137 lines
4.2 KiB
Java
137 lines
4.2 KiB
Java
|
|
package eu.dnetlib.dhp.bulktag.eosc;
|
|
|
|
import java.io.BufferedWriter;
|
|
import java.io.Closeable;
|
|
import java.io.IOException;
|
|
import java.io.OutputStreamWriter;
|
|
import java.nio.charset.StandardCharsets;
|
|
import java.sql.ResultSet;
|
|
import java.sql.SQLException;
|
|
import java.util.Arrays;
|
|
import java.util.List;
|
|
import java.util.function.Consumer;
|
|
import java.util.function.Function;
|
|
|
|
import org.apache.commons.io.IOUtils;
|
|
import org.apache.commons.lang3.StringUtils;
|
|
import org.apache.commons.logging.Log;
|
|
import org.apache.commons.logging.LogFactory;
|
|
import org.apache.hadoop.conf.Configuration;
|
|
import org.apache.hadoop.fs.FSDataOutputStream;
|
|
import org.apache.hadoop.fs.FileSystem;
|
|
import org.apache.hadoop.fs.Path;
|
|
|
|
/**
|
|
* @author miriam.baglioni
|
|
* @Date 21/07/22
|
|
*/
|
|
import com.fasterxml.jackson.databind.ObjectMapper;
|
|
|
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
|
import eu.dnetlib.dhp.common.DbClient;
|
|
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
|
import eu.dnetlib.dhp.schema.common.RelationInverse;
|
|
import eu.dnetlib.dhp.schema.oaf.Relation;
|
|
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
|
|
|
|
public class ReadMasterDatasourceFromDB implements Closeable {
|
|
|
|
private final DbClient dbClient;
|
|
private static final Log log = LogFactory.getLog(ReadMasterDatasourceFromDB.class);
|
|
|
|
private final BufferedWriter writer;
|
|
private final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
|
|
|
private static final String QUERY = "SELECT dso.id datasource, d.id master FROM " +
|
|
"(SELECT id FROM dsm_services WHERE id like 'eosc%') dso " +
|
|
"FULL JOIN " +
|
|
"(SELECT id, duplicate FROM dsm_dedup_services WHERE duplicate like 'eosc%')d " +
|
|
"ON dso.id = d.duplicate";
|
|
|
|
public static void main(final String[] args) throws Exception {
|
|
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
|
IOUtils
|
|
.toString(
|
|
ReadMasterDatasourceFromDB.class
|
|
.getResourceAsStream(
|
|
"/eu/dnetlib/dhp/bulktag/datasourcemaster_parameters.json")));
|
|
|
|
parser.parseArgument(args);
|
|
|
|
final String dbUrl = parser.get("postgresUrl");
|
|
final String dbUser = parser.get("postgresUser");
|
|
final String dbPassword = parser.get("postgresPassword");
|
|
final String hdfsPath = parser.get("hdfsPath") + "/datasourceMasters";
|
|
final String hdfsNameNode = parser.get("hdfsNameNode");
|
|
|
|
try (
|
|
final ReadMasterDatasourceFromDB rmd = new ReadMasterDatasourceFromDB(hdfsPath, hdfsNameNode, dbUrl, dbUser,
|
|
dbPassword)) {
|
|
|
|
log.info("Processing datasources...");
|
|
rmd.execute(QUERY, rmd::datasourceMasterMap);
|
|
|
|
}
|
|
}
|
|
|
|
public void execute(final String sql, final Function<ResultSet, DatasourceMaster> producer) {
|
|
|
|
dbClient.processResults(sql, rs -> writeMap(producer.apply(rs)));
|
|
}
|
|
|
|
public DatasourceMaster datasourceMasterMap(ResultSet rs) {
|
|
try {
|
|
DatasourceMaster dm = new DatasourceMaster();
|
|
String datasource = rs.getString("datasource");
|
|
dm.setDatasource(datasource);
|
|
String master = rs.getString("master");
|
|
if (StringUtils.isNotBlank(master))
|
|
dm.setMaster(OafMapperUtils.createOpenaireId(10, master, true));
|
|
else
|
|
dm.setMaster(OafMapperUtils.createOpenaireId(10, datasource, true));
|
|
return dm;
|
|
|
|
} catch (final SQLException e) {
|
|
throw new RuntimeException(e);
|
|
}
|
|
}
|
|
|
|
@Override
|
|
public void close() throws IOException {
|
|
dbClient.close();
|
|
writer.close();
|
|
}
|
|
|
|
public ReadMasterDatasourceFromDB(
|
|
final String hdfsPath, String hdfsNameNode, final String dbUrl, final String dbUser, final String dbPassword)
|
|
throws IOException {
|
|
|
|
this.dbClient = new DbClient(dbUrl, dbUser, dbPassword);
|
|
|
|
Configuration conf = new Configuration();
|
|
conf.set("fs.defaultFS", hdfsNameNode);
|
|
|
|
FileSystem fileSystem = FileSystem.get(conf);
|
|
Path hdfsWritePath = new Path(hdfsPath);
|
|
FSDataOutputStream fsDataOutputStream = null;
|
|
if (fileSystem.exists(hdfsWritePath)) {
|
|
fsDataOutputStream = fileSystem.append(hdfsWritePath);
|
|
} else {
|
|
fsDataOutputStream = fileSystem.create(hdfsWritePath);
|
|
}
|
|
|
|
this.writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8));
|
|
}
|
|
|
|
protected void writeMap(final DatasourceMaster dm) {
|
|
try {
|
|
writer.write(OBJECT_MAPPER.writeValueAsString(dm));
|
|
writer.newLine();
|
|
} catch (final IOException e) {
|
|
throw new RuntimeException(e);
|
|
}
|
|
}
|
|
|
|
}
|