diff --git a/dhp-build/dhp-build-assembly-resources/pom.xml b/dhp-build/dhp-build-assembly-resources/pom.xml index 012ff89a3..44165995d 100644 --- a/dhp-build/dhp-build-assembly-resources/pom.xml +++ b/dhp-build/dhp-build-assembly-resources/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp-build - 1.2.4-SNAPSHOT + 1.2.5-SNAPSHOT dhp-build-assembly-resources diff --git a/dhp-build/dhp-build-properties-maven-plugin/pom.xml b/dhp-build/dhp-build-properties-maven-plugin/pom.xml index 256017e2c..7579bdf45 100644 --- a/dhp-build/dhp-build-properties-maven-plugin/pom.xml +++ b/dhp-build/dhp-build-properties-maven-plugin/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp-build - 1.2.4-SNAPSHOT + 1.2.5-SNAPSHOT dhp-build-properties-maven-plugin diff --git a/dhp-build/dhp-code-style/pom.xml b/dhp-build/dhp-code-style/pom.xml index db0097d64..5a86efe17 100644 --- a/dhp-build/dhp-code-style/pom.xml +++ b/dhp-build/dhp-code-style/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp-code-style - 1.2.4-SNAPSHOT + 1.2.5-SNAPSHOT jar @@ -47,12 +47,16 @@ org.apache.maven.plugins maven-site-plugin 3.9.1 + + true + + UTF-8 sftp://dnet-hadoop@static-web.d4science.org/dnet-hadoop diff --git a/dhp-build/pom.xml b/dhp-build/pom.xml index 97fbdf45b..9040ea94e 100644 --- a/dhp-build/pom.xml +++ b/dhp-build/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp - 1.2.4-SNAPSHOT + 1.2.5-SNAPSHOT dhp-build pom diff --git a/dhp-common/pom.xml b/dhp-common/pom.xml index 7b18f0105..6df11f4ea 100644 --- a/dhp-common/pom.xml +++ b/dhp-common/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp - 1.2.4-SNAPSHOT + 1.2.5-SNAPSHOT ../pom.xml diff --git a/dhp-workflows/dhp-actionmanager/pom.xml b/dhp-workflows/dhp-actionmanager/pom.xml index f63f3aa01..29e1fab1f 100644 --- a/dhp-workflows/dhp-actionmanager/pom.xml +++ b/dhp-workflows/dhp-actionmanager/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp-workflows - 1.2.4-SNAPSHOT + 1.2.5-SNAPSHOT dhp-actionmanager diff --git a/dhp-workflows/dhp-aggregation/pom.xml b/dhp-workflows/dhp-aggregation/pom.xml index c89cc9d1d..53d349d2a 100644 --- a/dhp-workflows/dhp-aggregation/pom.xml +++ b/dhp-workflows/dhp-aggregation/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp-workflows - 1.2.4-SNAPSHOT + 1.2.5-SNAPSHOT dhp-aggregation diff --git a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala index 136b0fb93..8e41de83c 100644 --- a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala +++ b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala @@ -72,7 +72,6 @@ class DataciteToOAFTest extends AbstractVocabularyTest { spark.read.load(targetPath).printSchema(); - val result: Dataset[Oaf] = spark.read.load(targetPath).as[Oaf] result diff --git a/dhp-workflows/dhp-blacklist/pom.xml b/dhp-workflows/dhp-blacklist/pom.xml index 047767d33..479a9e8c6 100644 --- a/dhp-workflows/dhp-blacklist/pom.xml +++ b/dhp-workflows/dhp-blacklist/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.5-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-broker-events/pom.xml b/dhp-workflows/dhp-broker-events/pom.xml index afbd93dcb..5a41a0090 100644 --- a/dhp-workflows/dhp-broker-events/pom.xml +++ b/dhp-workflows/dhp-broker-events/pom.xml @@ -1,11 +1,9 @@ - + dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.5-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-dedup-openaire/pom.xml b/dhp-workflows/dhp-dedup-openaire/pom.xml index f47f8ba6e..a14076a78 100644 --- a/dhp-workflows/dhp-dedup-openaire/pom.xml +++ b/dhp-workflows/dhp-dedup-openaire/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.5-SNAPSHOT 4.0.0 dhp-dedup-openaire diff --git a/dhp-workflows/dhp-distcp/pom.xml b/dhp-workflows/dhp-distcp/pom.xml index 8c10538c0..c3d3a7375 100644 --- a/dhp-workflows/dhp-distcp/pom.xml +++ b/dhp-workflows/dhp-distcp/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.5-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-doiboost/pom.xml b/dhp-workflows/dhp-doiboost/pom.xml index f496ea9a2..37accbc4f 100644 --- a/dhp-workflows/dhp-doiboost/pom.xml +++ b/dhp-workflows/dhp-doiboost/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.5-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/sfi_funded_article.json b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/sfi_funded_article.json new file mode 100644 index 000000000..27580ba53 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/sfi_funded_article.json @@ -0,0 +1,982 @@ + +{ + + "indexed": { + "date-parts": [ + [ + 2022, + 4, + 5 + ] + ], + "date-time": "2022-04-05T11:07:00Z", + "timestamp": 1649156820730 + }, + "reference-count": 63, + "publisher": "Public Library of Science (PLoS)", + "issue": "5", + "license": [ + { + "start": { + "date-parts": [ + [ + 2020, + 5, + 29 + ] + ], + "date-time": "2020-05-29T00:00:00Z", + "timestamp": 1590710400000 + }, + "content-version": "vor", + "delay-in-days": 0, + "URL": "http://creativecommons.org/licenses/by/4.0/" + } + ], + "funder": [ + { + "DOI": "10.13039/501100001602", + "name": "Science Foundation Ireland", + "doi-asserted-by": "crossref", + "award": [ + "SFI/12/RC/2273" + ] + }, + { + "DOI": "10.13039/501100001602", + "name": "Science Foundation Ireland", + "doi-asserted-by": "crossref", + "award": [ + "SFI/12/RC/2273" + ] + }, + { + "DOI": "10.13039/501100001602", + "name": "Science Foundation Ireland", + "doi-asserted-by": "crossref", + "award": [ + "SFI/12/RC/2273" + ] + }, + { + "DOI": "10.13039/501100001602", + "name": "Science Foundation Ireland", + "doi-asserted-by": "crossref", + "award": [ + "SFI/12/RC/2273" + ] + } + ], + "content-domain": { + "domain": [ + "www.plosone.org" + ], + "crossmark-restriction": false + }, + "short-container-title": [ + "PLoS ONE" + ], + "DOI": "10.1371/journal.pone.0233284", + "type": "journal-article", + "created": { + "date-parts": [ + [ + 2020, + 5, + 29 + ] + ], + "date-time": "2020-05-29T17:53:47Z", + "timestamp": 1590774827000 + }, + "page": "e0233284", + "update-policy": "http://dx.doi.org/10.1371/journal.pone.corrections_policy", + "source": "Crossref", + "is-referenced-by-count": 13, + "title": [ + "Vancomycin and nisin A are effective against biofilms of multi-drug resistant Staphylococcus aureus isolates from human milk" + ], + "prefix": "10.1371", + "volume": "15", + "author": [ + { + "ORCID": "http://orcid.org/0000-0003-4107-0278", + "authenticated-orcid": true, + "given": "Angeliki", + "family": "Angelopoulou", + "sequence": "first", + "affiliation": [ + + ] + }, + { + "given": "Des", + "family": "Field", + "sequence": "additional", + "affiliation": [ + + ] + }, + { + "given": "Mariana", + "family": "Pérez-Ibarreche", + "sequence": "additional", + "affiliation": [ + + ] + }, + { + "ORCID": "http://orcid.org/0000-0001-8317-6455", + "authenticated-orcid": true, + "given": "Alicja K.", + "family": "Warda", + "sequence": "additional", + "affiliation": [ + + ] + }, + { + "given": "Colin", + "family": "Hill", + "sequence": "additional", + "affiliation": [ + + ] + }, + { + "given": "R. 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"crossref", + "first-page": "5572", + "DOI": "10.1128/AAC.00888-13", + "article-title": "Effects of bacteriocins on methicillin-resistant Staphylococcus aureus biofilm", + "volume": "57", + "author": "K Okuda", + "year": "2013", + "journal-title": "Antimicrob Agents Chemother" + }, + { + "issue": "6", + "key": "pone.0233284.ref040", + "doi-asserted-by": "crossref", + "first-page": "511", + "DOI": "10.1159/000335598", + "article-title": "In vitro activities of nisin alone or in combination with vancomycin and ciprofloxacin against methicillin-resistant and methicillin-susceptible Staphylococcus aureus strains", + "volume": "57", + "author": "S Dosler", + "year": "2011", + "journal-title": "Chemotherapy" + }, + { + "issue": "18", + "key": "pone.0233284.ref041", + "doi-asserted-by": "crossref", + "first-page": "5809", + "DOI": "10.1128/AEM.01104-07", + "article-title": "Dissection and modulation of the four distinct activities of nisin by mutagenesis of rings A and B and by C-terminal truncation", + "volume": "73", + "author": "R Rink", + "year": "2007", + "journal-title": "Appl Environ Microbiol" + }, + { + "issue": "6", + "key": "pone.0233284.ref042", + "doi-asserted-by": "crossref", + "first-page": "806", + "DOI": "10.1007/s00253-004-1599-1", + "article-title": "Site-directed mutagenesis of the hinge region of nisinZ and properties of nisinZ mutants", + "volume": "64", + "author": "J Yuan", + "year": "2004", + "journal-title": "Appl Microbiol Biotechnol" + }, + { + "key": "pone.0233284.ref043", + "doi-asserted-by": "crossref", + "first-page": "508", + "DOI": "10.3389/fmicb.2016.00508", + "article-title": "In vitro activities of nisin and nisin derivatives alone and in combination with antibiotics against Staphylococcus biofilms", + "volume": "7", + "author": "D Field", + "year": "2016", + "journal-title": "Front Microbiol" + }, + { + "issue": "18", + "key": "pone.0233284.ref044", + "doi-asserted-by": "crossref", + "first-page": "1573", + "DOI": "10.2217/fmb-2019-0153", + "article-title": "Nisin Z and lacticin 3147 improve efficacy of antibiotics against clinically significant bacteria", + "volume": "14", + "author": "JC Ellis", + "year": "2020", + "journal-title": "Future Microbiol" + }, + { + "issue": "3", + "key": "pone.0233284.ref045", + "doi-asserted-by": "crossref", + "first-page": "311", + "DOI": "10.1177/0890334408317435", + "article-title": "The bacteriocin nisin, an effective agent for the treatment of staphylococcal mastitis during lactation", + "volume": "24", + "author": "L Fernández", + "year": "2008", + "journal-title": "J Hum Lact" + }, + { + "issue": "1", + "key": "pone.0233284.ref046", + "doi-asserted-by": "crossref", + "first-page": "33", + "DOI": "10.1159/000272223", + "article-title": "Inflammatory breast diseases during lactation: milk stasis, puerperal mastitis, abscesses of the breast, and malignant tumors–current and evidence-based strategies for diagnosis and therapy", + "volume": "5", + "author": "M 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and enterotoxin-encoding genes among staphylococci isolated from expressed human breast milk", + "volume": "53", + "author": "LA Carneiro", + "year": "2004", + "journal-title": "J Med Microbiol" + }, + { + "issue": "2", + "key": "pone.0233284.ref050", + "doi-asserted-by": "crossref", + "first-page": "113", + "DOI": "10.1007/s00284-015-0925-4", + "article-title": "Antibiotic susceptibility of commensal bacteria from human milk", + "volume": "72", + "author": "PW Chen", + "year": "2016", + "journal-title": "Curr Microbiol" + }, + { + "key": "pone.0233284.ref051", + "doi-asserted-by": "crossref", + "first-page": "2512", + "DOI": "10.3389/fmicb.2018.02512", + "article-title": "Microbial community dynamics in mother's milk and infant's mouth and gut in moderately preterm infants", + "volume": "9", + "author": "E Biagi", + "year": "2018", + "journal-title": "Front Microbiol" + }, + { + "key": "pone.0233284.ref052", + "doi-asserted-by": "crossref", + "first-page": "4", + "DOI": "10.3410/M4-4", + "article-title": "Reduced vancomycin susceptibility among clinical Staphylococcus aureus isolates ('the MIC Creep'): implications for therapy", + "volume": "4", + "author": "A