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org.hl7.fhir.core
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Merge branch 'master' of https://github.com/hapifhir/org.hl7.fhir.core into IGRenderingChanges 

# Conflicts:
#	org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/AdditionalBindingsRenderer.java
This commit is contained in:
Lloyd McKenzie 2022-10-06 11:58:10 -06:00
parent 1bb4c27651 58b38cd5af
commit a59cfbe513
60 changed files with 952 additions and 254 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
org.hl7.fhir.convertors/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.6.68-SNAPSHOT</version>
<version>5.6.69-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

27
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/VSACImporter.java
View File

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

7
org.hl7.fhir.core.generator/configuration/CodeableConcept.java
View File

@ -93,4 +93,9 @@ public boolean hasCoding(String system, String code) {
public void addCoding(String system, String code, String display) {
getCoding().add(new Coding(system, code, display));
}
@Override
public String toString() {
return hasCoding() ? getCoding().toString() : "["+getText()+"]";
}

8
org.hl7.fhir.core.generator/configuration/OperationOutcomeIssueComponent.java Normal file
View File

@ -0,0 +1,8 @@
@Override
public String toString() {
if (getExpression().size() == 1) {
return getExpression().get(0)+" "+getDiagnostics()+" "+getSeverity().toCode()+"/"+getCode().toCode()+": "+getDetails().getText();
} else {
return getExpression()+" "+getDiagnostics()+" "+getSeverity().toCode()+"/"+getCode().toCode()+": "+getDetails().getText();
}
}

2
org.hl7.fhir.dstu2/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.6.68-SNAPSHOT</version>
<version>5.6.69-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.dstu2016may/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.6.68-SNAPSHOT</version>
<version>5.6.69-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.dstu3/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.6.68-SNAPSHOT</version>
<version>5.6.69-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.r4/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.6.68-SNAPSHOT</version>
<version>5.6.69-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.r4b/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.6.68-SNAPSHOT</version>
<version>5.6.69-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.r4b/src/main/java/org/hl7/fhir/r4b/renderers/DataRenderer.java
View File

@ -342,7 +342,7 @@ public class DataRenderer extends Renderer {
return true;
}
if (Utilities.existsInList(t,
"ActivityDefinition", "CapabilityStatement", "CapabilityStatement2", "ChargeItemDefinition", "Citation", "CodeSystem",
"ActivityDefinition", "CapabilityStatement", "ChargeItemDefinition", "Citation", "CodeSystem",
"CompartmentDefinition", "ConceptMap", "ConditionDefinition", "EventDefinition", "Evidence", "EvidenceReport", "EvidenceVariable",
"ExampleScenario", "GraphDefinition", "ImplementationGuide", "Library", "Measure", "MessageDefinition", "NamingSystem", "PlanDefinition"
))

2
org.hl7.fhir.r5/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.6.68-SNAPSHOT</version>
<version>5.6.69-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

22
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/AdditionalBindingsRenderer.java
View File

@ -31,6 +31,7 @@ public class AdditionalBindingsRenderer {
private String purpose;
private String valueSet;
private String doco;
private String docoShort;
private UsageContext usage;
private boolean any = false;
private boolean isUnchanged = false;
@ -52,6 +53,9 @@ public class AdditionalBindingsRenderer {
private boolean alreadyMatched() {
return matched;
}
public String getDoco(boolean full) {
return full ? doco : docoShort;
}
public boolean unchanged() {
if (!isUnchanged)
return false;
@ -161,6 +165,7 @@ public class AdditionalBindingsRenderer {
abr.purpose = ext.getExtensionString("purpose");
abr.valueSet = ext.getExtensionString("valueSet");
abr.doco = ext.getExtensionString("documentation");
abr.docoShort = ext.getExtensionString("shortDoco");
abr.usage = (ext.hasExtension("usage")) && ext.getExtensionByUrl("usage").hasValueUsageContext() ? ext.getExtensionByUrl("usage").getValueUsageContext() : null;
abr.any = "any".equals(ext.getExtensionString("scope"));
abr.isUnchanged = ext.hasUserData(ProfileUtilities.DERIVATION_EQUALS);
@ -188,12 +193,12 @@ public class AdditionalBindingsRenderer {
}
}
private void render(List<XhtmlNode> children, boolean doDoco) throws FHIRFormatError, DefinitionException, IOException {
public void render(List<XhtmlNode> children, boolean fullDoco) throws FHIRFormatError, DefinitionException, IOException {
boolean doco = false;
boolean usage = false;
boolean any = false;
for (AdditionalBindingDetail binding : bindings) {
doco = doco || (doDoco && (binding.doco != null || (binding.compare!=null && binding.compare.doco!=null)));
doco = doco || binding.getDoco(fullDoco)!=null || (binding.compare!=null && binding.compare.getDoco(fullDoco)!=null);
usage = usage || binding.usage != null || (binding.compare!=null && binding.compare.usage!=null);
any = any || binding.any || (binding.compare!=null && binding.compare.any);
}
@ -266,8 +271,8 @@ public class AdditionalBindingsRenderer {
}
if (doco) {
if (binding.doco != null) {
String d = md.processMarkdown("Binding.description", binding.doco);
String oldD = binding.compare==null ? null : md.processMarkdown("Binding.description.compare", binding.compare.doco);
String d = md.processMarkdown("Binding.description", fullDoco ? binding.doco : binding.docoShort);
String oldD = binding.compare==null ? null : md.processMarkdown("Binding.description.compare", fullDoco ? binding.compare.doco : binding.compare.docoShort);
tr.td().style("font-size: 11px").innerHTML(compareHtml(d, oldD));
} else {
tr.td().style("font-size: 11px");
@ -307,7 +312,10 @@ public class AdditionalBindingsRenderer {
td.ah(corePath+"extension-elementdefinition-minvalueset.html", "The minimum allowable value set - any conformant system SHALL support all these codes").tx("Min Binding");
break;
case "conformance" :
td.ah(corePath+"terminologies.html#strength", "Validators will check this binding (strength = required)").tx("Validation Criteria");
td.ah(corePath+"terminologies.html#strength", "Validators will check this binding (strength = required)").tx("Validation Binding");
break;
case "candidate" :
td.ah(corePath+"terminologies.html#strength", "This is a candidate binding that constraints on this profile may consider (see doco)").tx("Candidate Validation Binding");
break;
case "current" :
td.span(null, "New records are required to use this value set, but legacy records may use other codes").tx("Required");
@ -336,5 +344,9 @@ public class AdditionalBindingsRenderer {
return br;
}
public boolean hasBindings() {
return !bindings.isEmpty();
}
}

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

@ -4998,6 +4998,8 @@ public class ProfileUtilities extends TranslatingUtilities {
b.setDescription(o.getDescription());
b.getDescriptionElement().setUserData(DERIVATION_EQUALS, o.getDescriptionElement());
}
// todo: derivation?
b.getExtension().addAll(binding.getExtension());
return b;
}

10
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/ParserBase.java
View File

@ -43,6 +43,7 @@ import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.formats.FormatUtilities;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
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.utils.ToolingExtensions;
import org.hl7.fhir.utilities.Utilities;
@ -92,10 +93,13 @@ public abstract class ParserBase {
public enum ValidationPolicy { NONE, QUICK, EVERYTHING }
public boolean isPrimitive(String code) {
return Utilities.existsInList(code, "boolean", "integer", "integer64", "string", "decimal", "uri", "base64Binary", "instant", "date", "dateTime", "time", "code", "oid", "id", "markdown", "unsignedInt", "positiveInt", "xhtml", "url", "canonical");
StructureDefinition sd = context.fetchTypeDefinition(code);
if (sd != null) {
return sd.getKind() == StructureDefinitionKind.PRIMITIVETYPE;
}
return Utilities.existsInList(code, "boolean", "integer", "integer64", "string", "decimal", "uri", "base64Binary", "instant", "date", "dateTime", "time", "code", "oid", "id", "markdown", "unsignedInt", "positiveInt", "uuid", "xhtml", "url", "canonical");
// StructureDefinition sd = context.fetchTypeDefinition(code);
// return sd != null && sd.getKind() == StructureDefinitionKind.PRIMITIVETYPE;
}
protected IWorkerContext context;

69
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/XmlParser.java
View File

