Merge remote-tracking branch 'origin/master' into do-20230315-pathbuilder
This commit is contained in:
dotasek
commit
8ce7cd8323
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>org.hl7.fhir.core</artifactId>
|
||||
<version>5.6.113-SNAPSHOT</version>
|
||||
<version>5.6.115-SNAPSHOT</version>
|
||||
<relativePath>../pom.xml</relativePath>
|
||||
</parent>
|
||||
|
||||
|
|
|
|||
|
|
@ -2350,7 +2350,7 @@ public class ImplementationGuide40_50 {
|
|||
tgt.addParameter(convertImplementationGuideDefinitionParameterComponent(t));
|
||||
} else {
|
||||
org.hl7.fhir.r4.model.Extension e = new org.hl7.fhir.r4.model.Extension(EXT_IG_DEFINITION_PARAMETER);
|
||||
org.hl7.fhir.r4.model.Extension eCode = new org.hl7.fhir.r4.model.Extension("code", new org.hl7.fhir.r4.model.StringType(t.getCode().getCode()));
|
||||
org.hl7.fhir.r4.model.Extension eCode = new org.hl7.fhir.r4.model.Extension("code", new org.hl7.fhir.r4.model.CodeType(t.getCode().getCode()));
|
||||
org.hl7.fhir.r4.model.Extension eValue = new org.hl7.fhir.r4.model.Extension("value", new org.hl7.fhir.r4.model.StringType(t.getValue()));
|
||||
e.addExtension(eCode);
|
||||
e.addExtension(eValue);
|
||||
|
|
|
|||
|
|
@ -2344,7 +2344,7 @@ public class ImplementationGuide43_50 {
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|||
tgt.addParameter(convertImplementationGuideDefinitionParameterComponent(t));
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||||
else {
|
||||
org.hl7.fhir.r4b.model.Extension e = new org.hl7.fhir.r4b.model.Extension(EXT_IG_DEFINITION_PARAMETER);
|
||||
org.hl7.fhir.r4b.model.Extension eCode = new org.hl7.fhir.r4b.model.Extension("code", new org.hl7.fhir.r4b.model.StringType(t.getCode().getCode()));
|
||||
org.hl7.fhir.r4b.model.Extension eCode = new org.hl7.fhir.r4b.model.Extension("code", new org.hl7.fhir.r4b.model.CodeType(t.getCode().getCode()));
|
||||
org.hl7.fhir.r4b.model.Extension eValue = new org.hl7.fhir.r4b.model.Extension("value", new org.hl7.fhir.r4b.model.StringType(t.getValue()));
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||||
e.addExtension(eCode);
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||||
e.addExtension(eValue);
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||||
|
|
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|||
|
|
@ -24,6 +24,7 @@ import org.hl7.fhir.r5.model.ElementDefinition.TypeRefComponent;
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|||
import org.hl7.fhir.utilities.Utilities;
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||||
import org.hl7.fhir.utilities.VersionUtilities;
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||||
import org.hl7.fhir.utilities.npm.NpmPackage;
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||||
import org.hl7.fhir.utilities.npm.NpmPackage.PackageResourceInformation;
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||||
|
||||
import com.google.gson.JsonSyntaxException;
|
||||
|
||||
|
|
@ -40,6 +41,7 @@ public abstract class BaseLoaderR5 implements IContextResourceLoader {
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|||
@Getter @Setter protected boolean killPrimitives;
|
||||
@Getter protected List<String> types = new ArrayList<>();
|
||||
protected ILoaderKnowledgeProviderR5 lkp;
|
||||
private boolean loadProfiles = true;
|
||||
|
||||
public BaseLoaderR5(List<String> types, ILoaderKnowledgeProviderR5 lkp) {
|
||||
super();
|
||||
|
|
@ -169,6 +171,12 @@ public abstract class BaseLoaderR5 implements IContextResourceLoader {
|
|||
String url = URL_BASE+versionString()+"/StructureDefinition/"+code;
|
||||
ToolingExtensions.setUrlExtension(tr, ToolingExtensions.EXT_FHIR_TYPE, url);
|
||||
}
|
||||
for (CanonicalType c : tr.getProfile()) {
|
||||
c.setValue(patchUrl(c.getValue(), "StructureDefinition"));
|
||||
}
|
||||
for (CanonicalType c : tr.getTargetProfile()) {
|
||||
c.setValue(patchUrl(c.getValue(), "StructureDefinition"));
|
||||
}
|
||||
}
|
||||
if (ed.hasBinding()) {
|
||||
ed.getBinding().setValueSet(patchUrl(ed.getBinding().getValueSet(), "ValueSet"));
|
||||
|
|
@ -178,4 +186,20 @@ public abstract class BaseLoaderR5 implements IContextResourceLoader {
|
|||
}
|
||||
}
|
||||
|
||||
public IContextResourceLoader setLoadProfiles(boolean value) {
|
||||
loadProfiles = value;
|
||||
return this;
|
||||
}
|
||||
|
||||
public boolean wantLoad(NpmPackage pi, PackageResourceInformation pri) {
|
||||
if (pri.getResourceType().equals("StructureDefinition")) {
|
||||
if (loadProfiles) {
|
||||
return true;
|
||||
} else {
|
||||
return pi.isCore() && Utilities.tail(pri.getUrl()).equals(pri.getStatedType());
|
||||
}
|
||||
} else {
|
||||
return true;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -127,7 +127,7 @@ public class R4ToR5Loader extends BaseLoaderR5 implements IContextResourceLoader
|
|||
if (killPrimitives) {
|
||||
throw new FHIRException("Cannot kill primitives when using deferred loading");
|
||||
}
|
||||
if (r5 instanceof StructureDefinition && VersionUtilities.isR4BVer(version)) {
|
||||
if (r5 instanceof StructureDefinition && VersionUtilities.isR4Ver(version)) {
|
||||
r5 = new StructureDefinitionHacker(version).fixSD((StructureDefinition) r5);
|
||||
}
|
||||
if (patchUrls) {
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>org.hl7.fhir.core</artifactId>
|
||||
<version>5.6.113-SNAPSHOT</version>
|
||||
<version>5.6.115-SNAPSHOT</version>
|
||||
<relativePath>../pom.xml</relativePath>
|
||||
</parent>
|
||||
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>org.hl7.fhir.core</artifactId>
|
||||
<version>5.6.113-SNAPSHOT</version>
|
||||
<version>5.6.115-SNAPSHOT</version>
|
||||
<relativePath>../pom.xml</relativePath>
|
||||
</parent>
|
||||
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>org.hl7.fhir.core</artifactId>
|
||||
<version>5.6.113-SNAPSHOT</version>
|
||||
<version>5.6.115-SNAPSHOT</version>
|
||||
<relativePath>../pom.xml</relativePath>
|
||||
</parent>
|
||||
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>org.hl7.fhir.core</artifactId>
|
||||
<version>5.6.113-SNAPSHOT</version>
|
||||
<version>5.6.115-SNAPSHOT</version>
|
||||
<relativePath>../pom.xml</relativePath>
|
||||
</parent>
|
||||
|
||||
|
|
|
|||
Binary file not shown.
|
After Width: | Height: | Size: 714 B |
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>org.hl7.fhir.core</artifactId>
|
||||
<version>5.6.113-SNAPSHOT</version>
|
||||
<version>5.6.115-SNAPSHOT</version>
|
||||
<relativePath>../pom.xml</relativePath>
|
||||
</parent>
|
||||
|
||||
|
|
|
|||
|
|
@ -149,7 +149,7 @@ public class TestingUtilities extends BaseTestingUtilities {
|
|||
|
||||
public static String checkXMLIsSame(String f1, String f2) throws Exception {
|
||||
String result = compareXml(f1, f2);
|
||||
if (result != null && SHOW_DIFF) {
|
||||
if (result != null && SHOW_DIFF && System.getenv("ProgramFiles") != null) {
|
||||
String diff = Utilities.path(System.getenv("ProgramFiles"), "WinMerge", "WinMergeU.exe");
|
||||
if (new File(diff).exists()) {
|
||||
List<String> command = new ArrayList<String>();
|
||||
|
|
|
|||
Binary file not shown.
