Revision 54037
Added by Miriam Baglioni over 5 years ago
| modules/dnet-mapreduce-jobs/branches/master/src/main/java/eu/dnetlib/data/mapreduce/hbase/propagation/country/institutionalrepositories/PropagationCountryFromDsOrgResultFileReducer.java | ||
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package eu.dnetlib.data.mapreduce.hbase.propagation.country.institutionalrepositories; |
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import com.googlecode.protobuf.format.JsonFormat; |
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import eu.dnetlib.data.mapreduce.hbase.propagation.Value;
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import eu.dnetlib.data.proto.*;
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import eu.dnetlib.data.mapreduce.hbase.propagation.NotValidResultSequenceException; |
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import eu.dnetlib.data.mapreduce.hbase.propagation.ResultIterator;
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import eu.dnetlib.data.proto.OafProtos;
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import org.apache.commons.logging.Log; |
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import org.apache.commons.logging.LogFactory; |
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import org.apache.hadoop.io.Text; |
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import org.apache.hadoop.mapreduce.Reducer; |
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import java.io.IOException; |
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import java.util.Iterator; |
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import org.apache.commons.logging.LogFactory;
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import static eu.dnetlib.data.mapreduce.hbase.propagation.PropagationConstants.COUNTER_PROPAGATION;
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import static eu.dnetlib.data.mapreduce.hbase.propagation.PropagationConstants.*; |
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import static eu.dnetlib.data.mapreduce.hbase.propagation.Utils.getCountry; |
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public class PropagationCountryFromDsOrgResultFileReducer extends Reducer<InstOrgKey, Text, Text,Text> {
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private static final Log log = LogFactory.getLog(PropagationCountryFromDsOrgResultFileReducer.class); // NOPMD by marko on 11/24/08 5:02 PM |
| ... | ... | |
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private Text outValue; |
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private final static String DNETSCHEMA = "dnet:countries"; |
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private final static String CLASS_ID = "propagation::country::instrepos"; |
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@Override |
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protected void setup(final Context context) throws IOException, InterruptedException {
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super.setup(context); |
| ... | ... | |
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@Override |
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protected void reduce(InstOrgKey key, Iterable<Text> values, Context context) {
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final Iterator<Text> it = values.iterator(); |
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if(!it.hasNext()){
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context.getCounter(COUNTER_PROPAGATION,"empty information for key").increment(1); |
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ResultIterator rh = null; |
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try {
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rh = new ResultCountryIterator(values,key.getKeyType().get()); |
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} catch (NotValidResultSequenceException e) {
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context.getCounter(COUNTER_PROPAGATION,e.getMessage()).increment(1); |
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return; |
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} |
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context.getCounter(COUNTER_PROPAGATION,"institutional datasource").increment(1); |
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final Value first = Value.fromJson(it.next().toString()); |
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if (!(first.getValue().equals(ZERO) || first.getValue().equals(ONE))) {
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if (key.getKeyType().get() == TypeProtos.Type.organization.getNumber()) |
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context.getCounter(COUNTER_PROPAGATION,"First Element in reducer is not type of datasource, but the organization exists").increment(1); |
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else {
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// context.getCounter(COUNTER_PROPAGATION,String.format("WARNINGS: First element value is %s " , first));
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while (it.hasNext()) {
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while(rh.hasNext()){
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OafProtos.Oaf oafUpdate = rh.next(); |
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emit(context, rh.getResultId(), JsonFormat.printToString(oafUpdate)); |
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context.getCounter(COUNTER_PROPAGATION, " added country to product ").increment(1); |
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} |
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String resultId = Value.fromJson(it.next().toString()).getValue(); |
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if (!resultId.startsWith("50|"))
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context.getCounter(COUNTER_PROPAGATION,"ERROR ORDERING CHECK").increment(1); |
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} |
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} |
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if (!rh.getPropagate()){
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context.getCounter(COUNTER_PROPAGATION, "resultId expected in ordering was not found" ).increment(1); |
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} |
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//ensure we are dealing with an institutional repository |
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if (first.getValue().equals(ONE)) {
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context.getCounter(COUNTER_PROPAGATION,"institutional datasource").increment(1); |
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if(!it.hasNext()){
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context.getCounter(COUNTER_PROPAGATION,"no information apart of type of datasource").increment(1); |
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return; |
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} |
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final String country = Value.fromJson(it.next().toString()).getValue(); // need to update the information for the country to each element in the iterator |
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if(country.trim().length() != 2){
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context.getCounter(COUNTER_PROPAGATION,"second element in reducer is not country").increment(1); |
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return; |
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} |
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boolean propagate = true; |
