Merge pull request 'DOIBoost Mapping: change the creation of the instance in the DOIBoost result' (#155) from doiboost_url into beta

Reviewed-on: #155
This commit is contained in:
Claudio Atzori 2021-11-11 10:40:32 +01:00
commit 8bdca3413f
4 changed files with 653 additions and 27 deletions

View File

@ -70,7 +70,7 @@ case object Crossref2Oaf {
"reference-book" -> "0002 Book", "reference-book" -> "0002 Book",
"monograph" -> "0002 Book", "monograph" -> "0002 Book",
"journal-article" -> "0001 Article", "journal-article" -> "0001 Article",
"dissertation" -> "0006 Doctoral thesis", "dissertation" -> "0044 Thesis",
"other" -> "0038 Other literature type", "other" -> "0038 Other literature type",
"peer-review" -> "0015 Review", "peer-review" -> "0015 Review",
"proceedings" -> "0004 Conference object", "proceedings" -> "0004 Conference object",
@ -206,11 +206,16 @@ case object Crossref2Oaf {
else { else {
instance.setDateofacceptance(asField(createdDate.getValue)) instance.setDateofacceptance(asField(createdDate.getValue))
} }
val s: String = (json \ "URL").extract[String] val s: List[String] = List("https://doi.org/" + doi)
val links: List[String] = ((for {JString(url) <- json \ "link" \ "URL"} yield url) ::: List(s)).filter(p => p != null).distinct // val links: List[String] = ((for {JString(url) <- json \ "link" \ "URL"} yield url) ::: List(s)).filter(p => p != null && p.toLowerCase().contains(doi.toLowerCase())).distinct
if (links.nonEmpty) { // if (links.nonEmpty) {
instance.setUrl(links.asJava) // instance.setUrl(links.asJava)
} // }
if(s.nonEmpty)
{
instance.setUrl(s.asJava)
}
result.setInstance(List(instance).asJava) result.setInstance(List(instance).asJava)
//IMPORTANT //IMPORTANT

View File

@ -111,26 +111,9 @@ object SparkProcessMAG {
.map(item => ConversionUtil.updatePubsWithConferenceInfo(item)) .map(item => ConversionUtil.updatePubsWithConferenceInfo(item))
.write .write
.mode(SaveMode.Overwrite) .mode(SaveMode.Overwrite)
.save(s"$workingPath/merge_step_2_conference")
magPubs= spark.read.load(s"$workingPath/merge_step_2_conference").as[Publication]
.map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)]
val paperUrlDataset = spark.read.load(s"$sourcePath/PaperUrls").as[MagPaperUrl].groupBy("PaperId").agg(collect_list(struct("sourceUrl")).as("instances")).as[MagUrl]
logger.info("Phase 5) enrich publication with URL and Instances")
magPubs.joinWith(paperUrlDataset, col("_1").equalTo(paperUrlDataset("PaperId")), "left")
.map { a: ((String, Publication), MagUrl) => ConversionUtil.addInstances((a._1._2, a._2)) }
.write.mode(SaveMode.Overwrite)
.save(s"$workingPath/merge_step_3") .save(s"$workingPath/merge_step_3")
// logger.info("Phase 6) Enrich Publication with description")
// val pa = spark.read.load(s"${parser.get("sourcePath")}/PaperAbstractsInvertedIndex").as[MagPaperAbstract]
// pa.map(ConversionUtil.transformPaperAbstract).write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/PaperAbstract")
val paperAbstract = spark.read.load((s"$workingPath/PaperAbstract")).as[MagPaperAbstract] val paperAbstract = spark.read.load((s"$workingPath/PaperAbstract")).as[MagPaperAbstract]
@ -162,12 +145,14 @@ object SparkProcessMAG {
.write.mode(SaveMode.Overwrite) .write.mode(SaveMode.Overwrite)
.save(s"$workingPath/mag_publication") .save(s"$workingPath/mag_publication")
spark.read.load(s"$workingPath/mag_publication").as[Publication]
