honeymoose
/
org.hl7.fhir.core
mirror of https://github.com/hapifhir/org.hl7.fhir.core.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity

fix rendering on must-support view for must-support on types and target profiles

This commit is contained in:
Grahame Grieve 2020-11-13 14:46:57 +11:00
parent 25103f3653
commit 6ef8565563
3 changed files with 301 additions and 210 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

8
RELEASE_NOTES.md
View File

@ -0,0 +1,8 @@
Validator:
* Fix bug in unknown URL handling that could cause significant delays in validation (>1min / unknown URL)
* fix bug in processing excludes with filters in value sets
Other code changes:
* fix case problem with icons in questionnaire rendering
* fix problem with rendering nested slices on content references
* fix rendering on must-support view for must-support on types and target profiles

157
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/ProfileUtilities.java
View File

@ -150,6 +150,26 @@ import org.hl7.fhir.utilities.xml.SchematronWriter.Section;
*/
public class ProfileUtilities extends TranslatingUtilities {
public class ElementDefinitionResolution {
private StructureDefinition source;
private ElementDefinition element;
public ElementDefinitionResolution(StructureDefinition source, ElementDefinition element) {
this.source = source;
this.element = element;
}
public StructureDefinition getSource() {
return source;
}
public ElementDefinition getElement() {
return element;
}
}
public class ElementRedirection {
private String path;
@ -1154,15 +1174,24 @@ public class ProfileUtilities extends TranslatingUtilities {
while (diffCursor <= diffLimit && differential.getElement().size() > diffCursor && pathStartsWith(differential.getElement().get(diffCursor).getPath(), diffMatches.get(0).getPath()+"."))
diffCursor++;
if (outcome.hasContentReference()) {
ElementDefinition tgt = getElementById(srcSD, base.getElement(), outcome.getContentReference());
ElementDefinitionResolution tgt = getElementById(srcSD, base.getElement(), outcome.getContentReference());
if (tgt == null)
throw new DefinitionException(context.formatMessage(I18nConstants.UNABLE_TO_RESOLVE_REFERENCE_TO_, outcome.getContentReference()));
replaceFromContentReference(outcome, tgt);
int nbc = base.getElement().indexOf(tgt)+1;
replaceFromContentReference(outcome, tgt.getElement());
if (tgt.getSource() != srcSD) {
base = tgt.getSource().getSnapshot();
int nbc = base.getElement().indexOf(tgt.getElement())+1;
int nbl = nbc;
while (nbl < base.getElement().size() && base.getElement().get(nbl).getPath().startsWith(tgt.getPath()+"."))
while (nbl < base.getElement().size() && base.getElement().get(nbl).getPath().startsWith(tgt.getElement().getPath()+"."))
nbl++;
processPaths(indent+" ", result, base, differential, nbc, start - 1, nbl-1, diffCursor - 1, url, webUrl, profileName, tgt.getPath(), diffMatches.get(0).getPath(), trimDifferential, contextName, resultPathBase, false, null, null, redirectorStack(redirector, outcome, cpath), srcSD);
processPaths(indent+" ", result, base, differential, nbc, start - 1, nbl-1, diffCursor - 1, url, webUrl, profileName, tgt.getElement().getPath(), diffMatches.get(0).getPath(), trimDifferential, contextName, resultPathBase, false, null, null, redirectorStack(redirector, outcome, cpath), tgt.getSource());
} else {
int nbc = base.getElement().indexOf(tgt.getElement())+1;
int nbl = nbc;
while (nbl < base.getElement().size() && base.getElement().get(nbl).getPath().startsWith(tgt.getElement().getPath()+"."))
