Merge pull request 'Bulk Tagging single step' (#289) from bulkTagRefactor into beta

Reviewed-on: #289
This commit is contained in:
Claudio Atzori 2023-05-02 10:54:14 +02:00
commit f653640cd9
24 changed files with 1021 additions and 1675 deletions

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@ -4,12 +4,12 @@ package eu.dnetlib.dhp.bulktag;
import static eu.dnetlib.dhp.PropagationConstant.removeOutputDir;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.util.ArrayList;
import java.util.Objects;
import java.util.Optional;
import java.util.*;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.ForeachFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
@ -23,10 +23,17 @@ import com.google.gson.Gson;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.bulktag.community.*;
import eu.dnetlib.dhp.schema.oaf.Datasource;
import eu.dnetlib.dhp.schema.oaf.Result;
public class SparkBulkTagJob {
private static String OPENAIRE_3 = "openaire3.0";
private static String OPENAIRE_4 = "openaire-pub_4.0";
private static String OPENAIRE_CRIS = "openaire-cris_1.1";
private static String OPENAIRE_DATA = "openaire2.0_data";
private static String EOSC = "10|openaire____::2e06c1122c7df43765fdcf91080824fa";
private static final Logger log = LoggerFactory.getLogger(SparkBulkTagJob.class);
public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
@ -88,10 +95,47 @@ public class SparkBulkTagJob {
isSparkSessionManaged,
spark -> {
removeOutputDir(spark, outputPath);
extendCommunityConfigurationForEOSC(spark, inputPath, cc);
execBulkTag(spark, inputPath, outputPath, protoMappingParams, resultClazz, cc);
});
}
private static void extendCommunityConfigurationForEOSC(SparkSession spark, String inputPath,
CommunityConfiguration cc) {
Dataset<String> datasources = readPath(
spark, inputPath
.substring(
0,
inputPath.lastIndexOf("/"))
+ "/datasource",
Datasource.class)
.filter((FilterFunction<Datasource>) ds -> isOKDatasource(ds))
.map((MapFunction<Datasource, String>) ds -> ds.getId(), Encoders.STRING());
Map<String, List<Pair<String, SelectionConstraints>>> dsm = cc.getEoscDatasourceMap();
for (String ds : datasources.collectAsList()) {
final String dsId = ds.substring(3);
if (!dsm.containsKey(dsId)) {
ArrayList<Pair<String, SelectionConstraints>> eoscList = new ArrayList<>();
dsm.put(dsId, eoscList);
}
}
}
private static boolean isOKDatasource(Datasource ds) {
final String compatibility = ds.getOpenairecompatibility().getClassid();
boolean isOk = (compatibility.equalsIgnoreCase(OPENAIRE_3) ||
compatibility.equalsIgnoreCase(OPENAIRE_4) ||
compatibility.equalsIgnoreCase(OPENAIRE_CRIS) ||
compatibility.equalsIgnoreCase(OPENAIRE_DATA)) &&
ds.getCollectedfrom().stream().anyMatch(cf -> cf.getKey().equals(EOSC));
return isOk;
}
private static <R extends Result> void execBulkTag(
SparkSession spark,
String inputPath,

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@ -5,8 +5,6 @@ import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
import org.apache.avro.generic.GenericData;
import com.google.gson.Gson;
/** Created by miriam on 01/08/2018. */
@ -16,7 +14,7 @@ public class Community implements Serializable {
private List<String> subjects = new ArrayList<>();
private List<Provider> providers = new ArrayList<>();
private List<ZenodoCommunity> zenodoCommunities = new ArrayList<>();
private SelectionConstraints constraints;
private SelectionConstraints constraints = new SelectionConstraints();
public String toJson() {
final Gson g = new Gson();
@ -27,7 +25,7 @@ public class Community implements Serializable {
return !getSubjects().isEmpty()
|| !getProviders().isEmpty()
|| !getZenodoCommunities().isEmpty()
|| !getConstraints().getCriteria().isEmpty();
|| getConstraints().getCriteria() != null;
}
public String getId() {

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@ -26,6 +26,16 @@ public class CommunityConfiguration implements Serializable {
private Map<String, List<Pair<String, SelectionConstraints>>> zenodocommunityMap = new HashMap<>();
// map communityid -> selectionconstraints
private Map<String, SelectionConstraints> selectionConstraintsMap = new HashMap<>();
// map eosc datasource -> communityid
private Map<String, List<Pair<String, SelectionConstraints>>> eoscDatasourceMap = new HashMap<>();
public Map<String, List<Pair<String, SelectionConstraints>>> getEoscDatasourceMap() {
return eoscDatasourceMap;
}
public void setEoscDatasourceMap(Map<String, List<Pair<String, SelectionConstraints>>> eoscDatasourceMap) {
this.eoscDatasourceMap = eoscDatasourceMap;
}
public Map<String, List<Pair<String, SelectionConstraints>>> getSubjectMap() {
return subjectMap;
@ -146,6 +156,10 @@ public class CommunityConfiguration implements Serializable {
.collect(Collectors.toList());
}
public boolean isEoscDatasource(final String dts) {
return eoscDatasourceMap.containsKey(dts);
}
public List<Pair<String, SelectionConstraints>> getCommunityForZenodoCommunity(String zc) {
return zenodocommunityMap.get(zc);
}

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@ -7,7 +7,6 @@ import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
import java.io.Serializable;
import java.util.*;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import org.apache.commons.lang3.StringUtils;
import org.slf4j.Logger;
@ -17,9 +16,7 @@ import com.google.gson.Gson;
import com.jayway.jsonpath.DocumentContext;
import com.jayway.jsonpath.JsonPath;
import eu.dnetlib.dhp.bulktag.SparkBulkTagJob;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.bulktag.eosc.EoscIFTag;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
@ -67,6 +64,21 @@ public class ResultTagger implements Serializable {
return result;
}
// Execute the EOSCTag for the services
switch (result.getResulttype().getClassid()) {
case PUBLICATION_RESULTTYPE_CLASSID:
break;
case SOFTWARE_RESULTTYPE_CLASSID:
EoscIFTag.tagForSoftware(result);
break;
case DATASET_RESULTTYPE_CLASSID:
EoscIFTag.tagForDataset(result);
break;
case ORP_RESULTTYPE_CLASSID:
EoscIFTag.tagForOther(result);
break;
}
// communities contains all the communities to be added as context for the result
final Set<String> communities = new HashSet<>();
@ -89,24 +101,34 @@ public class ResultTagger implements Serializable {
// Tagging for datasource
final Set<String> datasources = new HashSet<>();
final Set<String> tmp = new HashSet<>();
final Set<String> collfrom = new HashSet<>();
final Set<String> hostdby = new HashSet<>();
if (Objects.nonNull(result.getInstance())) {
for (Instance i : result.getInstance()) {
if (Objects.nonNull(i.getCollectedfrom()) && Objects.nonNull(i.getCollectedfrom().getKey())) {
tmp.add(StringUtils.substringAfter(i.getCollectedfrom().getKey(), "|"));
collfrom.add(StringUtils.substringAfter(i.getCollectedfrom().getKey(), "|"));
}
if (Objects.nonNull(i.getHostedby()) && Objects.nonNull(i.getHostedby().getKey())) {
tmp.add(StringUtils.substringAfter(i.getHostedby().getKey(), "|"));
hostdby.add(StringUtils.substringAfter(i.getHostedby().getKey(), "|"));
}
}
tmp
collfrom
.forEach(
dsId -> datasources
.addAll(
conf.getCommunityForDatasource(dsId, param)));
hostdby.forEach(dsId -> {
datasources
.addAll(
conf.getCommunityForDatasource(dsId, param));
if (conf.isEoscDatasource(dsId)) {
datasources.add("eosc");
}
});
}
communities.addAll(datasources);
@ -142,7 +164,7 @@ public class ResultTagger implements Serializable {
.getSelectionConstraintsMap()
.keySet()
.forEach(communityId -> {
if (conf.getSelectionConstraintsMap().get(communityId) != null &&
if (conf.getSelectionConstraintsMap().get(communityId).getCriteria() != null &&
conf
.getSelectionConstraintsMap()
.get(communityId)

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@ -2,7 +2,6 @@
package eu.dnetlib.dhp.bulktag.criteria;
import java.io.Serializable;
import java.util.Locale;
@VerbClass("starts_with_caseinsensitive")
public class StartsWithVerbIgnoreCase implements Selection, Serializable {

