forked from D-Net/dnet-hadoop
modified code to use the the API. Removing not needed parameters. Rewritten the code to exploit the parallel stream on the entity types
This commit is contained in:
parent
34358afe75
commit
f206ff42d6
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@ -9,7 +9,6 @@ import java.util.*;
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import org.apache.commons.io.IOUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.function.FilterFunction;
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import org.apache.spark.api.java.function.ForeachFunction;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.Encoders;
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@ -21,8 +20,11 @@ import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import com.google.gson.Gson;
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import eu.dnetlib.dhp.api.Utils;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.bulktag.community.*;
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import eu.dnetlib.dhp.schema.common.EntityType;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.oaf.Datasource;
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import eu.dnetlib.dhp.schema.oaf.Result;
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@ -53,50 +55,38 @@ public class SparkBulkTagJob {
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.orElse(Boolean.TRUE);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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Boolean isTest = Optional
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.ofNullable(parser.get("isTest"))
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.map(Boolean::valueOf)
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.orElse(Boolean.FALSE);
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log.info("isTest: {} ", isTest);
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final String inputPath = parser.get("sourcePath");
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log.info("inputPath: {}", inputPath);
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final String outputPath = parser.get("outputPath");
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log.info("outputPath: {}", outputPath);
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final boolean production = Boolean.valueOf(parser.get("production"));
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log.info("production: {}", production);
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ProtoMap protoMappingParams = new Gson().fromJson(parser.get("pathMap"), ProtoMap.class);
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log.info("pathMap: {}", new Gson().toJson(protoMappingParams));
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final String resultClassName = parser.get("resultTableName");
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log.info("resultTableName: {}", resultClassName);
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final Boolean saveGraph = Optional
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.ofNullable(parser.get("saveGraph"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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log.info("saveGraph: {}", saveGraph);
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Class<? extends Result> resultClazz = (Class<? extends Result>) Class.forName(resultClassName);
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SparkConf conf = new SparkConf();
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CommunityConfiguration cc;
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String taggingConf = parser.get("taggingConf");
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String taggingConf = Optional
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.ofNullable(parser.get("taggingConf"))
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.map(String::valueOf)
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.orElse(null);
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if (isTest) {
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if (taggingConf != null) {
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cc = CommunityConfigurationFactory.newInstance(taggingConf);
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} else {
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cc = QueryInformationSystem.getCommunityConfiguration(parser.get("isLookUpUrl"));
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cc = Utils.getCommunityConfiguration(production);
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}
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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removeOutputDir(spark, outputPath);
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extendCommunityConfigurationForEOSC(spark, inputPath, cc);
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execBulkTag(spark, inputPath, outputPath, protoMappingParams, resultClazz, cc);
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execBulkTag(spark, inputPath, outputPath, protoMappingParams, cc);
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});
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}
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@ -105,10 +95,7 @@ public class SparkBulkTagJob {
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Dataset<String> datasources = readPath(
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spark, inputPath
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.substring(
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0,
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inputPath.lastIndexOf("/"))
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+ "/datasource",
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+ "datasource",
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Datasource.class)
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.filter((FilterFunction<Datasource>) ds -> isOKDatasource(ds))
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.map((MapFunction<Datasource, String>) ds -> ds.getId(), Encoders.STRING());
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@ -116,10 +103,10 @@ public class SparkBulkTagJob {
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Map<String, List<Pair<String, SelectionConstraints>>> dsm = cc.getEoscDatasourceMap();
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for (String ds : datasources.collectAsList()) {
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final String dsId = ds.substring(3);
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if (!dsm.containsKey(dsId)) {
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// final String dsId = ds.substring(3);
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if (!dsm.containsKey(ds)) {
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ArrayList<Pair<String, SelectionConstraints>> eoscList = new ArrayList<>();
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dsm.put(dsId, eoscList);
