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Merge pull request #405 from hapifhir/gg-v5.2.12 

Gg v5.2.12
This commit is contained in:
Grahame Grieve 2020-12-18 23:14:32 +11:00 committed by GitHub
parent ff49147146 9eca42afdb
commit 9ecd7f2933
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GPG Key ID: 4AEE18F83AFDEB23
7 changed files with 32 additions and 9 deletions
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4
RELEASE_NOTES.md
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@ -0,0 +1,4 @@
Validator:
* allow for URLs that are references to ISO standards (urn:std:)
* fix up validation of value set for code system and expansions
* fix up validation for R2B issues (value set references, profiled types)

4
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/DataRenderer.java
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@ -400,8 +400,10 @@ public class DataRenderer extends Renderer {
} else {
if (uri.getValue().contains("|")) {
x.ah(uri.getValue().substring(0, uri.getValue().indexOf("|"))).addText(uri.getValue());
} else {
} else if (url.startsWith("http:") || url.startsWith("https:") || url.startsWith("ftp:")) {
x.ah(uri.getValue()).addText(uri.getValue());
} else {
x.code().addText(uri.getValue());
}
}
}

3
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/Utilities.java
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@ -1090,7 +1090,8 @@ public class Utilities {
public static boolean isAbsoluteUrl(String ref) {
return ref != null && (ref.startsWith("http:") || ref.startsWith("https:") || ref.startsWith("urn:uuid:") || ref.startsWith("urn:oid:"));
return ref != null && (ref.startsWith("http:") || ref.startsWith("https:") || ref.startsWith("urn:uuid:") || ref.startsWith("urn:oid:") ||
Utilities.startsWithInList(ref, "urn:iso:", "urn:iso-iec:", "urn:iso-cie:", "urn:iso-astm:", "urn:iso-ieee:", "urn:iec:")); // rfc5141
}

2
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/i18n/I18nConstants.java
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@ -48,7 +48,7 @@ public class I18nConstants {
public static final String CODESYSTEM_CS_NO_VS_NOTCOMPLETE = "CODESYSTEM_CS_NO_VS_NOTCOMPLETE";
public static final String CODESYSTEM_CS_VS_INCLUDEDETAILS = "CodeSystem_CS_VS_IncludeDetails";
public static final String CODESYSTEM_CS_VS_INVALID = "CodeSystem_CS_VS_Invalid";
public static final String CODESYSTEM_CS_VS_MISMATCH = "CodeSystem_CS_VS_MisMatch";
public static final String CODESYSTEM_CS_VS_EXP_MISMATCH = "CODESYSTEM_CS_VS_EXP_MISMATCH";
public static final String CODESYSTEM_CS_VS_WRONGSYSTEM = "CodeSystem_CS_VS_WrongSystem";
public static final String CODE_FOUND_IN_EXPANSION_HOWEVER_ = "Code_found_in_expansion_however_";
public static final String CODING_HAS_NO_SYSTEM__CANNOT_VALIDATE = "Coding_has_no_system__cannot_validate";

4
org.hl7.fhir.utilities/src/main/resources/Messages.properties
View File

@ -24,7 +24,7 @@ Bundle_Document_Date_Missing_html = [(type = ''document'') implies (meta.lastUpd
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
CodeSystem_CS_VS_Invalid = CodeSystem {0} has an ''all system'' value set of {1}, but doesn''t have a single include
CodeSystem_CS_VS_MisMatch = CodeSystem {0} has an ''all system'' value set of {1}, but it is an expansion
CODESYSTEM_CS_VS_EXP_MISMATCH = CodeSystem {0} has an ''all system'' value set of {1}, but it is an expansion with the wrong number of concepts (found {2}, expected {3})
CodeSystem_CS_VS_WrongSystem = CodeSystem {0} has an ''all system'' value set of {1}, but doesn''t have a matching system ({2})
Extension_EXT_Context_Wrong = The extension {0} is not allowed to be used at this point (allowed = {1}; this element is [{2})
Extension_EXT_Count_Mismatch = Extensions count mismatch: expected {0} but found {1}
@ -617,7 +617,7 @@ SD_NESTED_MUST_SUPPORT_SNAPSHOT = The element {0} has types/profiles/targets tha
Unable_to_connect_to_terminology_server = Unable to connect to terminology server. Error = {0}
SD_ED_TYPE_PROFILE_UNKNOWN = Unable to resolve profile {0}
SD_ED_TYPE_PROFILE_NOTYPE = Found profile {0}, but unable to determine the type it applies it
SD_ED_TYPE_PROFILE_WRONG = Profile {0} is for type {1}, but the {3} element has type {2}
SD_ED_TYPE_PROFILE_WRONG = Extension {0} is for type {1}, but the {3} element has type {2}
SD_ED_TYPE_PROFILE_WRONG_TARGET = Profile {0} is for type {1}, which is not a {4} (which is required because the {3} element has type {2})
SD_ED_TYPE_NO_TARGET_PROFILE = Type {0} does not allow for target Profiles
TERMINOLOGY_TX_NOSVC_BOUND_REQ = Could not confirm that the codes provided are from the required value set {0} because there is no terminology service