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while(it.hasNext()) {
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String resultId = Value.fromJson(it.next().toString()).getValue(); |
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if (!resultId.startsWith(("50|"))) {
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if(!resultId.equalsIgnoreCase(country)) {
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context.getCounter(COUNTER_PROPAGATION, "resultId expected in ordering was not found" ).increment(1); |
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propagate = false; |
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} |
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}else{
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if (propagate){
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OafProtos.Oaf oafUpdate = getOafCountry(resultId, country,first.getTrust()); |
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emit(context, resultId, JsonFormat.printToString(oafUpdate)); |
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context.getCounter(COUNTER_PROPAGATION, " added country to product ").increment(1); |
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} |
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} |
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} |
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} else {
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context.getCounter(COUNTER_PROPAGATION,"not allowed dsType institutional datasource").increment(1); |
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} |
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} |
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private OafProtos.Oaf getOafCountry(String resultId, String countryValue, String trust) {
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final ResultProtos.Result.Metadata.Builder metadata = ResultProtos.Result.Metadata.newBuilder().addCountry( |
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getCountry(countryValue,trust,DNETSCHEMA,CLASS_ID,SCHEMA_ID,SCHEMA_NAME,DATA_INFO_TYPE,"Propagation of country information from datasources belonging to institutional repositories")); |
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final ResultProtos.Result.Builder result = ResultProtos.Result.newBuilder().setMetadata(metadata); |
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final OafProtos.OafEntity.Builder entity = OafProtos.OafEntity.newBuilder() |
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.setType(TypeProtos.Type.result) |
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.setId(resultId) |
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.setResult(result); |
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return OafProtos.Oaf.newBuilder() |
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.setKind(KindProtos.Kind.entity) |
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.setEntity(entity) |
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.build(); |
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} |
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} |
| modules/dnet-mapreduce-jobs/branches/master/src/main/java/eu/dnetlib/data/mapreduce/hbase/propagation/country/institutionalrepositories/PropagationCountryFromDsOrgResultReducer.java | ||
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| 1 | 1 |
package eu.dnetlib.data.mapreduce.hbase.propagation.country.institutionalrepositories; |
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import java.io.IOException; |
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import java.util.Iterator; |
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import com.google.gson.Gson; |
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import eu.dnetlib.data.mapreduce.hbase.propagation.NotValidResultSequenceException; |
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import eu.dnetlib.data.mapreduce.hbase.propagation.ResultIterator; |
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import eu.dnetlib.data.mapreduce.hbase.propagation.Value; |
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import eu.dnetlib.data.proto.*; |
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import org.apache.commons.lang3.StringUtils; |
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import org.apache.hadoop.hbase.io.ImmutableBytesWritable; |
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import org.apache.hadoop.hbase.mapreduce.TableReducer; |
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import org.apache.hadoop.hbase.util.Bytes; |
| ... | ... | |
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import org.apache.hadoop.io.Text; |
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import static eu.dnetlib.data.mapreduce.hbase.propagation.PropagationConstants.*; |
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import static eu.dnetlib.data.mapreduce.hbase.propagation.Utils.*; |
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public class PropagationCountryFromDsOrgResultReducer extends TableReducer<InstOrgKey, Text, ImmutableBytesWritable>{
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private static final Log log = LogFactory.getLog(PropagationCountryFromDsOrgResultReducer.class); |
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final static String DNETSCHEMA = "dnet:countries"; |
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private final static String CLASS_ID = "propagation::country::instrepos"; |
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private ImmutableBytesWritable keyOut; |
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@Override |
| ... | ... | |
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@Override |
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protected void reduce(final InstOrgKey key, final Iterable<Text> values, final Context context) throws IOException, InterruptedException {
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final Iterator<Text> it = values.iterator(); |
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if(!it.hasNext()){
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context.getCounter(COUNTER_PROPAGATION,"empty information for key").increment(1); |
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ResultIterator rh = null; |
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try {
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rh = new ResultCountryIterator(values,key.getKeyType().get()); |
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} catch (NotValidResultSequenceException e) {
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context.getCounter(COUNTER_PROPAGATION,e.getMessage()).increment(1); |
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return; |
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} |
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final Value first = Value.fromJson(it.next().toString()); |
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if (!(first.getValue().equals(ZERO) || first.getValue().equals(ONE))) {
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if (key.getKeyType().get() == TypeProtos.Type.organization.getNumber()) |
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context.getCounter(COUNTER_PROPAGATION,"First Element in reducer is not type of datasource, but the organization exists").increment(1); |
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else {
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context.getCounter(COUNTER_PROPAGATION, "WARNING: unexpected first element").increment(1); |
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while (it.hasNext()) {
