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classes test classes and resources for production of the actionset to include bipFinder score in results

This commit is contained in:
Miriam Baglioni 2020-11-30 20:14:23 +01:00
parent e731a7658d
commit db36e11912
10 changed files with 1637 additions and 0 deletions

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package eu.dnetlib.dhp.actionmanager.bipfinder;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
public class BipDeserialize extends HashMap<String, List<Score>> implements Serializable {
public BipDeserialize(){
super();
}
public List<Score> get(String key) {
if (super.get(key) == null) {
return new ArrayList<>();
}
return super.get(key);
}
}

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package eu.dnetlib.dhp.actionmanager.bipfinder;
import java.io.Serializable;
import java.util.List;
public class BipScore implements Serializable {
private String id;
private List<Score> scoreList;
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public List<Score> getScoreList() {
return scoreList;
}
public void setScoreList(List<Score> scoreList) {
this.scoreList = scoreList;
}
}

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package eu.dnetlib.dhp.actionmanager.bipfinder;
import java.io.Serializable;
public class KeyValue implements Serializable {
private String key;
private String value;
public String getKey() {
return key;
}
public void setKey(String key) {
this.key = key;
}
public String getValue() {
return value;
}
public void setValue(String value) {
this.value = value;
}
}

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package eu.dnetlib.dhp.actionmanager.bipfinder;
import java.io.Serializable;
public class PreparedResult implements Serializable {
private String id; //openaire id
private String value; //doi
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public String getValue() {
return value;
}
public void setValue(String value) {
this.value = value;
}
}

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package eu.dnetlib.dhp.actionmanager.bipfinder;
import java.io.Serializable;
import java.util.List;
public class Score implements Serializable {
private String id;
private List<KeyValue> unit;
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public List<KeyValue> getUnit() {
return unit;
}
public void setUnit(List<KeyValue> unit) {
this.unit = unit;
}
}

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package eu.dnetlib.dhp.actionmanager.bipfinder;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.schema.action.AtomicAction;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.hdfs.qjournal.protocol.QJournalProtocolProtos;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.mapred.SequenceFileOutputFormat;
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.FlatMapFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.api.java.function.MapGroupsFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.Row;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import scala.Tuple2;
import java.io.Serializable;
import java.util.List;
import java.util.Optional;
import java.util.stream.Collectors;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
public class SparkAtomicActionScoreJob implements Serializable {
private static String DOI = "doi";
private static final Logger log = LoggerFactory.getLogger(SparkAtomicActionScoreJob.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static <I extends Result> void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
SparkAtomicActionScoreJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/bipfinder/input_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 inputPath = parser.get("inputPath");
log.info("inputPath {}: ", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath {}: ", outputPath);
final String bipScorePath = parser.get("bipScorePath");
log.info("bipScorePath: {}", bipScorePath);
final String resultClassName = parser.get("resultTableName");
log.info("resultTableName: {}", resultClassName);
Class<I> inputClazz = (Class<I>) Class.forName(resultClassName);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
removeOutputDir(spark, outputPath);
prepareResults(spark, inputPath, outputPath, bipScorePath, inputClazz);
});
}
private static <I extends Result> void prepareResults(SparkSession spark, String inputPath, String outputPath,
String bipScorePath, Class<I> inputClazz) {
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<BipDeserialize> bipDeserializeJavaRDD = sc.textFile(bipScorePath)
.map(item -> OBJECT_MAPPER.readValue(item, BipDeserialize.class));
Dataset<BipScore> bipScores = 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));
System.out.println(bipScores.count());
Dataset<I> results = readPath(spark, inputPath, inputClazz);
results.createOrReplaceTempView("result");
Dataset<PreparedResult> preparedResult = spark.sql("select pIde.value value, id " +
"from result " +
"lateral view explode (pid) p as pIde " +
"where dataInfo.deletedbyinference = false and pIde.qualifier.classid = '" + DOI + "'")
.as(Encoders.bean(PreparedResult.class));
Dataset<BipScore> tmp = bipScores.joinWith(preparedResult, bipScores.col("id").equalTo(preparedResult.col("value")),
"inner")
.map((MapFunction<Tuple2<BipScore, PreparedResult>, BipScore>) value -> {
BipScore ret = value._1();
ret.setId(value._2().getId());
return ret;
}, Encoders.bean(BipScore.class));
tmp.groupByKey((MapFunction<BipScore, String>) value -> value.getId(), Encoders.STRING())
.mapGroups((MapGroupsFunction<String, BipScore, I>) (k, it) ->
{
Result ret = inputClazz.newInstance();
BipScore first = it.next();
ret.setId(first.getId());
ret.setMeasures(getMeasure(first));
it.forEachRemaining(value -> ret.getMeasures().addAll(getMeasure(value)));
return (I)ret;
}, Encoders.bean(inputClazz))
.toJavaRDD()
.map(p -> new AtomicAction(inputClazz, p))
.mapToPair(
aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
new Text(OBJECT_MAPPER.writeValueAsString(aa))))
.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);
;
}
public static Dataset<BipScore> getBipScoreDataset(Dataset<BipDeserialize> bipdeserialized){
return bipdeserialized.flatMap((FlatMapFunction<BipDeserialize, BipScore>) bip ->
bip.keySet().stream().map(key -> {
BipScore bs = new BipScore();
bs.setId(key);
bs.setScoreList(bip.get(key));
return bs;
}).collect(Collectors.toList()).iterator()
, Encoders.bean(BipScore.class));
}
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(getDataInfo());
return kv;
}).collect(Collectors.toList()));
return m;
}).collect(Collectors.toList());
}
private static DataInfo getDataInfo() {
DataInfo di = new DataInfo();
di.setInferred(false);
di.setInvisible(false);
di.setDeletedbyinference(false);
di.setTrust("");
Qualifier qualifier = new Qualifier();
qualifier.setClassid("sysimport:actionset");
qualifier.setClassname("Harvested");
qualifier.setSchemename("dnet:provenanceActions");
qualifier.setSchemeid("dnet:provenanceActions");
di.setProvenanceaction(qualifier);
return di;
}
private static void removeOutputDir(SparkSession spark, String path) {
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
}
public static <R> Dataset<R> readPath(
SparkSession spark, String inputPath, Class<R> clazz) {
return spark
.read()
.textFile(inputPath)
.map((MapFunction<String, R>) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz));
}
}

