diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/action/ReadDatasourceMasterDuplicateFromDB.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/action/ReadDatasourceMasterDuplicateFromDB.java new file mode 100644 index 000000000..5d39216f1 --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/action/ReadDatasourceMasterDuplicateFromDB.java @@ -0,0 +1,81 @@ + +package eu.dnetlib.dhp.common.action; + +import java.io.BufferedWriter; +import java.io.IOException; +import java.io.OutputStreamWriter; +import java.nio.charset.StandardCharsets; +import java.sql.ResultSet; +import java.sql.SQLException; + +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FSDataOutputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.common.DbClient; +import eu.dnetlib.dhp.common.action.model.MasterDuplicate; +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; + +public class ReadDatasourceMasterDuplicateFromDB { + + private static final Logger log = LoggerFactory.getLogger(ReadDatasourceMasterDuplicateFromDB.class); + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static final String QUERY = "SELECT distinct dd.id as masterId, d.officialname as masterName, dd.duplicate as duplicateId " + + + "FROM dsm_dedup_services dd join dsm_services d on (dd.id = d.id);"; + + public static int execute(String dbUrl, String dbUser, String dbPassword, String hdfsPath, String hdfsNameNode) + throws IOException { + int count = 0; + try (DbClient dbClient = new DbClient(dbUrl, dbUser, dbPassword)) { + Configuration conf = new Configuration(); + conf.set("fs.defaultFS", hdfsNameNode); + FileSystem fileSystem = FileSystem.get(conf); + FSDataOutputStream fos = fileSystem.create(new Path(hdfsPath)); + + log.info("running query: {}", QUERY); + log.info("storing results in: {}", hdfsPath); + + try (BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(fos, StandardCharsets.UTF_8))) { + dbClient.processResults(QUERY, rs -> writeMap(datasourceMasterMap(rs), writer)); + count++; + } + } + return count; + } + + private static MasterDuplicate datasourceMasterMap(ResultSet rs) { + try { + final MasterDuplicate md = new MasterDuplicate(); + + final String duplicateId = rs.getString("duplicateId"); + final String masterId = rs.getString("masterId"); + final String masterName = rs.getString("masterName"); + + md.setDuplicateId(OafMapperUtils.createOpenaireId(10, duplicateId, true)); + md.setMasterId(OafMapperUtils.createOpenaireId(10, masterId, true)); + md.setMasterName(masterName); + + return md; + } catch (final SQLException e) { + throw new RuntimeException(e); + } + } + + private static void writeMap(final MasterDuplicate dm, final BufferedWriter writer) { + try { + writer.write(OBJECT_MAPPER.writeValueAsString(dm)); + writer.newLine(); + } catch (final IOException e) { + throw new RuntimeException(e); + } + } + +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/action/model/MasterDuplicate.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/action/model/MasterDuplicate.java new file mode 100644 index 000000000..12a4407c4 --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/action/model/MasterDuplicate.java @@ -0,0 +1,38 @@ + +package eu.dnetlib.dhp.common.action.model; + +import java.io.Serializable; + +/** + * @author miriam.baglioni + * @Date 21/07/22 + */ +public class MasterDuplicate implements Serializable { + private String duplicateId; + private String masterId; + private String masterName; + + public String getDuplicateId() { + return duplicateId; + } + + public void setDuplicateId(String duplicateId) { + this.duplicateId = duplicateId; + } + + public String getMasterId() { + return masterId; + } + + public void setMasterId(String masterId) { + this.masterId = masterId; + } + + public String getMasterName() { + return masterName; + } + + public void setMasterName(String masterName) { + this.masterName = masterName; + } +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/Vocabulary.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/Vocabulary.java index 3a8df5c9e..2ab23bda6 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/Vocabulary.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/Vocabulary.java @@ -4,6 +4,7 @@ package eu.dnetlib.dhp.common.vocabulary; import java.io.Serializable; import java.util.HashMap; import java.util.Map; +import java.util.Objects; import java.util.Optional; import org.apache.commons.lang3.StringUtils; @@ -66,27 +67,39 @@ public class Vocabulary implements Serializable { } public Qualifier getTermAsQualifier(final String termId) { - if (StringUtils.isBlank(termId)) { + return getTermAsQualifier(termId, false); + } + + public Qualifier getTermAsQualifier(final String termId, boolean strict) { + final VocabularyTerm term = getTerm(termId); + if (Objects.nonNull(term)) { + return OafMapperUtils.qualifier(term.getId(), term.getName(), getId(), getName()); + } else if (Objects.isNull(term) && strict) { return OafMapperUtils.unknown(getId(), getName()); - } else if (termExists(termId)) { - final VocabularyTerm t = getTerm(termId); - return OafMapperUtils.qualifier(t.getId(), t.getName(), getId(), getName()); } else { return OafMapperUtils.qualifier(termId, termId, getId(), getName()); } } public Qualifier getSynonymAsQualifier(final String syn) { + return getSynonymAsQualifier(syn, false); + } + + public Qualifier getSynonymAsQualifier(final String syn, boolean strict) { return Optional .ofNullable(getTermBySynonym(syn)) - .map(term -> getTermAsQualifier(term.getId())) + .map(term -> getTermAsQualifier(term.getId(), strict)) .orElse(null); } public Qualifier lookup(String id) { + return lookup(id, false); + } + + public Qualifier lookup(String id, boolean strict) { return Optional - .ofNullable(getSynonymAsQualifier(id)) - .orElse(getTermAsQualifier(id)); + .ofNullable(getSynonymAsQualifier(id, strict)) + .orElse(getTermAsQualifier(id, strict)); } } diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java index 775f228eb..b24daaa5d 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java @@ -23,6 +23,8 @@ import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; import me.xuender.unidecode.Unidecode; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Encoders; public class GraphCleaningFunctions extends CleaningFunctions { @@ -201,6 +203,13 @@ public class GraphCleaningFunctions extends CleaningFunctions { .filter(sp -> StringUtils.isNotBlank(sp.getValue())) .filter(sp -> Objects.nonNull(sp.getQualifier())) .filter(sp -> StringUtils.isNotBlank(sp.getQualifier().getClassid())) + .map(s -> { + if ("dnet:result_subject".equals(s.getQualifier().getClassid())) { + s.getQualifier().setClassid(ModelConstants.DNET_SUBJECT_TYPOLOGIES); + s.getQualifier().setClassname(ModelConstants.DNET_SUBJECT_TYPOLOGIES); + } + return s; + }) .map(GraphCleaningFunctions::cleanValue) .collect( Collectors @@ -211,7 +220,7 @@ public class GraphCleaningFunctions extends CleaningFunctions { .orElse(s.getValue()), Function.identity(), (s1, s2) -> Collections - .min(Lists.newArrayList(s1, s1), new SubjectProvenanceComparator()))) + .min(Lists.newArrayList(s1, s2), new SubjectProvenanceComparator()))) .values()); r.setSubject(subjects); } @@ -333,7 +342,7 @@ public class GraphCleaningFunctions extends CleaningFunctions { if (Objects.isNull(i.getHostedby()) || StringUtils.isBlank(i.getHostedby().getKey())) { i.setHostedby(ModelConstants.UNKNOWN_REPOSITORY); } - if (Objects.isNull(i.getRefereed())) { + if (Objects.isNull(i.getRefereed()) || StringUtils.isBlank(i.getRefereed().getClassid())) { i.setRefereed(qualifier("0000", "Unknown", ModelConstants.DNET_REVIEW_LEVELS)); } if (Objects.nonNull(i.getDateofacceptance())) { diff --git a/dhp-common/src/test/java/eu/dnetlib/dhp/oa/merge/AuthorMergerTest.java b/dhp-common/src/test/java/eu/dnetlib/dhp/oa/merge/AuthorMergerTest.java deleted file mode 100644 index 3a7a41a1b..000000000 --- a/dhp-common/src/test/java/eu/dnetlib/dhp/oa/merge/AuthorMergerTest.java +++ /dev/null @@ -1,100 +0,0 @@ - -package eu.dnetlib.dhp.oa.merge; - -import java.io.BufferedReader; -import java.io.FileReader; -import java.io.IOException; -import java.nio.file.Paths; -import java.util.ArrayList; -import java.util.List; -import java.util.stream.Collectors; - -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeEach; -import org.junit.jupiter.api.Test; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.schema.oaf.Author; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; -import eu.dnetlib.pace.util.MapDocumentUtil; -import scala.Tuple2; - -class AuthorMergerTest { - - private String publicationsBasePath; - - private List> authors; - - @BeforeEach - public void setUp() throws Exception { - - publicationsBasePath = Paths - .get(AuthorMergerTest.class.getResource("/eu/dnetlib/dhp/oa/merge").toURI()) - .toFile() - .getAbsolutePath(); - - authors = readSample(publicationsBasePath + "/publications_with_authors.json", Publication.class) - .stream() - .map(p -> p._2().getAuthor()) - .collect(Collectors.toList()); - - } - - @Test - void mergeTest() { // used in the dedup: threshold set to 0.95 - - for (List authors1 : authors) { - System.out.println("List " + (authors.indexOf(authors1) + 1)); - for (Author author : authors1) { - System.out.println(authorToString(author)); - } - } - - List merge = AuthorMerger.merge(authors); - - System.out.println("Merge "); - for (Author author : merge) { - System.out.println(authorToString(author)); - } - - Assertions.assertEquals(7, merge.size()); - - } - - public List> readSample(String path, Class clazz) { - List> res = new ArrayList<>(); - BufferedReader reader; - try { - reader = new BufferedReader(new FileReader(path)); - String line = reader.readLine(); - while (line != null) { - res - .add( - new Tuple2<>( - MapDocumentUtil.getJPathString("$.id", line), - new ObjectMapper().readValue(line, clazz))); - // read next line - line = reader.readLine(); - } - reader.close(); - } catch (IOException e) { - e.printStackTrace(); - } - - return res; - } - - public String authorToString(Author a) { - - String print = "Fullname = "; - print += a.getFullname() + " pid = ["; - if (a.getPid() != null) - for (StructuredProperty sp : a.getPid()) { - print += sp.toComparableString() + " "; - } - print += "]"; - return print; - } -} diff --git a/dhp-common/src/test/resources/eu/dnetlib/dhp/oa/merge/publications_with_authors.json b/dhp-common/src/test/resources/eu/dnetlib/dhp/oa/merge/publications_with_authors.json deleted file mode 100644 index 600181ba5..000000000 --- a/dhp-common/src/test/resources/eu/dnetlib/dhp/oa/merge/publications_with_authors.json +++ /dev/null @@ -1,3 +0,0 @@ -{ "journal":{ "dataInfo":null, "conferenceplace":null, "issnPrinted":"0009-9260", "issnOnline":null, "issnLinking":null, "ep":"636", "iss":null, "sp":"632", "vol":"55", "edition":null, "conferencedate":null, "name":"Clinical Radiology" }, "measures":null, "author":[ { "rank":null, "fullname":"KARL TURETSCHEK", "affiliation":null, "pid":null, "surname":"TURETSCHEK", "name":"KARL" }, { "rank":null, "fullname":"WOLFGANG EBNER", "affiliation":null, "pid":null, "surname":"EBNER", "name":"WOLFGANG" }, { "rank":null, "fullname":"DOMINIK FLEISCHMANN", "affiliation":null, "pid":null, "surname":"FLEISCHMANN", "name":"DOMINIK" }, { "rank":null, "fullname":"PATRICK WUNDERBALDINGER", "affiliation":null, "pid":null, "surname":"WUNDERBALDINGER", "name":"PATRICK" }, { "rank":null, "fullname":"LUDWIG ERLACHER", "affiliation":null, "pid":null, "surname":"ERLACHER", "name":"LUDWIG" }, { "rank":null, "fullname":"THOMAS ZONTSICH", "affiliation":null, "pid":null, "surname":"ZONTSICH", "name":"THOMAS" }, { "rank":null, "fullname":"ALEXANDER A. BANKIER", "affiliation":null, "pid":null, "surname":"BANKIER", "name":"ALEXANDER A." } ], "resulttype":{ "classid":"publication", "schemeid":"dnet:result_typologies", "schemename":"dnet:result_typologies", "classname":"publication"}, "title":[ { "qualifier":{ "classid":"main title", "schemeid":"dnet:dataCite_title", "schemename":"dnet:dataCite_title", "classname":"main title" }, "dataInfo":null, "value":"Early Pulmonary Involvement in Ankylosing Spondylitis: Assessment With Thin-section CT" } ], "relevantdate":[ { "qualifier":{ "classid":"created", "schemeid":"dnet:dataCite_date", "schemename":"dnet:dataCite_date", "classname":"created" }, "dataInfo":null, "value":"2002-09-19T13:54:50Z" } ], "dateofacceptance":{ "dataInfo":null, "value":"2002-09-19T13:54:50Z" }, "publisher":{ "dataInfo":null, "value":"Elsevier BV" }, "embargoenddate":null, "fulltext":null, "contributor":null, "resourcetype":{ "classid":"0001", "schemeid":"dnet:dataCite_resource", "schemename":"dnet:dataCite_resource", "classname":"0001"}, "coverage":null, "bestaccessright":null, "externalReference":null, "format":null, "description":[ ], "source":[ { "dataInfo":null, "value":"Crossref" } ], "subject":[ { "qualifier":{ "classid":"keywords", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"keywords" }, "dataInfo":null, "value":"Radiology Nuclear Medicine and imaging" }, { "qualifier":{ "classid":"keywords", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"keywords" }, "dataInfo":null, "value":"General Medicine" } ], "language":null, "instance":[ { "processingchargecurrency":null, "refereed":null, "instancetype":{ "classid":"0001", "schemeid":"dnet:publication_resource", "schemename":"dnet:publication_resource", "classname":"Article" }, "hostedby":null, "distributionlocation":null, "processingchargeamount":null, "license":{ "dataInfo":null, "value":"https://www.elsevier.com/tdm/userlicense/1.0/" }, "accessright":{ "classid":"RESTRICTED", "schemeid":"dnet:access_modes", "schemename":"dnet:access_modes", "classname":"Restricted" }, "dateofacceptance":{ "dataInfo":null, "value":"2002-09-19T13:54:50Z" }, "collectedfrom":{ "dataInfo":null, "value":"Crossref", "key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2" }, "url":[ "https://api.elsevier.com/content/article/PII:S0009926000904987?httpAccept=text/xml", "https://api.elsevier.com/content/article/PII:S0009926000904987?httpAccept=text/plain", "http://dx.doi.org/10.1053/crad.2000.0498" ] } ], "context":null, "country":null, "originalId":[ "S0009926000904987", "10.1053/crad.2000.0498" ], "pid":[ { "qualifier":{ "classid":"doi", "schemeid":"dnet:pid_types", "schemename":"dnet:pid_types", "classname":"doi" }, "dataInfo":null, "value":"10.1053/crad.2000.0498" } ], "dateofcollection":"2020-02-06T20:40:22Z", "dateoftransformation":null, "oaiprovenance":null, "extraInfo":null, "id":"50|doiboost____::994b7e47b9e225ab6d5e14841cb45a7f", "collectedfrom":[ { "dataInfo":null, "value":"Crossref", "key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2" } ], "dataInfo":{ "trust":"0.9", "invisible":false, "inferred":false, "deletedbyinference":false, "inferenceprovenance":null, "provenanceaction":{ "classid":"sysimport:actionset", "schemeid":"dnet:provenanceActions", "schemename":"dnet:provenanceActions", "classname":"sysimport:actionset" } }, "lastupdatetimestamp":1581021622595 } -{ "journal":null, "measures":null, "author":[ { "rank":null, "fullname":"Dominik Fleischmann", "affiliation":null, "pid":[ { "qualifier":{ "classid":"ORCID", "schemeid":"dnet:pid_types", "schemename":"dnet:pid_types", "classname":"ORCID" }, "dataInfo":{ "trust":"0.91", "invisible":false, "inferred":false, "deletedbyinference":false, "inferenceprovenance":null, "provenanceaction":{ "classid":"sysimport:crosswalk:entityregistry", "schemeid":"dnet:provenanceActions", "schemename":"dnet:provenanceActions", "classname":"Harvested"} }, "value":"0000-0003-0715-0952" } ], "surname":"Fleischmann", "name":"Dominik" } ], "resulttype":{ "classid":"publication", "schemeid":"dnet:result_typologies", "schemename":"dnet:result_typologies", "classname":"publication"}, "title":[ ], "relevantdate":[ ], "dateofacceptance":null, "publisher":null, "embargoenddate":null, "fulltext":[ ], "contributor":[ ], "resourcetype":null, "coverage":[ ], "bestaccessright":null, "externalReference":[ ], "format":[ ], "description":null, "source":[ ], "subject":[ ], "language":null, "instance":[ ], "context":[ ], "country":[ ], "originalId":[ ], "pid":[ { "qualifier":{ "classid":"doi", "schemeid":"dnet:pid_types", "schemename":"dnet:pid_types", "classname":"doi"}, "dataInfo":null, "value":"10.1053/crad.2000.0498" } ], "dateofcollection":null, "dateoftransformation":null, "oaiprovenance":null, "extraInfo":[ ], "id":"50|doiboost____::994b7e47b9e225ab6d5e14841cb45a7f", "collectedfrom":[ { "dataInfo":null, "value":"ORCID", "key":"10|openaire____::806360c771262b4d6770e7cdf04b5c5a" } ], "dataInfo":{ "trust":"0.9", "invisible":false, "inferred":false, "deletedbyinference":false, "inferenceprovenance":null, "provenanceaction":{ "classid":"sysimport:actionset", "schemeid":"dnet:provenanceActions", "schemename":"dnet:provenanceActions", "classname":"sysimport:actionset" } }, "lastupdatetimestamp":null } -{ "journal":{ "dataInfo":null, "conferenceplace":null, "issnPrinted":"0009-9260", "issnOnline":null, "issnLinking":null, "ep":"636", "iss":"8", "sp":"632", "vol":"55", "edition":null, "conferencedate":null, "name":"Clinical Radiology" }, "measures":null, "author":[ { "rank":null, "fullname":"T. Zontsich", "affiliation":[ { "dataInfo":null, "value":"University of Vienna" } ], "pid":[ { "qualifier":{ "classid":"URL", "schemeid":"dnet:pid_types", "schemename":"dnet:pid_types", "classname":"URL"}, "dataInfo":null, "value":"https://academic.microsoft.com/#/detail/1966908432" } ], "surname":null, "name":null }, { "rank":null, "fullname":"L Erlacher", "affiliation":[ { "dataInfo":null, "value":"University of Vienna" } ], "pid":[ { "qualifier":{ "classid":"URL", "schemeid":"dnet:pid_types", "schemename":"dnet:pid_types", "classname":"URL"}, "dataInfo":null, "value":"https://academic.microsoft.com/#/detail/687931320" } ], "surname":null, "name":null }, { "rank":null, "fullname":"Dominik Fleischmann", "affiliation":[ { "dataInfo":null, "value":"University of Vienna" } ], "pid":[ { "qualifier":{ "classid":"URL", "schemeid":"dnet:pid_types", "schemename":"dnet:pid_types", "classname":"URL"}, "dataInfo":null, "value":"https://academic.microsoft.com/#/detail/2156559961" } ], "surname":null, "name":null }, { "rank":null, "fullname":"Alexander A. Bankier", "affiliation":[ { "dataInfo":null, "value":"University of Vienna" } ], "pid":[ { "qualifier":{ "classid":"URL", "schemeid":"dnet:pid_types", "schemename":"dnet:pid_types", "classname":"URL"}, "dataInfo":null, "value":"https://academic.microsoft.com/#/detail/1107971609" } ], "surname":null, "name":null }, { "rank":null, "fullname":"Patrick Wunderbaldinger", "affiliation":[ { "dataInfo":null, "value":"University of Vienna" } ], "pid":[ { "qualifier":{ "classid":"URL", "schemeid":"dnet:pid_types", "schemename":"dnet:pid_types", "classname":"URL" }, "dataInfo":null, "value":"https://academic.microsoft.com/#/detail/2422340537" } ], "surname":null, "name":null }, { "rank":null, "fullname":"Wolfgang Ebner", "affiliation":null, "pid":[ { "qualifier":{ "classid":"URL", "schemeid":"dnet:pid_types", "schemename":"dnet:pid_types", "classname":"URL" }, "dataInfo":null, "value":"https://academic.microsoft.com/#/detail/2186462571" } ], "surname":null, "name":null }, { "rank":null, "fullname":"K. Turetschek", "affiliation":[ { "dataInfo":null, "value":"University of Vienna" } ], "pid":[ { "qualifier":{ "classid":"URL", "schemeid":"dnet:pid_types", "schemename":"dnet:pid_types", "classname":"URL" }, "dataInfo":null, "value":"https://academic.microsoft.com/#/detail/321765676" } ], "surname":null, "name":null } ], "resulttype":{ "classid":"publication", "schemeid":"dnet:result_typologies", "schemename":"dnet:result_typologies", "classname":"publication" }, "title":[ { "qualifier":{ "classid":"main title", "schemeid":"dnet:dataCite_title", "schemename":"dnet:dataCite_title", "classname":"main title" }, "dataInfo":null, "value":"early pulmonary involvement in ankylosing spondylitis assessment with thin section ct" }, { "qualifier":{ "classid":"alternative title", "schemeid":"dnet:dataCite_title", "schemename":"dnet:dataCite_title", "classname":"alternative title" }, "dataInfo":null, "value":"Early pulmonary involvement in ankylosing spondylitis: assessment with thin-section CT." } ], "relevantdate":null, "dateofacceptance":{ "dataInfo":null, "value":"2000-08-01" }, "publisher":{ "dataInfo":null, "value":"Elsevier" }, "embargoenddate":null, "fulltext":null, "contributor":null, "resourcetype":null, "coverage":null, "bestaccessright":null, "externalReference":null, "format":null, "description":[ { "dataInfo":null, "value":"Abstract AIM: To determine the frequency and the distribution of early pulmonary lesions in patients with ankylosing spondylitis (AS) and a normal chest X-ray on thin-section CT and to correlate the CT findings with the results of pulmonary function tests and clinical data. MATERIALS AND METHODS: Twenty-five patients with clinically proven AS and no history of smoking underwent clinical examinations, pulmonary function tests (PFT), chest radiography, and thin-section CT. Four of 25 patients (16%), who had obvious signs on plain films suggestive of pre-existing disorders unrelated to AS were excluded. RESULTS: Fifteen of 21 patients (71%) had abnormalities on thin-section CT. The most frequent abnormalities were thickening of the interlobular septa in seven of 21 patients (33%), mild bronchial wall thickening in (6/21, 29%), pleural thickening and pleuropulmonary irregularities (both 29%) and linear septal thickening (6/21, 29%). In six patients there were no signs of pleuropulmonary involvement. Eight of 15 patients (53%) with abnormal and four of six patients (67%) with normal CT findings revealed mild restrictive lung function impairment. CONCLUSION: Patients with AS but a normal chest radiograph frequently have abnormalities on thin-section CT. As these abnormalities are usually subtle and their extent does not correlate with functional and clinical data, the overall routine impact of thin-section CT in the diagnosis of AS is limited. Turetschek, K , (2000) Clinical Radiology53, 632–636." } ], "source":[ { "dataInfo":null, "value":null } ], "subject":[ { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":null, "value":"Complication" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":null, "value":"Chest radiograph" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":{ "trust":"0.580897", "invisible":false, "inferred":false, "deletedbyinference":false, "inferenceprovenance":null, "provenanceaction":{ "classid":"sysimport:actionset", "schemeid":"dnet:provenanceActions", "schemename":"dnet:provenanceActions", "classname":"sysimport:actionset" } }, "value":"medicine.diagnostic_test" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":{ "trust":"0.580897", "invisible":false, "inferred":false, "deletedbyinference":false, "inferenceprovenance":null, "provenanceaction":{ "classid":"sysimport:actionset", "schemeid":"dnet:provenanceActions", "schemename":"dnet:provenanceActions", "classname":"sysimport:actionset" } }, "value":"medicine" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":null, "value":"In patient" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":null, "value":"Radiography" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":{ "trust":"0.4582326", "invisible":false, "inferred":false, "deletedbyinference":false, "inferenceprovenance":null, "provenanceaction":{ "classid":"sysimport:actionset", "schemeid":"dnet:provenanceActions", "schemename":"dnet:provenanceActions", "classname":"sysimport:actionset" } }, "value":"business.industry" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":{ "trust":"0.4582326", "invisible":false, "inferred":false, "deletedbyinference":false, "inferenceprovenance":null, "provenanceaction":{ "classid":"sysimport:actionset", "schemeid":"dnet:provenanceActions", "schemename":"dnet:provenanceActions", "classname":"sysimport:actionset" } }, "value":"business" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":null, "value":"Thin section ct" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":null, "value":"Respiratory disease" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":{ "trust":"0.49358836", "invisible":false, "inferred":false, "deletedbyinference":false, "inferenceprovenance":null, "provenanceaction":{ "classid":"sysimport:actionset", "schemeid":"dnet:provenanceActions", "schemename":"dnet:provenanceActions", "classname":"sysimport:actionset" } }, "value":"medicine.disease" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":{ "trust":"0.49358836", "invisible":false, "inferred":false, "deletedbyinference":false, "inferenceprovenance":null, "provenanceaction":{ "classid":"sysimport:actionset", "schemeid":"dnet:provenanceActions", "schemename":"dnet:provenanceActions", "classname":"sysimport:actionset" } }, "value":"medicine" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":null, "value":"Ankylosing spondylitis" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":{ "trust":"0.49937168", "invisible":false, "inferred":false, "deletedbyinference":false, "inferenceprovenance":null, "provenanceaction":{ "classid":"sysimport:actionset", "schemeid":"dnet:provenanceActions", "schemename":"dnet:provenanceActions", "classname":"sysimport:actionset" } }, "value":"medicine.disease" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":{ "trust":"0.49937168", "invisible":false, "inferred":false, "deletedbyinference":false, "inferenceprovenance":null, "provenanceaction":{ "classid":"sysimport:actionset", "schemeid":"dnet:provenanceActions", "schemename":"dnet:provenanceActions", "classname":"sysimport:actionset" } }, "value":"medicine" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":null, "value":"Radiology" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":{ "trust":"0.4573571", "invisible":false, "inferred":false, "deletedbyinference":false, "inferenceprovenance":null, "provenanceaction":{ "classid":"sysimport:actionset", "schemeid":"dnet:provenanceActions", "schemename":"dnet:provenanceActions", "classname":"sysimport:actionset" } }, "value":"medicine.medical_specialty" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":{ "trust":"0.4573571", "invisible":false, "inferred":false, "deletedbyinference":false, "inferenceprovenance":null, "provenanceaction":{ "classid":"sysimport:actionset", "schemeid":"dnet:provenanceActions", "schemename":"dnet:provenanceActions", "classname":"sysimport:actionset" } }, "value":"medicine" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":null, "value":"Medicine" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":{ "trust":"0.40295774", "invisible":false, "inferred":false, "deletedbyinference":false, "inferenceprovenance":null, "provenanceaction":{ "classid":"sysimport:actionset", "schemeid":"dnet:provenanceActions", "schemename":"dnet:provenanceActions", "classname":"sysimport:actionset" } }, "value":"business.industry" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":{ "trust":"0.40295774", "invisible":false, "inferred":false, "deletedbyinference":false, "inferenceprovenance":null, "provenanceaction":{ "classid":"sysimport:actionset", "schemeid":"dnet:provenanceActions", "schemename":"dnet:provenanceActions", "classname":"sysimport:actionset" } }, "value":"business" }, { "qualifier":{ "classid":"MAG", "schemeid":"dnet:subject_classification_typologies", "schemename":"dnet:subject_classification_typologies", "classname":"Microsoft Academic Graph classification" }, "dataInfo":null, "value":"Pulmonary function testing" } ], "language":null, "instance":[ { "processingchargecurrency":null, "refereed":null, "instancetype":null, "hostedby":null, "distributionlocation":null, "processingchargeamount":null, "license":null, "accessright":null, "dateofacceptance":null, "collectedfrom":{ "dataInfo":null, "value":"Microsoft Academic Graph", "key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a" }, "url":[ "https://www.ncbi.nlm.nih.gov/pubmed/10964736", "https://www.sciencedirect.com/science/article/pii/S0009926000904987", "https://academic.microsoft.com/#/detail/1990704599" ] } ], "context":null, "country":null, "originalId":[ "1990704599", "10.1053/crad.2000.0498" ], "pid":[ { "qualifier":{ "classid":"doi", "schemeid":"dnet:pid_types", "schemename":"dnet:pid_types", "classname":"doi" }, "dataInfo":null, "value":"10.1053/crad.2000.0498" } ], "dateofcollection":null, "dateoftransformation":null, "oaiprovenance":null, "extraInfo":null, "id":"50|doiboost____::994b7e47b9e225ab6d5e14841cb45a7f", "collectedfrom":[ { "dataInfo":null, "value":"Microsoft Academic Graph", "key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a" } ], "dataInfo":{ "trust":"0.9", "invisible":false, "inferred":false, "deletedbyinference":false, "inferenceprovenance":null, "provenanceaction":{ "classid":"sysimport:actionset", "schemeid":"dnet:provenanceActions", "schemename":"dnet:provenanceActions", "classname":"sysimport:actionset"} }, "lastupdatetimestamp":null } \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala index c29614d33..a7ad9e2d6 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala @@ -49,7 +49,7 @@ object DataciteToOAFTransformation { /** This method should skip record if json contains invalid text * defined in file datacite_filter * - * @param record : unparsed datacite record + * @param record : not parsed Datacite record * @param json : parsed record * @return True if the record should be skipped */ @@ -98,6 +98,10 @@ object DataciteToOAFTransformation { } + /** This utility method indicates whether the embargo date has been reached + * @param embargo_end_date + * @return True if the embargo date has been reached, false otherwise + */ def embargo_end(embargo_end_date: String): Boolean = { val dt = LocalDate.parse(embargo_end_date, DateTimeFormatter.ofPattern("[yyyy-MM-dd]")) val td = LocalDate.now() @@ -142,6 +146,21 @@ object DataciteToOAFTransformation { } } + /** * + * Use the vocabulary dnet:publication_resource to find a synonym to one of these terms and get the instance.type. + * Using the dnet:result_typologies vocabulary, we look up the instance.type synonym + * to generate one of the following main entities: + * - publication + * - dataset + * - software + * - otherresearchproduct + * + * @param resourceType + * @param resourceTypeGeneral + * @param schemaOrg + * @param vocabularies + * @return + */ def getTypeQualifier( resourceType: String, resourceTypeGeneral: String, @@ -330,6 +349,7 @@ object DataciteToOAFTransformation { if (result == null) return List() + // DOI is mapped on a PID inside a Instance object val doi_q = OafMapperUtils.qualifier( "doi", "doi", @@ -338,6 +358,8 @@ object DataciteToOAFTransformation { ) val pid = OafMapperUtils.structuredProperty(doi, doi_q, dataInfo) result.setPid(List(pid).asJava) + + // This identifiere will be replaced in a second moment using the PID logic generation result.setId(OafMapperUtils.createOpenaireId(50, s"datacite____::$doi", true)) result.setOriginalId(List(doi).asJava) @@ -386,6 +408,10 @@ object DataciteToOAFTransformation { a } + if (authors == null || authors.isEmpty || !authors.exists(a => a != null)) + return List() + result.setAuthor(authors.asJava) + val titles: List[TitleType] = (json \\ "titles").extractOrElse[List[TitleType]](List()) result.setTitle( @@ -409,10 +435,6 @@ object DataciteToOAFTransformation { .asJava ) - if (authors == null || authors.isEmpty || !authors.exists(a => a != null)) - return List() - result.setAuthor(authors.asJava) - val dates = (json \\ "dates").extract[List[DateType]] val publication_year = (json \\ "publicationYear").extractOrElse[String](null) diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkCreateBaselineDataFrame.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkCreateBaselineDataFrame.scala index 9c55ec7be..87116f00a 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkCreateBaselineDataFrame.