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Java implementation of openEHR OET Template Parser and Flattener
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/*
* component: "openEHR Java Reference Implementation"
* description: "Class Flattener"
* keywords: "oet-parser"
*
* author: "Rong Chen "
* copyright: "Copyright (c) 2009,2010 Cambio Healthcare Systems, Sweden"
* license: "See notice at bottom of class"
*
* file: "$URL$"
* revision: "$LastChangedRevision$"
* last_change: "$LastChangedDate$"
*/
package org.openehr.am.template;
import java.math.BigInteger;
import java.text.DecimalFormat;
import java.util.*;
import org.apache.log4j.Logger;
import openEHR.v1.template.ACTION;
import openEHR.v1.template.ADMINENTRY;
import openEHR.v1.template.Archetyped;
import openEHR.v1.template.COMPOSITION;
import openEHR.v1.template.ContentItem;
import openEHR.v1.template.ENTRY;
import openEHR.v1.template.EVALUATION;
import openEHR.v1.template.INSTRUCTION;
import openEHR.v1.template.ITEMSTRUCTURE;
import openEHR.v1.template.OBSERVATION;
import openEHR.v1.template.QuantityConstraint;
import openEHR.v1.template.QuantityUnitConstraint;
import openEHR.v1.template.SECTION;
import openEHR.v1.template.TEMPLATE;
import openEHR.v1.template.Statement;
import openEHR.v1.template.TextConstraint;
import openEHR.v1.template.ValueConstraint;
import openEHR.v1.template.MultipleConstraint;
import openEHR.v1.template.ITEM;
import org.openehr.am.archetype.Archetype;
import org.openehr.am.archetype.constraintmodel.*;
import org.openehr.am.archetype.constraintmodel.CAttribute.Existence;
import org.openehr.am.archetype.constraintmodel.primitive.CString;
import org.openehr.am.openehrprofile.datatypes.quantity.CDvQuantity;
import org.openehr.am.openehrprofile.datatypes.quantity.CDvQuantityItem;
import org.openehr.am.openehrprofile.datatypes.text.CCodePhrase;
import org.openehr.rm.common.archetyped.Locatable;
import org.openehr.rm.datatypes.text.CodePhrase;
import org.openehr.rm.support.basic.Interval;
/**
* A template flattener which can take OET object model generated by
* OET-template parser and join constraints from the parent archetype and
* all included children archetypes, and output the combined constraints
* in pure AOM instance.
*
* @author rong.chen
*
*/
public class Flattener {
/**
* Constructor
*/
public Flattener() {
archetypeMap = new HashMap();
termMap = new TermMap();
}
/**
* Flatten given template only with archetypes
*
* @param template
* @param archetypeMap
* @return
* @throws Exception
*/
public Archetype toFlattenedArchetype(TEMPLATE template,
Map archetypeMap) throws FlatteningException {
return toFlattenedArchetype(template, archetypeMap,
new HashMap());
}
/**
* Flatten given template with referenced archetypes and sub-templates
*
* @param template
* @param archetypeMap not null
* @param templateMap null if unspecified
* @return
* @throws FlatteningException if null archetypeMap
*/
public Archetype toFlattenedArchetype(TEMPLATE template,
Map archetypeMap,
Map templateMap) throws FlatteningException {
if(archetypeMap == null) {
throw new FlatteningException("null archetypeMap");
}
// make a internal copy of archetypeMap
this.archetypeMap.clear();
for(Map.Entry entry : archetypeMap.entrySet()) {
Archetype a = entry.getValue();
if(a != null) {
a = a.copy();
this.archetypeMap.put(entry.getKey(), a);
}
}
this.templateMap = templateMap;
log.debug("Loaded archetype/template maps, total archetypes: " +
archetypeMap.size() + ", total templates: " +
(templateMap == null ? 0 : templateMap.size()));
return toFlattenedArchetype(template);
}
/*
* Only used when archetype/template maps are initialized!
*/
private Archetype toFlattenedArchetype(TEMPLATE template)
throws FlatteningException {
log.debug("Flattening template.. STARTED");
Archetyped definition = template.getDefinition();
// start flattening
Archetype flattended = flattenArchetyped(definition);
flattended.reloadNodeMaps();
log.debug("Flattening template DONE");
return flattended;
}
/**
* Flattening entry point for root class archetyped
*
* @param parentArchetype provides the context of flattening, null for first
* entry of the recursive function
* @param definition
* @throws FlatteningException
*/
private Archetype flattenArchetyped(Archetyped definition) throws FlatteningException {
log.debug("flattening archetyped on archetype: " + definition.getArchetypeId());
// TODO handle template_id
if(definition instanceof COMPOSITION) {
// only exception when parentArchetype is always not set
return flattenComposition((COMPOSITION) definition);
} else if(definition instanceof ITEMSTRUCTURE) {
return flattenItemStructure(null, (ITEMSTRUCTURE) definition);
} else if(definition instanceof ContentItem) {
return flattenContentItem(null, (ContentItem) definition);
} else if(definition instanceof ITEM) {
return flattenItem(null, (ITEM) definition);
} else {
throw new FlatteningException("Unkown archetyped sub-type");
}
}
/*
* Flatten an item
*/
private Archetype flattenItem(Archetype parentArchetype, ITEM item)
throws FlatteningException {
String aid = parentArchetype == null ? "null" : parentArchetype.getArchetypeId().toString();
log.debug("flattening item on parentArchetype " + aid + " at path " + item.getPath());
Archetype archetype = retrieveArchetype(item.getArchetypeId());