|
After Width: | Height: | Size: 714 B |
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>org.hl7.fhir.core</artifactId>
|
||||
<version>5.6.113-SNAPSHOT</version>
|
||||
<version>5.6.115-SNAPSHOT</version>
|
||||
<relativePath>../pom.xml</relativePath>
|
||||
</parent>
|
||||
|
||||
|
|
|
|||
|
|
@ -1154,7 +1154,7 @@ public boolean prependLinks() {
|
|||
|
||||
@Override
|
||||
public String getLinkForUrl(String corePath, String s) {
|
||||
throw new NotImplementedError();
|
||||
return null;
|
||||
}
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -1,5 +1,6 @@
|
|||
package org.hl7.fhir.r5.conformance;
|
||||
|
||||
import org.hl7.fhir.r5.model.CanonicalType;
|
||||
import org.hl7.fhir.r5.model.ElementDefinition;
|
||||
import org.hl7.fhir.r5.model.ElementDefinition.TypeRefComponent;
|
||||
import org.hl7.fhir.r5.model.Resource;
|
||||
|
|
@ -22,8 +23,25 @@ public class StructureDefinitionHacker {
|
|||
}
|
||||
|
||||
public Resource fixSD(StructureDefinition sd) {
|
||||
if (VersionUtilities.isR4Ver(version) && "http://hl7.org/fhir/StructureDefinition/example-composition".equals(sd.getUrl())) {
|
||||
for (ElementDefinition ed : sd.getSnapshot().getElement()) {
|
||||
fixDocSecURL(ed);
|
||||
} for (ElementDefinition ed : sd.getDifferential().getElement()) {
|
||||
fixDocSecURL(ed);
|
||||
}
|
||||
}
|
||||
return sd;
|
||||
}
|
||||
|
||||
private void fixDocSecURL(ElementDefinition ed) {
|
||||
for (TypeRefComponent tr : ed.getType()) {
|
||||
for (CanonicalType c : tr.getProfile()) {
|
||||
if ("http://hl7.org/fhir/StructureDefinition/document-section-library".equals(c.getValue())) {
|
||||
c.setValue("http://hl7.org/fhir/StructureDefinition/example-section-library");
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -661,10 +661,7 @@ public class ProfileUtilities extends TranslatingUtilities {
|
|||
System.out.println(" "+ed.getId()+" = "+ed.getPath()+" : "+typeSummaryWithProfile(ed)+"["+ed.getMin()+".."+ed.getMax()+"]"+sliceSummary(ed)+" "+constraintSummary(ed));
|
||||
}
|
||||
}
|
||||
if (exception)
|
||||
throw new DefinitionException(msg);
|
||||
else
|
||||
messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url, msg, ValidationMessage.IssueSeverity.ERROR));
|
||||
handleError(url, msg);
|
||||
}
|
||||
// hack around a problem in R4 definitions (somewhere?)
|
||||
for (ElementDefinition ed : derived.getSnapshot().getElement()) {
|
||||
|
|
@ -712,14 +709,20 @@ public class ProfileUtilities extends TranslatingUtilities {
|
|||
if (ed.getPath().equals("Bundle.entry.response.outcome")) {
|
||||
wt = "OperationOutcome";
|
||||
}
|
||||
if (!sd.getType().equals(wt)) {
|
||||
boolean ok = isCompatibleType(wt, sd);
|
||||
String tt = sd.getType();
|
||||
boolean elementProfile = u.hasExtension(ToolingExtensions.EXT_PROFILE_ELEMENT);
|
||||
if (elementProfile) {
|
||||
ElementDefinition edt = sd.getSnapshot().getElementById(u.getExtensionString(ToolingExtensions.EXT_PROFILE_ELEMENT));
|
||||
if (edt == null) {
|
||||
handleError(url, "The profile "+u.getValue()+" has type "+sd.getType()+" which is not consistent with the stated type "+wt);
|
||||
} else {
|
||||
tt = edt.typeSummary();
|
||||
}
|
||||
}
|
||||
if (!tt.equals(wt)) {
|
||||
boolean ok = !elementProfile && isCompatibleType(wt, sd);
|
||||
if (!ok) {
|
||||
String smsg = "The profile "+u.getValue()+" has type "+sd.getType()+" which is not consistent with the stated type "+wt;
|
||||
if (exception)
|
||||
throw new DefinitionException(smsg);
|
||||
else
|
||||
messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url+"#"+ed.getId(), smsg, IssueSeverity.ERROR));
|
||||
handleError(url, "The profile "+u.getValue()+" has type "+sd.getType()+" which is not consistent with the stated type "+wt);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -738,6 +741,13 @@ public class ProfileUtilities extends TranslatingUtilities {
|
|||
}
|
||||
}
|
||||
|
||||
private void handleError(String url, String msg) {
|
||||
if (exception)
|
||||
throw new DefinitionException(msg);
|
||||
else
|
||||
messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url, msg, ValidationMessage.IssueSeverity.ERROR));
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
|
|
@ -1973,7 +1983,8 @@ public class ProfileUtilities extends TranslatingUtilities {
|
|||
base.getAlias().addAll(e.getAlias());
|
||||
base.getMapping().clear();
|
||||
base.getMapping().addAll(e.getMapping());
|
||||
} else if (source.getType().size() == 1 && source.getTypeFirstRep().hasProfile()) {
|
||||
} else if (source.getType().size() == 1 && source.getTypeFirstRep().hasProfile() && !source.getTypeFirstRep().getProfile().get(0).hasExtension(ToolingExtensions.EXT_PROFILE_ELEMENT)) {
|
||||
// todo: should we change down the profile_element if there's one?
|
||||
String type = source.getTypeFirstRep().getWorkingCode();
|
||||
if ("Extension".equals(type)) {
|
||||
System.out.println("Can't find Extension definition for "+source.getTypeFirstRep().getProfile().get(0).asStringValue()+" but trying to go on");
|
||||
|
|
@ -2270,11 +2281,11 @@ public class ProfileUtilities extends TranslatingUtilities {
|
|||
t.setUserData(UD_DERIVATION_EQUALS, true);
|
||||
}
|
||||
|
||||
if (derived.hasMapping()) {
|
||||
List<ElementDefinitionMappingComponent> list = new ArrayList<>();
|
||||
list.addAll(base.getMapping());
|
||||
base.getMapping().clear();
|
||||
addMappings(base.getMapping(), list);
|
||||
if (derived.hasMapping()) {
|
||||
addMappings(base.getMapping(), derived.getMapping());
|
||||
}
|
||||
for (ElementDefinitionMappingComponent m : base.getMapping()) {
|
||||
|
|
|
|||
|
|
@ -793,6 +793,9 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
|
|||
if (pIn == null) {
|
||||
throw new Error(formatMessage(I18nConstants.NO_PARAMETERS_PROVIDED_TO_EXPANDVS));
|
||||
}
|
||||
if (vs.getUrl().equals("http://hl7.org/fhir/ValueSet/all-time-units") || vs.getUrl().equals("http://hl7.org/fhir/ValueSet/all-distance-units")) {
|
||||
return new ValueSetExpansionOutcome("This value set is not expanded correctly at this time (will be fixed in a future version)", TerminologyServiceErrorClass.VALUESET_UNSUPPORTED);
|
||||
}
|
||||
|
||||
Parameters p = pIn.copy();
|
||||
|
||||
|
|
@ -1213,7 +1216,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
|
|||
if (isTxCaching && cacheId != null && vs.getUrl() != null && cached.contains(vs.getUrl()+"|"+vs.getVersion())) {
|
||||
pin.addParameter().setName("url").setValue(new UriType(vs.getUrl()+(vs.hasVersion() ? "|"+vs.getVersion() : "")));
|
||||
} else if (options.getVsAsUrl()){
|
||||
pin.addParameter().setName("url").setValue(new StringType(vs.getUrl()));
|
||||
pin.addParameter().setName("url").setValue(new UriType(vs.getUrl()));
|
||||
} else {
|
||||
pin.addParameter().setName("valueSet").setResource(vs);
|
||||
if (vs.getUrl() != null) {
|
||||
|
|
|
|||
|
|
@ -77,6 +77,7 @@ import org.hl7.fhir.utilities.TimeTracker;
|
|||
import org.hl7.fhir.utilities.TranslationServices;
|
||||
import org.hl7.fhir.utilities.npm.BasePackageCacheManager;
|
||||
import org.hl7.fhir.utilities.npm.NpmPackage;
|
||||
import org.hl7.fhir.utilities.npm.NpmPackage.PackageResourceInformation;
|
||||
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
|
||||
import org.hl7.fhir.utilities.validation.ValidationMessage;
|
||||
import org.hl7.fhir.utilities.validation.ValidationOptions;
|
||||
|
|
@ -338,6 +339,23 @@ public interface IWorkerContext {
|
|||
* @return
|
||||
*/
|
||||
String patchUrl(String url, String resourceType);
|
||||
|
||||
/**
|
||||
* set this to false (default is true) if you don't want profiles loaded
|
||||
* @param value
|
||||
* @return
|
||||
*/
|
||||
IContextResourceLoader setLoadProfiles(boolean value);
|
||||
|
||||
/**
|
||||
* Called during the loading process - the loader can decide which resources to load.
