current()), new ElementDefinitionNode(r.getStructure(), r.current()));
res.getChildren().add(sm);
compareElements(comp, sm, l.path(), null, l, r);
}
@ -310,7 +330,7 @@ public class ProfileComparer extends CanonicalResourceComparer {
for (DefinitionNavigator r : rc) {
if (!matchR.contains(r)) {
comp.getUnion().getSnapshot().getElement().add(r.current().copy());
res.getChildren().add(new StructuralMatch<ElementDefinition>(vmI(IssueSeverity.INFORMATION, "Added this element", path), r.current()));
res.getChildren().add(new StructuralMatch<ElementDefinitionNode>(vmI(IssueSeverity.INFORMATION, "Added this element", path), new ElementDefinitionNode(r.getStructure(), r.current())));
}
}
}
@ -324,7 +344,7 @@ public class ProfileComparer extends CanonicalResourceComparer {
return null;
}
private void ruleEqual(ProfileComparison comp, StructuralMatch<ElementDefinition> res, DataType vLeft, DataType vRight, String name, String path) throws IOException {
private void ruleEqual(ProfileComparison comp, StructuralMatch<ElementDefinitionNode> res, DataType vLeft, DataType vRight, String name, String path) throws IOException {
if (vLeft == null && vRight == null) {
// nothing
} else if (vLeft == null) {
@ -338,7 +358,7 @@ public class ProfileComparer extends CanonicalResourceComparer {
private String toString(DataType val, boolean left) throws IOException {
if (val instanceof PrimitiveType)
return "\"" + ((PrimitiveType) val).getValueAsString()+"\"";
return "'" + ((PrimitiveType) val).getValueAsString()+"'";
IParser jp = left ? session.getContextLeft().newJsonParser() : session.getContextRight().newJsonParser();
return jp.composeString(val, "value");
@ -356,14 +376,14 @@ public class ProfileComparer extends CanonicalResourceComparer {
return s;
}
private boolean rule(ProfileComparison comp, StructuralMatch<ElementDefinition> res, boolean test, String path, String message) {
private boolean rule(ProfileComparison comp, StructuralMatch<ElementDefinitionNode> res, boolean test, String path, String message) {
if (!test) {
vm(IssueSeverity.ERROR, message, path, comp.getMessages(), res.getMessages());
}
return test;
}
private String mergeText(ProfileComparison comp, StructuralMatch<ElementDefinition> res, String path, String name, String left, String right, boolean isError) {
private String mergeText(ProfileComparison comp, StructuralMatch<ElementDefinitionNode> res, String path, String name, String left, String right, boolean isError) {
if (left == null && right == null)
return null;
if (left == null)
@ -375,7 +395,7 @@ public class ProfileComparer extends CanonicalResourceComparer {
if (left.equalsIgnoreCase(right))
return left;
if (path != null) {
vm(isError ? IssueSeverity.ERROR : IssueSeverity.WARNING, "Elements differ in "+name+":\r\n \""+left+"\"\r\n \""+right+"\"", path, comp.getMessages(), res.getMessages());
vm(isError ? IssueSeverity.ERROR : IssueSeverity.WARNING, "Elements differ in "+name+": '"+left+"' vs '"+right+"'", path, comp.getMessages(), res.getMessages());
}
return "left: "+left+"; right: "+right;
}
@ -429,6 +449,36 @@ public class ProfileComparer extends CanonicalResourceComparer {
return right;
}
private void checkMinMax(ProfileComparison comp, StructuralMatch<ElementDefinitionNode> res, String path, int leftMin, int rightMin, int leftMax, int rightMax) {
if (leftMin != rightMin) {
if (leftMin == 0) {
vm(IssueSeverity.INFORMATION, "Element minimum cardinalities differ: '"+leftMin+"' vs '"+rightMin+"'", path, comp.getMessages(), res.getMessages());
} else if (rightMin == 0) {
vm(IssueSeverity.INFORMATION, "Element minimum cardinalities differ: '"+leftMin+"' vs '"+rightMin+"'", path, comp.getMessages(), res.getMessages());
} else {
vm(IssueSeverity.INFORMATION, "Element minimum cardinalities differ: '"+leftMin+"' vs '"+rightMin+"'", path, comp.getMessages(), res.getMessages());
}
}
if (leftMax != rightMax) {
if (leftMax == Integer.MAX_VALUE) {
vm(IssueSeverity.INFORMATION, "Element maximum cardinalities differ: '"+leftMax+"' vs '"+rightMax+"'", path, comp.getMessages(), res.getMessages());
} else if (rightMax == Integer.MAX_VALUE) {
vm(IssueSeverity.INFORMATION, "Element maximum cardinalities differ: '"+leftMax+"' vs '"+rightMax+"'", path, comp.getMessages(), res.getMessages());
} else {
vm(IssueSeverity.INFORMATION, "Element maximum cardinalities differ: '"+leftMax+"' vs '"+rightMax+"'", path, comp.getMessages(), res.getMessages());
}
}
// rule(comp, res, subset.getMax().equals("*") || Integer.parseInt(subset.getMax()) >= subset.getMin(), path, "Cardinality Mismatch: "+card(left)+"/"+card(right));
// cross comparison - if max > min in either direction, there can be no instances that are valid against both
if (leftMax < rightMin) {
vm(IssueSeverity.ERROR, "Element minimum cardinalities conflict: '"+leftMin+".."+leftMax+"' vs '"+rightMin+".."+rightMax+"': No instances can be valid against both profiles", path, comp.getMessages(), res.getMessages());
}
if (rightMax < leftMin) {
vm(IssueSeverity.ERROR, "Element minimum cardinalities conflict: '"+leftMin+".."+leftMax+"' vs '"+rightMin+".."+rightMax+"': No instances can be valid against both profiles", path, comp.getMessages(), res.getMessages());
}
}
private int unionMin(int left, int right) {
if (left > right)
return right;
@ -436,18 +486,14 @@ public class ProfileComparer extends CanonicalResourceComparer {
return left;
}
private String intersectMax(String left, String right) {
int l = "*".equals(left) ? Integer.MAX_VALUE : Integer.parseInt(left);
int r = "*".equals(right) ? Integer.MAX_VALUE : Integer.parseInt(right);
private String intersectMax(int l, int r, String left, String right) {
if (l < r)
return left;
else
return right;
}
private String unionMax(String left, String right) {
int l = "*".equals(left) ? Integer.MAX_VALUE : Integer.parseInt(left);
int r = "*".equals(right) ? Integer.MAX_VALUE : Integer.parseInt(right);
private String unionMax(int l, int r, String left, String right) {
if (l < r)
return right;
else
@ -480,7 +526,7 @@ public class ProfileComparer extends CanonicalResourceComparer {
return Integer.toString(defn.current().getMin())+".."+defn.current().getMax();
}
private Collection<? extends TypeRefComponent> unionTypes(ProfileComparison comp, StructuralMatch<ElementDefinition> res, String path, List<TypeRefComponent> left, List<TypeRefComponent> right) throws DefinitionException, IOException, FHIRFormatError {
private Collection<? extends TypeRefComponent> unionTypes(ProfileComparison comp, StructuralMatch<ElementDefinitionNode> res, String path, List<TypeRefComponent> left, List<TypeRefComponent> right) throws DefinitionException, IOException, FHIRFormatError {
List<TypeRefComponent> result = new ArrayList<TypeRefComponent>();
for (TypeRefComponent l : left)
checkAddTypeUnion(comp, res, path, result, l, session.getContextLeft());
@ -489,7 +535,7 @@ public class ProfileComparer extends CanonicalResourceComparer {
return result;
}
private void checkAddTypeUnion(ProfileComparison comp, StructuralMatch<ElementDefinition> res, String path, List<TypeRefComponent> results, TypeRefComponent nw, IWorkerContext ctxt) throws DefinitionException, IOException, FHIRFormatError {
private void checkAddTypeUnion(ProfileComparison comp, StructuralMatch<ElementDefinitionNode> res, String path, List<TypeRefComponent> results, TypeRefComponent nw, IWorkerContext ctxt) throws DefinitionException, IOException, FHIRFormatError {
boolean pfound = false;
boolean tfound = false;
nw = nw.copy();
@ -586,7 +632,7 @@ public class ProfileComparer extends CanonicalResourceComparer {
return false;
}
private Collection<? extends TypeRefComponent> intersectTypes(ProfileComparison comp, StructuralMatch<ElementDefinition> res, ElementDefinition ed, String path, List<TypeRefComponent> left, List<TypeRefComponent> right) throws DefinitionException, IOException, FHIRFormatError {
private Collection<? extends TypeRefComponent> intersectTypes(ProfileComparison comp, StructuralMatch<ElementDefinitionNode> res, ElementDefinition ed, String path, List<TypeRefComponent> left, List<TypeRefComponent> right) throws DefinitionException, IOException, FHIRFormatError {
List<TypeRefComponent> result = new ArrayList<TypeRefComponent>();
for (TypeRefComponent l : left) {
if (l.hasAggregation())
@ -665,7 +711,7 @@ public class ProfileComparer extends CanonicalResourceComparer {
return b.toString();
}
private boolean compareBindings(ProfileComparison comp, StructuralMatch<ElementDefinition> res, ElementDefinition subset, ElementDefinition superset, String path, ElementDefinition lDef, ElementDefinition rDef) throws FHIRFormatError, DefinitionException, IOException {
private boolean compareBindings(ProfileComparison comp, StructuralMatch<ElementDefinitionNode> res, ElementDefinition subset, ElementDefinition superset, String path, ElementDefinition lDef, ElementDefinition rDef) throws FHIRFormatError, DefinitionException, IOException {
assert(lDef.hasBinding() || rDef.hasBinding());
if (!lDef.hasBinding()) {
subset.setBinding(rDef.getBinding());
@ -801,7 +847,7 @@ public class ProfileComparer extends CanonicalResourceComparer {
}
// we can't really know about constraints. We create warnings, and collate them
private List<ElementDefinitionConstraintComponent> unionConstraints(ProfileComparison comp, StructuralMatch<ElementDefinition> res, String path, List<ElementDefinitionConstraintComponent> left, List<ElementDefinitionConstraintComponent> right) {
private List<ElementDefinitionConstraintComponent> unionConstraints(ProfileComparison comp, StructuralMatch<ElementDefinitionNode> res, String path, List<ElementDefinitionConstraintComponent> left, List<ElementDefinitionConstraintComponent> right) {
List<ElementDefinitionConstraintComponent> result = new ArrayList<ElementDefinitionConstraintComponent>();
for (ElementDefinitionConstraintComponent l : left) {
boolean found = false;
@ -829,7 +875,7 @@ public class ProfileComparer extends CanonicalResourceComparer {
return result;
}
private StructureDefinition resolveProfile(ProfileComparison comp, StructuralMatch<ElementDefinition> res, String path, String url, String name, IWorkerContext ctxt) {
private StructureDefinition resolveProfile(ProfileComparison comp, StructuralMatch<ElementDefinitionNode> res, String path, String url, String name, IWorkerContext ctxt) {
StructureDefinition sd = ctxt.fetchResource(StructureDefinition.class, url);
if (sd == null) {
ValidationMessage vm = vmI(IssueSeverity.WARNING, "Unable to resolve profile "+url+" in profile "+name, path);
@ -841,7 +887,7 @@ public class ProfileComparer extends CanonicalResourceComparer {
return binding.getStrength() == BindingStrength.EXAMPLE || binding.getStrength() == BindingStrength.PREFERRED;
}
private ElementDefinitionBindingComponent unionBindings(ProfileComparison comp, StructuralMatch<ElementDefinition> res, String path, ElementDefinitionBindingComponent left, ElementDefinitionBindingComponent right) throws FHIRFormatError, DefinitionException, IOException {
private ElementDefinitionBindingComponent unionBindings(ProfileComparison comp, StructuralMatch<ElementDefinitionNode> res, String path, ElementDefinitionBindingComponent left, ElementDefinitionBindingComponent right) throws FHIRFormatError, DefinitionException, IOException {
ElementDefinitionBindingComponent union = new ElementDefinitionBindingComponent();
if (left.getStrength().compareTo(right.getStrength()) < 0)
union.setStrength(left.getStrength());
@ -881,17 +927,17 @@ public class ProfileComparer extends CanonicalResourceComparer {
return gen.generate(model, prefix, 0, null);
}
private void genElementComp(String defPath, HierarchicalTableGenerator gen, List<Row> rows, StructuralMatch<ElementDefinition> combined, String corePath, String prefix, Row slicingRow, boolean root) throws IOException {
private void genElementComp(String defPath, HierarchicalTableGenerator gen, List<Row> rows, StructuralMatch<ElementDefinitionNode> combined, String corePath, String prefix, Row slicingRow, boolean root) throws IOException {
Row originalRow = slicingRow;
Row typesRow = null;
List<StructuralMatch<ElementDefinition>> children = combined.getChildren();
List<StructuralMatch<ElementDefinitionNode>> children = combined.getChildren();
Row row = gen.new Row();
rows.add(row);
String path = combined.either().getPath();
String path = combined.either().getDef().getPath();
row.setAnchor(path);
row.setColor(utilsRight.getRowColor(combined.either(), false));
row.setColor(utilsRight.getRowColor(combined.either().getDef(), false));
if (eitherHasSlicing(combined))
row.setLineColor(1);
else if (eitherHasSliceName(combined))
@ -917,7 +963,7 @@ public class ProfileComparer extends CanonicalResourceComparer {
row.setIcon("icon_choice.gif", HierarchicalTableGenerator.TEXT_ICON_CHOICE);
typesRow = row;
}
} else if (combined.either().hasContentReference())
} else if (combined.either().getDef().hasContentReference())
row.setIcon("icon_reuse.png", HierarchicalTableGenerator.TEXT_ICON_REUSE);
else if (isPrimitive(combined))
row.setIcon("icon_primitive.png", HierarchicalTableGenerator.TEXT_ICON_PRIMITIVE);
@ -927,7 +973,7 @@ public class ProfileComparer extends CanonicalResourceComparer {
row.setIcon("icon_datatype.gif", HierarchicalTableGenerator.TEXT_ICON_DATATYPE);
else
row.setIcon("icon_resource.png", HierarchicalTableGenerator.TEXT_ICON_RESOURCE);
String ref = defPath == null ? null : defPath + combined.either().getId();
String ref = defPath == null ? null : defPath + combined.either().getDef().getId();
String sName = tail(path);
String sn = getSliceName(combined);
if (sn != null)
@ -937,23 +983,23 @@ public class ProfileComparer extends CanonicalResourceComparer {
String leftColor = !combined.hasLeft() ? COLOR_NO_ROW_LEFT : combined.hasErrors() ? COLOR_DIFFERENT : null;
String rightColor = !combined.hasRight() ? COLOR_NO_ROW_LEFT : combined.hasErrors() ? COLOR_DIFFERENT : null;
if (combined.hasLeft()) {
nc = utilsRight.genElementNameCell(gen, combined.getLeft(), "??", true, corePath, prefix, root, false, false, null, typesRow, row, false, ext, used , ref, sName);
nc = utilsRight.genElementNameCell(gen, combined.getLeft().getDef(), "??", true, corePath, prefix, root, false, false, combined.getLeft().getSrc(), typesRow, row, false, ext, used , ref, sName);
} else {
nc = utilsRight.genElementNameCell(gen, combined.getRight(), "??", true, corePath, prefix, root, false, false, null, typesRow, row, false, ext, used , ref, sName);
nc = utilsRight.genElementNameCell(gen, combined.getRight().getDef(), "??", true, corePath, prefix, root, false, false, combined.getRight().getSrc(), typesRow, row, false, ext, used , ref, sName);
}
if (combined.hasLeft()) {
frame(utilsRight.genElementCells(gen, combined.getLeft(), "??", true, corePath, prefix, root, false, false, null, typesRow, row, false, ext, used , ref, sName, nc, false), leftColor);
frame(utilsRight.genElementCells(gen, combined.getLeft().getDef(), "??", true, corePath, prefix, root, false, false, combined.getLeft().getSrc(), typesRow, row, true, ext, used , ref, sName, nc, false, false), leftColor);
} else {
frame(spacers(row, 4, gen), leftColor);
}
if (combined.hasRight()) {
frame(utilsRight.genElementCells(gen, combined.getRight(), "??", true, corePath, prefix, root, false, false, null, typesRow, row, false, ext, used, ref, sName, nc, false), rightColor);
frame(utilsRight.genElementCells(gen, combined.getRight().getDef(), "??", true, corePath, prefix, root, false, false, combined.getRight().getSrc(), typesRow, row, true, ext, used, ref, sName, nc, false, false), rightColor);
} else {
frame(spacers(row, 4, gen), rightColor);
}
row.getCells().add(cellForMessages(gen, combined.getMessages()));
for (StructuralMatch<ElementDefinition> child : children) {
for (StructuralMatch<ElementDefinitionNode> child : children) {
genElementComp(defPath, gen, row.getSubRows(), child, corePath, prefix, originalRow, false);
}
}
@ -978,47 +1024,47 @@ public class ProfileComparer extends CanonicalResourceComparer {
return res;
}
private String getSliceName(StructuralMatch<ElementDefinition> combined) {
private String getSliceName(StructuralMatch<ElementDefinitionNode> combined) {
// TODO Auto-generated method stub
return null;
}
private boolean isDataType(StructuralMatch<ElementDefinition> combined) {
private boolean isDataType(StructuralMatch<ElementDefinitionNode> combined) {
// TODO Auto-generated method stub
return false;
}
private boolean hasTarget(StructuralMatch<ElementDefinition> combined) {
private boolean hasTarget(StructuralMatch<ElementDefinitionNode> combined) {
// TODO Auto-generated method stub
return false;
}
private boolean isPrimitive(StructuralMatch<ElementDefinition> combined) {
private boolean isPrimitive(StructuralMatch<ElementDefinitionNode> combined) {
// TODO Auto-generated method stub
return false;
}
private boolean allAreReference(StructuralMatch<ElementDefinition> combined) {
private boolean allAreReference(StructuralMatch<ElementDefinitionNode> combined) {
// TODO Auto-generated method stub
return false;
}
private boolean hasChoice(StructuralMatch<ElementDefinition> combined) {
private boolean hasChoice(StructuralMatch<ElementDefinitionNode> combined) {
// TODO Auto-generated method stub
return false;
}
private boolean elementIsComplex(StructuralMatch<ElementDefinition> combined) {
private boolean elementIsComplex(StructuralMatch<ElementDefinitionNode> combined) {
// TODO Auto-generated method stub velement.hasType() && element.getType().get(0).hasProfile() && extensionIsComplex(element.getType().get(0).getProfile().get(0).getValue()
return false;
}
private boolean eitherHasSliceName(StructuralMatch<ElementDefinition> combined) {
private boolean eitherHasSliceName(StructuralMatch<ElementDefinitionNode> combined) {
// TODO Auto-generated method stub
return false;
}
private boolean eitherHasSlicing(StructuralMatch<ElementDefinition> combined) {
private boolean eitherHasSlicing(StructuralMatch<ElementDefinitionNode> combined) {
// TODO Auto-generated method stub
return false;
}

436
org.hl7.fhir.r4b/src/main/java/org/hl7/fhir/r4b/conformance/ProfileUtilities.java
View File

