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WIP: various refactors

This commit is contained in:
Claudio Atzori 2023-06-26 15:02:51 +02:00 committed by Sandro La Bruzzo
parent 649679de8d
commit 521dd7f167
5 changed files with 562 additions and 289 deletions
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32
dhp-pace-core/pom.xml
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@ -15,6 +15,38 @@
<version>1.2.5-SNAPSHOT</version>
<packaging>jar</packaging>
<build>
<plugins>
<plugin>
<groupId>net.alchim31.maven</groupId>
<artifactId>scala-maven-plugin</artifactId>
<version>4.0.1</version>
<executions>
<execution>
<id>scala-compile-first</id>
<phase>initialize</phase>
<goals>
<goal>add-source</goal>
<goal>compile</goal>
</goals>
</execution>
<execution>
<id>scala-test-compile</id>
<phase>process-test-resources</phase>
<goals>
<goal>testCompile</goal>
</goals>
</execution>
</executions>
<configuration>
<scalaVersion>${scala.version}</scalaVersion>
<addScalacArgs>-target:jvm-1.8</addScalacArgs>
</configuration>
</plugin>
</plugins>
</build>
<dependencies>
<dependency>
<groupId>edu.cmu</groupId>

2
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkBlockStats.java
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@ -20,12 +20,12 @@ import org.xml.sax.SAXException;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.dedup.model.BlockStats;
import eu.dnetlib.pace.model.SparkDedupConfig;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import eu.dnetlib.pace.config.DedupConfig;
import eu.dnetlib.pace.model.RowDataOrderingComparator;
import eu.dnetlib.pace.model.SparkDedupConfig;
public class SparkBlockStats extends AbstractSparkAction {

307
dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/jpath/JsonPathTest.java
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File diff suppressed because one or more lines are too long

269
dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/oa/dedup/jpath/dedup_conf_organization.json Normal file
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@ -0,0 +1,269 @@
{
"wf" : {
"threshold" : "0.99",
"dedupRun" : "001",
"entityType" : "organization",
"subEntityValue": "organization",
"orderField" : "legalname",
"queueMaxSize" : "2000",
"groupMaxSize" : "50",
"slidingWindowSize" : "200",
"idPath":"$.id",
"rootBuilder" : [ "organization", "projectOrganization_participation_isParticipant", "datasourceOrganization_provision_isProvidedBy" ],
"includeChildren" : "true",
"maxIterations": "20"
},
"pace" : {
"clustering" : [
{ "name" : "sortedngrampairs", "fields" : [ "legalname" ], "params" : { "max" : 2, "ngramLen" : "3"} },
{ "name" : "suffixprefix", "fields" : [ "legalname" ], "params" : { "max" : 1, "len" : "3" } },
{ "name" : "urlclustering", "fields" : [ "websiteurl" ], "params" : { } },
{ "name" : "keywordsclustering", "fields" : [ "legalname" ], "params" : { "max": 2, "windowSize": 4} }
],
"decisionTree" : {
"start": {
"fields": [
{
"field": "gridid",
"comparator": "exactMatch",
"weight": 1,
"countIfUndefined": "false",
"params": {}
}
],
"threshold": 1,
"aggregation": "AVG",
"positive": "MATCH",
"negative": "NO_MATCH",
"undefined": "layer2",
"ignoreUndefined": "false"
},
"layer2": {
"fields": [
{
"field": "websiteurl",
"comparator": "domainExactMatch",
"weight": 1,
"countIfUndefined": "false",
"params": {}
},
{
"field": "country",
"comparator": "exactMatch",
"weight": 1,
"countIfUndefined": "true",
"params": {}
},
{
"field": "legalname",
"comparator": "numbersMatch",
"weight": 1,
"countIfUndefined": "true",
"params": {}
},
{
"field": "legalname",
"comparator": "romansMatch",
"weight": 1,
"countIfUndefined": "true",
"params": {}
}
],
"threshold": 1,
"aggregation": "AND",
"positive": "layer3",
"negative": "NO_MATCH",
"undefined": "layer3",
"ignoreUndefined": "true"
},
"layer3": {
"fields": [
{
"field": "legalname",
"comparator": "cityMatch",
"weight": 1.0,
"countIfUndefined": "true",
"params": {
"windowSize": "4"
}
}
],
"threshold": 0.1,