applyTemplateConstraints(archetype, item);
fillArchetypeSlot(parentArchetype, archetype, item.getPath(),
item.getName());
return archetype;
}
private Archetype flattenComposition(COMPOSITION composition) throws FlatteningException {
log.debug("flattening composition on archetype: " + composition.getArchetypeId());
Archetype archetype = retrieveArchetype(composition.getArchetypeId());
CComplexObject root = archetype.getDefinition();
CAttribute contentAttribute = root.getAttribute(CONTENT);
removeArchetypeSlots(contentAttribute);
// handle "/content" attribute
ContentItem[] items = composition.getContentArray();
if(items != null && items.length > 0) {
String path = "/" + CONTENT;
if(contentAttribute == null) {
List alternatives = new ArrayList();
contentAttribute = new CMultipleAttribute(path, CONTENT,
Existence.OPTIONAL, Cardinality.LIST, alternatives);
archetype.getDefinition().addAttribute(contentAttribute);
}
for(ContentItem item : items) {
log.debug("flattening composition.content..");
flattenContentItem(archetype, item);
}
}
// TODO handle "/context" attribute
// log.warn("flattening composition.context..not implemented");
applyRules(archetype, composition.getRuleArray());
applyNameConstraint(archetype, archetype.getDefinition(),
composition.getName(), "/");
return archetype;
}
private Archetype flattenContentItem(Archetype parentArchetype,
ContentItem definition) throws FlatteningException {
log.debug("flattening content_item on archetype: " +
definition.getArchetypeId() + " on path: " + definition.getPath());
Archetype archetype = null;
String templateId = definition.getTemplateId();
if(templateId == null) {
archetype = retrieveArchetype(definition.getArchetypeId());
} else {
// TODO only needed at SECTION level so far for ifk2
TEMPLATE template = retrieveTemplate(templateId);
archetype = toFlattenedArchetype(template);
}
applyTemplateConstraints(archetype, definition);
if(definition instanceof ENTRY) {
flattenEntry(parentArchetype, archetype, (ENTRY) definition);
} else if(definition instanceof SECTION) {
flattenSection(parentArchetype, archetype, (SECTION) definition);
} else {
throw new FlatteningException(
"Unexpected subtype of ContentItem: " + definition);
}
return archetype;
}
/*
* Apply common template constraints
*/
private void applyTemplateConstraints(Archetype archetype,
Archetyped definition) throws FlatteningException {
log.debug("applying common template constraints.. ");
if(archetype == null) {
return;
}
String name = null;
Statement[] rules = null;
BigInteger max = null;
BigInteger min = null;
boolean hideOnForm = false;
String annotation = null;
if(definition instanceof ContentItem) {
ContentItem item = (ContentItem) definition;
name = item.getName();
rules = item.getRuleArray();
max = item.getMax();
min = item.getMin();
hideOnForm = item.getHideOnForm();
annotation = item.getAnnotation();
} else if(definition instanceof ITEMSTRUCTURE) {
ITEMSTRUCTURE item = (ITEMSTRUCTURE) definition;
name = item.getName();
rules = item.getRuleArray();
max = item.getMax();
min = item.getMin();
hideOnForm = item.getHideOnForm();
annotation = item.getAnnotation();
} else if(definition instanceof ITEM) {
ITEM item = (ITEM) definition;
name = item.getName();
rules = item.getRuleArray();
max = item.getMax();
min = item.getMin();
hideOnForm = item.getHideOnForm();
annotation = item.getAnnotation();
} else {
log.warn("unsupported definition type: " + definition);
}
applyNameConstraint(archetype, archetype.getDefinition(), name , "/");
applyRules(archetype, rules);
applyOccurrencesConstraint(archetype, archetype.getDefinition(), max, min);
applyHideOnFormConstraint(archetype.getDefinition(), hideOnForm);
applyAnnotationConstraint(archetype.getDefinition(), annotation);
}
private void setPathPrefixOnCObjectTree(CObject cobj, String prefix)
throws FlatteningException {
// TODO shouldn't happen
if(cobj == null) {
log.warn("null cobj encountered at setPathPrefix(): " + prefix);
return;
}
String path = cobj.path();
if("/".equals(path)) {
path = prefix;
} else {
path = prefix + path;
}
cobj.setPath(path);
if(path.endsWith(VALUE)) {
// log.debug("setPathPrefixOnCObjectTree - value path: " + path);
}
if(cobj instanceof CComplexObject) {
CComplexObject ccobj = (CComplexObject) cobj;
for(CAttribute cattr : ccobj.getAttributes()) {
path = cattr.path();
cattr.setPath(prefix + path);
for(Iterator it = cattr.getChildren().iterator();
it.hasNext();) {
CObject child = it.next();
// TODO
if(child == null) {
it.remove();
log.warn("null child encountered remove in setPathPrefix()..");
}
setPathPrefixOnCObjectTree(child, prefix);
}
}
}
}
private void updatePathWithNamedNodeOnCObjectTree(CObject cobj,
String nodeId, String name) throws FlatteningException {
// TODO shouldn't happen
if (cobj == null) {
log.warn("null cobj in updatePathWithNamedNodeOnCObjectTree(): "
+ nodeId + "/" + name);
return;
}
String path = cobj.path();
path = replaceNodeIdWithNamedNode(path, nodeId, name);
cobj.setPath(path);
//log.debug("cobj.path: " + cobj.path());
if (cobj instanceof CComplexObject) {
CComplexObject ccobj = (CComplexObject) cobj;
for (CAttribute cattr : ccobj.getAttributes()) {
path = cattr.path();
path = replaceNodeIdWithNamedNode(path, nodeId, name);
cattr.setPath(path);
//log.debug("cattr.path: " + cattr.path());