@ -549,7 +549,17 @@ public class ProfileUtilities extends TranslatingUtilities {
}
public List<ElementDefinition> getChildList(StructureDefinition structure, ElementDefinition element) {
return getChildList(structure, element.getPath(), element.getId(), false);
if (element.hasContentReference()) {
ElementDefinition target = element;
for (ElementDefinition t : structure.getSnapshot().getElement()) {
if (t.getId().equals(element.getContentReference().substring(1))) {
target = t;
}
}
return getChildList(structure, target.getPath(), target.getId(), false);
} else {
return getChildList(structure, element.getPath(), element.getId(), false);
}
}
public void updateMaps(StructureDefinition base, StructureDefinition derived) throws DefinitionException {
@ -613,174 +623,178 @@ public class ProfileUtilities extends TranslatingUtilities {
}
derived.setUserData("profileutils.snapshot.generating", true);
snapshotStack.add(derived.getUrl());
if (!Utilities.noString(webUrl) && !webUrl.endsWith("/"))
webUrl = webUrl + '/';
if (defWebRoot == null)
defWebRoot = webUrl;
derived.setSnapshot(new StructureDefinitionSnapshotComponent());
try {
checkDifferential(derived.getDifferential().getElement(), typeName(derived.getType()), derived.getUrl());
checkDifferentialBaseType(derived);
// so we have two lists - the base list, and the differential list
// the differential list is only allowed to include things that are in the base list, but
// is allowed to include them multiple times - thereby slicing them
// our approach is to walk through the base list, and see whether the differential
// says anything about them.
int baseCursor = 0;
int diffCursor = 0; // we need a diff cursor because we can only look ahead, in the bound scoped by longer paths
if (!Utilities.noString(webUrl) && !webUrl.endsWith("/"))
webUrl = webUrl + '/';
if (defWebRoot == null)
defWebRoot = webUrl;
derived.setSnapshot(new StructureDefinitionSnapshotComponent());
try {
checkDifferential(derived.getDifferential().getElement(), typeName(derived.getType()), derived.getUrl());
checkDifferentialBaseType(derived);
// so we have two lists - the base list, and the differential list
// the differential list is only allowed to include things that are in the base list, but
// is allowed to include them multiple times - thereby slicing them
// our approach is to walk through the base list, and see whether the differential
// says anything about them.
int baseCursor = 0;
int diffCursor = 0; // we need a diff cursor because we can only look ahead, in the bound scoped by longer paths
for (ElementDefinition e : derived.getDifferential().getElement())
e.clearUserData(GENERATED_IN_SNAPSHOT);
for (ElementDefinition e : derived.getDifferential().getElement())
e.clearUserData(GENERATED_IN_SNAPSHOT);
// we actually delegate the work to a subroutine so we can re-enter it with a different cursors
StructureDefinitionDifferentialComponent diff = cloneDiff(derived.getDifferential()); // we make a copy here because we're sometimes going to hack the differential while processing it. Have to migrate user data back afterwards
StructureDefinitionSnapshotComponent baseSnapshot = base.getSnapshot();
if (derived.getDerivation() == TypeDerivationRule.SPECIALIZATION) {
String derivedType = derived.getType();
if (StructureDefinitionKind.LOGICAL.equals(derived.getKind()) && derived.getType().contains("/")) {
derivedType = derivedType.substring(derivedType.lastIndexOf("/")+1);
// we actually delegate the work to a subroutine so we can re-enter it with a different cursors
StructureDefinitionDifferentialComponent diff = cloneDiff(derived.getDifferential()); // we make a copy here because we're sometimes going to hack the differential while processing it. Have to migrate user data back afterwards
StructureDefinitionSnapshotComponent baseSnapshot = base.getSnapshot();
if (derived.getDerivation() == TypeDerivationRule.SPECIALIZATION) {
String derivedType = derived.getType();
if (StructureDefinitionKind.LOGICAL.equals(derived.getKind()) && derived.getType().contains("/")) {
derivedType = derivedType.substring(derivedType.lastIndexOf("/")+1);
}
baseSnapshot = cloneSnapshot(baseSnapshot, base.getType(), derivedType);
}
baseSnapshot = cloneSnapshot(baseSnapshot, base.getType(), derivedType);
}
// if (derived.getId().equals("2.16.840.1.113883.10.20.22.2.1.1")) {
// debug = true;
// }
processPaths("", derived.getSnapshot(), baseSnapshot, diff, baseCursor, diffCursor, baseSnapshot.getElement().size()-1,
derived.getDifferential().hasElement() ? derived.getDifferential().getElement().size()-1 : -1, url, webUrl, derived.present(), null, null, false, base.getUrl(), null, false, null, null, new ArrayList<ElementRedirection>(), base);
checkGroupConstraints(derived);
if (derived.getDerivation() == TypeDerivationRule.SPECIALIZATION) {
for (ElementDefinition e : diff.getElement()) {
if (!e.hasUserData(GENERATED_IN_SNAPSHOT)) {
ElementDefinition outcome = updateURLs(url, webUrl, e.copy());
e.setUserData(GENERATED_IN_SNAPSHOT, outcome);
derived.getSnapshot().addElement(outcome);
// if (derived.getId().equals("2.16.840.1.113883.10.20.22.2.1.1")) {
// debug = true;
// }
processPaths("", derived.getSnapshot(), baseSnapshot, diff, baseCursor, diffCursor, baseSnapshot.getElement().size()-1,
derived.getDifferential().hasElement() ? derived.getDifferential().getElement().size()-1 : -1, url, webUrl, derived.present(), null, null, false, base.getUrl(), null, false, null, null, new ArrayList<ElementRedirection>(), base);
checkGroupConstraints(derived);
if (derived.getDerivation() == TypeDerivationRule.SPECIALIZATION) {
for (ElementDefinition e : diff.getElement()) {
if (!e.hasUserData(GENERATED_IN_SNAPSHOT)) {
ElementDefinition outcome = updateURLs(url, webUrl, e.copy());
e.setUserData(GENERATED_IN_SNAPSHOT, outcome);
derived.getSnapshot().addElement(outcome);
}
}
}
}
if (derived.getKind() != StructureDefinitionKind.LOGICAL && !derived.getSnapshot().getElementFirstRep().getType().isEmpty())
throw new Error(context.formatMessage(I18nConstants.TYPE_ON_FIRST_SNAPSHOT_ELEMENT_FOR__IN__FROM_, derived.getSnapshot().getElementFirstRep().getPath(), derived.getUrl(), base.getUrl()));
updateMaps(base, derived);
setIds(derived, false);
if (debug) {
System.out.println("Differential: ");
for (ElementDefinition ed : derived.getDifferential().getElement())
System.out.println(" "+ed.getId()+" : "+typeSummaryWithProfile(ed)+"["+ed.getMin()+".."+ed.getMax()+"]"+sliceSummary(ed)+" "+constraintSummary(ed));
System.out.println("Snapshot: ");
for (ElementDefinition ed : derived.getSnapshot().getElement())
System.out.println(" "+ed.getId()+" : "+typeSummaryWithProfile(ed)+"["+ed.getMin()+".."+ed.getMax()+"]"+sliceSummary(ed)+" "+constraintSummary(ed));
}
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
//Check that all differential elements have a corresponding snapshot element
int ce = 0;
for (ElementDefinition e : diff.getElement()) {
if (!e.hasUserData("diff-source"))
throw new Error(context.formatMessage(I18nConstants.UNXPECTED_INTERNAL_CONDITION__NO_SOURCE_ON_DIFF_ELEMENT));
else {
if (e.hasUserData(DERIVATION_EQUALS))
((Base) e.getUserData("diff-source")).setUserData(DERIVATION_EQUALS, e.getUserData(DERIVATION_EQUALS));
if (e.hasUserData(DERIVATION_POINTER))
((Base) e.getUserData("diff-source")).setUserData(DERIVATION_POINTER, e.getUserData(DERIVATION_POINTER));
}
if (!e.hasUserData(GENERATED_IN_SNAPSHOT)) {
b.append(e.hasId() ? "id: "+e.getId() : "path: "+e.getPath());
ce++;
if (e.hasId()) {
String msg = "No match found in the generated snapshot: check that the path and definitions are legal in the differential (including order)";
messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url+"#"+e.getId(), msg, ValidationMessage.IssueSeverity.ERROR));
}
}
}
if (!Utilities.noString(b.toString())) {
String msg = "The profile "+derived.getUrl()+" has "+ce+" "+Utilities.pluralize("element", ce)+" in the differential ("+b.toString()+") that don't have a matching element in the snapshot: check that the path and definitions are legal in the differential (including order)";
System.out.println("Error in snapshot generation: "+msg);
if (!debug) {
if (derived.getKind() != StructureDefinitionKind.LOGICAL && !derived.getSnapshot().getElementFirstRep().getType().isEmpty())
throw new Error(context.formatMessage(I18nConstants.TYPE_ON_FIRST_SNAPSHOT_ELEMENT_FOR__IN__FROM_, derived.getSnapshot().getElementFirstRep().getPath(), derived.getUrl(), base.getUrl()));
updateMaps(base, derived);
setIds(derived, false);
if (debug) {
System.out.println("Differential: ");
for (ElementDefinition ed : derived.getDifferential().getElement())
System.out.println(" "+ed.getId()+" = "+ed.getPath()+" : "+typeSummaryWithProfile(ed)+"["+ed.getMin()+".."+ed.getMax()+"]"+sliceSummary(ed)+" "+constraintSummary(ed));
System.out.println(" "+ed.getId()+" : "+typeSummaryWithProfile(ed)+"["+ed.getMin()+".."+ed.getMax()+"]"+sliceSummary(ed)+" "+constraintSummary(ed));
System.out.println("Snapshot: ");
for (ElementDefinition ed : derived.getSnapshot().getElement())
System.out.println(" "+ed.getId()+" = "+ed.getPath()+" : "+typeSummaryWithProfile(ed)+"["+ed.getMin()+".."+ed.getMax()+"]"+sliceSummary(ed)+" "+constraintSummary(ed));
System.out.println(" "+ed.getId()+" : "+typeSummaryWithProfile(ed)+"["+ed.getMin()+".."+ed.getMax()+"]"+sliceSummary(ed)+" "+constraintSummary(ed));
}
if (exception)
throw new DefinitionException(msg);
else
messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url, msg, ValidationMessage.IssueSeverity.ERROR));
}
// hack around a problem in R4 definitions (somewhere?)
for (ElementDefinition ed : derived.getSnapshot().getElement()) {
for (ElementDefinitionMappingComponent mm : ed.getMapping()) {
if (mm.hasMap()) {
mm.setMap(mm.getMap().trim());
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
//Check that all differential elements have a corresponding snapshot element
int ce = 0;
for (ElementDefinition e : diff.getElement()) {
if (!e.hasUserData("diff-source"))
throw new Error(context.formatMessage(I18nConstants.UNXPECTED_INTERNAL_CONDITION__NO_SOURCE_ON_DIFF_ELEMENT));
else {
if (e.hasUserData(DERIVATION_EQUALS))
((Base) e.getUserData("diff-source")).setUserData(DERIVATION_EQUALS, e.getUserData(DERIVATION_EQUALS));
if (e.hasUserData(DERIVATION_POINTER))
((Base) e.getUserData("diff-source")).setUserData(DERIVATION_POINTER, e.getUserData(DERIVATION_POINTER));
}
}
for (ElementDefinitionConstraintComponent s : ed.getConstraint()) {
if (s.hasSource()) {
String ref = s.getSource();
if (!Utilities.isAbsoluteUrl(ref)) {
if (ref.contains(".")) {
s.setSource("http://hl7.org/fhir/StructureDefinition/"+ref.substring(0, ref.indexOf("."))+"#"+ref);
} else {
s.setSource("http://hl7.org/fhir/StructureDefinition/"+ref);
}
}
}
}
}
if (derived.getDerivation() == TypeDerivationRule.SPECIALIZATION) {
for (ElementDefinition ed : derived.getSnapshot().getElement()) {
if (!ed.hasBase()) {
ed.getBase().setPath(ed.getPath()).setMin(ed.getMin()).setMax(ed.getMax());
}
}
}
// last, check for wrong profiles or target profiles
for (ElementDefinition ed : derived.getSnapshot().getElement()) {
for (TypeRefComponent t : ed.getType()) {
for (UriType u : t.getProfile()) {
StructureDefinition sd = context.fetchResource(StructureDefinition.class, u.getValue());
if (sd == null) {
if (xver != null && xver.matchingUrl(u.getValue()) && xver.status(u.getValue()) == XVerExtensionStatus.Valid) {
sd = xver.makeDefinition(u.getValue());
}
if (!e.hasUserData(GENERATED_IN_SNAPSHOT)) {
b.append(e.hasId() ? "id: "+e.getId() : "path: "+e.getPath());
ce++;
if (e.hasId()) {
String msg = "No match found in the generated snapshot: check that the path and definitions are legal in the differential (including order)";
messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url+"#"+e.getId(), msg, ValidationMessage.IssueSeverity.ERROR));
}
if (sd == null) {
if (messages != null) {
messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url+"#"+ed.getId(), "The type of profile "+u.getValue()+" cannot be checked as the profile is not known", IssueSeverity.WARNING));
}
}
if (!Utilities.noString(b.toString())) {
String msg = "The profile "+derived.getUrl()+" has "+ce+" "+Utilities.pluralize("element", ce)+" in the differential ("+b.toString()+") that don't have a matching element in the snapshot: check that the path and definitions are legal in the differential (including order)";
System.out.println("Error in snapshot generation: "+msg);
if (!debug) {
System.out.println("Differential: ");
for (ElementDefinition ed : derived.getDifferential().getElement())
System.out.println(" "+ed.getId()+" = "+ed.getPath()+" : "+typeSummaryWithProfile(ed)+"["+ed.getMin()+".."+ed.getMax()+"]"+sliceSummary(ed)+" "+constraintSummary(ed));
System.out.println("Snapshot: ");
for (ElementDefinition ed : derived.getSnapshot().getElement())
System.out.println(" "+ed.getId()+" = "+ed.getPath()+" : "+typeSummaryWithProfile(ed)+"["+ed.getMin()+".."+ed.getMax()+"]"+sliceSummary(ed)+" "+constraintSummary(ed));
}
if (exception)
throw new DefinitionException(msg);
else
messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url, msg, ValidationMessage.IssueSeverity.ERROR));
}
// hack around a problem in R4 definitions (somewhere?)
for (ElementDefinition ed : derived.getSnapshot().getElement()) {
for (ElementDefinitionMappingComponent mm : ed.getMapping()) {
if (mm.hasMap()) {
mm.setMap(mm.getMap().trim());
}
}
for (ElementDefinitionConstraintComponent s : ed.getConstraint()) {
if (s.hasSource()) {
String ref = s.getSource();
if (!Utilities.isAbsoluteUrl(ref)) {
if (ref.contains(".")) {
s.setSource("http://hl7.org/fhir/StructureDefinition/"+ref.substring(0, ref.indexOf("."))+"#"+ref);
} else {
s.setSource("http://hl7.org/fhir/StructureDefinition/"+ref);
}
}
}
}
}
if (derived.getDerivation() == TypeDerivationRule.SPECIALIZATION) {
for (ElementDefinition ed : derived.getSnapshot().getElement()) {
if (!ed.hasBase()) {
ed.getBase().setPath(ed.getPath()).setMin(ed.getMin()).setMax(ed.getMax());
}
}
}
// last, check for wrong profiles or target profiles
for (ElementDefinition ed : derived.getSnapshot().getElement()) {
for (TypeRefComponent t : ed.getType()) {
for (UriType u : t.getProfile()) {
StructureDefinition sd = context.fetchResource(StructureDefinition.class, u.getValue());
if (sd == null) {
if (xver != null && xver.matchingUrl(u.getValue()) && xver.status(u.getValue()) == XVerExtensionStatus.Valid) {
sd = xver.makeDefinition(u.getValue());
}
}
} else {
String wt = t.getWorkingCode();
if (ed.getPath().equals("Bundle.entry.response.outcome")) {
wt = "OperationOutcome";
}
if (!sd.getType().equals(wt)) {
boolean ok = isCompatibleType(wt, sd);
if (!ok) {
String smsg = "The profile "+u.getValue()+" has type "+sd.getType()+" which is not consistent with the stated type "+wt;
if (exception)
throw new DefinitionException(smsg);
else
messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url+"#"+ed.getId(), smsg, IssueSeverity.ERROR));
if (sd == null) {
if (messages != null) {
messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url+"#"+ed.getId(), "The type of profile "+u.getValue()+" cannot be checked as the profile is not known", IssueSeverity.WARNING));
}
} else {
String wt = t.getWorkingCode();
if (ed.getPath().equals("Bundle.entry.response.outcome")) {
wt = "OperationOutcome";
}
if (!sd.getType().equals(wt)) {
boolean ok = isCompatibleType(wt, sd);
if (!ok) {
String smsg = "The profile "+u.getValue()+" has type "+sd.getType()+" which is not consistent with the stated type "+wt;
if (exception)
throw new DefinitionException(smsg);
else
messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url+"#"+ed.getId(), smsg, IssueSeverity.ERROR));
}
}
}
}
}
}
} catch (Exception e) {
// if we had an exception generating the snapshot, make sure we don't leave any half generated snapshot behind
derived.setSnapshot(null);
derived.clearUserData("profileutils.snapshot.generating");
throw e;
}
} catch (Exception e) {
// if we had an exception generating the snapshot, make sure we don't leave any half generated snapshot behind
derived.setSnapshot(null);
} finally {
derived.clearUserData("profileutils.snapshot.generating");
throw e;
snapshotStack.remove(derived.getUrl());
}
derived.clearUserData("profileutils.snapshot.generating");
}
public void checkDifferentialBaseType(StructureDefinition derived) throws Error {
@ -1077,6 +1091,7 @@ public class ProfileUtilities extends TranslatingUtilities {
ElementDefinition outcome = updateURLs(url, webUrl, currentBase.copy());
outcome.setPath(fixedPathDest(contextPathDst, outcome.getPath(), redirector, contextPathSrc));
updateFromBase(outcome, currentBase);
updateConstraintSources(outcome, srcSD.getUrl());
markDerived(outcome);
if (resultPathBase == null)
resultPathBase = outcome.getPath();
@ -1132,7 +1147,7 @@ public class ProfileUtilities extends TranslatingUtilities {
processPaths(indent+" ", result, base, differential, nbc, start, nbl-1, diffCursor-1, url, webUrl, profileName, tgt.getElement().getPath(), outcome.getPath(), trimDifferential, contextName, resultPathBase, false, null, null, redirectorStack(redirector, outcome, cpath), srcSD);
}
} else {
StructureDefinition dt = outcome.getType().size() > 1 ? context.fetchTypeDefinition("Element") : getProfileForDataType(outcome.getType().get(0));
StructureDefinition dt = outcome.getType().size() > 1 ? context.fetchTypeDefinition("Element") : getProfileForDataType(outcome.getType().get(0), webUrl);
if (dt == null) {
throw new DefinitionException(context.formatMessage(I18nConstants.UNKNOWN_TYPE__AT_, outcome.getType().get(0), cpath));
}
@ -1285,7 +1300,7 @@ public class ProfileUtilities extends TranslatingUtilities {
processPaths(indent+" ", result, base, differential, nbc, start - 1, nbl-1, diffCursor - 1, url, webUrl, profileName, tgt.getElement().getPath(), diffMatches.get(0).getPath(), trimDifferential, contextName, resultPathBase, false, null, null, redirectorStack(redirector, outcome, cpath), srcSD);
}
} else {
StructureDefinition dt = outcome.getType().size() == 1 ? getProfileForDataType(outcome.getType().get(0)) : getProfileForDataType("Element");
StructureDefinition dt = outcome.getType().size() == 1 ? getProfileForDataType(outcome.getType().get(0), webUrl) : getProfileForDataType("Element");
if (dt == null)
throw new DefinitionException(context.formatMessage(I18nConstants._HAS_CHILDREN__FOR_TYPE__IN_PROFILE__BUT_CANT_FIND_TYPE, diffMatches.get(0).getPath(), differential.getElement().get(diffCursor).getPath(), typeCode(outcome.getType()), profileName));
contextName = dt.getUrl();
@ -1496,7 +1511,7 @@ public class ProfileUtilities extends TranslatingUtilities {
if (baseHasChildren(base, currentBase)) { // not a new type here
throw new Error("This situation is not yet handled (constrain slicing to 1..1 and fix base slice for inline structure - please report issue to grahame@fhir.org along with a test case that reproduces this error (@ "+cpath+" | "+currentBase.getPath()+")");
} else {
StructureDefinition dt = getTypeForElement(differential, diffCursor, profileName, diffMatches, outcome);
StructureDefinition dt = getTypeForElement(differential, diffCursor, profileName, diffMatches, outcome, webUrl);
contextName = dt.getUrl();
diffCursor++;
start = diffCursor;
@ -1562,7 +1577,7 @@ public class ProfileUtilities extends TranslatingUtilities {
processPaths(indent+" ", result, base, differential, baseCursor+1, diffCursor, baseLimit, diffLimit, url, webUrl, profileName, contextPathSrc, contextPathDst, trimDifferential, contextName, resultPathBase, false, null, null, redirector, srcSD);
baseCursor = indexOfFirstNonChild(base, currentBase, baseCursor, baseLimit);
} else {
StructureDefinition dt = getTypeForElement(differential, diffCursor, profileName, diffMatches, outcome);
StructureDefinition dt = getTypeForElement(differential, diffCursor, profileName, diffMatches, outcome, webUrl);
contextName = dt.getUrl();
int start = diffCursor;
while (differential.getElement().size() > diffCursor && pathStartsWith(differential.getElement().get(diffCursor).getPath(), cpath+"."))
@ -1763,7 +1778,7 @@ public class ProfileUtilities extends TranslatingUtilities {
if (base.getElement().get(baseCursor).getType().size() != 1) {
throw new Error(context.formatMessage(I18nConstants.DIFFERENTIAL_WALKS_INTO____BUT_THE_BASE_DOES_NOT_AND_THERE_IS_NOT_A_SINGLE_FIXED_TYPE_THE_TYPE_IS__THIS_IS_NOT_HANDLED_YET, cpath, diffMatches.get(0).toString(), base.getElement().get(baseCursor).typeSummary()));
}
StructureDefinition dt = getProfileForDataType(base.getElement().get(baseCursor).getType().get(0));
StructureDefinition dt = getProfileForDataType(base.getElement().get(baseCursor).getType().get(0), webUrl);
if (dt == null) {
throw new DefinitionException(context.formatMessage(I18nConstants.UNKNOWN_TYPE__AT_, outcome.getType().get(0), diffMatches.get(0).getPath()));
}
@ -1879,7 +1894,7 @@ public class ProfileUtilities extends TranslatingUtilities {
diffCursor - 1, url, webUrl, profileName+pathTail(diffMatches, 0), base.getElement().get(0).getPath(), base.getElement().get(0).getPath(), trimDifferential, contextName, resultPathBase, false, null, null, redirector, srcSD);
} else {
StructureDefinition dt = getProfileForDataType(outcome.getType().get(0));
StructureDefinition dt = getProfileForDataType(outcome.getType().get(0), webUrl);
// if (t.getCode().equals("Extension") && t.hasProfile() && !t.getProfile().contains(":")) {
// lloydfix dt =
// }
@ -1913,6 +1928,15 @@ public class ProfileUtilities extends TranslatingUtilities {
return res;
}
private void updateConstraintSources(ElementDefinition ed, String url) {
for (ElementDefinitionConstraintComponent c : ed.getConstraint()) {
if (!c.hasSource()) {
c.setSource(url);
}
}
}
private Set<String> getListOfTypes(ElementDefinition e) {
Set<String> result = new HashSet<>();
for (TypeRefComponent t : e.getType()) {
@ -1922,7 +1946,7 @@ public class ProfileUtilities extends TranslatingUtilities {
}
public StructureDefinition getTypeForElement(StructureDefinitionDifferentialComponent differential, int diffCursor, String profileName,
List<ElementDefinition> diffMatches, ElementDefinition outcome) {
List<ElementDefinition> diffMatches, ElementDefinition outcome, String webUrl) {
if (outcome.getType().size() == 0) {
throw new DefinitionException(context.formatMessage(I18nConstants._HAS_NO_CHILDREN__AND_NO_TYPES_IN_PROFILE_, diffMatches.get(0).getPath(), differential.getElement().get(diffCursor).getPath(), profileName));
}
@ -1932,7 +1956,7 @@ public class ProfileUtilities extends TranslatingUtilities {
throw new DefinitionException(context.formatMessage(I18nConstants._HAS_CHILDREN__AND_MULTIPLE_TYPES__IN_PROFILE_, diffMatches.get(0).getPath(), differential.getElement().get(diffCursor).getPath(), typeCode(outcome.getType()), profileName));
}
}
StructureDefinition dt = getProfileForDataType(outcome.getType().get(0));
StructureDefinition dt = getProfileForDataType(outcome.getType().get(0), webUrl);
if (dt == null)
throw new DefinitionException(context.formatMessage(I18nConstants.UNKNOWN_TYPE__AT_, outcome.getType().get(0), diffMatches.get(0).getPath()));
return dt;
@ -2087,6 +2111,8 @@ public class ProfileUtilities extends TranslatingUtilities {
private void removeStatusExtensions(ElementDefinition outcome) {
outcome.removeExtension(ToolingExtensions.EXT_FMM_LEVEL);
outcome.removeExtension(ToolingExtensions.EXT_FMM_SUPPORT);
outcome.removeExtension(ToolingExtensions.EXT_FMM_DERIVED);
outcome.removeExtension(ToolingExtensions.EXT_STANDARDS_STATUS);
outcome.removeExtension(ToolingExtensions.EXT_NORMATIVE_VERSION);
outcome.removeExtension(ToolingExtensions.EXT_WORKGROUP);
@ -2402,10 +2428,16 @@ public class ProfileUtilities extends TranslatingUtilities {
return s;
}
private StructureDefinition getProfileForDataType(TypeRefComponent type) {
private StructureDefinition getProfileForDataType(TypeRefComponent type, String webUrl) {
StructureDefinition sd = null;
if (type.hasProfile()) {
sd = context.fetchResource(StructureDefinition.class, type.getProfile().get(0).getValue());
if (sd == null) {
if (xver != null && xver.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());
}
}
if (sd == null)
System.out.println("Failed to find referenced profile: " + type.getProfile());
}
@ -2475,19 +2507,19 @@ public class ProfileUtilities extends TranslatingUtilities {
if (webUrl != null) {
// also, must touch up the markdown
if (element.hasDefinition())
element.setDefinition(processRelativeUrls(element.getDefinition(), webUrl, baseSpecUrl(), context.getResourceNames(), masterSourceFileNames));
element.setDefinition(processRelativeUrls(element.getDefinition(), webUrl, baseSpecUrl(), context.getResourceNames(), masterSourceFileNames, true));
if (element.hasComment())
element.setComment(processRelativeUrls(element.getComment(), webUrl, baseSpecUrl(), context.getResourceNames(), masterSourceFileNames));
element.setComment(processRelativeUrls(element.getComment(), webUrl, baseSpecUrl(), context.getResourceNames(), masterSourceFileNames, true));
if (element.hasRequirements())
element.setRequirements(processRelativeUrls(element.getRequirements(), webUrl, baseSpecUrl(), context.getResourceNames(), masterSourceFileNames));
element.setRequirements(processRelativeUrls(element.getRequirements(), webUrl, baseSpecUrl(), context.getResourceNames(), masterSourceFileNames, true));
if (element.hasMeaningWhenMissing())
element.setMeaningWhenMissing(processRelativeUrls(element.getMeaningWhenMissing(), webUrl, baseSpecUrl(), context.getResourceNames(), masterSourceFileNames));
element.setMeaningWhenMissing(processRelativeUrls(element.getMeaningWhenMissing(), webUrl, baseSpecUrl(), context.getResourceNames(), masterSourceFileNames, true));
}
}
return element;
}
public static String processRelativeUrls(String markdown, String webUrl, String basePath, List<String> resourceNames, Set<String> filenames) {
public static String processRelativeUrls(String markdown, String webUrl, String basePath, List<String> resourceNames, Set<String> filenames, boolean processRelatives) {
StringBuilder b = new StringBuilder();
int i = 0;
while (i < markdown.length()) {
@ -2515,7 +2547,14 @@ public class ProfileUtilities extends TranslatingUtilities {
} else {
b.append("](");
// disabled 7-Dec 2021 GDG - we don't want to fool with relative URLs at all?
// b.append(webUrl);
// re-enabled 11-Feb 2022 GDG - we do want to do this. At least, $assemble in davinci-dtr, where the markdown comes from the SDC IG, and an SDC local reference must be changed to point to SDC. in this case, it's called when generating snapshots
// added processRelatives parameter to deal with this (well, to try)
if (processRelatives && webUrl != null) {
// System.out.println("Making "+url+" relative to '"+webUrl+"'");
b.append(webUrl);
} else {
// System.out.println("Not making "+url+" relative to '"+webUrl+"'");
}
i = i + 1;
}
} else
@ -2773,7 +2812,9 @@ public class ProfileUtilities extends TranslatingUtilities {
profile = source.getType().size() == 1 && source.getTypeFirstRep().hasProfile() ? context.fetchResource(StructureDefinition.class, source.getTypeFirstRep().getProfile().get(0).getValue()) : null;
if (profile != null) {
ElementDefinition e = profile.getSnapshot().getElement().get(0);
base.setDefinition(e.getDefinition());
String webroot = profile.getUserString("webroot");
base.setDefinition(processRelativeUrls(e.getDefinition(), webroot, baseSpecUrl(), context.getResourceNames(), masterSourceFileNames, true));
base.setShort(e.getShort());
if (e.hasCommentElement())
base.setCommentElement(e.getCommentElement());
@ -3502,7 +3543,7 @@ public class ProfileUtilities extends TranslatingUtilities {
List<TypeRefComponent> types = e.getType();
if (!e.hasType()) {
if (root) { // we'll use base instead of types then
StructureDefinition bsd = context.fetchResource(StructureDefinition.class, profile.getBaseDefinition());
StructureDefinition bsd = profile == null ? null : context.fetchResource(StructureDefinition.class, profile.getBaseDefinition());
if (bsd != null) {
if (bsd.hasUserData("path")) {
c.getPieces().add(gen.new Piece(Utilities.isAbsoluteUrl(bsd.getUserString("path")) ? bsd.getUserString("path") : imagePath +bsd.getUserString("path"), bsd.getName(), null));
@ -3584,7 +3625,7 @@ public class ProfileUtilities extends TranslatingUtilities {
c.addPiece(checkForNoChange(tl, gen.new Piece(null,", ", null)));
}
ref = pkp.getLinkForProfile(profile, p.getValue());
ref = pkp == null ? null : pkp.getLinkForProfile(profile, p.getValue());
if (ref != null) {
String[] parts = ref.split("\\|");
if (parts[0].startsWith("http:") || parts[0].startsWith("https:")) {
@ -3665,7 +3706,7 @@ public class ProfileUtilities extends TranslatingUtilities {
}
private String codeForAggregation(AggregationMode a) {
public static String codeForAggregation(AggregationMode a) {
switch (a) {
case BUNDLED : return "b";
case CONTAINED : return "c";
@ -3674,7 +3715,7 @@ public class ProfileUtilities extends TranslatingUtilities {
}
}
private String hintForAggregation(AggregationMode a) {
public static String hintForAggregation(AggregationMode a) {
if (a != null)
return a.getDefinition();
else
@ -3683,7 +3724,7 @@ public class ProfileUtilities extends TranslatingUtilities {
private String checkPrepend(String corePath, String path) {
if (pkp.prependLinks() && !(path.startsWith("http:") || path.startsWith("https:")))
if (pkp != null && pkp.prependLinks() && !(path.startsWith("http:") || path.startsWith("https:")))
return corePath+path;
else
return path;
@ -4055,7 +4096,7 @@ public class ProfileUtilities extends TranslatingUtilities {
if (logicalModel && element.hasRepresentation(PropertyRepresentation.XMLATTR))
sName = "@"+sName;
Cell nc = genElementNameCell(gen, element, profileBaseFileName, snapshot, corePath, imagePath, root, logicalModel, allInvariants, profile, typesRow, row, hasDef, ext, used, ref, sName);
genElementCells(gen, element, profileBaseFileName, snapshot, corePath, imagePath, root, logicalModel, allInvariants, profile, typesRow, row, hasDef, ext, used, ref, sName, nc, mustSupport);
genElementCells(gen, element, profileBaseFileName, snapshot, corePath, imagePath, root, logicalModel, allInvariants, profile, typesRow, row, hasDef, ext, used, ref, sName, nc, mustSupport, true);
if (element.hasSlicing()) {
if (standardExtensionSlicing(element)) {
used.used = true; // doesn't matter whether we have a type, we're used if we're setting up slicing ... element.hasType() && element.getType().get(0).hasProfile();
@ -4183,7 +4224,7 @@ public class ProfileUtilities extends TranslatingUtilities {
public List<Cell> genElementCells(HierarchicalTableGenerator gen, ElementDefinition element, String profileBaseFileName, boolean snapshot, String corePath,
String imagePath, boolean root, boolean logicalModel, boolean allInvariants, StructureDefinition profile, Row typesRow, Row row, boolean hasDef,
boolean ext, UnusedTracker used, String ref, String sName, Cell nameCell, boolean mustSupport) throws IOException {
boolean ext, UnusedTracker used, String ref, String sName, Cell nameCell, boolean mustSupport, boolean allowSubRows) throws IOException {
List<Cell> res = new ArrayList<>();
Cell gc = gen.new Cell();
row.getCells().add(gc);
@ -4209,7 +4250,7 @@ public class ProfileUtilities extends TranslatingUtilities {
if (extDefn == null) {
res.add(genCardinality(gen, element, row, hasDef, used, null));
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));
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));
} else {
String name = urltail(eurl);
nameCell.getPieces().get(0).setText(name);
@ -4222,7 +4263,7 @@ public class ProfileUtilities extends TranslatingUtilities {
else // if it's complex, we just call it nothing
// genTypes(gen, row, extDefn.getSnapshot().getElement().get(0), profileBaseFileName, profile);
res.add(addCell(row, gen.new Cell(null, null, "("+translate("sd.table", "Complex")+")", null, null)));
res.add(generateDescription(gen, row, element, extDefn.getElement(), used.used, null, extDefn.getUrl(), profile, corePath, imagePath, root, logicalModel, allInvariants, valueDefn, snapshot, mustSupport));
res.add(generateDescription(gen, row, element, extDefn.getElement(), used.used, null, extDefn.getUrl(), profile, corePath, imagePath, root, logicalModel, allInvariants, valueDefn, snapshot, mustSupport, allowSubRows));
}
} else {
res.add(genCardinality(gen, element, row, hasDef, used, null));
@ -4230,7 +4271,7 @@ public class ProfileUtilities extends TranslatingUtilities {
res.add(addCell(row, gen.new Cell()));
else
res.add(genTypes(gen, row, element, profileBaseFileName, profile, corePath, imagePath, root, mustSupport));
res.add(generateDescription(gen, row, element, (ElementDefinition) element.getUserData(DERIVATION_POINTER), used.used, null, null, profile, corePath, imagePath, root, logicalModel, allInvariants, snapshot, mustSupport));
res.add(generateDescription(gen, row, element, (ElementDefinition) element.getUserData(DERIVATION_POINTER), used.used, null, null, profile, corePath, imagePath, root, logicalModel, allInvariants, snapshot, mustSupport, allowSubRows));
}
} else {
res.add(genCardinality(gen, element, row, hasDef, used, null));
@ -4238,7 +4279,7 @@ public class ProfileUtilities extends TranslatingUtilities {
res.add(genTypes(gen, row, element, profileBaseFileName, profile, corePath, imagePath, root, mustSupport));
else
res.add(addCell(row, gen.new Cell()));
res.add(generateDescription(gen, row, element, (ElementDefinition) element.getUserData(DERIVATION_POINTER), used.used, null, null, profile, corePath, imagePath, root, logicalModel, allInvariants, snapshot, mustSupport));
res.add(generateDescription(gen, row, element, (ElementDefinition) element.getUserData(DERIVATION_POINTER), used.used, null, null, profile, corePath, imagePath, root, logicalModel, allInvariants, snapshot, mustSupport, allowSubRows));
}
return res;
}
@ -4289,12 +4330,12 @@ public class ProfileUtilities extends TranslatingUtilities {
private boolean isBaseCondition(IdType c) {
String key = c.asStringValue();
return key.startsWith("ele-") || key.startsWith("res-") || key.startsWith("ext-") || key.startsWith("dom-") || key.startsWith("dr-");
return key != null && key.startsWith("ele-") || key.startsWith("res-") || key.startsWith("ext-") || key.startsWith("dom-") || key.startsWith("dr-");
}
private boolean isBaseConstraint(ElementDefinitionConstraintComponent con) {
String key = con.getKey();
return key.startsWith("ele-") || key.startsWith("res-") || key.startsWith("ext-") || key.startsWith("dom-") || key.startsWith("dr-");
return key != null && key.startsWith("ele-") || key.startsWith("res-") || key.startsWith("ext-") || key.startsWith("dom-") || key.startsWith("dr-");
}
private void makeChoiceRows(List<Row> subRows, ElementDefinition element, HierarchicalTableGenerator gen, String corePath, String profileBaseFileName, boolean mustSupportMode) {
@ -4544,11 +4585,11 @@ public class ProfileUtilities extends TranslatingUtilities {
&& element.getSlicing().getRules() != SlicingRules.CLOSED && element.getSlicing().getDiscriminator().size() == 1 && element.getSlicing().getDiscriminator().get(0).getPath().equals("url") && element.getSlicing().getDiscriminator().get(0).getType().equals(DiscriminatorType.VALUE);
}
private Cell generateDescription(HierarchicalTableGenerator gen, Row row, ElementDefinition definition, ElementDefinition fallback, boolean used, String baseURL, String url, StructureDefinition profile, String corePath, String imagePath, boolean root, boolean logicalModel, boolean allInvariants, boolean snapshot, boolean mustSupportOnly) throws IOException, FHIRException {
return generateDescription(gen, row, definition, fallback, used, baseURL, url, profile, corePath, imagePath, root, logicalModel, allInvariants, null, snapshot, mustSupportOnly);
private Cell generateDescription(HierarchicalTableGenerator gen, Row row, ElementDefinition definition, ElementDefinition fallback, boolean used, String baseURL, String url, StructureDefinition profile, String corePath, String imagePath, boolean root, boolean logicalModel, boolean allInvariants, boolean snapshot, boolean mustSupportOnly, boolean allowSubRows) throws IOException, FHIRException {
return generateDescription(gen, row, definition, fallback, used, baseURL, url, profile, corePath, imagePath, root, logicalModel, allInvariants, null, snapshot, mustSupportOnly, allowSubRows);
}
private Cell generateDescription(HierarchicalTableGenerator gen, Row row, ElementDefinition definition, ElementDefinition fallback, boolean used, String baseURL, String url, StructureDefinition profile, String corePath, String imagePath, boolean root, boolean logicalModel, boolean allInvariants, ElementDefinition valueDefn, boolean snapshot, boolean mustSupportOnly) throws IOException, FHIRException {
private Cell generateDescription(HierarchicalTableGenerator gen, Row row, ElementDefinition definition, ElementDefinition fallback, boolean used, String baseURL, String url, StructureDefinition profile, String corePath, String imagePath, boolean root, boolean logicalModel, boolean allInvariants, ElementDefinition valueDefn, boolean snapshot, boolean mustSupportOnly, boolean allowSubRows) throws IOException, FHIRException {
Cell c = gen.new Cell();
row.getCells().add(c);
@ -4564,7 +4605,7 @@ public class ProfileUtilities extends TranslatingUtilities {
}
}
if (root) {
if (profile.getAbstract()) {
if (profile != null && profile.getAbstract()) {
if (!c.getPieces().isEmpty()) { c.addPiece(gen.new Piece("br")); }
c.addPiece(gen.new Piece(null, "This is an abstract profile", null));
}
@ -4659,7 +4700,7 @@ public class ProfileUtilities extends TranslatingUtilities {
if (binding!=null && !binding.isEmpty()) {
if (!c.getPieces().isEmpty())
c.addPiece(gen.new Piece("br"));
BindingResolution br = pkp.resolveBinding(profile, binding, definition.getPath());
BindingResolution br = pkp == null ? makeNullBr(binding) : pkp.resolveBinding(profile, binding, definition.getPath());
c.getPieces().add(checkForNoChange(binding, gen.new Piece(null, translate("sd.table", "Binding")+": ", null).addStyle("font-weight:bold")));
c.getPieces().add(checkForNoChange(binding.getValueSetElement(), gen.new Piece(br.url == null ? null : Utilities.isAbsoluteUrl(br.url) || !pkp.prependLinks() ? br.url : corePath+br.url, br.display, null)));
if (binding.hasStrength()) {
@ -4668,7 +4709,7 @@ public class ProfileUtilities extends TranslatingUtilities {
c.getPieces().add(checkForNoChange(binding.getStrengthElement(), gen.new Piece(null, ")", null)));
}
if (binding.hasExtension(ToolingExtensions.EXT_MAX_VALUESET)) {
br = pkp.resolveBinding(profile, ToolingExtensions.readStringExtension(binding, ToolingExtensions.EXT_MAX_VALUESET), definition.getPath());
br = pkp == null ? makeNullBr(binding) : pkp.resolveBinding(profile, ToolingExtensions.readStringExtension(binding, ToolingExtensions.EXT_MAX_VALUESET), definition.getPath());
c.addPiece(gen.new Piece("br"));
c.getPieces().add(checkForNoChange(binding, gen.new Piece(corePath+"extension-elementdefinition-maxvalueset.html", translate("sd.table", "Max Binding")+": ", "Max Value Set Extension").addStyle("font-weight:bold")));
c.getPieces().add(checkForNoChange(binding, gen.new Piece(br.url == null ? null : Utilities.isAbsoluteUrl(br.url) || !pkp.prependLinks() ? br.url : corePath+br.url, br.display, null)));
@ -4683,6 +4724,13 @@ public class ProfileUtilities extends TranslatingUtilities {
c.getPieces().add(gen.new Piece(null, ": ", null));
c.addMarkdownNoPara(PublicationHacker.fixBindingDescriptions(context, binding.getDescriptionElement()).asStringValue(), checkForNoChange(PublicationHacker.fixBindingDescriptions(context, binding.getDescriptionElement())));
}
if (binding.hasExtension(ToolingExtensions.EXT_BINDING_ADDITIONAL)) {
c.addPiece(gen.new Piece("br"));
c.getPieces().add(checkForNoChange(binding, gen.new Piece(null, translate("sd.table", "Additional Bindings")+": ", null).addStyle("font-weight:bold")));
for (Extension ext : binding.getExtensionsByUrl(ToolingExtensions.EXT_BINDING_ADDITIONAL)) {
renderAdditionalBinding(gen, c, ext);
}
}
}
for (ElementDefinitionConstraintComponent inv : definition.getConstraint()) {
if (!inv.hasSource() || profile == null || inv.getSource().equals(profile.getUrl()) || allInvariants) {
@ -4704,7 +4752,7 @@ public class ProfileUtilities extends TranslatingUtilities {
if (definition.hasFixed()) {
if (!c.getPieces().isEmpty()) { c.addPiece(gen.new Piece("br")); }
c.getPieces().add(checkForNoChange(definition.getFixed(), gen.new Piece(null, translate("sd.table", "Fixed Value")+": ", null).addStyle("font-weight:bold")));
if (!useTableForFixedValues || definition.getFixed().isPrimitive()) {
if (!useTableForFixedValues || !allowSubRows || definition.getFixed().isPrimitive()) {
String s = buildJson(definition.getFixed());
String link = null;
if (Utilities.isAbsoluteUrl(s))
@ -4712,7 +4760,7 @@ public class ProfileUtilities extends TranslatingUtilities {
c.getPieces().add(checkForNoChange(definition.getFixed(), gen.new Piece(link, s, null).addStyle("color: darkgreen")));
} else {
c.getPieces().add(checkForNoChange(definition.getFixed(), gen.new Piece(null, "As shown", null).addStyle("color: darkgreen")));
genFixedValue(gen, row, definition.getFixed(), snapshot, false, corePath, false);
genFixedValue(gen, row, definition.getFixed(), snapshot, false, corePath, false);
}
if (isCoded(definition.getFixed()) && !hasDescription(definition.getFixed())) {
Piece p = describeCoded(gen, definition.getFixed());
@ -4722,7 +4770,7 @@ public class ProfileUtilities extends TranslatingUtilities {
} else if (definition.hasPattern()) {
if (!c.getPieces().isEmpty()) { c.addPiece(gen.new Piece("br")); }
c.getPieces().add(checkForNoChange(definition.getPattern(), gen.new Piece(null, translate("sd.table", "Required Pattern")+": ", null).addStyle("font-weight:bold")));
if (!useTableForFixedValues || definition.getPattern().isPrimitive())
if (!useTableForFixedValues || !allowSubRows || definition.getPattern().isPrimitive())
c.getPieces().add(checkForNoChange(definition.getPattern(), gen.new Piece(null, buildJson(definition.getPattern()), null).addStyle("color: darkgreen")));
else {
c.getPieces().add(checkForNoChange(definition.getPattern(), gen.new Piece(null, "At least the following", null).addStyle("color: darkgreen")));
@ -4762,6 +4810,30 @@ public class ProfileUtilities extends TranslatingUtilities {
return c;
}
private void renderAdditionalBinding(HierarchicalTableGenerator gen, Cell c, Extension ext) {
// <nsbp>2 <sp> purpose <sp> value-set-link ([context]) {documentation}
String purpose = ext.getExtensionString("purpose");
String valueSet = ext.getExtensionString("valueSet");
String doco = ext.getExtensionString("documentation");
//UsageContext usage = (ext.hasExtension("usage")) ? ext.getExtensionByUrl("usage").getValueUsageContext() : null;
//
// purpose: code - defines how the binding is used
// usage : UsageContext - defines the contexts in which this binding is used for it's purpose
// valueSet : canonical(ValueSet)
// documentation : markdown
// !!
// c.getPieces().add(checkForNoChange(inv, gen.new Piece(null, inv.getKey()+": ", null).addStyle("font-weight:bold")));
// c.getPieces().add(checkForNoChange(inv, gen.new Piece(null, gt(inv.getHumanElement()), null)));
}
private BindingResolution makeNullBr(ElementDefinitionBindingComponent binding) {
BindingResolution br = new BindingResolution();
br.url = "http://none.none/none";
br.display = "todo";
return br;
}
private ElementDefinitionBindingComponent makeUnifiedBinding(ElementDefinitionBindingComponent binding, ElementDefinition element) {
if (!element.hasUserData(DERIVATION_POINTER)) {
return binding;