.filter(p => p.getId == null)
.groupByKey(p => p.getId)
.reduceGroups((a:Publication, b:Publication) => ConversionUtil.mergePublication(a,b))
.map(_._2)
.write.mode(SaveMode.Overwrite).save(s"$targetPath/magPublication")
val s:RDD[Publication] = spark.read.load(s"$workingPath/mag_publication").as[Publication]
.map(p=>Tuple2(p.getId, p)).rdd.reduceByKey((a:Publication, b:Publication) => ConversionUtil.mergePublication(a,b))
.map(_._2)
spark.createDataset(s).as[Publication].write.mode(SaveMode.Overwrite).save(s"$targetPath/magPublication")
} }
} }

View File

@ -612,4 +612,26 @@ class CrossrefMappingTest {
} }
@Test
def testMultipleURLs() :Unit = {
val json = Source.fromInputStream(getClass.getResourceAsStream("multiple_urls.json")).mkString
assertNotNull(json)
assertFalse(json.isEmpty);
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
assertTrue(resultList.nonEmpty)
val item : Result = resultList.filter(p => p.isInstanceOf[Result]).head.asInstanceOf[Result]
assertEquals(1, item.getInstance().size())
assertEquals(1, item.getInstance().get(0).getUrl().size())
assertEquals("https://doi.org/10.1016/j.jas.2019.105013", item.getInstance().get(0).getUrl().get(0))
//println(mapper.writeValueAsString(item))
}
} }

View File

@ -0,0 +1,614 @@
{
"indexed": {
"date-parts": [
[
2021,
10,
31
]
],
"date-time": "2021-10-31T15:48:01Z",
"timestamp": 1635695281393
},
"reference-count": 39,
"publisher": "Elsevier BV",
"license": [
{
"start": {
"date-parts": [
[
2019,
12,
1
]
],
"date-time": "2019-12-01T00:00:00Z",
"timestamp": 1575158400000
},
"content-version": "tdm",
"delay-in-days": 0,
"URL": "https://www.elsevier.com/tdm/userlicense/1.0/"
},
{
"start": {
"date-parts": [
[
2019,
9,
13
]
],
"date-time": "2019-09-13T00:00:00Z",
"timestamp": 1568332800000
},
"content-version": "vor",
"delay-in-days": 0,
"URL": "http://creativecommons.org/licenses/by/4.0/"
}
],
"funder": [
{
"DOI": "10.13039/100001182",
"name": "INSTAP",
"doi-asserted-by": "publisher"
},
{
"DOI": "10.13039/100014440",
"name": "Ministry of Science, Innovation and Universities",
"doi-asserted-by": "publisher",
"award": [
"RYC-2016-19637"
]
},
{
"DOI": "10.13039/100010661",
"name": "European Unions Horizon 2020",
"doi-asserted-by": "publisher",
"award": [
"746446"
]
}
],
"content-domain": {
"domain": [
"elsevier.com",
"sciencedirect.com"
],
"crossmark-restriction": true
},
"short-container-title": [
"Journal of Archaeological Science"
],
"published-print": {
"date-parts": [
[
2019,
12
]
]
},
"DOI": "10.1016/j.jas.2019.105013",
"type": "journal-article",
"created": {
"date-parts": [
[
2019,
9,
25
]
],
"date-time": "2019-09-25T20:05:08Z",
"timestamp": 1569441908000
},
"page": "105013",
"update-policy": "http://dx.doi.org/10.1016/elsevier_cm_policy",
"source": "Crossref",
"is-referenced-by-count": 21,
"title": [
"A brave new world for archaeological survey: Automated machine learning-based potsherd detection using high-resolution drone imagery"
],
"prefix": "10.1016",
"volume": "112",
"author": [
{
"given": "H.A.",
"family": "Orengo",
"sequence": "first",
"affiliation": [
]
},
{
"given": "A.",
"family": "Garcia-Molsosa",
"sequence": "additional",
"affiliation": [
]
}
],
"member": "78",
"reference": [
{
"key": "10.1016/j.jas.2019.105013_bib1",
"doi-asserted-by": "crossref",
"first-page": "85",
"DOI": "10.1080/17538947.2016.1250829",
