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42914
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eri.katsar
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package eu.dnetlib.data.mapreduce.hbase.lodExport.preprocessing;
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42692
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eri.katsar
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43143
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giorgos.al
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import java.io.IOException;
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43102
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eri.katsar
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import org.apache.commons.lang.StringUtils;
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42692
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eri.katsar
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import org.apache.hadoop.io.LongWritable;
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import org.apache.hadoop.io.Text;
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import org.apache.hadoop.mapreduce.Mapper;
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import org.apache.log4j.Logger;
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45843
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eri.katsar
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import eu.dnetlib.data.mapreduce.hbase.lodExport.utils.configuration.LodConfiguration;
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42692
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eri.katsar
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/**
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* Mapper Class that reads HBASE contents and prepares them for the StatsDB
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* export
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*/
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42802
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eri.katsar
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/*
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-> Parse LOD dump files
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Process lod input files and divide by entity type (both source and target)
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Transform to id, array of [ properties] format
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Store to HDFS
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For -> Multiple outputs and inputs
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Multiple inputs: all source and target datasets and their corresponding mappings
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M/O: separate output files for each dataset: mark records so that they are written to the correct one
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*/
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45528
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eri.katsar
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/*
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<http://lod.openaire.eu/data/result/doajarticles::89217af00809a91acc15a416e56b3782> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.eurocris.org/ontologies/cerif/1.3#ResultEntity> .
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<http://lod.openaire.eu/data/result/doajarticles::89217af00809a91acc15a416e56b3782> <http://www.eurocris.org/ontologies/cerif/1.3#name> "Une nouvelle anomalie a allure h r ditaire chez des agneaux it khouzistans /it" .
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*/
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42692
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eri.katsar
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public class SourceMapper extends Mapper<LongWritable, Text, Text, Text> {
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43347
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eri.katsar
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private Logger log = Logger.getLogger(SourceMapper.class);
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42692
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eri.katsar
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43347
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eri.katsar
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private LodConfiguration lodConfiguration;
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42802
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eri.katsar
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43485
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eri.katsar
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public static enum SOURCE_COUNTERS {
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45621
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eri.katsar
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SOURCE_ENTITIES, TOTAL_ENTITIES
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43347
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eri.katsar
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}
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43095
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eri.katsar
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42692
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eri.katsar
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43347
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eri.katsar
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@Override
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protected void setup(Context context) throws IOException, InterruptedException {
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lodConfiguration = new LodConfiguration();
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43526
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eri.katsar
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lodConfiguration.load(context.getConfiguration().get("lod.sourceMappings"));
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44137
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eri.katsar
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log.info("file loaded!" + context.getConfiguration().get("lod.sourceMappings"));
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45528
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eri.katsar
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43347
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eri.katsar
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}
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42692
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eri.katsar
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43347
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eri.katsar
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@Override
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protected void map(final LongWritable keyIn, final Text result, final Context context) throws IOException {
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42692
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eri.katsar
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43347
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eri.katsar
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try {
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45621
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eri.katsar
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context.getCounter(SOURCE_COUNTERS.TOTAL_ENTITIES).increment(1);
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43347
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eri.katsar
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//get ID - output source_recordID so we can group by id and get all props of a record
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43504
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eri.katsar
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43940
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eri.katsar
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StringBuilder value = new StringBuilder();
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45528
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eri.katsar
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String[] inputParts = result.toString().split("\"");
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42692
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eri.katsar
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43347
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eri.katsar
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int i = 0;
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while (i < inputParts.length) {
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inputParts[i] = inputParts[i].replaceAll("\\s", "\t");
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i += 2;
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}
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42692
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eri.katsar
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43347
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eri.katsar
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String output = StringUtils.join(inputParts, "\"");
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String[] Fields = output.split("\t");
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42918
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eri.katsar
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44174
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eri.katsar
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if (Fields.length >= 2) {
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//here addd all fields as array props and append "\t"
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// betweeen them so we can write directly to output
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//DO NOT enter id- we'll get it from key output
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42918
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eri.katsar
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44174
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eri.katsar
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i = 1;
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//extract entity type from subject
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String[] tmp = Fields[0].split("/");
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if (tmp.length >= 5) {
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String type = tmp[4];
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String subject = Fields[0];
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if (lodConfiguration.entityExists(type)) {
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while (i < Fields.length - 1) {
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String field = Fields[i];
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String fieldValue = Fields[i + 1];
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if (lodConfiguration.isValidField(field)) {
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45528
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eri.katsar
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value.append(subject).append("\t").append(field).append("\t").append(fieldValue).append("\t.\t");
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44174
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eri.katsar
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}
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i += 2;
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}
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45517
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eri.katsar
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// write out type,source_ID as key, and rest of props as value
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Text key = new Text("OA" + "," + type + "," + subject);
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45528
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eri.katsar
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if(value.toString().length()>0){
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45517
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eri.katsar
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context.write(key, new Text(value.toString()));
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context.getCounter(SOURCE_COUNTERS.SOURCE_ENTITIES).increment(1);
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45528
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eri.katsar
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}}
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43347
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eri.katsar
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}
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43537
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eri.katsar
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}
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44137
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eri.katsar
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} catch (Exception e) {
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43347
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eri.katsar
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log.error("Error writing entity to M/R output", e);
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45517
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eri.katsar
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// throw new InterruptedIOException(e.toString());
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43347
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eri.katsar
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}
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43102
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eri.katsar
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107 |
43347
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eri.katsar
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}
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108 |
43102
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eri.katsar
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43504
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eri.katsar
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private static String cleanInput(Text result) {
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44053
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eri.katsar
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String resulString = result.toString().replace("<", "").replace(">", "");
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43102
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eri.katsar
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43504
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eri.katsar
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int ind = resulString.lastIndexOf(".");
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if (ind >= 0) {
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resulString = resulString.substring(0, ind);
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}
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return resulString;
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}
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43347
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eri.katsar
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@Override
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protected void cleanup(Context context) throws IOException, InterruptedException {
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super.cleanup(context);
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}
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eri.katsar
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42692
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}
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