From d5867a19920d8acd232b263b5d4bb9a6a4d87de0 Mon Sep 17 00:00:00 2001 From: Claudio Atzori <claudio.atzori@isti.cnr.it> Date: Tue, 8 Oct 2024 14:58:28 +0200 Subject: [PATCH] merged #490 --- .../oaf/HashableStructuredProperty.java | 70 ++++++++++ .../schema/oaf/utils/CleaningFunctions.java | 30 ---- .../dhp/schema/oaf/utils/DoiCleaningRule.java | 14 +- .../oaf/utils/GraphCleaningFunctions.java | 18 ++- .../schema/oaf/utils/IdentifierFactory.java | 4 +- .../dhp/schema/oaf/utils/MergeUtils.java | 2 +- .../schema/oaf/utils/PidValueComparator.java | 4 +- .../java/eu/dnetlib/dhp/utils/DHPUtils.java | 3 +- .../oaf/utils/IdentifierFactoryTest.java | 4 +- .../schema/oaf/utils/publication_doi3.json | 2 +- .../schema/oaf/utils/publication_pmc2.json | 2 +- .../PrepareAffiliationRelations.java | 129 +++++++++++++++--- .../input_actionset_parameter.json | 12 +- .../collection/crossref/Crossref2Oaf.scala | 4 +- .../PrepareAffiliationRelationsTest.java | 67 ++++++--- .../CreateOpenCitationsASTest.java | 13 +- .../CreateTAActionSetTest.java | 13 +- .../bipaffiliations/doi_to_ror.json | 19 +-- .../bipaffiliations/doi_to_ror_old.json | 9 ++ .../bipaffiliations/publichers_old/publisher | 6 + .../bipaffiliations/publishers/publisher | 6 + .../raw/AbstractMdRecordToOafMapper.java | 35 ++--- .../dhp/oa/graph/raw/OafToOafMapper.java | 3 +- .../dhp/oa/graph/raw/OdfToOafMapper.java | 6 +- .../graph/clean/CleanGraphSparkJobTest.java | 16 +-- .../clean/GraphCleaningFunctionsTest.java | 12 +- .../raw/GenerateEntitiesApplicationTest.java | 8 +- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 97 ++++++++----- .../clean/graph/publication/publication.json | 2 +- .../eu/dnetlib/dhp/oa/graph/clean/result.json | 32 +---- .../dhp/oa/graph/raw/odf_record_base.xml | 129 ++++++++++++++++++ .../raw/organizations_resultset_entry.json | 5 + .../oa/graph/sample/person/person_10.json.gz | Bin 0 -> 1233 bytes .../graph/scholix/ScholixGenerationTest.scala | 3 +- 34 files changed, 540 insertions(+), 239 deletions(-) create mode 100644 dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/HashableStructuredProperty.java create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror_old.json create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/publichers_old/publisher create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/publishers/publisher create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_record_base.xml create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/sample/person/person_10.json.gz diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/HashableStructuredProperty.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/HashableStructuredProperty.java new file mode 100644 index 0000000000..aa60b097ab --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/HashableStructuredProperty.java @@ -0,0 +1,70 @@ +/* + * Copyright (c) 2024. + * SPDX-FileCopyrightText: © 2023 Consiglio Nazionale delle Ricerche + * SPDX-License-Identifier: AGPL-3.0-or-later + */ + +package eu.dnetlib.dhp.schema.oaf; + +import org.apache.commons.lang3.builder.EqualsBuilder; +import org.apache.commons.lang3.builder.HashCodeBuilder; + +public class HashableStructuredProperty extends StructuredProperty { + + private static final long serialVersionUID = 8371670185221126045L; + + public static HashableStructuredProperty newInstance(String value, Qualifier qualifier, DataInfo dataInfo) { + if (value == null) { + return null; + } + final HashableStructuredProperty sp = new HashableStructuredProperty(); + sp.setValue(value); + sp.setQualifier(qualifier); + sp.setDataInfo(dataInfo); + return sp; + } + + public static HashableStructuredProperty newInstance(StructuredProperty sp) { + HashableStructuredProperty hsp = new HashableStructuredProperty(); + hsp.setQualifier(sp.getQualifier()); + hsp.setValue(sp.getValue()); + hsp.setQualifier(sp.getQualifier()); + return hsp; + } + + public static StructuredProperty toStructuredProperty(HashableStructuredProperty hsp) { + StructuredProperty sp = new StructuredProperty(); + sp.setQualifier(hsp.getQualifier()); + sp.setValue(hsp.getValue()); + sp.setQualifier(hsp.getQualifier()); + return sp; + } + + @Override + public int hashCode() { + return new HashCodeBuilder(11, 91) + .append(getQualifier().getClassid()) + .append(getQualifier().getSchemeid()) + .append(getValue()) + .hashCode(); + } + + @Override + public boolean equals(Object obj) { + if (obj == null) { + return false; + } + if (obj == this) { + return true; + } + if (obj.getClass() != getClass()) { + return false; + } + final HashableStructuredProperty rhs = (HashableStructuredProperty) obj; + return new EqualsBuilder() + .append(getQualifier().getClassid(), rhs.getQualifier().getClassid()) + .append(getQualifier().getSchemeid(), rhs.getQualifier().getSchemeid()) + .append(getValue(), rhs.getValue()) + .isEquals(); + } +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/CleaningFunctions.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/CleaningFunctions.java index c0ef339bde..49b30897ca 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/CleaningFunctions.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/CleaningFunctions.java @@ -43,34 +43,4 @@ public class CleaningFunctions { return !PidBlacklistProvider.getBlacklist(s.getQualifier().getClassid()).contains(pidValue); } - /** - * Utility method that normalises PID values on a per-type basis. - * @param pid the PID whose value will be normalised. - * @return the PID containing the normalised value. - */ - public static StructuredProperty normalizePidValue(StructuredProperty pid) { - pid - .setValue( - normalizePidValue( - pid.getQualifier().getClassid(), - pid.getValue())); - - return pid; - } - - public static String normalizePidValue(String pidType, String pidValue) { - String value = Optional - .ofNullable(pidValue) - .map(String::trim) - .orElseThrow(() -> new IllegalArgumentException("PID value cannot be empty")); - - switch (pidType) { - - // TODO add cleaning for more PID types as needed - case "doi": - return value.toLowerCase().replaceFirst(DOI_PREFIX_REGEX, DOI_PREFIX); - } - return value; - } - } diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/DoiCleaningRule.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/DoiCleaningRule.java index 43fb0fedac..cd89577649 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/DoiCleaningRule.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/DoiCleaningRule.java @@ -6,18 +6,11 @@ import org.apache.commons.lang3.StringUtils; public class DoiCleaningRule { public static String clean(final String doi) { - return doi - .toLowerCase() - .replaceAll("\\s", "") - .replaceAll("^doi:", "") - .replaceFirst(CleaningFunctions.DOI_PREFIX_REGEX, CleaningFunctions.DOI_PREFIX); - } - - public static String normalizeDoi(final String input) { - if (input == null) + if (doi == null) return null; - final String replaced = input + final String replaced = doi .replaceAll("\\n|\\r|\\t|\\s", "") + .replaceAll("^doi:", "") .toLowerCase() .replaceFirst(CleaningFunctions.DOI_PREFIX_REGEX, CleaningFunctions.DOI_PREFIX); if (StringUtils.isEmpty(replaced)) @@ -32,7 +25,6 @@ public class DoiCleaningRule { return null; return ret; - } } 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 2be4e8e0ce..dfa9c5ad07 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 @@ -563,12 +563,24 @@ public class GraphCleaningFunctions extends CleaningFunctions { Optional .ofNullable(i.getPid()) .ifPresent(pid -> { - final Set<StructuredProperty> pids = Sets.newHashSet(pid); + final Set<HashableStructuredProperty> pids = pid + .stream() + .map(HashableStructuredProperty::newInstance) + .collect(Collectors.toCollection(HashSet::new)); Optional .ofNullable(i.getAlternateIdentifier()) .ifPresent(altId -> { - final Set<StructuredProperty> altIds = Sets.newHashSet(altId); - i.setAlternateIdentifier(Lists.newArrayList(Sets.difference(altIds, pids))); + final Set<HashableStructuredProperty> altIds = altId + .stream() + .map(HashableStructuredProperty::newInstance) + .collect(Collectors.toCollection(HashSet::new)); + i + .setAlternateIdentifier( + Sets + .difference(altIds, pids) + .stream() + .map(HashableStructuredProperty::toStructuredProperty) + .collect(Collectors.toList())); }); }); diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactory.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactory.java index 1d61c87df0..2c77c3b376 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactory.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactory.java @@ -175,7 +175,7 @@ public class IdentifierFactory implements Serializable { return entity .getPid() .stream() - .map(CleaningFunctions::normalizePidValue) + .map(PidCleaner::normalizePidValue) .filter(CleaningFunctions::pidFilter) .collect( Collectors @@ -207,7 +207,7 @@ public class IdentifierFactory implements Serializable { // filter away PIDs provided by a DS that is not considered an authority for the // given PID Type .filter(p -> shouldFilterPidByCriteria(collectedFrom, p, mapHandles)) - .map(CleaningFunctions::normalizePidValue) + .map(PidCleaner::normalizePidValue) .filter(p -> isNotFromDelegatedAuthority(collectedFrom, p)) .filter(CleaningFunctions::pidFilter)) .orElse(Stream.empty()); diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java index ac7694d188..e018131102 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java @@ -972,7 +972,7 @@ public class MergeUtils { private static String extractKeyFromPid(final StructuredProperty pid) { if (pid == null) return null; - final StructuredProperty normalizedPid = CleaningFunctions.normalizePidValue(pid); + final StructuredProperty normalizedPid = PidCleaner.normalizePidValue(pid); return String.format("%s::%s", normalizedPid.getQualifier().getClassid(), normalizedPid.getValue()); } diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidValueComparator.