[SKG-IF-EOSC] added possibility to filter for LOT1 constraints and results related to specific communities
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package eu.dnetlib.dhp.oa.graph.dump.filterentities;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.oaf.Result;
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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.sql.Encoders;
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import org.apache.spark.sql.SaveMode;
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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 java.io.Serializable;
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import java.util.Optional;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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/**
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* @author miriam.baglioni
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* @Date 20/03/24
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*/
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public class SelectCommunityEntities implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(SelectCommunityEntities.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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FilterEntities.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/graph/dump/skgif/eosc_entities_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 = Optional
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.ofNullable(parser.get("isSparkSessionManaged"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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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 filterPath = parser.get("filterPath");
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log.info("filterPath: {}", filterPath);
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final String communityId = parser.get("communityId");
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log.info("communityId: {}", communityId);
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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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selectEntities(spark, inputPath, filterPath, communityId);
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});
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}
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private static <R extends Result> void selectEntities(SparkSession spark, String inputPath, String filterPath, String communityId) {
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ModelSupport.entityTypes.keySet().forEach(e -> {
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if (ModelSupport.isResult(e)) {
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spark
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.read()
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.schema(Encoders.bean(Result.class).schema())
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.json(inputPath + e.name())
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.where("datainfo.deletedbyinference != true and datainfo.invisible != true")
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.select("id", "context")
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.where("array_contains(context.id,'"+communityId+"')")
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.drop("context")
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.distinct()
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.parquet(filterPath + e.name() + "_ids");
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}
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});
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}
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}
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@ -28,7 +28,6 @@ import scala.Tuple2;
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*/
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public class SelectEOSCEntities implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(SelectEOSCEntities.class);
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private static final String B2FIND_IDENTIFIER = "10|re3data_____::730f562f9efe8a3b3742d2da510d4335";
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public static void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils
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@ -68,17 +67,6 @@ public class SelectEOSCEntities implements Serializable {
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private static <R extends Result> void selectEntities(SparkSession spark, String inputPath, String filterPath) {
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ModelSupport.entityTypes.keySet().forEach(e -> {
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if (ModelSupport.isResult(e)) {
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// Utils
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// .readPath(spark, inputPath + e.name(), ModelSupport.entityTypes.get(e))
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// .filter(
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// (FilterFunction<R>) r -> !r.getDataInfo().getDeletedbyinference()
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// && !r.getDataInfo().getInvisible()
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// && (r.getContext().stream().anyMatch(c -> c.getId().equals("eosc")) ||
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// r
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// .getCollectedfrom()
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// .stream()
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// .anyMatch(cf -> cf.getValue().equalsIgnoreCase("B2FIND"))))
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// .map((MapFunction<R, String>) r -> r.getId(), Encoders.STRING())
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spark
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.read()
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@ -94,7 +82,6 @@ public class SelectEOSCEntities implements Serializable {
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.option("compression", "gzip")
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.parquet(filterPath + e.name() + "_ids");
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//
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}
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});
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@ -0,0 +1,133 @@
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package eu.dnetlib.dhp.oa.graph.dump.filterentities;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.oaf.*;
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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.sql.Encoders;
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import org.apache.spark.sql.SaveMode;
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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 static org.apache.spark.sql.functions.expr;
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import static org.apache.spark.sql.functions.max;
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import static org.apache.spark.sql.functions.col;
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import java.io.Serializable;
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import java.util.Optional;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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/**
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* @author miriam.baglioni
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* @Date 20/03/24
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*/
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public class SelectLOT1Entities implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(SelectLOT1Entities.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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FilterEntities.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/graph/dump/skgif/eosc_entities_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 = Optional
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.ofNullable(parser.get("isSparkSessionManaged"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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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 filterPath = parser.get("filterPath");
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log.info("filterPath: {}", filterPath);
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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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selectEntities(spark, inputPath, filterPath);
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});
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}
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private static <R extends Result> void selectEntities(SparkSession spark, String inputPath, String filterPath) {
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selectPublications(spark,inputPath,filterPath);
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selectDataset(spark,inputPath,filterPath);
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selectSoftware(spark,inputPath,filterPath);
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selectOthers(spark,inputPath,filterPath);
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}
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private static void selectOthers(SparkSession spark, String inputPath, String filterPath) {
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spark.read().schema(Encoders.bean(OtherResearchProduct.class).schema())
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.json(inputPath + "otherresearchproduct")
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.where("datainfo.deletedbyinference != true AND datainfo.invisible != true")
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.selectExpr("id", "instance", "explode(pid) as pid").where("pid.qualifier.classid IN ('doi', 'handle')") // filter by pid type
