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Merge pull request #363 from hapifhir/gg-v5117 

more fixes for next release
This commit is contained in:
Grahame Grieve 2020-10-14 14:40:01 +11:00 committed by GitHub
parent 7b0ef86c4e db870fc332
commit f5b02ff308
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68 changed files with 1110 additions and 490 deletions
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210
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/UTGVersionSorter.java Normal file
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@ -0,0 +1,210 @@
package org.hl7.fhir.convertors.misc;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.net.URISyntaxException;
import java.text.ParseException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.hl7.fhir.convertors.VersionConvertor_10_50;
import org.hl7.fhir.convertors.VersionConvertor_30_50;
import org.hl7.fhir.convertors.VersionConvertor_40_50;
import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.formats.XmlParser;
import org.hl7.fhir.r5.model.CanonicalResource;
import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.utils.ToolingExtensions;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.utilities.npm.NpmPackage.PackageResourceInformation;
import org.hl7.fhir.utilities.npm.ToolsVersion;
public class UTGVersionSorter {
private FilesystemPackageCacheManager pcm;
public class CanonicalResourceAnalysis {
private CanonicalResource resource;
private CanonicalResource r2;
private CanonicalResource r3;
private CanonicalResource r4;
private String fmm;
private boolean normative;
private String recommendation;
public CanonicalResourceAnalysis(CanonicalResource cr) {
this.resource = cr;
}
public String summary() {
// return "Relevant: "+resource.getUrl()+" [r2: "+r2Ver+"/"+r2Fmm+"]"+" [r3: "+r3Ver+"/"+r3Fmm+"]"+" [r4: "+r4Ver+"/"+r4Fmm+"/"+r4Normative+"] ---> "+recommendation;
return resource.getUrl()+" ---> "+recommendation;
}
public void analyse(Map<String, CanonicalResource> r2l, Map<String, CanonicalResource> r3l, Map<String, CanonicalResource> r4l) {
r2 = findMatch(r2l);
r3 = findMatch(r3l);
r4 = findMatch(r4l);
fmm = r4 != null ? ToolingExtensions.readStringExtension(r4, ToolingExtensions.EXT_FMM_LEVEL) : null;
normative = (r4 != null) && ToolingExtensions.readStringExtension(r4, ToolingExtensions.EXT_NORMATIVE_VERSION) != null;
if (normative) {
recommendation = "1.0.0";
} else if (Utilities.existsInList(fmm,"3", "4", "5")) {
recommendation = "0.5.0";
} else {
int i = 1;
if (r2 != null && r3 != null && !match(r2, r3, r2l, r3l)) {
i++;
}
if (r3 != null && r4 != null && !match(r3, r4, r3l, r4l)) {
i++;
}
recommendation = "0."+i+".0";
}
}
private boolean match(CanonicalResource l, CanonicalResource r, Map<String, CanonicalResource> ll, Map<String, CanonicalResource> rl) {
if (l instanceof CodeSystem && r instanceof CodeSystem) {
return matchCS((CodeSystem) l, (CodeSystem) r);
} else if (l instanceof ValueSet && r instanceof ValueSet) {
return matchVS((ValueSet) l, (ValueSet) r, ll, rl);
} else {
return false;
}
}
private boolean matchVS(ValueSet l, ValueSet r, Map<String, CanonicalResource> ll, Map<String, CanonicalResource> rl) {
if (l.getCompose().getInclude().size() == 1 && l.getCompose().getExclude().isEmpty() && l.getCompose().getIncludeFirstRep().hasSystem() && !l.getCompose().getIncludeFirstRep().hasConcept() && !l.getCompose().getIncludeFirstRep().hasFilter() &&
r.getCompose().getInclude().size() == 1 && r.getCompose().getExclude().isEmpty() && r.getCompose().getIncludeFirstRep().hasSystem() && !r.getCompose().getIncludeFirstRep().hasConcept() && !r.getCompose().getIncludeFirstRep().hasFilter()) {
CodeSystem lc = (CodeSystem) ll.get(l.getCompose().getIncludeFirstRep().getSystem());
CodeSystem rc = (CodeSystem) rl.get(l.getCompose().getIncludeFirstRep().getSystem());
if (lc != null && rc != null) {
return matchCS(lc, rc);
}
}
return false;
}
private boolean matchCS(CodeSystem l, CodeSystem r) {
return Base.compareDeep(l.getConcept(), r.getConcept(), false);
}
public CanonicalResource findMatch(Map<String, CanonicalResource> r2) {
CanonicalResource r = r2.get(resource.getUrl());
if (r == null) {
r = r2.get(resource.getUrl().replaceAll("http://terminology.hl7.org/", "http://hl7.org/fhir/"));
}
if (r == null) {
r = r2.get(resource.getUrl().replaceAll("http://terminology.hl7.org/CodeSystem", "http://hl7.org/fhir/"));
}
return r;
}
}
public static void main(String[] args) throws FileNotFoundException, FHIRException, IOException, ParseException, URISyntaxException {
new UTGVersionSorter().execute("C:\\work\\org.hl7.fhir.igs\\UTG\\input\\sourceOfTruth");
}
private void execute(String source) throws IOException {
List<CanonicalResourceAnalysis> list = new ArrayList<>();
System.out.println("Loading UTG");
loadFromSource(list, new File(source));
Map<String, CanonicalResource> r2 = loadPackageR2("hl7.fhir.r2.core");
Map<String, CanonicalResource> r3 = loadPackageR3("hl7.fhir.r3.core");
Map<String, CanonicalResource> r4 = loadPackageR4("hl7.fhir.r4.core");
System.out.println("Processing");
for (CanonicalResourceAnalysis cr : list) {
cr.analyse(r2,r3,r4);
}
System.out.println("Summary");
for (CanonicalResourceAnalysis cr : list) {
System.out.println(cr.summary());
}
System.out.println();
System.out.println("Done");
}
private Map<String, CanonicalResource> loadPackageR2(String id) throws IOException {
Map<String, CanonicalResource>res = new HashMap<>();
if (pcm == null) {
pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
}
System.out.println("Load "+id);
NpmPackage npm = pcm.loadPackage(id);
for (PackageResourceInformation p : npm.listIndexedResources("CodeSystem", "ValueSet")) {
CanonicalResource r = (CanonicalResource) VersionConvertor_10_50.convertResource(new org.hl7.fhir.dstu2.formats.JsonParser().parse(npm.load(p)));
res.put(r.getUrl(), r);
}
return res;
}
private Map<String, CanonicalResource> loadPackageR3(String id) throws IOException {
Map<String, CanonicalResource>res = new HashMap<>();
if (pcm == null) {
pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
}
System.out.println("Load "+id);
NpmPackage npm = pcm.loadPackage(id);
for (PackageResourceInformation p : npm.listIndexedResources("CodeSystem", "ValueSet")) {
CanonicalResource r = (CanonicalResource) VersionConvertor_30_50.convertResource(new org.hl7.fhir.dstu3.formats.JsonParser().parse(npm.load(p)), false);
res.put(r.getUrl(), r);
}
return res;
}
private Map<String, CanonicalResource> loadPackageR4(String id) throws IOException {
Map<String, CanonicalResource>res = new HashMap<>();
if (pcm == null) {
pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
}
System.out.println("Load "+id);
NpmPackage npm = pcm.loadPackage(id);
for (PackageResourceInformation p : npm.listIndexedResources("CodeSystem", "ValueSet")) {
CanonicalResource r = (CanonicalResource) VersionConvertor_40_50.convertResource(new org.hl7.fhir.r4.formats.JsonParser().parse(npm.load(p)));
res.put(r.getUrl(), r);
}
return res;
}
private void loadFromSource(List<CanonicalResourceAnalysis> list, File source) {
for (File f : source.listFiles()) {
if (f.isDirectory()) {
loadFromSource(list, f);
} else if (f.getName().endsWith(".xml")) {
try {
Resource r = new XmlParser().parse(new FileInputStream(f));
if (r instanceof CanonicalResource) {
CanonicalResource cr = (CanonicalResource) r;
cr.setUserData("path", f.getAbsolutePath());
if (cr.hasVersion() && cr.getVersion().startsWith("4.")) {
list.add(new CanonicalResourceAnalysis(cr));
}
}
} catch (Exception e) {
System.out.println(f.getAbsolutePath()+" not a resource? "+e.getMessage());
}
}
}
}
}

4
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/BaseWorkerContext.java
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@ -49,6 +49,7 @@ import org.apache.commons.lang3.StringUtils;
import org.fhir.ucum.UcumService;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.NoTerminologyServiceException;
import org.hl7.fhir.exceptions.TerminologyServiceException;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.context.CanonicalResourceManager.CanonicalResourceProxy;
@ -910,6 +911,9 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
txCache.cacheValidation(cacheToken, res, TerminologyCache.TRANSIENT);
return res;
} catch (Exception e) {
if (e instanceof NoTerminologyServiceException) {
return new ValidationResult(IssueSeverity.ERROR, "No Terminology Service", TerminologyServiceErrorClass.NOSERVICE);
}
}
}

14
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/SimpleWorkerContext.java
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@ -148,6 +148,7 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
private boolean ignoreProfileErrors;
private boolean progress;
private List<String> loadedPackages = new ArrayList<String>();
private boolean canNoTS;
public SimpleWorkerContext() throws FileNotFoundException, IOException, FHIRException {
super();
@ -299,7 +300,7 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
setTxCaps(txClient.getTerminologyCapabilities());
return cps.getSoftware().getVersion();
} catch (Exception e) {
throw new FHIRException(formatMessage(I18nConstants.UNABLE_TO_CONNECT_TO_TERMINOLOGY_SERVER_USE_PARAMETER_TX_NA_TUN_RUN_WITHOUT_USING_TERMINOLOGY_SERVICES_TO_VALIDATE_LOINC_SNOMED_ICDX_ETC_ERROR__, e.getMessage()), e);
throw new FHIRException(formatMessage(canNoTS ? I18nConstants.UNABLE_TO_CONNECT_TO_TERMINOLOGY_SERVER_USE_PARAMETER_TX_NA_TUN_RUN_WITHOUT_USING_TERMINOLOGY_SERVICES_TO_VALIDATE_LOINC_SNOMED_ICDX_ETC_ERROR__ : I18nConstants.UNABLE_TO_CONNECT_TO_TERMINOLOGY_SERVER, e.getMessage()), e);
}
}
@ -813,6 +814,15 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
public void setClock(TimeTracker tt) {
clock = tt;
}
public boolean isCanNoTS() {
return canNoTS;
}
public void setCanNoTS(boolean canNoTS) {
this.canNoTS = canNoTS;
}
}

3
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/CanonicalResource.java
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@ -442,7 +442,8 @@ public abstract class CanonicalResource extends DomainResource {
/**
* @param value A copyright statement relating to the canonical resource and/or its contents. Copyright statements are generally legal restrictions on the use and publishing of the canonical resource.
*/
public abstract CanonicalResource setCopyright(String value);
public abstract CanonicalResource setCopyright(String value);
protected void listChildren(List<Property> children) {
super.listChildren(children);
}

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/CodeType.java
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@ -34,6 +34,7 @@ package org.hl7.fhir.r5.model;
import static org.apache.commons.lang3.StringUtils.defaultString;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.xhtml.XhtmlNode;
import ca.uhn.fhir.model.api.annotation.DatatypeDef;
@ -137,4 +138,5 @@ public class CodeType extends StringType implements Comparable<CodeType>, ICodin
public boolean supportsDisplay() {
return false;
}
}

3
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/CompartmentDefinition.java
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@ -2323,6 +2323,9 @@ public class CompartmentDefinition extends CanonicalResource {
*/
public static final ca.uhn.fhir.rest.gclient.TokenClientParam VERSION = new ca.uhn.fhir.rest.gclient.TokenClientParam(SP_VERSION);
public boolean supportsCopyright() {
return false;
}
}

3
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/GraphDefinition.java
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@ -3766,6 +3766,9 @@ public class GraphDefinition extends CanonicalResource {
*/
public static final ca.uhn.fhir.rest.gclient.TokenClientParam VERSION = new ca.uhn.fhir.rest.gclient.TokenClientParam(SP_VERSION);
public boolean supportsCopyright() {
return false;
}
}

4
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/SearchParameter.java
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@ -3875,6 +3875,8 @@ public class SearchParameter extends CanonicalResource {
*/
public static final ca.uhn.fhir.rest.gclient.TokenClientParam VERSION = new ca.uhn.fhir.rest.gclient.TokenClientParam(SP_VERSION);
public boolean supportsCopyright() {
return false;
}
}

3
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/RendererFactory.java
View File

@ -36,6 +36,9 @@ public class RendererFactory {
if ("OperationDefinition".equals(resourceName)) {
return new OperationDefinitionRenderer(context);
}
if ("SearchParameter".equals(resourceName)) {
return new SearchParameterRenderer(context);
}
if ("CompartmentDefinition".equals(resourceName)) {
return new CompartmentDefinitionRenderer(context);
}

