org.molgenis.wikipathways.client.WikiPathwaysRESTBindingStub Maven / Gradle / Ivy
// WikiPathways Java library,
// Copyright 2014 WikiPathways
//
// 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 org.molgenis.wikipathways.client;
import org.apache.commons.codec.binary.Base64;
import org.apache.commons.io.IOUtils;
import org.apache.http.Consts;
import org.apache.http.HttpEntity;
import org.apache.http.HttpResponse;
import org.apache.http.NameValuePair;
import org.apache.http.client.HttpClient;
import org.apache.http.client.entity.UrlEncodedFormEntity;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.client.methods.HttpPost;
import org.apache.http.message.BasicNameValuePair;
import org.jdom.Document;
import org.jdom.Element;
import org.jdom.input.SAXBuilder;
import org.molgenis.wikipathways.utils.Utils;
import java.io.IOException;
import java.io.InputStream;
import java.net.URLEncoder;
import java.rmi.RemoteException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
/**
* connects to the new WikiPathways REST webservice
*
* @author msk
*/
@SuppressWarnings("unchecked")
public class WikiPathwaysRESTBindingStub implements WikiPathwaysPortType
{
private HttpClient client;
private String baseUrl;
public WikiPathwaysRESTBindingStub(HttpClient client, String baseUrl)
{
this.client = client;
this.baseUrl = baseUrl;
}
@Override
public WSSearchResult[] findInteractions(String query) throws RemoteException
{
try
{
query = query.replace(" ", "+");
String url = baseUrl + "/findInteractions?query=" + query;
Document jdomDocument = Utils.connect(url, client);
Element root = jdomDocument.getRootElement();
List list = root.getChildren("result", WSNamespaces.NS1);
WSSearchResult[] res = new WSSearchResult[list.size()];
for (int i = 0; i < list.size(); i++)
{
res[i] = Utils.parseWSSearchResult(list.get(i));
}
return res;
}
catch (Exception e)
{
throw new RemoteException(e.getMessage(), e.getCause());
}
}
@Override
public WSSearchResult[] findPathwaysByLiterature(String query) throws RemoteException
{
try
{
query = query.replace(" ", "+");
String url = baseUrl + "/findPathwaysByLiterature?query=" + query;
Document jdomDocument = Utils.connect(url, client);
Element root = jdomDocument.getRootElement();
List list = root.getChildren("result", WSNamespaces.NS1);
WSSearchResult[] res = new WSSearchResult[list.size()];
for (int i = 0; i < list.size(); i++)
{
res[i] = Utils.parseWSSearchResult(list.get(i));
}
return res;
}
catch (Exception e)
{
throw new RemoteException(e.getMessage(), e.getCause());
}
}
@Override
public WSSearchResult[] findPathwaysByText(String query, String species) throws RemoteException
{
try
{
query = query.replace(" ", "+");
String url = baseUrl + "/findPathwaysByText?query=" + query;
if (species != null)
{
species = species.replace(" ", "+");
url = url + "&species=" + species;
}
Document jdomDocument = Utils.connect(url, client);
Element root = jdomDocument.getRootElement();
List list = root.getChildren("result", WSNamespaces.NS1);
WSSearchResult[] res = new WSSearchResult[list.size()];
for (int i = 0; i < list.size(); i++)
{
res[i] = Utils.parseWSSearchResult(list.get(i));
}
return res;
}
catch (Exception e)
{
throw new RemoteException(e.getMessage(), e.getCause());
}
}
@Override
public WSSearchResult[] findPathwaysByXref(String[] ids, String[] codes) throws RemoteException
{
try
{
String url = baseUrl + "/findPathwaysByXref";
int count = 0;
for (String i : ids)
{
if (count == 0)
{
url = url + "?ids=" + i;
count++;
}
else
{
url = url + "&ids=" + i;
}
}
