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package org.eurekaclinical.i2b2.client.pdo;
/*
* #%L
* i2b2 Export Service
* %%
* Copyright (C) 2013 Emory University
* %%
* Licensed under the Apache License, Version 2.0 (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.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import org.eurekaclinical.i2b2.client.I2b2CommUtil;
import org.eurekaclinical.i2b2.client.xml.XmlUtil;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import javax.xml.xpath.XPathConstants;
import javax.xml.xpath.XPathExpressionException;
import java.text.DateFormat;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.Date;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
import org.eurekaclinical.i2b2.client.xml.I2b2XmlException;
/**
* Parser for i2b2 PDO result XML.
*
* @author Michel Mansour
* @since 1.0
*/
public class I2b2PdoResultParser {
private static final Logger LOGGER = LoggerFactory.getLogger(I2b2PdoResultParser.class);
/*
* the i2b2 date format
*/
private final DateFormat i2b2DateFormat;
/*
* maps from IDs to patients, events, and observers (providers)
*/
private final Map patients;
private final Map events;
private final Map observers;
/*
* the set of observations in the result XML
*/
private final Set observations;
/*
* the XML document to parse
*/
private final Document d;
/**
* Default constructor. Accepts an XML document for parsing.
*
* @param xmlDoc an XML {@link Document} to parse
*/
public I2b2PdoResultParser(Document xmlDoc) {
d = xmlDoc;
i2b2DateFormat = new SimpleDateFormat(I2b2CommUtil.I2B2_DATE_FMT);
patients = new HashMap<>();
events = new HashMap<>();
observers = new HashMap<>();
observations = new HashSet<>();
}
/**
* Parses the instance's XML document and returns the PDO results contained
* in it.
*
* @return an {@link I2b2PdoResults} containing all of the PDO results found
* in the XML
* @throws I2b2XmlException if there is a parsing error
*/
public I2b2PdoResults parse() throws I2b2XmlException {
try {
parseAll();
} catch (XPathExpressionException e) {
throw new I2b2XmlException("Unable to parse i2b2 PDO result XML", e);
}
return new I2b2PdoResults(patients.values(), events.values(), observers.values(), observations);
}
/**
* Parses all of the patients, events, observers and observations from the
* result XML and ties together all related entities.
*
* @throws XPathExpressionException if there is an XPath error
*/
private void parseAll() throws XPathExpressionException {
parsePatients();
parseEvents();
parseObservers();
parseObservations();
for (Observation o : observations) {
o.getEvent().addObservation(o);
if (observers.containsKey(o.getObserver())) {
observers.get(o.getObserver()).addObservation(o);
}
}
for (Event e : events.values()) {
e.getPatient().addEvent(e);
}
for (Patient p : patients.values()) {
p.sortEvents();
}
}
private NodeList pdoElement(String dataName) throws XPathExpressionException {
return (NodeList) XmlUtil.evalXPath(d, "//" + dataName,
XPathConstants.NODESET);
}
private void parsePatients() throws XPathExpressionException {
NodeList patientElts = pdoElement("patient");
for (int i = 0; i < patientElts.getLength(); i++) {
Node child = patientElts.item(i);
Patient p = parsePatient((Element) child);
patients.put(p.getPatientId(), p);
}
}
private void parseEvents() throws XPathExpressionException {
NodeList eventElts = pdoElement("event");
for (int i = 0; i < eventElts.getLength(); i++) {
Node child = eventElts.item(i);
Event e = parseEvent((Element) child);
events.put(e.getEventId(), e);
}
}
private void parseObservers() throws XPathExpressionException {
NodeList observerElts = pdoElement("observer");
for (int i = 0; i < observerElts.getLength(); i++) {
Node child = observerElts.item(i);
Observer o = parseObserver((Element) child);
observers.put(o.getObserverCode(), o);
}
}
private void parseObservations() throws XPathExpressionException {
NodeList obxElts = pdoElement("observation");
for (int i = 0; i < obxElts.getLength(); i++) {
Observation o = parseObservation((Element) obxElts.item(i));
observations.add(o);
}
}
private Patient parsePatient(Element patientXml) {