12
org.hl7.fhir.r4b/src/main/java/org/hl7/fhir/r4b/model/Enumerations.java
View File

@ -6169,9 +6169,9 @@ The primary difference between a medication statement and a medication administr
return _4_1_0;
if ("4.2.0".equals(codeString))
return _4_2_0;
if ("4.3.0-snapshot1".equals(codeString))
if ("4.3.0-snapshot1".equalsIgnoreCase(codeString))
return _4_3_0SNAPSHOT1;
if ("4.3.0-cibuild".equals(codeString))
if ("4.3.0-cibuild".equalsIgnoreCase(codeString))
return _4_3_0CIBUILD;
throw new FHIRException("Unknown FHIRVersion code '"+codeString+"'");
}
@ -6434,9 +6434,9 @@ public String toCode(int len) {
return FHIRVersion._4_1_0;
if ("4.2.0".equals(codeString))
return FHIRVersion._4_2_0;
if ("4.3.0-snapshot1".equals(codeString))
if ("4.3.0-snapshot1".equalsIgnoreCase(codeString))
return FHIRVersion._4_3_0SNAPSHOT1;
if ("4.3.0-cibuild".equals(codeString))
if ("4.3.0-cibuild".equalsIgnoreCase(codeString))
return FHIRVersion._4_3_0CIBUILD;
throw new IllegalArgumentException("Unknown FHIRVersion code '"+codeString+"'");
}
@ -6498,9 +6498,9 @@ public String toCode(int len) {
return new Enumeration<FHIRVersion>(this, FHIRVersion._4_1_0);
if ("4.2.0".equals(codeString))
return new Enumeration<FHIRVersion>(this, FHIRVersion._4_2_0);
if ("4.3.0-snapshot1".equals(codeString))
if ("4.3.0-snapshot1".equalsIgnoreCase(codeString))
return new Enumeration<FHIRVersion>(this, FHIRVersion._4_3_0SNAPSHOT1);
if ("4.3.0-cibuild".equals(codeString))
if ("4.3.0-cibuild".equalsIgnoreCase(codeString))
return new Enumeration<FHIRVersion>(this, FHIRVersion._4_3_0CIBUILD);
throw new FHIRException("Unknown FHIRVersion code '"+codeString+"'");
}

5
org.hl7.fhir.r4b/src/main/java/org/hl7/fhir/r4b/utils/ToolingExtensions.java
View File

@ -198,6 +198,9 @@ public class ToolingExtensions {
public static final String EXT_TARGET_ID = "http://hl7.org/fhir/StructureDefinition/targetElement";
public static final String EXT_TARGET_PATH = "http://hl7.org/fhir/StructureDefinition/targetPath";
public static final String EXT_VALUESET_SYSTEM = "http://hl7.org/fhir/StructureDefinition/valueset-system";
public static final String EXT_EXPAND_RULES = "http://hl7.org/fhir/StructureDefinition/valueset-expand-rules";
public static final String EXT_EXPAND_GROUP = "http://hl7.org/fhir/StructureDefinition/valueset-expand-group";
public static final String EXT_BINDING_ADDITIONAL = "http://hl7.org/fhir/tools/StructureDefinition/additional-binding";
// specific extension helpers
@ -511,7 +514,7 @@ public class ToolingExtensions {
* @return The extension, if on this element, else null
*/
public static Extension getExtension(DomainResource resource, String name) {
if (name == null)
if (resource == null || name == null)
return null;
if (!resource.hasExtension())
return null;

18
org.hl7.fhir.r4b/src/main/java/org/hl7/fhir/r4b/utils/XVerExtensionManager.java
View File

@ -50,9 +50,6 @@ public class XVerExtensionManager {
return XVerExtensionStatus.Invalid;
}
String v = url.substring(20, 23);
if ("5.0".equals(v)) {
v = "4.6"; // for now
}
String e = url.substring(54);
if (!lists.containsKey(v)) {
if (context.getBinaries().containsKey("xver-paths-"+v+".json")) {
@ -67,6 +64,9 @@ public class XVerExtensionManager {
}
JsonObject root = lists.get(v);
JsonObject path = root.getAsJsonObject(e);
if (path == null) {
path = root.getAsJsonObject(e+"[x]");
}
if (path == null) {
return XVerExtensionStatus.Unknown;
}
@ -83,13 +83,13 @@ public class XVerExtensionManager {
public StructureDefinition makeDefinition(String url) {
String verSource = url.substring(20, 23);
if ("5.0".equals(verSource)) {
verSource = "4.6"; // for now
}
String verTarget = VersionUtilities.getMajMin(context.getVersion());
String e = url.substring(54);
JsonObject root = lists.get(verSource);
JsonObject path = root.getAsJsonObject(e);
if (path == null) {
path = root.getAsJsonObject(e+"[x]");
}
StructureDefinition sd = new StructureDefinition();
sd.setUserData(XVER_EXT_MARKER, "true");
@ -117,16 +117,18 @@ public class XVerExtensionManager {
populateTypes(path, val, verSource, verTarget);
} else if (path.has("elements")) {
for (JsonElement i : path.getAsJsonArray("elements")) {
String s = i.getAsString();
JsonObject elt = root.getAsJsonObject(e+"."+i.getAsString());
if (elt != null) {
String s = i.getAsString().replace("[x]", "");
sd.getDifferential().addElement().setPath("Extension.extension").setSliceName(s);
sd.getDifferential().addElement().setPath("Extension.extension.extension").setMax("0");
sd.getDifferential().addElement().setPath("Extension.extension.url").setFixed(new UriType(s));
ElementDefinition val = sd.getDifferential().addElement().setPath("Extension.extension.value[x]").setMin(1);
JsonObject elt = root.getAsJsonObject(e+"."+s);
if (!elt.has("types")) {
throw new FHIRException("Internal error - nested elements not supported yet");
}
populateTypes(elt, val, verSource, verTarget);
}
}
sd.getDifferential().addElement().setPath("Extension.url").setFixed(new UriType(url));
sd.getDifferential().addElement().setPath("Extension.value[x]").setMax("0");

31
org.hl7.fhir.r4b/src/test/java/org/hl7/fhir/r4b/test/ProfileUtilitiesTests.java
View File

@ -4,6 +4,7 @@ import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r4b.conformance.ProfileUtilities;
import org.hl7.fhir.r4b.model.Base;
import org.hl7.fhir.r4b.model.ElementDefinition;
import org.hl7.fhir.r4b.model.ElementDefinition.ElementDefinitionConstraintComponent;
import org.hl7.fhir.r4b.model.IntegerType;
import org.hl7.fhir.r4b.model.StructureDefinition;
import org.hl7.fhir.r4b.model.StructureDefinition.TypeDerivationRule;
@ -51,6 +52,12 @@ public class ProfileUtilitiesTests {
f.setBase(null);
b.setRequirements(null);
f.setRequirements(null);
for (ElementDefinitionConstraintComponent c : b.getConstraint()) {
c.setSource(null);
}
for (ElementDefinitionConstraintComponent c : f.getConstraint()) {
c.setSource(null);
}
ok = Base.compareDeep(b, f, true);
}
}
@ -83,6 +90,12 @@ public class ProfileUtilitiesTests {
if (ok) {
ElementDefinition b = base.getSnapshot().getElement().get(i);
ElementDefinition f = focus.getSnapshot().getElement().get(i);
for (ElementDefinitionConstraintComponent c : b.getConstraint()) {
c.setSource(null);
}
for (ElementDefinitionConstraintComponent c : f.getConstraint()) {
c.setSource(null);
}
if (!f.hasBase() || !b.getPath().equals(f.getPath()))
ok = false;
else {
@ -128,6 +141,12 @@ public class ProfileUtilitiesTests {
ElementDefinition f = focus.getSnapshot().getElement().get(i);
b.setRequirements(null);
f.setRequirements(null);
for (ElementDefinitionConstraintComponent c : b.getConstraint()) {
c.setSource(null);
}
for (ElementDefinitionConstraintComponent c : f.getConstraint()) {
c.setSource(null);
}
if (!f.hasBase() || !b.getPath().equals(f.getPath())) {
ok = false;
}
@ -174,6 +193,12 @@ public class ProfileUtilitiesTests {
ElementDefinition f = focus.getSnapshot().getElement().get(i);
b.setRequirements(null);
f.setRequirements(null);
for (ElementDefinitionConstraintComponent c : b.getConstraint()) {
c.setSource(null);
}
for (ElementDefinitionConstraintComponent c : f.getConstraint()) {
c.setSource(null);
}
if (!f.hasBase() || !b.getPath().equals(f.getPath())) {
ok = false;
}
@ -221,6 +246,12 @@ public class ProfileUtilitiesTests {
ElementDefinition f = focus.getSnapshot().getElement().get(i);
b.setRequirements(null);
f.setRequirements(null);
for (ElementDefinitionConstraintComponent c : b.getConstraint()) {
c.setSource(null);
}
for (ElementDefinitionConstraintComponent c : f.getConstraint()) {
c.setSource(null);
}
if (!f.hasBase() || !b.getPath().equals(f.getPath())) {
ok = false;
}

59
org.hl7.fhir.r4b/src/test/java/org/hl7/fhir/r4b/test/SnapShotGenerationTests.java
View File

@ -49,6 +49,7 @@ import org.hl7.fhir.utilities.npm.ToolsVersion;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.junit.Assert;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.params.ParameterizedTest;
@ -137,7 +138,8 @@ public class SnapShotGenerationTests {
private boolean fail;
private boolean newSliceProcessing;
private boolean debug;
private boolean noR4b;
private List<Rule> rules = new ArrayList<>();
private StructureDefinition source;
private List<StructureDefinition> included = new ArrayList<>();
@ -161,6 +163,7 @@ public class SnapShotGenerationTests {
rules.add(new Rule(rule));
rule = XMLUtil.getNextSibling(rule);
}
noR4b = test.hasAttribute("r4b") && "false".equals(test.getAttribute("r4b"));
}
public String getId() {
@ -466,33 +469,37 @@ public class SnapShotGenerationTests {
fp.setHostServices(context);
messages = new ArrayList<ValidationMessage>();
System.out.println("---- "+id+" -----------------------------------------");
if (test.isFail()) {
boolean failed = true;
try {
if (test.isGen())
testGen(true, test, context);
else
testSort(test, context);
failed = false;
} catch (Throwable e) {
System.out.println("Error running test: " + e.getMessage());
if (!Utilities.noString(test.regex)) {
Assertions.assertTrue(e.getMessage().matches(test.regex), "correct error message");
} else if ("Should have failed".equals(e.getMessage())) {
throw e;
} else {
if (test.noR4b) {
Assert.assertTrue(true);
} else {
System.out.println("---- "+id+" -----------------------------------------");
if (test.isFail()) {
boolean failed = true;
try {
if (test.isGen())
testGen(true, test, context);
else
testSort(test, context);
failed = false;
} catch (Throwable e) {
System.out.println("Error running test: " + e.getMessage());
if (!Utilities.noString(test.regex)) {
Assertions.assertTrue(e.getMessage().matches(test.regex), "correct error message");
} else if ("Should have failed".equals(e.getMessage())) {
throw e;
} else {
}
}
Assertions.assertTrue(failed, "Should have failed");
} else if (test.isGen())
testGen(false, test, context);
else
testSort(test, context);
for (Rule r : test.getRules()) {
StructureDefinition sdn = new StructureDefinition();
boolean ok = fp.evaluateToBoolean(sdn, sdn, sdn, r.expression);
Assertions.assertTrue(ok, r.description);
}
Assertions.assertTrue(failed, "Should have failed");
} else if (test.isGen())
testGen(false, test, context);
else
testSort(test, context);
for (Rule r : test.getRules()) {
StructureDefinition sdn = new StructureDefinition();
boolean ok = fp.evaluateToBoolean(sdn, sdn, sdn, r.expression);
Assertions.assertTrue(ok, r.description);
}
}

2
org.hl7.fhir.r5/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.6.35</version>
<version>5.6.38-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

330
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/ProfileUtilities.java
View File