for (String c : codes)
{
url = url + "&codes=" + c;
}
Document jdomDocument = Utils.connect(url, client);
Element root = jdomDocument.getRootElement();
List list = root.getChildren("result", WSNamespaces.NS1);
WSSearchResult[] res = new WSSearchResult[list.size()];
for (int i = 0; i < list.size(); i++)
{
res[i] = Utils.parseWSSearchResult(list.get(i));
}
return res;
}
catch (Exception e)
{
throw new RemoteException(e.getMessage(), e.getCause());
}
}
@Override
public byte[] getColoredPathway(String pwId, String revision, String[] graphId, String[] color, String fileType)
throws RemoteException
{
try
{
String url = baseUrl + "/getColoredPathway?pwId=" + pwId + "&revision=" + revision;
for (String g : graphId)
{
url = url + "&graphId=" + g;
}
for (String c : color)
{
url = url + "&color=" + c;
}
url = url + "&fileType=" + fileType;
Document jdomDocument = Utils.connect(url, client);
Element data = jdomDocument.getRootElement().getChild("data", WSNamespaces.NS1);
return Base64.decodeBase64(data.getValue());
}
catch (Exception e)
{
throw new RemoteException(e.getMessage(), e.getCause());
}
}
@Override
public WSCurationTagHistory[] getCurationTagHistory(String pwId, String timestamp) throws RemoteException
{
try
{
String url = baseUrl + "/getCurationTagHistory?pwId=" + pwId;
if (timestamp != null)
{
url = url + "×tamp=" + timestamp;
}
Document jdomDocument = Utils.connect(url, client);
Element root = jdomDocument.getRootElement();
List list = root.getChildren("history", WSNamespaces.NS1);
WSCurationTagHistory[] hist = new WSCurationTagHistory[list.size()];
for (int i = 0; i < list.size(); i++)
{
hist[i] = Utils.parseCurationTagHistory(list.get(i));
}
return hist;
}
catch (Exception e)
{
throw new RemoteException(e.getMessage(), e.getCause());
}
}
@Override
public WSCurationTag[] getCurationTags(String pwId) throws RemoteException
{
try
{
String url = baseUrl + "/getCurationTags?pwId=" + pwId;
Document jdomDocument = Utils.connect(url, client);
Element root = jdomDocument.getRootElement();
List list = root.getChildren("tags", WSNamespaces.NS1);
WSCurationTag[] tags = new WSCurationTag[list.size()];
for (int i = 0; i < list.size(); i++)
{
tags[i] = Utils.parseCurationTag(list.get(i));
}
return tags;
}
catch (Exception e)
{
throw new RemoteException(e.getMessage(), e.getCause());
}
}
@Override
public WSCurationTag[] getCurationTagsByName(String tagName) throws RemoteException
{
try
{
String url = baseUrl + "/getCurationTagsByName?tagName=" + tagName;
Document jdomDocument = Utils.connect(url, client);
Element root = jdomDocument.getRootElement();
List list = root.getChildren("tags", WSNamespaces.NS1);
WSCurationTag[] tags = new WSCurationTag[list.size()];
for (int i = 0; i < list.size(); i++)
{
tags[i] = Utils.parseCurationTag(list.get(i));
}
return tags;
}
catch (Exception e)
{
throw new RemoteException(e.getMessage(), e.getCause());
}
}
@Override
public WSOntologyTerm[] getOntologyTermsByPathway(String pwId) throws RemoteException
{
try
{
String url = baseUrl + "/getOntologyTermsByPathway?pwId=" + pwId;
Document jdomDocument = Utils.connect(url, client);
Element root = jdomDocument.getRootElement();
List list = root.getChildren("terms", WSNamespaces.NS1);
WSOntologyTerm[] terms = new WSOntologyTerm[list.size()];
for (int i = 0; i < list.size(); i++)
{
terms[i] = Utils.parseOntologyTerm(list.get(i));
}
return terms;
}
catch (Exception e)
{
throw new RemoteException(e.getMessage(), e.getCause());
}
}
@Override
public WSPathway getPathway(String pwId, int revision) throws RemoteException
{
