Java tutorial
/* * See the NOTICE file distributed with this work for additional * information regarding copyright ownership. * * This is free software; you can redistribute it and/or modify it * under the terms of the GNU Lesser General Public License as * published by the Free Software Foundation; either version 2.1 of * the License, or (at your option) any later version. * * This software is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public * License along with this software; if not, write to the Free * Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA * 02110-1301 USA, or see the FSF site: http://www.fsf.org. */ package edu.toronto.cs.cidb.ncbieutils; import java.io.BufferedInputStream; import java.io.StringWriter; import java.net.URL; import java.util.ArrayList; import java.util.Collections; import java.util.HashMap; import java.util.LinkedList; import java.util.List; import java.util.Map; import javax.inject.Inject; import javax.inject.Named; import javax.inject.Singleton; import javax.xml.parsers.DocumentBuilder; import javax.xml.parsers.DocumentBuilderFactory; import javax.xml.transform.Result; import javax.xml.transform.Source; import javax.xml.transform.Transformer; import javax.xml.transform.TransformerFactory; import javax.xml.transform.dom.DOMSource; import javax.xml.transform.stream.StreamResult; import org.apache.commons.lang3.StringUtils; import org.slf4j.Logger; import org.w3c.dom.Document; import org.w3c.dom.Element; import org.w3c.dom.NamedNodeMap; import org.w3c.dom.Node; import org.w3c.dom.NodeList; import org.xwiki.component.annotation.Component; import org.xwiki.script.service.ScriptService; @Component @Named("ncbieutils") @Singleton public class NCBIEUtilsAccessService implements ScriptService { @Inject private Logger logger; protected static final String SERVER_URL = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/"; protected static final String TERM_SEARCH_QUERY_SCRIPT = "esearch.fcgi"; protected static final String TERM_SEARCH_PARAM_NAME = "term"; protected static final String TERM_SUMMARY_QUERY_SCRIPT = "esummary.fcgi"; protected static final String TERM_SUMMARY_PARAM_NAME = "id"; protected static final String SPELL_CHECK_QUERY_SCRIPT = "espell.fcgi"; protected static final String SPELL_CHECK_PARAM_NAME = "term"; protected static final String DB_PARAM_NAME = "db"; protected String getDatabaseName() { return ""; } protected List<Map<String, Object>> getSuggestions(final String query) { return getSuggestions(query, 10, 0); } protected List<Map<String, Object>> getSuggestions(final String query, final int rows, final int start) { // Step 1: get spelling suggestions for query String correctedQuery = getCorrectedQuery(query); // Step 2: get ID list matching the corrected query List<String> idList = getMatches(correctedQuery, rows, start); // step 3: get Summaries for ID list List<Map<String, Object>> result = getSummaries(idList); return result; } protected String getSuggestionsXML(final String query) { return getSuggestionsXML(query, 10, 0); } protected String getSuggestionsXML(final String query, final int rows, final int start) { // Step 1: get spelling suggestions for query String correctedQuery = getCorrectedQuery(query); // Step 2: get ID list matching the corrected query List<String> idList = getMatches(correctedQuery, rows, start); // step 3: get Summaries for ID list String result = getSummariesXML(idList); return result; } protected String getName(String id) { String url = composeURL(TERM_SUMMARY_QUERY_SCRIPT, TERM_SUMMARY_PARAM_NAME, id); String result = id; try { Document response = readXML(url); NodeList nodes = response.getElementsByTagName("DocSum"); if (nodes.getLength() > 0) { Map<String, String> idToName = this.getNameForId(nodes.item(0)); result = idToName.get(id); if (result != null && !id.equals(result)) { return result; } } this.logger.warn("Name not found for OMIM id " + id); return id; } catch (Exception ex) { this.logger.error("Error while trying to retrieve name for " + getDatabaseName() + " id " + id + " " + ex.getClass().getName() + " " + ex.getMessage(), ex); } return id; } protected