@ -621,180 +621,184 @@ public class ProfileUtilities extends TranslatingUtilities {
if (!base.getType().equals(derived.getType()) && derived.getDerivation() == TypeDerivationRule.CONSTRAINT) {
throw new DefinitionException(context.formatMessage(I18nConstants.BASE__DERIVED_PROFILES_HAVE_DIFFERENT_TYPES____VS___, base.getUrl(), base.getType(), derived.getUrl(), derived.getType()));
}
if (snapshotStack.contains(derived.getUrl())) {
throw new DefinitionException(context.formatMessage(I18nConstants.CIRCULAR_SNAPSHOT_REFERENCES_DETECTED_CANNOT_GENERATE_SNAPSHOT_STACK__, snapshotStack.toString()));
}
derived.setUserData("profileutils.snapshot.generating", true);
snapshotStack.add(derived.getUrl());
if (!Utilities.noString(webUrl) && !webUrl.endsWith("/"))
webUrl = webUrl + '/';
if (defWebRoot == null)
defWebRoot = webUrl;
derived.setSnapshot(new StructureDefinitionSnapshotComponent());
try {
checkDifferential(derived.getDifferential().getElement(), typeName(derived.getType()), derived.getUrl());
checkDifferentialBaseType(derived);
// so we have two lists - the base list, and the differential list
// the differential list is only allowed to include things that are in the base list, but
// is allowed to include them multiple times - thereby slicing them
// our approach is to walk through the base list, and see whether the differential
// says anything about them.
int baseCursor = 0;
int diffCursor = 0; // we need a diff cursor because we can only look ahead, in the bound scoped by longer paths
if (!Utilities.noString(webUrl) && !webUrl.endsWith("/"))
webUrl = webUrl + '/';
if (defWebRoot == null)
defWebRoot = webUrl;
derived.setSnapshot(new StructureDefinitionSnapshotComponent());
try {
checkDifferential(derived.getDifferential().getElement(), typeName(derived.getType()), derived.getUrl());
checkDifferentialBaseType(derived);
// so we have two lists - the base list, and the differential list
// the differential list is only allowed to include things that are in the base list, but
// is allowed to include them multiple times - thereby slicing them
// our approach is to walk through the base list, and see whether the differential
// says anything about them.
int baseCursor = 0;
int diffCursor = 0; // we need a diff cursor because we can only look ahead, in the bound scoped by longer paths
for (ElementDefinition e : derived.getDifferential().getElement())
e.clearUserData(GENERATED_IN_SNAPSHOT);
for (ElementDefinition e : derived.getDifferential().getElement())
e.clearUserData(GENERATED_IN_SNAPSHOT);
// we actually delegate the work to a subroutine so we can re-enter it with a different cursors
StructureDefinitionDifferentialComponent diff = cloneDiff(derived.getDifferential()); // we make a copy here because we're sometimes going to hack the differential while processing it. Have to migrate user data back afterwards
StructureDefinitionSnapshotComponent baseSnapshot = base.getSnapshot();
if (derived.getDerivation() == TypeDerivationRule.SPECIALIZATION) {
String derivedType = derived.getType();
if (StructureDefinitionKind.LOGICAL.equals(derived.getKind()) && derived.getType().contains("/")) {
derivedType = derivedType.substring(derivedType.lastIndexOf("/")+1);
// we actually delegate the work to a subroutine so we can re-enter it with a different cursors
StructureDefinitionDifferentialComponent diff = cloneDiff(derived.getDifferential()); // we make a copy here because we're sometimes going to hack the differential while processing it. Have to migrate user data back afterwards
StructureDefinitionSnapshotComponent baseSnapshot = base.getSnapshot();
if (derived.getDerivation() == TypeDerivationRule.SPECIALIZATION) {
String derivedType = derived.getType();
if (StructureDefinitionKind.LOGICAL.equals(derived.getKind()) && derived.getType().contains("/")) {
derivedType = derivedType.substring(derivedType.lastIndexOf("/")+1);
}
baseSnapshot = cloneSnapshot(baseSnapshot, base.getType(), derivedType);
}
baseSnapshot = cloneSnapshot(baseSnapshot, base.getType(), derivedType);
}
// if (derived.getId().equals("2.16.840.1.113883.10.20.22.2.1.1")) {
// debug = true;
// }
processPaths("", derived.getSnapshot(), baseSnapshot, diff, baseCursor, diffCursor, baseSnapshot.getElement().size()-1,
derived.getDifferential().hasElement() ? derived.getDifferential().getElement().size()-1 : -1, url, webUrl, derived.present(), null, null, false, base.getUrl(), null, false, null, null, new ArrayList<ElementRedirection>(), base);
checkGroupConstraints(derived);
if (derived.getDerivation() == TypeDerivationRule.SPECIALIZATION) {
for (ElementDefinition e : diff.getElement()) {
if (!e.hasUserData(GENERATED_IN_SNAPSHOT)) {
ElementDefinition outcome = updateURLs(url, webUrl, e.copy());
e.setUserData(GENERATED_IN_SNAPSHOT, outcome);
derived.getSnapshot().addElement(outcome);
// if (derived.getId().equals("2.16.840.1.113883.10.20.22.2.1.1")) {
// debug = true;
// }
processPaths("", derived.getSnapshot(), baseSnapshot, diff, baseCursor, diffCursor, baseSnapshot.getElement().size()-1,
derived.getDifferential().hasElement() ? derived.getDifferential().getElement().size()-1 : -1, url, webUrl, derived.present(), null, null, false, base.getUrl(), null, false, null, null, new ArrayList<ElementRedirection>(), base);
checkGroupConstraints(derived);
if (derived.getDerivation() == TypeDerivationRule.SPECIALIZATION) {
for (ElementDefinition e : diff.getElement()) {
if (!e.hasUserData(GENERATED_IN_SNAPSHOT)) {
ElementDefinition outcome = updateURLs(url, webUrl, e.copy());
e.setUserData(GENERATED_IN_SNAPSHOT, outcome);
derived.getSnapshot().addElement(outcome);
}
}
}
}
if (derived.getKind() != StructureDefinitionKind.LOGICAL && !derived.getSnapshot().getElementFirstRep().getType().isEmpty())
throw new Error(context.formatMessage(I18nConstants.TYPE_ON_FIRST_SNAPSHOT_ELEMENT_FOR__IN__FROM_, derived.getSnapshot().getElementFirstRep().getPath(), derived.getUrl(), base.getUrl()));
updateMaps(base, derived);
setIds(derived, false);
if (debug) {
System.out.println("Differential: ");
for (ElementDefinition ed : derived.getDifferential().getElement())
System.out.println(" "+ed.getId()+" : "+typeSummaryWithProfile(ed)+"["+ed.getMin()+".."+ed.getMax()+"]"+sliceSummary(ed)+" "+constraintSummary(ed));
System.out.println("Snapshot: ");
for (ElementDefinition ed : derived.getSnapshot().getElement())
System.out.println(" "+ed.getId()+" : "+typeSummaryWithProfile(ed)+"["+ed.getMin()+".."+ed.getMax()+"]"+sliceSummary(ed)+" "+constraintSummary(ed));
}
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
//Check that all differential elements have a corresponding snapshot element
int ce = 0;
for (ElementDefinition e : diff.getElement()) {
if (!e.hasUserData("diff-source"))
throw new Error(context.formatMessage(I18nConstants.UNXPECTED_INTERNAL_CONDITION__NO_SOURCE_ON_DIFF_ELEMENT));
else {
if (e.hasUserData(DERIVATION_EQUALS))
((Base) e.getUserData("diff-source")).setUserData(DERIVATION_EQUALS, e.getUserData(DERIVATION_EQUALS));
if (e.hasUserData(DERIVATION_POINTER))
((Base) e.getUserData("diff-source")).setUserData(DERIVATION_POINTER, e.getUserData(DERIVATION_POINTER));
}
if (!e.hasUserData(GENERATED_IN_SNAPSHOT)) {
b.append(e.hasId() ? "id: "+e.getId() : "path: "+e.getPath());
ce++;
if (e.hasId()) {
String msg = "No match found in the generated snapshot: check that the path and definitions are legal in the differential (including order)";
messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url+"#"+e.getId(), msg, ValidationMessage.IssueSeverity.ERROR));
}
}
}
if (!Utilities.noString(b.toString())) {
String msg = "The profile "+derived.getUrl()+" has "+ce+" "+Utilities.pluralize("element", ce)+" in the differential ("+b.toString()+") that don't have a matching element in the snapshot: check that the path and definitions are legal in the differential (including order)";
System.out.println("Error in snapshot generation: "+msg);
if (!debug) {
if (derived.getKind() != StructureDefinitionKind.LOGICAL && !derived.getSnapshot().getElementFirstRep().getType().isEmpty())
throw new Error(context.formatMessage(I18nConstants.TYPE_ON_FIRST_SNAPSHOT_ELEMENT_FOR__IN__FROM_, derived.getSnapshot().getElementFirstRep().getPath(), derived.getUrl(), base.getUrl()));
updateMaps(base, derived);
setIds(derived, false);
if (debug) {
System.out.println("Differential: ");
for (ElementDefinition ed : derived.getDifferential().getElement())
System.out.println(" "+ed.getId()+" = "+ed.getPath()+" : "+typeSummaryWithProfile(ed)+"["+ed.getMin()+".."+ed.getMax()+"]"+sliceSummary(ed)+" "+constraintSummary(ed));
System.out.println(" "+ed.getId()+" : "+typeSummaryWithProfile(ed)+"["+ed.getMin()+".."+ed.getMax()+"]"+sliceSummary(ed)+" "+constraintSummary(ed));
System.out.println("Snapshot: ");
for (ElementDefinition ed : derived.getSnapshot().getElement())
System.out.println(" "+ed.getId()+" = "+ed.getPath()+" : "+typeSummaryWithProfile(ed)+"["+ed.getMin()+".."+ed.getMax()+"]"+sliceSummary(ed)+" "+constraintSummary(ed));
System.out.println(" "+ed.getId()+" : "+typeSummaryWithProfile(ed)+"["+ed.getMin()+".."+ed.getMax()+"]"+sliceSummary(ed)+" "+constraintSummary(ed));
}
if (exception)
throw new DefinitionException(msg);
else
messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url, msg, ValidationMessage.IssueSeverity.ERROR));
}
// hack around a problem in R4 definitions (somewhere?)
for (ElementDefinition ed : derived.getSnapshot().getElement()) {
for (ElementDefinitionMappingComponent mm : ed.getMapping()) {
if (mm.hasMap()) {
mm.setMap(mm.getMap().trim());
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
//Check that all differential elements have a corresponding snapshot element
int ce = 0;
for (ElementDefinition e : diff.getElement()) {
if (!e.hasUserData("diff-source"))
throw new Error(context.formatMessage(I18nConstants.UNXPECTED_INTERNAL_CONDITION__NO_SOURCE_ON_DIFF_ELEMENT));
else {
if (e.hasUserData(DERIVATION_EQUALS))
((Base) e.getUserData("diff-source")).setUserData(DERIVATION_EQUALS, e.getUserData(DERIVATION_EQUALS));
if (e.hasUserData(DERIVATION_POINTER))
((Base) e.getUserData("diff-source")).setUserData(DERIVATION_POINTER, e.getUserData(DERIVATION_POINTER));
}
}
for (ElementDefinitionConstraintComponent s : ed.getConstraint()) {
if (s.hasSource()) {
String ref = s.getSource();
if (!Utilities.isAbsoluteUrl(ref)) {
if (ref.contains(".")) {
s.setSource("http://hl7.org/fhir/StructureDefinition/"+ref.substring(0, ref.indexOf("."))+"#"+ref);
} else {
s.setSource("http://hl7.org/fhir/StructureDefinition/"+ref);
}
}
}
}
}
if (derived.getDerivation() == TypeDerivationRule.SPECIALIZATION) {
for (ElementDefinition ed : derived.getSnapshot().getElement()) {
if (!ed.hasBase()) {
ed.getBase().setPath(ed.getPath()).setMin(ed.getMin()).setMax(ed.getMax());
}
}
}
// last, check for wrong profiles or target profiles
for (ElementDefinition ed : derived.getSnapshot().getElement()) {
for (TypeRefComponent t : ed.getType()) {
for (UriType u : t.getProfile()) {
StructureDefinition sd = context.fetchResource(StructureDefinition.class, u.getValue());
if (sd == null) {
if (xver != null && xver.matchingUrl(u.getValue()) && xver.status(u.getValue()) == XVerExtensionStatus.Valid) {
sd = xver.makeDefinition(u.getValue());
}
if (!e.hasUserData(GENERATED_IN_SNAPSHOT)) {
b.append(e.hasId() ? "id: "+e.getId() : "path: "+e.getPath());
ce++;
if (e.hasId()) {
String msg = "No match found in the generated snapshot: check that the path and definitions are legal in the differential (including order)";
messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url+"#"+e.getId(), msg, ValidationMessage.IssueSeverity.ERROR));
}
if (sd == null) {
if (messages != null) {
messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url+"#"+ed.getId(), "The type of profile "+u.getValue()+" cannot be checked as the profile is not known", IssueSeverity.WARNING));
}
}
if (!Utilities.noString(b.toString())) {
String msg = "The profile "+derived.getUrl()+" has "+ce+" "+Utilities.pluralize("element", ce)+" in the differential ("+b.toString()+") that don't have a matching element in the snapshot: check that the path and definitions are legal in the differential (including order)";
System.out.println("Error in snapshot generation: "+msg);
if (!debug) {
System.out.println("Differential: ");
for (ElementDefinition ed : derived.getDifferential().getElement())
System.out.println(" "+ed.getId()+" = "+ed.getPath()+" : "+typeSummaryWithProfile(ed)+"["+ed.getMin()+".."+ed.getMax()+"]"+sliceSummary(ed)+" "+constraintSummary(ed));
System.out.println("Snapshot: ");
for (ElementDefinition ed : derived.getSnapshot().getElement())
System.out.println(" "+ed.getId()+" = "+ed.getPath()+" : "+typeSummaryWithProfile(ed)+"["+ed.getMin()+".."+ed.getMax()+"]"+sliceSummary(ed)+" "+constraintSummary(ed));
}
if (exception)
throw new DefinitionException(msg);
else
messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url, msg, ValidationMessage.IssueSeverity.ERROR));
}
// hack around a problem in R4 definitions (somewhere?)
for (ElementDefinition ed : derived.getSnapshot().getElement()) {
for (ElementDefinitionMappingComponent mm : ed.getMapping()) {
if (mm.hasMap()) {
mm.setMap(mm.getMap().trim());
}
}
for (ElementDefinitionConstraintComponent s : ed.getConstraint()) {
if (s.hasSource()) {
String ref = s.getSource();
if (!Utilities.isAbsoluteUrl(ref)) {
if (ref.contains(".")) {
s.setSource("http://hl7.org/fhir/StructureDefinition/"+ref.substring(0, ref.indexOf("."))+"#"+ref);
} else {
s.setSource("http://hl7.org/fhir/StructureDefinition/"+ref);
}
}
}
}
}
if (derived.getDerivation() == TypeDerivationRule.SPECIALIZATION) {
for (ElementDefinition ed : derived.getSnapshot().getElement()) {
if (!ed.hasBase()) {
ed.getBase().setPath(ed.getPath()).setMin(ed.getMin()).setMax(ed.getMax());
}
}
}
// last, check for wrong profiles or target profiles
for (ElementDefinition ed : derived.getSnapshot().getElement()) {
for (TypeRefComponent t : ed.getType()) {
for (UriType u : t.getProfile()) {
StructureDefinition sd = context.fetchResource(StructureDefinition.class, u.getValue());
if (sd == null) {
if (xver != null && xver.matchingUrl(u.getValue()) && xver.status(u.getValue()) == XVerExtensionStatus.Valid) {
sd = xver.makeDefinition(u.getValue());
}
}
} else {
String wt = t.getWorkingCode();
if (ed.getPath().equals("Bundle.entry.response.outcome")) {
wt = "OperationOutcome";
}
if (!sd.getType().equals(wt)) {
boolean ok = isCompatibleType(wt, sd);
if (!ok) {
String smsg = "The profile "+u.getValue()+" has type "+sd.getType()+" which is not consistent with the stated type "+wt;
if (exception)
throw new DefinitionException(smsg);
else
messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url+"#"+ed.getId(), smsg, IssueSeverity.ERROR));
if (sd == null) {
if (messages != null) {
messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url+"#"+ed.getId(), "The type of profile "+u.getValue()+" cannot be checked as the profile is not known", IssueSeverity.WARNING));
}
} else {
String wt = t.getWorkingCode();
if (ed.getPath().equals("Bundle.entry.response.outcome")) {
wt = "OperationOutcome";
}
if (!sd.getType().equals(wt)) {
boolean ok = isCompatibleType(wt, sd);
if (!ok) {
String smsg = "The profile "+u.getValue()+" has type "+sd.getType()+" which is not consistent with the stated type "+wt;
if (exception)
throw new DefinitionException(smsg);
else
messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url+"#"+ed.getId(), smsg, IssueSeverity.ERROR));
}
}
}
}
}
}
} catch (Exception e) {
// if we had an exception generating the snapshot, make sure we don't leave any half generated snapshot behind
derived.setSnapshot(null);
derived.clearUserData("profileutils.snapshot.generating");
throw e;
}
} catch (Exception e) {
// if we had an exception generating the snapshot, make sure we don't leave any half generated snapshot behind
derived.setSnapshot(null);
} finally {
derived.clearUserData("profileutils.snapshot.generating");
throw e;
snapshotStack.remove(derived.getUrl());
}
derived.clearUserData("profileutils.snapshot.generating");
}
public void checkDifferentialBaseType(StructureDefinition derived) throws Error {
@ -1091,6 +1095,7 @@ public class ProfileUtilities extends TranslatingUtilities {
ElementDefinition outcome = updateURLs(url, webUrl, currentBase.copy());
outcome.setPath(fixedPathDest(contextPathDst, outcome.getPath(), redirector, contextPathSrc));
updateFromBase(outcome, currentBase);
updateConstraintSources(outcome, srcSD.getUrl());
markDerived(outcome);
if (resultPathBase == null)
resultPathBase = outcome.getPath();
@ -1146,7 +1151,7 @@ public class ProfileUtilities extends TranslatingUtilities {
processPaths(indent+" ", result, base, differential, nbc, start, nbl-1, diffCursor-1, url, webUrl, profileName, tgt.getElement().getPath(), outcome.getPath(), trimDifferential, contextName, resultPathBase, false, null, null, redirectorStack(redirector, outcome, cpath), srcSD);
}
} else {
StructureDefinition dt = outcome.getType().size() > 1 ? context.fetchTypeDefinition("Element") : getProfileForDataType(outcome.getType().get(0));
StructureDefinition dt = outcome.getType().size() > 1 ? context.fetchTypeDefinition("Element") : getProfileForDataType(outcome.getType().get(0), webUrl);
if (dt == null) {
throw new DefinitionException(context.formatMessage(I18nConstants.UNKNOWN_TYPE__AT_, outcome.getType().get(0), cpath));
}
@ -1299,7 +1304,7 @@ public class ProfileUtilities extends TranslatingUtilities {
processPaths(indent+" ", result, base, differential, nbc, start - 1, nbl-1, diffCursor - 1, url, webUrl, profileName, tgt.getElement().getPath(), diffMatches.get(0).getPath(), trimDifferential, contextName, resultPathBase, false, null, null, redirectorStack(redirector, outcome, cpath), srcSD);
}
} else {
StructureDefinition dt = outcome.getType().size() == 1 ? getProfileForDataType(outcome.getType().get(0)) : getProfileForDataType("Element");
StructureDefinition dt = outcome.getType().size() == 1 ? getProfileForDataType(outcome.getType().get(0), webUrl) : getProfileForDataType("Element");
if (dt == null)
throw new DefinitionException(context.formatMessage(I18nConstants._HAS_CHILDREN__FOR_TYPE__IN_PROFILE__BUT_CANT_FIND_TYPE, diffMatches.get(0).getPath(), differential.getElement().get(diffCursor).getPath(), typeCode(outcome.getType()), profileName));
contextName = dt.getUrl();
@ -1510,7 +1515,7 @@ public class ProfileUtilities extends TranslatingUtilities {
if (baseHasChildren(base, currentBase)) { // not a new type here
throw new Error("This situation is not yet handled (constrain slicing to 1..1 and fix base slice for inline structure - please report issue to grahame@fhir.org along with a test case that reproduces this error (@ "+cpath+" | "+currentBase.getPath()+")");
} else {
StructureDefinition dt = getTypeForElement(differential, diffCursor, profileName, diffMatches, outcome);
StructureDefinition dt = getTypeForElement(differential, diffCursor, profileName, diffMatches, outcome, webUrl);
contextName = dt.getUrl();
diffCursor++;
start = diffCursor;
@ -1576,7 +1581,7 @@ public class ProfileUtilities extends TranslatingUtilities {
processPaths(indent+" ", result, base, differential, baseCursor+1, diffCursor, baseLimit, diffLimit, url, webUrl, profileName, contextPathSrc, contextPathDst, trimDifferential, contextName, resultPathBase, false, null, null, redirector, srcSD);
baseCursor = indexOfFirstNonChild(base, currentBase, baseCursor, baseLimit);
} else {
StructureDefinition dt = getTypeForElement(differential, diffCursor, profileName, diffMatches, outcome);
StructureDefinition dt = getTypeForElement(differential, diffCursor, profileName, diffMatches, outcome, webUrl);
contextName = dt.getUrl();
int start = diffCursor;
while (differential.getElement().size() > diffCursor && pathStartsWith(differential.getElement().get(diffCursor).getPath(), cpath+"."))
@ -1777,7 +1782,7 @@ public class ProfileUtilities extends TranslatingUtilities {
if (base.getElement().get(baseCursor).getType().size() != 1) {
throw new Error(context.formatMessage(I18nConstants.DIFFERENTIAL_WALKS_INTO____BUT_THE_BASE_DOES_NOT_AND_THERE_IS_NOT_A_SINGLE_FIXED_TYPE_THE_TYPE_IS__THIS_IS_NOT_HANDLED_YET, cpath, diffMatches.get(0).toString(), base.getElement().get(baseCursor).typeSummary()));
}
StructureDefinition dt = getProfileForDataType(base.getElement().get(baseCursor).getType().get(0));
StructureDefinition dt = getProfileForDataType(base.getElement().get(baseCursor).getType().get(0), webUrl);
if (dt == null) {
throw new DefinitionException(context.formatMessage(I18nConstants.UNKNOWN_TYPE__AT_, outcome.getType().get(0), diffMatches.get(0).getPath()));
}
@ -1893,7 +1898,7 @@ public class ProfileUtilities extends TranslatingUtilities {
diffCursor - 1, url, webUrl, profileName+pathTail(diffMatches, 0), base.getElement().get(0).getPath(), base.getElement().get(0).getPath(), trimDifferential, contextName, resultPathBase, false, null, null, redirector, srcSD);
} else {
StructureDefinition dt = getProfileForDataType(outcome.getType().get(0));
StructureDefinition dt = getProfileForDataType(outcome.getType().get(0), webUrl);
// if (t.getCode().equals("Extension") && t.hasProfile() && !t.getProfile().contains(":")) {
// lloydfix dt =
// }
@ -1927,6 +1932,15 @@ public class ProfileUtilities extends TranslatingUtilities {
return res;
}
private void updateConstraintSources(ElementDefinition ed, String url) {
for (ElementDefinitionConstraintComponent c : ed.getConstraint()) {
if (!c.hasSource()) {
c.setSource(url);
}
}
}
private Set<String> getListOfTypes(ElementDefinition e) {
Set<String> result = new HashSet<>();
for (TypeRefComponent t : e.getType()) {
@ -1936,7 +1950,7 @@ public class ProfileUtilities extends TranslatingUtilities {
}
public StructureDefinition getTypeForElement(StructureDefinitionDifferentialComponent differential, int diffCursor, String profileName,
List<ElementDefinition> diffMatches, ElementDefinition outcome) {
List<ElementDefinition> diffMatches, ElementDefinition outcome, String webUrl) {
if (outcome.getType().size() == 0) {
throw new DefinitionException(context.formatMessage(I18nConstants._HAS_NO_CHILDREN__AND_NO_TYPES_IN_PROFILE_, diffMatches.get(0).getPath(), differential.getElement().get(diffCursor).getPath(), profileName));
}
@ -1946,7 +1960,7 @@ public class ProfileUtilities extends TranslatingUtilities {
throw new DefinitionException(context.formatMessage(I18nConstants._HAS_CHILDREN__AND_MULTIPLE_TYPES__IN_PROFILE_, diffMatches.get(0).getPath(), differential.getElement().get(diffCursor).getPath(), typeCode(outcome.getType()), profileName));
}
}
StructureDefinition dt = getProfileForDataType(outcome.getType().get(0));
StructureDefinition dt = getProfileForDataType(outcome.getType().get(0), webUrl);
if (dt == null)
throw new DefinitionException(context.formatMessage(I18nConstants.UNKNOWN_TYPE__AT_, outcome.getType().get(0), diffMatches.get(0).getPath()));
return dt;
@ -2418,10 +2432,16 @@ public class ProfileUtilities extends TranslatingUtilities {
return s;
}
private StructureDefinition getProfileForDataType(TypeRefComponent type) {
private StructureDefinition getProfileForDataType(TypeRefComponent type, String webUrl) {
StructureDefinition sd = null;
if (type.hasProfile()) {
sd = context.fetchResource(StructureDefinition.class, type.getProfile().get(0).getValue());
if (sd == null) {
if (xver != null && xver.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());
}
}
if (sd == null)
System.out.println("Failed to find referenced profile: " + type.getProfile());
}
@ -4314,12 +4334,12 @@ public class ProfileUtilities extends TranslatingUtilities {
private boolean isBaseCondition(IdType c) {
String key = c.asStringValue();
return key.startsWith("ele-") || key.startsWith("res-") || key.startsWith("ext-") || key.startsWith("dom-") || key.startsWith("dr-");
return key != null && key.startsWith("ele-") || key.startsWith("res-") || key.startsWith("ext-") || key.startsWith("dom-") || key.startsWith("dr-");
}
private boolean isBaseConstraint(ElementDefinitionConstraintComponent con) {
String key = con.getKey();
return key.startsWith("ele-") || key.startsWith("res-") || key.startsWith("ext-") || key.startsWith("dom-") || key.startsWith("dr-");
return key != null && key.startsWith("ele-") || key.startsWith("res-") || key.startsWith("ext-") || key.startsWith("dom-") || key.startsWith("dr-");
}
private void makeChoiceRows(List<Row> subRows, ElementDefinition element, HierarchicalTableGenerator gen, String corePath, String profileBaseFileName, boolean mustSupportMode) {

3
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/BaseWorkerContext.java
View File

@ -666,10 +666,11 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
@Override
public ValueSetExpansionOutcome expandVS(ConceptSetComponent inc, boolean hierarchical) throws TerminologyServiceException {
public ValueSetExpansionOutcome expandVS(ConceptSetComponent inc, boolean hierarchical, boolean noInactive) throws TerminologyServiceException {
ValueSet vs = new ValueSet();
vs.setStatus(PublicationStatus.ACTIVE);
vs.setCompose(new ValueSetComposeComponent());
vs.getCompose().setInactive(!noInactive);
vs.getCompose().getInclude().add(inc);
CacheToken cacheToken = txCache.generateExpandToken(vs, hierarchical);
ValueSetExpansionOutcome res;

3
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/CanonicalResourceManager.java
View File

@ -124,6 +124,9 @@ public class CanonicalResourceManager<T extends CanonicalResource> {
if (resource == null) {
@SuppressWarnings("unchecked")
T1 res = (T1) proxy.getResource();
if (res == null) {
throw new Error("Proxy loading a resource from "+packageInfo+" failed and returned null");
}
synchronized (this) {
resource = res;
}

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/IWorkerContext.java
View File

@ -547,7 +547,7 @@ public interface IWorkerContext {
* @return
* @throws FHIRException
*/
ValueSetExpansionOutcome expandVS(ConceptSetComponent inc, boolean hierarchical) throws TerminologyServiceException;
ValueSetExpansionOutcome expandVS(ConceptSetComponent inc, boolean hierarchical, boolean noInactive) throws TerminologyServiceException;
Locale getLocale();

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/SimpleWorkerContext.java
View File

@ -239,7 +239,7 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
public SimpleWorkerContext fromPackage(NpmPackage pi, IContextResourceLoader loader) throws IOException, FHIRException {
SimpleWorkerContext context = getSimpleWorkerContextInstance();
context.setAllowLoadingDuplicates(true);
context.setAllowLoadingDuplicates(allowLoadingDuplicates);
context.version = pi.getNpm().get("version").getAsString();
context.loadFromPackage(pi, loader);
context.finishLoading();

4
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/ElementDefinition.java
View File

@ -11568,6 +11568,10 @@ When pattern[x] is used to constrain a complex object, it means that each proper
public boolean isInlineType() {
return getType().size() == 1 && Utilities.existsInList(getType().get(0).getCode(), "Element", "BackboneElement");
}
public boolean prohibited() {
return "0".equals(getMax());
}

34
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/Enumerations.java
View File

@ -3741,8 +3741,8 @@ public class Enumerations {
*/
MEDICATIONREQUEST,
/**
* A record of a medication that is being consumed by a patient. A MedicationUsage may indicate that the patient may be taking the medication now or has taken the medication in the past or will be taking the medication in the future. The source of this information can be the patient, significant other (such as a family member or spouse), or a clinician. A common scenario where this information is captured is during the history taking process during a patient visit or stay. The medication information may come from sources such as the patient's memory, from a prescription bottle, or from a list of medications the patient, clinician or other party maintains.
* A record of a medication that is being consumed by a patient. A MedicationUsage may indicate that the patient may be taking the medication now or has taken the medication in the past or will be taking the medication in the future. The source of this information can be the patient, significant other (such as a family member or spouse), or a clinician. A common scenario where this information is captured is during the history taking process during a patient visit or stay. The medication information may come from sources such as the patient's memory, from a prescription bottle, or from a list of medications the patient, clinician or other party maintains.
The primary difference between a medicationusage and a medicationadministration is that the medication administration has complete administration information and is based on actual administration information from the person who administered the medication. A medicationusage is often, if not always, less specific. There is no required date/time when the medication was administered, in fact we only know that a source has reported the patient is taking this medication, where details such as time, quantity, or rate or even medication product may be incomplete or missing or less precise. As stated earlier, the Medication Usage information may come from the patient's memory, from a prescription bottle or from a list of medications the patient, clinician or other party maintains. Medication administration is more formal and is not missing detailed information.
*/
MEDICATIONUSAGE,
@ -6924,9 +6924,9 @@ The primary difference between a medicationusage and a medicationadministration
return _4_1_0;
if ("4.2.0".equals(codeString))
return _4_2_0;
if ("4.3.0-snapshot1".equals(codeString))
if ("4.3.0-snapshot1".equalsIgnoreCase(codeString))
return _4_3_0SNAPSHOT1;
if ("4.3.0-cibuild".equals(codeString))
if ("4.3.0-cibuild".equalsIgnoreCase(codeString))
return _4_3_0CIBUILD;
if ("4.4.0".equals(codeString))
return _4_4_0;
@ -6934,9 +6934,9 @@ The primary difference between a medicationusage and a medicationadministration
return _4_5_0;
if ("4.6.0".equals(codeString))
return _4_6_0;
if ("5.0.0-snapshot1".equals(codeString))
if ("5.0.0-snapshot1".equalsIgnoreCase(codeString))
return _5_0_0SNAPSHOT1;
if ("5.0.0-cibuild".equals(codeString))
if ("5.0.0-cibuild".equalsIgnoreCase(codeString))
return _5_0_0CIBUILD;
throw new FHIRException("Unknown FHIRVersion code '"+codeString+"'");
}
@ -7158,7 +7158,7 @@ public String toCode(int len) {
public boolean isR4B() {
return toCode().startsWith("4.3");
return toCode().startsWith("4.1") || toCode().startsWith("4.3");
}
// end addition
@ -7219,9 +7219,9 @@ public String toCode(int len) {
return FHIRVersion._4_1_0;
if ("4.2.0".equals(codeString))
return FHIRVersion._4_2_0;
if ("4.3.0-snapshot1".equals(codeString))
if ("4.3.0-snapshot1".equalsIgnoreCase(codeString))
return FHIRVersion._4_3_0SNAPSHOT1;
if ("4.3.0-cibuild".equals(codeString))
if ("4.3.0-cibuild".equalsIgnoreCase(codeString))
return FHIRVersion._4_3_0CIBUILD;
if ("4.4.0".equals(codeString))
return FHIRVersion._4_4_0;
@ -7229,9 +7229,9 @@ public String toCode(int len) {
return FHIRVersion._4_5_0;
if ("4.6.0".equals(codeString))
return FHIRVersion._4_6_0;
if ("5.0.0-snapshot1".equals(codeString))
if ("5.0.0-snapshot1".equalsIgnoreCase(codeString))
return FHIRVersion._5_0_0SNAPSHOT1;
if ("5.0.0-cibuild".equals(codeString))
if ("5.0.0-cibuild".equalsIgnoreCase(codeString))
return FHIRVersion._5_0_0CIBUILD;
throw new IllegalArgumentException("Unknown FHIRVersion code '"+codeString+"'");
}
@ -7293,9 +7293,9 @@ public String toCode(int len) {
return new Enumeration<FHIRVersion>(this, FHIRVersion._4_1_0);
if ("4.2.0".equals(codeString))
return new Enumeration<FHIRVersion>(this, FHIRVersion._4_2_0);
if ("4.3.0-snapshot1".equals(codeString))
if ("4.3.0-snapshot1".equalsIgnoreCase(codeString))
return new Enumeration<FHIRVersion>(this, FHIRVersion._4_3_0SNAPSHOT1);
if ("4.3.0-cibuild".equals(codeString))
if ("4.3.0-cibuild".equalsIgnoreCase(codeString))
return new Enumeration<FHIRVersion>(this, FHIRVersion._4_3_0CIBUILD);
if ("4.4.0".equals(codeString))
return new Enumeration<FHIRVersion>(this, FHIRVersion._4_4_0);
@ -7303,9 +7303,9 @@ public String toCode(int len) {
return new Enumeration<FHIRVersion>(this, FHIRVersion._4_5_0);
if ("4.6.0".equals(codeString))
return new Enumeration<FHIRVersion>(this, FHIRVersion._4_6_0);
if ("5.0.0-snapshot1".equals(codeString))
if ("5.0.0-snapshot1".equalsIgnoreCase(codeString))
return new Enumeration<FHIRVersion>(this, FHIRVersion._5_0_0SNAPSHOT1);
if ("5.0.0-cibuild".equals(codeString))
if ("5.0.0-cibuild".equalsIgnoreCase(codeString))
return new Enumeration<FHIRVersion>(this, FHIRVersion._5_0_0CIBUILD);
throw new FHIRException("Unknown FHIRVersion code '"+codeString+"'");
}
@ -9870,8 +9870,8 @@ public String toCode(int len) {
*/
MEDICATIONREQUEST,
/**
* A record of a medication that is being consumed by a patient. A MedicationUsage may indicate that the patient may be taking the medication now or has taken the medication in the past or will be taking the medication in the future. The source of this information can be the patient, significant other (such as a family member or spouse), or a clinician. A common scenario where this information is captured is during the history taking process during a patient visit or stay. The medication information may come from sources such as the patient's memory, from a prescription bottle, or from a list of medications the patient, clinician or other party maintains.
* A record of a medication that is being consumed by a patient. A MedicationUsage may indicate that the patient may be taking the medication now or has taken the medication in the past or will be taking the medication in the future. The source of this information can be the patient, significant other (such as a family member or spouse), or a clinician. A common scenario where this information is captured is during the history taking process during a patient visit or stay. The medication information may come from sources such as the patient's memory, from a prescription bottle, or from a list of medications the patient, clinician or other party maintains.
The primary difference between a medicationusage and a medicationadministration is that the medication administration has complete administration information and is based on actual administration information from the person who administered the medication. A medicationusage is often, if not always, less specific. There is no required date/time when the medication was administered, in fact we only know that a source has reported the patient is taking this medication, where details such as time, quantity, or rate or even medication product may be incomplete or missing or less precise. As stated earlier, the Medication Usage information may come from the patient's memory, from a prescription bottle or from a list of medications the patient, clinician or other party maintains. Medication administration is more formal and is not missing detailed information.
*/
MEDICATIONUSAGE,