try
{
String url = baseUrl + "/getPathway?pwId=" + pwId;
if (revision != 0)
{
url = url + "&revision=" + revision;
}
Document jdomDocument = Utils.connect(url, client);
Element root = jdomDocument.getRootElement();
Element p = root.getChild("pathway", WSNamespaces.NS1);
return Utils.parsePathway(p);
}
catch (Exception e)
{
throw new RemoteException(e.getMessage(), e.getCause());
}
}
@Override
public byte[] getPathwayAs(String fileType, String pwId, int revision) throws RemoteException
{
InputStream instream = null;
try
{
String url = baseUrl;
if (url.contains("webservice/webservice.php"))
{
url = url.replace("webservice/webservice.php", "wpi.php");
}
else if (url.contains("webservicetest"))
{
url = url.replace("webservicetest/webservice.php", "wpi.php");
}
else if (url.contains("webservice.wikipathways.org"))
{
url = "http://www.wikipathways.org/wpi/wpi.php";
}
url = url + "?action=downloadFile&type=" + fileType + "&pwTitle=Pathway:" + pwId + "&oldid=" + revision;
HttpGet httpget = new HttpGet(url);
HttpResponse response = client.execute(httpget);
HttpEntity entity = response.getEntity();
instream = entity.getContent();
return IOUtils.toByteArray(instream);
}
catch (Exception e)
{
throw new RemoteException(e.getMessage(), e.getCause());
}
finally
{
try
{
if (instream != null)
{
instream.close();
}
}
catch (IOException e)
{
throw new RemoteException(e.getMessage(), e.getCause());
}
}
}
@Override
public WSPathwayInfo[] getPathwaysByOntologyTerm(String term) throws RemoteException
{
try
{
term = term.replace(" ", "+");
String url = baseUrl + "/getPathwaysByOntologyTerm?term=" + term;
Document jdomDocument = Utils.connect(url, client);
Element root = jdomDocument.getRootElement();
List list = root.getChildren("pathways", WSNamespaces.NS1);
WSPathwayInfo[] info = new WSPathwayInfo[list.size()];
for (int i = 0; i < list.size(); i++)
{
info[i] = Utils.parseWSPathwayInfo(list.get(i));
}
return info;
}
catch (Exception e)
{
throw new RemoteException(e.getMessage(), e.getCause());
}
}
@Override
public WSPathwayInfo[] getPathwaysByParentOntologyTerm(String term) throws RemoteException
{
try
{
String url = baseUrl + "/getPathwaysByParentOntologyTerm?term=" + term;
Document jdomDocument = Utils.connect(url, client);
Element root = jdomDocument.getRootElement();
List list = root.getChildren("pathways", WSNamespaces.NS1);
WSPathwayInfo[] info = new WSPathwayInfo[list.size()];
for (int i = 0; i < list.size(); i++)
{
info[i] = Utils.parseWSPathwayInfo(list.get(i));
}
return info;
}
catch (Exception e)
{
throw new RemoteException(e.getMessage(), e.getCause());
}
}
@Override
public WSPathwayHistory getPathwayHistory(String pwId, String timestamp) throws RemoteException
{
try
{
String url = baseUrl + "/getPathwayHistory?pwId=" + pwId + "×tamp=" + timestamp;
Document jdomDocument = Utils.connect(url, client);
Element root = jdomDocument.getRootElement();
Element hist = root.getChild("history", WSNamespaces.NS1);
return Utils.parsePathwayHistory(hist);
}
catch (Exception e)
{
throw new RemoteException(e.getMessage(), e.getCause());
}
}
@Override
public WSPathwayInfo getPathwayInfo(String pwId) throws RemoteException
{
try
{
String url = baseUrl + "/getPathwayInfo?pwId=" + pwId;
Document jdomDocument = Utils.connect(url, client);
Element root = jdomDocument.getRootElement();
Element p = root.getChild("pathwayInfo", WSNamespaces.NS1);
return Utils.parseWSPathwayInfo(p);
}
catch (Exception e)
{
throw new RemoteException(e.getMessage(), e.getCause());
}
}
@Override