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@ -1,29 +0,0 @@
package eu.dnetlib.dhp.bulktag.eosc;
import java.io.Serializable;
/**
* @author miriam.baglioni
* @Date 21/07/22
*/
public class DatasourceMaster implements Serializable {
private String datasource;
private String master;
public String getDatasource() {
return datasource;
}
public void setDatasource(String datasource) {
this.datasource = datasource;
}
public String getMaster() {
return master;
}
public void setMaster(String master) {
this.master = master;
}
}

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@ -0,0 +1,145 @@
package eu.dnetlib.dhp.bulktag.eosc;
import java.util.*;
import eu.dnetlib.dhp.schema.oaf.*;
public class EoscIFTag {
public static final String EOSC_GALAXY_WORKFLOW = "EOSC::Galaxy Workflow";
public static final String EOSC_TWITTER_DATA = "EOSC::Twitter Data";
public static final String EOSC_JUPYTER_NOTEBOOK = "EOSC::Jupyter Notebook";
public static final String COMPLIES_WITH = "compliesWith";
public static EoscIfGuidelines newInstance(String code, String label, String url, String semantics) {
EoscIfGuidelines eig = new EoscIfGuidelines();
eig.setCode(code);
eig.setLabel(label);
eig.setUrl(url);
eig.setSemanticRelation(semantics);
return eig;
}
public static <R extends Result> void tagForSoftware(R s) {
if (!Optional.ofNullable(s.getEoscifguidelines()).isPresent())
s.setEoscifguidelines(new ArrayList<>());
if (containsCriteriaNotebook(s)) {
addEIG(
s.getEoscifguidelines(), EOSC_JUPYTER_NOTEBOOK, EOSC_JUPYTER_NOTEBOOK, "",
COMPLIES_WITH);
}
if (containsCriteriaGalaxy(s)) {
addEIG(
s.getEoscifguidelines(), EOSC_GALAXY_WORKFLOW, EOSC_GALAXY_WORKFLOW, "", COMPLIES_WITH);
}
}
public static <R extends Result> void tagForOther(R orp) {
if (!Optional.ofNullable(orp.getEoscifguidelines()).isPresent())
orp.setEoscifguidelines(new ArrayList<>());
if (containsCriteriaGalaxy(orp)) {
addEIG(
orp.getEoscifguidelines(), EOSC_GALAXY_WORKFLOW, EOSC_GALAXY_WORKFLOW, "",
COMPLIES_WITH);
}
if (containscriteriaTwitter(orp)) {
addEIG(orp.getEoscifguidelines(), EOSC_TWITTER_DATA, EOSC_TWITTER_DATA, "", COMPLIES_WITH);
}
}
public static <R extends Result> void tagForDataset(R d) {
if (!Optional.ofNullable(d.getEoscifguidelines()).isPresent())
d.setEoscifguidelines(new ArrayList<>());
if (containscriteriaTwitter(d)) {
addEIG(d.getEoscifguidelines(), EOSC_TWITTER_DATA, EOSC_TWITTER_DATA, "", COMPLIES_WITH);
}
}
private static void addEIG(List<EoscIfGuidelines> eoscifguidelines, String code, String label, String url,
String sem) {
if (!eoscifguidelines.stream().anyMatch(eig -> eig.getCode().equals(code)))
eoscifguidelines.add(newInstance(code, label, url, sem));
}
private static boolean containscriteriaTwitter(Result r) {
Set<String> words = getWordsSP(r.getTitle());
words.addAll(getWordsF(r.getDescription()));
if (words.contains("twitter") &&
(words.contains("data") || words.contains("dataset")))
return true;
return Optional
.ofNullable(r.getSubject())
.map(
s -> s.stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("twitter")) &&
s.stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("data")))
.orElse(false);
}
private static boolean containsCriteriaGalaxy(Result r) {
Set<String> words = getWordsSP(r.getTitle());
words.addAll(getWordsF(r.getDescription()));
if (words.contains("galaxy") &&
words.contains("workflow"))
return true;
return Optional
.ofNullable(r.getSubject())
.map(
s -> s.stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("galaxy")) &&
s.stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("workflow")))
.orElse(false);
}
private static <R extends Result> boolean containsCriteriaNotebook(R s) {
if (!Optional.ofNullable(s.getSubject()).isPresent())
return false;
if (s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("jupyter")))
return true;
if (s
.getSubject()
.stream()
.anyMatch(
sbj -> sbj.getValue().toLowerCase().contains("python") &&
sbj.getValue().toLowerCase().contains("notebook")))
return true;
if (s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("python")) &&
s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("notebook")))
return true;
return false;
}
private static Set<String> getWordsSP(List<StructuredProperty> elem) {
Set<String> words = new HashSet<>();
Optional
.ofNullable(elem)
.ifPresent(
e -> e
.forEach(
t -> words
.addAll(
Arrays.asList(t.getValue().toLowerCase().replaceAll("[^a-zA-Z ]", "").split(" ")))));
return words;
}
private static Set<String> getWordsF(List<Field<String>> elem) {
Set<String> words = new HashSet<>();
Optional
.ofNullable(elem)
.ifPresent(
e -> e
.forEach(
t -> words
.addAll(
Arrays.asList(t.getValue().toLowerCase().replaceAll("[^a-zA-Z ]", "").split(" ")))));
return words;
}
}

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@ -1,136 +0,0 @@
package eu.dnetlib.dhp.bulktag.eosc;
import java.io.BufferedWriter;
import java.io.Closeable;
import java.io.IOException;
import java.io.OutputStreamWriter;
import java.nio.charset.StandardCharsets;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.Arrays;
import java.util.List;
import java.util.function.Consumer;
import java.util.function.Function;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FSDataOutputStream;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
/**
* @author miriam.baglioni
* @Date 21/07/22
*/
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.DbClient;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.common.RelationInverse;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
public class ReadMasterDatasourceFromDB implements Closeable {
private final DbClient dbClient;
private static final Log log = LogFactory.getLog(ReadMasterDatasourceFromDB.class);
private final BufferedWriter writer;
private final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static final String QUERY = "SELECT dso.id datasource, d.id master FROM " +
"(SELECT id FROM dsm_services WHERE id like 'eosc%') dso " +
"FULL JOIN " +
"(SELECT id, duplicate FROM dsm_dedup_services WHERE duplicate like 'eosc%')d " +
"ON dso.id = d.duplicate";
public static void main(final String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
ReadMasterDatasourceFromDB.class
.getResourceAsStream(
"/eu/dnetlib/dhp/bulktag/datasourcemaster_parameters.json")));
parser.parseArgument(args);
final String dbUrl = parser.get("postgresUrl");
final String dbUser = parser.get("postgresUser");
final String dbPassword = parser.get("postgresPassword");
final String hdfsPath = parser.get("hdfsPath");
final String hdfsNameNode = parser.get("hdfsNameNode");
try (
final ReadMasterDatasourceFromDB rmd = new ReadMasterDatasourceFromDB(hdfsPath, hdfsNameNode, dbUrl, dbUser,
dbPassword)) {
log.info("Processing datasources...");
rmd.execute(QUERY, rmd::datasourceMasterMap);
}
}
public void execute(final String sql, final Function<ResultSet, DatasourceMaster> producer) {
dbClient.processResults(sql, rs -> writeMap(producer.apply(rs)));
}
public DatasourceMaster datasourceMasterMap(ResultSet rs) {
try {
DatasourceMaster dm = new DatasourceMaster();
String datasource = rs.getString("datasource");
dm.setDatasource(datasource);
String master = rs.getString("master");
if (StringUtils.isNotBlank(master))
dm.setMaster(OafMapperUtils.createOpenaireId(10, master, true));
else
dm.setMaster(OafMapperUtils.createOpenaireId(10, datasource, true));
return dm;
} catch (final SQLException e) {
throw new RuntimeException(e);
}
}
@Override
public void close() throws IOException {
dbClient.close();
writer.close();
}
public ReadMasterDatasourceFromDB(
final String hdfsPath, String hdfsNameNode, final String dbUrl, final String dbUser, final String dbPassword)
throws IOException {
this.dbClient = new DbClient(dbUrl, dbUser, dbPassword);
Configuration conf = new Configuration();
conf.set("fs.defaultFS", hdfsNameNode);
FileSystem fileSystem = FileSystem.get(conf);
Path hdfsWritePath = new Path(hdfsPath);
FSDataOutputStream fsDataOutputStream = null;
if (fileSystem.exists(hdfsWritePath)) {
fsDataOutputStream = fileSystem.append(hdfsWritePath);
} else {
fsDataOutputStream = fileSystem.create(hdfsWritePath);
}
this.writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8));
}
protected void writeMap(final DatasourceMaster dm) {
try {
writer.write(OBJECT_MAPPER.writeValueAsString(dm));
writer.newLine();
} catch (final IOException e) {
throw new RuntimeException(e);
}
}
}

