forked from D-Net/dnet-hadoop
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package eu.dnetlib.dhp.actionmanager.project;
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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 org.apache.commons.io.IOUtils;
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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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package eu.dnetlib.dhp.actionmanager.project;
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import java.io.BufferedWriter;
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import java.io.Closeable;
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@ -22,92 +12,104 @@ 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.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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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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public class ReadProjectsFromDB implements Closeable {
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private final DbClient dbClient;
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private static final Log log = LogFactory.getLog(ReadProjectsFromDB.class);
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private final Configuration conf;
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private final BufferedWriter writer;
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private final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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private final DbClient dbClient;
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private static final Log log = LogFactory.getLog(ReadProjectsFromDB.class);
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private final Configuration conf;
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private final BufferedWriter writer;
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private final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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private final static String query = "SELECT code " +
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"from projects where id like 'corda__h2020%' " ;
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private final static String query = "SELECT code " +
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"from projects where id like 'corda__h2020%' ";
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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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ReadProjectsFromDB.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/actionmanager/project/read_projects_db.json")));
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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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ReadProjectsFromDB.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/actionmanager/project/read_projects_db.json")));
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parser.parseArgument(args);
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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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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 (final ReadProjectsFromDB rbl = new ReadProjectsFromDB(hdfsPath, hdfsNameNode, dbUrl, dbUser,
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dbPassword)) {
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try (final ReadProjectsFromDB rbl = new ReadProjectsFromDB(hdfsPath, hdfsNameNode, dbUrl, dbUser,
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dbPassword)) {
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log.info("Processing blacklist...");
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rbl.execute(query, rbl::processProjectsEntry);
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log.info("Processing projects...");
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rbl.execute(query, rbl::processProjectsEntry);
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}
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}
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public void execute(final String sql, final Function<ResultSet, List<ProjectSubset>> producer) throws Exception {
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}
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}
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final Consumer<ResultSet> consumer = rs -> producer.apply(rs).forEach(r -> writeProject(r));
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public void execute(final String sql, final Function<ResultSet, List<ProjectSubset>> producer) throws Exception {
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dbClient.processResults(sql, consumer);
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}
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final Consumer<ResultSet> consumer = rs -> producer.apply(rs).forEach(r -> writeProject(r));
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public List<ProjectSubset> processProjectsEntry(ResultSet rs) {
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try {
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ProjectSubset p = new ProjectSubset();
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p.setCode(rs.getString("code"));
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dbClient.processResults(sql, consumer);
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}
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return Arrays.asList(p);
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public List<ProjectSubset> processProjectsEntry(ResultSet rs) {
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try {
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ProjectSubset p = new ProjectSubset();
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p.setCode(rs.getString("code"));
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} catch (final Exception e) {
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throw new RuntimeException(e);
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}
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}
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return Arrays.asList(p);
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protected void writeProject(final ProjectSubset r) {
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try {
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writer.write(OBJECT_MAPPER.writeValueAsString(r));
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writer.newLine();
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} catch (final Exception e) {
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throw new RuntimeException(e);
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}
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}
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} catch (final Exception e) {
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throw new RuntimeException(e);
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}
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}
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public ReadProjectsFromDB(
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final String hdfsPath, String hdfsNameNode, final String dbUrl, final String dbUser, final String dbPassword)
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throws Exception {
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protected void writeProject(final ProjectSubset r) {
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try {
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writer.write(OBJECT_MAPPER.writeValueAsString(r));
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writer.newLine();
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} catch (final Exception e) {
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throw new RuntimeException(e);
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}
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}
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this.dbClient = new DbClient(dbUrl, dbUser, dbPassword);
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this.conf = new Configuration();
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this.conf.set("fs.defaultFS", hdfsNameNode);
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FileSystem fileSystem = FileSystem.get(this.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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fileSystem.delete(hdfsWritePath, false);
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}
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fsDataOutputStream = fileSystem.create(hdfsWritePath);
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public ReadProjectsFromDB(
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final String hdfsPath, String hdfsNameNode, final String dbUrl, final String dbUser, final String dbPassword)
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throws Exception {
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this.dbClient = new DbClient(dbUrl, dbUser, dbPassword);
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this.conf = new Configuration();
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this.conf.set("fs.defaultFS", hdfsNameNode);
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FileSystem fileSystem = FileSystem.get(this.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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fileSystem.delete(hdfsWritePath, false);
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}
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fsDataOutputStream = fileSystem.create(hdfsWritePath);
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this.writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8));
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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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@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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@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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}
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