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.selectExpr("id", "explode(instance) as instance")
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.withColumn("CCL", expr("CASE WHEN instance.license.value LIKE 'CC%' OR instance.license.value LIKE '%/creativecommons.org/%' THEN 1 ELSE 0 END"))
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.groupBy("id")
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.agg(max(col("CCL")).as("CCL"))
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.parquet(filterPath + "otherresearchproduct_ids");
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}
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private static void selectSoftware(SparkSession spark, String inputPath, String filterPath) {
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spark.read().schema(Encoders.bean(Software.class).schema())
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.json(inputPath + "software")
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.where("datainfo.deletedbyinference != true AND datainfo.invisible != true")
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.selectExpr("id", "instance", "explode(pid) as pid").where("pid.qualifier.classid IN ('doi', 'swhid')") // filter by pid type
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.selectExpr("id", "explode(instance) as instance")
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.withColumn("CCL", expr("CASE WHEN instance.license.value LIKE 'CC%' OR instance.license.value LIKE '%/creativecommons.org/%' THEN 1 ELSE 0 END"))
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.groupBy("id")
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.agg(max(col("CCL")).as("CCL"))
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.parquet(filterPath + "software_ids");
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}
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private static void selectDataset(SparkSession spark, String inputPath, String filterPath) {
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spark.read().schema(Encoders.bean(Dataset.class).schema())
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.json(inputPath + "dataset")
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.where("datainfo.deletedbyinference != true AND datainfo.invisible != true")
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.selectExpr("id", "instance", "explode(pid) as pid").where("pid.qualifier.classid IN ('doi', 'handle', 'pdb', 'ena', 'uniprot')") // filter by pid type
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.selectExpr("id", "explode(instance) as instance")
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.withColumn("CCL", expr("CASE WHEN instance.license.value LIKE 'CC%' OR instance.license.value LIKE '%/creativecommons.org/%' THEN 1 ELSE 0 END"))
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.groupBy("id")
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.agg(max(col("CCL")).as("CCL"))
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.parquet(filterPath + "dataset_ids");
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}
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private static void selectPublications(SparkSession spark, String inputPath, String filterPath) {
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spark.read().schema(Encoders.bean(Publication.class).schema())
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.json(inputPath + "publication")
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.where("datainfo.deletedbyinference != true AND datainfo.invisible != true")
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.selectExpr("id", "instance", "explode(pid) as pid").where("pid.qualifier.classid IN ('doi', 'arXiv', 'pmid', 'handle')") // filter by pid type
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.selectExpr("id", "explode(instance) as instance").where("instance.instancetype.classname IN('Book', 'Article', 'Journal', 'Data Paper', 'Software Paper', 'Preprint', 'Part of book or chapter of book', 'Thesis', 'Master thesis', 'Bachelor thesis', 'Doctoral thesis', 'Conference object', 'Research', 'Other literature type')")
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.withColumn("CCL", expr("CASE WHEN instance.license.value LIKE 'CC%' OR instance.license.value LIKE '%/creativecommons.org/%' THEN 1 ELSE 0 END"))
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.groupBy("id")
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.agg(max(col("CCL")).as("CCL"))
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.parquet(filterPath + "publication_ids");
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}
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}
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@ -16,5 +16,10 @@
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"paramLongName": "isSparkSessionManaged",
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"paramDescription": "true if the spark session is managed, false otherwise",
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"paramRequired": false
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}
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},{
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"paramName": "ci",
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"paramLongName": "communityId",
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"paramDescription": "true if the spark session is managed, false otherwise",
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"paramRequired": false
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}
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]
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@ -77,7 +77,9 @@
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<decision name="select_subset">
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<switch>
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<!-- This one is if I hve to select the results as we do now for the eosc futere portal-->
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<case to="select_eosc_results">${wf:conf('filter') eq true}</case>
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<case to="select_eosc_results">${wf:conf('filter') eq 'EOSC'}</case>
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<case to="select_lot1_results">${wf:conf('filter') eq 'LOT1'}</case>
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<case to="select_community_results">${wf:conf('filter') eq 'Community'}</case>
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<!-- This one takes the identifier of the results matching different criteria and computed outside this code-->
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<default to="filter"/>
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</switch>
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@ -113,7 +115,59 @@
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<ok to="filter"/>
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<error to="Kill"/>
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</action>
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<action name="select_lot1_results">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Selecting graph results ids relevant for LOT1</name>
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<class>eu.dnetlib.dhp.oa.graph.dump.filterentities.SelectLOT1Entities</class>
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<jar>dump-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=4
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--executor-memory=4G
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--driver-memory=${sparkDriverMemory}
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--conf spark.executor.memoryOverhead=5G
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
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--conf spark.sql.shuffle.partitions=15000
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</spark-opts>
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<arg>--sourcePath</arg><arg>${sourcePath}</arg>
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<arg>--filterPath</arg><arg>${filterPath}/eoscIds/</arg>
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</spark>
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<ok to="filter"/>
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<error to="Kill"/>
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</action>
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<action name="select_community_results">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Selecting graph results ids relevant for Communities</name>
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<class>eu.dnetlib.dhp.oa.graph.dump.filterentities.SelectCommunityEntities</class>
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<jar>dump-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=4
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--executor-memory=4G
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--driver-memory=${sparkDriverMemory}
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--conf spark.executor.memoryOverhead=5G
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
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--conf spark.sql.shuffle.partitions=15000
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</spark-opts>
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<arg>--sourcePath</arg><arg>${sourcePath}</arg>
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<arg>--filterPath</arg><arg>${filterPath}/eoscIds/</arg>
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<arg>--communityId</arg><arg>${communityId}</arg>
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</spark>
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<ok to="filter"/>
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<error to="Kill"/>
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</action>
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<action name="filter">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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