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Merge pull request #287 from hapifhir/gg-work-202007 

more fixes
This commit is contained in:
Grahame Grieve 2020-07-30 14:06:31 +10:00 committed by GitHub
parent 9c044e5bb5 5aec9978bd
commit 490cecaced
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GPG Key ID: 4AEE18F83AFDEB23
22 changed files with 323 additions and 60 deletions
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4
RELEASE_NOTES.md
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@ -0,0 +1,4 @@
* Batch validation of codes in value sets
* Fix path problem doing comparisons
* Don't produce 2 columns for status for deprecated codes
* Fix errors in StructureDefinition validation

11
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/txClient/TerminologyClientR2.java
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@ -35,8 +35,10 @@ import java.net.URISyntaxException;
import java.util.Map;
import org.hl7.fhir.convertors.VersionConvertor_10_50;
import org.hl7.fhir.convertors.VersionConvertor_40_50;
import org.hl7.fhir.dstu2.utils.client.FHIRToolingClient;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.model.Bundle;
import org.hl7.fhir.r5.model.CapabilityStatement;
import org.hl7.fhir.r5.model.Parameters;
import org.hl7.fhir.r5.model.TerminologyCapabilities;
@ -116,6 +118,11 @@ public class TerminologyClientR2 implements TerminologyClient {
public int getRetryCount() throws FHIRException {
return client.getRetryCount();
}
@Override
public Bundle validateBatch(Bundle batch) {
return (Bundle) VersionConvertor_10_50.convertResource(client.transaction((org.hl7.fhir.dstu2.model.Bundle) VersionConvertor_10_50.convertResource(batch)));
}
}

10
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/txClient/TerminologyClientR3.java
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@ -35,8 +35,10 @@ import java.net.URISyntaxException;
import java.util.Map;
import org.hl7.fhir.convertors.VersionConvertor_30_50;
import org.hl7.fhir.convertors.VersionConvertor_40_50;
import org.hl7.fhir.dstu3.utils.client.FHIRToolingClient;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.model.Bundle;
import org.hl7.fhir.r5.model.CapabilityStatement;
import org.hl7.fhir.r5.model.Parameters;
import org.hl7.fhir.r5.model.TerminologyCapabilities;
@ -116,5 +118,11 @@ public class TerminologyClientR3 implements TerminologyClient {
public int getRetryCount() throws FHIRException {
return client.getRetryCount();
}
@Override
public Bundle validateBatch(Bundle batch) {
return (Bundle) VersionConvertor_30_50.convertResource(client.transaction((org.hl7.fhir.dstu3.model.Bundle) VersionConvertor_30_50.convertResource(batch, false)), false);
}
}

8
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/txClient/TerminologyClientR4.java
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@ -38,6 +38,7 @@ import org.hl7.fhir.convertors.VersionConvertor_40_50;
import org.hl7.fhir.convertors.conv40_50.TerminologyCapabilities40_50;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r4.utils.client.FHIRToolingClient;
import org.hl7.fhir.r5.model.Bundle;
import org.hl7.fhir.r5.model.CapabilityStatement;
import org.hl7.fhir.r5.model.Parameters;
import org.hl7.fhir.r5.model.TerminologyCapabilities;
@ -117,5 +118,10 @@ public class TerminologyClientR4 implements TerminologyClient {
public int getRetryCount() throws FHIRException {
return client.getRetryCount();
}
@Override
public Bundle validateBatch(Bundle batch) {
return (Bundle) VersionConvertor_40_50.convertResource(client.transaction((org.hl7.fhir.r4.model.Bundle) VersionConvertor_40_50.convertResource(batch)));
}
}

6
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/txClient/TerminologyClientR5.java
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@ -35,6 +35,7 @@ import java.net.URISyntaxException;
import java.util.Map;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.model.Bundle;
import org.hl7.fhir.r5.model.CapabilityStatement;
import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.Parameters;
@ -110,4 +111,9 @@ public class TerminologyClientR5 implements TerminologyClient {
return client.getRetryCount();
}
@Override
public Bundle validateBatch(Bundle batch) {
return client.transaction(batch);
}
}

