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Add steps to collect last visit data && archive not found repository URLs

This commit is contained in:
Serafeim Chatzopoulos 2023-09-27 19:00:54 +03:00
parent 9d44418d38
commit ed9c81a0b7
20 changed files with 848 additions and 218 deletions
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1
dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java
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@ -51,6 +51,7 @@ public class Constants {
public static final String RETRY_DELAY = "retryDelay";
public static final String CONNECT_TIMEOUT = "connectTimeOut";
public static final String READ_TIMEOUT = "readTimeOut";
public static final String REQUEST_METHOD = "requestMethod";
public static final String FROM_DATE_OVERRIDE = "fromDateOverride";
public static final String UNTIL_DATE_OVERRIDE = "untilDateOverride";

37
dhp-common/src/main/java/eu/dnetlib/dhp/common/collection/HttpClientParams.java
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@ -1,6 +1,9 @@
package eu.dnetlib.dhp.common.collection;
import java.util.HashMap;
import java.util.Map;
/**
* Bundles the http connection parameters driving the client behaviour.
*/
@ -13,6 +16,8 @@ public class HttpClientParams {
public static int _connectTimeOut = 10; // seconds
public static int _readTimeOut = 30; // seconds
public static String _requestMethod = "GET";
/**
* Maximum number of allowed retires before failing
*/
@ -38,17 +43,30 @@ public class HttpClientParams {
*/
private int readTimeOut;
/**
* Custom http headers
*/
private Map<String, String> headers;
/**
* Request method (i.e., GET, POST etc)
*/
private String requestMethod;
public HttpClientParams() {
this(_maxNumberOfRetry, _requestDelay, _retryDelay, _connectTimeOut, _readTimeOut);
this(_maxNumberOfRetry, _requestDelay, _retryDelay, _connectTimeOut, _readTimeOut, new HashMap<>(), _requestMethod);
}
public HttpClientParams(int maxNumberOfRetry, int requestDelay, int retryDelay, int connectTimeOut,
int readTimeOut) {
int readTimeOut, Map<String, String> headers, String requestMethod) {
this.maxNumberOfRetry = maxNumberOfRetry;
this.requestDelay = requestDelay;
this.retryDelay = retryDelay;
this.connectTimeOut = connectTimeOut;
this.readTimeOut = readTimeOut;
this.headers = headers;
this.requestMethod = requestMethod;
}
public int getMaxNumberOfRetry() {
@ -91,4 +109,19 @@ public class HttpClientParams {
this.readTimeOut = readTimeOut;
}
public Map<String, String> getHeaders() {
return headers;
}
public void setHeaders(Map<String, String> headers) {
this.headers = headers;
}
public String getRequestMethod() {
return requestMethod;
}
public void setRequestMethod(String requestMethod) {
this.requestMethod = requestMethod;
}
}

7
dhp-common/src/main/java/eu/dnetlib/dhp/common/collection/HttpConnector2.java
View File

@ -107,7 +107,14 @@ public class HttpConnector2 {
urlConn.setReadTimeout(getClientParams().getReadTimeOut() * 1000);
urlConn.setConnectTimeout(getClientParams().getConnectTimeOut() * 1000);
urlConn.addRequestProperty(HttpHeaders.USER_AGENT, userAgent);
urlConn.setRequestMethod(getClientParams().getRequestMethod());
// if provided, add custom headers
if (!getClientParams().getHeaders().isEmpty()) {
for (Map.Entry<String, String> headerEntry : getClientParams().getHeaders().entrySet()) {
urlConn.addRequestProperty(headerEntry.getKey(), headerEntry.getValue());
}
}
if (log.isDebugEnabled()) {
logHeaderFields(urlConn);
}

6
dhp-workflows/dhp-swh/pom.xml
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@ -99,6 +99,12 @@
<artifactId>httpclient</artifactId>
<version>4.5.13</version>
</dependency>
<dependency>
<groupId>org.datanucleus</groupId>
<artifactId>datanucleus-core</artifactId>
<version>3.2.10</version>
<scope>compile</scope>
</dependency>
</dependencies>
</project>

