/*******************************************************************************
* Copyright 2014 Virginia Polytechnic Institute and State 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.
******************************************************************************/
package edu.vt.vbi.patric.common;
import java.util.HashMap;
import java.util.Iterator;
import java.util.Map;
import javax.xml.namespace.QName;
import org.apache.axiom.om.OMAbstractFactory;
import org.apache.axiom.om.OMElement;
import org.apache.axiom.om.OMFactory;
import org.apache.axiom.om.OMNamespace;
import org.apache.axis2.AxisFault;
import org.apache.axis2.addressing.EndpointReference;
import org.apache.axis2.client.Options;
import org.apache.axis2.client.ServiceClient;
import org.json.simple.JSONArray;
import org.json.simple.JSONObject;
@SuppressWarnings("unchecked")
public class KLEIOInterface {
private final String kleioKey = "578e2b24fcf9c04e5464384a1ee7836e5e2327596c586189f76e2da0";
private final String endpointUrl = "http://nactem4.mc.man.ac.uk:18080/Kleio/services/KleioPort";
ServiceClient client = null;
private OMFactory omFactory = null;
private OMNamespace nsWeb = null;
private OMNamespace nsXsi = null;
private final String facets = "GENE,PROTEIN,MESHHEADING,METABOLITE,DRUG,BACTERIA,SYMPTOM,DISEASE,ORGAN,DIAG_PROC,THERAPEUTIC_PROC,INDICATOR";
private Map<String, String> hash = new HashMap<String, String>();
public KLEIOInterface() {
try {
client = new ServiceClient();
Options opts = new Options();
opts.setTo(new EndpointReference(endpointUrl));
opts.setTimeOutInMilliSeconds(300000);
client.setOptions(opts);
omFactory = OMAbstractFactory.getOMFactory();
nsWeb = omFactory.createOMNamespace("http://webservice.kleio.nactem.ac.uk/", "web");
nsXsi = omFactory.createOMNamespace("http://www.w3.org/2001/XMLSchema-instance", "xsi");
}
catch (AxisFault e) {
e.printStackTrace();
}
}
private OMElement getKLEIOKey() {
OMElement e = omFactory.createOMElement("key", null);
e.setText(kleioKey);
return e;
}
private OMElement getOptionalCriteria(String criteria, String value) {
OMElement e = omFactory.createOMElement(criteria, null);
if (value == null) {
if (criteria.equalsIgnoreCase("sortby")) {
value = "RELEVANCE";
}
else if (criteria.equalsIgnoreCase("nonullabstract")) {
value = "false";
}
else if (criteria.equalsIgnoreCase("startat")) {
value = "0";
}
else if (criteria.equalsIgnoreCase("hitsperpage")) {
value = "10";
}
}
e.addChild(omFactory.createOMText(value));
return e;
}
public JSONObject getDocumentList(String query, String sortby, boolean nullabstract, int startat, int hitsperpage) {
JSONObject r = new JSONObject();
JSONArray articles = new JSONArray();
OMElement res = null;
OMElement req = omFactory.createOMElement("getDocumentList", nsWeb);
req.addChild(getKLEIOKey());
req.addChild(getQueryNodes(query));
// optional
req.addChild(getOptionalCriteria("sortBy", sortby));
req.addChild(getOptionalCriteria("noNullAbstract", "" + nullabstract));
req.addChild(getOptionalCriteria("startAt", "" + startat));
req.addChild(getOptionalCriteria("hitsPerPage", "" + hitsperpage));
QName qnTotal = new QName("", "totalHits");
QName qnCitations = new QName("", "citations");
QName qnDate = new QName("", "dateString");
QName qnJournal = new QName("", "journalCite");
QName qnSnippet = new QName("", "docSnippet");
QName qnPMID = new QName("", "pmid");
QName qnTitle = new QName("", "title");
QName qnAuthors = new QName("", "authors");
try {
res = client.sendReceive(req);
OMElement rtrn = res.getFirstElement();
OMElement totalHits = rtrn.getFirstChildWithName(qnTotal);
System.out.println(totalHits.getText());
r.put("total", totalHits.getText());
if (rtrn.getFirstChildWithName(qnCitations) != null) {
Iterator<OMElement> itr = rtrn.getFirstChildWithName(qnCitations).getChildElements();
OMElement citation = null;
while (itr.hasNext()) {
citation = itr.next();
JSONObject article = new JSONObject();