12
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/comparison/ComparisonRenderer.java
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@ -146,8 +146,8 @@ public class ComparisonRenderer implements IEvaluationContext {
vars.put("concepts", new StringType(new XhtmlComposer(true).compose(cs.renderConcepts(comp, "", ""))));
String cnt = processTemplate(template, "CodeSystem", vars);
TextFile.stringToFile(cnt, file(comp.getId()+".html"));
new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, "comparison", comp.getId() + "-union.json")), comp.getUnion());
new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, "comparison", comp.getId() + "-intersection.json")), comp.getIntersection());
new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, comp.getId() + "-union.json")), comp.getUnion());
new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, comp.getId() + "-intersection.json")), comp.getIntersection());
}
private String file(String name) throws IOException {
@ -170,8 +170,8 @@ public class ComparisonRenderer implements IEvaluationContext {
vars.put("expansion", new StringType(new XhtmlComposer(true).compose(cs.renderExpansion(comp, "", ""))));
String cnt = processTemplate(template, "ValueSet", vars);
TextFile.stringToFile(cnt, file(comp.getId()+".html"));
new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, "comparison", comp.getId() + "-union.json")), comp.getUnion());
new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, "comparison", comp.getId() + "-intersection.json")), comp.getIntersection());
new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, comp.getId() + "-union.json")), comp.getUnion());
new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, comp.getId() + "-intersection.json")), comp.getIntersection());
}
private void renderProfile(String id, ProfileComparison comp) throws IOException {
@ -189,8 +189,8 @@ public class ComparisonRenderer implements IEvaluationContext {
vars.put("structure", new StringType(new XhtmlComposer(true).compose(cs.renderStructure(comp, "", "", "http://hl7.org/fhir"))));
String cnt = processTemplate(template, "CodeSystem", vars);
TextFile.stringToFile(cnt, file(comp.getId()+".html"));
new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, "comparison", comp.getId() + "-union.json")), comp.getUnion());
new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, "comparison", comp.getId() + "-intersection.json")), comp.getIntersection());
new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, comp.getId() + "-union.json")), comp.getUnion());
new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, comp.getId() + "-intersection.json")), comp.getIntersection());
}
private String processTemplate(String template, String name, Map<String, Base> vars) {

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/ProfileUtilities.java
View File

@ -2596,7 +2596,7 @@ public class ProfileUtilities extends TranslatingUtilities {
if (derived.hasIsSummaryElement()) {
if (!Base.compareDeep(derived.getIsSummaryElement(), base.getIsSummaryElement(), false)) {
if (base.hasIsSummary() && !context.getVersion().equals("1.4.0")) // work around a known issue with some 1.4.0 cosntraints
throw new Error(context.formatMessage(I18nConstants.ERROR_IN_PROFILE__AT__BASE_ISSUMMARY___DERIVED_ISSUMMARY__, pn, derived.getPath(), base.getIsSummaryElement().asStringValue(), derived.getIsSummaryElement().asStringValue()));
throw new Error(context.formatMessage(I18nConstants.ERROR_IN_PROFILE__AT__BASE_ISSUMMARY___DERIVED_ISSUMMARY__, purl, derived.getPath(), base.getIsSummaryElement().asStringValue(), derived.getIsSummaryElement().asStringValue()));
base.setIsSummaryElement(derived.getIsSummaryElement().copy());
} else if (trimDifferential)
derived.setIsSummaryElement(null);