|
||||
* At this point, only the .index.json is being read
|
||||
*
|
||||
* @param pi
|
||||
* @param pri
|
||||
* @return
|
||||
*/
|
||||
boolean wantLoad(NpmPackage pi, PackageResourceInformation pri);
|
||||
}
|
||||
|
||||
/**
|
||||
|
|
|
|||
|
|
@ -492,7 +492,7 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
|
|||
types = Utilities.strings("StructureDefinition", "ValueSet", "CodeSystem", "SearchParameter", "OperationDefinition", "Questionnaire", "ConceptMap", "StructureMap", "NamingSystem", "Measures" );
|
||||
}
|
||||
for (PackageResourceInformation pri : pi.listIndexedResources(types)) {
|
||||
if (!pri.getFilename().contains("ig-r4")) {
|
||||
if (!pri.getFilename().contains("ig-r4") && (loader == null || loader.wantLoad(pi, pri))) {
|
||||
try {
|
||||
registerResourceFromPackage(new PackageResourceLoader(pri, loader), new PackageInformation(pi));
|
||||
t++;
|
||||
|
|
|
|||
|
|
@ -394,7 +394,7 @@ public class FmlParser extends ParserBase {
|
|||
if (rule.getChildrenByName("source").size() != 1 || !rule.getChildrenByName("source").get(0).hasChild("element"))
|
||||
throw lexer.error("Complex rules must have an explicit name");
|
||||
if (rule.getChildrenByName("source").get(0).hasChild("type"))
|
||||
rule.makeElement("name").setValue(rule.getChildrenByName("source").get(0).getNamedChildValue("element") + rule.getChildrenByName("source").get(0).getNamedChildValue("type"));
|
||||
rule.makeElement("name").setValue(rule.getChildrenByName("source").get(0).getNamedChildValue("element") + Utilities.capitalize(rule.getChildrenByName("source").get(0).getNamedChildValue("type")));
|
||||
else
|
||||
rule.makeElement("name").setValue(rule.getChildrenByName("source").get(0).getNamedChildValue("element"));
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1245,6 +1245,20 @@ public class StructureDefinition extends CanonicalResource {
|
|||
return null;
|
||||
}
|
||||
|
||||
|
||||
public ElementDefinition getElementById(String id) {
|
||||
if (id == null) {
|
||||
return null;
|
||||
}
|
||||
for (ElementDefinition ed : getElement()) {
|
||||
if (id.equals(ed.getId())) {
|
||||
return ed;
|
||||
}
|
||||
}
|
||||
return null;
|
||||
}
|
||||
|
||||
|
||||
// end addition
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -72,7 +72,11 @@ public class QuestionnaireRenderer extends TerminologyRenderer {
|
|||
HierarchicalTableGenerator gen = new HierarchicalTableGenerator(context.getDestDir(), context.isInlineGraphics(), true);
|
||||
TableModel model = gen.new TableModel("qtree="+q.getId(), context.getRules() == GenerationRules.IG_PUBLISHER);
|
||||
model.setAlternating(true);
|
||||
model.setDocoImg(context.getLink(KnownLinkType.SPEC) +"help16.png");
|
||||
if (context.getRules() == GenerationRules.VALID_RESOURCE || context.isInlineGraphics()) {
|
||||
model.setDocoImg(HierarchicalTableGenerator.help16AsData());
|
||||
} else {
|
||||
model.setDocoImg(Utilities.pathURL(context.getLink(KnownLinkType.SPEC), "help16.png"));
|
||||
}
|
||||
model.setDocoRef(context.getLink(KnownLinkType.SPEC)+"formats.html#table");
|
||||
model.getTitles().add(gen.new Title(null, model.getDocoRef(), translate("sd.head", "LinkId"), translate("sd.hint", "The linkId for the item"), null, 0));
|
||||
model.getTitles().add(gen.new Title(null, model.getDocoRef(), translate("sd.head", "Text"), translate("sd.hint", "Text for the item"), null, 0));
|
||||
|
|
@ -446,7 +450,11 @@ public class QuestionnaireRenderer extends TerminologyRenderer {
|
|||
HierarchicalTableGenerator gen = new HierarchicalTableGenerator(context.getDestDir(), context.isInlineGraphics(), true);
|
||||
TableModel model = gen.new TableModel("qtree="+q.getId(), true);
|
||||
model.setAlternating(true);
|
||||
model.setDocoImg(context.getLink(KnownLinkType.SPEC) +"help16.png");
|
||||
if (context.getRules() == GenerationRules.VALID_RESOURCE || context.isInlineGraphics()) {
|
||||
model.setDocoImg(HierarchicalTableGenerator.help16AsData());
|
||||
} else {
|
||||
model.setDocoImg(Utilities.pathURL(context.getLink(KnownLinkType.SPEC), "help16.png"));
|
||||
}
|
||||
model.setDocoRef(context.getLink(KnownLinkType.SPEC)+"formats.html#table");
|
||||
model.getTitles().add(gen.new Title(null, model.getDocoRef(), translate("sd.head", "LinkId"), translate("sd.hint", "The linkId for the item"), null, 0));
|
||||
model.getTitles().add(gen.new Title(null, model.getDocoRef(), translate("sd.head", "Description & Constraints"), translate("sd.hint", "Additional information about the item"), null, 0));
|
||||
|
|
|
|||
|
|
@ -15,6 +15,7 @@ import org.hl7.fhir.r5.model.StructureDefinition;
|
|||
import org.hl7.fhir.r5.renderers.utils.BaseWrappers.BaseWrapper;
|
||||
import org.hl7.fhir.r5.renderers.utils.BaseWrappers.ResourceWrapper;
|
||||
import org.hl7.fhir.r5.renderers.utils.RenderingContext;
|
||||
import org.hl7.fhir.r5.renderers.utils.RenderingContext.GenerationRules;
|
||||
import org.hl7.fhir.r5.renderers.utils.RenderingContext.KnownLinkType;
|
||||
import org.hl7.fhir.utilities.Utilities;
|
||||
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator;
|
||||
|
|
@ -63,7 +64,11 @@ public class QuestionnaireResponseRenderer extends ResourceRenderer {
|
|||
HierarchicalTableGenerator gen = new HierarchicalTableGenerator(context.getDestDir(), context.isInlineGraphics(), true);
|
||||
TableModel model = gen.new TableModel("qtree="+qr.getId(), false);
|
||||
model.setAlternating(true);
|
||||
model.setDocoImg(context.getLink(KnownLinkType.SPEC) +"help16.png");
|
||||
if (context.getRules() == GenerationRules.VALID_RESOURCE || context.isInlineGraphics()) {
|
||||
model.setDocoImg(HierarchicalTableGenerator.help16AsData());
|
||||
} else {
|
||||
model.setDocoImg(Utilities.pathURL(context.getLink(KnownLinkType.SPEC), "help16.png"));
|
||||
}
|
||||
model.setDocoRef(context.getLink(KnownLinkType.SPEC)+"formats.html#table");
|
||||
model.getTitles().add(gen.new Title(null, model.getDocoRef(), translate("sd.head", "LinkId"), translate("sd.hint", "The linkId for the item"), null, 0));
|
||||
model.getTitles().add(gen.new Title(null, model.getDocoRef(), translate("sd.head", "Text"), translate("sd.hint", "Text for the item"), null, 0));
|
||||
|
|
@ -86,7 +91,11 @@ public class QuestionnaireResponseRenderer extends ResourceRenderer {
|
|||
HierarchicalTableGenerator gen = new HierarchicalTableGenerator(context.getDestDir(), context.isInlineGraphics(), true);
|
||||
TableModel model = gen.new TableModel("qtree="+q.getId(), true);
|
||||
model.setAlternating(true);
|
||||
model.setDocoImg(context.getLink(KnownLinkType.SPEC) +"help16.png");
|
||||
if (context.getRules() == GenerationRules.VALID_RESOURCE || context.isInlineGraphics()) {
|
||||
model.setDocoImg(HierarchicalTableGenerator.help16AsData());
|
||||
} else {
|
||||