"aggregation": "AVG",
"positive": "layer4",
"negative": "NO_MATCH",
"undefined": "NO_MATCH",
"ignoreUndefined": "true"
},
"layer4": {
"fields": [
{
"field": "legalname",
"comparator": "keywordMatch",
"weight": 1.0,
"countIfUndefined": "true",
"params": {
"windowSize": "4"
}
}
],
"threshold": 0.7,
"aggregation": "AVG",
"positive": "layer5",
"negative": "NO_MATCH",
"undefined": "layer5",
"ignoreUndefined": "true"
},
"layer5": {
"fields": [
{
"field": "legalname",
"comparator": "jaroWinklerNormalizedName",
"weight": 0.9,
"countIfUndefined": "true",
"params": {
"windowSize": "4"
}
},
{
"field": "legalshortname",
"comparator": "jaroWinklerNormalizedName",
"weight": 0.1,
"countIfUndefined": "false",
"params": {
"windowSize": 4
}
}
],
"threshold": 0.9,
"aggregation": "W_MEAN",
"positive": "MATCH",
"negative": "NO_MATCH",
"undefined": "NO_MATCH",
"ignoreUndefined": "true"
}
},
"model" : [
{ "name" : "country", "type" : "String", "path" : "$.country.classid"},
{ "name" : "legalshortname", "type" : "String", "path" : "$.legalshortname.value"},
{ "name" : "legalname", "type" : "String", "path" : "$.legalname.value" },
{ "name" : "websiteurl", "type" : "URL", "path" : "$.websiteurl.value" },
{ "name" : "gridid", "type" : "String", "path" : "$.pid[?(@.qualifier.classid =='grid')].value"},
{ "name" : "originalId", "type" : "String", "path" : "$.id" }
],
"blacklists" : {
"legalname" : []
},
"synonyms": {
"key::1": ["university","università", "universitas", "università studi","universitario","universitaria","université", "universite", "universitaire","universitaires","universidad","universitade","Universität","universitaet","Uniwersytet","университет","universiteit","πανεπιστήμιο","universitesi","universiteti", "universiti"],
"key::2": ["studies","studi","études","estudios","estudos","Studien","studia","исследования","studies","σπουδές"],
"key::3": ["advanced","superiore","supérieur","supérieure","supérieurs","supérieures","avancado","avancados","fortgeschrittene","fortgeschritten","zaawansowany","передовой","gevorderd","gevorderde","προχωρημένος","προχωρημένη","προχωρημένο","προχωρημένες","προχωρημένα","wyzsza"],
"key::4": ["institute","istituto","institut","instituto","instituto","Institut","instytut","институт","instituut","ινστιτούτο"],
"key::5": ["hospital","ospedale","hôpital","hospital","hospital","Krankenhaus","szpital","больница","ziekenhuis","νοσοκομείο"],
"key::6": ["research","ricerca","recherche","investigacion","pesquisa","Forschung","badania","исследования","onderzoek","έρευνα","erevna","erevnas"],
"key::7": ["college","collegio","colegio","faculdade","Hochschule","Szkoła Wyższa","Высшая школа","κολλέγιο"],
"key::8": ["foundation","fondazione","fondation","fundación","fundação","Stiftung","Fundacja","фонд","stichting","ίδρυμα","idryma"],
"key::9": ["center","centro","centre","centro","centro","zentrum","centrum","центр","centrum","κέντρο"],
"key::10": ["national","nazionale","national","nationale","nationaux","nationales","nacional","nacional","national","krajowy","национальный","nationaal","nationale","εθνικό"],
"key::11": ["association","associazione","association","asociación","associação","Verein","verband","stowarzyszenie","ассоциация","associatie"],
"key::12": ["society","societa","société","sociedad","sociedade","gesellschaft","społeczeństwo","общество","maatschappij","κοινωνία"],
"key::13": ["international","internazionale","international","internacional","internacional","international","międzynarodowy","Международный","internationaal","internationale","διεθνής","διεθνή","διεθνές"],
"key::14": ["community","comunita","communauté","comunidad","comunidade","Gemeinschaft","społeczność","сообщество","gemeenschap","κοινότητα"],
"key::15": ["school","scuola","école","escuela","escola","schule","Szkoła","школа","school","σχολείο"],
"key::16": ["education","educazione","éducation","educacion","Educação","Bildung","Edukacja","образование","opleiding","εκπαίδευση"],