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@ -1,209 +0,0 @@
package eu.dnetlib.dhp.bulktag.eosc;
import static eu.dnetlib.dhp.PropagationConstant.readPath;
import static eu.dnetlib.dhp.PropagationConstant.removeOutputDir;
import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.*;
import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.TAGGING_TRUST;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PROVENANCE_ACTIONS;
import java.io.Serializable;
import java.util.*;
import java.util.stream.Collectors;
import javax.print.attribute.DocAttributeSet;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.ForeachFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
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 com.google.gson.Gson;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.bulktag.SparkBulkTagJob;
import eu.dnetlib.dhp.bulktag.community.*;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
import scala.Tuple2;
/**
* @author miriam.baglioni
* @Date 21/07/22
*/
public class SparkEoscBulkTag implements Serializable {
private static final Logger log = LoggerFactory.getLogger(SparkEoscBulkTag.class);
public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static String OPENAIRE_3 = "openaire3.0";
private static String OPENAIRE_4 = "openaire-pub_4.0";
private static String OPENAIRE_CRIS = "openaire-cris_1.1";
private static String OPENAIRE_DATA = "openaire2.0_data";
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
SparkEoscBulkTag.class
.getResourceAsStream(
"/eu/dnetlib/dhp/bulktag/input_eosc_bulkTag_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
String datasourceMapPath = parser.get("datasourceMapPath");
log.info("datasourceMapPath: {}", datasourceMapPath);
final String resultClassName = parser.get("resultTableName");
log.info("resultTableName: {}", resultClassName);
final String resultType = parser.get("resultType");
log.info("resultType: {}", resultType);
Class<? extends Result> resultClazz = (Class<? extends Result>) Class.forName(resultClassName);
SparkConf conf = new SparkConf();
CommunityConfiguration cc;
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
removeOutputDir(spark, workingPath);
selectCompliantDatasources(spark, inputPath, workingPath, datasourceMapPath);
execBulkTag(spark, inputPath, workingPath, resultType, resultClazz);
});
}
private static void selectCompliantDatasources(SparkSession spark, String inputPath, String workingPath,
String datasourceMapPath) {
Dataset<Datasource> datasources = readPath(spark, inputPath + "datasource", Datasource.class)
.filter((FilterFunction<Datasource>) ds -> {
final String compatibility = ds.getOpenairecompatibility().getClassid();
return compatibility.equalsIgnoreCase(OPENAIRE_3) ||
compatibility.equalsIgnoreCase(OPENAIRE_4) ||
compatibility.equalsIgnoreCase(OPENAIRE_CRIS) ||
compatibility.equalsIgnoreCase(OPENAIRE_DATA);
});
Dataset<DatasourceMaster> datasourceMaster = readPath(spark, datasourceMapPath, DatasourceMaster.class);
datasources
.joinWith(datasourceMaster, datasources.col("id").equalTo(datasourceMaster.col("master")), "left")
.map(
(MapFunction<Tuple2<Datasource, DatasourceMaster>, DatasourceMaster>) t2 -> t2._2(),
Encoders.bean(DatasourceMaster.class))
.filter(Objects::nonNull)
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(workingPath + "datasource");
}
private static <R extends Result> void execBulkTag(
SparkSession spark,
String inputPath,
String workingPath,
String resultType,
Class<R> resultClazz) {
List<String> hostedByList = readPath(spark, workingPath + "datasource", DatasourceMaster.class)
.map((MapFunction<DatasourceMaster, String>) dm -> dm.getMaster(), Encoders.STRING())
.collectAsList();
readPath(spark, inputPath + resultType, resultClazz)
.map(
(MapFunction<R, R>) value -> enrich(value, hostedByList),
Encoders.bean(resultClazz))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(workingPath + resultType);
readPath(spark, workingPath + resultType, resultClazz)
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(inputPath + resultType);
}
private static <R extends Result> R enrich(R value, List<String> hostedByList) {
if (value.getDataInfo().getDeletedbyinference() == null) {
value.getDataInfo().setDeletedbyinference(false);
}
if (value.getContext() == null) {
value.setContext(new ArrayList<>());
}
if (value
.getInstance()
.stream()
.anyMatch(
i -> (hostedByList.contains(i.getHostedby().getKey())))
&&
!value.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) {
Context context = new Context();
context.setId("eosc");
context
.setDataInfo(
Arrays
.asList(
OafMapperUtils
.dataInfo(
false, BULKTAG_DATA_INFO_TYPE, true, false,
OafMapperUtils
.qualifier(
CLASS_ID_DATASOURCE, CLASS_NAME_BULKTAG_DATASOURCE,
DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS),
TAGGING_TRUST)));
value.getContext().add(context);
}
return value;
}
public static <R> Dataset<R> readPath(
SparkSession spark, String inputPath, Class<R> clazz) {
return spark
.read()
.textFile(inputPath)
.map((MapFunction<String, R>) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz));
}
// TODO remove this hack as soon as the values fixed by this method will be provided as NON null
private static <R extends Result> MapFunction<R, R> patchResult() {
return r -> {
if (r.getDataInfo().getDeletedbyinference() == null) {
r.getDataInfo().setDeletedbyinference(false);
}
if (r.getContext() == null) {
r.setContext(new ArrayList<>());
}
return r;
};
}
}