137
dhp-workflows/dhp-swh/src/main/java/eu/dnetlib/dhp/swh/ArchiveRepositoryURLs.java Normal file
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@ -0,0 +1,137 @@
package eu.dnetlib.dhp.swh;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.collection.CollectorException;
import eu.dnetlib.dhp.common.collection.HttpClientParams;
import eu.dnetlib.dhp.swh.models.LastVisitData;
import eu.dnetlib.dhp.swh.utils.SWHConnection;
import eu.dnetlib.dhp.swh.utils.SWHConstants;
import eu.dnetlib.dhp.swh.utils.SWHUtils;
import org.apache.commons.cli.ParseException;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.io.SequenceFile;
import org.apache.hadoop.io.Text;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.IOException;
import java.net.URL;
import java.util.Date;
import java.util.Optional;
import java.util.concurrent.TimeUnit;
import static eu.dnetlib.dhp.common.Constants.REQUEST_METHOD;
import static eu.dnetlib.dhp.utils.DHPUtils.getHadoopConfiguration;
/**
* Sends archive requests to the SWH API for those software repository URLs that are missing from them
*
* @author Serafeim Chatzopoulos
*/
public class ArchiveRepositoryURLs {
private static final Logger log = LoggerFactory.getLogger(ArchiveRepositoryURLs.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static SWHConnection swhConnection = null;
public static void main(final String[] args) throws IOException, ParseException {
final ArgumentApplicationParser argumentParser = new ArgumentApplicationParser(
IOUtils
.toString(
CollectLastVisitRepositoryData.class
.getResourceAsStream(
"/eu/dnetlib/dhp/swh/input_archive_repository_urls.json")));
argumentParser.parseArgument(args);
final String hdfsuri = argumentParser.get("namenode");
log.info("hdfsURI: {}", hdfsuri);
final String inputPath = argumentParser.get("lastVisitsPath");
log.info("inputPath: {}", inputPath);
final String outputPath = argumentParser.get("archiveRequestsPath");
log.info("outputPath: {}", outputPath);
final Integer archiveThresholdInDays = Integer.parseInt(argumentParser.get("archiveThresholdInDays"));
log.info("archiveThresholdInDays: {}", archiveThresholdInDays);
final HttpClientParams clientParams = SWHUtils.getClientParams(argumentParser);
swhConnection = new SWHConnection(clientParams);
final FileSystem fs = FileSystem.get(getHadoopConfiguration(hdfsuri));
archive(fs, inputPath, outputPath, archiveThresholdInDays);
}
private static void archive(FileSystem fs, String inputPath, String outputPath, Integer archiveThresholdInDays) throws IOException {
SequenceFile.Reader fr = SWHUtils.getSequenceFileReader(fs, inputPath);
SequenceFile.Writer fw = SWHUtils.getSequenceFileWriter(fs, outputPath);
// Create key and value objects to hold data
Text repoUrl = new Text();
Text lastVisitData = new Text();
// Read key-value pairs from the SequenceFile and handle appropriately
while (fr.next(repoUrl, lastVisitData)) {
String response = handleRecord(repoUrl.toString(), lastVisitData.toString(), archiveThresholdInDays);
// response is equal to null when no need for request
if (response != null) {
SWHUtils.appendToSequenceFile(fw, repoUrl.toString(), response);
}
}
// Close readers
fw.close();
fr.close();
}
public static String handleRecord(String repoUrl, String lastVisitData, Integer archiveThresholdInDays) throws IOException {
System.out.println("Key: " + repoUrl + ", Value: " + lastVisitData);
LastVisitData lastVisit = OBJECT_MAPPER.readValue(lastVisitData, LastVisitData.class);
// perform an archive request when no repoUrl was not found in previous step
if (lastVisit.getSnapshot() != null) {
// OR last visit was before (now() - archiveThresholdInDays)
long diffInMillies = Math.abs((new Date()).getTime() - lastVisit.getDate().getTime());
long diffInDays = TimeUnit.DAYS.convert(diffInMillies, TimeUnit.MILLISECONDS);
if (archiveThresholdInDays >= diffInDays) {
return null;
}
}
// if last visit data are available, re-use version control type, else use the default one (i.e., git)
String visitType = Optional
.ofNullable(lastVisit.getType())
.orElse(SWHConstants.DEFAULT_VISIT_TYPE);
URL url = new URL(String.format(SWHConstants.SWH_ARCHIVE_URL, visitType, repoUrl.trim()));
System.out.println(url.toString());
String response;
try {
response = swhConnection.call(url.toString());
} catch (CollectorException e) {
log.info("Error in request: {}", url);
response = "{}";
}
return response;
}
}

120
dhp-workflows/dhp-swh/src/main/java/eu/dnetlib/dhp/swh/CollectLastVisitRepositoryData.java Normal file
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@ -0,0 +1,120 @@
package eu.dnetlib.dhp.swh;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.collection.CollectorException;
import eu.dnetlib.dhp.common.collection.HttpClientParams;
import eu.dnetlib.dhp.swh.utils.SWHConnection;
import eu.dnetlib.dhp.swh.utils.SWHConstants;
import eu.dnetlib.dhp.swh.utils.SWHUtils;
import org.apache.commons.cli.ParseException;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.fs.FSDataInputStream;
import org.apache.hadoop.fs.FileStatus;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.SequenceFile;
import org.apache.hadoop.io.Text;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.net.URISyntaxException;
import java.net.URL;
import java.nio.charset.StandardCharsets;
import static eu.dnetlib.dhp.utils.DHPUtils.getHadoopConfiguration;
/**
* Given a file with software repository URLs, this class
* collects last visit data from the Software Heritage API.
*
* @author Serafeim Chatzopoulos
*/
public class CollectLastVisitRepositoryData {
private static final Logger log = LoggerFactory.getLogger(CollectLastVisitRepositoryData.class);
private static SWHConnection swhConnection = null;
public static void main(final String[] args)
throws IOException, ParseException, InterruptedException, URISyntaxException, CollectorException {
final ArgumentApplicationParser argumentParser = new ArgumentApplicationParser(
IOUtils
.toString(
CollectLastVisitRepositoryData.class
.getResourceAsStream(
"/eu/dnetlib/dhp/swh/input_collect_last_visit_repository_data.json")));
argumentParser.parseArgument(args);
log.info("Java Xmx: {}m", Runtime.getRuntime().maxMemory() / (1024 * 1024));
final String hdfsuri = argumentParser.get("namenode");
log.info("hdfsURI: {}", hdfsuri);
final String inputPath = argumentParser.get("softwareCodeRepositoryURLs");
log.info("inputPath: {}", inputPath);
final String outputPath = argumentParser.get("lastVisitsPath");
log.info("outputPath: {}", outputPath);
final HttpClientParams clientParams = SWHUtils.getClientParams(argumentParser);
swhConnection = new SWHConnection(clientParams);
final FileSystem fs = FileSystem.get(getHadoopConfiguration(hdfsuri));
collect(fs, inputPath, outputPath);
fs.close();
}
private static void collect(FileSystem fs, String inputPath, String outputPath)
throws IOException {
SequenceFile.Writer fw = SWHUtils.getSequenceFileWriter(fs, outputPath);
// Specify the HDFS directory path you want to read
Path directoryPath = new Path(inputPath);
// List all files in the directory
FileStatus[] partStatuses = fs.listStatus(directoryPath);
for (FileStatus partStatus : partStatuses) {
// Check if it's a file (not a directory)
if (partStatus.isFile()) {
handleFile(fs, partStatus.getPath(), fw);
}
}
fw.close();
}
private static void handleFile(FileSystem fs, Path partInputPath, SequenceFile.Writer fw)
throws IOException {
BufferedReader br = SWHUtils.getFileReader(fs, partInputPath);
String repoUrl;
while ((repoUrl = br.readLine()) != null) {
URL url = new URL(String.format(SWHConstants.SWH_LATEST_VISIT_URL, repoUrl.trim()));
String response;
try {
response = swhConnection.call(url.toString());
} catch (CollectorException e) {
log.info("Error in request: {}", url);
response = "{}";
}
SWHUtils.appendToSequenceFile(fw, repoUrl, response);
}
br.close();
}
}

