D-Net

package eu.dnetlib.data.mapreduce.hbase.propagation.projecttoresult;

import com.google.protobuf.InvalidProtocolBufferException;

import eu.dnetlib.data.mapreduce.hbase.propagation.Value;

import eu.dnetlib.data.mapreduce.util.OafRowKeyDecoder;

import eu.dnetlib.data.proto.OafProtos;

import eu.dnetlib.data.proto.TypeProtos;

import org.apache.commons.lang3.StringUtils;

import org.apache.hadoop.hbase.client.Result;

import org.apache.hadoop.hbase.io.ImmutableBytesWritable;

import org.apache.hadoop.hbase.mapreduce.TableMapper;

import org.apache.hadoop.hbase.util.Bytes;

import org.apache.hadoop.io.Text;

import java.io.IOException;

import java.util.*;

import java.util.stream.Collectors;

import static eu.dnetlib.data.mapreduce.hbase.propagation.PropagationConstants.*;

import static eu.dnetlib.data.mapreduce.hbase.propagation.Utils.getEntity;

//public class ProjectToResultMapper extends TableMapper<ProjectToResultKey, Text> {

public class ProjectToResultMapper extends TableMapper<ImmutableBytesWritable, Text> {

    private static final String SEPARATOR = ",";

    private String[] sem_rels;

    private String trust;

    private ImmutableBytesWritable keyOut;

    private Text valueOut;

    @Override

    protected void setup(final Context context) throws IOException, InterruptedException {

        keyOut = new ImmutableBytesWritable();

        valueOut = new Text();

        sem_rels = context.getConfiguration().getStrings("propagatetoproject.semanticrelations", DEFAULT_RELATION_SET);

        trust = context.getConfiguration().get("propagatetoproject.trust","0.85");

    }

    @Override

    protected void map(final ImmutableBytesWritable keyIn, final Result value, final Context context) throws IOException, InterruptedException {

        final TypeProtos.Type type = OafRowKeyDecoder.decode(keyIn.copyBytes()).getType();

        //If the type is not result I do not need to process it

        if(!type.equals(TypeProtos.Type.result)) {

            return;

        }

        //verify if entity is valid

        final OafProtos.OafEntity entity = getEntity(value, type);

        if (entity == null) {

            context.getCounter(COUNTER_PROPAGATION,"Del by inference or null body for result").increment(1);

            return;

        }

        context.getCounter(COUNTER_PROPAGATION, "Valid result ").increment(1);

        //selection of all the projects associated to this result

        String projectIdList = getProjectIdList(value);

        //if the list of projects is not empty, verify if it exists some allowed semantic relation to which propagate the project

        if(StringUtils.isNotBlank(projectIdList)){

            final Set<String> toemitrelations = new HashSet<>();

            //selection of all the results bind by this result considering all the allowed semantic relations

            for (String sem_rel : sem_rels)

                toemitrelations.addAll(getRelationTarget(value,sem_rel));

            emit(context, toemitrelations, projectIdList);

            context.getCounter(COUNTER_PROPAGATION, "emit for semantic relation").increment(toemitrelations.size());

        }

        keyOut.set(entity.getId().getBytes());

        valueOut.set(Value.newInstance(projectIdList,Type.fromresult).toJson());

        //context.write(ProjectToResultKey.create(FROM_RESULT,entity.getId()), valueOut);

        context.write(keyOut, valueOut);

        context.getCounter(COUNTER_PROPAGATION, "emit for result").increment(1);

    }

    //emit for each valid semantic relation the id of the relation target and the list of projects associated to the source of the relation

    private void emit( Context context, Set<String> toemitrelations, String projectIdList) throws IOException, InterruptedException {

        for(String relation : toemitrelations){

            keyOut.set(relation.getBytes());

            valueOut.set(Value.newInstance( projectIdList,trust,Type.fromsemrel).toJson());

            context.write(keyOut, valueOut);

        }

    }

    //starting from the Result gets the list of projects it is related to and returns it as a csv

    private String getProjectIdList(Result value) throws InvalidProtocolBufferException {

        Set<String> ret = getRelationTarget(value, OUTCOME_PRODUCEDBY);

        return ret.size() == 0 ? null : String.join(SEPARATOR, ret);

    }

    private Set<String> getRelationTarget(Result value, String sem_rel) throws InvalidProtocolBufferException {

        final Map<byte[], byte[]> relationMap = value.getFamilyMap(Bytes.toBytes(sem_rel));

        /*

        we could extract the target qualifiers from the familyMap's keyset, but we also need to check the relationship is not deletedbyinference

        return relationMap.keySet().stream()

                .map(String::new)

                .collect(Collectors.toCollection(HashSet::new));

        */

        return relationMap.values().stream()

                .map(this::asOaf)

                .filter(Objects::nonNull)

                .filter(o -> isValid(o))

                .filter(o -> !o.getDataInfo().getDeletedbyinference())

                .map(o -> o.getRel().getTarget())

                .collect(Collectors.toCollection(HashSet::new));

    }

    private OafProtos.Oaf asOaf(byte[] r) {

        try {

            return OafProtos.Oaf.parseFrom(r);

        } catch (InvalidProtocolBufferException e) {

            return null;

        }

    }

    private boolean isValid(final OafProtos.Oaf oaf) {

        return (oaf != null) && oaf.isInitialized();

    }

}