From fcbb4c148929c06756756f18a14cece1a5c232b3 Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Wed, 24 Jun 2020 16:29:32 +0200 Subject: [PATCH 01/37] parser of orcid publication data from xml original dump --- dhp-workflows/dhp-doiboost/pom.xml | 6 + .../doiboost/orcid/model/AuthorData.java | 9 + .../orcidnodoi/model/Contributor.java | 54 +++ .../doiboost/orcidnodoi/model/ExternalId.java | 32 ++ .../orcidnodoi/model/PublicationDate.java | 32 ++ .../orcidnodoi/model/WorkDataNoDoi.java | 101 ++++++ .../orcidnodoi/xml/XMLRecordParserNoDoi.java | 216 ++++++++++++ .../orcid/xml/XMLRecordParserTest.java | 2 +- .../orcidnodoi/xml/OrcidNoDoiTest.java | 326 ++++++++++++++++++ .../xml/activity_work_0000-0003-2760-1191.xml | 106 ++++++ .../xml/activity_work_0000-0002-5982-8983.xml | 0 ...ty_work_0000-0003-2760-1191-similarity.xml | 113 ++++++ .../xml/activity_work_0000-0003-2760-1191.xml | 106 ++++++ 13 files changed, 1102 insertions(+), 1 deletion(-) create mode 100644 dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/Contributor.java create mode 100644 dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/ExternalId.java create mode 100644 dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/PublicationDate.java create mode 100644 dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/WorkDataNoDoi.java create mode 100644 dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/xml/XMLRecordParserNoDoi.java create mode 100644 dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/xml/OrcidNoDoiTest.java create mode 100644 dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/xml/activity_work_0000-0003-2760-1191.xml rename dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/{orcid => orcidnodoi}/xml/activity_work_0000-0002-5982-8983.xml (100%) create mode 100644 dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/xml/activity_work_0000-0003-2760-1191-similarity.xml create mode 100644 dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/xml/activity_work_0000-0003-2760-1191.xml diff --git a/dhp-workflows/dhp-doiboost/pom.xml b/dhp-workflows/dhp-doiboost/pom.xml index 39bb81ec1..2662d0a39 100644 --- a/dhp-workflows/dhp-doiboost/pom.xml +++ b/dhp-workflows/dhp-doiboost/pom.xml @@ -84,6 +84,12 @@ spark-sql_2.11 + + org.apache.commons + commons-text + 1.8 + + diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/model/AuthorData.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/model/AuthorData.java index 29551c347..87f1f65c8 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/model/AuthorData.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/model/AuthorData.java @@ -9,6 +9,7 @@ public class AuthorData implements Serializable { private String name; private String surname; private String creditName; + private String otherName; private String errorCode; public String getErrorCode() { @@ -50,4 +51,12 @@ public class AuthorData implements Serializable { public void setOid(String oid) { this.oid = oid; } + + public String getOtherName() { + return otherName; + } + + public void setOtherName(String otherName) { + this.otherName = otherName; + } } diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/Contributor.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/Contributor.java new file mode 100644 index 000000000..42076de5d --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/Contributor.java @@ -0,0 +1,54 @@ + +package eu.dnetlib.doiboost.orcidnodoi.model; + +import java.io.Serializable; + +import eu.dnetlib.doiboost.orcid.model.AuthorData; + +public class Contributor extends AuthorData implements Serializable { + private String sequence; + private String role; + private boolean simpleMatch = false; + private Double score = 0.0; + private boolean bestMatch = false; + + public String getSequence() { + return sequence; + } + + public void setSequence(String sequence) { + this.sequence = sequence; + } + + public String getRole() { + return role; + } + + public void setRole(String role) { + this.role = role; + } + + public boolean isSimpleMatch() { + return simpleMatch; + } + + public void setSimpleMatch(boolean simpleMatch) { + this.simpleMatch = simpleMatch; + } + + public Double getScore() { + return score; + } + + public void setScore(Double score) { + this.score = score; + } + + public boolean isBestMatch() { + return bestMatch; + } + + public void setBestMatch(boolean bestMatch) { + this.bestMatch = bestMatch; + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/ExternalId.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/ExternalId.java new file mode 100644 index 000000000..865e54ae3 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/ExternalId.java @@ -0,0 +1,32 @@ + +package eu.dnetlib.doiboost.orcidnodoi.model; + +public class ExternalId { + private String type; + private String value; + private String relationShip; + + public String getType() { + return type; + } + + public void setType(String type) { + this.type = type; + } + + public String getValue() { + return value; + } + + public void setValue(String value) { + this.value = value; + } + + public String getRelationShip() { + return relationShip; + } + + public void setRelationShip(String relationShip) { + this.relationShip = relationShip; + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/PublicationDate.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/PublicationDate.java new file mode 100644 index 000000000..9282a80ba --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/PublicationDate.java @@ -0,0 +1,32 @@ + +package eu.dnetlib.doiboost.orcidnodoi.model; + +public class PublicationDate { + private String year; + private String month; + private String day; + + public String getYear() { + return year; + } + + public void setYear(String year) { + this.year = year; + } + + public String getMonth() { + return month; + } + + public void setMonth(String month) { + this.month = month; + } + + public String getDay() { + return day; + } + + public void setDay(String day) { + this.day = day; + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/WorkDataNoDoi.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/WorkDataNoDoi.java new file mode 100644 index 000000000..ee13454e1 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/WorkDataNoDoi.java @@ -0,0 +1,101 @@ + +package eu.dnetlib.doiboost.orcidnodoi.model; + +import java.io.Serializable; +import java.util.List; + +public class WorkDataNoDoi implements Serializable { + + private String oid; + private String id; + private String sourceName; + private String type; + private List titles; + private List urls; + List extIds; + List publicationDates; + List contributors; + + public String getOid() { + return oid; + } + + public void setOid(String oid) { + this.oid = oid; + } + + public String getErrorCode() { + return errorCode; + } + + public void setErrorCode(String errorCode) { + this.errorCode = errorCode; + } + + private String errorCode; + + public String getId() { + return id; + } + + public void setId(String id) { + this.id = id; + } + + public List getTitles() { + return titles; + } + + public void setTitles(List titles) { + this.titles = titles; + } + + public String getSourceName() { + return sourceName; + } + + public void setSourceName(String sourceName) { + this.sourceName = sourceName; + } + + public String getType() { + return type; + } + + public void setType(String type) { + this.type = type; + } + + public List getUrls() { + return urls; + } + + public void setUrls(List urls) { + this.urls = urls; + } + + public List getExtIds() { + return extIds; + } + + public void setExtIds(List extIds) { + this.extIds = extIds; + } + + public List getPublicationDates() { + return publicationDates; + } + + public void setPublicationDates(List publicationDates) { + this.publicationDates = publicationDates; + } + + public List getContributors() { + return contributors; + } + + public void setContributors(List contributors) { + this.contributors = contributors; + } + +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/xml/XMLRecordParserNoDoi.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/xml/XMLRecordParserNoDoi.java new file mode 100644 index 000000000..6e5771547 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/xml/XMLRecordParserNoDoi.java @@ -0,0 +1,216 @@ + +package eu.dnetlib.doiboost.orcidnodoi.xml; + +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.ximpleware.*; + +import eu.dnetlib.dhp.parser.utility.VtdException; +import eu.dnetlib.dhp.parser.utility.VtdUtilityParser; +import eu.dnetlib.doiboost.orcidnodoi.model.Contributor; +import eu.dnetlib.doiboost.orcidnodoi.model.ExternalId; +import eu.dnetlib.doiboost.orcidnodoi.model.PublicationDate; +import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi; + +public class XMLRecordParserNoDoi { + + private static final Logger logger = LoggerFactory.getLogger(XMLRecordParserNoDoi.class); + + private static final String NS_COMMON_URL = "http://www.orcid.org/ns/common"; + private static final String NS_COMMON = "common"; + private static final String NS_PERSON_URL = "http://www.orcid.org/ns/person"; + private static final String NS_PERSON = "person"; + private static final String NS_DETAILS_URL = "http://www.orcid.org/ns/personal-details"; + private static final String NS_DETAILS = "personal-details"; + private static final String NS_OTHER_URL = "http://www.orcid.org/ns/other-name"; + private static final String NS_OTHER = "other-name"; + private static final String NS_RECORD_URL = "http://www.orcid.org/ns/record"; + private static final String NS_RECORD = "record"; + private static final String NS_ERROR_URL = "http://www.orcid.org/ns/error"; + + private static final String NS_WORK = "work"; + private static final String NS_WORK_URL = "http://www.orcid.org/ns/work"; + + private static final String NS_ERROR = "error"; + + public static WorkDataNoDoi VTDParseWorkData(byte[] bytes) + throws VtdException, EncodingException, EOFException, EntityException, ParseException, XPathParseException, + NavException, XPathEvalException { + logger.info("parsing xml ..."); + final VTDGen vg = new VTDGen(); + vg.setDoc(bytes); + vg.parse(true); + final VTDNav vn = vg.getNav(); + final AutoPilot ap = new AutoPilot(vn); + ap.declareXPathNameSpace(NS_COMMON, NS_COMMON_URL); + ap.declareXPathNameSpace(NS_WORK, NS_WORK_URL); + ap.declareXPathNameSpace(NS_ERROR, NS_ERROR_URL); + + WorkDataNoDoi workData = new WorkDataNoDoi(); + final List errors = VtdUtilityParser.getTextValue(ap, vn, "//error:response-code"); + if (!errors.isEmpty()) { + workData.setErrorCode(errors.get(0)); + return workData; + } + + List workNodes = VtdUtilityParser + .getTextValuesWithAttributes(ap, vn, "//work:work", Arrays.asList("path", "put-code")); + if (!workNodes.isEmpty()) { + final String oid = (workNodes.get(0).getAttributes().get("path")).split("/")[1]; + workData.setOid(oid); + final String id = (workNodes.get(0).getAttributes().get("put-code")); + workData.setId(id); + } else { + return null; + } + + final List titles = VtdUtilityParser + .getTextValue( + ap, vn, "//common:title"); + if (!titles.isEmpty()) { + workData.setTitles(titles); + } + + final List sourceNames = VtdUtilityParser + .getTextValue( + ap, vn, "//common:source-name"); + if (!sourceNames.isEmpty()) { + workData.setSourceName(sourceNames.get(0)); + } + + final List types = VtdUtilityParser + .getTextValue( + ap, vn, "//work:type"); + if (!types.isEmpty()) { + workData.setType(types.get(0)); + } + + final List urls = VtdUtilityParser + .getTextValue( + ap, vn, "//common:url"); + if (!urls.isEmpty()) { + workData.setUrls(urls); + } + + workData.setPublicationDates(getPublicationDates(vg, vn, ap)); + workData.setExtIds(getExternalIds(vg, vn, ap)); + workData.setContributors(getContributors(vg, vn, ap)); + return workData; + + } + + private static List getPublicationDates(VTDGen vg, VTDNav vn, AutoPilot ap) + throws XPathParseException, NavException, XPathEvalException { + List publicationDates = new ArrayList(); + int yearIndex = 0; + ap.selectXPath("//common:publication-date/common:year"); + while (ap.evalXPath() != -1) { + PublicationDate publicationDate = new PublicationDate(); + int t = vn.getText(); + if (t >= 0) { + publicationDate.setYear(vn.toNormalizedString(t)); + publicationDates.add(yearIndex, publicationDate); + yearIndex++; + } + } + int monthIndex = 0; + ap.selectXPath("//common:publication-date/common:month"); + while (ap.evalXPath() != -1) { + int t = vn.getText(); + if (t >= 0) { + publicationDates.get(monthIndex).setMonth(vn.toNormalizedString(t)); + monthIndex++; + } + } + int dayIndex = 0; + ap.selectXPath("//common:publication-date/common:day"); + while (ap.evalXPath() != -1) { + int t = vn.getText(); + if (t >= 0) { + publicationDates.get(dayIndex).setDay(vn.toNormalizedString(t)); + dayIndex++; + } + } + return publicationDates; + } + + private static List getExternalIds(VTDGen vg, VTDNav vn, AutoPilot ap) + throws XPathParseException, NavException, XPathEvalException { + List extIds = new ArrayList(); + int typeIndex = 0; + ap.selectXPath("//common:external-id/common:external-id-type"); + while (ap.evalXPath() != -1) { + ExternalId extId = new ExternalId(); + int t = vn.getText(); + if (t >= 0) { + extId.setType(vn.toNormalizedString(t)); + extIds.add(typeIndex, extId); + typeIndex++; + } + } + int valueIndex = 0; + ap.selectXPath("//common:external-id/common:external-id-value"); + while (ap.evalXPath() != -1) { + int t = vn.getText(); + if (t >= 0) { + extIds.get(valueIndex).setValue(vn.toNormalizedString(t)); + valueIndex++; + } + } + int relationshipIndex = 0; + ap.selectXPath("//common:external-id/common:external-id-relationship"); + while (ap.evalXPath() != -1) { + int t = vn.getText(); + if (t >= 0) { + extIds.get(relationshipIndex).setRelationShip(vn.toNormalizedString(t)); + relationshipIndex++; + } + } + if (typeIndex == valueIndex) { + return extIds; + } + return new ArrayList(); + } + + private static List getContributors(VTDGen vg, VTDNav vn, AutoPilot ap) + throws XPathParseException, NavException, XPathEvalException { + List contributors = new ArrayList(); + int nameIndex = 0; + ap.selectXPath("//work:contributor/work:credit-name"); + while (ap.evalXPath() != -1) { + Contributor contributor = new Contributor(); + int t = vn.getText(); + if (t >= 0) { + contributor.setCreditName(vn.toNormalizedString(t)); + contributors.add(nameIndex, contributor); + nameIndex++; + } + } + + int sequenceIndex = 0; + ap.selectXPath("//work:contributor/work:contributor-attributes/work:contributor-sequence"); + while (ap.evalXPath() != -1) { + int t = vn.getText(); + if (t >= 0) { + contributors.get(sequenceIndex).setSequence(vn.toNormalizedString(t)); + sequenceIndex++; + } + } + + int roleIndex = 0; + ap.selectXPath("//work:contributor/work:contributor-attributes/work:contributor-role"); + while (ap.evalXPath() != -1) { + int t = vn.getText(); + if (t >= 0) { + contributors.get(roleIndex).setRole(vn.toNormalizedString(t)); + roleIndex++; + } + } + return contributors; + } +} diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParserTest.java b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParserTest.java index d5da4eec0..4d8237f77 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParserTest.java +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParserTest.java @@ -44,7 +44,7 @@ public class XMLRecordParserTest { String xml = IOUtils .toString( - this.getClass().getResourceAsStream("activity_work_0000-0002-5982-8983.xml")); + this.getClass().getResourceAsStream("activity_work_0000-0003-2760-1191.xml")); XMLRecordParser p = new XMLRecordParser(); diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/xml/OrcidNoDoiTest.java b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/xml/OrcidNoDoiTest.java new file mode 100644 index 000000000..31f8432ac --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/xml/OrcidNoDoiTest.java @@ -0,0 +1,326 @@ + +package eu.dnetlib.doiboost.orcidnodoi.xml; + +import com.ximpleware.NavException; +import com.ximpleware.ParseException; +import com.ximpleware.XPathEvalException; +import com.ximpleware.XPathParseException; +import eu.dnetlib.dhp.parser.utility.VtdException; +import eu.dnetlib.doiboost.orcid.model.AuthorData; +import eu.dnetlib.doiboost.orcidnodoi.model.Contributor; +import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi; +import jdk.nashorn.internal.ir.annotations.Ignore; +import org.apache.commons.io.IOUtils; +import org.apache.commons.text.similarity.JaccardSimilarity; +import org.apache.commons.text.similarity.JaroWinklerSimilarity; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.IOException; +import java.text.Normalizer; +import java.util.