From 262d7c581b56244cc3eab179bcb3ad82ba6174ae Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 31 Oct 2023 14:34:10 +0100 Subject: [PATCH 1/2] [graph cleaning] implemented further suggestions from https://support.openaire.eu/issues/8898 --- .../oaf/utils/GraphCleaningFunctions.java | 95 +++++++++++++++++-- .../graph/clean/CleanGraphSparkJobTest.java | 15 +++ .../clean/graph/publication/publication.json | 2 +- 3 files changed, 103 insertions(+), 9 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java index b4402a2fb..e8bada028 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java @@ -3,16 +3,20 @@ package eu.dnetlib.dhp.schema.oaf.utils; import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.getProvenance; +import java.net.MalformedURLException; +import java.net.URL; import java.time.LocalDate; import java.time.ZoneId; import java.time.format.DateTimeFormatter; import java.time.format.DateTimeParseException; import java.util.*; import java.util.function.Function; +import java.util.function.Supplier; import java.util.stream.Collectors; import java.util.stream.Stream; import org.apache.commons.lang3.StringUtils; +import org.apache.cxf.common.util.UrlUtils; import com.github.sisyphsu.dateparser.DateParserUtils; import com.google.common.collect.Lists; @@ -23,6 +27,7 @@ import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; import me.xuender.unidecode.Unidecode; +import sun.awt.HKSCS; public class GraphCleaningFunctions extends CleaningFunctions { @@ -36,6 +41,13 @@ public class GraphCleaningFunctions extends CleaningFunctions { public static final int TITLE_FILTER_RESIDUAL_LENGTH = 5; private static final String NAME_CLEANING_REGEX = "[\\r\\n\\t\\s]+"; + + private static final Set INVALID_AUTHOR_NAMES = new HashSet<>(); + + private static final Set INVALID_URLS = new HashSet<>(); + + private static final Set INVALID_URL_HOSTS = new HashSet<>(); + private static final HashSet PEER_REVIEWED_TYPES = new HashSet<>(); static { @@ -48,6 +60,47 @@ public class GraphCleaningFunctions extends CleaningFunctions { PEER_REVIEWED_TYPES.add("Thesis"); PEER_REVIEWED_TYPES.add("Bachelor thesis"); PEER_REVIEWED_TYPES.add("Conference object"); + + INVALID_AUTHOR_NAMES.add("(:null)"); + INVALID_AUTHOR_NAMES.add("(:unap)"); + INVALID_AUTHOR_NAMES.add("(:tba)"); + INVALID_AUTHOR_NAMES.add("(:unas)"); + INVALID_AUTHOR_NAMES.add("(:unav)"); + INVALID_AUTHOR_NAMES.add("(:unkn)"); + INVALID_AUTHOR_NAMES.add("(:unkn) unknown"); + INVALID_AUTHOR_NAMES.add(":none"); + INVALID_AUTHOR_NAMES.add(":null"); + INVALID_AUTHOR_NAMES.add(":unas"); + INVALID_AUTHOR_NAMES.add(":unav"); + INVALID_AUTHOR_NAMES.add(":unkn"); + INVALID_AUTHOR_NAMES.add("[autor desconocido]"); + INVALID_AUTHOR_NAMES.add("[s. n.]"); + INVALID_AUTHOR_NAMES.add("[s.n]"); + INVALID_AUTHOR_NAMES.add("[unknown]"); + INVALID_AUTHOR_NAMES.add("anonymous"); + INVALID_AUTHOR_NAMES.add("n.n."); + INVALID_AUTHOR_NAMES.add("nn"); + INVALID_AUTHOR_NAMES.add("no name supplied"); + INVALID_AUTHOR_NAMES.add("none"); + INVALID_AUTHOR_NAMES.add("none available"); + INVALID_AUTHOR_NAMES.add("not available not available"); + INVALID_AUTHOR_NAMES.add("null &na;"); + INVALID_AUTHOR_NAMES.add("null anonymous"); + INVALID_AUTHOR_NAMES.add("unbekannt"); + INVALID_AUTHOR_NAMES.add("unknown"); + + INVALID_URL_HOSTS.add("creativecommons.org"); + INVALID_URL_HOSTS.add("www.academia.edu"); + INVALID_URL_HOSTS.add("academia.edu"); + INVALID_URL_HOSTS.add("researchgate.net"); + INVALID_URL_HOSTS.add("www.researchgate.net"); + + INVALID_URLS.add("http://repo.scoap3.org/api"); + INVALID_URLS.add("http://ora.ox.ac.uk/objects/uuid:"); + INVALID_URLS.add("http://ntur.lib.ntu.edu.tw/news/agent_contract.pdf"); + INVALID_URLS.add("https://media.springer.com/full/springer-instructions-for-authors-assets/pdf/SN_BPF_EN.pdf"); + INVALID_URLS.add("http://www.tobaccoinduceddiseases.org/dl/61aad426c96519bea4040a374c6a6110/"); + INVALID_URLS.add("https://www.bilboard.nl/verenigingsbladen/bestuurskundige-berichten"); } public