nbl++;
processPaths(indent+" ", result, base, differential, nbc, start - 1, nbl-1, diffCursor - 1, url, webUrl, profileName, tgt.getElement().getPath(), diffMatches.get(0).getPath(), trimDifferential, contextName, resultPathBase, false, null, null, redirectorStack(redirector, outcome, cpath), srcSD);
}
} else {
StructureDefinition dt = outcome.getType().size() == 1 ? getProfileForDataType(outcome.getType().get(0)) : getProfileForDataType("Element");
if (dt == null)
@ -1263,16 +1292,6 @@ public class ProfileUtilities extends TranslatingUtilities {
e.getSlicing().addDiscriminator().setType(DiscriminatorType.TYPE).setPath("$this");
e.getSlicing().setRules(SlicingRules.CLOSED); // type slicing is always closed; the differential might call it open, but that just means it's not constraining the slices it doesn't mention
e.getSlicing().setOrdered(false);
// check that there's a slice for each allowed types
Set<String> allowedTypes = getListOfTypes(e);
for (TypeSlice t : typeList) {
allowedTypes.remove(t.type);
}
// GG - work in progress..
// if (!allowedTypes.isEmpty()) {
// System.out.println("!!: Error at "+cpath+": Allowed Types not sliced = "+allowedTypes);
// throw new Error("Error at "+cpath+": Allowed Types not sliced = "+allowedTypes);
// }
start++;
@ -1305,7 +1324,32 @@ public class ProfileUtilities extends TranslatingUtilities {
}
}
}
if (!"0".equals(e.getMax())) {
// check that there's a slice for each allowed types
Set<String> allowedTypes = getListOfTypes(e);
for (TypeSlice t : typeList) {
if (t.type != null) {
allowedTypes.remove(t.type);
} else if (t.getDefn().hasSliceName() && t.getDefn().getType().size() == 1) {
allowedTypes.remove(t.getDefn().getType().get(0).getCode());
}
}
if (!allowedTypes.isEmpty()) {
if (cpath.contains("xtension.value")) {
for (Iterator<TypeRefComponent> iter = e.getType().iterator(); iter.hasNext(); ) {
TypeRefComponent tr = iter.next();
if (allowedTypes.contains(tr.getCode())) {
iter.remove();
}
}
// System.out.println("!!: Extension Error at "+cpath+": Allowed Types not sliced = "+allowedTypes+". !Extension!!");
// throw new Error("Extension Error at "+cpath+": Allowed Types not sliced = "+allowedTypes+". !Extension!!");
} else {
e.getSlicing().setRules(SlicingRules.OPEN);
}
}
}
// ok, done with that - next in the base list
baseCursor = nbl+1;
diffCursor = ndl+1;
@ -2006,12 +2050,18 @@ public class ProfileUtilities extends TranslatingUtilities {
if (ed.hasSliceName() && ed.getType().size() == 1) {
typeList.add(new TypeSlice(ed, ed.getTypeFirstRep().getWorkingCode()));
} else if (ed.hasSliceName() && ed.getType().size() == 0) {
String tn = ed.getSliceName().substring(rn.length());
if (isDataType(s)) {
typeList.add(new TypeSlice(ed, s));
} else if (isPrimitive(Utilities.uncapitalize(s))) {
typeList.add(new TypeSlice(ed, Utilities.uncapitalize(s)));
} else {
String tn = ed.getSliceName().substring(n.length());
if (isDataType(tn)) {
typeList.add(new TypeSlice(ed, tn));
} else if (isPrimitive(Utilities.uncapitalize(tn))) {
typeList.add(new TypeSlice(ed, Utilities.uncapitalize(tn)));
}
}
} else if (!ed.hasSliceName() && !s.equals("[x]")) {
if (isDataType(s))
typeList.add(new TypeSlice(ed, s));
@ -3171,7 +3221,7 @@ public class ProfileUtilities extends TranslatingUtilities {
r1.getCells().add(gen.new Cell(null, defFile == null ? "" : defFile+"-definitions.html#extension."+ed.getName(), ((UriType) ued.getFixed()).getValue(), null, null));
r1.getCells().add(gen.new Cell());
r1.getCells().add(gen.new Cell(null, null, describeCardinality(c, null, new UnusedTracker()), null, null));
