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

This commit is contained in:
Lloyd McKenzie 2020-09-08 08:00:41 -06:00
parent 0191bfbbfb a92876ab4a
commit f2699a1d50
44 changed files with 1010 additions and 255 deletions
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2
org.hl7.fhir.convertors/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.1.8-SNAPSHOT</version>
<version>5.1.9-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

7
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/VersionConvertor_10_40.java
View File

@ -65,6 +65,7 @@ import org.hl7.fhir.convertors.conv10_40.ValueSet10_40;
import org.hl7.fhir.dstu2.model.CodeableConcept;
import org.hl7.fhir.dstu2.model.Parameters;
import org.hl7.fhir.dstu2.model.Parameters.ParametersParameterComponent;
import org.hl7.fhir.dstu2.model.PositiveIntType;
import org.hl7.fhir.dstu2.model.Reference;
import org.hl7.fhir.dstu2.utils.ToolingExtensions;
import org.hl7.fhir.exceptions.FHIRException;
@ -3423,4 +3424,10 @@ public class VersionConvertor_10_40 {
public static org.hl7.fhir.dstu2.model.Resource convertResource(org.hl7.fhir.r4.model.Resource src) throws FHIRException {
return convertResource(src, null);
}
public static UnsignedIntType convertUnsignedIntToPositive(PositiveIntType src) {
org.hl7.fhir.r4.model.UnsignedIntType tgt = src.hasValue() ? new org.hl7.fhir.r4.model.UnsignedIntType(src.getValue()) : new org.hl7.fhir.r4.model.UnsignedIntType();
copyElement(src, tgt);
return tgt;
}
}

8
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/VersionConvertor_40_50.java
View File

@ -3742,7 +3742,7 @@ public class VersionConvertor_40_50 {
return convertUsageContext((org.hl7.fhir.r4.model.UsageContext) src);
if (src instanceof org.hl7.fhir.r4.model.ElementDefinition)
return convertElementDefinition((org.hl7.fhir.r4.model.ElementDefinition) src);
throw new Error("Unknown type " + src.fhirType());
throw new FHIRException("Unknown type " + src.fhirType());
}
public static org.hl7.fhir.r4.model.Type convertType(org.hl7.fhir.r5.model.DataType src) throws FHIRException {
@ -3868,7 +3868,7 @@ public class VersionConvertor_40_50 {
return convertUsageContext((org.hl7.fhir.r5.model.UsageContext) src);
if (src instanceof org.hl7.fhir.r5.model.ElementDefinition)
return convertElementDefinition((org.hl7.fhir.r5.model.ElementDefinition) src);
throw new Error("Unknown type " + src.fhirType());
throw new FHIRException("Unknown type " + src.fhirType());
}
protected static void copyDomainResource(org.hl7.fhir.r4.model.DomainResource src, org.hl7.fhir.r5.model.DomainResource tgt) throws FHIRException {
@ -4174,7 +4174,7 @@ public class VersionConvertor_40_50 {
return VerificationResult40_50.convertVerificationResult((org.hl7.fhir.r4.model.VerificationResult) src);
if (src instanceof org.hl7.fhir.r4.model.VisionPrescription)
return VisionPrescription40_50.convertVisionPrescription((org.hl7.fhir.r4.model.VisionPrescription) src);
throw new Error("Unknown resource " + src.fhirType());
throw new FHIRException("Unknown resource " + src.fhirType());
}
public static org.hl7.fhir.r4.model.Resource convertResource(org.hl7.fhir.r5.model.Resource src) throws FHIRException {
@ -4441,7 +4441,7 @@ public class VersionConvertor_40_50 {
return VerificationResult40_50.convertVerificationResult((org.hl7.fhir.r5.model.VerificationResult) src);
if (src instanceof org.hl7.fhir.r5.model.VisionPrescription)
return VisionPrescription40_50.convertVisionPrescription((org.hl7.fhir.r5.model.VisionPrescription) src);
throw new Error("Unknown resource " + src.fhirType());
throw new FHIRException("Unknown resource " + src.fhirType());
}
protected static org.hl7.fhir.r5.model.CodeType convertResourceEnum(org.hl7.fhir.r4.model.CodeType src) {

1
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/conv10_40/AllergyIntolerance10_40.java
View File

@ -9,6 +9,7 @@ public class AllergyIntolerance10_40 {
if (src == null)
return null;
org.hl7.fhir.r4.model.AllergyIntolerance tgt = new org.hl7.fhir.r4.model.AllergyIntolerance();
VersionConvertor_10_40.copyDomainResource(src, tgt);
for (org.hl7.fhir.dstu2.model.Identifier t : src.getIdentifier()) tgt.addIdentifier(VersionConvertor_10_40.convertIdentifier(t));
if (src.hasOnset())
tgt.setOnset(VersionConvertor_10_40.convertType(src.getOnsetElement()));

6
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/conv10_40/MedicationRequest10_40.java
View File

@ -15,7 +15,7 @@ public class MedicationRequest10_40 {
tgt.setIntent(org.hl7.fhir.r4.model.MedicationRequest.MedicationRequestIntent.ORDER);
for (org.hl7.fhir.dstu2.model.Identifier identifier : src.getIdentifier()) tgt.addIdentifier(VersionConvertor_10_40.convertIdentifier(identifier));
if (src.hasDateWritten())
tgt.setAuthoredOn(src.getDateWritten());
tgt.setAuthoredOnElement(VersionConvertor_10_40.convertDateTime(src.getDateWrittenElement()));
if (src.hasStatus())
tgt.setStatus(org.hl7.fhir.r4.model.MedicationRequest.MedicationRequestStatus.fromCode(src.getStatus().toCode()));
if (src.hasPatient())
@ -48,7 +48,7 @@ public class MedicationRequest10_40 {
return null;
org.hl7.fhir.r4.model.Dosage tgt = new org.hl7.fhir.r4.model.Dosage();
if (src.hasText())
tgt.setText(src.getText());
tgt.setTextElement(VersionConvertor_10_40.convertString(src.getTextElement()));
if (src.hasAdditionalInstructions())
tgt.addAdditionalInstruction(VersionConvertor_10_40.convertCodeableConcept(src.getAdditionalInstructions()));
if (src.hasTiming())
@ -79,7 +79,7 @@ public class MedicationRequest10_40 {
if (src.hasValidityPeriod())
tgt.setValidityPeriod(VersionConvertor_10_40.convertPeriod(src.getValidityPeriod()));
if (src.hasNumberOfRepeatsAllowed())
tgt.setNumberOfRepeatsAllowed(src.getNumberOfRepeatsAllowed());
tgt.setNumberOfRepeatsAllowedElement(VersionConvertor_10_40.convertUnsignedIntToPositive(src.getNumberOfRepeatsAllowedElement()));
if (src.hasQuantity())
tgt.setQuantity(VersionConvertor_10_40.convertSimpleQuantity(src.getQuantity()));
if (src.hasExpectedSupplyDuration())

149
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/VSACImporter.java
View File

@ -1,26 +1,29 @@
package org.hl7.fhir.convertors.misc;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.model.Enumerations.PublicationStatus;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.r4.utils.client.FHIRToolingClient;
import org.hl7.fhir.r4.formats.JsonParser;
import org.hl7.fhir.r4.model.Enumerations.PublicationStatus;
import org.hl7.fhir.r4.model.ValueSet;
import org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.utilities.CSVReader;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.w3c.dom.Element;
import java.io.*;
import java.net.URISyntaxException;
import java.text.ParseException;
import java.util.ArrayList;
import java.util.List;
public class VSACImporter extends OIDBasedValueSetImporter {
public static void main(String[] args) throws FileNotFoundException, FHIRException, IOException, ParseException {
public static void main(String[] args) throws FileNotFoundException, FHIRException, IOException, ParseException, URISyntaxException {
// new PhinVadsImporter().importValueSet(TextFile.fileToBytes("C:\\work\\org.hl7.fhir\\packages\\us.cdc.phinvads-source\\source\\PHVS_BirthDefectsLateralityatDiagnosis_HL7_V1.txt"));
VSACImporter self = new VSACImporter();
self.process(args[0], args[1]);
self.process(args[0], args[1], args[2], args[3]);
}
public VSACImporter() throws FileNotFoundException, FHIRException, IOException {
@ -28,69 +31,87 @@ public class VSACImporter extends OIDBasedValueSetImporter {
init();
}
private void process(String source, String dest) {
for (File f : new File(source).listFiles()) {
private void process(String source, String dest, String username, String password) throws FHIRException, FileNotFoundException, IOException, URISyntaxException {
CSVReader csv = new CSVReader(new FileInputStream(source));
csv.readHeaders();
FHIRToolingClient client = new FHIRToolingClient("https://cts.nlm.nih.gov/fhir", username, password);
int i = 0;
while (csv.line()) {
String oid = csv.cell("OID");
try {
System.out.println("Process " + f.getName());
List<ValueSet> vsl = importValueSet(TextFile.fileToBytes(f));
for (ValueSet vs : vsl) {
if (vs.getId() != null) {
new JsonParser().compose(new FileOutputStream(Utilities.path(dest, "ValueSet-" + vs.getId() + ".json")), vs);
}
ValueSet vs = client.read(ValueSet.class, oid);
new JsonParser().compose(new FileOutputStream(Utilities.path(dest, "ValueSet-"+oid+".json")), vs);
i++;
if (i % 100 == 0) {
System.out.println(i);
}
} catch (Exception e) {
e.printStackTrace();
System.out.println("Unable to fetch OID "+oid+": "+e.getMessage());
}
}
System.out.println("Done. "+i+" ValueSets");
// for (File f : new File(source).listFiles()) {
// try {
// System.out.println("Process " + f.getName());
// List<ValueSet> vsl = importValueSet(TextFile.fileToBytes(f));
// for (ValueSet vs : vsl) {
// if (vs.getId() != null) {
// new JsonParser().compose(new FileOutputStream(Utilities.path(dest, "ValueSet-" + vs.getId() + ".json")), vs);
// }
// }
// } catch (Exception e) {
// e.printStackTrace();
// }
// }
}
private List<ValueSet> importValueSet(byte[] source) throws Exception {
List<ValueSet> res = new ArrayList<ValueSet>();
Element x = loadXml(new ByteArrayInputStream(source)).getDocumentElement();
List<Element> vl = XMLUtil.getNamedChildren(x, "DescribedValueSet");
for (Element v : vl) {
ValueSet vs = new ValueSet();
vs.setId(v.getAttribute("ID"));
vs.setUrl("http://vsac.nlm.nih.gov/fhir/ValueSet/" + vs.getId());
vs.getMeta().setSource("https://vsac.nlm.nih.gov/valueset/" + vs.getId() + "/expansion");
vs.setVersion(v.getAttribute("version"));
vs.setTitle(v.getAttribute("displayName"));
vs.setName(Utilities.titleize(vs.getTitle()).replace(" ", ""));
Element d = XMLUtil.getNamedChild(v, "Purpose");
if (d != null) {
vs.setDescription(d.getTextContent());
}
Element s = XMLUtil.getNamedChild(v, "Status");
if (s != null && "Active".equals(s.getTextContent())) {
vs.setStatus(PublicationStatus.ACTIVE);
} else {
vs.setStatus(PublicationStatus.DRAFT);
}
Element dt = XMLUtil.getNamedChild(v, "RevisionDate");
if (dt != null) {
vs.getDateElement().setValueAsString(dt.getTextContent());
}
Element cl = XMLUtil.getNamedChild(v, "ConceptList");
Element cc = XMLUtil.getFirstChild(cl);
while (cc != null) {
String code = cc.getAttribute("code");
String display = cc.getAttribute("displayName");
String csoid = cc.getAttribute("codeSystem");
String csver = cc.getAttribute("codeSystemVersion");
String url = context.oid2Uri(csoid);
if (url == null) {
url = "urn:oid:" + csoid;
}
csver = fixVersionforSystem(url, csver);
ConceptSetComponent inc = getInclude(vs, url, csver);
inc.addConcept().setCode(code).setDisplay(display);
cc = XMLUtil.getNextSibling(cc);
}
res.add(vs);
}
return res;
}
// private List<ValueSet> importValueSet(byte[] source) throws Exception {
// List<ValueSet> res = new ArrayList<ValueSet>();
// Element x = loadXml(new ByteArrayInputStream(source)).getDocumentElement();
// List<Element> vl = XMLUtil.getNamedChildren(x, "DescribedValueSet");
// for (Element v : vl) {
// ValueSet vs = new ValueSet();
// vs.setId(v.getAttribute("ID"));
// vs.setUrl("http://cts.nlm.nih.gov/fhir/ValueSet/" + vs.getId());
// vs.getMeta().setSource("https://vsac.nlm.nih.gov/valueset/" + vs.getId() + "/expansion");
// vs.setVersion(v.getAttribute("version"));
// vs.setTitle(v.getAttribute("displayName"));
// vs.setName(Utilities.titleize(vs.getTitle()).replace(" ", ""));
// Element d = XMLUtil.getNamedChild(v, "Purpose");
// if (d != null) {
// vs.setDescription(d.getTextContent());
// }
// Element s = XMLUtil.getNamedChild(v, "Status");
// if (s != null && "Active".equals(s.getTextContent())) {
// vs.setStatus(PublicationStatus.ACTIVE);
// } else {
// vs.setStatus(PublicationStatus.DRAFT);
// }
// Element dt = XMLUtil.getNamedChild(v, "RevisionDate");
// if (dt != null) {
// vs.getDateElement().setValueAsString(dt.getTextContent());
// }
//
// Element cl = XMLUtil.getNamedChild(v, "ConceptList");
// Element cc = XMLUtil.getFirstChild(cl);
//
// while (cc != null) {
// String code = cc.getAttribute("code");
// String display = cc.getAttribute("displayName");
// String csoid = cc.getAttribute("codeSystem");
// String csver = cc.getAttribute("codeSystemVersion");
// String url = context.oid2Uri(csoid);
// if (url == null) {
// url = "urn:oid:" + csoid;
// }
// csver = fixVersionforSystem(url, csver);
// ConceptSetComponent inc = getInclude(vs, url, csver);
// inc.addConcept().setCode(code).setDisplay(display);
// cc = XMLUtil.getNextSibling(cc);
// }
//
// res.add(vs);
// }
// return res;
// }
}