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidValueComparator.java index 0e20835902..1e591ce720 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidValueComparator.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidValueComparator.java @@ -18,8 +18,8 @@ public class PidValueComparator implements Comparator<StructuredProperty> { if (right == null) return -1; - StructuredProperty l = CleaningFunctions.normalizePidValue(left); - StructuredProperty r = CleaningFunctions.normalizePidValue(right); + StructuredProperty l = PidCleaner.normalizePidValue(left); + StructuredProperty r = PidCleaner.normalizePidValue(right); return Optional .ofNullable(l.getValue()) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java index e10d0c500c..77453e5f0f 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java @@ -28,6 +28,7 @@ import com.jayway.jsonpath.JsonPath; import eu.dnetlib.dhp.schema.mdstore.MDStoreWithInfo; import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions; +import eu.dnetlib.dhp.schema.oaf.utils.PidCleaner; import net.minidev.json.JSONArray; import scala.collection.JavaConverters; import scala.collection.Seq; @@ -104,7 +105,7 @@ public class DHPUtils { public static String generateUnresolvedIdentifier(final String pid, final String pidType) { - final String cleanedPid = CleaningFunctions.normalizePidValue(pidType, pid); + final String cleanedPid = PidCleaner.normalizePidValue(pidType, pid); return String.format("unresolved::%s::%s", cleanedPid, pidType.toLowerCase().trim()); } diff --git a/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactoryTest.java b/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactoryTest.java index bce4b76b58..9cc0698a4f 100644 --- a/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactoryTest.java +++ b/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactoryTest.java @@ -29,7 +29,7 @@ class IdentifierFactoryTest { "publication_doi2.json", "50|doi_________::79dbc7a2a56dc1532659f9038843256e", true); verifyIdentifier( - "publication_doi3.json", "50|pmc_________::94e4cb08c93f8733b48e2445d04002ac", true); + "publication_doi3.json", "50|pmc_________::e2a339e0e11bfbf55462e14a07f1b304", true); verifyIdentifier( "publication_doi4.json", "50|od______2852::38861c44e6052a8d49f59a4c39ba5e66", true); @@ -41,7 +41,7 @@ class IdentifierFactoryTest { "publication_pmc1.json", "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f", true); verifyIdentifier( - "publication_pmc2.json", "50|pmc_________::94e4cb08c93f8733b48e2445d04002ac", true); + "publication_pmc2.json", "50|pmc_________::e2a339e0e11bfbf55462e14a07f1b304", true); verifyIdentifier( "publication_openapc.json", "50|doi_________::79dbc7a2a56dc1532659f9038843256e", true); diff --git a/dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_doi3.json b/dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_doi3.json index b1ea01f605..303c023be8 100644 --- a/dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_doi3.json +++ b/dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_doi3.json @@ -29,7 +29,7 @@ }, { "qualifier": {"classid": "pmc"}, - "value": "21459329" + "value": "PMC21459329" } ] } diff --git a/dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_pmc2.json b/dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_pmc2.json index e7d49eebb9..3b7b6590ee 100644 --- a/dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_pmc2.json +++ b/dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_pmc2.json @@ -13,7 +13,7 @@ }, { "qualifier":{"classid":"pmc"}, - "value":"21459329" + "value":"PMC21459329" } ] } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java index 70ca1576c2..028fa47dc4 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java @@ -10,7 +10,6 @@ import java.util.List; import org.apache.commons.io.IOUtils; import org.apache.hadoop.io.Text; import org.apache.hadoop.io.compress.BZip2Codec; -import org.apache.hadoop.io.compress.GzipCodec; import org.apache.hadoop.mapred.SequenceFileOutputFormat; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaPairRDD; @@ -29,6 +28,7 @@ import eu.dnetlib.dhp.schema.action.AtomicAction; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions; +import eu.dnetlib.dhp.schema.oaf.utils.DoiCleaningRule; import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; import scala.Tuple2; @@ -46,6 +46,8 @@ public class PrepareAffiliationRelations implements Serializable { public static final String BIP_INFERENCE_PROVENANCE = "openaire:affiliation"; public static final String OPENAIRE_DATASOURCE_ID = "10|infrastruct_::f66f1bd369679b5b077dcdf006089556"; public static final String OPENAIRE_DATASOURCE_NAME = "OpenAIRE"; + public static final String DOI_URL_PREFIX = "https://doi.org/"; + public static final int DOI_URL_PREFIX_LENGTH = 16; public static <I extends Result> void main(String[] args) throws Exception { @@ -98,35 +100,26 @@ public class PrepareAffiliationRelations implements Serializable { private static void createActionSet(SparkSession spark, String crossrefInputPath, String pubmedInputPath, String openapcInputPath, String dataciteInputPath, String webcrawlInputPath, String publisherlInputPath, String outputPath) { - List<KeyValue> collectedFromCrossref = OafMapperUtils - .listKeyValues(ModelConstants.CROSSREF_ID, "Crossref"); - JavaPairRDD<Text, Text> crossrefRelations = prepareAffiliationRelations( - spark, crossrefInputPath, collectedFromCrossref); + List<KeyValue> collectedfromOpenAIRE = OafMapperUtils + .listKeyValues(OPENAIRE_DATASOURCE_ID, OPENAIRE_DATASOURCE_NAME); + + JavaPairRDD<Text, Text> crossrefRelations = prepareAffiliationRelationsNewModel( + spark, crossrefInputPath, collectedfromOpenAIRE); - List<KeyValue> collectedFromPubmed = OafMapperUtils - .listKeyValues(ModelConstants.PUBMED_CENTRAL_ID, "Pubmed"); JavaPairRDD<Text, Text> pubmedRelations = prepareAffiliationRelations( - spark, pubmedInputPath, collectedFromPubmed); + spark, pubmedInputPath, collectedfromOpenAIRE); - List<KeyValue> collectedFromOpenAPC = OafMapperUtils - .listKeyValues(ModelConstants.OPEN_APC_ID, "OpenAPC"); - JavaPairRDD<Text, Text> openAPCRelations = prepareAffiliationRelations( - spark, openapcInputPath, collectedFromOpenAPC); + JavaPairRDD<Text, Text> openAPCRelations = prepareAffiliationRelationsNewModel( + spark, openapcInputPath, collectedfromOpenAIRE); - List<KeyValue> collectedFromDatacite = OafMapperUtils - .listKeyValues(ModelConstants.DATACITE_ID, "Datacite"); JavaPairRDD<Text, Text> dataciteRelations = prepareAffiliationRelations( - spark, dataciteInputPath, collectedFromDatacite); + spark, dataciteInputPath, collectedfromOpenAIRE); - List<KeyValue> collectedFromWebCrawl = OafMapperUtils - .listKeyValues(OPENAIRE_DATASOURCE_ID, OPENAIRE_DATASOURCE_NAME); JavaPairRDD<Text, Text> webCrawlRelations = prepareAffiliationRelations( - spark, webcrawlInputPath, collectedFromWebCrawl); + spark, webcrawlInputPath, collectedfromOpenAIRE); - List<KeyValue> collectedfromPublisher = OafMapperUtils - .listKeyValues(OPENAIRE_DATASOURCE_ID, OPENAIRE_DATASOURCE_NAME); JavaPairRDD<Text, Text> publisherRelations = prepareAffiliationRelationFromPublisher( - spark, publisherlInputPath, collectedfromPublisher); + spark, publisherlInputPath, collectedfromOpenAIRE); crossrefRelations .union(pubmedRelations) @@ -138,6 +131,21 @@ public class PrepareAffiliationRelations implements Serializable { outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, BZip2Codec.class); } + private static JavaPairRDD<Text, Text> prepareAffiliationRelationFromPublisherNewModel(SparkSession spark, + String inputPath, + List<KeyValue> collectedfrom) { + + Dataset<Row> df = spark + .read() + .schema( + "`DOI` STRING, `Organizations` ARRAY<STRUCT<`PID`:STRING, `Value`:STRING,`Confidence`:DOUBLE, `Status`:STRING>>") + .json(inputPath) + .where("DOI is not null"); + + return getTextTextJavaPairRDD(collectedfrom, df.selectExpr("DOI", "Organizations as Matchings")); + + } + private static JavaPairRDD<Text, Text> prepareAffiliationRelationFromPublisher(SparkSession spark, String inputPath, List<KeyValue> collectedfrom) { @@ -165,6 +173,20 @@ public class PrepareAffiliationRelations implements Serializable { return getTextTextJavaPairRDD(collectedfrom, df); } + private static <I extends Result> JavaPairRDD<Text, Text> prepareAffiliationRelationsNewModel(SparkSession spark, + String inputPath, + List<KeyValue> collectedfrom) { + // load and parse affiliation relations from HDFS + Dataset<Row> df = spark + .read() + .schema( + "`DOI` STRING, `Matchings` ARRAY<STRUCT<`PID`:STRING, `Value`:STRING,`Confidence`:DOUBLE, `Status`:STRING>>") + .json(inputPath) + .where("DOI is not null"); + + return getTextTextJavaPairRDDNew(collectedfrom, df); + } + private static JavaPairRDD<Text, Text> getTextTextJavaPairRDD(List<KeyValue> collectedfrom, Dataset<Row> df) { // unroll nested arrays df = df @@ -181,7 +203,7 @@ public class PrepareAffiliationRelations implements Serializable { // DOI to OpenAIRE id final String paperId = ID_PREFIX - + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", row.getAs("doi"))); + + IdentifierFactory.md5(DoiCleaningRule.clean(removePrefix(row.getAs("doi")))); // ROR id to OpenAIRE id final String affId = GenerateRorActionSetJob.calculateOpenaireId(row.getAs("rorid")); @@ -213,6 +235,69 @@ public class PrepareAffiliationRelations implements Serializable { new Text(OBJECT_MAPPER.writeValueAsString(aa)))); } + private static JavaPairRDD<Text, Text> getTextTextJavaPairRDDNew(List<KeyValue> collectedfrom, Dataset<Row> df) { + // unroll nested arrays + df = df + .withColumn("matching", functions.explode(new Column("Matchings"))) + .select( + new Column("DOI").as("doi"), + new Column("matching.PID").as("pidtype"), + new Column("matching.Value").as("pidvalue"), + new