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dnet-hadoop
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Merge branch 'beta' of https://code-repo.d4science.org/D-Net/dnet-hadoop into beta

This commit is contained in:
Miriam Baglioni 2024-09-25 17:28:23 +02:00
parent 4d3e079590 6397141e56
commit 599e56dbc6
9 changed files with 132 additions and 73 deletions
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4
dhp-common/src/main/java/eu/dnetlib/dhp/common/collection/HttpConnector2.java
View File

@ -212,11 +212,11 @@ public class HttpConnector2 {
.format(
"Unexpected status code: %s errors: %s", urlConn.getResponseCode(),
MAPPER.writeValueAsString(report)));
} catch (MalformedURLException | UnknownHostException e) {
} catch (MalformedURLException e) {
log.error(e.getMessage(), e);
report.put(e.getClass().getName(), e.getMessage());
throw new CollectorException(e.getMessage(), e);
} catch (SocketTimeoutException | SocketException e) {
} catch (SocketTimeoutException | SocketException | UnknownHostException e) {
log.error(e.getMessage(), e);
report.put(e.getClass().getName(), e.getMessage());
backoffAndSleep(getClientParams().getRetryDelay() * retryNumber * 1000);

8
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/ReadCOCI.java
View File

@ -49,6 +49,9 @@ public class ReadCOCI implements Serializable {
final String workingPath = parser.get("inputPath");
log.info("workingPath {}", workingPath);
final String backupPath = parser.get("backupPath");
log.info("backupPath {}", backupPath);
SparkConf sconf = new SparkConf();
Configuration conf = new Configuration();
@ -68,12 +71,14 @@ public class ReadCOCI implements Serializable {
workingPath,
fileSystem,
outputPath,
backupPath,
delimiter);
});
}
private static void doRead(SparkSession spark, String workingPath, FileSystem fileSystem,
String outputPath,
String backupPath,
String delimiter) throws IOException {
RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem
.listFiles(
@ -107,7 +112,8 @@ public class ReadCOCI implements Serializable {
.mode(SaveMode.Append)
.option("compression", "gzip")
.json(outputPath);
fileSystem.rename(fileStatus.getPath(), new Path("/tmp/miriam/OC/DONE"));
fileSystem.rename(fileStatus.getPath(), new Path(backupPath));
}
}

89
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java
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@ -46,11 +46,11 @@ public class CollectorWorker extends ReportingJob {
private final HttpClientParams clientParams;
public CollectorWorker(
final ApiDescriptor api,
final FileSystem fileSystem,
final MDStoreVersion mdStoreVersion,
final HttpClientParams clientParams,
final AggregatorReport report) {
final ApiDescriptor api,
final FileSystem fileSystem,
final MDStoreVersion mdStoreVersion,
final HttpClientParams clientParams,
final AggregatorReport report) {
super(report);
this.api = api;
this.fileSystem = fileSystem;
@ -69,22 +69,25 @@ public class CollectorWorker extends ReportingJob {
scheduleReport(counter);
try (SequenceFile.Writer writer = SequenceFile
.createWriter(this.fileSystem.getConf(), SequenceFile.Writer.file(new Path(outputPath)), SequenceFile.Writer
.keyClass(IntWritable.class), SequenceFile.Writer
.valueClass(Text.class), SequenceFile.Writer.compression(SequenceFile.CompressionType.BLOCK, new DeflateCodec()))) {
.createWriter(
this.fileSystem.getConf(), SequenceFile.Writer.file(new Path(outputPath)), SequenceFile.Writer
.keyClass(IntWritable.class),
SequenceFile.Writer
.valueClass(Text.class),
SequenceFile.Writer.compression(SequenceFile.CompressionType.BLOCK, new DeflateCodec()))) {
final IntWritable key = new IntWritable(counter.get());
final Text value = new Text();
plugin
.collect(this.api, this.report)
.forEach(content -> {
key.set(counter.getAndIncrement());
value.set(content);
try {
writer.append(key, value);
} catch (final Throwable e) {
throw new RuntimeException(e);
}
});
.collect(this.api, this.report)
.forEach(content -> {
key.set(counter.getAndIncrement());
value.set(content);
try {
writer.append(key, value);
} catch (final Throwable e) {
throw new RuntimeException(e);
}
});
} catch (final Throwable e) {
this.report.put(e.getClass().getName(), e.getMessage());
throw new CollectorException(e);
@ -112,36 +115,36 @@ public class CollectorWorker extends ReportingJob {
private CollectorPlugin getCollectorPlugin() throws UnknownCollectorPluginException {
switch (CollectorPlugin.NAME.valueOf(this.api.getProtocol())) {
case oai:
return new OaiCollectorPlugin(this.clientParams);
case rest_json2xml:
return new RestCollectorPlugin(this.clientParams);
case file:
return new FileCollectorPlugin(this.fileSystem);
case fileGzip:
return new FileGZipCollectorPlugin(this.fileSystem);
case baseDump:
return new BaseCollectorPlugin(this.fileSystem);
case gtr2Publications:
return new Gtr2PublicationsCollectorPlugin(this.clientParams);
case osfPreprints:
return new OsfPreprintsCollectorPlugin(this.clientParams);
case other:
final CollectorPlugin.NAME.OTHER_NAME plugin = Optional
case oai:
return new OaiCollectorPlugin(this.clientParams);
case rest_json2xml:
return new RestCollectorPlugin(this.clientParams);
case file:
return new FileCollectorPlugin(this.fileSystem);
case fileGzip:
return new FileGZipCollectorPlugin(this.fileSystem);
case baseDump:
return new BaseCollectorPlugin(this.fileSystem);
case gtr2Publications:
return new Gtr2PublicationsCollectorPlugin(this.clientParams);
case osfPreprints:
return new OsfPreprintsCollectorPlugin(this.clientParams);
case other:
final CollectorPlugin.NAME.OTHER_NAME plugin = Optional
.ofNullable(this.api.getParams().get("other_plugin_type"))
.map(CollectorPlugin.NAME.OTHER_NAME::valueOf)
.orElseThrow(() -> new IllegalArgumentException("invalid other_plugin_type"));
switch (plugin) {
case mdstore_mongodb_dump:
return new MongoDbDumpCollectorPlugin(this.fileSystem);
case mdstore_mongodb:
return new MDStoreCollectorPlugin();
switch (plugin) {
case mdstore_mongodb_dump:
return new MongoDbDumpCollectorPlugin(this.fileSystem);
case mdstore_mongodb:
return new MDStoreCollectorPlugin();
default:
throw new UnknownCollectorPluginException("plugin is not managed: " + plugin);
}
default:
throw new UnknownCollectorPluginException("plugin is not managed: " + plugin);
}
default:
throw new UnknownCollectorPluginException("protocol is not managed: " + this.api.getProtocol());
throw new UnknownCollectorPluginException("protocol is not managed: " + this.api.getProtocol());
}
}

