changes in the blacklist and workflow definition
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@ -1,13 +1,5 @@
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package eu.dnetlib.dhp.blacklist;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.oa.graph.raw.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 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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package eu.dnetlib.dhp.blacklist;
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import java.io.BufferedWriter;
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import java.io.Closeable;
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@ -19,120 +11,125 @@ 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.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 com.fasterxml.jackson.databind.ObjectMapper;
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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.oa.graph.raw.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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public class ReadBlacklistFromDB implements Closeable {
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private final DbClient dbClient;
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private static final Log log = LogFactory.getLog(ReadBlacklistFromDB.class);
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private final Configuration conf;
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private final BufferedWriter writer;
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private final DbClient dbClient;
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private static final Log log = LogFactory.getLog(ReadBlacklistFromDB.class);
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private final Configuration conf;
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private final BufferedWriter writer;
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private final static String query = "SELECT source_type, unnest(original_source_objects) as source, " +
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"target_type, unnest(original_target_objects) as target, " +
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"relationship FROM blacklist WHERE status = 'ACCEPTED'";
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private final static String query = "SELECT source_type, unnest(original_source_objects) as source, " +
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"target_type, unnest(original_target_objects) as target, " +
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"relationship FROM blacklist WHERE status = 'ACCEPTED'";
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public static void main(final String[] args) throws Exception {
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final ArgumentApplicationParser parser =
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new ArgumentApplicationParser(
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IOUtils.toString(
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ReadBlacklistFromDB.class.getResourceAsStream(
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"/eu/dnetlib/dhp/blacklist/blacklist_parameters.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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ReadBlacklistFromDB.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/blacklist/blacklist_parameters.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 ReadBlacklistFromDB rbl = new ReadBlacklistFromDB(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::processBlacklistEntry);
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try (final ReadBlacklistFromDB rbl =
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new ReadBlacklistFromDB(hdfsPath, hdfsNameNode, dbUrl, dbUser, dbPassword)) {
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}
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}
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log.info("Processing blacklist...");
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rbl.execute(query, rbl::processBlacklistEntry);
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public void execute(final String sql, final Function<ResultSet, List<Relation>> producer)
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throws Exception {
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}
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}
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final Consumer<ResultSet> consumer = rs -> producer.apply(rs).forEach(r -> writeRelation(r));
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dbClient.processResults(sql, consumer);
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}
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public void execute(final String sql, final Function<ResultSet, List<Relation>> producer)
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throws Exception {
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public List<Relation> processBlacklistEntry(ResultSet rs) {
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try {
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Relation direct = new Relation();
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Relation inverse = new Relation();
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final Consumer<ResultSet> consumer = rs -> producer.apply(rs).forEach(r -> writeRelation(r));
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String source_prefix = ModelSupport.entityIdPrefix.get(rs.getString("source_type"));
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String target_prefix = ModelSupport.entityIdPrefix.get(rs.getString("target_type"));
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dbClient.processResults(sql, consumer);
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}
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String source_direct = source_prefix + "|" + rs.getString("source");
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direct.setSource(source_direct);
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inverse.setTarget(source_direct);
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public List<Relation> processBlacklistEntry(ResultSet rs){
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try {
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Relation direct = new Relation();
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Relation inverse = new Relation();
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String target_direct = target_prefix + "|" + rs.getString("target");
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direct.setTarget(target_direct);
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inverse.setSource(target_direct);
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String source_prefix = ModelSupport.entityIdPrefix.get(rs.getString("source_type"));
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String target_prefix = ModelSupport.entityIdPrefix.get(rs.getString("target_type"));
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String encoding = rs.getString("relationship");
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RelationInverse ri = ModelSupport.relationInverseMap.get(encoding);
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direct.setRelClass(ri.getRelation());
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inverse.setRelClass(ri.getInverse());
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direct.setRelType(ri.getRelType());
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inverse.setRelType(ri.getRelType());
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direct.setSubRelType(ri.getSubReltype());
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inverse.setSubRelType(ri.getSubReltype());
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String source_direct = source_prefix + "|" + rs.getString("source");
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direct.setSource(source_direct);
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inverse.setTarget(source_direct);
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return Arrays.asList(direct, inverse);
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String target_direct = target_prefix + "|" + rs.getString("target");
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direct.setTarget(target_direct);
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inverse.setSource(target_direct);
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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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String encoding = rs.getString("relationship");
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RelationInverse ri = ModelSupport.relationInverseMap.get(encoding);
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direct.setRelClass(ri.getRelation());
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inverse.setRelClass(ri.getInverse());
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direct.setRelType(ri.getRelType());
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inverse.setRelType(ri.getRelType());
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direct.setSubRelType(ri.getSubReltype());
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inverse.setSubRelType(ri.getSubReltype());
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return Arrays.asList(direct, inverse);
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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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@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 ReadBlacklistFromDB(
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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 = fileSystem.append(hdfsWritePath);
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this.writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8));
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}
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protected void writeRelation(final Relation r) {
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try {
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writer.write(new ObjectMapper().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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@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 ReadBlacklistFromDB(
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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 = fileSystem.append(hdfsWritePath);
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this.writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8));
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}
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protected void writeRelation(final Relation r) {
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try {
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writer.write(new ObjectMapper().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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}
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@ -1,5 +1,18 @@
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<workflow-app name="blacklsting" xmlns="uri:oozie:workflow:0.5">
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<workflow-app name="blacklisting" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>postgresURL</name>
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<description>the url of the postgress server to query</description>
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</property>
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<property>
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<name>postgresUser</name>
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<description>the username to access the postgres db</description>
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</property>
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<property>
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<name>postgresPassword</name>
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<description>the postgres password</description>
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</property>
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</parameters>
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<start to="reset-outputpath"/>
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<kill name="Kill">
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@ -8,7 +21,7 @@
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<action name="reset-outputpath">
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<fs>
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<delete path='${hdfsPath}'/>
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<delete path='${workingDir}/blacklist'/>
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</fs>
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<ok to="read_blacklist"/>
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<error to="Kill"/>
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@ -21,7 +34,7 @@
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<main-class>eu.dnetlib.dhp.blacklist.ReadBlacklistFromDB</main-class>
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<arg>--hdfsPath</arg><arg>${workingDir}/blacklist</arg>
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<arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
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<arg>--postgresUrl</arg><arg>${postgresUrl}</arg>
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<arg>--postgresUrl</arg><arg>${postgresURL}</arg>
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<arg>--postgresUser</arg><arg>${postgresUser}</arg>
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<arg>--postgresPassword</arg><arg>${postgresPassword}</arg>
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</java>
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