158
dhp-workflows/dhp-swh/src/main/java/eu/dnetlib/dhp/swh/CollectSoftwareRepositoryURLs.java
View File

@ -1,60 +1,37 @@
package eu.dnetlib.dhp.swh;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.IOException;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import java.util.Optional;
import java.util.concurrent.TimeUnit;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.Result;
import org.apache.commons.io.IOUtils;
import org.apache.http.Header;
import org.apache.http.HttpEntity;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClients;
import org.apache.http.util.EntityUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FlatMapFunction;
import org.apache.spark.sql.*;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.types.DataTypes;
import org.apache.spark.sql.types.StructType;
import org.apache.spark.sql.Row;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import java.io.Serializable;
import java.util.Optional;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
/**
* Creates action sets for Crossref affiliation relations inferred by BIP!
* Collects unique software repository URLs in the Graph using Hive
*
* @author Serafeim Chatzopoulos
*/
public class CollectSoftwareRepositoryURLs implements Serializable {
private static final Logger log = LoggerFactory.getLogger(CollectSoftwareRepositoryURLs.class);
// public static final String BIP_AFFILIATIONS_CLASSID = "result:organization:bipinference";
// public static final String BIP_AFFILIATIONS_CLASSNAME = "Affiliation relation inferred by BIP!";
// public static final String BIP_INFERENCE_PROVENANCE = "bip:affiliation:crossref";
private static final String DEFAULT_VISIT_TYPE = "git";
private static final int CONCURRENT_API_CALLS = 1;
private static final String SWH_LATEST_VISIT_URL = "https://archive.softwareheritage.org/api/1/origin/%s/visit/latest/";
public static <I extends Result> void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
CollectSoftwareRepositoryURLs.class
.getResourceAsStream("/eu/dnetlib/dhp/swh/input_parameters.json"));
.getResourceAsStream("/eu/dnetlib/dhp/swh/input_collect_software_repository_urls.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
@ -89,7 +66,10 @@ public class CollectSoftwareRepositoryURLs implements Serializable {
String queryTemplate = "SELECT distinct coderepositoryurl.value " +
"FROM %s.software " +
"WHERE coderepositoryurl.value IS NOT NULL";
"WHERE coderepositoryurl.value IS NOT NULL " +
"AND datainfo.deletedbyinference = FALSE " +
"AND datainfo.invisible = FALSE " +
"LIMIT 1000"; // TODO remove
String query = String.format(queryTemplate, hiveDbName);
log.info("Hive query to fetch software code URLs: {}", query);
@ -100,112 +80,6 @@ public class CollectSoftwareRepositoryURLs implements Serializable {
df
.write()
.mode(SaveMode.Overwrite)
// .option("compression", "gzip")
.csv(outputPath);
}
private static Dataset<Row> readSoftware(SparkSession spark, String inputPath) {
return spark
.read()
.json(inputPath)
.select(
new Column("codeRepositoryUrl.value").as("codeRepositoryUrl"),
new Column("dataInfo.deletedbyinference"),
new Column("dataInfo.invisible"));
}
private static Dataset<Row> filterSoftware(Dataset<Row> softwareDF, Integer limit) {
Dataset<Row> df = softwareDF
.where(softwareDF.col("codeRepositoryUrl").isNotNull())
.where("deletedbyinference = false")
.where("invisible = false")
.drop("deletedbyinference")
.drop("invisible");
// TODO remove when done
df = df.limit(limit);
return df;
}
public static Dataset<Row> makeParallelRequests(SparkSession spark, Dataset<Row> softwareDF) {
// TODO replace with coalesce ?
Dataset<Row> df = softwareDF.repartition(CONCURRENT_API_CALLS);
log.info("Number of partitions: {}", df.rdd().getNumPartitions());
ObjectMapper objectMapper = new ObjectMapper();
List<Row> collectedRows = df
.javaRDD()
// max parallelism should be equal to the number of partitions here
.mapPartitions((FlatMapFunction<Iterator<Row>, Row>) partition -> {
List<Row> resultRows = new ArrayList<>();
while (partition.hasNext()) {
Row row = partition.next();
String url = String.format(SWH_LATEST_VISIT_URL, row.getString(0));
// String snapshotId = null;
// String type = null;
// String date = null;
String responseBody = makeAPICall(url);
TimeUnit.SECONDS.sleep(1);
// Thread.sleep(500);
// if (responseBody != null) {
// LastVisitResponse visitResponse = objectMapper.readValue(responseBody, LastVisitResponse.class);
// snapshotId = visitResponse.getSnapshot();
// type = visitResponse.getType();
// date = visitResponse.getDate();
// }
// resultRows.add(RowFactory.create(url, snapshotId, type, date));
resultRows.add(RowFactory.create(url, responseBody));
}
return resultRows.iterator();
})
.collect();
StructType resultSchema = new StructType()
.add("codeRepositoryUrl", DataTypes.StringType)
.add("response", DataTypes.StringType);
// .add("snapshotId", DataTypes.StringType)
// .add("type", DataTypes.StringType)
// .add("date", DataTypes.StringType);
// create a DataFrame from the collected rows
return spark.createDataFrame(collectedRows, resultSchema);
}
private static String makeAPICall(String url) throws IOException {
System.out.println(java.time.LocalDateTime.now());
try (CloseableHttpClient httpClient = HttpClients.createDefault()) {
HttpGet httpGet = new HttpGet(url);
httpGet
.setHeader(
"Authorization",
"Bearer eyJhbGciOiJIUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJhMTMxYTQ1My1hM2IyLTQwMTUtODQ2Ny05MzAyZjk3MTFkOGEifQ.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.XHj1VIZu1dZ4Ej32-oU84mFmaox9cLNjXosNxwZM0Xs");
try (CloseableHttpResponse response = httpClient.execute(httpGet)) {
int statusCode = response.getStatusLine().getStatusCode();
// if (statusCode != 200)
// return null;
Header[] headers = response.getHeaders("X-RateLimit-Remaining");
for (Header header : headers) {
System.out
.println(
"Key : " + header.getName()
+ " ,Value : " + header.getValue());
}
HttpEntity entity = response.getEntity();
if (entity != null) {
return EntityUtils.toString(entity);
}
}
}
return null;
}
}

