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master #59

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claudio.atzori wants to merge 3221 commits from master into stable_ids
pull from: master
merge into: D-Net:stable_ids
Conversation 0 Commits 3221 Files Changed 2141 +363 -365
7 changed files with 363 additions and 365 deletions
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6
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java
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@ -232,9 +232,9 @@ public class PropagationConstant {
if (HdfsSupport.exists(inputPath, spark.sparkContext().hadoopConfiguration())) { if (HdfsSupport.exists(inputPath, spark.sparkContext().hadoopConfiguration())) {
return spark return spark
.read() .read()
.textFile(inputPath) .textFile(inputPath)
.map((MapFunction<String, R>) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)); .map((MapFunction<String, R>) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz));
} else { } else {
return spark.emptyDataset(Encoders.bean(clazz)); return spark.emptyDataset(Encoders.bean(clazz));
} }

1
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java
View File

@ -95,7 +95,6 @@ public class ResultTagger implements Serializable {
} }
tmp tmp
.forEach( .forEach(
dsId -> datasources dsId -> datasources

52
dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java
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@ -774,47 +774,47 @@ public class BulkTagJobTest {
void bulktagPublicationwithConstraintsTest() throws Exception { void bulktagPublicationwithConstraintsTest() throws Exception {
final String sourcePath = getClass() final String sourcePath = getClass()
.getResource( .getResource(
"/eu/dnetlib/dhp/bulktag/sample/publication/orcidbulktagfordatasource") "/eu/dnetlib/dhp/bulktag/sample/publication/orcidbulktagfordatasource")
.getPath(); .getPath();
SparkBulkTagJob SparkBulkTagJob
.main( .main(
new String[] { new String[] {
"-isTest", Boolean.TRUE.toString(), "-isTest", Boolean.TRUE.toString(),
"-isSparkSessionManaged", Boolean.FALSE.toString(), "-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath", sourcePath, "-sourcePath", sourcePath,
"-taggingConf", IOUtils "-taggingConf", IOUtils
.toString( .toString(
BulkTagJobTest.class BulkTagJobTest.class
.getResourceAsStream( .getResourceAsStream(
"/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf_neanias.xml")), "/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf_neanias.xml")),
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication",
"-outputPath", workingDir.toString() + "/publication", "-outputPath", workingDir.toString() + "/publication",
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL, "-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
"-pathMap", pathMap "-pathMap", pathMap
}); });
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Publication> tmp = sc JavaRDD<Publication> tmp = sc
.textFile(workingDir.toString() + "/publication") .textFile(workingDir.toString() + "/publication")
.map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); .map(item -> OBJECT_MAPPER.readValue(item, Publication.class));
Assertions.assertEquals(2, tmp.count()); Assertions.assertEquals(2, tmp.count());
org.apache.spark.sql.Dataset<Publication> verificationDataset = spark org.apache.spark.sql.Dataset<Publication> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(Publication.class)); .createDataset(tmp.rdd(), Encoders.bean(Publication.class));
verificationDataset.createOrReplaceTempView("dataset"); verificationDataset.createOrReplaceTempView("dataset");
String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name " String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name "
+ "from dataset " + "from dataset "
+ "lateral view explode(context) c as MyT " + "lateral view explode(context) c as MyT "
+ "lateral view explode(MyT.datainfo) d as MyD " + "lateral view explode(MyT.datainfo) d as MyD "