public WSPathwayInfo[] getRecentChanges(String timestamp) throws RemoteException
{
try
{
String url = baseUrl + "/getRecentChanges?timestamp=" + timestamp;
Document jdomDocument = Utils.connect(url, client);
Element root = jdomDocument.getRootElement();
List list = root.getChildren("pathways", WSNamespaces.NS1);
WSPathwayInfo[] info = new WSPathwayInfo[list.size()];
for (int i = 0; i < list.size(); i++)
{
info[i] = Utils.parseWSPathwayInfo(list.get(i));
}
return info;
}
catch (Exception e)
{
throw new RemoteException(e.getMessage(), e.getCause());
}
}
@Override
public String getUserByOrcid(String orcid) throws RemoteException
{
try
{
String url = baseUrl + "/getUserByOrcid?orcid=" + orcid;
Document jdomDocument = Utils.connect(url, client);
Element root = jdomDocument.getRootElement();
return root.getChildText("Result", WSNamespaces.NS1).substring(5);
}
catch (Exception e)
{
throw new RemoteException(e.getMessage(), e.getCause());
}
}
@Override
public String[] getXrefList(String pwId, String code) throws RemoteException
{
try
{
String url = baseUrl + "/getXrefList?pwId=" + pwId + "&code=" + code;
Document jdomDocument = Utils.connect(url, client);
Element root = jdomDocument.getRootElement();
List list = root.getChildren();
String[] xrefs = new String[list.size()];
for (int i = 0; i < list.size(); i++)
{
xrefs[i] = list.get(i).getValue();
}
return xrefs;
}
catch (Exception e)
{
throw new RemoteException(e.getMessage(), e.getCause());
}
}
@Override
public String[] listOrganisms() throws RemoteException
{
try
{
String url = baseUrl + "/listOrganisms";
Document jdomDocument = Utils.connect(url, client);
Element root = jdomDocument.getRootElement();
List list = root.getChildren();
String[] organisms = new String[list.size()];
for (int i = 0; i < list.size(); i++)
{
organisms[i] = list.get(i).getValue();
}
return organisms;
}
catch (Exception e)
{
throw new RemoteException(e.getMessage(), e.getCause());
}
}
@Override
public WSPathwayInfo[] listPathways(String organism) throws RemoteException
{
try
{
String url = "";
if (organism == null)
{
url = baseUrl + "/listPathways";
}
else
{
organism = organism.replace(" ", "+");
url = baseUrl + "/listPathways?organism=" + organism;
}
Document jdomDocument = Utils.connect(url, client);
Element root = jdomDocument.getRootElement();
List list = root.getChildren("pathways", WSNamespaces.NS1);
WSPathwayInfo[] info = new WSPathwayInfo[list.size()];
for (int i = 0; i < list.size(); i++)
{
info[i] = Utils.parseWSPathwayInfo(list.get(i));
}
return info;
}
catch (Exception e)
{
throw new RemoteException(e.getMessage(), e.getCause());
}
}
@Override
public String login(String name, String pass) throws RemoteException
{
try
{
String url = baseUrl + "/login?name=" + name + "&pass=" + pass;
Document jdomDocument = Utils.connect(url, client);
Element root = jdomDocument.getRootElement();
String auth = root.getChildText("auth", WSNamespaces.NS1);
if (auth == null)
{
throw new RemoteException("Invalid username or password");
}
return auth;
}
catch (Exception e)
{
throw new RemoteException(e.getMessage(), e.getCause());
}
}
@Override
public boolean removeCurationTag(String pwId, String tagName, WSAuth auth) throws RemoteException
{
try
{
String url = baseUrl + "/removeCurationTag?pwId=" + pwId + "&tagName=" + tagName + "&auth=" + auth.getKey()
+ "&username=" + auth.getUser();
Document jdomDocument = Utils.connect(url, client);
String success = jdomDocument.getRootElement().getChild("success", WSNamespaces.NS1).getValue();
if (success.equals("1"))
{
return true;
}
return false;
}
catch (Exception e)
