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org.molgenis.wikipathways.utils.Utils 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.utils;
import org.apache.commons.codec.binary.Base64;
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.JDOMException;
import org.jdom.input.SAXBuilder;
import org.molgenis.wikipathways.client.*;
import java.io.*;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
public class Utils
{
public static Document connect(String url, HttpClient client) throws IOException, JDOMException
{
HttpGet httpget = new HttpGet(url);
HttpResponse response = client.execute(httpget);
HttpEntity entity = response.getEntity();
InputStream instream = entity.getContent();
try
{
String content = "";
BufferedReader reader = new BufferedReader(new InputStreamReader(instream, "UTF-8"));
String line;
while ((line = reader.readLine()) != null)
{
content = content + line + "\n";
}
reader.close();
SAXBuilder jdomBuilder = new SAXBuilder();
Document jdomDocument = jdomBuilder.build(new StringReader(content));
return jdomDocument;
}
finally
{
instream.close();
}
}
public static String update(String url, HttpClient client, Map attributes) throws Exception
{
HttpPost httpost = new HttpPost(url);
// Adding all form parameters in a List of type NameValuePair
List nvps = new ArrayList();
for (String key : attributes.keySet())
{
nvps.add(new BasicNameValuePair(key, attributes.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());
String success = jdomDocument.getRootElement().getChildText("success", WSNamespaces.NS1);
return success;
}
public static WSPathwayInfo parseWSPathwayInfo(Element pathwayInfo)
{
String identifier = pathwayInfo.getChildText("id", WSNamespaces.NS2);
String url = pathwayInfo.getChildText("url", WSNamespaces.NS2);
String name = pathwayInfo.getChildText("name", WSNamespaces.NS2);
String species = pathwayInfo.getChildText("species", WSNamespaces.NS2);
String revision = pathwayInfo.getChildText("revision", WSNamespaces.NS2);
return new WSPathwayInfo(identifier, url, name, species, revision);
}
public static WSIndexField parseWSIndexField(Element indexField)
{
String name = indexField.getChildText("name", WSNamespaces.NS2);
String values = indexField.getChildText("values", WSNamespaces.NS2);
String[] v = new String[1];
v[0] = values;
WSIndexField field = new WSIndexField(name, v);
return field;
}
public static WSSearchResult parseWSSearchResult(Element searchResult)
{
WSSearchResult res = new WSSearchResult();
String score = searchResult.getChildText("score", WSNamespaces.NS2);
res.setScore(Double.parseDouble(score));
@SuppressWarnings("unchecked")
List fieldList = searchResult.getChildren("fields", WSNamespaces.NS2);
WSIndexField[] fields = new WSIndexField[fieldList.size()];
for (int i = 0; i < fieldList.size(); i++)
{
WSIndexField f = parseWSIndexField(fieldList.get(i));
fields[i] = f;
}
res.setFields(fields);
String id = searchResult.getChildText("id", WSNamespaces.NS2);
String url = searchResult.getChildText("url", WSNamespaces.NS2);
String name = searchResult.getChildText("name", WSNamespaces.NS2);
String species = searchResult.getChildText("species", WSNamespaces.NS2);
String revision = searchResult.getChildText("revision", WSNamespaces.NS2);
res.setId(id);
res.setName(name);
res.setUrl(url);
res.setSpecies(species);
res.setRevision(revision);
return res;
}
public static WSOntologyTerm parseOntologyTerm(Element term)
{
String ontology = term.getChildText("ontology", WSNamespaces.NS2);
String id = term.getChildText("id", WSNamespaces.NS2);
String name = term.getChildText("name", WSNamespaces.NS2);
WSOntologyTerm ontTerm = new WSOntologyTerm(ontology, id, name);
return ontTerm;
}
public static WSPathway parsePathway(Element pathway) throws UnsupportedEncodingException
{
String gpml = new String(Base64.decodeBase64(pathway.getChildText("gpml", WSNamespaces.NS2)), "UTF-8");
String id = pathway.getChildText("id", WSNamespaces.NS2);
String name = pathway.getChildText("name", WSNamespaces.NS2);
String url = pathway.getChildText("url", WSNamespaces.NS2);
String species = pathway.getChildText("species", WSNamespaces.NS2);
String revision = pathway.getChildText("revision", WSNamespaces.NS2);
WSPathway p = new WSPathway(gpml, id, url, name, species, revision);
return p;
}
public static WSPathwayHistory parsePathwayHistory(Element hist)
{
String id = hist.getChildText("id", WSNamespaces.NS2);
String url = hist.getChildText("url", WSNamespaces.NS2);
String name = hist.getChildText("name", WSNamespaces.NS2);
String species = hist.getChildText("species", WSNamespaces.NS2);
String revision = hist.getChildText("revision", WSNamespaces.NS2);
@SuppressWarnings("unchecked")
List list = hist.getChildren("history", WSNamespaces.NS2);
WSHistoryRow[] histRows = new WSHistoryRow[list.size()];
for (int i = 0; i < list.size(); i++)
{
histRows[i] = Utils.parseHistoryRow(list.get(i));
}
return new WSPathwayHistory(histRows, id, url, name, species, revision);
}
public static WSHistoryRow parseHistoryRow(Element historyRow)
{
String revision = historyRow.getChildText("revision", WSNamespaces.NS2);
String comment = historyRow.getChildText("comment", WSNamespaces.NS2);
String user = historyRow.getChildText("user", WSNamespaces.NS2);
String timestamp = historyRow.getChildText("timestamp", WSNamespaces.NS2);
return new WSHistoryRow(revision, comment, user, timestamp);
}
public static WSCurationTagHistory parseCurationTagHistory(Element history)
{
String tagName = history.getChildText("tagName", WSNamespaces.NS2);
String text = history.getChildText("text", WSNamespaces.NS2);
String pathwayId = history.getChildText("pathwayId", WSNamespaces.NS2);
String action = history.getChildText("action", WSNamespaces.NS2);
String user = history.getChildText("user", WSNamespaces.NS2);
String time = history.getChildText("time", WSNamespaces.NS2);
return new WSCurationTagHistory(tagName, text, pathwayId, action, user, time);
}
public static WSCurationTag parseCurationTag(Element tag)
{
String name = tag.getChildText("name", WSNamespaces.NS2);
String displayName = tag.getChildText("displayName", WSNamespaces.NS2);
String text = tag.getChildText("text", WSNamespaces.NS2);
String timeModified = tag.getChildText("timeModified", WSNamespaces.NS2);
String userModified = tag.getChildText("userModified", WSNamespaces.NS2);
WSPathwayInfo pathway = Utils.parseWSPathwayInfo(tag.getChild("pathway", WSNamespaces.NS2));
WSCurationTag t = new WSCurationTag(name, displayName, pathway, pathway.getRevision(), text,
Long.parseLong(timeModified), userModified);
return t;
}
}