110
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/BaseWorkerContext.java
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@ -55,6 +55,7 @@ import org.hl7.fhir.r5.context.CanonicalResourceManager.CanonicalResourceProxy;
import org.hl7.fhir.r5.context.IWorkerContext.ILoggingService.LogCategory;
import org.hl7.fhir.r5.context.TerminologyCache.CacheToken;
import org.hl7.fhir.r5.model.BooleanType;
import org.hl7.fhir.r5.model.Bundle;
import org.hl7.fhir.r5.model.CanonicalResource;
import org.hl7.fhir.r5.model.CapabilityStatement;
import org.hl7.fhir.r5.model.CodeSystem;
@ -74,6 +75,7 @@ import org.hl7.fhir.r5.model.NamingSystem;
import org.hl7.fhir.r5.model.NamingSystem.NamingSystemIdentifierType;
import org.hl7.fhir.r5.model.NamingSystem.NamingSystemUniqueIdComponent;
import org.hl7.fhir.r5.model.OperationDefinition;
import org.hl7.fhir.r5.model.OperationOutcome;
import org.hl7.fhir.r5.model.Parameters;
import org.hl7.fhir.r5.model.Parameters.ParametersParameterComponent;
import org.hl7.fhir.r5.model.PlanDefinition;
@ -88,8 +90,12 @@ import org.hl7.fhir.r5.model.StructureMap;
import org.hl7.fhir.r5.model.TerminologyCapabilities;
import org.hl7.fhir.r5.model.TerminologyCapabilities.TerminologyCapabilitiesCodeSystemComponent;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.r5.model.Bundle.BundleType;
import org.hl7.fhir.r5.model.Bundle.HTTPVerb;
import org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.r5.model.ValueSet.ValueSetComposeComponent;
import org.hl7.fhir.r5.renderers.OperationOutcomeRenderer;
import org.hl7.fhir.r5.terminologies.CodeSystemUtilities;
import org.hl7.fhir.r5.terminologies.TerminologyClient;
import org.hl7.fhir.r5.terminologies.ValueSetCheckerSimple;
@ -111,6 +117,8 @@ import org.hl7.fhir.utilities.validation.ValidationOptions.ValueSetMode;
import com.google.gson.JsonObject;
import ca.uhn.fhir.model.valueset.BundleEntrySearchModeEnum;
public abstract class BaseWorkerContext extends I18nBase implements IWorkerContext{
public class MetadataResourceVersionComparator<T extends CanonicalResource> implements Comparator<T> {
@ -685,10 +693,103 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
return validateCode(options.guessSystem(), c, vs);
}
@Override
public void validateCodeBatch(ValidationOptions options, List<? extends CodingValidationRequest> codes, ValueSet vs) {
if (options == null) {
options = ValidationOptions.defaults();
}
// 1st pass: what is in the cache?
// 2nd pass: What can we do internally
// 3rd pass: hit the server
for (CodingValidationRequest t : codes) {
t.setCacheToken(txCache != null ? txCache.generateValidationToken(options, t.getCoding(), vs) : null);
if (txCache != null) {
t.setResult(txCache.getValidation(t.getCacheToken()));
}
}
if (options.isUseClient()) {
for (CodingValidationRequest t : codes) {
if (!t.hasResult()) {
try {
ValueSetCheckerSimple vsc = new ValueSetCheckerSimple(options, vs, this);
ValidationResult res = vsc.validateCode(t.getCoding());
if (txCache != null)
txCache.cacheValidation(t.getCacheToken(), res, TerminologyCache.TRANSIENT);
t.setResult(res);
} catch (Exception e) {
}
}
}
}
for (CodingValidationRequest t : codes) {
if (!t.hasResult()) {
if (!options.isUseServer()) {
t.setResult(new ValidationResult(IssueSeverity.WARNING,formatMessage(I18nConstants.UNABLE_TO_VALIDATE_CODE_WITHOUT_USING_SERVER), TerminologyServiceErrorClass.BLOCKED_BY_OPTIONS));
} else if (unsupportedCodeSystems.contains(t.getCoding().getSystem())) {
t.setResult(new ValidationResult(IssueSeverity.ERROR,formatMessage(I18nConstants.TERMINOLOGY_TX_SYSTEM_NOTKNOWN, t.getCoding().getSystem()), TerminologyServiceErrorClass.CODESYSTEM_UNSUPPORTED));
} else if (noTerminologyServer) {
t.setResult(new ValidationResult(IssueSeverity.ERROR,formatMessage(I18nConstants.ERROR_VALIDATING_CODE_RUNNING_WITHOUT_TERMINOLOGY_SERVICES), TerminologyServiceErrorClass.NOSERVICE));
}
}
}
if (expParameters == null)
throw new Error(formatMessage(I18nConstants.NO_EXPANSIONPROFILE_PROVIDED));
// for those that that failed, we try to validate on the server
Bundle batch = new Bundle();
batch.setType(BundleType.BATCH);
Set<String> systems = new HashSet<>();
for (CodingValidationRequest t : codes) {
if (!t.hasResult()) {
Parameters pIn = new Parameters();
pIn.addParameter().setName("coding").setValue(t.getCoding());
if (options.isGuessSystem())
pIn.addParameter().setName("implySystem").setValue(new BooleanType(true));
if (vs != null) {
pIn.addParameter().setName("valueSet").setResource(vs);
}
pIn.addParameter().setName("profile").setResource(expParameters);
setTerminologyOptions(options, pIn);
BundleEntryComponent be = batch.addEntry();
be.setResource(pIn);
be.getRequest().setMethod(HTTPVerb.POST);
be.getRequest().setUrl("ValueSet/$validate-code");
be.setUserData("source", t);
systems.add(t.getCoding().getSystem());
}
}
if (batch.getEntry().size() > 0) {
tlog("$batch validate for "+batch.getEntry().size()+" codes on systems "+systems.toString());
if (txClient == null) {
throw new FHIRException(formatMessage(I18nConstants.ATTEMPT_TO_USE_TERMINOLOGY_SERVER_WHEN_NO_TERMINOLOGY_SERVER_IS_AVAILABLE));
}
if (txLog != null) {
txLog.clearLastId();
}
Bundle resp = txClient.validateBatch(batch);
for (int i = 0; i < batch.getEntry().size(); i++) {
CodingValidationRequest t = (CodingValidationRequest) batch.getEntry().get(i).getUserData("source");
BundleEntryComponent r = resp.getEntry().get(i);
if (r.getResource() instanceof Parameters) {
t.setResult(processValidationResult((Parameters) r.getResource()));
} else {
t.setResult(new ValidationResult(IssueSeverity.ERROR, getResponseText(r.getResource())).setTxLink(txLog == null ? null : txLog.getLastId()));
}
}
}
}
private String getResponseText(Resource resource) {
if (resource instanceof OperationOutcome) {
return OperationOutcomeRenderer.toString((OperationOutcome) resource);
}
return "Todo";
}
@Override
public ValidationResult validateCode(ValidationOptions options, Coding code, ValueSet vs) {
assert options != null;
if (options == null) {
options = ValidationOptions.defaults();
}
@ -813,6 +914,10 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
pOut = txClient.validateCS(pin);
else
pOut = txClient.validateVS(pin);
return processValidationResult(pOut);
}
public ValidationResult processValidationResult(Parameters pOut) {
boolean ok = false;
String message = "No Message returned";
String display = null;
@ -1622,4 +1727,5 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
return txClient;
}
}

