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Don't validate contained resources against Shareable* Profiles, + validate ShareableMeasure

This commit is contained in:
Grahame Grieve 2022-10-01 02:38:10 +10:00
parent 8893e0c0bc
commit 7f1e10a1e9
7 changed files with 72 additions and 20 deletions
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27
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/VSACImporter.java
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@ -1,5 +1,6 @@
package org.hl7.fhir.convertors.misc;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
@ -28,10 +29,10 @@ public class VSACImporter extends OIDBasedValueSetImporter {
public static void main(String[] args) throws FHIRException, IOException, ParseException, URISyntaxException {
VSACImporter self = new VSACImporter();
self.process(args[0], args[1], args[2]);
self.process(args[0], args[1], args[2], "true".equals(args[3]));
}
private void process(String source, String dest, String apiKey) throws FHIRException, IOException, URISyntaxException {
private void process(String source, String dest, String apiKey, boolean onlyNew) throws FHIRException, IOException, URISyntaxException {
CSVReader csv = new CSVReader(new FileInputStream(source));
csv.readHeaders();
Map<String, String> errs = new HashMap<>();
@ -39,23 +40,25 @@ public class VSACImporter extends OIDBasedValueSetImporter {
FHIRToolingClient fhirToolingClient = new FHIRToolingClient("https://cts.nlm.nih.gov/fhir", "fhir/vsac");
fhirToolingClient.setUsername("apikey");
fhirToolingClient.setPassword(apiKey);
fhirToolingClient.setTimeout(30000);
fhirToolingClient.setTimeout(120000);
int i = 0;
int j = 0;
while (csv.line()) {
String oid = csv.cell("OID");
try {
ValueSet vs = fhirToolingClient.read(ValueSet.class, oid);
try {
ValueSet vse = fhirToolingClient.expandValueset(vs.getUrl(), null);
vs.setExpansion(vse.getExpansion());
j++;
} catch (Exception e) {
errs.put(oid, "Expansion: " +e.getMessage());
System.out.println(e.getMessage());
if (!onlyNew || !(new File(Utilities.path(dest, "ValueSet-" + oid + ".json")).exists())) {
ValueSet vs = fhirToolingClient.read(ValueSet.class, oid);
try {
ValueSet vse = fhirToolingClient.expandValueset(vs.getUrl(), null);
vs.setExpansion(vse.getExpansion());
j++;
} catch (Exception e) {
errs.put(oid, "Expansion: " +e.getMessage());
System.out.println(e.getMessage());
}
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "ValueSet-" + oid + ".json")), vs);
}
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "ValueSet-" + oid + ".json")), vs);
i++;
if (i % 100 == 0) {
System.out.println(":"+i+" ("+j+")");

4
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/i18n/I18nConstants.java
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@ -635,6 +635,10 @@ public class I18nConstants {
public static final String CODESYSTEM_SHAREABLE_MISSING_HL7 = "CODESYSTEM_SHAREABLE_MISSING_HL7";
public static final String CODESYSTEM_SHAREABLE_EXTRA_MISSING_HL7 = "CODESYSTEM_SHAREABLE_EXTRA_MISSING_HL7";
public static final String CODESYSTEM_SHAREABLE_EXTRA_MISSING = "CODESYSTEM_SHAREABLE_EXTRA_MISSING";
public static final String MEASURE_SHAREABLE_MISSING = "MEASURE_SHAREABLE_MISSING";
public static final String MEASURE_SHAREABLE_MISSING_HL7 = "MEASURE_SHAREABLE_MISSING_HL7";
public static final String MEASURE_SHAREABLE_EXTRA_MISSING_HL7 = "MEASURE_SHAREABLE_EXTRA_MISSING_HL7";
public static final String MEASURE_SHAREABLE_EXTRA_MISSING = "MEASURE_SHAREABLE_EXTRA_MISSING";
public static final String VALUESET_UNC_SYSTEM_WARNING = "VALUESET_UNC_SYSTEM_WARNING";
public static final String VALUESET_UNC_SYSTEM_WARNING_VER = "VALUESET_UNC_SYSTEM_WARNING_VER";
public static final String VALUESET_IMPORT_UNION_INTERSECTION = "VALUESET_IMPORT_UNION_INTERSECTION";

