diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java index 982e8ea75..3186ed5c0 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java @@ -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 datasources = readPath( + spark, inputPath + .substring( + 0, + inputPath.lastIndexOf("/")) + + "/datasource", + Datasource.class) + .filter((FilterFunction) ds -> isOKDatasource(ds)) + .map((MapFunction) ds -> ds.getId(), Encoders.STRING()); + + Map>> dsm = cc.getEoscDatasourceMap(); + + for (String ds : datasources.collectAsList()) { + final String dsId = ds.substring(3); + if (!dsm.containsKey(dsId)) { + ArrayList> 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 void execBulkTag( SparkSession spark, String inputPath, diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Community.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Community.java index f0986a832..c218b0c2b 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Community.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Community.java @@ -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 subjects = new ArrayList<>(); private List providers = new ArrayList<>(); private List 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() { diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfiguration.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfiguration.java index 66407a4b3..a30e1cbbb 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfiguration.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfiguration.java @@ -26,6 +26,16 @@ public class CommunityConfiguration implements Serializable { private Map>> zenodocommunityMap = new HashMap<>(); // map communityid -> selectionconstraints private Map selectionConstraintsMap = new HashMap<>(); + // map eosc datasource -> communityid + private Map>> eoscDatasourceMap = new HashMap<>(); + + public Map>> getEoscDatasourceMap() { + return eoscDatasourceMap; + } + + public void setEoscDatasourceMap(Map>> eoscDatasourceMap) { + this.eoscDatasourceMap = eoscDatasourceMap; + } public Map>> 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> getCommunityForZenodoCommunity(String zc) { return zenodocommunityMap.get(zc); } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java index 31bb8d530..3f0954f38 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java @@ -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 communities = new HashSet<>(); @@ -89,24 +101,34 @@ public class ResultTagger implements Serializable { // Tagging for datasource final Set datasources = new HashSet<>(); - final Set tmp = new HashSet<>(); + final Set collfrom = new HashSet<>(); + final Set 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) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/StartsWithVerbIgnoreCase.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/StartsWithVerbIgnoreCase.java index fe439a614..e0c4a2f51 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/StartsWithVerbIgnoreCase.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/StartsWithVerbIgnoreCase.java @@ -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 { diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/DatasourceMaster.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/DatasourceMaster.java deleted file mode 100644 index ee01597e7..000000000 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/DatasourceMaster.java +++ /dev/null @@ -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; - } -} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/EoscIFTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/EoscIFTag.java new file mode 100644 index 000000000..2c9104c21 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/EoscIFTag.java @@ -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 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 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 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, 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 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 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(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 getWordsSP(List elem) { + Set 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 getWordsF(List> elem) { + Set 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; + } +} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java deleted file mode 100644 index e9b1d3cfd..000000000 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java +++ /dev/null @@ -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 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); - } - } - -} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java deleted file mode 100644 index 010ad5a87..000000000 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java +++ /dev/null @@ -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 resultClazz = (Class) 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 datasources = readPath(spark, inputPath + "datasource", Datasource.class) - .filter((FilterFunction) 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 = readPath(spark, datasourceMapPath, DatasourceMaster.class); - - datasources - .joinWith(datasourceMaster, datasources.col("id").equalTo(datasourceMaster.col("master")), "left") - .map( - (MapFunction, DatasourceMaster>) t2 -> t2._2(), - Encoders.bean(DatasourceMaster.class)) - .filter(Objects::nonNull) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(workingPath + "datasource"); - } - - private static void execBulkTag( - SparkSession spark, - String inputPath, - String workingPath, - String resultType, - Class resultClazz) { - - List hostedByList = readPath(spark, workingPath + "datasource", DatasourceMaster.class) - .map((MapFunction) dm -> dm.getMaster(), Encoders.STRING()) - .collectAsList(); - - readPath(spark, inputPath + resultType, resultClazz) - .map( - (MapFunction) 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 enrich(R value, List 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 Dataset readPath( - SparkSession spark, String inputPath, Class clazz) { - return spark - .read() - .textFile(inputPath) - .map((MapFunction) 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 MapFunction patchResult() { - return r -> { - if (r.getDataInfo().getDeletedbyinference() == null) { - r.getDataInfo().setDeletedbyinference(false); - } - if (r.getContext() == null) { - r.setContext(new ArrayList<>()); - } - return r; - }; - } - -} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscTag.java deleted file mode 100644 index c131399cc..000000000 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscTag.java +++ /dev/null @@ -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) 