String id = text(patientXml, "patient_id");
NodeList params = patientXml.getElementsByTagName("param");
Patient.Builder pb = new Patient.Builder(id);
Map pm = new CustomNullHashMap<>("N/A");
for (int i = 0; i < params.getLength(); i++) {
Node paramNode = params.item(i);
Node nameAttr = paramNode.getAttributes().getNamedItem("column");
if (nameAttr != null) {
if (paramNode.getChildNodes().getLength() > 0) {
pm.put(nameAttr.getNodeValue(), paramNode.getChildNodes()
.item(0).getNodeValue());
} else {
pm.put(nameAttr.getNodeValue(), "");
}
}
}
return pb.ageInYears(pm.get("age_in_years_num"))
.birthDate(pm.get("birth_date"))
.language(pm.get("language_cd"))
.maritalStatus(pm.get("marital_status_cd"))
.race(pm.get("race_cd")).religion(pm.get("religion_cd"))
.sex(pm.get("sex_cd"))
.stateCityZip(pm.get("statecityzip_path_char"))
.vitalStatus(pm.get("vital_status_cd"))
.zipCode(pm.get("zipcode_char")).build();
}
private Event parseEvent(Element eventXml) {
String id = text(eventXml, "event_id");
String patientId = text(eventXml, "patient_id");
Event.Builder eb = new Event.Builder(id, this.patients.get(patientId))
.startDate(date(eventXml, "start_date")).endDate(
date(eventXml, "end_date"));
NodeList params = eventXml.getElementsByTagName("param");
Map pm = new CustomNullHashMap<>("N/A");
for (int i = 0; i < params.getLength(); i++) {
Node paramNode = params.item(i);
Node nameAttr = paramNode.getAttributes().getNamedItem("column");
if (nameAttr != null) {
pm.put(nameAttr.getNodeValue(), paramNode.getTextContent());
}
}
return eb.activeStatus(pm.get("active_status_cd"))
.inOut(pm.get("inout_cd")).location(pm.get("location_cd"))
.build();
}
private Observer parseObserver(Element observerXml) {
String path = observerXml.getElementsByTagName("observer_path").item(0).getTextContent();
String code = observerXml.getElementsByTagName("observer_cd").item(0).getTextContent();
String name = observerXml.getElementsByTagName("name_char").item(0).getTextContent();
return new Observer.Builder(path, code).name(name).build();
}
private Observation parseObservation(Element obxXml) {
String eventId = obxXml.getElementsByTagName("event_id").item(0)
.getTextContent();
String conceptPath = obxXml.getParentNode().getAttributes().getNamedItem("panel_name").getNodeValue();
// some observations, like demographics, are timestamps and have no
// end date, so we just set it to the start date
Date startDate = date(obxXml, "start_date");
Date endDate;
if (obxXml.getElementsByTagName("end_date").getLength() == 1) {
endDate = date(obxXml, "end_date");
} else {
endDate = new Date(startDate.getTime());
}
return new Observation.Builder(this.events.get(eventId))
.conceptCode(text(obxXml, "concept_cd"))
.conceptPath(conceptPath)
.observer(text(obxXml, "observer_cd"))
.startDate(startDate)
.modifier(text(obxXml, "modifier_cd"))
.valuetype(text(obxXml, "valuetype_cd"))
.tval(text(obxXml, "tval_char")).nval(text(obxXml, "nval_num"))
.valueflag(text(obxXml, "valueflag_cd")).units(text(obxXml, "units_cd"))
.endDate(endDate)
.location(text(obxXml, "location_cd")).blob(text(obxXml, "observation_blob"))
.build();
}
private String text(Element elt, String tagName) {
try {
return elt.getElementsByTagName(tagName).item(0).getTextContent();
} catch (Exception e) {
return "";
}
}
private Date date(Element elt, String tagName) {
String dtTxt = text(elt, tagName);
// remove the last colon (:)
// we have to do this because Java's SimpleDateFormat does not directly
// support the format i2b2 is using: 2001-07-04T12:08:56.235-07:00
// even though it is a valid ISO-8601 date
// the closest Java has is: 2001-07-04T12:08:56.235-0700 (yyyy-MM-dd'T'HH:mm:ss.SSSZ)
// the other alternative is write our own date parser
int colonIdx = dtTxt.lastIndexOf(':');
if (colonIdx >= 0) {
dtTxt = dtTxt.substring(0, colonIdx).concat(dtTxt.substring(colonIdx + 1));
}
try {
return i2b2DateFormat.parse(dtTxt);
} catch (ParseException e) {
if (LOGGER.isDebugEnabled()) {
LOGGER.debug("Unable to parse date: {}", dtTxt);
} else if (null != dtTxt && !dtTxt.isEmpty()) {
LOGGER.warn("Unable to parse date: {}", dtTxt);
}
return null;
}
}
}
