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Improved paths in profile error messages, and fix problem with extension slicing being missed sometimes.

This commit is contained in:
Grahame Grieve 2023-08-04 11:47:08 +10:00
parent 73127f1f3a
commit 8cc698af5d
2 changed files with 125 additions and 28 deletions
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88
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/profile/ProfilePathProcessor.java
View File

@ -11,7 +11,9 @@ import org.hl7.fhir.r5.conformance.ElementRedirection;
import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.CanonicalType;
import org.hl7.fhir.r5.model.ElementDefinition;
import org.hl7.fhir.r5.model.ElementDefinition.DiscriminatorType;
import org.hl7.fhir.r5.model.ElementDefinition.ElementDefinitionSlicingComponent;
import org.hl7.fhir.r5.model.ElementDefinition.SlicingRules;
import org.hl7.fhir.r5.model.OperationOutcome.IssueType;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionSnapshotComponent;
@ -193,9 +195,16 @@ public class ProfilePathProcessor {
private void debugProcessPathsIteration(ProfilePathProcessorState cursors, String currentBasePath) {
if (profileUtilities.isDebug()) {
System.out.println(getDebugIndent() + " - " + currentBasePath + ": base = " + cursors.baseCursor + " (" + profileUtilities.descED(cursors.base.getElement(), cursors.baseCursor) + ") to " + getBaseLimit() + " (" + profileUtilities.descED(cursors.base.getElement(), getBaseLimit()) + "), diff = " + cursors.diffCursor + " (" + profileUtilities.descED(getDifferential().getElement(), cursors.diffCursor) + ") to " + getDiffLimit() + " (" + profileUtilities.descED(getDifferential().getElement(), getDiffLimit()) + ") " +
System.out.println(getDebugIndent() + " - " + currentBasePath + ": "+
"base = " + cursors.baseCursor + " (" + profileUtilities.descED(cursors.base.getElement(), cursors.baseCursor) + ") to " + getBaseLimit() +" (" + profileUtilities.descED(cursors.base.getElement(), getBaseLimit()) + "), "+
"diff = " + cursors.diffCursor + " (" + profileUtilities.descED(getDifferential().getElement(), cursors.diffCursor) + ") to " + getDiffLimit() + " (" + profileUtilities.descED(getDifferential().getElement(), getDiffLimit()) + ") " +
"(slicingDone = " + getSlicing().isDone() + ") (diffpath= " + (getDifferential().getElement().size() > cursors.diffCursor ? getDifferential().getElement().get(cursors.diffCursor).getPath() : "n/a") + ")");
String path = cursors.diffCursor >=0 && cursors.diffCursor < getDifferential().getElement().size() ? getDifferential().getElement().get(cursors.diffCursor).present() : null;
// if (path != null && path.contains(":populationBasis")) {
// System.out.println("!");
// }
}
}
private void debugProcessPathsEntry(ProfilePathProcessorState cursors) {
@ -294,7 +303,7 @@ public class ProfilePathProcessor {
// differential - if the first one in the list has a name, we'll process it. Else we'll treat it as the base definition of the slice.
if (!diffMatches.get(0).hasSliceName()) {
profileUtilities.updateFromDefinition(outcome, diffMatches.get(0), getProfileName(), isTrimDifferential(), getUrl(),getSourceStructureDefinition(), getDerived());
profileUtilities.updateFromDefinition(outcome, diffMatches.get(0), getProfileName(), isTrimDifferential(), getUrl(),getSourceStructureDefinition(), getDerived(), diffPath(diffMatches.get(0)));
profileUtilities.removeStatusExtensions(outcome);
if (!outcome.hasContentReference() && !outcome.hasType() && outcome.getPath().contains(".")) {
throw new DefinitionException(profileUtilities.getContext().formatMessage(I18nConstants.NOT_DONE_YET));
@ -354,6 +363,10 @@ public class ProfilePathProcessor {
cursors.diffCursor = newDiffLimit + 1;
}
private String diffPath(ElementDefinition ed) {
return "StructureDefinition.differential.element["+differential.getElement().indexOf(ed)+"]";
}
private String slicingSummary(ElementDefinitionSlicingComponent s) {
return s.toString();
}
@ -635,6 +648,11 @@ public class ProfilePathProcessor {
res = outcome;
profileUtilities.updateFromBase(outcome, currentBase, getSourceStructureDefinition().getUrl());
if (diffMatches.get(0).hasSliceName()) {
template = currentBase.copy();
template = profileUtilities.updateURLs(getUrl(), getWebUrl(), template);