*; + +import static org.junit.jupiter.api.Assertions.assertNotNull; + +public class OrcidNoDoiTest { + + private static final Logger logger = LoggerFactory.getLogger(OrcidNoDoiTest.class); + + String nameA = "Khairy"; + String surnameA = "Abdel Dayem"; + String otherNameA = "Dayem MKA"; + String nameB = "K"; + String surnameB = "Abdel-Dayem"; + String orcidIdA = "0000-0003-2760-1191"; + Double threshold = 0.8; + + @Test + @Ignore + private void similarityTest() throws Exception { + logger.info("running testSimilarity ...."); + logger + .info( + "JaroWinklerSimilarity: " + + Double.toString(similarityJaroWinkler(nameA, surnameA, nameB, surnameB))); + logger + .info( + "JaccardSimilarity: " + Double.toString(similarityJaccard(nameA, surnameA, nameB, surnameB))); + } + + @Test + @Ignore + private void bestMatchTest() throws Exception { + logger.info("running bestMatchTest ...."); + String contributor = surnameB + ", " + nameB; + logger.info("score: " + Double.toString(bestMatch(surnameA, nameA, contributor))); + } + + private static Double bestMatch(String authorSurname, String authorName, String contributor) { + logger.debug(authorSurname + " " + authorName + " vs " + contributor); + String[] contributorSplitted = contributor.split(" "); + if (contributorSplitted.length == 0) { + return 0.0; + } + final String contributorName = contributorSplitted[contributorSplitted.length - 1]; + String contributorSurname = ""; + if (contributorSplitted.length > 1) { + StringJoiner joiner = new StringJoiner(" "); + for (int i = 0; i < contributorSplitted.length - 1; i++) { + joiner.add(contributorSplitted[i]); + } + contributorSurname = joiner.toString(); + } + logger + .debug( + "contributorName: " + contributorName + + " contributorSurname: " + contributorSurname); + String authorNameNrm = normalize(authorName); + String authorSurnameNrm = normalize(authorSurname); + String contributorNameNrm = normalize(contributorName); + String contributorSurnameNrm = normalize(contributorSurname); + Double sm1 = similarity(authorNameNrm, authorSurnameNrm, contributorNameNrm, contributorSurnameNrm); + Double sm2 = similarity(authorNameNrm, authorSurnameNrm, contributorSurnameNrm, contributorNameNrm); + if (sm1.compareTo(sm2) >= 0) { + return sm1; + } + return sm2; + } + + private static Double similarity(String nameA, String surnameA, String nameB, String surnameB) { + Double score = similarityJaroWinkler(nameA, surnameA, nameB, surnameB); + logger + .debug(nameA + ", " + surnameA + " <> " + nameB + ", " + surnameB + " score: " + Double.toString(score)); + return score; + } + + private static Double similarityJaccard(String nameA, String surnameA, String nameB, String surnameB) { + return new JaccardSimilarity().apply(normalize(parse(nameA, surnameA)), normalize(parse(nameB, surnameB))); + } + + private static Double similarityJaroWinkler(String nameA, String surnameA, String nameB, String surnameB) { + return new JaroWinklerSimilarity().apply(normalize(parse(nameA, surnameA)), normalize(parse(nameB, surnameB))); + } + + private static String parse(String name, String surname) { + return surname + " " + name; + } + + private static String normalize(final String s) { + return nfd(s) + .toLowerCase() + // do not compact the regexes in a single expression, would cause StackOverflowError + // in case + // of large input strings + .replaceAll("(\\W)+", " ") + .replaceAll("(\\p{InCombiningDiacriticalMarks})+", " ") + .replaceAll("(\\p{Punct})+", " ") + .replaceAll("(\\d)+", " ") + .replaceAll("(\\n)+", " ") + .trim(); + } + + private static String nfd(final String s) { + return Normalizer.normalize(s, Normalizer.Form.NFD); + } + + @Test + @Ignore + public void readPublicationFieldsTest() + throws IOException, XPathEvalException, XPathParseException, NavException, VtdException, ParseException { + logger.info("running loadPublicationFieldsTest ...."); + String xml = IOUtils + .toString( + OrcidNoDoiTest.class.getResourceAsStream("activity_work_0000-0003-2760-1191.xml")); + + if (xml == null) { + logger.info("Resource not found"); + } + XMLRecordParserNoDoi p = new XMLRecordParserNoDoi(); + if (p == null) { + logger.info("XMLRecordParserNoDoi null"); + } + WorkDataNoDoi workData = null; + try { + workData = p.VTDParseWorkData(xml.getBytes()); + } catch (Exception e) { + logger.error("parsing xml", e); + } + assertNotNull(workData); + assertNotNull(workData.getOid()); + logger.info("oid: " + workData.getOid()); + assertNotNull(workData.getTitles()); + logger.info("titles: "); + workData.getTitles().forEach(t -> { + logger.info(t); + }); + logger.info("source: " + workData.getSourceName()); + logger.info("type: " + workData.getType()); + logger.info("urls: "); + workData.getUrls().forEach(u -> { + logger.info(u); + }); + logger.info("publication date: "); + workData.getPublicationDates().forEach(d -> { + logger.info(d.getYear() + " - " + d.getMonth() + " - " + d.getDay()); + }); + logger.info("external id: "); + workData.getExtIds().removeIf(e -> e.getRelationShip() != null && !e.getRelationShip().equals("self")); + workData.getExtIds().forEach(e -> { + logger.info(e.getType() + " - " + e.getValue() + " - " + e.getRelationShip()); + }); + logger.info("contributors: "); + workData.getContributors().forEach(c -> { + logger + .info( + c.getName() + " - " + c.getRole() + " - " + c.getSequence()); + }); + + } + + private void updateRanks(List contributors) { + boolean seqFound = false; + if (contributors + .stream() + .filter( + c -> c.getRole() != null && c.getSequence() != null && + c.getRole().equals("author") && (c.getSequence().equals("first") || + c.getSequence().equals("additional"))) + .count() > 0) { + seqFound = true; + logger.info("sequence data found"); + } + if (!seqFound) { + List seqIds = Arrays.asList(0); + contributors.forEach(c -> { + int currentSeq = seqIds.get(0) + 1; + seqIds.set(0, currentSeq); + c.setSequence(Integer.toString(seqIds.get(0))); + }); + } + } + + private void updateAuthorsSimpleMatch(List contributors, AuthorData author) { + contributors.forEach(c -> { + if (c.isSimpleMatch()) { + logger.info("simple match on : " + c.getCreditName()); + c.setName(author.getName()); + c.setSurname(author.getSurname()); + c.setOid(author.getOid()); + } + }); + updateRanks(contributors); + } + + private void updateAuthorsSimilarityMatch(List contributors, AuthorData author) { + logger.info("inside updateAuthorsSimilarityMatch ..."); + contributors.forEach(c -> { + logger + .info( + c.getOid() + " - " + c.getCreditName() + " - " + + c.getName() + " - " + c.getSurname() + " - " + + c.getRole() + " - " + c.getSequence() + " - best: " + c.isBestMatch() + " - simpe: " + + c.isSimpleMatch()); + }); + + contributors + .stream() + .filter(c -> c.isBestMatch()) + .forEach(c -> { + logger.info("similarity match on : " + c.getCreditName()); + c.setName(author.getName()); + c.setSurname(author.getSurname()); + c.setOid(author.getOid()); + }); + updateRanks(contributors); + } + + @Test + @Ignore + public void authorSimilarityMatchTest() throws Exception { + logger.info("running authorSimilarityMatchTest ...."); + authorMatchTest("activity_work_0000-0003-2760-1191-similarity.xml"); + } + + @Test + private void authorSimpleMatchTest() throws Exception { + logger.info("running authorSimpleMatchTest ...."); + authorMatchTest("activity_work_0000-0003-2760-1191.xml"); + } + + private void authorMatchTest(String orcidWork) + throws IOException, XPathEvalException, XPathParseException, NavException, VtdException, ParseException { + AuthorData author = new AuthorData(); + author.setName(nameA); + author.setSurname(surnameA); + author.setOid(orcidIdA); + String xml = IOUtils + .toString( + OrcidNoDoiTest.class.getResourceAsStream(orcidWork)); + + if (xml == null) { + logger.info("Resource not found"); + } + XMLRecordParserNoDoi p = new XMLRecordParserNoDoi(); + if (p == null) { + logger.info("XMLRecordParserNoDoi null"); + } + WorkDataNoDoi workData = null; + try { + workData = p.VTDParseWorkData(xml.getBytes()); + } catch (Exception e) { + logger.error("parsing xml", e); + } + assertNotNull(workData); + int matchCounter = 0; + List matchCounters = Arrays.asList(matchCounter); + Contributor contributor = null; + workData.getContributors().forEach(c -> { + if (normalize(c.getCreditName()).contains(normalize(author.getName())) || + normalize(c.getCreditName()).contains(normalize(author.getSurname())) || + ((author.getOtherName() != null) + && normalize(c.getCreditName()).contains(normalize(author.getOtherName())))) { + matchCounters.set(0, matchCounters.get(0) + 1); + c.setSimpleMatch(true); + } + }); + logger.info("match counter: " + Integer.toString(matchCounters.get(0))); + if (matchCounters.get(0) == 1) { + updateAuthorsSimpleMatch(workData.getContributors(), author); + } else if (matchCounters.get(0) > 1) { + Optional optCon = workData + .getContributors() + .stream() + .filter(c -> c.isSimpleMatch()) + .map(c -> { + c.setScore(bestMatch(nameA, surnameA, c.getCreditName())); + logger.debug("nella map: " + c.getCreditName() + " score: " + c.getScore()); + return c; + }) + .filter(c -> c.getScore() >= threshold) + .max(Comparator.comparing(c -> c.getScore())); + Contributor bestMatchContributor = null; + if (optCon.isPresent()) { + bestMatchContributor = optCon.get(); + bestMatchContributor.setBestMatch(true); + logger.info("best match: " + bestMatchContributor.getCreditName()); + updateAuthorsSimilarityMatch(workData.getContributors(), author); + } + + } + + logger.info("UPDATED contributors: "); + workData.getContributors().forEach(c -> { + logger + .info( + c.getOid() + " - " + c.getCreditName() + " - " + + c.getName() + " - " + c.getSurname() + " - " + + c.getRole() + " - " + c.getSequence()); + }); + } +} + +// +// orcid_RDD = sc.textFile(ORCID_DUMP_PATH) +// no_doi_works_RDD = orcid_RDD.map(orcid_map).filter(lambda x:x is not None).map(lambda x: json.dumps(x)).saveAsTextFile(path=ORCID_OPENAIRE_PATH,compressionCodecClass="org.apache.hadoop.io.compress.GzipCodec") +// \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/xml/activity_work_0000-0003-2760-1191.xml b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/xml/activity_work_0000-0003-2760-1191.xml new file mode 100644 index 000000000..485f4f8e8 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/xml/activity_work_0000-0003-2760-1191.xml @@ -0,0 +1,106 @@ + + + 2016-12-12T23:02:05.233Z + 2016-12-13T09:08:16.412Z + + + https://orcid.org/0000-0002-9157-3431 + 0000-0002-9157-3431 + orcid.org + + Europe PubMed Central + + + Cutoff Value of Admission N-Terminal Pro-Brain Natriuretic Peptide Which + Predicts Poor Myocardial Perfusion after Primary Percutaneous Coronary Intervention for + ST-Segment-Elevation Myocardial Infarction. + + + formatted-unspecified + Abdel-Dayem K, Eweda II, El-Sherbiny A, Dimitry MO, Nammas W, Acta + Cardiologica Sinica, 2016, vol. 32, no. 6, pp. 649-655, 2016 + + journal-article + + 2016 + 11 + + + + pmid + 27899851 + 27899851 + self + + + pmc + PMC5126442 + PMC5126442 + self + + + http://europepmc.org/abstract/med/27899851 + + + Abdel-Dayem K + + first + author + + + + Eweda II + + first + author + + + + El-Sherbiny A + + first + author + + + + Dimitry MO + + first + author + + + + Nammas W + + first + author + + + + diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/xml/activity_work_0000-0002-5982-8983.xml b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/xml/activity_work_0000-0002-5982-8983.xml similarity index 100% rename from dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/xml/activity_work_0000-0002-5982-8983.xml rename to dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/xml/activity_work_0000-0002-5982-8983.xml diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/xml/activity_work_0000-0003-2760-1191-similarity.xml b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/xml/activity_work_0000-0003-2760-1191-similarity.xml new file mode 100644 index 000000000..650d5a4cb --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/xml/activity_work_0000-0003-2760-1191-similarity.xml @@ -0,0 +1,113 @@ + + + 2016-12-12T23:02:05.233Z + 2016-12-13T09:08:16.412Z + + + https://orcid.org/0000-0002-9157-3431 + 0000-0002-9157-3431 + orcid.org + + Europe PubMed Central + + + Cutoff Value of Admission N-Terminal Pro-Brain Natriuretic Peptide Which + Predicts Poor Myocardial Perfusion after Primary Percutaneous Coronary Intervention for + ST-Segment-Elevation Myocardial Infarction. + + + formatted-unspecified + Abdel-Dayem K, Eweda II, El-Sherbiny A, Dimitry MO, Nammas W, Acta + Cardiologica Sinica, 2016, vol. 32, no. 6, pp. 649-655, 2016 + + journal-article + + 2016 + 11 + + + + pmid + 27899851 + 27899851 + self + + + pmc + PMC5126442 + PMC5126442 + self + + + http://europepmc.org/abstract/med/27899851 + + + Abdel-Dayem K + + first + author + + + + Abdel-Dayem Fake + + first + author + + + + Eweda II + + first + author + + + + El-Sherbiny A + + first + author + + + + Dimitry MO + + first + author + + + + Nammas W + + first + author + + + + diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/xml/activity_work_0000-0003-2760-1191.xml b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/xml/activity_work_0000-0003-2760-1191.xml new file mode 100644 index 000000000..485f4f8e8 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/xml/activity_work_0000-0003-2760-1191.xml @@ -0,0 +1,106 @@ + + + 2016-12-12T23:02:05.233Z + 2016-12-13T09:08:16.412Z + + + https://orcid.org/0000-0002-9157-3431 + 0000-0002-9157-3431 + orcid.org + + Europe PubMed Central + + + Cutoff Value of Admission N-Terminal Pro-Brain Natriuretic Peptide Which + Predicts Poor Myocardial Perfusion after Primary Percutaneous Coronary Intervention for + ST-Segment-Elevation Myocardial Infarction. + + + formatted-unspecified + Abdel-Dayem K, Eweda II, El-Sherbiny A, Dimitry MO, Nammas W, Acta + Cardiologica Sinica, 2016, vol. 32, no. 6, pp. 649-655, 2016 + + journal-article + + 2016 + 11 + + + + pmid + 27899851 + 27899851 + self + + + pmc + PMC5126442 + PMC5126442 + self + + + http://europepmc.org/abstract/med/27899851 + + + Abdel-Dayem K + + first + author + + + + Eweda II + + first + author + + + + El-Sherbiny A + + first + author + + + + Dimitry MO + + first + author + + + + Nammas W + + first + author + + + + From d6498278edc87aeb15ee61b33edf7f280829b56a Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Thu, 25 Jun 2020 18:43:29 +0200 Subject: [PATCH 02/37] added workflow to generate seq(orcidId,work) and seq(orcidId,enrichedWork) --- .../orcid/ActivitiesDecompressor.java | 2 +- .../doiboost/orcid/SummariesDecompressor.java | 2 +- .../doiboost/orcid/json/JsonHelper.java | 16 + .../orcidnodoi/ActivitiesDumpReader.java | 149 +++++ .../orcidnodoi/GenOrcidAuthorWork.java | 52 ++ .../SparkGenEnrichedOrcidWorks.java | 119 ++++ .../json/JsonWriter.java | 2 +- .../orcidnodoi/model/Contributor.java | 6 +- .../orcidnodoi/model/WorkDataNoDoi.java | 1 - .../orcidnodoi/similarity/AuthorMatcher.java | 204 +++++++ .../oozie_app/config-default.xml | 22 + .../oozie_app/workflow.xml | 524 ++++++++++++++++++ .../gen_enriched_orcid_works_parameters.json | 7 + .../orcidnodoi/xml/OrcidNoDoiTest.java | 250 +-------- 14 files changed, 1125 insertions(+), 231 deletions(-) create mode 100644 dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/json/JsonHelper.java create mode 100644 dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/ActivitiesDumpReader.java create mode 100644 dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/GenOrcidAuthorWork.java create mode 100644 dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java rename dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/{orcid => orcidnodoi}/json/JsonWriter.java (94%) create mode 100644 dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/similarity/AuthorMatcher.java create mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works/oozie_app/workflow.xml create mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works_parameters.json diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ActivitiesDecompressor.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ActivitiesDecompressor.java index 570fdef17..80ccd71a1 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ActivitiesDecompressor.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ActivitiesDecompressor.java @@ -19,7 +19,7 @@ import org.apache.hadoop.io.compress.CompressionCodec; import org.apache.hadoop.io.compress.CompressionCodecFactory; import org.mortbay.log.Log; -import eu.dnetlib.doiboost.orcid.json.JsonWriter; +import eu.dnetlib.doiboost.orcidnodoi.json.JsonWriter; import eu.dnetlib.doiboost.orcid.model.WorkData; import eu.dnetlib.doiboost.orcid.xml.XMLRecordParser; diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SummariesDecompressor.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SummariesDecompressor.java index f0bbb5c32..603bfedf6 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SummariesDecompressor.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SummariesDecompressor.java @@ -19,7 +19,7 @@ import org.apache.hadoop.io.compress.CompressionCodec; import org.apache.hadoop.io.compress.CompressionCodecFactory; import org.mortbay.log.Log; -import eu.dnetlib.doiboost.orcid.json.JsonWriter; +import eu.dnetlib.doiboost.orcidnodoi.json.JsonWriter; import eu.dnetlib.doiboost.orcid.model.AuthorData; import eu.dnetlib.doiboost.orcid.xml.XMLRecordParser; diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/json/JsonHelper.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/json/JsonHelper.java new file mode 100644 index 000000000..13a3cee8f --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/json/JsonHelper.java @@ -0,0 +1,16 @@ + +package eu.dnetlib.doiboost.orcid.json; + +import com.google.gson.Gson; +import com.google.gson.JsonObject; +import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi; + +public class JsonHelper { + + public static String createOidWork(WorkDataNoDoi workData) { + JsonObject oidWork = new JsonObject(); + oidWork.addProperty("oid", workData.getOid()); + oidWork.addProperty("work", new Gson().toJson(workData)); + return oidWork.toString(); + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/ActivitiesDumpReader.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/ActivitiesDumpReader.java new file mode 100644 index 000000000..7eb6faf54 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/ActivitiesDumpReader.java @@ -0,0 +1,149 @@ + +package eu.dnetlib.doiboost.orcidnodoi; + +import eu.dnetlib.doiboost.orcid.json.JsonHelper; +import eu.dnetlib.doiboost.orcidnodoi.json.JsonWriter; +import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi; +import eu.dnetlib.doiboost.orcidnodoi.xml.XMLRecordParserNoDoi; +import org.apache.commons.compress.archivers.tar.TarArchiveEntry; +import org.apache.commons.compress.archivers.tar.TarArchiveInputStream; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.apache.hadoop.io.IOUtils; +import org.apache.hadoop.io.SequenceFile; +import org.apache.hadoop.io.Text; +import org.apache.hadoop.io.compress.CompressionCodec; +import org.apache.hadoop.io.compress.CompressionCodecFactory; +import org.mortbay.log.Log; + +import java.io.BufferedReader; +import java.io.IOException; +import java.io.InputStream; +import java.io.InputStreamReader; +import java.net.URI; + +public class ActivitiesDumpReader { + + private static final int MAX_XML_WORKS_PARSED = -1; + private static final int XML_WORKS_PARSED_COUNTER_LOG_INTERVAL = 100000; + + public static void parseGzActivities(Configuration conf, String inputUri, Path outputPath) + throws Exception { + String uri = inputUri; + FileSystem fs = FileSystem.get(URI.create(uri), conf); + Path inputPath = new Path(uri); + CompressionCodecFactory factory = new CompressionCodecFactory(conf); + CompressionCodec codec = factory.getCodec(inputPath); + if (codec == null) { + System.err.println("No codec found for " + uri); + System.exit(1); + } + CompressionCodecFactory.removeSuffix(uri, codec.getDefaultExtension()); + InputStream gzipInputStream = null; + try { + gzipInputStream = codec.createInputStream(fs.open(inputPath)); + parseTarActivities(fs, conf, gzipInputStream, outputPath); + + } finally { + Log.debug("Closing gzip stream"); + IOUtils.closeStream(gzipInputStream); + } + } + + private static void parseTarActivities( + FileSystem fs, Configuration conf, InputStream gzipInputStream, Path outputPath) { + int counter = 0; + int noDoiFound = 0; + int errorFromOrcidFound = 0; + int xmlParserErrorFound = 0; + try (TarArchiveInputStream tais = new TarArchiveInputStream(gzipInputStream)) { + TarArchiveEntry entry = null; + + try (SequenceFile.Writer writer = SequenceFile + .createWriter( + conf, + SequenceFile.Writer.file(outputPath), + SequenceFile.Writer.keyClass(Text.class), + SequenceFile.Writer.valueClass(Text.class))) { + while ((entry = tais.getNextTarEntry()) != null) { + String filename = entry.getName(); + + try { + if (entry.isDirectory() || !filename.contains("works")) { + + } else { + Log.debug("XML work entry name: " + entry.getName()); + counter++; + BufferedReader br = new BufferedReader(new InputStreamReader(tais)); // Read directly from + // tarInput + String line; + StringBuffer buffer = new StringBuffer(); + while ((line = br.readLine()) != null) { + buffer.append(line); + } + WorkDataNoDoi workDataNoDoi = XMLRecordParserNoDoi.VTDParseWorkData(buffer.toString().getBytes()); + if (workDataNoDoi != null) { + if (workDataNoDoi.getErrorCode() != null) { + errorFromOrcidFound += 1; + Log + .debug( + "error from Orcid with code " + + workDataNoDoi.getErrorCode() + + " for entry " + + entry.getName()); + continue; + } + boolean isDoiFound = workDataNoDoi.getExtIds().stream() + .filter(e -> e.getType()!