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkCreateBaselineDataFrame.scala @@ -27,7 +27,7 @@ object SparkCreateBaselineDataFrame { def requestBaseLineUpdatePage(maxFile: String): List[(String, String)] = { val data = requestPage("https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/") - val result = data.lines + val result = data.linesWithSeparators.map(l =>l.stripLineEnd) .filter(l => l.startsWith("") diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/cnr_explora_tr.xslt b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/cnr_explora_tr.xslt index 78b167fde..33770ce47 100644 --- a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/cnr_explora_tr.xslt +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/cnr_explora_tr.xslt @@ -130,7 +130,7 @@ - + diff --git a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala index 827d23e72..24caaa553 100644 --- a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala +++ b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala @@ -63,7 +63,7 @@ class BioScholixTest extends AbstractVocabularyTest { val records: String = Source .fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed_dump")) .mkString - val r: List[Oaf] = records.lines.toList + val r: List[Oaf] = records.linesWithSeparators.map(l =>l.stripLineEnd).toList .map(s => mapper.readValue(s, classOf[PMArticle])) .map(a => PubMedToOaf.convert(a, vocabularies)) assertEquals(10, r.size) @@ -173,9 +173,9 @@ class BioScholixTest extends AbstractVocabularyTest { val records: String = Source .fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pdb_dump")) .mkString - records.lines.foreach(s => assertTrue(s.nonEmpty)) + records.linesWithSeparators.map(l =>l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty)) - val result: List[Oaf] = records.lines.toList.flatMap(o => BioDBToOAF.pdbTOOaf(o)) + val result: List[Oaf] = records.linesWithSeparators.map(l =>l.stripLineEnd).toList.flatMap(o => BioDBToOAF.pdbTOOaf(o)) assertTrue(result.nonEmpty) result.foreach(r => assertNotNull(r)) @@ -194,9 +194,9 @@ class BioScholixTest extends AbstractVocabularyTest { val records: String = Source .fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/uniprot_dump")) .mkString - records.lines.foreach(s => assertTrue(s.nonEmpty)) + records.linesWithSeparators.map(l =>l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty)) - val result: List[Oaf] = records.lines.toList.flatMap(o => BioDBToOAF.uniprotToOAF(o)) + val result: List[Oaf] = records.linesWithSeparators.map(l =>l.stripLineEnd).toList.flatMap(o => BioDBToOAF.uniprotToOAF(o)) assertTrue(result.nonEmpty) result.foreach(r => assertNotNull(r)) @@ -239,9 +239,9 @@ class BioScholixTest extends AbstractVocabularyTest { val records: String = Source .fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/crossref_links")) .mkString - records.lines.foreach(s => assertTrue(s.nonEmpty)) + records.linesWithSeparators.map(l =>l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty)) - val result: List[Oaf] = records.lines.map(s => BioDBToOAF.crossrefLinksToOaf(s)).toList + val result: List[Oaf] = records.linesWithSeparators.map(l =>l.stripLineEnd).map(s => BioDBToOAF.crossrefLinksToOaf(s)).toList assertNotNull(result) assertTrue(result.nonEmpty) @@ -276,11 +276,11 @@ class BioScholixTest extends AbstractVocabularyTest { getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/scholix_resolved") ) .mkString - records.lines.foreach(s => assertTrue(s.nonEmpty)) + records.linesWithSeparators.map(l =>l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty)) implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats - val l: List[ScholixResolved] = records.lines.map { input => + val l: List[ScholixResolved] = records.linesWithSeparators.map(l =>l.stripLineEnd).map { input => lazy val json = parse(input) json.extract[ScholixResolved] }.toList diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java index d345cf98f..7637cde93 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java @@ -1,10 +1,12 @@ package eu.dnetlib.dhp.oa.dedup; -import java.util.Collection; -import java.util.Iterator; -import java.util.List; +import java.lang.reflect.InvocationTargetException; +import java.util.*; +import java.util.stream.Collectors; +import org.apache.commons.beanutils.BeanUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapGroupsFunction; import org.apache.spark.sql.Dataset; @@ -15,6 +17,7 @@ import com.fasterxml.jackson.databind.DeserializationFeature; import com.fasterxml.jackson.databind.ObjectMapper; import com.google.common.collect.Lists; +import eu.dnetlib.dhp.oa.dedup.model.Identifier; import eu.dnetlib.dhp.oa.merge.AuthorMerger; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; @@ -74,33 +77,39 @@ public class DedupRecordFactory { public static T entityMerger( String id, Iterator> entities, long ts, DataInfo dataInfo, Class clazz) - throws IllegalAccessException, InstantiationException { + throws IllegalAccessException, InstantiationException, InvocationTargetException { - T entity = clazz.newInstance(); - entity.setDataInfo(dataInfo); + final Comparator> idComparator = new IdentifierComparator<>(); + + final LinkedList entityList = Lists + .newArrayList(entities) + .stream() + .map(t -> Identifier.newInstance(t._2())) + .sorted(idComparator) + .map(Identifier::getEntity) + .collect(Collectors.toCollection(LinkedList::new)); + + final T entity = clazz.newInstance(); + final T first = entityList.removeFirst(); + + BeanUtils.copyProperties(entity, first); - final Collection dates = Lists.newArrayList(); final List> authors = Lists.newArrayList(); - entities - .forEachRemaining( - t -> { - T duplicate = t._2(); - + entityList + .forEach( + duplicate -> { entity.mergeFrom(duplicate); if (ModelSupport.isSubClass(duplicate, Result.class)) { Result r1 = (Result) duplicate; - if (r1.getAuthor() != null && !r1.getAuthor().isEmpty()) - authors.add(r1.getAuthor()); - if (r1.getDateofacceptance() != null) - dates.add(r1.getDateofacceptance().getValue()); + Optional + .ofNullable(r1.getAuthor()) + .ifPresent(a -> authors.add(a)); } - }); // set authors and date if (ModelSupport.isSubClass(entity, Result.class)) { - ((Result) entity).setDateofacceptance(DatePicker.pick(dates)); ((Result) entity).setAuthor(AuthorMerger.merge(authors)); } diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/IdGenerator.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/IdGenerator.java index 81cd30f88..7e0d66062 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/IdGenerator.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/IdGenerator.java @@ -18,6 +18,10 @@ public class IdGenerator implements Serializable { if (pids == null || pids.isEmpty()) return defaultID; + return generateId(pids); + } + + private static String generateId(List> pids) { Identifier bp = pids .stream() .min(Identifier::compareTo) diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/IdentifierComparator.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/IdentifierComparator.java new file mode 100644 index 000000000..ba4e31128 --- /dev/null +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/IdentifierComparator.java @@ -0,0 +1,81 @@ + +package eu.dnetlib.dhp.oa.dedup; + +import java.util.Comparator; +import java.util.List; +import java.util.Optional; +import java.util.Set; +import java.util.stream.Collectors; + +import com.google.common.collect.Sets; + +import eu.dnetlib.dhp.oa.dedup.model.Identifier; +import eu.dnetlib.dhp.schema.common.EntityType; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.DataInfo; +import eu.dnetlib.dhp.schema.oaf.KeyValue; +import eu.dnetlib.dhp.schema.oaf.OafEntity; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; +import eu.dnetlib.dhp.schema.oaf.utils.PidComparator; +import eu.dnetlib.dhp.schema.oaf.utils.PidType; + +public class IdentifierComparator implements Comparator> { + + public static int compareIdentifiers(Identifier left, Identifier right) { + return new IdentifierComparator<>().compare(left, right); + } + + @Override + public int compare(Identifier left, Identifier i) { + // priority in comparisons: 1) pidtype, 2) collectedfrom (depending on the entity type) , 3) date 4) + // alphabetical order of the originalID + + Set lKeys = Optional + .ofNullable(left.getCollectedFrom()) + .map(c -> c.stream().map(KeyValue::getKey).collect(Collectors.toSet())) + .orElse(Sets.newHashSet()); + + final Optional> cf = Optional.ofNullable(i.getCollectedFrom()); + Set rKeys = cf + .map(c -> c.stream().map(KeyValue::getKey).collect(Collectors.toSet())) + .orElse(Sets.newHashSet()); + + if (left.getPidType().compareTo(i.getPidType()) == 0) { // same type + if (left.getEntityType() == EntityType.publication) { + if (isFromDatasourceID(lKeys, ModelConstants.CROSSREF_ID) + && !isFromDatasourceID(rKeys, ModelConstants.CROSSREF_ID)) + return -1; + if (isFromDatasourceID(rKeys, ModelConstants.CROSSREF_ID) + && !isFromDatasourceID(lKeys, ModelConstants.CROSSREF_ID)) + return 1; + } + if (left.getEntityType() == EntityType.dataset) { + if (isFromDatasourceID(lKeys, ModelConstants.DATACITE_ID) + && !isFromDatasourceID(rKeys, ModelConstants.DATACITE_ID)) + return -1; + if (isFromDatasourceID(rKeys, ModelConstants.DATACITE_ID) + && !isFromDatasourceID(lKeys, ModelConstants.DATACITE_ID)) + return 1; + } + + if (left.getDate().compareTo(i.getDate()) == 0) {// same date + // we need to take the alphabetically lower id + return left.getOriginalID().compareTo(i.getOriginalID()); + } else + // we need to take the elder date + return left.getDate().compareTo(i.getDate()); + } else { + return new PidComparator<>(left.getEntity()).compare(toSP(left.getPidType()), toSP(i.getPidType())); + } + } + + public boolean isFromDatasourceID(Set collectedFrom, String dsId) { + return collectedFrom.contains(dsId); + } + + private StructuredProperty toSP(PidType pidType) { + return OafMapperUtils.structuredProperty("", pidType.toString(), pidType.toString(), "", "", new DataInfo()); + } + +} diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/model/Identifier.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/model/Identifier.java index a25a853ef..0cba4fc3b 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/model/Identifier.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/model/Identifier.java @@ -11,6 +11,7 @@ import org.apache.commons.lang3.StringUtils; import com.google.common.collect.Sets; import eu.dnetlib.dhp.oa.dedup.DatePicker; +import eu.dnetlib.dhp.oa.dedup.IdentifierComparator; import eu.dnetlib.dhp.schema.common.EntityType; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelSupport; @@ -83,60 +84,12 @@ public class Identifier implements Serializable, Comparable return entity.getId(); } - private PidType getPidType() { + public PidType getPidType() { return PidType.tryValueOf(StringUtils.substringBefore(StringUtils.substringAfter(entity.getId(), "|"), "_")); } @Override public int compareTo(Identifier i) { - // priority in comparisons: 1) pidtype, 2) collectedfrom (depending on the entity type) , 3) date 4) - // alphabetical order of the originalID - - Set lKeys = Optional - .ofNullable(getCollectedFrom()) - .map(c -> c.stream().map(KeyValue::getKey).collect(Collectors.toSet())) - .orElse(Sets.newHashSet()); - - final Optional> cf = Optional.ofNullable(i.getCollectedFrom()); - Set rKeys = cf - .map(c -> c.stream().map(KeyValue::getKey).collect(Collectors.toSet())) - .orElse(Sets.newHashSet()); - - if (this.getPidType().compareTo(i.getPidType()) == 0) { // same type - if (getEntityType() == EntityType.publication) { - if (isFromDatasourceID(lKeys, ModelConstants.CROSSREF_ID) - && !isFromDatasourceID(rKeys, ModelConstants.CROSSREF_ID)) - return -1; - if (isFromDatasourceID(rKeys, ModelConstants.CROSSREF_ID) - && !isFromDatasourceID(lKeys, ModelConstants.CROSSREF_ID)) - return 1; - } - if (getEntityType() == EntityType.dataset) { - if (isFromDatasourceID(lKeys, ModelConstants.DATACITE_ID) - && !isFromDatasourceID(rKeys, ModelConstants.DATACITE_ID)) - return -1; - if (isFromDatasourceID(rKeys, ModelConstants.DATACITE_ID) - && !isFromDatasourceID(lKeys, ModelConstants.DATACITE_ID)) - return 1; - } - - if (this.getDate().compareTo(i.getDate()) == 0) {// same date - // we need to take the alphabetically lower id - return this.getOriginalID().compareTo(i.getOriginalID()); - } else - // we need to take the elder date - return this.getDate().compareTo(i.getDate()); - } else { - return new PidComparator<>(getEntity()).compare(toSP(getPidType()), toSP(i.getPidType())); - } - - } - - private StructuredProperty toSP(PidType pidType) { - return OafMapperUtils.structuredProperty("", pidType.toString(), pidType.toString(), "", "", new DataInfo()); - } - - public boolean isFromDatasourceID(Set collectedFrom, String dsId) { - return collectedFrom.contains(dsId); + return IdentifierComparator.compareIdentifiers(this, i); } } diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java index aa3722ce5..c9cfb8cb2 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java @@ -7,6 +7,7 @@ import java.io.BufferedReader; import java.io.FileReader; import java.io.IOException; import java.io.Serializable; +import java.lang.reflect.InvocationTargetException; import java.nio.file.Paths; import java.util.*; import java.util.stream.Collectors; @@ -54,7 +55,7 @@ class EntityMergerTest implements Serializable { } @Test - void softwareMergerTest() throws InstantiationException, IllegalAccessException { + void softwareMergerTest() throws InstantiationException, IllegalAccessException, InvocationTargetException { List> softwares = readSample( testEntityBasePath + "/software_merge.json", Software.class); @@ -69,7 +70,7 @@ class EntityMergerTest implements Serializable { } @Test - void publicationMergerTest() throws InstantiationException, IllegalAccessException { + void publicationMergerTest() throws InstantiationException, IllegalAccessException, InvocationTargetException { Publication pub_merged = DedupRecordFactory .entityMerger(dedupId, publications.iterator(), 0, dataInfo, Publication.class); @@ -134,7 +135,7 @@ class EntityMergerTest implements Serializable { } @Test - void publicationMergerTest2() throws InstantiationException, IllegalAccessException { + void publicationMergerTest2() throws InstantiationException, IllegalAccessException, InvocationTargetException { Publication pub_merged = DedupRecordFactory .entityMerger(dedupId, publications2.iterator(), 0, dataInfo, Publication.class); @@ -146,7 +147,7 @@ class EntityMergerTest implements Serializable { } @Test - void publicationMergerTest3() throws InstantiationException, IllegalAccessException { + void publicationMergerTest3() throws InstantiationException, IllegalAccessException, InvocationTargetException { Publication pub_merged = DedupRecordFactory .entityMerger(dedupId, publications3.iterator(), 0, dataInfo, Publication.class); @@ -156,7 +157,8 @@ class EntityMergerTest implements Serializable { } @Test - void publicationMergerTest4() throws InstantiationException, IllegalStateException, IllegalAccessException { + void publicationMergerTest4() + throws InstantiationException, IllegalStateException, IllegalAccessException, InvocationTargetException { Publication pub_merged = DedupRecordFactory .entityMerger(dedupId, publications4.iterator(), 0, dataInfo, Publication.class); @@ -166,7 +168,8 @@ class EntityMergerTest implements Serializable { } @Test - void publicationMergerTest5() throws InstantiationException, IllegalStateException, IllegalAccessException { + void publicationMergerTest5() + throws InstantiationException, IllegalStateException, IllegalAccessException, InvocationTargetException { System.out .println( diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java index 9c9ec43d5..3de14f577 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java @@ -4,8 +4,7 @@ package eu.dnetlib.dhp.oa.dedup; import static java.nio.file.Files.createTempDirectory; import static org.apache.spark.sql.functions.count; -import static org.junit.jupiter.api.Assertions.assertEquals; -import static org.junit.jupiter.api.Assertions.assertTrue; +import static org.junit.jupiter.api.Assertions.*; import static org.mockito.Mockito.lenient; import java.io.File; @@ -14,7 +13,11 @@ import java.io.IOException; import java.io.Serializable; import java.net.URISyntaxException; import java.nio.file.Paths; +import java.util.HashSet; import java.util.List; +import java.util.Optional; +import java.util.Set; +import java.util.stream.Collectors; import org.apache.commons.io.FileUtils; import org.apache.commons.io.IOUtils; @@ -35,10 +38,13 @@ import org.mockito.Mock; import org.mockito.Mockito; import org.mockito.junit.jupiter.MockitoExtension; +import com.fasterxml.jackson.databind.DeserializationFeature; import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.common.collect.Sets; import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import eu.dnetlib.pace.util.MapDocumentUtil; @@ -105,57 +111,27 @@ public class SparkDedupTest implements Serializable { lenient() .when(isLookUpService.getResourceProfileByQuery(Mockito.contains(testActionSetId))) - .thenReturn( - IOUtils - .toString( - SparkDedupTest.class - .getResourceAsStream( - "/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml"))); + .thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml")); lenient() .when(isLookUpService.getResourceProfileByQuery(Mockito.contains("organization"))) - .thenReturn( - IOUtils - .toString( - SparkDedupTest.class - .getResourceAsStream( - "/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json"))); + .thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json")); lenient() .when(isLookUpService.getResourceProfileByQuery(Mockito.contains("publication"))) - .thenReturn( - IOUtils - .toString( - SparkDedupTest.class - .getResourceAsStream( - "/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json"))); + .thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json")); lenient() .when(isLookUpService.getResourceProfileByQuery(Mockito.contains("software"))) - .thenReturn( - IOUtils - .toString( - SparkDedupTest.class - .getResourceAsStream( - "/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json"))); + .thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json")); lenient() .when(isLookUpService.getResourceProfileByQuery(Mockito.contains("dataset"))) - .thenReturn( - IOUtils - .toString( - SparkDedupTest.class - .getResourceAsStream( - "/eu/dnetlib/dhp/dedup/conf/ds.curr.conf.json"))); + .thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/conf/ds.curr.conf.json")); lenient() .when(isLookUpService.getResourceProfileByQuery(Mockito.contains("otherresearchproduct"))) - .thenReturn( - IOUtils - .toString( - SparkDedupTest.class - .getResourceAsStream( - "/eu/dnetlib/dhp/dedup/conf/orp.curr.conf.json"))); + .thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/conf/orp.curr.conf.json")); } @Test @@ -163,11 +139,7 @@ public class SparkDedupTest implements Serializable { void createSimRelsTest() throws Exception { ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - SparkCreateSimRels.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json"))); + classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json")); parser .parseArgument( @@ -207,7 +179,7 @@ public class SparkDedupTest implements Serializable { .count(); assertEquals(3076, orgs_simrel); - assertEquals(7040, pubs_simrel); + assertEquals(7046, pubs_simrel); assertEquals(336, sw_simrel); assertEquals(442, ds_simrel); assertEquals(6784, orp_simrel); @@ -223,11 +195,7 @@ public class SparkDedupTest implements Serializable { void whitelistSimRelsTest() throws Exception { ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - SparkWhitelistSimRels.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/dedup/whitelistSimRels_parameters.json"))); + classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/whitelistSimRels_parameters.json")); parser .parseArgument( @@ -264,7 +232,7 @@ public class SparkDedupTest implements Serializable { // entities simrels supposed to be equal to the number of previous step (no rels in whitelist) assertEquals(3076, orgs_simrel); - assertEquals(7040, pubs_simrel); + assertEquals(7046, pubs_simrel); assertEquals(442, ds_simrel); assertEquals(6784, orp_simrel); // System.out.println("orgs_simrel = " + orgs_simrel); @@ -306,11 +274,7 @@ public class SparkDedupTest implements Serializable { void cutMergeRelsTest() throws Exception { ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - SparkCreateMergeRels.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json"))); + classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json")); parser .parseArgument( @@ -402,11 +366,7 @@ public class SparkDedupTest implements Serializable { void createMergeRelsTest() throws Exception { ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - SparkCreateMergeRels.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json"))); + classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json")); parser .parseArgument( @@ -427,10 +387,10 @@ public class SparkDedupTest implements Serializable { .read() .load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel") .count(); - long pubs_mergerel = spark + final Dataset pubs = spark .read() .load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel") - .count(); + .as(Encoders.bean(Relation.class)); long sw_mergerel = spark .read() .load(testOutputBasePath + "/" + testActionSetId + "/software_mergerel") @@ -445,8 +405,35 @@ public class SparkDedupTest implements Serializable { .load(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_mergerel") .count(); + final List merges = pubs + .filter("source == '50|doi_dedup___::d5021b53204e4fdeab6ff5d5bc468032'") + .collectAsList(); + assertEquals(3, merges.size()); + Set dups = Sets + .newHashSet( + "50|doi_________::3b1d0d8e8f930826665df9d6b82fbb73", + "50|doi_________::d5021b53204e4fdeab6ff5d5bc468032", + "50|arXiv_______::c93aeb433eb90ed7a86e29be00791b7c"); + merges.forEach(r -> { + assertEquals(ModelConstants.RESULT_RESULT, r.getRelType()); + assertEquals(ModelConstants.DEDUP, r.getSubRelType()); + assertEquals(ModelConstants.MERGES, r.getRelClass()); + assertTrue(dups.contains(r.getTarget())); + }); + + final List mergedIn = pubs + .filter("target == '50|doi_dedup___::d5021b53204e4fdeab6ff5d5bc468032'") + .collectAsList(); + assertEquals(3, mergedIn.size()); + mergedIn.forEach(r -> { + assertEquals(ModelConstants.RESULT_RESULT, r.getRelType()); + assertEquals(ModelConstants.DEDUP, r.getSubRelType()); + assertEquals(ModelConstants.IS_MERGED_IN, r.getRelClass()); + assertTrue(dups.contains(r.getSource())); + }); + assertEquals(1268, orgs_mergerel); - assertEquals(1444, pubs_mergerel); + assertEquals(1450, pubs.count()); assertEquals(286, sw_mergerel); assertEquals(472, ds_mergerel); assertEquals(738, orp_mergerel); @@ -463,11 +450,7 @@ public class SparkDedupTest implements Serializable { void createDedupRecordTest() throws Exception { ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - SparkCreateDedupRecord.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json"))); + classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json")); parser .parseArgument( new String[] { @@ -483,12 +466,18 @@ public class SparkDedupTest implements Serializable { new SparkCreateDedupRecord(parser, spark).run(isLookUpService); + final ObjectMapper mapper = new ObjectMapper() + .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); + + final Dataset pubs = spark + .read() + .textFile(testOutputBasePath + "/" + testActionSetId + "/publication_deduprecord") + .map( + (MapFunction) value -> mapper.readValue(value, Publication.class), + Encoders.bean(Publication.class)); long orgs_deduprecord = jsc .textFile(testOutputBasePath + "/" + testActionSetId + "/organization_deduprecord") .count(); - long pubs_deduprecord = jsc - .textFile(testOutputBasePath + "/" + testActionSetId + "/publication_deduprecord") - .count(); long sw_deduprecord = jsc .textFile(testOutputBasePath + "/" + testActionSetId + "/software_deduprecord") .count(); @@ -499,11 +488,13 @@ public class SparkDedupTest implements Serializable { .count(); assertEquals(86, orgs_deduprecord); - assertEquals(67, pubs_deduprecord); + assertEquals(68, pubs.count()); assertEquals(49, sw_deduprecord); assertEquals(97, ds_deduprecord); assertEquals(92, orp_deduprecord); + verifyRoot_1(mapper, pubs); + // System.out.println("orgs_deduprecord = " + orgs_deduprecord); // System.out.println("pubs_deduprecord = " + pubs_deduprecord); // System.out.println("sw_deduprecord = " + sw_deduprecord); @@ -511,16 +502,63 @@ public class SparkDedupTest implements Serializable { // System.out.println("orp_deduprecord = " + orp_deduprecord); } + private static void verifyRoot_1(ObjectMapper mapper, Dataset pubs) { + Publication root = pubs + .filter("id = '50|doi_dedup___::d5021b53204e4fdeab6ff5d5bc468032'") + .first(); + assertNotNull(root); + + final Dataset publication = spark + .read() + .textFile(DedupUtility.createEntityPath(testGraphBasePath, "publication")); + + Publication crossref_duplicate = publication + .map( + (MapFunction) value -> mapper.readValue(value, Publication.class), + Encoders.bean(Publication.class)) + .filter("id = '50|doi_________::d5021b53204e4fdeab6ff5d5bc468032'") + .collectAsList() + .get(0); + + assertEquals(crossref_duplicate.getJournal().getName(), root.getJournal().getName()); + assertEquals(crossref_duplicate.getJournal().getIssnPrinted(), root.getJournal().getIssnPrinted()); + assertEquals(crossref_duplicate.getPublisher().getValue(), root.getPublisher().getValue()); + + Set rootPids = root + .getPid() + .stream() + .map(StructuredProperty::getValue) + .collect(Collectors.toCollection(HashSet::new)); + Set dupPids = crossref_duplicate + .getPid() + .stream() + .map(StructuredProperty::getValue) + .collect(Collectors.toCollection(HashSet::new)); + + assertFalse(Sets.intersection(rootPids, dupPids).isEmpty()); + assertTrue(rootPids.contains("10.1109/jstqe.2022.3205716")); + + Optional instance_cr = root + .getInstance() + .stream() + .filter(i -> i.getCollectedfrom().getValue().equals("Crossref")) + .findFirst(); + assertTrue(instance_cr.isPresent()); + assertEquals("OPEN", instance_cr.get().getAccessright().getClassid()); + assertEquals("Open Access", instance_cr.get().getAccessright().getClassname()); + assertEquals(OpenAccessRoute.hybrid, instance_cr.get().getAccessright().getOpenAccessRoute()); + assertEquals( + "IEEE Journal of Selected Topics in Quantum Electronics", instance_cr.get().getHostedby().getValue()); + assertEquals("0001", instance_cr.get().getInstancetype().getClassid()); + assertEquals("Article", instance_cr.get().getInstancetype().getClassname()); + } + @Test @Order(6) void updateEntityTest() throws Exception { ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - SparkUpdateEntity.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json"))); + classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json")); parser .parseArgument( new String[] { @@ -587,7 +625,7 @@ public class SparkDedupTest implements Serializable { .distinct() .count(); - assertEquals(898, publications); + assertEquals(902, publications); assertEquals(839, organizations); assertEquals(100, projects); assertEquals(100, datasource); @@ -640,11 +678,7 @@ public class SparkDedupTest implements Serializable { void propagateRelationTest() throws Exception { ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - SparkPropagateRelation.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json"))); + classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json")); parser .parseArgument( new String[] { @@ -714,4 +748,12 @@ public class SparkDedupTest implements Serializable { public boolean isDeletedByInference(String s) { return s.contains("\"deletedbyinference\":true"); } + + private static String classPathResourceAsString(String path) throws IOException { + return IOUtils + .toString( + SparkDedupTest.class + .getResourceAsStream(path)); + } + } diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkOpenorgsDedupTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkOpenorgsDedupTest.java index 9312d83b1..88c28ab2f 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkOpenorgsDedupTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkOpenorgsDedupTest.java @@ -143,7 +143,7 @@ public class SparkOpenorgsDedupTest implements Serializable { .load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "organization")) .count(); - assertEquals(288, orgs_simrel); + assertEquals(290, orgs_simrel); } @Test @@ -172,7 +172,7 @@ public class SparkOpenorgsDedupTest implements Serializable { .load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "organization")) .count(); - assertEquals(324, orgs_simrel); + assertEquals(326, orgs_simrel); } @Test diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkPublicationRootsTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkPublicationRootsTest.java new file mode 100644 index 000000000..3cff836eb --- /dev/null +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkPublicationRootsTest.java @@ -0,0 +1,403 @@ + +package eu.dnetlib.dhp.oa.dedup; + +import static java.nio.file.Files.createTempDirectory; + +import static org.apache.spark.sql.functions.count; +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.Mockito.lenient; + +import java.io.File; +import java.io.IOException; +import java.io.Serializable; +import java.net.URISyntaxException; +import java.nio.file.Path; +import java.nio.file.Paths; +import java.util.*; +import java.util.stream.Collectors; + +import org.apache.commons.cli.ParseException; +import org.apache.commons.io.FileUtils; +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.FilterFunction; +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.SparkSession; +import org.junit.jupiter.api.*; +import org.junit.jupiter.api.extension.ExtendWith; +import org.mockito.Mock; +import org.mockito.Mockito; +import org.mockito.junit.jupiter.MockitoExtension; + +import com.fasterxml.jackson.databind.DeserializationFeature; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.common.collect.Sets; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; + +@ExtendWith(MockitoExtension.class) +@TestMethodOrder(MethodOrderer.OrderAnnotation.class) +public class SparkPublicationRootsTest implements Serializable { + + @Mock(serializable = true) + ISLookUpService isLookUpService; + + private static SparkSession spark; + private static String workingPath; + + private static String graphInputPath; + private static String graphOutputPath; + private static final String testActionSetId = "test-orchestrator"; + + private static Path testBaseTmpPath; + + private static final ObjectMapper MAPPER = new ObjectMapper() + .