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Merge pull request #1073 from hapifhir/gg-202301-urn-validation 

Gg 202301 urn validation
This commit is contained in:
Grahame Grieve 2023-01-17 11:42:04 +11:00 committed by GitHub
parent e55b342674 41abbb21a0
commit bbad7717f7
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GPG Key ID: 4AEE18F83AFDEB23
12 changed files with 115 additions and 7 deletions
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3
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/BaseWorkerContext.java
View File

@ -2275,6 +2275,9 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
}
} catch (Exception e) {
System.out.println("Unable to generate snapshot for "+tail(sd.getUrl()) +" from "+tail(sd.getBaseDefinition())+" because "+e.getMessage());
if (logger.isDebugLogging()) {
e.printStackTrace();
}
}
}
System.out.print(":");

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/ContextUtilities.java
View File

@ -207,7 +207,7 @@ public class ContextUtilities implements ProfileKnowledgeProvider {
} catch (Exception e) {
if (!isSuppressDebugMessages()) {
System.out.println("Unable to generate snapshot for "+tail(sd.getUrl()) +" from "+tail(sd.getBaseDefinition())+" because "+e.getMessage());
if (true) {
if (context.getLogger().isDebugLogging()) {
e.printStackTrace();
}
}

3
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/SimpleWorkerContext.java
View File

@ -660,6 +660,9 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
} catch (Exception e) {
// not sure what to do in this case?
System.out.println("Unable to generate snapshot for "+uri+": "+e.getMessage());
if (logger.isDebugLogging()) {
e.printStackTrace();
}
}
}
return r;

2
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/FTPClient.java
View File

@ -57,7 +57,6 @@ public class FTPClient {
else {
clientImpl.connect(server);
}
//clientImpl.setFileTransferMode(FTP.BINARY_FILE_TYPE);
clientImpl.login(user, password);
@ -93,6 +92,7 @@ public class FTPClient {
String resolvedPath = resolveRemotePath(path);
FileInputStream localStream = new FileInputStream(source);
clientImpl.setFileType(FTP.BINARY_FILE_TYPE);
clientImpl.enterLocalPassiveMode();
clientImpl.storeFile( resolvedPath, localStream);
localStream.close();

2
org.hl7.fhir.utilities/src/main/resources/Messages.properties
View File

@ -222,7 +222,7 @@ Type_Specific_Checks_DT_URI_UUID = URI values cannot start with uuid:
Type_Specific_Checks_DT_URI_WS = URI values cannot have whitespace(''{0}'')
Type_Specific_Checks_DT_URL_Resolve = URL value ''{0}'' does not resolve
Type_Specific_Checks_DT_UUID_Strat = UUIDs must start with urn:uuid:
Type_Specific_Checks_DT_UUID_Valid = UUIDs must be valid (and lowercase)
Type_Specific_Checks_DT_UUID_Valid = UUIDs must be valid and lowercase ({0})
Validation_BUNDLE_Message = The first entry in a message must be a MessageHeader
Validation_VAL_Content_Unknown = Unrecognised Content {0}
Validation_VAL_NoType = Unknown type {0}

4
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/ValidationEngine.java
View File

@ -764,9 +764,9 @@ public class ValidationEngine implements IValidatorResourceFetcher, IValidationP
makeSnapshot(sd);
} catch (Exception e) {
System.out.println("Process Note: Unable to generate snapshot for " + sd.present() + ": " + e.getMessage());
// if (debug) {
if (context.getLogger().isDebugLogging()) {
e.printStackTrace();
// }
}
}
}
}

6
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java
View File

@ -2319,7 +2319,11 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
}
if (url != null && url.startsWith("urn:uuid:")) {
ok = rule(errors, NO_RULE_DATE, IssueType.INVALID, e.line(), e.col(), path, Utilities.isValidUUID(url.substring(9)), I18nConstants.TYPE_SPECIFIC_CHECKS_DT_UUID_VALID) && ok;
String s = url.substring(9);
if (s.contains("#")) {
s = s.substring(0, s.indexOf("#"));
}
ok = rule(errors, NO_RULE_DATE, IssueType.INVALID, e.line(), e.col(), path, Utilities.isValidUUID(s), I18nConstants.TYPE_SPECIFIC_CHECKS_DT_UUID_VALID, s) && ok;
}
if (url != null && url.startsWith("urn:oid:")) {
String cc = url.substring(8);

12
org.hl7.fhir.validation/src/test/resources/txCache/org.hl7.fhir.validation/4.0.1/http___standardterms.edqm.eu.cache Normal file
View File

@ -0,0 +1,12 @@
-------------------------------------------------------------------------------------
{"code" : {
"system" : "http://standardterms.edqm.eu",
"code" : "20049000",
"display" : "Nasal use"
}, "valueSet" :null, "lang":"null", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "versionFlexible":"false"}####
v: {
"display" : "Nasal use",
"code" : "20049000",
"system" : "http://standardterms.edqm.eu"
}
-------------------------------------------------------------------------------------

