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tools that operate on the archie reference models and archetype object model
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package com.nedap.archie.flattener;
import com.nedap.archie.aom.*;
import com.nedap.archie.aom.terminology.ArchetypeTerm;
import com.nedap.archie.aom.terminology.ArchetypeTerminology;
import com.nedap.archie.aom.terminology.ValueSet;
import com.nedap.archie.aom.utils.AOMUtils;
import com.nedap.archie.query.ComplexObjectProxyReplacement;
import java.util.*;
/**
* Creates operational templates. Not to be used externally, use the Flattener with the right parameters to
* create operational templates
*/
class OperationalTemplateCreator {
private final Flattener flattener;
OperationalTemplateCreator(Flattener flattener) {
this.flattener = flattener;
}
public static OperationalTemplate createOperationalTemplate(Archetype archetype) {
Archetype clone = archetype.clone(); //clone so we do not overwrite the parent archetype. never
OperationalTemplate result = new OperationalTemplate();
result.setArchetypeId((ArchetypeHRID) archetype.getArchetypeId().clone());
result.setDefinition(clone.getDefinition());
result.setDifferential(false);
result.setRmRelease(clone.getRmRelease());
result.setAdlVersion(clone.getAdlVersion());
result.setTerminology(clone.getTerminology());
result.setGenerated(true);
result.setOtherMetaData(clone.getOtherMetaData());
result.setRules(clone.getRules());
result.setBuildUid(clone.getBuildUid());
result.setDescription(clone.getDescription());
result.setOriginalLanguage(clone.getOriginalLanguage());
result.setTranslations(clone.getTranslations());
result.setAnnotations(clone.getAnnotations());
result.setRmOverlay(clone.getRmOverlay());
return result;
}
public static void overrideArchetypeId(Archetype result, Archetype override) {
result.setArchetypeId(override.getArchetypeId());
result.setParentArchetypeId(override.getParentArchetypeId());
}
public void fillSlots(OperationalTemplate archetype) { //should this be OperationalTemplate?
//TODO: closing archetype slots should be moved to AFTER including other archetypes
closeArchetypeSlots(archetype);
fillArchetypeRoots(archetype);
fillComplexObjectProxies(archetype);
}
static void expandValueSets(OperationalTemplate operationalTemplate) {
List terminologies = Arrays.asList(operationalTemplate.getTerminology());
// terminologies.addAll(operationalTemplate.getComponentTerminologies().values());
for(ArchetypeTerminology terminology:terminologies) {
for(ValueSet valueSet:terminology.getValueSets().values()) {
valueSet.setMembers(AOMUtils.getExpandedValueSetMembers(terminology.getValueSets(), valueSet));
}
}
}
/** Zero occurrences and existence constraint processing when creating OPT templates. Removes attributes */
public void removeZeroOccurrencesConstraints(Archetype archetype) {
Stack workList = new Stack<>();
workList.push(archetype.getDefinition());
while (!workList.isEmpty()) {
CObject object = workList.pop();
List attributesToRemove = new ArrayList<>();
for (CAttribute attribute : object.getAttributes()) {
if (attribute.getExistence() != null && attribute.getExistence().getUpper() == 0 && !attribute.getExistence().isUpperUnbounded()) {
attributesToRemove.add(attribute);
} else {
List objectsToRemove = new ArrayList<>();
for (CObject child : attribute.getChildren()) {
if (!child.isAllowed()) {
objectsToRemove.add(child);
}
workList.push(child);
}
FlattenerUtil.removeAnnotationsForArchetypeConstraints(archetype, objectsToRemove);
attribute.getChildren().removeAll(objectsToRemove);
}
}
FlattenerUtil.removeAnnotationsForArchetypeConstraints(archetype, attributesToRemove);
object.getAttributes().removeAll(attributesToRemove);
}
}
/** Zero occurrences and existence constraint processing when creating OPT templates. Removes attributes */
public void fillEmptyOccurrences(Archetype archetype) {
Stack workList = new Stack<>();
workList.push(archetype.getDefinition());
while (!workList.isEmpty()) {
CObject object = workList.pop();
if( (object instanceof CComplexObject || object instanceof ArchetypeSlot || object instanceof CComplexObjectProxy)
&& object.getOccurrences() == null) {
object.setOccurrences(object.effectiveOccurrences(flattener.getMetaModels()::referenceModelPropMultiplicity));
}
for (CAttribute attribute : object.getAttributes()) {
for (CObject child : attribute.getChildren()) {
workList.push(child);
}
}
}
}
private void closeArchetypeSlots(OperationalTemplate archetype) {
if(!getConfig().isCloseArchetypeSlots()) {
return;
}
Stack workList = new Stack<>();
workList.push(archetype.getDefinition());
while(!workList.isEmpty()) {
CObject object = workList.pop();
for(CAttribute attribute:object.getAttributes()) {
List toRemove = new ArrayList<>();
for(CObject child:attribute.getChildren()) {