Column("matching.Confidence").as("confidence"), + new Column("matching.Status").as("status")) + .where("status = 'active'"); + + // prepare action sets for affiliation relations + return df + .toJavaRDD() + .flatMap((FlatMapFunction<Row, Relation>) row -> { + + // DOI to OpenAIRE id + final String paperId = ID_PREFIX + + IdentifierFactory.md5(DoiCleaningRule.clean(removePrefix(row.getAs("doi")))); + + // Organization to OpenAIRE identifier + String affId = null; + if (row.getAs("pidtype").equals("ROR")) + // ROR id to OpenIARE id + affId = GenerateRorActionSetJob.calculateOpenaireId(row.getAs("pidvalue")); + else + // getting the OpenOrgs identifier for the organization + affId = row.getAs("pidvalue"); + + Qualifier qualifier = OafMapperUtils + .qualifier( + BIP_AFFILIATIONS_CLASSID, + BIP_AFFILIATIONS_CLASSNAME, + ModelConstants.DNET_PROVENANCE_ACTIONS, + ModelConstants.DNET_PROVENANCE_ACTIONS); + + // format data info; setting `confidence` into relation's `trust` + DataInfo dataInfo = OafMapperUtils + .dataInfo( + false, + BIP_INFERENCE_PROVENANCE, + true, + false, + qualifier, + Double.toString(row.getAs("confidence"))); + + // return bi-directional relations + return getAffiliationRelationPair(paperId, affId, collectedfrom, dataInfo).iterator(); + + }) + .map(p -> new AtomicAction(Relation.class, p)) + .mapToPair( + aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), + new Text(OBJECT_MAPPER.writeValueAsString(aa)))); + } + + private static String removePrefix(String doi) { + if (doi.startsWith(DOI_URL_PREFIX)) + return doi.substring(DOI_URL_PREFIX_LENGTH); + return doi; + } + private static List<Relation> getAffiliationRelationPair(String paperId, String affId, List<KeyValue> collectedfrom, DataInfo dataInfo) { return Arrays diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json index 4d85cf26b6..b3d1d742bc 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json @@ -28,13 +28,19 @@ "paramLongName": "dataciteInputPath", "paramDescription": "the path to get the input data from Datacite", "paramRequired": true - },{ + }, + { "paramName": "wip", "paramLongName": "webCrawlInputPath", "paramDescription": "the path to get the input data from Web Crawl", "paramRequired": true -} -, + }, + { + "paramName": "pub", + "paramLongName": "publisherInputPath", + "paramDescription": "the path to get the input data from publishers", + "paramRequired": true + }, { "paramName": "o", "paramLongName": "outputPath", diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala index 4bd6bcc098..7c45234f64 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala @@ -332,7 +332,7 @@ case object Crossref2Oaf { implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats //MAPPING Crossref DOI into PID - val doi: String = DoiCleaningRule.normalizeDoi((json \ "DOI").extract[String]) + val doi: String = DoiCleaningRule.clean((json \ "DOI").extract[String]) result.setPid( List( structuredProperty( @@ -673,7 +673,7 @@ case object Crossref2Oaf { val doi = input.getString(0) val rorId = input.getString(1) - val pubId = s"50|${PidType.doi.toString.padTo(12, "_")}::${DoiCleaningRule.normalizeDoi(doi)}" + val pubId = s"50|${PidType.doi.toString.padTo(12, "_")}::${DoiCleaningRule.clean(doi)}" val affId = GenerateRorActionSetJob.calculateOpenaireId(rorId) val r: Relation = new Relation diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java index ac9977a7ea..179cbecb5f 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java @@ -28,8 +28,8 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.schema.action.AtomicAction; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Relation; -import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions; import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; +import eu.dnetlib.dhp.schema.oaf.utils.PidCleaner; public class PrepareAffiliationRelationsTest { @@ -39,8 +39,7 @@ public class PrepareAffiliationRelationsTest { private static Path workingDir; private static final String ID_PREFIX = "50|doi_________::"; - private static final Logger log = LoggerFactory - .getLogger(PrepareAffiliationRelationsTest.class); + private static final Logger log = LoggerFactory.getLogger(PrepareAffiliationRelationsTest.class); @BeforeAll public static void beforeAll() throws IOException { @@ -74,26 +73,34 @@ public class PrepareAffiliationRelationsTest { @Test void testMatch() throws Exception { - String crossrefAffiliationRelationPath = getClass() + String crossrefAffiliationRelationPathNew = getClass() .getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json") .getPath(); + String crossrefAffiliationRelationPath = getClass() + .getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror_old.json") + .getPath(); + String publisherAffiliationRelationPath = getClass() .getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/publishers") .getPath(); + String publisherAffiliationRelationOldPath = getClass() + .getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/publichers_old") + .getPath(); + String outputPath = workingDir.toString() + "/actionSet"; PrepareAffiliationRelations .main( new String[] { "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-crossrefInputPath", crossrefAffiliationRelationPath, + "-crossrefInputPath", crossrefAffiliationRelationPathNew, "-pubmedInputPath", crossrefAffiliationRelationPath, - "-openapcInputPath", crossrefAffiliationRelationPath, + "-openapcInputPath", crossrefAffiliationRelationPathNew, "-dataciteInputPath", crossrefAffiliationRelationPath, "-webCrawlInputPath", crossrefAffiliationRelationPath, - "-publisherInputPath", publisherAffiliationRelationPath, + "-publisherInputPath", publisherAffiliationRelationOldPath, "-outputPath", outputPath }); @@ -104,13 +111,8 @@ public class PrepareAffiliationRelationsTest { .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) .map(aa -> ((Relation) aa.getPayload())); -// for (Relation r : tmp.collect()) { -// System.out.println( -// r.getSource() + "\t" + r.getTarget() + "\t" + r.getRelType() + "\t" + r.getRelClass() + "\t" + r.getSubRelType() + "\t" + r.getValidationDate() + "\t" + r.getDataInfo().getTrust() + "\t" + r.getDataInfo().getInferred() -// ); -// } // count the number of relations - assertEquals(138, tmp.count()); + assertEquals(150, tmp.count());// 18 + 24 *3 + 30 * 2 = Dataset<Relation> dataset = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class)); dataset.createOrReplaceTempView("result"); @@ -121,7 +123,7 @@ public class PrepareAffiliationRelationsTest { // verify that we have equal number of bi-directional relations Assertions .assertEquals( - 69, execVerification + 75, execVerification .filter( "relClass='" + ModelConstants.HAS_AUTHOR_INSTITUTION + "'") .collectAsList() @@ -129,21 +131,21 @@ public class PrepareAffiliationRelationsTest { Assertions .assertEquals( - 69, execVerification + 75, execVerification .filter( "relClass='" + ModelConstants.IS_AUTHOR_INSTITUTION_OF + "'") .collectAsList() .size()); // check confidence value of a specific relation - String sourceDOI = "10.1061/(asce)0733-9399(2002)128:7(759)"; + String sourceDOI = "10.1089/10872910260066679"; final String sourceOpenaireId = ID_PREFIX - + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", sourceDOI)); + + IdentifierFactory.md5(PidCleaner.normalizePidValue("doi", sourceDOI)); Assertions .assertEquals( - "0.7071067812", execVerification + "1.0", execVerification .filter( "source='" + sourceOpenaireId + "'") .collectAsList() @@ -151,11 +153,34 @@ public class PrepareAffiliationRelationsTest { .getString(4)); final String publisherid = ID_PREFIX - + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s00217-010-1268-9")); - final String rorId = "20|ror_________::" + IdentifierFactory.md5("https://ror.org/03265fv13"); + + IdentifierFactory.md5(PidCleaner.normalizePidValue("doi", "10.1089/10872910260066679")); + final String rorId = "20|ror_________::" + IdentifierFactory.md5("https://ror.org/05cf8a891"); Assertions .assertEquals( - 1, execVerification.filter("source = '" + publisherid + "' and target = '" + rorId + "'").count()); + 2, execVerification.filter("source = '" + publisherid + "' and target = '" + rorId + "'").count()); + + Assertions + .assertEquals( + 1, execVerification + .filter( + "source = '" + ID_PREFIX + + IdentifierFactory + .md5(PidCleaner.normalizePidValue("doi", "10.1007/s00217-010-1268-9")) + + "' and target = '" + "20|ror_________::" + + IdentifierFactory.md5("https://ror.org/03265fv13") + "'") + .count()); + + Assertions + .assertEquals( + 3, execVerification + .filter( + "source = '" + ID_PREFIX + + IdentifierFactory + .md5(PidCleaner.normalizePidValue("doi", "10.1007/3-540-47984-8_14")) + + "' and target = '" + "20|ror_________::" + + IdentifierFactory.md5("https://ror.org/00a0n9e72") + "'") + .count()); + } } diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateOpenCitationsASTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateOpenCitationsASTest.java index ed80ed5c53..b690b6228c 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateOpenCitationsASTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateOpenCitationsASTest.java @@ -31,6 +31,7 @@ import eu.dnetlib.dhp.schema.oaf.Publication; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions; import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; +import eu.dnetlib.dhp.schema.oaf.utils.PidCleaner; public class CreateOpenCitationsASTest { @@ -280,17 +281,17 @@ public class CreateOpenCitationsASTest { @Test void testRelationsSourceTargetCouple() throws Exception { final String doi1 = "50|doi_________::" - + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s10854-015-3684-x")); + + IdentifierFactory.md5(PidCleaner.normalizePidValue("doi", "10.1007/s10854-015-3684-x")); final String doi2 = "50|doi_________::" - + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1111/j.1551-2916.2008.02408.x")); + + IdentifierFactory.md5(PidCleaner.normalizePidValue("doi", "10.1111/j.1551-2916.2008.02408.x")); final String doi3 = "50|doi_________::" - + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s10854-014-2114-9")); + + IdentifierFactory.md5(PidCleaner.normalizePidValue("doi", "10.1007/s10854-014-2114-9")); final String doi4 = "50|doi_________::" - + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1016/j.ceramint.2013.09.069")); + + IdentifierFactory.md5(PidCleaner.normalizePidValue("doi", "10.1016/j.ceramint.2013.09.069")); final String doi5 = "50|doi_________::" - + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s10854-009-9913-4")); + + IdentifierFactory.md5(PidCleaner.normalizePidValue("doi", "10.1007/s10854-009-9913-4")); final String doi6 = "50|doi_________::" - + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1016/0038-1098(72)90370-5")); + + IdentifierFactory.md5(PidCleaner.normalizePidValue("doi", "10.1016/0038-1098(72)90370-5")); String inputPath = getClass() .getResource( diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/CreateTAActionSetTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/CreateTAActionSetTest.java index 0ec34311fd..592c6283a9 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/CreateTAActionSetTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/CreateTAActionSetTest.java @@ -28,6 +28,7 @@ import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions; import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; +import eu.dnetlib.dhp.schema.oaf.utils.PidCleaner; /** * @author miriam.baglioni @@ -270,17 +271,17 @@ public class CreateTAActionSetTest { @Test void testRelationsSourceTargetCouple() throws Exception { final String doi1 = "50|doi_________::" - + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s10854-015-3684-x")); + + IdentifierFactory.md5(PidCleaner.normalizePidValue("doi", "10.1007/s10854-015-3684-x")); final String doi2 = "50|doi_________::" - + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1111/j.1551-2916.2008.02408.x")); + + IdentifierFactory.md5(PidCleaner.normalizePidValue("doi", "10.1111/j.1551-2916.2008.02408.x")); final String doi3 = "50|doi_________::" - + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s10854-014-2114-9")); + + IdentifierFactory.md5(PidCleaner.normalizePidValue("doi", "10.1007/s10854-014-2114-9")); final String doi4 = "50|doi_________::" - + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1016/j.ceramint.2013.09.069")); + + IdentifierFactory.md5(PidCleaner.normalizePidValue("doi", "10.1016/j.ceramint.2013.09.069")); final String doi5 = "50|doi_________::" - + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s10854-009-9913-4")); + + IdentifierFactory.md5(PidCleaner.normalizePidValue("doi", "10.1007/s10854-009-9913-4")); final String doi6 = "50|doi_________::" - + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1016/0038-1098(72)90370-5")); + + IdentifierFactory.md5(PidCleaner.normalizePidValue("doi", "10.1016/0038-1098(72)90370-5")); String inputPath = getClass() .getResource( diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json index 08dc3f7eb5..b5a7116942 100644 --- a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json @@ -1,9 +1,10 @@ -{"DOI":"10.1061\/(asce)0733-9399(2002)128:7(759)","Matchings":[{"RORid":"https:\/\/ror.org\/03yxnpp24","Confidence":0.7071067812},{"RORid":"https:\/\/ror.org\/01teme464","Confidence":0.89}]} -{"DOI":"10.1105\/tpc.8.3.343","Matchings":[{"RORid":"https:\/\/ror.org\/02k40bc56","Confidence":0.7071067812}]} -{"DOI":"10.1161\/01.cir.0000013305.01850.37","Matchings":[{"RORid":"https:\/\/ror.org\/00qjgza05","Confidence":1}]} -{"DOI":"10.1142\/s021821650200186x","Matchings":[{"RORid":"https:\/\/ror.org\/035xkbk20","Confidence":1},{"RORid":"https:\/\/ror.org\/05apxxy63","Confidence":1}]} -{"DOI":"10.1061\/(asce)0733-9372(2002)128:7(575)","Matchings":[{"RORid":"https:\/\/ror.org\/04j198w64","Confidence":0.82}]} -{"DOI":"10.1061\/(asce)0733-9372(2002)128:7(588)","Matchings":[{"RORid":"https:\/\/ror.org\/03m8km719","Confidence":0.8660254038},{"RORid":"https:\/\/ror.org\/02aze4h65","Confidence":0.87}]} -{"DOI":"10.1161\/hy0202.103001","Matchings":[{"RORid":"https:\/\/ror.org\/057xtrt18","Confidence":0.7071067812}]} -{"DOI": "10.1080/13669877.2015.1042504", "Matchings": [{"Confidence": 1.0, "RORid": "https://ror.org/03265fv13"}]} -{"DOI": "10.1007/3-540-47984-8_14", "Matchings": [{"Confidence": 1.0, "RORid": "https://ror.org/00a0n9e72"}]} \ No newline at end of file +{"DOI":"10.1021\/ac020069k","Matchings":[{"PID":"ROR","Value":"https:\/\/ror.org\/01f5ytq51","Status":"active","Confidence":1}]} +{"DOI":"10.1161\/01.cir.0000013846.72805.7e","Matchings":[{"PID":"ROR","Value":"https:\/\/ror.org\/02pttbw34","Status":"active","Confidence":1}]} +{"DOI":"10.1161\/hy02t2.102992","Matchings":[{"PID":"ROR","Value":"https:\/\/ror.org\/00qqv6244","Status":"active","Confidence":1},{"PID":"ROR","Value":"https:\/\/ror.org\/00p991c53","Status":"active","Confidence":1}]} +{"DOI":"10.1126\/science.1073633","Matchings":[{"PID":"ROR","Value":"https:\/\/ror.org\/03xez1567","Status":"active","Confidence":1},{"PID":"ROR","Value":"https:\/\/ror.org\/006w34k90","Status":"active","Confidence":1}]} +{"DOI":"10.1089\/10872910260066679","Matchings":[{"PID":"ROR","Value":"https:\/\/ror.org\/05cf8a891","Status":"active","Confidence":1}]} +{"DOI":"10.1108\/02656719610116117","Matchings":[{"PID":"ROR","Value":"https:\/\/ror.org\/03mnm0t94","Status":"active","Confidence":1},{"PID":"ROR","Value":"https:\/\/ror.org\/007tn5k56","Status":"active","Confidence":1}]} +{"DOI":"10.1080\/01443610050111986","Matchings":[{"PID":"ROR","Value":"https:\/\/ror.org\/001x4vz59","Status":"active","Confidence":1},{"PID":"ROR","Value":"https:\/\/ror.org\/01tmqtf75","Status":"active","Confidence":1}]} +{"DOI":"10.1021\/cm020118+","Matchings":[{"PID":"ROR","Value":"https:\/\/ror.org\/02cf1je33","Confidence":1,"Status":"inactive"},{"PID":"ROR","Value":"https:\/\/ror.org\/01hvx5h04","Confidence":1,"Status":"active"}]} +{"DOI":"10.1161\/hc1202.104524","Matchings":[{"PID":"ROR","Value":"https:\/\/ror.org\/040r8fr65","Status":"active","Confidence":1},{"PID":"ROR","Value":"https:\/\/ror.org\/04fctr677","Status":"active","Confidence":1}]} +{"DOI":"10.1021\/ma011134f","Matchings":[{"PID":"ROR","Value":"https:\/\/ror.org\/04tj63d06","Status":"active","Confidence":1}]} \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror_old.json b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror_old.json new file mode 100644 index 0000000000..d7f004deb2 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror_old.json @@ -0,0 +1,9 @@ +{"DOI":"10.1061\/(asce)0733-9399(2002)128:7(759)","Matchings":[{"RORid":"https:\/\/ror.org\/03yxnpp24","Confidence":0.7071067812},{"RORid":"https:\/\/ror.org\/01teme464","Confidence":0.89}]} +{"DOI":"10.1105\/tpc.8.3.343","Matchings":[{"RORid":"https:\/\/ror.org\/02k40bc56","Confidence":0.7071067812}]} +{"DOI":"10.1161\/01.cir.0000013305.01850.37","Matchings":[{"RORid":"https:\/\/ror.org\/00qjgza05","Confidence":1}]} +{"DOI":"10.1142\/s021821650200186x","Matchings":[{"RORid":"https:\/\/ror.org\/035xkbk20","Confidence":1},{"RORid":"https:\/\/ror.org\/05apxxy63","Confidence":1}]} +{"DOI":"10.1061\/(asce)0733-9372(2002)128:7(575)","Matchings":[{"RORid":"https:\/\/ror.org\/04j198w64","Confidence":0.82}]} +{"DOI":"10.1061\/(asce)0733-9372(2002)128:7(588)","Matchings":[{"RORid":"https:\/\/ror.org\/03m8km719","Confidence":0.8660254038},{"RORid":"https:\/\/ror.org\/02aze4h65","Confidence":0.87}]} +{"DOI":"10.1161\/hy0202.103001","Matchings":[{"RORid":"https:\/\/ror.org\/057xtrt18","Confidence":0.7071067812}]} +{"DOI": "10.1080/13669877.2015.1042504", "Matchings": [{"Confidence": 1.0, "RORid": "https://ror.org/03265fv13"}]} +{"DOI": "https://doi.org/10.1007/3-540-47984-8_14", "Matchings": [{"Confidence": 1.0, "RORid": "https://ror.org/00a0n9e72"}]} \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/publichers_old/publisher b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/publichers_old/publisher new file mode 100644 index 0000000000..851263933d --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/publichers_old/publisher @@ -0,0 +1,6 @@ +{"DOI": "10.1007/s00217-010-1268-9", "Authors": [{"Name": {"Full": "Martin Zarnkow", "First": null, "Last": null}, "Raw_affiliations": ["TU M\u00fcnchen, Lehrstuhl f\u00fcr Brau- und Getr\u00e4nketechnologie"], "Organization_PIDs": []}, {"Name": {"Full": "Andrea Faltermaier", "First": null, "Last": null}, "Raw_affiliations": ["Lehrstuhl f\u00fcr Brau- und Getr\u00e4nketechnologie"], "Organization_PIDs": []}, {"Name": {"Full": "Werner Back", "First": null, "Last": null}, "Raw_affiliations": ["Lehrstuhl f\u00fcr Technologie der Brauerei I"], "Organization_PIDs": []}, {"Name": {"Full": "Martina Gastl", "First": null, "Last": null}, "Raw_affiliations": ["Lehrstuhl f\u00fcr Brau- und Getr\u00e4nketechnologie"], "Organization_PIDs": []}, {"Name": {"Full": "Elkek K. Arendt", "First": null, "Last": null}, "Raw_affiliations": ["University College Cork"], "Organization_PIDs": [{"RORid": "https://ror.org/03265fv13", "Confidence": 1}]}], "Organizations": [{"RORid": "https://ror.org/03265fv13", "Confidence": 1}]} +{"DOI": "10.1007/BF01154707", "Authors": [{"Name": {"Full": "Buggy, M.", "First": null, "Last": null}, "Raw_affiliations": ["Department of Materials Science and Technology, University of Limerick, Limerick, Ireland"], "Organization_PIDs": [{"RORid": "https://ror.org/00a0n9e72", "Confidence": 1}]}, {"Name": {"Full": "Carew, A.", "First": null, "Last": null}, "Raw_affiliations": ["Department of Materials Science and Technology, University of Limerick, Limerick, Ireland"], "Organization_PIDs": [{"RORid": "https://ror.org/00a0n9e72", "Confidence": 