160
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/SearchParameterRenderer.java Normal file
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@ -0,0 +1,160 @@
package org.hl7.fhir.r5.renderers;
import java.io.IOException;
import java.io.UnsupportedEncodingException;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.model.CodeType;
import org.hl7.fhir.r5.model.DomainResource;
import org.hl7.fhir.r5.model.Enumeration;
import org.hl7.fhir.r5.model.Extension;
import org.hl7.fhir.r5.model.OperationDefinition;
import org.hl7.fhir.r5.model.OperationDefinition.OperationDefinitionParameterComponent;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.SearchParameter;
import org.hl7.fhir.r5.model.SearchParameter.SearchComparator;
import org.hl7.fhir.r5.model.SearchParameter.SearchModifierCode;
import org.hl7.fhir.r5.model.SearchParameter.SearchParameterComponentComponent;
import org.hl7.fhir.r5.model.StringType;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.renderers.utils.RenderingContext;
import org.hl7.fhir.r5.renderers.utils.Resolver.ResourceContext;
import org.hl7.fhir.r5.utils.EOperationOutcome;
import org.hl7.fhir.r5.utils.ToolingExtensions;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.xhtml.XhtmlNode;
public class SearchParameterRenderer extends TerminologyRenderer {
public SearchParameterRenderer(RenderingContext context) {
super(context);
}
public SearchParameterRenderer(RenderingContext context, ResourceContext rcontext) {
super(context, rcontext);
}
public boolean render(XhtmlNode x, Resource dr) throws IOException, FHIRException, EOperationOutcome {
return render(x, (OperationDefinition) dr);
}
public boolean render(XhtmlNode x, SearchParameter spd) throws IOException, FHIRException, EOperationOutcome {
x.h2().addText(spd.getName());
XhtmlNode p = x.para();
p.tx("Parameter ");
p.code().tx(spd.getCode());
p.tx(":");
p.code().tx(spd.getType().toCode());
addMarkdown(x, spd.getDescription());
XhtmlNode tbl = x.table("grid");
XhtmlNode tr = tbl.tr();
tr.td().tx(Utilities.pluralize("Resource", spd.getBase().size()));
XhtmlNode td = tr.td();
for (CodeType t : spd.getBase()) {
StructureDefinition sd = context.getWorker().fetchTypeDefinition(t.toString());
if (sd != null && sd.hasUserData("path")) {
td.sep(", ").ah(sd.getUserString("path")).tx(t.getCode());
} else {
td.sep(", ").tx(t.getCode());
}
}
tr = tbl.tr();
tr.td().tx("Expression");
if (spd.hasExpression()) {
tr.td().code().tx(spd.getExpression());
} else {
tr.td().tx("(none)");
}
if (spd.hasXpathUsage()) {
tr = tbl.tr();
tr.td().tx("Usage");
tr.td().tx(spd.getXpathUsage().getDisplay());
}
if (spd.hasXpath()) {
tr = tbl.tr();
tr.td().tx("XPath");
tr.td().code().tx(spd.getXpath());
}
if (spd.hasTarget()) {
tr = tbl.tr();
tr.td().tx(Utilities.pluralize("Target Resources", spd.getTarget().size()));
td = tr.td();
for (CodeType t : spd.getTarget()) {
StructureDefinition sd = context.getWorker().fetchTypeDefinition(t.toString());
if (sd != null && sd.hasUserData("path")) {
td.sep(", ").ah(sd.getUserString("path")).tx(t.getCode());
} else {
td.sep(", ").tx(t.getCode());
}
}
}
tr = tbl.tr();
tr.td().tx("Multiples");
if (spd.getMultipleAnd() && spd.getMultipleOr()) {
tr.td().tx("The parameter can repeat (and) and can have repeating values (or)");
} else if (spd.getMultipleOr()) {
tr.td().tx("The parameter can repeat (and) but each repeat can only have one value");
} else if (spd.getMultipleAnd()) {
tr.td().tx("The parameter cannot repeat (and) but the single parameter can have multiple values (or)");
} else {
tr.td().tx("The parameter cannot repeat or have multiple values");
}
if (spd.hasComparator()) {
tr = tbl.tr();
tr.td().tx("Comparators");
td = tr.td().tx("Allowed: ");
for (Enumeration<SearchComparator> t : spd.getComparator()) {
td.sep(", ").tx(t.asStringValue());
}
}
if (spd.hasModifier()) {
tr = tbl.tr();
tr.td().tx("Modifiers");
td = tr.td().tx("Allowed: ");
for (Enumeration<SearchModifierCode> t : spd.getModifier()) {
td.sep(", ").tx(t.asStringValue());
}
}
if (spd.hasChain()) {
tr = tbl.tr();
tr.td().tx("Chains");
td = tr.td().tx("Allowed: ");
for (StringType t : spd.getChain()) {
td.sep(", ").tx(t.asStringValue());
}
}
if (spd.hasComponent()) {
x.para().b().tx("Components");
tbl = x.table("grid");
for (SearchParameterComponentComponent t : spd.getComponent()) {
tr = tbl.tr();
SearchParameter tsp = context.getWorker().fetchResource(SearchParameter.class, t.getDefinition());
if (tsp != null && tsp.hasUserData("path")) {
tr.td().ah(tsp.getUserString("path")).tx(tsp.present());
} else {
tr.td().tx(t.getDefinition());
}
tr.td().code().tx(t.getExpression());
}
}
return false;
}
public void describe(XhtmlNode x, OperationDefinition opd) {
x.tx(display(opd));
}
public String display(OperationDefinition opd) {
return opd.present();
}
@Override
public String display(Resource r) throws UnsupportedEncodingException, IOException {
return ((OperationDefinition) r).present();
}
}

4
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/ValueSetCheckerSimple.java
View File

@ -37,6 +37,7 @@ import java.util.List;
import java.util.Map;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.NoTerminologyServiceException;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.context.IWorkerContext.ValidationResult;
import org.hl7.fhir.r5.model.CanonicalType;
@ -515,6 +516,9 @@ public class ValueSetCheckerSimple implements ValueSetChecker {
if (res.getErrorClass() == TerminologyServiceErrorClass.UNKNOWN || res.getErrorClass() == TerminologyServiceErrorClass.CODESYSTEM_UNSUPPORTED || res.getErrorClass() == TerminologyServiceErrorClass.VALUESET_UNSUPPORTED) {
return null;
}
if (res.getErrorClass() == TerminologyServiceErrorClass.NOSERVICE) {
throw new NoTerminologyServiceException();
}
return res.isOk();
} else {
if (vsi.hasFilter()) {

8
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/IResourceValidator.java
View File

@ -184,6 +184,14 @@ public interface IResourceValidator {
public boolean isShowMessagesFromReferences();
public void setShowMessagesFromReferences(boolean value);
/**
* this is used internally in the publishing stack to ensure that everything is water tight, but
* this check is not necessary or appropriate at run time when the validator is hosted in HAPI
* @return
*/
public boolean isWantCheckSnapshotUnchanged();
public void setWantCheckSnapshotUnchanged(boolean wantCheckSnapshotUnchanged);
//FIXME: don't need that, gets never used?
// public String getValidationLanguage();
// public void setValidationLanguage(String value);

43
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/ResourceTests.java Normal file
View File

@ -0,0 +1,43 @@
package org.hl7.fhir.r5.test;
import static org.junit.jupiter.api.Assertions.*;
import org.hl7.fhir.r5.model.CapabilityStatement;
import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.CompartmentDefinition;
import org.hl7.fhir.r5.model.ConceptMap;
import org.hl7.fhir.r5.model.ExampleScenario;
import org.hl7.fhir.r5.model.GraphDefinition;
import org.hl7.fhir.r5.model.ImplementationGuide;
import org.hl7.fhir.r5.model.MessageDefinition;
import org.hl7.fhir.r5.model.NamingSystem;
import org.hl7.fhir.r5.model.OperationDefinition;
import org.hl7.fhir.r5.model.SearchParameter;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.model.StructureMap;
import org.hl7.fhir.r5.model.TerminologyCapabilities;
import org.hl7.fhir.r5.model.ValueSet;
import org.junit.jupiter.api.Test;
class ResourceTests {
@Test
void testSupportsCopyright() {
assertTrue(new CodeSystem().supportsCopyright());
assertTrue(new ValueSet().supportsCopyright());
assertTrue(new ConceptMap().supportsCopyright());
assertTrue(new TerminologyCapabilities().supportsCopyright());
assertTrue(new CapabilityStatement().supportsCopyright());
assertTrue(new StructureDefinition().supportsCopyright());
assertTrue(new ImplementationGuide().supportsCopyright());
assertTrue(new MessageDefinition().supportsCopyright());
assertTrue(new StructureMap().supportsCopyright());
assertTrue(new ExampleScenario().supportsCopyright());
assertFalse(new SearchParameter().supportsCopyright());
assertFalse(new NamingSystem().supportsCopyright());
assertFalse(new OperationDefinition().supportsCopyright());
assertFalse(new CompartmentDefinition().supportsCopyright());
assertFalse(new GraphDefinition().supportsCopyright());
}
}

8
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/i18n/I18nConstants.java
View File

@ -1,5 +1,7 @@
package org.hl7.fhir.utilities.i18n;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
public class I18nConstants {
@ -343,6 +345,9 @@ public class I18nConstants {
public static final String SD_MUST_HAVE_DERIVATION = "SD_MUST_HAVE_DERIVATION";
public static final String SD_NESTED_MUST_SUPPORT_DIFF = "SD_NESTED_MUST_SUPPORT_DIFF";
public static final String SD_NESTED_MUST_SUPPORT_SNAPSHOT = "SD_NESTED_MUST_SUPPORT_SNAPSHOT";
public static final String SD_ED_TYPE_PROFILE_UNKNOWN = "SD_ED_TYPE_PROFILE_UNKNOWN";
public static final String SD_ED_TYPE_PROFILE_NOTYPE = "SD_ED_TYPE_PROFILE_NOTYPE";
public static final String SD_ED_TYPE_PROFILE_WRONG = "SD_ED_TYPE_PROFILE_WRONG";
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";
@ -410,6 +415,8 @@ public class I18nConstants {
public static final String TERMINOLOGY_TX_SYSTEM_VALUESET2 = "Terminology_TX_System_ValueSet2";
public static final String TERMINOLOGY_TX_VALUESET_NOTFOUND = "Terminology_TX_ValueSet_NotFound";
public static final String TERMINOLOGY_TX_VALUESET_NOTFOUND2 = "Terminology_TX_ValueSet_NotFound2";
public static final String TERMINOLOGY_TX_NOSVC_BOUND_REQ = "TERMINOLOGY_TX_NOSVC_BOUND_REQ";
public static final String TERMINOLOGY_TX_NOSVC_BOUND_EXT = "TERMINOLOGY_TX_NOSVC_BOUND_EXT";
public static final String TEXT_SHOULD_NOT_BE_PRESENT = "Text_should_not_be_present";
public static final String THE_BASE_SNAPSHOT_MARKS_A_SLICING_AS_CLOSED_BUT_THE_DIFFERENTIAL_TRIES_TO_EXTEND_IT_IN__AT__ = "The_base_snapshot_marks_a_slicing_as_closed_but_the_differential_tries_to_extend_it_in__at__";
public static final String THIS_BASE_PROPERTY_MUST_BE_AN_ARRAY_NOT_A_ = "This_base_property_must_be_an_Array_not_a_";
@ -478,6 +485,7 @@ public class I18nConstants {
public static final String TYPE_SPECIFIC_CHECKS_DT_URL_RESOLVE = "Type_Specific_Checks_DT_URL_Resolve";
public static final String TYPE_SPECIFIC_CHECKS_DT_UUID_STRAT = "Type_Specific_Checks_DT_UUID_Strat";
public static final String TYPE_SPECIFIC_CHECKS_DT_UUID_VAID = "Type_Specific_Checks_DT_UUID_Vaid";
public static final String UNABLE_TO_CONNECT_TO_TERMINOLOGY_SERVER = "Unable_to_connect_to_terminology_server";
public static final String UNABLE_TO_CONNECT_TO_TERMINOLOGY_SERVER_USE_PARAMETER_TX_NA_TUN_RUN_WITHOUT_USING_TERMINOLOGY_SERVICES_TO_VALIDATE_LOINC_SNOMED_ICDX_ETC_ERROR__ = "Unable_to_connect_to_terminology_server_Use_parameter_tx_na_tun_run_without_using_terminology_services_to_validate_LOINC_SNOMED_ICDX_etc_Error__";
public static final String UNABLE_TO_FIND_BASE_DEFINITION_FOR_LOGICAL_MODEL__FROM_ = "Unable_to_find_base_definition_for_logical_model__from_";
public static final String UNABLE_TO_FIND_BASE__FOR_ = "Unable_to_find_base__for_";

5
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/NpmPackage.java
View File

@ -35,6 +35,7 @@ import java.io.BufferedOutputStream;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
@ -1095,6 +1096,10 @@ public class NpmPackage {
public boolean isNotForPublication() {
return JSONUtil.bool(npm, "notForPublication");
}
public InputStream load(PackageResourceInformation p) throws FileNotFoundException {
return new FileInputStream(p.filename);
}
}

13
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/xhtml/XhtmlNode.java
View File

@ -92,7 +92,7 @@ public class XhtmlNode implements IBaseXhtml {
private boolean notPretty;
private boolean inPara;
private boolean inLink;
private boolean seperated;
public XhtmlNode() {
super();
@ -842,6 +842,17 @@ public class XhtmlNode implements IBaseXhtml {
}
public XhtmlNode sep(String separator) {
// if there's already text, add the separator
if (seperated) {
return this;
}
seperated = true;
return tx(separator);
}

