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leftover for the properties and removal of bipfinder

This commit is contained in:
Miriam Baglioni 2023-10-10 12:53:57 +02:00
parent 110ce4b40f
commit a431b04814
4 changed files with 1 additions and 377 deletions
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178
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareBipFinder.java
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@ -1,178 +0,0 @@
package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
import static eu.dnetlib.dhp.actionmanager.Constants.*;
import static eu.dnetlib.dhp.actionmanager.Constants.UPDATE_CLASS_NAME;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.Arrays;
import java.util.List;
import java.util.Optional;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.actionmanager.bipmodel.BipScore;
import eu.dnetlib.dhp.actionmanager.bipmodel.score.deserializers.BipResultModel;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Instance;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import eu.dnetlib.dhp.schema.oaf.Measure;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
import eu.dnetlib.dhp.utils.DHPUtils;
public class PrepareBipFinder implements Serializable {
private static final Logger log = LoggerFactory.getLogger(PrepareBipFinder.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
PrepareBipFinder.class
.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/createunresolvedentities/prepare_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String sourcePath = parser.get("sourcePath");
log.info("sourcePath {}: ", sourcePath);
final String outputPath = parser.get("outputPath");
log.info("outputPath {}: ", outputPath);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration());
prepareResults(spark, sourcePath, outputPath);
});
}
private static void prepareResults(SparkSession spark, String inputPath, String outputPath) {
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<BipResultModel> bipDeserializeJavaRDD = sc
.textFile(inputPath)
.map(item -> OBJECT_MAPPER.readValue(item, BipResultModel.class));
spark
.createDataset(bipDeserializeJavaRDD.flatMap(entry -> entry.keySet().stream().map(key -> {
BipScore bs = new BipScore();
bs.setId(key);
bs.setScoreList(entry.get(key));
return bs;
}).collect(Collectors.toList()).iterator()).rdd(), Encoders.bean(BipScore.class))
.map((MapFunction<BipScore, Result>) v -> {
Result r = new Result();
final String cleanedPid = CleaningFunctions.normalizePidValue(DOI, v.getId());
r.setId(DHPUtils.generateUnresolvedIdentifier(v.getId(), DOI));
Instance inst = new Instance();
inst.setMeasures(getMeasure(v));
inst
.setPid(
Arrays
.asList(
OafMapperUtils
.structuredProperty(
cleanedPid,
OafMapperUtils
.qualifier(
DOI, DOI_CLASSNAME,
ModelConstants.DNET_PID_TYPES,
ModelConstants.DNET_PID_TYPES),
null)));
r.setInstance(Arrays.asList(inst));
r
.setDataInfo(
OafMapperUtils
.dataInfo(
false, null, true,
false,
OafMapperUtils
.qualifier(
ModelConstants.PROVENANCE_ENRICH,
null,
ModelConstants.DNET_PROVENANCE_ACTIONS,
ModelConstants.DNET_PROVENANCE_ACTIONS),
null));
return r;
}, Encoders.bean(Result.class))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath + "/bip");
}
private static List<Measure> getMeasure(BipScore value) {
return value
.getScoreList()
.stream()
.map(score -> {
Measure m = new Measure();
m.setId(score.getId());
m
.setUnit(
score
.getUnit()
.stream()
.map(unit -> {
KeyValue kv = new KeyValue();
kv.setValue(unit.getValue());
kv.setKey(unit.getKey());
kv
.setDataInfo(
OafMapperUtils
.dataInfo(
false,
UPDATE_DATA_INFO_TYPE,
true,
false,
OafMapperUtils
.qualifier(
UPDATE_MEASURE_BIP_CLASS_ID,
UPDATE_CLASS_NAME,
ModelConstants.DNET_PROVENANCE_ACTIONS,
ModelConstants.DNET_PROVENANCE_ACTIONS),
""));
return kv;
})
.collect(Collectors.toList()));
return m;
})
.collect(Collectors.toList());
}
}

31
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/oozie_app/workflow.xml
View File