11
org.hl7.fhir.validation/src/test/resources/txCache/org.hl7.fhir.validation/4.0.1/iso3166.cache
View File

@ -49,3 +49,14 @@ v: {
"system" : "urn:iso:std:iso:3166"
}
-------------------------------------------------------------------------------------
{"code" : {
"system" : "urn:iso:std:iso:3166",
"code" : "NO",
"display" : "Norway"
}, "valueSet" :null, "lang":"null", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "versionFlexible":"false"}####
v: {
"display" : "Norway",
"code" : "NO",
"system" : "urn:iso:std:iso:3166"
}
-------------------------------------------------------------------------------------

64
org.hl7.fhir.validation/src/test/resources/txCache/org.hl7.fhir.validation/4.0.1/loinc.cache
View File

@ -2184,3 +2184,67 @@ v: {
"system" : "http://loinc.org"
}
-------------------------------------------------------------------------------------
{"code" : {
"system" : "http://loinc.org",
"code" : "60591-5"
}, "url": "http://hl7.org/fhir/ValueSet/doc-typecodes--0", "version": "4.0.1", "lang":"null", "useServer":"true", "useClient":"false", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "versionFlexible":"false"}####
v: {
"display" : "Patient summary Document",
"code" : "60591-5",
"system" : "http://loinc.org"
}
-------------------------------------------------------------------------------------
{"code" : {
"system" : "http://loinc.org",
"code" : "60591-5",
"display" : "Patient Summary Document"
}, "url": "http://hl7.org/fhir/ValueSet/doc-typecodes", "version": "4.0.1", "lang":"null", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"NO_MEMBERSHIP_CHECK", "versionFlexible":"false"}####
v: {
"display" : "Patient summary Document",
"code" : "60591-5",
"system" : "http://loinc.org"
}
-------------------------------------------------------------------------------------
{"code" : {
"system" : "http://loinc.org",
"code" : "60591-5"
}, "valueSet" :null, "lang":"null", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "versionFlexible":"false"}####
v: {
"display" : "Patient summary Document",
"code" : "60591-5",
"system" : "http://loinc.org"
}
-------------------------------------------------------------------------------------
{"code" : {
"system" : "http://loinc.org",
"code" : "48765-2",
"display" : "Allergies and adverse reactions Document"
}, "valueSet" :null, "lang":"null", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "versionFlexible":"false"}####
v: {
"display" : "Allergies and adverse reactions Document",
"code" : "48765-2",
"system" : "http://loinc.org"
}
-------------------------------------------------------------------------------------
{"code" : {
"system" : "http://loinc.org",
"code" : "10160-0",
"display" : "History of Medication use Narrative"
}, "valueSet" :null, "lang":"null", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "versionFlexible":"false"}####
v: {
"display" : "History of Medication use Narrative",
"code" : "10160-0",
"system" : "http://loinc.org"
}
-------------------------------------------------------------------------------------
{"code" : {
"system" : "http://loinc.org",
"code" : "11450-4",
"display" : "Problem list - Reported"
}, "valueSet" :null, "lang":"null", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "versionFlexible":"false"}####
v: {
"display" : "Problem list - Reported",
"code" : "11450-4",
"system" : "http://loinc.org"
}
-------------------------------------------------------------------------------------

11
org.hl7.fhir.validation/src/test/resources/txCache/org.hl7.fhir.validation/4.0.1/rxnorm.cache
View File

@ -110,3 +110,14 @@ v: {
"system" : "http://www.nlm.nih.gov/research/umls/rxnorm"
}
-------------------------------------------------------------------------------------
{"code" : {
"system" : "http://www.nlm.nih.gov/research/umls/rxnorm",
"code" : "1000990",
"display" : "oxymetazoline hydrochloride 0.5 MG/ML Nasal Spray"
}, "valueSet" :null, "lang":"null", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "versionFlexible":"false"}####
v: {
"display" : "oxymetazoline hydrochloride 0.5 MG/ML Nasal Spray",
"code" : "1000990",
"system" : "http://www.nlm.nih.gov/research/umls/rxnorm"
}
-------------------------------------------------------------------------------------

2
pom.xml
View File

@ -19,7 +19,7 @@
<properties>
<hapi_fhir_version>6.2.1</hapi_fhir_version>
<validator_test_case_version>1.2.7</validator_test_case_version>
<validator_test_case_version>1.2.8-SNAPSHOT</validator_test_case_version>
<junit_jupiter_version>5.7.1</junit_jupiter_version>
<junit_platform_launcher_version>1.8.2</junit_platform_launcher_version>
<maven_surefire_version>3.0.0-M5</maven_surefire_version>