10
org.hl7.fhir.utilities/src/main/resources/Messages.properties
View File

@ -418,7 +418,7 @@ Parser_Type__not_supported = Parser Type {0} not supported
Version_mismatch_The_context_has_version__loaded_and_the_new_content_being_loaded_is_version_ = Version mismatch. The context has version {0} loaded, and the new content being loaded is version {1}
Error_reading__from_package__ = Error reading {0} from package {1}#{2}: {3}
Error_parsing_ = Error parsing {0}:{1}
Unable_to_connect_to_terminology_server_Use_parameter_tx_na_tun_run_without_using_terminology_services_to_validate_LOINC_SNOMED_ICDX_etc_Error__ = Unable to connect to terminology server. Use parameter ''-tx n/a'' tun run without using terminology services to validate LOINC, SNOMED, ICD-X etc. Error = {0}
Unable_to_connect_to_terminology_server_Use_parameter_tx_na_tun_run_without_using_terminology_services_to_validate_LOINC_SNOMED_ICDX_etc_Error__ = Unable to connect to terminology server. Use parameter ''-tx n/a'' to run without using terminology services to validate LOINC, SNOMED, ICD-X etc. Error = {0}
Display_Name_for__should_be_one_of__instead_of_ = Display Name for {0}#{1} should be one of ''{2}'' instead of ''{3}''
Unknown_Code__in_ = Unknown Code {0} in {1}
UNKNOWN_CODE__IN_FRAGMENT = Unknown Code {0} in {1} - note that the code system is labelled as a fragment, so the code may be valid in some other fragment
@ -611,4 +611,10 @@ UNSUPPORTED_IDENTIFIER_PATTERN_PROPERTY_NOT_SUPPORTED_FOR_DISCRIMINATOR_FOR_SLIC
UNSUPPORTED_IDENTIFIER_PATTERN_NO_PROPERTY_NOT_SUPPORTED_FOR_DISCRIMINATOR_FOR_SLICE = Unsupported: no properties with values found on type {2} for pattern for discriminator({0}) for slice {1}
SD_NESTED_MUST_SUPPORT_DIFF = The element {0} has types/profiles/targets that are marked as must support, but the element itself is not marked as must-support. The inner must-supports will be ignored unless the element inherits must-support = true
SD_NESTED_MUST_SUPPORT_SNAPSHOT = The element {0} has types/profiles/targets that are marked as must support, but the element itself is not marked as must-support
Unable_to_connect_to_terminology_server = Unable to connect to terminology server. Error = {0}
SD_ED_TYPE_PROFILE_UNKNOWN = Unable to resolve profile {0}
SD_ED_TYPE_PROFILE_NOTYPE = Found profile {0}, but unable to determine the type it applies it
SD_ED_TYPE_PROFILE_WRONG = Profile {0} is for type {1}, but this element has type {2}
TERMINOLOGY_TX_NOSVC_BOUND_REQ = Could not confirm that the codes provided are from the required value set {0} because there is no terminology service
TERMINOLOGY_TX_NOSVC_BOUND_EXT = Could not confirm that the codes provided are from the extensible value set {0} because there is no terminology service

5
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/BaseValidator.java
View File

@ -2,11 +2,7 @@ package org.hl7.fhir.validation;
import static org.apache.commons.lang3.StringUtils.isBlank;
import java.text.DateFormat;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Date;
import java.util.HashMap;
/*
@ -85,7 +81,6 @@ import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
import org.hl7.fhir.utilities.validation.ValidationMessage.Source;
import org.hl7.fhir.validation.BaseValidator.ValidationControl;
import org.hl7.fhir.validation.instance.utils.IndexedElement;
public class BaseValidator {

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

@ -34,7 +34,11 @@ package org.hl7.fhir.validation;
import java.io.ByteArrayOutputStream;
import java.io.IOException;
import org.hl7.fhir.convertors.*;
import org.hl7.fhir.convertors.VersionConvertorAdvisor50;
import org.hl7.fhir.convertors.VersionConvertor_10_50;
import org.hl7.fhir.convertors.VersionConvertor_14_50;
import org.hl7.fhir.convertors.VersionConvertor_30_50;
import org.hl7.fhir.convertors.VersionConvertor_40_50;
import org.hl7.fhir.exceptions.FHIRException;
/**

102
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/ValidationEngine.java
View File

@ -1,7 +1,46 @@
package org.hl7.fhir.validation;
import java.io.BufferedOutputStream;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.FilenameFilter;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.io.PrintWriter;
import java.net.HttpURLConnection;
import java.net.URISyntaxException;
import java.net.URL;
import java.net.URLConnection;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Locale;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
import java.util.UUID;
import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.convertors.*;
import org.hl7.fhir.convertors.VersionConvertorAdvisor50;
import org.hl7.fhir.convertors.VersionConvertor_10_30;
import org.hl7.fhir.convertors.VersionConvertor_10_40;
import org.hl7.fhir.convertors.VersionConvertor_10_50;
import org.hl7.fhir.convertors.VersionConvertor_14_30;
import org.hl7.fhir.convertors.VersionConvertor_14_40;
import org.hl7.fhir.convertors.VersionConvertor_14_50;
import org.hl7.fhir.convertors.VersionConvertor_30_40;
import org.hl7.fhir.convertors.VersionConvertor_30_50;
import org.hl7.fhir.convertors.VersionConvertor_40_50;
import org.hl7.fhir.convertors.loaders.BaseLoaderR5.NullLoaderKnowledgeProvider;
import org.hl7.fhir.convertors.loaders.R2016MayToR5Loader;
import org.hl7.fhir.convertors.loaders.R2ToR5Loader;
@ -23,50 +62,57 @@ import org.hl7.fhir.r5.formats.FormatUtilities;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.formats.XmlParser;
import org.hl7.fhir.r5.model.*;
import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.Bundle;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.Constants;
import org.hl7.fhir.r5.model.DomainResource;
import org.hl7.fhir.r5.model.FhirPublication;
import org.hl7.fhir.r5.model.ImplementationGuide;
import org.hl7.fhir.r5.model.ImplementationGuide.ImplementationGuideGlobalComponent;
import org.hl7.fhir.r5.model.OperationOutcome;
import org.hl7.fhir.r5.model.OperationOutcome.OperationOutcomeIssueComponent;
import org.hl7.fhir.r5.model.Parameters;
import org.hl7.fhir.r5.model.Reference;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.model.StructureMap;
import org.hl7.fhir.r5.renderers.RendererFactory;
import org.hl7.fhir.r5.renderers.utils.RenderingContext;
import org.hl7.fhir.r5.renderers.utils.RenderingContext.ResourceRendererMode;
import org.hl7.fhir.r5.terminologies.ConceptMapEngine;
import org.hl7.fhir.r5.utils.*;
import org.hl7.fhir.r5.utils.IResourceValidator.*;
import org.hl7.fhir.r5.utils.EOperationOutcome;
import org.hl7.fhir.r5.utils.FHIRPathEngine;
import org.hl7.fhir.r5.utils.IResourceValidator.BestPracticeWarningLevel;
import org.hl7.fhir.r5.utils.IResourceValidator.BundleValidationRule;
import org.hl7.fhir.r5.utils.IResourceValidator.CheckDisplayOption;
import org.hl7.fhir.r5.utils.IResourceValidator.IValidatorResourceFetcher;
import org.hl7.fhir.r5.utils.IResourceValidator.IdStatus;
import org.hl7.fhir.r5.utils.IResourceValidator.ReferenceValidationPolicy;
import org.hl7.fhir.r5.utils.OperationOutcomeUtilities;
import org.hl7.fhir.r5.utils.StructureMapUtilities;
import org.hl7.fhir.r5.utils.StructureMapUtilities.ITransformerServices;
import org.hl7.fhir.utilities.i18n.I18nConstants;
import org.hl7.fhir.utilities.npm.BasePackageCacheManager;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.utilities.npm.PackageClient;
import org.hl7.fhir.utilities.npm.ToolsVersion;
import org.hl7.fhir.validation.BaseValidator.ValidationControl;
import org.hl7.fhir.validation.Validator.QuestionnaireMode;
import org.hl7.fhir.validation.cli.services.StandAloneValidatorFetcher.IPackageInstaller;
import org.hl7.fhir.validation.instance.InstanceValidator;
import org.hl7.fhir.r5.utils.ToolingExtensions;
import org.hl7.fhir.utilities.IniFile;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.TimeTracker;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.i18n.I18nBase;
import org.hl7.fhir.utilities.i18n.I18nConstants;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.utilities.npm.ToolsVersion;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
import org.hl7.fhir.utilities.validation.ValidationMessage.Source;
import org.hl7.fhir.utilities.xhtml.XhtmlComposer;
import org.hl7.fhir.validation.BaseValidator.ValidationControl;
import org.hl7.fhir.validation.Validator.QuestionnaireMode;
import org.hl7.fhir.validation.cli.services.StandAloneValidatorFetcher.IPackageInstaller;
import org.hl7.fhir.validation.instance.InstanceValidator;
import org.xml.sax.SAXException;
import java.io.*;
import java.net.HttpURLConnection;
import java.net.URISyntaxException;
import java.net.URL;
import java.net.URLConnection;
import java.util.*;
import java.util.Map.Entry;
import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream;
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
@ -354,6 +400,7 @@ public class ValidationEngine implements IValidatorResourceFetcher, IPackageInst
public ValidationEngine() throws IOException {
pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
context = SimpleWorkerContext.fromNothing();
initContext(null);
}
public String setTerminologyServer(String src, String log, FhirPublication version) throws FHIRException, URISyntaxException {
@ -436,6 +483,11 @@ public class ValidationEngine implements IValidatorResourceFetcher, IPackageInst
context = SimpleWorkerContext.fromDefinitions(source, loaderForVersion(), new PackageVersion(src));
grabNatives(source, "http://hl7.org/fhir");
}
initContext(tt);
}
public void initContext(TimeTracker tt) throws IOException, FileNotFoundException {
context.setCanNoTS(true);
context.setCacheId(UUID.randomUUID().toString());
context.setAllowLoadingDuplicates(true); // because of Forge
context.setExpansionProfile(makeExpProfile());

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

@ -68,10 +68,12 @@ import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.validation.ValidationEngine.VersionSourceInformation;
import org.hl7.fhir.validation.cli.ValidatorGui;
import org.hl7.fhir.validation.cli.model.CliContext;
import org.hl7.fhir.validation.cli.services.ComparisonService;
import org.hl7.fhir.validation.cli.services.ValidationService;
import org.hl7.fhir.validation.cli.model.CliContext;
import org.hl7.fhir.validation.cli.utils.*;
import org.hl7.fhir.validation.cli.utils.Common;
import org.hl7.fhir.validation.cli.utils.Display;
import org.hl7.fhir.validation.cli.utils.Params;
/**
* A executable class that will validate one or more FHIR resources against

9
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/VersionUtil.java
View File

@ -1,5 +1,8 @@
package org.hl7.fhir.validation;
import static org.apache.commons.lang3.StringUtils.defaultIfBlank;
import static org.apache.commons.lang3.StringUtils.left;
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
@ -31,19 +34,13 @@ package org.hl7.fhir.validation;
import java.io.InputStream;
import java.text.SimpleDateFormat;
import java.time.Duration;
import java.time.Instant;
import java.time.OffsetDateTime;
import java.util.Date;
import java.util.Properties;
import org.hl7.fhir.r5.model.InstantType;
import org.hl7.fhir.utilities.Utilities;
import static org.apache.commons.lang3.StringUtils.defaultIfBlank;
import static org.apache.commons.lang3.StringUtils.left;
/**
* Used internally by HAPI to log the version of the HAPI FHIR framework
* once, when the framework is first loaded by the classloader.

5
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/RestEndpoints.java
View File

@ -1,12 +1,13 @@
package org.hl7.fhir.validation.cli;
import io.javalin.Javalin;
import org.hl7.fhir.validation.ValidationEngine;
import org.hl7.fhir.validation.cli.controller.CliContextController;
import org.hl7.fhir.validation.cli.controller.ValidationController;
import org.hl7.fhir.validation.cli.controller.UIController;
import org.hl7.fhir.validation.cli.controller.ValidationController;
import org.hl7.fhir.validation.cli.model.CliContext;
import io.javalin.Javalin;
public class RestEndpoints {
public UIController myUIController;

9
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/ValidatorGui.java
View File

@ -1,15 +1,14 @@
package org.hl7.fhir.validation.cli;
import io.javalin.Javalin;
import java.awt.Desktop;
import java.net.URI;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.validation.ValidationEngine;
import org.hl7.fhir.validation.cli.model.CliContext;
import org.hl7.fhir.validation.cli.utils.Common;
import java.awt.*;
import java.io.IOException;
import java.net.URI;
import java.net.URISyntaxException;
import io.javalin.Javalin;
public class ValidatorGui {

8
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/controller/CliContextController.java
View File

@ -1,12 +1,14 @@
package org.hl7.fhir.validation.cli.controller;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import io.javalin.http.Context;
import org.apache.http.HttpStatus;
import org.hl7.fhir.validation.cli.model.CliContext;
import org.jetbrains.annotations.NotNull;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import io.javalin.http.Context;
public class CliContextController {
private final String JSON_MIME_TYPE = "application/json";

7
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/controller/ValidationController.java
View File

@ -1,14 +1,15 @@
package org.hl7.fhir.validation.cli.controller;
import com.fasterxml.jackson.databind.ObjectMapper;
import io.javalin.http.Context;
import io.javalin.http.Handler;
import org.apache.http.HttpStatus;
import org.hl7.fhir.validation.ValidationEngine;
import org.hl7.fhir.validation.cli.model.ValidationRequest;
import org.hl7.fhir.validation.cli.model.ValidationResponse;
import org.hl7.fhir.validation.cli.services.ValidationService;
import com.fasterxml.jackson.databind.ObjectMapper;
import io.javalin.http.Context;
public class ValidationController {
private ValidationEngine myValidationEngine;

9
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/model/CliContext.java
View File

@ -1,11 +1,16 @@
package org.hl7.fhir.validation.cli.model;
import com.fasterxml.jackson.annotation.JsonProperty;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Locale;
import java.util.Map;
import java.util.Objects;
import org.hl7.fhir.r5.utils.IResourceValidator.BundleValidationRule;
import org.hl7.fhir.validation.Validator;
import java.util.*;
import com.fasterxml.jackson.annotation.JsonProperty;
/**
* A POJO for storing the flags/values for the CLI validator.