@ -155,7 +155,13 @@ public class XmlParser extends ParserBase {
doc = builder.parse(stream);
}
} catch (Exception e) {
logError(0, 0, "(syntax)", IssueType.INVALID, e.getMessage(), IssueSeverity.FATAL);
if (e.getMessage().contains("lineNumber:") && e.getMessage().contains("columnNumber:")) {
int line = Utilities.parseInt(extractVal(e.getMessage(), "lineNumber"), 0);
int col = Utilities.parseInt(extractVal(e.getMessage(), "columnNumber"), 0);
logError(line, col, "(xml)", IssueType.INVALID, e.getMessage().substring(e.getMessage().lastIndexOf(";")+1).trim(), IssueSeverity.FATAL);
} else {
logError(0, 0, "(xml)", IssueType.INVALID, e.getMessage(), IssueSeverity.FATAL);
}
doc = null;
}
if (doc != null) {
@ -168,12 +174,17 @@ public class XmlParser extends ParserBase {
}
private String extractVal(String src, String name) {
src = src.substring(src.indexOf(name)+name.length()+1);
src = src.substring(0, src.indexOf(";")).trim();
return src;
}
private void checkForProcessingInstruction(Document document) throws FHIRFormatError {
if (policy == ValidationPolicy.EVERYTHING && FormatUtilities.FHIR_NS.equals(document.getDocumentElement().getNamespaceURI())) {
Node node = document.getFirstChild();
while (node != null) {
if (node.getNodeType() == Node.PROCESSING_INSTRUCTION_NODE)
logError(line(document), col(document), "(document)", IssueType.INVALID, context.formatMessage(
logError(line(document, false), col(document, false), "(document)", IssueType.INVALID, context.formatMessage(
I18nConstants.NO_PROCESSING_INSTRUCTIONS_ALLOWED_IN_RESOURCES), IssueSeverity.ERROR);
node = node.getNextSibling();
}
@ -181,14 +192,14 @@ public class XmlParser extends ParserBase {
}
private int line(Node node) {
private int line(Node node, boolean end) {
XmlLocationData loc = node == null ? null : (XmlLocationData) node.getUserData(XmlLocationData.LOCATION_DATA_KEY);
return loc == null ? 0 : loc.getStartLine();
return loc == null ? 0 : end ? loc.getEndLine() : loc.getStartLine();
}
private int col(Node node) {
private int col(Node node, boolean end) {
XmlLocationData loc = node == null ? null : (XmlLocationData) node.getUserData(XmlLocationData.LOCATION_DATA_KEY);
return loc == null ? 0 : loc.getStartColumn();
return loc == null ? 0 : end ? loc.getEndColumn() : loc.getStartColumn();
}
public Element parse(Document doc) throws FHIRFormatError, DefinitionException, FHIRException, IOException {
@ -202,14 +213,14 @@ public class XmlParser extends ParserBase {
String name = element.getLocalName();
String path = "/"+pathPrefix(ns)+name;
StructureDefinition sd = getDefinition(line(element), col(element), (ns == null ? "noNamespace" : ns), name);
StructureDefinition sd = getDefinition(line(element, false), col(element, false), (ns == null ? "noNamespace" : ns), name);
if (sd == null)
return null;
Element result = new Element(element.getLocalName(), new Property(context, sd.getSnapshot().getElement().get(0), sd));
result.setPath(element.getLocalName());
checkElement(element, path, result.getProperty());
result.markLocation(line(element), col(element));
result.markLocation(line(element, false), col(element, false));
result.setType(element.getLocalName());
parseChildren(path, element, result);
result.numberChildren();
@ -253,14 +264,14 @@ public class XmlParser extends ParserBase {
private void checkElement(org.w3c.dom.Element element, String path, Property prop) throws FHIRFormatError {
if (policy == ValidationPolicy.EVERYTHING) {
if (empty(element) && FormatUtilities.FHIR_NS.equals(element.getNamespaceURI())) // this rule only applies to FHIR Content
logError(line(element), col(element), path, IssueType.INVALID, context.formatMessage(I18nConstants.ELEMENT_MUST_HAVE_SOME_CONTENT), IssueSeverity.ERROR);
logError(line(element, false), col(element, false), path, IssueType.INVALID, context.formatMessage(I18nConstants.ELEMENT_MUST_HAVE_SOME_CONTENT), IssueSeverity.ERROR);
String ns = prop.getXmlNamespace();
String elementNs = element.getNamespaceURI();
if (elementNs == null) {
elementNs = "noNamespace";
}
if (!elementNs.equals(ns))
logError(line(element), col(element), path, IssueType.INVALID, context.formatMessage(I18nConstants.WRONG_NAMESPACE__EXPECTED_, ns), IssueSeverity.ERROR);
logError(line(element, false), col(element, false), path, IssueType.INVALID, context.formatMessage(I18nConstants.WRONG_NAMESPACE__EXPECTED_, ns), IssueSeverity.ERROR);
}
}
@ -282,8 +293,8 @@ public class XmlParser extends ParserBase {
List<Property> properties = element.getProperty().getChildProperties(element.getName(), XMLUtil.getXsiType(node));
String text = XMLUtil.getDirectText(node).trim();
int line = line(node);
int col = col(node);
int line = line(node, false);
int col = col(node, false);
if (!Utilities.noString(text)) {
Property property = getTextProp(properties);
if (property != null) {
@ -307,16 +318,19 @@ public class XmlParser extends ParserBase {
Node n = node.getFirstChild();
while (n != null) {
if (n.getNodeType() == Node.TEXT_NODE && !Utilities.noString(n.getTextContent().trim())) {
while (n.getNextSibling() != null && n.getNodeType() != Node.ELEMENT_NODE) {
n = n.getNextSibling();
}
Node nt = n;
Node nt = n; // try to find the nearest element for a line/col location
boolean end = false;
while (nt.getPreviousSibling() != null && nt.getNodeType() != Node.ELEMENT_NODE) {
nt = nt.getPreviousSibling();
end = true;
}
line = line(nt);
col = col(nt);
logError(line, col, path, IssueType.STRUCTURE, context.formatMessage(I18nConstants.TEXT_SHOULD_NOT_BE_PRESENT, Utilities.makeSingleLine(text)), IssueSeverity.ERROR);
while (nt.getNextSibling() != null && nt.getNodeType() != Node.ELEMENT_NODE) {
nt = nt.getNextSibling();
end = false;
}
line = line(nt, end);
col = col(nt, end);
logError(line, col, path, IssueType.STRUCTURE, context.formatMessage(I18nConstants.TEXT_SHOULD_NOT_BE_PRESENT, Utilities.makeSingleLine(n.getTextContent().trim())), IssueSeverity.ERROR);
}
n = n.getNextSibling();
}
@ -351,8 +365,9 @@ public class XmlParser extends ParserBase {
} else
ok = ok || (attr.getLocalName().equals("schemaLocation")); // xsi:schemalocation allowed for non FHIR content
ok = ok || (hasTypeAttr(element) && attr.getLocalName().equals("type") && FormatUtilities.NS_XSI.equals(attr.getNamespaceURI())); // xsi:type allowed if element says so
if (!ok)
logError(line, col, path, IssueType.STRUCTURE, context.formatMessage(I18nConstants.UNDEFINED_ATTRIBUTE__ON__FOR_TYPE__PROPERTIES__, attr.getNodeName(), node.getNodeName(), element.fhirType(), properties), IssueSeverity.ERROR);
if (!ok) {
logError(line(node, false), col(node, false), path, IssueType.STRUCTURE, context.formatMessage(I18nConstants.UNDEFINED_ATTRIBUTE__ON__FOR_TYPE__PROPERTIES__, attr.getNodeName(), node.getNodeName(), element.fhirType(), properties), IssueSeverity.ERROR);
}
}
}
}
@ -376,12 +391,12 @@ public class XmlParser extends ParserBase {
xhtml = new CDANarrativeFormat().convert((org.w3c.dom.Element) child);
else
xhtml = new XhtmlParser().setValidatorMode(true).parseHtmlNode((org.w3c.dom.Element) child);
Element n = new Element(property.getName(), property, "xhtml", new XhtmlComposer(XhtmlComposer.XML, false).compose(xhtml)).setXhtml(xhtml).markLocation(line(child), col(child));
Element n = new Element(property.getName(), property, "xhtml", new XhtmlComposer(XhtmlComposer.XML, false).compose(xhtml)).setXhtml(xhtml).markLocation(line(child, false), col(child, false));
n.setPath(element.getPath()+"."+property.getName());
element.getChildren().add(n);
} else {
String npath = path+"/"+pathPrefix(child.getNamespaceURI())+child.getLocalName();
Element n = new Element(child.getLocalName(), property).markLocation(line(child), col(child));
Element n = new Element(child.getLocalName(), property).markLocation(line(child, false), col(child, false));
if (property.isList()) {
n.setPath(element.getPath()+"."+property.getName()+"["+repeatCount+"]");
} else {
@ -397,7 +412,7 @@ public class XmlParser extends ParserBase {
xsiType = ToolingExtensions.readStringExtension(property.getDefinition(), "http://hl7.org/fhir/StructureDefinition/elementdefinition-defaulttype");
n.setType(xsiType);
} else {
logError(line(child), col(child), path, IssueType.STRUCTURE, context.formatMessage(I18nConstants.NO_TYPE_FOUND_ON_, child.getLocalName()), IssueSeverity.ERROR);
logError(line(child, false), col(child, false), path, IssueType.STRUCTURE, context.formatMessage(I18nConstants.NO_TYPE_FOUND_ON_, child.getLocalName()), IssueSeverity.ERROR);
ok = false;
}
} else {
@ -418,11 +433,11 @@ public class XmlParser extends ParserBase {
}
}
} else
logError(line(child), col(child), path, IssueType.STRUCTURE, context.formatMessage(I18nConstants.UNDEFINED_ELEMENT_, child.getLocalName()), IssueSeverity.ERROR);
logError(line(child, false), col(child, false), path, IssueType.STRUCTURE, context.formatMessage(I18nConstants.UNDEFINED_ELEMENT_, child.getLocalName()), IssueSeverity.ERROR);
} else if (child.getNodeType() == Node.CDATA_SECTION_NODE){
logError(line(child), col(child), path, IssueType.STRUCTURE, context.formatMessage(I18nConstants.CDATA_IS_NOT_ALLOWED), IssueSeverity.ERROR);
logError(line(child, false), col(child, false), path, IssueType.STRUCTURE, context.formatMessage(I18nConstants.CDATA_IS_NOT_ALLOWED), IssueSeverity.ERROR);
} else if (!Utilities.existsInList(child.getNodeType(), 3, 8)) {
logError(line(child), col(child), path, IssueType.STRUCTURE, context.formatMessage(I18nConstants.NODE_TYPE__IS_NOT_ALLOWED, Integer.toString(child.getNodeType())), IssueSeverity.ERROR);
logError(line(child, false), col(child, false), path, IssueType.STRUCTURE, context.formatMessage(I18nConstants.NODE_TYPE__IS_NOT_ALLOWED, Integer.toString(child.getNodeType())), IssueSeverity.ERROR);
}
child = child.getNextSibling();
}

5
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/CodeableConcept.java
View File

@ -404,6 +404,11 @@ public boolean hasCoding(String system, String code) {
public void addCoding(String system, String code, String display) {
getCoding().add(new Coding(system, code, display));
}
@Override
public String toString() {
return hasCoding() ? getCoding().toString() : "["+getText()+"]";
}
// end addition

9
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/OperationOutcome.java
View File

@ -1299,6 +1299,15 @@ For resource issues, this will be a simple XPath limited to element names, repet
}
@Override
public String toString() {
if (getExpression().size() == 1) {
return getExpression().get(0)+" "+getDiagnostics()+" "+getSeverity().toCode()+"/"+getCode().toCode()+": "+getDetails().getText();
} else {
return getExpression()+" "+getDiagnostics()+" "+getSeverity().toCode()+"/"+getCode().toCode()+": "+getDetails().getText();
}
}
}
/**

29
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/BundleRenderer.java
View File

@ -79,8 +79,13 @@ public class BundleRenderer extends ResourceRenderer {
if (be.has("fullUrl")) {
root.an(makeInternalBundleLink(be.get("fullUrl").primitiveValue()));
}
if (be.has("resource") && be.getChildByName("resource").getValues().get(0).has("id")) {
root.an(be.get("resource").fhirType() + "_" + be.getChildByName("resource").getValues().get(0).get("id").primitiveValue());
if (be.has("resource")) {
if (be.getChildByName("resource").getValues().get(0).has("id")) {
root.an(be.get("resource").fhirType() + "_" + be.getChildByName("resource").getValues().get(0).get("id").primitiveValue());
} else {
String id = makeIdFromBundleEntry(be.get("fullUrl").primitiveValue());
root.an(be.get("resource").fhirType() + "_" + id);
}
}
root.hr();
if (be.has("fullUrl")) {
@ -101,6 +106,7 @@ public class BundleRenderer extends ResourceRenderer {
if (xn == null || xn.isEmpty()) {
ResourceRenderer rr = RendererFactory.factory(rw, context);
try {
rr.setRcontext(new ResourceContext(rcontext, rw));
xn = rr.render(rw);
} catch (Exception e) {
xn = new XhtmlNode();
@ -128,7 +134,7 @@ public class BundleRenderer extends ResourceRenderer {
if (subject.hasNarrative()) {
x.addChildren(subject.getNarrative());
} else {
RendererFactory.factory(subject, context).render(x, subject);
RendererFactory.factory(subject, context, new ResourceContext(rcontext, subject)).render(x, subject);
}
}
x.hr();
@ -204,12 +210,14 @@ public class BundleRenderer extends ResourceRenderer {
if (nx != null && !nx.isEmpty()) {
x.addChildren(nx);
} else {
RendererFactory.factory(subject, context).render(x, subject);
RendererFactory.factory(subject, context).setRcontext(new ResourceContext(rcontext, subject)).render(x, subject);
}
}
x.hr();
if (!comp.getText().hasDiv()) {
ResourceRenderer rr = RendererFactory.factory(comp, getContext()); rr.render(comp);
ResourceRenderer rr = RendererFactory.factory(comp, getContext());
rr.setRcontext(new ResourceContext(rcontext, comp));
rr.render(comp);
}
if (comp.getText().hasDiv()) {
x.addChildren(comp.getText().getDiv());
@ -292,8 +300,14 @@ public class BundleRenderer extends ResourceRenderer {
if (i > start) {
if (be.hasFullUrl())
x.an(makeInternalBundleLink(be.getFullUrl()));
if (be.hasResource() && be.getResource().hasId())
x.an(be.getResource().getResourceType().name() + "_" + be.getResource().getId());
if (be.hasResource()) {
if (be.getResource().hasId()) {
x.an(be.getResource().getResourceType().name() + "_" + be.getResource().getId());
} else {
String id = makeIdFromBundleEntry(be.getFullUrl());
x.an(be.getResource().getResourceType().name() + "_" + id);
}
}
x.hr();
if (docMode) {
if (be.hasFullUrl() && be.hasResource()) {
@ -329,6 +343,7 @@ public class BundleRenderer extends ResourceRenderer {
if (xn == null || xn.isEmpty()) {
ResourceRenderer rr = RendererFactory.factory(be.getResource(), context);
try {
rr.setRcontext(new ResourceContext(rcontext, be.getResource()));
xn = rr.build(be.getResource());
} catch (Exception e) {
xn = makeExceptionXhtml(e, "generating narrative");

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/DataRenderer.java
View File

@ -341,7 +341,7 @@ public class DataRenderer extends Renderer {
return true;
}
if (Utilities.existsInList(t,
"ActivityDefinition", "CapabilityStatement", "CapabilityStatement2", "ChargeItemDefinition", "Citation", "CodeSystem",
"ActivityDefinition", "CapabilityStatement", "ChargeItemDefinition", "Citation", "CodeSystem",
"CompartmentDefinition", "ConceptMap", "ConditionDefinition", "EventDefinition", "Evidence", "EvidenceReport", "EvidenceVariable",
"ExampleScenario", "GraphDefinition", "ImplementationGuide", "Library", "Measure", "MessageDefinition", "NamingSystem", "PlanDefinition"
))

7
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/ProfileDrivenRenderer.java
View File

@ -381,7 +381,7 @@ public class ProfileDrivenRenderer extends ResourceRenderer {
renderContactPoint(x, c);
}
} else if (e instanceof UriType) {
renderUri(x, (UriType) e, defn.getPath(), rcontext != null && rcontext.getResourceResource() != null ? rcontext.getResourceResource().getId() : null);
renderUri(x, (UriType) e, defn.getPath(), rcontext != null && rcontext.getResource() != null ? rcontext.getResource().getId() : null);
} else if (e instanceof Timing) {
renderTiming(x, (Timing) e);
} else if (e instanceof Range) {
@ -418,6 +418,7 @@ public class ProfileDrivenRenderer extends ResourceRenderer {
ctxtc.setAddGeneratedNarrativeHeader(false);
ctxtc.setContained(true);
ResourceRenderer rr = RendererFactory.factory(rw, ctxtc);
rr.setRcontext(new ResourceContext(rcontext, rw));
rr.render(parent.blockquote(), rw);
} else {
x.ah(ref).tx("See "+rw.fhirType());
@ -690,12 +691,12 @@ public class ProfileDrivenRenderer extends ResourceRenderer {
x.para().b().tx("Generated Narrative: "+profile.present()+(showCodeDetails ? " with Details" : ""));
}
try {
generateByProfile(rcontext.getResourceResource(), profile, rcontext.getResourceResource(), profile.getSnapshot().getElement(), profile.getSnapshot().getElement().get(0), getChildrenForPath(profile, profile.getSnapshot().getElement(), rcontext.getResourceResource().getResourceType().toString()), x, rcontext.getResourceResource().getResourceType().toString(), showCodeDetails);
generateByProfile(rcontext.getResource(), profile, rcontext.getResource(), profile.getSnapshot().getElement(), profile.getSnapshot().getElement().get(0), getChildrenForPath(profile, profile.getSnapshot().getElement(), rcontext.getResource().getResourceType().toString()), x, rcontext.getResource().getResourceType().toString(), showCodeDetails);
} catch (Exception e) {
e.printStackTrace();
x.para().b().style("color: maroon").tx("Exception generating Narrative: "+e.getMessage());
}
inject(rcontext.getResourceResource(), x, NarrativeStatus.GENERATED);
inject((DomainResource) rcontext.getResource(), x, NarrativeStatus.GENERATED);
return true;
}