genTypes(gen, r1, ved, defFile, ed, corePath, imagePath, false);
genTypes(gen, r1, ved, defFile, ed, corePath, imagePath, false, false);
Cell cell = gen.new Cell();
cell.addMarkdown(c.getDefinition());
r1.getCells().add(cell);
@ -3184,7 +3234,7 @@ public class ProfileUtilities extends TranslatingUtilities {
ved = ted;
}
genTypes(gen, r, ved, defFile, ed, corePath, imagePath, false);
genTypes(gen, r, ved, defFile, ed, corePath, imagePath, false, false);
r.setIcon("icon_"+m+"extension_simple.png", HierarchicalTableGenerator.TEXT_ICON_EXTENSION_SIMPLE);
}
@ -3243,7 +3293,7 @@ public class ProfileUtilities extends TranslatingUtilities {
private static final int AGG_GR = 2;
private static final boolean TABLE_FORMAT_FOR_FIXED_VALUES = false;
private Cell genTypes(HierarchicalTableGenerator gen, Row r, ElementDefinition e, String profileBaseFileName, StructureDefinition profile, String corePath, String imagePath, boolean root) {
private Cell genTypes(HierarchicalTableGenerator gen, Row r, ElementDefinition e, String profileBaseFileName, StructureDefinition profile, String corePath, String imagePath, boolean root, boolean mustSupportMode) {
Cell c = gen.new Cell();
r.getCells().add(c);
if (e.hasContentReference()) {
@ -3294,6 +3344,7 @@ public class ProfileUtilities extends TranslatingUtilities {
TypeRefComponent tl = null;
for (TypeRefComponent t : types) {
if (!mustSupportMode || allTypesMustSupport(e) || isMustSupport(t)) {
if (first) {
first = false;
} else {
@ -3302,23 +3353,25 @@ public class ProfileUtilities extends TranslatingUtilities {
tl = t;
if (t.hasTarget()) {
c.getPieces().add(gen.new Piece(corePath+"references.html", t.getWorkingCode(), null));
if (isMustSupportDirect(t) && e.getMustSupport()) {
if (!mustSupportMode && isMustSupportDirect(t) && e.getMustSupport()) {
c.addPiece(gen.new Piece(null, " ", null));
c.addStyledText(translate("sd.table", "This type must be supported"), "S", "white", "red", null, false);
}
c.getPieces().add(gen.new Piece(null, "(", null));
boolean tfirst = true;
for (CanonicalType u : t.getTargetProfile()) {
if (!mustSupportMode || allProfilesMustSupport(t.getTargetProfile()) || isMustSupport(u)) {
if (tfirst)
tfirst = false;
else
c.addPiece(gen.new Piece(null, " | ", null));
genTargetLink(gen, profileBaseFileName, corePath, c, t, u.getValue());
if (isMustSupport(u) && e.getMustSupport()) {
if (!mustSupportMode && isMustSupport(u) && e.getMustSupport()) {
c.addPiece(gen.new Piece(null, " ", null));
c.addStyledText(translate("sd.table", "This target must be supported"), "S", "white", "red", null, false);
}
}
}
c.getPieces().add(gen.new Piece(null, ")", null));
if (t.getAggregation().size() > 0) {
c.getPieces().add(gen.new Piece(corePath+"valueset-resource-aggregation-mode.html", " {", null));
@ -3336,6 +3389,7 @@ public class ProfileUtilities extends TranslatingUtilities {
String ref;
boolean pfirst = true;
for (CanonicalType p : t.getProfile()) {
if (!mustSupportMode || allProfilesMustSupport(t.getProfile()) || isMustSupport(p)) {
if (pfirst) {
pfirst = false;
} else {
@ -3354,11 +3408,12 @@ public class ProfileUtilities extends TranslatingUtilities {
}
} else
c.addPiece(checkForNoChange(t, gen.new Piece((p.getValue().startsWith(corePath)? corePath: "")+ref, t.getWorkingCode(), null)));
if (isMustSupport(p) && e.getMustSupport()) {
if (!mustSupportMode && isMustSupport(p) && e.getMustSupport()) {
c.addPiece(gen.new Piece(null, " ", null));
c.addStyledText(translate("sd.table", "This profile must be supported"), "S", "white", "red", null, false);