146
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/DataRenderer.java
View File

@ -30,6 +30,7 @@ import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.context.IWorkerContext.ValidationResult;
import org.hl7.fhir.r5.model.Address;
import org.hl7.fhir.r5.model.Annotation;
import org.hl7.fhir.r5.model.BackboneType;
import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.BaseDateTimeType;
import org.hl7.fhir.r5.model.CanonicalResource;
@ -48,6 +49,7 @@ import org.hl7.fhir.r5.model.ContactPoint.ContactPointSystem;
import org.hl7.fhir.r5.model.DataType;
import org.hl7.fhir.r5.model.DateTimeType;
import org.hl7.fhir.r5.model.DateType;
import org.hl7.fhir.r5.model.ElementDefinition;
import org.hl7.fhir.r5.model.Enumeration;
import org.hl7.fhir.r5.model.Expression;
import org.hl7.fhir.r5.model.Extension;
@ -357,8 +359,138 @@ public class DataRenderer extends Renderer {
return value.primitiveValue();
}
// -- 6. General purpose extension rendering ----------------------------------------------
// -- 5. Data type Rendering ----------------------------------------------
public boolean hasRenderableExtensions(DataType element) {
for (Extension ext : element.getExtension()) {
if (canRender(ext)) {
return true;
}
}
return false;
}
public boolean hasRenderableExtensions(BackboneType element) {
for (Extension ext : element.getExtension()) {
if (canRender(ext)) {
return true;
}
}
return element.hasModifierExtension();
}
private String getExtensionLabel(Extension ext) {
StructureDefinition sd = context.getWorker().fetchResource(StructureDefinition.class, ext.getUrl());
if (sd != null && ext.getValue().isPrimitive() && sd.hasSnapshot()) {
for (ElementDefinition ed : sd.getSnapshot().getElement()) {
if (Utilities.existsInList(ed.getPath(), "Extension", "Extension.value[x]") && ed.hasLabel()) {
return ed.getLabel();
}
}
}
return null;
}
private boolean canRender(Extension ext) {
return getExtensionLabel(ext) != null;
}
public void renderExtensionsInList(XhtmlNode ul, DataType element) throws FHIRFormatError, DefinitionException, IOException {
for (Extension ext : element.getExtension()) {
if (canRender(ext)) {
String lbl = getExtensionLabel(ext);
XhtmlNode li = ul.li();
li.tx(lbl);
li.tx(": ");
render(li, ext.getValue());
}
}
}
public void renderExtensionsInList(XhtmlNode ul, BackboneType element) throws FHIRFormatError, DefinitionException, IOException {
for (Extension ext : element.getModifierExtension()) {
if (canRender(ext)) {
String lbl = getExtensionLabel(ext);
XhtmlNode li = ul.li();
li = li.b();
li.tx(lbl);
li.tx(": ");
render(li, ext.getValue());
} else {
// somehow have to do better than this
XhtmlNode li = ul.li();
li.b().tx("WARNING: Unrenderable Modifier Extension!");
}
}
for (Extension ext : element.getExtension()) {
if (canRender(ext)) {
String lbl = getExtensionLabel(ext);
XhtmlNode li = ul.li();
li.tx(lbl);
li.tx(": ");
render(li, ext.getValue());
}
}
}
public void renderExtensionsInText(XhtmlNode div, DataType element, String sep) throws FHIRFormatError, DefinitionException, IOException {
boolean first = true;
for (Extension ext : element.getExtension()) {
if (canRender(ext)) {
if (first) {
first = false;
} else {
div.tx(sep);
div.tx(" ");
}
String lbl = getExtensionLabel(ext);
div.tx(lbl);
div.tx(": ");
render(div, ext.getValue());
}
}
}
public void renderExtensionsInList(XhtmlNode div, BackboneType element, String sep) throws FHIRFormatError, DefinitionException, IOException {
boolean first = true;
for (Extension ext : element.getModifierExtension()) {
if (first) {
first = false;
} else {
div.tx(sep);
div.tx(" ");
}
if (canRender(ext)) {
String lbl = getExtensionLabel(ext);
XhtmlNode b = div.b();
b.tx(lbl);
b.tx(": ");
render(div, ext.getValue());
} else {
// somehow have to do better than this
div.b().tx("WARNING: Unrenderable Modifier Extension!");
}
}
for (Extension ext : element.getExtension()) {
if (canRender(ext)) {
if (first) {
first = false;
} else {
div.tx(sep);
div.tx(" ");
}
String lbl = getExtensionLabel(ext);
div.tx(lbl);
div.tx(": ");
render(div, ext.getValue());
}
}
}
// -- 6. Data type Rendering ----------------------------------------------
public static String display(IWorkerContext context, DataType type) {
return new DataRenderer(new RenderingContext(context, null, null, "http://hl7.org/fhir/R4", "", null, ResourceRendererMode.END_USER)).display(type);
@ -866,11 +998,11 @@ public class DataRenderer extends Renderer {
return s;
}
protected void renderCodeableConcept(XhtmlNode x, CodeableConcept cc) {
protected void renderCodeableConcept(XhtmlNode x, CodeableConcept cc) throws FHIRFormatError, DefinitionException, IOException {
renderCodeableConcept(x, cc, false);
}
protected void renderCodeableReference(XhtmlNode x, CodeableReference e, boolean showCodeDetails) {
protected void renderCodeableReference(XhtmlNode x, CodeableReference e, boolean showCodeDetails) throws FHIRFormatError, DefinitionException, IOException {
if (e.hasConcept()) {
renderCodeableConcept(x, e.getConcept(), showCodeDetails);
}
@ -879,7 +1011,7 @@ public class DataRenderer extends Renderer {
}
}
protected void renderCodeableConcept(XhtmlNode x, CodeableConcept cc, boolean showCodeDetails) {
protected void renderCodeableConcept(XhtmlNode x, CodeableConcept cc, boolean showCodeDetails) throws FHIRFormatError, DefinitionException, IOException {
if (cc.isEmpty()) {
return;
}
@ -935,6 +1067,12 @@ public class DataRenderer extends Renderer {
sp.tx(" \""+c.getDisplay()+"\"");
}
}
if (hasRenderableExtensions(cc)) {
if (!first) {
sp.tx("; ");
}
renderExtensionsInText(sp, cc, ";");
}
sp.tx(")");
} else {

18
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/LiquidRenderer.java
View File

@ -32,12 +32,30 @@ public class LiquidRenderer extends ResourceRenderer {
this.rcontext = rcontext;
this.liquidTemplate = liquidTemplate;
}
/**
* This class provides an implementation of the ILiquidEngineIncludeResolver that makes use of the
* template provider available in the rendering context to support resolving includes.
*/
private class LiquidRendererIncludeResolver implements LiquidEngine.ILiquidEngineIncludeResolver {
public LiquidRendererIncludeResolver(RenderingContext context) {
this.context = context;
}
private RenderingContext context;
@Override
public String fetchInclude(LiquidEngine engine, String name) {
return context.getTemplateProvider().findTemplate(context, name);
}
}
@Override
public boolean render(XhtmlNode x, Resource r) throws FHIRFormatError, DefinitionException, IOException, FHIRException, EOperationOutcome {
LiquidEngine engine = new LiquidEngine(context.getWorker(), context.getServices());
XhtmlNode xn;
try {
engine.setIncludeResolver(new LiquidRendererIncludeResolver(context));
LiquidDocument doc = engine.parse(liquidTemplate, "template");
String html = engine.evaluate(doc, r, rcontext);
xn = new XhtmlParser().parseFragment(html);

6
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/ValueSetRenderer.java
View File

@ -213,7 +213,7 @@ public class ValueSetRenderer extends TerminologyRenderer {
XhtmlNode t = x.table( "codes");
XhtmlNode tr = t.tr();
if (doLevel)
tr.td().b().tx("Lvl");
tr.td().b().tx("Level");
tr.td().attribute("style", "white-space:nowrap").b().tx("Code");
if (doSystem)
tr.td().b().tx("System");
@ -242,7 +242,7 @@ public class ValueSetRenderer extends TerminologyRenderer {
addMapHeaders(tr, maps);
for (ValueSetExpansionContainsComponent c : vs.getExpansion().getContains()) {
addExpansionRowToTable(t, c, 0, doLevel, doSystem, doDefinition, maps, allCS, langs, doLangs);
addExpansionRowToTable(t, c, 1, doLevel, doSystem, doDefinition, maps, allCS, langs, doLangs);
}
// now, build observed languages
@ -1165,7 +1165,7 @@ public class ValueSetRenderer extends TerminologyRenderer {
ValueSetExpansionComponent vse = null;
if (!context.isNoSlowLookup() && !getContext().getWorker().hasCache()) {
try {
ValueSetExpansionOutcome vso = getContext().getWorker().expandVS(inc, false);
ValueSetExpansionOutcome vso = getContext().getWorker().expandVS(inc, false, false);
ValueSet valueset = vso.getValueset();
if (valueset == null)
throw new TerminologyServiceException("Error Expanding ValueSet: "+vso.getError());

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/CodeSystemUtilities.java
View File

@ -249,7 +249,7 @@ public class CodeSystemUtilities {
public static boolean isInactive(CodeSystem cs, ConceptDefinitionComponent def) throws FHIRException {
for (ConceptPropertyComponent p : def.getProperty()) {
if ("status".equals(p.getCode()) && p.hasValueStringType())
return "inactive".equals(p.getValueStringType());
return "inactive".equals(p.getValueStringType().primitiveValue()) || "retired".equals(p.getValueStringType().primitiveValue());
}
return false;
}

103
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/ValueSetCheckerSimple.java
View File

@ -33,8 +33,10 @@ package org.hl7.fhir.r5.terminologies;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.NoTerminologyServiceException;
@ -544,71 +546,92 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
private String systemForCodeInValueSet(String code) {
String sys = null;
Set<String> sys = new HashSet<>();
if (!scanForCodeInValueSet(code, sys)) {
return null;
}
if (sys.size() != 1) {
return null;
} else {
return sys.iterator().next();
}
}
private boolean scanForCodeInValueSet(String code, Set<String> sys) {
if (valueset.hasCompose()) {
if (valueset.getCompose().hasExclude()) {
return null;
}
// not sure what to do with the
// if (valueset.getCompose().hasExclude()) {
// return false;
// }
for (ConceptSetComponent vsi : valueset.getCompose().getInclude()) {
if (vsi.hasValueSet()) {
return null;
}
if (!vsi.hasSystem()) {
return null;
}
if (vsi.hasFilter()) {
return null;
}
CodeSystem cs = resolveCodeSystem(vsi.getSystem());
if (cs == null) {
return null;
}
if (vsi.hasConcept()) {
for (ConceptReferenceComponent cc : vsi.getConcept()) {
boolean match = cs.getCaseSensitive() ? cc.getCode().equals(code) : cc.getCode().equalsIgnoreCase(code);
if (match) {
if (sys == null) {
sys = vsi.getSystem();
} else if (!sys.equals(vsi.getSystem())) {
return null;
}
for (CanonicalType u : vsi.getValueSet()) {
if (!checkForCodeInValueSet(code, u.getValue(), sys)) {
return false;
}
}
} else {
ConceptDefinitionComponent cc = findCodeInConcept(cs.getConcept(), code);
if (cc != null) {
if (sys == null) {
sys = vsi.getSystem();
} else if (!sys.equals(vsi.getSystem())) {
return null;
} else if (!vsi.hasSystem()) {
return false;
}
if (vsi.hasSystem()) {
if (vsi.hasFilter()) {
return false;
}
CodeSystem cs = resolveCodeSystem(vsi.getSystem());
if (cs != null) {
if (vsi.hasConcept()) {
for (ConceptReferenceComponent cc : vsi.getConcept()) {
boolean match = cs.getCaseSensitive() ? cc.getCode().equals(code) : cc.getCode().equalsIgnoreCase(code);
if (match) {
sys.add(vsi.getSystem());
}
}
} else {
ConceptDefinitionComponent cc = findCodeInConcept(cs.getConcept(), code);
if (cc != null) {
sys.add(vsi.getSystem());
}
}
} else {
if (vsi.hasConcept()) {
for (ConceptReferenceComponent cc : vsi.getConcept()) {
boolean match = cc.getCode().equals(code);
if (match) {
sys.add(vsi.getSystem());
}
}
}
}
}
}
} else if (valueset.hasExpansion()) {
// Retrieve a list of all systems associated with this code in the expansion
List<String> systems = new ArrayList<String>();
checkSystems(valueset.getExpansion().getContains(), code, systems);
if (systems.size()==1)
sys = systems.get(0);
if (!checkSystems(valueset.getExpansion().getContains(), code, sys)) {
return false;
}
}
return true;
}
return sys;
private boolean checkForCodeInValueSet(String code, String uri, Set<String> sys) {
ValueSetCheckerSimple vs = getVs(uri);
return vs.scanForCodeInValueSet(code, sys);
}
/*
* Recursively go through all codes in the expansion and for any coding that matches the specified code, add the system for that coding
* to the passed list.
*/
private void checkSystems(List<ValueSetExpansionContainsComponent> contains, String code, List<String> systems) {
private boolean checkSystems(List<ValueSetExpansionContainsComponent> contains, String code, Set<String> systems) {
for (ValueSetExpansionContainsComponent c: contains) {
if (c.getCode().equals(code)) {
if (!systems.contains(c.getSystem()))
systems.add(c.getSystem());
systems.add(c.getSystem());
}
if (c.hasContains())
checkSystems(c.getContains(), code, systems);
}
return true;
}
@Override

81
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/ValueSetExpanderSimple.java
View File

@ -108,6 +108,8 @@ import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionParameterComponent;
import org.hl7.fhir.r5.utils.ToolingExtensions;
import org.hl7.fhir.utilities.Utilities;
import com.google.errorprone.annotations.NoAllocation;
public class ValueSetExpanderSimple extends ValueSetWorker implements ValueSetExpander {
public class PropertyFilter implements IConceptFilter {
@ -201,10 +203,15 @@ public class ValueSetExpanderSimple extends ValueSetWorker implements ValueSetEx
maxExpansionSize = theMaxExpansionSize;
}
private ValueSetExpansionContainsComponent addCode(String system, String code, String display, ValueSetExpansionContainsComponent parent, List<ConceptDefinitionDesignationComponent> designations, Parameters expParams, boolean isAbstract, boolean inactive, List<ValueSet> filters) {
private ValueSetExpansionContainsComponent addCode(String system, String code, String display, ValueSetExpansionContainsComponent parent, List<ConceptDefinitionDesignationComponent> designations, Parameters expParams,
boolean isAbstract, boolean inactive, List<ValueSet> filters, boolean noInactive) {
if (filters != null && !filters.isEmpty() && !filterContainsCode(filters, system, code))
return null;
if (noInactive && inactive) {
return null;
}
ValueSetExpansionContainsComponent n = new ValueSet.ValueSetExpansionContainsComponent();
n.setSystem(system);
n.setCode(code);
@ -267,12 +274,12 @@ public class ValueSetExpanderSimple extends ValueSetWorker implements ValueSetEx
return null;
}
private void addCodeAndDescendents(ValueSetExpansionContainsComponent focus, ValueSetExpansionContainsComponent parent, Parameters expParams, List<ValueSet> filters) throws FHIRException {
private void addCodeAndDescendents(ValueSetExpansionContainsComponent focus, ValueSetExpansionContainsComponent parent, Parameters expParams, List<ValueSet> filters, boolean noInactive) throws FHIRException {
focus.checkNoModifiers("Expansion.contains", "expanding");
ValueSetExpansionContainsComponent np = addCode(focus.getSystem(), focus.getCode(), focus.getDisplay(), parent,
convert(focus.getDesignation()), expParams, focus.getAbstract(), focus.getInactive(), filters);
convert(focus.getDesignation()), expParams, focus.getAbstract(), focus.getInactive(), filters, noInactive);
for (ValueSetExpansionContainsComponent c : focus.getContains())
addCodeAndDescendents(focus, np, expParams, filters);
addCodeAndDescendents(focus, np, expParams, filters, noInactive);
}
private List<ConceptDefinitionDesignationComponent> convert(List<ConceptReferenceDesignationComponent> designations) {
@ -287,7 +294,7 @@ public class ValueSetExpanderSimple extends ValueSetWorker implements ValueSetEx
return list;
}
private void addCodeAndDescendents(CodeSystem cs, String system, ConceptDefinitionComponent def, ValueSetExpansionContainsComponent parent, Parameters expParams, List<ValueSet> filters, ConceptDefinitionComponent exclusion, IConceptFilter filterFunc) throws FHIRException {
private void addCodeAndDescendents(CodeSystem cs, String system, ConceptDefinitionComponent def, ValueSetExpansionContainsComponent parent, Parameters expParams, List<ValueSet> filters, ConceptDefinitionComponent exclusion, IConceptFilter filterFunc, boolean noInactive) throws FHIRException {
def.checkNoModifiers("Code in Code System", "expanding");
if (exclusion != null) {
if (exclusion.getCode().equals(def.getCode()))
@ -298,30 +305,30 @@ public class ValueSetExpanderSimple extends ValueSetWorker implements ValueSetEx
boolean abs = CodeSystemUtilities.isNotSelectable(cs, def);
boolean inc = CodeSystemUtilities.isInactive(cs, def);
if ((includeAbstract || !abs) && filterFunc.includeConcept(cs, def)) {
np = addCode(system, def.getCode(), def.getDisplay(), parent, def.getDesignation(), expParams, abs, inc, filters);
np = addCode(system, def.getCode(), def.getDisplay(), parent, def.getDesignation(), expParams, abs, inc, filters, noInactive);
}
for (ConceptDefinitionComponent c : def.getConcept()) {
addCodeAndDescendents(cs, system, c, np, expParams, filters, exclusion, filterFunc);
addCodeAndDescendents(cs, system, c, np, expParams, filters, exclusion, filterFunc, noInactive);
}
if (def.hasUserData(CodeSystemUtilities.USER_DATA_CROSS_LINK)) {
List<ConceptDefinitionComponent> children = (List<ConceptDefinitionComponent>) def.getUserData(CodeSystemUtilities.USER_DATA_CROSS_LINK);
for (ConceptDefinitionComponent c : children)
addCodeAndDescendents(cs, system, c, np, expParams, filters, exclusion, filterFunc);
addCodeAndDescendents(cs, system, c, np, expParams, filters, exclusion, filterFunc, noInactive);
}
} else {
for (ConceptDefinitionComponent c : def.getConcept()) {
addCodeAndDescendents(cs, system, c, null, expParams, filters, exclusion, filterFunc);
addCodeAndDescendents(cs, system, c, null, expParams, filters, exclusion, filterFunc, noInactive);
}
if (def.hasUserData(CodeSystemUtilities.USER_DATA_CROSS_LINK)) {
List<ConceptDefinitionComponent> children = (List<ConceptDefinitionComponent>) def.getUserData(CodeSystemUtilities.USER_DATA_CROSS_LINK);
for (ConceptDefinitionComponent c : children)
addCodeAndDescendents(cs, system, c, null, expParams, filters, exclusion, filterFunc);
addCodeAndDescendents(cs, system, c, null, expParams, filters, exclusion, filterFunc, noInactive);
}
}
}
private void addCodes(ValueSetExpansionComponent expand, List<ValueSetExpansionParameterComponent> params, Parameters expParams, List<ValueSet> filters) throws ETooCostly, FHIRException {
private void addCodes(ValueSetExpansionComponent expand, List<ValueSetExpansionParameterComponent> params, Parameters expParams, List<ValueSet> filters, boolean noInactive) throws ETooCostly, FHIRException {
if (expand != null) {
if (expand.getContains().size() > maxExpansionSize)
throw failCostly("Too many codes to display (>" + Integer.toString(expand.getContains().size()) + ")");
@ -330,7 +337,7 @@ public class ValueSetExpanderSimple extends ValueSetWorker implements ValueSetEx
params.add(p);
}
copyImportContains(expand.getContains(), null, expParams, filters);
copyImportContains(expand.getContains(), null, expParams, filters, noInactive);
}
}
@ -354,7 +361,7 @@ public class ValueSetExpanderSimple extends ValueSetWorker implements ValueSetEx
CodeSystem cs = context.fetchCodeSystem(exc.getSystem());
if ((cs == null || cs.getContent() != CodeSystemContentMode.COMPLETE) && context.supportsSystem(exc.getSystem())) {
ValueSetExpansionOutcome vse = context.expandVS(exc, false);
ValueSetExpansionOutcome vse = context.expandVS(exc, false, false);
ValueSet valueset = vse.getValueset();
if (valueset == null)
throw failTSE("Error Expanding ValueSet: "+vse.getError());
@ -474,11 +481,11 @@ public class ValueSetExpanderSimple extends ValueSetWorker implements ValueSetEx
first = false;
else
canBeHeirarchy = false;
includeCodes(inc, exp, expParams, canBeHeirarchy, extensions);
includeCodes(inc, exp, expParams, canBeHeirarchy, compose.hasInactive() && !compose.getInactive(), extensions);
}
}
private ValueSet importValueSet(String value, ValueSetExpansionComponent exp, Parameters expParams) throws ETooCostly, TerminologyServiceException, FileNotFoundException, IOException, FHIRFormatError {
private ValueSet importValueSet(String value, ValueSetExpansionComponent exp, Parameters expParams, boolean noInactive) throws ETooCostly, TerminologyServiceException, FileNotFoundException, IOException, FHIRFormatError {
if (value == null)
throw fail("unable to find value set with no identity");
ValueSet vs = context.fetchResource(ValueSet.class, value);
@ -489,6 +496,10 @@ public class ValueSetExpanderSimple extends ValueSetWorker implements ValueSetEx
throw fail("Unable to find imported value set " + value);
}
}
if (noInactive) {
expParams = expParams.copy();
expParams.addParameter("activeOnly", true);
}
ValueSetExpansionOutcome vso = new ValueSetExpanderSimple(context, allErrors).expand(vs, expParams);
if (vso.getError() != null) {
addErrors(vso.getAllErrors());
@ -543,19 +554,19 @@ public class ValueSetExpanderSimple extends ValueSetWorker implements ValueSetEx
}
}
private void copyImportContains(List<ValueSetExpansionContainsComponent> list, ValueSetExpansionContainsComponent parent, Parameters expParams, List<ValueSet> filter) throws FHIRException {
private void copyImportContains(List<ValueSetExpansionContainsComponent> list, ValueSetExpansionContainsComponent parent, Parameters expParams, List<ValueSet> filter, boolean noInactive) throws FHIRException {
for (ValueSetExpansionContainsComponent c : list) {
c.checkNoModifiers("Imported Expansion in Code System", "expanding");
ValueSetExpansionContainsComponent np = addCode(c.getSystem(), c.getCode(), c.getDisplay(), parent, null, expParams, c.getAbstract(), c.getInactive(), filter);
copyImportContains(c.getContains(), np, expParams, filter);
ValueSetExpansionContainsComponent np = addCode(c.getSystem(), c.getCode(), c.getDisplay(), parent, null, expParams, c.getAbstract(), c.getInactive(), filter, noInactive);
copyImportContains(c.getContains(), np, expParams, filter, noInactive);
}
}
private void includeCodes(ConceptSetComponent inc, ValueSetExpansionComponent exp, Parameters expParams, boolean heirarchical, List<Extension> extensions) throws ETooCostly, FileNotFoundException, IOException, FHIRException {
private void includeCodes(ConceptSetComponent inc, ValueSetExpansionComponent exp, Parameters expParams, boolean heirarchical, boolean noInactive, List<Extension> extensions) throws ETooCostly, FileNotFoundException, IOException, FHIRException {
inc.checkNoModifiers("Compose.include", "expanding");
List<ValueSet> imports = new ArrayList<ValueSet>();
for (UriType imp : inc.getValueSet()) {
imports.add(importValueSet(imp.getValue(), exp, expParams));
imports.add(importValueSet(imp.getValue(), exp, expParams, noInactive));
}
if (!inc.hasSystem()) {
@ -564,19 +575,19 @@ public class ValueSetExpanderSimple extends ValueSetWorker implements ValueSetEx
ValueSet base = imports.get(0);
imports.remove(0);
base.checkNoModifiers("Imported ValueSet", "expanding");
copyImportContains(base.getExpansion().getContains(), null, expParams, imports);
copyImportContains(base.getExpansion().getContains(), null, expParams, imports, noInactive);
} else {
CodeSystem cs = context.fetchCodeSystem(inc.getSystem());
if (isServerSide(inc.getSystem()) || (cs == null || (cs.getContent() != CodeSystemContentMode.COMPLETE && cs.getContent() != CodeSystemContentMode.FRAGMENT))) {
doServerIncludeCodes(inc, heirarchical, exp, imports, expParams, extensions);
doServerIncludeCodes(inc, heirarchical, exp, imports, expParams, extensions, noInactive);
} else {
doInternalIncludeCodes(inc, exp, expParams, imports, cs);
doInternalIncludeCodes(inc, exp, expParams, imports, cs, noInactive);
}
}
}
private void doServerIncludeCodes(ConceptSetComponent inc, boolean heirarchical, ValueSetExpansionComponent exp, List<ValueSet> imports, Parameters expParams, List<Extension> extensions) throws FHIRException {
ValueSetExpansionOutcome vso = context.expandVS(inc, heirarchical);
private void doServerIncludeCodes(ConceptSetComponent inc, boolean heirarchical, ValueSetExpansionComponent exp, List<ValueSet> imports, Parameters expParams, List<Extension> extensions, boolean noInactive) throws FHIRException {
ValueSetExpansionOutcome vso = context.expandVS(inc, heirarchical, noInactive);
if (vso.getError() != null) {
throw failTSE("Unable to expand imported value set: " + vso.getError());
}
@ -599,7 +610,7 @@ public class ValueSetExpanderSimple extends ValueSetWorker implements ValueSetEx
}
}
for (ValueSetExpansionContainsComponent cc : vs.getExpansion().getContains()) {
addCodeAndDescendents(cc, null, expParams, imports);
addCodeAndDescendents(cc, null, expParams, imports, noInactive);
}
}
@ -612,7 +623,7 @@ public class ValueSetExpanderSimple extends ValueSetWorker implements ValueSetEx
return false;
}
public void doInternalIncludeCodes(ConceptSetComponent inc, ValueSetExpansionComponent exp, Parameters expParams, List<ValueSet> imports, CodeSystem cs) throws NoTerminologyServiceException, TerminologyServiceException, FHIRException {
public void doInternalIncludeCodes(ConceptSetComponent inc, ValueSetExpansionComponent exp, Parameters expParams, List<ValueSet> imports, CodeSystem cs, boolean noInactive) throws NoTerminologyServiceException, TerminologyServiceException, FHIRException {
if (cs == null) {
if (context.isNoTerminologyServer())
throw failTSE("Unable to find code system " + inc.getSystem().toString());
@ -629,7 +640,7 @@ public class ValueSetExpanderSimple extends ValueSetWorker implements ValueSetEx
if (inc.getConcept().size() == 0 && inc.getFilter().size() == 0) {
// special case - add all the code system
for (ConceptDefinitionComponent def : cs.getConcept()) {
addCodeAndDescendents(cs, inc.getSystem(), def, null, expParams, imports, null, new AllConceptsFilter());
addCodeAndDescendents(cs, inc.getSystem(), def, null, expParams, imports, null, new AllConceptsFilter(), noInactive);
}
if (cs.getContent() == CodeSystemContentMode.FRAGMENT) {
addFragmentWarning(exp, cs);
@ -658,7 +669,7 @@ public class ValueSetExpanderSimple extends ValueSetWorker implements ValueSetEx
} else {
inactive = CodeSystemUtilities.isInactive(cs, def);
}
addCode(inc.getSystem(), c.getCode(), !Utilities.noString(c.getDisplay()) ? c.getDisplay() : def == null ? null : def.getDisplay(), null, convertDesignations(c.getDesignation()), expParams, false, inactive, imports);
addCode(inc.getSystem(), c.getCode(), !Utilities.noString(c.getDisplay()) ? c.getDisplay() : def == null ? null : def.getDisplay(), null, convertDesignations(c.getDesignation()), expParams, false, inactive, imports, noInactive);
}
}
if (inc.getFilter().size() > 1) {
@ -675,14 +686,14 @@ public class ValueSetExpanderSimple extends ValueSetWorker implements ValueSetEx
ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), fc.getValue());
if (def == null)
throw failTSE("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'");
addCodeAndDescendents(cs, inc.getSystem(), def, null, expParams, imports, null, new AllConceptsFilter());
addCodeAndDescendents(cs, inc.getSystem(), def, null, expParams, imports, null, new AllConceptsFilter(), noInactive);
} else if ("concept".equals(fc.getProperty()) && fc.getOp() == FilterOperator.ISNOTA) {
// special: all codes in the target code system that are not under the value
ConceptDefinitionComponent defEx = getConceptForCode(cs.getConcept(), fc.getValue());
if (defEx == null)
throw failTSE("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'");
for (ConceptDefinitionComponent def : cs.getConcept()) {
addCodeAndDescendents(cs, inc.getSystem(), def, null, expParams, imports, defEx, new AllConceptsFilter());
addCodeAndDescendents(cs, inc.getSystem(), def, null, expParams, imports, defEx, new AllConceptsFilter(), noInactive);
}
} else if ("concept".equals(fc.getProperty()) && fc.getOp() == FilterOperator.DESCENDENTOF) {
// special: all codes in the target code system under the value
@ -690,11 +701,11 @@ public class ValueSetExpanderSimple extends ValueSetWorker implements ValueSetEx
if (def == null)
throw failTSE("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'");
for (ConceptDefinitionComponent c : def.getConcept())
addCodeAndDescendents(cs, inc.getSystem(), c, null, expParams, imports, null, new AllConceptsFilter());
addCodeAndDescendents(cs, inc.getSystem(), c, null, expParams, imports, null, new AllConceptsFilter(), noInactive);
if (def.hasUserData(CodeSystemUtilities.USER_DATA_CROSS_LINK)) {
List<ConceptDefinitionComponent> children = (List<ConceptDefinitionComponent>) def.getUserData(CodeSystemUtilities.USER_DATA_CROSS_LINK);
for (ConceptDefinitionComponent c : children)
addCodeAndDescendents(cs, inc.getSystem(), c, null, expParams, imports, null, new AllConceptsFilter());
addCodeAndDescendents(cs, inc.getSystem(), c, null, expParams, imports, null, new AllConceptsFilter(), noInactive);
}
} else if ("display".equals(fc.getProperty()) && fc.getOp() == FilterOperator.EQUAL) {
@ -705,13 +716,13 @@ public class ValueSetExpanderSimple extends ValueSetWorker implements ValueSetEx
if (isNotBlank(def.getDisplay()) && isNotBlank(fc.getValue())) {
if (def.getDisplay().contains(fc.getValue())) {
addCode(inc.getSystem(), def.getCode(), def.getDisplay(), null, def.getDesignation(), expParams, CodeSystemUtilities.isNotSelectable(cs, def), CodeSystemUtilities.isInactive(cs, def),
imports);
imports, noInactive);
}
}
}
} else if (isDefinedProperty(cs, fc.getProperty())) {
for (ConceptDefinitionComponent def : cs.getConcept()) {
addCodeAndDescendents(cs, inc.getSystem(), def, null, expParams, imports, null, new PropertyFilter(fc, getPropertyDefinition(cs, fc.getProperty())));
addCodeAndDescendents(cs, inc.getSystem(), def, null, expParams, imports, null, new PropertyFilter(fc, getPropertyDefinition(cs, fc.getProperty())), noInactive);
}
} else {
throw fail("Search by property[" + fc.getProperty() + "] and op[" + fc.getOp() + "] is not supported yet");