19
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/CodeSystemValidator.java
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@ -38,15 +38,30 @@ public class CodeSystemValidator extends BaseValidator {
vs = null;
}
if (vs != null) {
if (rule(errors, IssueType.BUSINESSRULE, stack.getLiteralPath(), vs.hasCompose() && !vs.hasExpansion(), I18nConstants.CODESYSTEM_CS_VS_MISMATCH, url, vsu))
if (rule(errors, IssueType.BUSINESSRULE, stack.getLiteralPath(), vs.getCompose().getInclude().size() == 1, I18nConstants.CODESYSTEM_CS_VS_INVALID, url, vsu))
if (rule(errors, IssueType.BUSINESSRULE, stack.getLiteralPath(), vs.hasCompose(), I18nConstants.CODESYSTEM_CS_VS_INVALID, url, vsu)) {
if (rule(errors, IssueType.BUSINESSRULE, stack.getLiteralPath(), vs.getCompose().getInclude().size() == 1, I18nConstants.CODESYSTEM_CS_VS_INVALID, url, vsu)) {
if (rule(errors, IssueType.BUSINESSRULE, stack.getLiteralPath(), vs.getCompose().getInclude().get(0).getSystem().equals(url), I18nConstants.CODESYSTEM_CS_VS_WRONGSYSTEM, url, vsu, vs.getCompose().getInclude().get(0).getSystem())) {
rule(errors, IssueType.BUSINESSRULE, stack.getLiteralPath(), !vs.getCompose().getInclude().get(0).hasValueSet()
&& !vs.getCompose().getInclude().get(0).hasConcept() && !vs.getCompose().getInclude().get(0).hasFilter(), I18nConstants.CODESYSTEM_CS_VS_INCLUDEDETAILS, url, vsu);
if (vs.hasExpansion()) {
int count = countConcepts(cs);
rule(errors, IssueType.BUSINESSRULE, stack.getLiteralPath(), vs.getExpansion().getContains().size() == count, I18nConstants.CODESYSTEM_CS_VS_EXP_MISMATCH, url, vsu, count, vs.getExpansion().getContains().size());
}
}
}
}
}
} // todo... try getting the value set the other way...
}
private int countConcepts(Element cs) {
List<Element> concepts = cs.getChildrenByName("concept");
int res = concepts.size();
for (Element concept : concepts) {
res = res + countConcepts(concept);
}
return res;
}
}

5
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/StructureDefinitionValidator.java
View File

@ -174,7 +174,7 @@ public class StructureDefinitionValidator extends BaseValidator {
rule(errors, IssueType.BUSINESSRULE, stack.getLiteralPath(), !snapshot || bindableType(typeCodes) != null, I18nConstants.SD_ED_BIND_NO_BINDABLE, path, typeCodes.toString());
if (binding.hasChild("valueSet")) {
Element valueSet = binding.getNamedChild("valueSet");
String ref = valueSet.hasPrimitiveValue() ? valueSet.primitiveValue() : valueSet.getNamedChildValue("refernece");
String ref = valueSet.hasPrimitiveValue() ? valueSet.primitiveValue() : valueSet.getNamedChildValue("reference");
if (warning(errors, IssueType.BUSINESSRULE, stack.getLiteralPath(), !snapshot || ref != null, I18nConstants.SD_ED_SHOULD_BIND_WITH_VS, path)) {
Resource vs = context.fetchResource(Resource.class, ref);
if (warning(errors, IssueType.BUSINESSRULE, stack.getLiteralPath(), vs != null, I18nConstants.SD_ED_BIND_UNKNOWN_VS, path, ref)) {
@ -300,10 +300,11 @@ public class StructureDefinitionValidator extends BaseValidator {
return true;
}
sd = sd.hasBaseDefinition() ? context.fetchResource(StructureDefinition.class, sd.getBaseDefinition()) : null;
if (sd != null && !sd.getAbstract()) {
if (!(VersionUtilities.isR2Ver(context.getVersion()) || VersionUtilities.isR2BVer(context.getVersion())) && sd != null && !sd.getAbstract()) {
sd = null;
}
}
return false;
}