25
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/ResourceRenderer.java
View File

@ -61,6 +61,15 @@ public abstract class ResourceRenderer extends DataRenderer {
this.rcontext = rcontext;
}
public ResourceContext getRcontext() {
return rcontext;
}
public ResourceRenderer setRcontext(ResourceContext rcontext) {
this.rcontext = rcontext;
return this;
}
public XhtmlNode build(Resource dr) throws FHIRFormatError, DefinitionException, FHIRException, IOException, EOperationOutcome {
XhtmlNode x = new XhtmlNode(NodeType.Element, "div");
render(x, dr);
@ -324,7 +333,11 @@ public abstract class ResourceRenderer extends DataRenderer {
if (rcontext != null) {
BundleEntryComponent bundleResource = rcontext.resolve(url);
if (bundleResource != null) {
String bundleUrl = "#" + bundleResource.getResource().getResourceType().name() + "_" + bundleResource.getResource().getId();
String id = bundleResource.getResource().getId();
if (id == null) {
id = makeIdFromBundleEntry(bundleResource.getFullUrl());
}
String bundleUrl = "#" + bundleResource.getResource().getResourceType().name() + "_" + id;
return new ResourceWithReference(bundleUrl, new ResourceWrapperDirect(this.context, bundleResource.getResource()));
}
org.hl7.fhir.r5.elementmodel.Element bundleElement = rcontext.resolveElement(url, version);
@ -350,6 +363,16 @@ public abstract class ResourceRenderer extends DataRenderer {
}
protected String makeIdFromBundleEntry(String url) {
if (url == null) {
return null;
}
if (url.startsWith("urn:uuid:")) {
return url.substring(9).toLowerCase();
}
return fullUrlToAnchor(url);
}
private String fullUrlToAnchor(String url) {
return url.replace(":", "").replace("/", "_");
}

4
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/utils/DirectWrappers.java
View File

@ -299,6 +299,10 @@ public class DirectWrappers {
return new PropertyWrapperDirect(context, p);
}
public Resource getResource() {
return wrapped;
}
}
}

4
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/utils/ElementWrappers.java
View File

@ -286,6 +286,10 @@ public class ElementWrappers {
return null;
}
public Element getElement() {
return wrapped;
}
}
public static class PropertyWrapperMetaElement extends RendererWrapperImpl implements PropertyWrapper {

126
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/utils/Resolver.java
View File

@ -7,15 +7,10 @@ import org.hl7.fhir.r5.model.Parameters;
import org.hl7.fhir.r5.model.Parameters.ParametersParameterComponent;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.renderers.utils.BaseWrappers.ResourceWrapper;
import org.hl7.fhir.r5.renderers.utils.Resolver.ResourceContextType;
import org.w3c.dom.Element;
public class Resolver {
public enum ResourceContextType {
PARAMETERS, BUNDLE
}
public interface IReferenceResolver {
ResourceWithReference resolve(RenderingContext context, String url);
@ -24,27 +19,24 @@ public class Resolver {
}
public static class ResourceContext {
private ResourceContextType type;
private Resource containerResource;
private org.hl7.fhir.r5.elementmodel.Element containerElement;
private ResourceContext container;
DomainResource resourceResource;
org.hl7.fhir.r5.elementmodel.Element resourceElement;
Resource resource;
org.hl7.fhir.r5.elementmodel.Element element;
public ResourceContext(ResourceContextType type, Resource bundle, DomainResource dr) {
public ResourceContext(ResourceContext container, Resource dr) {
super();
this.type = type;
this.containerResource = bundle;
this.resourceResource = dr;
this.container = container;
this.resource = dr;
}
public ResourceContext(ResourceContextType type, org.hl7.fhir.r5.elementmodel.Element bundle, org.hl7.fhir.r5.elementmodel.Element dr) {
public ResourceContext(ResourceContext container, org.hl7.fhir.r5.elementmodel.Element dr) {
super();
this.type = type;
this.containerElement = bundle;
this.resourceElement = dr;
this.container = container;
this.element = dr;
}
// public ResourceContext(Object bundle, Element doc) {
// // TODO Auto-generated constructor stub
// }
@ -54,22 +46,45 @@ public class Resolver {
// }
public ResourceContext(ResourceContext container, ResourceWrapper rw) {
super();
this.container = container;
// todo: howto do this better?
if (rw instanceof DirectWrappers.ResourceWrapperDirect) {
this.resource = ((DirectWrappers.ResourceWrapperDirect) rw).getResource();
} else if (rw instanceof ElementWrappers.ResourceWrapperMetaElement) {
this.element = ((ElementWrappers.ResourceWrapperMetaElement) rw).getElement();
} else {
throw new Error("Not supported yet");
}
}
public ResourceContext getContainer() {
return container;
}
public void setContainer(ResourceContext container) {
this.container = container;
}
// public org.hl7.fhir.r5.elementmodel.Element getBundleElement() {
// return containerElement;
// }
//
public DomainResource getResourceResource() {
return resourceResource;
public Resource getResource() {
return resource;
}
public org.hl7.fhir.r5.elementmodel.Element getResourceElement() {
return resourceElement;
public org.hl7.fhir.r5.elementmodel.Element getElement() {
return element;
}
public BundleEntryComponent resolve(String value) {
if (value.startsWith("#")) {
if (resourceResource != null) {
for (Resource r : resourceResource.getContained()) {
if (resource instanceof DomainResource) {
DomainResource dr = (DomainResource) resource;
for (Resource r : dr.getContained()) {
if (r.getId().equals(value.substring(1))) {
BundleEntryComponent be = new BundleEntryComponent();
be.setResource(r);
@ -79,44 +94,45 @@ public class Resolver {
}
return null;
}
if (type == ResourceContextType.BUNDLE) {
if (containerResource != null) {
for (BundleEntryComponent be : ((Bundle) containerResource).getEntry()) {
if (be.getFullUrl().equals(value))
return be;
if (value.equals(be.getResource().fhirType()+"/"+be.getResource().getId()))
return be;
if (resource instanceof Bundle) {
Bundle b = (Bundle) resource;
for (BundleEntryComponent be : b.getEntry()) {
if (be.getFullUrl().equals(value))
return be;
if (value.equals(be.getResource().fhirType()+"/"+be.getResource().getId()))
return be;
}
}
if (resource instanceof Parameters) {
Parameters pp = (Parameters) resource;
for (ParametersParameterComponent p : pp.getParameter()) {
if (p.getResource() != null && value.equals(p.getResource().fhirType()+"/"+p.getResource().getId())) {
BundleEntryComponent be = new BundleEntryComponent();
be.setResource(p.getResource());
return be;
}
}
}
if (type == ResourceContextType.PARAMETERS) {
if (containerResource != null) {
for (ParametersParameterComponent p : ((Parameters) containerResource).getParameter()) {
if (p.getResource() != null && value.equals(p.getResource().fhirType()+"/"+p.getResource().getId())) {
BundleEntryComponent be = new BundleEntryComponent();
be.setResource(p.getResource());
return be;
}
}
}
}
return null;
}
}
return container != null ? container.resolve(value) : null;
}
public org.hl7.fhir.r5.elementmodel.Element resolveElement(String value, String version) {
if (value.startsWith("#")) {
if (resourceElement != null) {
for (org.hl7.fhir.r5.elementmodel.Element r : resourceElement.getChildrenByName("contained")) {
if (element != null) {
for (org.hl7.fhir.r5.elementmodel.Element r : element.getChildrenByName("contained")) {
if (r.getChildValue("id").equals(value.substring(1)))
return r;
}
}
return null;
}
if (type == ResourceContextType.BUNDLE) {
if (containerElement != null) {
for (org.hl7.fhir.r5.elementmodel.Element be : containerElement.getChildren("entry")) {
if (element != null) {
if (element.fhirType().equals("Bundle")) {
for (org.hl7.fhir.r5.elementmodel.Element be : element.getChildren("entry")) {
org.hl7.fhir.r5.elementmodel.Element res = be.getNamedChild("resource");
if (res != null) {
if (value.equals(be.getChildValue("fullUrl"))) {
@ -132,10 +148,8 @@ public class Resolver {
}
}
}
}
if (type == ResourceContextType.PARAMETERS) {
if (containerElement != null) {
for (org.hl7.fhir.r5.elementmodel.Element p : containerElement.getChildren("parameter")) {
if (element.fhirType().equals("Parameters")) {
for (org.hl7.fhir.r5.elementmodel.Element p : element.getChildren("parameter")) {
org.hl7.fhir.r5.elementmodel.Element res = p.getNamedChild("resource");
if (res != null && value.equals(res.fhirType()+"/"+res.getChildValue("id"))) {
if (checkVersion(version, res)) {
@ -145,7 +159,7 @@ public class Resolver {
}
}
}
return null;
return container != null ? container.resolveElement(value, version) : null;
}
private boolean checkVersion(String version, org.hl7.fhir.r5.elementmodel.Element res) {

6
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/JurisdictionUtilities.java
View File

@ -11,7 +11,7 @@ public class JurisdictionUtilities {
}
public static String getJurisdictionFromLocale(String s) {
if (Utilities.existsInList(s,
if (Utilities.existsInList(s.toUpperCase(),
"AD", "AE", "AF", "AG", "AI", "AL", "AM", "AO", "AQ",
"AR", "AS", "AT", "AU", "AW", "AX", "AZ", "BA", "BB",
"BD", "BE", "BF", "BG", "BH", "BI", "BJ", "BL", "BM",
@ -41,7 +41,7 @@ public class JurisdictionUtilities {
"UZ", "VA", "VC", "VE", "VG", "VI", "VN", "VU", "WF",
"WS", "YE", "YT", "ZA", "ZM", "ZW"
)) {
return "urn:iso:std:iso:3166#"+s;
return "urn:iso:std:iso:3166#"+s.toUpperCase();
} else {
switch (s) {
case "uv" : return "http://unstats.un.org/unsd/methods/m49/m49.htm#001";
@ -54,7 +54,7 @@ public class JurisdictionUtilities {
}
public static String displayJurisdiction(String s) {
return displayJurisdiction(CodeSystemUtilities.readCoding(s));
return displayJurisdiction(CodeSystemUtilities.readCoding(getJurisdictionFromLocale(s)));
}
public static String displayJurisdiction(Coding c) {

17
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/ValueSetChecker.java
View File

@ -1,5 +1,6 @@
package org.hl7.fhir.r5.terminologies;
import java.util.ArrayList;
import java.util.List;
/*
@ -34,10 +35,24 @@ import java.util.List;
import org.hl7.fhir.r5.terminologies.ValueSetExpander.ETooCostly;
import org.hl7.fhir.r5.terminologies.ValueSetExpander.TerminologyServiceErrorClass;
import org.hl7.fhir.r5.utils.EOperationOutcome;
public interface ValueSetChecker {
Boolean codeInValueSet(String system, String code, List<String> warnings) throws ETooCostly, EOperationOutcome, Exception;
public static class ValidationProcessInfo {
private TerminologyServiceErrorClass err;
private List<String> warnings = new ArrayList<>();
public TerminologyServiceErrorClass getErr() {
return err;
}
public void setErr(TerminologyServiceErrorClass err) {
this.err = err;
}
public List<String> getWarnings() {
return warnings;
}
}
Boolean codeInValueSet(String system, String code, ValidationProcessInfo info) throws ETooCostly, EOperationOutcome, Exception;
}

59
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/ValueSetCheckerSimple.java
View File