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) 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) 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, 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 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 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 getWordsSP(List elem) { - Set 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 getWordsF(List> elem) { - Set 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; - } -} diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml index 8ac8097e8..b868e4c72 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml @@ -219,158 +219,9 @@ - + - - - yarn-cluster - cluster - EOSC_tagging - eu.dnetlib.dhp.bulktag.eosc.SparkEoscTag - dhp-enrichment-${projectVersion}.jar - - --num-executors=${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} - - --sourcePath${outputPath} - --workingPath${workingDir}/eoscTag - - - - - - - eu.dnetlib.dhp.bulktag.eosc.ReadMasterDatasourceFromDB - --hdfsPath${workingDir}/datasourcemaster - --hdfsNameNode${nameNode} - --postgresUrl${postgresURL} - --postgresUser${postgresUser} - --postgresPassword${postgresPassword} - - - - - - - - - - - - - - - yarn-cluster - cluster - EOSC tagging publication - eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag - dhp-enrichment-${projectVersion}.jar - - --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}${spark2EventLogDir} - - --sourcePath${outputPath}/ - --resultTypepublication - --workingPath${workingDir}/eoscContextTag/ - --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication - --datasourceMapPath${workingDir}/datasourcemaster - - - - - - - - yarn-cluster - cluster - EOSC tagging dataset - eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag - dhp-enrichment-${projectVersion}.jar - - --num-executors=${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} - - --sourcePath${outputPath}/ - --resultTypedataset - --workingPath${workingDir}/eoscContextTag/ - --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset - --datasourceMapPath${workingDir}/datasourcemaster - - - - - - - yarn-cluster - cluster - EOSC tagging software - eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag - dhp-enrichment-${projectVersion}.jar - - --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}${spark2EventLogDir} - - --sourcePath${outputPath}/ - --resultTypesoftware - --workingPath${workingDir}/eoscContextTag/ - --resultTableNameeu.dnetlib.dhp.schema.oaf.Software - --datasourceMapPath${workingDir}/datasourcemaster - - - - - - - yarn-cluster - cluster - EOSC tagging ORP - eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag - dhp-enrichment-${projectVersion}.jar - - --num-executors=${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} - - --sourcePath${outputPath}/ - --resultTypeotherresearchproduct - --workingPath${workingDir}/eoscContextTag/ - --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct - --datasourceMapPath${workingDir}/datasourcemaster - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java index 6c8dd157e..4432210f1 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java @@ -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 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 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 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 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 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 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 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 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 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()); } } diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCContextTaggingTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCContextTaggingTest.java deleted file mode 100644 index cbdab7628..000000000 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCContextTaggingTest.java +++ /dev/null @@ -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) 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 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()); - } - -} diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java deleted file mode 100644 index a640e2009..000000000 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java +++ /dev/null @@ -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) 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) 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) 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 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 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) 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) 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) 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 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 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) 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) 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) 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 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 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 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()); - - } -} diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/eosc/dataset/dataset_10.json b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/eosc/dataset/dataset_10.json index 63aa87e93..61484bb37 100644 --- a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/eosc/dataset/dataset_10.json +++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/eosc/dataset/dataset_10.json @@ -1,9 +1,7 @@ {"author":[{"affiliation":[],"fullname":"Government of Alberta | Gouvernement de l'Alberta","name":"Government Of Alberta Gouvernement L.","pid":[],"rank":1,"surname":"Alberta"}],"bestaccessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":[{"key":"10|openaire____::3795d6478e30e2c9f787d427ff160944","value":"Federated Research Data Repository / Dépôt fédéré de données de recherche"}],"context":[],"contributor":[{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"Federated Research Data Repository"},{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"Dépôt fédéré de données de recherche"}],"country":[],"coverage":[],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"dateofacceptance":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"2013-05-28"},"dateofcollection":"2022-06-26T00:09:49+0000","dateoftransformation":"2022-06-26T01:48:37.716Z","description":[{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"The number of people who are unemployed as a 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