=null) + .anyMatch(e -> e.getType().equals("doi")); + if (!isDoiFound) { + String jsonData = JsonHelper.createOidWork(workDataNoDoi); + Log.debug("oid: " + workDataNoDoi.getOid() + " data: " + jsonData); + + final Text key = new Text(workDataNoDoi.getOid()); + final Text value = new Text(jsonData); + + try { + writer.append(key, value); + } catch (IOException e) { + Log.debug("Writing to sequence file: " + e.getMessage()); + Log.debug(e); + throw new RuntimeException(e); + } + noDoiFound += 1; + } + + } else { + Log.warn("Data not retrievable [" + entry.getName() + "] " + buffer.toString()); + xmlParserErrorFound += 1; + } + } + } catch (Exception e) { + Log + .warn( + "Parsing work from tar archive and xml work: " + filename + " " + e.getMessage()); + Log.warn(e); + } + + if ((counter % XML_WORKS_PARSED_COUNTER_LOG_INTERVAL) == 0) { + Log.info("Current xml works parsed: " + counter); + } + + if ((MAX_XML_WORKS_PARSED > -1) && (counter > MAX_XML_WORKS_PARSED)) { + break; + } + } + } + } catch (IOException e) { + Log.warn("Parsing work from gzip archive: " + e.getMessage()); + Log.warn(e); + throw new RuntimeException(e); + } + Log.info("Activities parse completed"); + Log.info("Total XML works parsed: " + counter); + Log.info("Total no doi work found: " + noDoiFound); + Log.info("Error from Orcid found: " + errorFromOrcidFound); + Log.info("Error parsing xml work found: " + xmlParserErrorFound); + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/GenOrcidAuthorWork.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/GenOrcidAuthorWork.java new file mode 100644 index 000000000..b82f4bc4c --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/GenOrcidAuthorWork.java @@ -0,0 +1,52 @@ + +package eu.dnetlib.doiboost.orcidnodoi; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.doiboost.orcid.OrcidDSManager; +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.mortbay.log.Log; + +import java.io.IOException; + +public class GenOrcidAuthorWork extends OrcidDSManager { + + private String activitiesFileNameTarGz; + private String outputWorksPath; + private String workingPath; + + public static void main(String[] args) throws IOException, Exception { + GenOrcidAuthorWork genOrcidAuthorWork = new GenOrcidAuthorWork(); + genOrcidAuthorWork.loadArgs(args); + genOrcidAuthorWork.generateAuthorsDOIsData(); + } + + public void generateAuthorsDOIsData() throws Exception { + Configuration conf = initConfigurationObject(); + FileSystem fs = initFileSystemObject(conf); + String tarGzUri = hdfsServerUri.concat(workingPath).concat(activitiesFileNameTarGz); + Path outputPath = new Path(hdfsServerUri.concat(workingPath).concat(outputWorksPath)); + ActivitiesDumpReader.parseGzActivities(conf, tarGzUri, outputPath); + } + + private void loadArgs(String[] args) throws IOException, Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + GenOrcidAuthorWork.class + .getResourceAsStream( + "/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works_parameters.json"))); + parser.parseArgument(args); + + hdfsServerUri = parser.get("hdfsServerUri"); + Log.info("HDFS URI: " + hdfsServerUri); + workingPath = parser.get("workingPath"); + Log.info("Working Path: " + workingPath); + activitiesFileNameTarGz = parser.get("activitiesFileNameTarGz"); + Log.info("Activities File Name: " + activitiesFileNameTarGz); + outputWorksPath = parser.get("outputWorksPath"); + Log.info("Output Author Work Data: " + outputWorksPath); + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java new file mode 100644 index 000000000..6bb31bcf6 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java @@ -0,0 +1,119 @@ + +package eu.dnetlib.doiboost.orcidnodoi; + +import com.google.gson.Gson; +import com.google.gson.JsonElement; +import com.google.gson.JsonParser; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.doiboost.orcid.model.AuthorData; +import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi; +import eu.dnetlib.doiboost.orcidnodoi.similarity.AuthorMatcher; +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.io.Text; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaPairRDD; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import scala.Tuple2; + +import java.io.IOException; +import java.util.Objects; +import java.util.Optional; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +public class SparkGenEnrichedOrcidWorks { + + public static void main(String[] args) throws IOException, Exception { + Logger logger = LoggerFactory.getLogger(SparkGenEnrichedOrcidWorks.class); + logger.info("[ SparkGenerateDoiAuthorList STARTED]"); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + SparkGenEnrichedOrcidWorks.class + .getResourceAsStream( + "/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works_parameters.json"))); + parser.parseArgument(args); + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + logger.info("isSparkSessionManaged: {}", isSparkSessionManaged); + final String workingPath = parser.get("workingPath"); + logger.info("workingPath: ", workingPath); + final String outputEnrichedWorksPath = parser.get("outputEnrichedWorksPath"); + logger.info("outputEnrichedWorksPath: ", outputEnrichedWorksPath); + final String outputWorksPath = parser.get("outputWorksPath"); + logger.info("outputWorksPath: ", outputWorksPath); + + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaPairRDD summariesRDD = sc + .sequenceFile(workingPath + "../orcid_summaries/output/authors.seq", Text.class, Text.class); + Dataset summariesDataset = spark + .createDataset( + summariesRDD.map(seq -> loadAuthorFromJson(seq._1(), seq._2())).rdd(), + Encoders.bean(AuthorData.class)); + + JavaPairRDD activitiesRDD = sc + .sequenceFile(workingPath + outputWorksPath + "works_X.seq" , Text.class, Text.class); + Dataset activitiesDataset = spark + .createDataset( + activitiesRDD.map(seq -> loadWorkFromJson(seq._1(), seq._2())).rdd(), + Encoders.bean(WorkDataNoDoi.class)); + + activitiesDataset + .joinWith( + summariesDataset, + activitiesDataset.col("oid").equalTo(summariesDataset.col("oid")), "inner") + .map( + (MapFunction, Tuple2>) value -> { + WorkDataNoDoi w = value._1; + AuthorData a = value._2; + AuthorMatcher.match(a, w.getContributors()); + return new Tuple2<>(a.getOid(), w); + }, + Encoders.tuple(Encoders.STRING(), Encoders.bean(WorkDataNoDoi.class))) + .filter(Objects::nonNull) + .toJavaRDD() + .saveAsTextFile(workingPath + outputEnrichedWorksPath);; + }); + } + + private static AuthorData loadAuthorFromJson(Text orcidId, Text json) { + AuthorData authorData = new AuthorData(); + authorData.setOid(orcidId.toString()); + JsonElement jElement = new JsonParser().parse(json.toString()); + authorData.setName(getJsonValue(jElement, "name")); + authorData.setSurname(getJsonValue(jElement, "surname")); + authorData.setCreditName(getJsonValue(jElement, "creditname")); + return authorData; + } + + private static WorkDataNoDoi loadWorkFromJson(Text orcidId, Text json) { + WorkDataNoDoi workData = new Gson().fromJson(json.toString(), WorkDataNoDoi.class); + return workData; + } + + private static String getJsonValue(JsonElement jElement, String property) { + if (jElement.getAsJsonObject().has(property)) { + JsonElement name = null; + name = jElement.getAsJsonObject().get(property); + if (name != null && !name.isJsonNull()) { + return name.getAsString(); + } + } + return null; + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/json/JsonWriter.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/json/JsonWriter.java similarity index 94% rename from dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/json/JsonWriter.java rename to dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/json/JsonWriter.java index 35676d5ba..7f7e3a10a 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/json/JsonWriter.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/json/JsonWriter.java @@ -1,5 +1,5 @@ -package eu.dnetlib.doiboost.orcid.json; +package eu.dnetlib.doiboost.orcidnodoi.json; import com.google.gson.JsonObject; diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/Contributor.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/Contributor.java index 42076de5d..8a170de09 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/Contributor.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/Contributor.java @@ -8,9 +8,9 @@ import eu.dnetlib.doiboost.orcid.model.AuthorData; public class Contributor extends AuthorData implements Serializable { private String sequence; private String role; - private boolean simpleMatch = false; - private Double score = 0.0; - private boolean bestMatch = false; + private transient boolean simpleMatch = false; + private transient Double score = 0.0; + private transient boolean bestMatch = false; public String getSequence() { return sequence; diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/WorkDataNoDoi.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/WorkDataNoDoi.java index ee13454e1..5756521e7 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/WorkDataNoDoi.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/WorkDataNoDoi.java @@ -97,5 +97,4 @@ public class WorkDataNoDoi implements Serializable { public void setContributors(List contributors) { this.contributors = contributors; } - } diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/similarity/AuthorMatcher.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/similarity/AuthorMatcher.java new file mode 100644 index 000000000..09fd8b36b --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/similarity/AuthorMatcher.java @@ -0,0 +1,204 @@ + +package eu.dnetlib.doiboost.orcidnodoi.similarity; + +import java.io.IOException; +import java.text.Normalizer; +import java.util.*; + +import org.apache.commons.text.similarity.JaroWinklerSimilarity; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.google.gson.Gson; +import com.google.gson.GsonBuilder; +import com.ximpleware.NavException; +import com.ximpleware.ParseException; +import com.ximpleware.XPathEvalException; +import com.ximpleware.XPathParseException; + +import eu.dnetlib.dhp.parser.utility.VtdException; +import eu.dnetlib.doiboost.orcid.model.AuthorData; +import eu.dnetlib.doiboost.orcidnodoi.model.Contributor; +import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi; + +public class AuthorMatcher { + + private static final Logger logger = LoggerFactory.getLogger(AuthorMatcher.class); + private static final Double threshold = 0.8; + + public static void match(AuthorData author, List contributors) + throws IOException, XPathEvalException, XPathParseException, NavException, VtdException, ParseException { + + int matchCounter = 0; + List matchCounters = Arrays.asList(matchCounter); + Contributor contributor = null; + contributors.forEach(c -> { + if (normalize(c.getCreditName()).contains(normalize(author.getName())) || + normalize(c.getCreditName()).contains(normalize(author.getSurname())) || + ((author.getOtherName() != null) + && normalize(c.getCreditName()).contains(normalize(author.getOtherName())))) { + matchCounters.set(0, matchCounters.get(0) + 1); + c.setSimpleMatch(true); + } + }); + logger.info("match counter: " + Integer.toString(matchCounters.get(0))); + if (matchCounters.get(0) == 1) { + updateAuthorsSimpleMatch(contributors, author); + } else if (matchCounters.get(0) > 1) { + Optional optCon = contributors + .stream() + .filter(c -> c.isSimpleMatch()) + .map(c -> { + c.setScore(bestMatch(author.getName(), author.getSurname(), c.getCreditName())); + logger.debug("nella map: " + c.getCreditName() + " score: " + c.getScore()); + return c; + }) + .filter(c -> c.getScore() >= threshold) + .max(Comparator.comparing(c -> c.getScore())); + Contributor bestMatchContributor = null; + if (optCon.isPresent()) { + bestMatchContributor = optCon.get(); + bestMatchContributor.setBestMatch(true); + logger.info("best match: " + bestMatchContributor.getCreditName()); + updateAuthorsSimilarityMatch(contributors, author); + } + + } + + logger.info("UPDATED contributors: "); + contributors.forEach(c -> { + logger + .info( + c.getOid() + " - " + c.getCreditName() + " - " + + c.getName() + " - " + c.getSurname() + " - " + + c.getRole() + " - " + c.getSequence()); + }); + } + + private static Double bestMatch(String authorSurname, String authorName, String contributor) { + logger.debug(authorSurname + " " + authorName + " vs " + contributor); + String[] contributorSplitted = contributor.split(" "); + if (contributorSplitted.length == 0) { + return 0.0; + } + final String contributorName = contributorSplitted[contributorSplitted.length - 1]; + String contributorSurname = ""; + if (contributorSplitted.length > 1) { + StringJoiner joiner = new StringJoiner(" "); + for (int i = 0; i < contributorSplitted.length - 1; i++) { + joiner.add(contributorSplitted[i]); + } + contributorSurname = joiner.toString(); + } + logger + .debug( + "contributorName: " + contributorName + + " contributorSurname: " + contributorSurname); + String authorNameNrm = normalize(authorName); + String authorSurnameNrm = normalize(authorSurname); + String contributorNameNrm = normalize(contributorName); + String contributorSurnameNrm = normalize(contributorSurname); + Double sm1 = similarity(authorNameNrm, authorSurnameNrm, contributorNameNrm, contributorSurnameNrm); + Double sm2 = similarity(authorNameNrm, authorSurnameNrm, contributorSurnameNrm, contributorNameNrm); + if (sm1.compareTo(sm2) >= 0) { + return sm1; + } + return sm2; + } + + private static Double similarity(String nameA, String surnameA, String nameB, String surnameB) { + Double score = similarityJaroWinkler(nameA, surnameA, nameB, surnameB); + logger + .debug(nameA + ", " + surnameA + " <> " + nameB + ", " + surnameB + " score: " + Double.toString(score)); + return score; + } + + private static Double similarityJaroWinkler(String nameA, String surnameA, String nameB, String surnameB) { + return new JaroWinklerSimilarity().apply(normalize(parse(nameA, surnameA)), normalize(parse(nameB, surnameB))); + } + + private static String normalize(final String s) { + return nfd(s) + .toLowerCase() + // do not compact the regexes in a single expression, would cause StackOverflowError + // in case + // of large input strings + .replaceAll("(\\W)+", " ") + .replaceAll("(\\p{InCombiningDiacriticalMarks})+", " ") + .replaceAll("(\\p{Punct})+", " ") + .replaceAll("(\\d)+", " ") + .replaceAll("(\\n)+", " ") + .trim(); + } + + private static String nfd(final String s) { + return Normalizer.normalize(s, Normalizer.Form.NFD); + } + + private static String parse(String name, String surname) { + return surname + " " + name; + } + + private static void updateAuthorsSimpleMatch(List contributors, AuthorData author) { + contributors.forEach(c -> { + if (c.isSimpleMatch()) { + logger.info("simple match on : " + c.getCreditName()); + c.setName(author.getName()); + c.setSurname(author.getSurname()); + c.setOid(author.getOid()); + } + }); + updateRanks(contributors); + } + + private static void updateAuthorsSimilarityMatch(List contributors, AuthorData author) { + logger.info("inside updateAuthorsSimilarityMatch ..."); + contributors.forEach(c -> { + logger + .info( + c.getOid() + " - " + c.getCreditName() + " - " + + c.getName() + " - " + c.getSurname() + " - " + + c.getRole() + " - " + c.getSequence() + " - best: " + c.isBestMatch() + " - simpe: " + + c.isSimpleMatch()); + }); + + contributors + .stream() + .filter(c -> c.isBestMatch()) + .forEach(c -> { + logger.info("similarity match on : " + c.getCreditName()); + c.setName(author.getName()); + c.setSurname(author.getSurname()); + c.setOid(author.getOid()); + }); + updateRanks(contributors); + } + + private static void updateRanks(List contributors) { + boolean seqFound = false; + if (contributors + .stream() + .filter( + c -> c.getRole() != null && c.getSequence() != null && + c.getRole().equals("author") && (c.getSequence().equals("first") || + c.getSequence().equals("additional"))) + .count() > 0) { + seqFound = true; + logger.info("sequence data found"); + } + if (!seqFound) { + List seqIds = Arrays.asList(0); + contributors.forEach(c -> { + int currentSeq = seqIds.get(0) + 1; + seqIds.set(0, currentSeq); + c.setSequence(Integer.toString(seqIds.get(0))); + }); + } + } + + private static String toJson(WorkDataNoDoi work) { + GsonBuilder builder = new GsonBuilder(); + Gson gson = builder.create(); + return gson.toJson(work); + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works/oozie_app/config-default.xml new file mode 100644 index 000000000..f2d51e260 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works/oozie_app/config-default.xml @@ -0,0 +1,22 @@ + + + oozie.action.sharelib.for.java + spark2 + + + oozie.launcher.mapreduce.user.classpath.first + true + + + oozie.launcher.mapreduce.map.java.opts + -Xmx4g + + + jobTracker + hadoop-rm3.garr-pa1.d4science.org:8032 + + + nameNode + hdfs://hadoop-rm1.garr-pa1.d4science.org:8020 + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works/oozie_app/workflow.xml new file mode 100644 index 000000000..2486bdb24 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works/oozie_app/workflow.xml @@ -0,0 +1,524 @@ + + + + workingPath_activities + the working dir base path + + + shell_cmd_0 + wget -O /tmp/ORCID_2019_activites_0.tar.gz https://orcid.figshare.com/ndownloader/files/18017660 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_0.tar.gz /data/orcid_activities/ORCID_2019_activites_0.tar.gz ; rm -f /tmp/ORCID_2019_activites_0.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file 0 + + + shell_cmd_1 + wget -O /tmp/ORCID_2019_activites_1.tar.gz https://orcid.figshare.com/ndownloader/files/18017675 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_1.tar.gz /data/orcid_activities/ORCID_2019_activites_1.tar.gz ; rm -f /tmp/ORCID_2019_activites_1.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file 1 + + + shell_cmd_2 + wget -O /tmp/ORCID_2019_activites_2.tar.gz https://orcid.figshare.com/ndownloader/files/18017717 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_2.tar.gz /data/orcid_activities/ORCID_2019_activites_2.tar.gz ; rm -f /tmp/ORCID_2019_activites_2.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file 2 + + + shell_cmd_3 + wget -O /tmp/ORCID_2019_activites_3.tar.gz https://orcid.figshare.com/ndownloader/files/18017765 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_3.tar.gz /data/orcid_activities/ORCID_2019_activites_3.tar.gz ; rm -f /tmp/ORCID_2019_activites_3.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file 3 + + + shell_cmd_4 + wget -O /tmp/ORCID_2019_activites_4.tar.gz https://orcid.figshare.com/ndownloader/files/18017831 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_4.tar.gz /data/orcid_activities/ORCID_2019_activites_4.tar.gz ; rm -f /tmp/ORCID_2019_activites_4.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file 4 + + + shell_cmd_5 + wget -O /tmp/ORCID_2019_activites_5.tar.gz https://orcid.figshare.com/ndownloader/files/18017987 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_5.tar.gz /data/orcid_activities/ORCID_2019_activites_5.tar.gz ; rm -f /tmp/ORCID_2019_activites_5.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file 5 + + + shell_cmd_6 + wget -O /tmp/ORCID_2019_activites_6.tar.gz https://orcid.figshare.com/ndownloader/files/18018053 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_6.tar.gz /data/orcid_activities/ORCID_2019_activites_6.tar.gz ; rm -f /tmp/ORCID_2019_activites_6.