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Merge pull request #798 from hapifhir/gg-202204-validator-extensions 

enable -extension parameter for validator
This commit is contained in:
Grahame Grieve 2022-04-27 10:33:11 +10:00 committed by GitHub
parent 5fc2e9d6ec 0a58140163
commit 220f32a94b
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
11 changed files with 275 additions and 20 deletions
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1
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/FHIRPathEngine.java
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@ -5497,7 +5497,6 @@ public class FHIRPathEngine {
return list.size() != 1 ? true : Utilities.existsInList(list.get(0).getCode(), "Element", "BackboneElement", "Resource", "DomainResource");
}
private boolean hasType(ElementDefinition ed, String s) {
for (TypeRefComponent t : ed.getType()) {
if (s.equalsIgnoreCase(t.getCode())) {

12
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/FilesystemPackageCacheManager.java
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@ -95,6 +95,7 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
private boolean buildLoaded = false;
private Map<String, String> ciList = new HashMap<String, String>();
private JsonArray buildInfo;
private boolean suppressErrors;
/**
* Constructor
@ -354,7 +355,7 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
System.out.print(" Installing: ");
}
if (npm.name() == null || id == null || !id.equalsIgnoreCase(npm.name())) {
if (!suppressErrors && npm.name() == null || id == null || !id.equalsIgnoreCase(npm.name())) {
if (!id.equals("hl7.fhir.r5.core") && !id.equals("hl7.fhir.us.immds")) {// temporary work around
throw new IOException("Attempt to import a mis-identified package. Expected " + id + ", got " + npm.name());
}
@ -939,4 +940,13 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
return false;
}
public boolean isSuppressErrors() {
return suppressErrors;
}
public void setSuppressErrors(boolean suppressErrors) {
this.suppressErrors = suppressErrors;
}
}

4
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/ValidationEngine.java
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@ -159,6 +159,8 @@ public class ValidationEngine implements IValidatorResourceFetcher, IValidationP
@Getter @Setter private boolean showMessagesFromReferences;
@Getter @Setter private Locale locale;
@Getter @Setter private List<ImplementationGuide> igs = new ArrayList<>();
@Getter @Setter private List<String> extensionDomains = new ArrayList<>();
@Getter @Setter private boolean showTimes;
@Getter @Setter private List<BundleValidationRule> bundleValidationRules = new ArrayList<>();
@Getter @Setter private QuestionnaireMode questionnaireMode;
@ -596,6 +598,8 @@ public class ValidationEngine implements IValidatorResourceFetcher, IValidationP
InstanceValidator validator = new InstanceValidator(context, null, null);
validator.setHintAboutNonMustSupport(hintAboutNonMustSupport);
validator.setAnyExtensionsAllowed(anyExtensionsAllowed);
validator.getExtensionDomains().clear();
validator.getExtensionDomains().addAll(extensionDomains);
validator.setNoInvariantChecks(isNoInvariantChecks());
validator.setWantInvariantInMessage(isWantInvariantInMessage());
validator.setValidationLanguage(language);

22
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/model/CliContext.java
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@ -22,8 +22,6 @@ public class CliContext {
@JsonProperty("doNative")
private boolean doNative = false;
@JsonProperty("anyExtensionsAllowed")
private boolean anyExtensionsAllowed = true;
@JsonProperty("hintAboutNonMustSupport")
private boolean hintAboutNonMustSupport = false;
@JsonProperty("recursive")
@ -72,6 +70,8 @@ public class CliContext {
@JsonProperty("targetVer")
private String targetVer = null;
@JsonProperty("extensions")
private List<String> extensions = new ArrayList<String>();
@JsonProperty("igs")
private List<String> igs = new ArrayList<String>();
@JsonProperty("questionnaire")
@ -191,15 +191,9 @@ public class CliContext {
return this;
}
@JsonProperty("anyExtensionsAllowed")
public boolean isAnyExtensionsAllowed() {
return anyExtensionsAllowed;
}
@JsonProperty("anyExtensionsAllowed")
public CliContext setAnyExtensionsAllowed(boolean anyExtensionsAllowed) {
this.anyExtensionsAllowed = anyExtensionsAllowed;
return this;
@JsonProperty("extensions")
public List<String> getExtensions() {
return extensions;
}
@JsonProperty("hintAboutNonMustSupport")
@ -576,7 +570,6 @@ public class CliContext {
if (o == null || getClass() != o.getClass()) return false;
CliContext that = (CliContext) o;
return doNative == that.doNative &&
anyExtensionsAllowed == that.anyExtensionsAllowed &&
hintAboutNonMustSupport == that.hintAboutNonMustSupport &&
recursive == that.recursive &&
doDebug == that.doDebug &&
@ -587,6 +580,7 @@ public class CliContext {
noUnicodeBiDiControlChars == that.noUnicodeBiDiControlChars &&
noInvariants == that.noInvariants &&
wantInvariantsInMessages == that.wantInvariantsInMessages &&
Objects.equals(extensions, that.extensions) &&
Objects.equals(map, that.map) &&
Objects.equals(output, that.output) &&
Objects.equals(htmlOutput, that.htmlOutput) &&
@ -615,7 +609,7 @@ public class CliContext {
@Override
public int hashCode() {
return Objects.hash(doNative, anyExtensionsAllowed, hintAboutNonMustSupport, recursive, doDebug, assumeValidRestReferences, canDoNative, noInternalCaching,
return Objects.hash(doNative, extensions, hintAboutNonMustSupport, recursive, doDebug, assumeValidRestReferences, canDoNative, noInternalCaching,
noExtensibleBindingMessages, noInvariants, wantInvariantsInMessages, map, output, htmlOutput, txServer, sv, txLog, txCache, mapLog, lang, fhirpath, snomedCT,
targetVer, igs, questionnaireMode, level, profiles, sources, mode, locale, locations, crumbTrails, showTimes, allowExampleUrls, outputStyle, noUnicodeBiDiControlChars);
}
@ -624,7 +618,7 @@ public class CliContext {
public String toString() {
return "CliContext{" +
"doNative=" + doNative +
", anyExtensionsAllowed=" + anyExtensionsAllowed +
", extensions=" + extensions +
", hintAboutNonMustSupport=" + hintAboutNonMustSupport +
", recursive=" + recursive +
", doDebug=" + doDebug +

