private void loadValueSet(String n) throws FileNotFoundException, Exception {
XmlParser xml = new XmlParser();
ValueSet vs =
(ValueSet)
xml.parse(
new CSFileInputStream(
srcDir
+ ini.getStringProperty("valuesets", n).replace('\\', File.separatorChar)));
vs.setIdentifierSimple("http://hl7.org/fhir/vs/" + n);
definitions.getExtraValuesets().put(n, vs);
}
public static String describeBinding(
String prefix, ElementDefinitionBindingComponent def, PageProcessor page) throws Exception {
if (!def.hasValueSet()) return def.getDescription();
String ref =
def.getValueSet() instanceof UriType
? ((UriType) def.getValueSet()).asStringValue()
: ((Reference) def.getValueSet()).getReference();
ValueSet vs = page.getValueSets().get(ref);
if (vs != null) {
String pp = (String) vs.getUserData("path");
return def.getDescription()
+ "<br/>"
+ conf(def)
+ "<a href=\""
+ prefix
+ pp.replace(File.separatorChar, '/')
+ "\">"
+ vs.getName()
+ "</a>"
+ confTail(def);
}
if (ref.startsWith("http:") || ref.startsWith("https:"))
return def.getDescription()
+ "<br/>"
+ conf(def)
+ " <a href=\""
+ ref
+ "\">"
+ ref
+ "</a>"
+ confTail(def);
else
return def.getDescription()
+ "<br/>"
+ conf(def)
+ " ?? Broken Reference to "
+ ref
+ " ??"
+ confTail(def);
}
private void validateQuestionAnswers(
List<ValidationMessage> theErrors,
QuestionComponent theQuestion,
LinkedList<String> thePathStack,
AnswerFormat type,
org.hl7.fhir.instance.model.QuestionnaireResponse.QuestionComponent answerQuestion,
QuestionnaireResponse theAnswers,
boolean theValidateRequired) {
String linkId = theQuestion.getLinkId();
Set<Class<? extends Type>> allowedAnswerTypes = determineAllowedAnswerTypes(type);
if (allowedAnswerTypes.isEmpty()) {
for (QuestionAnswerComponent nextAnswer : answerQuestion.getAnswer()) {
rule(
theErrors,
IssueType.BUSINESSRULE,
thePathStack,
ElementUtil.isEmpty(nextAnswer.getValue()),
"Question with linkId[{0}] has no answer type but an answer was provided",
linkId);
}
} else {
rule(
theErrors,
IssueType.BUSINESSRULE,
thePathStack,
!(answerQuestion.getAnswer().size() > 1 && !theQuestion.getRepeats()),
"Multiple answers to non repeating question with linkId[{0}]",
linkId);
if (theValidateRequired) {
rule(
theErrors,
IssueType.BUSINESSRULE,
thePathStack,
!(theQuestion.getRequired() && answerQuestion.getAnswer().isEmpty()),
"Missing answer to required question with linkId[{0}]",
linkId);
} else {
hint(
theErrors,
IssueType.BUSINESSRULE,
thePathStack,
!(theQuestion.getRequired() && answerQuestion.getAnswer().isEmpty()),
"Missing answer to required question with linkId[{0}]",
linkId);
}
}
int answerIdx = -1;
for (QuestionAnswerComponent nextAnswer : answerQuestion.getAnswer()) {
answerIdx++;
try {
thePathStack.add("answer[" + answerIdx + "]");
Type nextValue = nextAnswer.getValue();
if (nextValue == null) {
continue;
}
if (!allowedAnswerTypes.contains(nextValue.getClass())) {
rule(
theErrors,
IssueType.BUSINESSRULE,
thePathStack,
false,
"Answer to question with linkId[{0}] found of type [{1}] but this is invalid for question of type [{2}]",
linkId,
nextValue.getClass().getSimpleName(),
type.toCode());
continue;
}
// Validate choice answers
if (type == AnswerFormat.CHOICE || type == AnswerFormat.OPENCHOICE) {