1
org.hl7.fhir.convertors/src/test/resources/0_allergy_intolerance_40.json
View File

@ -1,5 +1,6 @@
{
"resourceType" : "AllergyIntolerance",
"id" : "TBwnNbrAqC0Qw5Ha7AFT-2AB",
"clinicalStatus" : {
"coding" : [
{

1
org.hl7.fhir.convertors/src/test/resources/1_allergy_intolerance_40.json
View File

@ -1,5 +1,6 @@
{
"resourceType" : "AllergyIntolerance",
"id": "TKebKfLXzu6Sp.LY-IpvpmQB",
"clinicalStatus" : {
"coding" : [
{

2
org.hl7.fhir.dstu2/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.1.8-SNAPSHOT</version>
<version>5.1.9-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.dstu2016may/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.1.8-SNAPSHOT</version>
<version>5.1.9-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>5.1.8-SNAPSHOT</version>
<version>5.1.9-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

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>5.1.8-SNAPSHOT</version>
<version>5.1.9-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

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>5.1.8-SNAPSHOT</version>
<version>5.1.9-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

242
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/ProfileUtilities.java
View File

@ -78,6 +78,9 @@ import org.hl7.fhir.r5.model.Enumeration;
import org.hl7.fhir.r5.model.Enumerations.BindingStrength;
import org.hl7.fhir.r5.model.Enumerations.FHIRVersion;
import org.hl7.fhir.r5.model.Enumerations.PublicationStatus;
import org.hl7.fhir.r5.model.ExpressionNode;
import org.hl7.fhir.r5.model.ExpressionNode.Kind;
import org.hl7.fhir.r5.model.ExpressionNode.Operation;
import org.hl7.fhir.r5.model.Extension;
import org.hl7.fhir.r5.model.IdType;
import org.hl7.fhir.r5.model.IntegerType;
@ -99,6 +102,8 @@ import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionComponent;
import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionContainsComponent;
import org.hl7.fhir.r5.renderers.TerminologyRenderer;
import org.hl7.fhir.r5.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
import org.hl7.fhir.r5.utils.FHIRLexer;
import org.hl7.fhir.r5.utils.FHIRPathEngine;
import org.hl7.fhir.r5.utils.ToolingExtensions;
import org.hl7.fhir.r5.utils.TranslatingUtilities;
import org.hl7.fhir.r5.utils.XVerExtensionManager;
@ -200,6 +205,30 @@ public class ProfileUtilities extends TranslatingUtilities {
}
}
public static class ElementChoiceGroup {
private Row row;
private String name;
private boolean mandatory;
private List<String> elements = new ArrayList<>();
public ElementChoiceGroup(String name, boolean mandatory) {
super();
this.name = name;
this.mandatory = mandatory;
}
public Row getRow() {
return row;
}
public List<String> getElements() {
return elements;
}
public void setRow(Row row) {
this.row = row;
}
public String getName() {
return name;
}
}
private static final int MAX_RECURSION_LIMIT = 10;
@ -268,6 +297,7 @@ public class ProfileUtilities extends TranslatingUtilities {
// note that ProfileUtilities are used re-entrantly internally, so nothing with process state can be here
private final IWorkerContext context;
private FHIRPathEngine fpe;
private List<ValidationMessage> messages;
private List<String> snapshotStack = new ArrayList<String>();
private ProfileKnowledgeProvider pkp;
@ -284,6 +314,9 @@ public class ProfileUtilities extends TranslatingUtilities {
this.context = context;
this.messages = messages;
this.pkp = pkp;
if (context != null) {
this.fpe = new FHIRPathEngine(context, this);
}
}
public static class UnusedTracker {
@ -538,6 +571,7 @@ public class ProfileUtilities extends TranslatingUtilities {
}
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, new ArrayList<ElementRedirection>(), base);
checkGroupConstraints(derived);
if (derived.getDerivation() == TypeDerivationRule.SPECIALIZATION) {
for (ElementDefinition e : diff.getElement()) {
if (!e.hasUserData(GENERATED_IN_SNAPSHOT)) {
@ -666,6 +700,81 @@ public class ProfileUtilities extends TranslatingUtilities {
derived.clearUserData("profileutils.snapshot.generating");
}
private void checkGroupConstraints(StructureDefinition derived) {
List<ElementDefinition> toRemove = new ArrayList<>();
// List<ElementDefinition> processed = new ArrayList<>();
for (ElementDefinition element : derived.getSnapshot().getElement()) {
if (!toRemove.contains(element) && !element.hasSlicing() && !"0".equals(element.getMax())) {
checkForChildrenInGroup(derived, toRemove, element);
}
}
derived.getSnapshot().getElement().removeAll(toRemove);
}
public void checkForChildrenInGroup(StructureDefinition derived, List<ElementDefinition> toRemove, ElementDefinition element) throws Error {
List<ElementDefinition> children = getChildren(derived, element);
List<ElementChoiceGroup> groups = readChoices(element, children);
for (ElementChoiceGroup group : groups) {
System.out.println(children);
String mandated = null;
Set<String> names = new HashSet<>();
for (ElementDefinition ed : children) {
String name = tail(ed.getPath());
if (names.contains(name)) {
throw new Error("huh?");
} else {
names.add(name);
}
if (group.getElements().contains(name)) {
if (ed.getMin() == 1) {
if (mandated == null) {
mandated = name;
} else {
throw new Error("Error: there are two mandatory elements in "+derived.getUrl()+" when there can only be one: "+mandated+" and "+name);
}
}
}
}
if (mandated != null) {
for (ElementDefinition ed : children) {
String name = tail(ed.getPath());
if (group.getElements().contains(name) && !mandated.equals(name)) {
ed.setMax("0");
addAllChildren(derived, ed, toRemove);
}
}
}
}
}
private List<ElementDefinition> getChildren(StructureDefinition derived, ElementDefinition element) {
List<ElementDefinition> elements = derived.getSnapshot().getElement();
int index = elements.indexOf(element) + 1;
String path = element.getPath()+".";
List<ElementDefinition> list = new ArrayList<>();
while (index < elements.size()) {
ElementDefinition e = elements.get(index);
String p = e.getPath();
if (p.startsWith(path) && !e.hasSliceName()) {
if (!p.substring(path.length()).contains(".")) {
list.add(e);
}
index++;
} else {
break;
}
}
return list;
}
private void addAllChildren(StructureDefinition derived, ElementDefinition element, List<ElementDefinition> toRemove) {
List<ElementDefinition> children = getChildList(derived, element);
for (ElementDefinition child : children) {
toRemove.add(child);
addAllChildren(derived, child, toRemove);
}
}
private void checkDifferential(List<ElementDefinition> elements, String type, String url) {
boolean first = true;
for (ElementDefinition ed : elements) {
@ -3620,12 +3729,17 @@ public class ProfileUtilities extends TranslatingUtilities {
}
Row currRow = row;
List<ElementChoiceGroup> groups = readChoices(element, children);
boolean isExtension = Utilities.existsInList(tail(element.getPath()), "extension", "modifierExtension");
for (ElementDefinition child : children) {
if (!child.hasSliceName())
if (!child.hasSliceName()) {
currRow = row;
if (logicalModel || !child.getPath().endsWith(".id") || (child.getPath().endsWith(".id") && (profile != null) && (profile.getDerivation() == TypeDerivationRule.CONSTRAINT)))
currRow = genElement(defPath, gen, currRow.getSubRows(), child, all, profiles, showMissing, profileBaseFileName, isExtension, snapshot, corePath, imagePath, false, logicalModel, isConstraintMode, allInvariants, currRow, mustSupport);
}
Row childRow = chooseChildRowByGroup(gen, currRow, groups, child, element, isConstraintMode);
if (logicalModel || !child.getPath().endsWith(".id") || (child.getPath().endsWith(".id") && (profile != null) && (profile.getDerivation() == TypeDerivationRule.CONSTRAINT))) {
currRow = genElement(defPath, gen, childRow.getSubRows(), child, all, profiles, showMissing, profileBaseFileName, isExtension, snapshot, corePath, imagePath, false, logicalModel, isConstraintMode, allInvariants, currRow, mustSupport);
}
}
// if (!snapshot && (extensions == null || !extensions))
// for (ElementDefinition child : children)
@ -3639,6 +3753,34 @@ public class ProfileUtilities extends TranslatingUtilities {
return slicingRow;
}
private Row chooseChildRowByGroup(HierarchicalTableGenerator gen, Row row, List<ElementChoiceGroup> groups, ElementDefinition element, ElementDefinition parent, boolean isConstraintMode) {
String name = tail(element.getPath());
for (ElementChoiceGroup grp : groups) {
if (grp.getElements().contains(name)) {
if (grp.getRow() == null) {
grp.setRow(makeChoiceElementRow(gen, row, grp, parent, isConstraintMode));
}
return grp.getRow();
}
}
return row;
}
private Row makeChoiceElementRow(HierarchicalTableGenerator gen, Row prow, ElementChoiceGroup grp, ElementDefinition parent, boolean isConstraintMode) {
Row row = gen.new Row();
row.setAnchor(parent.getPath()+"-"+grp.getName());
row.setColor(getRowColor(parent, isConstraintMode));
row.setLineColor(1);
row.setIcon("icon_choice.gif", HierarchicalTableGenerator.TEXT_ICON_CHOICE);
row.getCells().add(gen.new Cell(null, null, "(Choice of one)", "", null));
row.getCells().add(gen.new Cell());
row.getCells().add(gen.new Cell(null, null, (grp.mandatory ? "1" : "0")+"..1", "", null));
row.getCells().add(gen.new Cell());
row.getCells().add(gen.new Cell());
prow.getSubRows().add(row);
return row;
}
public Cell genElementNameCell(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) throws IOException {
