Java tutorial
/* * Copyright: (c) 2004-2012 Mayo Foundation for Medical Education and * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the * triple-shield Mayo logo are trademarks and service marks of MFMER. * * Except as contained in the copyright notice above, or as used to identify * MFMER as the author of this software, the trade names, trademarks, service * marks, or product names of the copyright holder shall not be used in * advertising, promotion or otherwise in connection with this software without * prior written authorization of the copyright holder. * * 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 edu.mayo.cts2.framework.plugin.service.bprdf.dao.id; import java.util.ArrayList; import java.util.Arrays; import java.util.HashMap; import java.util.List; import java.util.Map; import java.util.Set; import java.util.Timer; import java.util.TimerTask; import javax.annotation.Resource; import org.apache.commons.lang.StringUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.springframework.beans.factory.InitializingBean; import org.springframework.stereotype.Component; import edu.mayo.twinkql.template.TwinkqlTemplate; /** * The Class DefaultIdService. * * @author <a href="mailto:kevin.peterson@mayo.edu">Kevin Peterson</a> */ @Component public class DefaultIdService implements IdService, InitializingBean { protected final Log log = LogFactory.getLog(getClass().getName()); private final static String BIOPORTAL_PURL_URI = "http://purl.bioontology.org/ontology/"; private final static String VERSION_SUBRESOURCE = "version"; private final static String BIOPORTAL_ONTOLOGIES_URI = "http://bioportal.bioontology.org/ontologies/"; private final static String PURL_OBO_OWL_URI = "http://purl.org/obo/owl/"; private final static String UTILITY_NAMESPACE = "util"; private final static String GET_IDS = "getIds"; @Resource private TwinkqlTemplate twinkqlTemplate; private Map<String, List<String>> ontologyIdToIds = new HashMap<String, List<String>>(); private Map<String, Integer> ontologyIdToLatestId = new HashMap<String, Integer>(); private Map<String, String> idToOntologyId = new HashMap<String, String>(); private Map<String, CodeSystemVersionName> csvNameToCsv = new HashMap<String, CodeSystemVersionName>(); private Map<String, CodeSystemVersionName> idToCsvName = new HashMap<String, CodeSystemVersionName>(); private Map<String, String> acronymToOntologyId = new HashMap<String, String>(); private Map<String, String> ontologyIdToAcronym = new HashMap<String, String>(); private Map<String, String> acronymToUri = new HashMap<String, String>(); private Map<String, String> uriToAcronym = new HashMap<String, String>(); private Map<String, String> ontologyIdToUri = new HashMap<String, String>(); private Map<String, String> idToDocumentUri = new HashMap<String, String>(); private Timer cacheClearingTimer = new Timer(); private static final int ONE_HOUR = 1000 * 60 * 60; private volatile boolean cacheBuilding = true; public void afterPropertiesSet() throws Exception { this.cacheClearingTimer.scheduleAtFixedRate(new TimerTask() { @Override public void run() { try { cacheBuilding = true; buildCache(); } finally { cacheBuilding = false; } } }, 0, ONE_HOUR); } /* * (non-Javadoc) * * @see * org.springframework.beans.factory.InitializingBean#afterPropertiesSet() */ // id = CodeSystemVersion // ontologyId = CodeSystem protected synchronized void buildCache() { List<IdResult> result = this.twinkqlTemplate.selectForList(UTILITY_NAMESPACE, GET_IDS, null, IdResult.class); for (IdResult idResult : result) { String id = idResult.getId(); String ontologyId = idResult.getOntologyId(); String acronym = idResult.getAcronym(); String uri = BIOPORTAL_ONTOLOGIES_URI + acronym; String documentUri = BIOPORTAL_ONTOLOGIES_URI + acronym + "/" + VERSION_SUBRESOURCE + "/" + id; if (acronym.equals("ontologia")) { System.out.println("here"); } if (!this.acronymToOntologyId.containsKey(acronym)) { this.acronymToOntologyId.put(acronym, ontologyId); } else { String foundOntologyId = this.acronymToOntologyId.get(acronym); if (!ontologyId.equals(foundOntologyId)) { log.warn("Found multiple OntologyIds (" + foundOntologyId + "," + ontologyId + ") for the same acronym (" + acronym + ")."); } } if (!this.ontologyIdToAcronym.containsKey(ontologyId)) { this.ontologyIdToAcronym.put(ontologyId, acronym); } else { String foundAcronym = this.ontologyIdToAcronym.get(ontologyId); if (!acronym.equals(foundAcronym)) { log.warn("Found multiple Acronyms (" + foundAcronym + "," + acronym + ") for the same ontologyId (" + ontologyId + ")."); } } if (!this.ontologyIdToIds.containsKey(ontologyId)) { this.ontologyIdToIds.put(ontologyId, new ArrayList<String>()); } this.ontologyIdToIds.get(ontologyId).add(id); Integer latestOntologyId = this.ontologyIdToLatestId.get(ontologyId); if (latestOntologyId == null) { ontologyIdToLatestId.put(ontologyId, Integer.parseInt(id)); } else { Integer foundOntologyId = Integer.parseInt(id); if (foundOntologyId > latestOntologyId) { ontologyIdToLatestId.put(ontologyId, foundOntologyId); } } this.idToOntologyId.put(id, ontologyId); CodeSystemVersionName csvName = new CodeSystemVersionName(acronym, id); this.csvNameToCsv.put(csvName.toString(), csvName); this.idToCsvName.put(id, csvName); this.acronymToUri.put(acronym, uri); this.uriToAcronym.put(uri, acronym); this.ontologyIdToUri.put(ontologyId, uri); this.idToDocumentUri.put(id, documentUri); } } /* * (non-Javadoc) * * @see edu.mayo.cts2.framework.plugin.service.bprdf.dao.id.IdService# * getOntologyIdForId(java.lang.String) */ @Override public String getOntologyIdForId(String id) { return this.getFromCache(idToOntologyId, id); } @Override public String getOntologyIdForAcronym(String acronym) { return this.getFromCache(acronymToOntologyId, acronym); } @Override public String getAcronymForOntologyId(String ontologyId) { return this.getFromCache(ontologyIdToAcronym, ontologyId); } /* * (non-Javadoc) * * @see edu.mayo.cts2.framework.plugin.service.bprdf.dao.id.IdService# * getIdsForOntologyId(java.lang.String) */ @Override public Iterable<String> getIdsForOntologyId(String ontologyId) { return this.getFromCache(ontologyIdToIds, ontologyId); } /* * (non-Javadoc) * * @see edu.mayo.cts2.framework.plugin.service.bprdf.dao.id.IdService# * getCurrentIdForOntologyId(java.lang.String) */ @Override public String getCurrentIdForOntologyId(String ontologyId) { Integer intOntologyId = this.getFromCache(ontologyIdToLatestId, ontologyId); if (intOntologyId == null) { return null; } else { return Integer.toString(intOntologyId); } } @Override public CodeSystemVersionName getCodeSystemVersionNameForName(String codeSystemVersionName) { return this.getFromCache(csvNameToCsv, codeSystemVersionName); } @Override public Set<String> getAllOntologyIds() { return this.getKeySetFromCache(ontologyIdToLatestId); } @Override public CodeSystemVersionName getCodeSystemVersionNameForId(String id) { return this.getFromCache(idToCsvName, id); } @Override public String getUriForAcronym(String acronym) { return this.getFromCache(acronymToUri, acronym); } @Override public String getDocumentUriForId(String id) { return this.getFromCache(idToDocumentUri, id); } @Override public String getUriForOntologyId(String ontologyId) { return this.getFromCache(this.ontologyIdToUri, ontologyId); } public boolean isAcronym(String acronym) { return this.getFromCache(this.acronymToUri, acronym) != null; } @Override public String getAcronymForUri(String uri) { // try adding a '/' if we don't find it for (String addition : Arrays.asList("", "/")) { String acronym = this.getFromCache(this.uriToAcronym, uri + addition); if (acronym != null) { return acronym; } } if (uri.startsWith(BIOPORTAL_PURL_URI)) { uri = StringUtils.removeStart(uri, BIOPORTAL_PURL_URI); uri = StringUtils.removeEnd(uri, "/"); uri = StringUtils.substringBefore(uri, "/"); uri = StringUtils.removeEnd(uri, ":"); uri = StringUtils.removeEnd(uri, "#"); return uri; } if (uri.startsWith(PURL_OBO_OWL_URI)) { uri = StringUtils.removeStart(uri, PURL_OBO_OWL_URI); uri = StringUtils.removeEnd(uri, "/"); uri = StringUtils.substringBefore(uri, "/"); uri = StringUtils.removeEnd(uri, ":"); uri = StringUtils.removeEnd(uri, "#"); return uri; } else { return null; } } protected <T> T getFromCache(Map<?, T> map, Object key) { while (cacheBuilding) { //wait for cache rebuild... } return map.get(key); } protected <T> Set<T> getKeySetFromCache(Map<T, ?> map) { while (cacheBuilding) { //wait for cache rebuild... } return map.keySet(); } }