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); + + @BeforeAll + public static void init() throws IOException, URISyntaxException { + + testBaseTmpPath = createTempDirectory(SparkPublicationRootsTest.class.getSimpleName() + "-"); + + final File entitiesSources = Paths + .get(SparkPublicationRootsTest.class.getResource("/eu/dnetlib/dhp/dedup/root").toURI()) + .toFile(); + + FileUtils + .copyDirectory( + entitiesSources, + testBaseTmpPath.resolve("input").toFile()); + + workingPath = testBaseTmpPath.resolve("workingPath").toString(); + graphInputPath = testBaseTmpPath.resolve("input").resolve("entities").toString(); + graphOutputPath = testBaseTmpPath.resolve("output").toString(); + + FileUtils.deleteDirectory(new File(workingPath)); + FileUtils.deleteDirectory(new File(graphOutputPath)); + + final SparkConf conf = new SparkConf(); + conf.set("spark.sql.shuffle.partitions", "10"); + spark = SparkSession + .builder() + .appName(SparkPublicationRootsTest.class.getSimpleName()) + .master("local[*]") + .config(conf) + .getOrCreate(); + } + + @BeforeEach + public void setUp() throws IOException, ISLookUpException { + + lenient() + .when(isLookUpService.getResourceProfileByQuery(Mockito.contains(testActionSetId))) + .thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator_publication.xml")); + + lenient() + .when(isLookUpService.getResourceProfileByQuery(Mockito.contains("publication"))) + .thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json")); + } + + @AfterAll + public static void tearDown() throws IOException { + FileUtils.deleteDirectory(testBaseTmpPath.toFile()); + spark.close(); + } + + @Test + @Order(1) + void createSimRelsTest() throws Exception { + new SparkCreateSimRels(args( + "/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json", + new String[] { + "--graphBasePath", graphInputPath, + "--actionSetId", testActionSetId, + "--isLookUpUrl", "lookupurl", + "--workingPath", workingPath, + "--numPartitions", "5" + }), spark) + .run(isLookUpService); + + long pubs_simrel = spark + .read() + .load(DedupUtility.createSimRelPath(workingPath, testActionSetId, "publication")) + .count(); + + assertEquals(74, pubs_simrel); + } + + @Test + @Order(2) + void cutMergeRelsTest() throws Exception { + new SparkCreateMergeRels(args( + "/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json", + new String[] { + "--graphBasePath", graphInputPath, + "--actionSetId", testActionSetId, + "--isLookUpUrl", "lookupurl", + "--workingPath", workingPath, + "--cutConnectedComponent", "3" + }), spark) + .run(isLookUpService); + + long pubs_mergerel = spark + .read() + .load(workingPath + "/" + testActionSetId + "/publication_mergerel") + .as(Encoders.bean(Relation.class)) + .filter((FilterFunction) r -> r.getRelClass().equalsIgnoreCase("merges")) + .groupBy("source") + .agg(count("target").alias("cnt")) + .select("source", "cnt") + .where("cnt > 3") + .count(); + + assertEquals(0, pubs_mergerel); + + FileUtils.deleteDirectory(new File(workingPath + "/" + testActionSetId + "/publication_mergerel")); + } + + @Test + @Order(3) + void createMergeRelsTest() throws Exception { + new SparkCreateMergeRels(args( + "/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json", + new String[] { + "--graphBasePath", graphInputPath, + "--actionSetId", testActionSetId, + "--isLookUpUrl", "lookupurl", + "--workingPath", workingPath + }), spark) + .run(isLookUpService); + + final Dataset merges = spark + .read() + .load(workingPath + "/" + testActionSetId + "/publication_mergerel") + .as(Encoders.bean(Relation.class)); + + final List mergeList = merges + .filter("source == '50|doi_dedup___::d5021b53204e4fdeab6ff5d5bc468032'") + .collectAsList(); + assertEquals(3, mergeList.size()); + Set dups = Sets + .newHashSet( + "50|doi_________::3b1d0d8e8f930826665df9d6b82fbb73", + "50|doi_________::d5021b53204e4fdeab6ff5d5bc468032", + "50|arXiv_______::c93aeb433eb90ed7a86e29be00791b7c"); + mergeList.forEach(r -> { + assertEquals(ModelConstants.RESULT_RESULT, r.getRelType()); + assertEquals(ModelConstants.DEDUP, r.getSubRelType()); + assertEquals(ModelConstants.MERGES, r.getRelClass()); + assertTrue(dups.contains(r.getTarget())); + }); + + final List mergedIn = merges + .filter("target == '50|doi_dedup___::d5021b53204e4fdeab6ff5d5bc468032'") + .collectAsList(); + assertEquals(3, mergedIn.size()); + mergedIn.forEach(r -> { + assertEquals(ModelConstants.RESULT_RESULT, r.getRelType()); + assertEquals(ModelConstants.DEDUP, r.getSubRelType()); + assertEquals(ModelConstants.IS_MERGED_IN, r.getRelClass()); + assertTrue(dups.contains(r.getSource())); + }); + + assertEquals(32, merges.count()); + } + + @Test + @Order(4) + void createDedupRecordTest() throws Exception { + new SparkCreateDedupRecord(args( + "/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json", + new String[] { + "--graphBasePath", graphInputPath, + "--actionSetId", testActionSetId, + "--isLookUpUrl", "lookupurl", + "--workingPath", workingPath + }), spark) + .run(isLookUpService); + + final Dataset roots = spark + .read() + .textFile(workingPath + "/" + testActionSetId + "/publication_deduprecord") + .map(asEntity(Publication.class), Encoders.bean(Publication.class)); + + assertEquals(3, roots.count()); + + final Dataset pubs = spark + .read() + .textFile(DedupUtility.createEntityPath(graphInputPath, "publication")) + .map(asEntity(Publication.class), Encoders.bean(Publication.class)); + + verifyRoot_case_1(roots, pubs); + verifyRoot_case_2(roots, pubs); + verifyRoot_case_3(roots, pubs); + } + + private static void verifyRoot_case_1(Dataset roots, Dataset pubs) { + Publication root = roots + .filter("id = '50|doi_dedup___::d5021b53204e4fdeab6ff5d5bc468032'") + .first(); + assertNotNull(root); + + Publication crossref_duplicate = pubs + .filter("id = '50|doi_________::d5021b53204e4fdeab6ff5d5bc468032'") + .collectAsList() + .get(0); + + assertEquals(crossref_duplicate.getJournal().getName(), root.getJournal().getName()); + assertEquals(crossref_duplicate.getJournal().getIssnPrinted(), root.getJournal().getIssnPrinted()); + assertEquals(crossref_duplicate.getPublisher().getValue(), root.getPublisher().getValue()); + + Set rootPids = root + .getPid() + .stream() + .map(StructuredProperty::getValue) + .collect(Collectors.toCollection(HashSet::new)); + Set dupPids = crossref_duplicate + .getPid() + .stream() + .map(StructuredProperty::getValue) + .collect(Collectors.toCollection(HashSet::new)); + + assertFalse(Sets.intersection(rootPids, dupPids).isEmpty()); + assertTrue(rootPids.contains("10.1109/jstqe.2022.3205716")); + + Optional instance_cr = root + .getInstance() + .stream() + .filter(i -> i.getCollectedfrom().getValue().equals("Crossref")) + .findFirst(); + assertTrue(instance_cr.isPresent()); + assertEquals("OPEN", instance_cr.get().getAccessright().getClassid()); + assertEquals("Open Access", instance_cr.get().getAccessright().getClassname()); + assertEquals(OpenAccessRoute.hybrid, instance_cr.get().getAccessright().getOpenAccessRoute()); + assertEquals( + "IEEE Journal of Selected Topics in Quantum Electronics", instance_cr.get().getHostedby().getValue()); + assertEquals("0001", instance_cr.get().getInstancetype().getClassid()); + assertEquals("Article", instance_cr.get().getInstancetype().getClassname()); + } + + private void verifyRoot_case_2(Dataset roots, Dataset pubs) { + Publication root = roots + .filter("id = '50|doi_dedup___::18aff3b55fb6876466a5d4bd82434885'") + .first(); + assertNotNull(root); + + Publication crossref_duplicate = pubs + .filter("id = '50|doi_________::18aff3b55fb6876466a5d4bd82434885'") + .first(); + + // System.err.println(new ObjectMapper().writeValueAsString(root)); + + assertEquals(crossref_duplicate.getJournal().getName(), root.getJournal().getName()); + assertEquals(crossref_duplicate.getJournal().getIssnOnline(), root.getJournal().getIssnOnline()); + assertEquals(crossref_duplicate.getJournal().getVol(), root.getJournal().getVol()); + + assertEquals(crossref_duplicate.getPublisher().getValue(), root.getPublisher().getValue()); + + Set dups_cf = pubs + .collectAsList() + .stream() + .flatMap(p -> p.getCollectedfrom().stream()) + .map(KeyValue::getValue) + .collect(Collectors.toCollection(HashSet::new)); + + Set root_cf = root + .getCollectedfrom() + .stream() + .map(KeyValue::getValue) + .collect(Collectors.toCollection(HashSet::new)); + + assertTrue(Sets.difference(root_cf, dups_cf).isEmpty()); + } + + private void verifyRoot_case_3(Dataset roots, Dataset pubs) { + Publication root = roots + .filter("id = '50|dedup_wf_001::31ca734cc22181b704c4aa8fd050062a'") + .first(); + assertNotNull(root); + + Publication pivot_duplicate = pubs + .filter("id = '50|od_______166::31ca734cc22181b704c4aa8fd050062a'") + .first(); + + assertEquals(pivot_duplicate.getPublisher().getValue(), root.getPublisher().getValue()); + + Set dups_cf = pubs + .collectAsList() + .stream() + .flatMap(p -> p.getCollectedfrom().stream()) + .map(KeyValue::getValue) + .collect(Collectors.toCollection(HashSet::new)); + + Set root_cf = root + .getCollectedfrom() + .stream() + .map(KeyValue::getValue) + .collect(Collectors.toCollection(HashSet::new)); + + assertTrue(Sets.difference(root_cf, dups_cf).isEmpty()); + } + + @Test + @Order(6) + void updateEntityTest() throws Exception { + new SparkUpdateEntity(args( + "/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json", + new String[] { + "--graphBasePath", graphInputPath, + "--workingPath", workingPath, + "--dedupGraphPath", graphOutputPath + }), spark) + .run(isLookUpService); + + long publications = spark.read().textFile(graphOutputPath + "/publication").count(); + + long mergedPubs = spark + .read() + .load(workingPath + "/" + testActionSetId + "/publication_mergerel") + .as(Encoders.bean(Relation.class)) + .where("relClass=='merges'") + .map((MapFunction) Relation::getTarget, Encoders.STRING()) + .distinct() + .count(); + + assertEquals(19, publications); // 16 originals + 3 roots + + long deletedPubs = spark + .read() + .textFile(graphOutputPath + "/publication") + .map(asEntity(Publication.class), Encoders.bean(Publication.class)) + .filter("datainfo.deletedbyinference == true") + .map((MapFunction) OafEntity::getId, Encoders.STRING()) + .distinct() + .count(); + + assertEquals(mergedPubs, deletedPubs); + } + + private static String classPathResourceAsString(String path) throws IOException { + return IOUtils + .toString( + SparkPublicationRootsTest.class + .getResourceAsStream(path)); + } + + private static MapFunction asEntity(Class clazz) { + return value -> MAPPER.readValue(value, clazz); + } + + private ArgumentApplicationParser args(String paramSpecs, String[] args) throws IOException, ParseException { + ArgumentApplicationParser parser = new ArgumentApplicationParser(classPathResourceAsString(paramSpecs)); + parser.parseArgument(args); + return parser; + } + +} diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkPublicationRootsTest2.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkPublicationRootsTest2.java new file mode 100644 index 000000000..9afe1e34b --- /dev/null +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkPublicationRootsTest2.java @@ -0,0 +1,251 @@ + +package eu.dnetlib.dhp.oa.dedup; + +import static java.nio.file.Files.createTempDirectory; + +import static org.apache.spark.sql.functions.count; +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.Mockito.lenient; + +import java.io.File; +import java.io.IOException; +import java.io.Serializable; +import java.net.URISyntaxException; +import java.nio.file.Path; +import java.nio.file.Paths; +import java.util.HashSet; +import java.util.List; +import java.util.Optional; +import java.util.Set; +import java.util.stream.Collectors; + +import org.apache.commons.cli.ParseException; +import org.apache.commons.io.FileUtils; +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.FilterFunction; +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.SparkSession; +import org.junit.jupiter.api.*; +import org.junit.jupiter.api.extension.ExtendWith; +import org.mockito.Mock; +import org.mockito.Mockito; +import org.mockito.junit.jupiter.MockitoExtension; + +import com.fasterxml.jackson.databind.DeserializationFeature; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.common.collect.Sets; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; + +@ExtendWith(MockitoExtension.class) +@TestMethodOrder(MethodOrderer.OrderAnnotation.class) +public class SparkPublicationRootsTest2 implements Serializable { + + @Mock(serializable = true) + ISLookUpService isLookUpService; + private static SparkSession spark; + + private static String workingPath; + + private static String graphInputPath; + + private static String graphOutputPath; + + private static final String testActionSetId = "test-orchestrator"; + + private static Path testBaseTmpPath; + + private static final ObjectMapper MAPPER = new ObjectMapper() + .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); + + @BeforeAll + public static void init() throws IOException, URISyntaxException { + + testBaseTmpPath = createTempDirectory(SparkPublicationRootsTest2.class.getSimpleName() + "-"); + + final File entitiesSources = Paths + .get(SparkPublicationRootsTest2.class.getResource("/eu/dnetlib/dhp/dedup/root").toURI()) + .toFile(); + + FileUtils + .copyDirectory( + entitiesSources, + testBaseTmpPath.resolve("input").toFile()); + + FileUtils + .copyFileToDirectory( + Paths + .get( + SparkPublicationRootsTest2.class + .getResource( + "/eu/dnetlib/dhp/dedup/root/alterations/publication/publication_1.gz") + .toURI()) + .toFile(), + testBaseTmpPath.resolve("input").resolve("entities").resolve("publication").toFile()); + + workingPath = testBaseTmpPath.resolve("workingPath").toString(); + graphInputPath = testBaseTmpPath.resolve("input").resolve("entities").toString(); + graphOutputPath = testBaseTmpPath.resolve("output").toString(); + + final SparkConf conf = new SparkConf(); + conf.set("spark.sql.shuffle.partitions", "10"); + spark = SparkSession + .builder() + .appName(SparkPublicationRootsTest2.class.getSimpleName()) + .master("local[*]") + .config(conf) + .getOrCreate(); + } + + @BeforeEach + public void setUp() throws IOException, ISLookUpException { + + lenient() + .when(isLookUpService.getResourceProfileByQuery(Mockito.contains(testActionSetId))) + .thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator_publication.xml")); + + lenient() + .when(isLookUpService.getResourceProfileByQuery(Mockito.contains("publication"))) + .thenReturn(classPathResourceAsString("/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json")); + } + + @AfterAll + public static void tearDown() throws IOException { + FileUtils.deleteDirectory(testBaseTmpPath.toFile()); + } + + @Test + @Order(7) + void dedupAlteredDatasetTest() throws Exception { + + new SparkCreateSimRels(args( + "/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json", + new String[] { + "--graphBasePath", graphInputPath, + "--actionSetId", testActionSetId, + "--isLookUpUrl", "lookupurl", + "--workingPath", workingPath, + "--numPartitions", "5" + }), spark) + .run(isLookUpService); + + new SparkCreateMergeRels(args( + "/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json", + new String[] { + "--graphBasePath", graphInputPath, + "--actionSetId", testActionSetId, + "--isLookUpUrl", "lookupurl", + "--workingPath", workingPath + }), spark) + .run(isLookUpService); + + final Dataset merges = spark + .read() + .load(workingPath + "/" + testActionSetId + "/publication_mergerel") + .as(Encoders.bean(Relation.class)); + + assertEquals( + 3, merges + .filter("relclass == 'isMergedIn'") + .map((MapFunction) Relation::getTarget, Encoders.STRING()) + .distinct() + .count()); + assertEquals( + 4, merges + .filter("source == '50|doi_dedup___::b3aec7985136e36827176aaa1dd5082d'") + .count()); + + new SparkCreateDedupRecord(args( + "/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json", + new String[] { + "--graphBasePath", graphInputPath, + "--actionSetId", testActionSetId, + "--isLookUpUrl", "lookupurl", + "--workingPath", workingPath + }), spark) + .run(isLookUpService); + + final Dataset roots = spark + .read() + .textFile(workingPath + "/" + testActionSetId + "/publication_deduprecord") + .map(asEntity(Publication.class), Encoders.bean(Publication.class)); + + assertEquals(3, roots.count()); + + final Dataset pubs = spark + .read() + .textFile(DedupUtility.createEntityPath(graphInputPath, "publication")) + .map(asEntity(Publication.class), Encoders.bean(Publication.class)); + + Publication root = roots + .filter("id = '50|doi_dedup___::b3aec7985136e36827176aaa1dd5082d'") + .first(); + assertNotNull(root); + + Publication crossref_duplicate = pubs + .filter("id = '50|doi_________::b3aec7985136e36827176aaa1dd5082d'") + .collectAsList() + .get(0); + + assertEquals(crossref_duplicate.getDateofacceptance().getValue(), root.getDateofacceptance().getValue()); + assertEquals(crossref_duplicate.getJournal().getName(), root.getJournal().getName()); + assertEquals(crossref_duplicate.getJournal().getIssnPrinted(), root.getJournal().getIssnPrinted()); + assertEquals(crossref_duplicate.getPublisher().getValue(), root.getPublisher().getValue()); + + Set rootPids = root + .getPid() + .stream() + .map(StructuredProperty::getValue) + .collect(Collectors.toCollection(HashSet::new)); + Set dupPids = crossref_duplicate + .getPid() + .stream() + .map(StructuredProperty::getValue) + .collect(Collectors.toCollection(HashSet::new)); + + assertFalse(Sets.intersection(rootPids, dupPids).isEmpty()); + assertTrue(rootPids.contains("10.1109/jstqe.2022.3205716")); + assertTrue(rootPids.contains("10.1109/jstqe.2023.9999999")); + + Optional instance_cr = root + .getInstance() + .stream() + .filter(i -> i.getCollectedfrom().getValue().equals("Crossref")) + .findFirst(); + assertTrue(instance_cr.isPresent()); + assertEquals("OPEN", instance_cr.get().getAccessright().getClassid()); + assertEquals("Open Access", instance_cr.get().getAccessright().getClassname()); + assertEquals(OpenAccessRoute.hybrid, instance_cr.get().getAccessright().getOpenAccessRoute()); + assertEquals( + "IEEE Journal of Selected Topics in Quantum Electronics", instance_cr.get().getHostedby().getValue()); + assertEquals("0001", instance_cr.get().getInstancetype().getClassid()); + assertEquals("Article", instance_cr.get().getInstancetype().getClassname()); + + } + + private static String classPathResourceAsString(String path) throws IOException { + return IOUtils + .toString( + SparkPublicationRootsTest2.class + .getResourceAsStream(path)); + } + + private static MapFunction asEntity(Class clazz) { + return value -> MAPPER.readValue(value, clazz); + } + + private ArgumentApplicationParser args(String paramSpecs, String[] args) throws IOException, ParseException { + ArgumentApplicationParser parser = new ArgumentApplicationParser(classPathResourceAsString(paramSpecs)); + parser.parseArgument(args); + return parser; + } + +} diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkStatsTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkStatsTest.java index 1ba2c717c..b33b627e7 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkStatsTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkStatsTest.java @@ -168,11 +168,11 @@ public class SparkStatsTest implements Serializable { .textFile(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_blockstats") .count(); - assertEquals(477, orgs_blocks); + assertEquals(480, orgs_blocks); assertEquals(295, pubs_blocks); assertEquals(122, sw_blocks); assertEquals(191, ds_blocks); - assertEquals(171, orp_blocks); + assertEquals(178, orp_blocks); } @AfterAll diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/publication/publication.gz b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/publication/publication.gz index cf513d730..a7457063b 100644 Binary files a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/publication/publication.gz and b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/publication/publication.gz differ diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator_publication.xml b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator_publication.xml new file mode 100644 index 000000000..b47d99b92 --- /dev/null +++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator_publication.xml @@ -0,0 +1,24 @@ + +
+ + + + + +
+ + + + + + + + + + + + + + SECURITY_PARAMETERS + + \ No newline at end of file diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/root/alterations/publication/publication_1.gz b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/root/alterations/publication/publication_1.gz new file mode 100644 index 000000000..89ed9671e Binary files /dev/null and b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/root/alterations/publication/publication_1.gz differ diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/root/entities/publication/publication_0.gz b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/root/entities/publication/publication_0.gz new file mode 100644 index 000000000..85706bc31 Binary files /dev/null and b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/root/entities/publication/publication_0.gz differ diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/log4j.properties b/dhp-workflows/dhp-dedup-openaire/src/test/resources/log4j.properties new file mode 100644 index 000000000..d3e717dfa --- /dev/null +++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/log4j.properties @@ -0,0 +1,47 @@ +# Root logger option +log4j.rootLogger=DEBUG, stdout + +# Direct log messages to stdout +log4j.appender.stdout=org.apache.log4j.ConsoleAppender +log4j.appender.stdout.Target=System.out +log4j.appender.stdout.layout=org.apache.log4j.PatternLayout +log4j.appender.stdout.layout.ConversionPattern=%d{yyyy-MM-dd HH:mm:ss} %-5p %c{1}:%L - %m%n + +# Change this to set Spark log level +log4j.logger.org.apache.spark=ERROR +log4j.rootCategory=WARN + +# Silence akka remoting +log4j.logger.Remoting=WARN + +# Ignore messages below warning level from Jetty, because it's a bit verbose +log4j.logger.org.eclipse.jetty=WARN + +log4j.logger.org.apache.hadoop.mapreduce.lib.output.FileOutputCommitterFactory=WARN +log4j.logger.org.apache.hadoop.mapreduce.lib.output.FileOutputCommitter=WARN +#log4j.logger.org.apache.parquet.hadoop.ParquetOutputFormat=WARN +#log4j.logger.org.apache.parquet.hadoop.InternalParquetRecordWriter=WARN +log4j.logger.org.apache.hadoop.io.compress.CodecPool=WARN +#log4j.logger.org.apache.hadoop.io.compress=WARN +#log4j.logger.org.apache.parquet.hadoop.codec.CodecConfig=WARN +log4j.logger.parquet.hadoop.ColumnChunkPageWriteStore=ERROR +log4j.logger.com.jayway.jsonpath.internal.path.CompiledPath=WARN +log4j.logger.org.apache.parquet.hadoop.ParquetRecordReader=ERROR +log4j.logger.parquet.hadoop=WARN +log4j.logger.org.eclipse.jetty.server.handler.ContextHandlerCollection=WARN +log4j.logger.org.spark_project.jetty.util.component.ContainerLifeCycle=WARN +log4j.logger.org.apache.hadoop.mapred.FileInputFormat=WARN +log4j.logger.org.spark_project.jetty.servlet.ServletHandler=WARN +log4j.logger.org.apache.commons.beanutils.converters.BooleanConverter=WARN +log4j.logger.org.apache.commons.beanutils.converters.StringConverter=WARN +log4j.logger.org.apache.commons.beanutils.converters.LongConverter=WARN +log4j.logger.org.apache.commons.beanutils.converters.ArrayConverter=WARN +log4j.logger.org.apache.commons.beanutils.converters.FloatConverter=WARN +log4j.logger.org.apache.commons.beanutils.converters.IntegerConverter=WARN +log4j.logger.org.apache.commons.beanutils.converters.DoubleConverter=WARN +log4j.logger.org.apache.commons.beanutils.converters.CharacterConverter=WARN +log4j.logger.org.apache.commons.beanutils.converters.ByteConverter=WARN +log4j.logger.org.apache.commons.beanutils.converters.BigIntegerConverter=WARN +log4j.logger.org.apache.commons.beanutils.converters.BigDecimalConverter=WARN +log4j.logger.org.apache.commons.beanutils.converters.ShortConverter=WARN +log4j.logger.org.apache.commons.beanutils.BeanUtils=WARN diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java index f92040c24..ba7c7dd01 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java @@ -554,7 +554,7 @@ public class PublicationToOaf implements Serializable { private KeyValue createCollectedFrom() { KeyValue cf = new KeyValue(); cf.setValue(ModelConstants.ORCID.toUpperCase()); - cf.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + "806360c771262b4d6770e7cdf04b5c5a"); + cf.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + "cd0f74b5955dc87fd0605745c4b49ee8"); return cf; } diff --git a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala index 98b5b708e..aba8cee12 100644 --- a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala +++ b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala @@ -31,13 +31,13 @@ class CrossrefMappingTest { .fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/funder_doi")) .mkString - for (line <- funder_doi.lines) { + for (line <- funder_doi.linesWithSeparators.map(l =>l.stripLineEnd)) { val json = template.replace("%s", line) val resultList: List[Oaf] = Crossref2Oaf.convert(json) assertTrue(resultList.nonEmpty) checkRelation(resultList) } - for (line <- funder_name.lines) { + for (line <- funder_name.linesWithSeparators.map(l =>l.stripLineEnd)) { val json = template.replace("%s", line) val resultList: List[Oaf] = Crossref2Oaf.convert(json) assertTrue(resultList.nonEmpty) diff --git a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/orcid/MappingORCIDToOAFTest.scala b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/orcid/MappingORCIDToOAFTest.scala index e5bf1bd5f..d7a6a94a5 100644 --- a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/orcid/MappingORCIDToOAFTest.scala +++ b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/orcid/MappingORCIDToOAFTest.scala @@ -25,7 +25,7 @@ class MappingORCIDToOAFTest { .mkString assertNotNull(json) assertFalse(json.isEmpty) - json.lines.foreach(s => { + json.linesWithSeparators.map(l =>l.stripLineEnd).foreach(s => { assertNotNull(ORCIDToOAF.extractValueFromInputString(s)) }) } diff --git a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/uw/UnpayWallMappingTest.scala b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/uw/UnpayWallMappingTest.scala index 542faa8ad..7fe0e9935 100644 --- a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/uw/UnpayWallMappingTest.scala +++ b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/uw/UnpayWallMappingTest.scala @@ -22,7 +22,7 @@ class UnpayWallMappingTest { .mkString var i: Int = 0 - for (line <- Ilist.lines) { + for (line <- Ilist.linesWithSeparators.map(l =>l.stripLineEnd)) { val p = UnpayWallToOAF.convertToOAF(line) if (p != null) { @@ -43,7 +43,7 @@ class UnpayWallMappingTest { i = i + 1 } - val l = Ilist.lines.next() + val l = Ilist.linesWithSeparators.map(l =>l.stripLineEnd).next() val item = UnpayWallToOAF.convertToOAF(l) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java index c12fb54d9..88ec9a142 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java @@ -230,10 +230,15 @@ public class PropagationConstant { 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)); + + if (HdfsSupport.exists(inputPath, spark.sparkContext().hadoopConfiguration())) { + return spark + .read() + .textFile(inputPath) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)); + } else { + return spark.emptyDataset(Encoders.bean(clazz)); + } } public static Dataset readOafKryoPath( diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfigurationFactory.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfigurationFactory.java index 52ca606fc..ae1deaa73 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfigurationFactory.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfigurationFactory.java @@ -90,12 +90,12 @@ public class CommunityConfigurationFactory { } private static SelectionConstraints parseConstrains(Node node) { - Node aconstraints = node.selectSingleNode("./advancedConstraints"); - if (aconstraints == null) { + Node advConstsNode = node.selectSingleNode("./advancedConstraints"); + if (advConstsNode == null || StringUtils.isBlank(StringUtils.trim(advConstsNode.getText()))) { return null; } SelectionConstraints selectionConstraints = new Gson() - .fromJson(aconstraints.getText(), SelectionConstraints.class); + .fromJson(advConstsNode.getText(), SelectionConstraints.class); selectionConstraints.setSelection(resolver); return selectionConstraints; diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/QueryInformationSystem.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/QueryInformationSystem.java index f06c0d47a..5fe3cf81f 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/QueryInformationSystem.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/QueryInformationSystem.java @@ -1,8 +1,10 @@ package eu.dnetlib.dhp.bulktag.community; +import java.io.IOException; import java.util.List; +import org.apache.commons.io.IOUtils; import org.dom4j.DocumentException; import org.xml.sax.SAXException; @@ -13,71 +15,17 @@ import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; public class QueryInformationSystem { - private static final String XQUERY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " - + " let $subj := $x//CONFIGURATION/context/param[./@name='subject']/text() " - + " let $datasources := $x//CONFIGURATION/context/category[./@id=concat($x//CONFIGURATION/context/@id,'::contentproviders')]/concept " - + " let $organizations := $x//CONFIGURATION/context/category[./@id=concat($x//CONFIGURATION/context/@id,'::resultorganizations')]/concept " - + " let $communities := $x//CONFIGURATION/context/category[./@id=concat($x//CONFIGURATION/context/@id,'::zenodocommunities')]/concept " - + " let $fos := $x//CONFIGURATION/context/param[./@name='fos']/text() " - + " let $sdg := $x//CONFIGURATION/context/param[./@name='sdg']/text() " - + - "let $zenodo := $x//param[./@name='zenodoCommunity']/text() " - + " where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] and $x//context/param[./@name = 'status']/text() != 'hidden' " - + " return " - + " " - + " { $x//CONFIGURATION/context/@id} " - + " " - + " {for $y in tokenize($subj,',') " - + " return " - + " {$y}} " - + " {for $y in tokenize($fos,',') " - + " return " - + " {$y}} " - + " {for $y in tokenize($sdg,',') " - + " return " - + " {$y}} " - + " " - + " " - + " {for $d in $datasources " - + " where $d/param[./@name='enabled']/text()='true' " - + " return " - + " " - + " " - + " {$d//param[./@name='openaireId']/text()} " - + " " - + " " - + " {$d/param[./@name='selcriteria']/text()} " - + " " - + " } " - + " " + - " " + - "{for $zc in $zenodo " + - "return " + - " " + - " " + - "{$zc} " + - " " + - "}" - + " {for $zc in $communities " - + " return " - + " " - + " " - + " {$zc/param[./@name='zenodoid']/text()} " - + " " - + " " - + " {$zc/param[./@name='selcriteria']/text()} " - + " " - + " } " - + " " - + "" - + "{$x//CONFIGURATION/context/param[./@name='advancedConstraint']/text()} " - + "" - + " "; public static CommunityConfiguration getCommunityConfiguration(final String isLookupUrl) - throws ISLookUpException, DocumentException, SAXException { + throws ISLookUpException, DocumentException, SAXException, IOException { ISLookUpService isLookUp = ISLookupClientFactory.getLookUpService(isLookupUrl); - final List res = isLookUp.quickSearchProfile(XQUERY); + final List res = isLookUp + .quickSearchProfile( + IOUtils + .toString( + QueryInformationSystem.class + .getResourceAsStream( + "/eu/dnetlib/dhp/bulktag/query.xq"))); final String xmlConf = "" + Joiner.on(" ").join(res) + ""; diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/ContainsVerbIgnoreCase.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/ContainsVerbIgnoreCase.java index a4a6f5663..501eb51b9 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/ContainsVerbIgnoreCase.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/ContainsVerbIgnoreCase.java @@ -3,7 +3,7 @@ package eu.dnetlib.dhp.bulktag.criteria; import java.io.Serializable; -@VerbClass("contains_ignorecase") +@VerbClass("contains_caseinsensitive") public class ContainsVerbIgnoreCase implements Selection, Serializable { private String param; diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/EqualVerbIgnoreCase.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/EqualVerbIgnoreCase.java index c5f0ce070..1cd07755c 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/EqualVerbIgnoreCase.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/EqualVerbIgnoreCase.java @@ -3,7 +3,7 @@ package eu.dnetlib.dhp.bulktag.criteria; import java.io.Serializable; -@VerbClass("equals_ignorecase") +@VerbClass("equals_caseinsensitive") public class EqualVerbIgnoreCase implements Selection, Serializable { private String param; diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/NotContainsVerbIgnoreCase.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/NotContainsVerbIgnoreCase.java index b21be83f0..e12b65a27 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/NotContainsVerbIgnoreCase.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/NotContainsVerbIgnoreCase.java @@ -3,7 +3,7 @@ package eu.dnetlib.dhp.bulktag.criteria; import java.io.Serializable; -@VerbClass("not_contains_ignorecase") +@VerbClass("not_contains_caseinsensitive") public class NotContainsVerbIgnoreCase implements Selection, Serializable { private String param; diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/NotEqualVerbIgnoreCase.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/NotEqualVerbIgnoreCase.java index c6958a641..c1749621e 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/NotEqualVerbIgnoreCase.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/NotEqualVerbIgnoreCase.java @@ -3,7 +3,7 @@ package eu.dnetlib.dhp.bulktag.criteria; import java.io.Serializable; -@VerbClass("not_equals_ignorecase") +@VerbClass("not_equals_caseinsensitive") public class NotEqualVerbIgnoreCase implements Selection, Serializable { private String param; diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/StartsWithVerb.