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code formatting

This commit is contained in:
Claudio Atzori 2024-09-30 15:13:23 +02:00
parent 3854fcc5e0
commit 6e0b6a886f
7 changed files with 135 additions and 125 deletions
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1
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeEntitiesComparator.java
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@ -1,3 +1,4 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.*;

98
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java
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@ -100,7 +100,7 @@ public class PrepareAffiliationRelations implements Serializable {
String openapcInputPath, String dataciteInputPath, String webcrawlInputPath, String publisherlInputPath,
String outputPath) {
List<KeyValue> collectedfromOpenAIRE = OafMapperUtils
.listKeyValues(OPENAIRE_DATASOURCE_ID, OPENAIRE_DATASOURCE_NAME);
.listKeyValues(OPENAIRE_DATASOURCE_ID, OPENAIRE_DATASOURCE_NAME);
JavaPairRDD<Text, Text> crossrefRelations = prepareAffiliationRelationsNewModel(
spark, crossrefInputPath, collectedfromOpenAIRE);
@ -130,7 +130,8 @@ public class PrepareAffiliationRelations implements Serializable {
outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, BZip2Codec.class);
}
private static JavaPairRDD<Text, Text> prepareAffiliationRelationFromPublisherNewModel(SparkSession spark, String inputPath,
private static JavaPairRDD<Text, Text> prepareAffiliationRelationFromPublisherNewModel(SparkSession spark,
String inputPath,
List<KeyValue> collectedfrom) {
Dataset<Row> df = spark
@ -145,29 +146,28 @@ public class PrepareAffiliationRelations implements Serializable {
}
private static JavaPairRDD<Text, Text> prepareAffiliationRelationFromPublisher(SparkSession spark, String inputPath,
List<KeyValue> collectedfrom) {
List<KeyValue> collectedfrom) {
Dataset<Row> df = spark
.read()
.schema("`DOI` STRING, `Organizations` ARRAY<STRUCT<`RORid`:STRING,`Confidence`:DOUBLE>>")
.json(inputPath)
.where("DOI is not null");
.read()
.schema("`DOI` STRING, `Organizations` ARRAY<STRUCT<`RORid`:STRING,`Confidence`:DOUBLE>>")
.json(inputPath)
.where("DOI is not null");
return getTextTextJavaPairRDD(collectedfrom, df.selectExpr("DOI", "Organizations as Matchings"));
}
private static <I extends Result> JavaPairRDD<Text, Text> prepareAffiliationRelations(SparkSession spark,
String inputPath,
List<KeyValue> collectedfrom) {
String inputPath,
List<KeyValue> collectedfrom) {
// load and parse affiliation relations from HDFS
Dataset<Row> df = spark
.read()
.schema("`DOI` STRING, `Matchings` ARRAY<STRUCT<`RORid`:STRING,`Confidence`:DOUBLE>>")
.json(inputPath)
.where("DOI is not null");
.read()
.schema("`DOI` STRING, `Matchings` ARRAY<STRUCT<`RORid`:STRING,`Confidence`:DOUBLE>>")
.json(inputPath)
.where("DOI is not null");
return getTextTextJavaPairRDD(collectedfrom, df);
}
@ -189,49 +189,49 @@ public class PrepareAffiliationRelations implements Serializable {
private static JavaPairRDD<Text, Text> getTextTextJavaPairRDD(List<KeyValue> collectedfrom, Dataset<Row> df) {
// unroll nested arrays
df = df
.withColumn("matching", functions.explode(new Column("Matchings")))
.select(
new Column("DOI").as("doi"),
new Column("matching.RORid").as("rorid"),
new Column("matching.Confidence").as("confidence"));
.withColumn("matching", functions.explode(new Column("Matchings")))
.select(
new Column("DOI").as("doi"),
new Column("matching.RORid").as("rorid"),
new Column("matching.Confidence").as("confidence"));
// prepare action sets for affiliation relations
return df
.toJavaRDD()
.flatMap((FlatMapFunction<Row, Relation>) row -> {
.toJavaRDD()
.flatMap((FlatMapFunction<Row, Relation>) row -> {
// DOI to OpenAIRE id
final String paperId = ID_PREFIX
+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", removePrefix(row.getAs("doi"))));
// DOI to OpenAIRE id
final String paperId = ID_PREFIX
+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", removePrefix(row.getAs("doi"))));
// ROR id to OpenAIRE id
final String affId = GenerateRorActionSetJob.calculateOpenaireId(row.getAs("rorid"));
// ROR id to OpenAIRE id
final String affId = GenerateRorActionSetJob.calculateOpenaireId(row.getAs("rorid"));
Qualifier qualifier = OafMapperUtils
.qualifier(
BIP_AFFILIATIONS_CLASSID,
BIP_AFFILIATIONS_CLASSNAME,
ModelConstants.DNET_PROVENANCE_ACTIONS,
ModelConstants.DNET_PROVENANCE_ACTIONS);
Qualifier qualifier = OafMapperUtils
.qualifier(
BIP_AFFILIATIONS_CLASSID,
BIP_AFFILIATIONS_CLASSNAME,
ModelConstants.DNET_PROVENANCE_ACTIONS,
ModelConstants.DNET_PROVENANCE_ACTIONS);
// format data info; setting `confidence` into relation's `trust`
DataInfo dataInfo = OafMapperUtils
.dataInfo(
false,
BIP_INFERENCE_PROVENANCE,
true,
false,
qualifier,
Double.toString(row.getAs("confidence")));
// format data info; setting `confidence` into relation's `trust`
DataInfo dataInfo = OafMapperUtils
.dataInfo(
false,
BIP_INFERENCE_PROVENANCE,
true,
false,
qualifier,
Double.toString(row.getAs("confidence")));
// return bi-directional relations
return getAffiliationRelationPair(paperId, affId, collectedfrom, dataInfo).iterator();
// return bi-directional relations
return getAffiliationRelationPair(paperId, affId, collectedfrom, dataInfo).iterator();
})
.map(p -> new AtomicAction(Relation.class, p))
.mapToPair(
aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
new Text(OBJECT_MAPPER.writeValueAsString(aa))));
})
.map(p -> new AtomicAction(Relation.class, p))
.mapToPair(
aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
new Text(OBJECT_MAPPER.writeValueAsString(aa))));
}
private static JavaPairRDD<Text, Text> getTextTextJavaPairRDDNew(List<KeyValue> collectedfrom, Dataset<Row> df) {
@ -292,7 +292,7 @@ public class PrepareAffiliationRelations implements Serializable {
}
private static String removePrefix(String doi) {
if(doi.startsWith(DOI_URL_PREFIX))
if (doi.startsWith(DOI_URL_PREFIX))
return doi.substring(DOI_URL_PREFIX_LENGTH);
return doi;
}

