de.bonn.limes.core.AbstractReposite.java Source code

Introduction

Here is the source code for de.bonn.limes.core.AbstractReposite.java

Source

/*
 * #Copyright (C) Peeyush Sahu <peeyush215[at]gmail.com>
 * #
 * #This program 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.
 * #
 * #This program 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 this program.  If not, see <http://www.gnu.org/licenses/>.
 */
package de.bonn.limes.core;

import de.bonn.limes.document.PubMedAbstract;
import de.bonn.limes.pubmed.PubMedFetcher;
import de.bonn.limes.pubmed.PubMedRecord;
import de.bonn.limes.pubmed.PubmedSearch;
import java.rmi.RemoteException;
import java.util.ArrayList;
import java.util.List;
import java.util.TreeMap;
import java.util.logging.Level;
import java.util.logging.Logger;
import org.apache.axis2.AxisFault;
import com.google.common.collect.Lists;
import static de.bonn.limes.gui.GeneMinerUI.progressbarCount;

/**
 *
 * @author peeyush
 *
 * this class will use the gene names to retrieve pubmed abstracts
 */
public class AbstractReposite {

    List<String> Glist; //To store gene list from user
    Integer noAbst;

    public TreeMap<String, ArrayList> getAbstracts(List<String> GeneList, Integer maxAbs, Integer perSec)
            throws InterruptedException {
        this.Glist = GeneList;
        this.noAbst = maxAbs;
        List<Integer> ids;
        try {
            TreeMap<String, ArrayList> geneWidAbstract = new TreeMap();// holds all PubMedAbstract object for gene list with genes
            List<PubMedAbstract> abstracts; // holds all PubMedAbstract object for gene list

            for (String gene : Glist) {
                System.out.println(gene.length());
                if (gene.length() != 0 && gene.length() > 2) {
                    //System.out.println("this is the count for progress bar: "+count);
                    abstracts = new ArrayList<>();
                    //System.out.println("Gene for abstract:  " + gene);
                    if (noAbst != null) {
                        ids = new PubmedSearch().getPubMedIDs(gene, noAbst);
                    } else {
                        ids = new PubmedSearch().getPubMedIDs(gene);
                    }
                    progressbarCount++;
                    //System.out.println("Size of fetched PMID list"+ids.size());
                    //ProgressBar.setValue(progressbarCount++);
                    //ProgressBar.repaint();
                    //System.out.println("This should be the progress:    "+ProgressBar.getValue());
                    //System.out.println("Are there no abstracts for gene:    " + ids.isEmpty());
                    if (ids.get(0) != 0) {
                        //System.out.println(ids);

                        // if PMID list has less than 50 ids
                        if (ids.size() < 50) {
                            List<PubMedRecord> records = new PubMedFetcher().getPubMedRecordForIDs(ids);
                            //System.out.println("Size of fetched PMID list"+records.size());
                            if (records == null) {
                                //System.out.println("No abstract to show..");
                            }

                            for (PubMedRecord record : records) {

                                PubMedAbstract abs = new PubMedAbstract();
                                abs.setAbstractText(record.getAbstract());
                                abs.setPMID(record.getPubMedID());
                                abs.setTitle(record.getTitle());
                                abs.setYear(String.valueOf(record.getYear()));
                                abstracts.add(abs);

                                /* WORKING
                                 System.out.println("+++++++++++++++++++++++++++"+record.getTitle());
                                 */
                            }
                        } // if
                        else {
                            int countabst = 0;
                            List<List<Integer>> parts = Lists.partition(ids, perSec);
                            for (List<Integer> Slist : parts) {

                                //System.out.println("Downloaded abstracts:"+Slist.size());
                                List<PubMedRecord> records = new PubMedFetcher().getPubMedRecordForIDs(Slist);
                                //System.out.println("Size of fetched PMID list"+records.size());
                                //System.out.println(gene);
                                if (!records.isEmpty()) {
                                    countabst++;
                                    //System.out.println("For "+gene +" Number of abstracts Fetched:   " + countabst * 500);

                                    for (PubMedRecord record : records) {

                                        PubMedAbstract abs = new PubMedAbstract();
                                        abs.setAbstractText(record.getAbstract());
                                        abs.setPMID(record.getPubMedID());
                                        abs.setTitle(record.getTitle());
                                        abs.setYear(String.valueOf(record.getYear()));
                                        abstracts.add(abs);
                                    }
                                } else {
                                    System.err.println("Empty list returned.");
                                }

                            }
                        }
                    }

                    //System.out.println("Size of Abstracts:  " + abstracts.size());
                    geneWidAbstract.put(gene, (ArrayList) abstracts);

                }
            }
            return geneWidAbstract;
        } catch (AxisFault ex) {
            Logger.getLogger(Main.class.getName()).log(Level.SEVERE, null, ex);
            return null;
        } catch (RemoteException ex) {
            Logger.getLogger(Main.class.getName()).log(Level.SEVERE, null, ex);
            return null;
        }

    }
}