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

This commit is contained in:
Grahame Grieve 2020-05-19 05:38:46 +10:00
parent 80d9102aee 9da81a1c4f
commit c7444745de
6 changed files with 43 additions and 18 deletions
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2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/ProfileUtilities.java
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@ -4252,7 +4252,7 @@ public class ProfileUtilities extends TranslatingUtilities {
private String commas(List<ElementDefinitionSlicingDiscriminatorComponent> list) {
CommaSeparatedStringBuilder c = new CommaSeparatedStringBuilder();
for (ElementDefinitionSlicingDiscriminatorComponent id : list)
c.append(id.getType().toCode()+":"+id.getPath());
c.append((id.hasType() ? id.getType().toCode() : "??")+":"+id.getPath());
return c.toString();
}

9
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/ValueSetRenderer.java
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@ -687,8 +687,13 @@ public class ValueSetRenderer extends TerminologyRenderer {
for (ConceptSetComponent inc : vs.getCompose().getInclude()) {
hasExtensions = genInclude(ul, inc, "Include", langs, maps) || hasExtensions;
}
for (ConceptSetComponent exc : vs.getCompose().getExclude()) {
hasExtensions = genInclude(ul, exc, "Exclude", langs, maps) || hasExtensions;
if (vs.getCompose().hasExclude()) {
p = x.para();
p.tx("This value set excludes codes based on the following rules:");
ul = x.ul();
for (ConceptSetComponent exc : vs.getCompose().getExclude()) {
hasExtensions = genInclude(ul, exc, "Exclude", langs, maps) || hasExtensions;
}
}
}

12
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/cache/PackageCacheManager.java vendored
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@ -257,7 +257,15 @@ public class PackageCacheManager {
for (File f : new File(cacheFolder).listFiles()) {
if (f.isDirectory()) {
Utilities.clearDirectory(f.getAbsolutePath());
try {
FileUtils.deleteDirectory(f);
} catch (Exception e1) {
try {
FileUtils.deleteDirectory(f);
} catch (Exception e2) {
// just give up
}
}
}
else if (!f.getName().equals("packages.ini"))
FileUtils.forceDelete(f);
@ -652,8 +660,8 @@ public class PackageCacheManager {
InputStream stream = fetchFromUrlSpecific(Utilities.pathURL(ciList.get(id), "package.tgz"), false);
return new InputStreamWithSrc(stream, Utilities.pathURL(ciList.get(id), "package.tgz"), "current");
} else if (id.startsWith("hl7.fhir.r5")) {
InputStream stream = fetchFromUrlSpecific(Utilities.pathURL("http://hl7.org/fhir/2020Feb", id+".tgz"), false);
return new InputStreamWithSrc(stream, Utilities.pathURL("http://hl7.org/fhir/2020Feb", id+".tgz"), "current");
InputStream stream = fetchFromUrlSpecific(Utilities.pathURL("http://build.fhir.org", id+".tgz"), false);
return new InputStreamWithSrc(stream, Utilities.pathURL("http://build.fhir.org", id+".tgz"), "current");
} else {
throw new FHIRException("The package '"+id+"' has not entry on the current build server");
}

2
org.hl7.fhir.utilities/src/main/resources/Messages.properties
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@ -17,7 +17,7 @@ Bundle_BUNDLE_FullUrl_NeedVersion = Entries matching fullURL {0} should declare
Bundle_BUNDLE_MultipleMatches = Multiple matches in bundle for reference {0}
Bundle_BUNDLE_Not_Local = URN reference is not locally contained within the bundle {0}
Bundle_MSG_Event_Count = Expected {0} but found {1} event elements
Bundle_Document_Date_Missing = A document must have a date {0}
Bundle_Document_Date_Missing = A document must have a date
Bundle_Document_Date_Missing_html = [(type = 'document') implies (meta.lastUpdated.hasValue())]
CapabalityStatement_CS_SP_WrongType = Type mismatch - SearchParameter "{0}" type is {1}, but type here is {2}
CodeSystem_CS_VS_IncludeDetails = CodeSystem {0} has an ''all system'' value set of {1}, but the include has extra details

