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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
parent 93f26fb742 064f9bbd87
commit 904e1c2667
3 changed files with 59 additions and 19 deletions
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69
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfromsemrel/SparkResultToOrganizationFromSemRel.java
View File

@ -6,6 +6,7 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
import java.io.Serializable;
import java.util.Arrays;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
@ -64,6 +65,18 @@ public class SparkResultToOrganizationFromSemRel implements Serializable {
final String workingPath = parser.get("workingDir");
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();
conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
@ -77,7 +90,8 @@ public class SparkResultToOrganizationFromSemRel implements Serializable {
resultOrganizationPath,
relationPath,
workingPath,
outputPath));
outputPath,
iterations));
}
public static void execPropagation(SparkSession spark,
@ -86,26 +100,45 @@ public class SparkResultToOrganizationFromSemRel implements Serializable {
String resultOrganizationPath,
String graphPath,
String workingPath,
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 iterationTwo = spark.sparkContext().longAccumulator(ITERATION_TWO);
final LongAccumulator iterationThree = spark.sparkContext().longAccumulator(ITERATION_THREE);
final LongAccumulator iterationFour = spark.sparkContext().longAccumulator(ITERATION_FOUR);
final LongAccumulator iterationFive = spark.sparkContext().longAccumulator(ITERATION_FIVE);
final LongAccumulator notReachedFirstParent = spark.sparkContext().longAccumulator(ITERATION_NO_PARENT);
final PropagationCounter propagationCounter = new PropagationCounter(iterationOne,
iterationTwo,
iterationThree,
iterationFour,
iterationFive,
notReachedFirstParent);
doPropagate(
spark, leavesPath, childParentPath, resultOrganizationPath, graphPath,
workingPath, outputPath, propagationCounter);
}
}
private static void doPropagateOnce(SparkSession spark, String leavesPath, String childParentPath,
String resultOrganizationPath, String graphPath, String workingPath,
String outputPath) {
final LongAccumulator iterationOne = spark.sparkContext().longAccumulator(ITERATION_ONE);
final LongAccumulator iterationTwo = spark.sparkContext().longAccumulator(ITERATION_TWO);
final LongAccumulator iterationThree = spark.sparkContext().longAccumulator(ITERATION_THREE);
final LongAccumulator iterationFour = spark.sparkContext().longAccumulator(ITERATION_FOUR);
final LongAccumulator iterationFive = spark.sparkContext().longAccumulator(ITERATION_FIVE);
final LongAccumulator notReachedFirstParent = spark.sparkContext().longAccumulator(ITERATION_NO_PARENT);
final PropagationCounter propagationCounter = new PropagationCounter(iterationOne,
iterationTwo,
iterationThree,
iterationFour,
iterationFive,
notReachedFirstParent);
doPropagate(
spark, leavesPath, childParentPath, resultOrganizationPath, graphPath,
workingPath, outputPath, propagationCounter);
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,

6
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttoorganizationfromsemrel/input_propagation_parameter.json
View File

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

3
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttoorganizationfromsemrel/oozie_app/workflow.xml
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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>
<property>
<name>sourcePath</name>
@ -181,6 +181,7 @@
<arg>--resultOrgPath</arg><arg>${workingDir}/preparedInfo/resultOrgPath</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--workingDir</arg><arg>${workingDir}/working</arg>
<arg>--iterations</arg><arg>${iterations}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>