}
}
}
} else {
String tc = t.getWorkingCode();
if (Utilities.isAbsoluteUrl(tc)) {
@ -3373,12 +3428,13 @@ public class ProfileUtilities extends TranslatingUtilities {
} else {
c.addPiece(checkForNoChange(t, gen.new Piece(null, tc, null)));
}
if (isMustSupportDirect(t) && e.getMustSupport()) {
if (!mustSupportMode && isMustSupportDirect(t) && e.getMustSupport()) {
c.addPiece(gen.new Piece(null, " ", null));
c.addStyledText(translate("sd.table", "This type must be supported"), "S", "white", "red", null, false);
}
}
}
}
return c;
}
@ -3485,7 +3541,7 @@ public class ProfileUtilities extends TranslatingUtilities {
// return null;
}
private ElementDefinition getElementById(StructureDefinition source, List<ElementDefinition> elements, String contentReference) {
private ElementDefinitionResolution getElementById(StructureDefinition source, List<ElementDefinition> elements, String contentReference) {
if (!contentReference.startsWith("#") && contentReference.contains("#")) {
String url = contentReference.substring(0, contentReference.indexOf("#"));
contentReference = contentReference.substring(contentReference.indexOf("#"));
@ -3499,7 +3555,7 @@ public class ProfileUtilities extends TranslatingUtilities {
}
for (ElementDefinition ed : elements)
if (ed.hasId() && ("#"+ed.getId()).equals(contentReference))
return ed;
return new ElementDefinitionResolution(source, ed);
return null;
}
@ -3882,7 +3938,7 @@ public class ProfileUtilities extends TranslatingUtilities {
// genElement(defPath, gen, row.getSubRows(), child, all, profiles, showMissing, profileBaseFileName, true, false, corePath, imagePath, false, logicalModel, isConstraintMode, allInvariants);
}
if (typesRow != null) {
makeChoiceRows(typesRow.getSubRows(), element, gen, corePath, profileBaseFileName);
makeChoiceRows(typesRow.getSubRows(), element, gen, corePath, profileBaseFileName, mustSupport);
}
}
return slicingRow;
@ -3967,7 +4023,7 @@ public class ProfileUtilities extends TranslatingUtilities {
res.add(genCardinality(gen, element, row, hasDef, used, extDefn.getElement()));
ElementDefinition valueDefn = extDefn.getExtensionValueDefinition();
if (valueDefn != null && !"0".equals(valueDefn.getMax()))
res.add(genTypes(gen, row, valueDefn, profileBaseFileName, profile, corePath, imagePath, root));
res.add(genTypes(gen, row, valueDefn, profileBaseFileName, profile, corePath, imagePath, root, mustSupport));
else // if it's complex, we just call it nothing
// genTypes(gen, row, extDefn.getSnapshot().getElement().get(0), profileBaseFileName, profile);
res.add(addCell(row, gen.new Cell(null, null, "("+translate("sd.table", "Complex")+")", null, null)));
@ -3978,7 +4034,7 @@ public class ProfileUtilities extends TranslatingUtilities {
if ("0".equals(element.getMax()))
res.add(addCell(row, gen.new Cell()));
else
res.add(genTypes(gen, row, element, profileBaseFileName, profile, corePath, imagePath, root));
res.add(genTypes(gen, row, element, profileBaseFileName, profile, corePath, imagePath, root, mustSupport));
res.add(generateDescription(gen, row, element, (ElementDefinition) element.getUserData(DERIVATION_POINTER), used.used, null, null, profile, corePath, imagePath, root, logicalModel, allInvariants, snapshot, mustSupport));
}
} else {
@ -3986,7 +4042,7 @@ public class ProfileUtilities extends TranslatingUtilities {
if (element.hasSlicing())
res.add(addCell(row, gen.new Cell(null, corePath+"profiling.html#slicing", "(Slice Definition)", null, null)));
else if (hasDef && !"0".equals(element.getMax()) && typesRow == null)