@ -61,6 +61,7 @@ import org.hl7.fhir.r5.model.ValueSet.ConceptReferenceDesignationComponent;
import org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.r5.model.ValueSet.ConceptSetFilterComponent;
import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionContainsComponent;
import org.hl7.fhir.r5.terminologies.ValueSetChecker.ValidationProcessInfo;
import org.hl7.fhir.r5.terminologies.ValueSetExpander.TerminologyServiceErrorClass;
import org.hl7.fhir.r5.utils.ToolingExtensions;
import org.hl7.fhir.r5.utils.validation.ValidationContextCarrier;
@ -129,11 +130,11 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
public ValidationResult validateCode(CodeableConcept code) throws FHIRException {
// first, we validate the codings themselves
List<String> errors = new ArrayList<String>();
List<String> warnings = new ArrayList<String>();
ValidationProcessInfo info = new ValidationProcessInfo();
if (options.getValueSetMode() != ValueSetMode.CHECK_MEMERSHIP_ONLY) {
for (Coding c : code.getCoding()) {
if (!c.hasSystem()) {
warnings.add(context.formatMessage(I18nConstants.CODING_HAS_NO_SYSTEM__CANNOT_VALIDATE));
info.getWarnings().add(context.formatMessage(I18nConstants.CODING_HAS_NO_SYSTEM__CANNOT_VALIDATE));
}
CodeSystem cs = resolveCodeSystem(c.getSystem());
ValidationResult res = null;
@ -145,7 +146,7 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
if (!res.isOk()) {
errors.add(res.getMessage());
} else if (res.getMessage() != null) {
warnings.add(res.getMessage());
info.getWarnings().add(res.getMessage());
}
}
}
@ -153,7 +154,7 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
if (valueset != null && options.getValueSetMode() != ValueSetMode.NO_MEMBERSHIP_CHECK) {
Boolean result = false;
for (Coding c : code.getCoding()) {
Boolean ok = codeInValueSet(c.getSystem(), c.getCode(), warnings);
Boolean ok = codeInValueSet(c.getSystem(), c.getCode(), info);
if (ok == null && result == false) {
result = null;
} else if (ok) {
@ -162,15 +163,15 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
}
}
if (result == null) {
warnings.add(0, context.formatMessage(I18nConstants.UNABLE_TO_CHECK_IF_THE_PROVIDED_CODES_ARE_IN_THE_VALUE_SET_, valueset.getUrl()));
info.getWarnings().add(0, context.formatMessage(I18nConstants.UNABLE_TO_CHECK_IF_THE_PROVIDED_CODES_ARE_IN_THE_VALUE_SET_, valueset.getUrl()));
} else if (!result) {
errors.add(0, context.formatMessage(I18nConstants.NONE_OF_THE_PROVIDED_CODES_ARE_IN_THE_VALUE_SET_, valueset.getUrl()));
}
}
if (errors.size() > 0) {
return new ValidationResult(IssueSeverity.ERROR, errors.toString());
} else if (warnings.size() > 0) {
return new ValidationResult(IssueSeverity.WARNING, warnings.toString());
} else if (info.getWarnings().size() > 0) {
return new ValidationResult(IssueSeverity.WARNING, info.getWarnings().toString());
} else {
ConceptDefinitionComponent cd = new ConceptDefinitionComponent(foundCoding.getCode());
cd.setDisplay(foundCoding.getDisplay());
@ -251,19 +252,24 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
inInclude = checkInclude(code);
}
List<String> warnings = new ArrayList<>();
ValidationProcessInfo info = new ValidationProcessInfo();
// then, if we have a value set, we check it's in the value set
if (valueset != null && options.getValueSetMode() != ValueSetMode.NO_MEMBERSHIP_CHECK) {
if ((res==null || res.isOk())) {
Boolean ok = codeInValueSet(system, code.getCode(), warnings);
Boolean ok = codeInValueSet(system, code.getCode(), info);
if (ok == null || !ok) {
if (res == null) {
res = new ValidationResult((IssueSeverity) null, null);
}
if (!inExpansion && !inInclude) {
if (warnings != null) {
res.setMessage("Not in value set "+valueset.getUrl()+" ("+warnings+")").setSeverity(IssueSeverity.ERROR);
if (info.getErr() != null) {
res.setErrorClass(info.getErr());
}
if (ok == null) {
res.setMessage("Unable to check whether code is in value set "+valueset.getUrl()+": "+info.getWarnings()).setSeverity(IssueSeverity.WARNING);
} else if (!inExpansion && !inInclude) {
if (!info.getWarnings().isEmpty()) {
res.setMessage("Not in value set "+valueset.getUrl()+": "+info.getWarnings()).setSeverity(IssueSeverity.ERROR);
} else {
res.setMessage("Not in value set "+valueset.getUrl()).setSeverity(IssueSeverity.ERROR);
}
@ -583,7 +589,7 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
return false;
}
CodeSystem cs = resolveCodeSystem(vsi.getSystem());
if (cs != null) {
if (cs != null && cs.getContent() == CodeSystemContentMode.COMPLETE) {
if (vsi.hasConcept()) {
for (ConceptReferenceComponent cc : vsi.getConcept()) {
@ -598,15 +604,15 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
sys.add(vsi.getSystem());
}
}
} else {
if (vsi.hasConcept()) {
for (ConceptReferenceComponent cc : vsi.getConcept()) {
boolean match = cc.getCode().equals(code);
if (match) {
sys.add(vsi.getSystem());
}
} else if (vsi.hasConcept()) {
for (ConceptReferenceComponent cc : vsi.getConcept()) {
boolean match = cc.getCode().equals(code);
if (match) {
sys.add(vsi.getSystem());
}
}
} else {
return false;
}
}
}
@ -640,7 +646,7 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
}
@Override
public Boolean codeInValueSet(String system, String code, List<String> warnings) throws FHIRException {
public Boolean codeInValueSet(String system, String code, ValidationProcessInfo info) throws FHIRException {
if (valueset == null) {
return false;
}
@ -651,7 +657,7 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
} else if (valueset.hasCompose()) {
int i = 0;
for (ConceptSetComponent vsi : valueset.getCompose().getInclude()) {
Boolean ok = inComponent(vsi, i, system, code, valueset.getCompose().getInclude().size() == 1, warnings);
Boolean ok = inComponent(vsi, i, system, code, valueset.getCompose().getInclude().size() == 1, info);
i++;
if (ok == null && result == false) {
result = null;
@ -662,7 +668,7 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
}
i = valueset.getCompose().getInclude().size();
for (ConceptSetComponent vsi : valueset.getCompose().getExclude()) {
Boolean nok = inComponent(vsi, i, system, code, valueset.getCompose().getInclude().size() == 1, warnings);
Boolean nok = inComponent(vsi, i, system, code, valueset.getCompose().getInclude().size() == 1, info);
i++;
if (nok == null && result == false) {
result = null;
@ -675,7 +681,7 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
return result;
}
private Boolean inComponent(ConceptSetComponent vsi, int vsiIndex, String system, String code, boolean only, List<String> warnings) throws FHIRException {
private Boolean inComponent(ConceptSetComponent vsi, int vsiIndex, String system, String code, boolean only, ValidationProcessInfo info) throws FHIRException {
boolean ok = true;
if (vsi.hasValueSet()) {
@ -721,8 +727,9 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
vs.getCompose().addInclude(vsi);
ValidationResult res = context.validateCode(options.noClient(), new Coding(system, code, null), vs);
if (res.getErrorClass() == TerminologyServiceErrorClass.UNKNOWN || res.getErrorClass() == TerminologyServiceErrorClass.CODESYSTEM_UNSUPPORTED || res.getErrorClass() == TerminologyServiceErrorClass.VALUESET_UNSUPPORTED) {
if (warnings != null && res.getErrorClass() == TerminologyServiceErrorClass.CODESYSTEM_UNSUPPORTED) {
warnings.add(context.formatMessage(I18nConstants.TERMINOLOGY_TX_SYSTEM_NOTKNOWN, system));
if (info != null && res.getErrorClass() == TerminologyServiceErrorClass.CODESYSTEM_UNSUPPORTED) {
info.getWarnings().add(context.formatMessage(I18nConstants.TERMINOLOGY_TX_SYSTEM_NOTKNOWN, system));
info.setErr(TerminologyServiceErrorClass.CODESYSTEM_UNSUPPORTED);
}
return null;
}

13
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/FHIRPathEngine.java
View File

@ -4503,7 +4503,18 @@ public class FHIRPathEngine {
return makeBoolean(false);
}
} else if (ns.equals("FHIR")) {
return makeBoolean(n.equals(focus.get(0).fhirType()));
if (n.equals(focus.get(0).fhirType())) {
return makeBoolean(true);
} else {
StructureDefinition sd = worker.fetchTypeDefinition(focus.get(0).fhirType());
while (sd != null) {
if (n.equals(sd.getType())) {
return makeBoolean(true);
}
sd = worker.fetchResource(StructureDefinition.class, sd.getBaseDefinition());
}
return makeBoolean(false);
}
} else {
return makeBoolean(false);
}

20
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/GraphQLSchemaGenerator.java
View File

@ -103,6 +103,9 @@ public class GraphQLSchemaGenerator {
if (sd.getKind() == StructureDefinitionKind.COMPLEXTYPE && sd.getDerivation() == TypeDerivationRule.SPECIALIZATION) {
tl.put(sd.getName(), sd);
}
if (sd.getKind() == StructureDefinitionKind.RESOURCE && sd.getDerivation() != TypeDerivationRule.CONSTRAINT && sd.getAbstract()) {
tl.put(sd.getName(), sd);
}
}
writer.write("# FHIR GraphQL Schema. Version " + version + "\r\n\r\n");
writer.write("# FHIR Defined Primitive types\r\n");
@ -290,16 +293,17 @@ public class GraphQLSchemaGenerator {
}
private void generateType(Map<String, String> existingTypeNames, Writer writer, StructureDefinition sd, EnumSet<FHIROperationType> operations) throws IOException {
if (sd.getAbstract()) {
return;
}
if (operations.contains(FHIROperationType.READ) || operations.contains(FHIROperationType.SEARCH)) {
List<StringBuilder> list = new ArrayList<>();
StringBuilder b = new StringBuilder();
list.add(b);
b.append("type ");
b.append(sd.getName());
StructureDefinition sdp = context.fetchResource(StructureDefinition.class, sd.getBaseDefinition());
if (sdp != null) {
b.append(" implements ");
b.append(sdp.getType());
}
b.append(" {\r\n");
ElementDefinition ed = sd.getSnapshot().getElementFirstRep();
generateProperties(existingTypeNames, list, b, sd.getName(), sd, ed, "type", "");
@ -370,7 +374,13 @@ public class GraphQLSchemaGenerator {
if (suffix)
b.append(Utilities.capitalize(typeDetails.getWorkingCode()));
b.append(": ");
b.append(n);
if (!child.getMax().equals("1")) {
b.append("[");
b.append(n);
b.append("]");
} else {
b.append(n);
}
if (!child.getPath().endsWith(".id")) {
b.append(" _");
b.append(tail(child.getPath(), suffix));

29
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/OperationOutcomeUtilities.java
View File

@ -129,4 +129,33 @@ public class OperationOutcomeUtilities {
}
return res;
}
public static OperationOutcomeIssueComponent convertToIssueSimple(ValidationMessage message, OperationOutcome op) {
OperationOutcomeIssueComponent issue = new OperationOutcome.OperationOutcomeIssueComponent();
issue.setUserData("source.vm", message);
issue.setCode(convert(message.getType()));
if (message.getLocation() != null) {
// message location has a fhirPath in it. We need to populate the expression
issue.addExpression(message.getLocation());
}
if (message.getLine() >= 0 && message.getCol() >= 0) {
issue.setDiagnostics("["+message.getLine()+","+message.getCol()+"]");
}
issue.setSeverity(convert(message.getLevel()));
CodeableConcept c = new CodeableConcept();
c.setText(message.getMessage());
issue.setDetails(c);
return issue;
}
public static OperationOutcome createOutcomeSimple(List<ValidationMessage> messages) {
OperationOutcome res = new OperationOutcome();
for (ValidationMessage vm : messages) {
res.addIssue(convertToIssueSimple(vm, res));
}
return res;
}
}

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

@ -205,6 +205,7 @@ public class ToolingExtensions {
public static final String EXT_REND_MD = "http://hl7.org/fhir/StructureDefinition/rendering-markdown";
public static final String EXT_CAP_STMT_EXPECT = "http://hl7.org/fhir/StructureDefinition/capabilitystatement-expectation";
public static final String EXT_ED_HEIRARCHY = "http://hl7.org/fhir/StructureDefinition/elementdefinition-heirarchy";
public static final String EXT_SD_DEPENDENCY = "http://hl7.org/fhir/StructureDefinition/structuredefinition-dependencies";
// in the tooling IG
public static final String EXT_BINDING_ADDITIONAL = "http://hl7.org/fhir/tools/StructureDefinition/additional-binding";

2
org.hl7.fhir.report/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.6.68-SNAPSHOT</version>
<version>5.6.69-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.utilities/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.6.68-SNAPSHOT</version>
<version>5.6.69-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

21
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/FileFormat.java Normal file
View File

@ -0,0 +1,21 @@
package org.hl7.fhir.utilities;
import java.io.PrintStream;
import java.nio.charset.Charset;
import java.nio.charset.StandardCharsets;
public class FileFormat {
public static boolean fileEncodingIsUtf8() {
return Charset.defaultCharset().equals(StandardCharsets.UTF_8);
}
public static void checkCharsetAndWarnIfNotUTF8(PrintStream out) {
if (fileEncodingIsUtf8()) return;
out.println("");
out.println("WARNING: Default file encoding is " + Charset.defaultCharset() + " which may cause unexpected results. ");
out.println(" To fix this issue, run this program with the parameter '-Dfile.encoding=UTF-8'");
out.println(" Future releases may not be able to run at all with encoding " + Charset.defaultCharset());
out.println("");
}
}

32
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/MarkDownProcessor.java
View File

