Revision 54039
Added by Miriam Baglioni over 5 years ago
| ProjectToResultMapper.java | ||
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import eu.dnetlib.data.mapreduce.util.OafRowKeyDecoder; |
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import eu.dnetlib.data.proto.OafProtos; |
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import eu.dnetlib.data.proto.TypeProtos; |
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import org.apache.commons.lang3.StringUtils; |
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import org.apache.hadoop.hbase.client.Result; |
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import org.apache.hadoop.hbase.io.ImmutableBytesWritable; |
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import org.apache.hadoop.hbase.mapreduce.TableMapper; |
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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 java.io.IOException; |
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import java.util.Collection; |
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import java.util.HashSet; |
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import java.util.Map; |
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import java.util.Set; |
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import java.util.*; |
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import java.util.stream.Collectors; |
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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.getEntity; |
| ... | ... | |
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private static final String SEPARATOR = ","; |
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private String[] sem_rels; |
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private String trust; |
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private ImmutableBytesWritable keyOut; |
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private Text valueOut; |
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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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keyOut = new ImmutableBytesWritable(); |
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valueOut = new Text(); |
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String[] default_set = {"resultResult_supplement_isSupplementedBy"};
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sem_rels = context.getConfiguration().getStrings("propagatetoproject.semanticrelations",default_set);
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sem_rels = context.getConfiguration().getStrings("propagatetoproject.semanticrelations", DEFAULT_RELATION_SET);
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trust = context.getConfiguration().get("propagatetoproject.trust","0.85");
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| ... | ... | |
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protected void map(final ImmutableBytesWritable keyIn, final Result value, final Context context) throws IOException, InterruptedException {
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final TypeProtos.Type type = OafRowKeyDecoder.decode(keyIn.copyBytes()).getType(); |
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//If the type is not result I do not need to process it |
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if(type!= TypeProtos.Type.result){
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if(!type.equals(TypeProtos.Type.result)) {
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return; |
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} |
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//verify if entity is valid |
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final OafProtos.OafEntity entity = getEntity(value,type); |
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final OafProtos.OafEntity entity = getEntity(value, type);
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if (entity == null) {
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context.getCounter(COUNTER_PROPAGATION,"Del by inference or null body for result").increment(1); |
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return; |
| ... | ... | |
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String projectIdList = getProjectIdList(value); |
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//if the list of projects is not empty, verify if it exists some allowed semantic relation to which propagate the project |
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if(projectIdList != null){
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if(StringUtils.isNotBlank(projectIdList)){
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final Set<String> toemitrelations = new HashSet<>(); |
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//selection of all the results bind by this result considering all the allowed semantic relations |
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for (String sem_rel : sem_rels) |
| ... | ... | |
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context.getCounter(COUNTER_PROPAGATION, "emit for semantic relation").increment(toemitrelations.size()); |
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} |
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valueOut.set(Value.newInstance(projectIdList,FROM_RESULT).toJson()); |
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keyOut.set(entity.getId().getBytes()); |
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valueOut.set(Value.newInstance(projectIdList,Type.fromresult).toJson()); |
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//context.write(ProjectToResultKey.create(FROM_RESULT,entity.getId()), valueOut); |
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context.write(new ImmutableBytesWritable(entity.getId().getBytes()), valueOut); |
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context.write(keyOut, valueOut); |
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context.getCounter(COUNTER_PROPAGATION, "emit for result").increment(1); |
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} |
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//emit for each valid semantic relation the id of the relation target and the list of projects associated to the source of the relation |
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private void emit( Context context, Set<String> toemitrelations, String projectIdList) throws IOException, InterruptedException {
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for(String relation:toemitrelations){
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valueOut.set(Value.newInstance( projectIdList,trust,FROM_SEM_REL).toJson());
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context.write(new ImmutableBytesWritable(relation.getBytes()), valueOut);
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for(String relation : toemitrelations){
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keyOut.set(relation.getBytes());
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valueOut.set(Value.newInstance( projectIdList,trust,Type.fromsemrel).toJson());
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context.write(keyOut, valueOut); |
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} |
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} |
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private Collection<? extends String> getRelationTarget(Result value, String sem_rel) throws InvalidProtocolBufferException {
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final Set<String> toemitrelations = new HashSet<>(); |
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//starting from the Result gets the list of projects it is related to and returns it as a csv |
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private String getProjectIdList(Result value) throws InvalidProtocolBufferException {
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Set<String> ret = getRelationTarget(value, OUTCOME_PRODUCEDBY); |
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return ret.size() == 0 ? null : String.join(SEPARATOR, ret); |
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} |
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private Set<String> getRelationTarget(Result value, String sem_rel) throws InvalidProtocolBufferException {
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final Map<byte[], byte[]> relationMap = value.getFamilyMap(Bytes.toBytes(sem_rel)); |
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for (byte[] relation : relationMap.values()) {
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final OafProtos.Oaf rel_oaf = OafProtos.Oaf.parseFrom(relation); |
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if (isValid(rel_oaf)) {
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if (!rel_oaf.getDataInfo().getDeletedbyinference()) {
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toemitrelations.add(rel_oaf.getRel().getTarget()); |
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} |
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} |
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} |
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return toemitrelations; |
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} |
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/* |
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we could extract the target qualifiers from the familyMap's keyset, but we also need to check the relationship is not deletedbyinference |
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return relationMap.keySet().stream() |
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.map(String::new) |
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.collect(Collectors.toCollection(HashSet::new)); |
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*/ |
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return relationMap.values().stream() |
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.map(this::asOaf) |
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.filter(Objects::nonNull) |
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.filter(o -> isValid(o)) |
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.filter(o -> !o.getDataInfo().getDeletedbyinference()) |
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.map(o -> o.getRel().getTarget()) |
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.collect(Collectors.toCollection(HashSet::new)); |
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//starting from the Result gets the list of projects it is related to and returns it as a csv |
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private String getProjectIdList(Result value) throws InvalidProtocolBufferException {
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Collection<? extends String> ret = getRelationTarget(value, "resultProject_outcome_isProducedBy"); |
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return ret.size() == 0 ? null : String.join(SEPARATOR,ret); |
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} |
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private OafProtos.Oaf asOaf(byte[] r) {
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try {
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return OafProtos.Oaf.parseFrom(r); |
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} catch (InvalidProtocolBufferException e) {
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return null; |
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} |
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} |
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private boolean isValid(final OafProtos.Oaf oaf) {
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Also available in: Unified diff
modified type for type variable. From int to Type