es.uvigo.ei.sing.gc.view.models.committee.enrichment.GeneEnrichmentSubtask.java Source code

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Here is the source code for es.uvigo.ei.sing.gc.view.models.committee.enrichment.GeneEnrichmentSubtask.java

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/*
   This file is part of GeneCommittee.
    
   GeneCommittee is free software: you can redistribute it and/or modify
   it under the terms of the GNU General Public License as published by
   the Free Software Foundation, either version 3 of the License, or
   (at your option) any later version.
    
   GeneCommittee 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 General Public License for more details.
    
   You should have received a copy of the GNU General Public License
   along with GeneCommittee.  If not, see <http://www.gnu.org/licenses/>.
*/
package es.uvigo.ei.sing.gc.view.models.committee.enrichment;

import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;

import org.hibernate.Session;

import es.uvigo.ei.sing.gc.execution.AbortException;
import es.uvigo.ei.sing.gc.execution.Subtask;
import es.uvigo.ei.sing.gc.execution.Task;
import es.uvigo.ei.sing.gc.model.entities.Committee;
import es.uvigo.ei.sing.gc.model.entities.GeneSetMetaData;
import es.uvigo.ei.sing.gc.model.entities.RankedGene;
import es.uvigo.ei.sing.gc.utils.HibernateUtil;
import es.uvigo.ei.sing.gc.ws.ArrayOfString;
import es.uvigo.ei.sing.gc.ws.GenebrowserClient;

final class GeneEnrichmentSubtask implements Subtask<Set<GeneSetMetaData>> {
    private static final Map<String, String> SOURCE_TRANSLATION = new HashMap<String, String>();

    static {
        SOURCE_TRANSLATION.put("MIM", "OMIM");
        SOURCE_TRANSLATION.put("KO", "KEGG Orthology");
        SOURCE_TRANSLATION.put("GO", "Gene Ontology");
        SOURCE_TRANSLATION.put("Reactome", "Reactome Pathways");
    }

    private final Integer committeeId;
    private final Set<RankedGene> geneList;
    private Task<Set<GeneSetMetaData>> task;
    private boolean aborted;

    public GeneEnrichmentSubtask(Integer committeeId, Set<RankedGene> geneList) {
        this.committeeId = committeeId;
        this.geneList = geneList;
        this.aborted = false;
    }

    @Override
    public Set<GeneSetMetaData> call() throws Exception {
        if (this.aborted)
            throw new AbortException();

        final ArrayOfString result = GeneEnrichmentSubtask.enrich("Homo sapiens (human)", geneList);

        if (this.aborted)
            throw new AbortException();

        final List<GeneSetMetaData> geneSets = new ArrayList<GeneSetMetaData>();

        int missingCount = 0;
        for (String data : result.getString()) {
            final String[] split = data.split(";");

            final String sourceId = split[0];
            final String sourceName = SOURCE_TRANSLATION.containsKey(sourceId) ? SOURCE_TRANSLATION.get(sourceId)
                    : sourceId;
            final String id = split[1];
            final String name = split[2].equals("-.") ? "[" + sourceId + "-" + ++missingCount + "]" : split[2];
            final String[] genes = split[3].split(",");
            final String pvalueString = split[4].replace(",", ".");
            final double pvalue = Double.parseDouble(pvalueString);

            final GeneSetMetaData gs = new GeneSetMetaData();
            gs.setSource(sourceName);
            gs.setGeneSetId(id);
            gs.setName(name);
            gs.setPValue(pvalue);

            gs.changeGenes(new HashSet<String>(Arrays.asList(genes)));

            geneSets.add(gs);
        }

        if (this.aborted)
            throw new AbortException();

        final Session session = HibernateUtil.getSessionFactory().openSession();
        session.beginTransaction();
        final Committee committee = (Committee) session.get(Committee.class, committeeId);

        for (GeneSetMetaData geneSet : geneSets) {
            session.persist(geneSet);
        }
        session.flush();

        committee.getGeneSets().addAll(geneSets);
        session.update(committee);

        session.getTransaction().commit();
        session.close();

        return committee.getGeneSets();
    }

    @Override
    public Task<Set<GeneSetMetaData>> getTask() {
        return this.task;
    }

    @Override
    public void setTask(Task<Set<GeneSetMetaData>> task) {
        this.task = task;
    }

    @Override
    public void abort() {
        this.aborted = true;
    }

    private static ArrayOfString enrich(String specieName, Set<RankedGene> geneList) {
        final StringBuilder sb = new StringBuilder();

        for (RankedGene genes : geneList) {
            if (sb.length() > 0)
                sb.append(',');
            sb.append(genes.getGene());
        }

        return GenebrowserClient.querySoap12(specieName, sb.toString());
    }
}