article.put("pmid", citation.getFirstChildWithName(qnPMID).getText());
String title = citation.getFirstChildWithName(qnTitle).getText();
StringBuffer z = new StringBuffer();
for (int i = 0; i < title.length(); i++) {
char c = title.charAt(i);
if (c > 127 || c == '"' || c == '<' || c == '>') {
z.append("&#" + (int) c + ";");
}
else {
z.append(c);
}
}
title = z.toString();
article.put("title", title);
article.put("date", citation.getFirstChildWithName(qnDate).getText());
article.put("journal", citation.getFirstChildWithName(qnJournal).getText());
article.put("snippet", citation.getFirstChildWithName(qnSnippet).getText());
// authors
JSONArray authors = new JSONArray();
Iterator<OMElement> itrAuthors = citation.getFirstChildWithName(qnAuthors).getChildElements();
OMElement a = null;
while (itrAuthors.hasNext()) {
a = itrAuthors.next();
authors.add(a.getText());
}
article.put("authors", authors);
articles.add(article);
}
}
r.put("result", articles);
}
catch (AxisFault e) {
e.printStackTrace();
}
return r;
}
public JSONObject getFacets(String query) {
JSONObject r = new JSONObject();
JSONArray facets = new JSONArray();
boolean flag = false;
OMElement res = null;
OMElement req = omFactory.createOMElement("getFacets", nsWeb);
req.addChild(getKLEIOKey());
req.addChild(getQueryNodes(query));
QName qnFacetName = new QName("", "facetName");
QName qnFacetFreq = new QName("", "facetFreq");
QName qnFacetValues = new QName("", "facetValues");
QName qnName = new QName("", "name");
QName qnFreq = new QName("", "freq");
try {
res = client.sendReceive(req);
// Iterator<OMElement> itr = res.getChildrenWithLocalName("getFacetResponse");
Iterator<OMElement> itr = res.getChildrenWithNamespaceURI(nsWeb.getNamespaceURI());
OMElement e = null;
OMElement v = null;
while (itr.hasNext()) {
e = itr.next(); // <return>
if (!e.getFirstChildWithName(qnFacetName).getText().toString().equals("HUMAN_PHENOM")
&& !e.getFirstChildWithName(qnFacetName).getText().toString().equals("GENERAL_PHENOM")
&& !e.getFirstChildWithName(qnFacetName).getText().toString().equals("NATURAL_PHENOM")
&& !e.getFirstChildWithName(qnFacetName).getText().toString().equals("PUBLICATIONTYPE")) {
flag = false;
JSONObject facet = new JSONObject();
if (e.getFirstChildWithName(qnFacetFreq).getText().toString().equals("0")) {
}
else {
if (e.getFirstChildWithName(qnFacetName).getText().toString().equals("DIAG_PROC")) {
facet.put("text",
"<span style=\"color: #CC6600; margin: 0; padding: 0 0 2px; font-weight: bold;\">Diagnostic Procedure</span><span style=\"color: #888;\"> ("
+ e.getFirstChildWithName(qnFacetFreq).getText() + "+) </span>");
}
else if (e.getFirstChildWithName(qnFacetName).getText().toString().equals("THERAPEUTIC_PROC")) {
facet.put("text",
"<span style=\"color: #CC6600; margin: 0; padding: 0 0 2px; font-weight: bold;\">Therapeutic Procedure</span><span style=\"color: #888;\"> ("
+ e.getFirstChildWithName(qnFacetFreq).getText() + "+) </span>");
}
else {
facet.put(
"text",
"<span style=\"color: #CC6600; margin: 0; padding: 0 0 2px; font-weight: bold;\">"
+ e.getFirstChildWithName(qnFacetName).getText().substring(0, 1).toUpperCase()
+ e.getFirstChildWithName(qnFacetName).getText().substring(1).toLowerCase()
+ "</span><span style=\"color: #888;\"> (" + e.getFirstChildWithName(qnFacetFreq).getText() + "+)</span>");
}
facet.put("id", e.getFirstChildWithName(qnFacetName).getText());
facet.put("leaf", false);
facet.put("expanded", true);
facet.put("renderstep", "1");
}
if (Integer.parseInt(e.getFirstChildWithName(qnFacetFreq).getText()) > 0) {
Iterator<OMElement> itrValues = e.getFirstChildWithName(qnFacetValues).getChildElements();
JSONArray jsonValues = new JSONArray();
int more_count = 0;
JSONArray morechildren = new JSONArray();
while (itrValues.hasNext()) {
v = itrValues.next(); // <facetValue>
if (v.getFirstChildWithName(qnFreq).getText().toString().equals("0")) {
}
else {
more_count++;
JSONObject jsonValue = null;
