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fixes for 5.1.8 (#336) 

* Fix up conversion for date problems

* Mark packages as unsuitable for publication

* rework rendering tests & fix bug in Parameters renderer

* fix test case depedency

* update VSACImporter to get value sets from VSAC directly

* Fix up rendering of Extensions

* Add support for choice groups, and markdownify some elements
This commit is contained in:
Grahame Grieve 2020-09-04 23:49:36 +10:00 committed by GitHub
parent 6cf6367b30
commit 7ca698f36a
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GPG Key ID: 4AEE18F83AFDEB23
20 changed files with 675 additions and 178 deletions
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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;
}
}

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;
// }
}

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;
}

102
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;
@ -778,6 +784,102 @@ 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())

10
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;
}
@ -87,7 +93,7 @@ public class ParametersRenderer extends ResourceRenderer {
}
} else if (p.has("part")) {
tr.td();
PropertyWrapper pw = getProperty(p, "parameter");
PropertyWrapper pw = getProperty(p, "part");
paramsW(tbl, pw.getValues(), 1);
}
}

64
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;
@ -82,6 +83,7 @@ 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 +110,13 @@ 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
@ -378,6 +381,9 @@ 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)) {
@ -386,7 +392,7 @@ public class ProfileDrivenRenderer extends ResourceRenderer {
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);
getChildrenForPath(sd.getSnapshot().getElement(), sd.getSnapshot().getElementFirstRep().getPath()), x, e.fhirType(), showCodeDetails, indent + 1);
}
}
@ -612,7 +618,19 @@ 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) {
@ -621,6 +639,9 @@ 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) {
@ -660,11 +681,33 @@ 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 +715,6 @@ public class ProfileDrivenRenderer extends ResourceRenderer {
}
}
}
}
}
}
}
private String getHeader() {
@ -699,6 +738,9 @@ public class ProfileDrivenRenderer extends ResourceRenderer {
}
private boolean canDoTable(String path, PropertyWrapper p, List<ElementDefinition> grandChildren) {
if (isExtension(p)) {
return false;
}
for (ElementDefinition e : grandChildren) {
List<PropertyWrapper> values = getValues(path, p, e);
if (values.size() > 1 || !isPrimitive(e) || !canCollapse(e))
@ -707,6 +749,10 @@ 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
@ -792,10 +838,10 @@ public class ProfileDrivenRenderer extends ResourceRenderer {
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), ed.getSnapshot().getElementFirstRep());
} 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;
}
}
}

14
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

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());

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).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");
}
}

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");
}
}

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

@ -741,6 +741,12 @@ public class XhtmlNode implements IBaseXhtml {
}
public XhtmlNode backgroundColor(String color) {
style("background-color: "+color);
return this;
}

2
pom.xml
View File

@ -17,7 +17,7 @@
<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-SNAPSHOT</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>