added DownloadCSV2 as alternative implementation of the same download procedure
This commit is contained in:
parent
5f0903d50d
commit
f74adc4752
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@ -7,16 +7,15 @@ import java.nio.charset.StandardCharsets;
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import java.util.Objects;
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import java.util.Optional;
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import eu.dnetlib.dhp.common.collection.CollectorException;
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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.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 eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.common.collection.CollectorException;
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import eu.dnetlib.dhp.common.collection.GetCSV;
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import eu.dnetlib.dhp.common.collection.HttpConnector2;
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@ -68,8 +67,9 @@ public class DownloadCSV {
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}
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protected void doDownload(String fileURL, String workingPath, String outputFile, String classForName, char delimiter, FileSystem fs)
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throws IOException, ClassNotFoundException, CollectorException {
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protected void doDownload(String fileURL, String workingPath, String outputFile, String classForName,
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char delimiter, FileSystem fs)
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throws IOException, ClassNotFoundException, CollectorException {
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final HttpConnector2 connector2 = new HttpConnector2();
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@ -78,11 +78,11 @@ public class DownloadCSV {
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try (BufferedReader in = new BufferedReader(
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new InputStreamReader(connector2.getInputSourceAsStream(fileURL)))) {
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try (BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(fs.create(path, true), Charset.defaultCharset()))) {
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try (PrintWriter writer = new PrintWriter(
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new OutputStreamWriter(fs.create(path, true), StandardCharsets.UTF_8))) {
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String line;
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while ((line = in.readLine()) != null) {
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writer.write(line.replace("\\\"", "\""));
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writer.newLine();
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writer.println(line.replace("\\\"", "\""));
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}
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}
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}
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@ -0,0 +1,84 @@
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package eu.dnetlib.dhp.oa.graph.hostedbymap;
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import java.io.*;
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import java.util.Objects;
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import java.util.Optional;
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import org.apache.commons.io.FileUtils;
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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.FileSystem;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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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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import eu.dnetlib.dhp.common.collection.HttpConnector2;
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public class DownloadCSV2 {
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private static final Logger log = LoggerFactory.getLogger(DownloadCSV2.class);
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public static final char DEFAULT_DELIMITER = ';';
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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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Objects
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.requireNonNull(
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DownloadCSV2.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/graph/hostedbymap/download_csv_parameters.json"))));
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parser.parseArgument(args);
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final String fileURL = parser.get("fileURL");
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log.info("fileURL {}", fileURL);
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final String tmpFile = parser.get("tmpFile");
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log.info("tmpFile {}", tmpFile);
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final String outputFile = parser.get("outputFile");
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log.info("outputFile {}", outputFile);
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final String hdfsNameNode = parser.get("hdfsNameNode");
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log.info("hdfsNameNode {}", hdfsNameNode);
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final String classForName = parser.get("classForName");
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log.info("classForName {}", classForName);
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final char delimiter = Optional
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.ofNullable(parser.get("delimiter"))
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.map(s -> s.charAt(0))
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.orElse(DEFAULT_DELIMITER);
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log.info("delimiter {}", delimiter);
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HttpConnector2 connector2 = new HttpConnector2();
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try (BufferedReader in = new BufferedReader(
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new InputStreamReader(connector2.getInputSourceAsStream(fileURL)))) {
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try (PrintWriter writer = new PrintWriter(new BufferedWriter(new FileWriter(tmpFile)))) {
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String line;
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while ((line = in.readLine()) != null) {
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writer.println(line.replace("\\\"", "\""));
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}
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}
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}
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try (BufferedReader in = new BufferedReader(new FileReader(tmpFile))) {
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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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GetCSV.getCsv(fileSystem, in, outputFile, classForName, delimiter);
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} finally {
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FileUtils.deleteQuietly(new File(tmpFile));
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}
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}
