use of org.hl7.fhir.r4b.model.DomainResource in project odm2fhir by num-codex.
the class StudyEvent method map.
public Stream<DomainResource> map(Subject subject, StudyEventData studyEventData) {
this.subject = subject;
var encounter = new Encounter();
if (ENVIRONMENT.getProperty("fhir.encounters.enabled", Boolean.class, true) && studyEventData.getStudyEventOID().matches("GECCOVISIT|Event.\\d_fall_arm_1")) {
var value = format("%s-%s.%s", studyEventData.getSubjectData().getSubjectKey(), studyEventData.getStudyEventOID(), studyEventData.getStudyEventRepeatKey());
if (!ENVIRONMENT.containsProperty("debug")) {
value = sha256Hex(value);
}
var encounterIdentifier = new Identifier().setSystem(getIdentifierSystem(ENCOUNTER)).setValue(value).setAssigner(subject.getOrganizationReference());
encounter.setStatus(UNKNOWN).setClass_(new Coding(IMP.getSystem(), IMP.toCode(), IMP.getDisplay())).addIdentifier(encounterIdentifier).setId(sha256Hex(encounterIdentifier.getSystem() + encounterIdentifier.getValue()));
encounterReference = new Reference(format("%s/%s", ENCOUNTER.toCode(), encounter.getId()));
}
var domainResources = studyEventData.getFormData().stream().flatMap(formData -> forms.stream().map(form -> form.map(this, formData))).flatMap(Function.identity());
return encounter.isEmpty() ? domainResources : Stream.concat(Stream.of(encounter), domainResources.peek(this::setEncounter));
}
use of org.hl7.fhir.r4b.model.DomainResource in project kindling by HL7.
the class ProfileGenerator method makeExtensionSlice.
private ElementDefinition makeExtensionSlice(String extensionName, StructureDefinition p, StructureDefinitionSnapshotComponent c, ElementDefn e, String path) throws URISyntaxException, Exception {
ElementDefinition ex = createBaseDefinition(p, path, definitions.getBaseResources().get("DomainResource").getRoot().getElementByName(definitions, extensionName, false, false, null));
c.getElement().add(ex);
if (!ex.hasBase())
ex.setBase(new ElementDefinitionBaseComponent());
ex.getBase().setPath("Element.extension");
ex.getBase().setMin(0);
ex.getBase().setMax("*");
ElementDefinitionConstraintComponent inv = ex.addConstraint();
inv.setKey("ext-1");
inv.setSeverity(ConstraintSeverity.ERROR);
inv.setHuman("Must have either extensions or value[x], not both");
inv.setExpression("extension.exists() != value.exists()");
inv.setXpath("exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])");
inv.setSource("http://hl7.org/fhir/StructureDefinition/Extension");
return ex;
}
use of org.hl7.fhir.r4b.model.DomainResource in project kindling by HL7.
the class ProfileGenerator method defineElement.
/**
* note: snapshot implies that we are generating a resource or a data type; for other profiles, the snapshot is generated elsewhere
* @param isInterface
*/
private ElementDefinition defineElement(Profile ap, StructureDefinition p, List<ElementDefinition> elements, ElementDefn e, String path, Set<String> slices, List<SliceHandle> parentSlices, SnapShotMode snapshot, boolean root, String defType, String inheritedType, boolean defaults) throws Exception {
boolean handleDiscriminator = true;
if (!Utilities.noString(e.getProfileName()) && !e.getDiscriminator().isEmpty() && !slices.contains(path)) {
handleDiscriminator = false;
// hey, we jumped straight into the slices with setting up the slicing (allowed in the spreadsheets, but not otherwise)
ElementDefinition slicer = new ElementDefinition();
elements.add(slicer);
slicer.setId(path);
slicer.setPath(path);
processDiscriminator(e, path, slicer);
if (e.getMaxCardinality() != null)
slicer.setMax(e.getMaxCardinality() == Integer.MAX_VALUE ? "*" : e.getMaxCardinality().toString());
slices.add(path);
}
// todo for task 12259
// if (ap != null) {
// String base = isImplicitTypeConstraint(path);
// if (base != null) {
// ElementDefinition typeConstrainer = new ElementDefinition(ElementDefinition.NOT_MODIFIER, ElementDefinition.NOT_IN_SUMMARY);
// elements.add(typeConstrainer);
// typeConstrainer.setId(base);
// typeConstrainer.setPath(base);
// String type = path.substring(base.length()-3);
// if (definitions.hasPrimitiveType(Utilities.uncapitalize(type)))
// type = Utilities.uncapitalize(type);
// typeConstrainer.addType().setCode(type);
// }
// }
ElementDefinition ce = new ElementDefinition(defaults, ElementDefinition.NOT_MODIFIER, ElementDefinition.NOT_IN_SUMMARY);
elements.add(ce);
if (e.getStandardsStatus() != null)
ToolingExtensions.setStandardsStatus(ce, e.getStandardsStatus(), e.getNormativeVersion());
ce.setId(path);
ce.setPath(path);
if (e.isXmlAttribute())
ce.addRepresentation(PropertyRepresentation.XMLATTR);
List<SliceHandle> myParents = new ArrayList<ProfileGenerator.SliceHandle>();
myParents.addAll(parentSlices);
// which holds Slicing information)
if (e.hasDescriminator() || !Utilities.noString(e.getProfileName())) {
if (e.getDiscriminator().size() > 0 && !slices.contains(path) && handleDiscriminator) {
processDiscriminator(e, path, ce);
slices.add(path);
}
if (!Utilities.noString(e.getProfileName())) {
SliceHandle hnd = new SliceHandle();
// though this it not used?