+ "where MyD.inferenceprovenance = 'bulktagging'"; + "where MyD.inferenceprovenance = 'bulktagging'";
org.apache.spark.sql.Dataset<Row> idExplodeCommunity = spark.sql(query); org.apache.spark.sql.Dataset<Row> idExplodeCommunity = spark.sql(query);
idExplodeCommunity.show(false); idExplodeCommunity.show(false);
Assertions.assertEquals(0, idExplodeCommunity.count()); Assertions.assertEquals(0, idExplodeCommunity.count());
} }
} }

280
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java
View File

@ -39,173 +39,173 @@ import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import eu.dnetlib.dhp.schema.oaf.utils.PidType; import eu.dnetlib.dhp.schema.oaf.utils.PidType;
public class CleanCountrySparkJob implements Serializable { public class CleanCountrySparkJob implements Serializable {
private static final Logger log = LoggerFactory.getLogger(CleanCountrySparkJob.class); private static final Logger log = LoggerFactory.getLogger(CleanCountrySparkJob.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static void main(String[] args) throws Exception { public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils String jsonConfiguration = IOUtils
.toString( .toString(
CleanCountrySparkJob.class CleanCountrySparkJob.class
.getResourceAsStream( .getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/input_clean_country_parameters.json")); "/eu/dnetlib/dhp/oa/graph/input_clean_country_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args); parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged")) .ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf) .map(Boolean::valueOf)
.orElse(Boolean.TRUE); .orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged); log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
String inputPath = parser.get("inputPath"); String inputPath = parser.get("inputPath");
log.info("inputPath: {}", inputPath); log.info("inputPath: {}", inputPath);
String workingDir = parser.get("workingDir"); String workingDir = parser.get("workingDir");
log.info("workingDir: {}", workingDir); log.info("workingDir: {}", workingDir);
String datasourcePath = parser.get("hostedBy"); String datasourcePath = parser.get("hostedBy");
log.info("datasourcePath: {}", datasourcePath); log.info("datasourcePath: {}", datasourcePath);
String country = parser.get("country"); String country = parser.get("country");
log.info("country: {}", country); log.info("country: {}", country);
String[] verifyParam = parser.get("verifyParam").split(";"); String[] verifyParam = parser.get("verifyParam").split(";");
log.info("verifyParam: {}", verifyParam); log.info("verifyParam: {}", verifyParam);
String collectedfrom = parser.get("collectedfrom"); String collectedfrom = parser.get("collectedfrom");
log.info("collectedfrom: {}", collectedfrom); log.info("collectedfrom: {}", collectedfrom);
String graphTableClassName = parser.get("graphTableClassName"); String graphTableClassName = parser.get("graphTableClassName");
log.info("graphTableClassName: {}", graphTableClassName); log.info("graphTableClassName: {}", graphTableClassName);
Class<? extends Result> entityClazz = (Class<? extends Result>) Class.forName(graphTableClassName); Class<? extends Result> entityClazz = (Class<? extends Result>) Class.forName(graphTableClassName);
SparkConf conf = new SparkConf(); SparkConf conf = new SparkConf();
runWithSparkSession( runWithSparkSession(
conf, conf,
isSparkSessionManaged, isSparkSessionManaged,
spark -> { spark -> {
cleanCountry( cleanCountry(
spark, country, verifyParam, inputPath, entityClazz, workingDir, collectedfrom, datasourcePath); spark, country, verifyParam, inputPath, entityClazz, workingDir, collectedfrom, datasourcePath);
}); });
} }
private static <T extends Result> void cleanCountry(SparkSession spark, String country, String[] verifyParam, private static <T extends Result> void cleanCountry(SparkSession spark, String country, String[] verifyParam,
String inputPath, Class<T> entityClazz, String workingDir, String collectedfrom, String datasourcePath) { String inputPath, Class<T> entityClazz, String workingDir, String collectedfrom, String datasourcePath) {