Dhand", + "year": "2012", + "journal-title": "F1000 Med Rep" + }, + { + "issue": "12", + "key": "pone.0233284.ref053", + "doi-asserted-by": "crossref", + "first-page": "1112", + "DOI": "10.1136/jcp.2009.069021", + "article-title": "Low concentrations of vancomycin stimulate biofilm formation in some clinical isolates of Staphylococcus epidermidis", + "volume": "62", + "author": "JS Cargill", + "year": "2009", + "journal-title": "J Clin Pathol" + }, + { + "issue": "2", + "key": "pone.0233284.ref054", + "doi-asserted-by": "crossref", + "first-page": "191", + "DOI": "10.1002/jobm.201000221", + "article-title": "Effect of sub-lethal doses of vancomycin and oxacillin on biofilm formation by vancomycin intermediate resistant Staphylococcus aureus", + "volume": "51", + "author": "ZA Mirani", + "year": "2011", + "journal-title": "J Basic Microbiol" + }, + { + "key": "pone.0233284.ref055", + "doi-asserted-by": "crossref", + "first-page": "225", + "DOI": "10.1016/j.micpath.2017.07.004", + "article-title": "Vancomycin-induced biofilm formation by methicillin-resistant Staphylococcus aureus is associated with the secretion of membrane vesicles", + "volume": "110", + "author": "X He", + "year": "2017", + "journal-title": "Microb Pathog" + }, + { + "issue": "9", + "key": "pone.0233284.ref056", + "doi-asserted-by": "crossref", + "first-page": "1627", + "DOI": "10.4315/0362-028X.JFP-12-001", + "article-title": "Effects of nisin and lysozyme on growth inhibition and biofilm formation capacity of Staphylococcus aureus strains isolated from raw milk and cheese samples", + "volume": "75", + "author": "M Sudagidan", + "year": "2012", + "journal-title": "J Food Prot" + }, + { + "issue": "3", + "key": "pone.0233284.ref057", + "doi-asserted-by": "crossref", + "first-page": "253", + "DOI": "10.1016/j.ijfoodmicro.2008.01.011", + "article-title": "Nisin-bacteriophage cross-resistance in Staphylococcus aureus", + "volume": "122", + "author": "B Martinez", + "year": "2008", + "journal-title": "Int J Food Microbiol" + }, + { + "issue": "1", + "key": "pone.0233284.ref058", + "doi-asserted-by": "crossref", + "first-page": "82", + "DOI": "10.2146/ajhp080434", + "article-title": "Therapeutic monitoring of vancomycin in adult patients: a consensus review of the american society of health-system pharmacists, the infectious diseases society of america, and the society of infectious diseases pharmacists", + "volume": "66", + "author": "M Rybak", + "year": "2009", + "journal-title": "Am J Health Syst Pharm" + }, + { + "issue": "2", + "key": "pone.0233284.ref059", + "doi-asserted-by": "crossref", + "first-page": "277", + "DOI": "10.1111/j.1574-695X.2007.00300.x", + "article-title": "Increased tolerance of Staphylococcus aureus to vancomycin in viscous media", + "volume": "51", + "author": "V Kostenko", + "year": "2007", + "journal-title": "FEMS Immunol Med Microbiol" + }, + { + "key": "pone.0233284.ref060", + "first-page": "107", + "article-title": "Multidrug tolerance of biofilms and persister cells", + "volume": "322", + "author": "K. Lewis", + "year": "2008", + "journal-title": "Curr Top Microbiol Immunol" + }, + { + "issue": "6", + "key": "pone.0233284.ref061", + "doi-asserted-by": "crossref", + "first-page": "ftw056", + "DOI": "10.1093/femspd/ftw056", + "article-title": "Penetration barrier contributes to bacterial biofilm-associated resistance against only select antibiotics, and exhibits genus-, strain- and antibiotic-specific differences", + "volume": "74", + "author": "R Singh", + "year": "2016", + "journal-title": "Pathog Dis" + }, + { + "issue": "12", + "key": "pone.0233284.ref062", + "doi-asserted-by": "crossref", + "first-page": "7273", + "DOI": "10.1128/AAC.03132-14", + "article-title": "Extracellular DNA impedes the transport of vancomycin in Staphylococcus epidermidis biofilms preexposed to subinhibitory concentrations of vancomycin", + "volume": "58", + "author": "N Doroshenko", + "year": "2014", + "journal-title": "Antimicrob Agents Chemotherapy" + }, + { + "issue": "1", + "key": "pone.0233284.ref063", + "doi-asserted-by": "crossref", + "first-page": "46", + "DOI": "10.1007/s00776-005-0968-7", + "article-title": "Antimicrobial susceptibility of Staphylococcus aureus and Staphylococcus epidermidis biofilms isolated from infected total hip arthroplasty cases", + "volume": "11", + "author": "S Nishimura", + "year": "2006", + "journal-title": "J Orthop Sci" + } + ], + "container-title": [ + "PLOS ONE" + ], + "original-title": [ + + ], + "language": "en", + "link": [ + { + "URL": "https://dx.plos.org/10.1371/journal.pone.0233284", + "content-type": "unspecified", + "content-version": "vor", + "intended-application": "similarity-checking" + } + ], + "deposited": { + "date-parts": [ + [ + 2020, + 5, + 29 + ] + ], + "date-time": "2020-05-29T17:54:37Z", + "timestamp": 1590774877000 + }, + "score": 1, + "resource": { + "primary": { + "URL": "https://dx.plos.org/10.1371/journal.pone.0233284" + } + }, + "subtitle": [ + + ], + "editor": [ + { + "given": "Rita G.", + "family": "Sobral", + "sequence": "first", + "affiliation": [ + + ] + } + ], + "short-title": [ + + ], + "issued": { + "date-parts": [ + [ + 2020, + 5, + 29 + ] + ] + }, + "references-count": 63, + "journal-issue": { + "issue": "5", + "published-online": { + "date-parts": [ + [ + 2020, + 5, + 29 + ] + ] + } + }, + "URL": "http://dx.doi.org/10.1371/journal.pone.0233284", + "relation": { + + }, + "ISSN": [ + "1932-6203" + ], + "issn-type": [ + { + "value": "1932-6203", + "type": "electronic" + } + ], + "subject": [ + "Multidisciplinary" + ], + "published": { + "date-parts": [ + [ + 2020, + 