hnd.name = path;
myParents.add(hnd);
if (path.contains(".")) {
// We don't want a slice name on the root
ce.setSliceName(e.getProfileName());
ce.setId(ce.getId() + ":" + e.getProfileName());
}
}
}
if (e.isTranslatable()) {
ce.addExtension(BuildExtensions.EXT_TRANSLATABLE, new BooleanType(true));
}
if (Utilities.existsInList(ce.getPath(), "Element.extension", "DomainResource.extension", "DomainResource.modifierExtension") && !ce.hasSlicing() && !ce.hasSliceName()) {
ce.getSlicing().setDescription("Extensions are always sliced by (at least) url").setRules(SlicingRules.OPEN).addDiscriminator().setType(DiscriminatorType.VALUE).setPath("url");
}
if (!Utilities.noString(inheritedType) && snapshot != SnapShotMode.None) {
ElementDefn inh = definitions.getElementDefn(inheritedType);
buildDefinitionFromElement(path, ce, inh, ap, p, inheritedType, definitions.getBaseResources().containsKey(inheritedType) && definitions.getBaseResources().get(inheritedType).isInterface());
} else if (path.contains(".") && Utilities.noString(e.typeCode()) && snapshot != SnapShotMode.None) {
addElementConstraints(defType, ce);
}
buildDefinitionFromElement(path, ce, e, ap, p, null, false);
if (!Utilities.noString(e.getStatedType())) {
ToolingExtensions.addStringExtension(ce, "http://hl7.org/fhir/StructureDefinition/structuredefinition-explicit-type-name", e.getStatedType());
}
if (e.isNoBindingAllowed()) {
ToolingExtensions.addBooleanExtension(ce, BuildExtensions.EXT_NO_BINDING, true);
}
if (!root) {
if (e.typeCode().startsWith("@")) {
ce.setContentReference("#" + getIdForPath(elements, e.typeCode().substring(1)));
} else if (Utilities.existsInList(path, "Element.id", "Extension.url") || path.endsWith(".id")) {
TypeRefComponent tr = ce.addType();
tr.getFormatCommentsPre().add("Note: special primitive values have a FHIRPath system type. e.g. this is compiler magic (j)");
tr.setCode(Constants.NS_SYSTEM_TYPE + "String");
if (path.equals("Extension.url")) {
ToolingExtensions.addUriExtension(tr, ToolingExtensions.EXT_FHIR_TYPE, "uri");
} else if (p.getKind() == StructureDefinitionKind.RESOURCE) {
ToolingExtensions.addUriExtension(tr, ToolingExtensions.EXT_FHIR_TYPE, "id");
} else {
ToolingExtensions.addUriExtension(tr, ToolingExtensions.EXT_FHIR_TYPE, "string");
}
} else {
List<TypeRef> expandedTypes = new ArrayList<TypeRef>();
for (TypeRef t : e.getTypes()) {
// Expand any Resource(A|B|C) references
if (t.hasParams() && !Utilities.existsInList(t.getName(), "Reference", "canonical", "CodeableReference")) {
throw new Exception("Only resource types can specify parameters. Path " + path + " in profile " + p.getName());
}
if (t.getParams().size() > 1) {
if (t.getProfile() != null && t.getParams().size() != 1) {
throw new Exception("Cannot declare profile on a resource reference declaring multiple resource types. Path " + path + " in profile " + p.getName());
}
for (String param : t.getParams()) {
if (definitions.hasLogicalModel(param)) {
for (String pn : definitions.getLogicalModel(param).getImplementations()) {
TypeRef childType = new TypeRef(t.getName());
childType.getParams().add(pn);
childType.getAggregations().addAll(t.getAggregations());
expandedTypes.add(childType);
}
} else {
TypeRef childType = new TypeRef(t.getName());
childType.getParams().add(param);
childType.getAggregations().addAll(t.getAggregations());
expandedTypes.add(childType);
}
}
} else if (t.isWildcardType()) {
// this list is filled out manually because it may be running before the types referred to have been loaded
for (String n : TypesUtilities.wildcardTypes(version.toString())) expandedTypes.add(new TypeRef(n));
} else if (!t.getName().startsWith("=")) {
