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 org.phenotips.solr; import org.phenotips.obo2solr.maps.CounterMap; import org.phenotips.obo2solr.maps.SumMap; import org.xwiki.component.annotation.Component; import org.xwiki.script.service.ScriptService; import java.util.Collection; import java.util.Collections; import java.util.HashMap; import java.util.HashSet; import java.util.LinkedList; import java.util.List; import java.util.Map; import java.util.Set; import javax.inject.Inject; import javax.inject.Named; import javax.inject.Singleton; import org.apache.commons.lang3.StringUtils; import org.apache.solr.client.solrj.SolrServerException; import org.apache.solr.client.solrj.response.QueryResponse; import org.apache.solr.common.SolrDocument; import org.apache.solr.common.SolrDocumentList; import org.apache.solr.common.params.CommonParams; import org.apache.solr.common.params.MapSolrParams; import org.apache.solr.common.util.SimpleOrderedMap; /** * Provides access to the Solr server, with the main purpose of providing access to the OMIM ontology. * * @version $Id: 311d84c18fb080c7dae58e070b92df838aa0c48a $ */ @Component @Named("omim") @Singleton public class OmimScriptService extends AbstractSolrScriptService { /** Provides access to the HPO ontology, for converting IDs into names and for getting all term ancestors. */ @Inject @Named("hpo") private ScriptService service; @Override protected String getName() { return "omim"; } /** * Compute a list of phenotypes to investigate, which maximize the probability of getting more accurate automatic * diagnosis suggestions. * * @param phenotypes the list of already selected phenotypes * @param limit the maximum number of phenotypes to return * @return a list of phenotype suggestions * @deprecated use {@link #getDifferentialPhenotypes(Collection, Collection, int)} which also has support for * negative phenotypes */ @Deprecated public List<SuggestedPhenotype> getDifferentialPhenotypes(Collection<String> phenotypes, int limit) { return getDifferentialPhenotypes(phenotypes, Collections.<String>emptyList(), limit); } /** * Compute a list of phenotypes to investigate, which maximize the probability of getting more accurate automatic * diagnosis suggestions. * * @param phenotypes the list of already selected phenotypes * @param nphenotypes phenotypes that are not observed in the patient * @param limit the maximum number of phenotypes to return * @return a list of phenotype suggestions */ public List<SuggestedPhenotype> getDifferentialPhenotypes(Collection<String> phenotypes, Collection<String> nphenotypes, int limit) { HPOScriptService hpoService = (HPOScriptService) this.service; QueryResponse response; List<SuggestedPhenotype> result = new LinkedList<SuggestedPhenotype>(); try { response = this.server.query(prepareParams(phenotypes, nphenotypes)); } catch (SolrServerException ex) { this.logger.warn("Failed to query OMIM index: {}", ex.getMessage()); return result; } SolrDocumentList matchingDisorders = response.getResults(); Map<?, ?> explanations = response.getExplainMap(); SumMap<String> cummulativeScore = new SumMap<String>(); CounterMap<String> matchCounter = new CounterMap<String>(); Set<String> allAncestors = new HashSet<String>(); for (String phenotype : phenotypes) { allAncestors.addAll(hpoService.getAllAncestorsAndSelfIDs(phenotype)); } for (SolrDocument disorder : matchingDisorders) { String omimId = (String) disorder.getFieldValue(ID_FIELD_NAME); @SuppressWarnings("unchecked") SimpleOrderedMap<Float> omimTerm = (SimpleOrderedMap<Float>) explanations.get(omimId); float score = omimTerm.get("value"); for (Object hpoId : disorder.getFieldValues("actual_symptom")) { if (allAncestors.contains(hpoId) || nphenotypes.contains(hpoId) || !hpoService.getAllAncestorsAndSelfIDs((String) hpoId).contains("HP:0000118")) { continue; } cummulativeScore.addTo((String) hpoId, (double) score); matchCounter.addTo((String) hpoId); } } if (matchCounter.getMinValue() <= matchingDisorders.size() / 2) { for (String hpoId : cummulativeScore.keySet()) { SolrDocument term = hpoService.get(hpoId); if (term == null) { continue; } result.add(new SuggestedPhenotype(hpoId, (String) term.getFieldValue("name"), cummulativeScore.get(hpoId) / (matchCounter.get(hpoId) * matchCounter.get(hpoId)))); } Collections.sort(result); } return result.subList(0, limit); } /** * Prepare the map of parameters that can be passed to a Solr query, in order to get a list of diseases matching the * selected positive and negative phenotypes. * * @param phenotypes the list of already selected phenotypes * @param nphenotypes phenotypes that are not observed in the patient * @return the computed Solr query parameters */ private MapSolrParams prepareParams(Collection<String> phenotypes, Collection<String> nphenotypes) { Map<String, String> params = new HashMap<String, String>(); String q = "symptom:" + StringUtils.join(phenotypes, " symptom:"); if (nphenotypes.size() > 0) { q += " not_symptom:" + StringUtils.join(nphenotypes, " not_symptom:"); } q += " -nameSort:\\** -nameSort:\\+* -nameSort:\\^*"; params.put(CommonParams.Q, q.replaceAll("HP:", "HP\\\\:")); params.put(CommonParams.ROWS, "100"); params.put(CommonParams.START, "0"); params.put(CommonParams.DEBUG_QUERY, Boolean.toString(true)); params.put(CommonParams.EXPLAIN_STRUCT, Boolean.toString(true)); return new MapSolrParams(params); } }