if(child instanceof ArchetypeSlot) { //use_archetype
if(((ArchetypeSlot) child).isClosed()) {
toRemove.add(child);
}
}
workList.push(child);
}
attribute.getChildren().removeAll(toRemove);
}
}
}
private void fillArchetypeRoots(OperationalTemplate result) {
if(!getConfig().isFillArchetypeRoots()) {
return;
}
Stack workList = new Stack<>();
workList.push(result.getDefinition());
while(!workList.isEmpty()) {
CObject object = workList.pop();
for(CAttribute attribute:object.getAttributes()) {
for(CObject child:attribute.getChildren()) {
if(child instanceof CArchetypeRoot) { //use_archetype
fillArchetypeRoot((CArchetypeRoot) child, result);
}
workList.push(child);
}
}
}
}
private void fillComplexObjectProxies(OperationalTemplate result) {
if(!getConfig().isReplaceUseNode()) {
return;
}
Stack workList = new Stack<>();
workList.push(result.getDefinition());
List replacements = new ArrayList<>();
while(!workList.isEmpty()) {
CObject object = workList.pop();
for(CAttribute attribute:object.getAttributes()) {
for(CObject child:attribute.getChildren()) {
if(child instanceof CComplexObjectProxy) { //use_node
ComplexObjectProxyReplacement possibleReplacement =
ComplexObjectProxyReplacement.getComplexObjectProxyReplacement((CComplexObjectProxy) child);
if(possibleReplacement != null) {
replacements.add(possibleReplacement);
} else {
throw new RuntimeException("cannot find target in CComplexObjectProxy");
}
}
workList.push(child);
}
}
}
for(ComplexObjectProxyReplacement replacement:replacements) {
replacement.replace();
}
}
/**
* Only fillArchetypeRoot if this is not done yet
*/
private void fillArchetypeRoot(CArchetypeRoot root, OperationalTemplate result) {
if(flattener.getCreateOperationalTemplate() && ( root.getAttributes() == null || root.getAttributes().isEmpty()) ) {
String archetypeRef = root.getArchetypeRef();
String newArchetypeRef = archetypeRef;
OverridingArchetypeRepository repository = flattener.getRepository();
Archetype archetype = repository.getArchetype(archetypeRef);
if(archetype instanceof TemplateOverlay){
//we want to be able to check which archetype this is in the UI. If it's an overlay, that means retrieving the non-operational template
//which is a hassle.
//That's a problem. Is this the way to fix is?
newArchetypeRef = archetype.getParentArchetypeId();
}
if (archetype == null) {
if(getConfig().isFailOnMissingUsedArchetype()) {
throw new IllegalArgumentException("Archetype with reference :" + archetypeRef + " not found.");
} else {
//just skip, as a form of graceful degradation.
return;
}
}
archetype = flattener.getNewFlattener().flatten(archetype);
//
CComplexObject rootToFill = root;
if(flattener.isUseComplexObjectForArchetypeSlotReplacement()) {
rootToFill = archetype.getDefinition();
root.getParent().replaceChild(root.getNodeId(), rootToFill);
} else {
rootToFill.setAttributes(archetype.getDefinition().getAttributes());
rootToFill.setAttributeTuples(archetype.getDefinition().getAttributeTuples());
rootToFill.setDefaultValue(archetype.getDefinition().getDefaultValue());
}
String newNodeId = archetype.getArchetypeId().getFullId();
ArchetypeTerminology terminology = archetype.getTerminology();
//The node id will be replaced from "id1" to something like "openEHR-EHR-COMPOSITION.template_overlay.v1.0.0
//so store it in the terminology as well
Map> termDefinitions = terminology.getTermDefinitions();
for(String language: termDefinitions.keySet()) {
Map translations = termDefinitions.get(language);
translations.put(newNodeId, TerminologyFlattener.getTerm(terminology.getTermDefinitions(), language, archetype.getDefinition().getNodeId()));
}
//rootToFill.setNodeId(newNodeId);
if(!flattener.isUseComplexObjectForArchetypeSlotReplacement()) {
root.setArchetypeRef(newNodeId);
}
//todo: should we filter this?
if(archetype instanceof OperationalTemplate) {
OperationalTemplate template = (OperationalTemplate) archetype;
//add all the component terminologies, otherwise we lose translation
for(String subarchetypeId:template.getComponentTerminologies().keySet()) {
result.addComponentTerminology(subarchetypeId, template.getComponentTerminologies().get(subarchetypeId));
}
}
result.addComponentTerminology(newNodeId, terminology);
String prefix = archetype.getArchetypeId().getConceptId() + "_";
flattener.getRulesFlattener().combineRules(archetype, root.getArchetype(), prefix, prefix, rootToFill.getPath(), false);
flattener.getAnnotationsAndOverlaysFlattener().addAnnotationsWithPathPrefix(rootToFill.getPath(), archetype, result);
flattener.getAnnotationsAndOverlaysFlattener().addVisibilityWithPathPrefix(rootToFill.getPath(), archetype, result);
//todo: do we have to put something in the terminology extracts?
//templateResult.addTerminologyExtract(child.getNodeId(), archetype.getTerminology().);
}
}
private FlattenerConfiguration getConfig() {
return flattener.getConfiguration();
}
}