"article-title": "Remote sensing heritage in a petabyte-scale: satellite data and heritage Earth Engine© applications",
"volume": "10",
"author": "Agapiou",
"year": "2017",
"journal-title": "Int. J. Digit. Earth"
},
{
"key": "10.1016/j.jas.2019.105013_bib2",
"series-title": "Extracting Meaning from Ploughsoil Assemblages",
"first-page": "1",
"article-title": "Extracting meaning from ploughsoil assemblages: assessments of the past, strategies for the future",
"author": "Alcock",
"year": "2000"
},
{
"key": "10.1016/j.jas.2019.105013_bib3",
"series-title": "Side-by-Side Survey. Comparative Regional Studies in the Mediterranean World",
"first-page": "1",
"article-title": "Introduction",
"author": "Alcock",
"year": "2004"
},
{
"key": "10.1016/j.jas.2019.105013_bib4",
"doi-asserted-by": "crossref",
"first-page": "93",
"DOI": "10.1111/j.1538-4632.1995.tb00338.x",
"article-title": "Local indicators of spatial association—LISA",
"volume": "27",
"author": "Anselin",
"year": "1995",
"journal-title": "Geogr. Anal."
},
{
"key": "10.1016/j.jas.2019.105013_bib5",
"series-title": "Archaeological Survey",
"author": "Banning",
"year": "2002"
},
{
"issue": "1/2",
"key": "10.1016/j.jas.2019.105013_bib6",
"doi-asserted-by": "crossref",
"first-page": "123",
"DOI": "10.2307/3181488",
"article-title": "GIS, archaeological survey and landscape archaeology on the island of Kythera, Greece",
"volume": "29",
"author": "Bevan",
"year": "2004",
"journal-title": "J. Field Archaeol."
},
{
"issue": "1",
"key": "10.1016/j.jas.2019.105013_bib8",
"doi-asserted-by": "crossref",
"first-page": "5",
"DOI": "10.1023/A:1010933404324",
"article-title": "Random forests",
"volume": "45",
"author": "Breiman",
"year": "2001",
"journal-title": "Mach. Learn."
},
{
"key": "10.1016/j.jas.2019.105013_bib9",
"series-title": "Sampling in Contemporary British Archaeology",
"author": "Cherry",
"year": "1978"
},
{
"issue": "3",
"key": "10.1016/j.jas.2019.105013_bib10",
"doi-asserted-by": "crossref",
"first-page": "273",
"DOI": "10.1016/0734-189X(84)90197-X",
"article-title": "Segmentation of a high-resolution urban scene using texture operators",
"volume": "25",
"author": "Conners",
"year": "1984",
"journal-title": "Comput. Vis. Graph Image Process"
},
{
"key": "10.1016/j.jas.2019.105013_bib11",
"first-page": "31",
"article-title": "Old land surfaces and modern ploughsoil: implications of recent work at Maxey, Cambridgeshire",
"volume": "2",
"author": "Crowther",
"year": "1983",
"journal-title": "Scott. Archaeol. Rev."
},
{
"key": "10.1016/j.jas.2019.105013_bib12",
"series-title": "Settlement Pattern Studies in the Americas: Fifty Years since Virú",
"first-page": "203",
"article-title": "Conclusions: the settlement pattern concept from an Americanist perspective",
"author": "Fish",
"year": "1999"
},
{
"key": "10.1016/j.jas.2019.105013_bib13",
"doi-asserted-by": "crossref",
"first-page": "21",
"DOI": "10.3390/geosciences9010021",
"article-title": "Remote sensing and historical morphodynamics of alluvial plains. The 1909 indus flood and the city of Dera Gazhi Khan (province of Punjab, Pakistan)",
"volume": "9",
"author": "Garcia",
"year": "2019",
"journal-title": "Geosciences"
},
{
"key": "10.1016/j.jas.2019.105013_bib14",
"unstructured": "Georgiadis, M.; Garcia-Molsosa, A.; Orengo, H.A.; Kefalidou, E. and Kallintzi, K. In Preparation. APAX Project 2015-2018: A Preliminary Report. (Hesperia)."
