diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscTag.java index b917d3980..a6767965d 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscTag.java @@ -119,8 +119,9 @@ public class SparkEoscTag { addEIG(orp.getEoscifguidelines(), EOSC_TWITTER_DATA, EOSC_TWITTER_DATA, "", COMPLIES_WITH); } if (containsCriteriaNotebook(orp)) { - addEIG(orp.getEoscifguidelines(), EOSC_JUPYTER_NOTEBOOK, EOSC_JUPYTER_NOTEBOOK, "", - COMPLIES_WITH); + addEIG( + orp.getEoscifguidelines(), EOSC_JUPYTER_NOTEBOOK, EOSC_JUPYTER_NOTEBOOK, "", + COMPLIES_WITH); } return orp; }, Encoders.bean(OtherResearchProduct.class)) @@ -199,6 +200,13 @@ public class SparkEoscTag { return false; if (s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("jupyter"))) return true; + if (s + .getSubject() + .stream() + .anyMatch( + sbj -> sbj.getValue().toLowerCase().contains("python") && + sbj.getValue().toLowerCase().contains("notebook"))) + return true; if (s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("python")) && s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("notebook"))) return true; 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 f3f1b02fe..e953129b1 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 @@ -31,26 +31,7 @@ import com.google.common.collect.Sets; 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.DataInfo; -import eu.dnetlib.dhp.schema.oaf.Dataset; -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.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.Relation; -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.*; import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; @@ -91,6 +72,17 @@ public abstract class AbstractMdRecordToOafMapper { nsContext.put("datacite", DATACITE_SCHEMA_KERNEL_3); } + // lowercase pidTypes as keys, normal casing for the values + protected static final Map pidTypeWithAuthority = new HashMap<>(); + + static { + IdentifierFactory.PID_AUTHORITY + .keySet() + .stream() + .forEach(entry -> pidTypeWithAuthority.put(entry.toString().toLowerCase(), entry.toString())); + + } + protected AbstractMdRecordToOafMapper(final VocabularyGroup vocs, final boolean invisible, final boolean shouldHashId, final boolean forceOriginalId) { this.vocs = vocs; @@ -377,10 +369,30 @@ 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); + 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); + } + private List prepareContexts(final Document doc, final DataInfo info) { final List list = new ArrayList<>(); for (final Object o : doc.selectNodes("//oaf:concept")) { 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 1b9e47408..a4a6ab224 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 @@ -19,6 +19,8 @@ import com.google.common.collect.Lists; import eu.dnetlib.dhp.common.PacePerson; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.schema.common.ModelSupport; +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; @@ -171,6 +173,9 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { for (final Object o : doc.selectNodes("//*[local-name()='identifier' and ./@identifierType='landingPage']")) { url.add(trimAndDecodeUrl(((Node) o).getText().trim())); } + for (final Object o : doc.selectNodes("//*[local-name()='identifier' and ./@identifierType='w3id']")) { + url.add(trimAndDecodeUrl(((Node) o).getText().trim())); + } for (final Object o : doc .selectNodes("//*[local-name()='alternateIdentifier' and ./@alternateIdentifierType='DOI']")) { url.add(HTTP_DOI_PREIFX + ((Node) o).getText().trim()); @@ -382,40 +387,53 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { final List res = new ArrayList<>(); for (final Object o : doc - .selectNodes("//*[local-name()='relatedIdentifier' and ./@relatedIdentifierType='OPENAIRE']")) { + .selectNodes("//*[local-name()='relatedIdentifier']")) { - final String originalId = ((Node) o).getText(); + final String originalId = ((Node) o).getText().trim(); if (StringUtils.isNotBlank(originalId)) { - final String otherId = createOpenaireId(50, originalId, false); - final String type = ((Node) o).valueOf("@relationType"); - - if (type.equalsIgnoreCase(IS_SUPPLEMENT_TO)) { - res - .add( - getRelation( - docId, otherId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENT_TO, entity)); - res - .add( - getRelation( - otherId, docId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENTED_BY, entity)); - } else if (type.equalsIgnoreCase(IS_PART_OF)) { - res - .add( - getRelation( - docId, otherId, RESULT_RESULT, PART, IS_PART_OF, entity)); - res - .add( - getRelation( - otherId, docId, RESULT_RESULT, PART, HAS_PART, entity)); - } else { - // TODO catch more semantics + final String idType = ((Node) o).valueOf("@relatedIdentifierType"); + final String relType = ((Node) o).valueOf("@relationType"); + String otherId = guessRelatedIdentifier(idType, originalId); + if (StringUtils.isNotBlank(otherId)) { + res.addAll(getRelations(relType, docId, otherId, entity)); } + } } return res; } + protected String guessRelatedIdentifier(final String idType, final String value) { + if (StringUtils.isBlank(idType) || StringUtils.isBlank(value)) + return null; + if (idType.equalsIgnoreCase("OPENAIRE")) + return createOpenaireId(50, value, false); + if (pidTypeWithAuthority.containsKey(idType.toLowerCase())) { + return IdentifierFactory.idFromPid("50", pidTypeWithAuthority.get(idType.toLowerCase()), value, true); + } + return null; + + } + + protected List getRelations(final String reltype, final String entityId, final String otherId, + final OafEntity entity) { + final List res = new ArrayList<>(); + RelationInverse rel = ModelSupport.findRelation(reltype); + if (rel != null) { + res + .add( + getRelation( + entityId, otherId, rel.getRelType(), rel.getSubReltype(), rel.getRelClass(), entity)); + res + .add( + getRelation( + otherId, entityId, rel.getRelType(), rel.getSubReltype(), rel.getInverseRelClass(), entity)); + + } + return res; + } + @Override protected Qualifier prepareResourceType(final Document doc, final DataInfo info) { return prepareQualifier( 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 806603880..421c916b0 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 @@ -579,7 +579,7 @@ class MappersTest { final List list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml); - assertEquals(1, list.size()); + assertEquals(3, list.size()); assertTrue(list.get(0) instanceof Software); final Software s = (Software) list.get(0); @@ -912,27 +912,62 @@ class MappersTest { } @Test - void