static T cleanContext(T value, String contextId, String verifyParam) { @@ -558,6 +611,15 @@ public class GraphCleaningFunctions extends CleaningFunctions { ModelConstants.DATASET_RESULTTYPE_CLASSID.equals(r.getResulttype().getClassid()))) { i.setFulltext(null); } + if (Objects.nonNull(i.getUrl())) { + i + .setUrl( + i + .getUrl() + .stream() + .filter(GraphCleaningFunctions::urlFilter) + .collect(Collectors.toList())); + } } } if (Objects.isNull(r.getBestaccessright()) @@ -580,8 +642,7 @@ public class GraphCleaningFunctions extends CleaningFunctions { .getAuthor() .stream() .filter(Objects::nonNull) - .filter(a -> StringUtils.isNotBlank(a.getFullname())) - .filter(a -> StringUtils.isNotBlank(a.getFullname().replaceAll("[\\W]", ""))) + .filter(GraphCleaningFunctions::isValidAuthorName) .map(GraphCleaningFunctions::cleanupAuthor) .collect(Collectors.toList())); @@ -739,12 +800,30 @@ public class GraphCleaningFunctions extends CleaningFunctions { // HELPERS private static boolean isValidAuthorName(Author a) { - return !Stream - .of(a.getFullname(), a.getName(), a.getSurname()) - .filter(s -> s != null && !s.isEmpty()) - .collect(Collectors.joining("")) - .toLowerCase() - .matches(INVALID_AUTHOR_REGEX); + return StringUtils.isNotBlank(a.getFullname()) && + StringUtils.isNotBlank(a.getFullname().replaceAll("[\\W]", "")) && + !INVALID_AUTHOR_NAMES.contains(StringUtils.lowerCase(a.getFullname()).trim()) && + !Stream + .of(a.getFullname(), a.getName(), a.getSurname()) + .filter(StringUtils::isNotBlank) + .collect(Collectors.joining("")) + .toLowerCase() + .matches(INVALID_AUTHOR_REGEX); + } + + private static boolean urlFilter(String u) { + try { + final URL url = new URL(u); + if (StringUtils.isBlank(url.getPath()) || "/".equals(url.getPath())) { + return false; + } + if (INVALID_URL_HOSTS.contains(url.getHost())) { + return false; + } + return !INVALID_URLS.contains(url.toString()); + } catch (MalformedURLException ex) { + return false; + } } private static List processPidCleaning(List pids) { diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java index 65182108e..a1a4c29cd 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java @@ -251,9 +251,19 @@ public class CleanGraphSparkJobTest { .filter(String.format("id = '%s'", id)) .first(); + final Set invalidURLs = new HashSet<>(); + invalidURLs.add("http://academia.edu/abcd"); + invalidURLs.add("http://repo.scoap3.org/api"); + invalidURLs.add("http://hdl.handle.net/"); + assertNull(p_in.getBestaccessright()); assertTrue(p_in instanceof Result); assertTrue(p_in instanceof Publication); + assertNotNull(p_in.getAuthor()); + assertEquals(14, p_in.getAuthor().size()); + assertNotNull(p_in.getInstance()); + assertNotNull(p_in.getInstance().get(0)); + assertEquals(3, p_in.getInstance().get(0).getUrl().stream().filter(invalidURLs::contains).count()); new CleanGraphSparkJob( args( @@ -273,6 +283,9 @@ public class CleanGraphSparkJobTest { assertNull(p.getPublisher()); + assertNotNull(p.getAuthor()); + assertEquals(12, p.getAuthor().size()); + assertEquals("und", p.getLanguage().getClassid()); assertEquals("Undetermined", p.getLanguage().getClassname()); @@ -364,6 +377,8 @@ public class CleanGraphSparkJobTest { .stream() .anyMatch(s -> s.getValue().equals("10.1009/qwerty"))); + assertTrue(p.getInstance().get(0).getUrl().stream().noneMatch(invalidURLs::contains)); + assertNotNull(p.getSubject()); List fos_subjects = p diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/graph/publication/publication.