refactoring, minor changes and implementation of the wf for openorgs with integration of organization phases into the scan wf
miconis
3 years ago
parent
1e1aab83e3
commit
8fea29177c
@ -0,0 +1,100 @@
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package eu.dnetlib.dhp.oa.dedup;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.common.EntityType;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.oaf.OafEntity;
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import eu.dnetlib.dhp.utils.ISLookupClientFactory;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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import org.apache.commons.io.IOUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SaveMode;
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import org.apache.spark.sql.SparkSession;
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import org.dom4j.DocumentException;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import java.io.IOException;
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import java.util.Optional;
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public class SparkCopyOpenorgs extends AbstractSparkAction{
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private static final Logger log = LoggerFactory.getLogger(SparkCopyRels.class);
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public SparkCopyOpenorgs(ArgumentApplicationParser parser, SparkSession spark) {
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super(parser, spark);
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}
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public static void main(String[] args) throws Exception {
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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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SparkCreateSimRels.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/dedup/copyOpenorgs_parameters.json")));
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parser.parseArgument(args);
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SparkConf conf = new SparkConf();
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new SparkCopyOpenorgs(parser, getSparkSession(conf))
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.run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl")));
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}
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@Override
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public void run(ISLookUpService isLookUpService)
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throws DocumentException, IOException, ISLookUpException {
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// read oozie parameters
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final String graphBasePath = parser.get("graphBasePath");
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final String actionSetId = parser.get("actionSetId");
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final String workingPath = parser.get("workingPath");
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final int numPartitions = Optional
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.ofNullable(parser.get("numPartitions"))
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.map(Integer::valueOf)
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.orElse(NUM_PARTITIONS);
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log.info("numPartitions: '{}'", numPartitions);
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log.info("graphBasePath: '{}'", graphBasePath);
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log.info("actionSetId: '{}'", actionSetId);
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log.info("workingPath: '{}'", workingPath);
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String subEntity = "organization";
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log.info("Copying openorgs to the working dir");
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final String outputPath = DedupUtility.createDedupRecordPath(workingPath, actionSetId, subEntity);
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removeOutputDir(spark, outputPath);
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final String entityPath = DedupUtility.createEntityPath(graphBasePath, subEntity);
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final Class<OafEntity> clazz = ModelSupport.entityTypes.get(EntityType.valueOf(subEntity));
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filterEntities(spark, entityPath, clazz)
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.json(outputPath);
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}
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public static <T extends OafEntity> Dataset<T> filterEntities(
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final SparkSession spark,
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final String entitiesInputPath,
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final Class<T> clazz) {
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// <id, json_entity>
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Dataset<T> entities = spark
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.read()
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.textFile(entitiesInputPath)
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.map(
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(MapFunction<String, T>) it -> {
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T entity = OBJECT_MAPPER.readValue(it, clazz);
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return entity;
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},
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Encoders.kryo(clazz));
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return entities.filter(entities.col("id").contains("openorgs____"));
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}
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}
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@ -0,0 +1,26 @@
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[
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{
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"paramName": "asi",
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"paramLongName": "actionSetId",
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"paramDescription": "action set identifier (name of the orchestrator)",
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"paramRequired": true
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},
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{
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"paramName": "i",
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"paramLongName": "graphBasePath",
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"paramDescription": "the base path of the raw graph",
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"paramRequired": true
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},
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{
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"paramName": "w",
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"paramLongName": "workingPath",
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"paramDescription": "path of the working directory",
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"paramRequired": true
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},
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{
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"paramName": "np",
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"paramLongName": "numPartitions",
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"paramDescription": "number of partitions for the similarity relations intermediate phases",
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"paramRequired": false
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}
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]
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@ -0,0 +1,32 @@
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[
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{
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"paramName": "asi",
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"paramLongName": "actionSetId",
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"paramDescription": "action set identifier (name of the orchestrator)",
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"paramRequired": true
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},
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{
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"paramName": "i",
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"paramLongName": "graphBasePath",
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"paramDescription": "the base path of the raw graph",
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"paramRequired": true
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},
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{
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"paramName": "w",
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"paramLongName": "workingPath",
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"paramDescription": "path of the working directory",
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"paramRequired": true
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},
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{
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"paramName": "e",
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"paramLongName": "entityType",
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"paramDescription": "type of the entity for the merge relations",
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"paramRequired": true
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},
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{
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"paramName": "np",
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"paramLongName": "numPartitions",
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"paramDescription": "number of partitions for the similarity relations intermediate phases",
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"paramRequired": false
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}
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]
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