"key::17": ["academy","accademia","académie","academia","academia","Akademie","akademie","академия","academie","ακαδημία"],
"key::18": ["public","pubblico","public","publique","publics","publiques","publico","publico","Öffentlichkeit","publiczny","публичный","publiek","publieke","δημόσιος","δημόσια","δημόσιο"],
"key::19": ["museum","museo","musée","mueso","museu","museum","muzeum","музей","museum","μουσείο"],
"key::20": ["group","gruppo","groupe","grupo","grupo","gruppe","grupa","группа","groep","ομάδα","όμιλος"],
"key::21": ["department","dipartimento","département","departamento","departamento","abteilung","departament","отдел","afdeling","τμήμα"],
"key::22": ["council","consiglio","conseil","Consejo","conselho","gesellschaft","rada","совет","raad","συμβούλιο"],
"key::23": ["library","biblioteca","bibliothèque","biblioteca","biblioteca","Bibliothek","biblioteka","библиотека","bibliotheek","βιβλιοθήκη"],
"key::24": ["ministry","ministero","ministère","ministerio","ministério","Ministerium","ministerstwo","министерство","ministerie","υπουργείο"],
"key::25": ["services","servizi","services","servicios","Serviços","Dienstleistungen","usługi","услуги","diensten","υπηρεσίες"],
"key::26": ["central","centrale","central","centrale","centrales","central","central","zentral","centralny","цетральный","centraal","κεντρικός","κεντρική","κεντρικό","κεντρικά"],
"key::27": ["general","generale","général","générale","généraux","générales","general","geral","general","Allgemeines","general","общий","algemeen","algemene","γενικός","γενική","γενικό","γενικά"],
"key::28": ["applied","applicati","appliqué","appliquée","appliqués","appliquées","aplicado","aplicada","angewendet","stosowany","прикладной","toegepast","toegepaste","εφαρμοσμένος","εφαρμοσμένη","εφαρμοσμένο","εφαρμοσμένα"],
"key::29": ["european","europee","europea","européen","européenne","européens","européennes","europeo","europeu","europäisch","europejski","европейский","Europees","Europese","ευρωπαϊκός","ευρωπαϊκή","ευρωπαϊκό","ευρωπαϊκά"],
"key::30": ["agency","agenzia","agence","agencia","agencia","agentur","agencja","агенция","agentschap","πρακτορείο"],
"key::31": ["laboratory","laboratorio","laboratoire","laboratorio","laboratorio","labor","laboratorium","лаборатория","laboratorium","εργαστήριο"],
"key::32": ["industry","industria","industrie","индустрия","industrie","βιομηχανία"],
"key::33": ["industrial","industriale","industriel","industrielle","industriels","industrielles","индустриальный","industrieel","βιομηχανικός","βιομηχανική","βιομηχανικό","βιομηχανικά","βιομηχανικές"],
"key::34": ["consortium","consorzio","consortium","консорциум","consortium","κοινοπραξία"],
"key::35": ["organization","organizzazione","organisation","organización","organização","organizacja","организация","organisatie","οργανισμός"],
"key::36": ["authority","autorità","autorité","авторитет","autoriteit"],
"key::37": ["federation","federazione","fédération","федерация","federatie","ομοσπονδία"],
"key::38": ["observatory","osservatorio","observatoire","обсерватория","observatorium","αστεροσκοπείο"],
"key::39": ["bureau","ufficio","bureau","офис","bureau","γραφείο"],
"key::40": ["company","impresa","compagnie","société","компания","bedrijf","εταιρία"],
"key::41": ["polytechnic","politecnico","polytechnique","политехника","polytechnisch","πολυτεχνείο","universita politecnica","polytechnic university","universidad politecnica","universitat politecnica","politechnika","politechniki","university technology","university science technology"],
"key::42": ["coalition","coalizione","coalition","коалиция","coalitie","συνασπισμός"],
"key::43": ["initiative","iniziativa","initiative","инициатива","initiatief","πρωτοβουλία"],
"key::44": ["academic","accademico","académique","universitaire","акадеческий academisch","ακαδημαϊκός","ακαδημαϊκή","ακαδημαϊκό","ακαδημαϊκές","ακαδημαϊκοί"],
"key::45": ["institution","istituzione","institution","институциональный","instelling","ινστιτούτο"],
"key::46": ["division","divisione","division","отделение","divisie","τμήμα"],
