updated unpaywall mapping
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@ -3,16 +3,20 @@ package eu.dnetlib.dhp.provision;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.provision.scholix.Scholix;
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import eu.dnetlib.dhp.utils.DHPUtils;
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import eu.dnetlib.dhp.provision.scholix.ScholixResource;
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import eu.dnetlib.dhp.provision.scholix.summary.ScholixSummary;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.io.compress.GzipCodec;
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import org.apache.spark.api.java.JavaPairRDD;
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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.api.java.function.PairFunction;
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import org.apache.spark.api.java.function.PairFlatMapFunction;
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import org.apache.spark.sql.SparkSession;
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import scala.Tuple2;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.Random;
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public class SparkGenerateScholix {
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private static final String jsonIDPath = "$.id";
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@ -21,6 +25,8 @@ public class SparkGenerateScholix {
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public static void main(String[] args) throws Exception {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkGenerateScholix.class.getResourceAsStream("/eu/dnetlib/dhp/provision/input_generate_summary_parameters.json")));
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parser.parseArgument(args);
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@ -37,29 +43,48 @@ public class SparkGenerateScholix {
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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final JavaRDD<String> relationToExport = sc.textFile(graphPath + "/relation").filter(ProvisionUtil::isNotDeleted).repartition(4000);
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final JavaPairRDD<String,String> scholixSummary = sc.textFile(workingDirPath + "/summary").mapToPair((PairFunction<String, String, String>) i -> new Tuple2<>(DHPUtils.getJPathString(jsonIDPath, i), i));
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scholixSummary.join(
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relationToExport
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.mapToPair((PairFunction<String, String, String>) i -> new Tuple2<>(DHPUtils.getJPathString(sourceIDPath, i), i)))
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.map(Tuple2::_2)
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.mapToPair(summaryRelation ->
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new Tuple2<>(
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DHPUtils.getJPathString(targetIDPath, summaryRelation._2()),
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Scholix.generateScholixWithSource(summaryRelation._1(), summaryRelation._2())))
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// .join(scholixSummary)
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// final JavaRDD<String> relationToExport = sc.textFile(graphPath + "/relation").filter(ProvisionUtil::isNotDeleted).repartition(4000);
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final JavaPairRDD<String,ScholixResource> scholixSummary =
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sc.textFile(workingDirPath + "/summary")
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.flatMapToPair((PairFlatMapFunction<String, String, ScholixResource>) i -> {
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final ObjectMapper mapper = new ObjectMapper();
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final ScholixSummary summary = mapper.readValue(i, ScholixSummary.class);
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ScholixResource tmp = ScholixResource.fromSummary(summary);
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final List<Tuple2<String, ScholixResource>> result = new ArrayList<>();
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for (int k = 0; k<10; k++)
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result.add(new Tuple2<>(String.format("%s::%d", tmp.getDnetIdentifier(), k), tmp));
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return result.iterator();
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});
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// scholixSummary.join(
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// relationToExport
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// .mapToPair((PairFunction<String, String, String>) i -> new Tuple2<>(DHPUtils.getJPathString(sourceIDPath, i), i)))
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// .map(Tuple2::_2)
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// .map(i -> i._1().addTarget(i._2()))
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.map(s-> {
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// .mapToPair(summaryRelation ->
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// new Tuple2<>(
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// DHPUtils.getJPathString(targetIDPath, summaryRelation._2()),
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// Scholix.generateScholixWithSource(summaryRelation._1(), summaryRelation._2())))
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//
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// .map(t-> t._2().setTarget(new ScholixResource().setDnetIdentifier(t._1())))
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// .map(s-> {
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// ObjectMapper mapper = new ObjectMapper();
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// return mapper.writeValueAsString(s);
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// })
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// .saveAsTextFile(workingDirPath + "/scholix", GzipCodec.class);
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sc.textFile(workingDirPath + "/scholix")
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.mapToPair(t -> {
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ObjectMapper mapper = new ObjectMapper();
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return mapper.writeValueAsString(s);
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Scholix scholix = mapper.readValue(t, Scholix.class);
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Random rand = new Random();
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return new Tuple2<>(String.format("%s::%d",scholix.getTarget().getDnetIdentifier(), rand.nextInt(10)), scholix);
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})
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.saveAsTextFile(workingDirPath + "/scholix", GzipCodec.class);
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;
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.join(scholixSummary)
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.map(t-> {
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Scholix item = t._2()._1().setTarget(t._2()._2());
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item.generateIdentifier();
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return item;
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})
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.map(s-> new ObjectMapper().writeValueAsString(s)).saveAsTextFile(workingDirPath + "/scholix_index", GzipCodec.class);
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}
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@ -24,6 +24,7 @@ public class SparkIndexCollectionOnES {
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final String sourcePath = parser.get("sourcePath");