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/StartsWithVerb.java new file mode 100644 index 000000000..f22e1a864 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/StartsWithVerb.java @@ -0,0 +1,30 @@ + +package eu.dnetlib.dhp.bulktag.criteria; + +import java.io.Serializable; + +@VerbClass("starts_with") +public class StartsWithVerb implements Selection, Serializable { + + private String param; + + public StartsWithVerb() { + } + + public StartsWithVerb(final String param) { + this.param = param; + } + + @Override + public boolean apply(String value) { + return value.startsWith(param); + } + + public String getParam() { + return param; + } + + public void setParam(String param) { + this.param = param; + } +} diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_bulkTag_parameters.json b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_bulkTag_parameters.json index a37d7d168..a8be7c32e 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_bulkTag_parameters.json +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_bulkTag_parameters.json @@ -38,13 +38,13 @@ { "paramName": "test", "paramLongName": "isTest", - "paramDescription": "true if the spark session is managed, false otherwise", + "paramDescription": "Parameter intended for testing purposes only. True if the reun is relatesd to a test and so the taggingConf parameter should be loaded", "paramRequired": false }, { "paramName": "tg", "paramLongName": "taggingConf", - "paramDescription": "true if the spark session is managed, false otherwise", + "paramDescription": "this parameter is intended for testing purposes only. It is a possible tagging configuration obtained via the XQUERY. Intended to be removed", "paramRequired": false } diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/query.xq b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/query.xq new file mode 100644 index 000000000..6fbd74c8f --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/query.xq @@ -0,0 +1,58 @@ +for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') +let $subj := $x//CONFIGURATION/context/param[./@name='subject']/text() +let $datasources := $x//CONFIGURATION/context/category[./@id=concat($x//CONFIGURATION/context/@id,'::contentproviders')]/concept +let $organizations := $x//CONFIGURATION/context/category[./@id=concat($x//CONFIGURATION/context/@id,'::resultorganizations')]/concept +let $communities := $x//CONFIGURATION/context/category[./@id=concat($x//CONFIGURATION/context/@id,'::zenodocommunities')]/concept +let $fos := $x//CONFIGURATION/context/param[./@name='fos']/text() +let $sdg := $x//CONFIGURATION/context/param[./@name='sdg']/text() +let $zenodo := $x//param[./@name='zenodoCommunity']/text() +where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] and $x//context/param[./@name = 'status']/text() != 'hidden' +return + +{ $x//CONFIGURATION/context/@id} + +{$x//CONFIGURATION/context/param[./@name='advancedConstraints']/text() } + + + {for $y in tokenize($subj,',') + return + {$y}} + {for $y in tokenize($fos,',') + return + {$y}} + {for $y in tokenize($sdg,',') + return + {$y}} + + + {for $d in $datasources + where $d/param[./@name='enabled']/text()='true' + return + + + {$d//param[./@name='openaireId']/text()} + + + {$d/param[./@name='selcriteria']/text()} + + } + + +{for $zc in $zenodo +return + + +{$zc} + +} +{for $zc in $communities +return + + +{$zc/param[./@name='zenodoid']/text()} + + +{$zc/param[./@name='selcriteria']/text()} + +} + \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java index def524156..2af3cdb2e 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java @@ -16,6 +16,7 @@ import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.ForeachFunction; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Row; import org.apache.spark.sql.SparkSession; @@ -45,7 +46,9 @@ public class BulkTagJobTest { + " \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\"," + " \"contributor\" : \"$['contributor'][*]['value']\"," + " \"description\" : \"$['description'][*]['value']\", " - + " \"subject\" :\"$['subject'][*]['value']\" }"; + + " \"subject\" :\"$['subject'][*]['value']\" , " + + + "\"fos\" : \"$['subject'][?(@['qualifier']['classid']=='subject:fos')].value\"} "; private static SparkSession spark; @@ -769,28 +772,14 @@ public class BulkTagJobTest { org.apache.spark.sql.Dataset idExplodeCommunity = spark.sql(query); idExplodeCommunity.show(false); - Assertions.assertEquals(4, idExplodeCommunity.count()); + Assertions.assertEquals(5, idExplodeCommunity.count()); Assertions .assertEquals( 3, idExplodeCommunity.filter("provenance = 'community:datasource'").count()); Assertions .assertEquals( - 1, idExplodeCommunity.filter("provenance = 'community:advconstraint'").count()); + 2, idExplodeCommunity.filter("provenance = 'community:advconstraint'").count()); } -// @Test -// void test1(){ -// ProtoMap params = new Gson().fromJson(pathMap, ProtoMap.class); -// HashMap param = new HashMap<>(); -// for (String key : params.keySet()) { -// try { -// param.put(key, jsonContext.read(params.get(key))); -// } catch (com.jayway.jsonpath.PathNotFoundException e) { -// param.put(key, new ArrayList<>()); -// } -// } -// return param; -// } -// } } diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/CommunityConfigurationFactoryTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/CommunityConfigurationFactoryTest.java index 861546adb..c8fd62c8e 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/CommunityConfigurationFactoryTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/CommunityConfigurationFactoryTest.java @@ -83,4 +83,36 @@ class CommunityConfigurationFactoryTest { Assertions.assertEquals("dariah", comm.get(0)); } + @Test + void loadSelCriteriaTest2() throws DocumentException, IOException, SAXException { + String xml = IOUtils + .toString( + getClass() + .getResourceAsStream( + "/eu/dnetlib/dhp/bulktag/communityconfiguration/community_configuration_selcrit2.xml")); + final CommunityConfiguration cc = CommunityConfigurationFactory.newInstance(xml); + Map> param = new HashMap<>(); + param.put("author", new ArrayList<>(Collections.singletonList("Pippo Pippi"))); + param + .put( + "description", + new ArrayList<>( + Collections + .singletonList( + "This work has been partially supported by DARIAH-EU infrastructure"))); + param + .put( + "contributor", + new ArrayList<>( + Collections + .singletonList( + "Author X helped to write the paper. X works for DARIAH"))); + List comm = cc + .getCommunityForDatasource( + "openaire____::1cfdb2e14977f31a98e0118283401f32", param); + + // TODO add more assertions + Assertions.assertEquals(0, comm.size()); + } + } diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/community_configuration_selcrit2.xml b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/community_configuration_selcrit2.xml new file mode 100644 index 000000000..b2b62e314 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/community_configuration_selcrit2.xml @@ -0,0 +1,4459 @@ + + + + + + + orp_________::9b49c76cf40a93f89944889678b741f9 + + + + + + egi + + + + + + + + + Ocean mapping + Multibeam Backscatter + Bathymetry + Seabed classification + Submarine Geomorphology + Underwater Photogrammetry + + + + issn___print::aedc6f1e34247e464bc8b45270e4b972 + {"criteria":[{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"bathymetry"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"bathymetry"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"backscatter"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"photogrammetry"},{"verb":"contains_caseinsensitive","field":"description","value":"underwater"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"multibeam"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"bathymetric"}]}]} + + + issn___print::ed5a370152cb6cafc3d5bff280a94c88 + {"criteria":[{"constraint":[{"verb":"equals_caseinsensitive","field":"title","value":"submarine geomorphology"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"bathymetry"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"marine"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"photogrammetry"},{"verb":"contains_caseinsensitive","field":"description","value":"underwater"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"backscatter"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"multibeam"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"bathymetric"}]}]} + + + opendoar____::99f59c0842e83c808dd1813b48a37c6a + {"criteria":[{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"bathymetry"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"bathymetry"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"photogrammetry"},{"verb":"contains_caseinsensitive","field":"description","value":"underwater"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"backscatter"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"multibeam"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"bathymetric"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"bathymetric"}]}]} + + + opendoar____::8f14e45fceea167a5a36dedd4bea2543 + {"criteria":[{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"bathymetry"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"backscatter"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"bathymetry"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"photogrammetry"},{"verb":"contains_caseinsensitive","field":"description","value":"underwater"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"multibeam"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"bathymetric"}]}]} + + + issn___print::d143b63af2b83be033d45d82f741761b + {"criteria":[{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"bathymetry"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"backscatter"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"photogrammetry"},{"verb":"contains_caseinsensitive","field":"description","value":"underwater"},{"verb":"contains_caseinsensitive","field":"description","value":"marine"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"underwater"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"marine"}]}]} + + + issn___print::780e93f1de06f8b0eb4e98606dfc7197 + {"criteria":[{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"underwater"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"bathymetric"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"backscatter"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"bathymetry"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"photogrammetry"},{"verb":"contains_caseinsensitive","field":"description","value":"underwater"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"multibeam"}]}]} + + + doajarticles::be08e041165577d36a805b13cd7d2ba7 + {"criteria":[{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"underwater"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"bathymetry"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"backscatter"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"photogrammetry"},{"verb":"contains_caseinsensitive","field":"description","value":"underwater"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"submarine"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"multibeam"}]}]} + + + opendoar____::ea119a40c1592979f51819b0bd38d39d + {"criteria":[{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"bathymetry"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"backscatter"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"submarine"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"underwater"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"backscatter"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"photogrammetry"},{"verb":"contains_caseinsensitive","field":"description","value":"underwater"}]}]} + + + doajarticles::795b5787c6d1515629042fd2f398dd0e + {"criteria":[{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"submarine"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"bathymetry"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"backscatter"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"underwater"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"photogrammetry"},{"verb":"contains_caseinsensitive","field":"description","value":"underwater"}]}]} + + + issn___print::bfcfaf0f496b008f5ab4381976a78743 + {"criteria":[{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"submarine"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"bathymetry"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"bathymetric"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"underwater"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"marine"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"multibeam"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"backscatter"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"photogrammetry"},{"verb":"contains_caseinsensitive","field":"description","value":"underwater"}]}]} + + + re3data_____::9633d1e8c4309c833c2c442abeb0cfeb + {"criteria":[{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"bathymetry"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"multibeam"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"backscatter"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"bathymetry"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"description","value":"backscatter"}]}]} + + + + + obsea + + + + openearth + + + + bermudabream + + + + marxiv + + + + meditmarsci + + + + sail + + + + greenmardata + + + + bluecloud + + + + emso-eric + + + + atlas + + + + medship-goship + + + + + + + + + + + + re3data_____::a507cdacc5bbcc08761c92185dee5cab + + + + + + oac_clarin + + + + + + + + + + + + rda-related + + + rda + + + + + + + + + + SDG13 - Climate action + SDG8 - Decent work and economic + growth + SDG15 - Life on land + SDG2 - Zero hunger + SDG17 - Partnerships for the + goals + SDG10 - Reduced inequalities + SDG5 - Gender equality + SDG12 - Responsible + consumption and production + SDG14 - Life below water + SDG6 - Clean water and + sanitation + SDG11 - Sustainable cities and communities + SDG1 - No poverty + SDG3 - + Good health and well being + SDG7 - Affordable and clean energy + SDG4 - Quality + education + SDG9 - Industry innovation and infrastructure + SDG16 - Peace justice + and strong institutions + + + + + oac_sdsn-greece + + + + + + + + + modern art + monuments + europeana data model + field walking + frescoes + LIDO metadata schema + art history + excavation + Arts and Humanities General + coins + temples + numismatics + lithics + environmental archaeology + digital cultural heritage + archaeological reports + history + CRMba + churches + cultural heritage + archaeological stratigraphy + religious art + digital humanities + archaeological sites + linguistic studies + bioarchaeology + architectural orders + palaeoanthropology + fine arts + europeana + CIDOC CRM + decorations + classic art + stratigraphy + digital archaeology + intangible cultural heritage + walls + chapels + CRMtex + Language and Literature + paintings + archaeology + mosaics + burials + medieval art + castles + CARARE metadata schema + statues + natural language processing + inscriptions + CRMsci + vaults + contemporary art + Arts and Humanities + CRMarchaeo + pottery + + + + re3data_____::9ebe127e5f3a0bf401875690f3bb6b81 + + + + doajarticles::c6cd4b532e12868c1d760a8d7cda6815 + + + + doajarticles::a6de4499bb87bf3c01add0a9e2c9ed0b + + + + doajarticles::6eb31d13b12bc06bbac06aef63cf33c9 + + + + doajarticles::0da84e9dfdc8419576169e027baa8028 + + + + re3data_____::a48f09c562b247a9919acfe195549b47 + + + + doajarticles::2899208a99aa7d142646e0a80bfeef05 + + + + issn___print::9c2ffbdfdc48f6df69a6a3e6a280fae1 + + + + issn___print::72d240a2d51f2c2d77326e010cf22b17 + + + + issn__online::92e1d78d81161cd33f11e8224a57c8b9 + + + + issn___print::0a35021b9120f06d707698476b7e1882 + + + + issn__online::fb8a8d9129fd90ab209688cf42f9baa7 + + + + re3data_____::69162d0a40bab7cc80b40ec90da874b9 + + + + doajarticles::cdccbf32233ba16782875c757ababf11 + + + + doajarticles::b451f47924a84a65fa51bc82516993ce + + + + openaire____::ec63975d4da67750eede546e4aac955c + + + + re3data_____::2201b9b181a9f8361b3d3fbf496d18d7 + + + + issn___print::9519433d216b7ef0c292a355a99d0fb7 + + + + issn___print::7e7ed6b3beb5404bbd9354b6809fc903 + + + + doajarticles::e7d82763b1b210e769fd10d6648504ea + + + + issn___print::b8cdab13c697a46c6c1c243d57bce3fe + + + + re3data_____::f52792889d64d1a688b43ed989f6464a + + + + re3data_____::a507cdacc5bbcc08761c92185dee5cab + + + + re3data_____::fe0d76581a60e1287a93e2ed2cb29339 + + + + re3data_____::d9b253653defb9c50dbf5eed44f68c73 + + + + re3data_____::b47b4a53d7ad3c7d1e60d5a6fbb8c640 + + + + re3data_____::0d863103c89be7344eb200475aca0647 + + + + re3data_____::afc322a1da36b057851bbd025e9b0115 + + + + + + oac_dh-ch + + + storm + + + + crosscult + + + + wholodance_eu + + + + digcur2013 + + + + gravitate + + + + dipp2014 + + + + digitalhumanities + + + + dimpo + + + + adho + + + + chc + + + + wahr + + + + ibe + + + + ariadne + + + + parthenos-hub + + + + parthenos-training + + + + gandhara + + + + cmsouthasia + + + + nilgirihills + + + + shamsa_mustecio + + + + bodhgaya + + + + + + + + + + brain mapping + brain imaging + electroencephalography + arterial spin labelling + brain fingerprinting + brain + neuroimaging + Multimodal Brain Image Analysis + fMRI + neuroinformatics + fetal brain + brain ultrasonic imaging + topographic brain mapping + diffusion tensor imaging + computerized knowledge assessment + connectome mapping + brain magnetic resonance imaging + brain abnormalities + + + + re3data_____::5b9bf9171d92df854cf3c520692e9122 + + + + doajarticles::c7d3de67dc77af72f6747157441252ec + + + + re3data_____::8515794670370f49c1d176c399c714f5 + + + + doajarticles::d640648c84b10d425f96f11c3de468f3 + + + + doajarticles::0c0e74daa5d95504eade9c81ebbd5b8a + + + + rest________::fb1a3d4523c95e63496e3bc7ba36244b + + + + issn___print::3a700379401534d8f70b632d72d05f9c + + + + + + oac_ni + + + neuroinformatics + + + + hbp + + + + from_neuroscience_to_machine_learning + + + + ci2c + + + + opensourcebrain + + + + brainspeak + + + + braincom + + + + nextgenvis + + + + meso-brain + + + + neuroplasticity-workshop + + + + bionics + + + + brainmattrain-676408 + + + + repronim + + + + affectiveneuro + + + + con + + + + lab_neurol_sperim_irfmn_irccs_milano_it + + + + + + + + + + marine + ocean + fish + aqua + sea + + + + opendoar____::8f14e45fceea167a5a36dedd4bea2543 + + + + opendoar____::ea119a40c1592979f51819b0bd38d39d + + + + opendoar____::35d02fef7d9a24e237057162abab82b7 + + + + doajarticles::e5934203928262dca69c4fc3e3e95ead + + + + issn___print::90b2464d021b3b394af968bc90ef660b + + + + openaire____::c739f47b413c0ca5f8577b9f6a5c35ce + + + + + + oac_mes + + + adriplan + + + + devotes-project + + + + euro-basin + + + + naclim + + + + discardless + + + + assisibf + + + + meece + + + + facts + + + + proeel + + + + aquatrace + + + + myfish + + + + atlas + + + + blue-actionh2020 + + + + sponges + + + + merces_project + + + + bigdataocean + + + + columbus + + + + h2020-aquainvad-ed + + + + aquarius + + + + southern-ocean-observing-system + + + + eawag + + + + mossco + + + + onc + + + + oceanbiogeochemistry + + + + oceanliteracy + + + + openearth + + + + ocean + + + + calcifierraman + + + + bermudabream + + + + brcorp1 + + + + mce + + + + biogeochem + + + + ecc2014 + + + + fisheries + + + + sedinstcjfas + + + + umr-entropie + + + + farfish2020 + + + + primefish + + + + zf-ilcs + + + + climefish + + + + afrimed_eu + + + + spi-ace + + + + cice-consortium + + + + nemo-ocean + + + + mesopp-h2020 + + + + marxiv + + + + + + + + + + + + + oac_instruct + + + instruct + + + + west-life + + + + + + + + + + + + + oaa_elixir-gr + + + + + + + + + + + opendoar____::7e7757b1e12abcb736ab9a754ffb617a + {"criteria":[{"constraint":[{"verb":"contains","field":"contributor","value":"DARIAH"}]}]} + + + opendoar____::96da2f590cd7246bbde0051047b0d6f7 + {"criteria":[{"constraint":[{"verb":"contains","field":"contributor","value":"DARIAH"}]}]} + + + re3data_____::f52792889d64d1a688b43ed989f6464a + {"criteria":[{"constraint":[{"verb":"equals","field":"contributor","value":"Architrave"}]},{"constraint":[{"verb":"equals","field":"contributor","value":"Fontane Notizbücher"}]},{"constraint":[{"verb":"equals","field":"contributor","value":"FreiDi"}]},{"constraint":[{"verb":"equals","field":"contributor","value":"Virtuelles Skriptorium St. Matthias"}]},{"constraint":[{"verb":"equals","field":"contributor","value":"ePoetics"}]}]} + + + + + dariah + + + dimpo + + + + + + + + + + + + + risis + + + + + + + + + + + + + + + + + Green Transport + City mobility systems + Vulnerable road users + Traffic engineering + Transport electrification + Intermodal freight transport + Clean vehicle fleets + Intelligent mobility + Inflight refueling + District mobility systems + Navigation and control systems for optimised planning and routing + European Space Technology Platform + European Transport networks + Green cars + Inter-modality infrastructures + Advanced Take Off and Landing Ideas + Sustainable urban systems + port-area railway networks + Innovative forms of urban transport + Alliance for Logistics Innovation through Collaboration in Europe + Advisory Council for Aeronautics Research in Europe + Mobility services for people and goods + Guidance and traffic management + Passenger mobility + Smart mobility and services + transport innovation + high-speed railway + Vehicle design + Inland shipping + public transportation + aviation’s climate impact + Road transport + On-demand public transport + Personal Air Transport + Pipeline transport + European Association of Aviation Training and Education Organisations + Defrosting of railway infrastructure + Inclusive and affordable transport + River Information Services + jel:L92 + Increased use of public transport + Seamless mobility + STRIA + trolleybus transport + Intelligent Transport System + Low-emission alternative energy for transport + Shared mobility for people and goods + Business model for urban mobility + Interoperability of transport systems + Cross-border train slot booking + Air transport + Transport pricing + Sustainable transport + European Rail Transport Research Advisory Council + Alternative aircraft configurations + Railways applications + urban transport + Environmental impact of transport + urban freight delivery systems + Automated Road Transport + Alternative fuels in public transport + Active LIDAR-sensor for GHG-measurements + Autonomous logistics operations + Rational use of motorised transport + Network and traffic management systems + electrification of railway wagons + Single European Sky + Electrified road systems + Railway dynamics + Motorway of the Sea + smart railway communications + Maritime transport + Environmental- friendly transport + Combined transport + Connected automated driving technology + Innovative freight logistics services + automated and shared vehicles + Alternative Aircraft Systems + Land-use and transport interaction + Public transport system + Business plan for shared mobility + Shared mobility + Growing of mobility demand + European Road Transport Research Advisory Council + WATERBORNE ETP + Effective transport management system + Short Sea Shipping + air traffic management + Sea hubs and the motorways of the sea + Urban mobility solutions + Smart city planning + Maritime spatial planning + EUropean rail Research Network of Excellence + ENERGY CONSUMPTION BY THE TRANSPORT SECTOR + Integrated urban plan + inland waterway services + European Conference of Transport Research Institutes + air vehicles + E-freight + Automated Driving + Automated ships + pricing for cross-border passenger transport + Vehicle efficiency + Railway transport + Electric vehicles + Road traffic monitoring + Deep sea shipping + Circular economy in transport + Traffic congestion + air transport system + Urban logistics + Rail transport + OpenStreetMap + high speed rail + Transportation engineering + Intermodal travel information + Flight Data Recorders + Advanced driver assistance systems + long distance freight transport + Inland waterway transport + Smart mobility + Mobility integration + Personal Rapid Transit system + Safety measures & requirements for roads + Green rail transport + Vehicle manufacturing + Future Airport Layout + Rail technologies + European Intermodal Research Advisory Council + inland navigation + Automated urban vehicles + ECSS-standards + Traveller services + Polluting transport + Air Traffic Control + Cooperative and connected and automated transport + Innovative powertrains + Quality of transport system and services + door-to- door logistics chain + Inter-modal aspects of urban mobility + Innovative freight 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100644 --- a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf.xml +++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf.xml @@ -844,6 +844,89 @@ + + { + "criteria": [ + { + "constraint": [ + { + "verb": "equals_caseinsensitive", + "field": "subject", + "value": "North America" + }, + { + "verb": "contains", + "field": "fos", + "value": "05" + } + ] + }, + { + "constraint": [ + { + "verb": "equals_caseinsensitive", + "field": "subject", + "value": "North America" + }, + { + "verb": "contains", + "field": "fos", + "value": "06" + } + ] + }, + { + "constraint": [ + { + "verb": "equals_caseinsensitive", + "field": "subject", + "value": "Mexico" + }, + { + "verb": "equals_caseinsensitive", + "field": "subject", + "value": "United States" + }, + { + "verb": "equals_caseinsensitive", + "field": "subject", + "value": "Canada" + }, + { + "verb": "contains", + "field": "fos", + "value": "05" + } + ] + }, + { + "constraint": [ + { + "verb": "equals_caseinsensitive", + "field": "subject", + "value": "Mexico" + }, + { + "verb": "equals_caseinsensitive", + "field": "subject", + "value": "United States" + }, + { + "verb": "equals_caseinsensitive", + "field": "subject", + "value": "Canada" + }, + { + "verb": "contains", + "field": "fos", + "value": "06" + } + ] + } + ] + } + + @@ -1174,7 +1257,9 @@ + + @@ -1193,7 +1278,7 @@ - {"criteria":[{"constraint":[{"verb":"equals_ignorecase","field":"subject","value":"ciencias de la comunicación"}, + {"criteria":[{"constraint":[{"verb":"equals_caseinsensitive","field":"subject","value":"ciencias de la comunicación"}, {"verb":"equals","field":"subject","value":"Miriam"}]}, {"constraint":[{"verb":"equals","field":"subject","value":"miriam"}]}]} @@ -1317,81 +1402,81 @@ opendoar____::358aee4cc897452c00244351e4d91f69 - {"criteria":[{"constraint":[{"verb":"contains_ignorecase","field":"title","value":"COVID-19"}]}, - 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{"criteria":[{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"COVID-19"}]}, + {"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"SARS-CoV-2"}]}, + {"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"2019-nCoV"}]}]} share_______::4719356ec8d7d55d3feb384ce879ad6c - {"criteria":[{"constraint":[{"verb":"contains_ignorecase","field":"title","value":"COVID-19"}]}, - {"constraint":[{"verb":"contains_ignorecase","field":"title","value":"SARS-CoV-2"}]}, - {"constraint":[{"verb":"contains_ignorecase","field":"title","value":"2019-nCoV"}]}]} + {"criteria":[{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"COVID-19"}]}, + {"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"SARS-CoV-2"}]}, + {"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"2019-nCoV"}]}]} share_______::bbd802baad85d1fd440f32a7a3a2c2b1 - 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a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject_datasource/dataset_10.json.gz and /dev/null differ diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/log4j.properties b/dhp-workflows/dhp-enrichment/src/test/resources/log4j.properties new file mode 100644 index 000000000..ce37270c6 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/test/resources/log4j.properties @@ -0,0 +1,25 @@ +# Root logger option +log4j.rootLogger=DEBUG, stdout + +# Direct log messages to stdout +log4j.appender.stdout=org.apache.log4j.ConsoleAppender +log4j.appender.stdout.Target=System.out +log4j.appender.stdout.layout=org.apache.log4j.PatternLayout +log4j.appender.stdout.layout.ConversionPattern=%d{yyyy-MM-dd HH:mm:ss} %-5p %c{1}:%L - %m%n + +# Change this to set Spark log level +log4j.logger.org.apache.spark=ERROR +log4j.rootCategory=WARN + +# Silence akka remoting +log4j.logger.Remoting=WARN + +# Ignore messages below warning level from Jetty, because it's a bit verbose +log4j.logger.org.eclipse.jetty=WARN + +log4j.logger.org.apache.hadoop.mapreduce.lib.output.FileOutputCommitterFactory=WARN +log4j.logger.org.apache.hadoop.mapreduce.lib.output.FileOutputCommitter=WARN +log4j.logger.org.apache.parquet.hadoop.ParquetOutputFormat=WARN +log4j.logger.org.apache.parquet.hadoop.InternalParquetRecordWriter=WARN +log4j.logger.org.apache.hadoop.io.compress.CodecPool=WARN +log4j.logger.org.apache.parquet.hadoop.codec.CodecConfig=WARN \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java index 55fdbac59..10a3d4465 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java @@ -47,8 +47,8 @@ public class CleanContextSparkJob implements Serializable { String inputPath = parser.get("inputPath"); log.info("inputPath: {}", inputPath); - String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); String contextId = parser.get("contextId"); log.info("contextId: {}", contextId); @@ -67,12 +67,12 @@ public class CleanContextSparkJob implements Serializable { isSparkSessionManaged, spark -> { - cleanContext(spark, contextId, verifyParam, inputPath, entityClazz, workingPath); + cleanContext(spark, contextId, verifyParam, inputPath, entityClazz, workingDir); }); } private static void cleanContext(SparkSession spark, String contextId, String verifyParam, - String inputPath, Class entityClazz, String workingPath) { + String inputPath, Class entityClazz, String workingDir) { Dataset res = spark .read() .textFile(inputPath) @@ -106,11 +106,11 @@ public class CleanContextSparkJob implements Serializable { .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") - .json(workingPath); + .json(workingDir); spark .read() - .textFile(workingPath) + .textFile(workingDir) .map( (MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), Encoders.bean(entityClazz)) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleMap.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleMap.java index 147e26699..3d501bb27 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleMap.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleMap.java @@ -3,6 +3,7 @@ package eu.dnetlib.dhp.oa.graph.clean; import java.io.Serializable; import java.util.HashMap; +import java.util.Objects; import java.util.concurrent.atomic.AtomicReference; import org.apache.commons.lang3.SerializationUtils; @@ -10,6 +11,7 @@ import org.apache.commons.lang3.StringUtils; import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableConsumer; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.common.vocabulary.VocabularyTerm; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.*; @@ -31,29 +33,30 @@ public class CleaningRuleMap extends HashMap, SerializableConsumer modified = new AtomicReference<>(false); + vocabularies.find(vocabularyId).ifPresent(vocabulary -> { - if (!ModelConstants.DNET_SUBJECT_KEYWORD.equalsIgnoreCase(subject.getQualifier().getClassid())) { - return; - } - Qualifier newValue = vocabulary.lookup(subject.getValue()); - if (!ModelConstants.UNKNOWN.equals(newValue.getClassid())) { - subject.setValue(newValue.getClassid()); - subject.getQualifier().setClassid(vocabularyId); - subject.getQualifier().setClassname(vocabulary.getName()); - modified.set(true); + if (ModelConstants.DNET_SUBJECT_KEYWORD.equalsIgnoreCase(subject.getQualifier().getClassid())) { + Qualifier newValue = vocabulary.lookup(subject.getValue(), true); + if (!ModelConstants.UNKNOWN.equals(newValue.getClassid())) { + subject.setValue(newValue.getClassid()); + subject.getQualifier().setClassid(vocabularyId); + subject.getQualifier().setClassname(vocabulary.getName()); + } + } else if (vocabularyId.equals(subject.getQualifier().getClassid())) { + Qualifier syn = vocabulary.getSynonymAsQualifier(subject.getValue()); + VocabularyTerm term = vocabulary.getTerm(subject.getValue()); + if (Objects.isNull(syn) && Objects.isNull(term)) { + subject.getQualifier().setClassid(ModelConstants.DNET_SUBJECT_KEYWORD); + subject.getQualifier().setClassname(ModelConstants.DNET_SUBJECT_KEYWORD); + } } }); - return modified.get(); } private static void cleanRelation(VocabularyGroup vocabularies, Relation r) { diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/MasterDuplicateAction.