forked from D-Net/dnet-hadoop
[OC New] last fix
This commit is contained in:
parent
fd34372c40
commit
48c052215c
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@ -95,7 +95,7 @@ public class SparkAtomicActionScoreJob implements Serializable {
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return projectScores.map((MapFunction<BipProjectModel, Project>) bipProjectScores -> {
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Project project = new Project();
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project.setId(bipProjectScores.getProjectId());
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// project.setId(bipProjectScores.getProjectId());
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project.setMeasures(bipProjectScores.toMeasures());
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return project;
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}, Encoders.bean(Project.class))
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@ -22,6 +22,7 @@ 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 com.fasterxml.jackson.core.JsonProcessingException;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.actionmanager.opencitations.model.COCI;
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@ -41,7 +42,9 @@ public class CreateActionSetSparkJob implements Serializable {
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private static final String DOI_PREFIX = "50|doi_________::";
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private static final String PMID_PREFIX = "50|pmid________::";
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private static final String ARXIV_PREFIX = "50|arXiv_______::";
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private static final String PMCID_PREFIX = "50|pmcid_______::";
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private static final String TRUST = "0.91";
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private static final Logger log = LoggerFactory.getLogger(CreateActionSetSparkJob.class);
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@ -74,25 +77,18 @@ public class CreateActionSetSparkJob implements Serializable {
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final String outputPath = parser.get("outputPath");
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log.info("outputPath {}", outputPath);
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final boolean shouldDuplicateRels = Optional
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.ofNullable(parser.get("shouldDuplicateRels"))
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.map(Boolean::valueOf)
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.orElse(Boolean.FALSE);
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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 -> extractContent(spark, inputPath, outputPath, shouldDuplicateRels));
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spark -> extractContent(spark, inputPath, outputPath));
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}
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private static void extractContent(SparkSession spark, String inputPath, String outputPath,
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boolean shouldDuplicateRels) {
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private static void extractContent(SparkSession spark, String inputPath, String outputPath) {
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getTextTextJavaPairRDD(spark, inputPath)
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// .union(getTextTextJavaPairRDD(spark, inputPath, shouldDuplicateRels, POCI))
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.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
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.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);// , GzipCodec.class);
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}
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private static JavaPairRDD<Text, Text> getTextTextJavaPairRDD(SparkSession spark, String inputPath) {
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@ -115,7 +111,7 @@ public class CreateActionSetSparkJob implements Serializable {
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new Text(OBJECT_MAPPER.writeValueAsString(aa))));
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}
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private static List<Relation> createRelation(COCI value) {
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private static List<Relation> createRelation(COCI value) throws JsonProcessingException {
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List<Relation> relationList = new ArrayList<>();
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@ -131,25 +127,52 @@ public class CreateActionSetSparkJob implements Serializable {
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case "pmid":
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citing = PMID_PREFIX
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+ IdentifierFactory
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.md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getCiting()));
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.md5(PidCleaner.normalizePidValue(PidType.pmid.toString(), value.getCiting()));
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break;
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case "arxiv":
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citing = ARXIV_PREFIX
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+ IdentifierFactory
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.md5(PidCleaner.normalizePidValue(PidType.arXiv.toString(), value.getCiting()));
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break;
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case "pmcid":
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citing = PMCID_PREFIX
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+ IdentifierFactory
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.md5(PidCleaner.normalizePidValue(PidType.pmc.toString(), value.getCiting()));
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break;
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case "isbn":
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case "issn":
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return relationList;
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default:
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throw new IllegalStateException("Invalid prefix: " + value.getCiting_pid());
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throw new IllegalStateException("Invalid prefix: " + new ObjectMapper().writeValueAsString(value));
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}
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switch (value.getCited_pid()) {
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case "doi":
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cited = DOI_PREFIX
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+ IdentifierFactory
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.md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getCiting()));
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.md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getCited()));
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break;
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case "pmid":
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cited = PMID_PREFIX
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+ IdentifierFactory
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.md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getCiting()));
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.md5(PidCleaner.normalizePidValue(PidType.pmid.toString(), value.getCited()));
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break;
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case "arxiv":
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cited = ARXIV_PREFIX
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+ IdentifierFactory
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.md5(PidCleaner.normalizePidValue(PidType.arXiv.toString(), value.getCited()));
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break;
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case "pmcid":
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cited = PMCID_PREFIX
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+ IdentifierFactory
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.md5(PidCleaner.normalizePidValue(PidType.pmc.toString(), value.getCited()));
