forked from D-Net/dnet-hadoop
84 lines
3.2 KiB
Java
84 lines
3.2 KiB
Java
package eu.dnetlib.dhp.oa.dedup;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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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 eu.dnetlib.pace.config.DedupConfig;
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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.sql.SparkSession;
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import org.dom4j.Document;
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import org.dom4j.DocumentException;
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import org.dom4j.Element;
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import org.dom4j.io.SAXReader;
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import scala.xml.Elem;
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import java.io.IOException;
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import java.io.Serializable;
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import java.io.StringReader;
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import java.util.ArrayList;
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import java.util.List;
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abstract class AbstractSparkAction implements Serializable {
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public ArgumentApplicationParser parser; //parameters for the spark action
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public ISLookUpService isLookUpService; //lookup service to take dedupconfig
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public AbstractSparkAction(ArgumentApplicationParser parser, ISLookUpService isLookUpService) throws Exception {
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this.parser = parser;
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this.isLookUpService = isLookUpService;
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}
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public List<DedupConfig> getConfigurations(String orchestrator) throws ISLookUpException, DocumentException, IOException {
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final String xquery = String.format("/RESOURCE_PROFILE[.//DEDUPLICATION/ACTION_SET/@id = '%s']", orchestrator);
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String orchestratorProfile = isLookUpService.getResourceProfileByQuery(xquery);
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final Document doc = new SAXReader().read(new StringReader(orchestratorProfile));
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final String actionSetId = doc.valueOf("//DEDUPLICATION/ACTION_SET/@id");
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final List<DedupConfig> configurations = new ArrayList<>();
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for (final Object o : doc.selectNodes("//SCAN_SEQUENCE/SCAN")) {
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configurations.add(loadConfig(isLookUpService, actionSetId, o));
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}
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return configurations;
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}
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public DedupConfig loadConfig(final ISLookUpService isLookUpService, final String actionSetId, final Object o)
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throws ISLookUpException, IOException {
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final Element s = (Element) o;
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final String configProfileId = s.attributeValue("id");
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final String conf =
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isLookUpService.getResourceProfileByQuery(String.format(
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"for $x in /RESOURCE_PROFILE[.//RESOURCE_IDENTIFIER/@value = '%s'] return $x//DEDUPLICATION/text()",
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configProfileId));
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DedupConfig dedupConfig = new ObjectMapper().readValue(conf, DedupConfig.class);
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dedupConfig.getPace().initModel();
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dedupConfig.getPace().initTranslationMap();
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dedupConfig.getWf().setConfigurationId(actionSetId);
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return dedupConfig;
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}
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abstract void run() throws DocumentException, IOException, ISLookUpException;
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protected SparkSession getSparkSession(ArgumentApplicationParser parser) {
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SparkConf conf = new SparkConf();
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return SparkSession
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.builder()
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.appName(SparkCreateSimRels.class.getSimpleName())
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.master(parser.get("master"))
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.config(conf)
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.getOrCreate();
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}
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}
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