List<String> hostedBy = spark List<String> hostedBy = spark
.read() .read()
.textFile(datasourcePath) .textFile(datasourcePath)
.collectAsList(); .collectAsList();
Dataset<T> res = spark Dataset<T> res = spark
.read() .read()
.textFile(inputPath) .textFile(inputPath)
.map( .map(
(MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, entityClazz), (MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, entityClazz),
Encoders.bean(entityClazz)); Encoders.bean(entityClazz));
res.map((MapFunction<T, T>) r -> { res.map((MapFunction<T, T>) r -> {
if (r.getInstance().stream().anyMatch(i -> hostedBy.contains(i.getHostedby().getKey())) || if (r.getInstance().stream().anyMatch(i -> hostedBy.contains(i.getHostedby().getKey())) ||
!r.getCollectedfrom().stream().anyMatch(cf -> cf.getValue().equals(collectedfrom))) { !r.getCollectedfrom().stream().anyMatch(cf -> cf.getValue().equals(collectedfrom))) {
return r; return r;
} }
List<StructuredProperty> ids = getPidsAndAltIds(r).collect(Collectors.toList()); List<StructuredProperty> ids = getPidsAndAltIds(r).collect(Collectors.toList());
if (ids if (ids
.stream() .stream()
.anyMatch( .anyMatch(
p -> p p -> p
.getQualifier() .getQualifier()
.getClassid() .getClassid()
.equals(PidType.doi.toString()) && pidInParam(p.getValue(), verifyParam))) { .equals(PidType.doi.toString()) && pidInParam(p.getValue(), verifyParam))) {
r r
.setCountry( .setCountry(
r r
.getCountry() .getCountry()
.stream() .stream()
.filter( .filter(
c -> toTakeCountry(c, country)) c -> toTakeCountry(c, country))
.collect(Collectors.toList())); .collect(Collectors.toList()));
} }
return r; return r;
}, Encoders.bean(entityClazz)) }, Encoders.bean(entityClazz))
.write() .write()
.mode(SaveMode.Overwrite) .mode(SaveMode.Overwrite)
.option("compression", "gzip") .option("compression", "gzip")
.json(workingDir); .json(workingDir);
spark spark
.read() .read()
.textFile(workingDir) .textFile(workingDir)
.map( .map(
(MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, entityClazz), (MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, entityClazz),
Encoders.bean(entityClazz)) Encoders.bean(entityClazz))
.write() .write()
.mode(SaveMode.Overwrite) .mode(SaveMode.Overwrite)
.option("compression", "gzip") .option("compression", "gzip")
.json(inputPath); .json(inputPath);
} }
private static <T extends Result> Stream<StructuredProperty> getPidsAndAltIds(T r) { private static <T extends Result> Stream<StructuredProperty> getPidsAndAltIds(T r) {
final Stream<StructuredProperty> resultPids = Optional final Stream<StructuredProperty> resultPids = Optional
.ofNullable(r.getPid()) .ofNullable(r.getPid())
.map(Collection::stream) .map(Collection::stream)
.orElse(Stream.empty()); .orElse(Stream.empty());
final Stream<StructuredProperty> instancePids = Optional final Stream<StructuredProperty> instancePids = Optional
.ofNullable(r.getInstance()) .ofNullable(r.getInstance())
.map( .map(
instance -> instance instance -> instance
.stream() .stream()
.flatMap( .flatMap(
i -> Optional i -> Optional
.ofNullable(i.getPid()) .ofNullable(i.getPid())
.map(Collection::stream) .map(Collection::stream)
.orElse(Stream.empty()))) .orElse(Stream.empty())))
.orElse(Stream.empty()); .orElse(Stream.empty());
final Stream<StructuredProperty> instanceAltIds = Optional final Stream<StructuredProperty> instanceAltIds = Optional
.ofNullable(r.getInstance()) .ofNullable(r.getInstance())
.map( .map(
instance -> instance instance -> instance
.stream() .stream()
.flatMap( .flatMap(
i -> Optional i -> Optional
.ofNullable(i.getAlternateIdentifier()) .ofNullable(i.getAlternateIdentifier())
.map(Collection::stream) .map(Collection::stream)
.orElse(Stream.empty()))) .orElse(Stream.empty())))
.orElse(Stream.empty()); .orElse(Stream.empty());
return Stream return Stream
.concat( .concat(
Stream.concat(resultPids, instancePids), Stream.concat(resultPids, instancePids),
