137 lines
4.2 KiB
Java
137 lines
4.2 KiB
Java
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package eu.dnetlib.dhp.bulktag.eosc;
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import java.io.BufferedWriter;
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import java.io.Closeable;
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import java.io.IOException;
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import java.io.OutputStreamWriter;
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import java.nio.charset.StandardCharsets;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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import java.util.Arrays;
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import java.util.List;
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import java.util.function.Consumer;
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import java.util.function.Function;
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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.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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import org.apache.hadoop.conf.Configuration;
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import org.apache.hadoop.fs.FSDataOutputStream;
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import org.apache.hadoop.fs.FileSystem;
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import org.apache.hadoop.fs.Path;
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/**
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* @author miriam.baglioni
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* @Date 21/07/22
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*/
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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.common.DbClient;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.common.RelationInverse;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
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public class ReadMasterDatasourceFromDB implements Closeable {
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private final DbClient dbClient;
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private static final Log log = LogFactory.getLog(ReadMasterDatasourceFromDB.class);
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private final BufferedWriter writer;
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private final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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private static final String QUERY = "SELECT dso.id datasource, d.id master FROM " +
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"(SELECT id FROM dsm_services WHERE id like 'eosc%') dso " +
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"FULL JOIN " +
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"(SELECT id, duplicate FROM dsm_dedup_services WHERE duplicate like 'eosc%')d " +
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"ON dso.id = d.duplicate";
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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(
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ReadMasterDatasourceFromDB.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/bulktag/datasourcemaster_parameters.json")));
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parser.parseArgument(args);
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final String dbUrl = parser.get("postgresUrl");
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final String dbUser = parser.get("postgresUser");
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final String dbPassword = parser.get("postgresPassword");
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final String hdfsPath = parser.get("hdfsPath");
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final String hdfsNameNode = parser.get("hdfsNameNode");
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try (
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final ReadMasterDatasourceFromDB rmd = new ReadMasterDatasourceFromDB(hdfsPath, hdfsNameNode, dbUrl, dbUser,
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dbPassword)) {
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log.info("Processing datasources...");
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rmd.execute(QUERY, rmd::datasourceMasterMap);
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}
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}
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public void execute(final String sql, final Function<ResultSet, DatasourceMaster> producer) {
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dbClient.processResults(sql, rs -> writeMap(producer.apply(rs)));
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}
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public DatasourceMaster datasourceMasterMap(ResultSet rs) {
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try {
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DatasourceMaster dm = new DatasourceMaster();
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String datasource = rs.getString("datasource");
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dm.setDatasource(datasource);
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String master = rs.getString("master");
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if (StringUtils.isNotBlank(master))
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dm.setMaster(OafMapperUtils.createOpenaireId(10, master, true));
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else
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dm.setMaster(OafMapperUtils.createOpenaireId(10, datasource, true));
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return dm;
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} catch (final SQLException e) {
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throw new RuntimeException(e);
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}
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}
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@Override
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public void close() throws IOException {
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dbClient.close();
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writer.close();
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}
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public ReadMasterDatasourceFromDB(
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final String hdfsPath, String hdfsNameNode, final String dbUrl, final String dbUser, final String dbPassword)
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throws IOException {
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this.dbClient = new DbClient(dbUrl, dbUser, dbPassword);
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Configuration conf = new Configuration();
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conf.set("fs.defaultFS", hdfsNameNode);
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FileSystem fileSystem = FileSystem.get(conf);
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Path hdfsWritePath = new Path(hdfsPath);
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FSDataOutputStream fsDataOutputStream = null;
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if (fileSystem.exists(hdfsWritePath)) {
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fsDataOutputStream = fileSystem.append(hdfsWritePath);
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} else {
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fsDataOutputStream = fileSystem.create(hdfsWritePath);
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}
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this.writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8));
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}
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protected void writeMap(final DatasourceMaster dm) {
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try {
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writer.write(OBJECT_MAPPER.writeValueAsString(dm));
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writer.newLine();
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} catch (final IOException e) {
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throw new RuntimeException(e);
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}
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}
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}
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