@ -5,11 +5,6 @@
<name>fosPath</name>
<description>the input path of the resources to be extended</description>
</property>
<!-- <property>-->
<!-- <name>bipScorePath</name>-->
<!-- <description>the path where to find the bipFinder scores</description>-->
<!-- </property>-->
<property>
<name>outputPath</name>
<description>the path where to store the actionset</description>
@ -77,35 +72,10 @@
<fork name="prepareInfo">
<!-- <path start="prepareBip"/>-->
<path start="getFOS"/>
<path start="getSDG"/>
</fork>
<!-- <action name="prepareBip">-->
<!-- <spark xmlns="uri:oozie:spark-action:0.2">-->
<!-- <master>yarn</master>-->
<!-- <mode>cluster</mode>-->
<!-- <name>Produces the unresolved from BIP! Finder</name>-->
<!-- <class>eu.dnetlib.dhp.actionmanager.createunresolvedentities.PrepareBipFinder</class>-->
<!-- <jar>dhp-aggregation-${projectVersion}.jar</jar>-->
<!-- <spark-opts>-->
<!-- &#45;&#45;executor-memory=${sparkExecutorMemory}-->
<!-- &#45;&#45;executor-cores=${sparkExecutorCores}-->
<!-- &#45;&#45;driver-memory=${sparkDriverMemory}-->
<!-- &#45;&#45;conf spark.extraListeners=${spark2ExtraListeners}-->
<!-- &#45;&#45;conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}-->
<!-- &#45;&#45;conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}-->
<!-- &#45;&#45;conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}-->
<!-- &#45;&#45;conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}-->
<!-- </spark-opts>-->
<!-- <arg>&#45;&#45;sourcePath</arg><arg>${bipScorePath}</arg>-->
<!-- <arg>&#45;&#45;outputPath</arg><arg>${workingDir}/prepared</arg>-->
<!-- </spark>-->
<!-- <ok to="join"/>-->
<!-- <error to="Kill"/>-->
<!-- </action>-->
<action name="getFOS">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
@ -125,6 +95,7 @@
</spark-opts>
<arg>--sourcePath</arg><arg>${fosPath}</arg>
<arg>--outputPath</arg><arg>${workingDir}/input/fos</arg>
<arg>--delimiter</arg><arg>${delimiter}</arg>
</spark>
<ok to="prepareFos"/>
<error to="Kill"/>