@ -64,11 +64,41 @@ public class MarkDownProcessor {
}
switch (dialect) {
case DARING_FIREBALL : return Processor.process(source);
case COMMON_MARK : return processCommonMark(source);
case COMMON_MARK : return processCommonMark(preProcess(source));
default: throw new Error("Unknown Markdown Dialect: "+dialect.toString()+" at "+context);
}
}
/**
* This deals with a painful problem created by the intersection of previous publishing processes
* and the way commonmark specifies that < is handled in content. For control reasons, the FHIR specification does
* not allow raw html tags in the markdown
*
* This check finds any raw <[x] where [x] is any alpha character, and prepends \ to it so that it
* renders as a < (e.g. gets escaped in the output HTML)
*
* This is public to enable testing (not for direct use otherwise)
*
* @param source
* @return
*/
public static String preProcess(String source) {
StringBuilder b = new StringBuilder();
for (int i = 0; i < source.length(); i++) {
char last = i > 0 ? source.charAt(i-1) : 0;
char current = source.charAt(i);
char next = i < source.length() -1 ? source.charAt(i+1) : 0;
if (current == '<' && Character.isAlphabetic(next) && last != '\\') {
b.append('\\');
b.append(current);
} else {
b.append(current);
}
}
return b.toString();
}
private String processCommonMark(String source) {
Set<Extension> extensions = Collections.singleton(TablesExtension.create());
Parser parser = Parser.builder().extensions(extensions).build();

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

@ -1758,4 +1758,12 @@ public class Utilities {
return text;
}
public static int parseInt(String value, int def) {
if (isInteger(value)) {
return Integer.parseInt(value);
} else {
return def;
}
}
}

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

@ -487,7 +487,6 @@ public class VersionUtilities {
res.add("ActivityDefinition");
res.add("CapabilityStatement");
res.add("CapabilityStatement2");
res.add("ChargeItemDefinition");
res.add("Citation");
res.add("CodeSystem");

7
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/i18n/I18nConstants.java
View File

@ -488,6 +488,7 @@ public class I18nConstants {
public static final String TYPE_SPECIFIC_CHECKS_DT_BASE64_VALID = "Type_Specific_Checks_DT_Base64_Valid";
public static final String TYPE_SPECIFIC_CHECKS_DT_BOOLEAN_VALUE = "Type_Specific_Checks_DT_Boolean_Value";
public static final String TYPE_SPECIFIC_CHECKS_DT_CODE_WS = "Type_Specific_Checks_DT_Code_WS";
public static final String TYPE_SPECIFIC_CHECKS_DT_MARKDOWN_HTML = "TYPE_SPECIFIC_CHECKS_DT_MARKDOWN_HTML";
public static final String TYPE_SPECIFIC_CHECKS_DT_DATETIME_REASONABLE = "Type_Specific_Checks_DT_DateTime_Reasonable";
public static final String TYPE_SPECIFIC_CHECKS_DT_DATETIME_REGEX = "Type_Specific_Checks_DT_DateTime_Regex";
public static final String TYPE_SPECIFIC_CHECKS_DT_DATETIME_TZ = "Type_Specific_Checks_DT_DateTime_TZ";
@ -610,6 +611,7 @@ public class I18nConstants {
public static final String VALIDATION_VAL_PROFILE_SIGNPOST = "VALIDATION_VAL_PROFILE_SIGNPOST";
public static final String VALIDATION_VAL_PROFILE_SIGNPOST_GLOBAL = "VALIDATION_VAL_PROFILE_SIGNPOST_GLOBAL";
public static final String VALIDATION_VAL_PROFILE_SIGNPOST_META = "VALIDATION_VAL_PROFILE_SIGNPOST_META";
public static final String VALIDATION_VAL_PROFILE_SIGNPOST_DEP = "VALIDATION_VAL_PROFILE_SIGNPOST_DEP";
public static final String VALIDATION_VAL_PROFILE_SIGNPOST_BUNDLE_PARAM = "VALIDATION_VAL_PROFILE_SIGNPOST_BUNDLE_PARAM";
public static final String VALIDATION_VAL_PROFILE_SLICEORDER = "Validation_VAL_Profile_SliceOrder";
public static final String VALIDATION_VAL_PROFILE_OTHER_VERSION = "VALIDATION_VAL_PROFILE_OTHER_VERSION";
@ -621,6 +623,7 @@ public class I18nConstants {
public static final String VALIDATION_VAL_PROFILE_WRONGTYPE = "Validation_VAL_Profile_WrongType";
public static final String VALIDATION_VAL_PROFILE_WRONGTYPE2 = "Validation_VAL_Profile_WrongType2";
public static final String VALIDATION_VAL_UNKNOWN_PROFILE = "Validation_VAL_Unknown_Profile";
public static final String VALIDATION_VAL_PROFILE_DEPENDS_NOT_RESOLVED = "VALIDATION_VAL_PROFILE_DEPENDS_NOT_RESOLVED";
public static final String VALUESET_INCLUDE_INVALID_CONCEPT_CODE = "VALUESET_INCLUDE_INVALID_CONCEPT_CODE";
public static final String VALUESET_INCLUDE_INVALID_CONCEPT_CODE_VER = "VALUESET_INCLUDE_INVALID_CONCEPT_CODE_VER";
@ -635,6 +638,10 @@ public class I18nConstants {
public static final String CODESYSTEM_SHAREABLE_MISSING_HL7 = "CODESYSTEM_SHAREABLE_MISSING_HL7";
public static final String CODESYSTEM_SHAREABLE_EXTRA_MISSING_HL7 = "CODESYSTEM_SHAREABLE_EXTRA_MISSING_HL7";
public static final String CODESYSTEM_SHAREABLE_EXTRA_MISSING = "CODESYSTEM_SHAREABLE_EXTRA_MISSING";
public static final String MEASURE_SHAREABLE_MISSING = "MEASURE_SHAREABLE_MISSING";
public static final String MEASURE_SHAREABLE_MISSING_HL7 = "MEASURE_SHAREABLE_MISSING_HL7";
public static final String MEASURE_SHAREABLE_EXTRA_MISSING_HL7 = "MEASURE_SHAREABLE_EXTRA_MISSING_HL7";
public static final String MEASURE_SHAREABLE_EXTRA_MISSING = "MEASURE_SHAREABLE_EXTRA_MISSING";
public static final String VALUESET_UNC_SYSTEM_WARNING = "VALUESET_UNC_SYSTEM_WARNING";
public static final String VALUESET_UNC_SYSTEM_WARNING_VER = "VALUESET_UNC_SYSTEM_WARNING_VER";
public static final String VALUESET_IMPORT_UNION_INTERSECTION = "VALUESET_IMPORT_UNION_INTERSECTION";

2
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/json/JsonTrackingParser.java
View File

@ -686,7 +686,7 @@ public class JsonTrackingParser {
}
public static void write(JsonObject json, File file) throws IOException {
Gson gson = new GsonBuilder().setPrettyPrinting().create();
Gson gson = new GsonBuilder().setPrettyPrinting().disableHtmlEscaping().create();
String jcnt = gson.toJson(json);
TextFile.stringToFile(jcnt, file);
}

18
org.hl7.fhir.utilities/src/main/resources/Messages.properties
View File

@ -236,6 +236,7 @@ Validation_VAL_Profile_Unknown = Profile reference ''{0}'' has not been checked
VALIDATION_VAL_PROFILE_UNKNOWN_NOT_POLICY = Profile reference ''{0}'' has not been checked because it is unknown, and the validator is set to not fetch unknown profiles
VALIDATION_VAL_PROFILE_UNKNOWN_ERROR = Profile reference ''{0}'' has not been checked because it is unknown, and fetching it resulted in the error {1}
Validation_VAL_Unknown_Profile = Unknown profile {0}
VALIDATION_VAL_PROFILE_DEPENDS_NOT_RESOLVED = Profile {1} identifies {2} as a dependency (using the extension http://hl7.org/fhir/StructureDefinition/structuredefinition-dependencies), but this profile could not be found
XHTML_XHTML_Attribute_Illegal = Illegal attribute name in the XHTML (''{0}'' on ''{1}'')
XHTML_XHTML_Element_Illegal = Illegal element name in the XHTML (''{0}'')
XHTML_XHTML_NS_InValid = Wrong namespace on the XHTML (''{0}'', should be ''{1}'')
@ -384,7 +385,7 @@ Error_parsing_JSON_ = Error parsing JSON: {0}
Node_type__is_not_allowed = Node type {0} is not allowed
CDATA_is_not_allowed = CDATA is not allowed
Undefined_element_ = Undefined element ''{0}''
Undefined_attribute__on__for_type__properties__ = Undefined attribute ''@{0}'' on {1} for type {2} (properties = {3})
Undefined_attribute__on__for_type__properties__ = Undefined attribute ''@{0}'' on {1} for type {2}
Text_should_not_be_present = Text should not be present (''{0}'')
Wrong_namespace__expected_ = Wrong namespace - expected ''{0}''
Element_must_have_some_content = Element must have some content
@ -536,6 +537,7 @@ VALIDATION_VAL_GLOBAL_PROFILE_UNKNOWN = Global Profile reference ''{0}'' from IG
VALIDATION_VAL_PROFILE_SIGNPOST_BASE = Validate resource against profile
VALIDATION_VAL_PROFILE_SIGNPOST = Validate resource against profile {0}
VALIDATION_VAL_PROFILE_SIGNPOST_META = Validate resource against profile {0} (per meta)
VALIDATION_VAL_PROFILE_SIGNPOST_DEP = Validate resource against profile {0} (per http://hl7.org/fhir/StructureDefinition/structuredefinition-dependencies in {1})
VALIDATION_VAL_PROFILE_SIGNPOST_BUNDLE_PARAM = Validate resource against profile {0} - provided as bundle param
VALIDATION_VAL_PROFILE_SIGNPOST_GLOBAL = Validate resource against profile {0} - a global profile in {1}
ERROR_GENERATING_SNAPSHOT = Error generating Snapshot: {0} (this usually arises from a problem in the differential)
@ -726,7 +728,13 @@ VALUESET_SHAREABLE_MISSING = The ShareableValueSet profile says that the {0} ele
VALUESET_SHAREABLE_EXTRA_MISSING = The ShareableValueSet profile recommends that the {0} element is populated, but it is not present. Published value sets SHOULD conform to the ShareableValueSet profile
VALUESET_SHAREABLE_MISSING_HL7 = The ShareableValueSet profile says that the {0} element is mandatory, but it is not found. HL7 Published value sets SHALL conform to the ShareableValueSet profile
VALUESET_SHAREABLE_EXTRA_MISSING_HL7 = The ShareableValueSet profile recommends that the {0} element is populated, but it is not found. HL7 Published value sets SHALL conform to the ShareableValueSet profile
CODESYSTEM_SHAREABLE_MISSING = The ShareableCodeSystem profile says that the {0} element is mandatory, but it is not present. Published value sets SHOULD conform to the ShareableCodeSystem profile
CODESYSTEM_SHAREABLE_EXTRA_MISSING = The ShareableCodeSystem profile recommends that the {0} element is populated, but it is not present. Published value sets SHOULD conform to the ShareableCodeSystem profile
CODESYSTEM_SHAREABLE_MISSING_HL7 = The ShareableCodeSystem profile says that the {0} element is mandatory, but it is not found. HL7 Published value sets SHALL conform to the ShareableCodeSystem profile
CODESYSTEM_SHAREABLE_EXTRA_MISSING_HL7 = The ShareableCodeSystem profile recommends that the {0} element is populated, but it is not found. HL7 Published value sets SHALL conform to the ShareableCodeSystem profile
CODESYSTEM_SHAREABLE_MISSING = The ShareableCodeSystem profile says that the {0} element is mandatory, but it is not present. Published code systems SHOULD conform to the ShareableCodeSystem profile
CODESYSTEM_SHAREABLE_EXTRA_MISSING = The ShareableCodeSystem profile recommends that the {0} element is populated, but it is not present. Published code systems SHOULD conform to the ShareableCodeSystem profile
CODESYSTEM_SHAREABLE_MISSING_HL7 = The ShareableCodeSystem profile says that the {0} element is mandatory, but it is not found. HL7 Published code systems SHALL conform to the ShareableCodeSystem profile
CODESYSTEM_SHAREABLE_EXTRA_MISSING_HL7 = The ShareableCodeSystem profile recommends that the {0} element is populated, but it is not found. HL7 Published code systems SHALL conform to the ShareableCodeSystem profile
MEASURE_SHAREABLE_MISSING = The ShareableMeasure profile says that the {0} element is mandatory, but it is not present. Published measures SHOULD conform to the ShareableMeasure profile
MEASURE_SHAREABLE_EXTRA_MISSING = The ShareableMeasure profile recommends that the {0} element is populated, but it is not present. Published measures SHOULD conform to the ShareableMeasure profile
MEASURE_SHAREABLE_MISSING_HL7 = The ShareableMeasure profile says that the {0} element is mandatory, but it is not found. HL7 Published measures SHALL conform to the ShareableMeasure profile
MEASURE_SHAREABLE_EXTRA_MISSING_HL7 = The ShareableMeasure profile recommends that the {0} element is populated, but it is not found. HL7 Published measures SHALL conform to the ShareableMeasure profile
TYPE_SPECIFIC_CHECKS_DT_MARKDOWN_HTML = The markdown contains content that appears to be an embedded HTML tag starting at ''{0}''. This will (or SHOULD) be escaped by the presentation layer. The content should be checked to confirm that this is the desired behaviour

35
org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/FileFormatTest.java Normal file
View File