for (Iterator it = cattr.getChildren().iterator(); it
.hasNext();) {
CObject child = it.next();
// TODO
if (child == null) {
it.remove();
log.warn("null child encountered remove in setPathPrefix()..");
}
updatePathWithNamedNodeOnCObjectTree(child, nodeId, name);
}
}
}
}
private String replaceNodeIdWithNamedNode(String path, String nodeId,
String name) {
return path.replaceFirst("\\[" + nodeId + "\\]",
"\\[" + namedNodeSegment(nodeId, name) + "\\]");
}
private String namedNodeSegment(String nodeId, String name) {
return nodeId + " and name/value='" + name + "'";
}
private Archetype flattenSection(Archetype parentArchetype,
Archetype archetype, SECTION section) throws FlatteningException {
log.debug("flattening section on archetype " + section.getArchetypeId()
+ " at path " + section.getPath());
ContentItem[] items = section.getItemArray();
String path = section.getPath();
CComplexObject root = archetype.getDefinition();
fillArchetypeSlot(parentArchetype, archetype, path, section.getName());
CAttribute itemsAttribute = root.getAttribute(ITEMS);
// handle SECTION.items
if(items != null && items.length > 0) {
// TODO shouldn't be necessary if the archetype has
// proper archetype_slots
if(itemsAttribute == null) {
if(parentArchetype == null) {
path = "";
} else {
path = root.path();
}
path += "/" + ITEMS;
List alternatives = new ArrayList();
itemsAttribute = new CMultipleAttribute(path, ITEMS,
Existence.OPTIONAL, Cardinality.LIST, alternatives);
root.addAttribute(itemsAttribute);
}
// flatten each item in the list
for(ContentItem item : items) {
log.debug("flattening section.items.. ");
flattenContentItem(archetype, item);
}
}
return archetype;
}
// validity check of node_id (archetype_id) and name among siblings
private void checkSiblingNodeIdAndName(CAttribute parent,
String nodeId, String name) throws FlatteningException {
for(CObject cobj : parent.getChildren()) {
if(nodeId.equals(cobj.path()) && name.equals(cobj.getNodeId())) {
throw new FlatteningException("duplicated node_id/name: " +
nodeId + "/" + name + "at path: " + parent.path());
}
}
}
private int countChildOfArchetypeId(CAttribute cattr, String archetypeId) {
int count = 0;
for(CObject cobj : cattr.getChildren()) {
String nodeId = cobj.getNodeId();
if(nodeId == null) {
continue;
}
if(nodeId.startsWith(archetypeId)) {
count++;
}
}
return count;
}
/**
* Overwrite recursively all the nodeIds in the given cobj tree with
* incremental number starting with given count value
*
* @param ccobj
* @param diff
* @return total number of nodeIds adjusted, used to update nodeId counter
*/
protected long adjustNodeIds(CObject cobj, long count)
throws FlatteningException {
if(cobj.getNodeId() != null) {
count++;
cobj.setNodeId(formatNodeId(count));
}
if(cobj instanceof CComplexObject) {
for(CAttribute attr : ((CComplexObject) cobj).getAttributes()) {
for(CObject child : attr.getChildren()) {
count = adjustNodeIds(child, count);
}
}
}
return count;
}
// TODO until this is in sync with pathNodeMap, this shouldn't be used
protected void adjustNodeIds(CObject root) throws FlatteningException {
this.nodeCount = adjustNodeIds(root, this.nodeCount);
}
// "/content" => "content"
// "/content/name" => "name"
// "/data[at0001]/items[at0002]" => "items"
private String lastAttribute(String path) {
int i = path.lastIndexOf("/");
String attr = path.substring(i + 1, path.length());
i = attr.indexOf("[");
if(i >= 0) {
attr = attr.substring(0, i);
}
log.debug("attribute name: " + attr);
return attr;
}
private Archetype flattenEntry(Archetype parentArchetype,
Archetype archetype, ENTRY definition) throws FlatteningException {
log.debug("flattening entry on archetype: " + definition.getArchetypeId()
+ ", path: " + ((ENTRY) definition).getPath());
String path = definition.getPath();
// bind current archetype to the parent
fillArchetypeSlot(parentArchetype, archetype, path, definition.getName());
// common part for all entries
ENTRY entry = (ENTRY) definition;
ITEM[] items = entry.getItemsArray();
if(items != null) {
for(ITEM item : items) {
flattenItem(archetype, item);
}
}
// more specialized handling of sub-entry
if(definition instanceof EVALUATION) {
// no special handling
} else if(definition instanceof OBSERVATION) {
// no special handling
} else if(definition instanceof ACTION) {
// TODO handle description item
ACTION action = (ACTION) definition;
ITEMSTRUCTURE description = action.getDescription();
if(description != null) {
flattenItemStructure(archetype, description);
}
} else if(definition instanceof INSTRUCTION) {
flattenInstruction(parentArchetype, archetype, (INSTRUCTION) definition);
} else if(definition instanceof ADMINENTRY) {
// no special handling
}
return archetype;
}
/**
* Fill archetype_slot at specified path of parentArchetype
* and remove all slots
*
* @param parentArchetype
* @param archetype
* @param path
* @throws FlatteningException
*/
private void fillArchetypeSlot(Archetype parentArchetype,
Archetype archetype, String path, String name) throws FlatteningException {
String archetypeId = archetype.getArchetypeId().toString();
CComplexObject root = archetype.getDefinition();
if(parentArchetype != null ) {
// TODO has a quick-fix for the following path syntax
// "/activities[at0001 and name/value='Medication activity']/description"
// WILL NOT WORK IN OTHER CASES!!