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final String index = parser.get("index");
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final String idPath = parser.get("idPath");
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final SparkSession spark = SparkSession.builder().config(conf).getOrCreate();
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@ -34,7 +35,7 @@ public class SparkIndexCollectionOnES {
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Map<String, String> esCfg = new HashMap<>();
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esCfg.put("es.nodes", "10.19.65.51, 10.19.65.52, 10.19.65.53, 10.19.65.54");
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esCfg.put("es.mapping.id", "id");
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esCfg.put("es.mapping.id", idPath);
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esCfg.put("es.batch.write.retry.count", "8");
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esCfg.put("es.batch.write.retry.wait", "60s");
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esCfg.put("es.batch.size.entries", "200");
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@ -47,7 +47,7 @@ public class Scholix implements Serializable {
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}
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private void generateIdentifier( ) {
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public void generateIdentifier( ) {
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setIdentifier(DHPUtils.md5(String.format("%s::%s::%s",source.getDnetIdentifier(),relationship.getName(), target.getDnetIdentifier())));
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}
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@ -25,9 +25,19 @@
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<description>number of cores used by single executor</description>
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</property>
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<property>
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<name>idScholix</name>
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<description>the </description>
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</property>
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<property>
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<name>idSummary</name>
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<description>number of cores used by single executor</description>
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</property>
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</parameters>
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<start to="generateScholix"/>
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<start to="indexScholix"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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@ -103,7 +113,7 @@
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<name-node>${nameNode}</name-node>
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>generate Summary</name>
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<name>generate Scholix</name>
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<class>eu.dnetlib.dhp.provision.SparkGenerateScholix</class>
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<jar>dhp-graph-provision-${projectVersion}.jar</jar>
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<spark-opts>--executor-memory ${sparkExecutorMemory} --driver-memory=${sparkDriverMemory} ${sparkExtraOPT}</spark-opts>
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@ -111,9 +121,29 @@
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<arg>--workingDirPath</arg><arg>${workingDirPath}</arg>
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<arg>--graphPath</arg><arg>${graphPath}</arg>
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</spark>
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<ok to="indexScholix"/>
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<error to="Kill"/>
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</action>
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<action name="indexScholix">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>index scholix</name>
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<class>eu.dnetlib.dhp.provision.SparkIndexCollectionOnES</class>
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<jar>dhp-graph-provision-${projectVersion}.jar</jar>
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<spark-opts>--executor-memory ${sparkExecutorMemory} --num-executors 20 --driver-memory=${sparkDriverMemory} ${sparkExtraOPT} --conf spark.dynamicAllocation.maxExecutors="32" </spark-opts>
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<arg>-mt</arg> <arg>yarn-cluster</arg>
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<arg>--sourcePath</arg><arg>${workingDirPath}/scholix_index</arg>
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<arg>--index</arg><arg>${index}_scholix</arg>
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</spark>
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<ok to="End"/>
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<error to="Kill"/>
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</action>
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<end name="End"/>
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</workflow-app>
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@ -16,5 +16,11 @@
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"paramLongName": "index",
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"paramDescription": "the index name",
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"paramRequired": true
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},
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{
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"paramName": "id",
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"paramLongName": "idPath",
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"paramDescription": "the identifier field name",
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"paramRequired": true
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}
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]
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@ -1,5 +1,6 @@
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package eu.dnetlib.dhp.provision;
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import com.fasterxml.jackson.core.type.TypeReference;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.provision.scholix.Scholix;
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import eu.dnetlib.dhp.provision.scholix.summary.ScholixSummary;
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@ -7,14 +8,13 @@ import org.apache.commons.io.IOUtils;
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import org.junit.Ignore;
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import org.junit.Test;
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import scala.Tuple2;
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public class ExtractInfoTest {
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@Test
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public void test() throws Exception {
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final String json = IOUtils.toString(getClass().getResourceAsStream("record.json"));
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ProvisionUtil.getItemType(json,ProvisionUtil.TARGETJSONPATH);
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}
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@ -43,6 +43,7 @@ public class ExtractInfoTest {
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}
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@Test
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@Ignore
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public void testIndex() throws Exception {
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