1}]}], "Organizations": [{"RORid": "https://ror.org/00a0n9e72", "Confidence": 1}]} +{"DOI": "10.1007/s10237-017-0974-7", "Authors": [{"Name": {"Full": "Donnacha J. McGrath", "First": null, "Last": null}, "Raw_affiliations": ["Biomechanics Research Centre (BMEC), Biomedical Engineering, College of Engineering and Informatics, NUI Galway, Galway, Ireland"], "Organization_PIDs": [{"RORid": "https://ror.org/03bea9k73", "Confidence": 1}]}, {"Name": {"Full": "Anja Lena Thiebes", "First": null, "Last": null}, "Raw_affiliations": ["Department of Biohybrid and Medical Textiles (BioTex), AME-Helmholtz Institute for Biomedical Engineering, ITA-Institut f\u00fcr Textiltechnik, RWTH Aachen University and at AMIBM Maastricht University, Maastricht, The Netherlands, Aachen, Germany"], "Organization_PIDs": [{"RORid": "https://ror.org/02jz4aj89", "Confidence": 0.82}, {"RORid": "https://ror.org/04xfq0f34", "Confidence": 0.87}]}, {"Name": {"Full": "Christian G. Cornelissen", "First": null, "Last": null}, "Raw_affiliations": ["Department of Biohybrid and Medical Textiles (BioTex), AME-Helmholtz Institute for Biomedical Engineering, ITA-Institut f\u00fcr Textiltechnik, RWTH Aachen University and at AMIBM Maastricht University, Maastricht, The Netherlands, Aachen, Germany"], "Organization_PIDs": [{"RORid": "https://ror.org/02jz4aj89", "Confidence": 0.82}, {"RORid": "https://ror.org/04xfq0f34", "Confidence": 0.87}]}, {"Name": {"Full": "Barry O\u2019Brien", "First": null, "Last": null}, "Raw_affiliations": ["Department for Internal Medicine \u2013 Section for Pneumology, Medical Faculty, RWTH Aachen University, Aachen, Germany"], "Organization_PIDs": [{"RORid": "https://ror.org/04xfq0f34", "Confidence": 1}]}, {"Name": {"Full": "Stefan Jockenhoevel", "First": null, "Last": null}, "Raw_affiliations": ["Biomechanics Research Centre (BMEC), Biomedical Engineering, College of Engineering and Informatics, NUI Galway, Galway, Ireland"], "Organization_PIDs": [{"RORid": "https://ror.org/03bea9k73", "Confidence": 1}]}, {"Name": {"Full": "Mark Bruzzi", "First": null, "Last": null}, "Raw_affiliations": ["Department of Biohybrid and Medical Textiles (BioTex), AME-Helmholtz Institute for Biomedical Engineering, ITA-Institut f\u00fcr Textiltechnik, RWTH Aachen University and at AMIBM Maastricht University, Maastricht, The Netherlands, Aachen, Germany"], "Organization_PIDs": [{"RORid": "https://ror.org/02jz4aj89", "Confidence": 0.82}, {"RORid": "https://ror.org/04xfq0f34", "Confidence": 0.87}]}, {"Name": {"Full": "Peter E. McHugh", "First": null, "Last": null}, "Raw_affiliations": ["Biomechanics Research Centre (BMEC), Biomedical Engineering, College of Engineering and Informatics, NUI Galway, Galway, Ireland"], "Organization_PIDs": [{"RORid": "https://ror.org/03bea9k73", "Confidence": 1}]}], "Organizations": [{"RORid": "https://ror.org/03bea9k73", "Confidence": 1}, {"RORid": "https://ror.org/02jz4aj89", "Confidence": 0.82}, {"RORid": "https://ror.org/04xfq0f34", "Confidence": 0.87}, {"RORid": "https://ror.org/04xfq0f34", "Confidence": 1}]} +{"DOI": "10.1007/BF03168973", "Authors": [{"Name": {"Full": "Sheehan, G.", "First": null, "Last": null}, "Raw_affiliations": ["Dept of Infectious Diseases, Mater Misercordiae Hospital, Dublin 7"], "Organization_PIDs": []}, {"Name": {"Full": "Chew, N.", "First": null, "Last": null}, "Raw_affiliations": ["Dept of Infectious Diseases, Mater Misercordiae Hospital, Dublin 7"], "Organization_PIDs": []}], "Organizations": []} +{"DOI": "10.1007/s00338-009-0480-1", "Authors": [{"Name": {"Full": "Gleason, D. F.", "First": null, "Last": null}, "Raw_affiliations": ["Department of Biology, Georgia Southern University, Statesboro, USA"], "Organization_PIDs": [{"RORid": "https://ror.org/04agmb972", "Confidence": 1}]}, {"Name": {"Full": "Danilowicz, B. S.", "First": null, "Last": null}, "Raw_affiliations": ["Department of Biology, Georgia Southern University, Statesboro, USA"], "Organization_PIDs": [{"RORid": "https://ror.org/04agmb972", "Confidence": 1}]}, {"Name": {"Full": "Nolan, C. J.", "First": null, "Last": null}, "Raw_affiliations": ["School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland"], "Organization_PIDs": [{"RORid": "https://ror.org/05m7pjf47", "Confidence": 1}]}], "Organizations": [{"RORid": "https://ror.org/04agmb972", "Confidence": 1}, {"RORid": "https://ror.org/05m7pjf47", "Confidence": 1}]} +{"DOI": "10.1007/s10993-010-9187-y", "Authors": [{"Name": {"Full": "Martin Howard", "First": null, "Last": null}, "Raw_affiliations": ["University College Cork"], "Organization_PIDs": [{"RORid": "https://ror.org/03265fv13", "Confidence": 1}]}], "Organizations": [{"RORid": "https://ror.org/03265fv13", "Confidence": 1}]} \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/publishers/publisher b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/publishers/publisher new file mode 100644 index 0000000000..426500e73a --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/publishers/publisher @@ -0,0 +1,6 @@ +{"DOI": "10.1007/s00217-010-1268-9", "Authors": [{"Name": {"Full": "Martin Zarnkow", "First": null, "Last": null}, "Raw_affiliations": ["TU M\u00fcnchen, Lehrstuhl f\u00fcr Brau- und Getr\u00e4nketechnologie"], "Organization_PIDs": []}, {"Name": {"Full": "Andrea Faltermaier", "First": null, "Last": null}, "Raw_affiliations": ["Lehrstuhl f\u00fcr Brau- und Getr\u00e4nketechnologie"], "Organization_PIDs": []}, {"Name": {"Full": "Werner Back", "First": null, "Last": null}, "Raw_affiliations": ["Lehrstuhl f\u00fcr Technologie der Brauerei I"], "Organization_PIDs": []}, {"Name": {"Full": "Martina Gastl", "First": null, "Last": null}, "Raw_affiliations": ["Lehrstuhl f\u00fcr Brau- und Getr\u00e4nketechnologie"], "Organization_PIDs": []}, {"Name": {"Full": "Elkek K. Arendt", "First": null, "Last": null}, "Raw_affiliations": ["University College Cork"], "Organization_PIDs": [{"Value": "https://ror.org/03265fv13", "Confidence": 1}]}], "Organizations": [{"Provenance":"AffRo","PID":"ROR","Status":"active","Value": "https://ror.org/03265fv13", "Confidence": 1}]} +{"DOI": "10.1007/BF01154707", "Authors": [{"Name": {"Full": "Buggy, M.", "First": null, "Last": null}, "Raw_affiliations": ["Department of Materials Science and Technology, University of Limerick, Limerick, Ireland"], "Organization_PIDs": [{"Value": "https://ror.org/00a0n9e72", "Confidence": 1}]}, {"Name": {"Full": "Carew, A.", "First": null, "Last": null}, "Raw_affiliations": ["Department of Materials Science and Technology, University of Limerick, Limerick, Ireland"], "Organization_PIDs": [{"Value": "https://ror.org/00a0n9e72", "Confidence": 1}]}], "Organizations": [{"Provenance":"AffRo","PID":"ROR","Status":"active","Value": "https://ror.org/00a0n9e72", "Confidence": 1}]} +{"DOI": "10.1007/s10237-017-0974-7", "Authors": [{"Name": {"Full": "Donnacha J. McGrath", "First": null, "Last": null}, "Raw_affiliations": ["Biomechanics Research Centre (BMEC), Biomedical Engineering, College of Engineering and Informatics, NUI Galway, Galway, Ireland"], "Organization_PIDs": [{"Value": "https://ror.org/03bea9k73", "Confidence": 1}]}, {"Name": {"Full": "Anja Lena Thiebes", "First": null, "Last": null}, "Raw_affiliations": ["Department of Biohybrid and Medical Textiles (BioTex), AME-Helmholtz Institute for Biomedical Engineering, ITA-Institut f\u00fcr Textiltechnik, RWTH Aachen University and at AMIBM Maastricht University, Maastricht, The Netherlands, Aachen, Germany"], "Organization_PIDs": [{"Value": "https://ror.org/02jz4aj89", "Confidence": 0.82}, {"Value": "https://ror.org/04xfq0f34", "Confidence": 0.87}]}, {"Name": {"Full": "Christian G. Cornelissen", "First": null, "Last": null}, "Raw_affiliations": ["Department of Biohybrid and Medical Textiles (BioTex), AME-Helmholtz Institute for Biomedical Engineering, ITA-Institut f\u00fcr Textiltechnik, RWTH Aachen University and at AMIBM Maastricht University, Maastricht, The Netherlands, Aachen, Germany"], "Organization_PIDs": [{"Value": "https://ror.org/02jz4aj89", "Confidence": 0.82}, {"Value": "https://ror.org/04xfq0f34", "Confidence": 0.87}]}, {"Name": {"Full": "Barry O\u2019Brien", "First": null, "Last": null}, "Raw_affiliations": ["Department for Internal Medicine \u2013 Section for Pneumology, Medical Faculty, RWTH Aachen University, Aachen, Germany"], "Organization_PIDs": [{"Value": "https://ror.org/04xfq0f34", "Confidence": 1}]}, {"Name": {"Full": "Stefan Jockenhoevel", "First": null, "Last": null}, "Raw_affiliations": ["Biomechanics Research Centre (BMEC), Biomedical Engineering, College of Engineering and Informatics, NUI Galway, Galway, Ireland"], "Organization_PIDs": [{"Value": "https://ror.org/03bea9k73", "Confidence": 1}]}, {"Name": {"Full": "Mark Bruzzi", "First": null, "Last": null}, "Raw_affiliations": ["Department of Biohybrid and Medical Textiles (BioTex), AME-Helmholtz Institute for Biomedical Engineering, ITA-Institut f\u00fcr Textiltechnik, RWTH Aachen University and at AMIBM Maastricht University, Maastricht, The Netherlands, Aachen, Germany"], "Organization_PIDs": [{"Value": "https://ror.org/02jz4aj89", "Confidence": 0.82}, {"Value": "https://ror.org/04xfq0f34", "Confidence": 0.87}]}, {"Name": {"Full": "Peter E. McHugh", "First": null, "Last": null}, "Raw_affiliations": ["Biomechanics Research Centre (BMEC), Biomedical Engineering, College of Engineering and Informatics, NUI Galway, Galway, Ireland"], "Organization_PIDs": [{"Value": "https://ror.org/03bea9k73", "Confidence": 1}]}], "Organizations": [{"Provenance":"AffRo","PID":"ROR","Status":"active","Value": "https://ror.org/03bea9k73", "Confidence": 1}, {"Provenance":"AffRo","PID":"ROR","Status":"active","Value": "https://ror.org/02jz4aj89", "Confidence": 0.82}, {"Provenance":"AffRo","PID":"ROR","Status":"active","Value": "https://ror.org/04xfq0f34", "Confidence": 