View File

@ -1,237 +0,0 @@
package eu.dnetlib.dhp.bulktag.eosc;
import static eu.dnetlib.dhp.PropagationConstant.readPath;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.util.*;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Encoders;
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 eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.*;
public class SparkEoscTag {
private static final Logger log = LoggerFactory.getLogger(SparkEoscTag.class);
public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static final String EOSC_GALAXY_WORKFLOW = "EOSC::Galaxy Workflow";
public static final String EOSC_TWITTER_DATA = "EOSC::Twitter Data";
public static final String EOSC_JUPYTER_NOTEBOOK = "EOSC::Jupyter Notebook";
public static final String COMPLIES_WITH = "compliesWith";
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
SparkEoscTag.class
.getResourceAsStream(
"/eu/dnetlib/dhp/bulktag/input_eoscTag_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
execEoscTag(spark, inputPath, workingPath);
});
}
public static EoscIfGuidelines newInstance(String code, String label, String url, String semantics) {
EoscIfGuidelines eig = new EoscIfGuidelines();
eig.setCode(code);
eig.setLabel(label);
eig.setUrl(url);
eig.setSemanticRelation(semantics);
return eig;
}
private static void execEoscTag(SparkSession spark, String inputPath, String workingPath) {
readPath(spark, inputPath + "/software", Software.class)
.map((MapFunction<Software, Software>) s -> {
if (containsCriteriaNotebook(s)) {
if (!Optional.ofNullable(s.getEoscifguidelines()).isPresent())
s.setEoscifguidelines(new ArrayList<>());
addEIG(
s.getEoscifguidelines(), EOSC_JUPYTER_NOTEBOOK, EOSC_JUPYTER_NOTEBOOK, "",
COMPLIES_WITH);
}
if (containsCriteriaGalaxy(s)) {
if (!Optional.ofNullable(s.getEoscifguidelines()).isPresent())
s.setEoscifguidelines(new ArrayList<>());
addEIG(
s.getEoscifguidelines(), EOSC_GALAXY_WORKFLOW, EOSC_GALAXY_WORKFLOW, "", COMPLIES_WITH);
}
return s;
}, Encoders.bean(Software.class))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(workingPath + "/software");
readPath(spark, workingPath + "/software", Software.class)
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(inputPath + "/software");
readPath(spark, inputPath + "/otherresearchproduct", OtherResearchProduct.class)
.map((MapFunction<OtherResearchProduct, OtherResearchProduct>) orp -> {
if (!Optional.ofNullable(orp.getEoscifguidelines()).isPresent())
orp.setEoscifguidelines(new ArrayList<>());
if (containsCriteriaGalaxy(orp)) {
addEIG(
orp.getEoscifguidelines(), EOSC_GALAXY_WORKFLOW, EOSC_GALAXY_WORKFLOW, "",
COMPLIES_WITH);
}
if (containscriteriaTwitter(orp)) {
addEIG(orp.getEoscifguidelines(), EOSC_TWITTER_DATA, EOSC_TWITTER_DATA, "", COMPLIES_WITH);
}
return orp;
}, Encoders.bean(OtherResearchProduct.class))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(workingPath + "/otherresearchproduct");
readPath(spark, workingPath + "/otherresearchproduct", OtherResearchProduct.class)
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(inputPath + "/otherresearchproduct");
readPath(spark, inputPath + "/dataset", Dataset.class)
.map((MapFunction<Dataset, Dataset>) d -> {
if (!Optional.ofNullable(d.getEoscifguidelines()).isPresent())
d.setEoscifguidelines(new ArrayList<>());
if (containscriteriaTwitter(d)) {
addEIG(d.getEoscifguidelines(), EOSC_TWITTER_DATA, EOSC_TWITTER_DATA, "", COMPLIES_WITH);
}
return d;
}, Encoders.bean(Dataset.class))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(workingPath + "/dataset");
readPath(spark, workingPath + "/dataset", Dataset.class)
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(inputPath + "/dataset");
}
private static void addEIG(List<EoscIfGuidelines> eoscifguidelines, String code, String label, String url,
String sem) {
if (!eoscifguidelines.stream().anyMatch(eig -> eig.getCode().equals(code)))
eoscifguidelines.add(newInstance(code, label, url, sem));
}
private static boolean containscriteriaTwitter(Result r) {
Set<String> words = getWordsSP(r.getTitle());
words.addAll(getWordsF(r.getDescription()));
if (words.contains("twitter") &&
(words.contains("data") || words.contains("dataset")))
return true;
return Optional
.ofNullable(r.getSubject())
.map(
s -> s.stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("twitter")) &&
s.stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("data")))
.orElse(false);
}
private static boolean containsCriteriaGalaxy(Result r) {
Set<String> words = getWordsSP(r.getTitle());
words.addAll(getWordsF(r.getDescription()));
if (words.contains("galaxy") &&
words.contains("workflow"))
return true;
return Optional
.ofNullable(r.getSubject())
.map(
s -> s.stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("galaxy")) &&
s.stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("workflow")))
.orElse(false);
}
private static boolean containsCriteriaNotebook(Software s) {
if (!Optional.ofNullable(s.getSubject()).isPresent())
return false;
if (s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("jupyter")))
return true;
if (s
.getSubject()
.stream()
.anyMatch(
sbj -> sbj.getValue().toLowerCase().contains("python") &&
sbj.getValue().toLowerCase().contains("notebook")))
return true;
if (s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("python")) &&
s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("notebook")))
return true;
return false;
}
private static Set<String> getWordsSP(List<StructuredProperty> elem) {
Set<String> words = new HashSet<>();
Optional
.ofNullable(elem)
.ifPresent(
e -> e
.forEach(
t -> words
.addAll(
Arrays.asList(t.getValue().toLowerCase().replaceAll("[^a-zA-Z ]", "").split(" ")))));
return words;
}
private static Set<String> getWordsF(List<Field<String>> elem) {
Set<String> words = new HashSet<>();
Optional
.ofNullable(elem)
.ifPresent(
e -> e
.forEach(
t -> words
.addAll(
Arrays.asList(t.getValue().toLowerCase().replaceAll("[^a-zA-Z ]", "").split(" ")))));
return words;
}
}

View File

@ -219,158 +219,9 @@
<error to="Kill"/>
</action>
<join name="wait" to="eosc_tag"/>
<join name="wait" to="End"/>
<action name="eosc_tag">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>EOSC_tagging</name>
<class>eu.dnetlib.dhp.bulktag.eosc.SparkEoscTag</class>
<jar>dhp-enrichment-${projectVersion}.jar</jar>
<spark-opts>
--num-executors=${sparkExecutorNumber}
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${outputPath}</arg>
<arg>--workingPath</arg><arg>${workingDir}/eoscTag</arg>
</spark>
<ok to="eosc_get_datasource_master"/>
<error to="Kill"/>
</action>
<action name="eosc_get_datasource_master">
<java>
<main-class>eu.dnetlib.dhp.bulktag.eosc.ReadMasterDatasourceFromDB</main-class>
<arg>--hdfsPath</arg><arg>${workingDir}/datasourcemaster</arg>
<arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
<arg>--postgresUrl</arg><arg>${postgresURL}</arg>
<arg>--postgresUser</arg><arg>${postgresUser}</arg>
<arg>--postgresPassword</arg><arg>${postgresPassword}</arg>
</java>
<ok to="fork_eosc_context_tag"/>
<error to="Kill"/>
</action>
<fork name="fork_eosc_context_tag">
<path start="eosc_context_tag_publication"/>
<path start="eosc_context_tag_dataset"/>
<path start="eosc_context_tag_otherresearchproduct"/>
<path start="eosc_context_tag_software"/>
</fork>
<action name="eosc_context_tag_publication">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>EOSC tagging publication</name>
<class>eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag</class>
<jar>dhp-enrichment-${projectVersion}.jar</jar>
<spark-opts>
--num-executors=${sparkExecutorNumber}
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${outputPath}/</arg>
<arg>--resultType</arg><arg>publication</arg>
<arg>--workingPath</arg><arg>${workingDir}/eoscContextTag/</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
<arg>--datasourceMapPath</arg><arg>${workingDir}/datasourcemaster</arg>
</spark>
<ok to="wait_eosc_context_tag"/>
<error to="Kill"/>
</action>
<action name="eosc_context_tag_dataset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>EOSC tagging dataset</name>
<class>eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag</class>
<jar>dhp-enrichment-${projectVersion}.jar</jar>
<spark-opts>
--num-executors=${sparkExecutorNumber}
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${outputPath}/</arg>
<arg>--resultType</arg><arg>dataset</arg>
<arg>--workingPath</arg><arg>${workingDir}/eoscContextTag/</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
<arg>--datasourceMapPath</arg><arg>${workingDir}/datasourcemaster</arg>
</spark>
<ok to="wait_eosc_context_tag"/>
<error to="Kill"/>
</action>
<action name="eosc_context_tag_software">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>EOSC tagging software</name>
<class>eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag</class>
<jar>dhp-enrichment-${projectVersion}.jar</jar>
<spark-opts>
--num-executors=${sparkExecutorNumber}
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${outputPath}/</arg>
<arg>--resultType</arg><arg>software</arg>
<arg>--workingPath</arg><arg>${workingDir}/eoscContextTag/</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
<arg>--datasourceMapPath</arg><arg>${workingDir}/datasourcemaster</arg>
</spark>
<ok to="wait_eosc_context_tag"/>
<error to="Kill"/>
</action>
<action name="eosc_context_tag_otherresearchproduct">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>EOSC tagging ORP</name>
<class>eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag</class>
<jar>dhp-enrichment-${projectVersion}.jar</jar>
<spark-opts>
--num-executors=${sparkExecutorNumber}
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${outputPath}/</arg>
<arg>--resultType</arg><arg>otherresearchproduct</arg>
<arg>--workingPath</arg><arg>${workingDir}/eoscContextTag/</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
<arg>--datasourceMapPath</arg><arg>${workingDir}/datasourcemaster</arg>
</spark>
<ok to="wait_eosc_context_tag"/>
<error to="Kill"/>
</action>
<join name="wait_eosc_context_tag" to="End"/>
<end name="End"/>
</workflow-app>