14
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPlugin.java
View File

@ -31,17 +31,19 @@ public class OsfPreprintsCollectorPlugin implements CollectorPlugin {
final String baseUrl = api.getBaseUrl();
final int pageSize = Optional
.ofNullable(api.getParams().get("pageSize"))
.filter(StringUtils::isNotBlank)
.map(s -> NumberUtils.toInt(s, PAGE_SIZE_VALUE_DEFAULT))
.orElse(PAGE_SIZE_VALUE_DEFAULT);
.ofNullable(api.getParams().get("pageSize"))
.filter(StringUtils::isNotBlank)
.map(s -> NumberUtils.toInt(s, PAGE_SIZE_VALUE_DEFAULT))
.orElse(PAGE_SIZE_VALUE_DEFAULT);
if (StringUtils.isBlank(baseUrl)) { throw new CollectorException("Param 'baseUrl' is null or empty"); }
if (StringUtils.isBlank(baseUrl)) {
throw new CollectorException("Param 'baseUrl' is null or empty");
}
final OsfPreprintsIterator it = new OsfPreprintsIterator(baseUrl, pageSize, getClientParams());
return StreamSupport
.stream(Spliterators.spliteratorUnknownSize(it, Spliterator.ORDERED), false);
.stream(Spliterators.spliteratorUnknownSize(it, Spliterator.ORDERED), false);
}
public HttpClientParams getClientParams() {