10
dhp-workflows/dhp-swh/src/main/java/eu/dnetlib/dhp/swh/models/LastVisitResponse.java → dhp-workflows/dhp-swh/src/main/java/eu/dnetlib/dhp/swh/models/LastVisitData.java
View File

@ -4,12 +4,14 @@ package eu.dnetlib.dhp.swh.models;
import com.cloudera.com.fasterxml.jackson.annotation.JsonProperty;
import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
import java.util.Date;
@JsonIgnoreProperties(ignoreUnknown = true)
public class LastVisitResponse {
public class LastVisitData {
private String type;
private String date;
private Date date;
@JsonProperty("snapshot")
private String snapshotId;
@ -22,11 +24,11 @@ public class LastVisitResponse {
this.type = type;
}
public String getDate() {
public Date getDate() {
return date;
}
public void setDate(String date) {
public void setDate(Date date) {
this.date = date;
}

138
dhp-workflows/dhp-swh/src/main/java/eu/dnetlib/dhp/swh/utils/SWHConnection.java Normal file
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@ -0,0 +1,138 @@
package eu.dnetlib.dhp.swh.utils;
import java.io.IOException;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.apache.commons.lang3.math.NumberUtils;
import org.apache.http.Header;
import org.apache.http.HttpHeaders;
import org.apache.http.HttpStatus;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.util.EntityUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.common.Constants;
import eu.dnetlib.dhp.common.collection.CollectorException;
import eu.dnetlib.dhp.common.collection.HttpClientParams;
import eu.dnetlib.dhp.common.collection.HttpConnector2;
public class SWHConnection {
private static final Logger log = LoggerFactory.getLogger(SWHConnection.class);
CloseableHttpClient httpClient;
HttpClientParams clientParams;
HttpConnector2 conn;
public SWHConnection(HttpClientParams clientParams) {
// // force http client to NOT transform double quotes (//) to single quote (/)
// RequestConfig requestConfig = RequestConfig.custom().setNormalizeUri(false).build();
//
// // Create an HttpClient instance
// httpClient = HttpClientBuilder
// .create()
// .setDefaultRequestConfig(requestConfig)
// .build();
//
// this.clientParams = clientParams;
// set custom headers
Map<String, String> headers = new HashMap<String, String>() {
{
put(HttpHeaders.ACCEPT, "application/json");
put(HttpHeaders.AUTHORIZATION, String.format("Bearer %s", SWHConstants.ACCESS_TOKEN));
}
};
clientParams.setHeaders(headers);
// create http connector
conn = new HttpConnector2(clientParams);
}
public String call(String url) throws CollectorException {
return conn.getInputSource(url);
}
public String getLib(String url) throws IOException, CollectorException {
// delay between requests
if (this.clientParams.getRequestDelay() > 0) {
log.info("Request delay: {}", this.clientParams.getRequestDelay());
this.backOff(this.clientParams.getRequestDelay());
}
// Create an HttpGet request with the URL
HttpGet httpGet = new HttpGet(url);
httpGet.setHeader("Accept", "application/json");
httpGet.setHeader("Authorization", String.format("Bearer %s", SWHConstants.ACCESS_TOKEN));
// Execute the request and get the response
try (CloseableHttpResponse response = httpClient.execute(httpGet)) {
System.out.println(url);
int responseCode = response.getStatusLine().getStatusCode();
if (responseCode != HttpStatus.SC_OK) {
}
System.out.println(responseCode);
List<Header> httpHeaders = Arrays.asList(response.getAllHeaders());
for (Header header : httpHeaders) {
System.out.println(header.getName() + ":\t" + header.getValue());
}
String rateRemaining = this.getRateRemaining(response);
// back off when rate remaining limit is approaching
if (rateRemaining != null && (Integer.parseInt(rateRemaining) < 2)) {
int retryAfter = this.getRetryAfter(response);
log.info("Rate Limit: {} - Backing off: {}", rateRemaining, retryAfter);
this.backOff(retryAfter);
}
return EntityUtils.toString(response.getEntity());
}
}
private String getRateRemaining(CloseableHttpResponse response) {
Header header = response.getFirstHeader(Constants.HTTPHEADER_IETF_DRAFT_RATELIMIT_REMAINING);
if (header != null) {
return header.getValue();
}
return null;
}
private int getRetryAfter(CloseableHttpResponse response) {
Header header = response.getFirstHeader(HttpHeaders.RETRY_AFTER);
if (header != null) {
String retryAfter = header.getValue();
if (NumberUtils.isCreatable(retryAfter)) {
return Integer.parseInt(retryAfter) + 10;
}
}
return 1000;
}
private void backOff(int sleepTimeMs) throws CollectorException {
try {
Thread.sleep(sleepTimeMs);
} catch (InterruptedException e) {
throw new CollectorException(e);
}
}
}