View File

@ -6,17 +6,13 @@ import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.ZENODO_COMMUNITY
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.ForeachFunction;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.Row;
import org.apache.spark.sql.SparkSession;
@ -28,11 +24,7 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.gson.Gson;
import com.jayway.jsonpath.DocumentContext;
import com.jayway.jsonpath.JsonPath;
import eu.dnetlib.dhp.bulktag.community.ProtoMap;
import eu.dnetlib.dhp.schema.oaf.*;
public class BulkTagJobTest {
@ -644,7 +636,8 @@ public class BulkTagJobTest {
new String[] {
"-isTest", Boolean.TRUE.toString(),
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath", getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/software/").getPath(),
"-sourcePath",
getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/software/software_10.json.gz").getPath(),
"-taggingConf", taggingConf,
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Software",
"-outputPath", workingDir.toString() + "/software",
@ -772,14 +765,764 @@ public class BulkTagJobTest {
org.apache.spark.sql.Dataset<Row> idExplodeCommunity = spark.sql(query);
idExplodeCommunity.show(false);
// Assertions.assertEquals(5, idExplodeCommunity.count());
//
// Assertions
// .assertEquals(
// 3, idExplodeCommunity.filter("provenance = 'community:datasource'").count());
// Assertions
// .assertEquals(
// 2, idExplodeCommunity.filter("provenance = 'community:advconstraint'").count());
}
@Test
void bulkTagOtherJupyter() throws Exception {
final String sourcePath = getClass()
.getResource(
"/eu/dnetlib/dhp/eosctag/jupyter/otherresearchproduct")
.getPath();
SparkBulkTagJob
.main(
new String[] {
"-isTest", Boolean.TRUE.toString(),
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath", sourcePath,
"-taggingConf", taggingConf,
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.OtherResearchProduct",
"-outputPath", workingDir.toString() + "/otherresearchproduct",
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
"-pathMap", pathMap
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
Assertions
.assertEquals(
10, sc
.textFile(workingDir.toString() + "/otherresearchproduct")
.map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class))
.count());
Assertions
.assertEquals(
0, sc
.textFile(workingDir.toString() + "/otherresearchproduct")
.map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class))
.filter(
orp -> orp
.getSubject()
.stream()
.anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook")))
.count());
Assertions
.assertEquals(
0, sc
.textFile(workingDir.toString() + "/otherresearchproduct")
.map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class))
.filter(
orp -> orp
.getSubject()
.stream()
.anyMatch(eig -> eig.getValue().equals("EOSC::Jupyter Notebook")))
.count());
}
@Test
public void bulkTagDatasetJupyter() throws Exception {
final String sourcePath = getClass()
.getResource(
"/eu/dnetlib/dhp/eosctag/jupyter/dataset")
.getPath();
SparkBulkTagJob
.main(
new String[] {
"-isTest", Boolean.TRUE.toString(),
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath", sourcePath,
"-taggingConf", taggingConf,
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset",
"-outputPath", workingDir.toString() + "/dataset",
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
"-pathMap", pathMap
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
Assertions
.assertEquals(
10, sc
.textFile(workingDir.toString() + "/dataset")
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class))
.count());
Assertions
.assertEquals(
0, sc
.textFile(workingDir.toString() + "/dataset")
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class))
.filter(
ds -> ds.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook")))
.count());
Assertions
.assertEquals(
0, sc
.textFile(workingDir.toString() + "/dataset")
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class))
.filter(
ds -> ds
.getEoscifguidelines()
.stream()
.anyMatch(eig -> eig.getCode().equals("EOSC::Jupyter Notebook")))
.count());
}
@Test
public void bulkTagSoftwareJupyter() throws Exception {
final String sourcePath = getClass()
.getResource(
"/eu/dnetlib/dhp/eosctag/jupyter/software")
.getPath();
SparkBulkTagJob
.main(
new String[] {
"-isTest", Boolean.TRUE.toString(),
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath", sourcePath,
"-taggingConf", taggingConf,
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Software",
"-outputPath", workingDir.toString() + "/software",
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
"-pathMap", pathMap
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Software> tmp = sc
.textFile(workingDir.toString() + "/software")
.map(item -> OBJECT_MAPPER.readValue(item, Software.class));
Assertions.assertEquals(10, tmp.count());
Assertions
.assertEquals(
4,
tmp
.filter(s -> s.getEoscifguidelines() != null)
.filter(
s -> s
.getEoscifguidelines()
.stream()
.anyMatch(eig -> eig.getCode().equals("EOSC::Jupyter Notebook")))
.count());
Assertions
.assertEquals(
1, tmp
.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4"))
.collect()
.get(0)
.getEoscifguidelines()
.size());
Assertions
.assertEquals(
1, tmp
.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4"))
.collect()
.get(0)
.getSubject()
.size());
Assertions
.assertTrue(
tmp
.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4"))
.collect()
.get(0)
.getEoscifguidelines()
.stream()
.anyMatch(s -> s.getCode().equals("EOSC::Jupyter Notebook")));
Assertions
.assertFalse(
tmp
.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4"))
.collect()
.get(0)
.getSubject()
.stream()
.anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook")));
Assertions
.assertEquals(
5, tmp
.filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11"))
.collect()
.get(0)
.getSubject()
.size());
Assertions
.assertFalse(
tmp
.filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11"))
.collect()
.get(0)
.getSubject()
.stream()
.anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook")));
Assertions
.assertEquals(
0,
tmp
.filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11"))
.collect()
.get(0)
.getEoscifguidelines()
.size());
Assertions
.assertEquals(
8, tmp
.filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56"))
.collect()
.get(0)
.getSubject()
.size());
Assertions
.assertFalse(
tmp
.filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56"))
.collect()
.get(0)
.getSubject()
.stream()
.anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook")));
Assertions
.assertEquals(
1, tmp
.filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56"))
.collect()
.get(0)
.getEoscifguidelines()
.size());
Assertions
.assertTrue(
tmp
.filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56"))
.collect()
.get(0)
.getEoscifguidelines()
.stream()
.anyMatch(s -> s.getCode().equals("EOSC::Jupyter Notebook")));
Assertions
.assertEquals(
5, tmp
.filter(sw -> sw.getId().equals("50|od______1582::5aec1186054301b66c0c5dc35972a589"))
.collect()
.get(0)
.getSubject()
.size());
Assertions
.assertFalse(
tmp
.filter(sw -> sw.getId().equals("50|od______1582::5aec1186054301b66c0c5dc35972a589"))
.collect()
.get(0)
.getSubject()
.stream()
.anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook")));
Assertions
.assertEquals(
0,
tmp
.filter(sw -> sw.getId().equals("50|od______1582::5aec1186054301b66c0c5dc35972a589"))
.collect()
.get(0)
.getEoscifguidelines()
.size());
Assertions
.assertEquals(
8, tmp
.filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0"))
.collect()
.get(0)
.getSubject()
.size());
Assertions
.assertFalse(
tmp
.filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0"))
.collect()
.get(0)
.getSubject()
.stream()
.anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook")));
Assertions
.assertEquals(
1,
tmp
.filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0"))
.collect()
.get(0)
.getEoscifguidelines()
.size());
Assertions
.assertTrue(
tmp
.filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0"))
.collect()
.get(0)
.getEoscifguidelines()
.stream()
.anyMatch(s -> s.getCode().equals("EOSC::Jupyter Notebook")));
List<Subject> subjects = tmp
.filter(sw -> sw.getId().equals("50|od______1582::6e7a9b21a2feef45673890432af34244"))
.collect()
.get(0)
.getSubject();
Assertions.assertEquals(7, subjects.size());
Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("jupyter")));
Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("Modeling and Simulation")));
Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("structure granulaire")));
Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("algorithme")));
Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("simulation numérique")));
Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("flux de gaz")));
Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("flux de liquide")));
}
@Test
void galaxyOtherTest() throws Exception {
final String sourcePath = getClass()
.getResource(
"/eu/dnetlib/dhp/eosctag/galaxy/otherresearchproduct")
.getPath();
SparkBulkTagJob
.main(
new String[] {
"-isTest", Boolean.TRUE.toString(),
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath", sourcePath,