int hybridStart = path.indexOf(" and name/value='");
if( hybridStart > 0) {
int i = path.indexOf("]");
path = path.substring(0, hybridStart) + path.substring(i);
log.debug("hybrid path detected, converted physical path: " + path);
}
CAttribute attribute = getParentAttribute(parentArchetype, path);
if(attribute == null) {
throw new FlatteningException("CAttribute not found at " + path);
}
removeArchetypeSlots(attribute);
root.setNodeId(archetypeId);
String pathSegment = archetypeId;
if(name != null) {
checkSiblingNodeIdAndName(attribute, archetypeId, name);
pathSegment = namedNodeSegment(archetypeId, name);
}
setPathPrefixOnCObjectTree(root, attribute.path() + "[" +
pathSegment + "]");
attribute.addChild(root);
}
}
private CAttribute getParentAttribute(Archetype archetype, String path)
throws FlatteningException {
String parentPath = Locatable.parentPath(path);
ArchetypeConstraint ac = archetype.node(parentPath);
if( ! (ac instanceof CComplexObject)) {
throw new FlatteningException("Parent node not found at " + path +
", computed parentPath: " + parentPath);
}
CComplexObject parentNode = (CComplexObject) ac;
String attributeName = lastAttribute(path);
CAttribute attribute = parentNode.getAttribute(attributeName);
return attribute;
}
private void flattenInstruction(Archetype parentArchetype,
Archetype archetype, INSTRUCTION instruction)
throws FlatteningException {
log.debug("flattening instruction on archetype: " + instruction.getArchetypeId()
+ ", path: " + ((ENTRY) instruction).getPath());
ITEMSTRUCTURE[] descriptions = instruction.getActivityDescriptionArray();
if(descriptions != null) {
for(ITEMSTRUCTURE item : descriptions) {
flattenItemStructure(archetype, item);
}
}
}
private void removeArchetypeSlots(CAttribute cattr) {
if(cattr == null) {
return;
}
// TODO verify slots by RM types
for(Iterator it = cattr.getChildren().iterator();
it.hasNext();) {
CObject cobj = it.next();
if(cobj instanceof ArchetypeSlot) {
it.remove();
log.debug("archetype_slot removed from attribute " +
cattr.getRmAttributeName());
}
}
}
/*
* Flatten any subclass of item_structure
*
* @param parentArchetype
* @param structure
* @return
* @throws FlatteningException
*/
private Archetype flattenItemStructure(Archetype parentArchetype,
ITEMSTRUCTURE structure) throws FlatteningException {
log.debug("flattening item_structure on archetype: " +
structure.getArchetypeId() + " on path: " + structure.getPath());
Archetype archetype = retrieveArchetype(structure.getArchetypeId());
applyTemplateConstraints(archetype, structure);
fillArchetypeSlot(parentArchetype, archetype, structure.getPath(),
structure.getName());
ITEM[] items = structure.getItemsArray();
if(items != null) {
for(ITEM item : items) {
flattenItem(archetype, item);
}
}
return archetype;
}
/**
* Apply a set of rules in the context of given archetype
*
* Important to keep passing the same archetype reference
* and keep the archetype updated when each rule is applied
*
* @param archetype
* @param rules
* @throws FlatteningException
*/
void applyRules(Archetype archetype, Statement[] rules)
throws FlatteningException {
if(rules == null) {
return;
}
String name = null;
String leadingPath = null;
for(Statement rule : rules) {
if(rule.getName() != null) {
if(name == null) {
name = rule.getName();
leadingPath = rule.getPath();
} else if(rule.getPath().equals(leadingPath)) {
// more than one named node for the same path,
// thus no need to rewrite the paths
log.debug("more than one named node [" + name +
"] on path: " + leadingPath );
name = null;
break;
}
}
}
// rewrite rule path for named nodes
// ASUMMING order is respected!!
for(Statement rule : rules) {
if(name != null && rule.getPath().startsWith(leadingPath)
&& rule.getPath().length() > leadingPath.length()) {
int len = leadingPath.length();
String path = rule.getPath();
path = path.substring(0, len - 1) + " and name/value='" +
name + "'" + path.substring(len - 1);
rule.setPath(path);
log.debug("rewrote path with named node: " + path);
}
applyRule(archetype, rule);
}
}
/**
* Apply a single rule on given archetype
*
* @param archetype
* @param rule
* @throws FlatteningException
*/
void applyRule(Archetype archetype, Statement rule)
throws FlatteningException {
log.debug("apply rule [" + rule + "] on archetype: " +
archetype.getArchetypeId().toString());
String path = rule.getPath();
ArchetypeConstraint constraint = archetype.node(rule.getPath());
if(constraint == null) {
throw new FlatteningException("no constraint on path: "
+ path + " of " + archetype.getArchetypeId());
}
constraint = applyNameConstraint(archetype, constraint, rule.getName(),
path);
applyOccurrencesConstraints(archetype, constraint, rule);
applyDefaultValueConstraint(constraint, rule.getDefault());
applyHideOnFormConstraint(constraint, rule.getHideOnForm());
applyAnnotationConstraint(constraint, rule.getAnnotation());
applyValueConstraint(archetype, constraint, rule);
archetype.updatePathNodeMap((CObject) constraint);
}
// TODO
protected void applyHideOnFormConstraint(ArchetypeConstraint constraint,
boolean hideOnForm) {
return;
}
// TODO
protected void applyAnnotationConstraint(ArchetypeConstraint constraint,
String annotation) {
if(annotation == null || annotation.length() == 0) {
return;
}
constraint.setAnnotation(annotation);
}
/**
* Apply a default value rule constraint
*
* Example:
* occurrences = new Interval(1,1);
// simple text value
if(defaultValue.indexOf("::") < 0) {
String path = cattr.path() + "/" + VALUE;
