Merge pull request 'Affiliation Propagation through semantic relation' (#183) from enrichment into beta

Reviewed-on: #183
This commit is contained in:
Miriam Baglioni 2022-01-07 19:18:16 +01:00
commit 904e1c2667
3 changed files with 59 additions and 19 deletions

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@ -6,6 +6,7 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
import java.io.Serializable; import java.io.Serializable;
import java.util.Arrays; import java.util.Arrays;
import java.util.Optional;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
@ -64,6 +65,18 @@ public class SparkResultToOrganizationFromSemRel implements Serializable {
final String workingPath = parser.get("workingDir"); final String workingPath = parser.get("workingDir");
log.info("workingPath: {}", workingPath); log.info("workingPath: {}", workingPath);
final int iterations = Optional
.ofNullable(parser.get("iterations"))
.map(v -> {
if (Integer.valueOf(v) < MAX_ITERATION) {
return Integer.valueOf(v);
} else
return MAX_ITERATION;
})
.orElse(MAX_ITERATION);
log.info("iterations: {}", iterations);
SparkConf conf = new SparkConf(); SparkConf conf = new SparkConf();
conf.set("hive.metastore.uris", parser.get("hive_metastore_uris")); conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
@ -77,7 +90,8 @@ public class SparkResultToOrganizationFromSemRel implements Serializable {
resultOrganizationPath, resultOrganizationPath,
relationPath, relationPath,
workingPath, workingPath,
outputPath)); outputPath,
iterations));
} }
public static void execPropagation(SparkSession spark, public static void execPropagation(SparkSession spark,
@ -86,7 +100,13 @@ public class SparkResultToOrganizationFromSemRel implements Serializable {
String resultOrganizationPath, String resultOrganizationPath,
String graphPath, String graphPath,
String workingPath, String workingPath,
String outputPath) { String outputPath,
int iterations) {
if (iterations == 1) {
doPropagateOnce(
spark, leavesPath, childParentPath, resultOrganizationPath, graphPath,
workingPath, outputPath);
} else {
final LongAccumulator iterationOne = spark.sparkContext().longAccumulator(ITERATION_ONE); final LongAccumulator iterationOne = spark.sparkContext().longAccumulator(ITERATION_ONE);
final LongAccumulator iterationTwo = spark.sparkContext().longAccumulator(ITERATION_TWO); final LongAccumulator iterationTwo = spark.sparkContext().longAccumulator(ITERATION_TWO);
@ -105,9 +125,22 @@ public class SparkResultToOrganizationFromSemRel implements Serializable {
doPropagate( doPropagate(
spark, leavesPath, childParentPath, resultOrganizationPath, graphPath, spark, leavesPath, childParentPath, resultOrganizationPath, graphPath,
workingPath, outputPath, propagationCounter); workingPath, outputPath, propagationCounter);
}
} }
private static void doPropagateOnce(SparkSession spark, String leavesPath, String childParentPath,
String resultOrganizationPath, String graphPath, String workingPath,
String outputPath) {
StepActions
.execStep(
spark, graphPath, workingPath + NEW_RELATION_PATH,
leavesPath, childParentPath, resultOrganizationPath);
addNewRelations(spark, workingPath + NEW_RELATION_PATH, outputPath);
}
private static void doPropagate(SparkSession spark, String leavesPath, String childParentPath, private static void doPropagate(SparkSession spark, String leavesPath, String childParentPath,
String resultOrganizationPath, String graphPath, String workingPath, String outputPath, String resultOrganizationPath, String graphPath, String workingPath, String outputPath,
PropagationCounter propagationCounter) { PropagationCounter propagationCounter) {

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@ -46,5 +46,11 @@
"paramLongName": "outputPath", "paramLongName": "outputPath",
"paramDescription": "the path used to store temporary output files", "paramDescription": "the path used to store temporary output files",
"paramRequired": true "paramRequired": true
},
{
"paramName": "it",
"paramLongName": "iterations",
"paramDescription": "the number of iterations to be computed",
"paramRequired": false
} }
] ]

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@ -1,4 +1,4 @@
<workflow-app name="affiliation_from_instrepo_propagation" xmlns="uri:oozie:workflow:0.5"> <workflow-app name="affiliation_from_semrel_propagation" xmlns="uri:oozie:workflow:0.5">
<parameters> <parameters>
<property> <property>
<name>sourcePath</name> <name>sourcePath</name>
@ -181,6 +181,7 @@
<arg>--resultOrgPath</arg><arg>${workingDir}/preparedInfo/resultOrgPath</arg> <arg>--resultOrgPath</arg><arg>${workingDir}/preparedInfo/resultOrgPath</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg> <arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--workingDir</arg><arg>${workingDir}/working</arg> <arg>--workingDir</arg><arg>${workingDir}/working</arg>
<arg>--iterations</arg><arg>${iterations}</arg>
</spark> </spark>
<ok to="End"/> <ok to="End"/>
<error to="Kill"/> <error to="Kill"/>