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dsm.put(ds, eoscList);
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}
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}
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@ -141,22 +128,30 @@ public class SparkBulkTagJob {
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String inputPath,
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String outputPath,
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ProtoMap protoMappingParams,
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Class<R> resultClazz,
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CommunityConfiguration communityConfiguration) {
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ResultTagger resultTagger = new ResultTagger();
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readPath(spark, inputPath, resultClazz)
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.map(patchResult(), Encoders.bean(resultClazz))
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.filter(Objects::nonNull)
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.map(
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(MapFunction<R, R>) value -> resultTagger
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.enrichContextCriteria(
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value, communityConfiguration, protoMappingParams),
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Encoders.bean(resultClazz))
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.json(outputPath);
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ModelSupport.entityTypes
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.keySet()
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.parallelStream()
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.filter(e -> ModelSupport.isResult(e))
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.forEach(e -> {
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removeOutputDir(spark, outputPath + e.name());
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ResultTagger resultTagger = new ResultTagger();
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Class<R> resultClazz = ModelSupport.entityTypes.get(e);
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readPath(spark, inputPath + e.name(), resultClazz)
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.map(patchResult(), Encoders.bean(resultClazz))
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.filter(Objects::nonNull)
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.map(
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(MapFunction<R, R>) value -> resultTagger
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.enrichContextCriteria(
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value, communityConfiguration, protoMappingParams),
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Encoders.bean(resultClazz))
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.json(outputPath + e.name());
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});
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}
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public static <R> Dataset<R> readPath(
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@ -4,6 +4,7 @@ package eu.dnetlib.dhp.bulktag.community;
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import java.io.Serializable;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.Optional;
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import com.google.gson.Gson;
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@ -13,7 +14,7 @@ public class Community implements Serializable {
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private String id;
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private List<String> subjects = new ArrayList<>();
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private List<Provider> providers = new ArrayList<>();
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private List<ZenodoCommunity> zenodoCommunities = new ArrayList<>();
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private List<String> zenodoCommunities = new ArrayList<>();
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private SelectionConstraints constraints = new SelectionConstraints();
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private SelectionConstraints removeConstraints = new SelectionConstraints();
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@ -26,7 +27,7 @@ public class Community implements Serializable {
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return !getSubjects().isEmpty()
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|| !getProviders().isEmpty()
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|| !getZenodoCommunities().isEmpty()
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|| getConstraints().getCriteria() != null;
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|| (Optional.ofNullable(getConstraints()).isPresent() && getConstraints().getCriteria() != null);
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}
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public String getId() {
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@ -53,11 +54,11 @@ public class Community implements Serializable {
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this.providers = providers;
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}
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public List<ZenodoCommunity> getZenodoCommunities() {
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public List<String> getZenodoCommunities() {
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return zenodoCommunities;
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}
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public void setZenodoCommunities(List<ZenodoCommunity> zenodoCommunities) {
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public void setZenodoCommunities(List<String> zenodoCommunities) {
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this.zenodoCommunities = zenodoCommunities;
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}
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@ -81,7 +81,7 @@ public class CommunityConfiguration implements Serializable {
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this.removeConstraintsMap = removeConstraintsMap;
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}
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CommunityConfiguration(final Map<String, Community> communities) {
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public CommunityConfiguration(final Map<String, Community> communities) {
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this.communities = communities;
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init();
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}
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@ -117,10 +117,10 @@ public class CommunityConfiguration implements Serializable {