0.87}, {"Provenance":"AffRo","PID":"ROR","Status":"active","Value": "https://ror.org/04xfq0f34", "Confidence": 1}]} +{"DOI": "10.1007/BF03168973", "Authors": [{"Name": {"Full": "Sheehan, G.", "First": null, "Last": null}, "Raw_affiliations": ["Dept of Infectious Diseases, Mater Misercordiae Hospital, Dublin 7"], "Organization_PIDs": []}, {"Name": {"Full": "Chew, N.", "First": null, "Last": null}, "Raw_affiliations": ["Dept of Infectious Diseases, Mater Misercordiae Hospital, Dublin 7"], "Organization_PIDs": []}], "Organizations": []} +{"DOI": "10.1007/s00338-009-0480-1", "Authors": [{"Name": {"Full": "Gleason, D. F.", "First": null, "Last": null}, "Raw_affiliations": ["Department of Biology, Georgia Southern University, Statesboro, USA"], "Organization_PIDs": [{"Value": "https://ror.org/04agmb972", "Confidence": 1}]}, {"Name": {"Full": "Danilowicz, B. S.", "First": null, "Last": null}, "Raw_affiliations": ["Department of Biology, Georgia Southern University, Statesboro, USA"], "Organization_PIDs": [{"Value": "https://ror.org/04agmb972", "Confidence": 1}]}, {"Name": {"Full": "Nolan, C. J.", "First": null, "Last": null}, "Raw_affiliations": ["School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland"], "Organization_PIDs": [{"Value": "https://ror.org/05m7pjf47", "Confidence": 1}]}], "Organizations": [{"Provenance":"AffRo","PID":"ROR","Status":"active","Value": "https://ror.org/04agmb972", "Confidence": 1}, {"Provenance":"AffRo","PID":"ROR","Status":"active","Value": "https://ror.org/05m7pjf47", "Confidence": 1}]} +{"DOI": "10.1007/s10993-010-9187-y", "Authors": [{"Name": {"Full": "Martin Howard", "First": null, "Last": null}, "Raw_affiliations": ["University College Cork"], "Organization_PIDs": [{"Value": "https://ror.org/03265fv13", "Confidence": 1}]}], "Organizations": [{"PID":"ROR","Status":"active","Value": "https://ror.org/03265fv13", "Confidence": 1}]} \ No newline at end of file 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 c95d5442a9..a85f47d99c 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 @@ -55,29 +55,7 @@ import eu.dnetlib.dhp.common.Constants; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.oaf.AccessRight; -import eu.dnetlib.dhp.schema.oaf.Author; -import eu.dnetlib.dhp.schema.oaf.Context; -import eu.dnetlib.dhp.schema.oaf.Country; -import eu.dnetlib.dhp.schema.oaf.DataInfo; -import eu.dnetlib.dhp.schema.oaf.Dataset; -import eu.dnetlib.dhp.schema.oaf.EoscIfGuidelines; -import eu.dnetlib.dhp.schema.oaf.Field; -import eu.dnetlib.dhp.schema.oaf.GeoLocation; -import eu.dnetlib.dhp.schema.oaf.Instance; -import eu.dnetlib.dhp.schema.oaf.InstanceTypeMapping; -import eu.dnetlib.dhp.schema.oaf.Journal; -import eu.dnetlib.dhp.schema.oaf.KeyValue; -import eu.dnetlib.dhp.schema.oaf.OAIProvenance; -import eu.dnetlib.dhp.schema.oaf.Oaf; -import eu.dnetlib.dhp.schema.oaf.OafEntity; -import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Qualifier; -import eu.dnetlib.dhp.schema.oaf.Result; -import eu.dnetlib.dhp.schema.oaf.Software; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; -import eu.dnetlib.dhp.schema.oaf.Subject; +import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; @@ -667,22 +645,25 @@ public abstract class AbstractMdRecordToOafMapper { return this.vocs.getTermAsQualifier(schemeId, classId); } - protected List<StructuredProperty> prepareListStructPropsWithValidQualifier( + protected List<HashableStructuredProperty> prepareListStructPropsWithValidQualifier( final Node node, final String xpath, final String xpathClassId, final String schemeId, final DataInfo info) { - final List<StructuredProperty> res = new ArrayList<>(); + final Set<HashableStructuredProperty> res = new HashSet<>(); for (final Object o : node.selectNodes(xpath)) { final Node n = (Node) o; final String classId = n.valueOf(xpathClassId).trim(); if (this.vocs.termExists(schemeId, classId)) { - res.add(structuredProperty(n.getText(), this.vocs.getTermAsQualifier(schemeId, classId), info)); + res + .add( + HashableStructuredProperty + .newInstance(n.getText(), this.vocs.getTermAsQualifier(schemeId, classId), info)); } } - return res; + return Lists.newArrayList(res); } protected List<StructuredProperty> prepareListStructProps( diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java index eee518353e..98da48f9e6 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java @@ -25,6 +25,7 @@ import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions; import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; import eu.dnetlib.dhp.schema.oaf.utils.ModelHardLimits; +import eu.dnetlib.dhp.schema.oaf.utils.PidCleaner; public class OafToOafMapper extends AbstractMdRecordToOafMapper { @@ -380,7 +381,7 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { return prepareListStructPropsWithValidQualifier( doc, "//oaf:identifier", "@identifierType", DNET_PID_TYPES, info) .stream() - .map(CleaningFunctions::normalizePidValue) + .map(PidCleaner::normalizePidValue) .collect(Collectors.toList()); } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java index 57e0d29555..41fc37cb13 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java @@ -24,6 +24,7 @@ import eu.dnetlib.dhp.schema.common.RelationInverse; import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions; import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; +import eu.dnetlib.dhp.schema.oaf.utils.PidCleaner; public class OdfToOafMapper extends AbstractMdRecordToOafMapper { @@ -504,7 +505,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { @Override protected List<StructuredProperty> prepareResultPids(final Document doc, final DataInfo info) { - final Set<StructuredProperty> res = new HashSet<>(); + final Set<HashableStructuredProperty> res = new HashSet<>(); res .addAll( prepareListStructPropsWithValidQualifier( @@ -524,7 +525,8 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { return res .stream() - .map(CleaningFunctions::normalizePidValue) + .map(PidCleaner::normalizePidValue) + .filter(CleaningFunctions::pidFilter) .collect(Collectors.toList()); } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java index 4ae3f82c2f..23de57204e 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java @@ -388,7 +388,7 @@ public class CleanGraphSparkJobTest { .collect(Collectors.toList()); assertNotNull(fos_subjects); - assertEquals(2, fos_subjects.size()); + assertEquals(3, fos_subjects.size()); assertTrue( fos_subjects @@ -396,18 +396,10 @@ public class CleanGraphSparkJobTest { .anyMatch( s -> "0101 mathematics".equals(s.getValue()) & ModelConstants.DNET_SUBJECT_FOS_CLASSID.equals(s.getQualifier().getClassid()) & - "sysimport:crosswalk:datasetarchive" - .equals(s.getDataInfo().getProvenanceaction().getClassid()))); + "subject:fos".equals(s.getDataInfo().getProvenanceaction().getClassid()))); - assertTrue( - fos_subjects - .stream() - .anyMatch( - s -> "0102 computer and information sciences".equals(s.getValue()) & - ModelConstants.DNET_SUBJECT_FOS_CLASSID.equals(s.getQualifier().getClassid()))); - - verify_keyword(p, "In Situ Hybridization"); - verify_keyword(p, "Avicennia"); + verify_keyword(p, "FOS: Mathematics"); + verify_keyword(p, "FOS: Computer and information sciences"); } @Test 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 8d10508a92..cdc052dfa7 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 @@ -266,7 +266,7 @@ public class GraphCleaningFunctionsTest { .collect(Collectors.toList()); assertNotNull(fos_subjects); - assertEquals(2, fos_subjects.size()); + assertEquals(3, fos_subjects.size()); assertTrue( fos_subjects @@ -274,18 +274,18 @@ public class GraphCleaningFunctionsTest { .anyMatch( s -> "0101 mathematics".equals(s.getValue()) & ModelConstants.DNET_SUBJECT_FOS_CLASSID.equals(s.getQualifier().getClassid()) & - "sysimport:crosswalk:datasetarchive" - .equals(s.getDataInfo().getProvenanceaction().getClassid()))); + "subject:fos".equals(s.getDataInfo().getProvenanceaction().getClassid()))); assertTrue( fos_subjects .stream() .anyMatch( s -> "0102 computer and information sciences".equals(s.getValue()) & - ModelConstants.DNET_SUBJECT_FOS_CLASSID.equals(s.getQualifier().getClassid()))); + ModelConstants.DNET_SUBJECT_FOS_CLASSID.equals(s.getQualifier().getClassid()) & + "subject:fos".equals(s.getDataInfo().getProvenanceaction().getClassid()))); - verify_keyword(p_cleaned, "In Situ Hybridization"); - verify_keyword(p_cleaned, "Avicennia"); + verify_keyword(p_cleaned, "FOS: Computer and information sciences"); + verify_keyword(p_cleaned, "FOS: Mathematics"); // TODO add more assertions to verity the cleaned values System.out.println(MAPPER.writeValueAsString(p_cleaned)); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java index 6ec2f1d51f..612e1d0b68 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java @@ -44,7 +44,7 @@ class GenerateEntitiesApplicationTest { } @Test - void testMergeResult() throws IOException, DocumentException { + void testMergeResult() throws IOException { Result publication = getResult("oaf_record.xml", Publication.class); Result dataset = getResult("odf_dataset.xml", Dataset.class); Result software = getResult("odf_software.xml", Software.class); @@ -69,15 +69,15 @@ class GenerateEntitiesApplicationTest { verifyMerge(orp, software, Software.class, ModelConstants.SOFTWARE_RESULTTYPE_CLASSID); } - protected <T extends Result> void verifyMerge(Result publication, Result dataset, Class<T> clazz, + protected <T extends Result> void verifyMerge(Result r1, Result r2, Class<T> clazz, String resultType) { - final Result merge = (Result) MergeUtils.merge(publication, dataset); + final Result merge = MergeUtils.checkedMerge(r1, r2, true); assertTrue(clazz.isAssignableFrom(merge.getClass())); assertEquals(resultType, merge.getResulttype().getClassid()); } protected <T extends Result> Result getResult(String xmlFileName, Class<T> clazz) - throws