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file 6 + + + shell_cmd_7 + wget -O /tmp/ORCID_2019_activites_7.tar.gz https://orcid.figshare.com/ndownloader/files/18018023 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_7.tar.gz /data/orcid_activities/ORCID_2019_activites_7.tar.gz ; rm -f /tmp/ORCID_2019_activites_7.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file 7 + + + shell_cmd_8 + wget -O /tmp/ORCID_2019_activites_8.tar.gz https://orcid.figshare.com/ndownloader/files/18018248 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_8.tar.gz /data/orcid_activities/ORCID_2019_activites_8.tar.gz ; rm -f /tmp/ORCID_2019_activites_8.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file 8 + + + shell_cmd_9 + wget -O /tmp/ORCID_2019_activites_9.tar.gz https://orcid.figshare.com/ndownloader/files/18018029 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_9.tar.gz /data/orcid_activities/ORCID_2019_activites_9.tar.gz ; rm -f /tmp/ORCID_2019_activites_9.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file 9 + + + shell_cmd_X + wget -O /tmp/ORCID_2019_activites_X.tar.gz https://orcid.figshare.com/ndownloader/files/18018182 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_X.tar.gz /data/orcid_activities/ORCID_2019_activites_X.tar.gz ; rm -f /tmp/ORCID_2019_activites_X.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file X + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_0.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_0} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork + -w${workingPath_activities}/ + -n${nameNode} + -fORCID_2019_activites_0.tar.gz + -owno_doi_works/works_0.seq + + + + + + + + + ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_1.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_1} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork + -w${workingPath_activities}/ + -n${nameNode} + -fORCID_2019_activites_1.tar.gz + -owno_doi_works/works_1.seq + + + + + + + + + ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_2.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_2} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork + -w${workingPath_activities}/ + -n${nameNode} + -fORCID_2019_activites_2.tar.gz + -owno_doi_works/works_2.seq + + + + + + + + + ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_3.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_3} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork + -w${workingPath_activities}/ + -n${nameNode} + -fORCID_2019_activites_3.tar.gz + -owno_doi_works/works_3.seq + + + + + + + + + ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_4.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_4} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork + -w${workingPath_activities}/ + -n${nameNode} + -fORCID_2019_activites_4.tar.gz + -owno_doi_works/works_4.seq + + + + + + + + + ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_5.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_5} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork + -w${workingPath_activities}/ + -n${nameNode} + -fORCID_2019_activites_5.tar.gz + -owno_doi_works/works_5.seq + + + + + + + + + ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_6.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_6} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork + -w${workingPath_activities}/ + -n${nameNode} + -fORCID_2019_activites_6.tar.gz + -owno_doi_works/works_6.seq + + + + + + + + + + ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_7.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_7} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork + -w${workingPath_activities}/ + -n${nameNode} + -fORCID_2019_activites_7.tar.gz + -owno_doi_works/works_7.seq + + + + + + + + + ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_8.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_8} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork + -w${workingPath_activities}/ + -n${nameNode} + -fORCID_2019_activites_8.tar.gz + -owno_doi_works/works_8.seq + + + + + + + + + ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_9.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_9} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork + -w${workingPath_activities}/ + -n${nameNode} + -fORCID_2019_activites_9.tar.gz + -owno_doi_works/works_9.seq + + + + + + + + + ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_X.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_X} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork + -w${workingPath_activities}/ + -n${nameNode} + -fORCID_2019_activites_X.tar.gz + -owno_doi_works/works_X.seq + + + + + + + + + + ${jobTracker} + ${nameNode} + yarn + cluster + Gen_Enriched_Orcid_Works + eu.dnetlib.doiboost.orcidnodoi.SparkGenEnrichedOrcidWorks + dhp-doiboost-1.2.3-SNAPSHOT.jar + --num-executors 10 --conf spark.yarn.jars="hdfs://hadoop-rm1.garr-pa1.d4science.org:8020/user/oozie/share/lib/lib_20180405103059/spark2" --executor-memory=${sparkExecutorMemory} --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} + + -w${workingPath}/ + -owno_doi_works/ + -oewno_doi_enriched_works/ + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works_parameters.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works_parameters.json new file mode 100644 index 000000000..c3a8f92ec --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works_parameters.json @@ -0,0 +1,7 @@ +[ + {"paramName":"n", "paramLongName":"hdfsServerUri", "paramDescription": "the server uri", "paramRequired": true}, + {"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the default work path", "paramRequired": true}, + {"paramName":"f", "paramLongName":"activitiesFileNameTarGz", "paramDescription": "the name of the activities orcid file", "paramRequired": true}, + {"paramName":"ow", "paramLongName":"outputWorksPath", "paramDescription": "the relative folder of the sequencial file to write", "paramRequired": true}, + {"paramName":"oew", "paramLongName":"outputEnrichedWorksPath", "paramDescription": "the relative folder of the sequencial file to write the data", "paramRequired": true} +] \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/xml/OrcidNoDoiTest.java b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/xml/OrcidNoDoiTest.java index 31f8432ac..6a5faddbd 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/xml/OrcidNoDoiTest.java +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/xml/OrcidNoDoiTest.java @@ -1,15 +1,12 @@ package eu.dnetlib.doiboost.orcidnodoi.xml; -import com.ximpleware.NavException; -import com.ximpleware.ParseException; -import com.ximpleware.XPathEvalException; -import com.ximpleware.XPathParseException; -import eu.dnetlib.dhp.parser.utility.VtdException; -import eu.dnetlib.doiboost.orcid.model.AuthorData; -import eu.dnetlib.doiboost.orcidnodoi.model.Contributor; -import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi; -import jdk.nashorn.internal.ir.annotations.Ignore; +import static org.junit.jupiter.api.Assertions.assertNotNull; + +import java.io.IOException; +import java.text.Normalizer; +import java.util.*; + import org.apache.commons.io.IOUtils; import org.apache.commons.text.similarity.JaccardSimilarity; import org.apache.commons.text.similarity.JaroWinklerSimilarity; @@ -17,11 +14,20 @@ import org.junit.jupiter.api.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.io.IOException; -import java.text.Normalizer; -import java.util.*; +import com.google.gson.Gson; +import com.google.gson.GsonBuilder; +import com.ximpleware.NavException; +import com.ximpleware.ParseException; +import com.ximpleware.XPathEvalException; +import com.ximpleware.XPathParseException; -import static org.junit.jupiter.api.Assertions.assertNotNull; +import eu.dnetlib.dhp.parser.utility.VtdException; +import eu.dnetlib.dhp.schema.oaf.Author; +import eu.dnetlib.doiboost.orcid.model.AuthorData; +import eu.dnetlib.doiboost.orcidnodoi.model.Contributor; +import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi; +import eu.dnetlib.doiboost.orcidnodoi.similarity.AuthorMatcher; +import jdk.nashorn.internal.ir.annotations.Ignore; public class OrcidNoDoiTest { @@ -33,100 +39,10 @@ public class OrcidNoDoiTest { String nameB = "K"; String surnameB = "Abdel-Dayem"; String orcidIdA = "0000-0003-2760-1191"; - Double threshold = 0.8; @Test @Ignore - private void similarityTest() throws Exception { - logger.info("running testSimilarity ...."); - logger - .info( - "JaroWinklerSimilarity: " - + Double.toString(similarityJaroWinkler(nameA, surnameA, nameB, surnameB))); - logger - .info( - "JaccardSimilarity: " + Double.toString(similarityJaccard(nameA, surnameA, nameB, surnameB))); - } - - @Test - @Ignore - private void bestMatchTest() throws Exception { - logger.info("running bestMatchTest ...."); - String contributor = surnameB + ", " + nameB; - logger.info("score: " + Double.toString(bestMatch(surnameA, nameA, contributor))); - } - - private static Double bestMatch(String authorSurname, String authorName, String contributor) { - logger.debug(authorSurname + " " + authorName + " vs " + contributor); - String[] contributorSplitted = contributor.split(" "); - if (contributorSplitted.length == 0) { - return 0.0; - } - final String contributorName = contributorSplitted[contributorSplitted.length - 1]; - String contributorSurname = ""; - if (contributorSplitted.length > 1) { - StringJoiner joiner = new StringJoiner(" "); - for (int i = 0; i < contributorSplitted.length - 1; i++) { - joiner.add(contributorSplitted[i]); - } - contributorSurname = joiner.toString(); - } - logger - .debug( - "contributorName: " + contributorName + - " contributorSurname: " + contributorSurname); - String authorNameNrm = normalize(authorName); - String authorSurnameNrm = normalize(authorSurname); - String contributorNameNrm = normalize(contributorName); - String contributorSurnameNrm = normalize(contributorSurname); - Double sm1 = similarity(authorNameNrm, authorSurnameNrm, contributorNameNrm, contributorSurnameNrm); - Double sm2 = similarity(authorNameNrm, authorSurnameNrm, contributorSurnameNrm, contributorNameNrm); - if (sm1.compareTo(sm2) >= 0) { - return sm1; - } - return sm2; - } - - private static Double similarity(String nameA, String surnameA, String nameB, String surnameB) { - Double score = similarityJaroWinkler(nameA, surnameA, nameB, surnameB); - logger - .debug(nameA + ", " + surnameA + " <> " + nameB + ", " + surnameB + " score: " + Double.toString(score)); - return score; - } - - private static Double similarityJaccard(String nameA, String surnameA, String nameB, String surnameB) { - return new JaccardSimilarity().apply(normalize(parse(nameA, surnameA)), normalize(parse(nameB, surnameB))); - } - - private static Double similarityJaroWinkler(String nameA, String surnameA, String nameB, String surnameB) { - return new JaroWinklerSimilarity().apply(normalize(parse(nameA, surnameA)), normalize(parse(nameB, surnameB))); - } - - private static String parse(String name, String surname) { - return surname + " " + name; - } - - private static String normalize(final String s) { - return nfd(s) - .toLowerCase() - // do not compact the regexes in a single expression, would cause StackOverflowError - // in case - // of large input strings - .replaceAll("(\\W)+", " ") - .replaceAll("(\\p{InCombiningDiacriticalMarks})+", " ") - .replaceAll("(\\p{Punct})+", " ") - .replaceAll("(\\d)+", " ") - .replaceAll("(\\n)+", " ") - .trim(); - } - - private static String nfd(final String s) { - return Normalizer.normalize(s, Normalizer.Form.NFD); - } - - @Test - @Ignore - public void readPublicationFieldsTest() + private void readPublicationFieldsTest() throws IOException, XPathEvalException, XPathParseException, NavException, VtdException, ParseException { logger.info("running loadPublicationFieldsTest ...."); String xml = IOUtils @@ -178,78 +94,10 @@ public class OrcidNoDoiTest { } - private void updateRanks(List contributors) { - boolean seqFound = false; - if (contributors - .stream() - .filter( - c -> c.getRole() != null && c.getSequence() != null && - c.getRole().equals("author") && (c.getSequence().equals("first") || - c.getSequence().equals("additional"))) - .count() > 0) { - seqFound = true; - logger.info("sequence data found"); - } - if (!seqFound) { - List seqIds = Arrays.asList(0); - contributors.forEach(c -> { - int currentSeq = seqIds.get(0) + 1; - seqIds.set(0, currentSeq); - c.setSequence(Integer.toString(seqIds.get(0))); - }); - } - } - - private void updateAuthorsSimpleMatch(List contributors, AuthorData author) { - contributors.forEach(c -> { - if (c.isSimpleMatch()) { - logger.info("simple match on : " + c.getCreditName()); - c.setName(author.getName()); - c.setSurname(author.getSurname()); - c.setOid(author.getOid()); - } - }); - updateRanks(contributors); - } - - private void updateAuthorsSimilarityMatch(List contributors, AuthorData author) { - logger.info("inside updateAuthorsSimilarityMatch ..."); - contributors.forEach(c -> { - logger - .info( - c.getOid() + " - " + c.getCreditName() + " - " + - c.getName() + " - " + c.getSurname() + " - " + - c.getRole() + " - " + c.getSequence() + " - best: " + c.isBestMatch() + " - simpe: " - + c.isSimpleMatch()); - }); - - contributors - .stream() - .filter(c -> c.isBestMatch()) - .forEach(c -> { - logger.info("similarity match on : " + c.getCreditName()); - c.setName(author.getName()); - c.setSurname(author.getSurname()); - c.setOid(author.getOid()); - }); - updateRanks(contributors); - } - @Test - @Ignore - public void authorSimilarityMatchTest() throws Exception { - logger.info("running authorSimilarityMatchTest ...."); - authorMatchTest("activity_work_0000-0003-2760-1191-similarity.xml"); - } - - @Test - private void authorSimpleMatchTest() throws Exception { + public void authorMatchTest() throws Exception { logger.info("running authorSimpleMatchTest ...."); - authorMatchTest("activity_work_0000-0003-2760-1191.xml"); - } - - private void authorMatchTest(String orcidWork) - throws IOException, XPathEvalException, XPathParseException, NavException, VtdException, ParseException { + String orcidWork = "activity_work_0000-0003-2760-1191-similarity.xml"; AuthorData author = new AuthorData(); author.setName(nameA); author.setSurname(surnameA); @@ -272,55 +120,9 @@ public class OrcidNoDoiTest { logger.error("parsing xml", e); } assertNotNull(workData); - int matchCounter = 0; - List matchCounters = Arrays.asList(matchCounter); - Contributor contributor = null; - workData.getContributors().forEach(c -> { - if (normalize(c.getCreditName()).contains(normalize(author.getName())) || - normalize(c.getCreditName()).contains(normalize(author.getSurname())) || - ((author.getOtherName() != null) - && normalize(c.getCreditName()).contains(normalize(author.getOtherName())))) { - matchCounters.set(0, matchCounters.get(0) + 1); - c.setSimpleMatch(true); - } - }); - logger.info("match counter: " + Integer.toString(matchCounters.get(0))); - if (matchCounters.get(0) == 1) { - updateAuthorsSimpleMatch(workData.getContributors(), author); - } else if (matchCounters.get(0) > 1) { - Optional optCon = workData - .getContributors() - .stream() - .filter(c -> c.isSimpleMatch()) - .map(c -> { - c.setScore(bestMatch(nameA, surnameA, c.getCreditName())); - logger.debug("nella map: " + c.getCreditName() + " score: " + c.getScore()); - return c; - }) - .filter(c -> c.getScore() >= threshold) - .max(Comparator.comparing(c -> c.getScore())); - Contributor bestMatchContributor = null; - if (optCon.isPresent()) { - bestMatchContributor = optCon.get(); - bestMatchContributor.setBestMatch(true); - logger.info("best match: " + bestMatchContributor.getCreditName()); - updateAuthorsSimilarityMatch(workData.getContributors(), author); - } - - } - - logger.info("UPDATED contributors: "); - workData.getContributors().forEach(c -> { - logger - .info( - c.getOid() + " - " + c.getCreditName() + " - " + - c.getName() + " - " + c.getSurname() + " - " + - c.getRole() + " - " + c.getSequence()); - }); + AuthorMatcher.match(author, workData.getContributors()); + GsonBuilder builder = new GsonBuilder(); + Gson gson = builder.create(); + logger.info(gson.toJson(workData)); } } - -// -// orcid_RDD = sc.textFile(ORCID_DUMP_PATH) -// no_doi_works_RDD = orcid_RDD.map(orcid_map).filter(lambda x:x is not None).map(lambda x: json.dumps(x)).saveAsTextFile(path=ORCID_OPENAIRE_PATH,compressionCodecClass="org.apache.hadoop.io.compress.GzipCodec") -// \ No newline at end of file From b2213b6435dd3180adff6a7546e9f03337e8056c Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Fri, 26 Jun 2020 17:27:34 +0200 Subject: [PATCH 03/37] merged with dnet version --- .../orcid/ActivitiesDecompressor.java | 2 +- .../doiboost/orcid/SummariesDecompressor.java | 2 +- .../doiboost/orcid/json/JsonHelper.java | 1 + .../orcidnodoi/ActivitiesDumpReader.java | 30 +- .../orcidnodoi/GenOrcidAuthorWork.java | 7 +- .../SparkGenEnrichedOrcidWorks.java | 59 +-- .../orcidnodoi/proto/ProtoWriter.java | 427 ++++++++++++++++++ .../oozie_app/workflow.xml | 2 +- 8 files changed, 483 insertions(+), 47 deletions(-) create mode 100644 dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/proto/ProtoWriter.java diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ActivitiesDecompressor.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ActivitiesDecompressor.java index 80ccd71a1..02d2b267b 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ActivitiesDecompressor.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ActivitiesDecompressor.java @@ -19,9 +19,9 @@ import org.apache.hadoop.io.compress.CompressionCodec; import org.apache.hadoop.io.compress.CompressionCodecFactory; import org.mortbay.log.Log; -import eu.dnetlib.doiboost.orcidnodoi.json.JsonWriter; import eu.dnetlib.doiboost.orcid.model.WorkData; import eu.dnetlib.doiboost.orcid.xml.XMLRecordParser; +import eu.dnetlib.doiboost.orcidnodoi.json.JsonWriter; public class ActivitiesDecompressor { diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SummariesDecompressor.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SummariesDecompressor.java index 603bfedf6..29d72ed0b 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SummariesDecompressor.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SummariesDecompressor.java @@ -19,9 +19,9 @@ import org.apache.hadoop.io.compress.CompressionCodec; import org.apache.hadoop.io.compress.CompressionCodecFactory; import org.mortbay.log.Log; -import eu.dnetlib.doiboost.orcidnodoi.json.JsonWriter; import eu.dnetlib.doiboost.orcid.model.AuthorData; import eu.dnetlib.doiboost.orcid.xml.XMLRecordParser; +import eu.dnetlib.doiboost.orcidnodoi.json.JsonWriter; public class SummariesDecompressor { diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/json/JsonHelper.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/json/JsonHelper.java index 13a3cee8f..bfd6f7447 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/json/JsonHelper.