@ -3985,7 +4127,7 @@ public class ProfileUtilities extends TranslatingUtilities {
}
if (root) {
if (profile.getAbstract()) {
if (!c.getPieces().isEmpty()) c.addPiece(gen.new Piece("br"));
if (!c.getPieces().isEmpty()) { c.addPiece(gen.new Piece("br")); }
c.addPiece(gen.new Piece(null, "This is an abstract profile", null));
}
}
@ -3993,10 +4135,10 @@ public class ProfileUtilities extends TranslatingUtilities {
c.getPieces().add(checkForNoChange(definition.getFixed(), gen.new Piece(null, "\""+buildJson(definition.getFixed())+"\"", null).addStyle("color: darkgreen")));
} else {
if (definition != null && definition.hasShort()) {
if (!c.getPieces().isEmpty()) c.addPiece(gen.new Piece("br"));
if (!c.getPieces().isEmpty()) { c.addPiece(gen.new Piece("br")); }
c.addPiece(checkForNoChange(definition.getShortElement(), gen.new Piece(null, gt(definition.getShortElement()), null)));
} else if (fallback != null && fallback.hasShort()) {
if (!c.getPieces().isEmpty()) c.addPiece(gen.new Piece("br"));
if (!c.getPieces().isEmpty()) { c.addPiece(gen.new Piece("br")); }
c.addPiece(gen.new Piece(null, gt(fallback.getShortElement()), null).addStyle("opacity: 0.5"));
}
if (url != null) {
@ -4041,7 +4183,7 @@ public class ProfileUtilities extends TranslatingUtilities {
}
if (definition.hasSlicing()) {
if (!c.getPieces().isEmpty()) c.addPiece(gen.new Piece("br"));
if (!c.getPieces().isEmpty()) { c.addPiece(gen.new Piece("br")); }
c.getPieces().add(gen.new Piece(null, translate("sd.table", "Slice")+": ", null).addStyle("font-weight:bold"));
c.getPieces().add(gen.new Piece(null, describeSlice(definition.getSlicing()), null));
}
@ -4095,7 +4237,7 @@ public class ProfileUtilities extends TranslatingUtilities {
}
if (definition.hasFixed()) {
if (!c.getPieces().isEmpty()) c.addPiece(gen.new Piece("br"));
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()) {
String s = buildJson(definition.getFixed());
@ -4113,7 +4255,7 @@ public class ProfileUtilities extends TranslatingUtilities {
c.getPieces().add(p);
}
} else if (definition.hasPattern()) {
if (!c.getPieces().isEmpty()) c.addPiece(gen.new Piece("br"));
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())
c.getPieces().add(checkForNoChange(definition.getPattern(), gen.new Piece(null, buildJson(definition.getPattern()), null).addStyle("color: darkgreen")));
@ -4123,13 +4265,13 @@ public class ProfileUtilities extends TranslatingUtilities {
}
} else if (definition.hasExample()) {
for (ElementDefinitionExampleComponent ex : definition.getExample()) {
if (!c.getPieces().isEmpty()) c.addPiece(gen.new Piece("br"));
if (!c.getPieces().isEmpty()) { c.addPiece(gen.new Piece("br")); }
c.getPieces().add(checkForNoChange(ex, gen.new Piece(null, translate("sd.table", "Example")+("".equals("General")? "" : " "+ex.getLabel())+": ", null).addStyle("font-weight:bold")));
c.getPieces().add(checkForNoChange(ex, gen.new Piece(null, buildJson(ex.getValue()), null).addStyle("color: darkgreen")));
}
}
if (definition.hasMaxLength() && definition.getMaxLength()!=0) {
if (!c.getPieces().isEmpty()) c.addPiece(gen.new Piece("br"));
if (!c.getPieces().isEmpty()) { c.addPiece(gen.new Piece("br")); }
c.getPieces().add(checkForNoChange(definition.getMaxLengthElement(), gen.new Piece(null, "Max Length: ", null).addStyle("font-weight:bold")));
c.getPieces().add(checkForNoChange(definition.getMaxLengthElement(), gen.new Piece(null, Integer.toString(definition.getMaxLength()), null).addStyle("color: darkgreen")));
}
@ -4367,7 +4509,7 @@ public class ProfileUtilities extends TranslatingUtilities {
}
if (definition.hasSlicing()) {
if (!c.getPieces().isEmpty()) c.addPiece(gen.new Piece("br"));
if (!c.getPieces().isEmpty()) { c.addPiece(gen.new Piece("br")); }
c.getPieces().add(gen.new Piece(null, "Slice: ", null).addStyle("font-weight:bold"));
c.getPieces().add(gen.new Piece(null, describeSlice(definition.getSlicing()), null));
}
@ -4389,12 +4531,16 @@ public class ProfileUtilities extends TranslatingUtilities {
}
}
for (ElementDefinitionConstraintComponent inv : definition.getConstraint()) {
if (!c.getPieces().isEmpty()) c.addPiece(gen.new Piece("br"));
if (!c.getPieces().isEmpty()) { c.addPiece(gen.new Piece("br")); }
c.getPieces().add(checkForNoChange(inv, gen.new Piece(null, inv.getKey()+": ", null).addStyle("font-weight:bold")));
if (inv.getHumanElement().hasExtension("http://hl7.org/fhir/StructureDefinition/rendering-markdown")) {
c.addMarkdown(inv.getHumanElement().getExtensionString("http://hl7.org/fhir/StructureDefinition/rendering-markdown"));
} else {
c.getPieces().add(checkForNoChange(inv, gen.new Piece(null, inv.getHuman(), null)));
}
}
if (definition.hasFixed()) {
if (!c.getPieces().isEmpty()) c.addPiece(gen.new Piece("br"));
if (!c.getPieces().isEmpty()) { c.addPiece(gen.new Piece("br")); }
c.getPieces().add(checkForNoChange(definition.getFixed(), gen.new Piece(null, "Fixed Value: ", null).addStyle("font-weight:bold")));
String s = buildJson(definition.getFixed());
String link = null;
@ -4402,18 +4548,18 @@ public class ProfileUtilities extends TranslatingUtilities {
link = pkp.getLinkForUrl(corePath, s);
c.getPieces().add(checkForNoChange(definition.getFixed(), gen.new Piece(link, s, null).addStyle("color: darkgreen")));
} else if (definition.hasPattern()) {
if (!c.getPieces().isEmpty()) c.addPiece(gen.new Piece("br"));
if (!c.getPieces().isEmpty()) { c.addPiece(gen.new Piece("br")); }
c.getPieces().add(checkForNoChange(definition.getPattern(), gen.new Piece(null, "Required Pattern: ", null).addStyle("font-weight:bold")));
c.getPieces().add(checkForNoChange(definition.getPattern(), gen.new Piece(null, buildJson(definition.getPattern()), null).addStyle("color: darkgreen")));
} else if (definition.hasExample()) {
for (ElementDefinitionExampleComponent ex : definition.getExample()) {
if (!c.getPieces().isEmpty()) c.addPiece(gen.new Piece("br"));
if (!c.getPieces().isEmpty()) { c.addPiece(gen.new Piece("br")); }
c.getPieces().add(checkForNoChange(ex, gen.new Piece(null, "Example'"+("".equals("General")? "" : " "+ex.getLabel()+"'")+": ", null).addStyle("font-weight:bold")));
c.getPieces().add(checkForNoChange(ex, gen.new Piece(null, buildJson(ex.getValue()), null).addStyle("color: darkgreen")));
}
}
if (definition.hasMaxLength() && definition.getMaxLength()!=0) {
if (!c.getPieces().isEmpty()) c.addPiece(gen.new Piece("br"));
if (!c.getPieces().isEmpty()) { c.addPiece(gen.new Piece("br")); }
c.getPieces().add(checkForNoChange(definition.getMaxLengthElement(), gen.new Piece(null, "Max Length: ", null).addStyle("font-weight:bold")));
c.getPieces().add(checkForNoChange(definition.getMaxLengthElement(), gen.new Piece(null, Integer.toString(definition.getMaxLength()), null).addStyle("color: darkgreen")));
}
@ -4434,14 +4580,14 @@ public class ProfileUtilities extends TranslatingUtilities {
}
}
if (definition.hasDefinition()) {
if (!c.getPieces().isEmpty()) c.addPiece(gen.new Piece("br"));
if (!c.getPieces().isEmpty()) { c.addPiece(gen.new Piece("br")); }
c.getPieces().add(gen.new Piece(null, "Definition: ", null).addStyle("font-weight:bold"));
c.addPiece(gen.new Piece("br"));
c.addMarkdown(definition.getDefinition());
// c.getPieces().add(checkForNoChange(definition.getCommentElement(), gen.new Piece(null, definition.getComment(), null)));
}
if (definition.getComment()!=null) {
if (!c.getPieces().isEmpty()) c.addPiece(gen.new Piece("br"));
if (!c.getPieces().isEmpty()) { c.addPiece(gen.new Piece("br")); }
c.getPieces().add(gen.new Piece(null, "Comments: ", null).addStyle("font-weight:bold"));
c.addPiece(gen.new Piece("br"));
c.addMarkdown(definition.getComment());
@ -5935,6 +6081,64 @@ public class ProfileUtilities extends TranslatingUtilities {
}
public List<ElementChoiceGroup> readChoices(ElementDefinition ed, List<ElementDefinition> children) {
List<ElementChoiceGroup> result = new ArrayList<>();
for (ElementDefinitionConstraintComponent c : ed.getConstraint()) {
ElementChoiceGroup grp = processConstraint(children, c);
if (grp != null) {
result.add(grp);
}
}
return result;
}
private ElementChoiceGroup processConstraint(List<ElementDefinition> children, ElementDefinitionConstraintComponent c) {
if (!c.hasExpression()) {
return null;
}
ExpressionNode expr = fpe.parse(c.getExpression());
if (expr.getKind() != Kind.Group || expr.getOpNext() == null || !(expr.getOperation() == Operation.Equals || expr.getOperation() == Operation.LessOrEqual)) {
return null;
}
ExpressionNode n1 = expr.getGroup();
ExpressionNode n2 = expr.getOpNext();
if (n2.getKind() != Kind.Constant || n2.getInner() != null || n2.getOpNext() != null || !"1".equals(n2.getConstant().primitiveValue())) {
return null;
}
ElementChoiceGroup grp = new ElementChoiceGroup(c.getKey(), expr.getOperation() == Operation.Equals);
while (n1 != null) {
if (n1.getKind() != Kind.Name || n1.getInner() != null) {
return null;
}
grp.elements.add(n1.getName());
if (n1.getOperation() == null || n1.getOperation() == Operation.Union) {
n1 = n1.getOpNext();
} else {
return null;
}
}
int total = 0;
for (String n : grp.elements) {
boolean found = false;
for (ElementDefinition child : children) {
String name = tail(child.getPath());
if (n.equals(name)) {
found = true;
if (!"0".equals(child.getMax())) {
total++;
}
}
}
if (!found) {
return null;
}
}
if (total <= 1) {
return null;
}
return grp;
}
}