"-taggingConf", taggingConf,
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.OtherResearchProduct",
"-outputPath", workingDir.toString() + "/otherresearchproduct",
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
"-pathMap", pathMap
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<OtherResearchProduct> orp = sc
.textFile(workingDir.toString() + "/otherresearchproduct")
.map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class));
Assertions.assertEquals(10, orp.count());
Assertions
.assertEquals(
0,
orp
.filter(
s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Galaxy Workflow")))
.count());
orp.foreach(o -> System.out.println(OBJECT_MAPPER.writeValueAsString(o)));
Assertions
.assertEquals(
1, orp
.filter(o -> o.getEoscifguidelines() != null)
.filter(
o -> o
.getEoscifguidelines()
.stream()
.anyMatch(eig -> eig.getCode().equals("EOSC::Galaxy Workflow")))
.count());
Assertions
.assertEquals(
2, orp
.filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07"))
.collect()
.get(0)
.getSubject()
.size());
Assertions
.assertFalse(
orp
.filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07"))
.collect()
.get(0)
.getSubject()
.stream()
.anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow")));
Assertions
.assertEquals(
1, orp
.filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07"))
.collect()
.get(0)
.getEoscifguidelines()
.size());
Assertions
.assertTrue(
orp
.filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07"))
.collect()
.get(0)
.getEoscifguidelines()
.stream()
.anyMatch(s -> s.getCode().equals("EOSC::Galaxy Workflow")));
Assertions
.assertEquals(
2, orp
.filter(sw -> sw.getId().equals("50|od______2017::1bd97baef19dbd2db3203b112bb83bc5"))
.collect()
.get(0)
.getSubject()
.size());
Assertions
.assertFalse(
orp
.filter(sw -> sw.getId().equals("50|od______2017::1bd97baef19dbd2db3203b112bb83bc5"))
.collect()
.get(0)
.getSubject()
.stream()
.anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow")));
Assertions
.assertEquals(
2, orp
.filter(sw -> sw.getId().equals("50|od______2017::1e400f1747487fd15998735c41a55c72"))
.collect()
.get(0)
.getSubject()
.size());
Assertions
.assertFalse(
orp
.filter(sw -> sw.getId().equals("50|od______2017::1e400f1747487fd15998735c41a55c72"))
.collect()
.get(0)
.getSubject()
.stream()
.anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow")));
}
@Test
void galaxySoftwareTest() throws Exception {
final String sourcePath = getClass()
.getResource(
"/eu/dnetlib/dhp/eosctag/galaxy/software")
.getPath();
SparkBulkTagJob
.main(
new String[] {
"-isTest", Boolean.TRUE.toString(),
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath", sourcePath,
"-taggingConf", taggingConf,
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Software",
"-outputPath", workingDir.toString() + "/software",
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
"-pathMap", pathMap
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Software> tmp = sc
.textFile(workingDir.toString() + "/software")
.map(item -> OBJECT_MAPPER.readValue(item, Software.class));
Assertions.assertEquals(11, tmp.count());
Assertions
.assertEquals(
0,
tmp
.filter(
s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Galaxy Workflow")))
.count());
Assertions
.assertEquals(
1,
tmp
.filter(
s -> s.getEoscifguidelines().size() > 0)
.count());
Assertions
.assertEquals(
1,
tmp
.filter(
s -> s.getEoscifguidelines().size() > 0)
.filter(
s -> s
.getEoscifguidelines()
.stream()
.anyMatch(eig -> eig.getCode().equals("EOSC::Galaxy Workflow")))
.count());
Assertions
.assertEquals(
1, tmp
.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4"))
.collect()
.get(0)
.getSubject()
.size());
Assertions
.assertFalse(
tmp
.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4"))
.collect()
.get(0)
.getSubject()
.stream()
.anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow")));
Assertions
.assertEquals(
1, tmp
.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4"))
.collect()
.get(0)
.getEoscifguidelines()
.size());
Assertions
.assertTrue(
tmp
.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4"))
.collect()
.get(0)
.getEoscifguidelines()
.stream()
.anyMatch(eig -> eig.getCode().equals("EOSC::Galaxy Workflow")));
Assertions
.assertEquals(
5, tmp
.filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11"))
.collect()
.get(0)
.getSubject()
.size());
Assertions
.assertEquals(
8, tmp
.filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56"))
.collect()
.get(0)
.getSubject()
.size());
Assertions
.assertFalse(
tmp
.filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56"))
.collect()
.get(0)
.getSubject()
.stream()
.anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow")));
}
@Test
void twitterDatasetTest() throws Exception {
final String sourcePath = getClass()
.getResource(
"/eu/dnetlib/dhp/eosctag/twitter/dataset")
.getPath();
SparkBulkTagJob
.main(
new String[] {
"-isTest", Boolean.TRUE.toString(),
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath", sourcePath,
"-taggingConf", taggingConf,
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset",
"-outputPath", workingDir.toString() + "/dataset",
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
"-pathMap", pathMap
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Dataset> dats = sc
.textFile(workingDir.toString() + "/dataset")
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
Assertions.assertEquals(11, dats.count());
Assertions
.assertEquals(
3,
dats
.filter(
s -> s
.getEoscifguidelines()
.stream()
.anyMatch(eig -> eig.getCode().equals("EOSC::Twitter Data")))
.count());
}
@Test
void twitterOtherTest() throws Exception {
final String sourcePath = getClass()
.getResource(
"/eu/dnetlib/dhp/eosctag/twitter/otherresearchproduct")
.getPath();
SparkBulkTagJob
.main(
new String[] {
"-isTest", Boolean.TRUE.toString(),
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath", sourcePath,
"-taggingConf", taggingConf,
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.OtherResearchProduct",
"-outputPath", workingDir.toString() + "/otherresearchproduct",
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
"-pathMap", pathMap
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<OtherResearchProduct> orp = sc
.textFile(workingDir.toString() + "/otherresearchproduct")
.map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class));
Assertions.assertEquals(10, orp.count());
Assertions
.assertEquals(
0,
orp
.filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Twitter Data")))
.count());
Assertions
.assertEquals(
3,
orp
.filter(
s -> s
.getEoscifguidelines()
.stream()
.anyMatch(eig -> eig.getCode().equals("EOSC::Twitter Data")))
.count());
}
@Test
void twitterSoftwareTest() throws Exception {
final String sourcePath = getClass()
.getResource(
"/eu/dnetlib/dhp/eosctag/twitter/software")
.getPath();
SparkBulkTagJob
.main(
new String[] {
"-isTest", Boolean.TRUE.toString(),
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath", sourcePath,
"-taggingConf", taggingConf,
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Software",
"-outputPath", workingDir.toString() + "/software",
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
"-pathMap", pathMap
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Software> tmp = sc
.textFile(workingDir.toString() + "/software")
.map(item -> OBJECT_MAPPER.readValue(item, Software.class));
Assertions.assertEquals(10, tmp.count());
Assertions
.assertEquals(
0,
tmp
.filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Twitter Data")))
.count());
}
@Test
void EoscContextTagTest() throws Exception {
final String sourcePath = getClass()
.getResource(
"/eu/dnetlib/dhp/bulktag/eosc/dataset/dataset_10.json")
.getPath();
SparkBulkTagJob
.main(
new String[] {
"-isTest", Boolean.TRUE.toString(),
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath", sourcePath,
"-taggingConf", taggingConf,
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset",
"-outputPath", workingDir.toString() + "/dataset",
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
"-pathMap", pathMap
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Dataset> tmp = sc
.textFile(workingDir.toString() + "/dataset")
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
Assertions.assertEquals(8, tmp.count());
Assertions
.assertEquals(
4,
tmp
.filter(
s -> s.getContext().stream().anyMatch(c -> c.getId().equals("eosc")))
.count());
Assertions
.assertEquals(
1,
tmp
.filter(
d -> d.getId().equals("50|475c1990cbb2::0fecfb874d9395aa69d2f4d7cd1acbea")
&&
d.getContext().stream().anyMatch(c -> c.getId().equals("eosc")))
.count());
Assertions
.assertEquals(
1,
tmp
.filter(
d -> d.getId().equals("50|475c1990cbb2::3185cd5d8a2b0a06bb9b23ef11748eb1")
&&
d.getContext().stream().anyMatch(c -> c.getId().equals("eosc")))
.count());
Assertions
.assertEquals(
1,
tmp
.filter(
d -> d.getId().equals("50|475c1990cbb2::3894c94123e96df8a21249957cf160cb")
&&
d.getContext().stream().anyMatch(c -> c.getId().equals("eosc")))
.count());
Assertions
.assertEquals(
1,
tmp
.filter(
d -> d.getId().equals("50|475c1990cbb2::449f28eefccf9f70c04ad70d61e041c7")
&&
d.getContext().stream().anyMatch(c -> c.getId().equals("eosc")))
.count());
}
}