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/json/JsonHelper.java @@ -3,6 +3,7 @@ package eu.dnetlib.doiboost.orcid.json; import com.google.gson.Gson; import com.google.gson.JsonObject; + import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi; public class JsonHelper { diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/ActivitiesDumpReader.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/ActivitiesDumpReader.java index 7eb6faf54..506641b81 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/ActivitiesDumpReader.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/ActivitiesDumpReader.java @@ -1,10 +1,12 @@ package eu.dnetlib.doiboost.orcidnodoi; -import eu.dnetlib.doiboost.orcid.json.JsonHelper; -import eu.dnetlib.doiboost.orcidnodoi.json.JsonWriter; -import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi; -import eu.dnetlib.doiboost.orcidnodoi.xml.XMLRecordParserNoDoi; +import java.io.BufferedReader; +import java.io.IOException; +import java.io.InputStream; +import java.io.InputStreamReader; +import java.net.URI; + import org.apache.commons.compress.archivers.tar.TarArchiveEntry; import org.apache.commons.compress.archivers.tar.TarArchiveInputStream; import org.apache.hadoop.conf.Configuration; @@ -17,11 +19,10 @@ import org.apache.hadoop.io.compress.CompressionCodec; import org.apache.hadoop.io.compress.CompressionCodecFactory; import org.mortbay.log.Log; -import java.io.BufferedReader; -import java.io.IOException; -import java.io.InputStream; -import java.io.InputStreamReader; -import java.net.URI; +import eu.dnetlib.doiboost.orcid.json.JsonHelper; +import eu.dnetlib.doiboost.orcidnodoi.json.JsonWriter; +import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi; +import eu.dnetlib.doiboost.orcidnodoi.xml.XMLRecordParserNoDoi; public class ActivitiesDumpReader { @@ -82,7 +83,8 @@ public class ActivitiesDumpReader { while ((line = br.readLine()) != null) { buffer.append(line); } - WorkDataNoDoi workDataNoDoi = XMLRecordParserNoDoi.VTDParseWorkData(buffer.toString().getBytes()); + WorkDataNoDoi workDataNoDoi = XMLRecordParserNoDoi + .VTDParseWorkData(buffer.toString().getBytes()); if (workDataNoDoi != null) { if (workDataNoDoi.getErrorCode() != null) { errorFromOrcidFound += 1; @@ -94,9 +96,11 @@ public class ActivitiesDumpReader { + entry.getName()); continue; } - boolean isDoiFound = workDataNoDoi.getExtIds().stream() - .filter(e -> e.getType()!=null) - .anyMatch(e -> e.getType().equals("doi")); + boolean isDoiFound = workDataNoDoi + .getExtIds() + .stream() + .filter(e -> e.getType() != null) + .anyMatch(e -> e.getType().equals("doi")); if (!isDoiFound) { String jsonData = JsonHelper.createOidWork(workDataNoDoi); Log.debug("oid: " + workDataNoDoi.getOid() + " data: " + jsonData); diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/GenOrcidAuthorWork.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/GenOrcidAuthorWork.java index b82f4bc4c..bbaa5acca 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/GenOrcidAuthorWork.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/GenOrcidAuthorWork.java @@ -1,15 +1,16 @@ package eu.dnetlib.doiboost.orcidnodoi; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.doiboost.orcid.OrcidDSManager; +import java.io.IOException; + import org.apache.commons.io.IOUtils; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.Path; import org.mortbay.log.Log; -import java.io.IOException; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.doiboost.orcid.OrcidDSManager; public class GenOrcidAuthorWork extends OrcidDSManager { diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java index 6bb31bcf6..9d9c5bc4a 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java @@ -1,13 +1,12 @@ package eu.dnetlib.doiboost.orcidnodoi; -import com.google.gson.Gson; -import com.google.gson.JsonElement; -import com.google.gson.JsonParser; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.doiboost.orcid.model.AuthorData; -import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi; -import eu.dnetlib.doiboost.orcidnodoi.similarity.AuthorMatcher; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.IOException; +import java.util.Objects; +import java.util.Optional; + import org.apache.commons.io.IOUtils; import org.apache.hadoop.io.Text; import org.apache.spark.SparkConf; @@ -19,14 +18,17 @@ import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.slf4j.Logger; import org.slf4j.LoggerFactory; + +import com.google.gson.Gson; +import com.google.gson.JsonElement; +import com.google.gson.JsonParser; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.doiboost.orcid.model.AuthorData; +import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi; +import eu.dnetlib.doiboost.orcidnodoi.similarity.AuthorMatcher; import scala.Tuple2; -import java.io.IOException; -import java.util.Objects; -import java.util.Optional; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - public class SparkGenEnrichedOrcidWorks { public static void main(String[] args) throws IOException, Exception { @@ -67,27 +69,28 @@ public class SparkGenEnrichedOrcidWorks { Encoders.bean(AuthorData.class)); JavaPairRDD activitiesRDD = sc - .sequenceFile(workingPath + outputWorksPath + "works_X.seq" , Text.class, Text.class); + .sequenceFile(workingPath + outputWorksPath + "works_X.seq", Text.class, Text.class); Dataset activitiesDataset = spark .createDataset( activitiesRDD.map(seq -> loadWorkFromJson(seq._1(), seq._2())).rdd(), Encoders.bean(WorkDataNoDoi.class)); activitiesDataset - .joinWith( - summariesDataset, - activitiesDataset.col("oid").equalTo(summariesDataset.col("oid")), "inner") - .map( - (MapFunction, Tuple2>) value -> { - WorkDataNoDoi w = value._1; - AuthorData a = value._2; - AuthorMatcher.match(a, w.getContributors()); - return new Tuple2<>(a.getOid(), w); - }, - Encoders.tuple(Encoders.STRING(), Encoders.bean(WorkDataNoDoi.class))) - .filter(Objects::nonNull) - .toJavaRDD() - .saveAsTextFile(workingPath + outputEnrichedWorksPath);; + .joinWith( + summariesDataset, + activitiesDataset.col("oid").equalTo(summariesDataset.col("oid")), "inner") + .map( + (MapFunction, Tuple2>) value -> { + WorkDataNoDoi w = value._1; + AuthorData a = value._2; + AuthorMatcher.match(a, w.getContributors()); + return new Tuple2<>(a.getOid(), w); + }, + Encoders.tuple(Encoders.STRING(), Encoders.bean(WorkDataNoDoi.class))) + .filter(Objects::nonNull) + .toJavaRDD() + .saveAsTextFile(workingPath + outputEnrichedWorksPath); + ; }); } diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/proto/ProtoWriter.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/proto/ProtoWriter.java new file mode 100644 index 000000000..01b172359 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/proto/ProtoWriter.java @@ -0,0 +1,427 @@ + +package eu.dnetlib.doiboost.orcidnodoi.proto; + +public class ProtoWriter { + +} +// +//import static eu.dnetlib.data.mapreduce.hbase.dataimport.DumpToActionsUtility.getArrayValues; +//import static eu.dnetlib.data.mapreduce.hbase.dataimport.DumpToActionsUtility.getDefaultResulttype; +//import static eu.dnetlib.data.mapreduce.hbase.dataimport.DumpToActionsUtility.getQualifier; +//import static eu.dnetlib.data.mapreduce.hbase.dataimport.DumpToActionsUtility.getStringValue; +//import static eu.dnetlib.data.mapreduce.hbase.dataimport.DumpToActionsUtility.isValidDate; +// +//import java.io.IOException; +//import java.io.InputStream; +//import java.util.ArrayList; +//import java.util.HashMap; +//import java.util.List; +//import java.util.Map; +// +//import org.apache.commons.io.IOUtils; +//import org.apache.commons.lang3.StringUtils; +// +//import com.google.gson.Gson; +//import com.google.gson.JsonArray; +//import com.google.gson.JsonElement; +//import com.google.gson.JsonObject; +//import com.googlecode.protobuf.format.JsonFormat; +// +//import eu.dnetlib.actionmanager.actions.ActionFactory; +//import eu.dnetlib.actionmanager.actions.AtomicAction; +//import eu.dnetlib.actionmanager.common.Agent; +//import eu.dnetlib.data.mapreduce.hbase.Reporter; +//import eu.dnetlib.data.mapreduce.util.StreamUtils; +//import eu.dnetlib.data.proto.FieldTypeProtos; +//import eu.dnetlib.data.proto.FieldTypeProtos.Author; +//import eu.dnetlib.data.proto.FieldTypeProtos.DataInfo; +//import eu.dnetlib.data.proto.FieldTypeProtos.KeyValue; +//import eu.dnetlib.data.proto.FieldTypeProtos.Qualifier; +//import eu.dnetlib.data.proto.FieldTypeProtos.StringField; +//import eu.dnetlib.data.proto.FieldTypeProtos.StructuredProperty; +//import eu.dnetlib.data.proto.KindProtos; +//import eu.dnetlib.data.proto.OafProtos; +//import eu.dnetlib.data.proto.ResultProtos; +//import eu.dnetlib.data.proto.TypeProtos; +//import eu.dnetlib.data.transform.xml.AbstractDNetXsltFunctions; +//import eu.dnetlib.miscutils.collections.Pair; +//import eu.dnetlib.miscutils.datetime.DateUtils; +//import eu.dnetlib.pace.model.Person; +// +//public class ProtoWriter { +// +// public static final String ORCID = "ORCID"; +// public final static String orcidPREFIX = "orcid_______"; +// public static final String OPENAIRE_PREFIX = "openaire____"; +// public static final String SEPARATOR = "::"; +// +// private static Map> datasources = new HashMap>() { +// +// { +// put(ORCID.toLowerCase(), new Pair<>(ORCID, OPENAIRE_PREFIX + SEPARATOR + "orcid")); +// +// } +// }; +// +// // json external id will be mapped to oaf:pid/@classid Map to oaf:pid/@classname +// private static Map> externalIds = new HashMap>() { +// +// { +// put("ark".toLowerCase(), new Pair<>("ark", "ark")); +// put("arxiv".toLowerCase(), new Pair<>("arxiv", "arXiv")); +// put("pmc".toLowerCase(), new Pair<>("pmc", "pmc")); +// put("pmid".toLowerCase(), new Pair<>("pmid", "pmid")); +// put("source-work-id".toLowerCase(), new Pair<>("orcidworkid", "orcidworkid")); +// put("urn".toLowerCase(), new Pair<>("urn", "urn")); +// } +// }; +// +// static Map> typologiesMapping; +// +// static { +// try { +// final InputStream is = OrcidToActions.class.getResourceAsStream("/eu/dnetlib/data/mapreduce/hbase/dataimport/mapping_typologies_orcid.json"); +// final String tt = IOUtils.toString(is); +// typologiesMapping = new Gson().fromJson(tt, Map.class); +// } catch (final IOException e) { +// e.printStackTrace(); +// } +// } +// +// public static final String PID_TYPES = "dnet:pid_types"; +// +// public static List generatePublicationActionsFromDump(final JsonObject rootElement, +// final ActionFactory factory, +// final String setName, +// final Agent agent, +// final Reporter context) { +// +// if (!isValid(rootElement, context)) { return null; } +// +// // Create OAF proto +// +// final OafProtos.Oaf.Builder oaf = OafProtos.Oaf.newBuilder(); +// +// oaf.setDataInfo( +// DataInfo.newBuilder() +// .setDeletedbyinference(false) +// .setInferred(false) +// .setTrust("0.9") +// .setProvenanceaction(getQualifier("sysimport:actionset:orcidworks-no-doi", "dnet:provenanceActions")) +// .build()); +// +// // Adding kind +// oaf.setKind(KindProtos.Kind.entity); +// +// oaf.setLastupdatetimestamp(DateUtils.now()); +// +// // creating result proto +// final OafProtos.OafEntity.Builder entity = OafProtos.OafEntity.newBuilder().setType(TypeProtos.Type.result); +// +// entity.setDateofcollection("2018-10-22"); +// entity.setDateoftransformation(DateUtils.now_ISO8601()); +// +// // Adding external ids +// StreamUtils.toStream(externalIds.keySet().iterator()) +// .forEach(jsonExtId -> { +// final String classid = externalIds.get(jsonExtId.toLowerCase()).getValue(); +// final String classname = externalIds.get(jsonExtId.toLowerCase()).getKey(); +// final String extId = getStringValue(rootElement, jsonExtId); +// if (StringUtils.isNotBlank(extId)) { +// entity.addPid(StructuredProperty.newBuilder() +// .setValue(extId) +// .setQualifier(Qualifier.newBuilder().setClassid(classid).setClassname(classname).setSchemeid("dnet:pid_types") +// .setSchemename("dnet:pid_types").build()) +// .build()); +// } +// }); +// +// // Create result field +// final ResultProtos.Result.Builder result = ResultProtos.Result.newBuilder(); +// +// // Create metadata proto +// final ResultProtos.Result.Metadata.Builder metadata = ResultProtos.Result.Metadata.newBuilder(); +// +// // Adding source +// final String source = getStringValue(rootElement, "source"); +// if (StringUtils.isNotBlank(source)) { +// metadata.addSource(StringField.newBuilder().setValue(source).build()); +// } +// +// // Adding title +// final String title = createRepeatedField(rootElement, "titles"); +// if (StringUtils.isBlank(title)) { +// context.incrementCounter("filtered", "title_not_found", 1); +// return null; +// } +// metadata.addTitle(FieldTypeProtos.StructuredProperty.newBuilder() +// .setValue(title) +// .setQualifier(getQualifier("main title", "dnet:dataCite_title")) +// .build()); +// +// // Adding identifier +// final String id = getStringValue(rootElement, "id"); +// String sourceId = null; +// if (id != null) { +// entity.addOriginalId(id); +// sourceId = String.format("50|%s" + SEPARATOR + "%s", orcidPREFIX, AbstractDNetXsltFunctions.md5(id)); +// } else { +// sourceId = String.format("50|%s" + SEPARATOR + "%s", orcidPREFIX, AbstractDNetXsltFunctions.md5(title)); +// } +// entity.setId(sourceId); +// +// // Adding relevant date +// settingRelevantDate(rootElement, metadata, "publication_date", "issued", true); +// +// // Adding collectedfrom +// final FieldTypeProtos.KeyValue collectedFrom = FieldTypeProtos.KeyValue.newBuilder() +// .setValue(ORCID) +// .setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + "806360c771262b4d6770e7cdf04b5c5a") +// .build(); +// entity.addCollectedfrom(collectedFrom); +// +// // Adding type +// final String type = getStringValue(rootElement, "type"); +// String cobjValue = ""; +// if (StringUtils.isNotBlank(type)) { +// +// metadata.setResourcetype(FieldTypeProtos.Qualifier.newBuilder() +// .setClassid(type) +// .setClassname(type) +// .setSchemeid("dnet:dataCite_resource") +// .setSchemename("dnet:dataCite_resource") +// .build()); +// +// final String typeValue = typologiesMapping.get(type).get("value"); +// cobjValue = typologiesMapping.get(type).get("cobj"); +// final ResultProtos.Result.Instance.Builder instance = ResultProtos.Result.Instance.newBuilder(); +// +// // Adding hostedby +// instance.setHostedby(FieldTypeProtos.KeyValue.newBuilder() +// .setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + "55045bd2a65019fd8e6741a755395c8c") +// .setValue("Unknown Repository") +// .build()); +// +// // Adding url +// final String url = createRepeatedField(rootElement, "urls"); +// if (StringUtils.isNotBlank(url)) { +// instance.addUrl(url); +// } +// +// final String pubDate = getPublicationDate(rootElement, "publication_date"); +// if (StringUtils.isNotBlank(pubDate)) { +// instance.setDateofacceptance(FieldTypeProtos.StringField.newBuilder().setValue(pubDate).build()); +// } +// +// instance.setCollectedfrom(collectedFrom); +// +// // Adding accessright +// instance.setAccessright(FieldTypeProtos.Qualifier.newBuilder() +// .setClassid("UNKNOWN") +// .setClassname("UNKNOWN") +// .setSchemeid("dnet:access_modes") +// .setSchemename("dnet:access_modes") +// .build()); +// +// // Adding type +// instance.setInstancetype(FieldTypeProtos.Qualifier.newBuilder() +// .setClassid(cobjValue) +// .setClassname(typeValue) +// .setSchemeid("dnet:publication_resource") +// .setSchemename("dnet:publication_resource") +// .build()); +// +// result.addInstance(instance); +// } else { +// context.incrementCounter("filtered", "type_not_found", 1); +// return null; +// } +// +// // Adding authors +// final List authors = createAuthors(rootElement); +// if (authors != null && authors.size() > 0) { +// metadata.addAllAuthor(authors); +// } else { +// context.incrementCounter("filtered", "author_not_found", 1); +// return null; +// } +// +// metadata.setResulttype(getQualifier(getDefaultResulttype(cobjValue), "dnet:result_typologies")); +// result.setMetadata(metadata.build()); +// entity.setResult(result.build()); +// oaf.setEntity(entity.build()); +// +// final List actionList = new ArrayList<>(); +// +// actionList.add(factory.createAtomicAction(setName, agent, oaf.getEntity().getId(), "result", "body", oaf.build().toByteArray())); +// +//// System.out.println(JsonFormat.printToString(oaf.build())); +// return actionList; +// +// } +// +// public static List createAuthors(final JsonObject root) { +// +// final String authorsJSONFieldName = "authors"; +// +// if (root.has(authorsJSONFieldName) && root.get(authorsJSONFieldName).isJsonArray()) { +// +// final List authors = new ArrayList<>(); +// final JsonArray jsonAuthors = root.getAsJsonArray(authorsJSONFieldName); +// int firstCounter = 0; +// int defaultCounter = 0; +// int rank = 1; +// int currentRank = 0; +// +// for (final JsonElement item : jsonAuthors) { +// final JsonObject author = item.getAsJsonObject(); +// final Author.Builder result = Author.newBuilder(); +// if (item.isJsonObject()) { +// final String surname = getStringValue(author, "surname"); +// final String name = getStringValue(author, "name"); +// final String oid = getStringValue(author, "oid"); +// final String seq = getStringValue(author, "seq"); +// if (StringUtils.isNotBlank(seq)) { +// if (seq.equals("first")) { +// firstCounter += 1; +// rank = firstCounter; +// +// } else if (seq.equals("additional")) { +// rank = currentRank + 1; +// } else { +// defaultCounter += 1; +// rank = defaultCounter; +// } +// } +// +// if (StringUtils.isNotBlank(oid)) { +// result.addPid(KeyValue.newBuilder() +// .setValue(oid) +// .setKey("ORCID") +// .build()); +// result.setFullname(name + " " + surname); +// if (StringUtils.isNotBlank(name)) { +// result.setName(name); +// } +// if (StringUtils.isNotBlank(surname)) { +// result.setSurname(surname); +// } +// } else { +// String fullname = ""; +// if (StringUtils.isNotBlank(name)) { +// fullname = name; +// } else { +// if (StringUtils.isNotBlank(surname)) { +// fullname = surname; +// } +// } +// Person p = new Person(fullname, false); +// if (p.isAccurate()) { +// result.setName(p.getNormalisedFirstName()); +// result.setSurname(p.getNormalisedSurname()); +// result.setFullname(p.getNormalisedFullname()); +// } +// else { +// result.setFullname(fullname); +// } +// } +// } +// result.setRank(rank); +// authors.add(result.build()); +// currentRank = rank; +// } +// return authors; +// +// } +// return null; +// } +// +// private static String createRepeatedField(final JsonObject rootElement, final String fieldName) { +// String field = ""; +// if (!rootElement.has(fieldName)) { return null; } +// if (rootElement.has(fieldName) && rootElement.get(fieldName).isJsonNull()) { return null; } +// if (rootElement.get(fieldName).isJsonArray()) { +// if (!isValidJsonArray(rootElement, fieldName)) { return null; } +// final StringBuilder ttl = new StringBuilder(); +// getArrayValues(rootElement, fieldName).forEach(ttl::append); +// field = ttl.toString(); +// } else { +// field = getStringValue(rootElement, fieldName); +// } +// +// if (field != null && !field.isEmpty() && field.charAt(0) == '"' && field.charAt(field.length() - 1) == '"') { +// field = field.substring(1, field.length() - 1); +// } +// return field; +// } +// +// private static void settingRelevantDate(final JsonObject rootElement, +// final ResultProtos.Result.Metadata.Builder metadata, +// final String jsonKey, +// final