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/graph/publication/publication.json index e5d7c88db..e2a2b9449 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/graph/publication/publication.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/graph/publication/publication.json @@ -1,4 +1,4 @@ -{"id":"50|CSC_________::2250a70c903c6ac6e4c01438259e9375","author":[{"affiliation":[],"fullname":"Brien, Tom","name":"Tom","pid":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"sysimport:crosswalk:datasetarchive","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"ORCID12","classname":"ORCID12","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"0000-0001-9613-6639"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"sysimport:crosswalk:datasetarchive","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"ORCID12","classname":"ORCID12","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"https://orcid.org/0000-0001-9613-6639"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"orcid","classname":"ORCID12","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"0000-0001-9613-6639"}],"rank":1,"surname":"Brien"},{"affiliation":[],"fullname":"Ade, Peter","name":"Peter","pid":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"sysimport:crosswalk:datasetarchive","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"xyz","classname":"XYZ","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"qwerty"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"sysimport:crosswalk:datasetarchive","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"ORCID","classname":"ORCID","schemeid":"","schemename":""},"value":"asdasd"}],"rank":2,"surname":"Ade"},{"affiliation":[],"fullname":"Barry, Peter S.","name":"Peter S.","pid":null,"rank":3,"surname":"Barry"},{"affiliation":[],"fullname":"Dunscombe, Chris J.","name":"Chris J.","pid":[],"rank":4,"surname":"Dunscombe"},{"affiliation":[],"fullname":"Leadley, David R.","name":"David R.","pid":[],"rank":5,"surname":"Leadley"},{"affiliation":[],"fullname":"Morozov, Dmitry V.","name":"Dmitry V.","pid":[],"rank":6,"surname":"Morozov"},{"affiliation":[],"fullname":"Myronov, Maksym","name":"Maksym","pid":[],"rank":7,"surname":"Myronov"},{"affiliation":[],"fullname":"Parker, Evan","name":"Evan","pid":[],"rank":8,"surname":"Parker"},{"affiliation":[],"fullname":"Prest, Martin J.","name":"Martin J.","pid":[],"rank":9,"surname":"Prest"},{"affiliation":[],"fullname":"Prunnila, Mika","name":"Mika","pid":[],"rank":10,"surname":"Prunnila"},{"affiliation":[],"fullname":"Sudiwala, Rashmi V.","name":"Rashmi V.","pid":[],"rank":11,"surname":"Sudiwala"},{"affiliation":[],"fullname":"Whall, Terry E.","name":"Terry E.","pid":[],"rank":12,"surname":"Whall"},{"affiliation":[],"fullname":"Mauskopf","name":"","pid":[],"rank":13,"surname":""},{"affiliation":[],"fullname":" P. 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deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java index e8bada028..7a8acbd36 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java @@ -11,12 +11,10 @@ import java.time.format.DateTimeFormatter; import java.time.format.DateTimeParseException; import java.util.*; import java.util.function.Function; -import java.util.function.Supplier; import java.util.stream.Collectors; import java.util.stream.Stream; import org.apache.commons.lang3.StringUtils; -import org.apache.cxf.common.util.UrlUtils; import com.github.sisyphsu.dateparser.DateParserUtils; import com.google.common.collect.Lists; @@ -27,7 +25,6 @@ import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; import me.xuender.unidecode.Unidecode; -import sun.awt.HKSCS; public class GraphCleaningFunctions extends CleaningFunctions {