@ -0,0 +1,35 @@
package org.hl7.fhir.utilities;
import org.junit.jupiter.api.Test;
import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.io.PrintStream;
import java.nio.charset.Charset;
import java.nio.charset.StandardCharsets;
import static org.hamcrest.CoreMatchers.containsString;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.junit.Assert.assertEquals;
public class FileFormatTest {
@Test
public void testCurrentFileFormat() throws IOException {
ByteArrayOutputStream bo = new ByteArrayOutputStream();
FileFormat.checkCharsetAndWarnIfNotUTF8(new PrintStream(bo));
bo.flush();
String allWrittenLines = new String(bo.toByteArray());
assertAWarningIsGivenWhenNotUTF8(allWrittenLines);
}
private static void assertAWarningIsGivenWhenNotUTF8(String allWrittenLines) {
if (Charset.defaultCharset().equals(StandardCharsets.UTF_8)) {
assertEquals(0, allWrittenLines.length());
} else {
assertThat(allWrittenLines, containsString("WARNING"));
}
}
}

30
org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/tests/MarkdownPreprocessorTesting.java Normal file
View File

@ -0,0 +1,30 @@
package org.hl7.fhir.utilities.tests;
import static org.junit.jupiter.api.Assertions.assertEquals;
import java.io.IOException;
import org.hl7.fhir.utilities.MarkDownProcessor;
import org.junit.jupiter.api.Test;
public class MarkdownPreprocessorTesting {
@Test
public void testSimple() throws IOException {
assertEquals(MarkDownProcessor.preProcess("1 < 2"), "1 < 2");
}
@Test
public void testHTML() throws IOException {
assertEquals(MarkDownProcessor.preProcess("<type>"), "\\<type>");
assertEquals(MarkDownProcessor.preProcess("\\<type>"), "\\<type>");
}
@Test
public void testBorder() throws IOException {
assertEquals(MarkDownProcessor.preProcess("<>"), "<>");
assertEquals(MarkDownProcessor.preProcess("><"), "><");
}
}

2
org.hl7.fhir.validation.cli/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.6.68-SNAPSHOT</version>
<version>5.6.69-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

4
org.hl7.fhir.validation/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.6.68-SNAPSHOT</version>
<version>5.6.69-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
@ -197,7 +197,7 @@
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
<version>2.12.6.1</version>
<version>2.14.0-rc1</version>
</dependency>
<dependency>
<groupId>org.thymeleaf</groupId>

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

@ -53,6 +53,7 @@ import org.hl7.fhir.utilities.npm.ToolsVersion;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.xhtml.XhtmlComposer;
import org.hl7.fhir.validation.BaseValidator.ValidationControl;
import org.hl7.fhir.validation.cli.model.HtmlInMarkdownCheck;
import org.hl7.fhir.validation.cli.services.IPackageInstaller;
import org.hl7.fhir.validation.cli.utils.*;
import org.hl7.fhir.validation.instance.InstanceValidator;
@ -160,6 +161,7 @@ public class ValidationEngine implements IValidatorResourceFetcher, IValidationP
@Getter @Setter private boolean allowExampleUrls;
@Getter @Setter private boolean showMessagesFromReferences;
@Getter @Setter private boolean doImplicitFHIRPathStringConversion;
@Getter @Setter private HtmlInMarkdownCheck htmlInMarkdownCheck;
@Getter @Setter private Locale locale;
@Getter @Setter private List<ImplementationGuide> igs = new ArrayList<>();
@Getter @Setter private List<String> extensionDomains = new ArrayList<>();
@ -625,6 +627,7 @@ public class ValidationEngine implements IValidatorResourceFetcher, IValidationP
validator.getValidationControl().putAll(validationControl);
validator.setQuestionnaireMode(questionnaireMode);
validator.setLevel(level);
validator.setHtmlInMarkdownCheck(htmlInMarkdownCheck);
validator.setNoUnicodeBiDiControlChars(noUnicodeBiDiControlChars);
validator.setDoImplicitFHIRPathStringConversion(doImplicitFHIRPathStringConversion);
if (format == FhirFormat.SHC) {

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

@ -61,6 +61,7 @@ POSSIBILITY OF SUCH DAMAGE.
import org.hl7.fhir.r5.model.ImplementationGuide;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.terminologies.JurisdictionUtilities;
import org.hl7.fhir.utilities.FileFormat;
import org.hl7.fhir.utilities.TimeTracker;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
@ -154,6 +155,8 @@ public class ValidatorCli {
CliContext cliContext = Params.loadCliContext(args);
FileFormat.checkCharsetAndWarnIfNotUTF8(System.out);
if (shouldDisplayHelpToUser(args)) {
Display.displayHelpDetails();
} else if (Params.hasParam(args, Params.COMPARE)) {

12
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/model/CliContext.java
View File

@ -48,6 +48,8 @@ public class CliContext {
private boolean wantInvariantsInMessages = false;
@JsonProperty("doImplicitFHIRPathStringConversion")
private boolean doImplicitFHIRPathStringConversion = false;
@JsonProperty("htmlInMarkdownCheck")
private HtmlInMarkdownCheck htmlInMarkdownCheck = HtmlInMarkdownCheck.WARNING;
@JsonProperty("map")
private String map = null;
@ -248,6 +250,16 @@ public class CliContext {
this.doImplicitFHIRPathStringConversion = doImplicitFHIRPathStringConversion;
}
@JsonProperty("htmlInMarkdownCheck")
public HtmlInMarkdownCheck getHtmlInMarkdownCheck() {
return htmlInMarkdownCheck;
}
@JsonProperty("htmlInMarkdownCheck")
public void setHtmlInMarkdownCheck(HtmlInMarkdownCheck htmlInMarkdownCheck) {
this.htmlInMarkdownCheck = htmlInMarkdownCheck;
}
@JsonProperty("locale")
public String getLanguageCode() {
return locale;

30
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/model/HtmlInMarkdownCheck.java Normal file
View File

@ -0,0 +1,30 @@
package org.hl7.fhir.validation.cli.model;
import org.hl7.fhir.utilities.Utilities;
public enum HtmlInMarkdownCheck {
NONE,
WARNING,
ERROR;
public static boolean isValidCode(String q) {
return fromCode(q) != null;
}
public static HtmlInMarkdownCheck fromCode(String q) {
if (Utilities.noString(q)) {
return null;
}
q = q.toLowerCase();
if (Utilities.existsInList(q, "n", "none", "ignore", "i")) {
return NONE;
}
if (Utilities.existsInList(q, "w", "warning", "warnings", "warn")) {
return WARNING;
}
if (Utilities.existsInList(q, "e", "error", "errors", "err")) {
return ERROR;
}
return null;
}
}

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

@ -372,6 +372,7 @@ public class ValidationService {
validator.setAssumeValidRestReferences(cliContext.isAssumeValidRestReferences());
validator.setShowMessagesFromReferences(cliContext.isShowMessagesFromReferences());
validator.setDoImplicitFHIRPathStringConversion(cliContext.isDoImplicitFHIRPathStringConversion());
validator.setHtmlInMarkdownCheck(cliContext.getHtmlInMarkdownCheck());
validator.setNoExtensibleBindingMessages(cliContext.isNoExtensibleBindingMessages());
validator.setNoUnicodeBiDiControlChars(cliContext.isNoUnicodeBiDiControlChars());
validator.setNoInvariantChecks(cliContext.isNoInvariants());

15
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/utils/Params.java
View File

@ -5,6 +5,7 @@ import org.hl7.fhir.r5.terminologies.JurisdictionUtilities;
import org.hl7.fhir.r5.utils.validation.BundleValidationRule;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.validation.cli.model.CliContext;
import org.hl7.fhir.validation.cli.model.HtmlInMarkdownCheck;
import java.io.File;
import java.util.Arrays;
@ -69,7 +70,8 @@ public class Params {
public static final String ALLOW_EXAMPLE_URLS = "-allow-example-urls";
public static final String OUTPUT_STYLE = "-output-style";
public static final String DO_IMPLICIT_FHIRPATH_STRING_CONVERSION = "-implicit-fhirpath-string-conversions";
private static final Object JURISDICTION = "-jurisdiction";
public static final String JURISDICTION = "-jurisdiction";
public static final String HTML_IN_MARKDOWN = "-html-in-markdown";
public static final String RUN_TESTS = "-run-tests";
@ -176,6 +178,17 @@ public class Params {
cliContext.setShowMessagesFromReferences(true);
} else if (args[i].equals(DO_IMPLICIT_FHIRPATH_STRING_CONVERSION)) {
cliContext.setDoImplicitFHIRPathStringConversion(true);
} else if (args[i].equals(HTML_IN_MARKDOWN)) {
if (i + 1 == args.length)
throw new Error("Specified "+HTML_IN_MARKDOWN+" without indicating mode");
else {
String q = args[++i];
if (!HtmlInMarkdownCheck.isValidCode(q)) {
throw new Error("Specified "+HTML_IN_MARKDOWN+" with na invalid code - must be ignore, warning, or error");
} else {
cliContext.setHtmlInMarkdownCheck(HtmlInMarkdownCheck.fromCode(q));
}
}
} else if (args[i].equals(LOCALE)) {
if (i + 1 == args.length) {
throw new Error("Specified -locale without indicating locale");