13
dhp-workflows/dhp-swh/src/main/java/eu/dnetlib/dhp/swh/utils/SWHConstants.java Normal file
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@ -0,0 +1,13 @@
package eu.dnetlib.dhp.swh.utils;
public class SWHConstants {
public static final String SWH_LATEST_VISIT_URL = "https://archive.softwareheritage.org/api/1/origin/%s/visit/latest/";
public static final String SWH_ARCHIVE_URL = "https://archive.softwareheritage.org/api/1/origin/save/%s/url/%s/";
public static final String ACCESS_TOKEN = "";
public static final String DEFAULT_VISIT_TYPE = "git";
}

94
dhp-workflows/dhp-swh/src/main/java/eu/dnetlib/dhp/swh/utils/SWHUtils.java Normal file
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@ -0,0 +1,94 @@
package eu.dnetlib.dhp.swh.utils;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.collection.HttpClientParams;
import org.apache.hadoop.fs.FSDataInputStream;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.SequenceFile;
import org.apache.hadoop.io.Text;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.nio.charset.StandardCharsets;
import java.util.Optional;
import static eu.dnetlib.dhp.common.Constants.*;
public class SWHUtils {
private static final Logger log = LoggerFactory.getLogger(SWHUtils.class);
public static HttpClientParams getClientParams(ArgumentApplicationParser argumentParser) {
final HttpClientParams clientParams = new HttpClientParams();
clientParams
.setMaxNumberOfRetry(
Optional
.ofNullable(argumentParser.get(MAX_NUMBER_OF_RETRY))
.map(Integer::parseInt)
.orElse(HttpClientParams._maxNumberOfRetry));
log.info("maxNumberOfRetry is {}", clientParams.getMaxNumberOfRetry());
clientParams
.setRequestDelay(
Optional
.ofNullable(argumentParser.get(REQUEST_DELAY))
.map(Integer::parseInt)
.orElse(HttpClientParams._requestDelay));
log.info("requestDelay is {}", clientParams.getRequestDelay());
clientParams
.setRetryDelay(
Optional
.ofNullable(argumentParser.get(RETRY_DELAY))
.map(Integer::parseInt)
.orElse(HttpClientParams._retryDelay));
log.info("retryDelay is {}", clientParams.getRetryDelay());
clientParams
.setRequestMethod(
Optional
.ofNullable(argumentParser.get(REQUEST_METHOD))
.orElse(HttpClientParams._requestMethod));
log.info("requestMethod is {}", clientParams.getRequestMethod());
return clientParams;
}
public static BufferedReader getFileReader(FileSystem fs, Path inputPath) throws IOException {
FSDataInputStream inputStream = fs.open(inputPath);
return new BufferedReader(
new InputStreamReader(inputStream, StandardCharsets.UTF_8));
}
public static SequenceFile.Writer getSequenceFileWriter(FileSystem fs, String outputPath) throws IOException {
return SequenceFile
.createWriter(
fs.getConf(),
SequenceFile.Writer.file(new Path(outputPath)),
SequenceFile.Writer.keyClass(Text.class),
SequenceFile.Writer.valueClass(Text.class));
}
public static SequenceFile.Reader getSequenceFileReader(FileSystem fs, String inputPath) throws IOException {
Path filePath = new Path(inputPath);
SequenceFile.Reader.Option fileOption = SequenceFile.Reader.file(filePath);
return new SequenceFile.Reader(fs.getConf(), fileOption);
}
public static void appendToSequenceFile(SequenceFile.Writer fw, String keyStr, String valueStr) throws IOException {
Text key = new Text();
key.set(keyStr);
Text value = new Text();
value.set(valueStr);
fw.append(key, value);
}
}