5, + 29 + ] + ] + } + +} \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala index 8124a5aae..c12f4c1f2 100644 --- a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala +++ b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala @@ -461,6 +461,86 @@ class CrossrefMappingTest { } + + @Test + def testConvertArticleFromCrossRef2OafSFI(): Unit = { + val json = Source + .fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/sfi_funded_article.json")) + .mkString + assertNotNull(json) + + assertFalse(json.isEmpty); + + val resultList: List[Oaf] = Crossref2Oaf.convert(json) + + assertTrue(resultList.nonEmpty) + + val items = resultList.filter(p => p.isInstanceOf[Publication]) + + assert(items.nonEmpty) + assert(items.size == 1) + val result: Result = items.head.asInstanceOf[Publication] + assertNotNull(result) + + logger.info(mapper.writeValueAsString(result)); + + assertNotNull(result.getDataInfo, "Datainfo test not null Failed"); + assertNotNull( + result.getDataInfo.getProvenanceaction, + "DataInfo/Provenance test not null Failed" + ); + assertFalse( + result.getDataInfo.getProvenanceaction.getClassid.isEmpty, + "DataInfo/Provenance/classId test not null Failed" + ); + assertFalse( + result.getDataInfo.getProvenanceaction.getClassname.isEmpty, + "DataInfo/Provenance/className test not null Failed" + ); + assertFalse( + result.getDataInfo.getProvenanceaction.getSchemeid.isEmpty, + "DataInfo/Provenance/SchemeId test not null Failed" + ); + assertFalse( + result.getDataInfo.getProvenanceaction.getSchemename.isEmpty, + "DataInfo/Provenance/SchemeName test not null Failed" + ); + + assertNotNull(result.getCollectedfrom, "CollectedFrom test not null Failed"); + assertFalse(result.getCollectedfrom.isEmpty); + + val collectedFromList = result.getCollectedfrom.asScala + assert( + collectedFromList.exists(c => c.getKey.equalsIgnoreCase("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")), + "Wrong collected from assertion" + ) + + assert( + collectedFromList.exists(c => c.getValue.equalsIgnoreCase("crossref")), + "Wrong collected from assertion" + ) + + val relevantDates = result.getRelevantdate.asScala + + assert( + relevantDates.exists(d => d.getQualifier.getClassid.equalsIgnoreCase("created")), + "Missing relevant date of type created" + ) + + val rels = resultList.filter(p => p.isInstanceOf[Relation]).asInstanceOf[List[Relation]] + assertFalse(rels.isEmpty) + rels.foreach(relation => { + assertNotNull(relation) + assertFalse(relation.getSource.isEmpty) + assertFalse(relation.getTarget.isEmpty) + assertFalse(relation.getRelClass.isEmpty) + assertFalse(relation.getRelType.isEmpty) + assertFalse(relation.getSubRelType.isEmpty) + + }) + + } + @Test def testSetDateOfAcceptanceCrossRef2Oaf(): Unit = { diff --git a/dhp-workflows/dhp-enrichment/pom.xml b/dhp-workflows/dhp-enrichment/pom.xml index 0b4269acd..591cad252 100644 --- a/dhp-workflows/dhp-enrichment/pom.xml +++ b/dhp-workflows/dhp-enrichment/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.5-SNAPSHOT 4.0.0 @@ -51,7 +51,7 @@ eu.dnetlib.dhp dhp-aggregation - 1.2.4-SNAPSHOT + 1.2.5-SNAPSHOT compile diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep1.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep1.java index f67447cd3..35b3700d9 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep1.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep1.java @@ -8,6 +8,7 @@ import java.util.ArrayList; import java.util.Arrays; import java.util.List; import java.util.Optional; +import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; @@ -56,7 +57,9 @@ public class PrepareResultOrcidAssociationStep1 { final String resultClassName = parser.get("resultTableName"); log.info("resultTableName: {}", resultClassName); - final List allowedsemrel = Arrays.asList(parser.get("allowedsemrels").split(";")); + final List allowedsemrel = Arrays.stream(parser.get("allowedsemrels").split(";")) + .map(s -> s.toLowerCase()).collect(Collectors.toList()); + log.info("allowedSemRel: {}", new Gson().toJson(allowedsemrel)); final List allowedPids = Arrays.asList(parser.get("allowedpids").split(";")); @@ -122,28 +125,27 @@ public class PrepareResultOrcidAssociationStep1 { Dataset result = readPath(spark, outputPath + "/resultSubset", resultClazz); result - .joinWith(relation, result.col("id").equalTo(relation.col("source"))) - .map((MapFunction, ResultOrcidList>) t2 -> { - ResultOrcidList rol = new ResultOrcidList(); - rol.setResultId(t2._2().getTarget()); - List aal = new ArrayList<>(); - t2._1().getAuthor().stream().forEach(a -> { - a.getPid().stream().forEach(p -> { - if (allowedPids.contains(p.getQualifier().getClassid().toLowerCase())) { - aal - .add( - AutoritativeAuthor - .newInstance(a.getName(), a.getSurname(), a.getFullname(), p.getValue())); - } + .joinWith(relation, result.col("id").equalTo(relation.col("source"))) + .map((MapFunction, ResultOrcidList>) t2 -> { + ResultOrcidList rol = new ResultOrcidList(); + rol.setResultId(t2._2().getTarget()); + List aal = new ArrayList<>(); + t2._1().getAuthor().stream().forEach(a -> { + a.getPid().stream().forEach(p -> { + if (allowedPids.contains(p.getQualifier().getClassid().toLowerCase())) { + aal + .add( + AutoritativeAuthor + .newInstance(a.getName(), a.getSurname(), a.getFullname(), p.getValue())); + } + }); }); - }); - return rol; - }, Encoders.bean(ResultOrcidList.class)) - .write() + return rol; + }, Encoders.bean(ResultOrcidList.class)).write() .option("compression", "gzip") .mode(SaveMode.Overwrite) .json(outputPath + "/" + resultType); - ; + } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep2.