Map<String, String> getNames(List<String> idList) { Map<String, String> result = new HashMap<String, String>(); String queryList = getSerializedList(idList); String url = composeURL(TERM_SUMMARY_QUERY_SCRIPT, TERM_SUMMARY_PARAM_NAME, queryList); try { Document response = readXML(url); NodeList nodes = response.getElementsByTagName("DocSum"); for (int i = 0; i < nodes.getLength(); ++i) { Map<String, String> idToName = this.getNameForId(nodes.item(i)); for (String id : idToName.keySet()) { if (idList.contains(id)) { result.put(id, idToName.get(id)); } else { this.logger.warn("Unrequested " + getDatabaseName() + " id " + id); } } } } catch (Exception ex) { this.logger.error("Error while trying to retrieve name for " + getDatabaseName() + " ids " + queryList + " " + ex.getClass().getName() + " " + ex.getMessage(), ex); } return result; } private Map<String, String> getNameForId(Node source) { Map<String, String> result = new HashMap<String, String>(); String id = null, name = null; NodeList data = source.getChildNodes(); for (int i = 0; i < data.getLength(); ++i) { Node n = data.item(i); if (n.getNodeType() != Node.ELEMENT_NODE) { continue; } if ("Id".equals(n.getNodeName())) { id = n.getTextContent(); } else if ("Item".equals(n.getNodeName())) { NamedNodeMap attrs = n.getAttributes(); if (attrs.getNamedItem("Name") != null && "Title".equals(attrs.getNamedItem("Name").getNodeValue())) { name = n.getTextContent(); } } } if (id != null) { if (name != null) { result.put(id, fixCase(name)); } else { result.put(id, id); } } return result; } protected String getCorrectedQuery(String query) { // response example at http://eutils.ncbi.nlm.nih.gov/entrez/eutils/espell.fcgi?db=omim&term=atention+sindrom // response type: XML // get corrected query from /eSpellResult/CorrectedQuery (single element) // use original query if this element is empty String url = composeURL(SPELL_CHECK_QUERY_SCRIPT, SPELL_CHECK_PARAM_NAME, query); try { Document response = readXML(url); NodeList nodes = response.getElementsByTagName("CorrectedQuery"); if (nodes.getLength() > 0) { String result = nodes.item(0).getTextContent(); if (result == null) { result = ""; } else { result.trim(); } return (!"".equals(result)) ? result : query; } } catch (Exception ex) { this.logger.error("Error while trying to retrieve corrected query for " + query + " " + ex.getClass().getName() + " " + ex.getMessage(), ex); } return query; } protected List<String> getMatches(final String query, final int rows, final int start) { // response example at http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=omim&term=down // response type: XML // get corrected query from /eSearchResult/IdList/Id (multiple elements) String url = composeURL(TERM_SEARCH_QUERY_SCRIPT, TERM_SEARCH_PARAM_NAME, query, rows, start); List<String> result = new ArrayList<String>(); try { Document response = readXML(url); NodeList nodes = response.getElementsByTagName("IdList"); if (nodes.getLength() > 0) { nodes = nodes.item(0).getChildNodes(); for (int i = 0; i < nodes.getLength(); ++i) { Node n = nodes.item(i); if (n.getNodeType() == Node.ELEMENT_NODE && n.getNodeName().equals("Id")) { result.add(n.getTextContent()); } } } } catch (Exception ex) { this.logger.error("Error while trying to retrieve matches for " + query + " " + ex.getClass().getName() + " " + ex.getMessage(), ex); } return result; } protected List<Map<String, Object>> getSummaries(List<String> idList) { // response example at // http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=omim&id=190685,605298,604829,602917,601088,602523,602259 // response type: XML // return it String queryList = getSerializedList(idList); String url = composeURL(TERM_SUMMARY_QUERY_SCRIPT, TERM_SUMMARY_PARAM_NAME, queryList); try { Document response = readXML(url); NodeList nodes = response.getElementsByTagName("Item"); // OMIM titles are all UPPERCASE, try to fix this for (int i = 0; i < nodes.getLength(); ++i) { Node n = nodes.item(i); if (n.getNodeType() == Node.ELEMENT_NODE) { if (n.getFirstChild() != null) { n.replaceChild(response.createTextNode(fixCase(n.getTextContent())), n.getFirstChild()); } } } List<Map<String, Object>> result = new LinkedList<Map<String, Object>>(); nodes = response.getElementsByTagName("DocSum"); for (int i = 0; i < nodes.getLength(); ++i) { Element n = (Element) nodes.item(i); Map<String, Object> doc = new HashMap<String, Object>(); doc.put("id", n.getElementsByTagName("Id").item(0).getTextContent()); NodeList items = n.getElementsByTagName("Item"); for (int j = 0; j < items.getLength(); ++j) { Element item = (Element) items.item(j); if ("List".equals(item.getAttribute("Type"))) { NodeList subitems = item.getElementsByTagName("Item"); if (subitems.getLength() > 0) { List<String> values = new ArrayList<String>(subitems.getLength()); for (int k = 0; k < subitems.getLength(); ++k) { values.add(subitems.item(k).getTextContent()); } doc.put(item.getAttribute("Name"), values); } } else { String value = item.getTextContent(); if (StringUtils.isNotEmpty(value)) { doc.put(item.getAttribute("Name"), value); } } } result.add(doc); } return result; } catch (Exception ex) { this.logger.error("Error while trying to retrieve summaries for ids " + idList + " " + ex.getClass().getName() + " " + ex.getMessage(), ex); } return Collections.emptyList(); } protected String getSummariesXML(List<String> idList) { // response example at // http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=omim&id=190685,605298,604829,602917,601088,602523,602259 // response type: XML // return it String queryList = getSerializedList(idList); String url = composeURL(TERM_SUMMARY_QUERY_SCRIPT, TERM_SUMMARY_PARAM_NAME, queryList); try { Document response = readXML(url); NodeList nodes = response.getElementsByTagName("Item"); // OMIM titles are all UPPERCASE, try to fix this for (int i = 0; i < nodes.getLength(); ++i) { Node n = nodes.item(i); if (n.getNodeType() == Node.ELEMENT_NODE) { if (n.getFirstChild() != null) { n.replaceChild(response.createTextNode(fixCase(n.getTextContent())), n.getFirstChild()); } } } Source source = new DOMSource(response); StringWriter stringWriter = new StringWriter(); Result result = new StreamResult(stringWriter); TransformerFactory factory = TransformerFactory.newInstance(); Transformer transformer = factory.newTransformer(); transformer.transform(source, result); return stringWriter.getBuffer().toString(); } catch (Exception ex) { this.logger.error("Error while trying to retrieve summaries for ids " + idList + " " + ex.getClass().getName() + " " + ex.getMessage(), ex); } return ""; } private String composeURL(String scriptName, String paramName, String query) { return SERVER_URL + scriptName + "?" + DB_PARAM_NAME + '=' + getDatabaseName() + "&" + paramName + "=" + query; } private String composeURL(String scriptName, String paramName, String query, final int rows, final int start) { return SERVER_URL + scriptName + "?" + DB_PARAM_NAME + '=' + getDatabaseName() + "&" + paramName + "=" + query + "&RetMax=" + rows + "&RetStart=" + start; } private org.w3c.dom.Document readXML(String url) { try { BufferedInputStream in = new BufferedInputStream(new URL(url).openStream()); DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance(); DocumentBuilder dBuilder = dbFactory.newDocumentBuilder(); org.w3c.dom.Document result = dBuilder.parse(in); result.getDocumentElement().normalize(); return result; } catch (Exception ex) { this.logger.error("Error while trying to retrieve data from URL " + url + " " + ex.getClass().getName() + " " + ex.getMessage(), ex); return null; } } private static String fixCase(String text) { if (text == null || text.length() == 0) { return ""; } if (StringUtils.isAllUpperCase(text.replaceAll("[^a-zA-Z]", ""))) { return StringUtils.capitalize(text.toLowerCase()); } return text; } private static String getSerializedList(List<String> list) { String result = ""; if (list.size() > 0) { StringBuilder listBuilder = new StringBuilder(); for (String item : list) { listBuilder.append(",").append(item); } result = listBuilder.substring(1); } return result; } public SpecializedNCBIEUtilsAccessService get(final String name) { return new SpecializedNCBIEUtilsAccessService() { @Override public String getDatabaseName() { return name; } }; } }