26
dhp-workflows/dhp-swh/src/main/resources/eu/dnetlib/dhp/swh/input_archive_repository_urls.json Normal file
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@ -0,0 +1,26 @@
[
{
"paramName": "n",
"paramLongName": "namenode",
"paramDescription": "the Name Node URI",
"paramRequired": true
},
{
"paramName": "lv",
"paramLongName": "lastVisitsPath",
"paramDescription": "the URL where to store last visits data",
"paramRequired": true
},
{
"paramName": "rqd",
"paramLongName": "requestDelay",
"paramDescription": "the delay (ms) between requests",
"paramRequired": false
},
{
"paramName": "atid",
"paramLongName": "archiveThresholdInDays",
"paramDescription": "the thershold (in days) required to issue an archive request",
"paramRequired": false
}
]

38
dhp-workflows/dhp-swh/src/main/resources/eu/dnetlib/dhp/swh/input_collect_last_visit_repository_data.json Normal file
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@ -0,0 +1,38 @@
[
{
"paramName": "n",
"paramLongName": "namenode",
"paramDescription": "the Name Node URI",
"paramRequired": true
},
{
"paramName": "scr",
"paramLongName": "softwareCodeRepositoryURLs",
"paramDescription": "the URL from where to read software repository URLs",
"paramRequired": true
},
{
"paramName": "lv",
"paramLongName": "lastVisitsPath",
"paramDescription": "the URL where to store last visits data",
"paramRequired": true
},
{
"paramName": "mnr",
"paramLongName": "maxNumberOfRetry",
"paramDescription": "the maximum number of admitted connection retries",
"paramRequired": false
},
{
"paramName": "rqd",
"paramLongName": "requestDelay",
"paramDescription": "the delay (ms) between requests",
"paramRequired": false
},
{
"paramName": "rtd",
"paramLongName": "retryDelay",
"paramDescription": "the delay (ms) between retries",
"paramRequired": false
}
]

2
dhp-workflows/dhp-swh/src/main/resources/eu/dnetlib/dhp/swh/input_parameters.json → dhp-workflows/dhp-swh/src/main/resources/eu/dnetlib/dhp/swh/input_collect_software_repository_urls.json
View File

@ -6,7 +6,7 @@
"paramRequired": false
},
{
"paramName": "ip",
"paramName": "scr",
"paramLongName": "softwareCodeRepositoryURLs",
"paramDescription": "the URL where to store software repository URLs",
"paramRequired": true

22
dhp-workflows/dhp-swh/src/main/resources/eu/dnetlib/dhp/swh/job.properties
View File

@ -1,25 +1,11 @@
# hive
hiveDbName=openaire_prod_20230914
hiveMetastoreUris=thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083
# oozie
oozie.action.sharelib.for.spark=spark2
oozie.use.system.libpath=true
oozie.wf.application.path=${oozieTopWfApplicationPath}
oozie.wf.application.path=${oozieTopWfApplicationPath}
oozieActionShareLibForSpark2=spark2
# spark
spark2EventLogDir=/user/spark/spark2ApplicationHistory
spark2ExtraListeners=com.cloudera.spark.lineage.NavigatorAppListener
spark2SqlQueryExecutionListeners=com.cloudera.spark.lineage.NavigatorQueryListener
spark2YarnHistoryServerAddress=http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089
sparkSqlWarehouseDir=/user/hive/warehouse
# misc
wfAppPath=${oozieTopWfApplicationPath}
resourceManager=http://iis-cdh5-test-m2.ocean.icm.edu.pl:8088/cluster
# input/output files
softwareCodeRepositoryURLs=${workingDir}/1_code_repo_urls.csv
lastVisitsPath=${workingDir}/2_last_visits.seq
archiveRequestsPath=${workingDir}/3_archive_requests.seq
# custom params
softwareCodeRepositoryURLs=${workingDir}/code_repo_urls.csv
resume=collect-software-repository-urls

50
dhp-workflows/dhp-swh/src/main/resources/eu/dnetlib/dhp/swh/oozie_app/config-default.xml Normal file
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@ -0,0 +1,50 @@
<configuration>
<property>
<name>jobTracker</name>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://nameservice1</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
<property>
<name>hiveMetastoreUris</name>
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
</property>
<property>
<name>spark2EventLogDir</name>
<value>/user/spark/spark2ApplicationHistory</value>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>"com.cloudera.spark.lineage.NavigatorAppListener"</value>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>"com.cloudera.spark.lineage.NavigatorQueryListener"</value>
</property>
<property>
<name>oozieActionShareLibForSpark2</name>
<value>spark2</value>
</property>
<property>
<name>resourceManager</name>
<value>http://iis-cdh5-test-m2.ocean.icm.edu.pl:8088/cluster</value>
</property>
<property>
<name>oozie.launcher.mapreduce.user.classpath.first</name>
<value>true</value>
</property>
</configuration>

