forked from D-Net/dnet-hadoop
Update to include a blackList that filters out the results we know are wrongly associated to IE
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parent
c3fe59bc78
commit
12ffde023f
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@ -12,6 +12,7 @@ import org.apache.hadoop.io.Text;
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import org.apache.hadoop.io.compress.GzipCodec;
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import org.apache.hadoop.mapred.SequenceFileOutputFormat;
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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.FlatMapFunction;
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import org.apache.spark.sql.*;
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import org.apache.spark.sql.types.StructType;
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@ -70,6 +71,9 @@ public class CreateActionSetFromWebEntries 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 blackListInputPath = parser.get("blackListPath");
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log.info("blackListInputPath: {}", blackListInputPath);
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SparkConf conf = new SparkConf();
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runWithSparkSession(
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@ -77,35 +81,40 @@ public class CreateActionSetFromWebEntries implements Serializable {
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isSparkSessionManaged,
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spark -> {
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createActionSet(spark, inputPath, outputPath);
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createActionSet(spark, inputPath, outputPath, blackListInputPath);
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});
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}
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public static void createActionSet(SparkSession spark, String inputPath,
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String outputPath) {
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String outputPath, String blackListInputPath) {
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final Dataset<Row> dataset = readWebCrawl(spark, inputPath)
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.filter("publication_year <= 2020 or country_code=='IE'")
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.filter("country_code=='IE'")
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.drop("publication_year");
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dataset.flatMap((FlatMapFunction<Row, Relation>) row -> {
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List<Relation> ret = new ArrayList<>();
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final String ror = ROR_PREFIX
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+ IdentifierFactory.md5(PidCleaner.normalizePidValue("ROR", row.getAs("ror")));
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ret.addAll(createAffiliationRelationPairDOI(row.getAs("doi"), ror));
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ret.addAll(createAffiliationRelationPairPMID(row.getAs("pmid"), ror));
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ret.addAll(createAffiliationRelationPairPMCID(row.getAs("pmcid"), ror));
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final Dataset<Row> blackList = readBlackList(spark, blackListInputPath);
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return ret
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.iterator();
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}, Encoders.bean(Relation.class))
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.toJavaRDD()
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.map(p -> new AtomicAction(p.getClass(), p))
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.mapToPair(
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aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
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new Text(OBJECT_MAPPER.writeValueAsString(aa))))
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.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
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dataset.join(blackList, dataset.col("id").equalTo(blackList.col("OpenAlexId")), "left")
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.filter((FilterFunction<Row>) r -> r.getAs("OpenAlexId") == null)
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.drop("OpenAlexId")
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.flatMap((FlatMapFunction<Row, Relation>) row -> {
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List<Relation> ret = new ArrayList<>();
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final String ror = ROR_PREFIX
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+ IdentifierFactory.md5(PidCleaner.normalizePidValue("ROR", row.getAs("ror")));
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ret.addAll(createAffiliationRelationPairDOI(row.getAs("doi"), ror));
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ret.addAll(createAffiliationRelationPairPMID(row.getAs("pmid"), ror));
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ret.addAll(createAffiliationRelationPairPMCID(row.getAs("pmcid"), ror));
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return ret
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.iterator();
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}, Encoders.bean(Relation.class))
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.toJavaRDD()
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.map(p -> new AtomicAction(p.getClass(), p))
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.mapToPair(
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aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
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new Text(OBJECT_MAPPER.writeValueAsString(aa))))
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.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);//, GzipCodec.class);
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}
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@ -136,6 +145,15 @@ public class CreateActionSetFromWebEntries implements Serializable {
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}
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private static Dataset<Row> readBlackList(SparkSession spark, String inputPath){
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return spark
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.read()
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.option("header", true)
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.csv(inputPath)
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.select("OpenAlexId");
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}
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private static List<Relation> createAffiliationRelationPairPMCID(String pmcid, String ror) {
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if (pmcid == null)
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return new ArrayList<>();
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@ -16,5 +16,10 @@
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"paramLongName": "isSparkSessionManaged",
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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": "bl",
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"paramLongName": "blackListPath",
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"paramDescription": "the working path",
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"paramRequired": true
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}
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]
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@ -75,8 +75,12 @@ public class CreateASTest {
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String inputPath = getClass()
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.getResource(
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"/eu/dnetlib/dhp/actionmanager/webcrawl/")
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"/eu/dnetlib/dhp/actionmanager/webcrawl/input/")
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.getPath();
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String blackListPath = getClass()
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.getResource(
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"/eu/dnetlib/dhp/actionmanager/webcrawl/blackList/")
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.getPath();
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CreateActionSetFromWebEntries
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.main(
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@ -86,7 +90,8 @@ public class CreateASTest {
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"-sourcePath",
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inputPath,
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"-outputPath",
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workingDir.toString() + "/actionSet1"
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workingDir.toString() + "/actionSet1",
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"-blackListPath", blackListPath
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});
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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@ -96,7 +101,7 @@ public class CreateASTest {
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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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Assertions.assertEquals(64, tmp.count());
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Assertions.assertEquals(58, tmp.count());
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}
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@ -109,6 +114,10 @@ public class CreateASTest {
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.getResource(
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"/eu/dnetlib/dhp/actionmanager/webcrawl/")
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.getPath();
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String blackListPath = getClass()
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.getResource(
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"/eu/dnetlib/dhp/actionmanager/webcrawl/blackList/")
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.getPath();
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CreateActionSetFromWebEntries
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.main(
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@ -118,7 +127,8 @@ public class CreateASTest {
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"-sourcePath",
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inputPath,
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"-outputPath",
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workingDir.toString() + "/actionSet1"
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workingDir.toString() + "/actionSet1",
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"-blackListPath", blackListPath
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});
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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@ -184,7 +194,7 @@ public class CreateASTest {
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Assertions
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.assertEquals(
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5, tmp
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2, tmp
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.filter(
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r -> r
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.getSource()
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@ -197,7 +207,7 @@ public class CreateASTest {
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Assertions
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.assertEquals(
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5, tmp
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2, tmp
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.filter(
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r -> r
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.getTarget()
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@ -210,7 +220,7 @@ public class CreateASTest {
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Assertions
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.assertEquals(
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2, tmp
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1, tmp
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.filter(
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r -> r
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.getTarget()
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@ -224,7 +234,7 @@ public class CreateASTest {
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Assertions
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.assertEquals(
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2, tmp
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1, tmp
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.filter(
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r -> r
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.getTarget()
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@ -238,7 +248,7 @@ public class CreateASTest {
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Assertions
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.assertEquals(
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1, tmp
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0, tmp
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.filter(
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r -> r
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.getTarget()
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