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/MasterDuplicateAction.java new file mode 100644 index 000000000..8bf36ff82 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/MasterDuplicateAction.java @@ -0,0 +1,45 @@ + +package eu.dnetlib.dhp.oa.graph.clean; + +import org.apache.commons.io.IOUtils; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.action.ReadDatasourceMasterDuplicateFromDB; + +public class MasterDuplicateAction { + + private static final Logger log = LoggerFactory.getLogger(MasterDuplicateAction.class); + + public static void main(final String[] args) throws Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + MasterDuplicateAction.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/datasourcemaster_parameters.json"))); + + parser.parseArgument(args); + + final String dbUrl = parser.get("postgresUrl"); + log.info("postgresUrl: {}", dbUrl); + + final String dbUser = parser.get("postgresUser"); + log.info("postgresUser: {}", dbUser); + + final String dbPassword = parser.get("postgresPassword"); + log.info("postgresPassword: {}", dbPassword); + + final String hdfsPath = parser.get("hdfsPath"); + log.info("hdfsPath: {}", hdfsPath); + + final String hdfsNameNode = parser.get("hdfsNameNode"); + log.info("hdfsNameNode: {}", hdfsNameNode); + + int rows = ReadDatasourceMasterDuplicateFromDB.execute(dbUrl, dbUser, dbPassword, hdfsPath, hdfsNameNode); + + log.info("written {} rows", rows); + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/cfhb/CleanCfHbSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/cfhb/CleanCfHbSparkJob.java new file mode 100644 index 000000000..531b415ed --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/cfhb/CleanCfHbSparkJob.java @@ -0,0 +1,227 @@ + +package eu.dnetlib.dhp.oa.graph.clean.cfhb; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.util.Iterator; +import java.util.List; +import java.util.Objects; +import java.util.Optional; +import java.util.stream.Collectors; +import java.util.stream.Stream; + +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FilterFunction; +import org.apache.spark.api.java.function.FlatMapFunction; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.api.java.function.MapGroupsFunction; +import org.apache.spark.sql.*; +import org.apache.spark.sql.expressions.Aggregator; +import org.jetbrains.annotations.NotNull; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.common.action.model.MasterDuplicate; +import eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob; +import eu.dnetlib.dhp.schema.oaf.Instance; +import eu.dnetlib.dhp.schema.oaf.KeyValue; +import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.utils.DHPUtils; +import scala.Tuple2; + +public class CleanCfHbSparkJob { + + private static final Logger log = LoggerFactory.getLogger(CleanCfHbSparkJob.class); + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static void main(String[] args) throws Exception { + + String jsonConfiguration = IOUtils + .toString( + CleanCountrySparkJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/input_clean_cfhb_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); + + String inputPath = parser.get("inputPath"); + log.info("inputPath: {}", inputPath); + + String resolvedPath = parser.get("resolvedPath"); + log.info("resolvedPath: {}", resolvedPath); + + String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); + + String dsMasterDuplicatePath = parser.get("masterDuplicatePath"); + log.info("masterDuplicatePath: {}", dsMasterDuplicatePath); + + String graphTableClassName = parser.get("graphTableClassName"); + log.info("graphTableClassName: {}", graphTableClassName); + + Class entityClazz = (Class) Class.forName(graphTableClassName); + + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration()); + HdfsSupport.remove(resolvedPath, spark.sparkContext().hadoopConfiguration()); + cleanCfHb( + spark, inputPath, entityClazz, resolvedPath, dsMasterDuplicatePath, outputPath); + }); + } + + private static void cleanCfHb(SparkSession spark, String inputPath, Class entityClazz, + String resolvedPath, String masterDuplicatePath, String outputPath) { + + // read the master-duplicate tuples + Dataset md = spark + .read() + .textFile(masterDuplicatePath) + .map(as(MasterDuplicate.class), Encoders.bean(MasterDuplicate.class)); + + // prepare the resolved CF|HB references with the corresponding EMPTY master ID + Dataset resolved = spark + .read() + .textFile(inputPath) + .map(as(entityClazz), Encoders.bean(entityClazz)) + .flatMap(flattenCfHbFn(), Encoders.bean(IdCfHbMapping.class)); + + // set the EMPTY master ID/NAME and save it + resolved + .joinWith(md, resolved.col("cfhb").equalTo(md.col("duplicateId"))) + .map(asIdCfHbMapping(), Encoders.bean(IdCfHbMapping.class)) + .filter((FilterFunction) m -> Objects.nonNull(m.getMasterId())) + .write() + .mode(SaveMode.Overwrite) + .json(resolvedPath); + + // read again the resolved CF|HB mapping + Dataset resolvedDS = spark + .read() + .textFile(resolvedPath) + .map(as(IdCfHbMapping.class), Encoders.bean(IdCfHbMapping.class)); + + // read the result table + Dataset res = spark + .read() + .textFile(inputPath) + .map(as(entityClazz), Encoders.bean(entityClazz)); + + // Join the results with the resolved CF|HB mapping, apply the mapping and save it + res + .joinWith(resolvedDS, res.col("id").equalTo(resolvedDS.col("resultId")), "left") + .groupByKey((MapFunction, String>) t -> t._1().getId(), Encoders.STRING()) + .mapGroups(getMapGroupsFunction(), Encoders.bean(entityClazz)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); + } + + private static MapFunction, IdCfHbMapping> asIdCfHbMapping() { + return t -> { + final IdCfHbMapping mapping = t._1(); + Optional + .ofNullable(t._2()) + .ifPresent(t2 -> { + mapping.setMasterId(t2.getMasterId()); + mapping.setMasterName(t2.getMasterName()); + + }); + return mapping; + }; + } + + private static FlatMapFunction flattenCfHbFn() { + return r -> Stream + .concat( + Optional + .ofNullable(r.getCollectedfrom()) + .map(cf -> cf.stream().map(KeyValue::getKey)) + .orElse(Stream.empty()), + Stream + .concat( + Optional + .ofNullable(r.getInstance()) + .map( + instances -> instances + .stream() + .map(i -> Optional.ofNullable(i.getHostedby()).map(KeyValue::getKey).orElse(""))) + .orElse(Stream.empty()) + .filter(StringUtils::isNotBlank), + Optional + .ofNullable(r.getInstance()) + .map( + instances -> instances + .stream() + .map( + i -> Optional + .ofNullable(i.getCollectedfrom()) + .map(KeyValue::getKey) + .orElse(""))) + .orElse(Stream.empty()) + .filter(StringUtils::isNotBlank))) + .distinct() + .filter(StringUtils::isNotBlank) + .map(cfHb -> asIdCfHbMapping(r.getId(), cfHb)) + .iterator(); + } + + private static MapGroupsFunction, T> getMapGroupsFunction() { + return new MapGroupsFunction, T>() { + @Override + public T call(String key, Iterator> values) { + final Tuple2 first = values.next(); + final T res = first._1(); + + updateResult(res, first._2()); + values.forEachRemaining(t -> updateResult(res, t._2())); + return res; + } + + private void updateResult(T res, IdCfHbMapping m) { + if (Objects.nonNull(m)) { + res.getCollectedfrom().forEach(kv -> updateKeyValue(kv, m)); + res.getInstance().forEach(i -> { + updateKeyValue(i.getHostedby(), m); + updateKeyValue(i.getCollectedfrom(), m); + }); + } + } + + private void updateKeyValue(final KeyValue kv, final IdCfHbMapping a) { + if (kv.getKey().equals(a.getCfhb())) { + kv.setKey(a.getMasterId()); + kv.setValue(a.getMasterName()); + } + } + + }; + } + + private static IdCfHbMapping asIdCfHbMapping(String resultId, String cfHb) { + IdCfHbMapping m = new IdCfHbMapping(resultId); + m.setCfhb(cfHb); + return m; + } + + private static MapFunction as(Class clazz) { + return s -> OBJECT_MAPPER.readValue(s, clazz); + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/cfhb/IdCfHbMapping.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/cfhb/IdCfHbMapping.java new file mode 100644 index 000000000..fad1129c5 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/cfhb/IdCfHbMapping.java @@ -0,0 +1,54 @@ + +package eu.dnetlib.dhp.oa.graph.clean.cfhb; + +import java.io.Serializable; + +public class IdCfHbMapping implements Serializable { + + private String resultId; + + private String cfhb; + + private String masterId; + + private String masterName; + + public IdCfHbMapping() { + } + + public IdCfHbMapping(String id) { + this.resultId = id; + } + + public String getResultId() { + return resultId; + } + + public void setResultId(String resultId) { + this.resultId = resultId; + } + + public String getCfhb() { + return cfhb; + } + + public void setCfhb(String cfhb) { + this.cfhb = cfhb; + } + + public String getMasterId() { + return masterId; + } + + public void setMasterId(String masterId) { + this.masterId = masterId; + } + + public String getMasterName() { + return masterName; + } + + public void setMasterName(String masterName) { + this.masterName = masterName; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java index cd77f342e..37e693de9 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java @@ -4,9 +4,12 @@ package eu.dnetlib.dhp.oa.graph.clean.country; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.io.Serializable; +import java.util.Collection; import java.util.List; import java.util.Optional; +import java.util.function.Function; import java.util.stream.Collectors; +import java.util.stream.Stream; import javax.swing.text.html.Option; @@ -30,6 +33,7 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob; import eu.dnetlib.dhp.schema.oaf.Country; +import eu.dnetlib.dhp.schema.oaf.Instance; import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.StructuredProperty; import eu.dnetlib.dhp.schema.oaf.utils.PidType; @@ -43,7 +47,7 @@ public class CleanCountrySparkJob implements Serializable { String jsonConfiguration = IOUtils .toString( - CleanContextSparkJob.class + CleanCountrySparkJob.class .getResourceAsStream( "/eu/dnetlib/dhp/oa/graph/input_clean_country_parameters.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); @@ -58,8 +62,8 @@ public class CleanCountrySparkJob implements Serializable { String inputPath = parser.get("inputPath"); log.info("inputPath: {}", inputPath); - String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + String workingDir = parser.get("workingDir"); + log.info("workingDir: {}", workingDir); String datasourcePath = parser.get("hostedBy"); log.info("datasourcePath: {}", datasourcePath); @@ -85,12 +89,12 @@ public class CleanCountrySparkJob implements Serializable { spark -> { cleanCountry( - spark, country, verifyParam, inputPath, entityClazz, workingPath, collectedfrom, datasourcePath); + spark, country, verifyParam, inputPath, entityClazz, workingDir, collectedfrom, datasourcePath); }); } private static void cleanCountry(SparkSession spark, String country, String[] verifyParam, - String inputPath, Class entityClazz, String workingPath, String collectedfrom, String datasourcePath) { + String inputPath, Class entityClazz, String workingDir, String collectedfrom, String datasourcePath) { List hostedBy = spark .read() @@ -110,8 +114,8 @@ public class CleanCountrySparkJob implements Serializable { return r; } - if (r - .getPid() + List ids = getPidsAndAltIds(r).collect(Collectors.toList()); + if (ids .stream() .anyMatch( p -> p @@ -134,11 +138,11 @@ public class CleanCountrySparkJob implements Serializable { .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") - .json(workingPath); + .json(workingDir); spark .read() - .textFile(workingPath) + .textFile(workingDir) .map( (MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), Encoders.bean(entityClazz)) @@ -148,6 +152,42 @@ public class CleanCountrySparkJob implements Serializable { .json(inputPath); } + private static Stream getPidsAndAltIds(T r) { + final Stream resultPids = Optional + .ofNullable(r.getPid()) + .map(Collection::stream) + .orElse(Stream.empty()); + + final Stream instancePids = Optional + .ofNullable(r.getInstance()) + .map( + instance -> instance + .stream() + .flatMap( + i -> Optional + .ofNullable(i.getPid()) + .map(Collection::stream) + .orElse(Stream.empty()))) + .orElse(Stream.empty()); + + final Stream instanceAltIds = Optional + .ofNullable(r.getInstance()) + .map( + instance -> instance + .stream() + .flatMap( + i -> Optional + .ofNullable(i.getAlternateIdentifier()) + .map(Collection::stream) + .orElse(Stream.empty()))) + .orElse(Stream.empty()); + + return Stream + .concat( + Stream.concat(resultPids, instancePids), + instanceAltIds); + } + private static boolean pidInParam(String value, String[] verifyParam) { for (String s : verifyParam) if (value.startsWith(s)) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/GetDatasourceFromCountry.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/GetDatasourceFromCountry.java index dd5af6998..598fccdd7 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/GetDatasourceFromCountry.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/GetDatasourceFromCountry.java @@ -54,8 +54,8 @@ public class GetDatasourceFromCountry implements Serializable { String inputPath = parser.get("inputPath"); log.info("inputPath: {}", inputPath); - String workingPath = parser.get("workingPath"); - log.info("workingPath: {}", workingPath); + String workingPath = parser.get("workingDir"); + log.info("workingDir: {}", workingPath); String country = parser.get("country"); log.info("country: {}", country); @@ -65,13 +65,12 @@ public class GetDatasourceFromCountry implements Serializable { conf, isSparkSessionManaged, spark -> { - getDatasourceFromCountry(spark, country, inputPath, workingPath); }); } private static void getDatasourceFromCountry(SparkSession spark, String country, String inputPath, - String workingPath) { + String workingDir) { Dataset organization = spark .read() @@ -83,7 +82,6 @@ public class GetDatasourceFromCountry implements Serializable { (FilterFunction) o -> !o.getDataInfo().getDeletedbyinference() && o.getCountry().getClassid().length() > 0 && o.getCountry().getClassid().equals(country)); - ; // filtering of the relations taking the non deleted by inference and those with IsProvidedBy as relclass Dataset relation = spark @@ -97,12 +95,12 @@ public class GetDatasourceFromCountry implements Serializable { !rel.getDataInfo().getDeletedbyinference()); organization - .joinWith(relation, organization.col("id").equalTo(relation.col("target")), "left") + .joinWith(relation, organization.col("id").equalTo(relation.col("target"))) .map((MapFunction, String>) t2 -> t2._2().getSource(), Encoders.STRING()) .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") - .json(workingPath); + .json(workingDir); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index c157be51a..7aa40cb8a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -366,6 +366,7 @@ public abstract class AbstractMdRecordToOafMapper { r.setInstance(instances); r.setBestaccessright(OafMapperUtils.createBestAccessRights(instances)); + r.setEoscifguidelines(prepareEOSCIfGuidelines(doc, info)); } protected abstract List prepareResultPids(Document doc, DataInfo info); @@ -384,6 +385,25 @@ public abstract class AbstractMdRecordToOafMapper { return list; } + private List prepareEOSCIfGuidelines(Document doc, DataInfo info) { + final Set set = Sets.newHashSet(); + for (final Object o : doc.selectNodes("//oaf:eoscifguidelines")) { + final String code = ((Node) o).valueOf("@code"); + final String label = ((Node) o).valueOf("@label"); + final String url = ((Node) o).valueOf("@url"); + final String semrel = ((Node) o).valueOf("@semanticrelation"); + if (StringUtils.isNotBlank(code)) { + final EoscIfGuidelines eig = new EoscIfGuidelines(); + eig.setCode(code); + eig.setLabel(label); + eig.setUrl(url); + eig.setSemanticRelation(semrel); + set.add(eig); + } + } + return Lists.newArrayList(set); + } + protected abstract Qualifier prepareResourceType(Document doc, DataInfo info); protected abstract List prepareInstances( diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml index 2ba0a7ad7..683c2417b 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml @@ -317,13 +317,13 @@ - + yarn @@ -343,7 +343,7 @@ --inputPath${graphOutputPath}/publication --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Publication - --workingPath${workingDir}/working/publication + --workingDir${workingDir}/working/publication --contextId${contextId} --verifyParam${verifyParam} @@ -370,7 +370,7 @@ --inputPath${graphOutputPath}/dataset --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Dataset - --workingPath${workingDir}/working/dataset + --workingDir${workingDir}/working/dataset --contextId${contextId} --verifyParam${verifyParam} @@ -397,7 +397,7 @@ --inputPath${graphOutputPath}/otherresearchproduct --graphTableClassNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct - --workingPath${workingDir}/working/otherresearchproduct + --workingDir${workingDir}/working/otherresearchproduct --contextId${contextId} --verifyParam${verifyParam} @@ -424,7 +424,7 @@ --inputPath${graphOutputPath}/software --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Software - --workingPath${workingDir}/working/software + --workingDir${workingDir}/working/software --contextId${contextId} --verifyParam${verifyParam} @@ -432,14 +432,13 @@ - + - - + yarn cluster - Clean publications context + Select datasource ID from country eu.dnetlib.dhp.oa.graph.clean.country.GetDatasourceFromCountry dhp-graph-mapper-${projectVersion}.jar @@ -453,25 +452,25 @@ --conf spark.sql.shuffle.partitions=7680 --inputPath${graphOutputPath} - --workingPath${workingDir}/working/hostedby + --workingDir${workingDir}/working/hostedby --country${country} - + yarn cluster - Clean publications counmtry + Clean publication country eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob dhp-graph-mapper-${projectVersion}.jar @@ -486,13 +485,13 @@ --inputPath${graphOutputPath}/publication --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Publication - --workingPath${workingDir}/working/publication + --workingDir${workingDir}/working/publication --country${country} --verifyParam${verifyCountryParam} - --datasourcePath${workingDir}/working/hostedby + --hostedBy${workingDir}/working/hostedby --collectedfrom${collectedfrom} - + @@ -500,7 +499,7 @@ yarn cluster - Clean datasets Country + Clean dataset country eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob dhp-graph-mapper-${projectVersion}.jar @@ -515,13 +514,13 @@ --inputPath${graphOutputPath}/dataset --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Dataset - --workingPath${workingDir}/working/dataset + --workingDir${workingDir}/working/dataset --country${country} --verifyParam${verifyCountryParam} - --datasourcePath${workingDir}/working/hostedby + --hostedBy${workingDir}/working/hostedby --collectedfrom${collectedfrom} - + @@ -529,7 +528,7 @@ yarn cluster - Clean otherresearchproducts country + Clean otherresearchproduct country eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob dhp-graph-mapper-${projectVersion}.jar @@ -544,13 +543,13 @@ --inputPath${graphOutputPath}/otherresearchproduct --graphTableClassNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct - --workingPath${workingDir}/working/otherresearchproduct + --workingDir${workingDir}/working/otherresearchproduct --country${country} --verifyParam${verifyCountryParam} - --datasourcePath${workingDir}/working/hostedby + --hostedBy${workingDir}/working/hostedby --collectedfrom${collectedfrom} - + @@ -558,7 +557,7 @@ yarn cluster - Clean softwares country + Clean software country eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob dhp-graph-mapper-${projectVersion}.jar @@ -573,17 +572,212 @@ --inputPath${graphOutputPath}/software --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Software - --workingPath${workingDir}/working/software + --workingDir${workingDir}/working/software --country${country} --verifyParam${verifyCountryParam} - --datasourcePath${workingDir}/working/hostedby + --hostedBy${workingDir}/working/hostedby --collectedfrom${collectedfrom} - + + + + + ${wf:conf('shouldClean') eq true} + + + + + + + eu.dnetlib.dhp.oa.graph.clean.MasterDuplicateAction + --postgresUrl${postgresURL} + --postgresUser${postgresUser} + --postgresPassword${postgresPassword} + --hdfsPath${workingDir}/masterduplicate + --hdfsNameNode${nameNode} + + + + + + + + + + + + + + + yarn + cluster + patch publication cfhb + eu.dnetlib.dhp.oa.graph.clean.cfhb.CleanCfHbSparkJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=7680 + + --inputPath${graphOutputPath}/publication + --resolvedPath${workingDir}/cfHbResolved/publication + --outputPath${workingDir}/cfHbPatched/publication + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Publication + --masterDuplicatePath${workingDir}/masterduplicate + + + + + + + + yarn + cluster + patch dataset cfhb + eu.dnetlib.dhp.oa.graph.clean.cfhb.CleanCfHbSparkJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=7680 + + --inputPath${graphOutputPath}/dataset + --resolvedPath${workingDir}/cfHbResolved/dataset + --outputPath${workingDir}/cfHbPatched/dataset + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Dataset + --masterDuplicatePath${workingDir}/masterduplicate + + + + + + + + yarn + cluster + patch otherresearchproduct cfhb + eu.dnetlib.dhp.oa.graph.clean.cfhb.CleanCfHbSparkJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=7680 + + --inputPath${graphOutputPath}/otherresearchproduct + --resolvedPath${workingDir}/cfHbResolved/otherresearchproduct + --outputPath${workingDir}/cfHbPatched/otherresearchproduct + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --masterDuplicatePath${workingDir}/masterduplicate + + + + + + + + yarn + cluster + patch software cfhb + eu.dnetlib.dhp.oa.graph.clean.cfhb.CleanCfHbSparkJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=7680 + + --inputPath${graphOutputPath}/software + --resolvedPath${workingDir}/cfHbResolved/software + --outputPath${workingDir}/cfHbPatched/software + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Software + --masterDuplicatePath${workingDir}/masterduplicate + + + + + + + + + + + + + + + + + + + + ${workingDir}/cfHbPatched/publication + ${graphOutputPath}/publication + + + + + + + + + + + ${workingDir}/cfHbPatched/dataset + ${graphOutputPath}/dataset + + + + + + + + + + + ${workingDir}/cfHbPatched/otherresearchproduct + ${graphOutputPath}/otherresearchproduct + + + + + + + + + + + ${workingDir}/cfHbPatched/software + ${graphOutputPath}/software + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/datasourcemaster_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/datasourcemaster_parameters.json new file mode 100644 index 000000000..fbe2cca10 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/datasourcemaster_parameters.json @@ -0,0 +1,32 @@ +[ + { + "paramName": "pu", + "paramLongName": "postgresUrl", + "paramDescription": "the jdbc url to the postgres", + "paramRequired": true + }, + { + "paramName": "uid", + "paramLongName": "postgresUser", + "paramDescription": "the postgres user", + "paramRequired": true + }, + { + "paramName": "pwd", + "paramLongName": "postgresPassword", + "paramDescription": "the postgres password=", + "paramRequired": true + }, + { + "paramName": "p", + "paramLongName": "hdfsPath", + "paramDescription": "the target path on HDFS", + "paramRequired": true + }, + { + "paramName": "nn", + "paramLongName": "hdfsNameNode", + "paramDescription": "the HDFS nameNode", + "paramRequired": true + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/workflow.xml index ba5f4f375..4468382be 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/workflow.xml @@ -126,6 +126,7 @@ --hiveDbName${hiveDbName} --classNameeu.dnetlib.dhp.schema.oaf.Publication --hiveMetastoreUris${hiveMetastoreUris} + --numPartitions8000 @@ -152,6 +153,7 @@ --hiveDbName${hiveDbName} --classNameeu.dnetlib.dhp.schema.oaf.Dataset --hiveMetastoreUris${hiveMetastoreUris} + --numPartitions4000 @@ -178,6 +180,7 @@ --hiveDbName${hiveDbName} --classNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct --hiveMetastoreUris${hiveMetastoreUris} + --numPartitions3000 @@ -204,6 +207,7 @@ --hiveDbName${hiveDbName} --classNameeu.dnetlib.dhp.schema.oaf.Software --hiveMetastoreUris${hiveMetastoreUris} + --numPartitions300 @@ -230,6 +234,7 @@ --hiveDbName${hiveDbName} --classNameeu.dnetlib.dhp.schema.oaf.Datasource --hiveMetastoreUris${hiveMetastoreUris} + --numPartitions100 @@ -256,6 +261,7 @@ --hiveDbName${hiveDbName} --classNameeu.dnetlib.dhp.schema.oaf.Organization --hiveMetastoreUris${hiveMetastoreUris} + --numPartitions400 @@ -309,6 +315,7 @@ --hiveDbName${hiveDbName} --classNameeu.dnetlib.dhp.schema.oaf.Relation --hiveMetastoreUris${hiveMetastoreUris} + --numPartitions10000 diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_cfhb_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_cfhb_parameters.json new file mode 100644 index 000000000..859350bbb --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_cfhb_parameters.json @@ -0,0 +1,38 @@ +[ + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false + }, + { + "paramName": "in", + "paramLongName": "inputPath", + "paramDescription": "the path to the graph data dump to read", + "paramRequired": true + }, + { + "paramName": "rp", + "paramLongName": "resolvedPath", + "paramDescription": "the path to store the resolved records", + "paramRequired": true + }, + { + "paramName": "out", + "paramLongName": "outputPath", + "paramDescription": "the path to store the output graph", + "paramRequired": true + }, + { + "paramName": "class", + "paramLongName": "graphTableClassName", + "paramDescription": "class name moelling the graph table", + "paramRequired": true + }, + { + "paramName": "md", + "paramLongName": "masterDuplicatePath", + "paramDescription": "path to the file on HDFS holding the datasource id tuples [master, duplicate]", + "paramRequired": true + } +] diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json index e3d31d69f..8be6496d8 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json @@ -12,8 +12,8 @@ "paramRequired": true }, { - "paramName": "wp", - "paramLongName": "workingPath", + "paramName": "wd", + "paramLongName": "workingDir", "paramDescription": "the path to store the output graph", "paramRequired": true }, diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_country_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_country_parameters.json index 318fb22f8..b38b5ac9f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_country_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_country_parameters.json @@ -12,8 +12,8 @@ "paramRequired": true }, { - "paramName": "wp", - "paramLongName": "workingPath", + "paramName": "wd", + "paramLongName": "workingDir", "paramDescription": "the path to store the output graph", "paramRequired": true }, diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_datasource_country_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_datasource_country_parameters.json index e0aa60328..01aa2e7b0 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_datasource_country_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_datasource_country_parameters.json @@ -12,8 +12,8 @@ "paramRequired": true }, { - "paramName": "wp", - "paramLongName": "workingPath", + "paramName": "wd", + "paramLongName": "workingDir", "paramDescription": "the path to store the output graph", "paramRequired": true }, diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala index 556106180..362cb2028 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala @@ -116,54 +116,45 @@ object SparkConvertRDDtoDataset { .map(s => mapper.readValue(s, classOf[Relation])) .filter(r => r.getDataInfo != null && !r.getDataInfo.getDeletedbyinference) .filter(r => r.getSource.startsWith("50") && r.getTarget.startsWith("50")) - .filter(r => filterRelations(subRelTypeFilter, relClassFilter, r)) - //filter OpenCitations relations - .filter(r => - r.getDataInfo.getProvenanceaction != null && - !"sysimport:crosswalk:opencitations".equals(r.getDataInfo.getProvenanceaction.getClassid) - ) + .filter(r => filterRelations(r)) + //filter OpenCitations relations +// .filter(r => +// r.getDataInfo.getProvenanceaction != null && +// !"sysimport:crosswalk:opencitations".equals(r.getDataInfo.getProvenanceaction.getClassid) +// ) spark.createDataset(rddRelation).as[Relation].write.mode(SaveMode.Overwrite).save(s"$relPath") } - private def filterRelations(subRelTypeFilter: String, relClassFilter: List[String], r: Relation): Boolean = { - if (StringUtils.isNotBlank(subRelTypeFilter)) { - subRelTypeFilter.equalsIgnoreCase(r.getSubRelType) - } else { - !relClassFilter.exists(k => k.equalsIgnoreCase(r.getRelClass)) + private def filterRelations(r: Relation): Boolean = { + + /** * + * We filter relation generated by dedups + * and all the relation that have one single collectedFrom OpenCitation + */ + + val relClassFilter = List( + ModelConstants.MERGES, + ModelConstants.IS_MERGED_IN, + ModelConstants.HAS_AMONG_TOP_N_SIMILAR_DOCS, + ModelConstants.IS_AMONG_TOP_N_SIMILAR_DOCS + ) + if (relClassFilter.exists(k => k.equalsIgnoreCase(r.getRelClass))) + false + else { + if (r.getCollectedfrom == null || r.getCollectedfrom.size() == 0) + false + else if (r.getCollectedfrom.size() > 1) + true + else if ( + r.getCollectedfrom.size() == 1 && r.getCollectedfrom.get(0) != null && "OpenCitations".equalsIgnoreCase( + r.getCollectedfrom.get(0).getValue + ) + ) + false + else + true } } - /* - //TODO: finalise implementation - private def processResult[T<: Result]( - implicit ct: ClassTag[T], - log: Logger, - spark: SparkSession, - sourcePath: String, - entityPath: String, - clazz: Class[T] - ): Unit = { - val entityType = clazz.getSimpleName.toLowerCase - - log.info(s"Converting $entityType") - - val mapper = new ObjectMapper() with ScalaObjectMapper - mapper.registerModule(DefaultScalaModule) - - val rdd = spark.sparkContext - .textFile(s"$sourcePath/$entityType") - .map(s => mapper.readValue(s, clazz)) - .filter(r => r.getDataInfo != null && !r.getDataInfo.getDeletedbyinference); - - implicit val encoder: Encoder[T] = Encoders.kryo(clazz) - spark - .createDataset(rdd) - .as[T] - .write - .mode(SaveMode.Overwrite) - .save(s"$entityPath/$entityType") - } - */ - } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java index e206c7c5a..91094f534 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java @@ -82,10 +82,10 @@ public class CleanContextTest { CleanContextSparkJob.main(new String[] { "--isSparkSessionManaged", Boolean.FALSE.toString(), "--inputPath", workingDir.toString() + "/publication", - "-graphTableClassName", Publication.class.getCanonicalName(), - "-workingPath", workingDir.toString() + "/working", - "-contextId", "sobigdata", - "-verifyParam", "gCube " + "--graphTableClassName", Publication.class.getCanonicalName(), + "--workingDir", workingDir.toString() + "/working", + "--contextId", "sobigdata", + "--verifyParam", "gCube " }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java index c9f846570..de9e4fc90 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java @@ -5,6 +5,7 @@ import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; +import eu.dnetlib.dhp.schema.oaf.Dataset; import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -83,12 +84,12 @@ public class CleanCountryTest { CleanCountrySparkJob.main(new String[] { "--isSparkSessionManaged", Boolean.FALSE.toString(), "--inputPath", workingDir.toString() + "/publication", - "-graphTableClassName", Publication.class.getCanonicalName(), - "-workingPath", workingDir.toString() + "/working", - "-country", "NL", - "-verifyParam", "10.17632", - "-collectedfrom", "NARCIS", - "-hostedBy", getClass() + "--graphTableClassName", Publication.class.getCanonicalName(), + "--workingDir", workingDir.toString() + "/working", + "--country", "NL", + "--verifyParam", "10.17632", + "--collectedfrom", "NARCIS", + "--hostedBy", getClass() .getResource("/eu/dnetlib/dhp/oa/graph/clean/hostedBy") .getPath() }); @@ -147,4 +148,44 @@ public class CleanCountryTest { .size()); } + @Test + public void testDatasetClean() throws Exception { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/clean/dataset_clean_country.json") + .getPath(); + + spark + .read() + .textFile(sourcePath) + .map( + (MapFunction) r -> OBJECT_MAPPER.readValue(r, Dataset.class), + Encoders.bean(Dataset.class)) + .write() + .json(workingDir.toString() + "/dataset"); + + CleanCountrySparkJob.main(new String[] { + "--isSparkSessionManaged", Boolean.FALSE.toString(), + "--inputPath", workingDir.toString() + "/dataset", + "-graphTableClassName", Dataset.class.getCanonicalName(), + "-workingDir", workingDir.toString() + "/working", + "-country", "NL", + "-verifyParam", "10.17632", + "-collectedfrom", "NARCIS", + "-hostedBy", getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/clean/hostedBy") + .getPath() + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); + + Assertions.assertEquals(1, tmp.count()); + + Assertions.assertEquals(0, tmp.first().getCountry().size()); + + + } + } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java index 6c43da832..fc7c6e5f1 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java @@ -7,6 +7,7 @@ import static org.mockito.Mockito.lenient; import java.io.IOException; import java.util.Collection; import java.util.List; +import java.util.Optional; import java.util.Set; import java.util.stream.Collectors; import java.util.stream.Stream; @@ -278,10 +279,25 @@ public class GraphCleaningFunctionsTest { s -> "0102 computer and information sciences".equals(s.getValue()) & ModelConstants.DNET_SUBJECT_FOS_CLASSID.equals(s.getQualifier().getClassid()))); + verify_keyword(p_cleaned, "In Situ Hybridization"); + verify_keyword(p_cleaned, "Avicennia"); + // TODO add more assertions to verity the cleaned values System.out.println(MAPPER.writeValueAsString(p_cleaned)); } + private static void verify_keyword(Publication p_cleaned, String subject) { + Optional s1 = p_cleaned + .getSubject() + .stream() + .filter(s -> s.getValue().equals(subject)) + .findFirst(); + + assertTrue(s1.isPresent()); + assertEquals(ModelConstants.DNET_SUBJECT_KEYWORD, s1.get().getQualifier().getClassid()); + assertEquals(ModelConstants.DNET_SUBJECT_KEYWORD, s1.get().getQualifier().getClassname()); + } + private Stream getAuthorPidTypes(Result pub) { return pub .getAuthor() diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/cfhb/CleanCfHbSparkJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/cfhb/CleanCfHbSparkJobTest.java new file mode 100644 index 000000000..9096180ef --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/cfhb/CleanCfHbSparkJobTest.java @@ -0,0 +1,213 @@ + +package eu.dnetlib.dhp.oa.graph.clean.cfhb; + +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertTrue; + +import java.io.File; +import java.io.IOException; +import java.net.URISyntaxException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.nio.file.Paths; + +import org.apache.commons.io.FileUtils; +import org.apache.spark.SparkConf; +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.SparkSession; +import org.junit.jupiter.api.*; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.schema.oaf.Dataset; +import eu.dnetlib.dhp.schema.oaf.Publication; + +public class CleanCfHbSparkJobTest { + + private static final Logger log = LoggerFactory.getLogger(CleanCfHbSparkJobTest.class); + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path testBaseTmpPath; + + private static String resolvedPath; + + private static String graphInputPath; + + private static String graphOutputPath; + + private static String dsMasterDuplicatePath; + + @BeforeAll + public static void beforeAll() throws IOException, URISyntaxException { + + testBaseTmpPath = Files.createTempDirectory(CleanCfHbSparkJobTest.class.getSimpleName()); + log.info("using test base path {}", testBaseTmpPath); + + final File entitiesSources = Paths + .get(CleanCfHbSparkJobTest.class.getResource("/eu/dnetlib/dhp/oa/graph/clean/cfhb/entities").toURI()) + .toFile(); + + FileUtils + .copyDirectory( + entitiesSources, + testBaseTmpPath.resolve("input").resolve("entities").toFile()); + + FileUtils + .copyFileToDirectory( + Paths + .get( + CleanCfHbSparkJobTest.class + .getResource("/eu/dnetlib/dhp/oa/graph/clean/cfhb/masterduplicate.json") + .toURI()) + .toFile(), + testBaseTmpPath.resolve("workingDir").resolve("masterduplicate").toFile()); + + graphInputPath = testBaseTmpPath.resolve("input").resolve("entities").toString(); + resolvedPath = testBaseTmpPath.resolve("workingDir").resolve("cfHbResolved").toString(); + graphOutputPath = testBaseTmpPath.resolve("workingDir").resolve("cfHbPatched").toString(); + dsMasterDuplicatePath = testBaseTmpPath.resolve("workingDir").resolve("masterduplicate").toString(); + + SparkConf conf = new SparkConf(); + conf.setAppName(CleanCfHbSparkJobTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("spark.ui.enabled", "false"); + + spark = SparkSession + .builder() + .appName(CleanCfHbSparkJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(testBaseTmpPath.toFile()); + spark.stop(); + } + + @Test + void testCleanCfHbSparkJob() throws Exception { + final String outputPath = graphOutputPath + "/dataset"; + final String inputPath = graphInputPath + "/dataset"; + + org.apache.spark.sql.Dataset records = read(spark, inputPath, Dataset.class); + Dataset d = records + .filter("id = '50|doi_________::09821844208a5cd6300b2bfb13bca1b9'") + .first(); + assertEquals("10|re3data_____::4c4416659cb74c2e0e891a883a047cbc", d.getCollectedfrom().get(0).getKey()); + assertEquals("Bacterial Protein Interaction Database - DUP", d.getCollectedfrom().get(0).getValue()); + assertEquals( + "10|re3data_____::4c4416659cb74c2e0e891a883a047cbc", d.getInstance().get(0).getCollectedfrom().getKey()); + assertEquals( + "Bacterial Protein Interaction Database - DUP", d.getInstance().get(0).getCollectedfrom().getValue()); + + d = records + .filter("id = '50|DansKnawCris::0dd644304b7116e8e58da3a5e3adc37a'") + .first(); + assertEquals("10|opendoar____::788b4ac1e172d8e520c2b9461c0a3d35", d.getCollectedfrom().get(0).getKey()); + assertEquals("FILUR DATA - DUP", d.getCollectedfrom().get(0).getValue()); + assertEquals( + "10|opendoar____::788b4ac1e172d8e520c2b9461c0a3d35", d.getInstance().get(0).getCollectedfrom().getKey()); + assertEquals("FILUR DATA - DUP", d.getInstance().get(0).getCollectedfrom().getValue()); + assertEquals( + "10|re3data_____::6ffd7bc058f762912dc494cd9c175341", d.getInstance().get(0).getHostedby().getKey()); + assertEquals("depositar - DUP", d.getInstance().get(0).getHostedby().getValue()); + + d = records + .filter("id = '50|DansKnawCris::203a27996ddc0fd1948258e5b7dec61c'") + .first(); + assertEquals("10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getCollectedfrom().get(0).getKey()); + assertEquals("DANS (Data Archiving and Networked Services)", d.getCollectedfrom().get(0).getValue()); + assertEquals( + "10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getInstance().get(0).getCollectedfrom().getKey()); + assertEquals( + "DANS (Data Archiving and Networked Services)", d.getInstance().get(0).getCollectedfrom().getValue()); + assertEquals( + "10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getInstance().get(0).getHostedby().getKey()); + assertEquals("DANS (Data Archiving and Networked Services)", d.getInstance().get(0).getHostedby().getValue()); + + CleanCfHbSparkJob + .main( + new String[] { + "--isSparkSessionManaged", Boolean.FALSE.toString(), + "--inputPath", inputPath, + "--outputPath", outputPath, + "--resolvedPath", resolvedPath + "/dataset", + "--graphTableClassName", Dataset.class.getCanonicalName(), + "--masterDuplicatePath", dsMasterDuplicatePath + }); + + assertTrue(Files.exists(Paths.get(graphOutputPath, "dataset"))); + + records = read(spark, outputPath, Dataset.class); + + assertEquals(3, records.count()); + + d = records + .filter("id = '50|doi_________::09821844208a5cd6300b2bfb13bca1b9'") + .first(); + assertEquals("10|fairsharing_::a29d1598024f9e87beab4b98411d48ce", d.getCollectedfrom().get(0).getKey()); + assertEquals("Bacterial Protein Interaction Database", d.getCollectedfrom().get(0).getValue()); + assertEquals( + "10|fairsharing_::a29d1598024f9e87beab4b98411d48ce", d.getInstance().get(0).getCollectedfrom().getKey()); + assertEquals("Bacterial Protein Interaction Database", d.getInstance().get(0).getCollectedfrom().getValue()); + + d = records + .filter("id = '50|DansKnawCris::0dd644304b7116e8e58da3a5e3adc37a'") + .first(); + assertEquals("10|re3data_____::fc1db64b3964826913b1e9eafe830490", d.getCollectedfrom().get(0).getKey()); + assertEquals("FULIR Data", d.getCollectedfrom().get(0).getValue()); + assertEquals( + "10|re3data_____::fc1db64b3964826913b1e9eafe830490", d.getInstance().get(0).getCollectedfrom().getKey()); + assertEquals("FULIR Data", d.getInstance().get(0).getCollectedfrom().getValue()); + assertEquals( + "10|fairsharing_::3f647cadf56541fb9513cb63ec370187", d.getInstance().get(0).getHostedby().getKey()); + assertEquals("depositar", d.getInstance().get(0).getHostedby().getValue()); + + d = records + .filter("id = '50|DansKnawCris::203a27996ddc0fd1948258e5b7dec61c'") + .first(); + assertEquals("10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getCollectedfrom().get(0).getKey()); + assertEquals("DANS (Data Archiving and Networked Services)", d.getCollectedfrom().get(0).getValue()); + assertEquals( + "10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getInstance().get(0).getCollectedfrom().getKey()); + assertEquals( + "DANS (Data Archiving and Networked Services)", d.getInstance().get(0).getCollectedfrom().getValue()); + assertEquals( + "10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getInstance().get(0).getHostedby().getKey()); + assertEquals("DANS (Data Archiving and Networked Services)", d.getInstance().get(0).getHostedby().getValue()); + + d = records + .filter("id = '50|DansKnawCris::203a27996ddc0fd1948258e5b7dec61c'") + .first(); + assertEquals("10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getCollectedfrom().get(0).getKey()); + assertEquals("DANS (Data Archiving and Networked Services)", d.getCollectedfrom().get(0).getValue()); + assertEquals( + "10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getInstance().get(0).getCollectedfrom().getKey()); + assertEquals( + "DANS (Data Archiving and Networked Services)", d.getInstance().get(0).getCollectedfrom().getValue()); + assertEquals( + "10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getInstance().get(0).getHostedby().getKey()); + assertEquals("DANS (Data Archiving and Networked Services)", d.getInstance().get(0).getHostedby().getValue()); + } + + private org.apache.spark.sql.Dataset read(SparkSession spark, String path, Class clazz) { + return spark + .read() + .textFile(path) + .map(as(clazz), Encoders.bean(clazz)); + } + + private static MapFunction as(Class clazz) { + return s -> OBJECT_MAPPER.readValue(s, clazz); + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index f0eadbd0d..d08545388 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -26,6 +26,7 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions; import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; import eu.dnetlib.dhp.schema.oaf.utils.PidType; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; @@ -238,7 +239,11 @@ class MappersTest { assertNotNull(i.getAccessright()); assertEquals("OPEN", i.getAccessright().getClassid()); }); - assertEquals("UNKNOWN", p.getInstance().get(0).getRefereed().getClassid()); + + Publication p_cleaned = cleanup(p, vocs); + assertEquals("0000", p_cleaned.getInstance().get(0).getRefereed().getClassid()); + assertEquals("Unknown", p_cleaned.getInstance().get(0).getRefereed().getClassname()); + assertNotNull(p.getInstance().get(0).getPid()); assertEquals(2, p.getInstance().get(0).getPid().size()); @@ -453,7 +458,10 @@ class MappersTest { assertNotNull(i.getAccessright()); assertEquals("OPEN", i.getAccessright().getClassid()); }); - assertEquals("UNKNOWN", p.getInstance().get(0).getRefereed().getClassid()); + + Publication p_cleaned = cleanup(p, vocs); + assertEquals("0000", p_cleaned.getInstance().get(0).getRefereed().getClassid()); + assertEquals("Unknown", p_cleaned.getInstance().get(0).getRefereed().getClassname()); } @Test @@ -570,7 +578,9 @@ class MappersTest { assertTrue(i.getUrl().contains("http://apps.who.int/trialsearch/Trial3.aspx?trialid=NCT02321059")); assertTrue(i.getUrl().contains("https://clinicaltrials.gov/ct2/show/NCT02321059")); - assertEquals("UNKNOWN", i.getRefereed().getClassid()); + Dataset d_cleaned = cleanup(d, vocs); + assertEquals("0000", d_cleaned.getInstance().get(0).getRefereed().getClassid()); + assertEquals("Unknown", d_cleaned.getInstance().get(0).getRefereed().getClassname()); } @Test @@ -871,7 +881,10 @@ class MappersTest { assertNotNull(i.getAccessright()); assertEquals("UNKNOWN", i.getAccessright().getClassid()); }); - assertEquals("UNKNOWN", p.getInstance().get(0).getRefereed().getClassid()); + + Dataset p_cleaned = cleanup(p, vocs); + assertEquals("0000", p_cleaned.getInstance().get(0).getRefereed().getClassid()); + assertEquals("Unknown", p_cleaned.getInstance().get(0).getRefereed().getClassname()); } @Test @@ -947,6 +960,11 @@ class MappersTest { Instance inst = p.getInstance().get(0); assertEquals("https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca", inst.getPid().get(0).getValue()); assertEquals("https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca", inst.getUrl().get(0)); + assertEquals(1, p.getEoscifguidelines().size()); + assertEquals("EOSC::RO-crate", p.getEoscifguidelines().get(0).getCode()); + assertEquals("EOSC::RO-crate", p.getEoscifguidelines().get(0).getLabel()); + assertEquals("", p.getEoscifguidelines().get(0).getUrl()); + assertEquals("compliesWith", p.getEoscifguidelines().get(0).getSemanticRelation()); } @@ -995,6 +1013,18 @@ class MappersTest { } + @Test + void testEOSCFuture_ROHub() throws IOException { + final String xml = IOUtils + .toString(Objects.requireNonNull(getClass().getResourceAsStream("photic-zone-transformed.xml"))); + final List list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml); + final OtherResearchProduct rocrate = (OtherResearchProduct) list.get(0); + assertNotNull(rocrate.getEoscifguidelines()); + System.out.println("***************"); + System.out.println(new ObjectMapper().writeValueAsString(rocrate)); + System.out.println("***************"); + } + @Test void testNotWellFormed() throws IOException { final String xml = IOUtils diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/cfhb/entities/dataset/dataset.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/cfhb/entities/dataset/dataset.json new file mode 100644 index 000000000..bf2f2d963 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/cfhb/entities/dataset/dataset.json @@ -0,0 +1,3 @@ +{"author":[{"affiliation":[],"fullname":"Greenough, B","name":"B","pid":[],"rank":1,"surname":"Greenough"}],"bestaccessright":{"classid":"UNKNOWN","classname":"not available","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":[{"key":"10|re3data_____::4c4416659cb74c2e0e891a883a047cbc","value":"Bacterial Protein Interaction Database - 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"classname": "Open Access", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "instancetype": {"classid": "0021", "classname": "Dataset", "schemeid": "dnet:publication_resource", "schemename": "dnet:publication_resource"}}], "dateofcollection": "2022-08-17T20:06:53+0000", "fulltext": [], "dateoftransformation": "2022-08-17T20:06:53+0000", "description": [{"dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:datasetarchive", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "value": "Unprocessed images for: Acinetobacter baumannii defends against oxidative stress through a Mn2+-dependent small RNA-mediated repression of type VI secretion system"}], "format": [], "measures": [{"id": "influence", "unit": [{"dataInfo": {"provenanceaction": {"classid": "measure:bip", "classname": "Inferred by OpenAIRE", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "update", "invisible": false, "trust": ""}, "key": "score", "value": "4.842839E-9"}, {"dataInfo": {"provenanceaction": {"classid": "measure:bip", "classname": "Inferred by OpenAIRE", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "update", "invisible": false, "trust": ""}, "key": "class", "value": "C"}]}, {"id": "popularity", "unit": [{"dataInfo": {"provenanceaction": {"classid": "measure:bip", "classname": "Inferred by OpenAIRE", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "update", "invisible": false, "trust": ""}, "key": "score", "value": "7.705171E-9"}, {"dataInfo": {"provenanceaction": {"classid": "measure:bip", "classname": "Inferred by OpenAIRE", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "update", "invisible": false, "trust": ""}, "key": "class", "value": "C"}]}, {"id": "influence_alt", "unit": [{"dataInfo": {"provenanceaction": {"classid": "measure:bip", "classname": "Inferred by OpenAIRE", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "update", "invisible": false, "trust": ""}, "key": "score", "value": "0"}, {"dataInfo": {"provenanceaction": {"classid": "measure:bip", "classname": "Inferred by OpenAIRE", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "update", "invisible": false, "trust": ""}, "key": "class", "value": "C"}]}, {"id": "popularity_alt", "unit": [{"dataInfo": {"provenanceaction": {"classid": "measure:bip", "classname": "Inferred by OpenAIRE", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "update", "invisible": false, "trust": ""}, "key": "score", "value": "0.0"}, {"dataInfo": {"provenanceaction": {"classid": "measure:bip", "classname": "Inferred by OpenAIRE", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "update", "invisible": false, "trust": ""}, "key": "class", "value": "C"}]}, {"id": "impulse", "unit": [{"dataInfo": {"provenanceaction": {"classid": "measure:bip", "classname": "Inferred by OpenAIRE", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "update", "invisible": false, "trust": ""}, "key": "score", "value": "0"}, {"dataInfo": {"provenanceaction": {"classid": "measure:bip", "classname": "Inferred by OpenAIRE", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "update", "invisible": false, "trust": ""}, "key": "class", "value": "C"}]}], "coverage": [], "externalReference": [], "publisher": {"value": "Mendeley"}, "context": [], "eoscifguidelines": [], "language": {"classid": "und", "classname": "Undetermined", "schemeid": "dnet:languages", "schemename": "dnet:languages"}, "resulttype": {"classid": "dataset", "classname": "dataset", "schemeid": "dnet:result_typologies", "schemename": "dnet:result_typologies"}, "country": [{"classid": "NL", "classname": "Netherlands", "dataInfo": {"provenanceaction": {"classid": "country:instrepos", "classname": "Propagation of country to result collected from datasources of type institutional repositories", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "propagation", "invisible": false, "trust": "0.85"}, "schemeid": "dnet:countries", "schemename": "dnet:countries"}], "extraInfo": [], "originalId": ["50|datacite____::e04c8cbefb6f0b8378a04c57e6edbd82", "10.17632/v6cgs4jpbk.2", "50|datacite____::1544eab177367edbc4d9d56517d482df", "10.17632/v6cgs4jpbk.3", "50|datacite____::f02e8a3c923d8e120e1cdc5d2dcda3ff", "10.17632/v6cgs4jpbk", "50|datacite____::fce3b034f047504961bc4baab3515295", "10.17632/v6cgs4jpbk.1", "50|DansKnawCris::3b86948c475d0efbde049b72579feb50", "oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:254617", "50|dris___00893::3b86948c475d0efbde049b72579feb50", "oai:easy.dans.knaw.nl:easy-dataset:254617", "50|r384e1237760::673150ea2ae00b606fd8c39897dfa3d7"], "source": [], "dateofacceptance": {"value": "2022-08-16"}, "title": [{"qualifier": {"classid": "main title", "classname": "main title", "schemeid": "dnet:dataCite_title", "schemename": "dnet:dataCite_title"}, "value": "Unprocessed images for: Acinetobacter baumannii defends against oxidative stress through a Mn2+-dependent small RNA-mediated repression of type VI secretion system"}]} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json index 8e4fc4545..8f35470e1 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json @@ -706,6 +706,28 @@ "source": [ ], "subject": [ + { + "dataInfo": { + "provenanceaction": { + "classid": "sysimport:crosswalk:repository", + "classname": "sysimport:crosswalk:repository", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + }, + "deletedbyinference": false, + "inferred": false, + "inferenceprovenance": "", + "invisible": false, + "trust": "0.9" + }, + "qualifier": { + "classid": "FOS", + "classname": "Fields of Science and Technology classification", + "schemeid": "dnet:result_subject", + "schemename": "dnet:result_subject" + }, + "value": "In Situ Hybridization" + }, { "dataInfo": { "deletedbyinference": false, @@ -885,24 +907,23 @@ { "dataInfo": { "deletedbyinference": false, - "inferenceprovenance": "", "inferred": false, "invisible": false, "provenanceaction": { - "classid": "sysimport:crosswalk:datasetarchive", - "classname": "sysimport:crosswalk:datasetarchive", + "classid": "sysimport:actionset", + "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions" }, "trust": "0.9" }, "qualifier": { - "classid": "", - "classname": "", - "schemeid": "", - "schemename": "" + "classid": "FOS", + "classname": "Fields of Science and Technology classification", + "schemeid": "dnet:subject_classification_typologies", + "schemename": "dnet:subject_classification_typologies" }, - "value": "doped silicon" + "value": "Avicennia" }, { "dataInfo": { diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/photic-zone-transformed.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/photic-zone-transformed.xml new file mode 100644 index 000000000..22bf0577e --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/photic-zone-transformed.xml @@ -0,0 +1,108 @@ + + +
+ fsh_____4119::68126da991bd76d8be494bddfbf7a1bb + https://w3id.org/ro-id/28499bdf-a0c6-46aa-a96f-50bd9490b8be + + + + + + 2022-11-15T12:29:19Z + 2022-11-15T12:29:19Z + fsh_____4119 + https://w3id.org/ro-id/28499bdf-a0c6-46aa-a96f-50bd9490b8be + 2022-11-15T12:29:19Z + rohub_data + ro-crate_data +
+ + + https://w3id.org/ro-id/28499bdf-a0c6-46aa-a96f-50bd9490b8be + + https://w3id.org/ro-id/28499bdf-a0c6-46aa-a96f-50bd9490b8be + + + https://w3id.org/ro-id/28499bdf-a0c6-46aa-a96f-50bd9490b8be/resources/b1b617b2-6b79-4bae-9fa6-b76945645626 + https://w3id.org/ro-id/28499bdf-a0c6-46aa-a96f-50bd9490b8be/resources/78103994-30be-4875-bf89-5acd752b5c3d + https://w3id.org/ro-id/28499bdf-a0c6-46aa-a96f-50bd9490b8be/resources/18fd1c70-249b-4c67-80ee-539f801a0da7 + https://w3id.org/ro-id/28499bdf-a0c6-46aa-a96f-50bd9490b8be/resources/32faa2eb-4cc8-401f-ac5c-bec2849b70e1 + https://w3id.org/ro-id/28499bdf-a0c6-46aa-a96f-50bd9490b8be/resources/4c253f5a-d427-40c2-9e9f-6063ae087239 + https://w3id.org/ro-id/28499bdf-a0c6-46aa-a96f-50bd9490b8be/resources/371b1957-078c-472b-a195-af7bce152c10 + https://w3id.org/ro-id/28499bdf-a0c6-46aa-a96f-50bd9490b8be/resources/82f9e4b8-01b4-4e50-9e27-ec9d337c8d74 + + RO-crate + + Creative Commons Attribution 4.0 International + open access + + + Mapping the photic zone of the Mediterranean Sea + + + Estimating the penetration of light along the water column from satellite data to map the photic zone in the Mediterranean Sea + + CNR-ISMAR + + + Giorgio Castellan + + + Lorenzo Angeletti + + + Paolo Montagna + + + Marco Taviani + + + + 2022-11-14T16:32:45Z + + + Estimating the penetration of light along the water column from satellite data to map the photic zone in the Mediterranean Sea + + 2022 + + open access + + + 813.478 KB + + + Earth sciences + Ecology + Optics + + + https://w3id.org/ro-id/28499bdf-a0c6-46aa-a96f-50bd9490b8be + 0048 + 2022-11-14 + OPEN + https://creativecommons.org/licenses/by/4.0/legalcode + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/rohub.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/rohub.xml index e1e30c3de..18f637ecc 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/rohub.xml +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/rohub.xml @@ -65,7 +65,6 @@ Ecology - EOSC::RO-crate https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca @@ -75,5 +74,9 @@ + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/oa/graph/resolution/ResolveEntitiesTest.scala b/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/oa/graph/resolution/ResolveEntitiesTest.scala index e333da1aa..d415b7fc9 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/oa/graph/resolution/ResolveEntitiesTest.scala +++ b/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/oa/graph/resolution/ResolveEntitiesTest.scala @@ -53,7 +53,7 @@ class ResolveEntitiesTest extends Serializable { def generateUpdates(spark: SparkSession): Unit = { val template = Source.fromInputStream(this.getClass.getResourceAsStream("updates")).mkString - val pids: List[String] = template.lines + val pids: List[String] = template.linesWithSeparators.map(l =>l.stripLineEnd) .map { id => val r = new Result r.setId(id.toLowerCase.trim) @@ -127,7 +127,7 @@ class ResolveEntitiesTest extends Serializable { entities.foreach { e => val template = Source.fromInputStream(this.getClass.getResourceAsStream(s"$e")).mkString spark - .createDataset(spark.sparkContext.parallelize(template.lines.toList)) + .createDataset(spark.sparkContext.parallelize(template.linesWithSeparators.map(l =>l.stripLineEnd).toList)) .as[String] .write .option("compression", "gzip") @@ -264,7 +264,7 @@ class ResolveEntitiesTest extends Serializable { Source .fromInputStream(this.getClass.getResourceAsStream(s"publication")) .mkString - .lines + .linesWithSeparators.map(l =>l.stripLineEnd) .next(), classOf[Publication] ) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/sx/graph/scholix/ScholixGraphTest.scala b/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/sx/graph/scholix/ScholixGraphTest.scala index e92f36896..0ea908290 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/sx/graph/scholix/ScholixGraphTest.scala +++ b/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/sx/graph/scholix/ScholixGraphTest.scala @@ -47,7 +47,7 @@ class ScholixGraphTest extends AbstractVocabularyTest { val inputRelations = Source .fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/oaf_to_summary")) .mkString - val items = inputRelations.lines.toList + val items = inputRelations.linesWithSeparators.map(l =>l.stripLineEnd).toList assertNotNull(items) items.foreach(i => assertTrue(i.nonEmpty)) val result = @@ -69,7 +69,7 @@ class ScholixGraphTest extends AbstractVocabularyTest { getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/merge_result_scholix") ) .mkString - val result: List[(Relation, ScholixSummary)] = inputRelations.lines + val result: List[(Relation, ScholixSummary)] = inputRelations.linesWithSeparators.map(l =>l.stripLineEnd) .sliding(2) .map(s => (s.head, s(1))) .map(p => (mapper.readValue(p._1, classOf[Relation]), mapper.readValue(p._2, classOf[ScholixSummary]))) diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/EOSCFuture_Test.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/EOSCFuture_Test.java new file mode 100644 index 000000000..3e1a501d1 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/EOSCFuture_Test.java @@ -0,0 +1,91 @@ + +package eu.dnetlib.dhp.oa.provision; + +import static org.junit.jupiter.api.Assertions.assertNotNull; + +import java.io.IOException; +import java.io.StringReader; + +import javax.xml.transform.Transformer; +import javax.xml.transform.TransformerException; + +import org.apache.commons.io.IOUtils; +import org.apache.solr.client.solrj.util.ClientUtils; +import org.apache.solr.common.SolrInputDocument; +import org.dom4j.Document; +import org.dom4j.DocumentException; +import org.dom4j.io.SAXReader; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; + +import com.fasterxml.jackson.databind.DeserializationFeature; +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.oa.provision.model.JoinedEntity; +import eu.dnetlib.dhp.oa.provision.utils.ContextMapper; +import eu.dnetlib.dhp.oa.provision.utils.StreamingInputDocumentFactory; +import eu.dnetlib.dhp.oa.provision.utils.XmlRecordFactory; +import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; +import eu.dnetlib.dhp.utils.saxon.SaxonTransformerFactory; + +public class EOSCFuture_Test { + + public static ObjectMapper OBJECT_MAPPER = new ObjectMapper() + .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); + + public static final String VERSION = "2021-04-15T10:05:53Z"; + public static final String DSID = "b9ee796a-c49f-4473-a708-e7d67b84c16d_SW5kZXhEU1Jlc291cmNlcy9JbmRleERTUmVzb3VyY2VUeXBl"; + + private ContextMapper contextMapper; + + @BeforeEach + public void setUp() { + contextMapper = new ContextMapper(); + } + + @Test + public void testEOSC_ROHub() throws IOException, DocumentException, TransformerException { + + final ContextMapper contextMapper = new ContextMapper(); + + final XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false, + XmlConverterJob.schemaLocation); + + final OtherResearchProduct p = OBJECT_MAPPER + .readValue( + IOUtils.toString(getClass().getResourceAsStream("eosc-future/photic-zone.json")), + OtherResearchProduct.class); + + final String xml = xmlRecordFactory.build(new JoinedEntity<>(p)); + + assertNotNull(xml); + + final Document doc = new SAXReader().read(new StringReader(xml)); + + assertNotNull(doc); + System.out.println(doc.asXML()); + + testRecordTransformation(xml); + } + + private void testRecordTransformation(final String record) throws IOException, TransformerException { + final String fields = IOUtils.toString(getClass().getResourceAsStream("fields.xml")); + final String xslt = IOUtils.toString(getClass().getResourceAsStream("layoutToRecordTransformer.xsl")); + + final String transformer = XmlIndexingJob.getLayoutTransformer("DMF", fields, xslt); + + final Transformer tr = SaxonTransformerFactory.newInstance(transformer); + + final String indexRecordXML = XmlIndexingJob.toIndexRecord(tr, record); + + final SolrInputDocument solrDoc = new StreamingInputDocumentFactory(VERSION, DSID) + .parseDocument(indexRecordXML); + + final String xmlDoc = ClientUtils.toXML(solrDoc); + + Assertions.assertNotNull(xmlDoc); + System.out.println(xmlDoc); + } + +} diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java index e0fbb2a2f..cd5e08426 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java @@ -128,6 +128,41 @@ public class IndexRecordTransformerTest { testRecordTransformation(record); } + @Test + public void testForEOSCFutureSoftwareNotebook() throws IOException, TransformerException { + final String record = IOUtils + .toString(getClass().getResourceAsStream("eosc-future/software-justthink.xml")); + testRecordTransformation(record); + } + + @Test + public void testForEOSCFutureSoftwareNotebookClaim() throws IOException, TransformerException { + final String record = IOUtils + .toString(getClass().getResourceAsStream("eosc-future/software-justthink-claim.xml")); + testRecordTransformation(record); + } + + @Test + public void testForEOSCFutureZenodo7353841() throws IOException, TransformerException { + final String record = IOUtils + .toString(getClass().getResourceAsStream("eosc-future/zenodo7353841.xml")); + testRecordTransformation(record); + } + + @Test + public void testForEOSCFutureZenodo7351393() throws IOException, TransformerException { + final String record = IOUtils + .toString(getClass().getResourceAsStream("eosc-future/zenodo7351393.xml")); + testRecordTransformation(record); + } + + @Test + public void testForEOSCFutureZenodo7351221() throws IOException, TransformerException { + final String record = IOUtils + .toString(getClass().getResourceAsStream("eosc-future/zenodo7351221.xml")); + testRecordTransformation(record); + } + @Test void testDoiUrlNormalization() throws MalformedURLException { diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/eosc-future/photic-zone.json b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/eosc-future/photic-zone.json new file mode 100644 index 000000000..9729c6051 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/eosc-future/photic-zone.json @@ -0,0 +1 @@ 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+ od______2659::3801993ea8f970cfc991277160edf277 + 2022-08-08T03:06:13Z + under curation + +
+ + + + JUSThink + Alignment Analysis + Norman, Utku + Dinkar, Tanvi + Bruno, Barbara + Clavel, Chloé + + + + +