if (nextAnswer.getValue() instanceof StringType) {
StringType answer = (StringType) nextAnswer.getValue();
if (answer == null || isBlank(answer.getValueAsString())) {
rule(
theErrors,
IssueType.BUSINESSRULE,
thePathStack,
false,
"Answer to question with linkId[{0}] is required but answer does not have a value",
linkId);
continue;
}
} else {
Coding coding = (Coding) nextAnswer.getValue();
if (isBlank(coding.getCode())) {
rule(
theErrors,
IssueType.BUSINESSRULE,
thePathStack,
false,
"Answer to question with linkId[{0}] is of type {1} but coding answer does not have a code",
linkId,
type.name());
continue;
}
if (isBlank(coding.getSystem())) {
rule(
theErrors,
IssueType.BUSINESSRULE,
thePathStack,
false,
"Answer to question with linkId[{0}] is of type {1} but coding answer does not have a system",
linkId,
type.name());
continue;
}
String optionsRef = theQuestion.getOptions().getReference();
if (isNotBlank(optionsRef)) {
ValueSet valueSet = getValueSet(theAnswers, theQuestion.getOptions());
if (valueSet == null) {
rule(
theErrors,
IssueType.BUSINESSRULE,
thePathStack,
false,
"Question with linkId[{0}] has options ValueSet[{1}] but this ValueSet can not be found",
linkId,
optionsRef);
continue;
}
boolean found = false;
if (coding.getSystem().equals(valueSet.getCodeSystem().getSystem())) {
for (ConceptDefinitionComponent next : valueSet.getCodeSystem().getConcept()) {
if (coding.getCode().equals(next.getCode())) {
found = true;
break;
}
}
}
if (!found) {
for (ConceptSetComponent nextCompose : valueSet.getCompose().getInclude()) {
if (coding.getSystem().equals(nextCompose.getSystem())) {
for (ConceptReferenceComponent next : nextCompose.getConcept()) {
if (coding.getCode().equals(next.getCode())) {
found = true;
break;
}
}
}
if (found) {
break;
}
}
}
rule(
theErrors,
IssueType.BUSINESSRULE,
thePathStack,
found,
"Question with linkId[{0}] has answer with system[{1}] and code[{2}] but this is not a valid answer for ValueSet[{3}]",
linkId,
coding.getSystem(),
coding.getCode(),
optionsRef);
}
}
}
} finally {
thePathStack.removeLast();
}
} // for answers
}
public static String describeBinding(String prefix, BindingSpecification cd, PageProcessor page)
throws Exception {
if (cd.getBinding() == BindingSpecification.BindingMethod.Unbound) return cd.getDefinition();
if (cd.getBinding() == BindingSpecification.BindingMethod.Special) {
if (cd.getValueSet().getName().equals("MessageEvent"))
return "the <a href=\""
+ prefix
+ "valueset-message-events.html\">Event List in the messaging framework</a>";
else if (cd.getValueSet().getName().equals("ResourceType"))
return "<a href=\""
+ prefix
+ "valueset-resource-types.html\">Any defined Resource Type name</a>";
else if (cd.getValueSet().getName().equals("DataType"))
return "<a href=\"" + prefix + "valueset-data-types.html\">Any defined Data Type name</a>";
else if (cd.getValueSet().getName().equals("FHIRDefinedType"))
return "<a href=\""
+ prefix
+ "valueset-defined-types.html\">Any defined Resource or Data Type name</a>";
else throw new Exception("Unknown special type " + cd.getValueSet().getName());
}
String bs =
"<a href=\""
+ prefix
+ "terminologies.html#"
+ cd.getStrength().toCode()
+ "\">"
+ cd.getStrength().getDisplay()
+ "</a>";
if (cd.getValueSet() != null) {
