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Add actionset creation for pubmed affiliations

This commit is contained in:
Serafeim Chatzopoulos 2023-10-19 19:58:25 +03:00
parent 94089878fd
commit 6ce9b600c1
4 changed files with 35 additions and 13 deletions

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@ -12,6 +12,7 @@ import org.apache.hadoop.io.Text;
import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.hadoop.mapred.SequenceFileOutputFormat;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaPairRDD;
import org.apache.spark.api.java.function.FlatMapFunction;
import org.apache.spark.sql.*;
import org.apache.spark.sql.Dataset;
@ -58,10 +59,13 @@ public class PrepareAffiliationRelations implements Serializable {
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("inputPath");
log.info("inputPath {}: ", inputPath);
log.info("inputPath: {}", inputPath);
final String pubmedInputPath = parser.get("pubmedInputPath");
log.info("pubmedInputPath: {}", pubmedInputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath {}: ", outputPath);
log.info("outputPath: {}", outputPath);
SparkConf conf = new SparkConf();
@ -70,12 +74,22 @@ public class PrepareAffiliationRelations implements Serializable {
isSparkSessionManaged,
spark -> {
Constants.removeOutputDir(spark, outputPath);
prepareAffiliationRelations(spark, inputPath, outputPath);
List<KeyValue> collectedFromCrossref = OafMapperUtils.listKeyValues(ModelConstants.CROSSREF_ID, "Crossref");
JavaPairRDD<Text, Text> crossrefRelations = prepareAffiliationRelations(spark, inputPath, collectedFromCrossref);
List<KeyValue> collectedFromPubmed = OafMapperUtils.listKeyValues(ModelConstants.PUBMED_CENTRAL_ID, "Pubmed");
JavaPairRDD<Text, Text> pubmedRelations = prepareAffiliationRelations(spark, inputPath, collectedFromPubmed);
crossrefRelations
.union(pubmedRelations)
.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
});
}
private static <I extends Result> void prepareAffiliationRelations(SparkSession spark, String inputPath,
String outputPath) {
private static <I extends Result> JavaPairRDD<Text, Text> prepareAffiliationRelations(SparkSession spark, String inputPath,
List<KeyValue> collectedfrom) {
// load and parse affiliation relations from HDFS
Dataset<Row> df = spark
@ -92,7 +106,7 @@ public class PrepareAffiliationRelations implements Serializable {
new Column("matching.Confidence").as("confidence"));
// prepare action sets for affiliation relations
df
return df
.toJavaRDD()
.flatMap((FlatMapFunction<Row, Relation>) row -> {
@ -120,8 +134,6 @@ public class PrepareAffiliationRelations implements Serializable {
qualifier,
Double.toString(row.getAs("confidence")));
List<KeyValue> collectedfrom = OafMapperUtils.listKeyValues(ModelConstants.CROSSREF_ID, "Crossref");
// return bi-directional relations
return getAffiliationRelationPair(paperId, affId, collectedfrom, dataInfo).iterator();
@ -129,9 +141,7 @@ public class PrepareAffiliationRelations implements Serializable {
.map(p -> new AtomicAction(Relation.class, p))
.mapToPair(
aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
new Text(OBJECT_MAPPER.writeValueAsString(aa))))
.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
new Text(OBJECT_MAPPER.writeValueAsString(aa))));
}
private static List<Relation> getAffiliationRelationPair(String paperId, String affId, List<KeyValue> collectedfrom,

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@ -8,7 +8,13 @@
{
"paramName": "ip",
"paramLongName": "inputPath",
"paramDescription": "the URL from where to get the programme file",
"paramDescription": "the path to get the input data from Crossref",
"paramRequired": true
},
{
"paramName": "pip",
"paramLongName": "pubmedInputPath",
"paramDescription": "the path to get the input data from Pubmed",
"paramRequired": true
},
{

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@ -32,4 +32,5 @@ spark2SqlQueryExecutionListeners=com.cloudera.spark.lineage.NavigatorQueryListen
oozie.wf.application.path=${oozieTopWfApplicationPath}
inputPath=/data/bip-affiliations/data.json
pubmedInputPath=/data/bip-affiiations/pubmed-data.json
outputPath=/tmp/crossref-affiliations-output-v5

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@ -3,7 +3,11 @@
<property>
<name>inputPath</name>
<description>the path where to find the inferred affiliation relations</description>
<description>the path where to find the inferred affiliation relations from Crossref</description>
</property>
<property>
<name>pubmedInputPath</name>
<description>the path where to find the inferred affiliation relations from Pubmed</description>
</property>
<property>
<name>outputPath</name>
@ -97,6 +101,7 @@
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--inputPath</arg><arg>${inputPath}</arg>
<arg>--pubmedInputPath</arg><arg>${pubmedInputPath}</arg>
<arg>--outputPath</arg><arg>${outputPath}</arg>
</spark>
<ok to="End"/>