109
dhp-workflows/dhp-swh/src/main/resources/eu/dnetlib/dhp/swh/oozie_app/workflow.xml
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@ -1,59 +1,31 @@
<workflow-app name="Software-Heritage-Integration-Workflow" xmlns="uri:oozie:workflow:0.5">
<!-- <parameters>-->
<!-- <property>-->
<!-- <name>apiDescription</name>-->
<!-- <description>A json encoding of the API Description class</description>-->
<!-- </property>-->
<!-- <property>-->
<!-- <name>dataSourceInfo</name>-->
<!-- <description>A json encoding of the Datasource Info</description>-->
<!-- </property>-->
<!-- <property>-->
<!-- <name>identifierPath</name>-->
<!-- <description>An xpath to retrieve the metadata identifier for the generation of DNet Identifier </description>-->
<!-- </property>-->
<!-- <property>-->
<!-- <name>metadataEncoding</name>-->
<!-- <description> The type of the metadata XML/JSON</description>-->
<!-- </property>-->
<!-- <property>-->
<!-- <name>timestamp</name>-->
<!-- <description>The timestamp of the collection date</description>-->
<!-- </property>-->
<!-- <property>-->
<!-- <name>workflowId</name>-->
<!-- <description>The identifier of the workflow</description>-->
<!-- </property>-->
<!-- <property>-->
<!-- <name>mdStoreID</name>-->
<!-- <description>The identifier of the mdStore</description>-->
<!-- </property>-->
<!-- <property>-->
<!-- <name>mdStoreManagerURI</name>-->
<!-- <description>The URI of the MDStore Manager</description>-->
<!-- </property>-->
<!-- <property>-->
<!-- <name>dnetMessageManagerURL</name>-->
<!-- <description>The URI of the Dnet Message Manager</description>-->
<!-- </property>-->
<!-- <property>-->
<!-- <name>collectionMode</name>-->
<!-- <description>Should be REFRESH or INCREMENTAL</description>-->
<!-- </property>-->
<!-- <property>-->
<!-- <name>collection_java_xmx</name>-->
<!-- <value>-Xmx200m</value>-->
<!-- <description>Used to configure the heap size for the map JVM process. Should be 80% of mapreduce.map.memory.mb.</description>-->
<!-- </property>-->
<!-- </parameters>-->
<!-- Custom parameters -->
<parameters>
<property>
<name>hiveDbName</name>
<description>The name of the Hive DB to be used</description>
</property>
<property>
<name>softwareCodeRepositoryURLs</name>
<description>The path in the HDSF to save the software repository URLs</description>
</property>
<property>
<name>resume</name>
<description>Variable that indicates the step to start from</description>
</property>
</parameters>
<!-- Global variables -->
<global>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<configuration>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>${oozieActionShareLibForSpark2}</value>
</property>
</configuration>
</global>
<start to="startFrom"/>
@ -90,8 +62,43 @@
<arg>--softwareCodeRepositoryURLs</arg><arg>${softwareCodeRepositoryURLs}</arg>
<arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
<arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
</spark>
<ok to="collect-repository-last-visit-data"/>
<error to="Kill"/>
</action>
<action name="collect-repository-last-visit-data">
<java>
<main-class>eu.dnetlib.dhp.swh.CollectLastVisitRepositoryData</main-class>
<arg>--namenode</arg><arg>${nameNode}</arg>
<arg>--softwareCodeRepositoryURLs</arg><arg>${softwareCodeRepositoryURLs}</arg>
<arg>--lastVisitsPath</arg><arg>${lastVisitsPath}</arg>
<arg>--maxNumberOfRetry</arg><arg>2</arg>
<arg>--requestDelay</arg><arg>0</arg>
<arg>--retryDelay</arg><arg>1</arg>
<arg>--requestMethod</arg><arg>GET</arg>
</java>
<ok to="archive-repository-urls"/>
<error to="Kill"/>
</action>
<action name="archive-repository-urls">
<java>
<main-class>eu.dnetlib.dhp.swh.ArchiveRepositoryURLs</main-class>
<arg>--namenode</arg><arg>${nameNode}</arg>
<arg>--lastVisitsPath</arg><arg>${lastVisitsPath}</arg>
<arg>--archiveThresholdInDays</arg><arg>365</arg>
<arg>--maxNumberOfRetry</arg><arg>2</arg>
<arg>--requestDelay</arg><arg>0</arg>
<arg>--retryDelay</arg><arg>1</arg>
<arg>--requestMethod</arg><arg>POST</arg>
</java>
<ok to="End"/>
<error to="Kill"/>
</action>

35
dhp-workflows/dhp-swh/src/test/java/eu/dnetlib/dhp/swh/ArchiveRepositoryURLsTest.java Normal file
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@ -0,0 +1,35 @@
package eu.dnetlib.dhp.swh;
import eu.dnetlib.dhp.swh.utils.SWHUtils;
import org.apache.hadoop.fs.FileSystem;
import org.junit.jupiter.api.Test;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.util.Arrays;
public class ArchiveRepositoryURLsTest {
@Test
void testArchive() throws IOException {
String inputPath = getClass()
.getResource("/eu/dnetlib/dhp/swh/lastVisitDataToArchive.csv")
.getPath();
File file = new File(inputPath);
FileReader fr = new FileReader(file);
BufferedReader br = new BufferedReader(fr); //creates a buffering character input stream
String line;
while((line = br.readLine()) != null) {
String[] tokens = line.split("\t");
String response = ArchiveRepositoryURLs.handleRecord(tokens[0], tokens[1], 365);
System.out.println(tokens[0] + "\t" + response);
System.out.println();
}
fr.close();
}
}