ValueSet vs = cd.getValueSet();
String pp = (String) vs.getUserData("path");
return "<a href=\""
+ prefix
+ pp.replace(File.separatorChar, '/')
+ "\">"
+ cd.getDefinition()
+ "</a> ("
+ bs
+ ")";
} else if (cd.getBinding() == BindingSpecification.BindingMethod.ValueSet) {
if (Utilities.noString(cd.getReference())) return cd.getDescription();
else if (cd.getValueSet() == null)
return bs
+ ": <a href=\""
+ (cd.getReference().startsWith("http")
? cd.getReference()
: prefix + cd.getReference() + ".html")
+ "\">See "
+ cd.getDescription()
+ "</a> ("
+ cd.getDefinition()
+ ")";
else
return bs
+ ": <a href=\""
+ prefix
+ cd.getReference()
+ ".html\">See "
+ cd.getValueSet().getUrl()
+ "</a> ("
+ cd.getDefinition()
+ ")";
} else if (cd.getBinding() == BindingSpecification.BindingMethod.CodeList) {
if (Utilities.noString(cd.getReference()))
return bs + ": " + cd.getDescription() + " (" + cd.getDefinition() + ")";
else
return bs
+ ": <a href=\""
+ prefix
+ "valueset-"
+ cd.getReference().substring(1)
+ ".html\">http://hl7.org/fhir/"
+ cd.getReference().substring(1)
+ "</a> ("
+ cd.getDefinition()
+ ")";
}
if (cd.getBinding() == BindingSpecification.BindingMethod.Reference) {
return bs
+ ": <a href=\""
+ prefix
+ cd.getReference()
+ "\">"
+ cd.getDescription()
+ "</a> ("
+ cd.getDefinition()
+ ")";
}
return "??";
}
private void gen(String prefix, Map<BindingSpecification, List<CDUsage>> txusages2)
throws Exception {
List<BindingSpecification> cds = new ArrayList<BindingSpecification>();
cds.addAll(txusages.keySet());
if (cds.size() == 0) return;
Collections.sort(cds, new MyCompare());
write("<h3>\r\nTerminology Bindings\r\n</h3>\r\n");
// 1. new form
write("<table class=\"grid\">\r\n");
write(" <tr><th>Path</th><th>Definition</th><th>Type</th><th>Reference</th></tr>\r\n");
for (BindingSpecification cd : cds) {
String path;
List<CDUsage> list = txusages.get(cd);
for (int i = 2; i < list.size(); i++) {
if (!list.get(i).element.typeCode().equals(list.get(1).element.typeCode()))
throw new Exception(
"Mixed types on one concept domain in one type - not yet supported by the build process for binding "
+ cd.getName());
}
String name = cd.getValueSet() != null ? cd.getValueSet().getName() : cd.getName();
write(" <tr><td valign=\"top\" title=\"" + name + "\">");
boolean first = true;
for (int i = 1; i < list.size(); i++) {
if (!first) write("<br/>");
first = false;
write(list.get(i).path);
}
write(" </td>");
write("<td valign=\"top\">" + Utilities.escapeXml(cd.getDefinition()) + "</td>");
if (cd.getBinding() == BindingMethod.Unbound)
write("<td>Unknown</td><td valign=\"top\">No details provided yet</td>");
else {
write(
"<td><a href=\""
+ prefix
+ "terminologies.html#"
+ cd.getStrength().toCode()
+ "\">"
+ cd.getStrength().getDisplay()
+ "</a></td>");
write("<td valign=\"top\">");
if (cd.getBinding() == BindingSpecification.BindingMethod.Special) {
if (name.equals("MessageEvent"))
write(
"<a href=\""
+ prefix
+ "valueset-message-events.html\">http://hl7.org/fhir/valueset/message-events</a>");
else if (name.equals("ResourceType"))
write(
"<a href=\""
+ prefix
+ "valueset-resource-types.html\">http://hl7.org/fhir/valueset/resource-types</a>");
else if (name.equals("DataType"))
write(
"<a href=\""
+ prefix