1
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/model/FileInfo.java
View File

@ -1,7 +1,6 @@
package org.hl7.fhir.validation.cli.model;
import com.fasterxml.jackson.annotation.JsonProperty;
import org.hl7.fhir.r5.elementmodel.Manager;
public class FileInfo {

7
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/model/ValidationOutcome.java
View File

@ -1,11 +1,12 @@
package org.hl7.fhir.validation.cli.model;
import com.fasterxml.jackson.annotation.JsonProperty;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import java.util.ArrayList;
import java.util.List;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import com.fasterxml.jackson.annotation.JsonProperty;
public class ValidationOutcome {
@JsonProperty("fileInfo")

4
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/model/ValidationRequest.java
View File

@ -1,10 +1,10 @@
package org.hl7.fhir.validation.cli.model;
import com.fasterxml.jackson.annotation.JsonProperty;
import java.util.ArrayList;
import java.util.List;
import com.fasterxml.jackson.annotation.JsonProperty;
public class ValidationRequest {
@JsonProperty("cliContext")

4
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/model/ValidationResponse.java
View File

@ -1,10 +1,10 @@
package org.hl7.fhir.validation.cli.model;
import com.fasterxml.jackson.annotation.JsonProperty;
import java.util.ArrayList;
import java.util.List;
import com.fasterxml.jackson.annotation.JsonProperty;
public class ValidationResponse {
@JsonProperty("outcomes")

16
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/services/ComparisonService.java
View File

@ -1,27 +1,19 @@
package org.hl7.fhir.validation.cli.services;
import java.awt.Desktop;
import java.io.File;
import java.io.IOException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.conformance.CapabilityStatementUtilities;
import org.hl7.fhir.r5.formats.IParser;
import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.formats.XmlParser;
import org.hl7.fhir.r5.model.CanonicalResource;
import org.hl7.fhir.r5.model.CapabilityStatement;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.utils.EOperationOutcome;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.validation.ValidationEngine;
import org.hl7.fhir.validation.cli.utils.Params;
import java.awt.*;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.util.UUID;
public class ComparisonService {
public static void doLeftRightComparison(String[] args, String dest, ValidationEngine validator) throws IOException, FHIRException, EOperationOutcome {

1
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/services/StandAloneValidatorFetcher.java
View File

@ -17,7 +17,6 @@ import org.hl7.fhir.utilities.VersionUtilities.VersionURLInfo;
import org.hl7.fhir.utilities.npm.BasePackageCacheManager;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.validation.cli.services.StandAloneValidatorFetcher.IPackageInstaller;
public class StandAloneValidatorFetcher implements IValidatorResourceFetcher {

28
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/services/ValidationService.java
View File

@ -1,11 +1,24 @@
package org.hl7.fhir.validation.cli.services;
import java.io.File;
import java.io.FileOutputStream;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import org.hl7.fhir.r5.context.TerminologyCache;
import org.hl7.fhir.r5.elementmodel.Manager;
import org.hl7.fhir.r5.formats.IParser;
import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.formats.XmlParser;
import org.hl7.fhir.r5.model.*;
import org.hl7.fhir.r5.model.Bundle;
import org.hl7.fhir.r5.model.DomainResource;
import org.hl7.fhir.r5.model.FhirPublication;
import org.hl7.fhir.r5.model.ImplementationGuide;
import org.hl7.fhir.r5.model.OperationOutcome;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionKind;
import org.hl7.fhir.r5.utils.ToolingExtensions;
import org.hl7.fhir.utilities.TextFile;
@ -14,14 +27,11 @@ import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.validation.ValidationEngine;
import org.hl7.fhir.validation.ValidationEngine.VersionSourceInformation;
import org.hl7.fhir.validation.cli.model.*;
import java.io.File;
import java.io.FileOutputStream;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import org.hl7.fhir.validation.cli.model.CliContext;
import org.hl7.fhir.validation.cli.model.FileInfo;
import org.hl7.fhir.validation.cli.model.ValidationOutcome;
import org.hl7.fhir.validation.cli.model.ValidationRequest;
import org.hl7.fhir.validation.cli.model.ValidationResponse;
public class ValidationService {

4
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/utils/Display.java
View File

@ -1,12 +1,12 @@
package org.hl7.fhir.validation.cli.utils;
import java.io.IOException;
import org.hl7.fhir.r5.model.Constants;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.ToolsVersion;
import java.io.IOException;
/**
* Class for displaying output to the cli user.
*

8
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/utils/Params.java
View File

@ -1,14 +1,14 @@
package org.hl7.fhir.validation.cli.utils;
import java.io.File;
import java.util.Arrays;
import java.util.Locale;
import org.hl7.fhir.r5.utils.IResourceValidator.BundleValidationRule;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.validation.Validator;
import org.hl7.fhir.validation.cli.model.CliContext;
import java.io.File;
import java.util.Arrays;
import java.util.Locale;
public class Params {
public static final String GUI = "-gui";

25
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/EnableWhenEvaluator.java
View File

@ -27,17 +27,26 @@ package org.hl7.fhir.validation.instance;
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
import java.util.*;
import java.util.stream.*;
*/
import java.util.ArrayList;
import java.util.List;
import java.util.stream.Collectors;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.elementmodel.Element;
import org.hl7.fhir.r5.model.*;
import org.hl7.fhir.r5.model.MeasureReport.MeasureReportGroupComponent;
import org.hl7.fhir.r5.model.Questionnaire.*;
import org.hl7.fhir.r5.model.BooleanType;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.DataType;
import org.hl7.fhir.r5.model.Expression;
import org.hl7.fhir.r5.model.ExpressionNode;
import org.hl7.fhir.r5.model.Factory;
import org.hl7.fhir.r5.model.PrimitiveType;
import org.hl7.fhir.r5.model.Quantity;
import org.hl7.fhir.r5.model.Questionnaire;
import org.hl7.fhir.r5.model.Questionnaire.EnableWhenBehavior;
import org.hl7.fhir.r5.model.Questionnaire.QuestionnaireItemComponent;
import org.hl7.fhir.r5.model.Questionnaire.QuestionnaireItemEnableWhenComponent;
import org.hl7.fhir.r5.model.Questionnaire.QuestionnaireItemOperator;
import org.hl7.fhir.r5.utils.FHIRPathEngine;
import org.hl7.fhir.validation.instance.utils.ValidatorHostContext;

