[ECclassification] added new classes
This commit is contained in:
parent
4f2df876cd
commit
c1f9848953
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@ -266,11 +266,15 @@ public class PrepareProgramme {
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String code = csvProgramme.getCode();
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if (!code.endsWith(".") && !code.contains("Euratom")
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&& !code.equals("H2020-EC"))
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&& !code.equals("H2020-EC") && !code.equals("H2020") &&
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!code.equals("H2020-Topics"))
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code += ".";
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if (map.containsKey(code)) {
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csvProgramme.setClassification(map.get(code)._1());
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csvProgramme.setClassification_short(map.get(code)._2());
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} else
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log.info("WARNING: No entry in map for code " + code);
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return csvProgramme;
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}).collect();
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@ -24,6 +24,7 @@ import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.actionmanager.project.utils.model.CSVProgramme;
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import eu.dnetlib.dhp.actionmanager.project.utils.model.CSVProject;
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import eu.dnetlib.dhp.actionmanager.project.utils.model.EXCELTopic;
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import eu.dnetlib.dhp.actionmanager.project.utils.model.JsonTopic;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.common.HdfsSupport;
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import eu.dnetlib.dhp.schema.action.AtomicAction;
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@ -110,7 +111,7 @@ public class SparkAtomicActionJob {
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Dataset<CSVProject> project = readPath(spark, projectPatH, CSVProject.class);
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Dataset<CSVProgramme> programme = readPath(spark, programmePath, CSVProgramme.class);
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Dataset<EXCELTopic> topic = readPath(spark, topicPath, EXCELTopic.class);
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Dataset<JsonTopic> topic = readPath(spark, topicPath, JsonTopic.class);
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Dataset<Project> aaproject = project
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.joinWith(programme, project.col("programme").equalTo(programme.col("code")), "left")
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@ -144,9 +145,9 @@ public class SparkAtomicActionJob {
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.filter(Objects::nonNull);
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aaproject
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.joinWith(topic, aaproject.col("h2020topiccode").equalTo(topic.col("code")), "left")
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.map((MapFunction<Tuple2<Project, EXCELTopic>, Project>) p -> {
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Optional<EXCELTopic> op = Optional.ofNullable(p._2());
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.joinWith(topic, aaproject.col("id").equalTo(topic.col("projectId")), "left")
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.map((MapFunction<Tuple2<Project, JsonTopic>, Project>) p -> {
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Optional<JsonTopic> op = Optional.ofNullable(p._2());
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Project rp = p._1();
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op.ifPresent(excelTopic -> rp.setH2020topicdescription(excelTopic.getTitle()));
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return rp;
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@ -1,12 +1,13 @@
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package eu.dnetlib.dhp.actionmanager.project.utils;
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import java.io.*;
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import java.io.BufferedWriter;
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import java.io.IOException;
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import java.io.OutputStreamWriter;
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import java.io.Serializable;
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import java.nio.charset.StandardCharsets;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.Optional;
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import java.util.zip.GZIPOutputStream;
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import java.util.zip.ZipEntry;
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import java.util.zip.ZipInputStream;
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@ -30,7 +31,7 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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* @author miriam.baglioni
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* @Date 28/02/23
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*/
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public class ExtractProjects implements Serializable {
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public class ExtractFromZip implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(PrepareProjects.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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@ -40,17 +41,17 @@ public class ExtractProjects implements Serializable {
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.toString(
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PrepareProjects.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/actionmanager/project/extract_project_parameters.json"));
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"/eu/dnetlib/dhp/actionmanager/project/extract_fromzip_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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final String projectPath = parser.get("projectPath");
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log.info("projectPath {}: ", projectPath);
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final String inputPath = parser.get("inputPath");
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log.info("inputPath {}: ", inputPath);
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final String workingPath = parser.get("workingPath");
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log.info("workingPath {}: ", workingPath);
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final String outputPath = parser.get("outputPath");