CComplexObject valueObj = CComplexObject.createSingleRequired(path, DV_TEXT);
CAttribute valueAttr = CSingleAttribute.createRequired(path, VALUE);
cattr.addChild(valueObj);
valueObj.addAttribute(valueAttr);
CString cstring = new CString(null, null, null, defaultValue);
CPrimitiveObject cpo = CPrimitiveObject.createSingleRequired(path, cstring);
valueAttr.addChild(cpo);
log.debug("c_string applied on path: " + constraint.path());
} else {
// or coded_text value
String path = ccobj.path() + "/" + VALUE;
CodePhrase codePhrase = parseCodePhraseAndCollectText(defaultValue,
path);
CCodePhrase ccp = new CCodePhrase(path, occurrences, null, cattr,
null, null, codePhrase, null);
cattr.addChild(ccp);
log.debug("c_code_phrase constraint applied on path: " + constraint.path());
}
}
protected void applyOccurrencesConstraints(Archetype archetype,
ArchetypeConstraint constraint, Statement rule) throws FlatteningException {
BigInteger max = rule.getMax();
BigInteger min = rule.getMin();
if(max != null || min != null) {
if(constraint instanceof CObject) {
applyOccurrencesConstraint(archetype, (CObject) constraint, rule.getMax(),
rule.getMin());
}
}
}
protected void applyOccurrencesConstraint(Archetype archetype,
CObject cobj, BigInteger max, BigInteger min) throws FlatteningException {
log.debug("applyOccurrencesConstraint, min: " + min + ", max: " + max
+ ", at: " + cobj.path());
if( !cobj.isRoot() ) {
//assert(cobj.getParent() != null);
}
String path = cobj.path();
Interval occurrences = cobj.getOccurrences();
// default occurrences, required [1,1]
// special-case in archetype root, then the default occurrences
// can be overriden
if(( !"/".equals(path)) && occurrences == null) {
log.warn("try to set occurrences constraint on default(null)" +
" occurrences: " + cobj.path());
return;
}
if(max != null && occurrences.getUpper() != null
&& max.intValue() > occurrences.getUpper().intValue()) {
throw new FlatteningException("more permissive max occurrences, " + path);
}
if(max != null && occurrences.getLower() != null
&& max.intValue() < occurrences.getLower().intValue()) {
throw new FlatteningException("contradicting max occurrences [max: "
+ max.intValue() + ", occurrences.lower: "
+ occurrences.getLower().intValue() + "] at path: " + path);
}
if(min != null && occurrences.getLower() != null
&& min.intValue() < occurrences.getLower().intValue()) {
throw new FlatteningException("more permissive min occurrences, " + path);
}
if(min != null && occurrences.getUpper() != null
&& min.intValue() > occurrences.getUpper().intValue()) {
throw new FlatteningException("contradicting min occurrences, " + path);
}
// it's required already
// special case for archetype node!
if(( !"/".equals(path)) && occurrences.getUpper() != null && occurrences.getLower() != null
&& occurrences.getUpper().intValue() == 1
&& occurrences.getLower().intValue() == 1) {
log.warn("try to set occurrences constraint on required node: "
+ cobj.path());
return;
}
// TODO temp fix for missing min=0 when setting
// optional occurrences in template designer
if(min == null && max != null) {
min = BigInteger.valueOf(0L);
}
Integer lower = null;
Integer upper = null;
if(occurrences != null) {
lower = occurrences.getLower();
upper = occurrences.getUpper();
}
if(min != null) {
lower = min.intValue();
if(upper != null && lower > upper) {
upper = lower;
}
}
if(max != null) {
upper = max.intValue();
if(lower != null && lower > upper) {
lower = upper;
}
}
Interval newOccurrences =
new Interval(lower, upper, lower != null, upper != null);
log.debug("newOccurrences: " + newOccurrences);
if(newOccurrences.getLower() != null
&& newOccurrences.getLower().intValue() > 0
&& !"/".equals(path)) {
CAttribute parent = getParentAttribute(archetype, path);
if(parent instanceof CMultipleAttribute) {
CMultipleAttribute cma = (CMultipleAttribute) parent;
log.debug("setting parent.cardinality: " + cma.getCardinality());
// TODO temporarily switched off
cma.getCardinality().getInterval().setLower(newOccurrences.getLower());
log.debug("AFTER parent.cardinality: " + cma.getCardinality());
} else {
if(parent == null) {
log.debug("parent null at " + cobj.path());
}
}
}
cobj.setOccurrences(newOccurrences);
}
// TODO add support for name-based hybrid path
// At least for Rule-based name constraint, if the node doesn't
// exist before, a copy of the node should be created with given name
protected CComplexObject applyNameConstraint(Archetype archetype,
ArchetypeConstraint constraint, String name, String localPath)
throws FlatteningException {
log.debug("applying name constraint [" + name + "] on path: " +
localPath + "constraint: " + constraint.path());
// preconditions
assert(constraint instanceof CComplexObject);
CComplexObject ccobj = (CComplexObject) constraint;
if(name == null) {
return ccobj;
}
//String path = ccobj.path();
String path = localPath;
if(! "/".equals(path)) {
CAttribute parent = getParentAttribute(archetype, path);
assert(parent != null);
// add a copy of the ccobj if sibling with same node_id exists
// this is the key to enable named-node path in template
if(hasSiblingNodeWithNodeId(parent, ccobj.getNodeId())) {
removeUnnamedSiblingNode(archetype, parent, ccobj.getNodeId());
ccobj = (CComplexObject) ccobj.copy();
parent.addChild(ccobj);
ccobj.setParent(parent);
checkSiblingNodeIdAndName(parent, ccobj.getNodeId(), name);
log.debug("sibling node with same node_id added, " + name);
}
}
// TODO check physicalPath needed
path = ccobj.path();
log.debug("applyNameConstraint - middle ccobj.path: " + ccobj.path());