51
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/IWorkerContext.java
View File

@ -44,6 +44,8 @@ import org.fhir.ucum.UcumService;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.TerminologyServiceException;
import org.hl7.fhir.r5.context.IWorkerContext.CodingValidationRequest;
import org.hl7.fhir.r5.context.TerminologyCache.CacheToken;
import org.hl7.fhir.r5.formats.IParser;
import org.hl7.fhir.r5.formats.ParserType;
import org.hl7.fhir.r5.model.Bundle;
@ -93,6 +95,53 @@ import com.google.gson.JsonSyntaxException;
*/
public interface IWorkerContext {
public class CodingValidationRequest {
private Coding coding;
private ValidationResult result;
private CacheToken cacheToken;
public CodingValidationRequest(Coding coding) {
super();
this.coding = coding;
}
public ValidationResult getResult() {
return result;
}
public void setResult(ValidationResult result) {
this.result = result;
}
public Coding getCoding() {
return coding;
}
public boolean hasResult() {
return result != null;
}
/**
* internal logic; external users of batch validation should ignore this property
*
* @return
*/
public CacheToken getCacheToken() {
return cacheToken;
}
/**
* internal logic; external users of batch validation should ignore this property
*
* @param cacheToken
*/
public void setCacheToken(CacheToken cacheToken) {
this.cacheToken = cacheToken;
}
}
public class PackageVersion {
private String id;
private String version;
@ -619,6 +668,8 @@ public interface IWorkerContext {
* @return
*/
public ValidationResult validateCode(ValidationOptions options, Coding code, ValueSet vs);
public void validateCodeBatch(ValidationOptions options, List<? extends CodingValidationRequest> codes, ValueSet vs);
/**
* returns the recommended tla for the type (from the structure definitions)

14
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/CodeSystemRenderer.java
View File

@ -138,6 +138,7 @@ public class CodeSystemRenderer extends TerminologyRenderer {
boolean display = false;
boolean hierarchy = false;
boolean version = false;
boolean ignoreStatus = false;
List<PropertyComponent> properties = new ArrayList<>();
for (PropertyComponent cp : cs.getProperty()) {
if (showPropertyInTable(cp)) {
@ -147,12 +148,15 @@ public class CodeSystemRenderer extends TerminologyRenderer {
}
if (exists) {
properties.add(cp);
if ("status".equals(cp.getCode())) {
ignoreStatus = true;
}
}
}
}
for (ConceptDefinitionComponent c : cs.getConcept()) {
commentS = commentS || conceptsHaveComments(c);
deprecated = deprecated || conceptsHaveDeprecated(cs, c);
deprecated = deprecated || conceptsHaveDeprecated(cs, c, ignoreStatus);
display = display || conceptsHaveDisplay(c);
version = version || conceptsHaveVersion(c);
hierarchy = hierarchy || c.hasConcept();
@ -255,11 +259,11 @@ public class CodeSystemRenderer extends TerminologyRenderer {
return false;
}
private boolean conceptsHaveDeprecated(CodeSystem cs, ConceptDefinitionComponent c) {
if (CodeSystemUtilities.isDeprecated(cs, c))
private boolean conceptsHaveDeprecated(CodeSystem cs, ConceptDefinitionComponent c, boolean ignoreStatus) {
if (CodeSystemUtilities.isDeprecated(cs, c, ignoreStatus))
return true;
for (ConceptDefinitionComponent g : c.getConcept())
if (conceptsHaveDeprecated(cs, g))
if (conceptsHaveDeprecated(cs, g, ignoreStatus))
return true;
return false;
}
@ -325,7 +329,7 @@ public class CodeSystemRenderer extends TerminologyRenderer {
}
if (deprecated) {
td = tr.td();
Boolean b = CodeSystemUtilities.isDeprecated(cs, c);
Boolean b = CodeSystemUtilities.isDeprecated(cs, c, false);
if (b != null && b) {
smartAddText(td, getContext().getWorker().translator().translate("xhtml-gen-cs", "Deprecated", getContext().getLang()));
hasExtensions = true;