},
{
"key": "10.1016/j.jas.2019.105013_bib15",
"series-title": "Geographical Information Systems and Landscape Archaeology",
"first-page": "35",
"article-title": "Regional survey and GIS: the boeotia project",
"author": "Gillings",
"year": "1999"
},
{
"key": "10.1016/j.jas.2019.105013_bib16",
"doi-asserted-by": "crossref",
"first-page": "18",
"DOI": "10.1016/j.rse.2017.06.031",
"article-title": "Google Earth engine: planetary-scale geospatial analysis for everyone",
"volume": "202",
"author": "Gorelick",
"year": "2017",
"journal-title": "Remote Sens. Environ."
},
{
"issue": "107",
"key": "10.1016/j.jas.2019.105013_bib17",
"doi-asserted-by": "crossref",
"first-page": "177",
"DOI": "10.1111/j.0031-868X.2004.00278.x",
"article-title": "Photogrammetric reconstruction of the great buddha of Bamiyan, Afghanistan",
"volume": "19",
"author": "Grün",
"year": "2004",
"journal-title": "Photogramm. Rec."
},
{
"issue": "6",
"key": "10.1016/j.jas.2019.105013_bib18",
"doi-asserted-by": "crossref",
"first-page": "610",
"DOI": "10.1109/TSMC.1973.4309314",
"article-title": "Textural features for image classification",
"author": "Haralick",
"year": "1973",
"journal-title": "IEEE Trans. Syst., Man, Cybernet., SMC-3"
},
{
"key": "10.1016/j.jas.2019.105013_bib19",
"doi-asserted-by": "crossref",
"first-page": "76",
"DOI": "10.1558/jmea.v14i1.76",
"article-title": "Excavating to excess? Implications of the last decade of archaeology in Israel",
"volume": "14",
"author": "Kletter",
"year": "2001",
"journal-title": "J. Mediterr. Archaeol."
},
{
"key": "10.1016/j.jas.2019.105013_bib20",
"first-page": "299",
"article-title": "Testing Google Earth Engine for the automatic identification and vectorization of archaeological features: a case study from Faynan, Jordan",
"volume": "15",
"author": "Liss",
"year": "2017",
"journal-title": "J. Archaeol. Sci.: Report"
},
{
"key": "10.1016/j.jas.2019.105013_bib21",
"series-title": "Geographical Information Systems and Landscape Archaeology",
"first-page": "55",
"article-title": "Towards a methodology for modelling surface survey data: the sangro valley project",
"author": "Lock",
"year": "1999"
},
{
"key": "10.1016/j.jas.2019.105013_bib22",
"series-title": "Extracting Meaning from Ploughsoil Assemblages",
"first-page": "5",
"article-title": "Methods of collection recording and quantification",
"author": "Mattingly",
"year": "2000"
},
{
"issue": "14",
"key": "10.1016/j.jas.2019.105013_bib23",
"doi-asserted-by": "crossref",
"first-page": "E778",
"DOI": "10.1073/pnas.1115472109",
"article-title": "Mapping patterns of long-term settlement in Northern Mesopotamia at a large scale",
"volume": "109",
"author": "Menze",
"year": "2012",
"journal-title": "Proc. Natl. Acad. Sci."
},
{
"key": "10.1016/j.jas.2019.105013_bib24",
"doi-asserted-by": "crossref",
"first-page": "80",
"DOI": "10.1016/j.jas.2015.04.002",
"article-title": "A supervised machine-learning approach towards geochemical predictive modelling in archaeology",
"volume": "59",
"author": "Oonk",
"year": "2015",
"journal-title": "J. Archaeol. Sci."