testROHub() throws IOException, DocumentException { + void testROHub() throws IOException { final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("rohub.xml"))); final List list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml); System.out.println("***************"); System.out.println(new ObjectMapper().writeValueAsString(list)); System.out.println("***************"); -// final Dataset p = (Dataset) list.get(0); -// assertValidId(p.getId()); -// assertValidId(p.getCollectedfrom().get(0).getKey()); -// System.out.println(p.getTitle().get(0).getValue()); -// assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue())); + assertEquals(5, list.size()); + final OtherResearchProduct p = (OtherResearchProduct) list.get(0); + assertValidId(p.getId()); + assertTrue(p.getId().startsWith("50|w3id")); + assertValidId(p.getCollectedfrom().get(0).getKey()); + assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue())); + assertEquals(1, p.getInstance().size()); + assertEquals("https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca", p.getPid().get(0).getValue()); + 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()); + } @Test - void testROHub2() throws IOException, DocumentException { + void testROHub2() throws IOException { final String xml = IOUtils .toString(Objects.requireNonNull(getClass().getResourceAsStream("rohub-modified.xml"))); final List list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml); System.out.println("***************"); System.out.println(new ObjectMapper().writeValueAsString(list)); System.out.println("***************"); + assertEquals(7, list.size()); + final OtherResearchProduct p = (OtherResearchProduct) list.get(0); + assertValidId(p.getId()); + assertValidId(p.getCollectedfrom().get(0).getKey()); + assertEquals("50|w3id________::afc7592914ae190a50570db90f55f9c2", p.getId()); + assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue())); + assertEquals("w3id", (p.getPid().get(0).getQualifier().getClassid())); + assertEquals("https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca", (p.getPid().get(0).getValue())); + + assertEquals(1, list.stream().filter(o -> o instanceof OtherResearchProduct).count()); + assertEquals(6, list.stream().filter(o -> o instanceof Relation).count()); + + for (Oaf oaf : list) { + if (oaf instanceof Relation) { + String source = ((Relation) oaf).getSource(); + String target = ((Relation) oaf).getTarget(); + assertNotEquals(source, target); + assertTrue(source.equals(p.getId()) || target.equals(p.getId())); + assertNotNull(((Relation) oaf).getSubRelType()); + assertNotNull(((Relation) oaf).getRelClass()); + assertNotNull(((Relation) oaf).getRelType()); + } + } } @Test diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_dataset.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_dataset.xml index 4f41ee6ea..4633d62c3 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_dataset.xml +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_dataset.xml @@ -69,7 +69,6 @@ - 10.5281/zenodo.3234525 https://zenodo.org/communities/epfl 1.0.0 diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_software.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_software.xml index 6a9170ce1..387b1ee86 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_software.xml +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_software.xml @@ -20,7 +20,7 @@ bio.tools http://maplab.imppc.org/chainy/ - 10.1093/bioinformatics/btw839 + 10.1093/bioinformatics/btw839 https://bio.tools/ diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/rohub-modified.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/rohub-modified.xml index 95d65ac8d..ce846a2cf 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/rohub-modified.xml +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/rohub-modified.xml @@ -30,6 +30,9 @@ https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca/resources/6d3427a8-352e-49f4-9796-f618c44dc16d + + fsh_____4119::afc7592914ae190a50570db90f55f9c3 + RO-crate 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 c85b55786..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 @@ -21,15 +21,13 @@ - https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca - + https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca + + https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca + - - https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca/resources/24fae96f-f986-46e1-bfd0-a21ca20ff0ce - - - https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca/resources/6d3427a8-352e-49f4-9796-f618c44dc16d - + https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca/resources/24fae96f-f986-46e1-bfd0-a21ca20ff0ce + https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca/resources/6d3427a8-352e-49f4-9796-f618c44dc16d RO-crate @@ -43,21 +41,17 @@ Poznań Supercomputing and Networking Center - - - Generation Service - + + Generation Service - - CNR-ISMAR - + CNR-ISMAR - 2018-06-20T11:21:46Z + 2018-06-20T11:21:46Z The use of biological effects tools offer enormous potential to meet the challenges outlined by the European Union Marine Strategy Framework Directive (MSFD) whereby Member States are required to develop a robust set of tools for defining 11 qualitative descriptors of Good Environmental Status (GES), such as demonstrating that "Concentrations of contaminants are at levels not giving rise to pollution effects" (GES Descriptor 8). This paper discusses the combined approach of monitoring chemical contaminant levels, along side biological effect measurements relating to the effect of pollutants, for undertaking assessments of GES across European marine regions. We outline the minimum standards that biological effects tools should meet if they are to be used for defining GES in relation to Descriptor 8 and describe the current international initiatives underway to develop assessment criteria for these biological effects techniques. Crown Copyright (C) 2010 Published by Elsevier Ltd. All rights reserved. @@ -71,15 +65,18 @@ Ecology - EOSC::RO-crate - https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca + https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca other research product - + 2018-06-20 OPEN + \ No newline at end of file diff --git a/pom.xml b/pom.xml index 821ce3124..fb132bb02 100644 --- a/pom.xml +++ b/pom.xml @@ -801,7 +801,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [2.12.1] + [2.12.1-patched] [4.0.3] [6.0.5] [3.1.6]