48
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/test/utils/TestingUtilities.java
View File

@ -75,11 +75,23 @@ public class TestingUtilities extends BaseTestingUtilities {
static public Map<String, IWorkerContext> fcontexts;
public static IWorkerContext context() {
return context("4.0.1");
final static public String DEFAULT_CONTEXT_VERSION = "4.0.1";
/** Get an existing instantiation of a WorkerContext if available
*
* This uses the DEFAULT_CONTEXT_VERSION
* */
public static IWorkerContext getSharedWorkerContext() {
return getSharedWorkerContext(DEFAULT_CONTEXT_VERSION);
}
public static IWorkerContext context(String version) {
/**
* Get an existing instantiation of a WorkerContext if available
*
* @param version FHIR Version to get context for
* @return
*/
public static IWorkerContext getSharedWorkerContext(String version) {
if ("4.5.0".equals(version)) {
version = "4.4.0"; // temporary work around
}
@ -89,30 +101,34 @@ public class TestingUtilities extends BaseTestingUtilities {
fcontexts = new HashMap<>();
}
if (!fcontexts.containsKey(v)) {
FilesystemPackageCacheManager pcm;
try {
pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
IWorkerContext fcontext = getWorkerContext(pcm.loadPackage(VersionUtilities.packageForVersion(version), version));
fcontext.setUcumService(new UcumEssenceService(TestingUtilities.loadTestResourceStream("ucum", "ucum-essence.xml")));
fcontext.setExpansionProfile(new Parameters());
// ((SimpleWorkerContext) fcontext).connectToTSServer(new TerminologyClientR5("http://tx.fhir.org/r4"), null);
IWorkerContext fcontext = getWorkerContext(version);
fcontexts.put(v, fcontext);
} catch (Exception e) {
e.printStackTrace();
throw new Error(e);
}
}
return fcontexts.get(v);
}
public static IWorkerContext getWorkerContext(String version) {
FilesystemPackageCacheManager pcm;
try {
pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
IWorkerContext fcontext = getWorkerContext(pcm.loadPackage(VersionUtilities.packageForVersion(version), version));
fcontext.setUcumService(new UcumEssenceService(TestingUtilities.loadTestResourceStream("ucum", "ucum-essence.xml")));
fcontext.setExpansionProfile(new Parameters());
return fcontext;
} catch (Exception e) {
e.printStackTrace();
throw new Error(e);
}
}
public static SimpleWorkerContext getWorkerContext(NpmPackage npmPackage) throws Exception {
SimpleWorkerContext swc = new SimpleWorkerContext.SimpleWorkerContextBuilder().withUserAgent(TestConstants.USER_AGENT).withTerminologyCachePath(TestConstants.TX_CACHE).fromPackage(npmPackage);
SimpleWorkerContext swc = new SimpleWorkerContext.SimpleWorkerContextBuilder().withAllowLoadingDuplicates(true).withUserAgent(TestConstants.USER_AGENT).withTerminologyCachePath(TestConstants.TX_CACHE).fromPackage(npmPackage);
TerminologyCache.setCacheErrors(true);
return swc;
}
public static SimpleWorkerContext getWorkerContext(NpmPackage npmPackage, IWorkerContext.IContextResourceLoader loader) throws Exception {
SimpleWorkerContext swc = new SimpleWorkerContext.SimpleWorkerContextBuilder().withUserAgent(TestConstants.USER_AGENT).withTerminologyCachePath(TestConstants.TX_CACHE).fromPackage(npmPackage, loader);
SimpleWorkerContext swc = new SimpleWorkerContext.SimpleWorkerContextBuilder().withAllowLoadingDuplicates(true).withUserAgent(TestConstants.USER_AGENT).withTerminologyCachePath(TestConstants.TX_CACHE).fromPackage(npmPackage, loader);
TerminologyCache.setCacheErrors(true);
return swc;
}

29
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/FHIRPathEngine.java
View File

@ -235,6 +235,18 @@ public class FHIRPathEngine {
}
return res;
}
public boolean hasType(String tn) {
if (type != null) {
return tn.equals(type);
} else {
for (TypeRefComponent t : element.getType()) {
if (tn.equals(t.getCode())) {
return true;
}
}
return false;
}
}
}
private IWorkerContext worker;
private IEvaluationContext hostServices;
@ -5472,7 +5484,7 @@ public class FHIRPathEngine {
* @throws PathEngineException
* @throws DefinitionException
*/
public TypedElementDefinition evaluateDefinition(ExpressionNode expr, StructureDefinition profile, TypedElementDefinition element, StructureDefinition source) throws DefinitionException {
public TypedElementDefinition evaluateDefinition(ExpressionNode expr, StructureDefinition profile, TypedElementDefinition element, StructureDefinition source, boolean dontWalkIntoReferences) throws DefinitionException {
StructureDefinition sd = profile;
TypedElementDefinition focus = null;
boolean okToNotResolve = false;
@ -5584,10 +5596,19 @@ public class FHIRPathEngine {
} else {
throw makeException(expr, I18nConstants.FHIRPATH_DISCRIMINATOR_CANT_FIND, expr.toString(), source.getUrl(), element.getElement().getId(), profile.getUrl());
}
} else if (expr.getInner() == null) {
return focus;
} else {
return evaluateDefinition(expr.getInner(), sd, focus, profile);
// gdg 26-02-2022. If we're walking towards a resolve() and we're on a reference, and we try to walk into the reference
// then we don't do that. .resolve() is allowed on the Reference.reference, but the target of the reference will be defined
// on the Reference, not the reference.reference.
ExpressionNode next = expr.getInner();
if (dontWalkIntoReferences && focus.hasType("Reference") && next != null && next.getKind() == Kind.Name && next.getName().equals("reference")) {
next = next.getInner();
}
if (next == null) {
return focus;
} else {
return evaluateDefinition(next, sd, focus, profile, dontWalkIntoReferences);
}
}
}

8
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/TypesUtilities.java
View File

@ -132,7 +132,9 @@ public class TypesUtilities {
res.add(new WildcardInformation("Annotation", TypeClassification.DATATYPE));
res.add(new WildcardInformation("Attachment", TypeClassification.DATATYPE));
res.add(new WildcardInformation("CodeableConcept", TypeClassification.DATATYPE));
res.add(new WildcardInformation("CodeableReference", TypeClassification.DATATYPE));
if (!VersionUtilities.isR4BVer(version)) {
res.add(new WildcardInformation("CodeableReference", TypeClassification.DATATYPE));
}
res.add(new WildcardInformation("Coding", TypeClassification.DATATYPE));
res.add(new WildcardInformation("ContactPoint", TypeClassification.DATATYPE));
res.add(new WildcardInformation("Count", TypeClassification.DATATYPE));
@ -145,7 +147,9 @@ public class TypesUtilities {
res.add(new WildcardInformation("Quantity", TypeClassification.DATATYPE));
res.add(new WildcardInformation("Range", TypeClassification.DATATYPE));
res.add(new WildcardInformation("Ratio", TypeClassification.DATATYPE));
res.add(new WildcardInformation("RatioRange", TypeClassification.DATATYPE));
if (!VersionUtilities.isR4BVer(version)) {
res.add(new WildcardInformation("RatioRange", TypeClassification.DATATYPE));
}
res.add(new WildcardInformation("Reference", " - a reference to another resource", TypeClassification.DATATYPE));
res.add(new WildcardInformation("SampledData", TypeClassification.DATATYPE));
res.add(new WildcardInformation("Signature", TypeClassification.DATATYPE));

12
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/XVerExtensionManager.java
View File

@ -50,9 +50,6 @@ public class XVerExtensionManager {
return XVerExtensionStatus.Invalid;
}
String v = url.substring(20, 23);
if ("5.0".equals(v)) {
v = "4.6"; // for now
}
String e = url.substring(54);
if (!lists.containsKey(v)) {
if (context.getBinaries().containsKey("xver-paths-"+v+".json")) {
@ -86,9 +83,6 @@ public class XVerExtensionManager {
public StructureDefinition makeDefinition(String url) {
String verSource = url.substring(20, 23);
if ("5.0".equals(verSource)) {
verSource = "4.6"; // for now
}
String verTarget = VersionUtilities.getMajMin(context.getVersion());
String e = url.substring(54);
JsonObject root = lists.get(verSource);
@ -123,16 +117,18 @@ public class XVerExtensionManager {
populateTypes(path, val, verSource, verTarget);
} else if (path.has("elements")) {
for (JsonElement i : path.getAsJsonArray("elements")) {
String s = i.getAsString();
JsonObject elt = root.getAsJsonObject(e+"."+i.getAsString());
if (elt != null) {
String s = i.getAsString().replace("[x]", "");
sd.getDifferential().addElement().setPath("Extension.extension").setSliceName(s);
sd.getDifferential().addElement().setPath("Extension.extension.extension").setMax("0");
sd.getDifferential().addElement().setPath("Extension.extension.url").setFixed(new UriType(s));
ElementDefinition val = sd.getDifferential().addElement().setPath("Extension.extension.value[x]").setMin(1);
JsonObject elt = root.getAsJsonObject(e+"."+s);
if (!elt.has("types")) {
throw new FHIRException("Internal error - nested elements not supported yet");
}
populateTypes(elt, val, verSource, verTarget);
}
}
sd.getDifferential().addElement().setPath("Extension.url").setFixed(new UriType(url));
sd.getDifferential().addElement().setPath("Extension.value[x]").setMax("0");

37
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/context/SimpleWorkerContextTests.java
View File

@ -1,13 +1,31 @@
package org.hl7.fhir.r5.context;
import org.hl7.fhir.r5.model.*;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.ArgumentMatchers.anyBoolean;
import static org.mockito.ArgumentMatchers.argThat;
import static org.mockito.ArgumentMatchers.eq;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.times;
import java.io.IOException;
import java.util.Arrays;
import java.util.HashMap;
import java.util.Map;
import org.hl7.fhir.r5.model.CapabilityStatement;
import org.hl7.fhir.r5.model.CodeableConcept;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.Enumerations;
import org.hl7.fhir.r5.model.Parameters;
import org.hl7.fhir.r5.model.TerminologyCapabilities;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.terminologies.TerminologyClient;
import org.hl7.fhir.r5.terminologies.ValueSetCheckerSimple;
import org.hl7.fhir.r5.terminologies.ValueSetExpander;
import org.hl7.fhir.r5.terminologies.ValueSetExpanderSimple;
import org.hl7.fhir.r5.utils.validation.ValidationContextCarrier;
import org.hl7.fhir.utilities.ToolingClientLogger;
import org.hl7.fhir.utilities.graphql.Value;
import org.hl7.fhir.utilities.validation.ValidationOptions;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
@ -18,15 +36,6 @@ import org.mockito.Mockito;
import org.mockito.Spy;
import org.mockito.junit.jupiter.MockitoExtension;
import java.io.IOException;
import java.util.Arrays;
import java.util.HashMap;
import java.util.Map;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.mockito.ArgumentMatchers.*;
import static org.mockito.Mockito.*;
@ExtendWith(MockitoExtension.class)
public class SimpleWorkerContextTests {
@ -251,12 +260,13 @@ public class SimpleWorkerContextTests {
ValueSet vs = new ValueSet();
vs.setStatus(Enumerations.PublicationStatus.ACTIVE);
vs.setCompose(new ValueSet.ValueSetComposeComponent());
vs.getCompose().setInactive(true);
vs.getCompose().getInclude().add(inc);
Mockito.doReturn(cacheToken).when(terminologyCache).generateExpandToken(argThat(new ValueSetMatcher(vs)),eq(true));
Mockito.doReturn(expectedExpansionResult).when(terminologyCache).getExpansion(cacheToken);
ValueSetExpander.ValueSetExpansionOutcome actualExpansionResult = context.expandVS(inc, true);
ValueSetExpander.ValueSetExpansionOutcome actualExpansionResult = context.expandVS(inc, true, false);
assertEquals(expectedExpansionResult, actualExpansionResult);
@ -273,6 +283,7 @@ public class SimpleWorkerContextTests {
ValueSet vs = new ValueSet();
vs.setStatus(Enumerations.PublicationStatus.ACTIVE);
vs.setCompose(new ValueSet.ValueSetComposeComponent());
vs.getCompose().setInactive(true);
vs.getCompose().getInclude().add(inc);
Mockito.doReturn(cacheToken).when(terminologyCache).generateExpandToken(argThat(new ValueSetMatcher(vs)),eq(true));
@ -285,7 +296,7 @@ public class SimpleWorkerContextTests {
Mockito.doReturn(expectedValueSet).when(terminologyClient).expandValueset(argThat(new ValueSetMatcher(vs)),
argThat(new ParametersMatcher(pInWithDependentResources)), eq(params));
ValueSetExpander.ValueSetExpansionOutcome actualExpansionResult = context.expandVS(inc, true);
ValueSetExpander.ValueSetExpansionOutcome actualExpansionResult = context.expandVS(inc, true, false);
assertEquals(expectedValueSet, actualExpansionResult.getValueset());

32
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/context/TerminologyCacheTests.java
View File

@ -1,15 +1,9 @@
package org.hl7.fhir.r5.context;
import com.google.gson.JsonElement;
import com.google.gson.JsonParser;
import org.hl7.fhir.r5.formats.IParser;
import org.hl7.fhir.r5.model.*;
import org.hl7.fhir.r5.terminologies.ValueSetExpander;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.Arguments;
import org.junit.jupiter.params.provider.MethodSource;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNull;
import static org.junit.jupiter.api.Assertions.assertTrue;
import java.io.File;
import java.io.IOException;
@ -25,8 +19,22 @@ import java.util.stream.Collectors;
import java.util.stream.IntStream;
import java.util.stream.Stream;
import static org.junit.jupiter.api.Assertions.*;
import static org.mockito.Mockito.mock;
import org.hl7.fhir.r5.formats.IParser;
import org.hl7.fhir.r5.model.CanonicalResource;
import org.hl7.fhir.r5.model.CapabilityStatement;
import org.hl7.fhir.r5.model.CodeableConcept;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.TerminologyCapabilities;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.terminologies.ValueSetExpander;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.Arguments;
import org.junit.jupiter.params.provider.MethodSource;
import com.google.gson.JsonElement;
import com.google.gson.JsonParser;
public class TerminologyCacheTests {

46
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/context/TestPackageLoader.java Normal file
View File

@ -0,0 +1,46 @@
package org.hl7.fhir.r5.context;
import java.io.IOException;
import java.io.InputStream;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.context.IWorkerContext.IContextResourceLoader;
import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.formats.XmlParser;
import org.hl7.fhir.r5.model.Bundle;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.utilities.npm.NpmPackage;
public class TestPackageLoader implements IContextResourceLoader {
private String[] types;
public TestPackageLoader(String[] types) {
this.types = types;
}
@Override
public Bundle loadBundle(InputStream stream, boolean isJson) throws FHIRException, IOException {
return null;
}
@Override
public Resource loadResource(InputStream stream, boolean isJson) throws FHIRException, IOException {
return isJson ? new JsonParser().parse(stream) : new XmlParser().parse(stream);
}
@Override
public String[] getTypes() {
return types;
}
@Override
public String getResourcePath(Resource resource) {
return null;
}
@Override
public IContextResourceLoader getNewLoader(NpmPackage npm) {
return this;
}
}

11
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/formats/FormatUtilitiesTest.java
View File

@ -1,14 +1,11 @@
package org.hl7.fhir.r5.formats;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.Arguments;
import org.junit.jupiter.params.provider.MethodSource;
import java.util.stream.Stream;
import static org.junit.jupiter.api.Assertions.*;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.Arguments;
import org.junit.jupiter.params.provider.MethodSource;
class FormatUtilitiesTest {

1
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/model/Base64BinaryTypeNullTest.java
View File

@ -1,6 +1,5 @@
package org.hl7.fhir.r5.model;
import org.hl7.fhir.r5.model.Base64BinaryType;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;

1
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/model/BooleanTypeNullTest.java
View File

@ -1,6 +1,5 @@
package org.hl7.fhir.r5.model;
import org.hl7.fhir.r5.model.BooleanType;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;

1
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/model/CanonicalTypeNullTest.java
View File

@ -1,6 +1,5 @@
package org.hl7.fhir.r5.model;
import org.hl7.fhir.r5.model.CanonicalType;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;

1
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/model/CodeTypeNullTest.java
View File

@ -1,6 +1,5 @@
package org.hl7.fhir.r5.model;
import org.hl7.fhir.r5.model.CodeType;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;

1
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/model/DateTimeTypeNullTest.java
View File

@ -1,6 +1,5 @@
package org.hl7.fhir.r5.model;
import org.hl7.fhir.r5.model.DateTimeType;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;

1
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/model/DateTypeNullTest.java
View File

@ -1,6 +1,5 @@
package org.hl7.fhir.r5.model;
import org.hl7.fhir.r5.model.DateType;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;

1
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/model/DecimalTypeNullTest.java
View File

@ -1,6 +1,5 @@
package org.hl7.fhir.r5.model;
import org.hl7.fhir.r5.model.DecimalType;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;

1
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/model/IdTypeNullTest.java
View File

@ -1,6 +1,5 @@
package org.hl7.fhir.r5.model;
import org.hl7.fhir.r5.model.IdType;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;

1
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/model/InstantTypeNullTest.java
View File

@ -1,6 +1,5 @@
package org.hl7.fhir.r5.model;
import org.hl7.fhir.r5.model.InstantType;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;

1
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/model/IntegerTypeNullTest.java
View File

@ -1,6 +1,5 @@
package org.hl7.fhir.r5.model;
import org.hl7.fhir.r5.model.IntegerType;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;

1
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/model/MarkdownTypeNullTest.java
View File

@ -1,6 +1,5 @@
package org.hl7.fhir.r5.model;
import org.hl7.fhir.r5.model.MarkdownType;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;

1
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/model/OidTypeNullTest.java
View File

@ -1,6 +1,5 @@
package org.hl7.fhir.r5.model;
import org.hl7.fhir.r5.model.OidType;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;

1
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/model/PositiveIntTypeNullTest.java
View File

@ -1,6 +1,5 @@
package org.hl7.fhir.r5.model;
import org.hl7.fhir.r5.model.PositiveIntType;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;

1
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/model/StringTypeNullTest.java
View File

@ -1,6 +1,5 @@
package org.hl7.fhir.r5.model;
import org.hl7.fhir.r5.model.StringType;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;

1
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/model/TimeTypeNullTest.java
View File

@ -1,6 +1,5 @@
package org.hl7.fhir.r5.model;
import org.hl7.fhir.r5.model.TimeType;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;

1
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/model/UnsignedIntTypeNullTest.java
View File

@ -1,6 +1,5 @@
package org.hl7.fhir.r5.model;
import org.hl7.fhir.r5.model.UnsignedIntType;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;

1
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/model/UriTypeNullTest.java
View File

@ -1,6 +1,5 @@
package org.hl7.fhir.r5.model;
import org.hl7.fhir.r5.model.UriType;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;

1
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/model/UrlTypeNullTest.java
View File

@ -1,6 +1,5 @@
package org.hl7.fhir.r5.model;
import org.hl7.fhir.r5.model.UrlType;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;

1
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/model/UuidTypeNullTest.java
View File

@ -1,6 +1,5 @@
package org.hl7.fhir.r5.model;
import org.hl7.fhir.r5.model.UuidType;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;

2
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/CDARoundTripTests.java
View File

@ -257,7 +257,7 @@ public class CDARoundTripTests {
value.setValue("öé");
ByteArrayOutputStream baosXml = new ByteArrayOutputStream();
Manager.compose(TestingUtilities.context(), xml, baosXml, FhirFormat.XML, OutputStyle.PRETTY, null);
Manager.compose(TestingUtilities.getSharedWorkerContext(), xml, baosXml, FhirFormat.XML, OutputStyle.PRETTY, null);
String cdaSerialised = baosXml.toString("UTF-8");
Assertions.assertTrue(cdaSerialised.indexOf("öé") > 0);
}

5
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/FHIRPathTests.java
View File

@ -25,7 +25,6 @@ import org.hl7.fhir.r5.model.Quantity;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.TypeDetails;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.test.FHIRPathTests.TestResultType;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.r5.utils.FHIRPathEngine;
import org.hl7.fhir.r5.utils.FHIRPathEngine.IEvaluationContext;
@ -94,7 +93,7 @@ public class FHIRPathTests {
@Override
public ValueSet resolveValueSet(Object appContext, String url) {
return TestingUtilities.context().fetchResource(ValueSet.class, url);
return TestingUtilities.getSharedWorkerContext().fetchResource(ValueSet.class, url);
}
}
@ -104,7 +103,7 @@ public class FHIRPathTests {
@BeforeAll
public static void setUp() {
fp = new FHIRPathEngine(TestingUtilities.context());
fp = new FHIRPathEngine(TestingUtilities.getSharedWorkerContext());
}
public static Stream<Arguments> data() throws ParserConfigurationException, SAXException, IOException {

2
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/GraphQLEngineTests.java
View File

@ -65,7 +65,7 @@ public class GraphQLEngineTests implements IGraphQLStorageServices {
stream = TestingUtilities.loadTestResourceStream("r5", parts[0].toLowerCase()+"-"+parts[1].toLowerCase()+".xml");
}
GraphQLEngine gql = new GraphQLEngine(TestingUtilities.context());
GraphQLEngine gql = new GraphQLEngine(TestingUtilities.getSharedWorkerContext());
gql.setServices(this);
if (stream != null)
gql.setFocus(new XmlParser().parse(stream));

2
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/LiquidEngineTests.java
View File

@ -37,7 +37,7 @@ public class LiquidEngineTests implements ILiquidEngineIncludeResolver {
@BeforeEach
public void setUp() throws Exception {
engine = new LiquidEngine(TestingUtilities.context(), null);
engine = new LiquidEngine(TestingUtilities.getSharedWorkerContext(), null);
engine.setIncludeResolver(this);
}

18
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/NarrativeGenerationTests.java
View File

@ -1,51 +1,35 @@
package org.hl7.fhir.r5.test;
import java.io.BufferedReader;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.IOException;
import java.time.ZoneId;
import java.time.format.DateTimeFormatter;
import java.util.ArrayList;
import java.util.List;
import java.util.stream.Stream;
import javax.xml.parsers.ParserConfigurationException;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.SystemUtils;
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.Manager;
import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.formats.XmlParser;
import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.DomainResource;
import org.hl7.fhir.r5.model.Questionnaire;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.renderers.RendererFactory;
import org.hl7.fhir.r5.renderers.ResourceRenderer;
import org.hl7.fhir.r5.renderers.utils.ElementWrappers;
import org.hl7.fhir.r5.renderers.utils.RenderingContext;
import org.hl7.fhir.r5.renderers.utils.RenderingContext.ITypeParser;
import org.hl7.fhir.r5.renderers.utils.RenderingContext.QuestionnaireRendererMode;
import org.hl7.fhir.r5.renderers.utils.RenderingContext.ResourceRendererMode;
import org.hl7.fhir.r5.test.NarrativeGenerationTests.TestTypeParser;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.utilities.TerminologyServiceOptions;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.xhtml.XhtmlComposer;
import org.hl7.fhir.utilities.xhtml.XhtmlNode;
import org.hl7.fhir.utilities.xhtml.XhtmlParser;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.Arguments;
import org.junit.jupiter.params.provider.MethodSource;
@ -119,7 +103,7 @@ public class NarrativeGenerationTests {
@BeforeAll
public static void setUp() {
context = TestingUtilities.context();
context = TestingUtilities.getSharedWorkerContext();
}
@ParameterizedTest(name = "{index}: file {0}")

