ubic.pubmedgate.organism.SpeciesLoader.java Source code

Introduction

Here is the source code for ubic.pubmedgate.organism.SpeciesLoader.java

Source

/*
 * The WhiteText project
 * 
 * Copyright (c) 2012 University of British Columbia
 * 
 * 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 ubic.pubmedgate.organism;

import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
import java.util.StringTokenizer;

import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.poi.hssf.usermodel.HSSFSheet;

import ubic.BAMSandAllen.Vocabulary;
import ubic.basecode.dataStructure.StringToStringSetMap;
import ubic.basecode.io.excel.ExcelUtil;
import ubic.pubmedgate.Config;
import ubic.pubmedgate.ConnectionsDocument;

import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.vocabulary.RDFS;

public class SpeciesLoader {

    // can turn species ID into species names
    // knows if a species should be filtered

    protected static Log log = LogFactory.getLog(SpeciesLoader.class);

    Set<String> filterOutIDs;
    Map<String, String> IDtoNames, IDtoSingleName;
    StringToStringSetMap commentToIDs;

    public Set<String> getFilteredIDs() {
        return filterOutIDs;
    }

    public SpeciesLoader() throws Exception {
        String excelFileName = Config.config.getString("whitetext.resolve.manual.species.filter");

        filterOutIDs = new HashSet<String>();
        IDtoNames = new HashMap<String, String>();
        IDtoSingleName = new HashMap<String, String>();
        commentToIDs = new StringToStringSetMap();

        HSSFSheet sheet = ExcelUtil.getSheetFromFile(excelFileName, "Sheet1");

        int row = 1;
        int namePos = 0;
        int IDPos = 1;
        int filterPos = 2;

        while (true) {
            String names = ExcelUtil.getValue(sheet, row, namePos);
            if (names == null)
                break;
            String ID = ExcelUtil.getValue(sheet, row, IDPos);
            String filter = ExcelUtil.getValue(sheet, row, filterPos);
            if (filter != null && filter.equals("Yes"))
                filterOutIDs.add(ID);
            // log.info( name + ID + filter );
            IDtoNames.put(ID, names);

            // find the shortest species string
            IDtoSingleName.put(ID, getSingleName(names));
            // log.info( "shortname:" + getSingleName( names ) );

            row++;
        }
        log.info("Filtered out species IDs:" + filterOutIDs.size());
        log.info("IDs total:" + IDtoNames.size());

        excelFileName = Config.config.getString("whitetext.resolve.annotated.species");
        sheet = ExcelUtil.getSheetFromFile(excelFileName, "Sheet1");
        row = 1;
        while (true) {
            String name = ExcelUtil.getValue(sheet, row, namePos);
            if (name == null)
                break;
            String ID = ExcelUtil.getValue(sheet, row, IDPos);
            if (ID != null) {
                commentToIDs.put(name, ID);
            }
            row++;
        }

        log.info("Annotated Species IDs:" + row);
        log.info("               mapped:" + commentToIDs.size());

    }

    public String getSingleName(String names) {
        StringTokenizer toker = new StringTokenizer(names, "[],");
        String shortest = toker.nextToken().toLowerCase().trim();
        while (toker.hasMoreElements()) {
            String current = toker.nextToken().toLowerCase().trim();
            // skip po as it's linked to rat.
            if (current.equals("po"))
                continue;
            // skip 'man' so human is used
            if (current.equals("man"))
                continue;
            if (current.length() < shortest.length())
                shortest = current;
        }
        return shortest;
    }

    public void addToModel(ConnectionsDocument doc, Model model) {
        Set<String> speciesSet = doc.getLinnaeusSpecies();
        speciesSet.removeAll(filterOutIDs);
        // filter
        String pmid = doc.getPMID();
        Resource docResource = model.createResource(Vocabulary.getpubmedURIPrefix() + pmid);
        for (String species : speciesSet) {
            // we only want the taxon ID at the end
            String fullSpeciesID = species;
            species = species.substring(species.lastIndexOf(":") + 1);
            Resource taxon = model.createResource("http://bio2rdf.org/taxon:" + species);
            // for the MScanner sets we don't have species names so the below line returns null
            String singleNameFromID = getSingleNameFromID(fullSpeciesID);
            if (singleNameFromID == null) {
                log.info(species + " has null single name label");
            } else {
                taxon.addLiteral(RDFS.label, singleNameFromID);
            }
            docResource.addProperty(Vocabulary.mentions_species, taxon);
            //            log.info( docResource.getURI() + "->" + taxon.getURI() );
        }
    }

    public String getTaggedNamesFromID(String ID) {
        return IDtoNames.get(ID);
    }

    public String getSingleNameFromID(String ID) {
        return IDtoSingleName.get(ID);
    }

    public Set<String> getAllIDs() {
        return new HashSet<String>(IDtoNames.keySet());
    }

    public boolean isFiltered(String ID) {
        return filterOutIDs.contains(ID);
    }

    public Set<String> getIDfromAnnotatedSpecies(String species) {
        return commentToIDs.get(species);
    }

    // requires mapping of annotated species to IDs

    /**
     * @param args
     */
    public static void main(String[] args) throws Exception {
        SpeciesLoader loader = new SpeciesLoader();
        log.info(loader.getTaggedNamesFromID("species:ncbi:10116").toString());

    }

}