8
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/OperationOutcomeRenderer.java
View File

@ -16,6 +16,7 @@ import org.hl7.fhir.r5.model.StringType;
import org.hl7.fhir.r5.renderers.utils.RenderingContext;
import org.hl7.fhir.r5.renderers.utils.Resolver.ResourceContext;
import org.hl7.fhir.r5.utils.ToolingExtensions;
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
import org.hl7.fhir.utilities.xhtml.XhtmlNode;
public class OperationOutcomeRenderer extends ResourceRenderer {
@ -89,4 +90,11 @@ public class OperationOutcomeRenderer extends ResourceRenderer {
return display((OperationOutcome) r);
}
public static String toString(OperationOutcome oo) {
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
for (OperationOutcomeIssueComponent issue : oo.getIssue()) {
b.append(issue.getSeverity().toCode()+": "+issue.getDetails().getText());
}
return b.toString();
}
}

18
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/ProfileDrivenRenderer.java
View File

@ -270,7 +270,7 @@ public class ProfileDrivenRenderer extends ResourceRenderer {
return null;
}
private void renderLeaf(ResourceWrapper res, BaseWrapper ew, ElementDefinition defn, XhtmlNode x, boolean title, boolean showCodeDetails, Map<String, String> displayHints, String path, int indent) throws FHIRException, UnsupportedEncodingException, IOException, EOperationOutcome {
private void renderLeaf(ResourceWrapper res, BaseWrapper ew, ElementDefinition defn, XhtmlNode parent, XhtmlNode x, boolean title, boolean showCodeDetails, Map<String, String> displayHints, String path, int indent) throws FHIRException, UnsupportedEncodingException, IOException, EOperationOutcome {
if (ew == null)
return;
@ -361,7 +361,7 @@ public class ProfileDrivenRenderer extends ResourceRenderer {
} else {
x.an(rw.getId());
ResourceRenderer rr = RendererFactory.factory(rw, context.copy().setAddGeneratedNarrativeHeader(false));
rr.render(x.blockquote(), rw);
rr.render(parent.blockquote(), rw);
}
}
} else {
@ -598,7 +598,7 @@ public class ProfileDrivenRenderer extends ResourceRenderer {
private void generateByProfile(ResourceWrapper res, StructureDefinition profile, BaseWrapper e, List<ElementDefinition> allElements, ElementDefinition defn, List<ElementDefinition> children, XhtmlNode x, String path, boolean showCodeDetails, int indent) throws FHIRException, UnsupportedEncodingException, IOException, EOperationOutcome {
if (children.isEmpty()) {
renderLeaf(res, e, defn, x, false, showCodeDetails, readDisplayHints(defn), path, indent);
renderLeaf(res, e, defn, x, x, false, showCodeDetails, readDisplayHints(defn), path, indent);
} else {
for (PropertyWrapper p : splitExtensions(profile, e.children())) {
if (p.hasValues()) {
@ -626,7 +626,7 @@ public class ProfileDrivenRenderer extends ResourceRenderer {
if (renderAsList(child) && p.getValues().size() > 1) {
XhtmlNode list = x.ul();
for (BaseWrapper v : p.getValues())
renderLeaf(res, v, child, list.li(), false, showCodeDetails, displayHints, path, indent);
renderLeaf(res, v, child, x, list.li(), false, showCodeDetails, displayHints, path, indent);
} else {
boolean first = true;
for (BaseWrapper v : p.getValues()) {
@ -634,7 +634,7 @@ public class ProfileDrivenRenderer extends ResourceRenderer {
first = false;
else
para.tx(", ");
renderLeaf(res, v, child, para, false, showCodeDetails, displayHints, path, indent);
renderLeaf(res, v, child, x, para, false, showCodeDetails, displayHints, path, indent);
}
}
}
@ -730,10 +730,12 @@ public class ProfileDrivenRenderer extends ResourceRenderer {
private void addColumnValues(ResourceWrapper res, XhtmlNode tr, List<ElementDefinition> grandChildren, BaseWrapper v, boolean showCodeDetails, Map<String, String> displayHints, String path, int indent) throws FHIRException, UnsupportedEncodingException, IOException, EOperationOutcome {
for (ElementDefinition e : grandChildren) {
PropertyWrapper p = v.getChildByName(e.getPath().substring(e.getPath().lastIndexOf(".")+1));
XhtmlNode td = tr.td();
if (p == null || p.getValues().size() == 0 || p.getValues().get(0) == null)
tr.td().tx(" ");
else
renderLeaf(res, p.getValues().get(0), e, tr.td(), false, showCodeDetails, displayHints, path, indent);
td.tx(" ");
else {
renderLeaf(res, p.getValues().get(0), e, td, td, false, showCodeDetails, displayHints, path, indent);
}
}
}