{
throw new RemoteException(e.getMessage(), e.getCause());
}
}
@Override
public boolean saveCurationTag(String pwId, String tagName, String tagText, int revision, WSAuth auth)
throws RemoteException
{
try
{
String url = baseUrl + "/saveCurationTag?pwId=" + pwId + "&tagName=" + tagName + "&text=" + URLEncoder
.encode(tagText, "UTF-8") + "&revision=" + revision + "&auth=" + auth.getKey() + "&username=" + auth
.getUser();
Document jdomDocument = Utils.connect(url, client);
String success = jdomDocument.getRootElement().getChild("success", WSNamespaces.NS1).getValue();
if (success.equals("1"))
{
return true;
}
return false;
}
catch (Exception e)
{
throw new RemoteException(e.getMessage(), e.getCause());
}
}
@Override
public boolean saveOntologyTag(String pwId, String term, String termId, WSAuth auth) throws RemoteException
{
try
{
String url =
baseUrl + "/saveOntologyTag?pwId=" + pwId + "&term=" + URLEncoder.encode(term, "UTF-8") + "&termId="
+ termId + "&auth=" + auth.getKey() + "&user=" + auth.getUser();
Document jdomDocument = Utils.connect(url, client);
String success = jdomDocument.getRootElement().getChild("success", WSNamespaces.NS1).getValue();
if (success.equals("1"))
{
return true;
}
return false;
}
catch (Exception e)
{
throw new RemoteException(e.getMessage(), e.getCause());
}
}
@Override
public boolean removeOntologyTag(String pwId, String termId, WSAuth auth) throws RemoteException
{
try
{
String url = baseUrl + "/removeOntologyTag?pwId=" + pwId + "&termId=" + termId + "&auth=" + auth.getKey()
+ "&user=" + auth.getUser();
Document jdomDocument = Utils.connect(url, client);
String success = jdomDocument.getRootElement().getChild("success", WSNamespaces.NS1).getValue();
if (success.equals("1"))
{
return true;
}
return false;
}
catch (Exception e)
{
throw new RemoteException(e.getMessage(), e.getCause());
}
}
@Override
public boolean updatePathway(String pwId, String description, String gpml, int revision, WSAuth auth)
throws RemoteException
{
try
{
Map map = new HashMap();
map.put("pwId", pwId);
map.put("description", description);
map.put("gpml", gpml);
map.put("revision", revision + "");
map.put("auth", auth.getKey());
map.put("username", auth.getUser());
String url = baseUrl + "/updatePathway";
String success = Utils.update(url, client, map);
if (success.equals("1"))
{
return true;
}
}
catch (Exception e)
{
e.printStackTrace();
throw new RemoteException(e.getMessage(), e.getCause());
}
return false;
}
@Override
public WSPathwayInfo createPathway(String gpml, WSAuth auth) throws RemoteException
{
try
{
Map map = new HashMap();
map.put("gpml", gpml);
map.put("auth", auth.getKey());
map.put("username", auth.getUser());
String url = baseUrl + "/createPathway";
HttpPost httpost = new HttpPost(url);
// Adding all form parameters in a List of type NameValuePair
List nvps = new ArrayList();
for (String key : map.keySet())
{
nvps.add(new BasicNameValuePair(key, map.get(key)));
}
httpost.addHeader("Accept-Encoding", "application/xml");
httpost.setEntity(new UrlEncodedFormEntity(nvps, Consts.UTF_8));
HttpResponse response = client.execute(httpost);
SAXBuilder jdomBuilder = new SAXBuilder();
Document jdomDocument = jdomBuilder.build(response.getEntity().getContent());
Element root = jdomDocument.getRootElement();
Element p = root.getChild("pathwayInfo", WSNamespaces.NS1);
return Utils.parseWSPathwayInfo(p);
}
catch (Exception e)
{
e.printStackTrace();
throw new RemoteException(e.getMessage(), e.getCause());
}
}
}
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