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add(d.getOpenaireId(), new Pair<>(id, d.getSelectionConstraints()), datasourceMap);
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}
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// get zenodo communities
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for (ZenodoCommunity zc : c.getZenodoCommunities()) {
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for (String zc : c.getZenodoCommunities()) {
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add(
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zc.getZenodoCommunityId(),
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new Pair<>(id, zc.getSelCriteria()),
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zc,
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new Pair<>(id, null),
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zenodocommunityMap);
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}
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selectionConstraintsMap.put(id, c.getConstraints());
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@ -143,16 +143,16 @@ public class CommunityConfigurationFactory {
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return providerList;
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}
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private static List<ZenodoCommunity> parseZenodoCommunities(final Node node) {
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private static List<String> parseZenodoCommunities(final Node node) {
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final List<Node> list = node.selectNodes("./zenodocommunities/zenodocommunity");
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final List<ZenodoCommunity> zenodoCommunityList = new ArrayList<>();
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final List<String> zenodoCommunityList = new ArrayList<>();
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for (Node n : list) {
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ZenodoCommunity zc = new ZenodoCommunity();
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zc.setZenodoCommunityId(n.selectSingleNode("./zenodoid").getText());
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zc.setSelCriteria(n.selectSingleNode("./selcriteria"));
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// ZenodoCommunity zc = new ZenodoCommunity();
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// zc.setZenodoCommunityId(n.selectSingleNode("./zenodoid").getText());
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// zc.setSelCriteria(n.selectSingleNode("./selcriteria"));
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zenodoCommunityList.add(zc);
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zenodoCommunityList.add(n.selectSingleNode("./zenodoid").getText());
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}
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log.info("size of the zenodo community list " + zenodoCommunityList.size());
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@ -4,6 +4,8 @@ package eu.dnetlib.dhp.bulktag.community;
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import java.io.Serializable;
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import java.lang.reflect.InvocationTargetException;
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import org.apache.htrace.fasterxml.jackson.annotation.JsonIgnore;
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import eu.dnetlib.dhp.bulktag.criteria.Selection;
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import eu.dnetlib.dhp.bulktag.criteria.VerbResolver;
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@ -11,7 +13,8 @@ public class Constraint implements Serializable {
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private String verb;
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private String field;
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private String value;
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// private String element;
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@JsonIgnore
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private Selection selection;
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public String getVerb() {
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@ -38,10 +41,8 @@ public class Constraint implements Serializable {
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this.value = value;
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}
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public void setSelection(Selection sel) {
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selection = sel;
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}
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@JsonIgnore
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public void setSelection(VerbResolver resolver)
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throws InvocationTargetException, NoSuchMethodException, InstantiationException,
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IllegalAccessException {
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@ -52,11 +53,5 @@ public class Constraint implements Serializable {
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return selection.apply(metadata);
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}
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// public String getElement() {
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// return element;
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// }
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//
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// public void setElement(String element) {
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// this.element = element;
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// }
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}
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@ -85,16 +85,18 @@ public class ResultTagger implements Serializable {
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conf
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.getRemoveConstraintsMap()
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.keySet()
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.forEach(communityId -> {
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if (conf.getRemoveConstraintsMap().get(communityId).getCriteria() != null &&
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conf
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.getRemoveConstraintsMap()
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.get(communityId)
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.getCriteria()
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.stream()
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.anyMatch(crit -> crit.verifyCriteria(param)))
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removeCommunities.add(communityId);
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});