JSONObject moreValue = null;
if (more_count == 4) {
jsonValue = new JSONObject();
jsonValue.put("parentID", e.getFirstChildWithName(qnFacetName).getText() + "_more");
jsonValue.put("id", v.getFirstChildWithName(qnName).getText() + "##" + e.getFirstChildWithName(qnFacetName));
jsonValue.put("leaf", true);
jsonValue.put("text", v.getFirstChildWithName(qnName).getText().substring(0, 1).toUpperCase()
+ v.getFirstChildWithName(qnName).getText().substring(1).toLowerCase()
+ "<span style=\"color: #888;\"> (" + v.getFirstChildWithName(qnFreq).getText() + "+)</span>");
jsonValue.put("checked",
keepState(v.getFirstChildWithName(qnName).getText(), e.getFirstChildWithName(qnFacetName).getText()));
jsonValue.put("renderstep", "2");
morechildren.add(jsonValue);
while (itrValues.hasNext()) {
v = itrValues.next();
jsonValue = new JSONObject();
jsonValue.put("parentID", e.getFirstChildWithName(qnFacetName).getText() + "_more");
jsonValue.put("id", v.getFirstChildWithName(qnName).getText() + "##" + e.getFirstChildWithName(qnFacetName));
jsonValue.put("leaf", true);
jsonValue.put("text", v.getFirstChildWithName(qnName).getText().substring(0, 1).toUpperCase()
+ v.getFirstChildWithName(qnName).getText().substring(1).toLowerCase()
+ "<span style=\"color: #888;\"> (" + v.getFirstChildWithName(qnFreq).getText() + "+)</span>");
jsonValue.put("renderstep", "2");
jsonValue.put("checked",
keepState(v.getFirstChildWithName(qnName).getText(), e.getFirstChildWithName(qnFacetName).getText()));
morechildren.add(jsonValue);
}
moreValue = new JSONObject();
moreValue.put("parentID", e.getFirstChildWithName(qnFacetName).getText());
moreValue.put("id", e.getFirstChildWithName(qnFacetName).getText() + "_more");
moreValue.put("leaf", false);
moreValue.put("text", "<b>more</b>");
moreValue.put("renderstep", "3");
JSONObject lessValue = new JSONObject();
lessValue.put("parentID", e.getFirstChildWithName(qnFacetName).getText());
lessValue.put("id", e.getFirstChildWithName(qnFacetName).getText() + "_less");
lessValue.put("leaf", true);
lessValue.put("text", "<b>less</b>");
lessValue.put("renderstep", "3");
morechildren.add(lessValue);
moreValue.put("children", morechildren);
jsonValues.add(moreValue);
}
else {
jsonValue = new JSONObject();
jsonValue.put("parentID", e.getFirstChildWithName(qnFacetName).getText());
jsonValue.put("id", v.getFirstChildWithName(qnName).getText() + "##" + e.getFirstChildWithName(qnFacetName));
jsonValue.put("leaf", true);
jsonValue.put("text", v.getFirstChildWithName(qnName).getText().substring(0, 1).toUpperCase()
+ v.getFirstChildWithName(qnName).getText().substring(1).toLowerCase()
+ "<span style=\"color: #888;\"> (" + v.getFirstChildWithName(qnFreq).getText() + "+)</span>");
jsonValue.put("checked",
keepState(v.getFirstChildWithName(qnName).getText(), e.getFirstChildWithName(qnFacetName).getText()));
jsonValues.add(jsonValue);
jsonValue.put("renderstep", "2");
}
}
}
if (!v.getFirstChildWithName(qnFreq).getText().toString().equals("0")) {
facet.put("children", jsonValues);
if (flag == true) {
facet.put("expanded", true);
}
}
}
if (!e.getFirstChildWithName(qnFacetFreq).getText().toString().equals("0")) {
facets.add(facet);
}
}
r.put("result", facets);
}
}
catch (AxisFault e) {
e.printStackTrace();
}
return r;
}
public boolean keepState(String text, String facet) {
boolean flag = false;
Iterator<?> it = hash.entrySet().iterator();
while (it.hasNext()) {
Map.Entry<?, ?> pairs = (Map.Entry<?, ?>) it.next();
if (!facet.equals("CONTENT") || !facet.equals("content")) {
String[] pairs_array = pairs.getValue().toString().split(";;");
if (pairs_array.length > 1) {
for (int i = 0; i < pairs_array.length; i++) {
if (text.equals(pairs_array[i]) && facet.equals(pairs.getKey().toString())) {
flag = true;
}
}
}
else {
if (text.equals(pairs.getValue().toString()) && facet.equals(pairs.getKey().toString())) {
flag = true;
}
}
}
}
return flag;
}
private OMElement getQueryNodes(String query) {