if (definitions.isLoaded() && (!definitions.hasResource(t.getName()) && !definitions.hasType(t.getName()) && !definitions.hasElementDefn(t.getName()) && !definitions.getBaseResources().containsKey(t.getName()) && !t.getName().equals("xhtml"))) {
throw new Exception("Bad Type '" + t.getName() + "' at " + path + " in profile " + p.getUrl());
}
expandedTypes.add(t);
}
}
if (expandedTypes.isEmpty()) {
if (defType != null)
ce.addType().setCode(defType);
} else
for (TypeRef t : expandedTypes) {
String profile = null;
String tc = null;
if (definitions.getConstraints().containsKey(t.getName())) {
ProfiledType pt = definitions.getConstraints().get(t.getName());
tc = pt.getBaseType();
profile = "http://hl7.org/fhir/StructureDefinition/" + pt.getName();
} else {
tc = t.getName();
profile = t.getProfile();
}
TypeRefComponent type = ce.getType(tc);
if (profile == null && t.hasParams()) {
profile = t.getParams().get(0);
}
if (t.getPatterns() != null) {
for (String s : t.getPatterns()) {
type.addExtension("http://hl7.org/fhir/StructureDefinition/elementdefinition-pattern", new CanonicalType("http://hl7.org/fhir/StructureDefinition/" + s));
}
}
if (profile != null) {
if (type.getWorkingCode().equals("Extension")) {
// check that the extension is being used correctly:
StructureDefinition ext = context.getExtensionStructure(null, profile);
if (ext == null) {
throw new Exception("Unable to resolve extension definition: " + profile);
}
boolean srcMod = ext.getSnapshot().getElement().get(0).getIsModifier();
boolean tgtMod = e.isModifier();
if (srcMod && !tgtMod)
throw new Exception("The extension '" + profile + "' is a modifier extension, but is being used as if it is not a modifier extension");
if (!srcMod && tgtMod)
throw new Exception("The extension '" + profile + "' is not a modifier extension, but is being used as if it is a modifier extension");
}
List<String> pr = new ArrayList<>();
if (profile.startsWith("http:") || profile.startsWith("#")) {
pr.add(profile);
} else if (definitions.hasLogicalModel(profile)) {
for (String pn : definitions.getLogicalModel(profile).getImplementations()) pr.add("http://hl7.org/fhir/StructureDefinition/" + pn);
} else
pr.add("http://hl7.org/fhir/StructureDefinition/" + (profile.equals("Any") ? "Resource" : profile));
if (type.getWorkingCode().equals("Reference") || type.getWorkingCode().equals("canonical") || type.getWorkingCode().equals("CodeableReference")) {
for (String pn : pr) {
type.addTargetProfile(pn);
if (e.hasHierarchy())
ToolingExtensions.addBooleanExtension(type, ToolingExtensions.EXT_HIERARCHY, e.getHierarchy());
}
} else
for (String pn : pr) {
type.addProfile(pn);
}
}
for (String aggregation : t.getAggregations()) {
type.addAggregation(AggregationMode.fromCode(aggregation));
}
}
}
}
String w5 = translateW5(e.getW5());
if (w5 != null)
addMapping(p, ce, "http://hl7.org/fhir/fivews", w5, ap);
if (e.isTranslatable())
ce.addExtension("http://hl7.org/fhir/StructureDefinition/elementdefinition-translatable", new BooleanType(true));
if (!Utilities.noString(e.getOrderMeaning()))
ce.setOrderMeaning(e.getOrderMeaning());
if (e.hasBinding()) {
ce.setBinding(generateBinding(e.getBinding()));
}
if (snapshot != SnapShotMode.None && !e.getElements().isEmpty()) {
// makeExtensionSlice("extension", p, c, e, path);
// if (snapshot == SnapShotMode.Resource) {
// makeExtensionSlice("modifierExtension", p, c, e, path);
// if (!path.contains(".")) {
// c.getElement().add(createBaseDefinition(p, path, definitions.getBaseResources().get("Resource").getRoot().getElementByName("language")));
// c.getElement().add(createBaseDefinition(p, path, definitions.getBaseResources().get("DomainResource").getRoot().getElementByName("text")));
// c.getElement().add(createBaseDefinition(p, path, definitions.getBaseResources().get("DomainResource").getRoot().getElementByName("contained")));
// }
// }
}
if (defaults)