instanceAltIds); instanceAltIds);
} }
private static boolean pidInParam(String value, String[] verifyParam) { private static boolean pidInParam(String value, String[] verifyParam) {
for (String s : verifyParam) for (String s : verifyParam)
if (value.startsWith(s)) if (value.startsWith(s))
return true; return true;
return false; return false;
} }
private static boolean toTakeCountry(Country c, String country) { private static boolean toTakeCountry(Country c, String country) {
// If dataInfo is not set, or dataInfo.inferenceprovenance is not set or not present then it cannot be // If dataInfo is not set, or dataInfo.inferenceprovenance is not set or not present then it cannot be
// inserted via propagation // inserted via propagation
if (!Optional.ofNullable(c.getDataInfo()).isPresent()) if (!Optional.ofNullable(c.getDataInfo()).isPresent())
return true; return true;
if (!Optional.ofNullable(c.getDataInfo().getInferenceprovenance()).isPresent()) if (!Optional.ofNullable(c.getDataInfo().getInferenceprovenance()).isPresent())
return true; return true;
return !(c return !(c
.getClassid() .getClassid()
.equalsIgnoreCase(country) && .equalsIgnoreCase(country) &&
c.getDataInfo().getInferenceprovenance().equals("propagation")); c.getDataInfo().getInferenceprovenance().equals("propagation"));
} }
} }

118
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/GetDatasourceFromCountry.java
View File

@ -31,76 +31,76 @@ import scala.Tuple2;
* @Date 22/07/22 * @Date 22/07/22
*/ */
public class GetDatasourceFromCountry implements Serializable { public class GetDatasourceFromCountry implements Serializable {
private static final Logger log = LoggerFactory.getLogger(GetDatasourceFromCountry.class); private static final Logger log = LoggerFactory.getLogger(GetDatasourceFromCountry.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static void main(String[] args) throws Exception { public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils String jsonConfiguration = IOUtils
.toString( .toString(
GetDatasourceFromCountry.class GetDatasourceFromCountry.class
.getResourceAsStream( .getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/input_datasource_country_parameters.json")); "/eu/dnetlib/dhp/oa/graph/input_datasource_country_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args); parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged")) .ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf) .map(Boolean::valueOf)
.orElse(Boolean.TRUE); .orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged); log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
String inputPath = parser.get("inputPath"); String inputPath = parser.get("inputPath");
log.info("inputPath: {}", inputPath); log.info("inputPath: {}", inputPath);
String workingPath = parser.get("workingDir"); String workingPath = parser.get("workingDir");
log.info("workingDir: {}", workingPath); log.info("workingDir: {}", workingPath);
String country = parser.get("country"); String country = parser.get("country");
log.info("country: {}", country); log.info("country: {}", country);
SparkConf conf = new SparkConf(); SparkConf conf = new SparkConf();
runWithSparkSession( runWithSparkSession(
conf, conf,
isSparkSessionManaged, isSparkSessionManaged,
spark -> { spark -> {
getDatasourceFromCountry(spark, country, inputPath, workingPath); getDatasourceFromCountry(spark, country, inputPath, workingPath);
}); });
} }
private static void getDatasourceFromCountry(SparkSession spark, String country, String inputPath, private static void getDatasourceFromCountry(SparkSession spark, String country, String inputPath,
String workingDir) { String workingDir) {
Dataset<Organization> organization = spark Dataset<Organization> organization = spark
.read() .read()
.textFile(inputPath + "/organization") .textFile(inputPath + "/organization")
.map( .map(
(MapFunction<String, Organization>) value -> OBJECT_MAPPER.readValue(value, Organization.class), (MapFunction<String, Organization>) value -> OBJECT_MAPPER.readValue(value, Organization.class),
