package edu.columbia.dbmi.ohdsims.util;
import java.io.IOException;
import java.io.UnsupportedEncodingException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.http.HttpResponse;
import org.apache.http.client.ClientProtocolException;
import org.apache.http.client.HttpClient;
import org.apache.http.client.methods.HttpGet;
//import org.apache.commons.httpclient.HttpClient;
//import org.apache.commons.httpclient.methods.PostMethod;
//import org.apache.commons.httpclient.methods.RequestEntity;
//import org.apache.commons.httpclient.methods.StringRequestEntity;
import org.apache.http.client.methods.HttpPost;
import org.apache.http.entity.StringEntity;
import org.apache.http.impl.client.DefaultHttpClient;
import org.apache.http.util.EntityUtils;
import com.google.gson.Gson;
import com.google.gson.JsonArray;
import com.google.gson.JsonObject;
import com.google.gson.JsonParser;
import com.google.gson.reflect.TypeToken;
import edu.columbia.dbmi.ohdsims.pojo.Concept;
import edu.columbia.dbmi.ohdsims.pojo.ConceptRecordCount;
import edu.columbia.dbmi.ohdsims.pojo.ConceptSet;
import edu.columbia.dbmi.ohdsims.pojo.ExtendConcept;
import edu.columbia.dbmi.ohdsims.pojo.GlobalSetting;
import edu.columbia.dbmi.ohdsims.pojo.Cdmentity;
import net.sf.json.JSONArray;
import net.sf.json.JSONNull;
import net.sf.json.JSONObject;
/*
* 使用的类：
* HttpClient
* HttpPost
* FileBody
* FormBodyPart
* MultipartEntity
* HttpResponse
* EntityUtils
*
*/
public class ATLASUtil {
// 接口地址
private final static String recordcounturl =GlobalSetting.ohdsi_api_base_url+ "cdmresults/1PCT/conceptRecordCount";
private final static String vocubularyurl =GlobalSetting.ohdsi_api_base_url+"vocabulary/1PCT/search";
private final static String conceptseturl = GlobalSetting.ohdsi_api_base_url+"conceptset/";
private final String pattern = "yyyy-MM-dd HH:mm:ss:SSS";
private HttpClient httpClient = null;
private HttpPost method = null;
private static long startTime = 0L;
private static long endTime = 0L;
private int status = 0;
public static void main(String[] args) throws IOException {
// Concept concept=getMaxCountConcept("type 2 diabetes","Condition");
// System.out.println("----->"+concept.getCONCEPT_NAME());
// System.out.println("conceptid="+conceptidindex.get(rindex));
searchConcept("insulin", "Drug");
//searchConceptByNameAndDomain("","");
}
// public static Concept getMaxCountConcept(String entity,String domainid)
// throws UnsupportedEncodingException, IOException, ClientProtocolException
// {
// Concept concept=new Concept();
// //<Integer,Integer> conceptidindex=new LinkedHashMap<Integer,Integer>();
// HashMap<Integer,ConceptRecordCount> hm=new
// HashMap<Integer,ConceptRecordCount>();
//
// JSONObject queryjson=new JSONObject();
// queryjson.accumulate("QUERY", entity);
// queryjson.accumulate("DOMAIN_ID", "['"+domainid+"']");
// queryjson.accumulate("VOCABULARY_ID", "['SNOMED']");
// System.out.println("queryjson:"+queryjson);
// String vocabularyresult=getConcept(queryjson);
// JSONArray array = JSONArray.fromObject(vocabularyresult);
// List<Concept> list = JSONArray.toList(array, Concept.class);// 过时方法
// //System.out.println(list.get(0).getCONCEPT_NAME());
// List<Integer> conceptidlist=new ArrayList<Integer>();
// for(int i=0;i<list.size();i++){
// conceptidlist.add(list.get(i).getCONCEPT_ID());
// }
// JSONArray conceptarr = JSONArray.fromObject(conceptidlist);
// if(conceptarr.size()>0){
// String co=getRecordCount(conceptarr);
// JSONArray carray = JSONArray.fromObject(co);
// //JSONNull jnull = new JSONNull();
// //List<ConceptRecordCount> rclist=new ArrayList<ConceptRecordCount>();
// for(int x=0;x<carray.size();x++){
// //if(){
//
// JSONObject js=(JSONObject)carray.get(x);
//
// JSONArray v=JSONArray.fromObject(js.get("value"));
// ConceptRecordCount crd=new ConceptRecordCount();
// crd.setRC((int) v.get(0));
// crd.setDRC((int) v.get(1));
// hm.put((Integer) js.get("key"),crd);
//
// }
//
// int rindex=0;
// int drcmax=0;
// int rcmax=0;