3
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/Base.java
View File

@ -171,8 +171,9 @@ private Map<String, Object> userData;
List<Property> children = new ArrayList<Property>();
listChildren(children);
for (Property c : children)
if (c.getName().equals(name))
if (c.getName().equals(name) || c.getName().equals(name+"[x]")) {
return c;
}
return null;
}

3
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/BundleRenderer.java
View File

@ -295,8 +295,7 @@ public class BundleRenderer extends ResourceRenderer {
try {
xn = rr.build(be.getResource());
} catch (Exception e) {
xn = new XhtmlNode();
xn.para().b().tx("Exception generating narrative: "+e.getMessage());
xn = makeExceptionXhtml(e, "generating narrative");
}
}
root.blockquote().getChildNodes().addAll(checkInternalLinks(b, xn.getChildNodes()));

118
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/DataRenderer.java
View File

@ -14,10 +14,16 @@ import org.hl7.fhir.r5.model.Annotation;
import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.BaseDateTimeType;
import org.hl7.fhir.r5.model.CanonicalResource;
import org.hl7.fhir.r5.model.CanonicalType;
import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.CodeableConcept;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.ContactPoint;
import org.hl7.fhir.r5.model.DataRequirement;
import org.hl7.fhir.r5.model.DataRequirement.DataRequirementCodeFilterComponent;
import org.hl7.fhir.r5.model.DataRequirement.DataRequirementDateFilterComponent;
import org.hl7.fhir.r5.model.DataRequirement.DataRequirementSortComponent;
import org.hl7.fhir.r5.model.DataRequirement.SortDirection;
import org.hl7.fhir.r5.model.ContactPoint.ContactPointSystem;
import org.hl7.fhir.r5.model.DataType;
import org.hl7.fhir.r5.model.DateTimeType;
@ -52,6 +58,7 @@ import org.hl7.fhir.utilities.MarkDownProcessor;
import org.hl7.fhir.utilities.MarkDownProcessor.Dialect;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.validation.ValidationOptions;
import org.hl7.fhir.utilities.xhtml.NodeType;
import org.hl7.fhir.utilities.xhtml.XhtmlNode;
import org.hl7.fhir.utilities.xhtml.XhtmlParser;
@ -778,6 +785,102 @@ public class DataRenderer extends Renderer {
x.addText(!p.hasEnd() ? "(ongoing)" : p.getEndElement().toHumanDisplay());
}
public void renderDataRequirement(XhtmlNode x, DataRequirement dr) {
XhtmlNode tbl = x.table("grid");
XhtmlNode tr = tbl.tr();
XhtmlNode td = tr.td().colspan("2");
td.b().tx("Type");
td.tx(": ");
StructureDefinition sd = context.getWorker().fetchTypeDefinition(dr.getType().toCode());
if (sd != null && sd.hasUserData("path")) {
td.ah(sd.getUserString("path")).tx(dr.getType().toCode());
} else {
td.tx(dr.getType().toCode());
}
if (dr.hasProfile()) {
td.tx(" (");
boolean first = true;
for (CanonicalType p : dr.getProfile()) {
if (first) first = false; else td.tx(" | ");
sd = context.getWorker().fetchResource(StructureDefinition.class, p.getValue());
if (sd != null && sd.hasUserData("path")) {
td.ah(sd.getUserString("path")).tx(sd.present());
} else {
td.tx(p.asStringValue());
}
}
td.tx(")");
}
if (dr.hasSubject()) {
tr = tbl.tr();
td = tr.td().colspan("2");
td.b().tx("Subject");
if (dr.hasSubjectReference()) {
renderReference(td, dr.getSubjectReference());
} else {
renderCodeableConcept(td, dr.getSubjectCodeableConcept());
}
}
if (dr.hasCodeFilter() || dr.hasDateFilter()) {
tr = tbl.tr().backgroundColor("#efefef");
tr.td().tx("Filter");
tr.td().tx("Value");
}
for (DataRequirementCodeFilterComponent cf : dr.getCodeFilter()) {
tr = tbl.tr();
if (cf.hasPath()) {
tr.td().tx(cf.getPath());
} else {
tr.td().tx("Search on " +cf.getSearchParam());
}
if (cf.hasValueSet()) {
td = tr.td();
td.tx("In ValueSet ");
render(td, cf.getValueSetElement());
} else {
boolean first = true;
td = tr.td();
td.tx("One of these codes: ");
for (Coding c : cf.getCode()) {
if (first) first = false; else td.tx(", ");
render(td, c);
}
}
}
for (DataRequirementDateFilterComponent cf : dr.getDateFilter()) {
tr = tbl.tr();
if (cf.hasPath()) {
tr.td().tx(cf.getPath());
} else {
tr.td().tx("Search on " +cf.getSearchParam());
}
render(tr.td(), cf.getValue());
}
if (dr.hasSort() || dr.hasLimit()) {
tr = tbl.tr();
td = tr.td().colspan("2");
if (dr.hasLimit()) {
td.b().tx("Limit");
td.tx(": ");
td.tx(dr.getLimit());
if (dr.hasSort()) {
td.tx(", ");
}
}
if (dr.hasSort()) {
td.b().tx("Sort");
td.tx(": ");
boolean first = true;
for (DataRequirementSortComponent p : dr.getSort()) {
if (first) first = false; else td.tx(" | ");
td.tx(p.getDirection() == SortDirection.ASCENDING ? "+" : "-");
td.tx(p.getPath());
}
}
}
}
private String displayTiming(Timing s) throws FHIRException {
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
if (s.hasCode())
@ -919,6 +1022,21 @@ public class DataRenderer extends Renderer {
}
public XhtmlNode makeExceptionXhtml(Exception e, String function) {
XhtmlNode xn;
xn = new XhtmlNode(NodeType.Element, "div");
xn.para().b().tx("Exception "+function+": "+e.getMessage()).addComment(getStackTrace(e));
return xn;
}
private String getStackTrace(Exception e) {
StringBuilder b = new StringBuilder();
b.append("\r\n");
for (StackTraceElement t : e.getStackTrace()) {
b.append(t.getClassName()+"."+t.getMethodName()+" ("+t.getFileName()+":"+t.getLineNumber());
b.append("\r\n");
}
return b.toString();
}
}

8
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/ParametersRenderer.java
View File

@ -31,13 +31,19 @@ import org.hl7.fhir.utilities.xhtml.XhtmlNode;
public class ParametersRenderer extends ResourceRenderer {
public ParametersRenderer(RenderingContext context) {
super(context);
}
public ParametersRenderer(RenderingContext context, ResourceContext rcontext) {
super(context, rcontext);
}
@Override
public boolean render(XhtmlNode x, Resource r) throws FHIRFormatError, DefinitionException, IOException, FHIRException, EOperationOutcome {
x.h2().tx("Parameters");
XhtmlNode tbl = x.table("grid");
params(tbl, ((Parameters) r).getParameter(), 0);
return false;
}

120
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/ProfileDrivenRenderer.java
View File

@ -27,6 +27,7 @@ import org.hl7.fhir.r5.model.CodeableReference;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.ContactDetail;
import org.hl7.fhir.r5.model.ContactPoint;
import org.hl7.fhir.r5.model.DataRequirement;
import org.hl7.fhir.r5.model.DateTimeType;
import org.hl7.fhir.r5.model.DomainResource;
import org.hl7.fhir.r5.model.Dosage;
@ -40,6 +41,7 @@ import org.hl7.fhir.r5.model.InstantType;
import org.hl7.fhir.r5.model.Meta;
import org.hl7.fhir.r5.model.Narrative;
import org.hl7.fhir.r5.model.Narrative.NarrativeStatus;
import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionKind;
import org.hl7.fhir.r5.model.Period;
import org.hl7.fhir.r5.model.PrimitiveType;
import org.hl7.fhir.r5.model.Property;
@ -82,6 +84,7 @@ import org.w3c.dom.Element;
public class ProfileDrivenRenderer extends ResourceRenderer {
private Set<String> containedIds = new HashSet<>();
private boolean hasExtensions;
public ProfileDrivenRenderer(RenderingContext context, ResourceContext rcontext) {
super(context, rcontext);
@ -108,12 +111,13 @@ public class ProfileDrivenRenderer extends ResourceRenderer {
System.out.println("hah!");
}
containedIds.clear();
hasExtensions = false;
generateByProfile(r, sd, r.root(), sd.getSnapshot().getElement(), ed, context.getProfileUtilities().getChildList(sd, ed), x, r.fhirType(), false, 0);
} catch (Exception e) {
e.printStackTrace();
x.para().b().style("color: maroon").tx("Exception generating Narrative: "+e.getMessage());
}
return false;
return hasExtensions;
}
@Override
@ -317,6 +321,12 @@ public class ProfileDrivenRenderer extends ResourceRenderer {
} else {
x.addText("??");
}
} else if (e instanceof org.hl7.fhir.r5.model.Integer64Type) {
if (((org.hl7.fhir.r5.model.Integer64Type) e).hasValue()) {
x.addText(Long.toString(((org.hl7.fhir.r5.model.Integer64Type) e).getValue()));
} else {
x.addText("??");
}
} else if (e instanceof org.hl7.fhir.r5.model.DecimalType) {
x.addText(((org.hl7.fhir.r5.model.DecimalType) e).getValue().toString());
} else if (e instanceof HumanName) {
@ -378,15 +388,13 @@ public class ProfileDrivenRenderer extends ResourceRenderer {
}
} else if (e instanceof Resource) {
return;
} else if (e instanceof DataRequirement) {
DataRequirement p = (DataRequirement) e;
renderDataRequirement(x, p);
} else if (e instanceof ElementDefinition) {
x.tx("todo-bundle");
} else if (e != null && !(e instanceof Attachment) && !(e instanceof Narrative) && !(e instanceof Meta)) {
StructureDefinition sd = getContext().getWorker().fetchTypeDefinition(e.fhirType());
if (sd == null)
throw new NotImplementedException("type "+e.getClass().getName()+" not handled yet, and no structure found");
else
generateByProfile(res, sd, ew, sd.getSnapshot().getElement(), sd.getSnapshot().getElementFirstRep(),
getChildrenForPath(sd.getSnapshot().getElement(), sd.getSnapshot().getElementFirstRep().getPath()), x, path, showCodeDetails, indent + 1);
throw new NotImplementedException("type "+e.getClass().getName()+" not handled - should not be here");
}
}
@ -547,12 +555,28 @@ public class ProfileDrivenRenderer extends ResourceRenderer {
private boolean isPrimitive(ElementDefinition e) {
//we can tell if e is a primitive because it has types
if (e.getType().isEmpty())
if (e.getType().isEmpty()) {
return false;
if (e.getType().size() == 1 && isBase(e.getType().get(0).getWorkingCode()))
}
if (e.getType().size() == 1 && isBase(e.getType().get(0).getWorkingCode())) {
return false;
}
if (e.getType().size() > 1) {
return true;
// return !e.getType().isEmpty()
}
StructureDefinition sd = context.getWorker().fetchTypeDefinition(e.getTypeFirstRep().getCode());
if (sd != null) {
if (sd.getKind() == StructureDefinitionKind.PRIMITIVETYPE) {
return true;
}
if (sd.getKind() == StructureDefinitionKind.COMPLEXTYPE) {
if (Utilities.existsInList(e.getTypeFirstRep().getCode(), "Extension", "CodeableConcept", "Coding", "Annotation", "Identifier", "HumanName", "SampledData",
"Address", "ContactPoint", "ContactDetail", "Timing", "Range", "Quantity", "Ratio", "Period", "Reference")) {
return true;
}
}
}
return false;
}
private boolean isBase(String code) {
@ -612,7 +636,19 @@ public class ProfileDrivenRenderer extends ResourceRenderer {
for (PropertyWrapper p : splitExtensions(profile, e.children())) {
if (p.hasValues()) {
ElementDefinition child = getElementDefinition(children, path+"."+p.getName(), p);
if (child == null) {
child = p.getElementDefinition();
}
if (child != null) {
generateElementByProfile(res, profile, allElements, x, path, showCodeDetails, indent, p, child);
}
}
}
}
}
public void generateElementByProfile(ResourceWrapper res, StructureDefinition profile, List<ElementDefinition> allElements, XhtmlNode x, String path,
boolean showCodeDetails, int indent, PropertyWrapper p, ElementDefinition child) throws UnsupportedEncodingException, IOException, EOperationOutcome {
Map<String, String> displayHints = readDisplayHints(child);
if ("DomainResource.contained".equals(child.getBase().getPath())) {
// if (p.getValues().size() > 0 && child != null) {
@ -621,11 +657,14 @@ public class ProfileDrivenRenderer extends ResourceRenderer {
// }
// }
} else if (!exemptFromRendering(child)) {
if (isExtension(p)) {
hasExtensions = true;
}
List<ElementDefinition> grandChildren = getChildrenForPath(allElements, path+"."+p.getName());
filterGrandChildren(grandChildren, path+"."+p.getName(), p);
if (p.getValues().size() > 0) {
if (isPrimitive(child)) {
XhtmlNode para = x.para();
XhtmlNode para = x.isPara() ? para = x : x.para();
String name = p.getName();
if (name.endsWith("[x]"))
name = name.substring(0, name.length() - 3);
@ -639,17 +678,18 @@ public class ProfileDrivenRenderer extends ResourceRenderer {
} else {
boolean first = true;
for (BaseWrapper v : p.getValues()) {
if (first)
if (first) {
first = false;
else
} else {
para.tx(", ");
}
renderLeaf(res, v, child, x, para, false, showCodeDetails, displayHints, path, indent);
}
}
}
} else if (canDoTable(path, p, grandChildren)) {
} else if (canDoTable(path, p, grandChildren, x)) {
x.addTag(getHeader()).addText(Utilities.capitalize(Utilities.camelCase(Utilities.pluralizeMe(p.getName()))));
XhtmlNode tbl = x.table( "grid");
XhtmlNode tbl = x.table("grid");
XhtmlNode tr = tbl.tr();
tr.td().tx("-"); // work around problem with empty table rows
addColumnHeadings(tr, grandChildren);
@ -660,11 +700,33 @@ public class ProfileDrivenRenderer extends ResourceRenderer {
addColumnValues(res, tr, grandChildren, v, showCodeDetails, displayHints, path, indent);
}
}
} else if (isExtension(p)) {
for (BaseWrapper v : p.getValues()) {
if (v != null) {
PropertyWrapper vp = v.getChildByName("value");
PropertyWrapper ev = v.getChildByName("extension");
if (vp.hasValues()) {
BaseWrapper vv = vp.value();
XhtmlNode para = x.para();
para.b().addText(p.getStructure().present());
para.tx(": ");
renderLeaf(res, v, child, x, para, false, showCodeDetails, displayHints, path, indent);
} else if (ev.hasValues()) {
XhtmlNode bq = x.addTag("blockquote");
bq.para().b().addText(isExtension(p) ? p.getStructure().present() : p.getName());
for (BaseWrapper vv : ev.getValues()) {
StructureDefinition ex = context.getWorker().fetchTypeDefinition("Extension");
List<ElementDefinition> children = getChildrenForPath(ex.getSnapshot().getElement(), "Extension");
generateByProfile(res, ex, vv, allElements, child, children, bq, "Extension", showCodeDetails, indent+1);
}
}
}
}
} else {
for (BaseWrapper v : p.getValues()) {
if (v != null) {
XhtmlNode bq = x.addTag("blockquote");
bq.para().b().addText(p.getName());
bq.para().b().addText(isExtension(p) ? p.getStructure().present() : p.getName());
generateByProfile(res, profile, v, allElements, child, grandChildren, bq, path+"."+p.getName(), showCodeDetails, indent+1);
}
}
@ -672,10 +734,6 @@ public class ProfileDrivenRenderer extends ResourceRenderer {
}
}
}
}
}
}
}
private String getHeader() {
@ -698,7 +756,13 @@ public class ProfileDrivenRenderer extends ResourceRenderer {
return res;
}
private boolean canDoTable(String path, PropertyWrapper p, List<ElementDefinition> grandChildren) {
private boolean canDoTable(String path, PropertyWrapper p, List<ElementDefinition> grandChildren, XhtmlNode x) {
if (isExtension(p)) {
return false;
}
if (x.getName().equals("p")) {
return false;
}
for (ElementDefinition e : grandChildren) {
List<PropertyWrapper> values = getValues(path, p, e);
if (values.size() > 1 || !isPrimitive(e) || !canCollapse(e))
@ -707,6 +771,10 @@ public class ProfileDrivenRenderer extends ResourceRenderer {
return true;
}
public boolean isExtension(PropertyWrapper p) {
return p.getName().contains("extension[");
}
private boolean canCollapse(ElementDefinition e) {
// we can collapse any data type
@ -784,18 +852,20 @@ public class ProfileDrivenRenderer extends ResourceRenderer {
getContext().getWorker().cacheResource(ed);
}
}
if (p.getName().equals("modifierExtension") && ed == null)
if (p.getName().equals("modifierExtension") && ed == null) {
throw new DefinitionException("Unknown modifier extension "+url);
}
PropertyWrapper pe = map.get(p.getName()+"["+url+"]");
if (pe == null) {
if (ed == null) {
if (url.startsWith("http://hl7.org/fhir") && !url.startsWith("http://hl7.org/fhir/us"))
if (url.startsWith("http://hl7.org/fhir") && !url.startsWith("http://hl7.org/fhir/us")) {
throw new DefinitionException("unknown extension "+url);
}
// System.out.println("unknown extension "+url);
pe = new PropertyWrapperDirect(this.context, new Property(p.getName()+"["+url+"]", p.getTypeCode(), p.getDefinition(), p.getMinCardinality(), p.getMaxCardinality(), ex));
pe = new PropertyWrapperDirect(this.context, new Property(p.getName()+"["+url+"]", p.getTypeCode(), p.getDefinition(), p.getMinCardinality(), p.getMaxCardinality(), ex), null);
} else {
ElementDefinition def = ed.getSnapshot().getElement().get(0);
pe = new PropertyWrapperDirect(this.context, new Property(p.getName()+"["+url+"]", "Extension", def.getDefinition(), def.getMin(), def.getMax().equals("*") ? Integer.MAX_VALUE : Integer.parseInt(def.getMax()), ex));
pe = new PropertyWrapperDirect(this.context, new Property(p.getName()+"["+url+"]", "Extension", def.getDefinition(), def.getMin(), def.getMax().equals("*") ? Integer.MAX_VALUE : Integer.parseInt(def.getMax()), ex), ed.getSnapshot().getElementFirstRep());
((PropertyWrapperDirect) pe).getWrapped().setStructure(ed);
}
results.add(pe);