8
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/CodeSystemUtilities.java
View File

@ -208,11 +208,13 @@ public class CodeSystemUtilities {
defineCodeSystemProperty(cs, "child", "The concept identified in this property is a child of the concept on which it is a property. The property type will be 'code'. The meaning of parent/child relationships is defined by the hierarchyMeaning attribute", PropertyType.CODE);
}
public static boolean isDeprecated(CodeSystem cs, ConceptDefinitionComponent def) {
public static boolean isDeprecated(CodeSystem cs, ConceptDefinitionComponent def, boolean ignoreStatus) {
try {
for (ConceptPropertyComponent p : def.getProperty()) {
if (p.getCode().equals("status") && p.hasValue() && p.hasValueCodeType() && p.getValueCodeType().getCode().equals("deprecated"))
return true;
if (!ignoreStatus) {
if (p.getCode().equals("status") && p.hasValue() && p.hasValueCodeType() && p.getValueCodeType().getCode().equals("deprecated"))
return true;
}
// this, though status should also be set
if (p.getCode().equals("deprecationDate") && p.hasValue() && p.getValue() instanceof DateTimeType)
return ((DateTimeType) p.getValue()).before(new DateTimeType(Calendar.getInstance()));

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/TerminologyClient.java
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@ -34,6 +34,7 @@ package org.hl7.fhir.r5.terminologies;
import java.util.Map;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.model.Bundle;
import org.hl7.fhir.r5.model.CapabilityStatement;
import org.hl7.fhir.r5.model.Parameters;
import org.hl7.fhir.r5.model.TerminologyCapabilities;
@ -52,4 +53,5 @@ public interface TerminologyClient {
public TerminologyClient setRetryCount(int retryCount) throws FHIRException;
public CapabilityStatement getCapabilitiesStatementQuick() throws FHIRException;
public Parameters lookupCode(Map<String, String> params) throws FHIRException;
public Bundle validateBatch(Bundle batch);
}

22
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/ValueSetCheckerSimple.java
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@ -402,18 +402,21 @@ public class ValueSetCheckerSimple implements ValueSetChecker {
private boolean inComponent(ConceptSetComponent vsi, String system, String code, boolean only) throws FHIRException {
for (UriType uri : vsi.getValueSet()) {
if (inImport(uri.getValue(), system, code))
if (inImport(uri.getValue(), system, code)) {
return true;
}
}
if (!vsi.hasSystem())
if (!vsi.hasSystem()) {
return false;
}
if (only && system == null) {
// whether we know the system or not, we'll accept the stated codes at face value
for (ConceptReferenceComponent cc : vsi.getConcept())
if (cc.getCode().equals(code))
for (ConceptReferenceComponent cc : vsi.getConcept()) {
if (cc.getCode().equals(code)) {
return true;
}
}
}
if (!system.equals(vsi.getSystem()))
@ -443,12 +446,15 @@ public class ValueSetCheckerSimple implements ValueSetChecker {
List<ConceptDefinitionComponent> list = cs.getConcept();
boolean ok = validateCodeInConceptList(code, cs, list);
if (ok && vsi.hasConcept()) {
for (ConceptReferenceComponent cc : vsi.getConcept())
if (cc.getCode().equals(code))
for (ConceptReferenceComponent cc : vsi.getConcept()) {
if (cc.getCode().equals(code)) {
return true;
}
}
return false;
} else
} else {
return ok;
}
}
}

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/ValueSetExpanderSimple.java
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@ -293,7 +293,7 @@ public class ValueSetExpanderSimple implements ValueSetExpander {
if (exclusion.getCode().equals(def.getCode()))
return; // excluded.
}
if (!CodeSystemUtilities.isDeprecated(cs, def)) {
if (!CodeSystemUtilities.isDeprecated(cs, def, false)) {
ValueSetExpansionContainsComponent np = null;
boolean abs = CodeSystemUtilities.isNotSelectable(cs, def);
boolean inc = CodeSystemUtilities.isInactive(cs, def);

1
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/client/FHIRToolingClient.java
View File

@ -513,7 +513,6 @@ public class FHIRToolingClient {
}
@SuppressWarnings("unchecked")
public <T extends Resource> OperationOutcome validate(Class<T> resourceClass, T resource, String id) {
ResourceRequest<T> result = null;
try {

1
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/i18n/I18nConstants.java
View File