+ 1. Description +

+

This repository contains tools to automatically analyse how + participants align their use of task-specific referents in their + dialogue and actions for a collaborative learning activity, and how + it relates to the task success (i.e. their learning + outcomes and task performance).

+

As a use case, it processes data from a collaborative problem solving + activity named JUSThink [1, 2], i.e. + JUSThink Dialogue and Actions Corpus data set that is available from the + Zenodo Repository, DOI: 10.5281/zenodo.4627104, and reproduces the results and figures + in [3].

+

In brief:

+
    +
  1. JUSThink Dialogue and Actions Corpus contains + transcripts, event logs, and test responses of children aged 9 + through 12, as they participate in the JUSThink activity [1, 2] + in pairs of two, to solve a problem on graphs together.
    2. +
  2. The JUSThink activity and its study is first + described in [1], and elaborated with findings concerning the link + between children's learning, performance in the activity, and + perception of self, the other and the robot in [2].
    3. +
  3. Alignment analysis in our work [3] studies the participants' use of + expressions that are related to the task at hand, their follow up + actions of these expressions, and how it links to task success.
    4. +
+

+ 2. Publications +

+

If you use this work in an academic context, please cite the following + publications:

+
    +
  • +

    Norman*, U., Dinkar*, T., Bruno, B., & Clavel, C. (2022). + Studying Alignment in a Collaborative Learning Activity via + Automatic Methods: The Link Between What We Say and Do. Dialogue + & Discourse, 13(2), 1 - ;48. *Contributed equally to this + work. https://doi.org/10.5210/dad.2022.201

    +
    • +
  • +

    Norman, U., Dinkar, T., Bruno, B., & Clavel, C. (2021). + JUSThink Alignment Analysis. In Dialogue & Discourse + (v1.0.0, Vol. 13, Number 2, pp. 1 - ;48). Zenodo. https://doi.org/10.5281/zenodo.4675070

    +
    • +
+

+ 3. Content +

+

The tools provided in this repository consists of 7 Jupyter Notebooks + written in Python 3, and two additional external tools utilised by the + notebooks.

+

+ 3.1. Jupyter Notebooks +

+

We highlight that the notebooks up until the last (i.e. to test the + hypotheses (tools/7_test_the_hypotheses.ipynb)) present a general + pipeline to process event logs, test responses and transcripts to + extract measures of task performance, learning outcomes, and measures of + alignment.