"key::47": ["committee","comitato","comité","комитет","commissie","επιτροπή"],
"key::48": ["promotion","promozione","продвижение","proothisis","forderung"],
"key::49": ["medical","medicine","clinical","medicina","clinici","médico","medicina","clínica","médico","medicina","clínica","medizinisch","Medizin","klinisch","medisch","geneeskunde","klinisch","ιατρικός","ιατρική","ιατρικό","ιατρικά","κλινικός","κλινική","κλινικό","κλινικά","tıbbi","tıp","klinik","orvosi","orvostudomány","klinikai","zdravniški","medicinski","klinični","meditsiini","kliinik","kliiniline"],
"key::50": ["technology","technological","tecnologia","tecnologie","tecnología","tecnológico","tecnologia","tecnológico","Technologie","technologisch","technologie","technologisch","τεχνολογία","τεχνολογικός","τεχνολογική","τεχνολογικό","teknoloji","teknolojik","technológia","technológiai","tehnologija","tehnološki","tehnoloogia","tehnoloogiline","technologii","technical","texniki","teknik"],
"key::51": ["science","scientific","scienza","scientifiche","scienze","ciencia","científico","ciência","científico","Wissenschaft","wissenschaftlich","wetenschap","wetenschappelijk","επιστήμη","επιστημονικός","επιστημονική","επιστημονικό","επιστημονικά","bilim","bilimsel","tudomány","tudományos","znanost","znanstveni","teadus","teaduslik",""],
"key::52": ["engineering","ingegneria","ingeniería","engenharia","Ingenieurwissenschaft","ingenieurswetenschappen","bouwkunde","μηχανικός","μηχανική","μηχανικό","mühendislik","mérnöki","Inženirstvo","inseneeria","inseneri",""],
"key::53": ["management","gestione","gestionale","gestionali","gestión","administración","gestão","administração","Verwaltung","management","διαχείριση","yönetim","menedzsment","vodstvo","upravljanje","management","juhtkond","juhtimine","haldus",""],
"key::54": ["energy","energia","energía","energia","Energie","energie","ενέργεια","enerji","energia","energija","energia",""],
"key::55": ["agricultural","agriculture","agricoltura","agricole","agrícola","agricultura","agrícola","agricultura","landwirtschaftlich","Landwirtschaft","landbouwkundig","landbouw","αγροτικός","αγροτική","αγροτικό","γεωργικός","γεωργική","γεωργικό","γεωργία","tarımsal","tarım","mezőgazdasági","mezőgazdaság","poljedelski","poljedelstvo","põllumajandus","põllumajanduslik",""],
"key::56": ["information","informazione","información","informação","Information","informatie","πληροφορία","bilgi","információ","informacija","informatsioon","informatycznych",""],
"key::57": ["social","sociali","social","social","Sozial","sociaal","maatschappelijk","κοινωνικός","κοινωνική","κοινωνικό","κοινωνικά","sosyal","szociális","družbeni","sotsiaal","sotsiaalne",""],
"key::58": ["environmental","ambiente","medioambiental","ambiente","medioambiente","meioambiente","Umwelt","milieu","milieuwetenschap","milieukunde","περιβαλλοντικός","περιβαλλοντική","περιβαλλοντικό","περιβαλλοντικά","çevre","környezeti","okoliški","keskonna",""],
"key::59": ["business","economia","economiche","economica","negocio","empresa","negócio","Unternehmen","bedrijf","bedrijfskunde","επιχείρηση","iş","üzleti","posel","ettevõte/äri",""],
"key::60": ["pharmaceuticals","pharmacy","farmacia","farmaceutica","farmacéutica","farmacia","farmacêutica","farmácia","Pharmazeutika","Arzneimittelkunde","farmaceutica","geneesmiddelen","apotheek","φαρμακευτικός","φαρμακευτική","φαρμακευτικό","φαρμακευτικά","φαρμακείο","ilaç","eczane","gyógyszerészeti","gyógyszertár","farmacevtika","lekarništvo","farmaatsia","farmatseutiline",""],
"key::61": ["healthcare","health services","salute","atenciónmédica","cuidadodelasalud","cuidadoscomasaúde","Gesundheitswesen","gezondheidszorg","ιατροφαρμακευτικήπερίθαλψη","sağlıkhizmeti","egészségügy","zdravstvo","tervishoid","tervishoiu",""],
"key::62": ["history","storia","historia","história","Geschichte","geschiedenis","geschiedkunde","ιστορία","tarih","történelem","zgodovina","ajalugu",""],