3
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/RendererFactory.java
View File

@ -72,6 +72,9 @@ public class RendererFactory {
if ("OperationOutcome".equals(resourceName)) {
return new OperationOutcomeRenderer(context);
}
if ("Parameters".equals(resourceName)) {
return new ParametersRenderer(context);
}
return new ProfileDrivenRenderer(context);
}

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

@ -8,6 +8,7 @@ import java.util.List;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.ElementDefinition;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.model.Narrative.NarrativeStatus;
import org.hl7.fhir.r5.renderers.ResourceRenderer;
@ -28,6 +29,7 @@ public class BaseWrappers {
public int getMinCardinality();
public int getMaxCardinality();
public StructureDefinition getStructure();
public ElementDefinition getElementDefinition();
public BaseWrapper value();
public ResourceWrapper getAsResource();
public String fhirType();
@ -87,7 +89,7 @@ public class BaseWrappers {
@Override
public boolean has(String name) {
for (PropertyWrapper p : children()) {
if (p.getName().equals(name)) {
if (p.getName().equals(name) || p.getName().equals(name+"[x]") ) {
return p.hasValues();
}
}
@ -97,7 +99,7 @@ public class BaseWrappers {
@Override
public Base get(String name) throws UnsupportedEncodingException, FHIRException, IOException {
for (PropertyWrapper p : children()) {
if (p.getName().equals(name)) {
if (p.getName().equals(name) || p.getName().equals(name+"[x]")) {
if (p.hasValues()) {
return p.getValues().get(0).getBase();
} else {
@ -111,7 +113,7 @@ public class BaseWrappers {
@Override
public List<BaseWrapper> children(String name) throws UnsupportedEncodingException, FHIRException, IOException {
for (PropertyWrapper p : children()) {
if (p.getName().equals(name)) {
if (p.getName().equals(name) || p.getName().equals(name+"[x]")) {
List<BaseWrapper> res = new ArrayList<>();
for (BaseWrapper b : p.getValues()) {
res.add(b);

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

@ -206,6 +206,11 @@ public class DOMWrappers {
return getTypeCode();
}
@Override
public ElementDefinition getElementDefinition() {
return definition;
}
}
public static class ResourceWrapperElement extends WrapperBaseImpl implements ResourceWrapper {

15
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/utils/DirectWrappers.java
View File

@ -8,6 +8,7 @@ import java.util.List;
import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.CanonicalResource;
import org.hl7.fhir.r5.model.DomainResource;
import org.hl7.fhir.r5.model.ElementDefinition;
import org.hl7.fhir.r5.model.Encounter;
import org.hl7.fhir.r5.model.Narrative.NarrativeStatus;
import org.hl7.fhir.r5.model.Patient;
@ -29,6 +30,7 @@ public class DirectWrappers {
public static class PropertyWrapperDirect extends RendererWrapperImpl implements PropertyWrapper {
private Property wrapped;
private List<BaseWrapper> list;
private ElementDefinition ed;
public PropertyWrapperDirect(RenderingContext context, Property wrapped) {
super(context);
@ -37,6 +39,14 @@ public class DirectWrappers {
this.wrapped = wrapped;
}
public PropertyWrapperDirect(RenderingContext context, Property wrapped, ElementDefinition ed) {
super(context);
if (wrapped == null)
throw new Error("wrapped == null");
this.wrapped = wrapped;
this.ed = ed;
}
@Override
public String getName() {
return wrapped.getName();
@ -106,6 +116,11 @@ public class DirectWrappers {
public String fhirType() {
return wrapped.getTypeCode();
}
@Override
public ElementDefinition getElementDefinition() {
return ed;
}
}
public static class BaseWrapperDirect extends WrapperBaseImpl implements BaseWrapper {

7
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/utils/ElementWrappers.java
View File

@ -58,7 +58,7 @@ public class ElementWrappers {
throw new FHIRException(e.getMessage(), e);
}
if (context.getParser() == null) {
System.out.println("Noe version specific parser provided");
System.out.println("No version specific parser provided");
}
if (context.getParser() == null) {
throw new Error("No type parser provided to renderer context");
@ -324,6 +324,11 @@ public class ElementWrappers {
return getTypeCode();
}
@Override
public ElementDefinition getElementDefinition() {
return definition;
}
}
}

117
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/FHIRPathEngine.java
View File

@ -319,6 +319,20 @@ public class FHIRPathEngine {
}
}
public FHIRPathEngine(IWorkerContext worker, ProfileUtilities utilities) {
super();
this.worker = worker;
profileUtilities = utilities;
for (StructureDefinition sd : worker.getStructures()) {
if (sd.getDerivation() == TypeDerivationRule.SPECIALIZATION && sd.getKind() != StructureDefinitionKind.LOGICAL) {
allTypes.put(sd.getName(), sd);
}
if (sd.getDerivation() == TypeDerivationRule.SPECIALIZATION && sd.getKind() == StructureDefinitionKind.PRIMITIVETYPE) {
primitiveTypes.add(sd.getName());
}
}
}
// --- 3 methods to override in children -------------------------------------------------------
// if you don't override, it falls through to the using the base reference implementation
@ -781,6 +795,10 @@ public class FHIRPathEngine {
return item.primitiveValue();
} else if (item instanceof Quantity) {
Quantity q = (Quantity) item;
if (q.hasUnit() && Utilities.existsInList(q.getUnit(), "year", "years", "month", "months", "week", "weeks", "day", "days", "hour", "hours", "minute", "minutes", "second", "seconds", "millisecond", "milliseconds")
&& (!q.hasSystem() || q.getSystem().equals("http://unitsofmeasure.org"))) {
return q.getValue().toPlainString()+" "+q.getUnit();
}
if (q.getSystem().equals("http://unitsofmeasure.org")) {
String u = "'"+q.getCode()+"'";
return q.getValue().toPlainString()+" "+u;
@ -940,12 +958,14 @@ public class FHIRPathEngine {
if (!isString && !lexer.done() && (result.getConstant() instanceof IntegerType || result.getConstant() instanceof DecimalType) && (lexer.isStringConstant() || lexer.hasToken("year", "years", "month", "months", "week", "weeks", "day", "days", "hour", "hours", "minute", "minutes", "second", "seconds", "millisecond", "milliseconds"))) {
// it's a quantity
String ucum = null;
String unit = null;
if (lexer.hasToken("year", "years", "month", "months", "week", "weeks", "day", "days", "hour", "hours", "minute", "minutes", "second", "seconds", "millisecond", "milliseconds")) {
String s = lexer.take();
unit = s;
if (s.equals("year") || s.equals("years")) {
ucum = "a";
// this is not the UCUM year
} else if (s.equals("month") || s.equals("months")) {
ucum = "mo";
// this is not the UCUM month
} else if (s.equals("week") || s.equals("weeks")) {
ucum = "wk";
} else if (s.equals("day") || s.equals("days")) {
@ -962,7 +982,7 @@ public class FHIRPathEngine {
} else {
ucum = lexer.readConstant("units");
}
result.setConstant(new Quantity().setValue(new BigDecimal(result.getConstant().primitiveValue())).setSystem("http://unitsofmeasure.org").setCode(ucum));
result.setConstant(new Quantity().setValue(new BigDecimal(result.getConstant().primitiveValue())).setUnit(unit).setSystem(ucum == null ? null : "http://unitsofmeasure.org").setCode(ucum));
}
result.setEnd(lexer.getCurrentLocation());
} else if ("(".equals(lexer.getCurrent())) {
@ -1920,18 +1940,50 @@ public class FHIRPathEngine {
}
}
private boolean qtyEqual(Quantity left, Quantity right) {
private Boolean qtyEqual(Quantity left, Quantity right) {
if (!left.hasValue() && !right.hasValue()) {
return true;
}
if (!left.hasValue() || !right.hasValue()) {
return null;
}
if (worker.getUcumService() != null) {
DecimalType dl = qtyToCanonical(left);
DecimalType dr = qtyToCanonical(right);
Pair dl = qtyToCanonicalPair(left);
Pair dr = qtyToCanonicalPair(right);
if (dl != null && dr != null) {
return doEquals(dl, dr);
if (dl.getCode().equals(dr.getCode())) {
return doEquals(new DecimalType(dl.getValue().asDecimal()), new DecimalType(dr.getValue().asDecimal()));
} else {
return false;
}
}
return left.equals(right);
}
if (left.hasCode() || right.hasCode()) {
if (!(left.hasCode() && right.hasCode()) || !left.getCode().equals(right.getCode())) {
return null;
}
} else if (!left.hasUnit() || right.hasUnit()) {
if (!(left.hasUnit() && right.hasUnit()) || !left.getUnit().equals(right.getUnit())) {
return null;
}
}
return doEquals(new DecimalType(left.getValue()), new DecimalType(right.getValue()));
}
private DecimalType qtyToCanonical(Quantity q) {
private Pair qtyToCanonicalPair(Quantity q) {
if (!"http://unitsofmeasure.org".equals(q.getSystem())) {
return null;
}
try {
Pair p = new Pair(new Decimal(q.getValue().toPlainString()), q.getCode() == null ? "1" : q.getCode());
Pair c = worker.getUcumService().getCanonicalForm(p);
return c;
} catch (UcumException e) {
return null;
}
}
private DecimalType qtyToCanonicalDecimal(Quantity q) {
if (!"http://unitsofmeasure.org".equals(q.getSystem())) {
return null;
}
@ -1961,15 +2013,34 @@ public class FHIRPathEngine {
}
private boolean qtyEquivalent(Quantity left, Quantity right) throws PathEngineException {
private Boolean qtyEquivalent(Quantity left, Quantity right) throws PathEngineException {
if (!left.hasValue() && !right.hasValue()) {
return true;
}
if (!left.hasValue() || !right.hasValue()) {
return null;
}
if (worker.getUcumService() != null) {
DecimalType dl = qtyToCanonical(left);
DecimalType dr = qtyToCanonical(right);
Pair dl = qtyToCanonicalPair(left);
Pair dr = qtyToCanonicalPair(right);
if (dl != null && dr != null) {
return doEquivalent(dl, dr);
if (dl.getCode().equals(dr.getCode())) {
return doEquivalent(new DecimalType(dl.getValue().asDecimal()), new DecimalType(dr.getValue().asDecimal()));
} else {
return false;
}
}
return left.equals(right);
}
if (left.hasCode() || right.hasCode()) {
if (!(left.hasCode() && right.hasCode()) || !left.getCode().equals(right.getCode())) {
return null;
}
} else if (!left.hasUnit() || right.hasUnit()) {
if (!(left.hasUnit() && right.hasUnit()) || !left.getUnit().equals(right.getUnit())) {
return null;
}
}
return doEquivalent(new DecimalType(left.getValue()), new DecimalType(right.getValue()));
}
@ -2058,9 +2129,9 @@ public class FHIRPathEngine {
return makeBoolean(false);
} else {
List<Base> dl = new ArrayList<Base>();
dl.add(qtyToCanonical((Quantity) left.get(0)));
dl.add(qtyToCanonicalDecimal((Quantity) left.get(0)));
List<Base> dr = new ArrayList<Base>();
dr.add(qtyToCanonical((Quantity) right.get(0)));
dr.add(qtyToCanonicalDecimal((Quantity) right.get(0)));
return opLessThan(dl, dr);
}
}
@ -2105,9 +2176,9 @@ public class FHIRPathEngine {
return makeBoolean(false);
} else {
List<Base> dl = new ArrayList<Base>();
dl.add(qtyToCanonical((Quantity) left.get(0)));
dl.add(qtyToCanonicalDecimal((Quantity) left.get(0)));
List<Base> dr = new ArrayList<Base>();
dr.add(qtyToCanonical((Quantity) right.get(0)));
dr.add(qtyToCanonicalDecimal((Quantity) right.get(0)));
return opGreater(dl, dr);
}
}
@ -2155,9 +2226,9 @@ public class FHIRPathEngine {
return makeBoolean(false);
} else {
List<Base> dl = new ArrayList<Base>();
dl.add(qtyToCanonical((Quantity) left.get(0)));
dl.add(qtyToCanonicalDecimal((Quantity) left.get(0)));
List<Base> dr = new ArrayList<Base>();
dr.add(qtyToCanonical((Quantity) right.get(0)));
dr.add(qtyToCanonicalDecimal((Quantity) right.get(0)));
return opLessOrEqual(dl, dr);
}
}
@ -2203,9 +2274,9 @@ public class FHIRPathEngine {
return makeBoolean(false);
} else {
List<Base> dl = new ArrayList<Base>();
dl.add(qtyToCanonical((Quantity) left.get(0)));
dl.add(qtyToCanonicalDecimal((Quantity) left.get(0)));
List<Base> dr = new ArrayList<Base>();
dr.add(qtyToCanonical((Quantity) right.get(0)));
dr.add(qtyToCanonicalDecimal((Quantity) right.get(0)));
return opGreaterOrEqual(dl, dr);
}
}
@ -4843,7 +4914,7 @@ public class FHIRPathEngine {
if (s.equals("year") || s.equals("years")) {
return Quantity.fromUcum(v, "a");
} else if (s.equals("month") || s.equals("months")) {
return Quantity.fromUcum(v, "mo");
return Quantity.fromUcum(v, "mo_s");
} else if (s.equals("week") || s.equals("weeks")) {
return Quantity.fromUcum(v, "wk");
} else if (s.equals("day") || s.equals("days")) {