System.out.print("KLEIO query" + query);
String[] splitted = query.split(" AND | OR ");
if (splitted.length > 1) {
for (int i = 0; i < splitted.length; i++) {
String[] row = splitted[i].split(":");
if (row[0] != null && facets.indexOf(row[0]) < 0) {
if (hash.containsKey("content")) {
String exists = hash.get("content") + ";;" + row[0].trim();
hash.put("content", exists);
}
else {
hash.put("content", row[0].trim());
}
}
else {
if (hash.containsKey(row[0].trim())) {
String exists = hash.get(row[0].trim()) + ";;" + row[1].trim();
hash.put(row[0].trim(), exists);
}
else {
hash.put(row[0].trim(), row[1].trim());
}
}
}
}
else {
splitted = query.split(":");
if (splitted[0] != null && facets.indexOf(splitted[0]) < 0)
hash.put("content", splitted[0].trim());
else
hash.put(splitted[0].trim(), splitted[1].trim());
}
Iterator<?> it = hash.entrySet().iterator();
OMElement e = omFactory.createOMElement("query", null);
OMElement eall = omFactory.createOMElement("node", null);
if (hash.size() > 1) {
eall.addAttribute("type", "web:andNode", nsXsi);
}
while (it.hasNext()) {
Map.Entry<?, ?> pairs = (Map.Entry<?, ?>) it.next();
OMElement etemp = omFactory.createOMElement("node", null);
if (pairs.getKey().equals("content") || pairs.getKey().equals("CONTENT")) {
String[] pairs_array = pairs.getValue().toString().split(";;");
if (pairs_array.length > 1) {
etemp.addAttribute("type", "web:andNode", nsXsi);
for (int i = 0; i < pairs_array.length; i++) {
OMElement eNode = omFactory.createOMElement("node", null);
eNode.addAttribute("type", "web:stringNode", nsXsi);
OMElement eValue = omFactory.createOMElement("value", null);
eValue.setText(pairs_array[i]);
eNode.addChild(eValue);
etemp.addChild(eNode);
}
}
else {
etemp.addAttribute("type", "web:stringNode", nsXsi);
OMElement eValue = omFactory.createOMElement("value", null);
eValue.setText(pairs.getValue().toString());
etemp.addChild(eValue);
}
}
else {
String[] pairs_array = pairs.getValue().toString().split(";;");
if (pairs_array.length > 1) {
etemp.addAttribute("type", "web:orNode", nsXsi);
for (int i = 0; i < pairs_array.length; i++) {
OMElement eNode = omFactory.createOMElement("node", null);
eNode.addAttribute("type", "web:facetNode", nsXsi);
OMElement eValue1 = omFactory.createOMElement("facet", null);
OMElement eValue2 = omFactory.createOMElement("value", null);
eValue1.setText(pairs.getKey().toString());
eValue2.setText(pairs_array[i]);
eNode.addChild(eValue1);
eNode.addChild(eValue2);
etemp.addChild(eNode);
}
}
else {
etemp.addAttribute("type", "web:facetNode", nsXsi);
OMElement eValue1 = omFactory.createOMElement("facet", null);
OMElement eValue2 = omFactory.createOMElement("value", null);
eValue1.setText(pairs.getKey().toString());
eValue2.setText(pairs.getValue().toString());
etemp.addChild(eValue1);
etemp.addChild(eValue2);
}
}
if (hash.size() > 1) {
eall.addChild(etemp);
}
else {
eall = etemp;
}
}
e.addChild(eall);
// System.out.print(e.toString());
return e;
}
public JSONObject getDocument(String pubmedID) {
JSONObject r = new JSONObject();
OMElement req = omFactory.createOMElement("getDocument", nsWeb);
OMElement res = null;
QName qnAuthors = new QName("", "authors");
QName qnAbstract = new QName("", "abstract");
QName qnTitle = new QName("", "title");
QName qnJournal = new QName("", "journalCite");
QName qnPMID = new QName("", "pmid");
QName qnMesh = new QName("", "meshHeadings");
req.addChild(getKLEIOKey());
OMElement documentID = omFactory.createOMElement("documentId", null);
documentID.setText(pubmedID);
req.addChild(documentID);
try {
res = client.sendReceive(req);
OMElement article = res.getFirstElement();
// authors
JSONArray authors = new JSONArray();
Iterator<OMElement> itrAuthors = article.getFirstChildWithName(qnAuthors).getChildElements();
OMElement a = null;
while (itrAuthors.hasNext()) {
a = itrAuthors.next();
authors.add(a.getText());
}
r.put("authors", authors);
r.put("abstract", article.getFirstChildWithName(qnAbstract).getText());