View File

@ -1,162 +0,0 @@
package eu.dnetlib.dhp.bulktag;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.List;
import org.apache.commons.io.FileUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* @author miriam.baglioni
* @Date 22/07/22
*/
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag;
import eu.dnetlib.dhp.schema.oaf.Dataset;
import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct;
import eu.dnetlib.dhp.schema.oaf.Software;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
//"50|475c1990cbb2::0fecfb874d9395aa69d2f4d7cd1acbea" has instance hostedby eosc
//"50|475c1990cbb2::3185cd5d8a2b0a06bb9b23ef11748eb1" has instance hostedby eosc
//"50|475c1990cbb2::449f28eefccf9f70c04ad70d61e041c7" has two instance one hostedby eosc
//"50|475c1990cbb2::3894c94123e96df8a21249957cf160cb" has EoscTag
public class EOSCContextTaggingTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static SparkSession spark;
private static Path workingDir;
private static final Logger log = LoggerFactory.getLogger(EOSCContextTaggingTest.class);
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files.createTempDirectory(EOSCContextTaggingTest.class.getSimpleName());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf();
conf.setAppName(EOSCContextTaggingTest.class.getSimpleName());
conf.setMaster("local[*]");
conf.set("spark.driver.host", "localhost");
conf.set("hive.metastore.local", "true");
conf.set("spark.ui.enabled", "false");
conf.set("spark.sql.warehouse.dir", workingDir.toString());
conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
spark = SparkSession
.builder()
.appName(EOSCTagJobTest.class.getSimpleName())
.config(conf)
.getOrCreate();
}
@AfterAll
public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
spark.stop();
}
@Test
void EoscContextTagTest() throws Exception {
spark
.read()
.textFile(getClass().getResource("/eu/dnetlib/dhp/bulktag/eosc/dataset/dataset_10.json").getPath())
.map(
(MapFunction<String, Dataset>) value -> OBJECT_MAPPER.readValue(value, Dataset.class),
Encoders.bean(Dataset.class))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(workingDir.toString() + "/input/dataset");
SparkEoscBulkTag
.main(
new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath",
workingDir.toString() + "/input/dataset",
"-workingPath", workingDir.toString() + "/working/dataset",
"-datasourceMapPath",
getClass()
.getResource("/eu/dnetlib/dhp/bulktag/eosc/datasourceMasterAssociation/datasourceMaster")
.getPath(),
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset"
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Dataset> tmp = sc
.textFile(workingDir.toString() + "/input/dataset")
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
Assertions.assertEquals(10, tmp.count());
Assertions
.assertEquals(
4,
tmp
.filter(
s -> s.getContext().stream().anyMatch(c -> c.getId().equals("eosc")))
.count());
Assertions
.assertEquals(
1,
tmp
.filter(
d -> d.getId().equals("50|475c1990cbb2::0fecfb874d9395aa69d2f4d7cd1acbea")
&&
d.getContext().stream().anyMatch(c -> c.getId().equals("eosc")))
.count());
Assertions
.assertEquals(
1,
tmp
.filter(
d -> d.getId().equals("50|475c1990cbb2::3185cd5d8a2b0a06bb9b23ef11748eb1")
&&
d.getContext().stream().anyMatch(c -> c.getId().equals("eosc")))
.count());
Assertions
.assertEquals(
1,
tmp
.filter(
d -> d.getId().equals("50|475c1990cbb2::3894c94123e96df8a21249957cf160cb")
&&
d.getContext().stream().anyMatch(c -> c.getId().equals("eosc")))
.count());
Assertions
.assertEquals(
1,
tmp
.filter(
d -> d.getId().equals("50|475c1990cbb2::3894c94123e96df8a21249957cf160cb")
&&
d.getContext().stream().anyMatch(c -> c.getId().equals("eosc")))
.count());
}
}