ce.makeBase();
Set<String> containedSlices = new HashSet<String>();
if (snapshot != SnapShotMode.None) {
if (!root && Utilities.noString(e.typeCode())) {
if (snapshot == SnapShotMode.Resource)
defineAncestorElements("BackboneElement", path, snapshot, containedSlices, p, elements, defType, defaults);
else
defineAncestorElements("Element", path, snapshot, containedSlices, p, elements, defType, defaults);
} else if (root && !Utilities.noString(e.typeCode()))
defineAncestorElements(e.typeCode(), path, snapshot, containedSlices, p, elements, defType, defaults);
}
for (ElementDefn child : e.getElements()) defineElement(ap, p, elements, child, path + "." + child.getName(), containedSlices, myParents, snapshot, false, defType, null, defaults);
return ce;
}
use of org.hl7.fhir.r4b.model.DomainResource in project kindling by HL7.
the class XmlSpecGenerator method generateInner.
private void generateInner(ElementDefn root, boolean resource, boolean isAbstract) throws IOException, Exception {
String rn;
if (root.getName().equals("Extension"))
rn = "extension|modifierExtension";
else if (root.getName().equals("Meta"))
rn = "meta";
else if (root.getTypes().size() > 0 && (root.getTypes().get(0).getName().equals("Type") || (root.getTypes().get(0).getName().equals("Structure"))) || isAbstract)
rn = "[name]";
else
rn = root.getName();
write("<");
if (defPage == null)
write("<span title=\"" + Utilities.escapeXml(root.getDefinition()) + "\"><b>");
else
write("<a href=\"" + (defPage + "#" + root.getName()) + "\" title=\"" + Utilities.escapeXml(root.getDefinition()) + "\" class=\"dict\"><b>");
write(rn);
if ((defPage == null))
write("</b></span>");
else
write("</b></a>");
boolean hasXmlLang = false;
for (ElementDefn elem : root.getElements()) {
hasXmlLang = hasXmlLang || elem.typeCode().equals("xml:lang");
}
if (hasXmlLang)
write(" xml:lang?");
if (resource)
write(" xmlns=\"http://hl7.org/fhir\"");
else
write(" xmlns=\"http://hl7.org/fhir\"");
for (ElementDefn elem : root.getElements()) {
if (elem.isXmlAttribute()) {
generateAttribute(elem);
}
}
if (resource) {
write("> <span style=\"float: right\"><a title=\"Documentation for this format\" href=\"" + prefix + "xml.html\"><img src=\"" + prefix + "help.png\" alt=\"doco\"/></a></span>\r\n");
} else
write(">\r\n");
if (rn.equals(root.getName()) && resource) {
if (!Utilities.noString(root.typeCode())) {
write(" <!-- from <a href=\"" + prefix + "resource.html\">Resource</a>: <a href=\"" + prefix + "resource.html#id\">id</a>, <a href=\"" + prefix + "resource.html#meta\">meta</a>, <a href=\"" + prefix + "resource.html#implicitRules\">implicitRules</a>, and <a href=\"" + prefix + "resource.html#language\">language</a> -->\r\n");
if (root.typeCode().equals("DomainResource"))
write(" <!-- from <a href=\"" + prefix + "domainresource.html\">DomainResource</a>: <a href=\"" + prefix + "narrative.html#Narrative\">text</a>, <a href=\"" + prefix + "references.html#contained\">contained</a>, <a href=\"" + prefix + "extensibility.html\">extension</a>, and <a href=\"" + prefix + "extensibility.html#modifierExtension\">modifierExtension</a> -->\r\n");
}
} else if (root.typeCode().equals("BackboneElement")) {
write(" <!-- from BackboneElement: <a href=\"" + prefix + "extensibility.html\">extension</a>, <a href=\"" + prefix + "extensibility.html\">modifierExtension</a> -->\r\n");
} else {
write(" <!-- from Element: <a href=\"" + prefix + "extensibility.html\">extension</a> -->\r\n");
}
for (ElementDefn elem : root.getElements()) {
if (!elem.typeCode().equals("xml:lang") && !elem.isXmlAttribute())
generateCoreElem(elem, 1, rn, root.getName(), rn.equals(root.getName()) && resource);
}
write("</");
write(rn);
write(">\r\n");
}
use of org.hl7.fhir.r4b.model.DomainResource in project kindling by HL7.