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break;
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case "isbn":
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case "issn":
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return relationList;
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default:
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throw new IllegalStateException("Invalid prefix: " + value.getCited_pid());
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throw new IllegalStateException("Invalid prefix: " + new ObjectMapper().writeValueAsString(value));
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}
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if (!citing.equals(cited)) {
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@ -9,11 +9,19 @@ import java.util.Arrays;
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import java.util.Objects;
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import java.util.Optional;
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import java.util.stream.Collectors;
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import java.util.zip.ZipEntry;
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import java.util.zip.ZipInputStream;
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import org.apache.commons.cli.ParseException;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.conf.Configuration;
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import org.apache.hadoop.fs.FSDataInputStream;
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import org.apache.hadoop.fs.FSDataOutputStream;
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import org.apache.hadoop.fs.FileSystem;
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import org.apache.hadoop.fs.Path;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.function.FlatMapFunction;
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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.*;
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import org.slf4j.Logger;
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@ -62,6 +70,10 @@ public class MapOCIdsInPids implements Serializable {
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final String outputPath = parser.get("outputPath");
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log.info("outputPath {}", outputPath);
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final String nameNode = parser.get("nameNode");
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log.info("nameNode {}", nameNode);
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unzipCorrespondenceFile(inputPath, nameNode);
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SparkConf conf = new SparkConf();
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runWithSparkSession(
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conf,
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@ -70,6 +82,41 @@ public class MapOCIdsInPids implements Serializable {
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}
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private static void unzipCorrespondenceFile(String inputPath, String hdfsNameNode) throws IOException {
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Configuration conf = new Configuration();
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conf.set("fs.defaultFS", hdfsNameNode);
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final Path path = new Path(inputPath + "/correspondence/omid.zip");
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FileSystem fileSystem = FileSystem.get(conf);
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FSDataInputStream project_zip = fileSystem.open(path);
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try (ZipInputStream zis = new ZipInputStream(project_zip)) {
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ZipEntry entry = null;
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while ((entry = zis.getNextEntry()) != null) {
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if (!entry.isDirectory()) {
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String fileName = entry.getName();
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byte buffer[] = new byte[1024];
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int count;
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try (
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FSDataOutputStream out = fileSystem
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.create(new Path(inputPath + "/correspondence/omid.csv"))) {
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while ((count = zis.read(buffer, 0, buffer.length)) != -1)
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out.write(buffer, 0, count);
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}
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}
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}
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}
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}
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private static void mapIdentifiers(SparkSession spark, String inputPath, String outputPath) {
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Dataset<COCI> coci = spark
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.read()
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@ -85,7 +132,7 @@ public class MapOCIdsInPids implements Serializable {
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.option("inferSchema", "true")
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.option("header", "true")
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.option("quotes", "\"")
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.load(inputPath + "/correspondence/omid.zip")
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.load(inputPath + "/correspondence/omid.csv")
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.repartition(5000)
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.flatMap((FlatMapFunction<Row, Tuple2<String, String>>) r -> {
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String ocIdentifier = r.getAs("omid");
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@ -98,7 +145,7 @@ public class MapOCIdsInPids implements Serializable {
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}, Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
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Dataset<COCI> mappedCitingDataset = coci
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.joinWith(correspondenceData, coci.col("citing").equalTo(correspondenceData.col("_1")), "left")
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.joinWith(correspondenceData, coci.col("citing").equalTo(correspondenceData.col("_1")))
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.map((MapFunction<Tuple2<COCI, Tuple2<String, String>>, COCI>) t2 -> {
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String correspondent = t2._2()._2();
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t2._1().setCiting_pid(correspondent.substring(0, correspondent.indexOf(":")));
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@ -118,6 +165,16 @@ public class MapOCIdsInPids implements Serializable {
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.mode(SaveMode.Append)
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.option("compression", "gzip")
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.json(outputPath);
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mappedCitingDataset
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.joinWith(correspondenceData, mappedCitingDataset.col("cited").equalTo(correspondenceData.col("_1")))
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.map((MapFunction<Tuple2<COCI, Tuple2<String, String>>, COCI>) t2 -> {
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String correspondent = t2._2()._2();
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t2._1().setCited_pid(correspondent.substring(0, correspondent.indexOf(":")));
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t2._1().setCited(correspondent.substring(correspondent.indexOf(":") + 1));
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return t2._1();
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}, Encoders.bean(COCI.class))
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.foreach((ForeachFunction<COCI>) c -> System.out.println(OBJECT_MAPPER.writeValueAsString(c)));
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}
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}
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@ -14,6 +14,7 @@ import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.conf.Configuration;