6
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/NarrativeGeneratorTests.java
View File

@ -5,11 +5,7 @@ import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.time.ZoneId;
import java.time.ZonedDateTime;
import java.time.format.DateTimeFormatter;
import java.time.format.FormatStyle;
import java.util.Locale;
import java.util.TimeZone;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
@ -38,7 +34,7 @@ public class NarrativeGeneratorTests {
@BeforeAll
public static void setUp() throws FHIRException {
rc = new RenderingContext(TestingUtilities.context(), null, null, "http://hl7.org/fhir", "", null, ResourceRendererMode.END_USER);
rc = new RenderingContext(TestingUtilities.getSharedWorkerContext(), null, null, "http://hl7.org/fhir", "", null, ResourceRendererMode.END_USER);
}
@Test

2
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/OpenApiGeneratorTest.java
View File

@ -32,7 +32,7 @@ public class OpenApiGeneratorTest {
public void run(InputStream sfn, String dfn) throws IOException, FHIRFormatError, FileNotFoundException {
CapabilityStatement cs = (CapabilityStatement) new JsonParser().parse(sfn);
Writer oa = new Writer(new FileOutputStream(dfn));
OpenApiGenerator gen = new OpenApiGenerator(TestingUtilities.context(), cs, oa);
OpenApiGenerator gen = new OpenApiGenerator(TestingUtilities.getSharedWorkerContext(), cs, oa);
gen.generate("test-lic", "http://spdx.org/licenses/test-lic.html");
oa.commit();
}

57
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/ProfileUtilitiesTests.java
View File

@ -1,9 +1,13 @@
package org.hl7.fhir.r5.test;
import java.util.ArrayList;
import java.util.List;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.ElementDefinition;
import org.hl7.fhir.r5.model.ElementDefinition.ElementDefinitionConstraintComponent;
import org.hl7.fhir.r5.model.IntegerType;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.model.StructureDefinition.TypeDerivationRule;
@ -13,9 +17,6 @@ import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
import java.util.ArrayList;
import java.util.List;
public class ProfileUtilitiesTests {
// /**
@ -29,13 +30,13 @@ public class ProfileUtilitiesTests {
public void testSimple() throws FHIRException {
StructureDefinition focus = new StructureDefinition();
StructureDefinition base = TestingUtilities.context().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Patient").copy();
StructureDefinition base = TestingUtilities.getSharedWorkerContext().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Patient").copy();
focus.setUrl(Utilities.makeUuidUrn());
focus.setBaseDefinition(base.getUrl());
focus.setType("Patient");
focus.setDerivation(TypeDerivationRule.CONSTRAINT);
List<ValidationMessage> messages = new ArrayList<>();
new ProfileUtilities(TestingUtilities.context(), messages, null).generateSnapshot(base, focus, focus.getUrl(), "http://test.org/test", "Simple Test");
new ProfileUtilities(TestingUtilities.getSharedWorkerContext(), messages, null).generateSnapshot(base, focus, focus.getUrl(), "http://test.org/test", "Simple Test");
boolean ok = base.getSnapshot().getElement().size() == focus.getSnapshot().getElement().size();
for (int i = 0; i < base.getSnapshot().getElement().size(); i++) {
@ -51,6 +52,12 @@ public class ProfileUtilitiesTests {
f.setBase(null);
b.setRequirements(null);
f.setRequirements(null);
for (ElementDefinitionConstraintComponent c : b.getConstraint()) {
c.setSource(null);
}
for (ElementDefinitionConstraintComponent c : f.getConstraint()) {
c.setSource(null);
}
ok = Base.compareDeep(b, f, true);
}
}
@ -70,19 +77,25 @@ public class ProfileUtilitiesTests {
// */
@Test
public void testSimple2() {
StructureDefinition base = TestingUtilities.context().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/ValueSet").copy();
StructureDefinition base = TestingUtilities.getSharedWorkerContext().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/ValueSet").copy();
StructureDefinition focus = base.copy();
focus.setUrl(Utilities.makeUuidUrn());
focus.setSnapshot(null);
focus.setDifferential(null);
List<ValidationMessage> messages = new ArrayList<>();
new ProfileUtilities(TestingUtilities.context(), messages, null).generateSnapshot(base, focus, focus.getUrl(), "http://test.org", "Simple Test");
new ProfileUtilities(TestingUtilities.getSharedWorkerContext(), messages, null).generateSnapshot(base, focus, focus.getUrl(), "http://test.org", "Simple Test");
boolean ok = base.getSnapshot().getElement().size() == focus.getSnapshot().getElement().size();
for (int i = 0; i < base.getSnapshot().getElement().size(); i++) {
if (ok) {
ElementDefinition b = base.getSnapshot().getElement().get(i);
ElementDefinition f = focus.getSnapshot().getElement().get(i);
for (ElementDefinitionConstraintComponent c : b.getConstraint()) {
c.setSource(null);
}
for (ElementDefinitionConstraintComponent c : f.getConstraint()) {
c.setSource(null);
}
if (!f.hasBase() || !b.getPath().equals(f.getPath()))
ok = false;
else {
@ -110,7 +123,7 @@ public class ProfileUtilitiesTests {
@Test
void testCardinalityChange() {
StructureDefinition focus = new StructureDefinition();
StructureDefinition base = TestingUtilities.context().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Patient").copy();
StructureDefinition base = TestingUtilities.getSharedWorkerContext().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Patient").copy();
focus.setUrl(Utilities.makeUuidUrn());
focus.setBaseDefinition(base.getUrl());
focus.setType(base.getType());
@ -119,7 +132,7 @@ public class ProfileUtilitiesTests {
id.setPath("Patient.identifier");
id.setMin(1);
List<ValidationMessage> messages = new ArrayList<>();
new ProfileUtilities(TestingUtilities.context(), messages, null).generateSnapshot(base, focus, focus.getUrl(), "http://test.org", "Simple Test");
new ProfileUtilities(TestingUtilities.getSharedWorkerContext(), messages, null).generateSnapshot(base, focus, focus.getUrl(), "http://test.org", "Simple Test");
boolean ok = base.getSnapshot().getElement().size() == focus.getSnapshot().getElement().size();
for (int i = 0; i < base.getSnapshot().getElement().size(); i++) {
@ -128,6 +141,12 @@ public class ProfileUtilitiesTests {
ElementDefinition f = focus.getSnapshot().getElement().get(i);
b.setRequirements(null);
f.setRequirements(null);
for (ElementDefinitionConstraintComponent c : b.getConstraint()) {
c.setSource(null);
}
for (ElementDefinitionConstraintComponent c : f.getConstraint()) {
c.setSource(null);
}
if (!f.hasBase() || !b.getPath().equals(f.getPath())) {
ok = false;
}
@ -155,7 +174,7 @@ public class ProfileUtilitiesTests {
void testMinValueChange() {
// Given
StructureDefinition focus = new StructureDefinition();
StructureDefinition base = TestingUtilities.context().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Appointment").copy();
StructureDefinition base = TestingUtilities.getSharedWorkerContext().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Appointment").copy();
focus.setUrl(Utilities.makeUuidUrn());
focus.setBaseDefinition(base.getUrl());
focus.setType(base.getType());
@ -165,7 +184,7 @@ public class ProfileUtilitiesTests {
id.setMinValue(new IntegerType(1));
List<ValidationMessage> messages = new ArrayList<>();
// When
new ProfileUtilities(TestingUtilities.context(), messages, null).generateSnapshot(base, focus, focus.getUrl(), "http://test.org", "Simple Test");
new ProfileUtilities(TestingUtilities.getSharedWorkerContext(), messages, null).generateSnapshot(base, focus, focus.getUrl(), "http://test.org", "Simple Test");
// Then
boolean ok = base.getSnapshot().getElement().size() == focus.getSnapshot().getElement().size();
for (int i = 0; i < base.getSnapshot().getElement().size(); i++) {
@ -174,6 +193,12 @@ public class ProfileUtilitiesTests {
ElementDefinition f = focus.getSnapshot().getElement().get(i);
b.setRequirements(null);
f.setRequirements(null);
for (ElementDefinitionConstraintComponent c : b.getConstraint()) {
c.setSource(null);
}
for (ElementDefinitionConstraintComponent c : f.getConstraint()) {
c.setSource(null);
}
if (!f.hasBase() || !b.getPath().equals(f.getPath())) {
ok = false;
}
@ -202,7 +227,7 @@ public class ProfileUtilitiesTests {
void testMaxValueChange() {
// Given
StructureDefinition focus = new StructureDefinition();
StructureDefinition base = TestingUtilities.context().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Appointment").copy();
StructureDefinition base = TestingUtilities.getSharedWorkerContext().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Appointment").copy();
focus.setUrl(Utilities.makeUuidUrn());
focus.setBaseDefinition(base.getUrl());
focus.setType(base.getType());
@ -212,7 +237,7 @@ public class ProfileUtilitiesTests {
id.setMaxValue(new IntegerType(1));
List<ValidationMessage> messages = new ArrayList<>();
// When
new ProfileUtilities(TestingUtilities.context(), messages, null).generateSnapshot(base, focus, focus.getUrl(), "http://test.org", "Simple Test");
new ProfileUtilities(TestingUtilities.getSharedWorkerContext(), messages, null).generateSnapshot(base, focus, focus.getUrl(), "http://test.org", "Simple Test");
// Then
boolean ok = base.getSnapshot().getElement().size() == focus.getSnapshot().getElement().size();
for (int i = 0; i < base.getSnapshot().getElement().size(); i++) {
@ -221,6 +246,12 @@ public class ProfileUtilitiesTests {
ElementDefinition f = focus.getSnapshot().getElement().get(i);
b.setRequirements(null);
f.setRequirements(null);
for (ElementDefinitionConstraintComponent c : b.getConstraint()) {
c.setSource(null);
}
for (ElementDefinitionConstraintComponent c : f.getConstraint()) {
c.setSource(null);
}
if (!f.hasBase() || !b.getPath().equals(f.getPath())) {
ok = false;
}

4
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/ResourceCopyTests.java
View File

@ -1,5 +1,7 @@
package org.hl7.fhir.r5.test;
import java.io.IOException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.model.Enumerations;
import org.hl7.fhir.r5.model.Extension;
@ -7,8 +9,6 @@ import org.hl7.fhir.r5.model.Observation;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
import java.io.IOException;
public class ResourceCopyTests {

8
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/ResourceRoundTripTests.java
View File

@ -19,7 +19,6 @@ import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.formats.XmlParser;
import org.hl7.fhir.r5.model.Bundle;
import org.hl7.fhir.r5.model.DateTimeType;
import org.hl7.fhir.r5.model.DomainResource;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.renderers.RendererFactory;
@ -27,7 +26,6 @@ import org.hl7.fhir.r5.renderers.utils.RenderingContext;
import org.hl7.fhir.r5.renderers.utils.RenderingContext.ResourceRendererMode;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.r5.utils.EOperationOutcome;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
public class ResourceRoundTripTests {
@ -35,7 +33,7 @@ public class ResourceRoundTripTests {
@Test
public void test() throws IOException, FHIRException, EOperationOutcome {
DomainResource res = (DomainResource) new XmlParser().parse(TestingUtilities.loadTestResourceStream("r5", "unicode.xml"));
RenderingContext rc = new RenderingContext(TestingUtilities.context(), null, null, "http://hl7.org/fhir", "", null, ResourceRendererMode.END_USER);
RenderingContext rc = new RenderingContext(TestingUtilities.getSharedWorkerContext(), null, null, "http://hl7.org/fhir", "", null, ResourceRendererMode.END_USER);
RendererFactory.factory(res, rc).render(res);
IOUtils.copy(TestingUtilities.loadTestResourceStream("r5", "unicode.xml"), new FileOutputStream(TestingUtilities.tempFile("gen", "unicode.xml")));
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(TestingUtilities.tempFile("gen", "unicode.out.xml")), res);
@ -66,7 +64,7 @@ public class ResourceRoundTripTests {
* verify that umlaut like äö etc are not encoded in UTF-8 in attributes
*/
public void testSerializeUmlaut() throws IOException {
Element xml = Manager.parseSingle(TestingUtilities.context(), TestingUtilities.loadTestResourceStream("r5", "unicode.xml"),
Element xml = Manager.parseSingle(TestingUtilities.getSharedWorkerContext(), TestingUtilities.loadTestResourceStream("r5", "unicode.xml"),
FhirFormat.XML);
List<Element> concept = xml.getChildrenByName("concept");
assertTrue(concept!=null && concept.size()==1);
@ -74,7 +72,7 @@ public class ResourceRoundTripTests {
assertTrue(code!=null && code.size()==1);
code.get(0).setValue("ö");
ByteArrayOutputStream baosXml = new ByteArrayOutputStream();
Manager.compose(TestingUtilities.context(), xml, baosXml, FhirFormat.XML, OutputStyle.PRETTY, null);
Manager.compose(TestingUtilities.getSharedWorkerContext(), xml, baosXml, FhirFormat.XML, OutputStyle.PRETTY, null);
String cdaSerialised = baosXml.toString("UTF-8");
assertTrue(cdaSerialised.indexOf("ö")>0);
}

4
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/ResourceTests.java
View File

@ -1,6 +1,8 @@
package org.hl7.fhir.r5.test;
import static org.junit.jupiter.api.Assertions.*;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertTrue;
import java.io.IOException;

4
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/ShexGeneratorTests.java
View File

@ -18,12 +18,12 @@ import org.junit.jupiter.api.Test;
public class ShexGeneratorTests {
private void doTest(String name) throws FileNotFoundException, IOException, FHIRException, UcumException {
StructureDefinition sd = TestingUtilities.context().fetchResource(StructureDefinition.class, ProfileUtilities.sdNs(name, null));
StructureDefinition sd = TestingUtilities.getSharedWorkerContext().fetchResource(StructureDefinition.class, ProfileUtilities.sdNs(name, null));
if (sd == null) {
throw new FHIRException("StructuredDefinition for " + name + "was null");
}
Path outPath = FileSystems.getDefault().getPath(System.getProperty("java.io.tmpdir"), name.toLowerCase() + ".shex");
TextFile.stringToFile(new ShExGenerator(TestingUtilities.context()).generate(HTMLLinkPolicy.NONE, sd), outPath.toString());
TextFile.stringToFile(new ShExGenerator(TestingUtilities.getSharedWorkerContext()).generate(HTMLLinkPolicy.NONE, sd), outPath.toString());
}
@Test

95
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/SnapShotGenerationTests.java
View File

@ -4,7 +4,6 @@ import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.List;
import java.util.stream.Stream;
@ -19,28 +18,27 @@ import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.exceptions.PathEngineException;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.conformance.ProfileUtilities.ProfileKnowledgeProvider;
import org.hl7.fhir.r5.context.IWorkerContext.IContextResourceLoader;
import org.hl7.fhir.r5.context.TestPackageLoader;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.formats.XmlParser;
import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.Bundle;
import org.hl7.fhir.r5.model.ElementDefinition.ElementDefinitionBindingComponent;
import org.hl7.fhir.r5.model.ExpressionNode.CollectionStatus;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionKind;
import org.hl7.fhir.r5.model.StructureDefinition.TypeDerivationRule;
import org.hl7.fhir.r5.model.TypeDetails;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.renderers.RendererFactory;
import org.hl7.fhir.r5.renderers.utils.RenderingContext;
import org.hl7.fhir.r5.renderers.utils.RenderingContext.ResourceRendererMode;
import org.hl7.fhir.r5.model.TypeDetails;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.r5.utils.FHIRPathEngine;
import org.hl7.fhir.r5.utils.FHIRPathEngine.IEvaluationContext;
import org.hl7.fhir.r5.utils.validation.IResourceValidator;
import org.hl7.fhir.r5.utils.XVerExtensionManager;
import org.hl7.fhir.r5.utils.validation.IResourceValidator;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.npm.CommonPackages;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
@ -60,41 +58,6 @@ import org.xml.sax.SAXException;
public class SnapShotGenerationTests {
public class TestLoader implements IContextResourceLoader {
private String[] types;
public TestLoader(String[] types) {
this.types = types;
}
@Override
public Bundle loadBundle(InputStream stream, boolean isJson) throws FHIRException, IOException {
return null;
}
@Override
public Resource loadResource(InputStream stream, boolean isJson) throws FHIRException, IOException {
return null;
}
@Override
public String[] getTypes() {
return types;
}
@Override
public String getResourcePath(Resource resource) {
return null;
}
@Override
public IContextResourceLoader getNewLoader(NpmPackage npm) {
return this;
}
}
public enum TestFetchMode {
INPUT,
OUTPUT,
@ -248,13 +211,13 @@ public class SnapShotGenerationTests {
@Override
public boolean isDatatype(String name) {
StructureDefinition sd = TestingUtilities.context().fetchTypeDefinition(name);
StructureDefinition sd = TestingUtilities.getSharedWorkerContext().fetchTypeDefinition(name);
return (sd != null) && (sd.getDerivation() == TypeDerivationRule.SPECIALIZATION) && (sd.getKind() == StructureDefinitionKind.PRIMITIVETYPE || sd.getKind() == StructureDefinitionKind.COMPLEXTYPE);
}
@Override
public boolean isResource(String typeSimple) {
StructureDefinition sd = TestingUtilities.context().fetchTypeDefinition(typeSimple);
StructureDefinition sd = TestingUtilities.getSharedWorkerContext().fetchTypeDefinition(typeSimple);
return (sd != null) && (sd.getDerivation() == TypeDerivationRule.SPECIALIZATION) && (sd.getKind() == StructureDefinitionKind.RESOURCE);
}
@ -286,7 +249,7 @@ public class SnapShotGenerationTests {
@Override
public String getLinkForProfile(StructureDefinition profile, String url) {
StructureDefinition sd = TestingUtilities.context().fetchResource(StructureDefinition.class, url);
StructureDefinition sd = TestingUtilities.getSharedWorkerContext().fetchResource(StructureDefinition.class, url);
if (sd == null)
return url + "|" + url;
else
@ -312,15 +275,15 @@ public class SnapShotGenerationTests {
public Resource fetchFixture(String id) {
TestFetchMode mode = TestFetchMode.INPUT;
if (id.equals("patient"))
return TestingUtilities.context().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Patient");
return TestingUtilities.getSharedWorkerContext().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Patient");
if (id.equals("valueset"))
return TestingUtilities.context().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/ValueSet");
return TestingUtilities.getSharedWorkerContext().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/ValueSet");
if (id.equals("organization"))
return TestingUtilities.context().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Organization");
return TestingUtilities.getSharedWorkerContext().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Organization");
if (id.equals("operationoutcome"))
return TestingUtilities.context().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/OperationOutcome");
return TestingUtilities.getSharedWorkerContext().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/OperationOutcome");
if (id.equals("parameters"))
return TestingUtilities.context().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Parameters");
return TestingUtilities.getSharedWorkerContext().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Parameters");
if (id.contains("-")) {
String[] p = id.split("\\-");
@ -376,7 +339,7 @@ public class SnapShotGenerationTests {
@Override
public TypeDetails checkFunction(Object appContext, String functionName, List<TypeDetails> parameters) throws PathEngineException {
if ("fixture".equals(functionName))
return new TypeDetails(CollectionStatus.SINGLETON, TestingUtilities.context().getResourceNamesAsSet());
return new TypeDetails(CollectionStatus.SINGLETON, TestingUtilities.getSharedWorkerContext().getResourceNamesAsSet());
return null;
}
@ -403,7 +366,7 @@ public class SnapShotGenerationTests {
@Override
public boolean conformsToProfile(Object appContext, Base item, String url) throws FHIRException {
IResourceValidator val = TestingUtilities.context().newValidator();
IResourceValidator val = TestingUtilities.getSharedWorkerContext().newValidator();
List<ValidationMessage> valerrors = new ArrayList<ValidationMessage>();
if (item instanceof Resource) {
val.validate(appContext, valerrors, (Resource) item, url);
@ -441,7 +404,7 @@ public class SnapShotGenerationTests {
@BeforeAll
public static void setUp() {
fp = new FHIRPathEngine(TestingUtilities.context());
fp = new FHIRPathEngine(TestingUtilities.getSharedWorkerContext());
}
public static Stream<Arguments> data() throws ParserConfigurationException, IOException, FHIRFormatError, SAXException {
@ -499,7 +462,7 @@ public class SnapShotGenerationTests {
private void testSort(TestDetails test, SnapShotGenerationTestsContext context) throws DefinitionException, FHIRException, IOException {
StructureDefinition base = getSD(test.getSource().getBaseDefinition(), context);
test.setOutput(test.getSource().copy());
ProfileUtilities pu = new ProfileUtilities(TestingUtilities.context(), null, null);
ProfileUtilities pu = new ProfileUtilities(TestingUtilities.getSharedWorkerContext(), null, null);
pu.setIds(test.getSource(), false);
List<String> errors = new ArrayList<String>();
pu.sortDifferential(base, test.getOutput(), test.getOutput().getUrl(), errors, false);
@ -513,17 +476,17 @@ public class SnapShotGenerationTests {
private void testGen(boolean fail, TestDetails test, SnapShotGenerationTestsContext context) throws Exception {
if (!Utilities.noString(test.register)) {
List<ValidationMessage> messages = new ArrayList<ValidationMessage>();
ProfileUtilities pu = new ProfileUtilities(TestingUtilities.context(), messages, null);
ProfileUtilities pu = new ProfileUtilities(TestingUtilities.getSharedWorkerContext(), messages, null);
pu.setNewSlicingProcessing(true);
for (StructureDefinition sd : test.included) {
pu.setIds(sd, false);
}
for (StructureDefinition sd : test.included) {
if (!TestingUtilities.context().hasResource(StructureDefinition.class, sd.getUrl())) {
TestingUtilities.context().cacheResource(sd);
if (!TestingUtilities.getSharedWorkerContext().hasResource(StructureDefinition.class, sd.getUrl())) {
TestingUtilities.getSharedWorkerContext().cacheResource(sd);
}
}
StructureDefinition base = TestingUtilities.context().fetchResource(StructureDefinition.class, test.included.get(0).getBaseDefinition());
StructureDefinition base = TestingUtilities.getSharedWorkerContext().fetchResource(StructureDefinition.class, test.included.get(0).getBaseDefinition());
if (base != null) {
pu.generateSnapshot(base, test.included.get(0), test.included.get(0).getUrl(), "http://test.org/profile", test.included.get(0).getName());
}
@ -542,16 +505,16 @@ public class SnapShotGenerationTests {
throw new Exception("URL mismatch on base: " + base.getUrl() + " wanting " + test.getSource().getBaseDefinition());
StructureDefinition output = test.getSource().copy();
ProfileUtilities pu = new ProfileUtilities(TestingUtilities.context(), messages, new TestPKP());
ProfileUtilities pu = new ProfileUtilities(TestingUtilities.getSharedWorkerContext(), messages, new TestPKP());
pu.setNewSlicingProcessing(test.isNewSliceProcessing());
pu.setThrowException(false);
pu.setDebug(test.isDebug());
pu.setIds(test.getSource(), false);
if (!TestingUtilities.context().hasPackage(CommonPackages.ID_XVER, CommonPackages.VER_XVER)) {
if (!TestingUtilities.getSharedWorkerContext().hasPackage(CommonPackages.ID_XVER, CommonPackages.VER_XVER)) {
NpmPackage npm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION).loadPackage(CommonPackages.ID_XVER, CommonPackages.VER_XVER);
TestingUtilities.context().loadFromPackage(npm, new TestLoader(new String[]{"StructureDefinition"}), new String[]{"StructureDefinition"});
TestingUtilities.getSharedWorkerContext().loadFromPackage(npm, new TestPackageLoader(new String[]{"StructureDefinition"}), new String[]{"StructureDefinition"});
}
pu.setXver(new XVerExtensionManager(TestingUtilities.context()));
pu.setXver(new XVerExtensionManager(TestingUtilities.getSharedWorkerContext()));
if (test.isSort()) {
List<String> errors = new ArrayList<String>();
int lastCount = output.getDifferential().getElement().size();
@ -576,14 +539,14 @@ public class SnapShotGenerationTests {
throw e;
}
if (output.getDifferential().hasElement()) {
RenderingContext rc = new RenderingContext(TestingUtilities.context(), null, null, "http://hl7.org/fhir", "", null, ResourceRendererMode.END_USER);
RenderingContext rc = new RenderingContext(TestingUtilities.getSharedWorkerContext(), null, null, "http://hl7.org/fhir", "", null, ResourceRendererMode.END_USER);
rc.setDestDir(Utilities.path("[tmp]", "snapshot"));
rc.setProfileUtilities(new ProfileUtilities(TestingUtilities.context(), null, new TestPKP()));
rc.setProfileUtilities(new ProfileUtilities(TestingUtilities.getSharedWorkerContext(), null, new TestPKP()));
RendererFactory.factory(output, rc).render(output);
}
if (!fail) {
test.output = output;
TestingUtilities.context().cacheResource(output);
TestingUtilities.getSharedWorkerContext().cacheResource(output);
File dst = new File(TestingUtilities.tempFile("snapshot", test.getId() + "-expected.xml"));
if (dst.exists())
dst.delete();
@ -600,14 +563,14 @@ public class SnapShotGenerationTests {
private StructureDefinition getSD(String url, SnapShotGenerationTestsContext context) throws DefinitionException, FHIRException, IOException {
StructureDefinition sd = context.getByUrl(url);
if (sd == null) {
sd = TestingUtilities.context().fetchResource(StructureDefinition.class, url);
sd = TestingUtilities.getSharedWorkerContext().fetchResource(StructureDefinition.class, url);
}
if (sd == null) {
throw new DefinitionException("Unable to find profile "+url);
}
if (!sd.hasSnapshot()) {
StructureDefinition base = getSD(sd.getBaseDefinition(), context);
ProfileUtilities pu = new ProfileUtilities(TestingUtilities.context(), messages, new TestPKP());
ProfileUtilities pu = new ProfileUtilities(TestingUtilities.getSharedWorkerContext(), messages, new TestPKP());
pu.setNewSlicingProcessing(true);
List<String> errors = new ArrayList<String>();
pu.sortDifferential(base, sd, url, errors, false);

8
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/StructureMapUtilitiesTest.java
View File

@ -1,5 +1,8 @@
package org.hl7.fhir.r5.test;
import java.io.IOException;
import java.util.List;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.context.SimpleWorkerContext;
import org.hl7.fhir.r5.model.Base;
@ -7,17 +10,14 @@ import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.StructureMap;
import org.hl7.fhir.r5.model.StructureMap.StructureMapGroupRuleTargetComponent;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.r5.utils.structuremap.StructureMapUtilities;
import org.hl7.fhir.r5.utils.structuremap.ITransformerServices;
import org.hl7.fhir.r5.utils.structuremap.StructureMapUtilities;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.ToolsVersion;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import java.io.IOException;
import java.util.List;
public class StructureMapUtilitiesTest implements ITransformerServices {
static private SimpleWorkerContext context;

166
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/VocabTests.java Normal file
View File