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context.getCounter(COUNTER_PROPAGATION,"institutional datasource").increment(1); |
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String resultId = Value.fromJson(it.next().toString()).getValue(); |
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if (!resultId.startsWith("50|")) {
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context.getCounter(COUNTER_PROPAGATION,"ERROR ORDERING CHECK").increment(1); |
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} |
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} |
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} |
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} |
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while(rh.hasNext()){
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byte[] oafUpdate = rh.next().toByteArray(); |
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//ensure we are dealing with an institutional repository |
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if (first.getValue().equals(ONE)) {
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context.getCounter(COUNTER_PROPAGATION,"institutional datasource").increment(1); |
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if(!it.hasNext()) {
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context.getCounter(COUNTER_PROPAGATION,"no information apart of type of datasource").increment(1); |
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return; |
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} |
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byte[] targetRowKey = Bytes.toBytes(rh.getResultId()); |
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final Put put = new Put(targetRowKey).add(Bytes.toBytes("result"), Bytes.toBytes("update_" + System.nanoTime()), oafUpdate);
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keyOut.set(targetRowKey); |
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context.write(keyOut, put); |
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context.getCounter(COUNTER_PROPAGATION, "added country to product").increment(1); |
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} |
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final String country = Value.fromJson(it.next().toString()).getValue(); // need to update the information for the country to each element in the iterator |
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if(country.trim().length() != 2) {
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try {
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Integer.parseInt(country.trim()); |
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} catch(Exception e) { }
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context.getCounter(COUNTER_PROPAGATION,"second element in reducer is not country").increment(1); |
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return; |
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} |
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if (!rh.getPropagate()){
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context.getCounter(COUNTER_PROPAGATION, "resultId expected in ordering was not found" ).increment(1); |
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} |
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boolean propagate = true; |
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while(it.hasNext()) {
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final String resultId = Value.fromJson(it.next().toString()).getValue(); |
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if (!resultId.startsWith(("50|"))) {
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if(!resultId.equalsIgnoreCase(country)) {
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context.getCounter(COUNTER_PROPAGATION, "resultId expected in ordering was not found").increment(1); |
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//throw new RuntimeException("Problem in country values of institutional repositories" + targetRowKey);
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propagate = false; |
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} |
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} else {
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if (propagate) {
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byte[] oafUpdate = getOafCountry(resultId, country, first.getTrust()); |
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byte[] targetRowKey = Bytes.toBytes(resultId); |
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final Put put = new Put(targetRowKey).add(Bytes.toBytes("result"), Bytes.toBytes("update_" + System.nanoTime()), oafUpdate);
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keyOut.set(targetRowKey); |
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context.write(keyOut, put); |
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context.getCounter(COUNTER_PROPAGATION, "added country to product").increment(1); |
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} |
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} |
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} |
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} else {
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context.getCounter(COUNTER_PROPAGATION,"not allowed dsType institutional datasource").increment(1); |
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} |
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} |
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private byte[] getOafCountry(String resultId, String countryValue, String trust) {
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final ResultProtos.Result.Metadata.Builder metadata = ResultProtos.Result.Metadata.newBuilder().addCountry( |
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getCountry(countryValue,trust,DNETSCHEMA,CLASS_ID,SCHEMA_ID,SCHEMA_NAME,DATA_INFO_TYPE,"Propagation of country information from datasources belonging to institutional repositories")); |
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final ResultProtos.Result.Builder result = ResultProtos.Result.newBuilder().setMetadata(metadata); |
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final OafProtos.OafEntity.Builder entity = OafProtos.OafEntity.newBuilder() |
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.setType(TypeProtos.Type.result) |
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.setId(resultId) |
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.setResult(result); |
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return OafProtos.Oaf.newBuilder() |
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.setKind(KindProtos.Kind.entity) |
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.setEntity(entity) |
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.build() |
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.toByteArray(); |
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} |
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} |
| modules/dnet-mapreduce-jobs/branches/master/src/main/java/eu/dnetlib/data/mapreduce/hbase/propagation/country/institutionalrepositories/PropagationCountryFromDsOrgResultMapper.java | ||
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} |
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private String getTrust(Result value) throws InvalidProtocolBufferException {
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final Map<byte[],byte[]> map = value.getFamilyMap(Bytes.toBytes("datasource"));
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final byte[] body = map.get(Bytes.toBytes("body"));
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Also available in: Unified diff
updated implementation to use iterator