// for (Entry<Integer, ConceptRecordCount> entry : hm.entrySet()) {
// if(entry.getValue().getDRC()>=drcmax){
// drcmax=entry.getValue().getDRC();
// rcmax=entry.getValue().getRC();
// rindex=entry.getKey();
// }
//
// }
// for(int y=0;y<list.size();y++){
// if(list.get(y).getCONCEPT_ID()==rindex){
// concept=list.get(y);
//// concept.setRC(rcmax);
//// concept.setDRC(drcmax);
//
// }
// }
// return concept;
// }else{
// return concept;
// }
// }
public static String getConcept(JSONObject jjj)
throws UnsupportedEncodingException, IOException, ClientProtocolException {
HttpPost httppost = new HttpPost(vocubularyurl);
// httppost.setHeader("X-GWT-Permutation",
// "3DE824138FE65400740EC1816A73CACC");
httppost.setHeader("Content-Type", "application/json");
StringEntity se = new StringEntity(jjj.toString());
httppost.setEntity(se);
startTime = System.currentTimeMillis();
HttpResponse httpresponse = new DefaultHttpClient().execute(httppost);
endTime = System.currentTimeMillis();
System.out.println("statusCode:" + httpresponse.getStatusLine().getStatusCode());
System.out.println("Call API time (unit:millisecond)：" + (endTime - startTime));
if (httpresponse.getStatusLine().getStatusCode() == 200) {
// System.out.println("succeed!");
String strResult = EntityUtils.toString(httpresponse.getEntity());
return strResult;
// httppost.
} else {
return null;
}
}
public static String getRecordCount(JsonArray array)
throws UnsupportedEncodingException, IOException, ClientProtocolException {
HttpPost httppost = new HttpPost(recordcounturl);
httppost.setHeader("Content-Type", "application/json");
StringEntity se = new StringEntity(array.toString());
httppost.setEntity(se);
startTime = System.currentTimeMillis();
HttpResponse httpresponse = new DefaultHttpClient().execute(httppost);
endTime = System.currentTimeMillis();
System.out.println("statusCode:" + httpresponse.getStatusLine().getStatusCode());
System.out.println("Call API time (unit:millisecond)：" + (endTime - startTime));
if (httpresponse.getStatusLine().getStatusCode() == 200) {
String strResult = EntityUtils.toString(httpresponse.getEntity());
return strResult;
} else {
return null;
}
}
public static List<ConceptSet> getallConceptSet() {
String strResult = HttpUtil.doGet(conceptseturl);
JSONArray array = JSONArray.fromObject(strResult);
// System.out.println("-->"+array);
List<ConceptSet> list = JSONArray.toList(array, ConceptSet.class);// 过时方法
return list;
}
public static LinkedHashMap<ConceptSet, Integer> matchConceptSetByEntity(String entityname) {
HashMap<ConceptSet, Integer> candidatecs = new HashMap<ConceptSet, Integer>();
// arrange by length similarity
int distance = 0;
List<ConceptSet> cslist = getallConceptSet();
for (int k = 0; k < cslist.size(); k++) {
if (cslist.get(k).getName().toLowerCase().contains(entityname.toLowerCase().trim())) {
System.out.println("match=" + cslist.get(k).getName());
distance = cslist.get(k).getName().length() - entityname.trim().length();
candidatecs.put(cslist.get(k), distance);
}
}
List<Map.Entry<ConceptSet, Integer>> sort = new ArrayList<>();
sort.addAll(candidatecs.entrySet());
ValueComparator vc = new ValueComparator();
Collections.sort(sort, vc);
LinkedHashMap<ConceptSet, Integer> lm = new LinkedHashMap<ConceptSet, Integer>();
for (int i = sort.size() - 1; i >= 0; i--) {
lm.put(sort.get(i).getKey(), sort.get(i).getValue());
}
return lm;
}
public static Map<Concept, ConceptRecordCount> searchConcept(String entity, String domainid)
throws UnsupportedEncodingException, IOException, ClientProtocolException {
List<Concept> conceptlist = new ArrayList<Concept>();
HashMap<Concept, ConceptRecordCount> hm = new HashMap<Concept, ConceptRecordCount>();
List<Concept> list = searchConceptByNameAndDomain(entity, domainid);
// extract concept id
List<Integer> conceptidlist = new ArrayList<Integer>();
for (int i = 0; i < list.size(); i++) {
System.out.println(list.get(i).getCONCEPT_ID() + "--" + list.get(i).getCONCEPT_NAME());
conceptidlist.add(list.get(i).getCONCEPT_ID());
