forked from D-Net/dnet-hadoop
job for the population of the oai database
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package eu.dnetlib.dhp.oa.oaipmh;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.io.ByteArrayOutputStream;
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import java.io.IOException;
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import java.time.LocalDateTime;
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import java.util.ArrayList;
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import java.util.Optional;
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import java.util.Properties;
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import java.util.zip.GZIPOutputStream;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.function.FilterFunction;
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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.Encoder;
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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.dom4j.Document;
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import org.dom4j.DocumentHelper;
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import org.dom4j.Node;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.oa.provision.XmlConverterJob;
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import eu.dnetlib.dhp.oa.provision.model.SerializableSolrInputDocument;
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import eu.dnetlib.dhp.oa.provision.model.TupleWrapper;
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public class IrishOaiExporterJob {
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private static final Logger log = LoggerFactory.getLogger(IrishOaiExporterJob.class);
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protected static final int NUM_CONNECTIONS = 20;
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public static void main(final String[] args) throws Exception {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(XmlConverterJob.class
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.getResourceAsStream("/eu/dnetlib/dhp/oa/oaipmh/input_params_irish_oai_exporter.json")));
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parser.parseArgument(args);
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final Boolean isSparkSessionManaged = Optional
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.ofNullable(parser.get("isSparkSessionManaged"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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final String inputPath = parser.get("inputPath");
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final String dbUrl = parser.get("dbUrl");
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final String dbTable = parser.get("dbTable");
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final String dbUser = parser.get("dbUser");
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final String dbPwd = parser.get("dbPwd");
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final int numConnections = Optional
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.ofNullable(parser.get("numConnections"))
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.map(Integer::valueOf)
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.orElse(NUM_CONNECTIONS);
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log.info("inputPath: '{}'", inputPath);
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log.info("dbUrl: '{}'", dbUrl);
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log.info("dbUser: '{}'", dbUser);
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log.info("table: '{}'", dbTable);
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log.info("dbPwd: '{}'", "xxx");
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log.info("numPartitions: '{}'", numConnections);
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final Properties connectionProperties = new Properties();
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connectionProperties.put("user", dbUser);
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connectionProperties.put("password", dbPwd);
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final SparkConf conf = new SparkConf();
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conf.registerKryoClasses(new Class[] {
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SerializableSolrInputDocument.class
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});
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final Encoder<TupleWrapper> encoderTuple = Encoders.bean(TupleWrapper.class);
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final Encoder<OaiRecordWrapper> encoderOaiRecord = Encoders.bean(OaiRecordWrapper.class);
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runWithSparkSession(conf, isSparkSessionManaged, spark -> {
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final Dataset<OaiRecordWrapper> docs = spark
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.read()
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.schema(encoderTuple.schema())
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.json(inputPath)
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.as(encoderTuple)
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.map((MapFunction<TupleWrapper, String>) TupleWrapper::getXml, Encoders.STRING())
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.map((MapFunction<String, OaiRecordWrapper>) IrishOaiExporterJob::asIrishOaiResult, encoderOaiRecord)
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.filter((FilterFunction<OaiRecordWrapper>) obj -> (obj != null) && StringUtils.isNotBlank(obj.getId()));
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docs.repartition(numConnections)
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.write()
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.mode(SaveMode.Overwrite)
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.jdbc(dbUrl, dbTable, connectionProperties);
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});
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}
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private static OaiRecordWrapper asIrishOaiResult(final String xml) {
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try {
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final Document doc = DocumentHelper.parseText(xml);
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final OaiRecordWrapper r = new OaiRecordWrapper();
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if (isValid(doc)) {
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r.setId(doc.valueOf("//*[local-name()='objIdentifier']").trim());
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r.setBody(gzip(xml));
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r.setDate(LocalDateTime.now());
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r.setSets(new ArrayList<>());
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}
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return r;
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} catch (final Exception e) {
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log.error("Error parsing record: " + xml, e);
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throw new RuntimeException("Error parsing record: " + xml, e);
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}
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}
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private static boolean isValid(final Document doc) {
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final Node n = doc.selectSingleNode("//*[local-name()='entity']/*[local-name()='result']");
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if (n != null) {
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for (final Object o : n.selectNodes(".//*[local-name()='datainfo']/*[local-name()='deletedbyinference']")) {
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if ("true".equals(((Node) o).getText().trim())) { return false; }
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}
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for (final Object o : n.selectNodes("./*[local-name()='country']")) {
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if ("IE".equals(((Node) o).valueOf("@classid").trim())) { return true; }
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}
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for (final Object o : n.selectNodes(".//*[local-name()='rel']")) {
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final String relType = ((Node) o).valueOf("./[local-name() = 'to']/@type").trim();
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final String relCountry = ((Node) o).valueOf("./*[local-name() = 'country']/@classid").trim();
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if ("organization".equals(relType) && "IE".equals(relCountry)) { return true; }
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}
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}
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return false;
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}
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private static byte[] gzip(final String str) {
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if (StringUtils.isBlank(str)) { return null; }
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try {
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final ByteArrayOutputStream obj = new ByteArrayOutputStream();
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final GZIPOutputStream gzip = new GZIPOutputStream(obj);
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gzip.write(str.getBytes("UTF-8"));
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gzip.flush();
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gzip.close();
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return obj.toByteArray();
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} catch (final IOException e) {
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throw new RuntimeException("error in gzip", e);
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}
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}
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}
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@ -0,0 +1,50 @@
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package eu.dnetlib.dhp.oa.oaipmh;
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import java.io.Serializable;
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import java.time.LocalDateTime;
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import java.util.List;
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public class OaiRecordWrapper implements Serializable {
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private static final long serialVersionUID = 8997046455575004880L;
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private String id;
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private byte[] body;
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private LocalDateTime date;
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private List<String> sets;
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public OaiRecordWrapper() {}
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public String getId() {
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return this.id;
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}
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public void setId(final String id) {
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this.id = id;
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}
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public byte[] getBody() {
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return this.body;
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}
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public void setBody(final byte[] body) {
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this.body = body;
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}
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public LocalDateTime getDate() {
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return this.date;
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}
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public void setDate(final LocalDateTime date) {
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this.date = date;
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}
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public List<String> getSets() {
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return this.sets;
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}
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public void setSets(final List<String> sets) {
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this.sets = sets;
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}
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}
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