master #11
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@ -9,131 +9,115 @@ import org.apache.hadoop.fs.FileSystem;
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import org.apache.spark.SparkConf;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaPairRDD;
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import org.apache.spark.api.java.JavaPairRDD;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.*;
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import org.apache.spark.sql.Row;
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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.SparkSession;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import scala.Tuple2;
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import scala.Tuple2;
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import java.util.*;
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import java.util.*;
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import static eu.dnetlib.dhp.PropagationConstant.*;
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import static eu.dnetlib.dhp.PropagationConstant.*;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
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public class SparkOrcidToResultFromSemRelJob3 {
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private static final Logger log = LoggerFactory.getLogger(SparkOrcidToResultFromSemRelJob3.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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public class SparkOrcidToResultFromSemRelJob2 {
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public static void main(String[] args) throws Exception {
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public static void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils.toString(SparkOrcidToResultFromSemRelJob3.class
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.getResourceAsStream("/eu/dnetlib/dhp/orcidtoresultfromsemrel/input_orcidtoresult_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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jsonConfiguration);
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkOrcidToResultFromSemRelJob2.class.getResourceAsStream("/eu/dnetlib/dhp/orcidtoresultfromremrel/input_orcidtoresult_parameters.json")));
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parser.parseArgument(args);
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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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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 String possibleUpdates = parser.get("possibleUpdatesPath");
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log.info("possibleUpdatesPath: {}", possibleUpdates);
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final String resultClassName = parser.get("resultTableName");
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log.info("resultTableName: {}", resultClassName);
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final String resultType = resultClassName.substring(resultClassName.lastIndexOf(".") + 1).toLowerCase();
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log.info("resultType: {}", resultType);
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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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SparkConf conf = new SparkConf();
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conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
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conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
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final SparkSession spark = SparkSession
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.builder()
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.appName(SparkOrcidToResultFromSemRelJob2.class.getSimpleName())
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.master(parser.get("master"))
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.config(conf)
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.enableHiveSupport()
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.getOrCreate();
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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runWithSparkHiveSession(conf, isSparkSessionManaged,
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final String inputPath = parser.get("sourcePath");
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spark -> {
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final String outputPath = "/tmp/provision/propagation/orcidtoresult";
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if(isTest(parser)) {
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removeOutputDir(spark, outputPath);
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final List<String> allowedsemrel = Arrays.asList(parser.get("allowedsemrels").split(";"));
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}
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boolean writeUpdate = TRUE.equals(parser.get("writeUpdate"));
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if(saveGraph)
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boolean saveGraph = TRUE.equals(parser.get("saveGraph"));
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execPropagation(spark, possibleUpdates, inputPath, outputPath, resultClazz);
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});
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createOutputDirs(outputPath, FileSystem.get(spark.sparkContext().hadoopConfiguration()));
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org.apache.spark.sql.Dataset<Relation> relation = spark.createDataset(sc.textFile(inputPath + "/relation")
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.map(item -> new ObjectMapper().readValue(item, Relation.class)).rdd(), Encoders.bean(Relation.class));
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org.apache.spark.sql.Dataset<Dataset> dataset = spark.createDataset(sc.textFile(inputPath + "/dataset")
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.map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.Dataset.class)).rdd(),