IOException, DocumentException { + throws IOException { final String xml = IOUtils.toString(getClass().getResourceAsStream(xmlFileName)); return new OdfToOafMapper(vocs, false, true) .processMdRecord(xml) 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 4fb8f86f75..228c6308ca 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 @@ -216,7 +216,7 @@ class MappersTest { } @Test - void testPublication_PubMed() throws IOException, DocumentException { + void testPublication_PubMed() throws IOException { final String xml = IOUtils .toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_record_pubmed.xml"))); @@ -264,8 +264,17 @@ class MappersTest { assertFalse(p.getSubject().isEmpty()); assertFalse(p.getPid().isEmpty()); - assertEquals("PMC1517292", p.getPid().get(0).getValue()); - assertEquals("pmc", p.getPid().get(0).getQualifier().getClassid()); + + assertTrue(p.getPid().stream().anyMatch(pi -> "pmc".equals(pi.getQualifier().getClassid()))); + assertEquals( + "PMC1517292", + p + .getPid() + .stream() + .filter(pi -> "pmc".equals(pi.getQualifier().getClassid())) + .findFirst() + .get() + .getValue()); assertNotNull(p.getInstance()); assertFalse(p.getInstance().isEmpty()); @@ -292,7 +301,7 @@ class MappersTest { } @Test - void testPublicationInvisible() throws IOException, DocumentException { + void testPublicationInvisible() throws IOException { final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_record.xml"))); @@ -307,6 +316,25 @@ class MappersTest { } + @Test + void testPublicationInvisible_BASE() throws IOException { + + final String xml = IOUtils + .toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_record_base.xml"))); + + final List<Oaf> list = new OdfToOafMapper(vocs, true, true).processMdRecord(xml); + + assertFalse(list.isEmpty()); + assertTrue(list.get(0) instanceof Publication); + + final Publication p = (Publication) list.get(0); + + assertTrue(p.getDataInfo().getInvisible()); + + System.out.println(new ObjectMapper().writeValueAsString(p)); + + } + @Test void testOdfFwfEBookLibrary() throws IOException { final String xml = IOUtils @@ -318,7 +346,7 @@ class MappersTest { } @Test - void testDataset() throws IOException, DocumentException { + void testDataset() throws IOException { final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_dataset.xml"))); final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml); @@ -332,19 +360,19 @@ class MappersTest { final Relation r1 = (Relation) list.get(1); final Relation r2 = (Relation) list.get(2); - assertEquals(d.getId(), r1.getSource()); - assertEquals("40|corda_______::e06332dee33bec6c2ba4c98601053229", r1.getTarget()); + assertEquals(d.getId(), r1.getTarget()); + assertEquals("40|corda_______::e06332dee33bec6c2ba4c98601053229", r1.getSource()); assertEquals(ModelConstants.RESULT_PROJECT, r1.getRelType()); assertEquals(ModelConstants.OUTCOME, r1.getSubRelType()); - assertEquals(ModelConstants.IS_PRODUCED_BY, r1.getRelClass()); + assertEquals(ModelConstants.PRODUCES, r1.getRelClass()); assertTrue(r1.getValidated()); assertEquals("2020-01-01", r1.getValidationDate()); - assertEquals(d.getId(), r2.getTarget()); - assertEquals("40|corda_______::e06332dee33bec6c2ba4c98601053229", r2.getSource()); + assertEquals(d.getId(), r2.getSource()); + assertEquals("40|corda_______::e06332dee33bec6c2ba4c98601053229", r2.getTarget()); assertEquals(ModelConstants.RESULT_PROJECT, r2.getRelType()); assertEquals(ModelConstants.OUTCOME, r2.getSubRelType()); - assertEquals(ModelConstants.PRODUCES, r2.getRelClass()); + assertEquals(ModelConstants.IS_PRODUCED_BY, r2.getRelClass()); assertTrue(r2.getValidated()); assertEquals("2020-01-01", r2.getValidationDate()); @@ -450,7 +478,7 @@ class MappersTest { } @Test - void testOdfBielefeld() throws IOException, DocumentException { + void testOdfBielefeld() throws IOException { final String xml = IOUtils .toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_bielefeld.xml"))); @@ -501,7 +529,7 @@ class MappersTest { } @Test - void testOpentrial() throws IOException, DocumentException { + void testOpentrial() throws IOException { final String xml = IOUtils .toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_opentrial.xml"))); @@ -741,7 +769,7 @@ class MappersTest { } @Test - void testSoftware() throws IOException, DocumentException { + void testSoftware() throws IOException { final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_software.xml"))); final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml); @@ -763,22 +791,21 @@ class MappersTest { final Relation r1 = (Relation) list.get(1); final Relation r2 = (Relation) list.get(2); - assertEquals(s.getId(), r1.getSource()); - assertEquals("50|doi_________::b453e7b4b2130ace57ff0c3db470a982", r1.getTarget()); + assertEquals(s.getId(), r1.getTarget()); + assertEquals("50|doi_________::b453e7b4b2130ace57ff0c3db470a982", r1.getSource()); assertEquals(ModelConstants.RESULT_RESULT, r1.getRelType()); assertEquals(ModelConstants.RELATIONSHIP, r1.getSubRelType()); - assertEquals(ModelConstants.IS_REFERENCED_BY, r1.getRelClass()); + assertEquals(ModelConstants.REFERENCES, r1.getRelClass()); - assertEquals(s.getId(), r2.getTarget()); - assertEquals("50|doi_________::b453e7b4b2130ace57ff0c3db470a982", r2.getSource()); + assertEquals(s.getId(), r2.getSource()); + assertEquals("50|doi_________::b453e7b4b2130ace57ff0c3db470a982", r2.getTarget()); assertEquals(ModelConstants.RESULT_RESULT, r2.getRelType()); assertEquals(ModelConstants.RELATIONSHIP, r2.getSubRelType()); - assertEquals(ModelConstants.REFERENCES, r2.getRelClass()); - + assertEquals(ModelConstants.IS_REFERENCED_BY, r2.getRelClass()); } @Test - void testClaimDedup() throws IOException, DocumentException { + void testClaimDedup() throws IOException { final String xml = IOUtils .toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_claim_dedup.xml"))); final List<Oaf> list = new OafToOafMapper(vocs, false, true).processMdRecord(xml); @@ -792,7 +819,7 @@ class MappersTest { } @Test - void testNakala() throws IOException, DocumentException { + void testNakala() throws IOException { final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_nakala.xml"))); final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml); @@ -820,7 +847,7 @@ class MappersTest { } @Test - void testEnermaps() throws IOException, DocumentException { + void testEnermaps() throws IOException { final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("enermaps.xml"))); final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml); @@ -845,7 +872,7 @@ class MappersTest { } @Test - void testClaimFromCrossref() throws IOException, DocumentException { + void testClaimFromCrossref() throws IOException { final String xml = IOUtils .toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_claim_crossref.xml"))); final List<Oaf> list = new OafToOafMapper(vocs, false, true).processMdRecord(xml); @@ -862,7 +889,7 @@ class MappersTest { } @Test - void testODFRecord() throws IOException, DocumentException { + void testODFRecord() throws IOException { final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_record.xml"))); final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml); System.out.println("***************"); @@ -882,7 +909,7 @@ class MappersTest { } @Test - void testTextGrid() throws IOException, DocumentException { + void testTextGrid() throws IOException { final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("textgrid.xml"))); final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml); @@ -916,7 +943,7 @@ class MappersTest { } @Test - void testBologna() throws IOException, DocumentException { + void testBologna() throws IOException { final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf-bologna.xml"))); final List<Oaf> list = new OafToOafMapper(vocs, false, true).processMdRecord(xml); @@ -933,7 +960,7 @@ class MappersTest { } @Test - void testJairo() throws IOException, DocumentException { + void testJairo() throws IOException { final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_jairo.xml"))); final List<Oaf> list = new OafToOafMapper(vocs, false, true).processMdRecord(xml); @@ -971,7 +998,7 @@ class MappersTest { } @Test - void testZenodo() throws IOException, DocumentException { + void testZenodo() throws IOException { final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_zenodo.xml"))); final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml); @@ -1016,7 +1043,7 @@ class MappersTest { } @Test - void testOdfFromHdfs() throws IOException, DocumentException { + void testOdfFromHdfs() throws IOException { final String xml = IOUtils .toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_from_hdfs.xml"))); @@ -1065,7 +1092,7 @@ class MappersTest { } @Test - void testXMLEncodedURL() throws IOException, DocumentException { + void testXMLEncodedURL() throws IOException { final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("encoded-url.xml"))); final List<Oaf> list = new OafToOafMapper(vocs, false, true).processMdRecord(xml); @@ -1081,7 +1108,7 @@ class MappersTest { } @Test - void testXMLEncodedURL_ODF() throws IOException, DocumentException { + void testXMLEncodedURL_ODF() throws IOException { final String xml = IOUtils .toString(Objects.requireNonNull(getClass().getResourceAsStream("encoded-url_odf.xml"))); final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml); @@ -1245,7 +1272,7 @@ class MappersTest { } @Test - void testRiunet() throws IOException, DocumentException { + void testRiunet() throws IOException { final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("riunet.xml"))); final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml); System.out.println("***************"); @@ -1291,7 +1318,7 @@ class MappersTest { } @Test - void testIRISPub() throws IOException, DocumentException { + void testIRISPub() throws IOException { final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("iris-odf.xml"))); final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml); System.out.println("***************"); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/graph/publication/publication.