View File

@ -1,713 +0,0 @@
package eu.dnetlib.dhp.bulktag;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.List;
import org.apache.commons.io.FileUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.bulktag.eosc.SparkEoscTag;
import eu.dnetlib.dhp.schema.oaf.*;
public class EOSCTagJobTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static SparkSession spark;
private static Path workingDir;
private static final Logger log = LoggerFactory.getLogger(EOSCTagJobTest.class);
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files.createTempDirectory(EOSCTagJobTest.class.getSimpleName());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf();
conf.setAppName(EOSCTagJobTest.class.getSimpleName());
conf.setMaster("local[*]");
conf.set("spark.driver.host", "localhost");
conf.set("hive.metastore.local", "true");
conf.set("spark.ui.enabled", "false");
conf.set("spark.sql.warehouse.dir", workingDir.toString());
conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
spark = SparkSession
.builder()
.appName(EOSCTagJobTest.class.getSimpleName())
.config(conf)
.getOrCreate();
}
@AfterAll
public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
spark.stop();
}
@Test
void jupyterUpdatesTest() throws Exception {
spark
.read()
.textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/jupyter/software").getPath())
.map(
(MapFunction<String, Software>) value -> OBJECT_MAPPER.readValue(value, Software.class),
Encoders.bean(Software.class))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(workingDir.toString() + "/input/software");
spark
.read()
.textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/jupyter/dataset").getPath())
.map(
(MapFunction<String, Dataset>) value -> OBJECT_MAPPER.readValue(value, Dataset.class),
Encoders.bean(Dataset.class))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(workingDir.toString() + "/input/dataset");
spark
.read()
.textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/jupyter/otherresearchproduct").getPath())
.map(
(MapFunction<String, OtherResearchProduct>) value -> OBJECT_MAPPER
.readValue(value, OtherResearchProduct.class),
Encoders.bean(OtherResearchProduct.class))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(workingDir.toString() + "/input/otherresearchproduct");
SparkEoscTag
.main(
new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath",
workingDir.toString() + "/input",
"-workingPath", workingDir.toString() + "/working"
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Software> tmp = sc
.textFile(workingDir.toString() + "/input/software")
.map(item -> OBJECT_MAPPER.readValue(item, Software.class));
Assertions.assertEquals(10, tmp.count());
Assertions
.assertEquals(
4,
tmp
.filter(s -> s.getEoscifguidelines() != null)
.filter(
s -> s
.getEoscifguidelines()
.stream()
.anyMatch(eig -> eig.getCode().equals("EOSC::Jupyter Notebook")))
.count());
Assertions
.assertEquals(
1, tmp
.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4"))
.collect()
.get(0)
.getEoscifguidelines()
.size());
Assertions
.assertEquals(
1, tmp
.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4"))
.collect()
.get(0)
.getSubject()
.size());
Assertions
.assertTrue(
tmp
.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4"))
.collect()
.get(0)
.getEoscifguidelines()
.stream()
.anyMatch(s -> s.getCode().equals("EOSC::Jupyter Notebook")));
Assertions
.assertFalse(
tmp
.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4"))
.collect()
.get(0)
.getSubject()
.stream()
.anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook")));
Assertions
.assertEquals(
5, tmp
.filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11"))
.collect()
.get(0)
.getSubject()
.size());
Assertions
.assertFalse(
tmp
.filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11"))
.collect()
.get(0)
.getSubject()
.stream()
.anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook")));
Assertions
.assertTrue(
tmp
.filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11"))
.collect()
.get(0)
.getEoscifguidelines() == null);
Assertions
.assertEquals(
8, tmp
.filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56"))
.collect()
.get(0)
.getSubject()
.size());
Assertions
.assertFalse(
tmp
.filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56"))
.collect()
.get(0)
.getSubject()
.stream()
.anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook")));
Assertions
.assertEquals(
1, tmp
.filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56"))
.collect()
.get(0)
.getEoscifguidelines()
.size());
Assertions
.assertTrue(
tmp
.filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56"))
.collect()
.get(0)
.getEoscifguidelines()
.stream()
.anyMatch(s -> s.getCode().equals("EOSC::Jupyter Notebook")));
Assertions
.assertEquals(
5, tmp
.filter(sw -> sw.getId().equals("50|od______1582::5aec1186054301b66c0c5dc35972a589"))
.collect()
.get(0)
.getSubject()
.size());
Assertions
.assertFalse(
tmp
.filter(sw -> sw.getId().equals("50|od______1582::5aec1186054301b66c0c5dc35972a589"))
.collect()
.get(0)
.getSubject()
.stream()
.anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook")));
Assertions
.assertTrue(
tmp
.filter(sw -> sw.getId().equals("50|od______1582::5aec1186054301b66c0c5dc35972a589"))
.collect()
.get(0)
.getEoscifguidelines() == null);
Assertions
.assertEquals(
8, tmp
.filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0"))
.collect()
.get(0)
.getSubject()
.size());
Assertions
.assertFalse(
tmp
.filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0"))
.collect()
.get(0)
.getSubject()
.stream()
.anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook")));
Assertions
.assertEquals(
1,
tmp
.filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0"))
.collect()
.get(0)
.getEoscifguidelines()
.size());
Assertions
.assertTrue(
tmp
.filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0"))
.collect()
.get(0)
.getEoscifguidelines()
.stream()
.anyMatch(s -> s.getCode().equals("EOSC::Jupyter Notebook")));
List<Subject> subjects = tmp
.filter(sw -> sw.getId().equals("50|od______1582::6e7a9b21a2feef45673890432af34244"))
.collect()
.get(0)
.getSubject();
Assertions.assertEquals(7, subjects.size());
Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("jupyter")));
Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("Modeling and Simulation")));
Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("structure granulaire")));
Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("algorithme")));
Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("simulation numérique")));
Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("flux de gaz")));
Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("flux de liquide")));
Assertions
.assertEquals(
10, sc
.textFile(workingDir.toString() + "/input/dataset")
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class))
.count());
Assertions
.assertEquals(
0, sc
.textFile(workingDir.toString() + "/input/dataset")
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class))
.filter(
ds -> ds.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook")))
.count());
Assertions
.assertEquals(
0, sc
.textFile(workingDir.toString() + "/input/dataset")
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class))
.filter(
ds -> ds
.getEoscifguidelines()
.stream()
.anyMatch(eig -> eig.getCode().equals("EOSC::Jupyter Notebook")))
.count());
Assertions
.assertEquals(
10, sc
.textFile(workingDir.toString() + "/input/otherresearchproduct")
.map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class))
.count());
Assertions
.assertEquals(
0, sc
.textFile(workingDir.toString() + "/input/otherresearchproduct")
.map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class))
.filter(
orp -> orp
.getSubject()
.stream()
.anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook")))
.count());
Assertions
.assertEquals(
0, sc
.textFile(workingDir.toString() + "/input/otherresearchproduct")
.map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class))
.filter(
orp -> orp
.getSubject()
.stream()
.anyMatch(eig -> eig.getValue().equals("EOSC::Jupyter Notebook")))
.count());
// spark.stop();
}
@Test
void galaxyUpdatesTest() throws Exception {
spark
.read()
.textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/galaxy/software").getPath())
.map(
(MapFunction<String, Software>) value -> OBJECT_MAPPER.readValue(value, Software.class),
Encoders.bean(Software.class))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(workingDir.toString() + "/input/software");
spark
.read()
.textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/galaxy/dataset").getPath())
.map(
(MapFunction<String, Dataset>) value -> OBJECT_MAPPER.readValue(value, Dataset.class),
Encoders.bean(Dataset.class))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(workingDir.toString() + "/input/dataset");
spark
.read()
.textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/galaxy/otherresearchproduct").getPath())
.map(
(MapFunction<String, OtherResearchProduct>) value -> OBJECT_MAPPER
.readValue(value, OtherResearchProduct.class),
Encoders.bean(OtherResearchProduct.class))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(workingDir.toString() + "/input/otherresearchproduct");
SparkEoscTag
.main(
new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath",
workingDir.toString() + "/input",
"-workingPath", workingDir.toString() + "/working"
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Software> tmp = sc
.textFile(workingDir.toString() + "/input/software")
.map(item -> OBJECT_MAPPER.readValue(item, Software.class));
Assertions.assertEquals(11, tmp.count());
Assertions
.assertEquals(
0,
tmp
.filter(
s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Galaxy Workflow")))
.count());
Assertions
.assertEquals(
1,
tmp
.filter(
s -> s.getEoscifguidelines() != null)
.count());
Assertions
.assertEquals(
1,
tmp
.filter(
s -> s.getEoscifguidelines() != null)
.filter(
s -> s
.getEoscifguidelines()
.stream()
.anyMatch(eig -> eig.getCode().equals("EOSC::Galaxy Workflow")))
.count());
Assertions
.assertEquals(
1, tmp
.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4"))
.collect()
.get(0)
.getSubject()
.size());
Assertions
.assertFalse(
tmp
.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4"))
.collect()
.get(0)
.getSubject()
.stream()
.anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow")));
Assertions
.assertEquals(
1, tmp
.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4"))
.collect()
.get(0)
.getEoscifguidelines()
.size());
Assertions
.assertTrue(
tmp
.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4"))
.collect()
.get(0)
.getEoscifguidelines()
.stream()
.anyMatch(eig -> eig.getCode().equals("EOSC::Galaxy Workflow")));
Assertions
.assertEquals(
5, tmp
.filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11"))
.collect()
.get(0)
.getSubject()
.size());
Assertions
.assertEquals(
8, tmp
.filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56"))
.collect()
.get(0)
.getSubject()
.size());
Assertions
.assertFalse(
tmp
.filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56"))
.collect()
.get(0)
.getSubject()
.stream()
.anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow")));
JavaRDD<OtherResearchProduct> orp = sc
.textFile(workingDir.toString() + "/input/otherresearchproduct")
.map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class));
Assertions.assertEquals(10, orp.count());
Assertions
.assertEquals(
0,
orp
.filter(
s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Galaxy Workflow")))
.count());
orp.foreach(o -> System.out.println(OBJECT_MAPPER.writeValueAsString(o)));
Assertions
.assertEquals(
1, orp
.filter(o -> o.getEoscifguidelines() != null)
.filter(
o -> o
.getEoscifguidelines()
.stream()
.anyMatch(eig -> eig.getCode().equals("EOSC::Galaxy Workflow")))
.count());
Assertions
.assertEquals(
2, orp
.filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07"))
.collect()
.get(0)
.getSubject()
.size());
Assertions
.assertFalse(
orp
.filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07"))
.collect()
.get(0)
.getSubject()
.stream()
.anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow")));
Assertions
.assertEquals(
1, orp
.filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07"))
.collect()
.get(0)
.getEoscifguidelines()
.size());
Assertions
.assertTrue(
orp
.filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07"))
.collect()
.get(0)
.getEoscifguidelines()
.stream()
.anyMatch(s -> s.getCode().equals("EOSC::Galaxy Workflow")));
Assertions
.assertEquals(
2, orp
.filter(sw -> sw.getId().equals("50|od______2017::1bd97baef19dbd2db3203b112bb83bc5"))
.collect()
.get(0)
.getSubject()
.size());
Assertions
.assertFalse(
orp
.filter(sw -> sw.getId().equals("50|od______2017::1bd97baef19dbd2db3203b112bb83bc5"))
.collect()
.get(0)
.getSubject()
.stream()
.anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow")));
Assertions
.assertEquals(
2, orp
.filter(sw -> sw.getId().equals("50|od______2017::1e400f1747487fd15998735c41a55c72"))
.collect()
.get(0)
.getSubject()
.size());
Assertions
.assertFalse(
orp
.filter(sw -> sw.getId().equals("50|od______2017::1e400f1747487fd15998735c41a55c72"))
.collect()
.get(0)
.getSubject()
.stream()
.anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow")));
}
@Test
void twitterUpdatesTest() throws Exception {
spark
.read()
.textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/twitter/software").getPath())
.map(
(MapFunction<String, Software>) value -> OBJECT_MAPPER.readValue(value, Software.class),
Encoders.bean(Software.class))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(workingDir.toString() + "/input/software");
spark
.read()
.textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/twitter/dataset").getPath())
.map(
(MapFunction<String, Dataset>) value -> OBJECT_MAPPER.readValue(value, Dataset.class),
Encoders.bean(Dataset.class))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(workingDir.toString() + "/input/dataset");
spark
.read()
.textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/twitter/otherresearchproduct").getPath())
.map(
(MapFunction<String, OtherResearchProduct>) value -> OBJECT_MAPPER
.readValue(value, OtherResearchProduct.class),
Encoders.bean(OtherResearchProduct.class))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(workingDir.toString() + "/input/otherresearchproduct");
SparkEoscTag
.main(
new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath",
workingDir.toString() + "/input",
"-workingPath", workingDir.toString() + "/working"
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Software> tmp = sc
.textFile(workingDir.toString() + "/input/software")
.map(item -> OBJECT_MAPPER.readValue(item, Software.class));
Assertions.assertEquals(10, tmp.count());
Assertions
.assertEquals(
0,
tmp
.filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Twitter Data")))
.count());
JavaRDD<OtherResearchProduct> orp = sc
.textFile(workingDir.toString() + "/input/otherresearchproduct")
.map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class));
Assertions.assertEquals(10, orp.count());
Assertions
.assertEquals(
0,
orp
.filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Twitter Data")))
.count());
Assertions
.assertEquals(
3,
orp
.filter(
s -> s
.getEoscifguidelines()
.stream()
.anyMatch(eig -> eig.getCode().equals("EOSC::Twitter Data")))
.count());
JavaRDD<Dataset> dats = sc
.textFile(workingDir.toString() + "/input/dataset")
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
Assertions.assertEquals(11, dats.count());
Assertions
.assertEquals(
3,
dats
.filter(
s -> s
.getEoscifguidelines()
.stream()
.anyMatch(eig -> eig.getCode().equals("EOSC::Twitter Data")))
.count());
}
}

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