163
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java
View File

@ -42,6 +42,8 @@ import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.Calendar;
import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
@ -142,6 +144,7 @@ import org.hl7.fhir.r5.utils.ToolingExtensions;
import org.hl7.fhir.r5.utils.XVerExtensionManager;
import org.hl7.fhir.r5.utils.validation.constants.*;
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
import org.hl7.fhir.utilities.MarkDownProcessor;
import org.hl7.fhir.utilities.SIDUtilities;
import org.hl7.fhir.utilities.SimpleTimeTracker;
import org.hl7.fhir.utilities.TimeTracker;
@ -159,9 +162,12 @@ 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.cli.model.HtmlInMarkdownCheck;
import org.hl7.fhir.validation.cli.utils.QuestionnaireMode;
import org.hl7.fhir.validation.cli.utils.ValidationLevel;
import org.hl7.fhir.validation.instance.InstanceValidator.CanonicalResourceLookupResult;
import org.hl7.fhir.validation.instance.InstanceValidator.CanonicalTypeSorter;
import org.hl7.fhir.validation.instance.InstanceValidator.StructureDefinitionSorterByUrl;
import org.hl7.fhir.validation.instance.type.BundleValidator;
import org.hl7.fhir.validation.instance.type.CodeSystemValidator;
import org.hl7.fhir.validation.instance.type.MeasureValidator;
@ -199,6 +205,25 @@ import com.google.gson.JsonObject;
*/
public class InstanceValidator extends BaseValidator implements IResourceValidator {
public class StructureDefinitionSorterByUrl implements Comparator<StructureDefinition> {
@Override
public int compare(StructureDefinition o1, StructureDefinition o2) {
return o1.getUrl().compareTo(o2.getUrl());
}
}
public class CanonicalTypeSorter implements Comparator<CanonicalType> {
@Override
public int compare(CanonicalType o1, CanonicalType o2) {
return o1.getValue().compareTo(o2.getValue());
}
}
public class CanonicalResourceLookupResult {
private CanonicalResource resource;
@ -387,6 +412,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
private boolean noCheckAggregation;
private boolean wantCheckSnapshotUnchanged;
private boolean noUnicodeBiDiControlChars;
private HtmlInMarkdownCheck htmlInMarkdownCheck;
private List<ImplementationGuide> igs = new ArrayList<>();
private List<String> extensionDomains = new ArrayList<String>();
@ -792,15 +818,31 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
setParents(element);
long t = System.nanoTime();
NodeStack stack = new NodeStack(context, path, element, validationLanguage);
if (profiles == null || profiles.isEmpty()) {
validateResource(new ValidatorHostContext(appContext, element), errors, element, element, null, resourceIdRule, new NodeStack(context, path, element, validationLanguage).resetIds(), null);
validateResource(new ValidatorHostContext(appContext, element), errors, element, element, null, resourceIdRule, stack.resetIds(), null);
} else {
int i = 0;
while (i < profiles.size()) {
StructureDefinition sd = profiles.get(i);
if (sd.hasExtension(ToolingExtensions.EXT_SD_DEPENDENCY)) {
for (Extension ext : sd.getExtensionsByUrl(ToolingExtensions.EXT_SD_DEPENDENCY)) {
StructureDefinition dep = context.fetchResource( StructureDefinition.class, ext.getValue().primitiveValue());
if (dep == null) {
warning(errors, IssueType.BUSINESSRULE, element.line(), element.col(), stack.getLiteralPath(), false, I18nConstants.VALIDATION_VAL_PROFILE_DEPENDS_NOT_RESOLVED, ext.getValue().primitiveValue(), sd.getUrl());
} else if (!profiles.contains(dep)) {
profiles.add(dep);
}
}
}
i++;
}
for (StructureDefinition defn : profiles) {
validateResource(new ValidatorHostContext(appContext, element), errors, element, element, defn, resourceIdRule, new NodeStack(context, path, element, validationLanguage).resetIds(), null);
validateResource(new ValidatorHostContext(appContext, element), errors, element, element, defn, resourceIdRule, stack.resetIds(), null);
}
}
if (hintAboutNonMustSupport) {
checkElementUsage(errors, element, new NodeStack(context, path, element, validationLanguage));
checkElementUsage(errors, element, stack);
}
errors.removeAll(messagesToRemove);
timeTracker.overall(t);
@ -1191,7 +1233,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
checkBindings(errors, path, element, stack, valueset, nextCoding);
}
}
timeTracker.tx(t, "vc "+DataRenderer.display(context, cc));
timeTracker.tx(t, "vc "+cc.toString());
}
}
} catch (Exception e) {
@ -1666,6 +1708,8 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
txHint(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_NOVALID_14, describeReference(binding.getValueSet(), valueset), getErrorMessage(vr.getMessage()), theSystem+"#"+theCode);
}
}
} else if (vr != null && vr.getMessage() != null) {
txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, vr.getMessage());
}
} catch (Exception e) {
if (STACK_TRACE) e.printStackTrace();
@ -2134,7 +2178,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
if (!"xhtml".equals(type)) {
if (securityChecks) {
rule(errors, IssueType.INVALID, e.line(), e.col(), path, !containsHtmlTags(e.primitiveValue()), I18nConstants.SECURITY_STRING_CONTENT_ERROR);
} else {
} else if (!"markdown".equals(type)){
hint(errors, IssueType.INVALID, e.line(), e.col(), path, !containsHtmlTags(e.primitiveValue()), I18nConstants.SECURITY_STRING_CONTENT_WARNING);
}
}
@ -2318,6 +2362,17 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
checkPrimitiveBinding(hostContext, errors, path, type, context, e, profile, node);
}
if (type.equals("markdown") && htmlInMarkdownCheck != HtmlInMarkdownCheck.NONE) {
String raw = e.primitiveValue();
String processed = MarkDownProcessor.preProcess(raw);
if (!raw.equals(processed)) {
int i = 0;
while (i < raw.length() && raw.charAt(1) == processed.charAt(i)) {
i++;
}
warningOrError(htmlInMarkdownCheck == HtmlInMarkdownCheck.ERROR, errors, IssueType.INVALID, e.line(), e.col(), path, false, I18nConstants.TYPE_SPECIFIC_CHECKS_DT_MARKDOWN_HTML, raw.subSequence(i, 2));
}
}
if (type.equals("xhtml")) {
XhtmlNode xhtml = e.getXhtml();
if (xhtml != null) { // if it is null, this is an error already noted in the parsers
@ -3226,7 +3281,10 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
return true;
}
private String asListByUrl(Collection<StructureDefinition> list) {
private String asListByUrl(Collection<StructureDefinition> coll) {
List<StructureDefinition> list = new ArrayList<>();
list.addAll(coll);
Collections.sort(list, new StructureDefinitionSorterByUrl());
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
for (StructureDefinition sd : list) {
b.append(sd.getUrl());
@ -3234,7 +3292,10 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
return b.toString();
}
private String asList(Collection<CanonicalType> list) {
private String asList(Collection<CanonicalType> coll) {
List<CanonicalType> list = new ArrayList<>();
list.addAll(coll);
Collections.sort(list, new CanonicalTypeSorter());
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
for (CanonicalType c : list) {
b.append(c.getValue());
@ -3670,7 +3731,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
}
private String getErrorMessage(String message) {
return message != null ? " (error message = " + message + ")" : "";
return message != null ? " (error message = " + message + ")" : "";
}
public boolean isSuppressLoincSnomedMessages() {
@ -4474,28 +4535,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
} else if (!fetcher.fetchesCanonicalResource(this, profile.primitiveValue())) {
warning(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath() + ".meta.profile[" + i + "]", false, I18nConstants.VALIDATION_VAL_PROFILE_UNKNOWN_NOT_POLICY, profile.primitiveValue());
} else {
sd = null;
String url = profile.primitiveValue();
CanonicalResourceLookupResult cr = crLookups.get(url);
if (cr != null) {
if (cr.error != null) {
warning(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath() + ".meta.profile[" + i + "]", false, I18nConstants.VALIDATION_VAL_PROFILE_UNKNOWN_ERROR, url, cr.error);
} else {
sd = (StructureDefinition) cr.resource;
}
} else {
try {
sd = (StructureDefinition) fetcher.fetchCanonicalResource(this, url);
crLookups.put(url, new CanonicalResourceLookupResult(sd));
} catch (Exception e) {
if (STACK_TRACE) { e.printStackTrace(); }
crLookups.put(url, new CanonicalResourceLookupResult(e.getMessage()));
warning(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath() + ".meta.profile[" + i + "]", false, I18nConstants.VALIDATION_VAL_PROFILE_UNKNOWN_ERROR, profile.primitiveValue(), e.getMessage());
}
if (sd != null) {
context.cacheResource(sd);
}
}
sd = lookupProfileReference(errors, element, stack, i, profile, sd);
}
}
if (sd != null) {
@ -4510,6 +4550,27 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
if (pctOwned) {
pct.done();
}
if (sd.hasExtension(ToolingExtensions.EXT_SD_DEPENDENCY)) {
for (Extension ext : sd.getExtensionsByUrl(ToolingExtensions.EXT_SD_DEPENDENCY)) {
StructureDefinition sdi = context.fetchResource(StructureDefinition.class, ext.getValue().primitiveValue());
if (sdi == null) {
warning(errors, IssueType.BUSINESSRULE, element.line(), element.col(), stack.getLiteralPath() + ".meta.profile[" + i + "]", false, I18nConstants.VALIDATION_VAL_PROFILE_DEPENDS_NOT_RESOLVED, ext.getValue().primitiveValue(), sd.getUrl());
} else {
if (crumbTrails) {
element.addMessage(signpost(errors, IssueType.INFORMATIONAL, element.line(), element.col(), stack.getLiteralPath(), I18nConstants.VALIDATION_VAL_PROFILE_SIGNPOST_DEP, sdi.getUrl(), sd.getUrl()));
}
stack.resetIds();
if (pctOwned) {
pct = new PercentageTracker(resource.countDescendents(), resource.fhirType(), sdi.getUrl(), logProgress);
}
startInner(hostContext, errors, resource, element, sdi, stack, false, pct);
if (pctOwned) {
pct.done();
}
}
}
}
}
}
}
@ -4540,6 +4601,32 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
// System.out.println("start: "+(System.currentTimeMillis()-st)+" ("+resource.fhirType()+")");
}
private StructureDefinition lookupProfileReference(List<ValidationMessage> errors, Element element, NodeStack stack,
int i, Element profile, StructureDefinition sd) {
String url = profile.primitiveValue();
CanonicalResourceLookupResult cr = crLookups.get(url);
if (cr != null) {
if (cr.error != null) {
warning(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath() + ".meta.profile[" + i + "]", false, I18nConstants.VALIDATION_VAL_PROFILE_UNKNOWN_ERROR, url, cr.error);
} else {
sd = (StructureDefinition) cr.resource;
}
} else {
try {
sd = (StructureDefinition) fetcher.fetchCanonicalResource(this, url);
crLookups.put(url, new CanonicalResourceLookupResult(sd));
} catch (Exception e) {
if (STACK_TRACE) { e.printStackTrace(); }
crLookups.put(url, new CanonicalResourceLookupResult(e.getMessage()));
warning(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath() + ".meta.profile[" + i + "]", false, I18nConstants.VALIDATION_VAL_PROFILE_UNKNOWN_ERROR, profile.primitiveValue(), e.getMessage());
}
if (sd != null) {
context.cacheResource(sd);
}
}
return sd;
}
// private void plog(String msg) {
// long n = System.currentTimeMillis();
// String elapsed = Utilities.padLeft(Long.toString(n-start), ' ', 5);
@ -4638,9 +4725,9 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
} else if (element.getType().equals("QuestionnaireResponse")) {
new QuestionnaireValidator(context, myEnableWhenEvaluator, fpe, timeTracker, questionnaireMode, xverManager, jurisdiction).validateQuestionannaireResponse(hostContext, errors, element, stack);
} else if (element.getType().equals("Measure")) {
new MeasureValidator(context, timeTracker, xverManager, jurisdiction).validateMeasure(hostContext, errors, element, stack);
new MeasureValidator(context, timeTracker, xverManager, jurisdiction, this).validateMeasure(hostContext, errors, element, stack);
} else if (element.getType().equals("MeasureReport")) {
new MeasureValidator(context, timeTracker, xverManager, jurisdiction).validateMeasureReport(hostContext, errors, element, stack);
new MeasureValidator(context, timeTracker, xverManager, jurisdiction, this).validateMeasureReport(hostContext, errors, element, stack);
} else if (element.getType().equals("CapabilityStatement")) {
validateCapabilityStatement(errors, element, stack);
} else if (element.getType().equals("CodeSystem")) {
@ -5677,7 +5764,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
boolean ok;
try {
long t = System.nanoTime();
ok = fpe.evaluateToBoolean(hostContext, resource, hostContext.getRootResource(), element, n);
ok = fpe.evaluateToBoolean(hostContext, resource, hostContext.getRootResource(), element, n);
timeTracker.fpe(t);
msg = fpe.forLog();
} catch (Exception ex) {
@ -6025,6 +6112,16 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
this.noUnicodeBiDiControlChars = noUnicodeBiDiControlChars;
}
public HtmlInMarkdownCheck getHtmlInMarkdownCheck() {
return htmlInMarkdownCheck;
}
public void setHtmlInMarkdownCheck(HtmlInMarkdownCheck htmlInMarkdownCheck) {
this.htmlInMarkdownCheck = htmlInMarkdownCheck;
}
public Coding getJurisdiction() {
return jurisdiction;
}

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

@ -84,7 +84,9 @@ public class CodeSystemValidator extends BaseValidator {
}
}
checkShareableCodeSystem(errors, cs, stack);
if (!stack.isContained()) {
checkShareableCodeSystem(errors, cs, stack);
}
}

38
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/MeasureValidator.java
View File

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

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

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

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

@ -61,7 +61,9 @@ public class ValueSetValidator extends BaseValidator {
cc++;
}
}
checkShareableValueSet(errors, vs, stack);
if (!stack.isContained()) {
checkShareableValueSet(errors, vs, stack);
}
}
private void checkShareableValueSet(List<ValidationMessage> errors, Element vs, NodeStack stack) {

7
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/utils/FHIRPathExpressionFixer.java
View File

@ -45,6 +45,13 @@ public class FHIRPathExpressionFixer {
return ("name.exists() implies name.matches('[A-Z]([A-Za-z0-9_]){0,254}')");
}
// R5 ballot
if (expr.equals("url.matches('([^|#])*')")) {
return ("$this.matches('([^|#])*')");
}
// clarification in FHIRPath spec
if ("eld-19".equals(key)) {

36
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/r5/test/GeneralTests.java Normal file
View File

@ -0,0 +1,36 @@
package org.hl7.fhir.r5.test;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.List;
import org.hl7.fhir.r5.elementmodel.ParserBase.ValidationPolicy;
import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.junit.jupiter.api.Test;
public class GeneralTests {
@Test
void testXMLParse() throws IOException {
System.out.println(System.getProperty("java.vm.name"));
InputStream stream = TestingUtilities.loadTestResourceStream("validator",
"xml_v10.xml");
org.hl7.fhir.r5.elementmodel.XmlParser xp = new org.hl7.fhir.r5.elementmodel.XmlParser(TestingUtilities.getSharedWorkerContext());
xp.setAllowXsiLocation(true);
List<ValidationMessage> errorList = new ArrayList<>();
xp.setupValidation(ValidationPolicy.EVERYTHING, errorList);
try {
Object resource = xp.parse(stream);
} catch (Exception e) {
e.printStackTrace();
}
for (ValidationMessage message : errorList) {
System.out.println(message.getMessage());
}
}
}

181
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/ValidationTests.java
View File