model.setDocoImg(Utilities.pathURL(context.getLink(KnownLinkType.SPEC), "help16.png"));
|
||||
}
|
||||
model.setDocoRef(context.getLink(KnownLinkType.SPEC)+"formats.html#table");
|
||||
model.getTitles().add(gen.new Title(null, model.getDocoRef(), translate("sd.head", "LinkId"), translate("sd.hint", "The linkId for the item"), null, 0));
|
||||
model.getTitles().add(gen.new Title(null, model.getDocoRef(), translate("sd.head", "Text"), translate("sd.hint", "Text for the item"), null, 0));
|
||||
|
|
|
|||
|
|
@ -3,10 +3,12 @@ package org.hl7.fhir.r5.renderers;
|
|||
import org.hl7.fhir.r5.context.IWorkerContext;
|
||||
import org.hl7.fhir.r5.renderers.utils.RenderingContext;
|
||||
import org.hl7.fhir.r5.renderers.utils.RenderingContext.GenerationRules;
|
||||
import org.hl7.fhir.r5.renderers.utils.RenderingContext.KnownLinkType;
|
||||
import org.hl7.fhir.r5.renderers.utils.RenderingContext.ResourceRendererMode;
|
||||
import org.hl7.fhir.r5.utils.TranslatingUtilities;
|
||||
import org.hl7.fhir.utilities.MarkDownProcessor;
|
||||
import org.hl7.fhir.utilities.StandardsStatus;
|
||||
import org.hl7.fhir.utilities.Utilities;
|
||||
import org.hl7.fhir.utilities.MarkDownProcessor.Dialect;
|
||||
import org.hl7.fhir.utilities.validation.ValidationOptions;
|
||||
import org.hl7.fhir.utilities.xhtml.XhtmlNode;
|
||||
|
|
@ -76,7 +78,7 @@ public class Renderer extends TranslatingUtilities {
|
|||
public void genStandardsStatus(XhtmlNode td, StandardsStatus ss) {
|
||||
if (ss != null) {
|
||||
td.tx(" ");
|
||||
XhtmlNode a = td.ah("versions.html#std-process", "Standards Status = "+ss.toDisplay());
|
||||
XhtmlNode a = td.ah(Utilities.pathURL(context.getLink(KnownLinkType.SPEC), "versions.html#std-process"), "Standards Status = "+ss.toDisplay());
|
||||
a.style("padding-left: 3px; padding-right: 3px; border: 1px grey solid; font-weight: bold; color: black; background-color: "+ss.getColor());
|
||||
a.tx(ss.getAbbrev());
|
||||
}
|
||||
|
|
|
|||
|
|
@ -516,11 +516,15 @@ public class StructureDefinitionRenderer extends ResourceRenderer {
|
|||
}
|
||||
}
|
||||
|
||||
public TableModel initCustomTable(HierarchicalTableGenerator gen, String prefix, boolean isLogical, boolean alternating, String id, boolean isActive, List<Column> columns) {
|
||||
public TableModel initCustomTable(HierarchicalTableGenerator gen, String prefix, boolean isLogical, boolean alternating, String id, boolean isActive, List<Column> columns) throws IOException {
|
||||
TableModel model = gen.new TableModel(id, isActive);
|
||||
|
||||
model.setAlternating(alternating);
|
||||
if (context.getRules() == GenerationRules.VALID_RESOURCE || context.isInlineGraphics()) {
|
||||
model.setDocoImg(HierarchicalTableGenerator.help16AsData());
|
||||
} else {
|
||||
model.setDocoImg(Utilities.pathURL(prefix, "help16.png"));
|
||||
}
|
||||
model.setDocoRef(Utilities.pathURL("https://build.fhir.org/ig/FHIR/ig-guidance", "readingIgs.html#table-views"));
|
||||
model.getTitles().add(gen.new Title(null, model.getDocoRef(), translate("sd.head", "Name"), translate("sd.hint", "The logical name of the element"), null, 0));
|
||||
for (Column col : columns) {
|
||||
|
|
@ -2586,10 +2590,14 @@ public class StructureDefinitionRenderer extends ResourceRenderer {
|
|||
}
|
||||
|
||||
|
||||
private TableModel initSpanningTable(HierarchicalTableGenerator gen, String prefix, boolean isLogical, String id) {
|
||||
private TableModel initSpanningTable(HierarchicalTableGenerator gen, String prefix, boolean isLogical, String id) throws IOException {
|
||||
TableModel model = gen.new TableModel(id, true);
|
||||
|
||||
model.setDocoImg(prefix+"help16.png");
|
||||
if (context.getRules() == GenerationRules.VALID_RESOURCE || context.isInlineGraphics()) {
|
||||
model.setDocoImg(HierarchicalTableGenerator.help16AsData());
|
||||
} else {
|
||||
model.setDocoImg(Utilities.pathURL(prefix, "help16.png"));
|
||||
}
|
||||
model.setDocoRef(Utilities.pathURL(prefix, "formats.html#table")); // todo: change to graph definition
|
||||
model.getTitles().add(gen.new Title(null, model.getDocoRef(), "Property", "A profiled resource", null, 0));
|
||||
model.getTitles().add(gen.new Title(null, model.getDocoRef(), "Card.", "Minimum and Maximum # of times the the element can appear in the instance", null, 0));
|
||||
|
|
|
|||
|
|
@ -461,7 +461,7 @@ public class StructureMapRenderer extends TerminologyRenderer {
|
|||
if (n.equals(s) || n.equals("\"" + s + "\""))
|
||||
return true;
|
||||
if (source.get(0).hasType()) {
|
||||
s = source.get(0).getElement() + "-" + source.get(0).getType();
|
||||
s = source.get(0).getElement() + Utilities.capitalize(source.get(0).getType());
|
||||
return n.equals(s) || n.equals("\"" + s + "\"");
|
||||
}
|
||||
return false;
|
||||
|
|
|
|||
|
|
@ -13,6 +13,7 @@ import org.hl7.fhir.r5.model.Bundle;
|
|||
import org.hl7.fhir.r5.model.CodeSystem;
|
||||
import org.hl7.fhir.r5.model.Resource;
|
||||
import org.hl7.fhir.utilities.npm.NpmPackage;
|
||||
import org.hl7.fhir.utilities.npm.NpmPackage.PackageResourceInformation;
|
||||
|
||||
public class TestPackageLoader implements IContextResourceLoader {
|
||||
|
||||
|
|
@ -62,4 +63,14 @@ public class TestPackageLoader implements IContextResourceLoader {
|
|||
return url;
|
||||
}
|
||||
|
||||
@Override
|
||||
public IContextResourceLoader setLoadProfiles(boolean value) {
|
||||
return this;
|
||||
}
|
||||
|
||||
@Override
|
||||
public boolean wantLoad(NpmPackage pi, PackageResourceInformation pri) {
|
||||
return true;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1000,7 +1000,7 @@ public class StructureMapUtilities {
|
|||
if (rule.getSource().size() != 1 || !rule.getSourceFirstRep().hasElement() && exceptionsForChecks )
|
||||
throw lexer.error("Complex rules must have an explicit name");
|
||||
if (rule.getSourceFirstRep().hasType())
|
||||
rule.setName(rule.getSourceFirstRep().getElement() + "-" + rule.getSourceFirstRep().getType());
|
||||
rule.setName(rule.getSourceFirstRep().getElement() + Utilities.capitalize(rule.getSourceFirstRep().getType()));
|
||||
else
|
||||
rule.setName(rule.getSourceFirstRep().getElement());
|
||||
}
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>org.hl7.fhir.core</artifactId>
|
||||
<version>5.6.113-SNAPSHOT</version>
|
||||
<version>5.6.115-SNAPSHOT</version>
|
||||
<relativePath>../pom.xml</relativePath>
|
||||
</parent>
|
||||
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>org.hl7.fhir.core</artifactId>
|
||||
<version>5.6.113-SNAPSHOT</version>
|
||||
<version>5.6.115-SNAPSHOT</version>
|
||||
<relativePath>../pom.xml</relativePath>
|
||||
</parent>
|
||||
|
||||
|
|
|
|||
|
|
@ -115,15 +115,28 @@ public class FTPClient {
|
|||
|
||||
resetTimers();
|
||||
|
||||
logger.debug("Initial Working directory: " + clientImpl.printWorkingDirectory());
|
||||