139
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareTest.java
View File

@ -67,92 +67,6 @@ public class PrepareTest {
spark.stop();
}
@Test
void bipPrepareTest() throws Exception {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/bip/bip.json")
.getPath();
PrepareBipFinder
.main(
new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(),
"--sourcePath", sourcePath,
"--outputPath", workingDir.toString() + "/work"
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Result> tmp = sc
.textFile(workingDir.toString() + "/work/bip")
.map(item -> OBJECT_MAPPER.readValue(item, Result.class));
Assertions.assertEquals(86, tmp.count());
String doi1 = "unresolved::10.0000/096020199389707::doi";
Assertions.assertEquals(1, tmp.filter(r -> r.getId().equals(doi1)).count());
Assertions.assertEquals(1, tmp.filter(r -> r.getId().equals(doi1)).collect().get(0).getInstance().size());
Assertions
.assertEquals(
3, tmp.filter(r -> r.getId().equals(doi1)).collect().get(0).getInstance().get(0).getMeasures().size());
Assertions
.assertEquals(
"6.34596412687e-09", tmp
.filter(r -> r.getId().equals(doi1))
.collect()
.get(0)
.getInstance()
.get(0)
.getMeasures()
.stream()
.filter(sl -> sl.getId().equals("influence"))
.collect(Collectors.toList())
.get(0)
.getUnit()
.get(0)
.getValue());
Assertions
.assertEquals(
"0.641151896994", tmp
.filter(r -> r.getId().equals(doi1))
.collect()
.get(0)
.getInstance()
.get(0)
.getMeasures()
.stream()
.filter(sl -> sl.getId().equals("popularity_alt"))
.collect(Collectors.toList())
.get(0)
.getUnit()
.get(0)
.getValue());
Assertions
.assertEquals(
"2.33375102921e-09", tmp
.filter(r -> r.getId().equals(doi1))
.collect()
.get(0)
.getInstance()
.get(0)
.getMeasures()
.stream()
.filter(sl -> sl.getId().equals("popularity"))
.collect(Collectors.toList())
.get(0)
.getUnit()
.get(0)
.getValue());
final String doi2 = "unresolved::10.3390/s18072310::doi";
Assertions.assertEquals(1, tmp.filter(r -> r.getId().equals(doi2)).count());
Assertions.assertEquals(1, tmp.filter(r -> r.getId().equals(doi2)).collect().get(0).getInstance().size());
}
@Test
void fosPrepareTest() throws Exception {
final String sourcePath = getClass()
@ -338,57 +252,4 @@ public class PrepareTest {
}
// @Test
// void test3() throws Exception {
// final String sourcePath = "/Users/miriam.baglioni/Downloads/doi_fos_results_20_12_2021.csv.gz";
//
// final String outputPath = workingDir.toString() + "/fos.json";
// GetFOSSparkJob
// .main(
// new String[] {
// "--isSparkSessionManaged", Boolean.FALSE.toString(),
// "--sourcePath", sourcePath,
//
// "-outputPath", outputPath
//
// });
//
// final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
//
// JavaRDD<FOSDataModel> tmp = sc
// .textFile(outputPath)
// .map(item -> OBJECT_MAPPER.readValue(item, FOSDataModel.class));
//
// tmp.foreach(t -> Assertions.assertTrue(t.getDoi() != null));
// tmp.foreach(t -> Assertions.assertTrue(t.getLevel1() != null));
// tmp.foreach(t -> Assertions.assertTrue(t.getLevel2() != null));
// tmp.foreach(t -> Assertions.assertTrue(t.getLevel3() != null));
//
// }
//
// @Test
// void test4() throws Exception {
// final String sourcePath = "/Users/miriam.baglioni/Downloads/doi_sdg_results_20_12_21.csv.gz";
//
// final String outputPath = workingDir.toString() + "/sdg.json";
// GetSDGSparkJob
// .main(
// new String[] {
// "--isSparkSessionManaged", Boolean.FALSE.toString(),
// "--sourcePath", sourcePath,
//
// "-outputPath", outputPath
//
// });
//
// final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
//
// JavaRDD<SDGDataModel> tmp = sc
// .textFile(outputPath)
// .map(item -> OBJECT_MAPPER.readValue(item, SDGDataModel.class));
//
// tmp.foreach(t -> Assertions.assertTrue(t.getDoi() != null));
// tmp.foreach(t -> Assertions.assertTrue(t.getSbj() != null));
//
// }
}

30
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/ProduceTest.java
View File

@ -340,18 +340,7 @@ public class ProduceTest {
}
private JavaRDD<Result> getResultJavaRDD() throws Exception {
final String bipPath = getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/bip/bip.json")
.getPath();
PrepareBipFinder
.main(
new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(),
"--sourcePath", bipPath,
"--outputPath", workingDir.toString() + "/work"
});
final String fosPath = getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/fos.json")
.getPath();
@ -449,18 +438,7 @@ public class ProduceTest {
}
private JavaRDD<Result> getResultJavaRDDPlusSDG() throws Exception {
final String bipPath = getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/bip/bip.json")
.getPath();
PrepareBipFinder
.main(
new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(),
"--sourcePath", bipPath,
"--outputPath", workingDir.toString() + "/work"
});
final String fosPath = getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/fos.json")
.getPath();
@ -517,14 +495,6 @@ public class ProduceTest {
.filter(row -> row.getSubject() != null)
.count());
Assertions
.assertEquals(
85,
tmp
.filter(row -> !row.getId().equals(doi))
.filter(r -> r.getInstance() != null && r.getInstance().size() > 0)
.count());
}
@Test