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import org.apache.hadoop.fs.*;
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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.MapFunction;
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import org.apache.spark.sql.*;
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import org.slf4j.Logger;
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@ -79,7 +80,7 @@ public class ReadCOCI implements Serializable {
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new Path(workingPath), true);
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while (fileStatusListIterator.hasNext()) {
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LocatedFileStatus fileStatus = fileStatusListIterator.next();
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log.info("extracting file {}", fileStatus.getPath().toString());
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Dataset<Row> cociData = spark
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.read()
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.format("csv")
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@ -91,6 +92,7 @@ public class ReadCOCI implements Serializable {
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.repartition(100);
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cociData.map((MapFunction<Row, COCI>) row -> {
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COCI coci = new COCI();
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coci.setCiting(row.getString(1));
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@ -100,10 +102,12 @@ public class ReadCOCI implements Serializable {
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return coci;
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}, Encoders.bean(COCI.class))
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.filter((FilterFunction<COCI>) c -> c != null)
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.write()
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.mode(SaveMode.Append)
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.option("compression", "gzip")
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.json(outputPath);
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fileSystem.rename(fileStatus.getPath(), new Path("/tmp/miriam/OC/DONE"));
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}
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}
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@ -27,6 +27,8 @@ public class COCI implements Serializable {
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}
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public void setCiting(String citing) {
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if (citing != null && citing.startsWith("omid:"))
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citing = citing.substring(5);
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this.citing = citing;
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}
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@ -35,6 +37,8 @@ public class COCI implements Serializable {
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}
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public void setCited(String cited) {
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if (cited != null && cited.startsWith("omid:"))
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cited = cited.substring(5);
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this.cited = cited;
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}
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@ -27,6 +27,7 @@
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<case to="download">${wf:conf('resumeFrom') eq 'DownloadDump'}</case>
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<case to="extract">${wf:conf('resumeFrom') eq 'ExtractContent'}</case>
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<case to="read">${wf:conf('resumeFrom') eq 'ReadContent'}</case>
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<case to="remap">${wf:conf('resumeFrom') eq 'MapContent'}</case>
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<case to="create_actionset">${wf:conf('resumeFrom') eq 'CreateAS'}</case>
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<default to="deleteoutputpath"/> <!-- first action to be done when downloadDump is to be performed -->
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</switch>
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@ -154,6 +155,7 @@
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</spark-opts>
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<arg>--inputPath</arg><arg>${inputPath}</arg>
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<arg>--outputPath</arg><arg>${outputPathExtraction}</arg>
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<arg>--nameNode</arg><arg>${nameNode}</arg>
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</spark>
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<ok to="create_actionset"/>
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<error to="Kill"/>
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@ -16,5 +16,10 @@
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"paramLongName": "isSparkSessionManged",
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"paramDescription": "the hdfs name node",
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"paramRequired": false
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}
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},{
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"paramName": "nn",
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"paramLongName": "nameNode",
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"paramDescription": "the hdfs name node",
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"paramRequired": true
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}
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]
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@ -76,7 +76,7 @@ public class CreateOpenCitationsASTest {
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String inputPath = getClass()
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.getResource(
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"/eu/dnetlib/dhp/actionmanager/opencitations/COCI")
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"/eu/dnetlib/dhp/actionmanager/opencitations/COCI/inputremap/jsonforas")
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.getPath();
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CreateActionSetSparkJob
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@ -84,8 +84,6 @@ public class CreateOpenCitationsASTest {
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new String[] {
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"-isSparkSessionManaged",
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Boolean.FALSE.toString(),
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"-shouldDuplicateRels",
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Boolean.TRUE.toString(),
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"-inputPath",
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inputPath,
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"-outputPath",
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@ -99,9 +97,10 @@ public class CreateOpenCitationsASTest {
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.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
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.map(aa -> ((Relation) aa.getPayload()));
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assertEquals(31, tmp.count());
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Assertions.assertEquals(27, tmp.count());
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tmp.foreach(r -> Assertions.assertEquals(1, r.getCollectedfrom().size()));
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// tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r)));
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tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r)));
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}
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@ -0,0 +1,90 @@
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package eu.dnetlib.dhp.actionmanager.opencitations;
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import java.io.IOException;
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import java.nio.file.Files;
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import java.nio.file.Path;