// perhaps unnecessary
CAttribute nameAttr = ccobj.getAttribute(NAME);
CPrimitiveObject cpo = null;
if(nameAttr == null) {
CString cstring = cString(name);
if("/".equals(path)) {
path = path + NAME;
} else {
path = path+ "/" + NAME;
}
CComplexObject nameObj = CComplexObject.createSingleRequired(path, DV_TEXT);
nameAttr = CSingleAttribute.createRequired(path, NAME);
nameAttr.addChild(nameObj);
path = path + "/" + VALUE;
CAttribute valueAttr = CSingleAttribute.createRequired(path, VALUE);
nameObj.addAttribute(valueAttr);
cpo = CPrimitiveObject.createSingleRequired(path, cstring);
valueAttr.addChild(cpo);
}
ccobj.addAttribute(nameAttr);
updatePathWithNamedNodeOnCObjectTree(ccobj, ccobj.getNodeId(), name);
archetype.updatePathNodeMapRecursively(ccobj);
log.debug("after setting name, cobj.path: " + ccobj.path());
return ccobj;
}
private void removeUnnamedSiblingNode(Archetype archetype,
CAttribute parent, String nodeId) throws FlatteningException {
for(Iterator it = parent.getChildren().iterator();
it.hasNext();) {
CObject cobj = it.next();
if(nodeId.equals(cobj.getNodeId())) {
if( ! (cobj instanceof CComplexObject)) {
throw new FlatteningException("unexpected constraint type: "
+ cobj.getClass() + " for node_id[" + nodeId + "] at " +
parent.path());
}
CComplexObject ccobj = (CComplexObject) cobj;
if( ! ccobj.hasAttribute(NAME)) {
it.remove();
// seems unnecessary
// archetype.reloadNodeMaps();
log.debug("Unnamed sibling node[" + nodeId + "] removed..");
break;
}
}
}
}
/*
* Check if given path is a hybrid of physical and runtime path
*
* Example:
* "/data[at0001]/items[at0002 and name/value='one']/items[at0003]"
*/
private boolean isHybridPath(String path) {
// TODO validity check
return path.indexOf(" and name") > 0;
}
// temporary solution until a proper
// archetype-terminology based solution is specified
protected void __applyNameConstraint(ArchetypeConstraint constraint,
String name) throws FlatteningException {
}
/**
* Checks if there is any sibling node with the same node_id
*
* @param parent
* @param nodeId
* @return
*/
private boolean hasSiblingNodeWithNodeId(CAttribute parent, String nodeId) {
for(CObject cobj : parent.getChildren()) {
if(nodeId.equals(cobj.getNodeId())) {
return true;
}
}
return false;
}
protected void applyValueConstraint(Archetype archetype,
ArchetypeConstraint constraint, Statement rule)
throws FlatteningException {
if(rule.getConstraint() == null) {
return;
}
log.debug("applying value constraint on path: " + constraint.path());
if( ! (constraint instanceof CComplexObject)) {
throw new FlatteningException("Unexpected constraint type: " + constraint.getClass());
}
CComplexObject ccobj = (CComplexObject) constraint;
if( ! ccobj.getRmTypeName().equalsIgnoreCase(ELEMENT)) {
throw new FlatteningException("Unexpected constraint rmType: " +
ccobj.getRmTypeName());
}
ValueConstraint vc = rule.getConstraint();
if(vc instanceof TextConstraint) {
TextConstraint tc = (TextConstraint) vc;
applyTextConstraint(ccobj, tc);
} if(vc instanceof QuantityConstraint) {
QuantityConstraint tc = (QuantityConstraint) vc;
applyQuantityConstraint(ccobj, tc);
archetype.updatePathNodeMapRecursively(ccobj);
} else if(vc instanceof MultipleConstraint) {
MultipleConstraint mc = (MultipleConstraint) vc;
applyMultipleConstraint(ccobj, mc);
}
}
protected void applyQuantityConstraint(CComplexObject ccobj,
QuantityConstraint qc) throws FlatteningException {
log.debug("applying quantity constraint on path: " + ccobj.path());
String[] includedUnits = qc.getIncludedUnitsArray();
String[] excludedUnits = qc.getExcludedUnitsArray();
QuantityUnitConstraint[] magnitudeUnits = qc.getUnitMagnitudeArray() ;
CDvQuantityItem item = null;
CAttribute valueAttr = ccobj.getAttribute(VALUE);
String valuePath = ccobj.path() + "/" + VALUE;
if(magnitudeUnits != null && magnitudeUnits.length == 1) {
log.debug("setting unit_magnitude quantity constraint");
QuantityUnitConstraint quc = magnitudeUnits[0];
Interval magnitude = new Interval(
quc.getMinMagnitude(), quc.getMaxMagnitude(),
quc.getIncludesMinimum(), quc.getIncludesMaximum());
item = new CDvQuantityItem(magnitude, quc.getUnit());
if(valueAttr != null) {
valueAttr.removeAllChildren();
CDvQuantity cdq = CDvQuantity.singleRequired(valuePath, item);
valueAttr.addChild(cdq);
}
} else if(includedUnits != null && includedUnits.length == 1) {
//
// mmol/L
//
log.debug("setting included_units quantity constraint");
item = new CDvQuantityItem(includedUnits[0]);
} else if(excludedUnits != null && excludedUnits.length > 0) {
log.debug("setting excluded_units quantity constraint");
//
// in
//
if(valueAttr == null) {
throw new FlatteningException(
"Missing value attribute for quantityConstraint.excludedUnits");
}
if(valueAttr.getChildren() == null || valueAttr.getChildren().isEmpty()) {
throw new FlatteningException(
"Missing child obj for quantityConstraint.excludedUnits");
}
if(valueAttr.getChildren().size() > 1) {
throw new FlatteningException(
"More than one child obj for quantityConstraint.excludedUnits");
}
CObject child = valueAttr.getChildren().get(0);
if( ! (child instanceof CDvQuantity)) {
throw new FlatteningException(
"Non-CDvQuantity child obj for quantityConstraint.excludedUnits");
}
CDvQuantity cdq = (CDvQuantity) child;
if(cdq.getList() == null || cdq.getList().isEmpty()) {
throw new FlatteningException(
"Empty CDvQuantity.list for quantityConstraint.excludedUnits");
}
cdq.removeItemByUnitsList(excludedUnits);
return;
} else {
// TODO > 1 in the array etc
throw new FlatteningException(