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}
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@ -6,9 +6,9 @@
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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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"paramDescription": "the path where to find the pre-processed data for unibi gold list and doj artciles",
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"paramName":"tf",
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"paramLongName":"tmpFile",
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"paramDescription": "the temporary local file storing the cleaned CSV contents for unibi gold list and doj artciles",
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"paramRequired": true
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},
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{
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@ -73,7 +73,8 @@
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<decision name="resume_from">
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<switch>
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<case to="remove_hbmpath">${wf:conf('resumeFrom') eq 'ProduceHBM'}</case>
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<case to="produceHBM">${wf:conf('resumeFrom') eq 'ProduceHBM'}</case>
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<case to="remove_hbmpath">${wf:conf('resumeFrom') eq 'download_csv'}</case>
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<default to="prepareInfo"/>
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</switch>
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</decision>
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@ -98,10 +99,10 @@
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<action name="download_gold">
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<java>
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<main-class>eu.dnetlib.dhp.oa.graph.hostedbymap.DownloadCSV</main-class>
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<main-class>eu.dnetlib.dhp.oa.graph.hostedbymap.DownloadCSV2</main-class>
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<arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
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<arg>--fileURL</arg><arg>${unibiFileURL}</arg>
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<arg>--workingPath</arg><arg>${workingDir}/unibi_gold</arg>
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<arg>--tmpFile</arg><arg>/tmp/unibi_gold_replaced.csv</arg>
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<arg>--outputFile</arg><arg>${workingDir}/unibi_gold.json</arg>
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<arg>--classForName</arg><arg>eu.dnetlib.dhp.oa.graph.hostedbymap.model.UnibiGoldModel</arg>
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</java>
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@ -111,10 +112,10 @@
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<action name="download_doaj">
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<java>
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<main-class>eu.dnetlib.dhp.oa.graph.hostedbymap.DownloadCSV</main-class>
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<main-class>eu.dnetlib.dhp.oa.graph.hostedbymap.DownloadCSV2</main-class>
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<arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
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<arg>--fileURL</arg><arg>${doajFileURL}</arg>
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<arg>--workingPath</arg><arg>${workingDir}/doaj</arg>
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<arg>--tmpFile</arg><arg>/tmp/doaj_replaced.csv</arg>
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<arg>--outputFile</arg><arg>${workingDir}/doaj.json</arg>
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<arg>--classForName</arg><arg>eu.dnetlib.dhp.oa.graph.hostedbymap.model.DOAJModel</arg>
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</java>
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@ -141,7 +142,7 @@
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--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
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</spark-opts>
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<arg>--datasourcePath</arg><arg>${sourcePath}/datasource</arg>
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<arg>--workingPath</arg><arg>${workingDir}</arg>
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<arg>--workingPath</arg><arg>/user/${wf:user()}/data</arg>
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<arg>--outputPath</arg><arg>${hostedByMapPath}</arg>
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<arg>--master</arg><arg>yarn-cluster</arg>
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</spark>
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@ -1,133 +1,149 @@
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package eu.dnetlib.dhp.oa.graph.hostedbymap;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.common.collection.CollectorException;
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import eu.dnetlib.dhp.common.collection.GetCSV;
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import eu.dnetlib.dhp.common.collection.HttpConnector2;
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import eu.dnetlib.dhp.oa.graph.hostedbymap.model.DOAJModel;
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import eu.dnetlib.dhp.oa.graph.hostedbymap.model.UnibiGoldModel;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import static org.junit.jupiter.api.Assertions.assertTrue;
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import java.io.BufferedReader;
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import java.io.File;
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import java.io.IOException;
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import java.io.InputStreamReader;
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import java.nio.file.Files;
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import org.apache.commons.io.FileUtils;
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import org.apache.hadoop.conf.Configuration;
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import org.apache.hadoop.fs.FileSystem;
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import org.apache.hadoop.fs.LocalFileSystem;
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import org.apache.hadoop.fs.Path;
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import org.junit.jupiter.api.*;
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import org.junit.jupiter.api.AfterAll;
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import org.junit.jupiter.api.BeforeAll;
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import org.junit.jupiter.api.Disabled;
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import org.junit.jupiter.api.Test;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import java.io.*;
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import java.nio.file.Files;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import static org.junit.jupiter.api.Assertions.assertTrue;
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import eu.dnetlib.dhp.common.collection.CollectorException;
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import eu.dnetlib.dhp.oa.graph.hostedbymap.model.DOAJModel;
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import eu.dnetlib.dhp.oa.graph.hostedbymap.model.UnibiGoldModel;
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public class DownloadCsvTest {