the class JsonSpecGenerator method generateInner.
private void generateInner(ElementDefn root, boolean resource, boolean isAbstract) throws IOException, Exception {
String rn;
if (root.getTypes().size() > 0 && (root.getTypes().get(0).getName().equals("Type") || root.getName().equals("Extension") || (root.getTypes().get(0).getName().equals("Structure")) && root.getName().equals("Element") || root.getName().equals("BackboneElement") || root.getName().equals("Meta")))
rn = null;
else if (isAbstract)
rn = "[name]";
else
rn = root.getName();
write("{<span style=\"float: right\"><a title=\"Documentation for this format\" href=\"" + prefix + "json.html\"><img src=\"" + prefix + "help.png\" alt=\"doco\"/></a></span>\r\n");
if (definitions.hasResource(root.getName()) || Utilities.existsInList(root.getName(), "Parameters")) {
write(" \"resourceType\" : \"");
if (defPage == null)
write("<span title=\"" + Utilities.escapeXml(root.getDefinition()) + "\"><b>");
else
write("<a href=\"" + (defPage + "#" + root.getName()) + "\" title=\"" + Utilities.escapeXml(root.getDefinition()) + "\" class=\"dict\"><b>");
write(rn);
if ((defPage == null))
write("</b></span>\",\r\n");
else
write("</b></a>\",\r\n");
}
if ((root.getName().equals(rn) || "[name]".equals(rn)) && resource) {
if (!Utilities.noString(root.typeCode())) {
write(" // from <a href=\"" + prefix + "resource.html\">Resource</a>: <a href=\"" + prefix + "resource.html#id\">id</a>, <a href=\"" + prefix + "resource.html#meta\">meta</a>, <a href=\"" + prefix + "resource.html#implicitRules\">implicitRules</a>, and <a href=\"" + prefix + "resource.html#language\">language</a>\r\n");
if (root.typeCode().equals("DomainResource"))
write(" // from <a href=\"" + prefix + "domainresource.html\">DomainResource</a>: <a href=\"" + prefix + "narrative.html#Narrative\">text</a>, <a href=\"" + prefix + "references.html#contained\">contained</a>, <a href=\"" + prefix + "extensibility.html\">extension</a>, and <a href=\"" + prefix + "extensibility.html#modifierExtension\">modifierExtension</a>\r\n");
}
} else if (!resource) {
if (root.typeCode().equals("BackboneElement"))
write(" // from BackboneElement: <a href=\"" + prefix + "extensibility.html\">extension</a>, <a href=\"" + prefix + "extensibility.html\">modifierExtension</a>\r\n");
else
write(" // from Element: <a href=\"" + prefix + "extensibility.html\">extension</a>\r\n");
}
// if (root.getName().equals("Extension")) {
// ElementDefn urld = root.getElements().get(0);
// write(" \"<span title=\"" + Utilities.escapeXml(urld.getDefinition()) + "\"><a href=\"" + (defPage + "#Extension.url") + "\" title=\"" + Utilities.escapeXml(urld.getDefinition()) + "\" class=\"dict\">");
// write("<url></a></span>");
// write("\" : { // <span style=\"color: navy; opacity: 0.8\">" + Utilities.escapeXml(root.getElements().get(0).getShortDefn()) + "</span>\r\n");
// generateCoreElem(root.getElements().get(1), 2, rn, root.getName(), false, true);
// write(" }\r\n");
// } else {
int c = 0;
for (ElementDefn elem : root.getElements()) {
generateCoreElem(elem, 1, rn, root.getName(), root.getName().equals(rn) && resource, ++c == root.getElements().size());
// }
}
write("}\r\n");
}
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