String dictionaryKey, +// final boolean addToDateOfAcceptance) { +// +// final String pubDate = getPublicationDate(rootElement, "publication_date"); +// if (StringUtils.isNotBlank(pubDate)) { +// if (addToDateOfAcceptance) { +// metadata.setDateofacceptance(FieldTypeProtos.StringField.newBuilder().setValue(pubDate).build()); +// } +// metadata.addRelevantdate(FieldTypeProtos.StructuredProperty.newBuilder() +// .setValue(pubDate) +// .setQualifier(getQualifier(dictionaryKey, "dnet:dataCite_date")) +// .build()); +// } +// } +// +// private static String getPublicationDate(final JsonObject rootElement, +// final String jsonKey) { +// +// final JsonObject pubDateJson = rootElement.getAsJsonObject(jsonKey); +// if (pubDateJson == null) { return null; } +// final String year = getStringValue(pubDateJson, "year"); +// final String month = getStringValue(pubDateJson, "month"); +// final String day = getStringValue(pubDateJson, "day"); +// +// if (StringUtils.isBlank(year)) { return null; } +// String pubDate = "".concat(year); +// if (StringUtils.isNotBlank(month)) { +// pubDate = pubDate.concat("-" + month); +// if (StringUtils.isNotBlank(day)) { +// pubDate = pubDate.concat("-" + day); +// } else { +// pubDate += "-01"; +// } +// } else { +// pubDate += "-01-01"; +// } +// if (isValidDate(pubDate)) { return pubDate; } +// return null; +// } +// +// protected static boolean isValid(final JsonObject rootElement, final Reporter context) { +// +// final String type = getStringValue(rootElement, "type"); +// if (!typologiesMapping.containsKey(type)) { +// context.incrementCounter("filtered", "unknowntype_" + type, 1); +// return false; +// } +// +// if (!isValidJsonArray(rootElement, "titles")) { +// context.incrementCounter("filtered", "invalid_title", 1); +// return false; +// } +// return true; +// } +// +// private static boolean isValidJsonArray(final JsonObject rootElement, final String fieldName) { +// if (!rootElement.has(fieldName)) { return false; } +// final JsonElement jsonElement = rootElement.get(fieldName); +// if (jsonElement.isJsonNull()) { return false; } +// if (jsonElement.isJsonArray()) { +// final JsonArray jsonArray = jsonElement.getAsJsonArray(); +// if (jsonArray.isJsonNull()) { return false; } +// if (jsonArray.get(0).isJsonNull()) { return false; } +// } +// return true; +// } +//} diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works/oozie_app/workflow.xml index 2486bdb24..33fbdf875 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works/oozie_app/workflow.xml @@ -509,7 +509,7 @@ cluster Gen_Enriched_Orcid_Works eu.dnetlib.doiboost.orcidnodoi.SparkGenEnrichedOrcidWorks - dhp-doiboost-1.2.3-SNAPSHOT.jar + dhp-doiboost-1.2.2-SNAPSHOT.jar --num-executors 10 --conf spark.yarn.jars="hdfs://hadoop-rm1.garr-pa1.d4science.org:8020/user/oozie/share/lib/lib_20180405103059/spark2" --executor-memory=${sparkExecutorMemory} --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} -w${workingPath}/ From b7b6be12a51c81b2b7469684cf18bc8a3014aec4 Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Mon, 29 Jun 2020 18:03:16 +0200 Subject: [PATCH 04/37] fixed enriched works generation --- .../doiboost/orcid/json/JsonHelper.java | 6 +-- .../orcidnodoi/ActivitiesDumpReader.java | 4 +- .../orcidnodoi/GenOrcidAuthorWork.java | 1 + .../SparkGenEnrichedOrcidWorks.java | 29 +++++------ .../orcidnodoi/similarity/AuthorMatcher.java | 48 +++++-------------- .../orcidnodoi/xml/XMLRecordParserNoDoi.java | 4 +- .../oozie_app/config-default.xml | 17 +++++-- .../oozie_app/workflow.xml | 24 +++++++--- 8 files changed, 66 insertions(+), 67 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/json/JsonHelper.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/json/JsonHelper.java index bfd6f7447..94f7d8c91 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/json/JsonHelper.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/json/JsonHelper.java @@ -2,16 +2,12 @@ package eu.dnetlib.doiboost.orcid.json; import com.google.gson.Gson; -import com.google.gson.JsonObject; import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi; public class JsonHelper { public static String createOidWork(WorkDataNoDoi workData) { - JsonObject oidWork = new JsonObject(); - oidWork.addProperty("oid", workData.getOid()); - oidWork.addProperty("work", new Gson().toJson(workData)); - return oidWork.toString(); + return new Gson().toJson(workData); } } diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/ActivitiesDumpReader.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/ActivitiesDumpReader.java index 506641b81..bf63568d8 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/ActivitiesDumpReader.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/ActivitiesDumpReader.java @@ -26,8 +26,8 @@ import eu.dnetlib.doiboost.orcidnodoi.xml.XMLRecordParserNoDoi; public class ActivitiesDumpReader { - private static final int MAX_XML_WORKS_PARSED = -1; - private static final int XML_WORKS_PARSED_COUNTER_LOG_INTERVAL = 100000; + private static final int MAX_XML_WORKS_PARSED = 100; + private static final int XML_WORKS_PARSED_COUNTER_LOG_INTERVAL = 10; public static void parseGzActivities(Configuration conf, String inputUri, Path outputPath) throws Exception { diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/GenOrcidAuthorWork.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/GenOrcidAuthorWork.java index bbaa5acca..8dcee796c 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/GenOrcidAuthorWork.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/GenOrcidAuthorWork.java @@ -45,6 +45,7 @@ public class GenOrcidAuthorWork extends OrcidDSManager { Log.info("HDFS URI: " + hdfsServerUri); workingPath = parser.get("workingPath"); Log.info("Working Path: " + workingPath); + hdfsOrcidDefaultPath = workingPath; activitiesFileNameTarGz = parser.get("activitiesFileNameTarGz"); Log.info("Activities File Name: " + activitiesFileNameTarGz); outputWorksPath = parser.get("outputWorksPath"); diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java index 9d9c5bc4a..ae1e4dae6 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java @@ -24,6 +24,7 @@ import com.google.gson.JsonElement; import com.google.gson.JsonParser; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.doiboost.orcid.json.JsonHelper; import eu.dnetlib.doiboost.orcid.model.AuthorData; import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi; import eu.dnetlib.doiboost.orcidnodoi.similarity.AuthorMatcher; @@ -31,9 +32,9 @@ import scala.Tuple2; public class SparkGenEnrichedOrcidWorks { + static Logger logger = LoggerFactory.getLogger(SparkGenEnrichedOrcidWorks.class); + public static void main(String[] args) throws IOException, Exception { - Logger logger = LoggerFactory.getLogger(SparkGenEnrichedOrcidWorks.class); - logger.info("[ SparkGenerateDoiAuthorList STARTED]"); final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils @@ -46,13 +47,9 @@ public class SparkGenEnrichedOrcidWorks { .ofNullable(parser.get("isSparkSessionManaged")) .map(Boolean::valueOf) .orElse(Boolean.TRUE); - logger.info("isSparkSessionManaged: {}", isSparkSessionManaged); final String workingPath = parser.get("workingPath"); - logger.info("workingPath: ", workingPath); final String outputEnrichedWorksPath = parser.get("outputEnrichedWorksPath"); - logger.info("outputEnrichedWorksPath: ", outputEnrichedWorksPath); final String outputWorksPath = parser.get("outputWorksPath"); - logger.info("outputWorksPath: ", outputWorksPath); SparkConf conf = new SparkConf(); runWithSparkSession( @@ -67,30 +64,33 @@ public class SparkGenEnrichedOrcidWorks { .createDataset( summariesRDD.map(seq -> loadAuthorFromJson(seq._1(), seq._2())).rdd(), Encoders.bean(AuthorData.class)); + logger.info("Authors data loaded: " + summariesDataset.count()); JavaPairRDD activitiesRDD = sc - .sequenceFile(workingPath + outputWorksPath + "works_X.seq", Text.class, Text.class); + .sequenceFile(workingPath + outputWorksPath + "*.seq", Text.class, Text.class); Dataset activitiesDataset = spark .createDataset( activitiesRDD.map(seq -> loadWorkFromJson(seq._1(), seq._2())).rdd(), Encoders.bean(WorkDataNoDoi.class)); + logger.info("Works data loaded: " + activitiesDataset.count()); - activitiesDataset + JavaRDD> enrichedWorksRDD = activitiesDataset .joinWith( summariesDataset, activitiesDataset.col("oid").equalTo(summariesDataset.col("oid")), "inner") .map( - (MapFunction, Tuple2>) value -> { + (MapFunction, Tuple2>) value -> { WorkDataNoDoi w = value._1; AuthorData a = value._2; AuthorMatcher.match(a, w.getContributors()); - return new Tuple2<>(a.getOid(), w); + return new Tuple2<>(a.getOid(), JsonHelper.createOidWork(w)); }, - Encoders.tuple(Encoders.STRING(), Encoders.bean(WorkDataNoDoi.class))) + Encoders.tuple(Encoders.STRING(), Encoders.STRING())) .filter(Objects::nonNull) - .toJavaRDD() - .saveAsTextFile(workingPath + outputEnrichedWorksPath); - ; + .toJavaRDD(); + logger.info("Works enriched data created: " + enrichedWorksRDD.count()); + enrichedWorksRDD.repartition(10).saveAsTextFile(workingPath + outputEnrichedWorksPath); + logger.info("Works enriched data saved"); }); } @@ -105,6 +105,7 @@ public class SparkGenEnrichedOrcidWorks { } private static WorkDataNoDoi loadWorkFromJson(Text orcidId, Text json) { + WorkDataNoDoi workData = new Gson().fromJson(json.toString(), WorkDataNoDoi.class); return workData; } diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/similarity/AuthorMatcher.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/similarity/AuthorMatcher.java index 09fd8b36b..1e4c38bef 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/similarity/AuthorMatcher.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/similarity/AuthorMatcher.java @@ -33,15 +33,13 @@ public class AuthorMatcher { List matchCounters = Arrays.asList(matchCounter); Contributor contributor = null; contributors.forEach(c -> { - if (normalize(c.getCreditName()).contains(normalize(author.getName())) || - normalize(c.getCreditName()).contains(normalize(author.getSurname())) || - ((author.getOtherName() != null) - && normalize(c.getCreditName()).contains(normalize(author.getOtherName())))) { + if (simpleMatch(c.getCreditName(), author.getName()) || + simpleMatch(c.getCreditName(), author.getSurname()) || + simpleMatch(c.getCreditName(), author.getOtherName())) { matchCounters.set(0, matchCounters.get(0) + 1); c.setSimpleMatch(true); } }); - logger.info("match counter: " + Integer.toString(matchCounters.get(0))); if (matchCounters.get(0) == 1) { updateAuthorsSimpleMatch(contributors, author); } else if (matchCounters.get(0) > 1) { @@ -50,7 +48,6 @@ public class AuthorMatcher { .filter(c -> c.isSimpleMatch()) .map(c -> { c.setScore(bestMatch(author.getName(), author.getSurname(), c.getCreditName())); - logger.debug("nella map: " + c.getCreditName() + " score: " + c.getScore()); return c; }) .filter(c -> c.getScore() >= threshold) @@ -59,24 +56,21 @@ public class AuthorMatcher { if (optCon.isPresent()) { bestMatchContributor = optCon.get(); bestMatchContributor.setBestMatch(true); - logger.info("best match: " + bestMatchContributor.getCreditName()); updateAuthorsSimilarityMatch(contributors, author); } } - logger.info("UPDATED contributors: "); - contributors.forEach(c -> { - logger - .info( - c.getOid() + " - " + c.getCreditName() + " - " + - c.getName() + " - " + c.getSurname() + " - " + - c.getRole() + " - " + c.getSequence()); - }); + } + + private static boolean simpleMatch(String name, String searchValue) { + if (searchValue == null) { + return false; + } + return normalize(name).contains(normalize(searchValue)); } private static Double bestMatch(String authorSurname, String authorName, String contributor) { - logger.debug(authorSurname + " " + authorName + " vs " + contributor); String[] contributorSplitted = contributor.split(" "); if (contributorSplitted.length == 0) { return 0.0; @@ -90,10 +84,6 @@ public class AuthorMatcher { } contributorSurname = joiner.toString(); } - logger - .debug( - "contributorName: " + contributorName + - " contributorSurname: " + contributorSurname); String authorNameNrm = normalize(authorName); String authorSurnameNrm = normalize(authorSurname); String contributorNameNrm = normalize(contributorName); @@ -108,8 +98,6 @@ public class AuthorMatcher { private static Double similarity(String nameA, String surnameA, String nameB, String surnameB) { Double score = similarityJaroWinkler(nameA, surnameA, nameB, surnameB); - logger - .debug(nameA + ", " + surnameA + " <> " + nameB + ", " + surnameB + " score: " + Double.toString(score)); return score; } @@ -118,6 +106,9 @@ public class AuthorMatcher { } private static String normalize(final String s) { + if (s == null) { + return new String(""); + } return nfd(s) .toLowerCase() // do not compact the regexes in a single expression, would cause StackOverflowError @@ -142,7 +133,6 @@ public class AuthorMatcher { private static void updateAuthorsSimpleMatch(List contributors, AuthorData author) { contributors.forEach(c -> { if (c.isSimpleMatch()) { - logger.info("simple match on : " + c.getCreditName()); c.setName(author.getName()); c.setSurname(author.getSurname()); c.setOid(author.getOid()); @@ -152,21 +142,10 @@ public class AuthorMatcher { } private static void updateAuthorsSimilarityMatch(List contributors, AuthorData author) { - logger.info("inside updateAuthorsSimilarityMatch ..."); - contributors.forEach(c -> { - logger - .info( - c.getOid() + " - " + c.getCreditName() + " - " + - c.getName() + " - " + c.getSurname() + " - " + - c.getRole() + " - " + c.getSequence() + " - best: " + c.isBestMatch() + " - simpe: " - + c.isSimpleMatch()); - }); - contributors .stream() .filter(c -> c.isBestMatch()) .forEach(c -> { - logger.info("similarity match on : " + c.getCreditName()); c.setName(author.getName()); c.setSurname(author.getSurname()); c.setOid(author.getOid()); @@ -184,7 +163,6 @@ public class AuthorMatcher { c.getSequence().equals("additional"))) .count() > 0) { seqFound = true; - logger.info("sequence data found"); } if (!seqFound) { List seqIds = Arrays.asList(0); diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/xml/XMLRecordParserNoDoi.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/xml/XMLRecordParserNoDoi.java index 6e5771547..ae96a322f 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/xml/XMLRecordParserNoDoi.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/xml/XMLRecordParserNoDoi.java @@ -41,7 +41,6 @@ public class XMLRecordParserNoDoi { public static WorkDataNoDoi VTDParseWorkData(byte[] bytes) throws VtdException, EncodingException, EOFException, EntityException, ParseException, XPathParseException, NavException, XPathEvalException { - logger.info("parsing xml ..."); final VTDGen vg = new VTDGen(); vg.setDoc(bytes); vg.parse(true); @@ -191,6 +190,9 @@ public class XMLRecordParserNoDoi { nameIndex++; } } + if (contributors.size() == 0) { + return contributors; + } int sequenceIndex = 0; ap.selectXPath("//work:contributor/work:contributor-attributes/work:contributor-sequence"); diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works/oozie_app/config-default.xml index f2d51e260..3068562d0 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works/oozie_app/config-default.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works/oozie_app/config-default.xml @@ -8,15 +8,24 @@ true - oozie.launcher.mapreduce.map.java.opts - -Xmx4g + oozie.launcher.mapreduce.map.java.opts + -Xmx4g jobTracker - hadoop-rm3.garr-pa1.d4science.org:8032 + yarnRM nameNode - hdfs://hadoop-rm1.garr-pa1.d4science.org:8020 + hdfs://nameservice1 + + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works/oozie_app/workflow.xml index 33fbdf875..df5e0e76f 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works/oozie_app/workflow.xml @@ -71,10 +71,9 @@ the shell command that downloads and puts to hdfs orcid activity file X - + - - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] @@ -133,6 +132,7 @@ -n${nameNode} -fORCID_2019_activites_0.tar.gz -owno_doi_works/works_0.seq + -oewno_doi_enriched_works/ @@ -169,6 +169,7 @@ -n${nameNode} -fORCID_2019_activites_1.tar.gz -owno_doi_works/works_1.seq + -oewno_doi_enriched_works/ @@ -205,6 +206,7 @@ -n${nameNode} -fORCID_2019_activites_2.tar.gz -owno_doi_works/works_2.seq + -oewno_doi_enriched_works/ @@ -241,6 +243,7 @@ -n${nameNode} -fORCID_2019_activites_3.tar.gz -owno_doi_works/works_3.seq + -oewno_doi_enriched_works/ @@ -277,6 +280,7 @@ -n${nameNode} -fORCID_2019_activites_4.tar.gz -owno_doi_works/works_4.seq + -oewno_doi_enriched_works/ @@ -313,6 +317,7 @@ -n${nameNode} -fORCID_2019_activites_5.tar.gz -owno_doi_works/works_5.seq + -oewno_doi_enriched_works/ @@ -349,6 +354,7 @@ -n${nameNode} -fORCID_2019_activites_6.tar.gz -owno_doi_works/works_6.seq + -oewno_doi_enriched_works/ @@ -386,6 +392,7 @@ -n${nameNode} -fORCID_2019_activites_7.tar.gz -owno_doi_works/works_7.seq + -oewno_doi_enriched_works/ @@ -422,6 +429,7 @@ -n${nameNode} -fORCID_2019_activites_8.tar.gz -owno_doi_works/works_8.seq + -oewno_doi_enriched_works/ @@ -458,6 +466,7 @@ -n${nameNode} -fORCID_2019_activites_9.tar.gz -owno_doi_works/works_9.seq + -oewno_doi_enriched_works/ @@ -494,11 +503,12 @@ -n${nameNode} -fORCID_2019_activites_X.tar.gz -owno_doi_works/works_X.seq + -oewno_doi_enriched_works/ - + @@ -509,12 +519,14 @@ cluster Gen_Enriched_Orcid_Works eu.dnetlib.doiboost.orcidnodoi.SparkGenEnrichedOrcidWorks - dhp-doiboost-1.2.2-SNAPSHOT.jar + dhp-doiboost-1.2.4-SNAPSHOT.jar --num-executors 10 --conf spark.yarn.jars="hdfs://hadoop-rm1.garr-pa1.d4science.org:8020/user/oozie/share/lib/lib_20180405103059/spark2" --executor-memory=${sparkExecutorMemory} --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} -w${workingPath}/ + -n${nameNode} + -f- -owno_doi_works/ - -oewno_doi_enriched_works/ + -oewno_doi_enriched_works/output From 5525f57ec8f9ef07d74ab30c54ab8d39e924d413 Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Wed, 1 Jul 2020 18:36:14 +0200 Subject: [PATCH 05/37] converter from orcid work json to oaf --- .../orcidnodoi/oaf/OrcidWorkToOAF.java | 420 +++++++++++++++++ .../orcidnodoi/proto/ProtoWriter.java | 427 ------------------ .../orcidnodoi/util/DumpToActionsUtility.java | 107 +++++ .../doiboost/orcidnodoi/util/Pair.java | 30 ++ .../orcidnodoi/mappings/typologies.json | 41 ++ 5 files changed, 598 insertions(+), 427 deletions(-) create mode 100644 dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/OrcidWorkToOAF.java delete mode 100644 dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/proto/ProtoWriter.java create mode 100644 dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/util/DumpToActionsUtility.java create mode 100644 dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/util/Pair.java create mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcidnodoi/mappings/typologies.json diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/OrcidWorkToOAF.