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Encoders.bean(eu.dnetlib.dhp.schema.oaf.Dataset.class));
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org.apache.spark.sql.Dataset<OtherResearchProduct> other = spark.createDataset(sc.textFile(inputPath + "/otherresearchproduct")
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.map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.OtherResearchProduct.class)).rdd(),
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Encoders.bean(eu.dnetlib.dhp.schema.oaf.OtherResearchProduct.class));
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org.apache.spark.sql.Dataset<Software> software = spark.createDataset(sc.textFile(inputPath + "/software")
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.map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.Software.class)).rdd(),
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Encoders.bean(eu.dnetlib.dhp.schema.oaf.Software.class));
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org.apache.spark.sql.Dataset<Publication> publication = spark.createDataset(sc.textFile(inputPath + "/publication")
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.map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.Publication.class)).rdd(),
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Encoders.bean(eu.dnetlib.dhp.schema.oaf.Publication.class));
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relation.createOrReplaceTempView("relation");
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String query = "Select source, target " +
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"from relation " +
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"where datainfo.deletedbyinference = false " + getConstraintList(" relclass = '" , allowedsemrel);
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org.apache.spark.sql.Dataset<Row> result_result = spark.sql(query);
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publication.createOrReplaceTempView("publication");
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org.apache.spark.sql.Dataset<ResultWithOrcid> pubs_with_orcid = getResultWithOrcid("publication", spark)
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.as(Encoders.bean(ResultWithOrcid.class));
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dataset.createOrReplaceTempView("dataset");
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org.apache.spark.sql.Dataset<ResultWithOrcid> dats_with_orcid = getResultWithOrcid("dataset", spark)
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.as(Encoders.bean(ResultWithOrcid.class));
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other.createOrReplaceTempView("orp");
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org.apache.spark.sql.Dataset<ResultWithOrcid> orp_with_orcid = getResultWithOrcid("orp", spark)
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.as(Encoders.bean(ResultWithOrcid.class));
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dataset.createOrReplaceTempView("software");
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org.apache.spark.sql.Dataset<ResultWithOrcid> software_with_orcid = getResultWithOrcid("software", spark)
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.as(Encoders.bean(ResultWithOrcid.class));
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//get the results having at least one author pid we are interested in
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//target of the relation from at least one source with orcid.
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//the set of authors contains all those that have orcid and are related to target
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//from any source with allowed semantic relationship
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JavaPairRDD<String, List<AutoritativeAuthor>> target_authorlist_from_pubs = getTargetAutoritativeAuthorList(pubs_with_orcid);
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JavaPairRDD<String, List<AutoritativeAuthor>> target_authorlist_from_dats = getTargetAutoritativeAuthorList(dats_with_orcid);
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JavaPairRDD<String, List<AutoritativeAuthor>> target_authorlist_from_orp = getTargetAutoritativeAuthorList(orp_with_orcid);
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JavaPairRDD<String, List<AutoritativeAuthor>> target_authorlist_from_sw = getTargetAutoritativeAuthorList(software_with_orcid);
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if(writeUpdate){
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target_authorlist_from_dats.map(r -> new ObjectMapper().writeValueAsString(r))
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.saveAsTextFile(outputPath + "/" + "update_dats");
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target_authorlist_from_pubs.map(r -> new ObjectMapper().writeValueAsString(r))
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.saveAsTextFile(outputPath + "/" + "update_pubs");
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target_authorlist_from_orp.map(r -> new ObjectMapper().writeValueAsString(r))
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.saveAsTextFile(outputPath + "/" + "update_orp");
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target_authorlist_from_sw.map(r -> new ObjectMapper().writeValueAsString(r))
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.saveAsTextFile(outputPath + "/" + "update_sw");
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}
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if(saveGraph){
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sc.textFile(inputPath + "/publication")
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.map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.Publication.class))
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.mapToPair(p -> new Tuple2<>(p.getId(),p))
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.leftOuterJoin(target_authorlist_from_pubs)
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.map(c -> {
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Result r = c._2()._1();
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if(!c._2()._2().isPresent()){