String title = article.getFirstChildWithName(qnTitle).getText();
// System.out.print("title"+title);
StringBuffer z = new StringBuffer();
for (int i = 0; i < title.length(); i++) {
char c = title.charAt(i);
if (c > 127 || c == '"' || c == '<' || c == '>') {
z.append("&#" + (int) c + ";");
}
else {
z.append(c);
}
}
title = z.toString();
r.put("title", title);
r.put("journal", article.getFirstChildWithName(qnJournal).getText());
r.put("pmid", article.getFirstChildWithName(qnPMID).getText());
// mesh
JSONArray mesh = new JSONArray();
Iterator<OMElement> itrMesh = article.getFirstChildWithName(qnMesh).getChildElements();
OMElement m = null;
while (itrMesh.hasNext()) {
m = itrMesh.next();
mesh.add(m.getText());
}
r.put("mesh", mesh);
}
catch (AxisFault e) {
e.printStackTrace();
}
return r;
}
public JSONArray getFacetNames() {
JSONArray r = new JSONArray();
OMElement res = null;
OMElement req = omFactory.createOMElement("getFacetNames", nsWeb);
req.addChild(getKLEIOKey());
try {
res = client.sendReceive(req);
Iterator<OMElement> itr = res.getChildrenWithLocalName("getFacetNamesResponse");
while (itr.hasNext()) {
OMElement e = itr.next();
r.add(e.getText());
}
}
catch (AxisFault e) {
e.printStackTrace();
}
return r;
}
public JSONObject getNamedEntities(String pubmedID) {
JSONObject r = new JSONObject();
JSONArray results = new JSONArray();
OMElement req = omFactory.createOMElement("getNamedEntities", nsWeb);
OMElement res = null;
// QName qnannotation = new QName("","annotation");
QName qnexternalReferences = new QName("", "externalReferences");
QName qnid = new QName("", "id");
QName qnnamespace = new QName("", "namespace");
QName qnbegin = new QName("", "begin");
QName qnend = new QName("", "end");
QName qnexpandedForm = new QName("", "expandedForm");
QName qnlocation = new QName("", "location");
QName qnnamedEntity = new QName("", "namedEntity");
QName qnnormalisedForm = new QName("", "normalisedForm");
QName qnshortForm = new QName("", "shortForm");
QName qnsurfaceForm = new QName("", "surfaceForm");
req.addChild(getKLEIOKey());
OMElement documentID = omFactory.createOMElement("documentId", null);
documentID.setText(pubmedID);
req.addChild(documentID);
try {
res = client.sendReceive(req);
Iterator<OMElement> itr = res.getChildrenWithLocalName("getNamedEntitiesResponse");
OMElement entities = null;
while (itr.hasNext()) {
entities = itr.next();
JSONObject entity = new JSONObject();
entity.put("begin", entities.getFirstChildWithName(qnbegin).getText());
entity.put("end", entities.getFirstChildWithName(qnend).getText());
entity.put("expandedForm", entities.getFirstChildWithName(qnexpandedForm).getText());
entity.put("location", entities.getFirstChildWithName(qnlocation).getText());
if (entities.getFirstChildWithName(qnnamedEntity) != null) {
entity.put("namedEntity", entities.getFirstChildWithName(qnnamedEntity).getText());
}
entity.put("normalisedForm", entities.getFirstChildWithName(qnnormalisedForm).getText());
entity.put("shortForm", entities.getFirstChildWithName(qnshortForm).getText());
entity.put("surfaceForm", entities.getFirstChildWithName(qnsurfaceForm).getText());
Iterator<OMElement> itrreferences = entities.getFirstChildWithName(qnexternalReferences).getChildElements();
JSONObject extreferences = new JSONObject();
OMElement references = null;
while (itrreferences.hasNext()) {
references = itrreferences.next();
JSONObject reference = new JSONObject();
reference.put("namespace", references.getFirstChildWithName(qnnamespace).getText());
reference.put("id", references.getFirstChildWithName(qnid).getText());
extreferences.put("reference", reference);
}
entity.put("externalReferences", extreferences);
results.add(entity);
}
r.put("result", results);
}
catch (AxisFault e) {
e.printStackTrace();
}
return r;
}
public void clean() {
try {
client.cleanup();
client.cleanupTransport();
}
catch (AxisFault e) {
e.printStackTrace();
}
}
}