51
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/NPMPackageGenerator.java
View File

@ -104,17 +104,17 @@ public class NPMPackageGenerator {
private NpmPackageIndexBuilder indexer;
public NPMPackageGenerator(String destFile, String canonical, String url, PackageType kind, ImplementationGuide ig, Date date) throws FHIRException, IOException {
public NPMPackageGenerator(String destFile, String canonical, String url, PackageType kind, ImplementationGuide ig, Date date, boolean notForPublication) throws FHIRException, IOException {
super();
this.destFile = destFile;
start();
List<String> fhirVersion = new ArrayList<>();
for (Enumeration<FHIRVersion> v : ig.getFhirVersion())
fhirVersion.add(v.asStringValue());
buildPackageJson(canonical, kind, url, date, ig, fhirVersion);
buildPackageJson(canonical, kind, url, date, ig, fhirVersion, notForPublication);
}
public static NPMPackageGenerator subset(NPMPackageGenerator master, String destFile, String id, String name, Date date) throws FHIRException, IOException {
public static NPMPackageGenerator subset(NPMPackageGenerator master, String destFile, String id, String name, Date date, boolean notForPublication) throws FHIRException, IOException {
JsonObject p = master.packageJ.deepCopy();
p.remove("name");
p.addProperty("name", id);
@ -122,24 +122,30 @@ public class NPMPackageGenerator {
p.addProperty("type", PackageType.SUBSET.getCode());
p.remove("title");
p.addProperty("title", name);
return new NPMPackageGenerator(destFile, p, date);
if (notForPublication) {
p.addProperty("notForPublication", true);
}
public NPMPackageGenerator(String destFile, String canonical, String url, PackageType kind, ImplementationGuide ig, Date date, List<String> fhirVersion) throws FHIRException, IOException {
return new NPMPackageGenerator(destFile, p, date, notForPublication);
}
public NPMPackageGenerator(String destFile, String canonical, String url, PackageType kind, ImplementationGuide ig, Date date, List<String> fhirVersion, boolean notForPublication) throws FHIRException, IOException {
super();
this.destFile = destFile;
start();
buildPackageJson(canonical, kind, url, date, ig, fhirVersion);
buildPackageJson(canonical, kind, url, date, ig, fhirVersion, notForPublication);
}
public NPMPackageGenerator(String destFile, JsonObject npm, Date date) throws FHIRException, IOException {
public NPMPackageGenerator(String destFile, JsonObject npm, Date date, boolean notForPublication) throws FHIRException, IOException {
super();
String dt = new SimpleDateFormat("yyyyMMddHHmmss").format(date);
packageJ = npm;
packageManifest = new JsonObject();
packageManifest.addProperty("version", npm.get("version").getAsString());
packageManifest.addProperty("date", dt);
if (notForPublication) {
packageManifest.addProperty("notForPublication", true);
}
npm.addProperty("date", dt);
packageManifest.addProperty("name", npm.get("name").getAsString());
this.destFile = destFile;
@ -152,19 +158,23 @@ public class NPMPackageGenerator {
}
}
private void buildPackageJson(String canonical, PackageType kind, String web, Date date, ImplementationGuide ig, List<String> fhirVersion) throws FHIRException, IOException {
private void buildPackageJson(String canonical, PackageType kind, String web, Date date, ImplementationGuide ig, List<String> fhirVersion, boolean notForPublication) throws FHIRException, IOException {
String dtHuman = new SimpleDateFormat("EEE, MMM d, yyyy HH:mmZ", new Locale("en", "US")).format(date);
String dt = new SimpleDateFormat("yyyyMMddHHmmss").format(date);
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
if (!ig.hasPackageId())
if (!ig.hasPackageId()) {
b.append("packageId");
if (!ig.hasVersion())
}
if (!ig.hasVersion()) {
b.append("version");
if (!ig.hasFhirVersion())
}
if (!ig.hasFhirVersion()) {
b.append("fhirVersion");
if (!ig.hasLicense())
}
if (!ig.hasLicense()) {
b.append("license");
}
for (ImplementationGuideDependsOnComponent d : ig.getDependsOn()) {
if (!d.hasVersion()) {
b.append("dependsOn.version("+d.getUri()+")");
@ -177,14 +187,20 @@ public class NPMPackageGenerator {
npm.addProperty("tools-version", ToolsVersion.TOOLS_VERSION);
npm.addProperty("type", kind.getCode());
npm.addProperty("date", dt);
if (ig.hasLicense())
if (ig.hasLicense()) {
npm.addProperty("license", ig.getLicense().toCode());
}
npm.addProperty("canonical", canonical);
if (notForPublication) {
npm.addProperty("notForPublication", true);
}
npm.addProperty("url", web);
if (ig.hasTitle())
if (ig.hasTitle()) {
npm.addProperty("title", ig.getTitle());
if (ig.hasDescription())
}
if (ig.hasDescription()) {
npm.addProperty("description", ig.getDescription()+ " (built "+dtHuman+timezone()+")");
}
JsonArray vl = new JsonArray();
npm.add("fhirVersions", vl);
@ -205,8 +221,9 @@ public class NPMPackageGenerator {
dep.addProperty(d.getPackageId(), d.getVersion());
}
}
if (ig.hasPublisher())
if (ig.hasPublisher()) {
npm.addProperty("author", ig.getPublisher());
}
JsonArray m = new JsonArray();
for (ContactDetail t : ig.getContact()) {
String email = email(t.getTelecom());

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

@ -178,6 +178,7 @@ public class FHIRPathTests {
outcome.clear();
outcome.add(new BooleanType(ok));
}
System.out.println(name);
if (fp.hasLog()) {
System.out.println(name);
System.out.println(fp.takeLog());

60
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/NarrativeGenerationTests.java
View File

@ -11,22 +11,32 @@ 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;
@ -40,6 +50,15 @@ import org.xml.sax.SAXException;
public class NarrativeGenerationTests {
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);
}
}
public static final String WINDOWS = "WINDOWS";
private static final String HEADER = "<html><head>"+
@ -57,11 +76,13 @@ public class NarrativeGenerationTests {
public static class TestDetails {
private String id;
private boolean header;
private boolean meta;
public TestDetails(Element test) {
super();
id = test.getAttribute("id");
header = "true".equals(test.getAttribute("header"));
meta = "true".equals(test.getAttribute("meta"));
}
public String getId() {
@ -72,6 +93,10 @@ public class NarrativeGenerationTests {
return header;
}
public boolean isMeta() {
return meta;
}
}
public static Stream<Arguments> data() throws ParserConfigurationException, IOException, FHIRFormatError, SAXException {
@ -107,19 +132,30 @@ public class NarrativeGenerationTests {
rc.setHeader(test.isHeader());
rc.setDefinitionsTarget("test.html");
rc.setTerminologyServiceOptions(TerminologyServiceOptions.defaults());
IOUtils.copy(TestingUtilities.loadTestResourceStream("r5", "narrative", test.getId() + "-expected.xml"), new FileOutputStream(TestingUtilities.tempFile("narrative", test.getId() + "-expected.xml")));
DomainResource source;
if (TestingUtilities.findTestResource("r5", "narrative", test.getId() + "-input.json")) {
source = (DomainResource) new JsonParser().parse(TestingUtilities.loadTestResourceStream("r5", "narrative", test.getId() + "-input.json"));
rc.setParser(new TestTypeParser());
Resource source;
if (TestingUtilities.findTestResource("r5", "narrative", test.getId() + ".json")) {
source = (Resource) new JsonParser().parse(TestingUtilities.loadTestResourceStream("r5", "narrative", test.getId() + ".json"));
} else {
source = (DomainResource) new XmlParser().parse(TestingUtilities.loadTestResourceStream("r5", "narrative", test.getId() + "-input.xml"));
source = (Resource) new XmlParser().parse(TestingUtilities.loadTestResourceStream("r5", "narrative", test.getId() + ".xml"));
}
DomainResource target = (DomainResource) new XmlParser().parse(TestingUtilities.loadTestResourceStream("r5", "narrative", test.getId() + "-expected.xml"));
RendererFactory.factory(source, rc).render(source);
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(TestingUtilities.tempFile("narrative", test.getId() + "-actual.xml")), source);
source = (DomainResource) new XmlParser().parse(new FileInputStream(TestingUtilities.tempFile("narrative", test.getId() + "-actual.xml")));
String html = HEADER+new XhtmlComposer(true).compose(source.getText().getDiv())+FOOTER;
TextFile.stringToFile(html, TestingUtilities.tempFile("narrative", test.getId() + ".html"));
Assertions.assertTrue(source.equalsDeep(target), "Output does not match expected");
XhtmlNode x = RendererFactory.factory(source, rc).build(source);
String target = TextFile.streamToString(TestingUtilities.loadTestResourceStream("r5", "narrative", test.getId() + ".html"));
String output = HEADER+new XhtmlComposer(true, true).compose(x)+FOOTER;
TextFile.stringToFile(target, TestingUtilities.tempFile("narrative", test.getId() + ".target.html"));
TextFile.stringToFile(output, TestingUtilities.tempFile("narrative", test.getId() + ".output.html"));
Assertions.assertTrue(output.equals(target), "Output does not match expected");
if (test.isMeta()) {
org.hl7.fhir.r5.elementmodel.Element e = Manager.parse(context, TestingUtilities.loadTestResourceStream("r5", "narrative", test.getId() + ".xml"), FhirFormat.XML);
x = RendererFactory.factory(source, rc).render(new ElementWrappers.ResourceWrapperMetaElement(rc, e));
target = TextFile.streamToString(TestingUtilities.loadTestResourceStream("r5", "narrative", test.getId() + "-meta.html"));
output = HEADER+new XhtmlComposer(true, true).compose(x)+FOOTER;
TextFile.stringToFile(output, TestingUtilities.tempFile("narrative", test.getId() + "-meta.output.html"));
Assertions.assertTrue(output.equals(target), "Output does not match expected (meta)");
}
}
}