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return r;
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}
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List<eu.dnetlib.dhp.schema.oaf.Author> toenrich_author = r.getAuthor();
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List<AutoritativeAuthor> autoritativeAuthors = c._2()._2().get();
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for(eu.dnetlib.dhp.schema.oaf.Author author: toenrich_author){
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if (!containsAllowedPid(author)){
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enrichAuthor(author, autoritativeAuthors);
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}
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}
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return r;
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});
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}
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}
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}
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private static void enrichAuthor(eu.dnetlib.dhp.schema.oaf.Author a, List<AutoritativeAuthor> au){
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private static <R extends Result> void execPropagation(SparkSession spark, String possibleUpdatesPath, String inputPath,
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String outputPath, Class<R> resultClazz ) {
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//read possible updates (resultId and list of possible orcid to add
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Dataset<ResultOrcidList> possible_updates = readAssocResultOrcidList(spark, possibleUpdatesPath);
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//read the result we have been considering
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Dataset<R> result = readPathEntity(spark, inputPath, resultClazz);
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//make join result left_outer with possible updates
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result.joinWith(possible_updates, result.col("id").equalTo(possible_updates.col("resultId")),
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"left_outer")
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.map(value -> {
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R ret = value._1();
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Optional<ResultOrcidList> rol = Optional.ofNullable(value._2());
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if(rol.isPresent()) {
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List<Author> toenrich_author = ret.getAuthor();
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List<AutoritativeAuthor> autoritativeAuthors = rol.get().getAuthorList();
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for(Author author: toenrich_author){
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if (!containsAllowedPid(author)){
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enrichAuthor(author, autoritativeAuthors);
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}
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}
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}
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return ret;
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}, Encoders.bean(resultClazz))
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.toJSON()
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression","gzip")
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.text(outputPath);
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}
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private static Dataset<ResultOrcidList> readAssocResultOrcidList(SparkSession spark, String relationPath) {
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return spark
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.read()
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.textFile(relationPath)
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.map(value -> OBJECT_MAPPER.readValue(value, ResultOrcidList.class), Encoders.bean(ResultOrcidList.class));
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}
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private static void enrichAuthor(Author a, List<AutoritativeAuthor> au){
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for (AutoritativeAuthor aa: au){
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for (AutoritativeAuthor aa: au){
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if(enrichAuthor(aa, a)){
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if(enrichAuthor(aa, a)){
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return;
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return;
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@ -142,77 +126,9 @@ public class SparkOrcidToResultFromSemRelJob2 {
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}
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}
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// private static JavaPairRDD<String, List<AutoritativeAuthor>> getTargetAutoritativeAuthorList(org.apache.spark.sql.Dataset<Row> result_result, org.apache.spark.sql.Dataset<ResultWithOrcid> pubs_with_orcid) {
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// return pubs_with_orcid
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// .toJavaRDD()
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// .mapToPair(p -> new Tuple2<>(p.getId(), p.getAuthorList()))
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// .join(result_result.toJavaRDD().mapToPair(rel -> new Tuple2<>(rel.getString(0), rel.getString(1))))
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// .mapToPair(c -> new Tuple2<>(c._2._2(), c._2()._1()))
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// .reduceByKey((a, b) -> {
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// if(a == null){
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// return b;
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// }
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// if(b==null){
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// return a;
