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Add support for choice groups, and markdownify some elements

This commit is contained in:
Grahame Grieve 2020-09-04 16:23:27 +10:00
parent a964d4fcd5
commit 2adb9a7b68
2 changed files with 239 additions and 21 deletions
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246
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;
@ -200,7 +205,31 @@ 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;
public class ExtensionContext {
@ -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")));
c.getPieces().add(checkForNoChange(inv, gen.new Piece(null, inv.getHuman(), null)));
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;
}
}

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