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private static String workingDir;
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private static final Logger log = LoggerFactory.getLogger(DownloadCsvTest.class);
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private static LocalFileSystem fs;
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private static String workingDir;
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@BeforeAll
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public static void beforeAll() throws IOException {
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workingDir = Files
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.createTempDirectory(DownloadCsvTest.class.getSimpleName())
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.toString();
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private static LocalFileSystem fs;
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fs = FileSystem.getLocal(new Configuration());
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}
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@BeforeAll
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public static void beforeAll() throws IOException {
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workingDir = Files
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.createTempDirectory(DownloadCsvTest.class.getSimpleName())
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.toString();
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@Disabled
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@Test
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void getUnibiFileTest() throws CollectorException, IOException, ClassNotFoundException {
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fs = FileSystem.getLocal(new Configuration());
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}
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String fileURL = "https://pub.uni-bielefeld.de/download/2944717/2944718/issn_gold_oa_version_4.csv";
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@Disabled
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@Test
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void getUnibiFileTest() throws CollectorException, IOException, ClassNotFoundException {
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final String outputFile = workingDir + "/unibi_gold.json";
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new DownloadCSV().doDownload(
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fileURL,
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workingDir + "/unibi_gold",
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outputFile,
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UnibiGoldModel.class.getName(),
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',',
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fs);
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String fileURL = "https://pub.uni-bielefeld.de/download/2944717/2944718/issn_gold_oa_version_4.csv";
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BufferedReader in = new BufferedReader(new InputStreamReader(fs.open(new Path(outputFile))));
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final String outputFile = workingDir + "/unibi_gold.json";
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new DownloadCSV()
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.doDownload(
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fileURL,
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workingDir + "/unibi_gold",
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outputFile,
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UnibiGoldModel.class.getName(),
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',',
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fs);
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String line;
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int count = 0;
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while ((line = in.readLine()) != null) {
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UnibiGoldModel unibi = new ObjectMapper().readValue(line, UnibiGoldModel.class);
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if (count == 0) {
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assertTrue(unibi.getIssn().equals("0001-625X"));
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assertTrue(unibi.getIssnL().equals("0001-625X"));
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assertTrue(unibi.getTitle().equals("Acta Mycologica"));
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BufferedReader in = new BufferedReader(new InputStreamReader(fs.open(new Path(outputFile))));
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}
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if (count == 43158) {
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assertTrue(unibi.getIssn().equals("2088-6330"));
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assertTrue(unibi.getIssnL().equals("2088-6330"));
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assertTrue(unibi.getTitle().equals("Religió: Jurnal Studi Agama-agama"));
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String line;
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int count = 0;
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while ((line = in.readLine()) != null) {
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UnibiGoldModel unibi = new ObjectMapper().readValue(line, UnibiGoldModel.class);
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if (count == 0) {
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assertTrue(unibi.getIssn().equals("0001-625X"));
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assertTrue(unibi.getIssnL().equals("0001-625X"));
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assertTrue(unibi.getTitle().equals("Acta Mycologica"));
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}
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if (count == 67027) {
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assertTrue(unibi.getIssn().equals("2658-7068"));
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assertTrue(unibi.getIssnL().equals("2308-2488"));
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assertTrue(unibi.getTitle().equals("Istoriko-èkonomičeskie issledovaniâ."));
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}
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}
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if (count == 43158) {
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assertTrue(unibi.getIssn().equals("2088-6330"));
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assertTrue(unibi.getIssnL().equals("2088-6330"));
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assertTrue(unibi.getTitle().equals("Religió: Jurnal Studi Agama-agama"));
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count += 1;
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}
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}
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if (count == 67027) {
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assertTrue(unibi.getIssn().equals("2658-7068"));
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assertTrue(unibi.getIssnL().equals("2308-2488"));
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assertTrue(unibi.getTitle().equals("Istoriko-èkonomičeskie issledovaniâ."));
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}
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Assertions.assertEquals(67028, count);
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}
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count += 1;