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// }
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//
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// Set<String> authSet = new HashSet<>();
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// a.stream().forEach(au -> authSet.add(au.getOrcid()));
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//
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// b.stream().forEach(au -> {
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// if (!authSet.contains(au.getOrcid())) {
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// a.add(au);
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// }
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// }
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// );
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// return a;
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// });
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// }
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private static JavaPairRDD<String, List<AutoritativeAuthor>> getTargetAutoritativeAuthorList( org.apache.spark.sql.Dataset<ResultWithOrcid> pubs_with_orcid) {
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return pubs_with_orcid
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.toJavaRDD()
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.mapToPair(p -> new Tuple2<>(p.getId(), p.getAuthorList()))
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.reduceByKey((a, b) -> {
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if(a == null){
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return b;
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}
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if(b==null){
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return a;
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}
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Set<String> authSet = new HashSet<>();
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a.stream().forEach(au -> authSet.add(au.getOrcid()));
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b.stream().forEach(au -> {
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if (!authSet.contains(au.getOrcid())) {
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a.add(au);
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}
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}
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);
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return a;
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});
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}
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private static org.apache.spark.sql.Dataset<Row> getResultWithOrcid(String table, SparkSession spark){
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String query = " select target, author " +
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" from (select id, collect_set(named_struct('name', name, 'surname', surname, 'fullname', fullname, 'orcid', orcid)) author " +
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" from ( " +
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" select id, MyT.fullname, MyT.name, MyT.surname, MyP.value orcid " +
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" from " + table +
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" lateral view explode (author) a as MyT " +
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" lateral view explode (MyT.pid) p as MyP " +
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" where MyP.qualifier.classid = 'ORCID') tmp " +
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" group by id) r_t " +
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" join (" +
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" select source, target " +
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" from relation " +
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" where datainfo.deletedbyinference = false and (relclass = 'isSupplementedBy' or relclass = 'isSupplementTo') rel_rel " +
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" on source = id";
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return spark.sql(query);
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}
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private static boolean enrichAuthor(AutoritativeAuthor autoritative_author, eu.dnetlib.dhp.schema.oaf.Author author) {
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private static boolean enrichAuthor(AutoritativeAuthor autoritative_author, Author author) {
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boolean toaddpid = false;
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boolean toaddpid = false;
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if (StringUtils.isNoneEmpty(autoritative_author.getSurname())) {
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if (StringUtils.isNoneEmpty(autoritative_author.getSurname())) {
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@ -252,100 +168,9 @@ private static JavaPairRDD<String, List<AutoritativeAuthor>> getTargetAutoritati
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}
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}
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// private static List<Author> enrichAuthors(List<Author> autoritative_authors, List<Author> to_enrich_authors, boolean filter){
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//// List<Author> autoritative_authors = p._2()._2().get().getAuthors();
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//// List<Author> to_enrich_authors = r.getAuthor();
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//
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// return to_enrich_authors
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// .stream()
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// .map(a -> {
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// if (filter) {
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// if (containsAllowedPid(a)) {
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// return a;