@ -333,6 +333,7 @@ public class I18nConstants {
public static final String RESOURCE_RES_ID_PROHIBITED = "Resource_RES_ID_Prohibited";
public static final String RESOURCE_TYPE_MISMATCH_FOR___ = "Resource_type_mismatch_for___";
public static final String SAME_ID_ON_MULTIPLE_ELEMENTS__IN_ = "Same_id_on_multiple_elements__in_";
public static final String SD_MUST_HAVE_DERIVATION = "SD_MUST_HAVE_DERIVATION";
public static final String SEARCHPARAMETER_BASE_WRONG = "SEARCHPARAMETER_BASE_WRONG";
public static final String SEARCHPARAMETER_EXP_WRONG = "SEARCHPARAMETER_EXP_WRONG";
public static final String SEARCHPARAMETER_NOTFOUND = "SEARCHPARAMETER_NOTFOUND";

1
org.hl7.fhir.utilities/src/main/resources/Messages.properties
View File

@ -570,3 +570,4 @@ XHTML_XHTML_DOCTYPE_ILLEGAL = Malformed XHTML: Found a DocType declaration, and
PACKAGE_VERSION_MISMATCH = FHIR Version mismatch in package {0}: version is {2} but must be {1} (path: {3})
VALUESET_REFERENCE_UNKNOWN = The value set import {0} could not be found so cannot be checked
VALUESET_REFERENCE_INVALID_TYPE = The value set import {0} points to a resource of type {1} which is not valid
SD_MUST_HAVE_DERIVATION = StructureDefinition {0} must have a derivation, since it has a baseDefinition

39
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/StructureDefinitionValidator.java
View File

@ -24,6 +24,7 @@ import org.hl7.fhir.r5.model.ElementDefinition;
import org.hl7.fhir.r5.model.ExpressionNode;
import org.hl7.fhir.r5.model.ExpressionNode.Kind;
import org.hl7.fhir.r5.model.ExpressionNode.Operation;
import org.hl7.fhir.r5.model.StructureDefinition.TypeDerivationRule;
import org.hl7.fhir.r5.model.SearchParameter;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.utils.FHIRPathEngine;
@ -66,27 +67,31 @@ public class StructureDefinitionValidator extends BaseValidator {
sd.setSnapshot(null);
StructureDefinition base = context.fetchResource(StructureDefinition.class, sd.getBaseDefinition());
if (warning(errors, IssueType.NOTFOUND, stack.getLiteralPath(), base != null, I18nConstants.UNABLE_TO_FIND_BASE__FOR_, sd.getBaseDefinition(), "StructureDefinition, so can't check the differential")) {
List<ValidationMessage> msgs = new ArrayList<>();
ProfileUtilities pu = new ProfileUtilities(context, msgs, null);
pu.generateSnapshot(base, sd, sd.getUrl(), "http://hl7.org/fhir", sd.getName());
if (msgs.size() > 0) {
for (ValidationMessage msg : msgs) {
// we need to set the location for the context
String loc = msg.getLocation();
if (loc.contains("#")) {
msg.setLocation(stack.getLiteralPath()+".differential.element.where(path = '"+loc.substring(loc.indexOf("#")+1)+"')");
} else {
msg.setLocation(stack.getLiteralPath());
if (rule(errors, IssueType.NOTFOUND, stack.getLiteralPath(), sd.hasDerivation(), I18nConstants.SD_MUST_HAVE_DERIVATION, sd.getUrl())) {
if (sd.getDerivation() == TypeDerivationRule.CONSTRAINT) {
List<ValidationMessage> msgs = new ArrayList<>();
ProfileUtilities pu = new ProfileUtilities(context, msgs, null);
pu.generateSnapshot(base, sd, sd.getUrl(), "http://hl7.org/fhir", sd.getName());
if (msgs.size() > 0) {
for (ValidationMessage msg : msgs) {
// we need to set the location for the context
String loc = msg.getLocation();
if (loc.contains("#")) {
msg.setLocation(stack.getLiteralPath()+".differential.element.where(path = '"+loc.substring(loc.indexOf("#")+1)+"')");
} else {
msg.setLocation(stack.getLiteralPath());
}
errors.add(msg);
}
}
if (!snapshot.isEmpty()) {
int was = snapshot.size();
int is = sd.getSnapshot().getElement().size();
rule(errors, IssueType.NOTFOUND, stack.getLiteralPath(), was == is, I18nConstants.SNAPSHOT_EXISTING_PROBLEM, was, is);
}
errors.add(msg);
}
}
}
if (!snapshot.isEmpty()) {
int was = snapshot.size();
int is = sd.getSnapshot().getElement().size();
rule(errors, IssueType.NOTFOUND, stack.getLiteralPath(), was == is, I18nConstants.SNAPSHOT_EXISTING_PROBLEM, was, is);
}
} catch (FHIRException | IOException e) {
rule(errors, IssueType.EXCEPTION, stack.getLiteralPath(), false, I18nConstants.ERROR_GENERATING_SNAPSHOT, e.getMessage());
}