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep2.java index c60012a74..f2ce0526e 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep2.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep2.java @@ -10,6 +10,8 @@ import java.util.Set; import org.apache.commons.io.IOUtils; import org.apache.hadoop.io.compress.GzipCodec; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.api.java.function.MapGroupsFunction; import org.apache.spark.sql.*; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -63,33 +65,30 @@ public class PrepareResultOrcidAssociationStep2 { .union(readPath(spark, inputPath + "/software", ResultOrcidList.class)); resultOrcidAssoc - .toJavaRDD() - .mapToPair(r -> new Tuple2<>(r.getResultId(), r)) - .reduceByKey( - (a, b) -> { - if (a == null) { - return b; - } - if (b == null) { - return a; - } + .groupByKey((MapFunction) rol -> rol.getResultId(), Encoders.STRING()) + .mapGroups((MapGroupsFunction) (k, it) ->{ + ResultOrcidList resultOrcidList = it.next(); + if(it.hasNext()) + { Set orcid_set = new HashSet<>(); - a.getAuthorList().stream().forEach(aa -> orcid_set.add(aa.getOrcid())); - b - .getAuthorList() - .stream() - .forEach( - aa -> { - if (!orcid_set.contains(aa.getOrcid())) { - a.getAuthorList().add(aa); - orcid_set.add(aa.getOrcid()); - } - }); - return a; - }) - .map(Tuple2::_2) - .map(r -> OBJECT_MAPPER.writeValueAsString(r)) - .saveAsTextFile(outputPath, GzipCodec.class); + resultOrcidList.getAuthorList().stream().forEach(aa -> orcid_set.add(aa.getOrcid())); + it.forEachRemaining(val -> val + .getAuthorList() + .stream() + .forEach( + aa -> { + if (!orcid_set.contains(aa.getOrcid())) { + resultOrcidList.getAuthorList().add(aa); + orcid_set.add(aa.getOrcid()); + } + })); + } + return resultOrcidList; + },Encoders.bean(ResultOrcidList.class) ) + .write() + .mode(SaveMode.Overwrite) + .option("compression","gzip") + .json(outputPath); } } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java index ebc4853cf..6b5f5163c 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob.java @@ -3,6 +3,7 @@ package eu.dnetlib.dhp.orcidtoresultfromsemrel; import static eu.dnetlib.dhp.PropagationConstant.*; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.util.List; import java.util.Optional; @@ -59,9 +60,9 @@ public class SparkOrcidToResultFromSemRelJob { Class resultClazz = (Class) Class.forName(resultClassName); SparkConf conf = new SparkConf(); - conf.set("hive.metastore.uris", parser.get("hive_metastore_uris")); - runWithSparkHiveSession( + + runWithSparkSession( conf, isSparkSessionManaged, spark -> { diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/SparkResultToOrganizationFromIstRepoJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/SparkResultToOrganizationFromIstRepoJob.java index d49d8a5c8..650aa338b 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/SparkResultToOrganizationFromIstRepoJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/SparkResultToOrganizationFromIstRepoJob.java @@ -11,10 +11,7 @@ import java.util.Optional; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.FlatMapFunction; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; +import org.apache.spark.sql.*; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -159,8 +156,14 @@ public class SparkResultToOrganizationFromIstRepoJob { Dataset result = readPath(spark, inputPath, resultClazz); result.createOrReplaceTempView("result"); - createCfHbforResult(spark); + Dataset cfhb = spark.sql("select distinct r.id, inst.collectedfrom.key cf, inst.hostedby.key hb " + + + "from result r " + + "lateral view explode(instance) i as inst " + + "where r.datainfo.deletedbyinference=false"); + //createCfHbforResult(spark); + cfhb.createOrReplaceTempView("cfhb"); dsOrg.createOrReplaceTempView("rels"); return spark diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/countrypropagation/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/countrypropagation/oozie_app/workflow.xml index ea5ec91f4..89287b6ba 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/countrypropagation/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/countrypropagation/oozie_app/workflow.xml @@ -228,8 +228,12 @@ --conf spark.sql.shuffle.partitions=3840 --sourcePath${sourcePath}/publication +<<<<<<< HEAD:dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/countrypropagation/oozie_app/workflow.xml --preparedInfoPath${workingDir}/country/publication --saveGraph${saveGraph} +======= + --preparedInfoPath${workingDir}/publication +>>>>>>> beta:dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/oozie_app/workflow.xml --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication --outputPath${outputPath}/publication @@ -258,8 +262,12 @@ --conf spark.sql.shuffle.partitions=3840 --sourcePath${sourcePath}/dataset +<<<<<<< HEAD:dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/countrypropagation/oozie_app/workflow.xml --preparedInfoPath${workingDir}/country/dataset --saveGraph${saveGraph} +======= + --preparedInfoPath${workingDir}/dataset +>>>>>>> beta:dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/oozie_app/workflow.xml --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset --outputPath${outputPath}/dataset @@ -288,8 +296,12 @@ --conf spark.sql.shuffle.partitions=3840 --sourcePath${sourcePath}/otherresearchproduct +<<<<<<< HEAD:dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/countrypropagation/oozie_app/workflow.xml --preparedInfoPath${workingDir}/country/otherresearchproduct --saveGraph${saveGraph} +======= + --preparedInfoPath${workingDir}/otherresearchproduct +>>>>>>> beta:dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/oozie_app/workflow.xml --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct --outputPath${outputPath}/otherresearchproduct @@ -319,7 +331,6 @@ --sourcePath${sourcePath}/software --preparedInfoPath${workingDir}/software - --saveGraph${saveGraph} --resultTableNameeu.dnetlib.dhp.schema.oaf.Software --outputPath${outputPath}/software diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareStep1Test.