Encoders.bean(Organization.class)) Encoders.bean(Organization.class))
.filter( .filter(
(FilterFunction<Organization>) o -> !o.getDataInfo().getDeletedbyinference() && (FilterFunction<Organization>) o -> !o.getDataInfo().getDeletedbyinference() &&
o.getCountry().getClassid().length() > 0 && o.getCountry().getClassid().length() > 0 &&
o.getCountry().getClassid().equals(country)); o.getCountry().getClassid().equals(country));
// filtering of the relations taking the non deleted by inference and those with IsProvidedBy as relclass // filtering of the relations taking the non deleted by inference and those with IsProvidedBy as relclass
Dataset<Relation> relation = spark Dataset<Relation> relation = spark
.read() .read()
.textFile(inputPath + "/relation") .textFile(inputPath + "/relation")
.map( .map(
(MapFunction<String, Relation>) value -> OBJECT_MAPPER.readValue(value, Relation.class), (MapFunction<String, Relation>) value -> OBJECT_MAPPER.readValue(value, Relation.class),
Encoders.bean(Relation.class)) Encoders.bean(Relation.class))
.filter( .filter(
(FilterFunction<Relation>) rel -> rel.getRelClass().equalsIgnoreCase(ModelConstants.IS_PROVIDED_BY) && (FilterFunction<Relation>) rel -> rel.getRelClass().equalsIgnoreCase(ModelConstants.IS_PROVIDED_BY) &&
!rel.getDataInfo().getDeletedbyinference()); !rel.getDataInfo().getDeletedbyinference());
organization organization
.joinWith(relation, organization.col("id").equalTo(relation.col("target"))) .joinWith(relation, organization.col("id").equalTo(relation.col("target")))
.map((MapFunction<Tuple2<Organization, Relation>, String>) t2 -> t2._2().getSource(), Encoders.STRING()) .map((MapFunction<Tuple2<Organization, Relation>, String>) t2 -> t2._2().getSource(), Encoders.STRING())
.write() .write()
.mode(SaveMode.Overwrite) .mode(SaveMode.Overwrite)
.option("compression", "gzip") .option("compression", "gzip")
.json(workingDir); .json(workingDir);
} }
} }

267
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java
View File

@ -5,7 +5,6 @@ import java.io.IOException;
import java.nio.file.Files; import java.nio.file.Files;
import java.nio.file.Path; import java.nio.file.Path;
import eu.dnetlib.dhp.schema.oaf.Dataset;
import org.apache.commons.io.FileUtils; import org.apache.commons.io.FileUtils;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaRDD;
@ -27,165 +26,165 @@ import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob; import eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob;
import eu.dnetlib.dhp.schema.oaf.Dataset;
import eu.dnetlib.dhp.schema.oaf.Publication; import eu.dnetlib.dhp.schema.oaf.Publication;
public class CleanCountryTest { public class CleanCountryTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static SparkSession spark; private static SparkSession spark;
private static Path workingDir; private static Path workingDir;
private static final Logger log = LoggerFactory.getLogger(CleanContextTest.class); private static final Logger log = LoggerFactory.getLogger(CleanContextTest.class);
@BeforeAll @BeforeAll
public static void beforeAll() throws IOException { public static void beforeAll() throws IOException {
workingDir = Files.createTempDirectory(CleanCountryTest.class.getSimpleName()); workingDir = Files.createTempDirectory(CleanCountryTest.class.getSimpleName());
log.info("using work dir {}", workingDir); log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf(); SparkConf conf = new SparkConf();
conf.setAppName(CleanCountryTest.class.getSimpleName()); conf.setAppName(CleanCountryTest.class.getSimpleName());
conf.setMaster("local[*]"); conf.setMaster("local[*]");
conf.set("spark.driver.host", "localhost"); conf.set("spark.driver.host", "localhost");
conf.set("hive.metastore.local", "true"); conf.set("hive.metastore.local", "true");
conf.set("spark.ui.enabled", "false"); conf.set("spark.ui.enabled", "false");
conf.set("spark.sql.warehouse.dir", workingDir.toString()); conf.set("spark.sql.warehouse.dir", workingDir.toString());
conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
spark = SparkSession spark = SparkSession
.builder() .builder()
.appName(CleanCountryTest.class.getSimpleName()) .appName(CleanCountryTest.class.getSimpleName())
.config(conf) .config(conf)
.getOrCreate(); .getOrCreate();
} }
@AfterAll @AfterAll
public static void afterAll() throws IOException { public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile()); FileUtils.deleteDirectory(workingDir.toFile());
spark.stop(); spark.stop();
} }
@Test @Test
public void testResultClean() throws Exception { public void testResultClean() throws Exception {
final String sourcePath = getClass() final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/clean/publication_clean_country.json") .getResource("/eu/dnetlib/dhp/oa/graph/clean/publication_clean_country.json")
.getPath(); .getPath();
spark spark
.read() .read()
.textFile(sourcePath) .textFile(sourcePath)
.map( .map(
(MapFunction<String, Publication>) r -> OBJECT_MAPPER.readValue(r, Publication.class), (MapFunction<String, Publication>) r -> OBJECT_MAPPER.readValue(r, Publication.class),
Encoders.bean(Publication.class)) Encoders.bean(Publication.class))
.write() .write()
.json(workingDir.toString() + "/publication"); .json(workingDir.toString() + "/publication");
CleanCountrySparkJob.main(new String[] { CleanCountrySparkJob.main(new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(), "--isSparkSessionManaged", Boolean.FALSE.toString(),
"--inputPath", workingDir.toString() + "/publication", "--inputPath", workingDir.toString() + "/publication",
"--graphTableClassName", Publication.class.getCanonicalName(), "--graphTableClassName", Publication.class.getCanonicalName(),
"--workingDir", workingDir.toString() + "/working", "--workingDir", workingDir.toString() + "/working",
"--country", "NL", "--country", "NL",
"--verifyParam", "10.17632", "--verifyParam", "10.17632",
"--collectedfrom", "NARCIS", "--collectedfrom", "NARCIS",
"--hostedBy", getClass() "--hostedBy", getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/clean/hostedBy") .getResource("/eu/dnetlib/dhp/oa/graph/clean/hostedBy")
.getPath() .getPath()
}); });
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Publication> tmp = sc JavaRDD<Publication> tmp = sc
.textFile(workingDir.toString() + "/publication") .textFile(workingDir.toString() + "/publication")
.map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); .map(item -> OBJECT_MAPPER.readValue(item, Publication.class));
Assertions.assertEquals(8, tmp.count()); Assertions.assertEquals(8, tmp.count());
// original result with NL country and doi starting with Mendely prefix, but not collectedfrom NARCIS // original result with NL country and doi starting with Mendely prefix, but not collectedfrom NARCIS
Assertions Assertions
.assertEquals( .assertEquals(
1, 1,
tmp tmp
.filter(p -> p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95")) .filter(p -> p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95"))
.collect() .collect()
.get(0) .get(0)
.getCountry() .getCountry()
.size()); .size());
// original result with NL country and pid not starting with Mendely prefix // original result with NL country and pid not starting with Mendely prefix
Assertions Assertions
.assertEquals( .assertEquals(
1, 1,
tmp tmp
.filter(p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")) .filter(p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9"))
.collect() .collect()
.get(0) .get(0)
.getCountry() .getCountry()
.size()); .size());
// original result with NL country and doi starting with Mendely prefix and collectedfrom NARCIS but not // original result with NL country and doi starting with Mendely prefix and collectedfrom NARCIS but not
// inserted with propagation // inserted with propagation
Assertions Assertions
.assertEquals( .assertEquals(
1, 1,
tmp tmp
.filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")) .filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af"))