12
org.hl7.fhir.utilities/src/main/resources/Messages.properties
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@ -726,7 +726,11 @@ VALUESET_SHAREABLE_MISSING = The ShareableValueSet profile says that the {0} ele
VALUESET_SHAREABLE_EXTRA_MISSING = The ShareableValueSet profile recommends that the {0} element is populated, but it is not present. Published value sets SHOULD conform to the ShareableValueSet profile
VALUESET_SHAREABLE_MISSING_HL7 = The ShareableValueSet profile says that the {0} element is mandatory, but it is not found. HL7 Published value sets SHALL conform to the ShareableValueSet profile
VALUESET_SHAREABLE_EXTRA_MISSING_HL7 = The ShareableValueSet profile recommends that the {0} element is populated, but it is not found. HL7 Published value sets SHALL conform to the ShareableValueSet profile
CODESYSTEM_SHAREABLE_MISSING = The ShareableCodeSystem profile says that the {0} element is mandatory, but it is not present. Published value sets SHOULD conform to the ShareableCodeSystem profile
CODESYSTEM_SHAREABLE_EXTRA_MISSING = The ShareableCodeSystem profile recommends that the {0} element is populated, but it is not present. Published value sets SHOULD conform to the ShareableCodeSystem profile
CODESYSTEM_SHAREABLE_MISSING_HL7 = The ShareableCodeSystem profile says that the {0} element is mandatory, but it is not found. HL7 Published value sets SHALL conform to the ShareableCodeSystem profile
CODESYSTEM_SHAREABLE_EXTRA_MISSING_HL7 = The ShareableCodeSystem profile recommends that the {0} element is populated, but it is not found. HL7 Published value sets SHALL conform to the ShareableCodeSystem profile
CODESYSTEM_SHAREABLE_MISSING = The ShareableCodeSystem profile says that the {0} element is mandatory, but it is not present. Published code systems SHOULD conform to the ShareableCodeSystem profile
CODESYSTEM_SHAREABLE_EXTRA_MISSING = The ShareableCodeSystem profile recommends that the {0} element is populated, but it is not present. Published code systems SHOULD conform to the ShareableCodeSystem profile
CODESYSTEM_SHAREABLE_MISSING_HL7 = The ShareableCodeSystem profile says that the {0} element is mandatory, but it is not found. HL7 Published code systems SHALL conform to the ShareableCodeSystem profile
CODESYSTEM_SHAREABLE_EXTRA_MISSING_HL7 = The ShareableCodeSystem profile recommends that the {0} element is populated, but it is not found. HL7 Published code systems SHALL conform to the ShareableCodeSystem profile
MEASURE_SHAREABLE_MISSING = The ShareableMeasure profile says that the {0} element is mandatory, but it is not present. Published measures SHOULD conform to the ShareableMeasure profile
MEASURE_SHAREABLE_EXTRA_MISSING = The ShareableMeasure profile recommends that the {0} element is populated, but it is not present. Published measures SHOULD conform to the ShareableMeasure profile
MEASURE_SHAREABLE_MISSING_HL7 = The ShareableMeasure profile says that the {0} element is mandatory, but it is not found. HL7 Published measures SHALL conform to the ShareableMeasure profile
MEASURE_SHAREABLE_EXTRA_MISSING_HL7 = The ShareableMeasure profile recommends that the {0} element is populated, but it is not found. HL7 Published measures SHALL conform to the ShareableMeasure profile

4
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/CodeSystemValidator.java
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@ -84,7 +84,9 @@ public class CodeSystemValidator extends BaseValidator {
}
}
checkShareableCodeSystem(errors, cs, stack);
if (!stack.isContained()) {
checkShareableCodeSystem(errors, cs, stack);
}
}