clientImpl.setFileType(FTP.BINARY_FILE_TYPE);
|
||||
clientImpl.enterLocalPassiveMode();
|
||||
|
||||
logger.debug("Setting initial working directory: " + clientImpl.printWorkingDirectory());
|
||||
|
||||
clientImpl.changeWorkingDirectory(path);
|
||||
|
||||
throwExceptionForNegativeCompletion("FTP server could not establish default working directory", true);
|
||||
logger.debug("Set initial working directory.");
|
||||
|
||||
logger.debug("Resolving remote resolved path.");
|
||||
resolvedPath = clientImpl.printWorkingDirectory();
|
||||
|
||||
logger.debug("Resolved working directory: " + resolvedPath);
|
||||
logger.debug("Resolved remote resolved path: " + resolvedPath);
|
||||
}
|
||||
|
||||
public void setBufferSize(int bufferSize) {
|
||||
clientImpl.setBufferSize(bufferSize);
|
||||
}
|
||||
|
||||
public int getBufferSize() {
|
||||
return clientImpl.getBufferSize();
|
||||
}
|
||||
|
||||
private void resetTimers() {
|
||||
|
|
@ -208,7 +221,6 @@ public class FTPClient {
|
|||
String resolvedPath = resolveRemotePath(path);
|
||||
logger.debug("Uploading file to remote path: " + resolvedPath);
|
||||
|
||||
|
||||
attemptUpload(source, resolvedPath);
|
||||
|
||||
FTPReplyCodeAndString reply = getFTPReplyCodeAndString();
|
||||
|
|
@ -239,8 +251,6 @@ public class FTPClient {
|
|||
private void attemptUpload(String source, String resolvedPath) throws IOException {
|
||||
final long startTime = System.nanoTime();
|
||||
FileInputStream localStream = new FileInputStream(source);
|
||||
clientImpl.setFileType(FTP.BINARY_FILE_TYPE);
|
||||
clientImpl.enterLocalPassiveMode();
|
||||
clientImpl.storeFile(resolvedPath, localStream);
|
||||
localStream.close();
|
||||
this.storeFileTimeNanos += System.nanoTime() - startTime;
|
||||
|
|
|
|||
|
|
@ -905,6 +905,15 @@ public class Utilities {
|
|||
return false;
|
||||
}
|
||||
|
||||
public static boolean containsInList(String value, String... array) {
|
||||
if (value == null)
|
||||
return false;
|
||||
for (String s : array)
|
||||
if (value.contains(s))
|
||||
return true;
|
||||
return false;
|
||||
}
|
||||
|
||||
public static boolean existsInList(String value, String... array) {
|
||||
if (value == null)
|
||||
return false;
|
||||
|
|
@ -1491,10 +1500,13 @@ public class Utilities {
|
|||
ZipEntry zipEntry = zis.getNextEntry();
|
||||
while (zipEntry != null) {
|
||||
boolean isDirectory = false;
|
||||
if (zipEntry.getName().endsWith("/") || zipEntry.getName().endsWith("\\")) {
|
||||
|
||||
String n = makeOSSafe(zipEntry.getName());
|
||||
|
||||
if (n.endsWith(File.separator)) {
|
||||
isDirectory = true;
|
||||
}
|
||||
Path newPath = zipSlipProtect(zipEntry, target);
|
||||
Path newPath = zipSlipProtect(n, target);
|
||||
if (isDirectory) {
|
||||
Files.createDirectories(newPath);
|
||||
} else {
|
||||
|
|
@ -1511,19 +1523,23 @@ public class Utilities {
|
|||
}
|
||||
}
|
||||
|
||||
public static Path zipSlipProtect(ZipEntry zipEntry, Path targetDir)
|
||||
public static String makeOSSafe(String name) {
|
||||
return name.replace("\\", File.separator).replace("/", File.separator);
|
||||
}
|
||||
|
||||
public static Path zipSlipProtect(String zipName, Path targetDir)
|
||||
throws IOException {
|
||||
|
||||
// test zip slip vulnerability
|
||||
// Path targetDirResolved = targetDir.resolve("../../" + zipEntry.getName());
|
||||
|
||||
Path targetDirResolved = targetDir.resolve(zipEntry.getName());
|
||||
Path targetDirResolved = targetDir.resolve(zipName);
|
||||
|
||||
// make sure normalized file still has targetDir as its prefix
|
||||
// else throws exception
|
||||
Path normalizePath = targetDirResolved.normalize();
|
||||
if (!normalizePath.startsWith(targetDir)) {
|
||||
throw new IOException("Bad zip entry: " + zipEntry.getName());
|
||||
throw new IOException("Bad zip entry: " + zipName);
|
||||
}
|
||||
|
||||
return normalizePath;
|
||||
|
|
@ -1868,7 +1884,7 @@ public class Utilities {
|
|||
if (ignoreList == null || !ignoreList.contains(f.getAbsolutePath())) {
|
||||
if (f.isDirectory()) {
|
||||
addAllFiles(res, root, f, ignoreList);
|
||||
} else {
|
||||
} else if (!f.getName().equals(".DS_Store")) {
|
||||
res.add(getRelativePath(root, f.getAbsolutePath()));
|
||||
}
|
||||
}
|
||||
|
|
@ -1932,7 +1948,7 @@ public class Utilities {
|
|||
|
||||
public static String tail(String url) {
|
||||
int i = url.length()-1;
|
||||
while (i >= 0 && isTokenChar(url.charAt(i))) {
|
||||
while (i >= 0 && (isTokenChar(url.charAt(i)) || isDigit(url.charAt(i))) ) {
|
||||
i--;
|
||||
}
|
||||
if (i < 0) {
|
||||
|
|
|
|||
|
|
@ -668,6 +668,8 @@ public class I18nConstants {
|
|||
public static final String MEASURE_SHAREABLE_MISSING_HL7 = "MEASURE_SHAREABLE_MISSING_HL7";
|
||||
public static final String MEASURE_SHAREABLE_EXTRA_MISSING_HL7 = "MEASURE_SHAREABLE_EXTRA_MISSING_HL7";
|
||||
public static final String MEASURE_SHAREABLE_EXTRA_MISSING = "MEASURE_SHAREABLE_EXTRA_MISSING";
|
||||
public static final String VALUESET_EXAMPLE_SYSTEM_ERROR = "VALUESET_EXAMPLE_SYSTEM_ERROR";
|
||||
public static final String VALUESET_EXAMPLE_SYSTEM_HINT = "VALUESET_EXAMPLE_SYSTEM_HINT";
|
||||
public static final String VALUESET_UNC_SYSTEM_WARNING = "VALUESET_UNC_SYSTEM_WARNING";
|
||||
public static final String VALUESET_UNC_SYSTEM_WARNING_VER = "VALUESET_UNC_SYSTEM_WARNING_VER";
|
||||
public static final String VALUESET_IMPORT_UNION_INTERSECTION = "VALUESET_IMPORT_UNION_INTERSECTION";
|
||||
|
|
|
|||
|
|
@ -66,6 +66,7 @@ import java.io.ByteArrayOutputStream;
|
|||
import java.io.File;
|
||||
import java.io.FileOutputStream;
|
||||
import java.io.IOException;
|
||||
import java.io.InputStream;
|
||||
import java.io.OutputStream;
|
||||
import java.util.ArrayList;
|
||||
import java.util.HashMap;
|
||||
|
|
@ -82,9 +83,9 @@ import org.commonmark.node.Node;
|
|||
import org.commonmark.parser.Parser;
|
||||
import org.commonmark.renderer.html.HtmlRenderer;
|
||||
import org.hl7.fhir.exceptions.FHIRException;
|
||||
import org.hl7.fhir.utilities.TextFile;
|
||||
import org.hl7.fhir.utilities.TranslatingUtilities;
|
||||
import org.hl7.fhir.utilities.Utilities;
|
||||
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.TableGenerationMode;
|
||||
|
||||
|
||||
public class HierarchicalTableGenerator extends TranslatingUtilities {
|
||||
|
|
@ -634,13 +635,17 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
|
|||
checkSetup();
|
||||
}
|
||||
|
||||
public TableModel initNormalTable(String prefix, boolean isLogical, boolean alternating, String id, boolean isActive, TableGenerationMode mode) {
|
||||
public TableModel initNormalTable(String prefix, boolean isLogical, boolean alternating, String id, boolean isActive, TableGenerationMode mode) throws IOException {
|
||||
this.mode = mode;
|
||||
|
||||
TableModel model = new TableModel(id, isActive);