490
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java
View File

@ -37,10 +37,8 @@ import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.nio.charset.Charset;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.Base64;
import java.util.Calendar;
import java.util.Collection;
import java.util.HashMap;
@ -51,15 +49,10 @@ import java.util.Set;
import java.util.UUID;
import org.apache.commons.codec.binary.Base64InputStream;
import org.apache.commons.io.Charsets;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.NotImplementedException;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.r5.model.Reference;
import org.hl7.fhir.convertors.*;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.exceptions.PathEngineException;
import org.hl7.fhir.exceptions.TerminologyServiceException;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
@ -86,6 +79,7 @@ import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.r5.model.CodeableConcept;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.ContactPoint;
import org.hl7.fhir.r5.model.DataType;
import org.hl7.fhir.r5.model.DateTimeType;
import org.hl7.fhir.r5.model.DateType;
import org.hl7.fhir.r5.model.DecimalType;
@ -114,6 +108,7 @@ import org.hl7.fhir.r5.model.PrimitiveType;
import org.hl7.fhir.r5.model.Quantity;
import org.hl7.fhir.r5.model.Range;
import org.hl7.fhir.r5.model.Ratio;
import org.hl7.fhir.r5.model.Reference;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.SampledData;
import org.hl7.fhir.r5.model.SearchParameter;
@ -127,18 +122,30 @@ import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionSnapshotComp
import org.hl7.fhir.r5.model.StructureDefinition.TypeDerivationRule;
import org.hl7.fhir.r5.model.TimeType;
import org.hl7.fhir.r5.model.Timing;
import org.hl7.fhir.r5.model.DataType;
import org.hl7.fhir.r5.model.TypeDetails;
import org.hl7.fhir.r5.model.UriType;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionContainsComponent;
import org.hl7.fhir.r5.terminologies.ValueSetExpander.TerminologyServiceErrorClass;
import org.hl7.fhir.r5.utils.FHIRLexer.FHIRLexerException;
import org.hl7.fhir.r5.utils.FHIRPathEngine;
import org.hl7.fhir.r5.utils.FHIRPathEngine.IEvaluationContext;
import org.hl7.fhir.r5.utils.IResourceValidator;
import org.hl7.fhir.r5.utils.ToolingExtensions;
import org.hl7.fhir.r5.utils.XVerExtensionManager;
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.Utilities.DecimalStatus;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.VersionUtilities.VersionURLInfo;
import org.hl7.fhir.utilities.i18n.I18nConstants;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
import org.hl7.fhir.utilities.validation.ValidationMessage.Source;
import org.hl7.fhir.utilities.validation.ValidationOptions;
import org.hl7.fhir.utilities.xhtml.NodeType;
import org.hl7.fhir.utilities.xhtml.XhtmlNode;
import org.hl7.fhir.validation.BaseValidator;
import org.hl7.fhir.validation.Validator.QuestionnaireMode;
import org.hl7.fhir.validation.instance.type.BundleValidator;
@ -148,19 +155,13 @@ import org.hl7.fhir.validation.instance.type.QuestionnaireValidator;
import org.hl7.fhir.validation.instance.type.SearchParameterValidator;
import org.hl7.fhir.validation.instance.type.StructureDefinitionValidator;
import org.hl7.fhir.validation.instance.type.ValueSetValidator;
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.Utilities.DecimalStatus;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.VersionUtilities.VersionURLInfo;
import org.hl7.fhir.utilities.validation.ValidationOptions;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
import org.hl7.fhir.utilities.validation.ValidationMessage.Source;
import org.hl7.fhir.utilities.xhtml.NodeType;
import org.hl7.fhir.utilities.xhtml.XhtmlNode;
import org.hl7.fhir.validation.instance.utils.*;
import org.hl7.fhir.validation.instance.utils.ChildIterator;
import org.hl7.fhir.validation.instance.utils.ElementInfo;
import org.hl7.fhir.validation.instance.utils.IndexedElement;
import org.hl7.fhir.validation.instance.utils.NodeStack;
import org.hl7.fhir.validation.instance.utils.ResolvedReference;
import org.hl7.fhir.validation.instance.utils.ResourceValidationTracker;
import org.hl7.fhir.validation.instance.utils.ValidatorHostContext;
import org.w3c.dom.Document;
import com.google.gson.Gson;
@ -343,6 +344,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
private String validationLanguage;
private boolean baseOnly;
private boolean noCheckAggregation;
private boolean wantCheckSnapshotUnchanged;
private List<ImplementationGuide> igs = new ArrayList<>();
private List<String> extensionDomains = new ArrayList<String>();
@ -1004,7 +1006,13 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
ValidationResult vr = checkCodeOnServer(stack, valueset, cc, true); // we're going to validate the codings directly, so only check the valueset
if (!vr.isOk()) {
bindingsOk = false;
if (vr.getErrorClass() != null && vr.getErrorClass().isInfrastructure()) {
if (vr.getErrorClass() != null && vr.getErrorClass() == TerminologyServiceErrorClass.NOSERVICE) {
if (binding.getStrength() == BindingStrength.REQUIRED || (binding.getStrength() == BindingStrength.EXTENSIBLE && binding.hasExtension("http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet"))) {
hint(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_NOSVC_BOUND_REQ, describeReference(binding.getValueSet()));
} else if (binding.getStrength() == BindingStrength.EXTENSIBLE) {
hint(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_NOSVC_BOUND_EXT, describeReference(binding.getValueSet()));
}
} else if (vr.getErrorClass() != null && vr.getErrorClass().isInfrastructure()) {
if (binding.getStrength() == BindingStrength.REQUIRED)
txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_CONFIRM_1, describeReference(binding.getValueSet()), vr.getErrorClass().toString());
else if (binding.getStrength() == BindingStrength.EXTENSIBLE) {
@ -3860,7 +3868,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
} else if (element.getType().equals("SearchParameter")) {
new SearchParameterValidator(context, timeTracker, fpe).validateSearchParameter(errors, element, stack);
} else if (element.getType().equals("StructureDefinition")) {
new StructureDefinitionValidator(context, timeTracker, fpe).validateStructureDefinition(errors, element, stack);
new StructureDefinitionValidator(context, timeTracker, fpe, wantCheckSnapshotUnchanged).validateStructureDefinition(errors, element, stack);
} else if (element.getType().equals("ValueSet")) {
new ValueSetValidator(context, timeTracker, this).validateValueSet(errors, element, stack);
}
@ -4128,236 +4136,252 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
Element resource, Element element, String actualType, NodeStack stack, boolean inCodeableConcept, boolean checkDisplayInContext, ElementInfo ei, String extensionUrl)
throws FHIRException, DefinitionException {
List<String> profiles = new ArrayList<String>();
if (ei.definition != null) {
String type = null;
ElementDefinition typeDefn = null;
checkMustSupport(profile, ei);
checkChildByDefinition(hostContext, errors, profile, definition, resource, element, actualType, stack, inCodeableConcept, checkDisplayInContext, ei,
extensionUrl, ei.definition, false);
}
if (ei.slice != null) {
checkChildByDefinition(hostContext, errors, profile, definition, resource, element, actualType, stack, inCodeableConcept, checkDisplayInContext, ei,
extensionUrl, ei.slice, true);
}
}
if (ei.definition.getType().size() == 1 && !"*".equals(ei.definition.getType().get(0).getWorkingCode()) && !"Element".equals(ei.definition.getType().get(0).getWorkingCode())
&& !"BackboneElement".equals(ei.definition.getType().get(0).getWorkingCode())) {
type = ei.definition.getType().get(0).getWorkingCode();
String stype = ei.getElement().fhirType();
if (ei.definition.isChoice() && !stype.equals(type)) {
if ("Extension".equals(profile.getType())) {
// error will be raised elsewhere
} else {
rule(errors, IssueType.STRUCTURE, element.line(), element.col(), ei.getPath(), false, I18nConstants.EXTENSION_PROF_TYPE, profile.getUrl(), type, stype);
}
}
//
// Excluding reference is a kludge to get around versioning issues
if (ei.definition.getType().get(0).hasProfile()) {
for (CanonicalType p : ei.definition.getType().get(0).getProfile()) {
profiles.add(p.getValue());
}
}
} else if (ei.definition.getType().size() == 1 && "*".equals(ei.definition.getType().get(0).getWorkingCode())) {
String prefix = tail(ei.definition.getPath());
assert prefix.endsWith("[x]");
type = ei.getName().substring(prefix.length() - 3);
if (isPrimitiveType(type))
type = Utilities.uncapitalize(type);
if (ei.definition.getType().get(0).hasProfile()) {
for (CanonicalType p : ei.definition.getType().get(0).getProfile()) {
profiles.add(p.getValue());
}
}
} else if (ei.definition.getType().size() > 1) {
public void checkChildByDefinition(ValidatorHostContext hostContext, List<ValidationMessage> errors, StructureDefinition profile,
ElementDefinition definition, Element resource, Element element, String actualType, NodeStack stack, boolean inCodeableConcept,
boolean checkDisplayInContext, ElementInfo ei, String extensionUrl, ElementDefinition checkDefn, boolean isSlice) {
List<String> profiles = new ArrayList<String>();
String type = null;
ElementDefinition typeDefn = null;
checkMustSupport(profile, ei);
String prefix = tail(ei.definition.getPath());
assert typesAreAllReference(ei.definition.getType()) || ei.definition.hasRepresentation(PropertyRepresentation.TYPEATTR) || prefix.endsWith("[x]") : prefix;
if (ei.definition.hasRepresentation(PropertyRepresentation.TYPEATTR))
type = ei.getElement().getType();
else {
prefix = prefix.substring(0, prefix.length() - 3);
for (TypeRefComponent t : ei.definition.getType())
if ((prefix + Utilities.capitalize(t.getWorkingCode())).equals(ei.getName())) {
type = t.getWorkingCode();
// Excluding reference is a kludge to get around versioning issues
if (t.hasProfile() && !type.equals("Reference"))
profiles.add(t.getProfile().get(0).getValue());
}
}
if (type == null) {
TypeRefComponent trc = ei.definition.getType().get(0);
if (trc.getWorkingCode().equals("Reference"))
type = "Reference";
else
rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), stack.getLiteralPath(), false, I18nConstants.VALIDATION_VAL_PROFILE_NOTYPE, ei.getName(), describeTypes(ei.definition.getType()));
}
} else if (ei.definition.getContentReference() != null) {
typeDefn = resolveNameReference(profile.getSnapshot(), ei.definition.getContentReference());
} else if (ei.definition.getType().size() == 1 && ("Element".equals(ei.definition.getType().get(0).getWorkingCode()) || "BackboneElement".equals(ei.definition.getType().get(0).getWorkingCode()))) {
if (ei.definition.getType().get(0).hasProfile()) {
CanonicalType pu = ei.definition.getType().get(0).getProfile().get(0);
if (pu.hasExtension(ToolingExtensions.EXT_PROFILE_ELEMENT))
profiles.add(pu.getValue() + "#" + pu.getExtensionString(ToolingExtensions.EXT_PROFILE_ELEMENT));
else
profiles.add(pu.getValue());
if (checkDefn.getType().size() == 1 && !"*".equals(checkDefn.getType().get(0).getWorkingCode()) && !"Element".equals(checkDefn.getType().get(0).getWorkingCode())
&& !"BackboneElement".equals(checkDefn.getType().get(0).getWorkingCode())) {
type = checkDefn.getType().get(0).getWorkingCode();
String stype = ei.getElement().fhirType();
if (checkDefn.isChoice() && !stype.equals(type)) {
if ("Extension".equals(profile.getType())) {
// error will be raised elsewhere
} else {
rule(errors, IssueType.STRUCTURE, element.line(), element.col(), ei.getPath(), false, I18nConstants.EXTENSION_PROF_TYPE, profile.getUrl(), type, stype);
}
}
if (type != null) {
if (type.startsWith("@")) {
ei.definition = findElement(profile, type.substring(1));
type = null;
//
// Excluding reference is a kludge to get around versioning issues
if (checkDefn.getType().get(0).hasProfile()) {
for (CanonicalType p : checkDefn.getType().get(0).getProfile()) {
profiles.add(p.getValue());
}
}
NodeStack localStack = stack.push(ei.getElement(), ei.count, ei.definition, type == null ? typeDefn : resolveType(type, ei.definition.getType()));
} else if (checkDefn.getType().size() == 1 && "*".equals(checkDefn.getType().get(0).getWorkingCode())) {
String prefix = tail(checkDefn.getPath());
assert prefix.endsWith("[x]");
type = ei.getName().substring(prefix.length() - 3);
if (isPrimitiveType(type))
type = Utilities.uncapitalize(type);
if (checkDefn.getType().get(0).hasProfile()) {
for (CanonicalType p : checkDefn.getType().get(0).getProfile()) {
profiles.add(p.getValue());
}
}
} else if (checkDefn.getType().size() > 1) {
String prefix = tail(checkDefn.getPath());
assert typesAreAllReference(checkDefn.getType()) || checkDefn.hasRepresentation(PropertyRepresentation.TYPEATTR) || prefix.endsWith("[x]") : prefix;
if (checkDefn.hasRepresentation(PropertyRepresentation.TYPEATTR))
type = ei.getElement().getType();
else {
prefix = prefix.substring(0, prefix.length() - 3);
for (TypeRefComponent t : checkDefn.getType())
if ((prefix + Utilities.capitalize(t.getWorkingCode())).equals(ei.getName())) {
type = t.getWorkingCode();
// Excluding reference is a kludge to get around versioning issues
if (t.hasProfile() && !type.equals("Reference"))
profiles.add(t.getProfile().get(0).getValue());
}
}
if (type == null) {
TypeRefComponent trc = checkDefn.getType().get(0);
if (trc.getWorkingCode().equals("Reference"))
type = "Reference";
else
rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), stack.getLiteralPath(), false, I18nConstants.VALIDATION_VAL_PROFILE_NOTYPE, ei.getName(), describeTypes(checkDefn.getType()));
}
} else if (checkDefn.getContentReference() != null) {
typeDefn = resolveNameReference(profile.getSnapshot(), checkDefn.getContentReference());
} else if (checkDefn.getType().size() == 1 && ("Element".equals(checkDefn.getType().get(0).getWorkingCode()) || "BackboneElement".equals(checkDefn.getType().get(0).getWorkingCode()))) {
if (checkDefn.getType().get(0).hasProfile()) {
CanonicalType pu = checkDefn.getType().get(0).getProfile().get(0);
if (pu.hasExtension(ToolingExtensions.EXT_PROFILE_ELEMENT))
profiles.add(pu.getValue() + "#" + pu.getExtensionString(ToolingExtensions.EXT_PROFILE_ELEMENT));
else
profiles.add(pu.getValue());
}
}
if (type != null) {
if (type.startsWith("@")) {
checkDefn = findElement(profile, type.substring(1));
if (isSlice) {
ei.slice = ei.definition;
} else {
ei.definition = ei.definition;
}
type = null;
}
}
NodeStack localStack = stack.push(ei.getElement(), ei.count, checkDefn, type == null ? typeDefn : resolveType(type, checkDefn.getType()));
// if (debug) {
// System.out.println(" check " + localStack.getLiteralPath()+" against "+ei.getDefinition().getId()+" in profile "+profile.getUrl());
// }
String localStackLiterapPath = localStack.getLiteralPath();
String eiPath = ei.getPath();
assert (eiPath.equals(localStackLiterapPath)) : "ei.path: " + ei.getPath() + " - localStack.getLiteralPath: " + localStackLiterapPath;
boolean thisIsCodeableConcept = false;
String thisExtension = null;
boolean checkDisplay = true;
String localStackLiterapPath = localStack.getLiteralPath();
String eiPath = ei.getPath();
assert (eiPath.equals(localStackLiterapPath)) : "ei.path: " + ei.getPath() + " - localStack.getLiteralPath: " + localStackLiterapPath;
boolean thisIsCodeableConcept = false;
String thisExtension = null;
boolean checkDisplay = true;
checkInvariants(hostContext, errors, profile, typeDefn != null ? typeDefn : ei.definition, resource, ei.getElement(), localStack, true);
checkInvariants(hostContext, errors, profile, typeDefn != null ? typeDefn : checkDefn, resource, ei.getElement(), localStack, true);
ei.getElement().markValidation(profile, ei.definition);
boolean elementValidated = false;
if (type != null) {
if (isPrimitiveType(type)) {
checkPrimitive(hostContext, errors, ei.getPath(), type, ei.definition, ei.getElement(), profile, stack);
} else {