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareStep1Test.java index a86527c3e..ab9d5a619 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareStep1Test.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareStep1Test.java @@ -5,9 +5,9 @@ import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; - -import com.google.gson.Gson; +import eu.dnetlib.dhp.schema.oaf.Relation; import org.apache.commons.io.FileUtils; +import org.apache.neethi.Assertion; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; @@ -22,6 +22,7 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.gson.Gson; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Dataset; @@ -63,8 +64,7 @@ public class PrepareStep1Test { } @Test - void noUpdateTest() throws Exception { - //7 relationi fra issupplementedby e issupplementto + void noMatchTest() throws Exception { final String sourcePath = getClass() .getResource("/eu/dnetlib/dhp/orcidtoresultfromsemrel/preparestep1") @@ -77,19 +77,25 @@ public class PrepareStep1Test { "-sourcePath", sourcePath, "-resultTableName", Dataset.class.getCanonicalName(), "-outputPath", workingDir.toString() + "/preparedInfo", - "-allowedsemrels", "IsSupplementedBy;IsSupplementTo", - "-allowedpids","orcid;orcid_pending" + "-allowedsemrels", "IsSupplementedBy;IsSupplementTo", + "-allowedpids", "orcid;orcid_pending" }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/preparedInfo") + .textFile(workingDir.toString() + "/preparedInfo/dataset") .map(item -> OBJECT_MAPPER.readValue(item, ResultOrcidList.class)); - System.out.println("***************** COUNT ********************* \n" + tmp.count()); - tmp.map(s -> new Gson().toJson(s)).foreach(s -> System.out.println(s)); + Assertions.assertEquals(0, tmp.count()); + Assertions.assertEquals(7, sc + .textFile(workingDir.toString() + "/preparedInfo/relationSubset") + .map(item -> OBJECT_MAPPER.readValue(item, Relation.class)).count()); + + Assertions.assertEquals(0, sc + .textFile(workingDir.toString() + "/preparedInfo/resultSubset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)).count()); } diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/orcidtoresultfromsemrel/preparestep1/publication/part00000 b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/orcidtoresultfromsemrel/preparestep1/publication/part00000 index 7fa6c7bff..81ef9aed0 100644 --- a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/orcidtoresultfromsemrel/preparestep1/publication/part00000 +++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/orcidtoresultfromsemrel/preparestep1/publication/part00000 @@ -11,3 +11,4 @@ +{u'dataInfo': {u'invisible': False, u'provenanceaction': {u'classid': u'sysimport:crosswalk:entityregistry', u'classname': u'Harvested', u'schemeid': u'dnet:provenanceActions', u'schemename': u'dnet:provenanceActions'}, u'trust': u'0.91', u'inferred': False, u'deletedbyinference': False}, u'qualifier': {u'classid': u'orcid', u'classname': u'Open Researcher and Contributor ID', u'schemeid': u'dnet:pid_types', u'schemename': u'dnet:pid_types'}, u'value': u'0000-0002-5001-6911'} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/pom.xml b/dhp-workflows/dhp-graph-mapper/pom.xml index 17146903a..687f0de66 100644 --- a/dhp-workflows/dhp-graph-mapper/pom.xml +++ b/dhp-workflows/dhp-graph-mapper/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.5-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/BibJson.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/BibJson.java index f7c0d501f..4de687ec7 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/BibJson.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/BibJson.java @@ -4,8 +4,6 @@ package eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj; import java.io.Serializable; import java.util.List; -import com.fasterxml.jackson.annotation.JsonIgnore; - public class BibJson implements Serializable { private Editorial editorial; private PidScheme pid_scheme; diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index 1f8c23ac3..b5801ca5c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -42,10 +42,7 @@ import java.io.IOException; import java.sql.Array; import java.sql.ResultSet; import java.sql.SQLException; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Date; -import java.util.List; +import java.util.*; import java.util.function.Consumer; import java.util.function.Function; import java.util.function.Predicate; @@ -311,7 +308,13 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i ds.setContentpolicies(prepareListOfQualifiers(rs.getArray("contentpolicies"))); ds.setConsenttermsofuse(rs.getBoolean("consenttermsofuse")); ds.setFulltextdownload(rs.getBoolean("fulltextdownload")); - ds.setConsenttermsofusedate(rs.getDate("consenttermsofusedate").toString()); + ds + .setConsenttermsofusedate( + Optional + .ofNullable( + rs.getDate("consenttermsofusedate")) + .map(c -> c.toString()) + .orElse(null)); return Arrays.asList(ds); } catch (final Exception e) { diff --git a/dhp-workflows/dhp-graph-provision/pom.xml b/dhp-workflows/dhp-graph-provision/pom.xml index e402d0600..ae8f3b53a 100644 --- a/dhp-workflows/dhp-graph-provision/pom.xml +++ b/dhp-workflows/dhp-graph-provision/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.5-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-stats-promote/pom.xml