}
JsonArray conceptarr = (JsonArray) new Gson().toJsonTree(conceptidlist, new TypeToken<List<Integer>>() {
}.getType());
// get record count by concept id array
if (conceptarr.size() > 0) {
String co = getRecordCount(conceptarr);
JSONArray carray = JSONArray.fromObject(co);
System.out.println("carray-" + carray.size());
for (int c = 0; c < list.size(); c++) {
if (carray.size() == 0) {
ConceptRecordCount crd = new ConceptRecordCount(-1,-1);
hm.put(list.get(c), crd);
} else {
for (int x = 0; x < carray.size(); x++) {
JSONObject js = (JSONObject) carray.get(x);
System.out.println("js="+js);
Set<String> keyset=js.keySet();
String conceptID="0";
for(String ss:keyset){
System.out.println("ss=>"+ss);
conceptID=ss;
}
JSONArray v = JSONArray.fromObject(js.get(conceptID.toString()));
System.out.println("v="+v);
System.out.println("Size="+v.size());
//v.size()
if(v.get(0).equals(JSONNull.getInstance())){
ConceptRecordCount crd = new ConceptRecordCount(-1,-1);
hm.put(list.get(c), crd);
}else{
int rc=(int) v.get(0);
int drc=(int) v.get(1);
ConceptRecordCount crd = new ConceptRecordCount(rc,drc);
// System.out.println("=====>"+rc+"\t"+drc);
// System.out.println(c);
// System.out.println("=====>"+list.get(c).getCONCEPT_ID()+"\t"+conceptID.toString());
if (list.get(c).getCONCEPT_ID().equals(js.get(conceptID.toString()))) {
System.out.println("=ID==>"+list.get(c).getCONCEPT_ID()+"\t"+conceptID.toString());
hm.put(list.get(c), crd);
}
}
}
}
}
System.out.println("yes!!");
return hm;
} else {
System.out.println("no!!");
return null;
}
}
public static List<Concept> searchConceptByNameAndDomain(String entity, String domainid)
throws UnsupportedEncodingException, IOException, ClientProtocolException {
JSONObject queryjson = new JSONObject();
queryjson.accumulate("QUERY", entity);
queryjson.accumulate("DOMAIN_ID", "['" + domainid + "']");
queryjson.accumulate("STANDARD_CONCEPT","S");//only standard concept
// queryjson.accumulate("VOCABULARY_ID", "['SNOMED']");
System.out.println("queryjson:" + queryjson);
String vocabularyresult = getConcept(queryjson);
System.out.println("vocabularyresult length=" + vocabularyresult.length());
Gson gson = new Gson();
JsonArray ja = new JsonParser().parse(vocabularyresult).getAsJsonArray();
if (ja.size() == 0) {
System.out.println("size=" + ja.size());
return null;
}
List<Concept> list = gson.fromJson(ja, new TypeToken<List<Concept>>() {
}.getType());
return list;
}
public static List<Concept> searchConceptByName(String entity)
throws UnsupportedEncodingException, IOException, ClientProtocolException {
JSONObject queryjson = new JSONObject();
queryjson.accumulate("QUERY", entity);
System.out.println("queryjson:" + queryjson);
String vocabularyresult = getConcept(queryjson);
System.out.println("vocabularyresult length=" + vocabularyresult.length());
Gson gson = new Gson();
JsonArray ja = new JsonParser().parse(vocabularyresult).getAsJsonArray();
if (ja.size() == 0) {
System.out.println("size=" + ja.size());
return null;
}
List<Concept> list = gson.fromJson(ja, new TypeToken<List<Concept>>() {
}.getType());
return list;
}
public static JSONObject querybyconceptid(int conceptid){
JSONObject jot=new JSONObject();
String re2=HttpUtil.doGet("http://api.ohdsi.org/WebAPI/conceptset/"+conceptid);
JSONObject jore2=JSONObject.fromObject(re2);
jot.accumulateAll(jore2);
String re3=HttpUtil.doGet("http://api.ohdsi.org/WebAPI/conceptset/"+conceptid+"/expression");
JSONObject expression=JSONObject.fromObject(re3);
jot.accumulate("expression",expression);
return jot;
}
public static JSONObject querybyconceptSetid(int conceptid){
JSONObject jot=new JSONObject();
String re2=HttpUtil.doGet("http://api.ohdsi.org/WebAPI/conceptset/"+conceptid);
JSONObject jore2=JSONObject.fromObject(re2);
jot.accumulateAll(jore2);
String re3=HttpUtil.doGet("http://api.ohdsi.org/WebAPI/conceptset/"+conceptid+"/expression");
JSONObject expression=JSONObject.fromObject(re3);
jot.accumulate("expression",expression);
return jot;
}
}