"key::63": ["materials","materiali","materia","materiales","materiais","materialen","υλικά","τεκμήρια","malzemeler","anyagok","materiali","materjalid","vahendid",""],
"key::64": ["economics","economia","economiche","economica","economía","economia","Wirtschaft","economie","οικονομικά","οικονομικέςεπιστήμες","ekonomi","közgazdaságtan","gospodarstvo","ekonomija","majanduslik","majandus",""],
"key::65": ["therapeutics","terapeutica","terapéutica","terapêutica","therapie","θεραπευτική","tedavibilimi","gyógykezelés","terapevtika","terapeutiline","ravi",""],
"key::66": ["oncology","oncologia","oncologico","oncología","oncologia","Onkologie","oncologie","ογκολογία","onkoloji","onkológia","onkologija","onkoloogia",""],
"key::67": ["natural","naturali","naturale","natural","natural","natürlich","natuurlijk","φυσικός","φυσική","φυσικό","φυσικά","doğal","természetes","naraven","loodus",""],
"key::68": ["educational","educazione","pedagogia","educacional","educativo","educacional","pädagogisch","educatief","εκπαιδευτικός","εκπαιδευτική","εκπαιδευτικό","εκπαιδευτικά","eğitimsel","oktatási","izobraževalen","haridus","hariduslik",""],
"key::69": ["biomedical","biomedica","biomédico","biomédico","biomedizinisch","biomedisch","βιοιατρικός","βιοιατρική","βιοιατρικό","βιοιατρικά","biyomedikal","orvosbiológiai","biomedicinski","biomeditsiiniline",""],
"key::70": ["veterinary","veterinaria","veterinarie","veterinaria","veterinária","tierärtzlich","veterinair","veeartsenijlkunde","κτηνιατρικός","κτηνιατρική","κτηνιατρικό","κτηνιατρικά","veteriner","állatorvosi","veterinar","veterinarski","veterinaaria",""],
"key::71": ["chemistry","chimica","química","química","Chemie","chemie","scheikunde","χημεία","kimya","kémia","kemija","keemia",""],
"key::72": ["security","sicurezza","seguridad","segurança","Sicherheit","veiligheid","ασφάλεια","güvenlik","biztonsági","varnost","turvalisus","julgeolek",""],
"key::73": ["biotechnology","biotecnologia","biotecnologie","biotecnología","biotecnologia","Biotechnologie","biotechnologie","βιοτεχνολογία","biyoteknoloji","biotechnológia","biotehnologija","biotehnoloogia",""],
"key::74": ["military","militare","militari","militar","militar","Militär","militair","leger","στρατιωτικός","στρατιωτική","στρατιωτικό","στρατιωτικά","askeri","katonai","vojaški","vojni","militaar","wojskowa",""],
"key::75": ["theological","teologia","teologico","teológico","tecnológica","theologisch","theologisch","θεολογικός","θεολογική","θεολογικό","θεολογικά","teolojik","technológiai","teološki","teoloogia","usuteadus","teoloogiline",""],
"key::76": ["electronics","elettronica","electrónica","eletrônicos","Elektronik","elektronica","ηλεκτρονική","elektronik","elektronika","elektronika","elektroonika",""],
"key::77": ["forestry","forestale","forestali","silvicultura","forestal","floresta","Forstwirtschaft","bosbouw","δασοκομία","δασολογία","ormancılık","erdészet","gozdarstvo","metsandus",""],
"key::78": ["maritime","marittima","marittime","marittimo","marítimo","marítimo","maritiem","ναυτικός","ναυτική","ναυτικό","ναυτικά","ναυτιλιακός","ναυτιλιακή","ναυτιλιακό","ναυτιλιακά","θαλάσσιος","θαλάσσια","θαλάσσιο","denizcilik","tengeri","morski","mere","merendus",""],
"key::79": ["sports","sport","deportes","esportes","Sport","sport","sportwetenschappen","άθληση","γυμναστικήδραστηριότητα","spor","sport","šport","sport","spordi",""],
"key::80": ["surgery","chirurgia","chirurgiche","cirugía","cirurgia","Chirurgie","chirurgie","heelkunde","εγχείρηση","επέμβαση","χειρουργικήεπέμβαση","cerrahi","sebészet","kirurgija","kirurgia",""],
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"key::106" : ["seminary", "seminario", "seminaire", "seminar"],
"key::107" : ["agricultural forestry", "af", "a f"],
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}
}
}

241
dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/oa/dedup/jpath/organization.json Normal file
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@ -0,0 +1,241 @@
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