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fixed CSV downloader & tests

This commit is contained in:
Claudio Atzori 2021-08-13 14:17:54 +02:00
parent 17cefe6a97
commit 5f0903d50d
2 changed files with 36 additions and 32 deletions
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26
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/DownloadCSV.java
View File

@ -2,9 +2,12 @@
package eu.dnetlib.dhp.oa.graph.hostedbymap;
import java.io.*;
import java.nio.charset.Charset;
import java.nio.charset.StandardCharsets;
import java.util.Objects;
import java.util.Optional;
import eu.dnetlib.dhp.common.collection.CollectorException;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FSDataOutputStream;
@ -56,30 +59,37 @@ public class DownloadCSV {
.orElse(DEFAULT_DELIMITER);
log.info("delimiter {}", delimiter);
final HttpConnector2 connector2 = new HttpConnector2();
Configuration conf = new Configuration();
conf.set("fs.defaultFS", hdfsNameNode);
FileSystem fileSystem = FileSystem.get(conf);
new DownloadCSV().doDownload(fileURL, workingPath, outputFile, classForName, delimiter, fileSystem);
}
protected void doDownload(String fileURL, String workingPath, String outputFile, String classForName, char delimiter, FileSystem fs)
throws IOException, ClassNotFoundException, CollectorException {
final HttpConnector2 connector2 = new HttpConnector2();
final Path path = new Path(workingPath + "/replaced.csv");
try (BufferedReader in = new BufferedReader(
new InputStreamReader(connector2.getInputSourceAsStream(fileURL)))) {
try (FSDataOutputStream fos = fileSystem.create(path, true)) {
try (BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(fs.create(path, true), Charset.defaultCharset()))) {
String line;
while ((line = in.readLine()) != null) {
fos.writeUTF(line.replace("\\\"", "\""));
fos.writeUTF("\n");
writer.write(line.replace("\\\"", "\""));
writer.newLine();
}
}
}
try (InputStreamReader reader = new InputStreamReader(fileSystem.open(path))) {
GetCSV.getCsv(fileSystem, reader, outputFile, classForName, delimiter);
try (InputStreamReader reader = new InputStreamReader(fs.open(path))) {
GetCSV.getCsv(fs, reader, outputFile, classForName, delimiter);
}
}
}

42
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/DownloadCsvTest.java
View File

@ -39,14 +39,16 @@ public class DownloadCsvTest {
String fileURL = "https://pub.uni-bielefeld.de/download/2944717/2944718/issn_gold_oa_version_4.csv";
GetCSV
.getCsv(
fs, new BufferedReader(
new InputStreamReader(new HttpConnector2().getInputSourceAsStream(fileURL))),
workingDir + "/programme",
UnibiGoldModel.class.getName());
final String outputFile = workingDir + "/unibi_gold.json";
new DownloadCSV().doDownload(
fileURL,
workingDir + "/unibi_gold",
outputFile,
UnibiGoldModel.class.getName(),
',',
fs);
BufferedReader in = new BufferedReader(new InputStreamReader(fs.open(new Path(workingDir + "/programme"))));
BufferedReader in = new BufferedReader(new InputStreamReader(fs.open(new Path(outputFile))));
String line;
int count = 0;
@ -82,24 +84,16 @@ public class DownloadCsvTest {
String fileURL = "https://doaj.org/csv";
try (BufferedReader in = new BufferedReader(
new InputStreamReader(new HttpConnector2().getInputSourceAsStream(fileURL)))) {
try (PrintWriter writer = new PrintWriter(new BufferedWriter(new FileWriter("/tmp/DOAJ_1.csv")))) {
String line;
while ((line = in.readLine()) != null) {
writer.println(line.replace("\\\"", "\""));
}
}
}
final String outputFile = workingDir + "/doaj.json";
new DownloadCSV().doDownload(
fileURL,
workingDir + "/doaj",
outputFile,
DOAJModel.class.getName(),
',',
fs);
GetCSV
.getCsv(
fs, new BufferedReader(
new FileReader("/tmp/DOAJ_1.csv")),
workingDir + "/programme",
DOAJModel.class.getName());
BufferedReader in = new BufferedReader(new InputStreamReader(fs.open(new Path(workingDir + "/programme"))));
BufferedReader in = new BufferedReader(new InputStreamReader(fs.open(new Path(outputFile))));
String line;
int count = 0;