if (ei.definition.hasFixed()) {
checkFixedValue(errors, ei.getPath(), ei.getElement(), ei.definition.getFixed(), profile.getUrl(), ei.definition.getSliceName(), null);
}
if (ei.definition.hasPattern()) {
checkFixedValue(errors, ei.getPath(), ei.getElement(), ei.definition.getPattern(), profile.getUrl(), ei.definition.getSliceName(), null, true);
}
}
if (type.equals("Identifier")) {
checkIdentifier(errors, ei.getPath(), ei.getElement(), ei.definition);
} else if (type.equals("Coding")) {
checkCoding(errors, ei.getPath(), ei.getElement(), profile, ei.definition, inCodeableConcept, checkDisplayInContext, stack);
} else if (type.equals("Quantity")) {
checkQuantity(errors, ei.getPath(), ei.getElement(), profile, ei.definition, stack);
} else if (type.equals("Attachment")) {
checkAttachment(errors, ei.getPath(), ei.getElement(), profile, ei.definition, inCodeableConcept, checkDisplayInContext, stack);
} else if (type.equals("CodeableConcept")) {
checkDisplay = checkCodeableConcept(errors, ei.getPath(), ei.getElement(), profile, ei.definition, stack);
thisIsCodeableConcept = true;
} else if (type.equals("Reference")) {
checkReference(hostContext, errors, ei.getPath(), ei.getElement(), profile, ei.definition, actualType, localStack);
// We only check extensions if we're not in a complex extension or if the element we're dealing with is not defined as part of that complex extension
} else if (type.equals("Extension")) {
Element eurl = ei.getElement().getNamedChild("url");
if (rule(errors, IssueType.INVALID, ei.getPath(), eurl != null, I18nConstants.EXTENSION_EXT_URL_NOTFOUND)) {
String url = eurl.primitiveValue();
thisExtension = url;
if (rule(errors, IssueType.INVALID, ei.getPath(), !Utilities.noString(url), I18nConstants.EXTENSION_EXT_URL_NOTFOUND)) {
if (rule(errors, IssueType.INVALID, ei.getPath(), (extensionUrl != null) || Utilities.isAbsoluteUrl(url), I18nConstants.EXTENSION_EXT_URL_ABSOLUTE)) {
checkExtension(hostContext, errors, ei.getPath(), resource, element, ei.getElement(), ei.definition, profile, localStack, stack, extensionUrl);
}
}
}
} else if (type.equals("Resource") || isResource(type)) {
validateContains(hostContext, errors, ei.getPath(), ei.definition, definition, resource, ei.getElement(), localStack, idStatusForEntry(element, ei)); // if
elementValidated = true;
// (str.matches(".*([.,/])work\\1$"))
} else if (Utilities.isAbsoluteUrl(type)) {
StructureDefinition defn = context.fetchTypeDefinition(type);
if (defn != null && hasMapping("http://hl7.org/fhir/terminology-pattern", defn, defn.getSnapshot().getElementFirstRep())) {
List<String> txtype = getMapping("http://hl7.org/fhir/terminology-pattern", defn, defn.getSnapshot().getElementFirstRep());
if (txtype.contains("CodeableConcept")) {
checkTerminologyCodeableConcept(errors, ei.getPath(), ei.getElement(), profile, ei.definition, stack, defn);
thisIsCodeableConcept = true;
} else if (txtype.contains("Coding")) {
checkTerminologyCoding(errors, ei.getPath(), ei.getElement(), profile, ei.definition, inCodeableConcept, checkDisplayInContext, stack, defn);
}
}
}
ei.getElement().markValidation(profile, checkDefn);
boolean elementValidated = false;
if (type != null) {
if (isPrimitiveType(type)) {
checkPrimitive(hostContext, errors, ei.getPath(), type, checkDefn, ei.getElement(), profile, stack);
} else {
if (rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), stack.getLiteralPath(), ei.definition != null, I18nConstants.VALIDATION_VAL_CONTENT_UNKNOWN, ei.getName()))
validateElement(hostContext, errors, profile, ei.definition, null, null, resource, ei.getElement(), type, localStack, false, true, null);
}
StructureDefinition p = null;
String tail = null;
if (profiles.isEmpty()) {
if (type != null) {
p = getProfileForType(type, ei.definition.getType());
// If dealing with a primitive type, then we need to check the current child against
// the invariants (constraints) on the current element, because otherwise it only gets
// checked against the primary type's invariants: LLoyd
//if (p.getKind() == StructureDefinitionKind.PRIMITIVETYPE) {
// checkInvariants(hostContext, errors, ei.path, profile, ei.definition, null, null, resource, ei.element);
//}
rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.getPath(), p != null, I18nConstants.VALIDATION_VAL_NOTYPE, type);
if (checkDefn.hasFixed()) {
checkFixedValue(errors, ei.getPath(), ei.getElement(), checkDefn.getFixed(), profile.getUrl(), checkDefn.getSliceName(), null);
}
} else if (profiles.size() == 1) {
String url = profiles.get(0);
if (checkDefn.hasPattern()) {
checkFixedValue(errors, ei.getPath(), ei.getElement(), checkDefn.getPattern(), profile.getUrl(), checkDefn.getSliceName(), null, true);
}
}
if (type.equals("Identifier")) {
checkIdentifier(errors, ei.getPath(), ei.getElement(), checkDefn);
} else if (type.equals("Coding")) {
checkCoding(errors, ei.getPath(), ei.getElement(), profile, checkDefn, inCodeableConcept, checkDisplayInContext, stack);
} else if (type.equals("Quantity")) {
checkQuantity(errors, ei.getPath(), ei.getElement(), profile, checkDefn, stack);
} else if (type.equals("Attachment")) {
checkAttachment(errors, ei.getPath(), ei.getElement(), profile, checkDefn, inCodeableConcept, checkDisplayInContext, stack);
} else if (type.equals("CodeableConcept")) {
checkDisplay = checkCodeableConcept(errors, ei.getPath(), ei.getElement(), profile, checkDefn, stack);
thisIsCodeableConcept = true;
} else if (type.equals("Reference")) {
checkReference(hostContext, errors, ei.getPath(), ei.getElement(), profile, checkDefn, actualType, localStack);
// We only check extensions if we're not in a complex extension or if the element we're dealing with is not defined as part of that complex extension
} else if (type.equals("Extension")) {
Element eurl = ei.getElement().getNamedChild("url");
if (rule(errors, IssueType.INVALID, ei.getPath(), eurl != null, I18nConstants.EXTENSION_EXT_URL_NOTFOUND)) {
String url = eurl.primitiveValue();
thisExtension = url;
if (rule(errors, IssueType.INVALID, ei.getPath(), !Utilities.noString(url), I18nConstants.EXTENSION_EXT_URL_NOTFOUND)) {
if (rule(errors, IssueType.INVALID, ei.getPath(), (extensionUrl != null) || Utilities.isAbsoluteUrl(url), I18nConstants.EXTENSION_EXT_URL_ABSOLUTE)) {
checkExtension(hostContext, errors, ei.getPath(), resource, element, ei.getElement(), checkDefn, profile, localStack, stack, extensionUrl);
}
}
}
} else if (type.equals("Resource") || isResource(type)) {
validateContains(hostContext, errors, ei.getPath(), checkDefn, definition, resource, ei.getElement(), localStack, idStatusForEntry(element, ei)); // if
elementValidated = true;
// (str.matches(".*([.,/])work\\1$"))
} else if (Utilities.isAbsoluteUrl(type)) {
StructureDefinition defn = context.fetchTypeDefinition(type);
if (defn != null && hasMapping("http://hl7.org/fhir/terminology-pattern", defn, defn.getSnapshot().getElementFirstRep())) {
List<String> txtype = getMapping("http://hl7.org/fhir/terminology-pattern", defn, defn.getSnapshot().getElementFirstRep());
if (txtype.contains("CodeableConcept")) {
checkTerminologyCodeableConcept(errors, ei.getPath(), ei.getElement(), profile, checkDefn, stack, defn);
thisIsCodeableConcept = true;
} else if (txtype.contains("Coding")) {
checkTerminologyCoding(errors, ei.getPath(), ei.getElement(), profile, checkDefn, inCodeableConcept, checkDisplayInContext, stack, defn);
}
}
}
} else {
if (rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), stack.getLiteralPath(), checkDefn != null, I18nConstants.VALIDATION_VAL_CONTENT_UNKNOWN, ei.getName()))
validateElement(hostContext, errors, profile, checkDefn, null, null, resource, ei.getElement(), type, localStack, false, true, null);
}
StructureDefinition p = null;
String tail = null;
if (profiles.isEmpty()) {
if (type != null) {
p = getProfileForType(type, checkDefn.getType());
// If dealing with a primitive type, then we need to check the current child against
// the invariants (constraints) on the current element, because otherwise it only gets
// checked against the primary type's invariants: LLoyd
//if (p.getKind() == StructureDefinitionKind.PRIMITIVETYPE) {
// checkInvariants(hostContext, errors, ei.path, profile, ei.definition, null, null, resource, ei.element);
//}
rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.getPath(), p != null, I18nConstants.VALIDATION_VAL_NOTYPE, type);
}
} else if (profiles.size() == 1) {
String url = profiles.get(0);
if (url.contains("#")) {
tail = url.substring(url.indexOf("#") + 1);
url = url.substring(0, url.indexOf("#"));
}
p = this.context.fetchResource(StructureDefinition.class, url);
rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.getPath(), p != null, I18nConstants.VALIDATION_VAL_UNKNOWN_PROFILE, profiles.get(0));
} else {
elementValidated = true;
HashMap<String, List<ValidationMessage>> goodProfiles = new HashMap<String, List<ValidationMessage>>();
HashMap<String, List<ValidationMessage>> badProfiles = new HashMap<String, List<ValidationMessage>>();
for (String typeProfile : profiles) {
String url = typeProfile;
tail = null;
if (url.contains("#")) {
tail = url.substring(url.indexOf("#") + 1);
url = url.substring(0, url.indexOf("#"));
}
p = this.context.fetchResource(StructureDefinition.class, url);
rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.getPath(), p != null, I18nConstants.VALIDATION_VAL_UNKNOWN_PROFILE, profiles.get(0));
} else {
elementValidated = true;
HashMap<String, List<ValidationMessage>> goodProfiles = new HashMap<String, List<ValidationMessage>>();
HashMap<String, List<ValidationMessage>> badProfiles = new HashMap<String, List<ValidationMessage>>();
for (String typeProfile : profiles) {
String url = typeProfile;
tail = null;
if (url.contains("#")) {
tail = url.substring(url.indexOf("#") + 1);
url = url.substring(0, url.indexOf("#"));
}
p = this.context.fetchResource(StructureDefinition.class, typeProfile);
if (rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.getPath(), p != null, I18nConstants.VALIDATION_VAL_UNKNOWN_PROFILE, typeProfile)) {
List<ValidationMessage> profileErrors = new ArrayList<ValidationMessage>();
validateElement(hostContext, profileErrors, p, getElementByTail(p, tail), profile, ei.definition, resource, ei.getElement(), type, localStack, thisIsCodeableConcept, checkDisplay, thisExtension);
if (hasErrors(profileErrors))
badProfiles.put(typeProfile, profileErrors);
else
goodProfiles.put(typeProfile, profileErrors);
p = this.context.fetchResource(StructureDefinition.class, typeProfile);
if (rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.getPath(), p != null, I18nConstants.VALIDATION_VAL_UNKNOWN_PROFILE, typeProfile)) {
List<ValidationMessage> profileErrors = new ArrayList<ValidationMessage>();
validateElement(hostContext, profileErrors, p, getElementByTail(p, tail), profile, checkDefn, resource, ei.getElement(), type, localStack, thisIsCodeableConcept, checkDisplay, thisExtension);
if (hasErrors(profileErrors))
badProfiles.put(typeProfile, profileErrors);
else
goodProfiles.put(typeProfile, profileErrors);
}
}
if (goodProfiles.size() == 1) {
errors.addAll(goodProfiles.values().iterator().next());
} else if (goodProfiles.size() == 0) {
rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.getPath(), false, I18nConstants.VALIDATION_VAL_PROFILE_NOMATCH, StringUtils.join("; ", profiles));
for (String m : badProfiles.keySet()) {
p = this.context.fetchResource(StructureDefinition.class, m);
for (ValidationMessage message : badProfiles.get(m)) {
message.setMessage(message.getMessage() + " (validating against " + p.getUrl() + (p.hasVersion() ? "|" + p.getVersion() : "") + " [" + p.getName() + "])");
errors.add(message);
}
}
if (goodProfiles.size() == 1) {
errors.addAll(goodProfiles.values().iterator().next());
} else if (goodProfiles.size() == 0) {
rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.getPath(), false, I18nConstants.VALIDATION_VAL_PROFILE_NOMATCH, StringUtils.join("; ", profiles));
for (String m : badProfiles.keySet()) {
p = this.context.fetchResource(StructureDefinition.class, m);
for (ValidationMessage message : badProfiles.get(m)) {
message.setMessage(message.getMessage() + " (validating against " + p.getUrl() + (p.hasVersion() ? "|" + p.getVersion() : "") + " [" + p.getName() + "])");
errors.add(message);
}
}
} else {
warning(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.getPath(), false, I18nConstants.VALIDATION_VAL_PROFILE_MULTIPLEMATCHES, StringUtils.join("; ", goodProfiles.keySet()));
for (String m : goodProfiles.keySet()) {
p = this.context.fetchResource(StructureDefinition.class, m);
for (ValidationMessage message : goodProfiles.get(m)) {
message.setMessage(message.getMessage() + " (validating against " + p.getUrl() + (p.hasVersion() ? "|" + p.getVersion() : "") + " [" + p.getName() + "])");
errors.add(message);
}
} else {
warning(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.getPath(), false, I18nConstants.VALIDATION_VAL_PROFILE_MULTIPLEMATCHES, StringUtils.join("; ", goodProfiles.keySet()));
for (String m : goodProfiles.keySet()) {
p = this.context.fetchResource(StructureDefinition.class, m);
for (ValidationMessage message : goodProfiles.get(m)) {
message.setMessage(message.getMessage() + " (validating against " + p.getUrl() + (p.hasVersion() ? "|" + p.getVersion() : "") + " [" + p.getName() + "])");
errors.add(message);
}
}
}
if (p != null) {
trackUsage(p, hostContext, element);
}
if (p != null) {
trackUsage(p, hostContext, element);
if (!elementValidated) {
if (ei.getElement().getSpecial() == SpecialElement.BUNDLE_ENTRY || ei.getElement().getSpecial() == SpecialElement.BUNDLE_OUTCOME || ei.getElement().getSpecial() == SpecialElement.PARAMETER)
validateElement(hostContext, errors, p, getElementByTail(p, tail), profile, ei.definition, ei.getElement(), ei.getElement(), type, localStack.resetIds(), thisIsCodeableConcept, checkDisplay, thisExtension);
else
validateElement(hostContext, errors, p, getElementByTail(p, tail), profile, ei.definition, resource, ei.getElement(), type, localStack, thisIsCodeableConcept, checkDisplay, thisExtension);
}
int index = profile.getSnapshot().getElement().indexOf(ei.definition);
if (index < profile.getSnapshot().getElement().size() - 1) {
String nextPath = profile.getSnapshot().getElement().get(index + 1).getPath();
if (!nextPath.equals(ei.definition.getPath()) && nextPath.startsWith(ei.definition.getPath()))
validateElement(hostContext, errors, profile, ei.definition, null, null, resource, ei.getElement(), type, localStack, thisIsCodeableConcept, checkDisplay, thisExtension);
}
if (!elementValidated) {
if (ei.getElement().getSpecial() == SpecialElement.BUNDLE_ENTRY || ei.getElement().getSpecial() == SpecialElement.BUNDLE_OUTCOME || ei.getElement().getSpecial() == SpecialElement.PARAMETER)
validateElement(hostContext, errors, p, getElementByTail(p, tail), profile, checkDefn, ei.getElement(), ei.getElement(), type, localStack.resetIds(), thisIsCodeableConcept, checkDisplay, thisExtension);
else
validateElement(hostContext, errors, p, getElementByTail(p, tail), profile, checkDefn, resource, ei.getElement(), type, localStack, thisIsCodeableConcept, checkDisplay, thisExtension);
}
int index = profile.getSnapshot().getElement().indexOf(checkDefn);
if (index < profile.getSnapshot().getElement().size() - 1) {
String nextPath = profile.getSnapshot().getElement().get(index + 1).getPath();
if (!nextPath.equals(checkDefn.getPath()) && nextPath.startsWith(checkDefn.getPath()))
validateElement(hostContext, errors, profile, checkDefn, null, null, resource, ei.getElement(), type, localStack, thisIsCodeableConcept, checkDisplay, thisExtension);
}
}
}
@ -5091,4 +5115,12 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
return questionnaireMode;
}
public boolean isWantCheckSnapshotUnchanged() {
return wantCheckSnapshotUnchanged;
}
public void setWantCheckSnapshotUnchanged(boolean wantCheckSnapshotUnchanged) {
this.wantCheckSnapshotUnchanged = wantCheckSnapshotUnchanged;
}
}