"Unsupported quantityConstraint in Template: " + qc);
}
if(valueAttr == null) {
valueAttr = new CSingleAttribute(valuePath, VALUE, Existence.REQUIRED);
CDvQuantity cdq = CDvQuantity.singleRequired(valuePath, item);
valueAttr.addChild(cdq);
ccobj.addAttribute(valueAttr);
} else {
// deal with empty c_dv_quantity to add new items
if(valueAttr.getChildren() == null || valueAttr.getChildren().isEmpty()) {
throw new FlatteningException(
"Missing child obj for quantityConstraint.excludedUnits");
}
if(valueAttr.getChildren().size() > 1) {
throw new FlatteningException(
"More than one child obj for quantityConstraint.excludedUnits");
}
CObject child = valueAttr.getChildren().get(0);
if( ! (child instanceof CDvQuantity)) {
throw new FlatteningException(
"Non-CDvQuantity child obj for quantityConstraint.excludedUnits");
}
CDvQuantity cdq = (CDvQuantity) child;
cdq.addItem(item);
}
}
protected void applyTextConstraint(CComplexObject ccobj,
TextConstraint tc) throws FlatteningException {
log.debug("applying text constraint on path: " + ccobj.path());
String[] includedValues = tc.getIncludedValuesArray();
String[] excludedValues = tc.getExcludedValuesArray();
CAttribute valueAttr = ccobj.getAttribute(VALUE);
String valuePath = ccobj.path() + "/" + VALUE;
String definingCodePath = valuePath + "/" + DEFINING_CODE;
if(includedValues != null && includedValues.length > 0) {
if(valueAttr == null) {
valueAttr = new CSingleAttribute(valuePath, VALUE,
Existence.REQUIRED);
ccobj.addAttribute(valueAttr);
} else if (valueAttr.getChildren().size() > 0) {
valueAttr.removeAllChildren();
}
CComplexObject valueObj = CComplexObject.createSingleRequired(
valuePath, DV_CODED_TEXT);
valueAttr.addChild(valueObj);
CAttribute definingCode = CSingleAttribute.createRequired(
definingCodePath, DEFINING_CODE);
valueObj.addAttribute(definingCode);
List codeList = new ArrayList();
String terminology = null;
String text = null;
String code = null;
for(String value : includedValues) {
int i = value.indexOf("::");
int j = value.lastIndexOf("::");
if(i == j || j > value.length() - 2) {
throw new FlatteningException(
"wrong syntax for coded text: " + value);
}
terminology = value.substring(0, i);
code = value.substring(i + 2, j);
text = value.substring(j + 2);
codeList.add(code);
termMap.addTerm(terminology, code, text, valuePath);
}
CCodePhrase ccp = CCodePhrase.singleRequired(definingCodePath,
terminology, codeList);
definingCode.addChild(ccp);
} else if(excludedValues != null && excludedValues.length > 0) {
if(valueAttr == null) {
throw new FlatteningException(
"failed to set excluded values on text constraint, " +
"VALUE attribute missing");
}
if (valueAttr.getChildren().size() == 1) {
CObject child = valueAttr.getChildren().get(0);
if(child instanceof CComplexObject) {
CComplexObject childCCObj = (CComplexObject) child;
if(childCCObj.getRmTypeName().equals(DV_CODED_TEXT)) {
CAttribute definingCodeAttr =
childCCObj.getAttribute(DEFINING_CODE);
if(definingCodeAttr == null) {
throw new FlatteningException(
"Missing defining_code attribute");
}
CCodePhrase ccp =
(CCodePhrase) definingCodeAttr.getChildren().get(0);
log.debug("before codeList.size: " + ccp.getCodeList().size());
for(Iterator it = ccp.getCodeList().iterator();
it.hasNext();) {
String code = it.next();
for(String value : excludedValues) {
int i = value.indexOf("::");
if(code.equals(value.substring(i + 2))) {
it.remove();
}
}
}
log.debug("after codeList.size: " + ccp.getCodeList().size());
} else {
// TODO other data types?
}
} else {
throw new FlatteningException(
"Unexpected VALUE.child constrainType: " +
(child == null ? "null" : child.getClass()));
}
} else {
throw new FlatteningException("Unexpected VALUE.children.size: "
+ valueAttr.getChildren().size());
}
}
}
protected void applyMultipleConstraint(CComplexObject ccobj,
MultipleConstraint mc) throws FlatteningException {
log.debug("applying multiple constraint on path: " + ccobj.path());
String[] includedTypes = mc.getIncludedTypesArray();
CAttribute cattr = ccobj.getAttribute(VALUE);
if(cattr != null) {
if(cattr.getChildren() == null || cattr.getChildren().isEmpty()) {
throw new FlatteningException(
"failed to set value constraint, null/empty children list");
}
List newChildrenList = new ArrayList();
for(CObject child : cattr.getChildren()) {
String childType = child.getRmTypeName();
for(String type : includedTypes) {
if((DATA_TYPES_PREFIX + type).equalsIgnoreCase(childType)
|| type.equalsIgnoreCase(childType)) {
newChildrenList.add(child);
break;
}
}
}
cattr.removeAllChildren();
for(CObject child : newChildrenList) {
cattr.addChild(child);
}
log.debug("total " + newChildrenList.size() + " children left");
} else {
// in case value attribute doesn't exist in archetype
String valuePath = ccobj.path() + "/" + VALUE;
cattr = new CSingleAttribute(valuePath, VALUE, Existence.REQUIRED);
ccobj.addAttribute(cattr);
for(String rmType : includedTypes) {
rmType = rmType.toUpperCase();
if( ! rmType.startsWith("DV_")) {
rmType = DATA_TYPES_PREFIX + rmType;
}
CComplexObject child =
CComplexObject.createSingleRequired(valuePath, rmType);
cattr.addChild(child);
}
log.debug("value attribute added with total "
+ cattr.getChildren().size() + "child(s)");
}
}
/*
* Returns next unique nodeId in "at0001" format
*/
protected String formatNodeId(long count) {
String nextId = AT + format.format(count);
return nextId;
}
/*
* Gets next unique id and increase the counter
*/
private String nextNodeId() {
nodeCount++;
String nextId = formatNodeId(nodeCount);