3
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/ResourceRoundTripTests.java
View File

@ -13,6 +13,7 @@ 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;
@ -20,6 +21,7 @@ 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 {
@ -52,4 +54,5 @@ public class ResourceRoundTripTests {
if (result == null)
throw new FHIRException("Bundle was null");
}
}

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>5.1.8-SNAPSHOT</version>
<version>5.1.9-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>5.1.8-SNAPSHOT</version>
<version>5.1.9-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

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

@ -56,6 +56,12 @@ public class MarkDownProcessor {
public String process(String source, String context) {
if (source == null) {
return null;
}
if ("".equals(source)) {
return "";
}
switch (dialect) {
case DARING_FIREBALL : return Processor.process(source);
case COMMON_MARK : return processCommonMark(source);

4
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/cache/NpmPackage.java vendored
View File

@ -1092,5 +1092,9 @@ public class NpmPackage {
return true;
}
public boolean isNotForPublication() {
return JSONUtil.bool(npm, "notForPublication");
}
}

4
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/i18n/I18nConstants.java
View File

@ -161,7 +161,7 @@ public class I18nConstants {
public static final String FHIRPATH_UNKNOWN_CONSTANT = "FHIRPATH_UNKNOWN_CONSTANT";
public static final String FHIRPATH_UNKNOWN_CONTEXT = "FHIRPATH_UNKNOWN_CONTEXT";
public static final String FHIRPATH_UNKNOWN_CONTEXT_ELEMENT = "FHIRPATH_UNKNOWN_CONTEXT_ELEMENT";
public static final String FHIRPATH_UNKNOWN_NAME = "FHIRPATH_UNWKNOWN_NAME";
public static final String FHIRPATH_UNKNOWN_NAME = "FHIRPATH_UNKNOWN_NAME";
public static final String FHIRPATH_WRONG_PARAM_TYPE = "FHIRPATH_WRONG_PARAM_TYPE";
public static final String FIXED_TYPE_CHECKS_DT_ADDRESS_LINE = "Fixed_Type_Checks_DT_Address_Line";
public static final String FIXED_TYPE_CHECKS_DT_NAME_FAMILY = "Fixed_Type_Checks_DT_Name_Family";
@ -466,6 +466,7 @@ public class I18nConstants {
public static final String TYPE_SPECIFIC_CHECKS_DT_PRIMITIVE_REGEX = "Type_Specific_Checks_DT_Primitive_Regex";
public static final String TYPE_SPECIFIC_CHECKS_DT_PRIMITIVE_VALUEEXT = "Type_Specific_Checks_DT_Primitive_ValueExt";
public static final String TYPE_SPECIFIC_CHECKS_DT_PRIMITIVE_WS = "Type_Specific_Checks_DT_Primitive_WS";
public static final String TYPE_SPECIFIC_CHECKS_DT_QTY_NO_ANNOTATIONS = "TYPE_SPECIFIC_CHECKS_DT_QTY_NO_ANNOTATIONS";
public static final String TYPE_SPECIFIC_CHECKS_DT_STRING_LENGTH = "Type_Specific_Checks_DT_String_Length";
public static final String TYPE_SPECIFIC_CHECKS_DT_STRING_WS = "Type_Specific_Checks_DT_String_WS";
public static final String TYPE_SPECIFIC_CHECKS_DT_TIME_VALID = "Type_Specific_Checks_DT_Time_Valid";
@ -578,6 +579,7 @@ public class I18nConstants {
public static final String XHTML_XHTML_ATTRIBUTE_ILLEGAL = "XHTML_XHTML_Attribute_Illegal";
public static final String XHTML_XHTML_DOCTYPE_ILLEGAL = "XHTML_XHTML_DOCTYPE_ILLEGAL";
public static final String XHTML_XHTML_ELEMENT_ILLEGAL = "XHTML_XHTML_Element_Illegal";
public static final String XHTML_XHTML_ELEMENT_ILLEGAL_IN_PARA = "XHTML_XHTML_ELEMENT_ILLEGAL_IN_PARA";
public static final String XHTML_XHTML_NAME_INVALID = "XHTML_XHTML_Name_Invalid";
public static final String XHTML_XHTML_NS_INVALID = "XHTML_XHTML_NS_InValid";
public static final String XML_ATTR_VALUE_INVALID = "xml_attr_value_invalid";

59
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/xhtml/XhtmlNode.java
View File

@ -41,7 +41,10 @@ import java.util.Map;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.IBaseXhtml;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.i18n.I18nConstants;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
import ca.uhn.fhir.model.api.annotation.ChildOrder;
import ca.uhn.fhir.model.primitive.XhtmlDt;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
@ -137,11 +140,53 @@ public class XhtmlNode implements IBaseXhtml {
return this;
}
public void validate(List<String> errors, String path, boolean inResource, boolean inPara) {
if (nodeType == NodeType.Element || nodeType == NodeType.Document) {
path = Utilities.noString(path) ? name : path+"/"+name;
if (inResource) {
if (!Utilities.existsInList(name, "p", "br", "div", "h1", "h2", "h3", "h4", "h5", "h6", "a", "span", "b", "em", "i", "strong",
"small", "big", "tt", "small", "dfn", "q", "var", "abbr", "acronym", "cite", "blockquote", "hr", "address", "bdo", "kbd", "q", "sub", "sup",
"ul", "ol", "li", "dl", "dt", "dd", "pre", "table", "caption", "colgroup", "col", "thead", "tr", "tfoot", "tbody", "th", "td",
"code", "samp", "img", "map", "area")) {
errors.add("Error at "+path+": Found "+name+" in a resource");
}
for (String an : attributes.keySet()) {
boolean ok = an.startsWith("xmlns") || Utilities.existsInList(an,
"title", "style", "class", "ID", "lang", "xml:lang", "dir", "accesskey", "tabindex",
// tables
"span", "width", "align", "valign", "char", "charoff", "abbr", "axis", "headers", "scope", "rowspan", "colspan") ||
Utilities.existsInList(name + "." + an, "a.href", "a.name", "img.src", "img.border", "div.xmlns", "blockquote.cite", "q.cite",
"a.charset", "a.type", "a.name", "a.href", "a.hreflang", "a.rel", "a.rev", "a.shape", "a.coords", "img.src",
"img.alt", "img.longdesc", "img.height", "img.width", "img.usemap", "img.ismap", "map.name", "area.shape",
"area.coords", "area.href", "area.nohref", "area.alt", "table.summary", "table.width", "table.border",
"table.frame", "table.rules", "table.cellspacing", "table.cellpadding", "pre.space", "td.nowrap"
);
if (!ok)
errors.add("Error at "+path+": Found attribute "+name+"."+an+" in a resource");
}
}
if (inPara && Utilities.existsInList(name, "div", "blockquote", "table", "ol", "ul", "p")) {
errors.add("Error at "+path+": Found "+name+" inside an html paragraph");
}
if (childNodes != null) {
if ("p".equals(name)) {
inPara = true;
}
for (XhtmlNode child : childNodes) {
child.validate(errors, path, inResource, inPara);
}
}
}
}
public XhtmlNode addTag(String name)
{
if (!(nodeType == NodeType.Element || nodeType == NodeType.Document))
if (!(nodeType == NodeType.Element || nodeType == NodeType.Document)) {
throw new Error("Wrong node type - node is "+nodeType.toString()+" ('"+getName()+"/"+getContent()+"')");
}
XhtmlNode node = new XhtmlNode(NodeType.Element);
node.setName(name);
childNodes.add(node);
@ -188,7 +233,6 @@ public class XhtmlNode implements IBaseXhtml {
childNodes.add(node);
return node;
}
public XhtmlNode addText(String content)
{
if (!(nodeType == NodeType.Element || nodeType == NodeType.Document))
@ -741,6 +785,17 @@ public class XhtmlNode implements IBaseXhtml {
}
public XhtmlNode backgroundColor(String color) {
style("background-color: "+color);
return this;
}
public boolean isPara() {
return "p".equals(name);
}

3
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/xhtml/XhtmlParser.java
View File

@ -536,8 +536,9 @@ private boolean elementIsOk(String name) throws FHIRFormatError {
return;
else
{
if (mustBeWellFormed)
if (mustBeWellFormed) {
throw new FHIRFormatError("Malformed XHTML: Found \"</"+n.getName()+">\" expecting \"</"+node.getName()+">\""+descLoc());
}
for (int i = parents.size() - 1; i >= 0; i--)
{
if (parents.get(i).getName().equals(n))

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

@ -605,3 +605,5 @@ FHIRPATH_NUMERICAL_ONLY = Error evaluating FHIRPath expression: The function {0}
FHIRPATH_DECIMAL_ONLY = Error evaluating FHIRPath expression: The function {0} can only be used on a decimal but found {1}
FHIRPATH_FOCUS_PLURAL = Error evaluating FHIRPath expression: focus for {0} has more than one value
REFERENCE_REF_SUSPICIOUS = The syntax of the reference ''{0}'' looks incorrect, and it should be checked
TYPE_SPECIFIC_CHECKS_DT_QTY_NO_ANNOTATIONS = UCUM Codes that contain human readable annotations like {0} can be misleading. Best Practice is not to use annotations in the UCUM code, and rather to make sure that Quantity.unit is correctly human readable
XHTML_XHTML_ELEMENT_ILLEGAL_IN_PARA = Illegal element name inside in a paragraph in the XHTML (''{0}'')

2
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>5.1.8-SNAPSHOT</version>
<version>5.1.9-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

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>5.1.8-SNAPSHOT</version>
<version>5.1.9-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

66
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/BaseValidator.java
View File

@ -2,7 +2,12 @@ package org.hl7.fhir.validation;
import static org.apache.commons.lang3.StringUtils.isBlank;
import java.text.DateFormat;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Date;
import java.util.HashMap;
/*
Copyright (c) 2011+, HL7, Inc.
@ -64,6 +69,8 @@ POSSIBILITY OF SUCH DAMAGE.
*/
import java.util.List;
import java.util.Map;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.elementmodel.Element;
@ -78,10 +85,28 @@ import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
import org.hl7.fhir.utilities.validation.ValidationMessage.Source;
import org.hl7.fhir.validation.BaseValidator.ValidationControl;
import org.hl7.fhir.validation.instance.utils.IndexedElement;
public class BaseValidator {
public class ValidationControl {
private boolean allowed;
private IssueSeverity level;
public ValidationControl(boolean allowed, IssueSeverity level) {
super();
this.allowed = allowed;
this.level = level;
}
public boolean isAllowed() {
return allowed;
}
public IssueSeverity getLevel() {
return level;
}
}
protected final String META = "meta";
protected final String ENTRY = "entry";
protected final String DOCUMENT = "document";
@ -99,6 +124,15 @@ public class BaseValidator {
protected IWorkerContext context;
protected TimeTracker timeTracker = new TimeTracker();
/**
* Use to control what validation the validator performs.
* Using this, you can turn particular kinds of validation on and off
* In addition, you can override the error | warning | hint level and make it a different level
*
* There is no way to do this using the command line validator; it's a service that is only
* offered when the validator is hosted in some other process
*/
private Map<String, ValidationControl> validationControl = new HashMap<>();
public BaseValidator(IWorkerContext context){
this.context = context;
@ -287,7 +321,10 @@ public class BaseValidator {
protected boolean txRule(List<ValidationMessage> errors, String txLink, IssueType type, int line, int col, String path, boolean thePass, String theMessage, Object... theMessageArguments) {
if (!thePass) {
String message = context.formatMessage(theMessage, theMessageArguments);
errors.add(new ValidationMessage(Source.TerminologyEngine, type, line, col, path, message, IssueSeverity.ERROR).setTxLink(txLink));
ValidationMessage vm = new ValidationMessage(Source.TerminologyEngine, type, line, col, path, message, IssueSeverity.ERROR).setMessageId(theMessage);
if (checkMsgId(theMessage, vm)) {
errors.add(vm.setTxLink(txLink));
}
}
return thePass;
}
@ -415,10 +452,23 @@ public class BaseValidator {
protected ValidationMessage addValidationMessage(List<ValidationMessage> errors, IssueType type, int line, int col, String path, String msg, IssueSeverity theSeverity, Source theSource, String id) {
ValidationMessage validationMessage = new ValidationMessage(theSource, type, line, col, path, msg, theSeverity).setMessageId(id);
if (checkMsgId(id, validationMessage)) {
errors.add(validationMessage);
}
return validationMessage;
}
public boolean checkMsgId(String id, ValidationMessage vm) {
if (id != null && validationControl.containsKey(id)) {
ValidationControl control = validationControl.get(id);
if (control.level != null) {
vm.setLevel(control.level);
}
return control.isAllowed();
}
return true;
}
/**
* Test a rule and add a {@link IssueSeverity#WARNING} validation message if the validation fails
*
@ -429,7 +479,10 @@ public class BaseValidator {
protected boolean txWarning(List<ValidationMessage> errors, String txLink, IssueType type, int line, int col, String path, boolean thePass, String msg, Object... theMessageArguments) {
if (!thePass) {
String nmsg = context.formatMessage(msg, theMessageArguments);
errors.add(new ValidationMessage(Source.TerminologyEngine, type, line, col, path, nmsg, IssueSeverity.WARNING).setTxLink(txLink).setMessageId(msg));
ValidationMessage vmsg = new ValidationMessage(Source.TerminologyEngine, type, line, col, path, nmsg, IssueSeverity.WARNING).setTxLink(txLink).setMessageId(msg);
if (checkMsgId(msg, vmsg)) {
errors.add(vmsg);
}
}
return thePass;
@ -567,7 +620,10 @@ public class BaseValidator {
}
protected void addValidationMessage(List<ValidationMessage> errors, IssueType type, String path, String msg, String html, IssueSeverity theSeverity, String id) {
errors.add(new ValidationMessage(source, type, -1, -1, path, msg, html, theSeverity).setMessageId(id));
ValidationMessage vm = new ValidationMessage(source, type, -1, -1, path, msg, html, theSeverity);
if (checkMsgId(id, vm)) {
errors.add(vm.setMessageId(id));
}
}
/**
@ -802,5 +858,9 @@ public class BaseValidator {
}
}
public Map<String, ValidationControl> getValidationControl() {
return validationControl;
}
}

