<commit_before>package org.intermine.bio.dataconversion;

/*
 * Copyright (C) 2002-2017 FlyMine
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  See the LICENSE file for more
 * information or http://www.gnu.org/copyleft/lesser.html.
 *
 */

import java.io.Reader;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;

import org.apache.log4j.Logger;
import org.intermine.dataconversion.ItemWriter;
import org.intermine.metadata.Model;
import org.intermine.objectstore.ObjectStoreException;
import org.intermine.util.FormattedTextParser;
import org.intermine.xml.full.Item;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;

/**
 *
 * @author <NAME>
 */
public class GtexConverter extends BioDirectoryConverter
{
    //
    private static final String DATASET_TITLE = "GTex data set";
    private static final String DATA_SOURCE_NAME = "GTex";
    private Map<String, Item> genes = new HashMap<String, Item>();
    private static final String TAXON_ID = "9606";
    protected IdResolver rslv;
    private static final Logger LOG = Logger.getLogger(GtexConverter.class);

    /**
     * Constructor
     * @param writer the ItemWriter used to handle the resultant items
     * @param model the Model
     */
    public GtexConverter(ItemWriter writer, Model model) {
        super(writer, model, DATA_SOURCE_NAME, DATASET_TITLE);
    }

    @Override
    public void process(File dataDir) throws Exception {

        if (rslv == null) {
            rslv = IdResolverService.getIdResolverByTaxonId(TAXON_ID, false);
        }
<commit_msg>fail on error<commit_after>package org.intermine.bio.dataconversion;

/*
 * Copyright (C) 2002-2017 FlyMine
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  See the LICENSE file for more
 * information or http://www.gnu.org/copyleft/lesser.html.
 *
 */

import java.io.Reader;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;

import org.apache.log4j.Logger;
import org.intermine.dataconversion.ItemWriter;
import org.intermine.metadata.Model;
import org.intermine.objectstore.ObjectStoreException;
import org.intermine.util.FormattedTextParser;
import org.intermine.xml.full.Item;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;

/**
 *
 * @author <NAME>
 */
public class GtexConverter extends BioDirectoryConverter
{
    //
    private static final String DATASET_TITLE = "GTex data set";
    private static final String DATA_SOURCE_NAME = "GTex";
    private Map<String, Item> genes = new HashMap<String, Item>();
    private static final String TAXON_ID = "9606";
    protected IdResolver rslv;
    private static final Logger LOG = Logger.getLogger(GtexConverter.class);

    /**
     * Constructor
     * @param writer the ItemWriter used to handle the resultant items
     * @param model the Model
     */
    public GtexConverter(ItemWriter writer, Model model) {
        super(writer, model, DATA_SOURCE_NAME, DATASET_TITLE);
    }

    @Override
    public void process(File dataDir) throws Exception {

        if (rslv == null) {
            rslv = IdResolverService.getIdResolverByOrganism(TAXON_ID);
        }

{'fraction_non_alphanumeric': 0.09306987399770905, 'fraction_numerical': 0.0074455899198167235, 'mean_word_length': 3.7330623306233064, 'pattern_counts': {'":': 0, '<': 9, '<?xml version=': 0, '>': 9, 'https://': 0, 'lorem ipsum': 0, 'www.': 2, 'xml': 2}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '7153331', 'n_tokens_mistral': 1052, 'n_tokens_neox': 1023, 'n_words': 301}