template.setPath(profileUtilities.fixedPathDest(getContextPathTarget(), template.getPath(), getRedirector(), getContextPathSource()));
checkToSeeIfSlicingExists(diffMatches.get(0), template);
outcome.setSliceName(diffMatches.get(0).getSliceName());
if (!diffMatches.get(0).hasMin() && (diffMatches.size() > 1 || getSlicing().getElementDefinition()== null || getSlicing().getElementDefinition().getSlicing().getRules() != ElementDefinition.SlicingRules.CLOSED) && !currentBase.hasSliceName()) {
if (!currentBasePath.endsWith("xtension.value[x]")) { // hack work around for problems with snapshots in official releases
@ -642,7 +660,7 @@ public class ProfilePathProcessor {
}
}
}
profileUtilities.updateFromDefinition(outcome, diffMatches.get(0), getProfileName(), isTrimDifferential(), getUrl(), getSourceStructureDefinition(), getDerived());
profileUtilities.updateFromDefinition(outcome, diffMatches.get(0), getProfileName(), isTrimDifferential(), getUrl(), getSourceStructureDefinition(), getDerived(), diffPath(diffMatches.get(0)));
profileUtilities.removeStatusExtensions(outcome);
// if (outcome.getPath().endsWith("[x]") && outcome.getType().size() == 1 && !outcome.getType().get(0).getCode().equals("*") && !diffMatches.get(0).hasSlicing()) // if the base profile allows multiple types, but the profile only allows one, rename it
// outcome.setPath(outcome.getPath().substring(0, outcome.getPath().length()-3)+Utilities.capitalize(outcome.getType().get(0).getCode()));
@ -743,6 +761,66 @@ public class ProfilePathProcessor {
return res;
}
private void checkToSeeIfSlicingExists(ElementDefinition ed, ElementDefinition template) {
List<ElementDefinition> ss = result.getElement();
int i = ss.size() -1;
ElementDefinition m = null;
System.out.println("check for "+ed.getPath());
while (i >= 0) {
ElementDefinition t = ss.get(i);
System.out.println(""+i+": "+t.getPath());
if (pathsMatch(t.getPath(), ed.getPath())) {
if (t.hasSlicing() || t.hasSliceName() || t.getPath().endsWith("[x]")) {
m = t;
break;
}
}
if (t.getPath().length() < ed.getPath().length()) {
break;
}
i--;
}
if (m == null) {
if (template.getPath().endsWith(".extension")) {
template.getSlicing().setRules(SlicingRules.OPEN);
template.getSlicing().setOrdered(false);
template.getSlicing().addDiscriminator().setType(DiscriminatorType.VALUE).setPath("url");
result.getElement().add(template);
} else {
System.err.println("checkToSeeIfSlicingExists: "+ed.getPath()+":"+ed.getSliceName()+" is not sliced");
}
m = ed;
}
}
private boolean pathsMatch(String path1, String path2) {
String[] p1 = path1.split("\\.");
String[] p2 = path2.split("\\.");
if (p1.length != p2.length) {
return false;
}
for (int i = 0; i < p1.length; i++) {
String pp1 = p1[i];
String pp2 = p2[i];
if (!pp1.equals(pp2)) {
if (pp1.endsWith("[x]")) {
if (!pp2.startsWith(pp1.substring(0, pp1.length()-3))) {
return false;
}
} else if (pp2.endsWith("[x]")) {
if (!pp1.startsWith(pp2.substring(0, pp2.length()-3))) {
return false;
}
} else {
return false;
}
}
}
return true;
}
private int indexOfFirstNonChild(StructureDefinitionSnapshotComponent base, ElementDefinition currentBase, int i, int baseLimit) {
return baseLimit+1;
}
@ -937,7 +1015,7 @@ public class ProfilePathProcessor {
profileUtilities.updateFromBase(outcome, currentBase, getSourceStructureDefinition().getUrl());
if (diffMatches.get(0).hasSlicing() || !diffMatches.get(0).hasSliceName()) {
profileUtilities.updateFromSlicing(outcome.getSlicing(), diffMatches.get(0).getSlicing());
profileUtilities.updateFromDefinition(outcome, diffMatches.get(0), getProfileName(), closed, getUrl(), getSourceStructureDefinition(), getDerived()); // if there's no slice, we don't want to update the unsliced description
profileUtilities.updateFromDefinition(outcome, diffMatches.get(0), getProfileName(), closed, getUrl(), getSourceStructureDefinition(), getDerived(), diffPath(diffMatches.get(0))); // if there's no slice, we don't want to update the unsliced description
profileUtilities.removeStatusExtensions(outcome);
} else if (!diffMatches.get(0).hasSliceName()) {
diffMatches.get(0).setUserData(profileUtilities.UD_GENERATED_IN_SNAPSHOT, outcome); // because of updateFromDefinition isn't called