+ "valueset-data-types.html\">http://hl7.org/fhir/valueset/data-types</a>");
else if (name.equals("FHIRDefinedType"))
write(
"<a href=\""
+ prefix
+ "valueset-defined-types.html\">http://hl7.org/fhir/valueset/defined-types</a>");
else throw new Exception("Unknown special type " + name);
}
if (cd.getValueSet() != null) {
ValueSet vs = cd.getValueSet();
String pp = (String) vs.getUserData("path");
if (pp == null) throw new Exception("unknown path on " + cd.getReference());
write(
"<a href=\""
+ prefix
+ pp.replace(File.separatorChar, '/')
+ "\">"
+ vs.getName()
+ "</a><!-- b -->");
} else if (cd.getBinding() == BindingSpecification.BindingMethod.ValueSet) {
if (Utilities.noString(cd.getReference())) write("??");
else if (cd.getReference().startsWith("valueset-"))
write(
"<a href=\""
+ prefix
+ cd.getReference()
+ ".html\">http://hl7.org/fhir/ValueSet/"
+ cd.getReference().substring(9)
+ "</a><!-- a -->");
else if (cd.getReference().startsWith("http://hl7.org/fhir")) {
if (cd.getReference().startsWith("http://hl7.org/fhir/ValueSet/v3-")) {
ValueSet vs = page.getValueSets().get(cd.getReference());
String pp = (String) vs.getUserData("path");
if (pp == null) throw new Exception("unknown path on " + cd.getReference());
write(
"<a href=\""
+ prefix
+ pp.replace(File.separatorChar, '/')
+ "\">"
+ cd.getReference()
+ "</a><!-- b -->");
} else if (cd.getReference().startsWith("http://hl7.org/fhir/ValueSet/v2-")) {
ValueSet vs = page.getValueSets().get(cd.getReference());
String pp = (String) vs.getUserData("path");
write(
"<a href=\""
+ prefix
+ pp.replace(File.separatorChar, '/')
+ "\">"
+ cd.getReference()
+ "</a><!-- c -->");
} else if (cd.getReference().startsWith("http://hl7.org/fhir/ValueSet/")) {
String ref = getBindingLink(cd);
write("<a href=\"" + prefix + ref + "\">" + cd.getReference() + "</a><!-- d -->");
// BindingSpecification bs1 =
// page.getDefinitions().getBindingByURL(cd.getReference());
// if (bs1 != null)
// write("<a
// href=\""+cd.getReference().substring(23)+".html\">"+cd.getReference()+"</a><!-- d
// -->");
// else
// write("<a
// href=\"valueset-"+cd.getReference().substring(23)+".html\">"+cd.getReference()+"</a><!-- d -->");
} else
throw new Exception("Internal reference " + cd.getReference() + " not handled yet");
} else if (cd.getReference().startsWith("http:"))
write("<a href=\"" + cd.getReference() + "\">" + cd.getReference() + "</a><!-- e -->");
else
write(
"<a href=\""
+ prefix
+ "valueset-"
+ cd.getReference()
+ ".html\">http://hl7.org/fhir/"
+ cd.getReference()
+ "</a><!-- e -->");
} else if (cd.getBinding() == BindingSpecification.BindingMethod.CodeList) {
write(
"<a href=\""
+ prefix
+ "valueset-"
+ cd.getReference().substring(1)
+ ".html\">http://hl7.org/fhir/"
+ cd.getReference().substring(1)
+ "</a><!-- f -->");
} else if (cd.getBinding() == BindingSpecification.BindingMethod.Reference) {
write(
"<a href=\""
+ prefix
+ cd.getReference()
+ "\">"
+ cd.getDescription()
+ "</a><!-- g -->");
}
write("</td>");
}
write(" </tr>\r\n");
}
write("</table>\r\n<p> </p>\r\n");
}
public void validate(ValueSet vs, boolean internal) throws Exception {
if (internal && vs.getDefine() != null) {
for (ValueSetDefineConceptComponent t : vs.getDefine().getConcept()) checkLowercase(t);
}
}