35
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsIterator.java
View File

@ -5,6 +5,7 @@ import java.util.Iterator;
import java.util.Queue;
import java.util.concurrent.PriorityBlockingQueue;
import org.apache.commons.lang3.StringUtils;
import org.dom4j.Document;
import org.dom4j.DocumentHelper;
import org.dom4j.Element;
@ -33,9 +34,9 @@ public class OsfPreprintsIterator implements Iterator<String> {
private final Queue<String> recordQueue = new PriorityBlockingQueue<>();
public OsfPreprintsIterator(
final String baseUrl,
final int pageSize,
final HttpClientParams clientParams) {
final String baseUrl,
final int pageSize,
final HttpClientParams clientParams) {
this.clientParams = clientParams;
this.baseUrl = baseUrl;
@ -46,13 +47,15 @@ public class OsfPreprintsIterator implements Iterator<String> {
private void initQueue() {
this.currentUrl = this.baseUrl + "?filter:is_published:d=true&format=json&page[size]=" + this.pageSize;
log.info("REST calls starting with {}", this.currentUrl);
}
@Override
public boolean hasNext() {
synchronized (this.recordQueue) {
while (this.recordQueue.isEmpty() && !this.currentUrl.isEmpty()) {
while (this.recordQueue.isEmpty() && StringUtils.isNotBlank(this.currentUrl)
&& this.currentUrl.startsWith("http")) {
try {
this.currentUrl = downloadPage(this.currentUrl);
} catch (final CollectorException e) {
@ -61,7 +64,9 @@ public class OsfPreprintsIterator implements Iterator<String> {
}
}
if (!this.recordQueue.isEmpty()) { return true; }
if (!this.recordQueue.isEmpty()) {
return true;
}
return false;
}
@ -83,17 +88,23 @@ public class OsfPreprintsIterator implements Iterator<String> {
final Element n = (Element) ((Element) o).detach();
final Element group = DocumentHelper.createElement("group");
group.addAttribute("id", n.valueOf(".//data/id"));
group.addAttribute("id", n.valueOf("./id"));
group.addElement("preprint").add(n);
for (final Object o1 : n.selectNodes(".//contributors//href")) {
final Document doc1 = downloadUrl(((Node) o1).getText(), 0);
group.addElement("contributors").add(doc1.getRootElement().detach());
final String href = ((Node) o1).getText();
if (StringUtils.isNotBlank(href) && href.startsWith("http")) {
final Document doc1 = downloadUrl(href, 0);
group.addElement("contributors").add(doc1.getRootElement().detach());
}
}
for (final Object o1 : n.selectNodes(".//primary_file//href")) {
final Document doc1 = downloadUrl(((Node) o1).getText(), 0);
group.addElement("primary_file").add(doc1.getRootElement().detach());
final String href = ((Node) o1).getText();
if (StringUtils.isNotBlank(href) && href.startsWith("http")) {
final Document doc1 = downloadUrl(href, 0);
group.addElement("primary_file").add(doc1.getRootElement().detach());
}
}
this.recordQueue.add(DocumentHelper.createDocument(group).asXML());
@ -104,7 +115,9 @@ public class OsfPreprintsIterator implements Iterator<String> {
}
private Document downloadUrl(final String url, final int attempt) throws CollectorException {
if (attempt > MAX_ATTEMPTS) { throw new CollectorException("Max Number of attempts reached, url:" + url); }
if (attempt > MAX_ATTEMPTS) {
throw new CollectorException("Max Number of attempts reached, url:" + url);
}
if (attempt > 0) {
final int delay = (attempt * 5000);

19
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/input_readcoci_parameters.json
View File

@ -24,12 +24,19 @@
"paramLongName": "outputPath",
"paramDescription": "the hdfs name node",
"paramRequired": true
}, {
"paramName": "nn",
"paramLongName": "hdfsNameNode",
"paramDescription": "the hdfs name node",
"paramRequired": true
}
},
{
"paramName": "nn",
"paramLongName": "hdfsNameNode",
"paramDescription": "the hdfs name node",
"paramRequired": true
},
{
"paramName": "bp",
"paramLongName": "backupPath",
"paramDescription": "the hdfs path to move the OC data after the extraction",
"paramRequired": true
}
]

1
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/oozie_app/workflow.xml
View File

@ -129,6 +129,7 @@
</spark-opts>
<arg>--inputPath</arg><arg>${inputPath}/Extracted</arg>
<arg>--outputPath</arg><arg>${inputPath}/JSON</arg>
<arg>--backupPath</arg><arg>${inputPath}/backup</arg>
<arg>--delimiter</arg><arg>${delimiter}</arg>
<arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
</spark>

18
dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala
View File

@ -504,6 +504,24 @@ case object Crossref2Oaf {
)
}
val is_review = json \ "relation" \ "is-review-of" \ "id"
if (is_review != JNothing) {
instance.setInstancetype(
OafMapperUtils.qualifier(
"0015",
"peerReviewed",
ModelConstants.DNET_REVIEW_LEVELS,
ModelConstants.DNET_REVIEW_LEVELS
)
)
}
if (doi.startsWith("10.3410") || doi.startsWith("10.12703"))
instance.setHostedby(
OafMapperUtils.keyValue(OafMapperUtils.createOpenaireId(10, "openaire____::H1Connect", true), "H1Connect")
)
instance.setAccessright(
decideAccessRight(instance.getLicense, result.getDateofacceptance.getValue)
)

17
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPluginTest.java
View File

@ -18,6 +18,7 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.collection.ApiDescriptor;
import eu.dnetlib.dhp.collection.plugin.utils.JsonUtils;
import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
import eu.dnetlib.dhp.common.collection.CollectorException;
import eu.dnetlib.dhp.common.collection.HttpClientParams;
@ -49,9 +50,10 @@ public class OsfPreprintsCollectorPluginTest {
@Test
@Disabled
void test_one() throws CollectorException {
this.plugin.collect(this.api, new AggregatorReport())
.limit(1)
.forEach(log::info);
this.plugin
.collect(this.api, new AggregatorReport())
.limit(1)
.forEach(log::info);
}
@Test
@ -94,7 +96,8 @@ public class OsfPreprintsCollectorPluginTest {
final HttpConnector2 connector = new HttpConnector2();
try {
final String res = connector.getInputSource("https://api.osf.io/v2/preprints/ydtzx/contributors/?format=json");
final String res = connector
.getInputSource("https://api.osf.io/v2/preprints/ydtzx/contributors/?format=json");
System.out.println(res);
fail();
} catch (final Throwable e) {
@ -110,4 +113,10 @@ public class OsfPreprintsCollectorPluginTest {
}
@Test
void testXML() {
final String xml = JsonUtils.convertToXML("{'next':null}");
System.out.println(xml);
}
}