},
{
"key": "10.1016/j.jas.2019.105013_bib25",
"doi-asserted-by": "crossref",
"first-page": "49",
"DOI": "10.1016/j.isprsjprs.2012.07.005",
"article-title": "Combining terrestrial stereophotogrammetry, DGPS and GIS-based 3D voxel modelling in the volumetric recording of archaeological features",
"volume": "76",
"author": "Orengo",
"year": "2013",
"journal-title": "ISPRS J. Photogrammetry Remote Sens."
},
{
"key": "10.1016/j.jas.2019.105013_bib26",
"doi-asserted-by": "crossref",
"first-page": "100",
"DOI": "10.1016/j.jas.2015.10.008",
"article-title": "Photogrammetric re-discovery of the Eastern Thessalian hidden long-term landscapes",
"volume": "64",
"author": "Orengo",
"year": "2015",
"journal-title": "J. Archaeol. Sci."
},
{
"issue": "3",
"key": "10.1016/j.jas.2019.105013_bib27",
"doi-asserted-by": "crossref",
"first-page": "479",
"DOI": "10.3764/aja.122.3.0479",
"article-title": "Towards a definition of Minoan agro-pastoral landscapes: results of the survey at Palaikastro (Crete)",
"volume": "122",
"author": "Orengo",
"year": "2018",
"journal-title": "Am. J. Archaeol."
},
{
"issue": "7",
"key": "10.1016/j.jas.2019.105013_bib28",
"doi-asserted-by": "crossref",
"first-page": "735",
"DOI": "10.3390/rs9070735",
"article-title": "Large-scale, multi-temporal remote sensing of palaeo-river networks: a case study from Northwest India and its implications for the Indus civilisation",
"volume": "9",
"author": "Orengo",
"year": "2017",
"journal-title": "Remote Sens."
},
{
"key": "10.1016/j.jas.2019.105013_bib29",
"doi-asserted-by": "crossref",
"first-page": "1361",
"DOI": "10.1002/esp.4317",
"article-title": "Multi-scale relief model (MSRM): a new algorithm for the visualization of subtle topographic change of variable size in digital elevation models",
"volume": "43",
"author": "Orengo",
"year": "2018",
"journal-title": "Earth Surf. Process. Landforms"
},
{
"key": "10.1016/j.jas.2019.105013_bib30",
"series-title": "Submitted to Proceedings of the National Academy of Sciences",
"article-title": "Living on the edge of the desert: automated detection of archaeological mounds in Cholistan (Pakistan) using machine learning classification of multi-sensor multi-temporal satellite data",
"author": "Orengo",
"year": "2019"
},
{
"key": "10.1016/j.jas.2019.105013_bib31",
"first-page": "154",
"article-title": "How many trees in a random forest?",
"volume": "vol. 7376",
"author": "Oshiro",
"year": "2012"
},
{
"key": "10.1016/j.jas.2019.105013_bib32",
"article-title": "Decision-making in modern surveys",
"volume": "ume 1",
"author": "Plog",
"year": "1978"
},
{
"issue": "4",
"key": "10.1016/j.jas.2019.105013_bib33",
"doi-asserted-by": "crossref",
"first-page": "100",
"DOI": "10.3390/geosciences7040100",
"article-title": "From above and on the ground: geospatial methods for recording endangered archaeology in the Middle East and north africa",
"volume": "7",
"author": "Rayne",
"year": "2017",
"journal-title": "Geosciences"
},
{
"issue": "1",
"key": "10.1016/j.jas.2019.105013_bib34",
"doi-asserted-by": "crossref",
"first-page": "1",
"DOI": "10.1080/00438243.1978.9979712",
"article-title": "The design of archaeological surveys",
"volume": "10",
"author": "Schiffer",
"year": "1978",
"journal-title": "World Archaeol."