res.add(genTypes(gen, row, element, profileBaseFileName, profile, corePath, imagePath, root));
res.add(genTypes(gen, row, element, profileBaseFileName, profile, corePath, imagePath, root, mustSupport));
else
res.add(addCell(row, gen.new Cell()));
res.add(generateDescription(gen, row, element, (ElementDefinition) element.getUserData(DERIVATION_POINTER), used.used, null, null, profile, corePath, imagePath, root, logicalModel, allInvariants, snapshot, mustSupport));
@ -4048,9 +4104,10 @@ public class ProfileUtilities extends TranslatingUtilities {
return key.startsWith("ele-") || key.startsWith("res-") || key.startsWith("ext-") || key.startsWith("dom-") || key.startsWith("dr-");
}
private void makeChoiceRows(List<Row> subRows, ElementDefinition element, HierarchicalTableGenerator gen, String corePath, String profileBaseFileName) {
private void makeChoiceRows(List<Row> subRows, ElementDefinition element, HierarchicalTableGenerator gen, String corePath, String profileBaseFileName, boolean mustSupportMode) {
// create a child for each choice
for (TypeRefComponent tr : element.getType()) {
if (!mustSupportMode || allTypesMustSupport(element) || isMustSupport(tr)) {
Row choicerow = gen.new Row();
String t = tr.getWorkingCode();
if (isReference(t)) {
@ -4065,7 +4122,7 @@ public class ProfileUtilities extends TranslatingUtilities {
c.getPieces().add(gen.new Piece(corePath+"datatypes.html#canonical", "canonical", null));
else
c.getPieces().add(gen.new Piece(corePath+"references.html#Reference", "Reference", null));
if (isMustSupportDirect(tr) && element.getMustSupport()) {
if (!mustSupportMode && isMustSupportDirect(tr) && element.getMustSupport()) {
c.addPiece(gen.new Piece(null, " ", null));
c.addStyledText(translate("sd.table", "This type must be supported"), "S", "white", "red", null, false);
}
@ -4073,15 +4130,17 @@ public class ProfileUtilities extends TranslatingUtilities {
}
boolean first = true;
for (CanonicalType rt : tr.getTargetProfile()) {
if (!mustSupportMode || allProfilesMustSupport(tr.getTargetProfile()) || isMustSupport(rt)) {
if (!first)
c.getPieces().add(gen.new Piece(null, " | ", null));
genTargetLink(gen, profileBaseFileName, corePath, c, tr, rt.getValue());
if (isMustSupport(rt) && element.getMustSupport()) {
if (!mustSupportMode && isMustSupport(rt) && element.getMustSupport()) {
c.addPiece(gen.new Piece(null, " ", null));
c.addStyledText(translate("sd.table", "This target must be supported"), "S", "white", "red", null, false);
}
first = false;
}
}
if (first)
c.getPieces().add(gen.new Piece(null, "Any", null));
@ -4100,7 +4159,7 @@ public class ProfileUtilities extends TranslatingUtilities {
choicerow.setIcon("icon_primitive.png", HierarchicalTableGenerator.TEXT_ICON_PRIMITIVE);
Cell c = gen.new Cell(null, corePath+"datatypes.html#"+t, sd.getType(), null, null);
choicerow.getCells().add(c);
if (isMustSupport(tr) && element.getMustSupport()) {
if (!mustSupportMode && isMustSupport(tr) && element.getMustSupport()) {
c.addPiece(gen.new Piece(null, " ", null));
c.addStyledText(translate("sd.table", "This type must be supported"), "S", "white", "red", null, false);
}
@ -4111,7 +4170,7 @@ public class ProfileUtilities extends TranslatingUtilities {
choicerow.setIcon("icon_datatype.gif", HierarchicalTableGenerator.TEXT_ICON_DATATYPE);
Cell c = gen.new Cell(null, pkp.getLinkFor(corePath, t), sd.getType(), null, null);
choicerow.getCells().add(c);
if (isMustSupport(tr) && element.getMustSupport()) {
if (!mustSupportMode && isMustSupport(tr) && element.getMustSupport()) {
c.addPiece(gen.new Piece(null, " ", null));