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[
{
"paramName": "issm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "when true will stop SparkSession after job execution",
"paramRequired": false
},
{
"paramName": "ip",
"paramLongName": "inputPath",
"paramDescription": "the URL from where to get the programme file",
"paramRequired": true
},
{
"paramName": "o",
"paramLongName": "outputPath",
"paramDescription": "the path of the new ActionSet",
"paramRequired": true
},
{
"paramName": "rtn",
"paramLongName": "resultTableName",
"paramDescription": "the path of the new ActionSet",
"paramRequired": true
},
{
"paramName": "bsp",
"paramLongName": "bipScorePath",
"paramDescription": "the path of the new ActionSet",
"paramRequired": true
}
]

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package eu.dnetlib.dhp.actionmanager.bipfinder;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.action.AtomicAction;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import org.apache.commons.io.FileUtils;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.mapred.SequenceFileOutputFormat;
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.FilterFunction;
import org.apache.spark.api.java.function.ForeachFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.api.java.function.MapGroupsFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import scala.Tuple2;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.List;
import java.util.stream.Collectors;
public class SparkAtomicActionScoreJobTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static SparkSession spark;
private static Path workingDir;
private static final Logger log = LoggerFactory
.getLogger(SparkAtomicActionScoreJobTest.class);
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files
.createTempDirectory(SparkAtomicActionScoreJobTest.class.getSimpleName());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf();
conf.setAppName(SparkAtomicActionScoreJobTest.class.getSimpleName());
conf.setMaster("local[*]");
conf.set("spark.driver.host", "localhost");
conf.set("hive.metastore.local", "true");
conf.set("spark.ui.enabled", "false");
conf.set("spark.sql.warehouse.dir", workingDir.toString());
conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
spark = SparkSession
.builder()
.appName(SparkAtomicActionScoreJobTest.class.getSimpleName())
.config(conf)
.getOrCreate();
}
@AfterAll
public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
spark.stop();
}
@Test
public <I extends Result> void numberDistinctProjectTest() throws Exception {
String bipScoresPath = getClass().getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json").getPath();
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/bipfinder/publication.json")
.getPath();
SparkAtomicActionScoreJob.main(
new String[] {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-inputPath",
inputPath,
"-bipScorePath",
bipScoresPath,
"-resultTableName",
"eu.dnetlib.dhp.schema.oaf.Publication",
"-outputPath",
workingDir.toString() + "/actionSet"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Publication> tmp = sc
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Publication) aa.getPayload()));
Assertions.assertTrue(tmp.count() == 1);
// Dataset<Publication> verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Publication.class));
// verificationDataset.createOrReplaceTempView("project");
// Dataset<Row> execverification = spark
// .sql(
// "SELECT id, class classification, h2020topiccode, h2020topicdescription FROM project LATERAL VIEW EXPLODE(h2020classification) c as class ");
//
// Assertions
// .assertEquals(
// "H2020-EU.3.4.7.",
// execverification
// .filter("id = '40|corda__h2020::2c7298913008865ba784e5c1350a0aa5'")
// .select("classification.h2020Programme.code")
// .collectAsList()
// .get(0)
// .getString(0));
}
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 -> {
eu.dnetlib.dhp.schema.oaf.KeyValue kv = new KeyValue();
kv.setValue(unit.getValue());
kv.setKey(unit.getKey());
kv.setDataInfo(getDataInfo());
return kv;
}).collect(Collectors.toList()));
return m;
}).collect(Collectors.toList());
}
private static DataInfo getDataInfo() {
DataInfo di = new DataInfo();
di.setInferred(false);
di.setInvisible(false);
di.setDeletedbyinference(false);
di.setTrust("");
Qualifier qualifier = new Qualifier();
qualifier.setClassid("sysimport:actionset");
qualifier.setClassname("Harvested");
qualifier.setSchemename("dnet:provenanceActions");
qualifier.setSchemeid("dnet:provenanceActions");
di.setProvenanceaction(qualifier);
return di;
}
}

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