@ -1075,7 +1153,7 @@ public class ProfilePathProcessor {
throw new DefinitionException(profileUtilities.getContext().formatMessage(I18nConstants.ADDING_WRONG_PATH));
debugCheck(outcome);
getResult().getElement().add(outcome);
profileUtilities.updateFromDefinition(outcome, diffItem, getProfileName(), isTrimDifferential(), getUrl(), getSourceStructureDefinition(), getDerived());
profileUtilities.updateFromDefinition(outcome, diffItem, getProfileName(), isTrimDifferential(), getUrl(), getSourceStructureDefinition(), getDerived(), diffPath(diffItem));
profileUtilities.removeStatusExtensions(outcome);
// --- LM Added this
cursors.diffCursor = getDifferential().getElement().indexOf(diffItem) + 1;

65
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/profile/ProfileUtilities.java
View File

@ -139,11 +139,13 @@ public class ProfileUtilities extends TranslatingUtilities {
public class ElementDefinitionCounter {
int countMin = 0;
int countMax = 0;
int index = 0;
ElementDefinition focus;
Set<String> names = new HashSet<>();
public ElementDefinitionCounter(ElementDefinition ed) {
public ElementDefinitionCounter(ElementDefinition ed, int i) {
focus = ed;
index = i;
}
public int checkMin() {
@ -192,6 +194,11 @@ public class ProfileUtilities extends TranslatingUtilities {
public boolean checkMinMax() {
return countMin <= countMax;
}
public int getIndex() {
return index;
}
}
public enum MappingMergeModeOption {
@ -683,11 +690,12 @@ public class ProfileUtilities extends TranslatingUtilities {
checkGroupConstraints(derived);
if (derived.getDerivation() == TypeDerivationRule.SPECIALIZATION) {
int i = 0;
for (ElementDefinition e : diff.getElement()) {
if (!e.hasUserData(UD_GENERATED_IN_SNAPSHOT) && e.getPath().contains(".")) {
ElementDefinition existing = getElementInCurrentContext(e.getPath(), derived.getSnapshot().getElement());
if (existing != null) {
updateFromDefinition(existing, e, profileName, false, url, base, derived);
updateFromDefinition(existing, e, profileName, false, url, base, derived, "StructureDefinition.differential.element["+i+"]");
} else {
ElementDefinition outcome = updateURLs(url, webUrl, e.copy());
e.setUserData(UD_GENERATED_IN_SNAPSHOT, outcome);
@ -701,6 +709,7 @@ public class ProfileUtilities extends TranslatingUtilities {
}
}
}
i++;
}
}
@ -723,6 +732,7 @@ public class ProfileUtilities extends TranslatingUtilities {
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
//Check that all differential elements have a corresponding snapshot element
int ce = 0;
int i = 0;
for (ElementDefinition e : diff.getElement()) {
if (!e.hasUserData("diff-source"))
throw new Error(context.formatMessage(I18nConstants.UNXPECTED_INTERNAL_CONDITION__NO_SOURCE_ON_DIFF_ELEMENT));
@ -736,15 +746,16 @@ public class ProfileUtilities extends TranslatingUtilities {
b.append(e.hasId() ? "id: "+e.getId() : "path: "+e.getPath());
ce++;
if (e.hasId()) {
String msg = "No match found in the generated snapshot: check that the path and definitions are legal in the differential (including order)";
messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url+"#"+e.getId(), msg, ValidationMessage.IssueSeverity.ERROR));
String msg = "No match found for "+e.getId()+" in the generated snapshot: check that the path and definitions are legal in the differential (including order)";
messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, "StructureDefinition.differential.element["+i+"]", msg, ValidationMessage.IssueSeverity.ERROR));
}
}
i++;
}
if (!Utilities.noString(b.toString())) {
String msg = "The profile "+derived.getUrl()+" has "+ce+" "+Utilities.pluralize("element", ce)+" in the differential ("+b.toString()+") that don't have a matching element in the snapshot: check that the path and definitions are legal in the differential (including order)";
if (debug) {
System.out.println("Error in snapshot generation: "+msg);
System.err.println("Error in snapshot generation: "+msg);
if (!debug) {
System.out.println("Differential: ");
for (ElementDefinition ed : derived.getDifferential().getElement())
@ -789,10 +800,10 @@ public class ProfileUtilities extends TranslatingUtilities {
tn = tn.substring(tn.lastIndexOf("/")+1);
}
Map<String, ElementDefinitionCounter> slices = new HashMap<>();
int i = 0;
i = 0;