},
{
"key": "10.1016/j.jas.2019.105013_bib35",
"series-title": "Experiments in the Collection and Analysis of Archaeological Survey Data: the East Hampshire Survey",
"author": "Shennan",
"year": "1985"
},
{
"key": "10.1016/j.jas.2019.105013_bib36",
"doi-asserted-by": "crossref",
"first-page": "1066",
"DOI": "10.1016/j.culher.2016.06.006",
"article-title": "Drones over Mediterranean landscapes. The potential of small UAV's (drones) for site detection and heritage management in archaeological survey projects: a case study from Le Pianelle in the Tappino Valley, Molise (Italy)",
"volume": "22",
"author": "Stek",
"year": "2016",
"journal-title": "J. Cult. Herit."
},
{
"key": "10.1016/j.jas.2019.105013_bib37",
"series-title": "Side-by-Side Survey. Comparative Regional Studies in the Mediterranean World",
"first-page": "65",
"article-title": "Side-by-side and back to front: exploring intra-regional latitudinal and longitudinal comparability in survey data. Three case studies from Metaponto, southern Italy",
"author": "Thomson",
"year": "2004"
},
{
"key": "10.1016/j.jas.2019.105013_bib38",
"series-title": "Digital Discovery. Exploring New Frontiers in Human Heritage. Computer Applications and Quantitative Methods in Archaeology",
"article-title": "Computer vision and machine learning for archaeology",
"author": "van der Maaten",
"year": "2007"
},
{
"key": "10.1016/j.jas.2019.105013_bib39",
"doi-asserted-by": "crossref",
"first-page": "1114",
"DOI": "10.1111/j.1475-4754.2012.00667.x",
"article-title": "Computer vision-based orthophoto mapping of complex archaeological sites: the ancient quarry of Pitaranha (Portugal-Spain)",
"volume": "54",
"author": "Verhoeven",
"year": "2012",
"journal-title": "Archaeometry"
},
{
"key": "10.1016/j.jas.2019.105013_bib40",
"series-title": "A Guide for Salvage Archeology",
"author": "Wendorf",
"year": "1962"
}
],
"container-title": [
"Journal of Archaeological Science"
],
"original-title": [
],
"language": "en",
"link": [
{
"URL": "https://api.elsevier.com/content/article/PII:S0305440319301001?httpAccept=text/xml",
"content-type": "text/xml",
"content-version": "vor",
"intended-application": "text-mining"
},
{
"URL": "https://api.elsevier.com/content/article/PII:S0305440319301001?httpAccept=text/plain",
"content-type": "text/plain",
"content-version": "vor",
"intended-application": "text-mining"
}
],
"deposited": {
"date-parts": [
[
2019,
11,
25
]
],
"date-time": "2019-11-25T06:46:34Z",
"timestamp": 1574664394000
},
"score": 1,
"subtitle": [
],
"short-title": [
],
"issued": {
"date-parts": [
[
2019,
12
]
]
},
"references-count": 39,
"alternative-id": [
"S0305440319301001"
],
"URL": "http://dx.doi.org/10.1016/j.jas.2019.105013",
"relation": {
},
"ISSN": [
"0305-4403"
],
"issn-type": [
{
"value": "0305-4403",
"type": "print"
}
],
"subject": [
"Archaeology",
"Archaeology"
],
"published": {
"date-parts": [
[
2019,
12
]
]
},
"assertion": [
{
"value": "Elsevier",
"name": "publisher",
"label": "This article is maintained by"
},
{
"value": "A brave new world for archaeological survey: Automated machine learning-based potsherd detection using high-resolution drone imagery",
"name": "articletitle",
"label": "Article Title"
},
{
"value": "Journal of Archaeological Science",
"name": "journaltitle",
"label": "Journal Title"
},
{
"value": "https://doi.org/10.1016/j.jas.2019.105013",
"name": "articlelink",
"label": "CrossRef DOI link to publisher maintained version"
},
{
"value": "article",
"name": "content_type",
"label": "Content Type"
},
{
"value": "© 2019 The Authors. Published by Elsevier Ltd.",
"name": "copyright",
"label": "Copyright"
}
],
"article-number": "105013"
}