|
||||
|
||||
model.setAlternating(alternating);
|
||||
if (mode == TableGenerationMode.XML) {
|
||||
model.setDocoImg(help16AsData());
|
||||
} else {
|
||||
model.setDocoImg(Utilities.pathURL(prefix, "help16.png"));
|
||||
}
|
||||
model.setDocoRef(Utilities.pathURL("https://build.fhir.org/ig/FHIR/ig-guidance", "readingIgs.html#table-views"));
|
||||
model.getTitles().add(new Title(null, model.getDocoRef(), translate("sd.head", "Name"), translate("sd.hint", "The logical name of the element"), null, 0));
|
||||
model.getTitles().add(new Title(null, model.getDocoRef(), translate("sd.head", "Flags"), translate("sd.hint", "Information about the use of the element"), null, 0));
|
||||
|
|
@ -653,11 +658,15 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
|
|||
return model;
|
||||
}
|
||||
|
||||
public TableModel initComparisonTable(String prefix, String id) {
|
||||
public TableModel initComparisonTable(String prefix, String id) throws IOException {
|
||||
TableModel model = new TableModel(id, true);
|
||||
|
||||
model.setAlternating(true);
|
||||
if (mode == TableGenerationMode.XML) {
|
||||
model.setDocoImg(help16AsData()); // #FIXME
|
||||
} else {
|
||||
model.setDocoImg(Utilities.pathURL(prefix, "help16.png"));
|
||||
}
|
||||
model.setDocoRef(Utilities.pathURL(prefix, "formats.html#table"));
|
||||
model.getTitles().add(new Title(null, model.getDocoRef(), translate("sd.head", "Name"), translate("sd.hint", "The logical name of the element"), null, 0));
|
||||
model.getTitles().add(new Title(null, model.getDocoRef(), translate("sd.head", "L Flags"), translate("sd.hint", "Information about the use of the element - Left Structure"), null, 0).setStyle("border-left: 1px grey solid"));
|
||||
|
|
@ -913,6 +922,15 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
|
|||
return corePrefix+filename;
|
||||
}
|
||||
|
||||
public static String help16AsData() throws IOException {
|
||||
ClassLoader classLoader = HierarchicalTableGenerator.class.getClassLoader();
|
||||
InputStream help = classLoader.getResourceAsStream("help16.png");
|
||||
StringBuilder b = new StringBuilder();
|
||||
b.append("data:image/png;base64,");
|
||||
byte[] bytes = TextFile.streamToBytes(help);
|
||||
b.append(new String(Base64.encodeBase64(bytes)));
|
||||
return b.toString();
|
||||
}
|
||||
|
||||
private void checkModel(TableModel model) throws FHIRException {
|
||||
check(!model.getTitles().isEmpty(), "Must have titles");
|
||||
|
|
|
|||
|
|
@ -187,7 +187,11 @@ public class XhtmlGenerator {
|
|||
out.write(" ");
|
||||
if (adorner != null) {
|
||||
XhtmlGeneratorAdornerState attrState = adorner.getAttributeMarkup(this, newstate, node, node.getAttributes().item(i).getNodeName(), node.getAttributes().item(i).getTextContent());
|
||||
if (attrState.getAltText() != null) {
|
||||
out.write(node.getAttributes().item(i).getNodeName()+"=\"<span class=\"xmlattrvalue\">"+attrState.getPrefix()+escapeHtml(Utilities.escapeXml(attrState.getAltText()), level)+attrState.getSuffix()+"</span>\"");
|
||||
} else {
|
||||
out.write(node.getAttributes().item(i).getNodeName()+"=\"<span class=\"xmlattrvalue\">"+attrState.getPrefix()+escapeHtml(Utilities.escapeXml(node.getAttributes().item(i).getTextContent()), level)+attrState.getSuffix()+"</span>\"");
|
||||
}
|
||||
} else
|
||||
out.write(node.getAttributes().item(i).getNodeName()+"=\"<span class=\"xmlattrvalue\">"+escapeHtml(Utilities.escapeXml(node.getAttributes().item(i).getTextContent()), level)+"</span>\"");
|
||||
}
|
||||
|
|
|
|||
|
|
@ -41,6 +41,7 @@ public interface XhtmlGeneratorAdorner {
|
|||
private String suffix;
|
||||
private String supressionMessage;
|
||||
private String path;
|
||||
private String altText;
|
||||
|
||||
public XhtmlGeneratorAdornerState(String path, String prefix, String suffix) {
|
||||
super();
|
||||
|
|
@ -49,6 +50,15 @@ public interface XhtmlGeneratorAdorner {
|
|||
this.suffix = suffix;
|
||||
}
|
||||
|
||||
|
||||
public XhtmlGeneratorAdornerState(String path, String prefix, String suffix, String altText) {
|
||||
super();
|
||||
this.path = path;
|
||||
this.prefix = prefix;
|
||||
this.suffix = suffix;
|
||||
this.altText = altText;
|
||||
}
|
||||
|
||||
public XhtmlGeneratorAdornerState(String path, String supressionMessage) {
|
||||
super();
|
||||
this.path = path;
|
||||
|
|
@ -70,6 +80,11 @@ public interface XhtmlGeneratorAdorner {
|
|||
public String getPath() {
|
||||
return path;
|
||||
}
|
||||
|
||||
public String getAltText() {
|
||||
return altText;
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
XhtmlGeneratorAdornerState getState(XhtmlGenerator ref, XhtmlGeneratorAdornerState state, Element node) throws Exception;
|
||||
|
|
|
|||
|
|
@ -558,6 +558,8 @@ SEARCHPARAMETER_EXP_WRONG = The expression ''{2}'' is not compatible with the ex
|
|||
VALUESET_NO_SYSTEM_WARNING = No System specified, so Concepts and Filters can't be checked
|
||||
VALUESET_INCLUDE_INVALID_CONCEPT_CODE = The code {1} is not valid in the system {0}
|
||||
VALUESET_INCLUDE_INVALID_CONCEPT_CODE_VER = The code {2} is not valid in the system {0} version {1}
|
||||
VALUESET_EXAMPLE_SYSTEM_HINT = Example System ''{0}'' specified, so Concepts and Filters can''t be checked
|
||||
VALUESET_EXAMPLE_SYSTEM_ERROR = Example System ''{0}'' specified, which is illegal. Concepts and Filters can''t be checked
|
||||
VALUESET_UNC_SYSTEM_WARNING = Unknown System ''{0}'' specified, so Concepts and Filters can''t be checked (Details: {1})
|
||||
VALUESET_UNC_SYSTEM_WARNING_VER = Unknown System/Version ''{0}'' specified, so Concepts and Filters can''t be checked (Details: {1})
|
||||
Extension_PROF_Type = The Profile ''{0}'' definition allows for the type {1} but found type {2}
|
||||
|
|
@ -855,7 +857,7 @@ SM_NO_LIST_RULE_ID_NEEDED = A list ruleId should not be provided since this is a
|
|||
SM_LIST_RULE_ID_ONLY_WHEN_SHARE = A ruleId should only be provided when the rule mode is ''share''
|
||||
SM_RULE_SOURCE_UNASSIGNED = The source statement doesn''t assign a variable to the source - check that this is what is intended
|
||||
SM_TARGET_PATH_MULTIPLE_MATCHES = The target path {0}.{1} refers to the path {2} which is could be a reference to multiple elements ({3}). No further checking can be performed
|
||||
SM_SOURCE_TYPE_INVALID = The type {0} is not valid in this source context {1}. The possible types are [{2}]
|
||||
SM_SOURCE_TYPE_INVALID = The type {0} is not valid in the source context {1}. The possible types are [{2}]
|
||||
SM_TARGET_TRANSFORM_PARAM_COUNT_RANGE = Transform {0} takes {1}-{2} parameter(s) but {3} were found
|
||||
SM_TARGET_TRANSFORM_PARAM_COUNT_SINGLE = Transform {0} takes {1} parameter(s) but {2} were found
|
||||
SM_TARGET_TRANSFORM_NOT_CHECKED = Transform {0} not checked dyet
|
||||
|
|
|
|||
Binary file not shown.