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// }
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// }
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//
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// List<Author> lst = autoritative_authors.stream()
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// .map(aa -> enrichAuthor(aa, a)).filter(au -> !(au == null)).collect(Collectors.toList());
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// if (lst.size() == 0) {
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// return a;
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// }
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// return lst.get(0);//Each author can be enriched at most once. It cannot be the same as many different people
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//
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// }).collect(Collectors.toList());
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// }
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//
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// private static void writeResult(JavaPairRDD<String, Result> results, JavaPairRDD<String, TypedRow> toupdateresult,
|
|
||||||
// String outputPath, String type) {
|
|
||||||
//
|
|
||||||
// results.join(toupdateresult)
|
|
||||||
// .map(p -> {
|
|
||||||
// Result r = p._2()._1();
|
|
||||||
//
|
|
||||||
// List<Author> autoritative_authors = p._2()._2().getAuthors();
|
|
||||||
// List<eu.dnetlib.dhp.schema.oaf.Author> to_enrich_authors = r.getAuthor();
|
|
||||||
//
|
|
||||||
// r.setAuthor(enrichAutors(autoritative_authors, to_enrich_authors, false));
|
|
||||||
//// .stream()
|
|
||||||
//// .map(a -> {
|
|
||||||
//// if(filter) {
|
|
||||||
//// if (containsAllowedPid(a)) {
|
|
||||||
//// return a;
|
|
||||||
//// }
|
|
||||||
//// }
|
|
||||||
////
|
|
||||||
//// List<Author> lst = autoritative_authors.stream()
|
|
||||||
//// .map(aa -> enrichAuthor(aa, a)).filter(au -> !(au == null)).collect(Collectors.toList());
|
|
||||||
//// if(lst.size() == 0){
|
|
||||||
//// return a;
|
|
||||||
//// }
|
|
||||||
//// return lst.get(0);//Each author can be enriched at most once. It cannot be the same as many different people
|
|
||||||
////
|
|
||||||
//// }).collect(Collectors.toList()));
|
|
||||||
//
|
|
||||||
// return r;
|
|
||||||
// })
|
|
||||||
// .map(p -> new ObjectMapper().writeValueAsString(p))
|
|
||||||
// .saveAsTextFile(outputPath + "/" + type + "_update");
|
|
||||||
// }
|
|
||||||
|
|
||||||
|
|
||||||
// private static void updateResult(JavaPairRDD<String, Result> results, JavaPairRDD<String, TypedRow> toupdateresult,
|
private static boolean containsAllowedPid(Author a) {
|
||||||
// String outputPath, String type) {
|
|
||||||
// results.leftOuterJoin(toupdateresult)
|
|
||||||
// .map(p -> {
|
|
||||||
// Result r = p._2()._1();
|
|
||||||
// if (p._2()._2().isPresent()){
|
|
||||||
// List<AutoritativeAuthor> autoritative_authors = p._2()._2().get().getAuthors();
|
|
||||||
// List<eu.dnetlib.dhp.schema.oaf.Author> to_enrich_authors = r.getAuthor();
|
|
||||||
//
|
|
||||||
// r.setAuthor(enrichAutors(autoritative_authors, to_enrich_authors, true));
|
|
||||||
//// .stream()
|
|
||||||
//// .map(a -> {
|
|
||||||
//// if(filter) {
|
|
||||||
//// if (containsAllowedPid(a)) {
|
|
||||||
//// return a;
|
|
||||||
//// }
|
|
||||||
//// }
|
|
||||||
////
|
|
||||||
//// List<Author> lst = autoritative_authors.stream()
|
|
||||||
//// .map(aa -> enrichAuthor(aa, a)).filter(au -> !(au == null)).collect(Collectors.toList());
|
|
||||||
//// if(lst.size() == 0){
|
|
||||||
//// return a;
|
|
||||||
//// }
|
|
||||||
//// return lst.get(0);//Each author can be enriched at most once. It cannot be the same as many different people
|
|
||||||
////
|
|
||||||
//// }).collect(Collectors.toList()));
|
|
||||||
// }
|
|
||||||
// return r;
|
|
||||||
// })
|
|
||||||
// .map(p -> new ObjectMapper().writeValueAsString(p))
|
|
||||||
// .saveAsTextFile(outputPath+"/"+type);
|
|
||||||
// }
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
private static boolean containsAllowedPid(eu.dnetlib.dhp.schema.oaf.Author a) {
|
|
||||||
for (StructuredProperty pid : a.getPid()) {
|
for (StructuredProperty pid : a.getPid()) {
|
||||||
if (PROPAGATION_AUTHOR_PID.equals(pid.getQualifier().getClassid())) {
|
if (PROPAGATION_AUTHOR_PID.equals(pid.getQualifier().getClassid())) {
|
||||||
return true;
|
return true;
|
||||||
|
|
@ -355,44 +180,3 @@ private static JavaPairRDD<String, List<AutoritativeAuthor>> getTargetAutoritati
|
||||||
}
|
}
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
/*private ResultProtos.Result.Metadata.Builder searchMatch(List<FieldTypeProtos.Author> author_list){
|
|
||||||
ResultProtos.Result.Metadata.Builder metadataBuilder = ResultProtos.Result.Metadata.newBuilder();
|
|
||||||
boolean updated = false;
|
|
||||||
|
|
||||||
for (FieldTypeProtos.Author a: author_list){
|
|
||||||
FieldTypeProtos.Author.Builder author = searchAuthor(a, autoritative_authors);
|
|
||||||
if(author != null){
|
|
||||||
updated = true;
|
|
||||||
metadataBuilder.addAuthor(author);
|
|
||||||
}else{
|
|
||||||
metadataBuilder.addAuthor(FieldTypeProtos.Author.newBuilder(a));
|
|
||||||
}
|
|
||||||
}
|
|
||||||
if(updated)
|
|
||||||
return metadataBuilder;
|
|
||||||
return null;
|
|
||||||
}
|
|
||||||
private FieldTypeProtos.Author.Builder searchAuthor(FieldTypeProtos.Author a, List<FieldTypeProtos.Author> author_list){
|
|
||||||
if(containsOrcid(a.getPidList()))
|
|
||||||
return null;
|
|
||||||
for(FieldTypeProtos.Author autoritative_author : author_list) {
|
|
||||||
if (equals(autoritative_author, a)) {
|
|
||||||
if(!containsOrcid(a.getPidList()))
|
|
||||||
return update(a, autoritative_author);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
return null;
|
|
||||||
|
|
||||||
}
|
|
||||||
|
|
||||||
private boolean containsOrcid(List<FieldTypeProtos.KeyValue> pidList){
|
|
||||||
if(pidList == null)
|
|
||||||
return false;
|
|
||||||
return pidList
|
|
||||||
.stream()
|
|
||||||
.filter(kv -> kv.getKey().equals(PropagationConstants.AUTHOR_PID))
|
|
||||||
.collect(Collectors.toList()).size() > 0;
|
|
||||||
}
|
|
||||||
*/
|
|
||||||
Loading…
Reference in New Issue