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}
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@Disabled
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@Test
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void getDoajFileTest() throws CollectorException, IOException, ClassNotFoundException {
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assertEquals(67028, count);
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}
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String fileURL = "https://doaj.org/csv";
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@Disabled
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@Test
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void getDoajFileTest() throws CollectorException, IOException, ClassNotFoundException {
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final String outputFile = workingDir + "/doaj.json";
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new DownloadCSV().doDownload(
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fileURL,
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workingDir + "/doaj",
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outputFile,
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DOAJModel.class.getName(),
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',',
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fs);
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String fileURL = "https://doaj.org/csv";
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BufferedReader in = new BufferedReader(new InputStreamReader(fs.open(new Path(outputFile))));
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final String outputFile = workingDir + "/doaj.json";
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new DownloadCSV()
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.doDownload(
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fileURL,
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workingDir + "/doaj",
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outputFile,
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DOAJModel.class.getName(),
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',',
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fs);
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String line;
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int count = 0;
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while ((line = in.readLine()) != null) {
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DOAJModel doaj = new ObjectMapper().readValue(line, DOAJModel.class);
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if (count == 0) {
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Assertions.assertEquals("0001-3765", doaj.getIssn());
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Assertions.assertEquals("1678-2690", doaj.getEissn());
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Assertions.assertEquals("Anais da Academia Brasileira de Ciências", doaj.getJournalTitle());
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BufferedReader in = new BufferedReader(new InputStreamReader(fs.open(new Path(outputFile))));
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}
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if (count == 7904) {
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System.out.println(new ObjectMapper().writeValueAsString(doaj));
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Assertions.assertEquals("", doaj.getIssn());
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Assertions.assertEquals("2055-7159", doaj.getEissn());
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Assertions.assertEquals("BJR|case reports", doaj.getJournalTitle());
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}
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if (count == 16707) {
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String line;
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int count = 0;
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while ((line = in.readLine()) != null) {
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DOAJModel doaj = new ObjectMapper().readValue(line, DOAJModel.class);
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if (count == 0) {
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assertEquals("0001-3765", doaj.getIssn());
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assertEquals("1678-2690", doaj.getEissn());
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assertEquals("Anais da Academia Brasileira de Ciências", doaj.getJournalTitle());
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}
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if (count == 22) {
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log.info(new ObjectMapper().writeValueAsString(doaj));
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System.out.println(new ObjectMapper().writeValueAsString(doaj));
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}
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if (count == 7904) {
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// log.info(new ObjectMapper().writeValueAsString(doaj));
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assertEquals("", doaj.getIssn());
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assertEquals("2055-7159", doaj.getEissn());
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assertEquals("BJR|case reports", doaj.getJournalTitle());
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}
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if (count == 16707) {
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Assertions.assertEquals("", doaj.getIssn());
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Assertions.assertEquals("2788-6298", doaj.getEissn());
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Assertions
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.assertEquals("Teacher Education through Flexible Learning in Africa", doaj.getJournalTitle());
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}
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assertEquals("2783-1043", doaj.getIssn());
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assertEquals("2783-1051", doaj.getEissn());
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assertEquals("فیزیک کاربردی ایران", doaj.getJournalTitle());
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}
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count += 1;
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}
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count += 1;
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}
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Assertions.assertEquals(16713, count);
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}
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assertEquals(16715, count);
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}
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@AfterAll
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public static void cleanup() {
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FileUtils.deleteQuietly(new File(workingDir));
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}
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@AfterAll
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public static void cleanup() {
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FileUtils.deleteQuietly(new File(workingDir));
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}
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}
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Reference in New Issue