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log.info("outputPath {}: ", outputPath);
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final String hdfsNameNode = parser.get("hdfsNameNode");
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log.info("hdfsNameNode {}", hdfsNameNode);
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@ -60,8 +61,8 @@ public class ExtractProjects implements Serializable {
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FileSystem fs = FileSystem.get(conf);
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doExtract(projectPath, workingPath, fs);
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readProjects(workingPath + "json/project.json", workingPath + "projects/h2020_projects_nld.json", fs);
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doExtract(inputPath, outputPath, fs);
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}
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private static void doExtract(String inputFile, String workingPath, FileSystem fileSystem)
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@ -97,30 +98,4 @@ public class ExtractProjects implements Serializable {
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}
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private static void readProjects(String inputFile, String workingPath, FileSystem fs) throws IOException {
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Path hdfsreadpath = new Path(inputFile);
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FSDataInputStream inputStream = fs.open(hdfsreadpath);
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ArrayList<Project> projects = OBJECT_MAPPER
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.readValue(
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IOUtils.toString(inputStream, "UTF-8"),
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new TypeReference<List<Project>>() {
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});
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Path hdfsWritePath = new Path(workingPath);
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if (fs.exists(hdfsWritePath)) {
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fs.delete(hdfsWritePath, false);
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}
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FSDataOutputStream fos = fs.create(hdfsWritePath);
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try (BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(fos, StandardCharsets.UTF_8))) {
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for (Project p : projects) {
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writer.write(OBJECT_MAPPER.writeValueAsString(p));
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writer.newLine();
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}
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}
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}
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}
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@ -6,7 +6,9 @@ import java.util.Optional;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.conf.Configuration;
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import org.apache.hadoop.fs.FSDataInputStream;
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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 eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.common.collection.GetCSV;
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@ -40,8 +42,11 @@ public class ReadCSV {
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conf.set("fs.defaultFS", hdfsNameNode);
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FileSystem fileSystem = FileSystem.get(conf);
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FSDataInputStream inputStream = fileSystem.open(new Path(fileURL));
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BufferedReader reader = new BufferedReader(
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new InputStreamReader(new HttpConnector2().getInputSourceAsStream(fileURL)));
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new InputStreamReader(inputStream));
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GetCSV.getCsv(fileSystem, reader, hdfsPath, classForName, del);
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@ -0,0 +1,90 @@
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package eu.dnetlib.dhp.actionmanager.project.utils;
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import java.io.*;
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import java.nio.charset.StandardCharsets;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.zip.ZipEntry;
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import java.util.zip.ZipInputStream;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.conf.Configuration;
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import org.apache.hadoop.fs.FSDataInputStream;
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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 org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.core.type.TypeReference;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.actionmanager.project.PrepareProjects;
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import eu.dnetlib.dhp.actionmanager.project.utils.model.Project;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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/**
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* @author miriam.baglioni
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* @Date 28/02/23
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*/
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public class ReadProjects implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(ReadProjects.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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public static void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils
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.toString(
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PrepareProjects.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/actionmanager/project/read_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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final String inputPath = parser.get("inputPath");
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log.info("inputPath {}: ", inputPath);
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final String outputPath = parser.get("outputPath");
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log.info("outputPath {}: ", outputPath);
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final String hdfsNameNode = parser.get("hdfsNameNode");
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log.info("hdfsNameNode {}", hdfsNameNode);