38
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/MeasureValidator.java
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@ -37,17 +37,20 @@ import org.hl7.fhir.utilities.validation.ValidationMessage.Source;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.hl7.fhir.validation.BaseValidator;
import org.hl7.fhir.validation.TimeTracker;
import org.hl7.fhir.validation.instance.InstanceValidator;
import org.hl7.fhir.validation.instance.utils.NodeStack;
import org.hl7.fhir.validation.instance.utils.ValidatorHostContext;
import org.w3c.dom.Document;
public class MeasureValidator extends BaseValidator {
public MeasureValidator(IWorkerContext context, TimeTracker timeTracker, XVerExtensionManager xverManager, Coding jurisdiction) {
private InstanceValidator parent;
public MeasureValidator(IWorkerContext context, TimeTracker timeTracker, XVerExtensionManager xverManager, Coding jurisdiction, InstanceValidator parent) {
super(context, xverManager);
source = Source.InstanceValidator;
this.timeTracker = timeTracker;
this.jurisdiction = jurisdiction;
this.parent = parent;
}
@ -105,8 +108,41 @@ public class MeasureValidator extends BaseValidator {
c++;
}
}
if (!stack.isContained()) {
checkShareableMeasure(errors, element, stack);
}
}
private void checkShareableMeasure(List<ValidationMessage> errors, Element cs, NodeStack stack) {
if (parent.isForPublication()) {
if (isHL7(cs)) {
rule(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("url"), I18nConstants.MEASURE_SHAREABLE_MISSING_HL7, "url");
rule(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("version"), I18nConstants.MEASURE_SHAREABLE_MISSING_HL7, "version");
rule(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("title"), I18nConstants.MEASURE_SHAREABLE_MISSING_HL7, "title");
warning(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("name"), I18nConstants.MEASURE_SHAREABLE_EXTRA_MISSING_HL7, "name");
rule(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("status"), I18nConstants.MEASURE_SHAREABLE_MISSING_HL7, "status");
rule(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("experimental"), I18nConstants.MEASURE_SHAREABLE_MISSING_HL7, "experimental");
rule(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("description"), I18nConstants.MEASURE_SHAREABLE_MISSING_HL7, "description");
rule(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("content"), I18nConstants.MEASURE_SHAREABLE_MISSING_HL7, "content");
if (!"supplement".equals(cs.getChildValue("content"))) {
rule(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("caseSensitive"), I18nConstants.MEASURE_SHAREABLE_MISSING_HL7, "caseSensitive");
}
} else {
warning(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("url"), I18nConstants.MEASURE_SHAREABLE_MISSING, "url");
warning(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("version"), I18nConstants.MEASURE_SHAREABLE_MISSING, "version");
warning(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("title"), I18nConstants.MEASURE_SHAREABLE_MISSING, "title");
warning(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("name"), I18nConstants.MEASURE_SHAREABLE_EXTRA_MISSING, "name");
warning(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("status"), I18nConstants.MEASURE_SHAREABLE_MISSING, "status");
warning(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("experimental"), I18nConstants.MEASURE_SHAREABLE_MISSING, "experimental");
warning(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("description"), I18nConstants.MEASURE_SHAREABLE_MISSING, "description");
warning(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("content"), I18nConstants.MEASURE_SHAREABLE_MISSING, "content");
if (!"supplement".equals(cs.getChildValue("content"))) {
warning(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("caseSensitive"), I18nConstants.MEASURE_SHAREABLE_MISSING, "caseSensitive");
}
}
}
}
private void validateMeasureCriteria(ValidatorHostContext hostContext, List<ValidationMessage> errors, MeasureContext mctxt, Element crit, NodeStack nsc) {
String mimeType = crit.getChildValue("language");
if (!Utilities.noString(mimeType)) { // that would be an error elsewhere

3
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/StructureDefinitionValidator.java
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@ -115,8 +115,9 @@ public class StructureDefinitionValidator extends BaseValidator {
for (Element snapshot : snapshots) {
validateElementList(errors, snapshot, stack.push(snapshot, -1, null, null), true, true, sd);
}
}
private void validateElementList(List<ValidationMessage> errors, Element elementList, NodeStack stack, boolean snapshot, boolean hasSnapshot, StructureDefinition sd) {
List<Element> elements = elementList.getChildrenByName("element");
int cc = 0;

4
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/ValueSetValidator.java
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@ -61,7 +61,9 @@ public class ValueSetValidator extends BaseValidator {
cc++;
}
}
checkShareableValueSet(errors, vs, stack);
if (!stack.isContained()) {
checkShareableValueSet(errors, vs, stack);
}
}
private void checkShareableValueSet(List<ValidationMessage> errors, Element vs, NodeStack stack) {