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This commit is contained in:
Grahame Grieve 2021-11-03 10:35:47 +11:00
commit 36ea3f5b45
15 changed files with 66 additions and 42 deletions
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2
org.hl7.fhir.convertors/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.5.9-SNAPSHOT</version>
<version>5.5.10-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

6
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/context/VersionConvertorContext.java
View File

@ -79,7 +79,7 @@ public class VersionConvertorContext<T> {
stack = new Stack<>();
}
stack.push(path);
logger.debug("Pushing path <" + path + "> onto stack. Current path -> " + String.join(",", stack));
// logger.debug("Pushing path <" + path + "> onto stack. Current path -> " + String.join(",", stack));
threadLocalPath.set(stack);
}
@ -96,7 +96,7 @@ public class VersionConvertorContext<T> {
throw new FHIRException("Cannot close path <" + path + ">. Reached unstable state, no stack path available.");
}
String currentPath = stack.pop();
logger.debug("Popping path <" + currentPath + "> off stack. Current path -> " + String.join(",", stack));
// logger.debug("Popping path <" + currentPath + "> off stack. Current path -> " + String.join(",", stack));
if (!path.equals(currentPath)) {
throw new FHIRException("Reached unstable state, current path doesn't match expected path.");
}
@ -127,7 +127,7 @@ public class VersionConvertorContext<T> {
public T getVersionConvertor() {
T result = threadLocalVersionConverter.get();
if (result != null && logger != null) {
logger.debug(result.toString());
// logger.debug(result.toString());
}
return result;
}

22
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/DicomPackageBuilder.java
View File

@ -36,6 +36,7 @@ public class DicomPackageBuilder {
private String version;
private String dest;
private String source;
private String pattern = "fhir.dicom#{version}.tgz";
public static void main(String[] args) throws FileNotFoundException, ParserConfigurationException, SAXException, IOException {
if (args.length == 0 || args[0].equals("-help")) {
@ -55,12 +56,16 @@ public class DicomPackageBuilder {
DicomPackageBuilder self = new DicomPackageBuilder();
self.setSource(source);
self.setDest(dest);
self.setPattern("{version}/package.tgz");
self.execute();
}
private void execute() throws FileNotFoundException, ParserConfigurationException, SAXException, IOException {
public void execute() throws FileNotFoundException, ParserConfigurationException, SAXException, IOException {
CodeSystem cs = buildCodeSystem();
NPMPackageGenerator gen = new NPMPackageGenerator(Utilities.path(dest, "fhir.dicom#"+version+".tgz"), buildPackage());
String fn = Utilities.path(dest, pattern.replace("{version}", version));
Utilities.createDirectory(Utilities.getDirectoryForFile(fn));
NPMPackageGenerator gen = new NPMPackageGenerator(fn, buildPackage());
int i = 2;
gen.addFile(Category.RESOURCE, "CodeSystem-"+cs.getId()+".json", new JsonParser().setOutputStyle(OutputStyle.NORMAL).composeBytes(cs));
ValueSet vs = buildAllValueSet();
@ -168,15 +173,16 @@ public class DicomPackageBuilder {
return p[0].substring(0, 4)+"."+(1+(p[0].charAt(4) - 'a'))+"."+p[1];
}
private void setVersion(String version) {
this.version = version;
}
private void setDest(String dest) {
public void setDest(String dest) {
this.dest = dest;
}
private void setSource(String source) {
public void setSource(String source) {
this.source = source;
}
public void setPattern(String pattern) {
this.pattern = pattern;
}
}

2
org.hl7.fhir.dstu2/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.5.9-SNAPSHOT</version>
<version>5.5.10-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.dstu2016may/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.5.9-SNAPSHOT</version>
<version>5.5.10-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.dstu3/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.5.9-SNAPSHOT</version>
<version>5.5.10-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.r4/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.5.9-SNAPSHOT</version>
<version>5.5.10-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.r5/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.5.9-SNAPSHOT</version>
<version>5.5.10-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.report/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.5.9-SNAPSHOT</version>
<version>5.5.10-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.utilities/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.5.9-SNAPSHOT</version>
<version>5.5.10-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.validation.cli/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.5.9-SNAPSHOT</version>
<version>5.5.10-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.validation/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.5.9-SNAPSHOT</version>
<version>5.5.10-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