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.forEach(
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communityId -> {
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if (conf.getRemoveConstraintsMap().keySet().contains(communityId) &&
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conf.getRemoveConstraintsMap().get(communityId).getCriteria() != null &&
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conf
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.getRemoveConstraintsMap()
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.get(communityId)
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.getCriteria()
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.stream()
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.anyMatch(crit -> crit.verifyCriteria(param)))
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removeCommunities.add(communityId);
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});
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// communities contains all the communities to be added as context for the result
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final Set<String> communities = new HashSet<>();
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@ -124,10 +126,10 @@ public class ResultTagger implements Serializable {
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if (Objects.nonNull(result.getInstance())) {
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for (Instance i : result.getInstance()) {
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if (Objects.nonNull(i.getCollectedfrom()) && Objects.nonNull(i.getCollectedfrom().getKey())) {
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collfrom.add(StringUtils.substringAfter(i.getCollectedfrom().getKey(), "|"));
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collfrom.add(i.getCollectedfrom().getKey());
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}
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if (Objects.nonNull(i.getHostedby()) && Objects.nonNull(i.getHostedby().getKey())) {
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hostdby.add(StringUtils.substringAfter(i.getHostedby().getKey(), "|"));
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hostdby.add(i.getHostedby().getKey());
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}
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}
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@ -7,11 +7,13 @@ import java.util.Collection;
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import java.util.List;
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import java.util.Map;
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import com.fasterxml.jackson.annotation.JsonAutoDetect;
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import com.google.gson.Gson;
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import com.google.gson.reflect.TypeToken;
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import eu.dnetlib.dhp.bulktag.criteria.VerbResolver;
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@JsonAutoDetect
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public class SelectionConstraints implements Serializable {
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private List<Constraints> criteria;
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@ -0,0 +1,225 @@
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package eu.dnetlib.dhp.resulttocommunityfromorganization;
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/**
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* @author miriam.baglioni
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* @Date 16/10/23
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*/
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/**
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* @author miriam.baglioni
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* @Date 16/10/23
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*/
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import static eu.dnetlib.dhp.PropagationConstant.*;
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import static eu.dnetlib.dhp.PropagationConstant.OBJECT_MAPPER;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.util.*;
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import java.util.stream.Collectors;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.io.ObjectWritable;
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import org.apache.hadoop.io.compress.GzipCodec;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.function.*;
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import org.apache.spark.api.java.function.FilterFunction;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.*;
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import org.apache.spark.sql.types.DataTypes;
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import org.apache.spark.sql.types.StructType;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import com.google.gson.Gson;
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import eu.dnetlib.dhp.api.Utils;
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import eu.dnetlib.dhp.api.model.CommunityEntityMap;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import scala.Tuple2;
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public class PrepareResultCommunity2 {
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private static final Logger log = LoggerFactory
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.getLogger(eu.dnetlib.dhp.resulttocommunityfromorganization.PrepareResultCommunitySet.class);
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public static void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils
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.toString(
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eu.dnetlib.dhp.resulttocommunityfromorganization.PrepareResultCommunitySet.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/resulttocommunityfromorganization/input_preparecommunitytoresult_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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String inputPath = parser.get("sourcePath");
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log.info("inputPath: {}", inputPath);
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final String outputPath = parser.get("outputPath");
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log.info("outputPath: {}", outputPath);
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final boolean production = Boolean.valueOf(parser.get("production"));
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log.info("production: {}", production);
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final CommunityEntityMap organizationMap = Utils.getCommunityOrganization(production);
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log.info("organizationMap: {}", new Gson().toJson(organizationMap));
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SparkConf conf = new SparkConf();