for (ElementDefinition ed : derived.getSnapshot().getElement()) {
if (ed.hasSlicing()) {
slices.put(ed.getPath(), new ElementDefinitionCounter(ed));
slices.put(ed.getPath(), new ElementDefinitionCounter(ed, i));
} else {
Set<String> toRemove = new HashSet<>();
for (String s : slices.keySet()) {
@ -809,37 +820,43 @@ public class ProfileUtilities extends TranslatingUtilities {
slice.getFocus().setMin(count);
} else {
String msg = "The slice definition for "+slice.getFocus().getId()+" has a minimum of "+slice.getFocus().getMin()+" but the slices add up to a minimum of "+count;
messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url+"#"+slice.getFocus().getId(), msg, forPublication ? ValidationMessage.IssueSeverity.ERROR : ValidationMessage.IssueSeverity.INFORMATION).setIgnorableError(true));
messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE,
"StructureDefinition.snapshot.element["+slice.getIndex()+"]", msg, forPublication ? ValidationMessage.IssueSeverity.ERROR : ValidationMessage.IssueSeverity.INFORMATION).setIgnorableError(true));
}
}
count = slice.checkMax();
if (count > -1 && repeats) {
String msg = "The slice definition for "+slice.getFocus().getId()+" has a maximum of "+slice.getFocus().getMax()+" but the slices add up to a maximum of "+count+". Check that this is what is intended";
messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url+"#"+slice.getFocus().getId(), msg, ValidationMessage.IssueSeverity.INFORMATION));
messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE,
"StructureDefinition.snapshot.element["+slice.getIndex()+"]", msg, ValidationMessage.IssueSeverity.INFORMATION));
}
if (!slice.checkMinMax()) {
String msg = "The slice definition for "+slice.getFocus().getId()+" has a maximum of "+slice.getFocus().getMax()+" which is less than the minimum of "+slice.getFocus().getMin();
messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url+"#"+"#"+slice.getFocus().getId(), msg, ValidationMessage.IssueSeverity.WARNING));
messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE,
"StructureDefinition.snapshot.element["+slice.getIndex()+"]", msg, ValidationMessage.IssueSeverity.WARNING));
}
slices.remove(s);
}
}
if (ed.getPath().contains(".") && !ed.getPath().startsWith(tn+".")) {
throw new Error("The element "+ed.getId()+" in the profile '"+derived.getVersionedUrl()+" (["+i+"]) doesn't have the right path (should start with "+tn+".");
throw new Error("The element "+ed.getId()+" in the profile '"+derived.getVersionedUrl()+" doesn't have the right path (should start with "+tn+".");
}
if (ed.hasSliceName() && !slices.containsKey(ed.getPath())) {
String msg = "The element "+ed.getId()+" (["+i+"]) launches straight into slicing without the slicing being set up properly first";
messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url+"#"+ed.getId(), msg, ValidationMessage.IssueSeverity.ERROR).setIgnorableError(true));
String msg = "The element "+ed.getId()+" launches straight into slicing without the slicing being set up properly first";
messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE,
"StructureDefinition.snapshot.element["+i+"]", msg, ValidationMessage.IssueSeverity.ERROR).setIgnorableError(true));
}
if (ed.hasSliceName() && slices.containsKey(ed.getPath())) {
if (!slices.get(ed.getPath()).count(ed, ed.getSliceName())) {
String msg = "Duplicate slice name "+ed.getSliceName()+" on "+ed.getId()+" (["+i+"])";
messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url+"#"+ed.getId(), msg, ValidationMessage.IssueSeverity.ERROR).setIgnorableError(true));
messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE,
"StructureDefinition.snapshot.element["+i+"]", msg, ValidationMessage.IssueSeverity.ERROR).setIgnorableError(true));
}
}
i++;
}
i = 0;
// last, check for wrong profiles or target profiles
for (ElementDefinition ed : derived.getSnapshot().getElement()) {
for (TypeRefComponent t : ed.getType()) {
@ -852,7 +869,8 @@ public class ProfileUtilities extends TranslatingUtilities {
}
if (sd == null) {
if (messages != null) {
messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url+"#"+ed.getId(), "The type of profile "+u.getValue()+" cannot be checked as the profile is not known", IssueSeverity.WARNING));
messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE,
"StructureDefinition.snapshot.element["+i+"]", "The type of profile "+u.getValue()+" cannot be checked as the profile is not known", IssueSeverity.WARNING));
}
} else {
String wt = t.getWorkingCode();
@ -878,6 +896,7 @@ public class ProfileUtilities extends TranslatingUtilities {
}
}
}
i++;
}
} catch (Exception e) {
// if we had an exception generating the snapshot, make sure we don't leave any half generated snapshot behind
@ -1365,7 +1384,7 @@ public class ProfileUtilities extends TranslatingUtilities {
return true;
}
if (tr.getWorkingCode().equals(t.getCode())) {
System.out.println("Type error: use of a simple type \""+t.getCode()+"\" wrongly constraining "+base.getPath());
System.err.println("Type error: use of a simple type \""+t.getCode()+"\" wrongly constraining "+base.getPath());
return true;
}
}
@ -1773,7 +1792,7 @@ public class ProfileUtilities extends TranslatingUtilities {
}
if (sd == null) {
if (debug) {
System.out.println("Failed to find referenced profile: " + type.getProfile());
System.err.println("Failed to find referenced profile: " + type.getProfile());
}
}
@ -1781,14 +1800,14 @@ public class ProfileUtilities extends TranslatingUtilities {
if (sd == null)
sd = context.fetchTypeDefinition(type.getWorkingCode());
if (sd == null)
System.out.println("XX: failed to find profle for type: " + type.getWorkingCode()); // debug GJM
System.err.println("XX: failed to find profle for type: " + type.getWorkingCode()); // debug GJM
return sd;
}
protected StructureDefinition getProfileForDataType(String type) {
StructureDefinition sd = context.fetchTypeDefinition(type);
if (sd == null)
System.out.println("XX: failed to find profle for type: " + type); // debug GJM
System.err.println("XX: failed to find profle for type: " + type); // debug GJM
return sd;
}
@ -2259,7 +2278,7 @@ public class ProfileUtilities extends TranslatingUtilities {
}
protected void updateFromDefinition(ElementDefinition dest, ElementDefinition source, String pn, boolean trimDifferential, String purl, StructureDefinition srcSD, StructureDefinition derivedSrc) throws DefinitionException, FHIRException {
protected void updateFromDefinition(ElementDefinition dest, ElementDefinition source, String pn, boolean trimDifferential, String purl, StructureDefinition srcSD, StructureDefinition derivedSrc, String path) throws DefinitionException, FHIRException {
source.setUserData(UD_GENERATED_IN_SNAPSHOT, dest);
// we start with a clone of the base profile ('dest') and we copy from the profile ('source')
// over the top for anything the source has
@ -2690,7 +2709,7 @@ public class ProfileUtilities extends TranslatingUtilities {
if (!Base.compareDeep(derived.getType(), base.getType(), false)) {
if (base.hasType()) {
for (TypeRefComponent ts : derived.getType()) {
checkTypeDerivation(purl, derivedSrc, base, derived, ts);
checkTypeDerivation(purl, derivedSrc, base, derived, ts, path);
}
}
base.getType().clear();
@ -2816,7 +2835,7 @@ public class ProfileUtilities extends TranslatingUtilities {
}
}
private void checkTypeDerivation(String purl, StructureDefinition srcSD, ElementDefinition base, ElementDefinition derived, TypeRefComponent ts) {
private void checkTypeDerivation(String purl, StructureDefinition srcSD, ElementDefinition base, ElementDefinition derived, TypeRefComponent ts, String path) {
boolean ok = false;
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
String t = ts.getWorkingCode();
@ -2854,7 +2873,7 @@ public class ProfileUtilities extends TranslatingUtilities {
StructureDefinition sd = context.fetchResource(StructureDefinition.class, url);
if (sd == null) {
if (messages != null) {
messages.add(new ValidationMessage(Source.InstanceValidator, IssueType.BUSINESSRULE, purl + "#" + derived.getPath(), "Cannot check whether the target profile " + url + " is valid constraint on the base because it is not known", IssueSeverity.WARNING));
messages.add(new ValidationMessage(Source.InstanceValidator, IssueType.BUSINESSRULE, path, "Cannot check whether the target profile " + url + " on "+derived.getPath()+" is valid constraint on the base because it is not known", IssueSeverity.WARNING));
}
url = null;
tgtOk = true; // suppress error message