|
After Width: | Height: | Size: 714 B |
|
|
@ -30,8 +30,11 @@ public class FTPClientTest implements ResourceLoaderTests {
|
|||
public static final String DUMMY_FILE_TO_DELETE = "dummyFileToDelete";
|
||||
|
||||
public static final String DUMMY_FILE_TO_UPLOAD = "dummyFileToUpload";
|
||||
|
||||
public static final String DUMMY_FILE_TO_UPLOAD_2 = "dummyFileToUpload2";
|
||||
public static final int FAKE_FTP_PORT = 8022;
|
||||
public static final String DUMMY_FILE_CONTENT = "Dummy file content\nMore content\n";
|
||||
public static final String DUMMY_FILE_CONTENT_2 = "Dummy file content 2\nMore content\n";
|
||||
public static final String LOCALHOST = "localhost";
|
||||
|
||||
|
||||
|
|
@ -48,26 +51,31 @@ public class FTPClientTest implements ResourceLoaderTests {
|
|||
|
||||
|
||||
Path dummyFileToUploadPath;
|
||||
|
||||
Path dummyFileToUploadPath2;
|
||||
Path dummyUploadedFilePath;
|
||||
Path dummyUploadedFilePath2;
|
||||
|
||||
String dummyFileContent;
|
||||
|
||||
String dummyFileContent2;
|
||||
|
||||
@BeforeEach
|
||||
public void setup() throws IOException {
|
||||
setupDummyFileToUpload();
|
||||
setupDummyFilesToUpload();
|
||||
setupFakeFtpDirectory();
|
||||
setupFakeFtpServer();
|
||||
}
|
||||
|
||||
private void setupDummyFileToUpload() throws IOException {
|
||||
dummyFileContent = createDummyFileContent();
|
||||
private void setupDummyFilesToUpload() throws IOException {
|
||||
dummyFileContent = DUMMY_FILE_CONTENT;
|
||||
dummyFileContent2 = DUMMY_FILE_CONTENT;
|
||||
|
||||
dummyFileToUploadPath = Files.createTempFile("dummyFtpFileToUpload", "dummy");
|
||||
Files.write(dummyFileToUploadPath, DUMMY_FILE_CONTENT.getBytes(StandardCharsets.UTF_8));
|
||||
}
|
||||
|
||||
private String createDummyFileContent() {
|
||||
return DUMMY_FILE_CONTENT;
|
||||
dummyFileToUploadPath2 = Files.createTempFile("dummyFtpFileToUpload2", "dummy");
|
||||
Files.write(dummyFileToUploadPath2, DUMMY_FILE_CONTENT_2.getBytes(StandardCharsets.UTF_8));
|
||||
}
|
||||
|
||||
public void setupFakeFtpServer() throws IOException {
|
||||
|
|
@ -101,6 +109,7 @@ public class FTPClientTest implements ResourceLoaderTests {
|
|||
|
||||
dummyFileToDeletePath = Files.createFile(relativePath2.resolve(DUMMY_FILE_TO_DELETE));
|
||||
dummyUploadedFilePath = relativePath2.resolve(DUMMY_FILE_TO_UPLOAD);
|
||||
dummyUploadedFilePath2 = relativePath2.resolve(DUMMY_FILE_TO_UPLOAD_2);
|
||||
}
|
||||
|
||||
@AfterEach
|
||||
|
|
@ -141,6 +150,7 @@ public class FTPClientTest implements ResourceLoaderTests {
|
|||
|
||||
private FTPClient connectToFTPClient() throws IOException {
|
||||
FTPClient client = new FTPClient(LOCALHOST, FAKE_FTP_PORT, RELATIVE_PATH_1, DUMMY_USER, DUMMY_PASSWORD);
|
||||
client.setBufferSize(16000);
|
||||
client.connect();
|
||||
|
||||
assertAllMillisFieldsAreZero(client);
|
||||
|
|
@ -175,21 +185,43 @@ public class FTPClientTest implements ResourceLoaderTests {
|
|||
|
||||
client.upload(dummyFileToUploadPath.toFile().getAbsolutePath(), RELATIVE_PATH_2 + "/" + DUMMY_FILE_TO_UPLOAD);
|
||||
|
||||
assertUploadedFileCorrect(uploadFilePath);
|
||||
assertUploadedFileCorrect(uploadFilePath, DUMMY_FILE_CONTENT);
|
||||
|
||||
assertTrue(client.getDeleteFileTimeNanos() == 0);
|
||||
assertTrue(client.getStoreFileTimeNanos() > 0);
|
||||
assertTrue(client.getCreateRemotePathIfNotExistsNanos() == 0);
|
||||
}
|
||||
|
||||
private void assertUploadedFileCorrect(String uploadedFilePath) throws IOException {
|
||||
@Test
|
||||
public void testMultiUpload() throws IOException {
|
||||
FTPClient client = connectToFTPClient();
|
||||
|
||||
String uploadFilePath = dummyUploadedFilePath.toFile().getAbsolutePath();
|
||||
assertFalse(fakeFtpServer.getFileSystem().exists(uploadFilePath));
|
||||
|
||||
String uploadFilePath2 = dummyUploadedFilePath2.toFile().getAbsolutePath();
|
||||
assertFalse(fakeFtpServer.getFileSystem().exists(uploadFilePath));
|
||||
|
||||
client.upload(dummyFileToUploadPath.toFile().getAbsolutePath(), RELATIVE_PATH_2 + "/" + DUMMY_FILE_TO_UPLOAD);
|
||||
|
||||
client.upload(dummyFileToUploadPath2.toFile().getAbsolutePath(), RELATIVE_PATH_2 + "/" + DUMMY_FILE_TO_UPLOAD_2);
|
||||
|
||||
assertUploadedFileCorrect(uploadFilePath, DUMMY_FILE_CONTENT);
|
||||
assertUploadedFileCorrect(uploadFilePath2, DUMMY_FILE_CONTENT_2);
|
||||
|
||||
assertTrue(client.getDeleteFileTimeNanos() == 0);
|
||||
assertTrue(client.getStoreFileTimeNanos() > 0);
|
||||
assertTrue(client.getCreateRemotePathIfNotExistsNanos() == 0);
|
||||
}
|
||||
|
||||
private void assertUploadedFileCorrect(String uploadedFilePath, String expectedFileContent) throws IOException {
|
||||
assertTrue(fakeFtpServer.getFileSystem().exists(uploadedFilePath));
|
||||
FileEntry fileEntry = (FileEntry)fakeFtpServer.getFileSystem().getEntry(uploadedFilePath);
|
||||
assertNotNull(fileEntry);
|
||||
InputStream inputStream = fileEntry.createInputStream();
|
||||
byte[] bytes = IOUtils.toByteArray(inputStream);
|
||||
String actualContent = new String(bytes, StandardCharsets.UTF_8);
|
||||
assertEquals(DUMMY_FILE_CONTENT,actualContent);
|
||||
assertEquals(expectedFileContent,actualContent);
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
@ -237,7 +269,7 @@ public class FTPClientTest implements ResourceLoaderTests {
|
|||
assertTrue(fakeFtpServer.getFileSystem().exists(newPath1.toFile().getAbsolutePath()));
|
||||
assertTrue(fakeFtpServer.getFileSystem().exists(newPath2.toFile().getAbsolutePath()));
|
||||
|
||||
assertUploadedFileCorrect(uploadFilePath.toFile().getAbsolutePath());
|
||||
assertUploadedFileCorrect(uploadFilePath.toFile().getAbsolutePath(), DUMMY_FILE_CONTENT);
|
||||
|
||||
assertTrue(client.getDeleteFileTimeNanos() == 0);
|
||||
assertTrue(client.getStoreFileTimeNanos() > 0);
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>org.hl7.fhir.core</artifactId>
|
||||
<version>5.6.113-SNAPSHOT</version>
|
||||
<version>5.6.115-SNAPSHOT</version>
|
||||
<relativePath>../pom.xml</relativePath>
|
||||
</parent>
|
||||
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>org.hl7.fhir.core</artifactId>
|
||||
<version>5.6.113-SNAPSHOT</version>
|
||||
<version>5.6.115-SNAPSHOT</version>
|
||||
<relativePath>../pom.xml</relativePath>
|
||||
</parent>
|
||||
|
||||
|
|
|
|||
|
|
@ -155,6 +155,7 @@ public class BaseValidator implements IValidationContextResourceLoader {
|
|||
protected List<ValidationMessage> messagesToRemove = new ArrayList<>();
|
||||
private ValidationLevel level = ValidationLevel.HINTS;
|
||||
protected Coding jurisdiction;
|
||||
protected boolean allowExamples;
|
||||
|
||||
public BaseValidator(IWorkerContext context, XVerExtensionManager xverManager) {
|
||||
super();
|
||||
|
|
@ -1231,4 +1232,17 @@ public class BaseValidator implements IValidationContextResourceLoader {
|
|||
String url = cr.getChildValue("url");
|
||||
return url != null && url.contains("hl7");
|
||||
}
|
||||
|
||||
public boolean isAllowExamples() {
|
||||
return this.allowExamples;
|
||||
}
|
||||
|
||||
public void setAllowExamples(boolean value) {
|
||||
this.allowExamples = value;
|
||||
}
|
||||
|
||||
protected boolean isExampleUrl(String url) {
|
||||
return Utilities.containsInList(url, "example.org", "acme.com", "acme.org");
|
||||
|
||||
}
|
||||
}
|
||||
|
|
@ -65,8 +65,10 @@ public class CodeSystemValidator extends BaseValidator {
|
|||
|
||||
private void checkCodes(Set<String> codes, List<ConceptDefinitionComponent> list, String path, List<ValidationMessage> errors) {
|
||||
for (ConceptDefinitionComponent cc : list) {
|
||||
String npath = path+".concept.descendents().where(code = '"+cc.getCode()+"')";
|
||||
rule(errors, NO_RULE_DATE, IssueType.BUSINESSRULE, npath, !codes.contains(cc.getCode()), "Duplicate Code "+cc.getCode());
|
||||
String npath = path+".concept.where(code = '"+cc.getCode()+"')";
|
||||
if (codes.contains(cc.getCode())) {
|
||||
rule(errors, NO_RULE_DATE, IssueType.BUSINESSRULE, npath, false, "Duplicate Code "+cc.getCode());
|
||||
}
|
||||
codes.add(cc.getCode());
|
||||