35
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java
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@ -2185,10 +2185,12 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
boolean matchingResource = false;
for (CanonicalType target : containerType.getTargetProfile()) {
StructureDefinition sd = resolveProfile(profile, target.asStringValue());
if (rule(errors, IssueType.NOTFOUND, element.line(), element.col(), path, sd != null, I18nConstants.REFERENCE_REF_CANTRESOLVEPROFILE, target.asStringValue())) {
if (("http://hl7.org/fhir/StructureDefinition/" + sd.getType()).equals(tu)) {
matchingResource = true;
break;
}
}
}
rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path, matchingResource, I18nConstants.REFERENCE_REF_WRONGTARGET, reference.getType(), container.getType("Reference").getTargetProfile());
@ -3627,6 +3629,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
}
} else if (ei.definition.getContentReference() != null) {
typeDefn = resolveNameReference(profile.getSnapshot(), ei.definition.getContentReference());
} else if (ei.definition.getType().size() == 1 && ("Element".equals(ei.definition.getType().get(0).getWorkingCode()) || "BackboneElement".equals(ei.definition.getType().get(0).getWorkingCode()))) {
if (ei.definition.getType().get(0).hasProfile()) {
CanonicalType pu = ei.definition.getType().get(0).getProfile().get(0);
@ -3654,7 +3657,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
String thisExtension = null;
boolean checkDisplay = true;
checkInvariants(hostContext, errors, profile, ei.definition, resource, ei.getElement(), localStack, true);
checkInvariants(hostContext, errors, profile, typeDefn != null ? typeDefn : ei.definition, resource, ei.getElement(), localStack, true);
ei.getElement().markValidation(profile, ei.definition);
boolean elementValidated = false;
@ -3910,18 +3913,20 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
ElementDefinition ed = childDefinitions.get(i);
boolean childUnsupportedSlicing = false;
boolean process = true;
if (ed.hasSlicing() && !ed.getSlicing().getOrdered())
if (ed.hasSlicing() && !ed.getSlicing().getOrdered()) {
slicingPath = ed.getPath();
else if (slicingPath != null && ed.getPath().equals(slicingPath))
} else if (slicingPath != null && ed.getPath().equals(slicingPath)) {
; // nothing
else if (slicingPath != null && !ed.getPath().startsWith(slicingPath))
} else if (slicingPath != null && !ed.getPath().startsWith(slicingPath)) {
slicingPath = null;
}
// where are we with slicing
if (ed.hasSlicing()) {
if (slicer != null && slicer.getPath().equals(ed.getPath())) {
String errorContext = "profile " + profile.getUrl();
if (!resource.getChildValue(ID).isEmpty())
if (!resource.getChildValue(ID).isEmpty()) {
errorContext += "; instance " + resource.getChildValue("id");
}
throw new DefinitionException(context.formatMessage(I18nConstants.SLICE_ENCOUNTERED_MIDWAY_THROUGH_SET_PATH___ID___, slicer.getPath(), slicer.getId(), errorContext));
}
slicer = ed;
@ -3941,9 +3946,10 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
int lastSlice = -1;
for (ElementInfo ei : children) {
String sliceInfo = "";
if (slicer != null)
if (slicer != null) {
sliceInfo = " (slice: " + slicer.getPath() + ")";
if (!unsupportedSlicing)
}
if (!unsupportedSlicing) {
if (ei.additionalSlice && ei.definition != null) {
if (ei.definition.getSlicing().getRules().equals(ElementDefinition.SlicingRules.OPEN) ||
ei.definition.getSlicing().getRules().equals(ElementDefinition.SlicingRules.OPENATEND) && true /* TODO: replace "true" with condition to check that this element is at "end" */) {
@ -3956,9 +3962,11 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
}
} else {
// Don't raise this if we're in an abstract profile, like Resource
if (!profile.getAbstract())
if (!profile.getAbstract()) {
rule(errors, IssueType.NOTSUPPORTED, ei.line(), ei.col(), ei.getPath(), (ei.definition != null), I18nConstants.VALIDATION_VAL_PROFILE_NOTALLOWED, profile.getUrl());
}
}
}
// TODO: Should get the order of elements correct when parsing elements that are XML attributes vs. elements
boolean isXmlAttr = false;
if (ei.definition != null) {
@ -3974,14 +3982,17 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
boolean ok = (ei.definition == null) || (ei.index >= last) || isXmlAttr;
rule(errors, IssueType.INVALID, ei.line(), ei.col(), ei.getPath(), ok, I18nConstants.VALIDATION_VAL_PROFILE_OUTOFORDER, profile.getUrl(), ei.getName());
}
if (ei.slice != null && ei.index == last && ei.slice.getSlicing().getOrdered())
if (ei.slice != null && ei.index == last && ei.slice.getSlicing().getOrdered()) {
rule(errors, IssueType.INVALID, ei.line(), ei.col(), ei.getPath(), (ei.definition == null) || (ei.sliceindex >= lastSlice) || isXmlAttr, I18nConstants.VALIDATION_VAL_PROFILE_SLICEORDER, profile.getUrl(), ei.getName());
if (ei.definition == null || !isXmlAttr)
}
if (ei.definition == null || !isXmlAttr) {
last = ei.index;
if (ei.slice != null)
}
if (ei.slice != null) {
lastSlice = ei.sliceindex;
else
} else {
lastSlice = -1;
}
}
return problematicPaths;
}

1
release-notes-validator.md
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@ -6,6 +6,7 @@ title: FHIR Validator Release Notes
## Current (not released yet)
* Fix to check invariants on Elements with type redirections (e.g. ValueSet.compose.exclude)
* fix fatal NPE validating bundles when resource is missing
* fix tests for R5 changes