c.addStyledText(translate("sd.table", "This type must be supported"), "S", "white", "red", null, false);
}
@ -4121,17 +4180,18 @@ public class ProfileUtilities extends TranslatingUtilities {
typeCell.addPiece(gen.new Piece(null, "(", null));
boolean first = true;
for (CanonicalType pt : tr.getProfile()) {
if (!mustSupportMode || allProfilesMustSupport(tr.getProfile()) || isMustSupport(pt)) {
if (first) first = false; else typeCell.addPiece(gen.new Piece(null, " | ", null));
StructureDefinition psd = context.fetchResource(StructureDefinition.class, pt.getValue());
if (psd == null)
typeCell.addPiece(gen.new Piece(null, "?gen-e2?", null));
else
typeCell.addPiece(gen.new Piece(psd.getUserString("path"), psd.getName(), psd.present()));
if (isMustSupport(pt) && element.getMustSupport()) {
if (!mustSupportMode && isMustSupport(pt) && element.getMustSupport()) {
typeCell.addPiece(gen.new Piece(null, " ", null));
typeCell.addStyledText(translate("sd.table", "This profile must be supported"), "S", "white", "red", null, false);
}
}
}
typeCell.addPiece(gen.new Piece(null, ")", null));
}
@ -4140,6 +4200,7 @@ public class ProfileUtilities extends TranslatingUtilities {
subRows.add(choicerow);
}
}
}
private boolean isReference(String t) {
return t.equals("Reference") || t.equals("canonical");
@ -4182,7 +4243,7 @@ public class ProfileUtilities extends TranslatingUtilities {
ExtensionContext extDefn = null;
genCardinality(gen, element, row, hasDef, used, null);
if (hasDef && !"0".equals(element.getMax()))
genTypes(gen, row, element, profileBaseFileName, profile, corePath, imagePath, root);
genTypes(gen, row, element, profileBaseFileName, profile, corePath, imagePath, root, false);
else
row.getCells().add(gen.new Cell());
generateGridDescription(gen, row, element, null, used.used, null, null, profile, corePath, imagePath, root, null);
@ -5072,6 +5133,9 @@ public class ProfileUtilities extends TranslatingUtilities {
if (ref.substring(1, 2).toUpperCase().equals(ref.substring(1,2))) {
actual = base+(ref.substring(1)+"."+path.substring(p.length()+1)).substring(prefixLength);
path = actual;
} else if (ref.startsWith("http:")) {
actual = base+(ref.substring(ref.indexOf("#")+1)+"."+path.substring(p.length()+1)).substring(prefixLength);
path = actual;
} else {
// Older versions of FHIR (e.g. 2016May) had reference of the style #parameter instead of #Parameters.parameter, so we have to handle that
actual = base+(path.substring(0, path.indexOf(".")+1) + ref.substring(1)+"."+path.substring(p.length()+1)).substring(prefixLength);
@ -6365,6 +6429,25 @@ public class ProfileUtilities extends TranslatingUtilities {
return grp;
}
public static boolean allTypesMustSupport(ElementDefinition e) {
boolean all = true;
boolean any = false;
for (TypeRefComponent tr : e.getType()) {
all = all && isMustSupport(tr);
any = any || isMustSupport(tr);
}
return !all && !any;
}
public static boolean allProfilesMustSupport(List<CanonicalType> profiles) {
boolean all = true;
boolean any = false;
for (CanonicalType u : profiles) {
all = all && isMustSupport(u);
any = any || isMustSupport(u);
}
return !all && !any;
}
public static boolean isMustSupportDirect(TypeRefComponent tr) {
return ("true".equals(ToolingExtensions.readStringExtension(tr, ToolingExtensions.EXT_MUST_SUPPORT)));
}

2
pom.xml
View File

@ -19,7 +19,7 @@
<properties>
<hapi_fhir_version>5.1.0</hapi_fhir_version>
<validator_test_case_version>1.1.49</validator_test_case_version>
<validator_test_case_version>1.1.50-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>