23
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/ValidationEngine.java
View File

@ -34,6 +34,7 @@ import org.hl7.fhir.r5.utils.*;
import org.hl7.fhir.r5.utils.IResourceValidator.*;
import org.hl7.fhir.r5.utils.StructureMapUtilities.ITransformerServices;
import org.hl7.fhir.utilities.i18n.I18nConstants;
import org.hl7.fhir.validation.BaseValidator.ValidationControl;
import org.hl7.fhir.validation.cli.services.StandAloneValidatorFetcher.IPackageInstaller;
import org.hl7.fhir.validation.instance.InstanceValidator;
import org.hl7.fhir.utilities.IniFile;
@ -309,6 +310,7 @@ public class ValidationEngine implements IValidatorResourceFetcher, IPackageInst
private List<ImplementationGuide> igs = new ArrayList<>();
private boolean showTimes;
private List<BundleValidationRule> bundleValidationRules = new ArrayList<>();
private Map<String, ValidationControl> validationControl = new HashMap<>();
private class AsteriskFilter implements FilenameFilter {
String dir;
@ -1580,6 +1582,7 @@ public class ValidationEngine implements IValidatorResourceFetcher, IPackageInst
validator.setFetcher(this);
validator.getImplementationGuides().addAll(igs);
validator.getBundleValidationRules().addAll(bundleValidationRules);
validator.getValidationControl().putAll(validationControl );
return validator;
}
@ -2391,9 +2394,27 @@ public class ValidationEngine implements IValidatorResourceFetcher, IPackageInst
return pcm.packageExists(id, ver);
}
public void loadPackage(String id, String ver) throws IOException, FHIRException {
loadIg(id+(ver == null ? "" : "#"+ver), true);
}
/**
* Systems that host the ValidationEngine can use this to control what validation the validator performs.
*
* Using this, you can turn particular kinds of validation on and off. In addition, you can override
* the error | warning | hint level and make it a different level.
*
* Each entry has
* * 'allowed': a boolean flag. if this is false, the Validator will not report the error.
* * 'level' : set to error, warning, information
*
* Entries are registered by ID, using the IDs in /org.hl7.fhir.utilities/src/main/resources/Messages.properties
*
* This feature is not supported by the validator CLI - and won't be. It's for systems hosting
* the validation framework in their own implementation context
*/
public Map<String, ValidationControl> getValidationControl() {
return validationControl;
}
}

31
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java
View File

@ -491,17 +491,17 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
return false;
}
private void bpCheck(List<ValidationMessage> errors, IssueType invalid, int line, int col, String literalPath, boolean test, String message) {
private void bpCheck(List<ValidationMessage> errors, IssueType invalid, int line, int col, String literalPath, boolean test, String message, Object... theMessageArguments) {
if (bpWarnings != null) {
switch (bpWarnings) {
case Error:
rule(errors, invalid, line, col, literalPath, test, message);
rule(errors, invalid, line, col, literalPath, test, message, theMessageArguments);
break;
case Warning:
warning(errors, invalid, line, col, literalPath, test, message);
warning(errors, invalid, line, col, literalPath, test, message, theMessageArguments);
break;
case Hint:
hint(errors, invalid, line, col, literalPath, test, message);
hint(errors, invalid, line, col, literalPath, test, message, theMessageArguments);
break;
default: // do nothing
break;
@ -2070,7 +2070,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
checkInnerNS(errors, e, path, xhtml.getChildNodes());
rule(errors, IssueType.INVALID, e.line(), e.col(), path, "div".equals(xhtml.getName()), I18nConstants.XHTML_XHTML_NAME_INVALID, ns);
// check that no illegal elements and attributes have been used
checkInnerNames(errors, e, path, xhtml.getChildNodes());
checkInnerNames(errors, e, path, xhtml.getChildNodes(), false);
checkUrls(errors, e, path, xhtml.getChildNodes());
}
}
@ -2171,7 +2171,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
"http://hl7.org/fhirpath/System.Decimal", "http://hl7.org/fhirpath/System.Date", "http://hl7.org/fhirpath/System.Time", "http://hl7.org/fhirpath/System.DateTime", "http://hl7.org/fhirpath/System.Quantity");
}
private void checkInnerNames(List<ValidationMessage> errors, Element e, String path, List<XhtmlNode> list) {
private void checkInnerNames(List<ValidationMessage> errors, Element e, String path, List<XhtmlNode> list, boolean inPara) {
for (XhtmlNode node : list) {
if (node.getNodeType() == NodeType.Comment) {
rule(errors, IssueType.INVALID, e.line(), e.col(), path, !node.getContent().startsWith("DOCTYPE"), I18nConstants.XHTML_XHTML_DOCTYPE_ILLEGAL);
@ -2181,9 +2181,8 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
"p", "br", "div", "h1", "h2", "h3", "h4", "h5", "h6", "a", "span", "b", "em", "i", "strong",
"small", "big", "tt", "small", "dfn", "q", "var", "abbr", "acronym", "cite", "blockquote", "hr", "address", "bdo", "kbd", "q", "sub", "sup",
"ul", "ol", "li", "dl", "dt", "dd", "pre", "table", "caption", "colgroup", "col", "thead", "tr", "tfoot", "tbody", "th", "td",
"code", "samp", "img", "map", "area"
"code", "samp", "img", "map", "area"), I18nConstants.XHTML_XHTML_ELEMENT_ILLEGAL, node.getName());
), I18nConstants.XHTML_XHTML_ELEMENT_ILLEGAL, node.getName());
for (String an : node.getAttributes().keySet()) {
boolean ok = an.startsWith("xmlns") || Utilities.existsInList(an,
"title", "style", "class", ID, "lang", "xml:lang", "dir", "accesskey", "tabindex",
@ -2196,10 +2195,14 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
"area.coords", "area.href", "area.nohref", "area.alt", "table.summary", "table.width", "table.border",
"table.frame", "table.rules", "table.cellspacing", "table.cellpadding", "pre.space", "td.nowrap"
);
if (!ok)
if (!ok) {
rule(errors, IssueType.INVALID, e.line(), e.col(), path, false, I18nConstants.XHTML_XHTML_ATTRIBUTE_ILLEGAL, an, node.getName());
}
checkInnerNames(errors, e, path, node.getChildNodes());
}
rule(errors, IssueType.INVALID, e.line(), e.col(), path, !(inPara && Utilities.existsInList(node.getName(), "div", "blockquote", "table", "ol", "ul", "p")) , I18nConstants.XHTML_XHTML_ELEMENT_ILLEGAL_IN_PARA, node.getName());
checkInnerNames(errors, e, path, node.getChildNodes(), inPara || "p".equals(node.getName()));
}
}
}
@ -2320,6 +2323,14 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
if (system != null || code != null ) {
checkCodedElement(theErrors, thePath, element, theProfile, definition, false, false, theStack, code, system, unit);
}
if (code != null && "http://unitsofmeasure.org".equals(system)) {
int b = code.indexOf("{");
int e = code.indexOf("}");
if (b >= 0 && e > 0 && b < e) {
bpCheck(theErrors, IssueType.BUSINESSRULE, element.line(), element.col(), thePath, !code.contains("{"), I18nConstants.TYPE_SPECIFIC_CHECKS_DT_QTY_NO_ANNOTATIONS, code.substring(b, e+1));
}
}
}
private void checkAttachment(List<ValidationMessage> errors, String path, Element element, StructureDefinition theProfile, ElementDefinition definition, boolean theInCodeableConcept, boolean theCheckDisplayInContext, NodeStack theStack) {

10
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/ValidationTestSuite.java
View File

@ -36,6 +36,7 @@ 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.IResourceValidator;
import org.hl7.fhir.r5.utils.IResourceValidator.BestPracticeWarningLevel;
import org.hl7.fhir.r5.utils.IResourceValidator.BundleValidationRule;
import org.hl7.fhir.r5.utils.IResourceValidator.IValidatorResourceFetcher;
import org.hl7.fhir.r5.utils.IResourceValidator.ReferenceValidationPolicy;
@ -204,6 +205,9 @@ public class ValidationTestSuite implements IEvaluationContext, IValidatorResour
} else {
val.setDebug(false);
}
if (content.has("best-practice")) {
val.setBestPracticeWarningLevel(BestPracticeWarningLevel.valueOf(content.get("best-practice").getAsString()));
}
if (content.has("examples")) {
val.setAllowExamples(content.get("examples").getAsBoolean());
} else {
@ -367,11 +371,13 @@ public class ValidationTestSuite implements IEvaluationContext, IValidatorResour
}
if (!TestingUtilities.context(version).isNoTerminologyServer() || !focus.has("tx-dependent")) {
Assert.assertEquals("Test " + name + (profile == null ? "" : " profile: "+ profile) + ": Expected " + Integer.toString(java.get("errorCount").getAsInt()) + " errors, but found " + Integer.toString(ec) + ".", java.get("errorCount").getAsInt(), ec);
if (java.has("warningCount"))
if (java.has("warningCount")) {
Assert.assertEquals( "Test " + name + (profile == null ? "" : " profile: "+ profile) + ": Expected " + Integer.toString(java.get("warningCount").getAsInt()) + " warnings, but found " + Integer.toString(wc) + ".", java.get("warningCount").getAsInt(), wc);
if (java.has("infoCount"))
}
if (java.has("infoCount")) {
Assert.assertEquals( "Test " + name + (profile == null ? "" : " profile: "+ profile) + ": Expected " + Integer.toString(java.get("infoCount").getAsInt()) + " hints, but found " + Integer.toString(hc) + ".", java.get("infoCount").getAsInt(), hc);
}
}
if (java.has("error-locations")) {
JsonArray el = java.getAsJsonArray("error-locations");
Assert.assertEquals( "locations count is not correct", errLocs.size(), el.size());

4
pom.xml
View File

@ -13,11 +13,11 @@
each other. It is fine to bump the point version of this POM without affecting
HAPI FHIR.
-->
<version>5.1.8-SNAPSHOT</version>
<version>5.1.9-SNAPSHOT</version>
<properties>
<hapi_fhir_version>5.1.0</hapi_fhir_version>
<validator_test_case_version>1.1.35</validator_test_case_version>
<validator_test_case_version>1.1.36</validator_test_case_version>
<junit_jupiter_version>5.6.2</junit_jupiter_version>
<maven_surefire_version>3.0.0-M4</maven_surefire_version>
<jacoco_version>0.8.5</jacoco_version>