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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removeOutputDir(spark, outputPath);
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prepareInfo(spark, inputPath, outputPath, organizationMap);
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});
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}
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private static void prepareInfo(
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SparkSession spark,
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String inputPath,
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String outputPath,
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CommunityEntityMap organizationMap) {
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final StructType structureSchema = new StructType()
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.add(
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"dataInfo", new StructType()
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.add("deletedbyinference", DataTypes.BooleanType)
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.add("invisible", DataTypes.BooleanType))
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.add("source", DataTypes.StringType)
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.add("target", DataTypes.StringType)
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.add("relClass", DataTypes.StringType);
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readPath(spark, inputPath, Relation.class)
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.foreach((ForeachFunction<Relation>) r -> System.out.println(new ObjectMapper().writeValueAsString(r)));
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Dataset<Row> resultOrganization = spark
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.read()
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.schema(Encoders.bean(Relation.class).schema())
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.json(inputPath)
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.filter(
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"dataInfo.deletedbyinference != true " +
|
||||
"and relClass == '" + ModelConstants.HAS_AUTHOR_INSTITUTION + "'")
|
||||
.select(
|
||||
new Column("source").as("resultId"),
|
||||
new Column("target").as("organizationId"));
|
||||
|
||||
resultOrganization
|
||||
.foreach((ForeachFunction<Row>) r -> System.out.println(new ObjectMapper().writeValueAsString(r)));
|
||||
|
||||
Dataset<Row> organizationOrganization = spark
|
||||
.read()
|
||||
.schema(structureSchema)
|
||||
.json(inputPath)
|
||||
.filter(
|
||||
"dataInfo.deletedbyinference != true " +
|
||||
"and relClass == '" + ModelConstants.MERGES + "'")
|
||||
.select(
|
||||
new Column("source").as("masterOrganization"),
|
||||
new Column("target").as("duplicateOrganization"));
|
||||
|
||||
resultOrganization
|
||||
.joinWith(
|
||||
organizationOrganization, resultOrganization
|
||||
.col("organizationId")
|
||||
.equalTo(organizationOrganization.col("masterOrganization")),
|
||||
"left")
|
||||
.groupByKey(
|
||||
(MapFunction<Tuple2<Row, Row>, String>) t2 -> (String) t2._1().getAs("resultId"), Encoders.STRING())
|
||||
.mapGroups((MapGroupsFunction<String, Tuple2<Row, Row>, ResultCommunityList>) (k, v) -> {
|
||||
ResultCommunityList rcl = new ResultCommunityList();
|
||||
rcl.setResultId(k);
|
||||
ArrayList<String> cl = new ArrayList<>();
|
||||
Tuple2<Row, Row> first = v.next();
|
||||
cl.addAll(organizationMap.get(first._1().getAs("organizationId")));
|
||||
if (Optional.ofNullable(first._2()).isPresent()) {
|
||||
cl.addAll(organizationMap.get(first._2().getAs(("duplicateOrganization"))));
|
||||
}
|
||||
v.forEachRemaining(o -> cl.addAll(organizationMap.get(o._2().getAs("duplicateOrganization"))));
|
||||
if (cl.size() == 0)
|
||||
return null;
|
||||
rcl.setCommunityList(new ArrayList<>(cl.stream().distinct().collect(Collectors.toList())));
|
||||
return rcl;
|
||||
}, Encoders.bean(ResultCommunityList.class))
|
||||
.filter(Objects::nonNull)
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression", "gzip")
|
||||
.json(outputPath);
|
||||
|
||||
// Dataset<Relation> relation = readPath(spark, inputPath, Relation.class)
|
||||
// .filter((FilterFunction<Relation>) r -> !r.getDataInfo().getDeletedbyinference() );
|
||||
//
|
||||
// relation.createOrReplaceTempView("relation");
|
||||
//
|
||||
// String query = "SELECT result_organization.source resultId, result_organization.target orgId, org_set merges "
|
||||
// + "FROM (SELECT source, target "
|
||||
// + " FROM relation "
|
||||
// + " AND lower(relClass) = '"
|
||||
// + ModelConstants.HAS_AUTHOR_INSTITUTION.toLowerCase()
|
||||
// + "') result_organization "
|
||||
// + "LEFT JOIN (SELECT source, collect_set(target) org_set "
|
||||
// + " FROM relation "
|
||||
// + " AND lower(relClass) = '"
|
||||
// + ModelConstants.MERGES.toLowerCase()
|
||||
// + "' "
|
||||
// + " GROUP BY source) organization_organization "
|
||||
// + "ON result_organization.target = organization_organization.source ";
|
||||
//
|
||||
// Dataset<ResultOrganizations> result_organizationset = spark
|
||||
// .sql(query)
|
||||
// .as(Encoders.bean(ResultOrganizations.class));
|
||||
//
|
||||
// result_organizationset
|
||||
// .map(mapResultCommunityFn(organizationMap), Encoders.bean(ResultCommunityList.class))
|
||||
// .filter(Objects::nonNull)
|
||||
// .toJavaRDD()
|
||||
// .mapToPair(value -> new Tuple2<>(value.getResultId(), value))
|
||||
// .reduceByKey((a, b) -> {
|
||||
// ArrayList<String> cl = a.getCommunityList();
|
||||
// b.getCommunityList().stream().forEach(s -> {
|
||||
// if (!cl.contains(s)) {
|
||||
// cl.add(s);
|
||||
// }
|
||||
// });
|
||||
// a.setCommunityList(cl);
|
||||
// return a;
|
||||
// })
|
||||
// .map(value -> OBJECT_MAPPER.writeValueAsString(value._2()))
|
||||
// .saveAsTextFile(outputPath, GzipCodec.class);
|
||||
}
|
||||
|
||||
private static MapFunction<ResultOrganizations, ResultCommunityList> mapResultCommunityFn(
|
||||
CommunityEntityMap organizationMap) {
|
||||
return value -> {
|
||||
String rId = value.getResultId();
|
||||
Optional<List<String>> orgs = Optional.ofNullable(value.getMerges());
|
||||
String oTarget = value.getOrgId();
|
||||
Set<String> communitySet = new HashSet<>();
|
||||
if (organizationMap.containsKey(oTarget)) {
|
||||
communitySet.addAll(organizationMap.get(oTarget));
|
||||
}
|
||||
if (orgs.isPresent())
|
||||
for (String oId : orgs.get()) {
|
||||
if (organizationMap.containsKey(oId)) {
|
||||
communitySet.addAll(organizationMap.get(oId));
|
||||
}
|
||||
}
|
||||
if (!communitySet.isEmpty()) {
|
||||
ResultCommunityList rcl = new ResultCommunityList();
|
||||
rcl.setResultId(rId);
|
||||
ArrayList<String> communityList = new ArrayList<>();
|
||||
communityList.addAll(communitySet);
|
||||
rcl.setCommunityList(communityList);
|
||||
return rcl;
|
||||
}
|
||||
return null;
|
||||
};
|
||||
}
|
||||
}
|
||||
Loading…
Reference in New Issue