b/dhp-workflows/dhp-stats-promote/pom.xml index c64c2f58e..ce3e739a5 100644 --- a/dhp-workflows/dhp-stats-promote/pom.xml +++ b/dhp-workflows/dhp-stats-promote/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.5-SNAPSHOT 4.0.0 dhp-stats-promote diff --git a/dhp-workflows/dhp-stats-update/pom.xml b/dhp-workflows/dhp-stats-update/pom.xml index 52f35ff07..2bc610c42 100644 --- a/dhp-workflows/dhp-stats-update/pom.xml +++ b/dhp-workflows/dhp-stats-update/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.5-SNAPSHOT 4.0.0 dhp-stats-update diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql index a95ee74d8..24e6bff7e 100755 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql @@ -12,6 +12,8 @@ and (ri.accessright = 'Open Access' or ri.accessright = 'Embargo' or ri.accessright = 'Open Source')) tmp on p.id= tmp.id; +compute stats indi_pub_green_oa; + create table indi_pub_grey_lit stored as parquet as select distinct p.id, coalesce(grey_lit, 0) as grey_lit from publication p @@ -22,6 +24,8 @@ join result_classifications rt on rt.id = p.id where rt.type not in ('Article','Part of book or chapter of book','Book','Doctoral thesis','Master thesis','Data Paper', 'Thesis', 'Bachelor thesis', 'Conference object') and not exists (select 1 from result_classifications rc where type ='Other literature type' and rc.id=p.id)) tmp on p.id=tmp.id; +compute stats indi_pub_grey_lit; + create table indi_pub_doi_from_crossref stored as parquet as select distinct p.id, coalesce(doi_from_crossref, 0) as doi_from_crossref from publication p @@ -31,6 +35,7 @@ join datasource d on d.id = ri.collectedfrom where pidtype='Digital Object Identifier' and d.name ='Crossref') tmp on tmp.id=p.id; +compute stats indi_pub_doi_from_crossref; ---- Sprint 2 ---- create table indi_result_has_cc_licence stored as parquet as select distinct r.id, (case when lic='' or lic is null then 0 else 1 end) as has_cc_license @@ -40,6 +45,8 @@ join result_licenses as license on license.id = r.id where lower(license.type) LIKE '%creativecommons.org%' OR lower(license.type) LIKE '%cc-%') tmp on r.id= tmp.id; +compute stats indi_result_has_cc_licence; + create table indi_result_has_cc_licence_url stored as parquet as select distinct r.id, case when lic_host='' or lic_host is null then 0 else 1 end as has_cc_license_url from result r @@ -49,16 +56,21 @@ join result_licenses as license on license.id = r.id WHERE lower(parse_url(license.type, "HOST")) = "creativecommons.org") tmp on r.id= tmp.id; +compute stats indi_result_has_cc_licence_url; + create table indi_pub_has_abstract stored as parquet as select distinct publication.id, coalesce(abstract, 1) has_abstract from publication; +compute stats indi_pub_has_abstract; + create table indi_result_with_orcid stored as parquet as select distinct r.id, coalesce(has_orcid, 0) as has_orcid from result r left outer join (select id, 1 as has_orcid from result_orcid) tmp on r.id= tmp.id; +compute stats indi_result_with_orcid; ---- Sprint 3 ---- create table indi_funded_result_with_fundref stored as parquet as @@ -68,6 +80,8 @@ left outer join (select distinct id, 1 as fundref from project_results where provenance='Harvested') tmp on r.id= tmp.id; +compute stats indi_funded_result_with_fundref; + create table indi_result_org_country_collab stored as parquet as with tmp as (select o.id as id, o.country , ro.id as result,r.type from organization o @@ -79,6 +93,8 @@ join tmp as o2 on o1.result=o2.result where o1.id<>o2.id and o1.country<>o2.country group by o1.id, o1.type,o2.country; +compute stats indi_result_org_country_collab; + create table indi_result_org_collab stored as parquet as with tmp as (select o.id, ro.id as result,r.type from organization o @@ -90,6 +106,8 @@ join tmp as o2 on o1.result=o2.result where o1.id<>o2.id group by o1.id, o2.id, o1.type; +compute stats indi_result_org_collab; + create table indi_funder_country_collab stored as parquet as with tmp as (select funder, project, country from organization_projects op join organization o on o.id=op.id @@ -101,6 +119,8 @@ join tmp as f2 on f1.project=f2.project where f1.country<>f2.country group by f1.funder, f2.country, f1.country; +compute stats indi_funder_country_collab; + create table indi_result_country_collab stored as parquet as with tmp as (select country, ro.id as result,r.type from organization o @@ -112,6 +132,8 @@ join tmp as o2 on o1.result=o2.result where o1.country<>o2.country group by o1.country, o2.country, o1.type; +compute stats indi_result_country_collab; + ---- Sprint 4 ---- create table indi_pub_diamond stored as parquet as select distinct pd.id, coalesce(in_diamond_journal, 0) as in_diamond_journal @@ -123,6 +145,8 @@ join stats_ext.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_onli and (ps.journal_is_in_doaj=true or ps.journal_is_oa=true) and ps.has_apc=false) tmp on pd.id=tmp.id; +compute stats indi_pub_diamond; + create table indi_pub_hybrid stored as parquet as select distinct pd.id, coalesce(is_hybrid, 0) as is_hybrid from publication_datasources pd @@ -133,6 +157,8 @@ join stats_ext.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_onli and (ps.journal_is_in_doaj=false and ps.journal_is_oa=false)) tmp on pd.id=tmp.id; +compute stats indi_pub_hybrid; + create table indi_pub_in_transformative stored as parquet as select distinct pd.id, coalesce(is_transformative, 0) as is_transformative from publication pd @@ -143,6 +169,8 @@ join stats_ext.