57
dhp-workflows/dhp-swh/src/test/java/eu/dnetlib/dhp/swh/SWHConnectionTest.java Normal file
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@ -0,0 +1,57 @@
package eu.dnetlib.dhp.swh;
import eu.dnetlib.dhp.common.collection.CollectorException;
import eu.dnetlib.dhp.common.collection.HttpClientParams;
import eu.dnetlib.dhp.swh.utils.SWHConnection;
import eu.dnetlib.dhp.swh.utils.SWHConstants;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.IOException;
import java.net.MalformedURLException;
import java.net.URL;
//import org.apache.hadoop.hdfs.MiniDFSCluster;
public class SWHConnectionTest {
private static final Logger log = LoggerFactory.getLogger(SWHConnectionTest.class);
@Test
void testGetCall() throws IOException {
HttpClientParams clientParams = new HttpClientParams();
clientParams.setRequestMethod("GET");
SWHConnection swhConnection = new SWHConnection(clientParams);
String repoUrl = "https://github.com/stanford-futuredata/FAST";
URL url = new URL(String.format(SWHConstants.SWH_LATEST_VISIT_URL, repoUrl));
String response = null;
try {
response = swhConnection.call(url.toString());
} catch (CollectorException e) {
System.out.println("Error in request: " + url);
}
System.out.println(response);
}
@Test
void testPostCall() throws MalformedURLException {
HttpClientParams clientParams = new HttpClientParams();
clientParams.setRequestMethod("POST");
SWHConnection swhConnection = new SWHConnection(clientParams);
String repoUrl = "https://github.com/stanford-futuredata/FAST";
URL url = new URL(String.format(SWHConstants.SWH_ARCHIVE_URL, SWHConstants.DEFAULT_VISIT_TYPE, repoUrl));
String response = null;
try {
response = swhConnection.call(url.toString());
} catch (CollectorException e) {
System.out.println("Error in request: " + url);
}
System.out.println(response);
}
}

6
dhp-workflows/dhp-swh/src/test/resources/eu/dnetlib/dhp/swh/lastVisitDataToArchive.csv Normal file
View File

@ -0,0 +1,6 @@
https://github.com/bioinsilico/BIPSPI {"origin":"https://github.com/bioinsilico/BIPSPI","visit":1,"date":"2020-03-18T14:50:21.541822+00:00","status":"full","snapshot":"c6c69d2cd73ce89811448da5f031611df6f63bdb","type":"git","metadata":{},"origin_url":"https://archive.softwareheritage.org/api/1/origin/https://github.com/bioinsilico/BIPSPI/get/","snapshot_url":"https://archive.softwareheritage.org/api/1/snapshot/c6c69d2cd73ce89811448da5f031611df6f63bdb/"}
https://github.com/mloop/kdiff-type1-error-rate/blob/master/analysis/simulation.R {}
https://github.com/schwanbeck/YSMR {"origin":"https://github.com/schwanbeck/YSMR","visit":6,"date":"2023-08-02T15:25:02.650676+00:00","status":"full","snapshot":"a9d1c5f0bca2def198b89f65bc9f7da3be8439ed","type":"git","metadata":{},"origin_url":"https://archive.softwareheritage.org/api/1/origin/https://github.com/schwanbeck/YSMR/get/","snapshot_url":"https://archive.softwareheritage.org/api/1/snapshot/a9d1c5f0bca2def198b89f65bc9f7da3be8439ed/"}
https://github.com/lvclark/TASSELGBS_combine {"origin":"https://github.com/lvclark/TASSELGBS_combine","visit":1,"date":"2020-04-12T20:44:09.405589+00:00","status":"full","snapshot":"ffa6fefd3f5becefbea9fe0e6d5d93859c95c071","type":"git","metadata":{},"origin_url":"https://archive.softwareheritage.org/api/1/origin/https://github.com/lvclark/TASSELGBS_combine/get/","snapshot_url":"https://archive.softwareheritage.org/api/1/snapshot/ffa6fefd3f5becefbea9fe0e6d5d93859c95c071/"}
https://github.com/PRIDE-Toolsuite/inspector-example-files {"origin":"https://github.com/PRIDE-Toolsuite/inspector-example-files","visit":12,"date":"2021-01-25T08:54:13.394674+00:00","status":"full","snapshot":"0b56eb0ad07cf778df6dabefc4b73636e0ae8b37","type":"git","metadata":{},"origin_url":"https://archive.softwareheritage.org/api/1/origin/https://github.com/PRIDE-Toolsuite/inspector-example-files/get/","snapshot_url":"https://archive.softwareheritage.org/api/1/snapshot/0b56eb0ad07cf778df6dabefc4b73636e0ae8b37/"}
https://bitbucket.org/matwey/chelyabinsk {"origin":"https://bitbucket.org/matwey/chelyabinsk","visit":6,"date":"2021-09-24T19:32:43.322909+00:00","status":"full","snapshot":"215913858c3ee0e61e1aaea18241c5ee006da1b0","type":"hg","metadata":{},"origin_url":"https://archive.softwareheritage.org/api/1/origin/https://bitbucket.org/matwey/chelyabinsk/get/","snapshot_url":"https://archive.softwareheritage.org/api/1/snapshot/215913858c3ee0e61e1aaea18241c5ee006da1b0/"}
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