//log.debug("next nodeId: " + nextId);
return nextId;
}
/*
* Parse coded text like 'SNOMED-CT::258835005::mg/dygn'
* the last segment of actual text value
* is now collected in termMap as a quick fix
*
*/
private CodePhrase parseCodePhraseAndCollectText(String value, String path)
throws FlatteningException {
int i = value.indexOf("::");
int j = value.lastIndexOf("::");
if(i == j) {
throw new FlatteningException(
"wrong syntax for coded text: " + value);
}
String terminology = value.substring(0, i);
String code = value.substring(i + 2, j);
String text = value.substring(j + 2);
CodePhrase codePhrase = new CodePhrase(terminology, code);
termMap.addTerm(terminology, code, text, path);
return codePhrase;
}
private CString cString(String value) {
List values = new ArrayList();
values.add(value);
CString cstring = new CString(null, values, null);
return cstring;
}
/**
* Finds and replaces according archetypeSlot with fully flattened cobj
*
* @param cattr
* @param definition
* @param cobj
*/
void replaceSlotWithFlattened(CAttribute cattr, Archetyped definition,
CObject cobj) {
List children = cattr.getChildren();
if(children == null) {
return;
}
for(int i = 0, j = children.size(); i < j; i++) {
CObject child = children.get(i);
if(child instanceof ArchetypeSlot) {
// if the slot matches the template def
children.remove(i);
cobj.setPath(child.path());
children.add(i, cobj);
}
}
}
private TEMPLATE retrieveTemplate(String templateId)
throws FlatteningException {
TEMPLATE template = templateMap.get(templateId);
if(template == null) {
throw new UnknownTemplateException(templateId);
}
return template;
}
private Archetype retrieveArchetype(String archetypeId)
throws FlatteningException {
Archetype archetype = archetypeMap.get(archetypeId);
if(archetype == null) {
throw new UnknownArchetypeException(archetypeId);
}
// make a deep copy
archetype = archetype.copy();
return archetype;
}
/**
* Find the largest node id
*
* @param archetype
* @return
*/
protected int findLargestNodeId(Archetype archetype)
throws FlatteningException {
return findLargestNodeId(archetype.getDefinition(), 0);
}
// Traverse given cobj tree and find the largest node id
protected int findLargestNodeId(CObject cobj, int largest)
throws FlatteningException {
int current = largest;
int last = 0;
current = parseNodeId(cobj.getNodeID());
if(largest > current) {
current = largest;
}
if(cobj instanceof CComplexObject) {
CComplexObject ccobj = (CComplexObject) cobj;
for(CAttribute cattr : ccobj.getAttributes()) {
for(CObject child : cattr.getChildren()) {
last = findLargestNodeId(child, current);
if(last > current) {
current = last;
}
}
}
}
return current;
}
/*
* Parses given nodeId and returns the integer value
*/
protected int parseNodeId(String nodeId) throws FlatteningException {
if(nodeId == null) {
return 0;
}
if(nodeId.length() <= AT.length()) {
throw new FlatteningException("Too short nodeId: " + nodeId);
}
nodeId = nodeId.substring(AT.length());
int dot = nodeId.indexOf(".");
if(dot > 0) {
nodeId = nodeId.substring(0, dot);
} else if(dot == 0) {
throw new FlatteningException("Bad format of nodeId: " + nodeId);
}
int value = 0;
try {
value = Integer.parseInt(nodeId);
} catch(NumberFormatException nfe) {
throw new FlatteningException("Bad format of nodeId: " + nodeId);
}
return value;
}
protected ArchetypeConstraint nodeAtHybridPath(String path)
throws FlatteningException {
return null;
}
public TermMap getTermMap() {
return termMap;
}
/* constant values */
private static final String DV_TEXT = "DV_TEXT";
private static final String DV_CODED_TEXT = "DV_CODED_TEXT";
private static final String ELEMENT = "ELEMENT";
private static final String NAME = "name";
private static final String VALUE = "value";
private static final String ITEMS = "items";
private static final String CONTENT = "content";
private static final String DESCRIPTION = "description";
private static final String DEFINING_CODE = "defining_code";
private static final String AT = "at";
private static final String DATA_TYPES_PREFIX = "DV_";
/* static fields */
private static DecimalFormat format = new DecimalFormat("####");
static {
// number of digits is not limited according to the specs
// using 4 as minimum is by convention
format.setMinimumIntegerDigits(4);
format.setMaximumIntegerDigits(8);
}
private static Logger log = Logger.getLogger(Flattener.class);
/* fields */
private Map archetypeMap;
private Map templateMap;
private TermMap termMap;
private long nodeCount;
}
/*
* ***** BEGIN LICENSE BLOCK ***** Version: MPL 1.1/GPL 2.0/LGPL 2.1
*
* The contents of this file are subject to the Mozilla Public License Version
* 1.1 (the 'License'); you may not use this file except in compliance with the
* License. You may obtain a copy of the License at http://www.mozilla.org/MPL/
*
* Software distributed under the License is distributed on an 'AS IS' basis,
* WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License for
* the specific language governing rights and limitations under the License.
*
* The Original Code is Flattener.java
*
* The Initial Developer of the Original Code is Rong Chen. Portions created by
* the Initial Developer are Copyright (C) 2009-2010 the Initial Developer. All
* Rights Reserved.
*
* Contributor(s):
*
* Software distributed under the License is distributed on an 'AS IS' basis,
* WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License for
* the specific language governing rights and limitations under the License.
*
* ***** END LICENSE BLOCK *****
*/