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Configuration conf = new Configuration();
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conf.set("fs.defaultFS", hdfsNameNode);
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FileSystem fs = FileSystem.get(conf);
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readProjects(inputPath, outputPath, fs);
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}
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private static void readProjects(String inputFile, String workingPath, FileSystem fs) throws IOException {
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Path hdfsreadpath = new Path(inputFile);
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FSDataInputStream inputStream = fs.open(hdfsreadpath);
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ArrayList<Project> projects = OBJECT_MAPPER
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.readValue(
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IOUtils.toString(inputStream, "UTF-8"),
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new TypeReference<List<Project>>() {
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});
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Path hdfsWritePath = new Path(workingPath);
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if (fs.exists(hdfsWritePath)) {
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fs.delete(hdfsWritePath, false);
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}
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FSDataOutputStream fos = fs.create(hdfsWritePath);
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try (BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(fos, StandardCharsets.UTF_8))) {
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for (Project p : projects) {
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writer.write(OBJECT_MAPPER.writeValueAsString(p));
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writer.newLine();
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}
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}
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}
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}
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@ -0,0 +1,92 @@
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package eu.dnetlib.dhp.actionmanager.project.utils;
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import java.io.BufferedWriter;
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import java.io.IOException;
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import java.io.OutputStreamWriter;
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import java.io.Serializable;
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import java.nio.charset.StandardCharsets;
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import java.util.ArrayList;
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import java.util.List;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.conf.Configuration;
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import org.apache.hadoop.fs.FSDataInputStream;
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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 org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.core.type.TypeReference;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.actionmanager.project.PrepareProjects;
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import eu.dnetlib.dhp.actionmanager.project.utils.model.JsonTopic;
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import eu.dnetlib.dhp.actionmanager.project.utils.model.Project;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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/**
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* @author miriam.baglioni
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* @Date 28/02/23
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*/
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public class ReadTopics implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(ReadTopics.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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public static void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils
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.toString(
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PrepareProjects.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/actionmanager/project/read_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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final String inputPath = parser.get("inputPath");
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log.info("inputPath {}: ", inputPath);
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final String outputPath = parser.get("outputPath");
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log.info("outputPath {}: ", outputPath);
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final String hdfsNameNode = parser.get("hdfsNameNode");
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log.info("hdfsNameNode {}", hdfsNameNode);
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Configuration conf = new Configuration();
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conf.set("fs.defaultFS", hdfsNameNode);
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FileSystem fs = FileSystem.get(conf);
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readTopics(inputPath, outputPath, fs);
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}
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private static void readTopics(String inputFile, String workingPath, FileSystem fs) throws IOException {
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Path hdfsreadpath = new Path(inputFile);
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FSDataInputStream inputStream = fs.open(hdfsreadpath);
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ArrayList<JsonTopic> topics = OBJECT_MAPPER
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.readValue(
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IOUtils.toString(inputStream, "UTF-8"),
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new TypeReference<List<JsonTopic>>() {
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});
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Path hdfsWritePath = new Path(workingPath);
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if (fs.exists(hdfsWritePath)) {
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fs.delete(hdfsWritePath, false);
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}
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FSDataOutputStream fos = fs.create(hdfsWritePath);
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try (BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(fos, StandardCharsets.UTF_8))) {
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for (JsonTopic p : topics) {