@ -0,0 +1,166 @@
package org.hl7.fhir.r5.test;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.stream.Stream;
import javax.xml.parsers.ParserConfigurationException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.context.TestPackageLoader;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.formats.XmlParser;
import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.renderers.utils.RenderingContext.ITypeParser;
import org.hl7.fhir.r5.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.utilities.npm.ToolsVersion;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.Arguments;
import org.junit.jupiter.params.provider.MethodSource;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.xml.sax.SAXException;
public class VocabTests {
public enum TestType {
Expansion;
}
public class TestTypeParser implements ITypeParser {
@Override
public Base parseType(String xml, String type) throws FHIRFormatError, IOException, FHIRException {
return new org.hl7.fhir.r5.formats.XmlParser().parseType(xml, type);
}
}
private static IWorkerContext context;
public static class TestDetails {
private String id;
private Map<String, String> parameters = new HashMap<>();
private String source;
private String target;
private TestType type;
public TestDetails(Element test) {
super();
id = test.getAttribute("id");
source = XMLUtil.getNamedChildValue(test, "source");
target = XMLUtil.getNamedChildValue(test, "target");
type = TestType.Expansion;
}
public String getId() {
return id;
}
public Map<String, String> getParameters() {
return parameters;
}
public String getSource() {
return source;
}
public String getTarget() {
return target;
}
public TestType getType() {
return type;
}
}
public static Stream<Arguments> data() throws ParserConfigurationException, IOException, FHIRFormatError, SAXException {
Document tests = XMLUtil.parseToDom(TestingUtilities.loadTestResource("r5", "vocab", "manifest.xml"));
Element test = XMLUtil.getFirstChild(tests.getDocumentElement());
List<Arguments> objects = new ArrayList<>();
while (test != null && test.getNodeName().equals("test")) {
TestDetails t = new TestDetails(test);
objects.add(Arguments.of(t.getId(), t));
test = XMLUtil.getNextSibling(test);
}
return objects.stream();
}
@BeforeAll
public static void setUp() throws FHIRException, IOException {
/* Do NOT get a shared worker context from Testing Utilities or else the terminology package loaded below
will appear in tests where it causes failures.
*/
context = TestingUtilities.getWorkerContext(VersionUtilities.getMajMin(TestingUtilities.DEFAULT_CONTEXT_VERSION));
if (!context.hasPackage("hl7.terminology", null)) {
NpmPackage utg = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION).loadPackage("hl7.terminology");
System.out.println("Loading THO: "+utg.name()+"#"+utg.version());
context.loadFromPackage(utg, new TestPackageLoader(new String[]{"CodeSystem", "ValueSet"}));
}
}
@ParameterizedTest(name = "{index}: file {0}")
@MethodSource("data")
public void test(String id, TestDetails test) throws Exception {
Resource source;
if (test.getSource().endsWith(".json")) {
source = (Resource) new JsonParser().parse(TestingUtilities.loadTestResourceStream("r5", "vocab", test.getSource()));
} else {
source = (Resource) new XmlParser().parse(TestingUtilities.loadTestResourceStream("r5", "vocab", test.getSource()));
}
Resource target;
if (test.getTarget().endsWith(".json")) {
target = (Resource) new JsonParser().parse(TestingUtilities.loadTestResourceStream("r5", "vocab", test.getTarget()));
} else {
target = (Resource) new XmlParser().parse(TestingUtilities.loadTestResourceStream("r5", "vocab", test.getTarget()));
}
if (test.getType() == TestType.Expansion) {
testExpansion(test, (ValueSet) source, (ValueSet) target);
} else {
Assertions.fail("not done yet");
}
}
private void testExpansion(TestDetails test, ValueSet sourceVS, ValueSet targetVS) throws Exception {
ValueSetExpansionOutcome outcome = context.expandVS(sourceVS, false, test.getParameters().containsKey("hierarchical"));
if (outcome.isOk()) {
outcome.getValueset().getExpansion().setIdentifier(null);
outcome.getValueset().getExpansion().setTimestamp(null);
String target = new XmlParser().setOutputStyle(OutputStyle.PRETTY).composeString(targetVS);
String output = new XmlParser().setOutputStyle(OutputStyle.PRETTY).composeString(outcome.getValueset());
String tfn = TestingUtilities.tempFile("vocab", test.getId() + ".target.html");
String ofn = TestingUtilities.tempFile("vocab", test.getId() + ".output.html");
TextFile.stringToFile(target, tfn);
TextFile.stringToFile(output, ofn);
String msg = TestingUtilities.checkXMLIsSame(ofn, tfn);
Assertions.assertTrue(msg == null, "Output does not match expected: "+msg);
} else {
Assertions.fail("Expansion Failed: "+outcome.getError());
}
}
}

6
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/misc/ResourceTest.java
View File

@ -86,9 +86,9 @@ public class ResourceTest {
}
public Element testEM() throws Exception {
Element resource = Manager.parseSingle(TestingUtilities.context(), new FileInputStream(source), isJson() ? FhirFormat.JSON : FhirFormat.XML);
Manager.compose(TestingUtilities.context(), resource, new FileOutputStream(source.getAbsoluteFile()+".out.json"), FhirFormat.JSON, OutputStyle.PRETTY, null);
Manager.compose(TestingUtilities.context(), resource, new FileOutputStream(source.getAbsoluteFile()+".out.json"), FhirFormat.XML, OutputStyle.PRETTY, null);
Element resource = Manager.parseSingle(TestingUtilities.getSharedWorkerContext(), new FileInputStream(source), isJson() ? FhirFormat.JSON : FhirFormat.XML);
Manager.compose(TestingUtilities.getSharedWorkerContext(), resource, new FileOutputStream(source.getAbsoluteFile()+".out.json"), FhirFormat.JSON, OutputStyle.PRETTY, null);
Manager.compose(TestingUtilities.getSharedWorkerContext(), resource, new FileOutputStream(source.getAbsoluteFile()+".out.json"), FhirFormat.XML, OutputStyle.PRETTY, null);
return resource;
}

2
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/utils/FHIRLexerTest.java
View File

@ -4,8 +4,6 @@ import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;
import static org.junit.jupiter.api.Assertions.*;
class FHIRLexerTest {
@Test
@DisplayName("Test that a 'null' current value returns 'false' when FHIRLexer.isConstant() is called, and not NPE.")

29
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/utils/client/FHIRToolingClientTest.java
View File

@ -1,9 +1,22 @@
package org.hl7.fhir.r5.utils.client;
import okhttp3.Headers;
import okhttp3.Request;
import okhttp3.internal.http2.Header;
import org.hl7.fhir.r5.model.*;
import java.io.IOException;
import java.net.URI;
import java.net.URISyntaxException;
import java.util.ArrayList;
import java.util.Arrays;
import org.hl7.fhir.r5.model.Bundle;
import org.hl7.fhir.r5.model.CapabilityStatement;
import org.hl7.fhir.r5.model.Enumerations;
import org.hl7.fhir.r5.model.IdType;
import org.hl7.fhir.r5.model.Observation;
import org.hl7.fhir.r5.model.OperationOutcome;
import org.hl7.fhir.r5.model.Patient;
import org.hl7.fhir.r5.model.Quantity;
import org.hl7.fhir.r5.model.Reference;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.TerminologyCapabilities;
import org.hl7.fhir.r5.utils.client.network.Client;
import org.hl7.fhir.r5.utils.client.network.ResourceRequest;
import org.junit.jupiter.api.Assertions;
@ -13,11 +26,9 @@ import org.mockito.ArgumentCaptor;
import org.mockito.ArgumentMatchers;
import org.mockito.Mockito;
import java.io.IOException;
import java.net.URI;
import java.net.URISyntaxException;
import java.util.ArrayList;
import java.util.Arrays;
import okhttp3.Headers;
import okhttp3.Request;
import okhttp3.internal.http2.Header;
class FHIRToolingClientTest {

7
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/utils/client/network/ClientHeadersTest.java
View File

@ -1,14 +1,15 @@
package org.hl7.fhir.r5.utils.client.network;
import okhttp3.internal.http2.Header;
import java.util.Arrays;
import java.util.List;
import org.hl7.fhir.exceptions.FHIRException;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;
import java.util.Arrays;
import java.util.List;
import okhttp3.internal.http2.Header;
class ClientHeadersTest {

29
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/utils/client/network/ClientTest.java
View File

@ -1,21 +1,30 @@
package org.hl7.fhir.r5.utils.client.network;
import okhttp3.HttpUrl;
import okhttp3.mockwebserver.MockResponse;
import okhttp3.mockwebserver.MockWebServer;
import okhttp3.mockwebserver.RecordedRequest;
import org.hl7.fhir.r5.context.HTMLClientLogger;
import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.model.*;
import org.junit.jupiter.api.*;
import org.mockito.Mockito;
import java.io.IOException;
import java.net.URI;
import java.net.URISyntaxException;
import java.util.Random;
import java.util.concurrent.TimeUnit;
import org.hl7.fhir.r5.context.HTMLClientLogger;
import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.model.Address;
import org.hl7.fhir.r5.model.Enumerations;
import org.hl7.fhir.r5.model.HumanName;
import org.hl7.fhir.r5.model.Patient;
import org.hl7.fhir.r5.model.Resource;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.TestInstance;
import org.mockito.Mockito;
import okhttp3.HttpUrl;
import okhttp3.mockwebserver.MockResponse;
import okhttp3.mockwebserver.MockWebServer;
import okhttp3.mockwebserver.RecordedRequest;
@TestInstance(TestInstance.Lifecycle.PER_CLASS)
class ClientTest {

12
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/utils/client/network/FhirRequestBuilderTest.java
View File

@ -1,17 +1,15 @@
package org.hl7.fhir.r5.utils.client.network;
import okhttp3.Headers;
import okhttp3.OkHttpClient;
import okhttp3.Request;
import java.util.List;
import java.util.Map;
import org.hl7.fhir.r5.model.OperationOutcome;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;
import java.util.HashMap;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import okhttp3.Headers;
import okhttp3.Request;
class FhirRequestBuilderTest {

2
org.hl7.fhir.report/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.6.35</version>
<version>5.6.38-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.utilities/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.6.35</version>
<version>5.6.38-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/i18n/I18nConstants.java
View File

@ -366,6 +366,8 @@ public class I18nConstants {
public static final String SD_ED_TYPE_PROFILE_UNKNOWN = "SD_ED_TYPE_PROFILE_UNKNOWN";
public static final String SD_ED_TYPE_PROFILE_NOTYPE = "SD_ED_TYPE_PROFILE_NOTYPE";
public static final String SD_ED_TYPE_PROFILE_WRONG = "SD_ED_TYPE_PROFILE_WRONG";
public static final String SD_ED_TYPE_PROFILE_IS_MODIFIER = "SD_ED_TYPE_PROFILE_IS_MODIFIER";
public static final String SD_ED_TYPE_PROFILE_NOT_MODIFIER = "SD_ED_TYPE_PROFILE_NOT_MODIFIER";
public static final String SD_ED_TYPE_PROFILE_WRONG_TARGET = "SD_ED_TYPE_PROFILE_WRONG_TARGET";
public static final String SD_ED_TYPE_NO_TARGET_PROFILE = "SD_ED_TYPE_NO_TARGET_PROFILE";
public static final String SD_ED_SHOULD_BIND = "SD_ED_SHOULD_BIND";

2
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/CommonPackages.java
View File

@ -3,7 +3,7 @@ package org.hl7.fhir.utilities.npm;
public class CommonPackages {
public static final String ID_XVER = "hl7.fhir.xver-extensions";
public static final String VER_XVER = "0.0.8";
public static final String VER_XVER = "0.0.11";
public static final String ID_PUBPACK = "hl7.fhir.pubpack";
public static final String VER_PUBPACK = "0.0.9";

78
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/PackageClient.java
View File

@ -16,7 +16,6 @@ import java.io.ByteArrayInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
import java.net.URL;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Date;
@ -82,10 +81,10 @@ public class PackageClient {
if (versions != null) {
for (String v : sorted(versions.keySet())) {
JsonObject obj = versions.getAsJsonObject(v);
res.add(new PackageInfo(JSONUtil.str(obj, "name"),
JSONUtil.str(obj, "version"),
JSONUtil.str(obj, "FhirVersion"),
JSONUtil.str(obj, "description"),
res.add(new PackageInfo(JSONUtil.str(obj, "Name", "name"),
JSONUtil.str(obj, "Version", "version"),
JSONUtil.str(obj, "FhirVersion", "fhirVersion"),
JSONUtil.str(obj, "Description", "description"),
JSONUtil.str(obj, "url"),
JSONUtil.str(obj, "canonical"),
address));
@ -192,42 +191,51 @@ public class PackageClient {
}
}
protected PackageInfo getPackageInfoFromJSON(JsonObject o, String name, String canonical, String fhirVersion) {
String id = JSONUtil.str(o, "npm-name");
String pname = JSONUtil.str(o, "name");
String pcanonical = JSONUtil.str(o, "canonical");
String description = JSONUtil.str(o, "description");
boolean ok = true;
if (ok && !Utilities.noString(name)) {
ok = (pname != null && pname.contains(name)) || (description != null && description.contains(name)) || (id != null && id.contains(name));
}
if (ok && !Utilities.noString(canonical)) {
ok = pcanonical.contains(canonical);
}
String version = null;
String fVersion = null;
String url = null;
if (ok) {
// if we can find something...
for (JsonObject e : JSONUtil.objects(o, "editions")) {
if (fhirVersion == null || fhirVersion.equals(JSONUtil.str(e, "fhir-version"))) {
String v = JSONUtil.str(e, "ig-version");
if (version == null || VersionUtilities.isThisOrLater(version, v)) {
version = v;
fVersion = e.getAsJsonArray("fhir-version").get(0).getAsString();
url = JSONUtil.str(e, "url");
String npmPackage = JSONUtil.str(e, "package");
if (npmPackage != null && id == null) {
id = npmPackage.substring(0, npmPackage.indexOf("#"));
}
}
}
}
}
return new PackageInfo(id, version, fVersion, description, url, pcanonical, address);
}
public List<PackageInfo> listFromRegistry(String name, String canonical, String fhirVersion) throws IOException {
List<PackageInfo> result = new ArrayList<>();
JsonObject packages = JsonTrackingParser.fetchJson("https://raw.githubusercontent.com/FHIR/ig-registry/master/fhir-ig-list.json?nocache=" + System.currentTimeMillis());
for (JsonObject o : JSONUtil.objects(packages, "guides")) {
if (o.has("canonical")) {
String id = JSONUtil.str(o, "npm-name");
String pname = JSONUtil.str(o, "name");
String pcanonical = JSONUtil.str(o, "canonical");
String description = JSONUtil.str(o, "description");
boolean ok = true;
if (ok && !Utilities.noString(name)) {
ok = (pname != null && pname.contains(name)) || (description != null && description.contains(name)) || (id != null && id.contains(name));
}
if (ok && !Utilities.noString(canonical)) {
ok = pcanonical.contains(canonical);
}
String version = null;
String fVersion = null;
String url = null;
if (ok) {
// if we can find something...
for (JsonObject e : JSONUtil.objects(o, "editions")) {
if (fhirVersion == null || fhirVersion.equals(JSONUtil.str(e, "fhir-version"))) {
String v = JSONUtil.str(e, "ig-version");
if (version == null || VersionUtilities.isThisOrLater(version, v)) {
version = v;
fVersion = e.getAsJsonArray("fhir-version").get(0).getAsString();
url = JSONUtil.str(e, "url");
}
}
}
}
if (version != null) {
result.add(new PackageInfo(id, version, fVersion, description, url, pcanonical, address));
final PackageInfo packageInfo = getPackageInfoFromJSON(o, name, canonical, fhirVersion);
if (packageInfo.getVersion() != null) {
result.add(packageInfo);
}
}
}

5
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/xhtml/HierarchicalTableGenerator.java
View File

@ -403,6 +403,11 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
pieces.add(p);
return p;
}
public Piece addText(String text) {
Piece p = new Piece(null, text, null);
pieces.add(p);
return p;
}
public String text() {
StringBuilder b = new StringBuilder();
for (Piece p : pieces)

6
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/xml/XMLUtil.java
View File

@ -273,9 +273,9 @@ public class XMLUtil {
for (int i = 0; i < rawContent.length(); i++) {
char ch = rawContent.charAt(i);
if (ch == '\'')
sb.append("&#39;");
else if (ch == '&')
// We don't escape ' because our code always spits out attributes surrounded by "", which means
// it's not necessary to escape ' - and it's *much* less ugly and more bandwidth-efficient when we don't.
if (ch == '&')
sb.append("&amp;");
else if (ch == '"')
sb.append("&quot;");

2
org.hl7.fhir.utilities/src/main/resources/Messages.properties
View File

@ -629,6 +629,8 @@ Unable_to_connect_to_terminology_server = Unable to connect to terminology serve
SD_ED_TYPE_PROFILE_UNKNOWN = Unable to resolve profile {0}
SD_ED_TYPE_PROFILE_NOTYPE = Found profile {0}, but unable to determine the type it applies to
SD_ED_TYPE_PROFILE_WRONG = Profile {0} is for type {1}, but the {3} element has type {2}
SD_ED_TYPE_PROFILE_IS_MODIFIER = Profile {0} is for not for a modifier extension, but the {3} element is a modifier
SD_ED_TYPE_PROFILE_NOT_MODIFIER = Profile {0} is for a modifier extension, but the {3} element is not a modifier
SD_ED_TYPE_PROFILE_WRONG_TARGET = Profile {0} is for type {1}, which is not a {4} (which is required because the {3} element has type {2})
SD_ED_TYPE_NO_TARGET_PROFILE = Type {0} does not allow for target Profiles
TERMINOLOGY_TX_NOSVC_BOUND_REQ = Could not confirm that the codes provided are from the required value set {0} because there is no terminology service

6
org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/UtilitiesTest.java
View File

@ -39,7 +39,11 @@ class UtilitiesTest {
@Test
@DisplayName("Test Utilities.path maps temp directory correctly")
public void testTempDirPath() throws IOException {
Assertions.assertEquals(Utilities.path("[tmp]", TEST_TXT), getTempDirectory() + TEST_TXT);
if (ToolGlobalSettings.hasTempPath()) {
Assertions.assertEquals(Utilities.path("[tmp]", TEST_TXT), ToolGlobalSettings.getTempPath() +File.separator+ TEST_TXT);
} else {
Assertions.assertEquals(Utilities.path("[tmp]", TEST_TXT), getTempDirectory() + TEST_TXT);
}
}
@Test

44
org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/npm/PackageClientTest.java Normal file
View File

@ -0,0 +1,44 @@
package org.hl7.fhir.utilities.npm;
import com.google.gson.Gson;
import com.google.gson.JsonObject;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;
import java.nio.file.Files;
import java.nio.file.Paths;
import static org.junit.jupiter.api.Assertions.assertEquals;
public class PackageClientTest {
PackageClient packageClient = new PackageClient(PackageClient.PRIMARY_SERVER);
private void assertExpectedFields(final PackageInfo packageInfo) {
assertEquals("dummy.package", packageInfo.getId());
assertEquals("1.2.3", packageInfo.getVersion());
assertEquals("4.5.6", packageInfo.getFhirVersion());
assertEquals("Dummy description",
packageInfo.getDescription());
assertEquals("https://d.e.f", packageInfo.getUrl());
assertEquals("https://a.b.c", packageInfo.getCanonical());
}
@Test
@DisplayName("test getting package from JSON works")
public void getPackageInfoFromJSONTest() throws java.io.IOException{
final JsonObject jsonObject = new Gson().fromJson(Files.newBufferedReader(Paths.get("src", "test", "resources", "npm", "PackageClient-baseTestCase.json")), JsonObject.class);
final PackageInfo packageInfo = packageClient.getPackageInfoFromJSON(jsonObject, null, null, null);
assertExpectedFields(packageInfo);
}
@Test
@DisplayName("test getting package from JSON works")
public void getPackageInfoWithIdFromJSONTest() throws java.io.IOException {
final JsonObject jsonObject = new Gson().fromJson(Files.newBufferedReader(Paths.get("src", "test", "resources", "npm", "PackageClient-testCaseWithId.json")), JsonObject.class);
final PackageInfo packageInfo = packageClient.getPackageInfoFromJSON(jsonObject, null, null, null);
assertExpectedFields(packageInfo);
}
}

25
org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/tests/RegexTests.java Normal file
View File

@ -0,0 +1,25 @@
package org.hl7.fhir.utilities.tests;
import java.io.IOException;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
public class RegexTests {
@Test
public void testPath1() throws IOException {
Assertions.assertFalse("http://fhir.org/guides/cqf/common/Library/FHIR-ModelInfo|4.0.1".matches("Library"));
}
@Test
public void testPath2() throws IOException {
Assertions.assertTrue("http://fhir.org/guides/cqf/common/Library/FHIR-ModelInfo|4.0.1".matches(".*Library.*"));
}
@Test
public void testPath3() throws IOException {
Assertions.assertTrue("http://fhir.org/guides/cqf/common/Library/FHIR-ModelInfo|4.0.1".matches("(?s).*Library.*"));
}
}

16
org.hl7.fhir.utilities/src/test/resources/npm/PackageClient-baseTestCase.json Normal file
View File

@ -0,0 +1,16 @@
{
"name": "Pan-Canadian Patient Summary",
"description": "Dummy description",
"canonical": "https://a.b.c",
"editions": [
{
"name": "Dummy name",
"ig-version": "1.2.3",
"package": "dummy.package#1.2.3",
"fhir-version": [
"4.5.6"
],
"url": "https://d.e.f"
}
]
}

17
org.hl7.fhir.utilities/src/test/resources/npm/PackageClient-testCaseWithId.json Normal file
View File

@ -0,0 +1,17 @@
{
"name": "Pan-Canadian Patient Summary",
"description": "Dummy description",
"canonical": "https://a.b.c",
"npm-name": "dummy.package",
"editions": [
{
"name": "Dummy name",
"ig-version": "1.2.3",
"package": "not.a.dummy.package#1.2.3",
"fhir-version": [
"4.5.6"
],
"url": "https://d.e.f"
}
]
}

4
org.hl7.fhir.validation.cli/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.6.35</version>
<version>5.6.38-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
@ -76,7 +76,7 @@
<goal>unpack-dependencies</goal>
</goals>
<configuration>
<excludes>**/module-info.class,META-INF/*.SF,META-INF/*.DSA,META-INF/*.RSA</excludes>
<excludes>**/module-info.class,META-INF/*</excludes>
<outputDirectory>${project.build.directory}/classes</outputDirectory>
<overWriteReleases>false</overWriteReleases>
<overWriteSnapshots>true</overWriteSnapshots>

2
org.hl7.fhir.validation/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.6.35</version>
<version>5.6.38-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

10
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java
View File

@ -3405,13 +3405,17 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
return elements;
}
boolean dontFollowReference = false;
if (removeResolve) { // if we're doing profile slicing, we don't want to walk into the last resolve.. we need the profile on the source not the target
if (discriminator.equals("resolve()")) {
elements.add(element);
return elements;
}
if (discriminator.endsWith(".resolve()"))
if (discriminator.endsWith(".resolve()")) {
discriminator = discriminator.substring(0, discriminator.length() - 10);
dontFollowReference = true;
}
}
TypedElementDefinition ted = null;
@ -3424,7 +3428,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
throw new FHIRException(context.formatMessage(I18nConstants.DISCRIMINATOR_BAD_PATH, e.getMessage(), fp), e);
}
long t2 = System.nanoTime();
ted = fpe.evaluateDefinition(expr, profile, new TypedElementDefinition(element), srcProfile);
ted = fpe.evaluateDefinition(expr, profile, new TypedElementDefinition(element), srcProfile, dontFollowReference);
timeTracker.sd(t2);
if (ted != null)
elements.add(ted.getElement());
@ -3449,7 +3453,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
}
expr = fpe.parse(fp);
t2 = System.nanoTime();
ted = fpe.evaluateDefinition(expr, profile, new TypedElementDefinition(element), srcProfile);
ted = fpe.evaluateDefinition(expr, profile, new TypedElementDefinition(element), srcProfile, dontFollowReference);
timeTracker.sd(t2);
if (ted != null)
elements.add(ted.getElement());

2
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/BundleValidator.java
View File

@ -27,7 +27,7 @@ import org.hl7.fhir.validation.instance.utils.IndexedElement;
import org.hl7.fhir.validation.instance.utils.NodeStack;
import org.hl7.fhir.validation.instance.utils.ValidatorHostContext;
public class BundleValidator extends BaseValidator{
public class BundleValidator extends BaseValidator {
public final static String URI_REGEX3 = "((http|https)://([A-Za-z0-9\\\\\\.\\:\\%\\$]*\\/)*)?(Account|ActivityDefinition|AllergyIntolerance|AdverseEvent|Appointment|AppointmentResponse|AuditEvent|Basic|Binary|BodySite|Bundle|CapabilityStatement|CarePlan|CareTeam|ChargeItem|Claim|ClaimResponse|ClinicalImpression|CodeSystem|Communication|CommunicationRequest|CompartmentDefinition|Composition|ConceptMap|Condition (aka Problem)|Consent|Contract|Coverage|DataElement|DetectedIssue|Device|DeviceComponent|DeviceMetric|DeviceRequest|DeviceUseStatement|DiagnosticReport|DocumentManifest|DocumentReference|EligibilityRequest|EligibilityResponse|Encounter|Endpoint|EnrollmentRequest|EnrollmentResponse|EpisodeOfCare|ExpansionProfile|ExplanationOfBenefit|FamilyMemberHistory|Flag|Goal|GraphDefinition|Group|GuidanceResponse|HealthcareService|ImagingManifest|ImagingStudy|Immunization|ImmunizationRecommendation|ImplementationGuide|Library|Linkage|List|Location|Measure|MeasureReport|Media|Medication|MedicationAdministration|MedicationDispense|MedicationRequest|MedicationStatement|MessageDefinition|MessageHeader|NamingSystem|NutritionOrder|Observation|OperationDefinition|OperationOutcome|Organization|Parameters|Patient|PaymentNotice|PaymentReconciliation|Person|PlanDefinition|Practitioner|PractitionerRole|Procedure|ProcedureRequest|ProcessRequest|ProcessResponse|Provenance|Questionnaire|QuestionnaireResponse|ReferralRequest|RelatedPerson|RequestGroup|ResearchStudy|ResearchSubject|RiskAssessment|Schedule|SearchParameter|Sequence|ServiceDefinition|Slot|Specimen|StructureDefinition|StructureMap|Subscription|Substance|SupplyDelivery|SupplyRequest|Task|TestScript|TestReport|ValueSet|VisionPrescription)\\/[A-Za-z0-9\\-\\.]{1,64}(\\/_history\\/[A-Za-z0-9\\-\\.]{1,64})?";
private String serverBase;
private InstanceValidator validator;

23
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/StructureDefinitionValidator.java
View File

@ -294,6 +294,15 @@ public class StructureDefinitionValidator extends BaseValidator {
rule(errors, IssueType.EXCEPTION, stack.getLiteralPath(), false, I18nConstants.SD_ED_TYPE_PROFILE_NOTYPE, p);
} else {
rule(errors, IssueType.EXCEPTION, stack.getLiteralPath(), isInstanceOf(t, code), I18nConstants.SD_ED_TYPE_PROFILE_WRONG, p, t, code, path);
if (t.getType().equals("Extension")) {
boolean isModifierDefinition = checkIsModifierExtension(sd);
boolean isModifierContext = path.endsWith(".modifierExtension");
if (isModifierDefinition) {
rule(errors, IssueType.EXCEPTION, stack.getLiteralPath(), isModifierContext, I18nConstants.SD_ED_TYPE_PROFILE_NOT_MODIFIER, p, t, code, path);
} else {
rule(errors, IssueType.EXCEPTION, stack.getLiteralPath(), !isModifierContext, I18nConstants.SD_ED_TYPE_PROFILE_IS_MODIFIER, p, t, code, path);
}
}
}
}
}
@ -325,10 +334,24 @@ public class StructureDefinitionValidator extends BaseValidator {
rule(errors, IssueType.EXCEPTION, stack.getLiteralPath(), false, I18nConstants.SD_ED_TYPE_PROFILE_NOTYPE, p);
} else if (!isInstanceOf(t, code)) {
rule(errors, IssueType.EXCEPTION, stack.getLiteralPath(), false, I18nConstants.SD_ED_TYPE_PROFILE_WRONG, p, t, code, path);
} else {
if (t.getType().equals("Extension")) {
boolean isModifierDefinition = checkIsModifierExtension(sd);
boolean isModifierContext = path.endsWith(".modifierExtension");
if (isModifierDefinition) {
rule(errors, IssueType.EXCEPTION, stack.getLiteralPath(), isModifierContext, I18nConstants.SD_ED_TYPE_PROFILE_NOT_MODIFIER, p, t, code, path);
} else {
rule(errors, IssueType.EXCEPTION, stack.getLiteralPath(), !isModifierContext, I18nConstants.SD_ED_TYPE_PROFILE_IS_MODIFIER, p, t, code, path);
}
}
}
}
}
private boolean checkIsModifierExtension(StructureDefinition t) {
return t.getSnapshot().getElementFirstRep().getIsModifier();
}
private void validateTargetProfile(List<ValidationMessage> errors, Element profile, String code, NodeStack stack, String path) {
String p = profile.primitiveValue();
StructureDefinition sd = context.fetchResource(StructureDefinition.class, p);

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