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_onli and ps.is_transformative_journal=true) tmp on pd.id=tmp.id; +compute stats indi_pub_in_transformative; + create table indi_pub_closed_other_open stored as parquet as select distinct ri.id, coalesce(pub_closed_other_open, 0) as pub_closed_other_open from result_instance ri left outer join @@ -153,11 +181,12 @@ where d.type like '%Journal%' and ri.accessright='Closed Access' and (p.bestlicence='Open Access' or p.bestlicence='Open Source')) tmp on tmp.id=ri.id; - +compute stats indi_pub_closed_other_open; ---- Sprint 5 ---- create table indi_result_no_of_copies stored as parquet as select id, count(id) as number_of_copies from result_instance group by id; +compute stats indi_result_no_of_copies; ---- Sprint 6 ---- create table indi_pub_gold_oa stored as parquet as WITH gold_oa AS ( @@ -183,6 +212,8 @@ LEFT OUTER JOIN ( JOIN issn on issn.id=pd.datasource JOIN gold_oa on issn.issn = gold_oa.issn) tmp ON pd.id=tmp.id; +compute stats indi_pub_gold_oa; + create table indi_datasets_gold_oa stored as parquet as WITH gold_oa AS ( SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_1 as issn @@ -210,6 +241,8 @@ LEFT OUTER JOIN ( JOIN issn on issn.id=pd.datasource JOIN gold_oa on issn.issn = gold_oa.issn) tmp ON pd.id=tmp.id; +compute stats indi_datasets_gold_oa; + create table indi_software_gold_oa stored as parquet as WITH gold_oa AS ( SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_1 as issn @@ -237,6 +270,8 @@ LEFT OUTER JOIN ( JOIN issn on issn.id=pd.datasource JOIN gold_oa on issn.issn = gold_oa.issn) tmp ON pd.id=tmp.id; +compute stats indi_software_gold_oa; + create table indi_org_findable stored as parquet as with result_with_pid as ( select ro.organization organization, count(distinct rp.id) no_result_with_pid from result_organization ro @@ -263,6 +298,8 @@ join result_with_pid_share on result_with_pid_share.organization=allresults.orga left outer join ( select organization, abstract_share from result_with_abstract_share) tmp on tmp.organization=allresults.organization; +compute stats indi_org_findable; + create table indi_org_openess stored as parquet as WITH datasets_oa as ( SELECT ro.organization, count(dg.id) no_oadatasets FROM indi_datasets_gold_oa dg @@ -313,6 +350,8 @@ left outer join ( left outer join ( select organization,s from allsoftwaresshare) tmp1 on tmp1.organization=allpubsshare.organization; +compute stats indi_org_openess; + create table indi_pub_hybrid_oa_with_cc stored as parquet as WITH hybrid_oa AS ( SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_print as issn @@ -343,6 +382,8 @@ LEFT OUTER JOIN ( JOIN indi_result_has_cc_licence cc on pd.id=cc.id where cc.has_cc_license=1) tmp on pd.id=tmp.id; +compute stats indi_pub_hybrid_oa_with_cc; + create table indi_pub_downloads stored as parquet as SELECT result_id, sum(downloads) no_dowloads from openaire_prod_usage_stats.usage_stats join publication on result_id=id @@ -350,6 +391,8 @@ where downloads>0 GROUP BY result_id order by no_dowloads desc; +compute stats indi_pub_downloads; + create table indi_pub_downloads_datasource stored as parquet as SELECT result_id, repository_id, sum(downloads) no_dowloads from openaire_prod_usage_stats.usage_stats join publication on result_id=id @@ -357,15 +400,21 @@ where downloads>0 GROUP BY result_id, repository_id order by result_id; +compute stats indi_pub_downloads_datasource; + create table indi_pub_downloads_year stored as parquet as SELECT result_id, substring(us.`date`, 1,4) as `year`, sum(downloads) no_dowloads from openaire_prod_usage_stats.usage_stats us join publication on result_id=id where downloads>0 GROUP BY result_id, `year` order by `year` asc; +compute stats indi_pub_downloads_year; + create table indi_pub_downloads_datasource_year stored as parquet as SELECT result_id, substring(us.`date`, 1,4) as `year`, repository_id, sum(downloads) no_dowloads from openaire_prod_usage_stats.usage_stats us join publication on result_id=id where downloads>0 GROUP BY result_id, repository_id, `year` order by `year` asc, result_id; + +compute stats indi_pub_downloads_datasource_year; \ No newline at end of file diff --git a/dhp-workflows/dhp-usage-raw-data-update/pom.xml b/dhp-workflows/dhp-usage-raw-data-update/pom.xml index a78f92d41..954c8bd39 100644 --- a/dhp-workflows/dhp-usage-raw-data-update/pom.xml +++ b/dhp-workflows/dhp-usage-raw-data-update/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.5-SNAPSHOT 4.0.0 dhp-usage-raw-data-update diff --git a/dhp-workflows/dhp-usage-stats-build/pom.xml b/dhp-workflows/dhp-usage-stats-build/pom.xml index 20d2f5b76..54e18580b 100644 --- a/dhp-workflows/dhp-usage-stats-build/pom.xml +++ b/dhp-workflows/dhp-usage-stats-build/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.5-SNAPSHOT 4.0.0 dhp-usage-stats-build diff --git a/dhp-workflows/dhp-workflow-profiles/pom.xml b/dhp-workflows/dhp-workflow-profiles/pom.xml index b1c51c497..8c71a5ca1 100644 --- a/dhp-workflows/dhp-workflow-profiles/pom.xml +++ b/dhp-workflows/dhp-workflow-profiles/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.2.4-SNAPSHOT + 1.2.5-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/pom.xml b/dhp-workflows/pom.xml index 143178560..541d59007 100644 --- a/dhp-workflows/pom.xml +++ b/dhp-workflows/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp - 1.2.4-SNAPSHOT + 1.2.5-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 6a14954e5..136b9b867 100644 --- a/pom.xml +++ b/pom.xml @@ -3,7 +3,7 @@ 4.0.0 eu.dnetlib.dhp dhp - 1.2.4-SNAPSHOT + 1.2.5-SNAPSHOT pom @@ -551,6 +551,9 @@ org.apache.maven.plugins maven-site-plugin 3.9.1 + + ${dhp.site.skip} + @@ -791,6 +794,7 @@ 2.4.0.cloudera2 2.9.6 3.5 + true 11.0.2 2.11.12 5.6.1