8
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/services/ValidationService.java
View File

@ -340,7 +340,13 @@ public class ValidationService {
validator.setLevel(cliContext.getLevel());
validator.setDoNative(cliContext.isDoNative());
validator.setHintAboutNonMustSupport(cliContext.isHintAboutNonMustSupport());
validator.setAnyExtensionsAllowed(cliContext.isAnyExtensionsAllowed());
for (String s : cliContext.getExtensions()) {
if ("*".equals(s)) {
validator.setAnyExtensionsAllowed(true);
} else {
validator.getExtensionDomains().add(s);
}
}
validator.setLanguage(cliContext.getLang());
validator.setLocale(cliContext.getLocale());
validator.setSnomedExtension(cliContext.getSnomedCTCode());

6
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/utils/Params.java
View File

@ -26,7 +26,7 @@ public class Params {
public static final String RECURSE = "-recurse";
public static final String SHOW_MESSAGES_FROM_REFERENCES = "-showReferenceMessages";
public static final String LOCALE = "-locale";
public static final String STRICT_EXTENSIONS = "-strictExtensions";
public static final String EXTENSIONS = "-extensions";
public static final String HINT_ABOUT_NON_MUST_SUPPORT = "-hintAboutNonMustSupport";
public static final String TO_VERSION = "-to-version";
public static final String DO_NATIVE = "-do-native";
@ -169,8 +169,8 @@ public class Params {
} else {
cliContext.setLocale(new Locale(args[++i]));
}
} else if (args[i].equals(STRICT_EXTENSIONS)) {
cliContext.setAnyExtensionsAllowed(false);
} else if (args[i].equals(EXTENSIONS)) {
cliContext.getExtensions().add(args[++i]);
} else if (args[i].equals(NO_INTERNAL_CACHING)) {
cliContext.setNoInternalCaching(true);
} else if (args[i].equals(NO_EXTENSIBLE_BINDING_WARNINGS)) {

19
org.hl7.fhir.validation/src/test/resources/txCache/iso4217.cache Normal file
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@ -0,0 +1,19 @@
-------------------------------------------------------------------------------------
{"hierarchical" : false, "valueSet" :{
"resourceType" : "ValueSet",
"compose" : {
"inactive" : true,
"include" : [{
"system" : "urn:iso:std:iso:4217"
}]
}
}}####
e: {
"error" : "java.lang.NullPointerException"
}
-------------------------------------------------------------------------------------
{"hierarchical" : false, "url": "http://hl7.org/fhir/ValueSet/currencies", "version": "4.0.1"}####
e: {
"error" : "java.lang.NullPointerException"
}
-------------------------------------------------------------------------------------

11
org.hl7.fhir.validation/src/test/resources/txCache/lang.cache Normal file
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@ -0,0 +1,11 @@
-------------------------------------------------------------------------------------
{"code" : {
"system" : "urn:ietf:bcp:47",
"code" : "fr-CA"
}, "valueSet" :null, "lang":"en-US", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "versionFlexible":"true"}####
v: {
"severity" : "error",
"error" : "Attempt to use Terminology server when no Terminology server is available",
"class" : "SERVER_ERROR"
}
-------------------------------------------------------------------------------------