50
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/ValueSetValidator.java
View File

@ -1,9 +1,11 @@
package org.hl7.fhir.validation.instance.type;
import java.util.ArrayList;
import java.util.List;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.context.IWorkerContext.CodingValidationRequest;
import org.hl7.fhir.r5.context.IWorkerContext.ValidationResult;
import org.hl7.fhir.r5.elementmodel.Element;
import org.hl7.fhir.r5.model.CodeSystem;
@ -19,10 +21,26 @@ import org.hl7.fhir.utilities.validation.ValidationMessage.Source;
import org.hl7.fhir.utilities.validation.ValidationOptions;
import org.hl7.fhir.validation.BaseValidator;
import org.hl7.fhir.validation.TimeTracker;
import org.hl7.fhir.validation.instance.type.ValueSetValidator.VSCodingValidationRequest;
import org.hl7.fhir.validation.instance.utils.NodeStack;
public class ValueSetValidator extends BaseValidator {
public class VSCodingValidationRequest extends CodingValidationRequest {
private NodeStack stack;
public VSCodingValidationRequest(NodeStack stack, Coding code) {
super(code);
this.stack = stack;
}
public NodeStack getStack() {
return stack;
}
}
public ValueSetValidator(IWorkerContext context, TimeTracker timeTracker) {
super(context);
source = Source.InstanceValidator;
@ -58,7 +76,6 @@ public class ValueSetValidator extends BaseValidator {
private void validateValueSetInclude(List<ValidationMessage> errors, Element include, NodeStack stack) {
String system = include.getChildValue("system");
String version = include.getChildValue("version");
boolean systemOk = true;
List<Element> valuesets = include.getChildrenByName("valueSet");
int i = 0;
for (Element ve : valuesets) {
@ -79,13 +96,31 @@ public class ValueSetValidator extends BaseValidator {
List<Element> concepts = include.getChildrenByName("concept");
List<Element> filters = include.getChildrenByName("filter");
if (!Utilities.noString(system)) {
boolean systemOk = true;
int cc = 0;
List<VSCodingValidationRequest> batch = new ArrayList<>();
boolean first = true;
for (Element concept : concepts) {
if (systemOk && !validateValueSetIncludeConcept(errors, concept, stack.push(concept, cc, null, null), system, version)) {
systemOk = false;
// we treat the first differently because we want to know if tbe system is worth validating. if it is, then we batch the rest
if (first) {
systemOk = validateValueSetIncludeConcept(errors, concept, stack.push(concept, cc, null, null), system, version);
first = false;
} else if (systemOk) {
batch.add(prepareValidateValueSetIncludeConcept(errors, concept, stack.push(concept, cc, null, null), system, version));
}
cc++;
}
if (batch.size() > 0) {
context.validateCodeBatch(ValidationOptions.defaults(), batch, null);
for (VSCodingValidationRequest cv : batch) {
if (version == null) {
warning(errors, IssueType.BUSINESSRULE, cv.getStack().getLiteralPath(), cv.getResult().isOk(), I18nConstants.VALUESET_INCLUDE_INVALID_CONCEPT_CODE, system, cv.getCoding().getCode());
} else {
warning(errors, IssueType.BUSINESSRULE, cv.getStack().getLiteralPath(), cv.getResult().isOk(), I18nConstants.VALUESET_INCLUDE_INVALID_CONCEPT_CODE_VER, system, version, cv.getCoding().getCode());
}
}
}
int cf = 0;
for (Element filter : filters) {
if (systemOk && !validateValueSetIncludeFilter(errors, include, stack.push(filter, cf, null, null), system, version)) {
@ -121,6 +156,15 @@ public class ValueSetValidator extends BaseValidator {
return true;
}
private VSCodingValidationRequest prepareValidateValueSetIncludeConcept(List<ValidationMessage> errors, Element concept, NodeStack stack, String system, String version) {
String code = concept.getChildValue("code");
Coding c = new Coding(system, code, null);
if (version != null) {
c.setVersion(version);
}
return new VSCodingValidationRequest(stack, c);
}
private boolean validateValueSetIncludeFilter(List<ValidationMessage> errors, Element include, NodeStack push, String system, String version) {
return true;
}

3
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/ValidationTestSuite.java
View File

@ -98,7 +98,8 @@ public class ValidationTestSuite implements IEvaluationContext, IValidatorResour
private String version;
private String name;
private static final String DEF_TX = "http://tx.fhir.org";
private static final String DEF_TX = "http://tx.fhir.org";
// private static final String DEF_TX = "http://local.fhir.org:960";
private static Map<String, ValidationEngine> ve = new HashMap<>();
private static ValidationEngine vCurr;