55
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java
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@ -5384,57 +5384,76 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
// this is a hack work around for past publication of wrong FHIRPath expressions
// R4
// waiting for 4.0.2
//TODO is this expression below correct? @grahamegrieve
if ("probability is decimal implies (probability as decimal) <= 100".equals(expr)) {
return "probablility.empty() or ((probability is decimal) implies ((probability as decimal) <= 100))";
}
if ("enableWhen.count() > 2 implies enableBehavior.exists()".equals(expr)) {
return "enableWhen.count() >= 2 implies enableBehavior.exists()";
}
if ("txt-2".equals(key)) {
return "htmlChecks2()";
}
// handled in 4.0.1
if ("(component.empty() and hasMember.empty()) implies (dataAbsentReason or value)".equals(expr))
if ("(component.empty() and hasMember.empty()) implies (dataAbsentReason or value)".equals(expr)) {
return "(component.empty() and hasMember.empty()) implies (dataAbsentReason.exists() or value.exists())";
if ("isModifier implies isModifierReason.exists()".equals(expr))
}
if ("isModifier implies isModifierReason.exists()".equals(expr)) {
return "(isModifier.exists() and isModifier) implies isModifierReason.exists()";
if ("(%resource.kind = 'logical' or element.first().path.startsWith(%resource.type)) and (element.tail().not() or element.tail().all(path.startsWith(%resource.differential.element.first().path.replaceMatches('\\\\..*','')&'.')))".equals(expr))
}
if ("(%resource.kind = 'logical' or element.first().path.startsWith(%resource.type)) and (element.tail().not() or element.tail().all(path.startsWith(%resource.differential.element.first().path.replaceMatches('\\\\..*','')&'.')))".equals(expr)) {
return "(%resource.kind = 'logical' or element.first().path.startsWith(%resource.type)) and (element.tail().empty() or element.tail().all(path.startsWith(%resource.differential.element.first().path.replaceMatches('\\\\..*','')&'.')))";
if ("differential.element.all(id) and differential.element.id.trace('ids').isDistinct()".equals(expr))
}
if ("differential.element.all(id) and differential.element.id.trace('ids').isDistinct()".equals(expr)) {
return "differential.element.all(id.exists()) and differential.element.id.trace('ids').isDistinct()";
if ("snapshot.element.all(id) and snapshot.element.id.trace('ids').isDistinct()".equals(expr))
}
if ("snapshot.element.all(id) and snapshot.element.id.trace('ids').isDistinct()".equals(expr)) {
return "snapshot.element.all(id.exists()) and snapshot.element.id.trace('ids').isDistinct()";
}
// R3
if ("(code or value.empty()) and (system.empty() or system = 'urn:iso:std:iso:4217')".equals(expr))
if ("(code or value.empty()) and (system.empty() or system = 'urn:iso:std:iso:4217')".equals(expr)) {
return "(code.exists() or value.empty()) and (system.empty() or system = 'urn:iso:std:iso:4217')";
if ("value.empty() or code!=component.code".equals(expr))
}
if ("value.empty() or code!=component.code".equals(expr)) {
return "value.empty() or (code in component.code).not()";
if ("(code or value.empty()) and (system.empty() or system = %ucum) and (value.empty() or value > 0)".equals(expr))
}
if ("(code or value.empty()) and (system.empty() or system = %ucum) and (value.empty() or value > 0)".equals(expr)) {
return "(code.exists() or value.empty()) and (system.empty() or system = %ucum) and (value.empty() or value > 0)";
if ("element.all(definition and min and max)".equals(expr))
}
if ("element.all(definition and min and max)".equals(expr)) {
return "element.all(definition.exists() and min.exists() and max.exists())";
if ("telecom or endpoint".equals(expr))
}
if ("telecom or endpoint".equals(expr)) {
return "telecom.exists() or endpoint.exists()";
if ("(code or value.empty()) and (system.empty() or system = %ucum) and (value.empty() or value > 0)".equals(expr))
}
if ("(code or value.empty()) and (system.empty() or system = %ucum) and (value.empty() or value > 0)".equals(expr)) {
return "(code.exists() or value.empty()) and (system.empty() or system = %ucum) and (value.empty() or value > 0)";
if ("searchType implies type = 'string'".equals(expr))
}
if ("searchType implies type = 'string'".equals(expr)) {
return "searchType.exists() implies type = 'string'";
if ("abatement.empty() or (abatement as boolean).not() or clinicalStatus='resolved' or clinicalStatus='remission' or clinicalStatus='inactive'".equals(expr))
}
if ("abatement.empty() or (abatement as boolean).not() or clinicalStatus='resolved' or clinicalStatus='remission' or clinicalStatus='inactive'".equals(expr)) {
return "abatement.empty() or (abatement is boolean).not() or (abatement as boolean).not() or (clinicalStatus = 'resolved') or (clinicalStatus = 'remission') or (clinicalStatus = 'inactive')";
if ("(component.empty() and related.empty()) implies (dataAbsentReason or value)".equals(expr))
}
if ("(component.empty() and related.empty()) implies (dataAbsentReason or value)".equals(expr)) {
return "(component.empty() and related.empty()) implies (dataAbsentReason.exists() or value.exists())";
}
if ("reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))".equals(expr)) {
return "(reference = '#') or reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))";
}
if ("reference.startsWith('#').not() or (reference.substring(1).trace('url') in %resource.contained.id.trace('ids'))".equals(expr)) {
return "(reference = '#') or reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))";
}
if ("".equals(expr))
if ("probability is decimal implies probability.as(decimal) <= 100".equals(expr)) {
if (key.equals("ras-2")) {
return "probability.empty() or (probability is decimal implies probability.as(decimal) <= 100)";
}
}
if ("".equals(expr)) {
return "";
}
return expr;
}

1
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/ValidationTests.java
View File

@ -100,7 +100,6 @@ public class ValidationTests implements IEvaluationContext, IValidatorResourceFe
List<Object[]> objects = new ArrayList<Object[]>(examples.size());
for (String id : names) {
//if (id.equals("bundle-documentation-miss-last-updated"))
objects.add(new Object[]{id, examples.get(id)});
}
return objects;

4
pom.xml
View File

@ -14,12 +14,12 @@
HAPI FHIR
-->
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.5.9-SNAPSHOT</version>
<version>5.5.10-SNAPSHOT</version>
<packaging>pom</packaging>
<properties>
<hapi_fhir_version>5.1.0</hapi_fhir_version>
<validator_test_case_version>1.1.71-SNAPSHOT</validator_test_case_version>
<validator_test_case_version>1.1.72-SNAPSHOT</validator_test_case_version>
<junit_jupiter_version>5.7.1</junit_jupiter_version>
<junit_platform_launcher_version>1.7.1</junit_platform_launcher_version>
<maven_surefire_version>3.0.0-M4</maven_surefire_version>