90
org.hl7.fhir.validation/src/test/resources/txCache/loinc.cache Normal file
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@ -0,0 +1,90 @@
-------------------------------------------------------------------------------------
{"hierarchical" : false, "valueSet" :{
"resourceType" : "ValueSet",
"compose" : {
"inactive" : true,
"include" : [{
"system" : "http://loinc.org",
"concept" : [{
"extension" : [{
"url" : "http://hl7.org/fhir/StructureDefinition/valueset-label",
"valueString" : "A."
}],
"code" : "LA20752-4",
"display" : "Within 24 hours"
},
{
"extension" : [{
"url" : "http://hl7.org/fhir/StructureDefinition/valueset-label",
"valueString" : "B."
}],
"code" : "LA20753-2",
"display" : "After 24 hours but before 3 days"
},
{
"extension" : [{
"url" : "http://hl7.org/fhir/StructureDefinition/valueset-label",
"valueString" : "C."
}],
"code" : "LA20754-0",
"display" : "Three days or later"
},
{
"extension" : [{
"url" : "http://hl7.org/fhir/StructureDefinition/valueset-label",
"valueString" : "D."
}],
"code" : "LA4489-6",
"display" : "Unknown"
}]
}]
}
}}####
e: {
"error" : "java.lang.NullPointerException"
}
-------------------------------------------------------------------------------------
{"hierarchical" : false, "valueSet" :{
"resourceType" : "ValueSet",
"compose" : {
"include" : [{
"system" : "http://loinc.org",
"concept" : [{
"extension" : [{
"url" : "http://hl7.org/fhir/StructureDefinition/valueset-label",
"valueString" : "A."
}],
"code" : "LA20752-4",
"display" : "Within 24 hours"
},
{
"extension" : [{
"url" : "http://hl7.org/fhir/StructureDefinition/valueset-label",
"valueString" : "B."
}],
"code" : "LA20753-2",
"display" : "After 24 hours but before 3 days"
},
{
"extension" : [{
"url" : "http://hl7.org/fhir/StructureDefinition/valueset-label",
"valueString" : "C."
}],
"code" : "LA20754-0",
"display" : "Three days or later"
},
{
"extension" : [{
"url" : "http://hl7.org/fhir/StructureDefinition/valueset-label",
"valueString" : "D."
}],
"code" : "LA4489-6",
"display" : "Unknown"
}]
}]
}
}}####
e: {
"error" : "java.lang.NullPointerException"
}
-------------------------------------------------------------------------------------

19
org.hl7.fhir.validation/src/test/resources/txCache/mimetypes.cache Normal file
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@ -0,0 +1,19 @@
-------------------------------------------------------------------------------------
{"hierarchical" : false, "valueSet" :{
"resourceType" : "ValueSet",
"compose" : {
"inactive" : true,
"include" : [{
"system" : "urn:ietf:bcp:13"
}]
}
}}####
e: {
"error" : "java.lang.NullPointerException"
}
-------------------------------------------------------------------------------------
{"hierarchical" : false, "url": "http://hl7.org/fhir/ValueSet/mimetypes", "version": "4.0.1"}####
e: {
"error" : "java.lang.NullPointerException"
}
-------------------------------------------------------------------------------------

103
org.hl7.fhir.validation/src/test/resources/txCache/ucum.cache Normal file
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@ -0,0 +1,103 @@
-------------------------------------------------------------------------------------
{"hierarchical" : false, "valueSet" :{
"resourceType" : "ValueSet",
"compose" : {
"inactive" : true,
"include" : [{
"system" : "http://unitsofmeasure.org",
"concept" : [{
"extension" : [{
"url" : "http://hl7.org/fhir/StructureDefinition/valueset-concept-definition",
"valueString" : "second"
}],
"code" : "s",
"display" : "second",
"designation" : [{
"language" : "zh",
"value" : "秒"
}]
},
{
"extension" : [{
"url" : "http://hl7.org/fhir/StructureDefinition/valueset-concept-definition",
"valueString" : "minute"
}],
"code" : "min",
"display" : "minute",
"designation" : [{
"language" : "zh",
"value" : "分钟"
}]
},
{
"extension" : [{
"url" : "http://hl7.org/fhir/StructureDefinition/valueset-concept-definition",
"valueString" : "hour"
}],
"code" : "h",
"display" : "hour",
"designation" : [{
"language" : "zh",
"value" : "小时"
}]
},
{
"extension" : [{
"url" : "http://hl7.org/fhir/StructureDefinition/valueset-concept-definition",
"valueString" : "day"
}],
"code" : "d",
"display" : "day",
"designation" : [{
"language" : "zh",
"value" : "天"
}]
},
{
"extension" : [{
"url" : "http://hl7.org/fhir/StructureDefinition/valueset-concept-definition",
"valueString" : "week"
}],
"code" : "wk",
"display" : "week",
"designation" : [{
"language" : "zh",
"value" : "星期"
}]
},
{
"extension" : [{
"url" : "http://hl7.org/fhir/StructureDefinition/valueset-concept-definition",
"valueString" : "month"
}],
"code" : "mo",
"display" : "month",
"designation" : [{
"language" : "zh",
"value" : "月"
}]
},
{
"extension" : [{
"url" : "http://hl7.org/fhir/StructureDefinition/valueset-concept-definition",
"valueString" : "year"
}],
"code" : "a",
"display" : "year",
"designation" : [{
"language" : "zh",
"value" : "年"
}]
}]
}]
}
}}####
e: {
"error" : "java.lang.NullPointerException"
}
-------------------------------------------------------------------------------------
{"hierarchical" : false, "url": "http://hl7.org/fhir/ValueSet/units-of-time", "version": "4.0.1"}####
e: {
"error" : "java.lang.NullPointerException"
}
-------------------------------------------------------------------------------------