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writer.write(OBJECT_MAPPER.writeValueAsString(p));
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writer.newLine();
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}
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}
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}
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}
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@ -0,0 +1,38 @@
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package eu.dnetlib.dhp.actionmanager.project.utils.model;
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import java.io.Serializable;
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/**
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* @author miriam.baglioni
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* @Date 28/02/23
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*/
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public class JsonTopic implements Serializable {
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private String projectID;
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private String title;
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private String topic;
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public String getProjectID() {
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return projectID;
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}
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public void setProjectID(String projectID) {
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this.projectID = projectID;
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}
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public String getTitle() {
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return title;
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}
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public void setTitle(String title) {
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this.title = title;
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}
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public String getTopic() {
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return topic;
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}
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public void setTopic(String topic) {
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this.topic = topic;
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}
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}
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@ -1,16 +1,16 @@
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[
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{
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"paramName": "pjp",
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"paramLongName": "projectPath",
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"paramName": "ip",
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"paramLongName": "inputPath",
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"paramDescription": "the path where the projects are stored ",
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"paramRequired": true
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},
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{
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"paramName": "wp",
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"paramLongName": "workingPath",
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"paramName": "op",
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"paramLongName": "outputPath",
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"paramDescription": "the path for the extracted folder",
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"paramRequired": true
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},
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@ -0,0 +1,3 @@
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#!/bin/bash
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hdfs dfs -rm $2
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curl -LSs $1 | hdfs dfs -put - $2
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@ -14,7 +14,6 @@
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</property>
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<property>
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<name>outputPath</name>
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<value>noneed</value>
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<description>path where to store the action set</description>
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</property>
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<property>
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@ -35,42 +34,104 @@
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<delete path='${workingDir}'/>
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<mkdir path='${workingDir}'/>
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</fs>
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<ok to="fork_get_projects"/>
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<ok to="fork_download_info"/>
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<error to="Kill"/>
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</action>
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<fork name="fork_get_info">
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<fork name="fork_download_info">
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<path start="fork_get_projects"/>
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<path start="get_programme_file"/>
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<path start="get_topic_file"/>
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<path start="download_programme_file"/>
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<!-- <path start="read_topic_file"/>-->
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</fork>
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<fork name="fork_get_projects">
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<path start="extract_projects"/>
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<path start="read_projects"/>
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<path start="download_projects"/>
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<path start="read_projects_from_db"/>
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</fork>
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<action name="extract_projects">
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<java>
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<main-class>eu.dnetlib.dhp.actionmanager.project.utils.ExtractProjects</main-class>
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<arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