+
    +
  1. Extract task performance (and other features) from the logs + (tools/1_extract_performance_and_other_features_from_logs.ipynb): + Extracts various measures of task behaviour from the logs, at + varying granularities of the activity (i.e. the whole corpus, task, + attempt, and turn levels). In later notebooks, we focus on one of + the features to estimate the task performance of a team: (minimum) + error.
    2. +
  2. Extract learning outcomes from the test responses + (tools/2_extract_learning_gain_from_test_responses.ipynb): Extracts + measures of learning outcomes from the responses to the pre-test and + the post-test. In later notebooks, we focus on one of the features + to estimate the learning outcome of a team: relative learning gain + [4]
    3. +
  3. Select and visualise a subset of teams for + transcription + (tools/3_visualise_transcribed_teams.ipynb): Visualises the + transcribed teams among the other teams in the feature space spanned + by task performance and learning outcome, as well as the + distribution of their number of attempts and turns.
    4. +
  4. Extract routines from transcripts + (tools/4_extract_routines_from_transcripts.ipynb) (uses dialign to + extract routines): Extracts routines of referring expressions that + are "fixed", i.e. become shared or established amongst + interlocutors.
    5. +
  5. Combine transcripts with logs + (tools/5_construct_the_corpus_by_combining_transcripts_with_logs.ipynb): + Merges transcripts with event logs to have a combined dialogue and + actions corpus, to be processed e.g. to detect follow-up + actions.
    6. +
  6. Recognise instructions and detect follow-up actions + (tools/6_recognise_instructions_detect_follow-up_actions.ipynb): + Extracts verbalised instruction such as "connect Mount Basel to + Montreux", and pairs them with the follow-up action that may + match (e.g. if the other connects Basel to Montreux) or + mismatch (e.g. if the other connects Basel to + Neuchatel) with the instruction.
    7. +
  7. Test the hypotheses in [3] (tools/7_test_the_hypotheses.ipynb) (uses + effsize to estimate effect size, specifically + Cliff's Delta): Considers each research questions and hypotheses + studied in [3] and generates the results in [3].
    8. +
+

+ 3.2. External Tools +

+
    +
  1. dialign + tool to extract routines, specifically Release 1.0 from dialign-1.0.zip:\n It extracts routine expressions that are + "shared" among the participants from transcripts. \n It is + used as an external module (in accordance with its CeCILL-B License, + see License).
    2. +
  2. effsize tool to compute estimators of effect + size.\n We specifically use it to compute Cliff's Delta, which + quantifies the amount difference between two groups of observations, + by computing the Cliff's Delta statistic.\n It is taken from + project DABEST (see License).
    3. +
+

+ 4. Research Questions and Hypotheses in [3] +

+
    +
  • RQ1 Lexical alignment: How do the interlocutors + use expressions related to the task? Is this associated + with task success?
      +
    • H1.1: Task-specific referents become + routine early for more successful teams.
      • +
    • H1.2: Hesitation phenomena are more likely + to occur in the vicinity of priming and establishment of + task-specific referents for more successful teams.
      • +
    +
    • +
  • RQ2 Behavioural alignment: How do the interlocutors + follow up these expressions with actions? Is this + associated with task success?
      +
    • H2.1: Instructions are more likely to be + followed by a corresponding action early in the dialogue for + more successful teams.
      • +
    • H2.2: When instructions are followed by a + corresponding or a different action, the action is more + likely to be in the vicinity of information management + phenomena for more successful teams.
      • +
    +
    • +
+

The RQs and Hs are addressed in the notebook for testing the hypotheses + (i.e. tools/7_test_the_hypotheses.ipynb).

+

+ Acknowledgements +

+

This project has received funding from the European Union's Horizon + 2020 research and innovation programme under grant agreement No 765955. + Namely, the ANIMATAS Project.

+

+ License +

+

The whole package is under MIT License, see the LICENSE + file.

+

Classes under the tools/effsize package were taken from + project DABEST, Copyright 2016-2020 Joses W. Ho. + These classes are licensed under the BSD 3-Clause Clear License. See + tools/effsize/LICENSE file for additional + details.

+

Classes under the tools/dialign-1.0 package were taken + from project dialign. These classes are licensed under the + CeCILL-B License. This package is used as an "external + module", see tools/dialign-1.0/LICENSE.txt for + additional details.

+ + + + + Zenodo + + + + + + + + + + + + + + + + + + + oai:zenodo.org:4675070 + + oai:zenodo.org:4675070 + 10.5281/zenodo.4675070 + + + + false + false + 0.9 + + + + + + corda__h2020::c4515ebef538a734cf11f795347f5dac + 765955 + ANIMATAS + Advancing intuitive human-machine interaction with human-like + social capabilities for education in schools + + + + ec__________::EC::H2020 + + + + + + + + + + + + + https://zenodo.org/record/4675070 + + + + + + + + diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/eosc-future/software-justthink.xml b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/eosc-future/software-justthink.xml new file mode 100644 index 000000000..9c0f4ea7d --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/eosc-future/software-justthink.xml @@ -0,0 +1,429 @@ + + +
+ doi_dedup___::c054151b6a8c4f41c7acf160651a6503 + 2022-10-13T00:15:44+0000 + 2022-10-13T07:44:29.152Z +
+ + + + + + oai:zenodo.org:4675070 + 50|od______2659::3801993ea8f970cfc991277160edf277 + oai:zenodo.org:6974562 + 50|od______2659::9c87ff4a5e7710052b873088e7265072 + 10.5281/zenodo.4675069 + 10.5281/zenodo.4675070 + 10.5281/zenodo.6974562 + 10.5281/zenodo.4675069 + + + + + + JUSThink Alignment + Analysis + + Norman, Utku + Dinkar, Tanvi + Bruno, Barbara + Clavel, Chloé + 2022-08-08 + &lt;strong>1. Description&lt;/strong> This repository + contains&lt;strong> tools to automatically analyse how participants align + their use of task-specific referents in their dialogue and actions for a + collaborative learning activity, and how it relates to the task + success&lt;/strong> (i.e. their learning outcomes and task performance). As + a use case, it processes data from a collaborative problem solving activity + named JUSThink [1, 2], i.e. JUSThink Dialogue and Actions Corpus data set that + is available from the Zenodo Repository, DOI: 10.5281/zenodo.4627104, and + reproduces the results and figures in [3]. In brief: &lt;strong>JUSThink + Dialogue and Actions Corpus&lt;/strong> contains transcripts, event logs, + and test responses of children aged 9 through 12, as they participate in the + JUSThink activity [1, 2] in pairs of two, to solve a problem on graphs together. + &lt;strong>The JUSThink activity and its study&lt;/strong> is first + described in [1], and elaborated with findings concerning the link between + children's learning, performance in the activity, and perception of self, the + other and the robot in [2]. &lt;strong>Alignment analysis in our work + [3]&lt;/strong> studies the participants' use of expressions that are + related to the task at hand, their follow up actions of these expressions, and + how it links to task success. &lt;strong>Changes in Release + v1.1.0:&lt;/strong> updated with the publication information, finalized + paper structure, research questions and hypotheses as in the published article: + U. Norman*&lt;em>, &lt;/em>T. Dinkar*, B. Bruno, and C. Clavel, + "Studying Alignment in a Collaborative Learning Activity via Automatic Methods: + The Link Between What We Say and Do," Dialogue &amp;amp; Discourse, 13(2), + 1–48. *Contributed equally to this work. 10.5210/dad.2022.201. + &lt;strong>Full Changelog:&lt;/strong> + https://github.com/chili-epfl/justhink-alignment-analysis/compare/v1.0.0...v1.1.0 + &lt;strong>2. Publications&lt;/strong> If you use this work in an + academic context, please cite the following publications: Norman*, U., Dinkar*, + T., Bruno, B., &amp;amp; Clavel, C. (2022). Studying Alignment in a + Collaborative Learning Activity via Automatic Methods: The Link Between What We + Say and Do. Dialogue &amp;amp; Discourse, 13(2), 1–48. *Contributed equally + to this work. https://doi.org/10.5210/dad.2022.201 Norman, U., Dinkar, T., + Bruno, B., &amp;amp; Clavel, C. (2021). JUSThink Alignment Analysis. In + Dialogue &amp;amp; Discourse (v1.1.0, Vol. 13, Number 2, pp. 1–48). Zenodo. + https://doi.org/10.5281/zenodo.6974562 &lt;strong>3. Content&lt;/strong> + The tools provided in this repository consists of 7 Jupyter Notebooks written in + Python 3, and two additional external tools utilised by the notebooks. + &lt;strong>3.1. Jupyter Notebooks&lt;/strong> We highlight that the + notebooks up until the last (i.e. to test the hypotheses + (tools/7_test_the_hypotheses.ipynb)) present a general pipeline to process event + logs, test responses and transcripts to extract measures of task performance, + learning outcomes, and measures of alignment. &lt;strong>Extract task + performance (and other features) from the logs + &lt;/strong>(tools/1_extract_performance_and_other_features_from_logs.ipynb): + Extracts various measures of task behaviour from the logs, at varying + granularities of the activity (i.e. the whole corpus, task, attempt, and turn + levels). In later notebooks, we focus on one of the features to estimate the + task performance of a team: (minimum) error. &lt;strong>Extract learning + outcomes from the test responses&lt;/strong> + (tools/2_extract_learning_gain_from_test_responses.ipynb): Extracts measures of + learning outcomes from the responses to the pre-test and the post-test. In later + notebooks, we focus on one of the features to estimate the learning outcome of a + team: relative learning gain [4] &lt;strong>Select and visualise a subset of + teams for transcription&lt;/strong> + (tools/3_visualise_transcribed_teams.ipynb): Visualises the transcribed teams + among the other teams in the feature space spanned by task performance and + learning outcome, as well as the distribution of their number of attempts and + turns. &lt;strong>Extract routines from transcripts&lt;/strong> + (tools/4_extract_routines_from_transcripts.ipynb) (uses dialign to extract + routines): Extracts routines of referring expressions that are "fixed", i.e. + become shared or established amongst interlocutors. &lt;strong>Combine + transcripts with logs&lt;/strong> + (tools/5_construct_the_corpus_by_combining_transcripts_with_logs.ipynb): Merges + transcripts with event logs to have a combined dialogue and actions corpus, to + be processed e.g. to detect follow-up actions. &lt;strong>Recognise + instructions and detect follow-up actions&lt;/strong> + (tools/6_recognise_instructions_detect_follow-up_actions.ipynb): Extracts + verbalised instruction such as "connect Mount Basel to Montreux", and pairs them + with the follow-up action that may &lt;em>match&lt;/em> (e.g. if the + other connects Basel to Montreux) or &lt;em>mismatch&lt;/em> (e.g. if + the other connects Basel to Neuchatel) with the instruction. &lt;strong>Test + the hypotheses &lt;/strong>in [3] (tools/7_test_the_hypotheses.ipynb) (uses + &lt;strong>effsize&lt;/strong> to estimate effect size, specifically + Cliff's Delta): Considers each research questions and hypotheses studied in [3] + and generates the results in [3]. &lt;strong>3.2. External + Tools&lt;/strong> &lt;strong>dialign tool&lt;/strong> to extract + routines, specifically Release 1.0 from dialign-1.0.zip:&lt;br> It extracts + routine expressions that are "shared" among the participants from transcripts. + &lt;br> It is used as an external module (in accordance with its CeCILL-B + License, see &lt;strong>License&lt;/strong>). &lt;strong>effsize + tool&lt;/strong> to compute estimators of effect size.&lt;br> We + specifically use it to compute Cliff's Delta, which quantifies the amount + difference between two groups of observations, by computing the Cliff's Delta + statistic.&lt;br> It is taken from project DABEST (see + &lt;strong>License&lt;/strong>). &lt;strong>4. Research Questions + and Hypotheses in [3]&lt;/strong> &lt;strong>RQ1 Lexical + alignment&lt;/strong>: How do the interlocutors &lt;em>use&lt;/em> + expressions related to the task? Is this associated with task success? + &lt;strong>H1.1&lt;/strong>: Task-specific referents become routine + early for more successful teams. &lt;strong>H1.2&lt;/strong>: Hesitation + phenomena are more likely to occur in the vicinity of priming and establishment + of task-specific referents for more successful teams. &lt;strong>RQ2 + Behavioural alignment&lt;/strong>: How do the interlocutors + &lt;em>follow up&lt;/em> these expressions with actions? Is this + associated with task success? &lt;strong>H2.1&lt;/strong>: Instructions + are more likely to be followed by a corresponding action early in the dialogue + for more successful teams. &lt;strong>H2.2&lt;/strong>: When + instructions are followed by a corresponding or a different action, the action + is more likely to be in the vicinity of information management phenomena for + more successful teams. The RQs and Hs are addressed in the notebook for testing + the hypotheses (i.e. tools/7_test_the_hypotheses.ipynb). + &lt;strong>Acknowledgements&lt;/strong> This project has received + funding from the European Union's Horizon 2020 research and innovation programme + under grant agreement No 765955. Namely, the ANIMATAS Project. + &lt;strong>License&lt;/strong> The whole package is under MIT License, + see the &lt;strong>LICENSE&lt;/strong> file. Classes under the + &lt;strong>tools/effsize&lt;/strong> package were taken from project + &lt;strong>DABEST&lt;/strong>, Copyright 2016-2020 Joses W. Ho. These + classes are licensed under the BSD 3-Clause Clear License. See + &lt;strong>tools/effsize/LICENSE&lt;/strong> file for additional + details. Classes under the &lt;strong>tools/dialign-1.0&lt;/strong> + package were taken from project &lt;strong>dialign&lt;/strong>. These + classes are licensed under the CeCILL-B License. This package is used as an + "external module", see&lt;strong> + tools/dialign-1.0/LICENSE.txt&lt;/strong> for additional + details. + {"references": ["[1] J. Nasir, U. Norman, B. Bruno, and P. Dillenbourg, + \"You Tell, I Do, and We Swap until we Connect All the Gold Mines!,\" ERCIM + News, vol. 2020, no. 120, 2020, [Online]. Available: + https://ercim-news.ercim.eu/en120/special/you-tell-i-do-and-we-swap-until-we-connect-all-the-gold-mines", + "[2] J. Nasir*, U. Norman*, B. Bruno, and P. Dillenbourg, \"When Positive + Perception of the Robot Has No Effect on Learning,\" in 2020 29th IEEE + International Conference on Robot and Human Interactive Communication (RO-MAN), + Aug. 2020, pp. 313\u2013320, doi: 10.1109/RO-MAN47096.2020.9223343", "[3] U. + Norman*, T. Dinkar*, B. Bruno, and C. Clavel, \"Studying Alignment in a + Collaborative Learning Activity via Automatic Methods: The Link Between What We + Say and Do,\" Dialogue &amp;amp; Discourse, vol. 13, no. 2, pp. 1\u201348, + Aug. 2022, doi: 10.5210/dad.2022.201.", "[4] M. Sangin, G. Molinari, M.-A. + N\u00fcssli, and P. Dillenbourg, \"Facilitating peer knowledge modeling: Effects + of a knowledge awareness tool on collaborative learning outcomes and + processes,\"\" Computers in Human Behavior, vol. 27, no. 3, pp. 1059\u20131067, + May 2011, doi: 10.1016/j.chb.2010.05.032."]} + alignment + situated + dialogue + collaborative + learning + spontaneous + speech + disfluency + mutual + understanding + + 2021-04-09 + 2022-08-08 + Zenodo + + + + + + + + + + + true + false + 0.8 + dedup-result-decisiontree-v3 + + + + + doi_dedup___::ae235765bbc422195a6c9f632b2d77eb + + 2104.04429 + + arXiv + + 2022-08-05 + Studying + Alignment in a Collaborative Learning Activity via Automatic Methods: + The Link Between What We Say and Do + + + 10.48550/arxiv.2104.04429 + 10.5210/dad.2022.201 + + + corda__h2020::c4515ebef538a734cf11f795347f5dac + Advancing intuitive human-machine interaction with human-like social + capabilities for education in schools + 765955 + + + ec__________::EC::H2020 + ec__________::EC::H2020::MSCA-ITN-ETN + + ANIMATAS + + + doi_dedup___::0a6314b0ed275d915f5b57a259375691 + 2021-03-22 + Zenodo + 10.5281/zenodo.4627104 + JUSThink Dialogue and Actions Corpus + 10.5281/zenodo.4627103 + + + + + + + Zenodo + 10.5281/zenodo.4675070 + JUSThink Alignment Analysis + 2021-04-09 + + + + 2022-08-08 + Zenodo + 10.5281/zenodo.6974562 + + JUSThink Alignment Analysis (v1.1.0) + + + JUSThink + Alignment Analysis (v1.1.0) + 2022-08-08 + Zenodo + 10.5281/zenodo.4675069 + + + + + + + 2022-08-08 + + 10.5281/zenodo.4675069 + + https://opensource.org/licenses/MIT + + https://doi.org/10.5281/zenodo.4675069 + + + + + + + 2022-08-08 + + 10.5281/zenodo.6974562 + + https://opensource.org/licenses/MIT + + https://doi.org/10.5281/zenodo.6974562 + + + + + + + 2021-04-09 + + 10.5281/zenodo.4675070 + + https://opensource.org/licenses/MIT + + https://doi.org/10.5281/zenodo.4675070 + + + + + + + + diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/eosc-future/zenodo7351221.xml b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/eosc-future/zenodo7351221.xml new file mode 100644 index 000000000..7f1e66dac --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/eosc-future/zenodo7351221.xml @@ -0,0 +1,99 @@ + + +
+ doi_________::9cb0664d4c891c4baaf73f007c0c9de0 + 2022-11-25T12:55:13Z + under curation + +
+ + + + + COVID-19 Knowledge Graph: A semantic resource embedding biological and chemical entities + Karki, Reagon + + + +

A Knowledge graph representation of compounds and associated biological entities in the BY-COVID and EOSC Future project.

Current status

  • Number of Nodes: 35952
  • Number of Edges: 279462
  • Human Proteins: 1347
  • Assay: 15835
  • Chemical/Compound: 4096
  • Mechanism of Action: 739
  • Pathway: 1513
  • Disease: 1585
  • SideEffect: 7420
  • Biological Process: 2085
  • Molecular Function: 1332

Please check the BY_COVID_update_August.ipynb for understanding step wise process of KG generation and KG statistics. The KG has been exported to formats such as graphml, sif and so on for visualizations in other platforms. For example, the graphml file can be imported to Cytoscape directly. These files are located in 'data\export' folder.

 + + + + Zenodo + + + + + + + + + + + + + + + + + + + oai:zenodo.org:7351221 + + oai:zenodo.org:7351221 + 10.5281/zenodo.7351221 + + + + false + false + 0.9 + + + + + + corda__h2020::256485716fdb9f5ca69007b7ca5a072b + 101017536 + EOSC Future + EOSC Future + + + + ec__________::EC::H2020 + + + + + corda__h2020::4a3254eac2997eee0a9dcb7a7daedb81 + 101046203 + BY-COVID + Beyond COVID + + + + ec__________::EC::Horizon Europe Framework Programme - HORIZON-RIA\HORIZON Action Grant Budget-Based + + + + + + + + + + + + + https://zenodo.org/record/7351221 + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/eosc-future/zenodo7351393.xml b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/eosc-future/zenodo7351393.xml new file mode 100644 index 000000000..21b656d2c --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/eosc-future/zenodo7351393.xml @@ -0,0 +1,100 @@ + + +
+ doi_________::07fdccabd77830e3caccf0b33c083f1b + 2022-11-25T01:08:31Z + under curation + +
+ + + + Monkeypox Knowledge Graph: A semantic resource embedding biological and chemical entities + Karki, Reagon + Andrea, Zaliani + Gadiya, Yojana + Gribbon, Philip + + + +

The Monkeypox KG is built using viral and human proteins reported in different resources. Additionally, the KG represents chemicals tested against Monkeypox and their targets, associated biological processes, molecular functions, diseases and side effects.

KG status

Version 1 stats:

  • Number of Nodes: 8235
  • Number of Edges: 40422

Version 2 stats (2nd September) :

  • Number of Nodes: 9129
  • Number of Edges: 44568

Please check the graph.ipynb for understanding step wise process of KG generation and KG statistics. The KG has been exported to formats such as graphml, sif and so on for visualizations in other platforms. For example, the graphml file can be imported to Cytoscape directly. These files are located in 'data\export' folder.

 + + + + Zenodo + + + + + + + + + + + + + + + + + + + oai:zenodo.org:7351393 + + oai:zenodo.org:7351393 + 10.5281/zenodo.7351393 + + + false + false + 0.9 + + + + + + corda__h2020::256485716fdb9f5ca69007b7ca5a072b + 101017536 + EOSC Future + EOSC Future + + + + ec__________::EC::H2020 + + + + + corda__h2020::4a3254eac2997eee0a9dcb7a7daedb81 + 101046203 + BY-COVID + Beyond COVID + + + + ec__________::EC::Horizon Europe Framework Programme - HORIZON-RIA\HORIZON Action Grant Budget-Based + + + + + + + + + + + + + https://zenodo.org/record/7351393 + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/eosc-future/zenodo7353841.xml b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/eosc-future/zenodo7353841.xml new file mode 100644 index 000000000..4bd287e50 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/eosc-future/zenodo7353841.xml @@ -0,0 +1,85 @@ + + +
+ doi_________::93d39dd7edef016928788c3500e149f1 + 2022-11-24T08:41:37Z + under curation + +
+ + + + ENVRI SP - Dashboard State of the Environment - Ocean Indicators + Tjerk Krijger + + + +

The attached .yaml file is used as input to the Dashboard State of the Environment, which is a science project of the ENVRI-FAIR science cluster within EOSC-FUTURE. The contents of the file enable the visualization of Ocean indicators on the dashboard. It is possible to download the attached file and change the contents to include indicators from different domains such as atmosphere or biodiversity.

 + + + + Zenodo + + + + + + + + + + + + + + + + + + + oai:zenodo.org:7353841 + + oai:zenodo.org:7353841 + 10.5281/zenodo.7353841 + + + false + false + 0.9 + + + + + + corda__h2020::256485716fdb9f5ca69007b7ca5a072b + 101017536 + EOSC Future + EOSC Future + + + + ec__________::EC::H2020 + + + + + + + + + + + + + https://zenodo.org/record/7353841 + + + + + + + + diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/fields.xml b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/fields.xml index 910a366f6..be2ee7b98 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/fields.xml +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/fields.xml @@ -2,11 +2,11 @@ - - - - - + + + + + @@ -14,17 +14,16 @@ - - - - + + + - - - - - - + + + + + + @@ -34,18 +33,17 @@ - - - + + - - - + + + - + - + @@ -54,35 +52,36 @@ - + - + - + - - + + - + - - + + + - - - + + + @@ -94,26 +93,29 @@ - + - - + + + + + - - + + - + - + - - + + - + @@ -132,13 +134,15 @@ + - + + - + @@ -156,20 +160,6 @@ - - - - - - - - - - - - - - - + \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/config-default.xml b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/config-default.xml index 9331d4ac5..63fc84d75 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/config-default.xml +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/config-default.xml @@ -21,7 +21,7 @@ hive_jdbc_url - jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 + jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000/;UseNativeQuery=1;?spark.executor.memory=19166291558;spark.yarn.executor.memoryOverhead=3225;spark.driver.memory=11596411699;spark.yarn.driver.memoryOverhead=1228 oozie.wf.workflow.notification.url diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql index d699b68c3..41c3ed751 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql @@ -42,7 +42,9 @@ SELECT p.id, CASE WHEN prr2.id IS NULL THEN 0 ELSE prr2.dp END AS delayedpubs, p.callidentifier, p.code, - p.totalcost + p.totalcost, + p.fundedamount, + p.currency FROM ${stats_db_name}.project_tmp p LEFT JOIN (SELECT pr.id, count(distinct pr.result) AS np FROM ${stats_db_name}.project_results pr diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql index aee66fd5e..24e1a1355 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql @@ -59,7 +59,7 @@ UNION ALL SELECT * FROM ${stats_db_name}.otherresearchproduct_sources; -create table ${stats_db_name}.result_orcid STORED AS PARQUET as +CREATE TABLE IF NOT EXISTS ${stats_db_name}.result_orcid STORED AS PARQUET as select distinct res.id, regexp_replace(res.orcid, 'http://orcid.org/' ,'') as orcid from ( SELECT substr(res.id, 4) as id, auth_pid.value as orcid @@ -69,7 +69,7 @@ from ( LATERAL VIEW explode(auth.pid.qualifier.classid) apt as author_pid_type WHERE res.datainfo.deletedbyinference = FALSE and res.datainfo.invisible = FALSE and author_pid_type = 'orcid') as res; -create table ${stats_db_name}.result_result stored as parquet as +CREATE TABLE IF NOT EXISTS ${stats_db_name}.result_result stored as parquet as select substr(rel.source, 4) as source, substr(rel.target, 4) as target, relclass, subreltype from ${openaire_db_name}.relation rel join ${openaire_db_name}.result r1 on rel.source=r1.id @@ -82,7 +82,7 @@ where reltype='resultResult' and r2.resulttype.classname != 'other' and rel.datainfo.deletedbyinference=false and rel.datainfo.invisible = FALSE; -create table ${stats_db_name}.result_citations_oc stored as parquet as +CREATE TABLE IF NOT EXISTS ${stats_db_name}.result_citations_oc stored as parquet as select substr(target, 4) as id, count(distinct substr(source, 4)) as citations from ${openaire_db_name}.relation rel join ${openaire_db_name}.result r1 on rel.source=r1.id @@ -97,7 +97,7 @@ where relClass='Cites' and rel.datainfo.provenanceaction.classid = 'sysimport:cr and rel.datainfo.deletedbyinference=false and rel.datainfo.invisible = FALSE group by substr(target, 4); -create table ${stats_db_name}.result_references_oc stored as parquet as +CREATE TABLE IF NOT EXISTS ${stats_db_name}.result_references_oc stored as parquet as select substr(source, 4) as id, count(distinct substr(target, 4)) as references from ${openaire_db_name}.relation rel join ${openaire_db_name}.result r1 on rel.source=r1.id diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql index 2505c3a34..2bdcbfa3d 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql @@ -48,7 +48,9 @@ create table TARGET.result stored as parquet as 'openorgs____::3e8d1f8c3f6cd7f418b09f1f58b4873b', -- Aristotle University of Thessaloniki 'openorgs____::3fcef6e1c469c10f2a84b281372c9814', -- World Bank 'openorgs____::1698a2eb1885ef8adb5a4a969e745ad3', -- École des Ponts ParisTech - 'openorgs____::e15adb13c4dadd49de4d35c39b5da93a' -- Nanyang Technological University + 'openorgs____::e15adb13c4dadd49de4d35c39b5da93a', -- Nanyang Technological University + 'openorgs____::4b34103bde246228fcd837f5f1bf4212', -- Autonomous University of Barcelona + 'openorgs____::72ec75fcfc4e0df1a76dc4c49007fceb' -- McMaster University ) )) foo; compute stats TARGET.result; diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql index 5461afde6..c31180c14 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql @@ -48,7 +48,9 @@ CREATE TABLE ${stats_db_name}.project_tmp delayedpubs INT, callidentifier STRING, code STRING, - totalcost FLOAT + totalcost FLOAT, + fundedamount FLOAT, + currency STRING ) CLUSTERED BY (id) INTO 100 buckets stored AS orc tblproperties ('transactional' = 'true'); INSERT INTO ${stats_db_name}.project_tmp @@ -72,7 +74,9 @@ SELECT substr(p.id, 4) AS id, 0 AS delayedpubs, p.callidentifier.value AS callidentifier, p.code.value AS code, - p.totalcost AS totalcost + p.totalcost AS totalcost, + p.fundedamount AS fundedamount, + p.currency.value AS currency FROM ${openaire_db_name}.project p WHERE p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;