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/graph/publication/publication.json index e2a2b9449e..2536934c59 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/graph/publication/publication.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/graph/publication/publication.json @@ -1,4 +1,4 @@ -{"id":"50|CSC_________::2250a70c903c6ac6e4c01438259e9375","author":[{"affiliation":[],"fullname":"Brien, Tom","name":"Tom","pid":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"sysimport:crosswalk:datasetarchive","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"ORCID12","classname":"ORCID12","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"0000-0001-9613-6639"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"sysimport:crosswalk:datasetarchive","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"ORCID12","classname":"ORCID12","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"https://orcid.org/0000-0001-9613-6639"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"orcid","classname":"ORCID12","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"0000-0001-9613-6639"}],"rank":1,"surname":"Brien"},{"affiliation":[],"fullname":"Ade, 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"classid": "FOS", + "classname": "Fields of Science and Technology classification", "schemeid": "dnet:subject_classification_typologies", "schemename": "dnet:subject_classification_typologies" }, @@ -910,8 +888,8 @@ "inferred": false, "invisible": false, "provenanceaction": { - "classid": "sysimport:actionset", - "classname": "Harvested", + "classid": "subject:fos", + "classname": "subject:fos", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions" }, @@ -923,7 +901,7 @@ "schemeid": "dnet:subject_classification_typologies", "schemename": "dnet:subject_classification_typologies" }, - "value": "Avicennia" + "value": "0102 computer and information sciences" }, { "dataInfo": { diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_record_base.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_record_base.xml new file mode 100644 index 0000000000..6ae4a7f801 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_record_base.xml @@ -0,0 +1,129 @@ +<?xml version="1.0" encoding="UTF-8"?> +<record xmlns:oaire="http://namespace.openaire.eu/schema/oaire/" + xmlns:datacite="http://datacite.org/schema/kernel-4" + xmlns:dr="http://www.driver-repository.eu/namespace/dr" + xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" + xmlns:oaf="http://namespace.openaire.eu/oaf" + xmlns:oai="http://www.openarchives.org/OAI/2.0/" + xmlns:dri="http://www.driver-repository.eu/namespace/dri" + xmlns:xs="http://www.w3.org/2001/XMLSchema" + xmlns:dc="http://purl.org/dc/elements/1.1/"> + <header xmlns="http://www.openarchives.org/OAI/2.0/"> + <dri:objIdentifier>base_oa_____::7ecf1ef502253efffe203ca9a22bb9f1</dri:objIdentifier> + <identifier>ftunivqespace:oai:espace.library.uq.edu.au:UQ:336902</identifier> + <datestamp>2020-12-22T10:30:27Z</datestamp> + <dr:dateOfTransformation>2024-09-10T17:21:36.972Z</dr:dateOfTransformation> + </header> + <metadata> + <datacite:resource> + <datacite:identifier identifierType="DOI">https://doi.org/10.1016/j.envint.2014.07.004</datacite:identifier> + <datacite:alternateIdentifiers> + <datacite:identifier alternateIdentifierType="url">https://espace.library.uq.edu.au/view/UQ:336902</datacite:identifier> + <datacite:identifier alternateIdentifierType="oai-original">ftunivqespace:oai:espace.library.uq.edu.au:UQ:336902</datacite:identifier> + </datacite:alternateIdentifiers> + <datacite:relatedIdentifiers/> + <datacite:resourceType>Article contribution</datacite:resourceType> + <datacite:titles> + <datacite:title>The role of environmental factors in the spatial distribution of Japanese encephalitis in mainland China</datacite:title> + </datacite:titles> + <datacite:creators> + <datacite:creator> + <datacite:creatorName>Wang, Liya</datacite:creatorName> + </datacite:creator> + <datacite:creator> + <datacite:creatorName>Hu, Wenbiao</datacite:creatorName> + </datacite:creator> + <datacite:creator> + <datacite:creatorName>Soares Magalhaes, Ricardo J.</datacite:creatorName> + </datacite:creator> + <datacite:creator> + <datacite:creatorName>Bi, Peng</datacite:creatorName> + </datacite:creator> + <datacite:creator> + <datacite:creatorName>Ding, Fan</datacite:creatorName> + </datacite:creator> + <datacite:creator> + <datacite:creatorName>Sun, Hailong</datacite:creatorName> + </datacite:creator> + <datacite:creator> + <datacite:creatorName>Li, Shenlong</datacite:creatorName> + </datacite:creator> + <datacite:creator> + <datacite:creatorName>Yin, Wenwu</datacite:creatorName> + </datacite:creator> + <datacite:creator> + <datacite:creatorName>Wei, Lan</datacite:creatorName> + </datacite:creator> + <datacite:creator> + <datacite:creatorName>Liu, Qiyong</datacite:creatorName> + </datacite:creator> + <datacite:creator> + <datacite:creatorName>Haque, Ubydul</datacite:creatorName> + </datacite:creator> + <datacite:creator> + <datacite:creatorName>Sun, Yansong</datacite:creatorName> + </datacite:creator> + <datacite:creator> + <datacite:creatorName>Huang, Liuyu</datacite:creatorName> + </datacite:creator> + <datacite:creator> + <datacite:creatorName>Tong, Shilu</datacite:creatorName> + </datacite:creator> + <datacite:creator> + <datacite:creatorName>Clements, Archie C.A.</datacite:creatorName> + </datacite:creator> + <datacite:creator> + <datacite:creatorName>Zhang, Wenyi</datacite:creatorName> + </datacite:creator> + <datacite:creator> + <datacite:creatorName>Li, Chengyi</datacite:creatorName> + </datacite:creator> + </datacite:creators> + <datacite:contributors/> + <datacite:descriptions> + <datacite:description descriptionType="Abstract">Japanese encephalitis (JE) is the most common cause of viral encephalitis and an important public health concern in the Asia-Pacific region, particularly in China where 50% of global cases are notified. To explore the association between environmental factors and human JE cases and identify the high risk areas for JE transmission in China, we used annual notified data on JE cases at the center of administrative township and environmental variables with a pixel resolution of 1. km. ×. 1. km from 2005 to 2011 to construct models using ecological niche modeling (ENM) approaches based on maximum entropy. These models were then validated by overlaying reported human JE case localities from 2006 to 2012 onto each prediction map. ENMs had good discriminatory ability with the area under the curve (AUC) of the receiver operating curve (ROC) of 0.82-0.91, and low extrinsic omission rate of 5.44-7.42%. Resulting maps showed JE being presented extensively throughout southwestern and central China, with local spatial variations in probability influenced by minimum temperatures, human population density, mean temperatures, and elevation, with contribution of 17.94%-38.37%, 15.47%-21.82%, 3.86%-21.22%, and 12.05%-16.02%, respectively. Approximately 60% of JE cases occurred in predicted high risk areas, which covered less than 6% of areas in mainland China. Our findings will help inform optimal geographical allocation of the limited resources available for JE prevention and control in China, find hidden high-risk areas, and increase the effectiveness of public health interventions against JE transmission.</datacite:description> + </datacite:descriptions> + <datacite:subjects> + <datacite:subject>Japanese encephalitis</datacite:subject> + <datacite:subject>Ecological niche model</datacite:subject> + <datacite:subject>MaxEnt</datacite:subject> + <datacite:subject>China</datacite:subject> + <datacite:subject>2300 Environmental Science</datacite:subject> + <datacite:subject classificationCode="950" subjectScheme="ddc">950</datacite:subject> + </datacite:subjects> + <datacite:publisher>Pergamon Press</datacite:publisher> + <datacite:publicationYear>2014</datacite:publicationYear> + <datacite:formats/> + <datacite:language>eng</datacite:language> + <oaf:accessrights/> + </datacite:resource> + <dr:CobjCategory 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Academic Search Engine (BASE)" + id="openaire____::base_search"/> + <oaf:dateAccepted>2014-12-01</oaf:dateAccepted> + <oaf:relation relClass="hasAuthorInstitution" + relType="resultOrganization" + subRelType="affiliation" + targetType="organization">ror_________::https://ror.org/00rqy9422</oaf:relation> + <oaf:datainfo> + <oaf:inferred>false</oaf:inferred> + <oaf:deletedbyinference>false</oaf:deletedbyinference> + <oaf:trust>0.89</oaf:trust> + <oaf:inferenceprovenance/> + <oaf:provenanceaction classid="sysimport:crosswalk:aggregator" + classname="sysimport:crosswalk:aggregator" + schemeid="dnet:provenanceActions" + schemename="dnet:provenanceActions"/> + </oaf:datainfo> + </metadata> +</record> \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/organizations_resultset_entry.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/organizations_resultset_entry.json index 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eu.dnetlib.dhp.schema.sx.scholix.ScholixResource import eu.dnetlib.dhp.sx.graph.SparkCreateScholexplorerDump import org.apache.spark.SparkConf import org.apache.spark.sql.{Encoder, Encoders, SparkSession} -import org.junit.jupiter.api.Test +import org.junit.jupiter.api.{Disabled, Test} import org.objenesis.strategy.StdInstantiatorStrategy class ScholixGenerationTest { @Test + @Disabled def generateScholix(): Unit = { val spark: SparkSession = SparkSession.builder().master("local[*]").getOrCreate()