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
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@ -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() {

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

@ -34,9 +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;
@ -54,7 +54,8 @@ public class OsfPreprintsIterator implements Iterator<String> {
@Override
public boolean hasNext() {
synchronized (this.recordQueue) {
while (this.recordQueue.isEmpty() && StringUtils.isNotBlank(this.currentUrl) && this.currentUrl.startsWith("http")) {
while (this.recordQueue.isEmpty() && StringUtils.isNotBlank(this.currentUrl)
&& this.currentUrl.startsWith("http")) {
try {
this.currentUrl = downloadPage(this.currentUrl);
} catch (final CollectorException e) {
@ -63,7 +64,9 @@ public class OsfPreprintsIterator implements Iterator<String> {
}
}
if (!this.recordQueue.isEmpty()) { return true; }
if (!this.recordQueue.isEmpty()) {
return true;
}
return false;
}
@ -112,7 +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);

31
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java
View File

@ -79,16 +79,16 @@ public class PrepareAffiliationRelationsTest {
.getPath();
String crossrefAffiliationRelationPath = getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror_old.json")
.getPath();
.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror_old.json")
.getPath();
String publisherAffiliationRelationPath = getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/publishers")
.getPath();
String publisherAffiliationRelationOldPath = getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/publichers_old")
.getPath();
.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/publichers_old")
.getPath();
String outputPath = workingDir.toString() + "/actionSet";
@ -112,9 +112,8 @@ public class PrepareAffiliationRelationsTest {
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Relation) aa.getPayload()));
// count the number of relations
assertEquals(150, tmp.count());// 18 + 24 *3 + 30 * 2 =
assertEquals(150, tmp.count());// 18 + 24 *3 + 30 * 2 =
Dataset<Relation> dataset = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
dataset.createOrReplaceTempView("result");
@ -173,18 +172,16 @@ public class PrepareAffiliationRelationsTest {
+ IdentifierFactory.md5("https://ror.org/03265fv13") + "'")
.count());
Assertions
.assertEquals(
3, execVerification
.filter(
"source = '" + ID_PREFIX
+ IdentifierFactory
.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/3-540-47984-8_14"))
+ "' and target = '" + "20|ror_________::"
+ IdentifierFactory.md5("https://ror.org/00a0n9e72") + "'")
.count());
.assertEquals(
3, execVerification
.filter(
"source = '" + ID_PREFIX
+ IdentifierFactory
.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/3-540-47984-8_14"))
+ "' and target = '" + "20|ror_________::"
+ IdentifierFactory.md5("https://ror.org/00a0n9e72") + "'")
.count());
}
}

10
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPluginTest.java
View File

@ -50,9 +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
@ -95,7 +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) {