3
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/SpecialExtensions.java
View File

@ -1,12 +1,9 @@
package org.hl7.fhir.validation.instance;
import java.io.IOException;
import java.io.InputStream;
import org.hl7.fhir.convertors.VersionConvertorConstants;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.formats.XmlParser;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.utilities.Utilities;

5
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/MeasureContext.java
View File

@ -1,19 +1,14 @@
package org.hl7.fhir.validation.instance.type;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import javax.xml.parsers.ParserConfigurationException;
import org.hl7.fhir.r5.elementmodel.Element;
import org.hl7.fhir.r5.model.Attachment;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.Library;
import org.hl7.fhir.r5.model.Measure;
import org.hl7.fhir.r5.model.Measure.MeasureGroupComponent;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.xml.sax.SAXException;
public class MeasureContext {

11
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/MeasureValidator.java
View File

@ -5,7 +5,6 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.math.BigDecimal;
import java.math.BigInteger;
import java.util.ArrayList;
import java.util.List;
@ -22,27 +21,23 @@ import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.FhirPublication;
import org.hl7.fhir.r5.model.Library;
import org.hl7.fhir.r5.model.Measure;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.renderers.DataRenderer;
import org.hl7.fhir.r5.renderers.utils.RenderingContext;
import org.hl7.fhir.r5.renderers.utils.RenderingContext.ResourceRendererMode;
import org.hl7.fhir.r5.model.Measure.MeasureGroupComponent;
import org.hl7.fhir.r5.model.Measure.MeasureGroupPopulationComponent;
import org.hl7.fhir.r5.model.Measure.MeasureGroupStratifierComponent;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.renderers.DataRenderer;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.i18n.I18nConstants;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
import org.hl7.fhir.utilities.validation.ValidationMessage.Source;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.hl7.fhir.validation.instance.utils.NodeStack;
import org.hl7.fhir.validation.BaseValidator;
import org.hl7.fhir.validation.TimeTracker;
import org.hl7.fhir.validation.instance.utils.NodeStack;
import org.hl7.fhir.validation.instance.utils.ValidatorHostContext;
import org.w3c.dom.Document;
import net.sf.saxon.tree.tiny.LargeStringBuffer;
public class MeasureValidator extends BaseValidator {
public MeasureValidator(IWorkerContext context, TimeTracker timeTracker) {

11
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/QuestionnaireValidator.java
View File

@ -23,26 +23,25 @@ import org.hl7.fhir.r5.elementmodel.ObjectConverter;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.DateType;
import org.hl7.fhir.r5.model.Enumerations.FHIRVersion;
import org.hl7.fhir.r5.model.FhirPublication;
import org.hl7.fhir.r5.model.IntegerType;
import org.hl7.fhir.r5.model.Questionnaire;
import org.hl7.fhir.r5.model.Questionnaire.QuestionnaireItemAnswerOptionComponent;
import org.hl7.fhir.r5.model.Questionnaire.QuestionnaireItemComponent;
import org.hl7.fhir.r5.model.Questionnaire.QuestionnaireItemType;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.StringType;
import org.hl7.fhir.r5.model.TimeType;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.model.ElementDefinition.TypeRefComponent;
import org.hl7.fhir.r5.model.Enumerations.FHIRVersion;
import org.hl7.fhir.r5.model.Questionnaire.QuestionnaireItemAnswerOptionComponent;
import org.hl7.fhir.r5.model.Questionnaire.QuestionnaireItemComponent;
import org.hl7.fhir.r5.model.Questionnaire.QuestionnaireItemType;
import org.hl7.fhir.r5.utils.FHIRPathEngine;
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.i18n.I18nConstants;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationOptions;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
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.Validator.QuestionnaireMode;

3
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/SearchParameterValidator.java
View File

@ -5,14 +5,12 @@ import java.util.Collections;
import java.util.Comparator;
import java.util.List;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.elementmodel.Element;
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.SearchParameter;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.utils.FHIRPathEngine;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.i18n.I18nConstants;
@ -21,7 +19,6 @@ import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
import org.hl7.fhir.utilities.validation.ValidationMessage.Source;
import org.hl7.fhir.validation.BaseValidator;
import org.hl7.fhir.validation.TimeTracker;
import org.hl7.fhir.validation.instance.type.SearchParameterValidator.FhirPathSorter;
import org.hl7.fhir.validation.instance.utils.NodeStack;
public class SearchParameterValidator extends BaseValidator {

79
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/StructureDefinitionValidator.java
View File

@ -3,18 +3,15 @@ package org.hl7.fhir.validation.instance.type;
import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.List;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.convertors.VersionConvertor_10_50;
import org.hl7.fhir.convertors.VersionConvertor_14_50;
import org.hl7.fhir.convertors.VersionConvertor_30_50;
import org.hl7.fhir.convertors.VersionConvertor_40_50;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.conformance.ProfileUtilities.ProfileKnowledgeProvider;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.elementmodel.Element;
import org.hl7.fhir.r5.elementmodel.Manager;
@ -22,14 +19,10 @@ import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
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;
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;
import org.hl7.fhir.r5.utils.ToolingExtensions;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.i18n.I18nConstants;
import org.hl7.fhir.utilities.validation.ValidationMessage;
@ -37,7 +30,6 @@ import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
import org.hl7.fhir.utilities.validation.ValidationMessage.Source;
import org.hl7.fhir.validation.BaseValidator;
import org.hl7.fhir.validation.TimeTracker;
import org.hl7.fhir.validation.instance.type.StructureDefinitionValidator.FhirPathSorter;
import org.hl7.fhir.validation.instance.utils.NodeStack;
public class StructureDefinitionValidator extends BaseValidator {
@ -52,16 +44,18 @@ public class StructureDefinitionValidator extends BaseValidator {
}
private FHIRPathEngine fpe;
private boolean wantCheckSnapshotUnchanged;
public StructureDefinitionValidator(IWorkerContext context, TimeTracker timeTracker, FHIRPathEngine fpe) {
public StructureDefinitionValidator(IWorkerContext context, TimeTracker timeTracker, FHIRPathEngine fpe, boolean wantCheckSnapshotUnchanged) {
super(context);
source = Source.InstanceValidator;
this.fpe = fpe;
this.timeTracker = timeTracker;
this.wantCheckSnapshotUnchanged = wantCheckSnapshotUnchanged;
}
public void validateStructureDefinition(List<ValidationMessage> errors, Element src, NodeStack stack) {
StructureDefinition sd;
StructureDefinition sd = null;
try {
sd = loadAsSD(src);
List<ElementDefinition> snapshot = sd.getSnapshot().getElement();
@ -85,7 +79,7 @@ public class StructureDefinitionValidator extends BaseValidator {
errors.add(msg);
}
}
if (!snapshot.isEmpty()) {
if (!snapshot.isEmpty() && wantCheckSnapshotUnchanged) {
int was = snapshot.size();
int is = sd.getSnapshot().getElement().size();
rule(errors, IssueType.NOTFOUND, stack.getLiteralPath(), was == is, I18nConstants.SNAPSHOT_EXISTING_PROBLEM, was, is);
@ -99,29 +93,33 @@ public class StructureDefinitionValidator extends BaseValidator {
List<Element> differentials = src.getChildrenByName("differential");
List<Element> snapshots = src.getChildrenByName("snapshot");
for (Element differential : differentials) {
validateElementList(errors, differential, stack.push(differential, -1, null, null), false, snapshots.size() > 0);
validateElementList(errors, differential, stack.push(differential, -1, null, null), false, snapshots.size() > 0, sd);
}
for (Element snapshot : snapshots) {
validateElementList(errors, snapshot, stack.push(snapshot, -1, null, null), true, true);
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) {
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;
for (Element element : elements) {
validateElementDefinition(errors, element, stack.push(element, cc, null, null), snapshot, hasSnapshot);
validateElementDefinition(errors, element, stack.push(element, cc, null, null), snapshot, hasSnapshot, sd);
cc++;
}
}
private void validateElementDefinition(List<ValidationMessage> errors, Element element, NodeStack stack, boolean snapshot, boolean hasSnapshot) {
private void validateElementDefinition(List<ValidationMessage> errors, Element element, NodeStack stack, boolean snapshot, boolean hasSnapshot, StructureDefinition sd) {
boolean typeMustSupport = false;
List<Element> types = element.getChildrenByName("type");
for (Element type : types) {
if (hasMustSupportExtension(type)) {
typeMustSupport = true;
}
// check the stated profile - must be a constraint on the type
if (snapshot || sd != null) {
validateElementType(errors, type, stack.push(type, -1, null, null), sd, element.getChildValue("path"));
}
}
if (typeMustSupport) {
if (snapshot) {
@ -132,6 +130,53 @@ public class StructureDefinitionValidator extends BaseValidator {
}
}
private void validateElementType(List<ValidationMessage> errors, Element type, NodeStack stack, StructureDefinition sd, String path) {
String code = type.getNamedChildValue("code");
if (code == null && path != null) {
code = getTypeCodeFromSD(sd, path);
}
if (code != null) {
List<Element> profiles = type.getChildrenByName("profile");
for (Element profile : profiles) {
validateTypeProfile(errors, profile, code, stack.push(type, -1, null, null));
}
}
}
private String getTypeCodeFromSD(StructureDefinition sd, String path) {
ElementDefinition ed = null;
for (ElementDefinition t : sd.getSnapshot().getElement()) {
if (t.hasPath() && t.getPath().equals(path)) {
if (ed == null) {
ed = t;
} else {
return null; // more than one match, we don't know which is which
}
}
}
return ed != null && ed.getType().size() == 1 ? ed.getTypeFirstRep().getCode() : null;
}
private void validateTypeProfile(List<ValidationMessage> errors, Element profile, String code, NodeStack stack) {
String p = profile.primitiveValue();
StructureDefinition sd = context.fetchResource(StructureDefinition.class, p);
if (warning(errors, IssueType.EXCEPTION, stack.getLiteralPath(), sd != null, I18nConstants.SD_ED_TYPE_PROFILE_UNKNOWN, p)) {
String t = determineBaseType(sd);
if (t == null) {
rule(errors, IssueType.EXCEPTION, stack.getLiteralPath(), code.equals(t), I18nConstants.SD_ED_TYPE_PROFILE_NOTYPE, p);
} else {
rule(errors, IssueType.EXCEPTION, stack.getLiteralPath(), code.equals(t), I18nConstants.SD_ED_TYPE_PROFILE_WRONG, p, t, code);
}
}
}
private String determineBaseType(StructureDefinition sd) {
while (sd != null && !sd.hasType() && sd.getDerivation() == TypeDerivationRule.CONSTRAINT) {
sd = context.fetchResource(StructureDefinition.class, sd.getBaseDefinition());
}
return sd == null ? null : sd.getType();
}
private boolean hasMustSupportExtension(Element type) {
if ("true".equals(getExtensionValue(type, ToolingExtensions.EXT_MUST_SUPPORT))) {
return true;

4
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/ValueSetValidator.java
View File

@ -3,14 +3,13 @@ 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;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.terminologies.ValueSetExpander.TerminologyServiceErrorClass;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
@ -22,7 +21,6 @@ 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.InstanceValidator;
import org.hl7.fhir.validation.instance.type.ValueSetValidator.VSCodingValidationRequest;
import org.hl7.fhir.validation.instance.utils.NodeStack;
public class ValueSetValidator extends BaseValidator {

2
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/utils/ChildIterator.java
View File

@ -1,8 +1,8 @@
package org.hl7.fhir.validation.instance.utils;
import org.hl7.fhir.r5.elementmodel.Element;
import org.hl7.fhir.validation.instance.InstanceValidator;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.validation.instance.InstanceValidator;
public class ChildIterator {
private final InstanceValidator instanceValidator;

4
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/utils/ElementInfo.java
View File

@ -1,11 +1,11 @@
package org.hl7.fhir.validation.instance.utils;
import java.util.List;
import org.hl7.fhir.r5.elementmodel.Element;
import org.hl7.fhir.r5.model.ElementDefinition;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import java.util.List;
public class ElementInfo {
public List<ValidationMessage> sliceInfo;

4
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/utils/EntrySummary.java
View File

@ -1,10 +1,10 @@
package org.hl7.fhir.validation.instance.utils;
import org.hl7.fhir.r5.elementmodel.Element;
import java.util.ArrayList;
import java.util.List;
import org.hl7.fhir.r5.elementmodel.Element;
public class EntrySummary {
Element entry;

2
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/utils/NodeStack.java
View File

@ -2,10 +2,8 @@ package org.hl7.fhir.validation.instance.utils;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.elementmodel.Element;

1
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/utils/ResolvedReference.java
View File

@ -2,7 +2,6 @@ package org.hl7.fhir.validation.instance.utils;
import org.hl7.fhir.r5.elementmodel.Element;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.validation.instance.InstanceValidator;
public class ResolvedReference {

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

@ -1,13 +1,13 @@
package org.hl7.fhir.validation.instance.utils;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.utilities.validation.ValidationMessage;
/**
* The validator keeps one of these classes for each resource it validates (e.g. when chasing references)
* <p>