.collect() .collect()
.get(0) .get(0)
.getCountry() .getCountry()
.size()); .size());
// original result with NL country and doi starting with Mendely prefix and collectedfrom NARCIS inserted with // original result with NL country and doi starting with Mendely prefix and collectedfrom NARCIS inserted with
// propagation // propagation
Assertions Assertions
.assertEquals( .assertEquals(
0, 0,
tmp tmp
.filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6ag")) .filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6ag"))
.collect() .collect()
.get(0) .get(0)
.getCountry() .getCountry()
.size()); .size());
} }
@Test @Test
public void testDatasetClean() throws Exception { public void testDatasetClean() throws Exception {
final String sourcePath = getClass() final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/clean/dataset_clean_country.json") .getResource("/eu/dnetlib/dhp/oa/graph/clean/dataset_clean_country.json")
.getPath(); .getPath();
spark spark
.read() .read()
.textFile(sourcePath) .textFile(sourcePath)
.map( .map(
(MapFunction<String, Dataset>) r -> OBJECT_MAPPER.readValue(r, Dataset.class), (MapFunction<String, Dataset>) r -> OBJECT_MAPPER.readValue(r, Dataset.class),
Encoders.bean(Dataset.class)) Encoders.bean(Dataset.class))
.write() .write()
.json(workingDir.toString() + "/dataset"); .json(workingDir.toString() + "/dataset");
CleanCountrySparkJob.main(new String[] { CleanCountrySparkJob.main(new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(), "--isSparkSessionManaged", Boolean.FALSE.toString(),
"--inputPath", workingDir.toString() + "/dataset", "--inputPath", workingDir.toString() + "/dataset",
"-graphTableClassName", Dataset.class.getCanonicalName(), "-graphTableClassName", Dataset.class.getCanonicalName(),
"-workingDir", workingDir.toString() + "/working", "-workingDir", workingDir.toString() + "/working",
"-country", "NL", "-country", "NL",
"-verifyParam", "10.17632", "-verifyParam", "10.17632",
"-collectedfrom", "NARCIS", "-collectedfrom", "NARCIS",
"-hostedBy", getClass() "-hostedBy", getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/clean/hostedBy") .getResource("/eu/dnetlib/dhp/oa/graph/clean/hostedBy")
.getPath() .getPath()
}); });
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Dataset> tmp = sc JavaRDD<Dataset> tmp = sc
.textFile(workingDir.toString() + "/dataset") .textFile(workingDir.toString() + "/dataset")
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
Assertions.assertEquals(1, tmp.count()); Assertions.assertEquals(1, tmp.count());
Assertions.assertEquals(0, tmp.first().getCountry().size()); Assertions.assertEquals(0, tmp.first().getCountry().size());
}
}
} }

4
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java
View File

@ -12,7 +12,6 @@ import java.util.Objects;
import java.util.Optional; import java.util.Optional;
import java.util.stream.Collectors; import java.util.stream.Collectors;
import com.fasterxml.jackson.core.JsonProcessingException;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.StringUtils;
import org.dom4j.DocumentException; import org.dom4j.DocumentException;
@ -22,6 +21,7 @@ import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.Mock; import org.mockito.Mock;
import org.mockito.junit.jupiter.MockitoExtension; import org.mockito.junit.jupiter.MockitoExtension;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
@ -995,7 +995,7 @@ class MappersTest {
@Test @Test
void testEoscFutureHackZenodo() throws IOException { void testEoscFutureHackZenodo() throws IOException {
final String xml = IOUtils final String xml = IOUtils
.toString(Objects.requireNonNull(getClass().getResourceAsStream("zenodo7351221.xml"))); .toString(Objects.requireNonNull(getClass().getResourceAsStream("zenodo7351221.xml")));
final List<Oaf> actual = new OdfToOafMapper(vocs, false, true).processMdRecord(xml); final List<Oaf> actual = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
actual.forEach(a -> { actual.forEach(a -> {