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<arg>--projectPath</arg><arg>/tmp/miriam/cordis-h2020projects-json_.zip</arg>
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<!-- <arg>--workingPath</arg><arg>/tmp/miriam/cordis_h2020/</arg>-->
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<!-- <arg>--projectPath</arg><arg>${projectPath}</arg>-->
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<arg>--workingPath</arg><arg>${workingDir}/</arg>
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</java>
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<ok to="wait_projects"/>
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<!-- <ok to="End"/>-->
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<action name="download_projects">
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<shell xmlns="uri:oozie:shell-action:0.2">
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<configuration>
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<property>
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<name>mapred.job.queue.name</name>
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<value>${queueName}</value>
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</property>
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</configuration>
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<exec>download.sh</exec>
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<argument>${downloadH2020Projects}</argument>
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<argument>${projectPath}</argument>
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<env-var>HADOOP_USER_NAME=${wf:user()}</env-var>
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<file>download.sh</file>
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||||
<capture-output/>
|
||||
</shell>
|
||||
<ok to="extract_projects"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="get_programme_file">
|
||||
<action name="extract_projects">
|
||||
<java>
|
||||
<main-class>eu.dnetlib.dhp.actionmanager.project.utils.ExtractFromZip</main-class>
|
||||
<arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
|
||||
<arg>--inputPath</arg><arg>${projectPath}</arg>
|
||||
<arg>--outputPath</arg><arg>${workingDir}/</arg>
|
||||
</java>
|
||||
<ok to="read_from_folder"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<fork name="read_from_folder">
|
||||
<path start="read_projects"/>
|
||||
<path start="read_topic_file"/>
|
||||
</fork>
|
||||
|
||||
<action name="read_projects">
|
||||
<java>
|
||||
<main-class>eu.dnetlib.dhp.actionmanager.project.utils.ReadProjects</main-class>
|
||||
<arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
|
||||
<arg>--inputPath</arg><arg>${workingDir}/json/project.json</arg>
|
||||
<arg>--outputPath</arg><arg>${workingDir}/projects</arg>
|
||||
</java>
|
||||
<ok to="wait_read_from_folder"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="download_programme_file">
|
||||
<shell xmlns="uri:oozie:shell-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<configuration>
|
||||
<property>
|
||||
<name>mapred.job.queue.name</name>
|
||||
<value>${queueName}</value>
|
||||
</property>
|
||||
</configuration>
|
||||
<exec>download.sh</exec>
|
||||
<argument>${downloadH2020Programme}</argument>
|
||||
<argument>${programmePath}</argument>
|
||||
<env-var>HADOOP_USER_NAME=${wf:user()}</env-var>
|
||||
<file>download.sh</file>
|
||||
<capture-output/>
|
||||
</shell>
|
||||
<ok to="extract_programme"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
<action name="extract_programme">
|
||||
<java>
|
||||
<main-class>eu.dnetlib.dhp.actionmanager.project.utils.ExtractFromZip</main-class>
|
||||
<arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
|
||||
<arg>--inputPath</arg><arg>${programmePath}</arg>
|
||||
<arg>--outputPath</arg><arg>${workingDir}/downloadedProgramme/</arg>
|
||||
</java>
|
||||
<ok to="read_programme"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
<action name="read_programme">
|
||||
<java>
|
||||
<main-class>eu.dnetlib.dhp.actionmanager.project.utils.ReadCSV</main-class>
|
||||
<arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
|
||||
<arg>--fileURL</arg><arg>${programmeFileURL}</arg>
|
||||
<arg>--fileURL</arg><arg>${workingDir}/downloadedProgramme/csv/programme.csv</arg>
|
||||
<arg>--hdfsPath</arg><arg>${workingDir}/programme</arg>
|
||||
<arg>--classForName</arg><arg>eu.dnetlib.dhp.actionmanager.project.utils.model.CSVProgramme</arg>
|
||||
</java>
|
||||
|
@ -78,20 +139,18 @@
|
|||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="get_topic_file">
|
||||
<action name="read_topic_file">
|
||||
<java>
|
||||
<main-class>eu.dnetlib.dhp.actionmanager.project.utils.ReadExcel</main-class>
|
||||
<main-class>eu.dnetlib.dhp.actionmanager.project.utils.ReadTopics</main-class>
|
||||
<arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
|
||||
<arg>--fileURL</arg><arg>${topicFileURL}</arg>
|
||||
<arg>--hdfsPath</arg><arg>${workingDir}/topic</arg>
|
||||
<arg>--sheetName</arg><arg>${sheetName}</arg>
|
||||
<arg>--classForName</arg><arg>eu.dnetlib.dhp.actionmanager.project.utils.model.EXCELTopic</arg>
|
||||
<arg>--inputPath</arg><arg>${workingDir}/json/topics.json</arg>
|
||||
<arg>--outputPath</arg><arg>${workingDir}/topic</arg>
|
||||
</java>
|
||||
<ok to="wait"/>
|
||||
<ok to="wait_read_from_folder"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="read_projects">
|
||||
<action name="read_projects_from_db">
|
||||
<java>
|
||||
<main-class>eu.dnetlib.dhp.actionmanager.project.ReadProjectsFromDB</main-class>
|
||||
<arg>--hdfsPath</arg><arg>${workingDir}/dbProjects</arg>
|
||||
|
@ -125,9 +184,11 @@
|
|||
<arg>--outputPath</arg><arg>${workingDir}/preparedProgramme</arg>
|
||||
</spark>
|
||||
<ok to="wait"/>
|
||||
<!-- <ok to="End"/>-->
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<join name="wait_read_from_folder" to="wait_projects"/>
|
||||
<join name="wait" to="create_updates"/>
|
||||
|
||||
<join name="wait_projects" to="prepare_project"/>
|
||||
|
@ -154,8 +215,8 @@
|
|||
<arg>--outputPath</arg><arg>${workingDir}/preparedProjects</arg>
|
||||
<arg>--dbProjectPath</arg><arg>${workingDir}/dbProjects</arg>
|
||||
</spark>
|
||||
<!-- <ok to="wait"/>-->
|
||||
<ok to="End"/>
|
||||
<ok to="wait"/>
|
||||
<!-- <ok to="End"/>-->
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
|
|
|
@ -0,0 +1,23 @@
|
|||
[
|
||||
|
||||
{
|
||||
"paramName": "ip",
|
||||
"paramLongName": "inputPath",
|
||||
"paramDescription": "the path where the projects are stored ",
|
||||
"paramRequired": true
|
||||
},
|
||||
|
||||
|
||||
{
|
||||
"paramName": "op",
|
||||
"paramLongName": "outputPath",
|
||||
"paramDescription": "the path for the extracted folder",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "hnn",
|
||||
"paramLongName": "hdfsNameNode",
|
||||
"paramDescription": "the hdfs namenode",
|
||||
"paramRequired": true
|
||||
}
|
||||
]
|
Loading…
Reference in New Issue