Java tutorial
// WikiPathways Java library, // Copyright 2014-2015 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.wikipathways.client.utils; import java.io.BufferedReader; import java.io.IOException; import java.io.InputStream; import java.io.InputStreamReader; import java.io.StringReader; import java.io.UnsupportedEncodingException; import java.util.ArrayList; import java.util.List; import java.util.Map; 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.pathvisio.wikipathways.webservice.WSCurationTag; import org.pathvisio.wikipathways.webservice.WSCurationTagHistory; import org.pathvisio.wikipathways.webservice.WSHistoryRow; import org.pathvisio.wikipathways.webservice.WSIndexField; import org.pathvisio.wikipathways.webservice.WSNamespaces; import org.pathvisio.wikipathways.webservice.WSOntologyTerm; import org.pathvisio.wikipathways.webservice.WSPathway; import org.pathvisio.wikipathways.webservice.WSPathwayHistory; import org.pathvisio.wikipathways.webservice.WSPathwayInfo; import org.pathvisio.wikipathways.webservice.WSSearchResult; 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)); 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<String, String> attributes) throws Exception { HttpPost httpost = new HttpPost(url); // Adding all form parameters in a List of type NameValuePair List<NameValuePair> nvps = new ArrayList<NameValuePair>(); 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)); List<Element> 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); List<Element> 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; } }