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import org.apache.commons.io.FileUtils;
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import org.apache.hadoop.conf.Configuration;
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import org.apache.hadoop.fs.FileSystem;
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import org.apache.hadoop.fs.LocalFileSystem;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaRDD;
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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.SparkSession;
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import org.junit.jupiter.api.AfterAll;
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import org.junit.jupiter.api.Assertions;
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import org.junit.jupiter.api.BeforeAll;
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import org.junit.jupiter.api.Test;
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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 eu.dnetlib.dhp.actionmanager.opencitations.model.COCI;
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/**
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* @author miriam.baglioni
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* @Date 07/03/24
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*/
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public class RemapTest {
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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private static SparkSession spark;
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private static Path workingDir;
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private static final Logger log = LoggerFactory
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.getLogger(RemapTest.class);
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@BeforeAll
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public static void beforeAll() throws IOException {
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workingDir = Files
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.createTempDirectory(RemapTest.class.getSimpleName());
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log.info("using work dir {}", workingDir);
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SparkConf conf = new SparkConf();
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conf.setAppName(RemapTest.class.getSimpleName());
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conf.setMaster("local[*]");
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conf.set("spark.driver.host", "localhost");
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conf.set("hive.metastore.local", "true");
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conf.set("spark.ui.enabled", "false");
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conf.set("spark.sql.warehouse.dir", workingDir.toString());
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conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
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spark = SparkSession
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.builder()
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.appName(RemapTest.class.getSimpleName())
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.config(conf)
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.getOrCreate();
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}
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@AfterAll
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public static void afterAll() throws IOException {
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FileUtils.deleteDirectory(workingDir.toFile());
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spark.stop();
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}
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@Test
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void testRemap() throws Exception {
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String inputPath = getClass()
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.getResource(
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"/eu/dnetlib/dhp/actionmanager/opencitations/COCI/inputremap")
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.getPath();
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MapOCIdsInPids
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.main(
|
||||
new String[] {
|
||||
"-isSparkSessionManged",
|
||||
Boolean.FALSE.toString(),
|
||||
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|
||||
inputPath,
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||||
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|
||||
workingDir.toString() + "/out/",
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||||
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||||
});
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||||
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}
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||||
}
|
||||
|
|
@ -0,0 +1,31 @@
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||||
|
|
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|||
omid,id
|
||||
br/061201599020,doi:10.1142/s0219887817501687
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br/06210273177,doi:10.1090/qam/20394
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br/06502272390,pmid:32235596 doi:10.3390/nano10040644
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br/0660613430,doi:10.1007/bf00470411
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br/06120941789,doi:10.1098/rspa.2006.1747
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br/062602732073,doi:10.1007/978-3-642-38844-6_25
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br/06230199640,pmid:25088780 doi:10.1016/j.ymeth.2014.07.008
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br/061103703697,pmid:2682767
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br/0670517081,doi:10.1016/j.foodpol.2021.102189
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br/06502310477,doi:10.1142/s0218127416500450
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br/06520113284,doi:10.1109/cfasta57821.2023.10243367
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br/062303652439,pmid:5962654 doi:10.1016/0020-708x(66)90001-9
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br/06250691436,doi:10.1042/bst20150052 pmid:26009172
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br/061201665577,doi:10.1097/00115550-200205000-00018
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br/06503490336,pmid:34689254 doi:10.1007/s10072-021-05687-0
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br/06220615942,pmid:25626134 doi:10.1016/j.jcis.2015.01.008
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br/061103389243,doi:10.4324/9780203702819-10
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br/062303011271,doi:10.1109/icassp.2011.5946250
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br/061302926083,doi:10.4018/978-1-6684-3937-1.ch002
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br/061402485360,doi:10.1109/iciict.2015.7396079
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br/06410101083,doi:10.1016/j.autcon.2023.104828
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br/062202243386,doi:10.1016/0001-8791(81)90022-1
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br/06170421486,doi:10.1130/0016-7606(2003)115<0166:dsagmf>2.0.co;2
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br/061201983865,doi:10.4324/9781315109008 isbn:9781315109008
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br/061701697230,doi:10.1016/j.trd.2012.07.006
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br/061201137111,doi:10.1109/access.2020.2971656
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br/0648013560,doi:10.1080/14772000.2012.705356
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br/0690214059,doi:10.2752/175630608x329217
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br/06450133713,doi:10.1093/acprof:oso/9780199670888.003.0008
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br/0628074892,doi:10.1097/hnp.0000000000000597
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br/061601032219,doi:10.1002/bdm.2102
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br/06602079930,doi:10.1101/2020.08.25.267500
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br/0604192147,doi:10.11501/3307395
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br/061101933800,doi:10.1142/s0217732398002242
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Reference in New Issue