10
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/utils/ValidatorHostContext.java
View File

@ -1,15 +1,13 @@
package org.hl7.fhir.validation.instance.utils;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.hl7.fhir.r5.elementmodel.Element;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Stack;
public class ValidatorHostContext {
private Object appContext;

2
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/packages/PackageValidator.java
View File

@ -10,8 +10,8 @@ import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.npm.CachingPackageClient;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.utilities.npm.ToolsVersion;
import org.hl7.fhir.utilities.npm.PackageClient.PackageInfo;
import org.hl7.fhir.utilities.npm.ToolsVersion;
public class PackageValidator {

33
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/comparison/tests/ComparisonTests.java
View File

@ -1,15 +1,25 @@
package org.hl7.fhir.comparison.tests;
import com.google.common.base.Charsets;
import com.google.gson.JsonElement;
import com.google.gson.JsonObject;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.stream.Stream;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.convertors.VersionConvertor_10_50;
import org.hl7.fhir.convertors.VersionConvertor_14_50;
import org.hl7.fhir.convertors.VersionConvertor_30_50;
import org.hl7.fhir.convertors.VersionConvertor_40_50;
import org.hl7.fhir.convertors.loaders.R4ToR5Loader;
import org.hl7.fhir.convertors.loaders.BaseLoaderR5.NullLoaderKnowledgeProvider;
import org.hl7.fhir.convertors.loaders.R4ToR5Loader;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
@ -49,18 +59,9 @@ import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.Arguments;
import org.junit.jupiter.params.provider.MethodSource;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.stream.Stream;
import com.google.common.base.Charsets;
import com.google.gson.JsonElement;
import com.google.gson.JsonObject;
public class ComparisonTests {

38
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/conversion/tests/R3R4ConversionTests.java
View File

@ -1,6 +1,21 @@
package org.hl7.fhir.conversion.tests;
import com.google.gson.*;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.stream.Stream;
import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream;
import javax.xml.parsers.ParserConfigurationException;
import org.hl7.fhir.convertors.loaders.R3ToR4Loader;
import org.hl7.fhir.exceptions.DefinitionException;
@ -11,8 +26,16 @@ import org.hl7.fhir.r4.context.SimpleWorkerContext;
import org.hl7.fhir.r4.elementmodel.Element;
import org.hl7.fhir.r4.elementmodel.Manager;
import org.hl7.fhir.r4.formats.IParser.OutputStyle;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.Base;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.MetadataResource;
import org.hl7.fhir.r4.model.PractitionerRole;
import org.hl7.fhir.r4.model.Resource;
import org.hl7.fhir.r4.model.ResourceFactory;
import org.hl7.fhir.r4.model.StructureDefinition;
import org.hl7.fhir.r4.model.StructureDefinition.StructureDefinitionKind;
import org.hl7.fhir.r4.model.StructureMap;
import org.hl7.fhir.r4.model.UriType;
import org.hl7.fhir.r4.test.utils.TestingUtilities;
import org.hl7.fhir.r4.utils.IResourceValidator;
import org.hl7.fhir.r4.utils.IResourceValidator.IValidatorResourceFetcher;
@ -32,12 +55,11 @@ import org.junit.jupiter.params.provider.Arguments;
import org.junit.jupiter.params.provider.MethodSource;
import org.xml.sax.SAXException;
import javax.xml.parsers.ParserConfigurationException;
import java.io.*;
import java.util.*;
import java.util.stream.Stream;
import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream;
import com.google.gson.Gson;
import com.google.gson.GsonBuilder;
import com.google.gson.JsonArray;
import com.google.gson.JsonObject;
import com.google.gson.JsonPrimitive;
@Disabled
public class R3R4ConversionTests implements ITransformerServices, IValidatorResourceFetcher {

21
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/conversion/tests/SnapShotGenerationXTests.java
View File

@ -1,5 +1,14 @@
package org.hl7.fhir.conversion.tests;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import javax.xml.parsers.ParserConfigurationException;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.NotImplementedException;
import org.hl7.fhir.exceptions.DefinitionException;
@ -18,12 +27,12 @@ import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionKind;
import org.hl7.fhir.r5.model.StructureDefinition.TypeDerivationRule;
import org.hl7.fhir.r5.model.TypeDetails;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.renderers.RendererFactory;
import org.hl7.fhir.r5.renderers.utils.RenderingContext;
import org.hl7.fhir.r5.renderers.utils.RenderingContext.ResourceRendererMode;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.r5.model.TypeDetails;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.utils.FHIRPathEngine;
import org.hl7.fhir.r5.utils.FHIRPathEngine.IEvaluationContext;
import org.hl7.fhir.r5.utils.IResourceValidator;
@ -38,14 +47,6 @@ import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.xml.sax.SAXException;
import javax.xml.parsers.ParserConfigurationException;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
public class SnapShotGenerationXTests {
public enum TestFetchMode {

4
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/conversion/tests/UtilitiesXTests.java
View File

@ -46,14 +46,14 @@ import javax.xml.parsers.DocumentBuilderFactory;
import org.apache.commons.codec.binary.Base64;
import org.apache.commons.io.IOUtils;
import org.fhir.ucum.UcumEssenceService;
import org.hl7.fhir.convertors.loaders.BaseLoaderR5.NullLoaderKnowledgeProvider;
import org.hl7.fhir.convertors.loaders.R2016MayToR5Loader;
import org.hl7.fhir.convertors.loaders.R2ToR5Loader;
import org.hl7.fhir.convertors.loaders.R3ToR5Loader;
import org.hl7.fhir.convertors.loaders.R4ToR5Loader;
import org.hl7.fhir.convertors.loaders.BaseLoaderR5.NullLoaderKnowledgeProvider;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.context.SimpleWorkerContext;
import org.hl7.fhir.r5.context.IWorkerContext.IContextResourceLoader;
import org.hl7.fhir.r5.context.SimpleWorkerContext;
import org.hl7.fhir.r5.model.Parameters;
import org.hl7.fhir.utilities.CSFile;
import org.hl7.fhir.utilities.TextFile;

2
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/r5/test/FHIRMappingLanguageTests.java
View File

@ -6,7 +6,6 @@ import java.io.ByteArrayOutputStream;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.stream.Stream;
@ -24,7 +23,6 @@ import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.hl7.fhir.validation.ValidationEngine;
import org.hl7.fhir.validation.instance.InstanceValidatorFactory;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.params.ParameterizedTest;

7
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/cli/BaseRestTest.java
View File

@ -1,14 +1,15 @@
package org.hl7.fhir.validation.cli;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
import java.io.IOException;
import org.apache.http.HttpResponse;
import org.apache.http.util.EntityUtils;
import org.hl7.fhir.validation.cli.model.CliContext;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.BeforeAll;
import java.io.IOException;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
public abstract class BaseRestTest {

18
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/cli/ValidatorGuiTest.java
View File

@ -1,17 +1,8 @@
package org.hl7.fhir.validation.cli;
import io.github.bonigarcia.wdm.WebDriverManager;
import org.hl7.fhir.r5.elementmodel.Manager;
import org.hl7.fhir.r5.model.FhirPublication;
import org.hl7.fhir.r5.model.OperationOutcome;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.r5.utils.EOperationOutcome;
import org.hl7.fhir.validation.ValidationEngine;
import java.io.IOException;
import org.hl7.fhir.validation.cli.model.CliContext;
import org.hl7.fhir.validation.cli.model.FileInfo;
import org.hl7.fhir.validation.cli.model.ValidationRequest;
import org.hl7.fhir.validation.cli.model.ValidationResponse;
import org.hl7.fhir.validation.cli.services.ValidationService;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;
@ -19,10 +10,7 @@ import org.openqa.selenium.WebDriver;
import org.openqa.selenium.chrome.ChromeDriver;
import org.openqa.selenium.chrome.ChromeOptions;
import java.io.IOException;
import java.io.InputStream;
import java.net.URISyntaxException;
import java.util.Arrays;
import io.github.bonigarcia.wdm.WebDriverManager;
class ValidatorGuiTest {

4
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/cli/controller/HttpGetContextTest.java
View File

@ -1,5 +1,7 @@
package org.hl7.fhir.validation.cli.controller;
import java.io.IOException;
import org.apache.http.HttpResponse;
import org.apache.http.HttpStatus;
import org.apache.http.client.methods.HttpGet;
@ -13,8 +15,6 @@ import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;
import java.io.IOException;
class HttpGetContextTest extends BaseRestTest {
private final String GET_CONTEXT_URL = "http://localhost:" + ValidatorGui.getPort() + "/context";

6
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/cli/controller/HttpPutContextTest.java
View File

@ -1,12 +1,12 @@
package org.hl7.fhir.validation.cli.controller;
import io.javalin.http.Context;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.verify;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.verify;
import io.javalin.http.Context;
class HttpPutContextTest {

6
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/JsonSchemaTests.java
View File

@ -1,5 +1,8 @@
package org.hl7.fhir.validation.tests;
import java.io.FileNotFoundException;
import java.io.IOException;
import org.everit.json.schema.Schema;
import org.everit.json.schema.ValidationException;
import org.everit.json.schema.loader.SchemaLoader;
@ -9,9 +12,6 @@ import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import java.io.FileNotFoundException;
import java.io.IOException;
public class JsonSchemaTests {

2
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/LoadIgTests.java
View File

@ -8,8 +8,6 @@ import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.validation.ValidationEngine;
import org.junit.Test;
import net.sf.saxon.expr.instruct.Message;
public class LoadIgTests {
@Test

2
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/TransformationTests.java
View File

@ -3,8 +3,8 @@ package org.hl7.fhir.validation.tests;
import java.io.File;
import org.hl7.fhir.r4.test.utils.TestingUtilities;
import org.hl7.fhir.validation.Validator;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.validation.Validator;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;

6
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/ValidationEngineTests.java
View File

@ -1,5 +1,8 @@
package org.hl7.fhir.validation.tests;
import java.util.ArrayList;
import java.util.List;
import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
import org.hl7.fhir.r5.model.FhirPublication;
import org.hl7.fhir.r5.model.OperationOutcome;
@ -11,9 +14,6 @@ import org.hl7.fhir.validation.tests.utilities.TestUtilities;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
import java.util.ArrayList;
import java.util.List;
public class ValidationEngineTests {
private static final String DEF_TX = "http://tx.fhir.org";

51
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/ValidationTests.java
View File

@ -1,10 +1,19 @@
package org.hl7.fhir.validation.tests;
import com.google.common.base.Charsets;
import com.google.gson.GsonBuilder;
import com.google.gson.JsonArray;
import com.google.gson.JsonElement;
import com.google.gson.JsonObject;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
import java.net.MalformedURLException;
import java.net.URL;
import java.net.URLConnection;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Locale;
import java.util.Map;
import java.util.Map.Entry;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.NotImplementedException;
import org.hl7.fhir.convertors.VersionConvertor_10_50;
@ -43,11 +52,11 @@ import org.hl7.fhir.r5.utils.IResourceValidator.ReferenceValidationPolicy;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.hl7.fhir.validation.ValidationEngine;
import org.hl7.fhir.validation.instance.InstanceValidator;
import org.junit.AfterClass;
import org.junit.Assert;
import org.junit.Test;
@ -55,19 +64,11 @@ import org.junit.runner.RunWith;
import org.junit.runners.Parameterized;
import org.junit.runners.Parameterized.Parameters;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
import java.net.MalformedURLException;
import java.net.URL;
import java.net.URLConnection;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Locale;
import java.util.Map;
import java.util.Map.Entry;
import com.google.common.base.Charsets;
import com.google.gson.GsonBuilder;
import com.google.gson.JsonArray;
import com.google.gson.JsonElement;
import com.google.gson.JsonObject;
@RunWith(Parameterized.class)
public class ValidationTests implements IEvaluationContext, IValidatorResourceFetcher {
@ -100,7 +101,7 @@ public class ValidationTests implements IEvaluationContext, IValidatorResourceFe
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;
@ -154,8 +155,8 @@ public class ValidationTests implements IEvaluationContext, IValidatorResourceFe
return;
String testCaseContent = TestingUtilities.loadTestResource("validator", name);
InstanceValidator val = vCurr.getValidator();
val.setWantCheckSnapshotUnchanged(true);
val.getContext().setClientRetryCount(4);
val.setDebug(false);
if (content.has("allowed-extension-domain"))
@ -170,7 +171,13 @@ public class ValidationTests implements IEvaluationContext, IValidatorResourceFe
val.setFetcher(this);
if (content.has("packages")) {
for (JsonElement e : content.getAsJsonArray("packages")) {
vCurr.loadIg(e.getAsString(), true);
String n = e.getAsString();
InputStream cnt = n.endsWith(".tgz") ? TestingUtilities.loadTestResourceStream("validator", n) : null;
if (cnt != null) {
vCurr.loadPackage(NpmPackage.fromPackage(cnt));
} else {
vCurr.loadIg(n, true);
}
}
}
if (content.has("crumb-trail")) {

2
pom.xml
View File

@ -19,7 +19,7 @@
<properties>
<hapi_fhir_version>5.1.0</hapi_fhir_version>
<validator_test_case_version>1.1.45</validator_test_case_version>
<validator_test_case_version>1.1.46</validator_test_case_version>
<junit_jupiter_version>5.6.2</junit_jupiter_version>
<maven_surefire_version>3.0.0-M4</maven_surefire_version>
<jacoco_version>0.8.5</jacoco_version>