@ -1,6 +1,10 @@
package org.hl7.fhir.validation.tests;
import static org.junit.Assert.assertFalse;
import static org.junit.jupiter.api.Assertions.assertEquals;
import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
@ -22,6 +26,8 @@ import org.hl7.fhir.convertors.factory.VersionConvertorFactory_10_50;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_14_50;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_30_50;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_40_50;
import org.hl7.fhir.r5.model.OperationOutcome;
import org.hl7.fhir.r5.model.OperationOutcome.OperationOutcomeIssueComponent;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
@ -31,6 +37,7 @@ import org.hl7.fhir.r5.elementmodel.Element;
import org.hl7.fhir.r5.elementmodel.Manager;
import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
import org.hl7.fhir.r5.elementmodel.ObjectConverter;
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.Base;
@ -46,6 +53,7 @@ import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.r5.utils.FHIRPathEngine;
import org.hl7.fhir.r5.utils.FHIRPathEngine.IEvaluationContext;
import org.hl7.fhir.r5.utils.OperationOutcomeUtilities;
import org.hl7.fhir.r5.utils.validation.IResourceValidator;
import org.hl7.fhir.r5.utils.validation.IValidationPolicyAdvisor;
import org.hl7.fhir.r5.utils.validation.constants.BestPracticeWarningLevel;
@ -56,17 +64,20 @@ import org.hl7.fhir.r5.utils.validation.IValidatorResourceFetcher;
import org.hl7.fhir.r5.utils.validation.constants.ContainedReferenceValidationPolicy;
import org.hl7.fhir.r5.utils.validation.constants.ReferenceValidationPolicy;
import org.hl7.fhir.utilities.SimpleHTTPClient.HTTPResult;
import org.hl7.fhir.utilities.json.JsonTrackingParser;
import org.hl7.fhir.utilities.json.JsonUtilities;
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.IgLoader;
import org.hl7.fhir.validation.ValidationEngine;
import org.hl7.fhir.validation.cli.model.HtmlInMarkdownCheck;
import org.hl7.fhir.validation.cli.services.StandAloneValidatorFetcher;
import org.hl7.fhir.validation.instance.InstanceValidator;
import org.junit.AfterClass;
import org.junit.Assert;
import org.junit.Test;
import org.junit.jupiter.api.Assertions;
import org.junit.runner.RunWith;
import org.junit.runners.Parameterized;
import org.junit.runners.Parameterized.Parameters;
@ -82,6 +93,7 @@ import com.google.gson.JsonObject;
public class ValidationTests implements IEvaluationContext, IValidatorResourceFetcher, IValidationPolicyAdvisor {
public final static boolean PRINT_OUTPUT_TO_CONSOLE = true;
private static final boolean BUILD_NEW = false;
@Parameters(name = "{index}: id {0}")
public static Iterable<Object[]> data() throws IOException {
@ -128,7 +140,7 @@ public class ValidationTests implements IEvaluationContext, IValidatorResourceFe
long setup = System.nanoTime();
this.name = name;
System.out.println("---- " + name + " ----------------------------------------------------------------");
System.out.println("---- " + name + " ---------------------------------------------------------------- ("+System.getProperty("java.vm.name")+")");
System.out.println("** Core: ");
String txLog = null;
if (content.has("txLog")) {
@ -254,7 +266,9 @@ public class ValidationTests implements IEvaluationContext, IValidatorResourceFe
if (content.has("security-checks")) {
val.setSecurityChecks(content.get("security-checks").getAsBoolean());
}
if (content.has("noHtmlInMarkdown")) {
val.setHtmlInMarkdownCheck(HtmlInMarkdownCheck.ERROR);
}
if (content.has("logical")==false) {
val.setAssumeValidRestReferences(content.has("assumeValidRestReferences") ? content.get("assumeValidRestReferences").getAsBoolean() : false);
System.out.println(String.format("Start Validating (%d to set up)", (System.nanoTime() - setup) / 1000000));
@ -333,6 +347,9 @@ public class ValidationTests implements IEvaluationContext, IValidatorResourceFe
checkOutcomes(errorsLogical, logical, "logical", name);
}
logger.verifyHasNoRequests();
if (BUILD_NEW) {
JsonTrackingParser.write(manifest, new File(Utilities.path("[tmp]", "validator", "manifest.new.json")));
}
}
@ -400,57 +417,139 @@ public class ValidationTests implements IEvaluationContext, IValidatorResourceFe
}
}
private void checkOutcomes(List<ValidationMessage> errors, JsonObject focus, String profile, String name) {
private void checkOutcomes(List<ValidationMessage> errors, JsonObject focus, String profile, String name) throws IOException {
JsonObject java = focus.getAsJsonObject("java");
int ec = 0;
int wc = 0;
int hc = 0;
List<String> errLocs = new ArrayList<>();
for (ValidationMessage vm : errors) {
if (vm.getLevel() == IssueSeverity.FATAL || vm.getLevel() == IssueSeverity.ERROR) {
ec++;
if (PRINT_OUTPUT_TO_CONSOLE) {
System.out.println(vm.getDisplay());
}
errLocs.add(vm.getLocation());
}
if (vm.getLevel() == IssueSeverity.WARNING) {
wc++;
if (PRINT_OUTPUT_TO_CONSOLE) {
System.out.println(vm.getDisplay());
}
}
if (vm.getLevel() == IssueSeverity.INFORMATION) {
hc++;
if (PRINT_OUTPUT_TO_CONSOLE) {
System.out.println(vm.getDisplay());
}
OperationOutcome goal = java.has("outcome") ? (OperationOutcome) new JsonParser().parse(java.getAsJsonObject("outcome")) : new OperationOutcome();
OperationOutcome actual = OperationOutcomeUtilities.createOutcomeSimple(errors);
actual.setText(null);
String json = new JsonParser().setOutputStyle(OutputStyle.PRETTY).composeString(actual);
List<String> fails = new ArrayList<>();
Map<OperationOutcomeIssueComponent, OperationOutcomeIssueComponent> map = new HashMap<>();
for (OperationOutcomeIssueComponent issGoal : goal.getIssue()) {
OperationOutcomeIssueComponent issActual = findMatchingIssue(actual, issGoal);
if (issActual == null) {
fails.add("Expected Issue not found: "+issGoal.toString());
} else {
map.put(issActual, issGoal);
}
}
if (!TestingUtilities.getSharedWorkerContext(version).isNoTerminologyServer() || !focus.has("tx-dependent")) {
Assert.assertEquals("Test " + name + (profile == null ? "" : " profile: "+ profile) + ": Expected " + Integer.toString(java.get("errorCount").getAsInt()) + " errors, but found " + Integer.toString(ec) + ".", java.get("errorCount").getAsInt(), ec);
for (OperationOutcomeIssueComponent issActual : actual.getIssue()) {
if (PRINT_OUTPUT_TO_CONSOLE) {
System.out.println(issActual.toString());
}
OperationOutcomeIssueComponent issGoal = map.get(issActual);
if (issGoal == null) {
fails.add("Unexpected Issue found: "+issActual.toString());
}
}
if (goal.getIssue().size() != actual.getIssue().size() && fails.isEmpty()) {
fails.add("Issue count mismatch (check for duplicate error messages)");
}
if (fails.size() > 0) {
for (String s : fails) {
System.out.println(s);
}
System.out.println("");
System.out.println("========================================================");
System.out.println("");
System.out.println(json);
System.out.println("");
System.out.println("========================================================");
System.out.println("");
Assertions.fail(fails.toString());
}
// int ec = 0;
// int wc = 0;
// int hc = 0;
// List<String> errLocs = new ArrayList<>();
// for (ValidationMessage vm : errors) {
// if (vm.getLevel() == IssueSeverity.FATAL || vm.getLevel() == IssueSeverity.ERROR) {
// ec++;
// if (PRINT_OUTPUT_TO_CONSOLE) {
// System.out.println(vm.getDisplay());
// }
// errLocs.add(vm.getLocation());
// }
// if (vm.getLevel() == IssueSeverity.WARNING) {
// wc++;
// if (PRINT_OUTPUT_TO_CONSOLE) {
// System.out.println(vm.getDisplay());
// }
// }
// if (vm.getLevel() == IssueSeverity.INFORMATION) {
// hc++;
// if (PRINT_OUTPUT_TO_CONSOLE) {
// System.out.println(vm.getDisplay());
// }
// }
// }
// if (!TestingUtilities.getSharedWorkerContext(version).isNoTerminologyServer() || !focus.has("tx-dependent")) {
// Assert.assertEquals("Test " + name + (profile == null ? "" : " profile: "+ profile) + ": Expected " + Integer.toString(java.get("errorCount").getAsInt()) + " errors, but found " + Integer.toString(ec) + ".", java.get("errorCount").getAsInt(), ec);
// if (java.has("warningCount")) {
// Assert.assertEquals( "Test " + name + (profile == null ? "" : " profile: "+ profile) + ": Expected " + Integer.toString(java.get("warningCount").getAsInt()) + " warnings, but found " + Integer.toString(wc) + ".", java.get("warningCount").getAsInt(), wc);
// }
// if (java.has("infoCount")) {
// Assert.assertEquals( "Test " + name + (profile == null ? "" : " profile: "+ profile) + ": Expected " + Integer.toString(java.get("infoCount").getAsInt()) + " hints, but found " + Integer.toString(hc) + ".", java.get("infoCount").getAsInt(), hc);
// }
// }
// if (java.has("error-locations")) {
// JsonArray el = java.getAsJsonArray("error-locations");
// Assert.assertEquals( "locations count is not correct", errLocs.size(), el.size());
// for (int i = 0; i < errLocs.size(); i++) {
// Assert.assertEquals("Location should be " + el.get(i).getAsString() + ", but was " + errLocs.get(i), errLocs.get(i), el.get(i).getAsString());
// }
// }
if (BUILD_NEW) {
if (java.has("output")) {
java.remove("output");
}
if (java.has("error-locations")) {
java.remove("error-locations");
}
if (java.has("warningCount")) {
Assert.assertEquals( "Test " + name + (profile == null ? "" : " profile: "+ profile) + ": Expected " + Integer.toString(java.get("warningCount").getAsInt()) + " warnings, but found " + Integer.toString(wc) + ".", java.get("warningCount").getAsInt(), wc);
java.remove("warningCount");
}
if (java.has("infoCount")) {
Assert.assertEquals( "Test " + name + (profile == null ? "" : " profile: "+ profile) + ": Expected " + Integer.toString(java.get("infoCount").getAsInt()) + " hints, but found " + Integer.toString(hc) + ".", java.get("infoCount").getAsInt(), hc);
java.remove("infoCount");
}
if (java.has("errorCount")) {
java.remove("errorCount");
}
if (java.has("outcome")) {
java.remove("outcome");
}
if (actual.hasIssue()) {
JsonObject oj = JsonTrackingParser.parse(json, null);
java.add("outcome", oj);
}
}
if (java.has("error-locations")) {
JsonArray el = java.getAsJsonArray("error-locations");
Assert.assertEquals( "locations count is not correct", errLocs.size(), el.size());
for (int i = 0; i < errLocs.size(); i++) {
Assert.assertEquals("Location should be " + el.get(i).getAsString() + ", but was " + errLocs.get(i), errLocs.get(i), el.get(i).getAsString());
}
private OperationOutcomeIssueComponent findMatchingIssue(OperationOutcome oo, OperationOutcomeIssueComponent iss) {
for (OperationOutcomeIssueComponent t : oo.getIssue()) {
if (t.getExpression().get(0).getValue().equals(iss.getExpression().get(0).getValue()) && t.getCode() == iss.getCode() && t.getSeverity() == iss.getSeverity()
&& (t.hasDiagnostics() ? t.getDiagnostics().equals(iss.getDiagnostics()) : !iss.hasDiagnostics()) && textMatches(t.getDetails().getText(), iss.getDetails().getText())) {
return t;
}
}
if (focus.has("output")) {
focus.remove("output");
return null;
}
private boolean textMatches(String t1, String t2) {
if (t1.endsWith("...")) {
t2 = t2.substring(0, t1.length()-3);
t1 = t1.substring(0, t1.length()-3);
}
JsonArray vr = new JsonArray();
java.add("output", vr);
for (ValidationMessage vm : errors) {
vr.add(vm.getDisplay());
if (t2.endsWith("...")) {
t1 = t1.substring(0, t2.length()-3);
t2 = t2.substring(0, t2.length()-3);
}
t1 = t1.trim();
t2 = t2.trim();
return t1.equals(t2);
}
private org.hl7.fhir.r4.model.Parameters makeExpProfile() {

21
org.hl7.fhir.validation/src/test/resources/txCache/org.hl7.fhir.validation/4.0.1/snomed.cache
View File

@ -1843,3 +1843,24 @@ v: {
"error" : "Unable to find code 2 in http://snomed.info/sct (version http://snomed.info/sct/900000000000207008/version/20220731); The code \"2\" is not valid in the system http://snomed.info/sct; The code provided (http://snomed.info/sct#2) is not valid in the value set 'All codes known to the system' (from http://tx.fhir.org/r4)"
}
-------------------------------------------------------------------------------------
{"code" : {
"system" : "http://snomed.info/sct",
"code" : "56248011000036107",
"display" : "Panadol 500 mg tablet, 50"
}, "valueSet" :null, "lang":"null", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "versionFlexible":"false"}####
v: {
"severity" : "error",
"error" : "Unable to find code 56248011000036107 in http://snomed.info/sct (version http://snomed.info/sct/900000000000207008/version/20220731); The code \"56248011000036107\" is not valid in the system http://snomed.info/sct; The code provided (http://snomed.info/sct#56248011000036107) is not valid in the value set 'All codes known to the system' (from http://tx.fhir.org/r4)"
}
-------------------------------------------------------------------------------------
{"code" : {
"system" : "http://snomed.info/sct",
"code" : "361055000",
"display" : "Misuses drugs (finding)"
}, "valueSet" :null, "lang":"null", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "versionFlexible":"false"}####
v: {
"display" : "Misuses drugs",
"code" : "361055000",
"system" : "http://snomed.info/sct"
}
-------------------------------------------------------------------------------------

4
pom.xml
View File

@ -14,12 +14,12 @@
HAPI FHIR
-->
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.6.68-SNAPSHOT</version>
<version>5.6.69-SNAPSHOT</version>
<packaging>pom</packaging>
<properties>
<hapi_fhir_version>5.4.0</hapi_fhir_version>
<validator_test_case_version>1.1.113</validator_test_case_version>
<validator_test_case_version>1.1.114-SNAPSHOT</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>