checkCodes(codes, cc.getConcept(), npath, errors);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -471,7 +471,6 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
|
|||
private IValidationProfileUsageTracker tracker;
|
||||
private ValidatorHostServices validatorServices;
|
||||
private boolean assumeValidRestReferences;
|
||||
private boolean allowExamples;
|
||||
private boolean securityChecks;
|
||||
private ProfileUtilities profileUtilities;
|
||||
private boolean crumbTrails;
|
||||
|
|
@ -586,14 +585,6 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
|
|||
this.assumeValidRestReferences = value;
|
||||
}
|
||||
|
||||
public boolean isAllowExamples() {
|
||||
return this.allowExamples;
|
||||
}
|
||||
|
||||
public void setAllowExamples(boolean value) {
|
||||
this.allowExamples = value;
|
||||
}
|
||||
|
||||
public boolean isAllowComments() {
|
||||
return allowComments;
|
||||
}
|
||||
|
|
@ -2646,7 +2637,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
|
|||
if (fetcher != null && !type.equals("uuid")) {
|
||||
boolean found;
|
||||
try {
|
||||
found = isDefinitionURL(url) || (allowExamples && (url.contains("example.org") || url.contains("acme.com")) || url.contains("acme.org")) || (url.startsWith("http://hl7.org/fhir/tools")) ||
|
||||
found = isDefinitionURL(url) || (allowExamples && (url.contains("example.org") || url.contains("acme.com")) || url.contains("acme.org")) /* || (url.startsWith("http://hl7.org/fhir/tools")) */ ||
|
||||
SpecialExtensions.isKnownExtension(url) || isXverUrl(url);
|
||||
if (!found) {
|
||||
found = fetcher.resolveURL(this, hostContext, path, url, type);
|
||||
|
|
@ -5043,7 +5034,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
|
|||
} else if (element.getType().equals("StructureMap")) {
|
||||
return new StructureMapValidator(context, timeTracker, fpe, xverManager,profileUtilities, jurisdiction).validateStructureMap(errors, element, stack);
|
||||
} else if (element.getType().equals("ValueSet")) {
|
||||
return new ValueSetValidator(context, timeTracker, this, xverManager, jurisdiction).validateValueSet(errors, element, stack);
|
||||
return new ValueSetValidator(context, timeTracker, this, xverManager, jurisdiction, allowExamples).validateValueSet(errors, element, stack);
|
||||
} else {
|
||||
return true;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -199,6 +199,11 @@ public class StructureMapValidator extends BaseValidator {
|
|||
return sd.getUrl().equals(other.sd.getUrl()) && ed.getPath().equals(other.ed.getPath()) && Utilities.stringsEqual(type, other.type);
|
||||
}
|
||||
|
||||
@Override
|
||||
public String toString() {
|
||||
return summary();
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
public class VariableSet {
|
||||
|
|
@ -623,10 +628,16 @@ public class StructureMapValidator extends BaseValidator {
|
|||
} else {
|
||||
ok = false;
|
||||
}
|
||||
}
|
||||
// check condition
|
||||
// check check
|
||||
}
|
||||
} else {
|
||||
String variable = source.getChildValue("variable");
|
||||
if (variable != null) {
|
||||
variables.add(variable, v.getMode()); // may overwrite
|
||||
|
||||
}
|
||||
}
|
||||
}
|
||||
return ok;
|
||||
}
|
||||
|
|
@ -873,7 +884,7 @@ public class StructureMapValidator extends BaseValidator {
|
|||
// under some special conditions, we can infer what the type will be:
|
||||
// * there's a nominated default variable
|
||||
// * that variable has as single type
|
||||
// * there's a create with no param
|
||||
// * there's a create/copy with no param
|
||||
// * there's a single dependent rule with name = StructureMapUtilities.DEF_GROUP_NAME
|
||||
// * there's a default type group for the type of the source type
|
||||
// otherwise, we can't know the target type.
|
||||
|
|
@ -882,11 +893,25 @@ public class StructureMapValidator extends BaseValidator {
|
|||
VariableDefn v = variables.getVariable(ruleInfo.getDefVariable(), SOURCE);
|
||||
if (v != null && v.getEd() != null && (v.getEd().getType().size() == 1 || v.getType() != null)) {
|
||||
List<Element> dependents = rule.getChildrenByName("dependent");
|
||||
if (dependents.size() == 1 && StructureMapUtilities.DEF_GROUP_NAME.equals(dependents.get(0).getChildValue("name"))) {
|
||||
String type = v.getType() != null ? getTypeFromDefn(v.getEd(), v.getType()) : v.getEd().getTypeFirstRep().getWorkingCode();
|
||||
if (dependents.size() == 1 && StructureMapUtilities.DEF_GROUP_NAME.equals(dependents.get(0).getChildValue("name"))) {
|
||||
// now, we look for a default group.
|
||||
// todo: look in this source
|
||||
// now look through the inputs
|
||||
for (StructureMap map : imports) {
|
||||
for (StructureMapGroupComponent grp : map.getGroup()) {
|
||||
if (grp.getTypeMode() != StructureMapGroupTypeMode.NULL && grp.getInput().size() == 2) {
|
||||
String grpType = getTypeForGroupInput(map, grp, grp.getInput().get(0));
|
||||
if (sameTypes(type, grpType)) {
|
||||
String tgtType = getTypeForGroupInput(map, grp, grp.getInput().get(1));
|
||||
if (tgtType != null) {
|
||||
return tgtType;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
} else if (dependents.size() == 0) {
|
||||
for (StructureMap map : imports) {
|
||||
for (StructureMapGroupComponent grp : map.getGroup()) {
|
||||
if (grp.getTypeMode() == StructureMapGroupTypeMode.TYPEANDTYPES && grp.getInput().size() == 2) {
|
||||
|
|
@ -900,6 +925,7 @@ public class StructureMapValidator extends BaseValidator {
|
|||
}
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -43,13 +43,13 @@ public class ValueSetValidator extends BaseValidator {
|
|||
|
||||
private InstanceValidator parent;
|
||||
|
||||
public ValueSetValidator(IWorkerContext context, TimeTracker timeTracker, InstanceValidator parent, XVerExtensionManager xverManager, Coding jurisdiction) {
|
||||
public ValueSetValidator(IWorkerContext context, TimeTracker timeTracker, InstanceValidator parent, XVerExtensionManager xverManager, Coding jurisdiction, boolean allowExamples) {
|
||||
super(context, xverManager);
|
||||
source = Source.InstanceValidator;
|
||||
this.timeTracker = timeTracker;
|
||||
this.parent = parent;
|
||||
this.jurisdiction = jurisdiction;
|
||||
|
||||
this.allowExamples = allowExamples;
|
||||
}
|
||||
|
||||
public boolean validateValueSet(List<ValidationMessage> errors, Element vs, NodeStack stack) {
|
||||
|
|
@ -190,7 +190,15 @@ public class ValueSetValidator extends BaseValidator {
|
|||
if (version == null) {
|
||||
ValidationResult vv = context.validateCode(ValidationOptions.defaults(), new Coding(system, code, null), null);
|
||||
if (vv.getErrorClass() == TerminologyServiceErrorClass.CODESYSTEM_UNSUPPORTED) {
|
||||
if (isExampleUrl(system)) {
|
||||
if (isAllowExamples()) {
|
||||
hint(errors, NO_RULE_DATE, IssueType.BUSINESSRULE, stackInc.getLiteralPath(), false, I18nConstants.VALUESET_EXAMPLE_SYSTEM_HINT, system);
|
||||
} else {
|
||||
rule(errors, NO_RULE_DATE, IssueType.BUSINESSRULE, stackInc.getLiteralPath(), false, I18nConstants.VALUESET_EXAMPLE_SYSTEM_ERROR, system);
|
||||
}
|
||||
} else {
|
||||
warning(errors, NO_RULE_DATE, IssueType.BUSINESSRULE, stackInc.getLiteralPath(), false, I18nConstants.VALUESET_UNC_SYSTEM_WARNING, system, vv.getMessage());
|
||||
}
|
||||
return false;
|
||||
} else {
|
||||
boolean ok = vv.isOk();
|
||||
|
|
|
|||
Binary file not shown.
|
After Width: | Height: | Size: 714 B |
4
pom.xml
4
pom.xml
|
|
@ -14,12 +14,12 @@
|
|||
HAPI FHIR
|
||||
-->
|
||||
<artifactId>org.hl7.fhir.core</artifactId>
|
||||
<version>5.6.113-SNAPSHOT</version>
|
||||
<version>5.6.115-SNAPSHOT</version>
|
||||
<packaging>pom</packaging>
|
||||
|
||||
<properties>
|
||||
<hapi_fhir_version>6.2.1</hapi_fhir_version>
|
||||
<validator_test_case_version>1.2.21</validator_test_case_version>
|
||||
<validator_test_case_version>1.2.23</validator_test_case_version>
|
||||
<junit_jupiter_version>5.7.1</junit_jupiter_version>
|
||||
<junit_platform_launcher_version>1.8.2</junit_platform_launcher_version>
|
||||
<maven_surefire_version>3.0.0-M5</maven_surefire_version>
|
||||
|
|
|
|||
Loading…
Reference in New Issue