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/OrcidWorkToOAF.java new file mode 100644 index 000000000..673abb407 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/OrcidWorkToOAF.java @@ -0,0 +1,420 @@ + +package eu.dnetlib.doiboost.orcidnodoi.oaf; + +import com.google.gson.Gson; +import com.google.gson.JsonArray; +import com.google.gson.JsonElement; +import com.google.gson.JsonObject; +import eu.dnetlib.dhp.common.PacePerson; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.utils.DHPUtils; +import eu.dnetlib.doiboost.orcidnodoi.SparkGenEnrichedOrcidWorks; +import eu.dnetlib.doiboost.orcidnodoi.util.DumpToActionsUtility; +import eu.dnetlib.doiboost.orcidnodoi.util.Pair; +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.util.*; +import java.util.stream.Collectors; + +import static eu.dnetlib.doiboost.orcidnodoi.util.DumpToActionsUtility.*; + +public class OrcidWorkToOAF { + + static Logger logger = LoggerFactory.getLogger(OrcidWorkToOAF.class); + + public static final String ORCID = "ORCID"; + public final static String orcidPREFIX = "orcid_______"; + public static final String OPENAIRE_PREFIX = "openaire____"; + public static final String SEPARATOR = "::"; + + private static Map> datasources = new HashMap>() { + + { + put(ORCID.toLowerCase(), new Pair<>(ORCID, OPENAIRE_PREFIX + SEPARATOR + "orcid")); + + } + }; + + // json external id will be mapped to oaf:pid/@classid Map to oaf:pid/@classname + private static Map> externalIds = new HashMap>() { + + { + put("ark".toLowerCase(), new Pair<>("ark", "ark")); + put("arxiv".toLowerCase(), new Pair<>("arxiv", "arXiv")); + put("pmc".toLowerCase(), new Pair<>("pmc", "pmc")); + put("pmid".toLowerCase(), new Pair<>("pmid", "pmid")); + put("source-work-id".toLowerCase(), new Pair<>("orcidworkid", "orcidworkid")); + put("urn".toLowerCase(), new Pair<>("urn", "urn")); + } + }; + + static Map> typologiesMapping; + + static { + try { + final String tt = IOUtils.toString(OrcidWorkToOAF.class.getResourceAsStream( + "/eu/dnetlib/dhp/doiboost/orcidnodoi/mappings/typologies.json")); + typologiesMapping = new Gson().fromJson(tt, Map.class); + } catch (final Exception e) { + logger.error("loading typologies", e); + } + } + + public static final String PID_TYPES = "dnet:pid_types"; + + public static Oaf generatePublicationActionsFromDump(final JsonObject rootElement, final String setName) { + + if (!isValid(rootElement/*, context*/)) { return null; } + + Publication publication = new Publication(); + + final DataInfo dataInfo = new DataInfo(); + dataInfo.setDeletedbyinference(false); + dataInfo.setInferred(false); + dataInfo.setTrust("0.9"); + dataInfo.setProvenanceaction( + mapQualifier( + "sysimport:actionset:orcidworks-no-doi", + "sysimport:actionset:orcidworks-no-doi", + "dnet:provenanceActions", + "dnet:provenanceActions")); + publication.setDataInfo(dataInfo); + + publication.setLastupdatetimestamp(new Date().getTime()); + + publication.setDateofcollection("2019-10-22"); + publication.setDateoftransformation(DumpToActionsUtility.now_ISO8601()); + + // Adding external ids + externalIds.keySet().stream() + .forEach(jsonExtId -> { + final String classid = externalIds.get(jsonExtId.toLowerCase()).getValue(); + final String classname = externalIds.get(jsonExtId.toLowerCase()).getKey(); + final String extId = getStringValue(rootElement, jsonExtId); + if (StringUtils.isNotBlank(extId)) { + publication.getExternalReference().add( + convertExtRef(extId, classid, classname, "dnet:pid_types", "dnet:pid_types")); + } + }); + + // Adding source +// final String source = getStringValue(rootElement, "source"); +// if (StringUtils.isNotBlank(source)) { +// metadata.addSource(StringField.newBuilder().setValue(source).build()); +// } + + // Adding titles + final List titles = createRepeatedField(rootElement, "titles"); + if (titles==null || titles.isEmpty()) { +// context.incrementCounter("filtered", "title_not_found", 1); + return null; + } + Qualifier q = mapQualifier("main title","main title","dnet:dataCite_title","dnet:dataCite_title"); + publication.setTitle( + titles + .stream() + .map(t -> { + return mapStructuredProperty(t, q, null); + }) + .collect(Collectors.toList())); + // Adding identifier + final String id = getStringValue(rootElement, "id"); + String sourceId = null; + if (id != null) { + publication.setOriginalId(Arrays.asList(id)); + sourceId = String.format("50|%s" + SEPARATOR + "%s", orcidPREFIX, DHPUtils.md5(id.toLowerCase())); + } else { + String mergedTitle = titles.stream().map(Object::toString).collect(Collectors.joining(",")); + sourceId = String.format("50|%s" + SEPARATOR + "%s", orcidPREFIX, DHPUtils.md5(mergedTitle.toLowerCase())); + } + publication.setId(sourceId); + + // Adding relevant date + settingRelevantDate(rootElement, publication, "publication_date", "issued", true); + + // Adding collectedfrom + publication.setCollectedfrom(Arrays.asList(createCollectedFrom())); + + // Adding type + final String type = getStringValue(rootElement, "type"); + String cobjValue = ""; + if (StringUtils.isNotBlank(type)) { + publication.setResourcetype(mapQualifier(type, type, "dnet:dataCite_resource", "dnet:dataCite_resource")); + + final String typeValue = typologiesMapping.get(type).get("value"); + cobjValue = typologiesMapping.get(type).get("cobj"); + final Instance instance = new Instance(); + + // Adding hostedby + instance.setHostedby(createHostedBy()); + + // Adding url + final List urls = createRepeatedField(rootElement, "urls"); + if (urls!=null && !urls.isEmpty()) { + instance.setUrl(urls); + } + + final String pubDate = getPublicationDate(rootElement, "publication_date"); + if (StringUtils.isNotBlank(pubDate)) { + instance.setDateofacceptance(mapStringField(pubDate, null)); + } + + instance.setCollectedfrom(createCollectedFrom()); + + // Adding accessright + instance.setAccessright(mapQualifier("UNKNOWN", "UNKNOWN", "dnet:access_modes", "dnet:access_modes")); + + // Adding type + instance.setInstancetype(mapQualifier(cobjValue, typeValue, "dnet:publication_resource", "dnet:publication_resource")); + + publication.setInstance(Arrays.asList(instance)); + } else { +// context.incrementCounter("filtered", "type_not_found", 1); + return null; + } + + // Adding authors + final List authors = createAuthors(rootElement); + if (authors != null && authors.size() > 0) { + publication.setAuthor(authors); + } else { +// context.incrementCounter("filtered", "author_not_found", 1); + return null; + } + String classValue = getDefaultResulttype(cobjValue); + publication.setResulttype(mapQualifier(classValue, classValue,"dnet:result_typologies", "dnet:result_typologies")); + return publication; + } + + public static List createAuthors(final JsonObject root) { + + final String authorsJSONFieldName = "authors"; + + if (root.has(authorsJSONFieldName) && root.get(authorsJSONFieldName).isJsonArray()) { + + final List authors = new ArrayList<>(); + final JsonArray jsonAuthors = root.getAsJsonArray(authorsJSONFieldName); + int firstCounter = 0; + int defaultCounter = 0; + int rank = 1; + int currentRank = 0; + + for (final JsonElement item : jsonAuthors) { + final JsonObject jsonAuthor = item.getAsJsonObject(); + final Author author = new Author(); + if (item.isJsonObject()) { + final String surname = getStringValue(jsonAuthor, "surname"); + final String name = getStringValue(jsonAuthor, "name"); + final String oid = getStringValue(jsonAuthor, "oid"); + final String seq = getStringValue(jsonAuthor, "seq"); + if (StringUtils.isNotBlank(seq)) { + if (seq.equals("first")) { + firstCounter += 1; + rank = firstCounter; + + } else if (seq.equals("additional")) { + rank = currentRank + 1; + } else { + defaultCounter += 1; + rank = defaultCounter; + } + } + + if (StringUtils.isNotBlank(oid)) { + author.setPid(Arrays.asList(mapAuthorId(oid))); + author.setFullname(name + " " + surname); + if (StringUtils.isNotBlank(name)) { + author.setName(name); + } + if (StringUtils.isNotBlank(surname)) { + author.setSurname(surname); + } + } else { + String fullname = ""; + if (StringUtils.isNotBlank(name)) { + fullname = name; + } else { + if (StringUtils.isNotBlank(surname)) { + fullname = surname; + } + } + PacePerson p = new PacePerson(fullname, false); + if (p.isAccurate()) { + author.setName(p.getNormalisedFirstName()); + author.setSurname(p.getNormalisedSurname()); + author.setFullname(p.getNormalisedFullname()); + } + else { + author.setFullname(fullname); + } + } + } + author.setRank(rank); + authors.add(author); + currentRank = rank; + } + return authors; + + } + return null; + } + + private static List createRepeatedField(final JsonObject rootElement, final String fieldName) { + if (!rootElement.has(fieldName)) { return null; } + if (rootElement.has(fieldName) && rootElement.get(fieldName).isJsonNull()) { return null; } + if (rootElement.get(fieldName).isJsonArray()) { + if (!isValidJsonArray(rootElement, fieldName)) { return null; } + return getArrayValues(rootElement, fieldName); + } else { + String field = getStringValue(rootElement, fieldName); + return Arrays.asList(cleanField(field)); + } + } + + private static String cleanField(String value) { + if (value != null && !value.isEmpty() && value.charAt(0) == '"' && value.charAt(value.length() - 1) == '"') { + value = value.substring(1, value.length() - 1); + } + return value; + } + + private static void settingRelevantDate(final JsonObject rootElement, + final Publication publication, + final String jsonKey, + final String dictionaryKey, + final boolean addToDateOfAcceptance) { + + final String pubDate = getPublicationDate(rootElement, "publication_date"); + if (StringUtils.isNotBlank(pubDate)) { + if (addToDateOfAcceptance) { + publication.setDateofacceptance(mapStringField(pubDate, null)); + } + Qualifier q = mapQualifier(dictionaryKey,dictionaryKey,"dnet:dataCite_date","dnet:dataCite_date"); + publication.setRelevantdate( + Arrays.asList(pubDate) + .stream() + .map(r -> { + return mapStructuredProperty(r, q, null); + }) + .collect(Collectors.toList())); + } + } + + private static String getPublicationDate(final JsonObject rootElement, + final String jsonKey) { + + final JsonObject pubDateJson = rootElement.getAsJsonObject(jsonKey); + if (pubDateJson == null) { return null; } + final String year = getStringValue(pubDateJson, "year"); + final String month = getStringValue(pubDateJson, "month"); + final String day = getStringValue(pubDateJson, "day"); + + if (StringUtils.isBlank(year)) { return null; } + String pubDate = "".concat(year); + if (StringUtils.isNotBlank(month)) { + pubDate = pubDate.concat("-" + month); + if (StringUtils.isNotBlank(day)) { + pubDate = pubDate.concat("-" + day); + } else { + pubDate += "-01"; + } + } else { + pubDate += "-01-01"; + } + if (isValidDate(pubDate)) { return pubDate; } + return null; + } + + protected static boolean isValid(final JsonObject rootElement/*, final Reporter context*/) { + + final String type = getStringValue(rootElement, "type"); + if (!typologiesMapping.containsKey(type)) { +// context.incrementCounter("filtered", "unknowntype_" + type, 1); + return false; + } + + if (!isValidJsonArray(rootElement, "titles")) { +// context.incrementCounter("filtered", "invalid_title", 1); + return false; + } + return true; + } + + private static boolean isValidJsonArray(final JsonObject rootElement, final String fieldName) { + if (!rootElement.has(fieldName)) { return false; } + final JsonElement jsonElement = rootElement.get(fieldName); + if (jsonElement.isJsonNull()) { return false; } + if (jsonElement.isJsonArray()) { + final JsonArray jsonArray = jsonElement.getAsJsonArray(); + if (jsonArray.isJsonNull()) { return false; } + if (jsonArray.get(0).isJsonNull()) { return false; } + } + return true; + } + + private static Qualifier mapQualifier(String classId, String className, String schemeId, String schemeName) { + final Qualifier qualifier = new Qualifier(); + qualifier.setClassid(classId); + qualifier.setClassname(className); + qualifier.setSchemeid(schemeId); + qualifier.setSchemename(schemeName); + return qualifier; + } + + private static ExternalReference convertExtRef(String extId, String classId, String className, String schemeId, String schemeName) { + ExternalReference ex = new ExternalReference(); + ex.setRefidentifier(extId); + ex.setQualifier(mapQualifier(classId, className, schemeId, schemeName )); + return ex; + } + + private static StructuredProperty mapStructuredProperty(String value, Qualifier qualifier, DataInfo dataInfo) { + if (value == null | StringUtils.isBlank(value)) { + return null; + } + + final StructuredProperty structuredProperty = new StructuredProperty(); + structuredProperty.setValue(value); + structuredProperty.setQualifier(qualifier); + structuredProperty.setDataInfo(dataInfo); + return structuredProperty; + } + + private static Field mapStringField(String value, DataInfo dataInfo) { + if (value == null || StringUtils.isBlank(value)) { + return null; + } + + final Field stringField = new Field<>(); + stringField.setValue(value); + stringField.setDataInfo(dataInfo); + return stringField; + } + + private static KeyValue createCollectedFrom() { + KeyValue cf = new KeyValue(); + cf.setValue(ORCID); + cf.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + "806360c771262b4d6770e7cdf04b5c5a"); + return cf; + } + + private static KeyValue createHostedBy() { + KeyValue hb = new KeyValue(); + hb.setValue("Unknown Repository"); + hb.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + "55045bd2a65019fd8e6741a755395c8c"); + return hb; + } + + private static StructuredProperty mapAuthorId(String orcidId) { + final StructuredProperty sp = new StructuredProperty(); + sp.setValue(orcidId); + final Qualifier q = new Qualifier(); + q.setClassid("ORCID"); + q.setClassname("ORCID"); + sp.setQualifier(q); + return sp; + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/proto/ProtoWriter.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/proto/ProtoWriter.java deleted file mode 100644 index 01b172359..000000000 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/proto/ProtoWriter.java +++ /dev/null @@ -1,427 +0,0 @@ - -package eu.dnetlib.doiboost.orcidnodoi.proto; - -public class ProtoWriter { - -} -// -//import static eu.dnetlib.data.mapreduce.hbase.dataimport.DumpToActionsUtility.getArrayValues; -//import static eu.dnetlib.data.mapreduce.hbase.dataimport.DumpToActionsUtility.getDefaultResulttype; -//import static eu.dnetlib.data.mapreduce.hbase.dataimport.DumpToActionsUtility.getQualifier; -//import static eu.dnetlib.data.mapreduce.hbase.dataimport.DumpToActionsUtility.getStringValue; -//import static eu.dnetlib.data.mapreduce.hbase.dataimport.DumpToActionsUtility.isValidDate; -// -//import java.io.IOException; -//import java.io.InputStream; -//import java.util.ArrayList; -//import java.util.HashMap; -//import java.util.List; -//import java.util.Map; -// -//import org.apache.commons.io.IOUtils; -//import org.apache.commons.lang3.StringUtils; -// -//import com.google.gson.Gson; -//import com.google.gson.JsonArray; -//import com.google.gson.JsonElement; -//import com.google.gson.JsonObject; -//import com.googlecode.protobuf.format.JsonFormat; -// -//import eu.dnetlib.actionmanager.actions.ActionFactory; -//import eu.dnetlib.actionmanager.actions.AtomicAction; -//import eu.dnetlib.actionmanager.common.Agent; -//import eu.dnetlib.data.mapreduce.hbase.Reporter; -//import eu.dnetlib.data.mapreduce.util.StreamUtils; -//import eu.dnetlib.data.proto.FieldTypeProtos; -//import eu.dnetlib.data.proto.FieldTypeProtos.Author; -//import eu.dnetlib.data.proto.FieldTypeProtos.DataInfo; -//import eu.dnetlib.data.proto.FieldTypeProtos.KeyValue; -//import eu.dnetlib.data.proto.FieldTypeProtos.Qualifier; -//import eu.dnetlib.data.proto.FieldTypeProtos.StringField; -//import eu.dnetlib.data.proto.FieldTypeProtos.StructuredProperty; -//import eu.dnetlib.data.proto.KindProtos; -//import eu.dnetlib.data.proto.OafProtos; -//import eu.dnetlib.data.proto.ResultProtos; -//import eu.dnetlib.data.proto.TypeProtos; -//import eu.dnetlib.data.transform.xml.AbstractDNetXsltFunctions; -//import eu.dnetlib.miscutils.collections.Pair; -//import eu.dnetlib.miscutils.datetime.DateUtils; -//import eu.dnetlib.pace.model.Person; -// -//public class ProtoWriter { -// -// public static final String ORCID = "ORCID"; -// public final static String orcidPREFIX = "orcid_______"; -// public static final String OPENAIRE_PREFIX = "openaire____"; -// public static final String SEPARATOR = "::"; -// -// private static Map> datasources = new HashMap>() { -// -// { -// put(ORCID.toLowerCase(), new Pair<>(ORCID, OPENAIRE_PREFIX + SEPARATOR + "orcid")); -// -// } -// }; -// -// // json external id will be mapped to oaf:pid/@classid Map to oaf:pid/@classname -// private static Map> externalIds = new HashMap>() { -// -// { -// put("ark".toLowerCase(), new Pair<>("ark", "ark")); -// put("arxiv".toLowerCase(), new Pair<>("arxiv", "arXiv")); -// put("pmc".toLowerCase(), new Pair<>("pmc", "pmc")); -// put("pmid".toLowerCase(), new Pair<>("pmid", "pmid")); -// put("source-work-id".toLowerCase(), new Pair<>("orcidworkid", "orcidworkid")); -// put("urn".toLowerCase(), new Pair<>("urn", "urn")); -// } -// }; -// -// static Map> typologiesMapping; -// -// static { -// try { -// final InputStream is = OrcidToActions.class.getResourceAsStream("/eu/dnetlib/data/mapreduce/hbase/dataimport/mapping_typologies_orcid.json"); -// final String tt = IOUtils.toString(is); -// typologiesMapping = new Gson().fromJson(tt, Map.class); -// } catch (final IOException e) { -// e.printStackTrace(); -// } -// } -// -// public static final String PID_TYPES = "dnet:pid_types"; -// -// public static List generatePublicationActionsFromDump(final JsonObject rootElement, -// final ActionFactory factory, -// final String setName, -// final Agent agent, -// final Reporter context) { -// -// if (!isValid(rootElement, context)) { return null; } -// -// // Create OAF proto -// -// final OafProtos.Oaf.Builder oaf = OafProtos.Oaf.newBuilder(); -// -// oaf.setDataInfo( -// DataInfo.newBuilder() -// .setDeletedbyinference(false) -// .setInferred(false) -// .setTrust("0.9") -// .setProvenanceaction(getQualifier("sysimport:actionset:orcidworks-no-doi", "dnet:provenanceActions")) -// .build()); -// -// // Adding kind -// oaf.setKind(KindProtos.Kind.entity); -// -// oaf.setLastupdatetimestamp(DateUtils.now()); -// -// // creating result proto -// final OafProtos.OafEntity.Builder entity = OafProtos.OafEntity.newBuilder().setType(TypeProtos.Type.result); -// -// entity.setDateofcollection("2018-10-22"); -// entity.setDateoftransformation(DateUtils.now_ISO8601()); -// -// // Adding external ids -// StreamUtils.toStream(externalIds.keySet().iterator()) -// .forEach(jsonExtId -> { -// final String classid = externalIds.get(jsonExtId.toLowerCase()).getValue(); -// final String classname = externalIds.get(jsonExtId.toLowerCase()).getKey(); -// final String extId = getStringValue(rootElement, jsonExtId); -// if (StringUtils.isNotBlank(extId)) { -// entity.addPid(StructuredProperty.newBuilder() -// .setValue(extId) -// .setQualifier(Qualifier.newBuilder().setClassid(classid).setClassname(classname).setSchemeid("dnet:pid_types") -// .setSchemename("dnet:pid_types").build()) -// .build()); -// } -// }); -// -// // Create result field -// final ResultProtos.Result.Builder result = ResultProtos.Result.newBuilder(); -// -// // Create metadata proto -// final ResultProtos.Result.Metadata.Builder metadata = ResultProtos.Result.Metadata.newBuilder(); -// -// // Adding source -// final String source = getStringValue(rootElement, "source"); -// if (StringUtils.isNotBlank(source)) { -// metadata.addSource(StringField.newBuilder().setValue(source).build()); -// } -// -// // Adding title -// final String title = createRepeatedField(rootElement, "titles"); -// if (StringUtils.isBlank(title)) { -// context.incrementCounter("filtered", "title_not_found", 1); -// return null; -// } -// metadata.addTitle(FieldTypeProtos.StructuredProperty.newBuilder() -// .setValue(title) -// .setQualifier(getQualifier("main title", "dnet:dataCite_title")) -// .build()); -// -// // Adding identifier -// final String id = getStringValue(rootElement, "id"); -// String sourceId = null; -// if (id != null) { -// entity.addOriginalId(id); -// sourceId = String.format("50|%s" + SEPARATOR + "%s", orcidPREFIX, AbstractDNetXsltFunctions.md5(id)); -// } else { -// sourceId = String.format("50|%s" + SEPARATOR + "%s", orcidPREFIX, AbstractDNetXsltFunctions.md5(title)); -// } -// entity.setId(sourceId); -// -// // Adding relevant date -// settingRelevantDate(rootElement, metadata, "publication_date", "issued", true); -// -// // Adding collectedfrom -// final FieldTypeProtos.KeyValue collectedFrom = FieldTypeProtos.KeyValue.newBuilder() -// .setValue(ORCID) -// .setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + "806360c771262b4d6770e7cdf04b5c5a") -// .build(); -// entity.addCollectedfrom(collectedFrom); -// -// // Adding type -// final String type = getStringValue(rootElement, "type"); -// String cobjValue = ""; -// if (StringUtils.isNotBlank(type)) { -// -// metadata.setResourcetype(FieldTypeProtos.Qualifier.newBuilder() -// .setClassid(type) -// .setClassname(type) -// .setSchemeid("dnet:dataCite_resource") -// .setSchemename("dnet:dataCite_resource") -// .build()); -// -// final String typeValue = typologiesMapping.get(type).get("value"); -// cobjValue = typologiesMapping.get(type).get("cobj"); -// final ResultProtos.Result.Instance.Builder instance = ResultProtos.Result.Instance.newBuilder(); -// -// // Adding hostedby -// instance.setHostedby(FieldTypeProtos.KeyValue.newBuilder() -// .setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + "55045bd2a65019fd8e6741a755395c8c") -// .setValue("Unknown Repository") -// .build()); -// -// // Adding url -// final String url = createRepeatedField(rootElement, "urls"); -// if (StringUtils.isNotBlank(url)) { -// instance.addUrl(url); -// } -// -// final String pubDate = getPublicationDate(rootElement, "publication_date"); -// if (StringUtils.isNotBlank(pubDate)) { -// instance.setDateofacceptance(FieldTypeProtos.StringField.newBuilder().setValue(pubDate).build()); -// } -// -// instance.setCollectedfrom(collectedFrom); -// -// // Adding accessright -// instance.setAccessright(FieldTypeProtos.Qualifier.newBuilder() -// .setClassid("UNKNOWN") -// .setClassname("UNKNOWN") -// .setSchemeid("dnet:access_modes") -// .setSchemename("dnet:access_modes") -// .build()); -// -// // Adding type -// instance.setInstancetype(FieldTypeProtos.Qualifier.newBuilder() -// .setClassid(cobjValue) -// .setClassname(typeValue) -// .setSchemeid("dnet:publication_resource") -// .setSchemename("dnet:publication_resource") -// .build()); -// -// result.addInstance(instance); -// } else { -// context.incrementCounter("filtered", "type_not_found", 1); -// return null; -// } -// -// // Adding authors -// final List authors = createAuthors(rootElement); -// if (authors != null && authors.size() > 0) { -// metadata.addAllAuthor(authors); -// } else { -// context.incrementCounter("filtered", "author_not_found", 1); -// return null; -// } -// -// metadata.setResulttype(getQualifier(getDefaultResulttype(cobjValue), "dnet:result_typologies")); -// result.setMetadata(metadata.build()); -// entity.setResult(result.build()); -// oaf.setEntity(entity.build()); -// -// final List actionList = new ArrayList<>(); -// -// actionList.add(factory.createAtomicAction(setName, agent, oaf.getEntity().getId(), "result", "body", oaf.build().toByteArray())); -// -//// System.out.println(JsonFormat.printToString(oaf.build())); -// return actionList; -// -// } -// -// public static List createAuthors(final JsonObject root) { -// -// final String authorsJSONFieldName = "authors"; -// -// if (root.has(authorsJSONFieldName) && root.get(authorsJSONFieldName).isJsonArray()) { -// -// final List authors = new ArrayList<>(); -// final JsonArray jsonAuthors = root.getAsJsonArray(authorsJSONFieldName); -// int firstCounter = 0; -// int defaultCounter = 0; -// int rank = 1; -// int currentRank = 0; -// -// for (final JsonElement item : jsonAuthors) { -// final JsonObject author = item.getAsJsonObject(); -// final Author.Builder result = Author.newBuilder(); -// if (item.isJsonObject()) { -// final String surname = getStringValue(author, "surname"); -// final String name = getStringValue(author, "name"); -// final String oid = getStringValue(author, "oid"); -// final String seq = getStringValue(author, "seq"); -// if (StringUtils.isNotBlank(seq)) { -// if (seq.equals("first")) { -// firstCounter += 1; -// rank = firstCounter; -// -// } else if (seq.equals("additional")) { -// rank = currentRank + 1; -// } else { -// defaultCounter += 1; -// rank = defaultCounter; -// } -// } -// -// if (StringUtils.isNotBlank(oid)) { -// result.addPid(KeyValue.newBuilder() -// .setValue(oid) -// .setKey("ORCID") -// .build()); -// result.setFullname(name + " " + surname); -// if (StringUtils.isNotBlank(name)) { -// result.setName(name); -// } -// if (StringUtils.isNotBlank(surname)) { -// result.setSurname(surname); -// } -// } else { -// String fullname = ""; -// if (StringUtils.isNotBlank(name)) { -// fullname = name; -// } else { -// if (StringUtils.isNotBlank(surname)) { -// fullname = surname; -// } -// } -// Person p = new Person(fullname, false); -// if (p.isAccurate()) { -// result.setName(p.getNormalisedFirstName()); -// result.setSurname(p.getNormalisedSurname()); -// result.setFullname(p.getNormalisedFullname()); -// } -// else { -// result.setFullname(fullname); -// } -// } -// } -// result.setRank(rank); -// authors.add(result.build()); -// currentRank = rank; -// } -// return authors; -// -// } -// return null; -// } -// -// private static String createRepeatedField(final JsonObject rootElement, final String fieldName) { -// String field = ""; -// if (!rootElement.has(fieldName)) { return null; } -// if (rootElement.has(fieldName) && rootElement.get(fieldName).isJsonNull()) { return null; } -// if (rootElement.get(fieldName).isJsonArray()) { -// if (!isValidJsonArray(rootElement, fieldName)) { return null; } -// final StringBuilder ttl = new StringBuilder(); -// getArrayValues(rootElement, fieldName).forEach(ttl::append); -// field = ttl.toString(); -// } else { -// field = getStringValue(rootElement, fieldName); -// } -// -// if (field != null && !field.isEmpty() && field.charAt(0) == '"' && field.charAt(field.length() - 1) == '"') { -// field = field.substring(1, field.length() - 1); -// } -// return field; -// } -// -// private static void settingRelevantDate(final JsonObject rootElement, -// final ResultProtos.Result.Metadata.Builder metadata, -// final String jsonKey, -// final String dictionaryKey, -// final boolean addToDateOfAcceptance) { -// -// final String pubDate = getPublicationDate(rootElement, "publication_date"); -// if (StringUtils.isNotBlank(pubDate)) { -// if (addToDateOfAcceptance) { -// metadata.setDateofacceptance(FieldTypeProtos.StringField.newBuilder().setValue(pubDate).build()); -// } -// metadata.addRelevantdate(FieldTypeProtos.StructuredProperty.newBuilder() -// .setValue(pubDate) -// .setQualifier(getQualifier(dictionaryKey, "dnet:dataCite_date")) -// .build()); -// } -// } -// -// private static String getPublicationDate(final JsonObject rootElement, -// final String jsonKey) { -// -// final JsonObject pubDateJson = rootElement.getAsJsonObject(jsonKey); -// if (pubDateJson == null) { return null; } -// final String year = getStringValue(pubDateJson, "year"); -// final String month = getStringValue(pubDateJson, "month"); -// final String day = getStringValue(pubDateJson, "day"); -// -// if (StringUtils.isBlank(year)) { return null; } -// String pubDate = "".concat(year); -// if (StringUtils.isNotBlank(month)) { -// pubDate = pubDate.concat("-" + month); -// if (StringUtils.isNotBlank(day)) { -// pubDate = pubDate.concat("-" + day); -// } else { -// pubDate += "-01"; -// } -// } else { -// pubDate += "-01-01"; -// } -// if (isValidDate(pubDate)) { return pubDate; } -// return null; -// } -// -// protected static boolean isValid(final JsonObject rootElement, final Reporter context) { -// -// final String type = getStringValue(rootElement, "type"); -// if (!typologiesMapping.containsKey(type)) { -// context.incrementCounter("filtered", "unknowntype_" + type, 1); -// return false; -// } -// -// if (!isValidJsonArray(rootElement, "titles")) { -// context.incrementCounter("filtered", "invalid_title", 1); -// return false; -// } -// return true; -// } -// -// private static boolean isValidJsonArray(final JsonObject rootElement, final String fieldName) { -// if (!rootElement.has(fieldName)) { return false; } -// final JsonElement jsonElement = rootElement.get(fieldName); -// if (jsonElement.isJsonNull()) { return false; } -// if (jsonElement.isJsonArray()) { -// final JsonArray jsonArray = jsonElement.getAsJsonArray(); -// if (jsonArray.isJsonNull()) { return false; } -// if (jsonArray.get(0).isJsonNull()) { return false; } -// } -// return true; -// } -//} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/util/DumpToActionsUtility.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/util/DumpToActionsUtility.java new file mode 100644 index 000000000..c460f6299 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/util/DumpToActionsUtility.java @@ -0,0 +1,107 @@ +package eu.dnetlib.doiboost.orcidnodoi.util; + +import com.google.gson.JsonArray; +import com.google.gson.JsonObject; +import org.apache.commons.lang3.StringUtils; + +import java.text.SimpleDateFormat; +import java.util.*; + +public class DumpToActionsUtility { + + private static final SimpleDateFormat ISO8601FORMAT = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ssZ", Locale.US); + + public static String getStringValue(final JsonObject root, final String key) { + if (root.has(key) && !root.get(key).isJsonNull()) + return root.get(key).getAsString(); + return null; + } + + public static List getArrayValues(final JsonObject root, final String key) { + if (root.has(key) && root.get(key).isJsonArray()) { + final JsonArray asJsonArray = root.get(key).getAsJsonArray(); + final List result = new ArrayList<>(); + + + asJsonArray.forEach(it -> { + if (StringUtils.isNotBlank(it.getAsString())) { + result.add(it.getAsString()); + } + }); + return result; + } + return new ArrayList<>(); + } + public static List getArrayObjects(final JsonObject root, final String key) { + if (root.has(key) && root.get(key).isJsonArray()) { + final JsonArray asJsonArray = root.get(key).getAsJsonArray(); + final List result = new ArrayList<>(); + asJsonArray.forEach(it -> { + if (it.getAsJsonObject() != null) { + result.add(it.getAsJsonObject()); + } + }); + return result; + } + return new ArrayList<>(); + } + + public static boolean isValidDate(final String date) { + return date.matches("\\d{4}-\\d{2}-\\d{2}"); + } + + public static String now_ISO8601() { // NOPMD + String result; + synchronized (ISO8601FORMAT) { + result = ISO8601FORMAT.format(new Date()); + } + //convert YYYYMMDDTHH:mm:ss+HH00 into YYYYMMDDTHH:mm:ss+HH:00 + //- note the added colon for the Timezone + return result.substring(0, result.length() - 2) + ":" + result.substring(result.length() - 2); + } + + public static String getDefaultResulttype(final String cobjcategory) { + switch (cobjcategory) { + case "0029": + return "software"; + case "0021": + case "0024": + case "0025": + case "0030": + return "dataset"; + case "0000": + case "0010": + case "0018": + case "0020": + case "0022": + case "0023": + case "0026": + case "0027": + case "0028": + case "0037": + return "other"; + case "0001": + case "0002": + case "0004": + case "0005": + case "0006": + case "0007": + case "0008": + case "0009": + case "0011": + case "0012": + case "0013": + case "0014": + case "0015": + case "0016": + case "0017": + case "0019": + case "0031": + case "0032": + return "publication"; + default: + return "publication"; + } + } + +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/util/Pair.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/util/Pair.java new file mode 100644 index 000000000..58c09af60 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/util/Pair.java @@ -0,0 +1,30 @@ +package eu.dnetlib.doiboost.orcidnodoi.util; + +public class Pair { + + private K k; + + private V v; + + public Pair(K k, V v) { + this.k = k; + this.v = v; + } + + public K getKey() { + return k; + } + + public V getValue() { + return v; + } + + @Override + public boolean equals(Object obj) { + if (obj instanceof Pair) { + Pair tmp = (Pair) obj; + return k.equals(tmp.getKey()) && v.equals(tmp.getValue()); + } else return false; + } + +} diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcidnodoi/mappings/typologies.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcidnodoi/mappings/typologies.json new file mode 100644 index 000000000..cb696f279 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcidnodoi/mappings/typologies.json @@ -0,0 +1,41 @@ +{ + "reference-entry": {"cobj":"0013", "value": "Part of book or chapter of book"}, + "report": {"cobj":"0017", "value": "Report"}, + "dataset": {"cobj":"0021", "value": "Dataset"}, + "journal-article": {"cobj":"0001", "value": "Article"}, + "reference-book": {"cobj":"0002", "value": "Book"}, + "other": {"cobj":"0020", "value": "Other ORP type"}, + "proceedings-article": {"cobj":"0004", "value": "Conference object"}, + "standard": {"cobj":"0038", "value": "Other literature type"}, + "book-part": {"cobj":"0002", "value": "Book"}, + "monograph": {"cobj":"0002", "value": "Book"}, + "report-series": {"cobj":"0017", "value": "Report"}, + "book": {"cobj":"0002", "value": "Book"}, + "book-chapter": {"cobj":"0013", "value": "Part of book or chapter of book"}, + "peer-review": {"cobj":"0015", "value": "Review"}, + "book-section": {"cobj":"0013", "value": "Part of book or chapter of book"}, + "book-review": {"cobj":"0015", "value": "Review"}, + "conference-abstract": {"cobj":"0004", "value": "Conference object"}, + "conference-paper": {"cobj":"0004", "value": "Conference object"}, + "conference-poster": {"cobj":"0004", "value": "Conference object"}, + "data-set": {"cobj":"0021", "value": "Dataset"}, + "dictionary-entry": {"cobj":"0038", "value": "Other literature type"}, + "disclosure": {"cobj":"0038", "value": "Other literature type"}, + "dissertation": {"cobj":"0006", "value": "Doctoral thesis"}, + "edited-book": {"cobj":"0002", "value": "Book"}, + "encyclopedia-entry": {"cobj":"0038", "value": "Other literature type"}, + "lecture-speech": {"cobj":"0010", "value": "Lecture"}, + "license": {"cobj":"0038", "value": "Other literature type"}, + "magazine-article": {"cobj":"0005", "value": "Contribution for newspaper or weekly magazine"}, + "manual": {"cobj":"0038", "value": "Other literature type"}, + "newsletter-article": {"cobj":"0012", "value": "Newsletter"}, + "newspaper-article": {"cobj":"0005", "value": "Contribution for newspaper or weekly magazine"}, + "patent": {"cobj":"0019", "value": "Patent"}, + "research-technique": {"cobj":"0020", "value": "Other ORP type"}, + "research-tool": {"cobj":"0020", "value": "Other ORP type"}, + "standards-and-policy": {"cobj":"0038", "value": "Other literature type"}, + "supervised-student-publication": {"cobj":"0001", "value": "Article"}, + "technical-standard": {"cobj":"0038", "value": "Other literature type"}, + "website": {"cobj":"0020", "value": "Other ORP type"}, + "working-paper": {"cobj":"0014", "value": "Research"} +} \ No newline at end of file From 1729cc5cf320c32cdafa2523d884d965ccefdc98 Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Thu, 2 Jul 2020 18:46:20 +0200 Subject: [PATCH 06/37] publication conversion from json to oaf test --- .../orcidnodoi/oaf/OrcidWorkToOAF.java | 420 ---------------- .../orcidnodoi/oaf/PublicationToOaf.java | 456 ++++++++++++++++++ .../orcidnodoi/util/DumpToActionsUtility.java | 184 +++---- .../doiboost/orcidnodoi/util/Pair.java | 40 +- .../doiboost/orcid/OrcidClientTest.java | 2 +- .../orcidnodoi/PublicationToOafTest.java | 76 +++ .../orcidnodoi/xml/OrcidNoDoiTest.java | 3 +- .../doiboost/orcidnodoi/publication.json | 1 + 8 files changed, 650 insertions(+), 532 deletions(-) delete mode 100644 dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/OrcidWorkToOAF.java create mode 100644 dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java create mode 100644 dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/PublicationToOafTest.java create mode 100644 dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/publication.json diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/OrcidWorkToOAF.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/OrcidWorkToOAF.java deleted file mode 100644 index 673abb407..000000000 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/OrcidWorkToOAF.java +++ /dev/null @@ -1,420 +0,0 @@ - -package eu.dnetlib.doiboost.orcidnodoi.oaf; - -import com.google.gson.Gson; -import com.google.gson.JsonArray; -import com.google.gson.JsonElement; -import com.google.gson.JsonObject; -import eu.dnetlib.dhp.common.PacePerson; -import eu.dnetlib.dhp.schema.oaf.*; -import eu.dnetlib.dhp.utils.DHPUtils; -import eu.dnetlib.doiboost.orcidnodoi.SparkGenEnrichedOrcidWorks; -import eu.dnetlib.doiboost.orcidnodoi.util.DumpToActionsUtility; -import eu.dnetlib.doiboost.orcidnodoi.util.Pair; -import org.apache.commons.io.IOUtils; -import org.apache.commons.lang3.StringUtils; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import java.util.*; -import java.util.stream.Collectors; - -import static eu.dnetlib.doiboost.orcidnodoi.util.DumpToActionsUtility.*; - -public class OrcidWorkToOAF { - - static Logger logger = LoggerFactory.getLogger(OrcidWorkToOAF.class); - - public static final String ORCID = "ORCID"; - public final static String orcidPREFIX = "orcid_______"; - public static final String OPENAIRE_PREFIX = "openaire____"; - public static final String SEPARATOR = "::"; - - private static Map> datasources = new HashMap>() { - - { - put(ORCID.toLowerCase(), new Pair<>(ORCID, OPENAIRE_PREFIX + SEPARATOR + "orcid")); - - } - }; - - // json external id will be mapped to oaf:pid/@classid Map to oaf:pid/@classname - private static Map> externalIds = new HashMap>() { - - { - put("ark".toLowerCase(), new Pair<>("ark", "ark")); - put("arxiv".toLowerCase(), new Pair<>("arxiv", "arXiv")); - put("pmc".toLowerCase(), new Pair<>("pmc", "pmc")); - put("pmid".toLowerCase(), new Pair<>("pmid", "pmid")); - put("source-work-id".toLowerCase(), new Pair<>("orcidworkid", "orcidworkid")); - put("urn".toLowerCase(), new Pair<>("urn", "urn")); - } - }; - - static Map> typologiesMapping; - - static { - try { - final String tt = IOUtils.toString(OrcidWorkToOAF.class.getResourceAsStream( - "/eu/dnetlib/dhp/doiboost/orcidnodoi/mappings/typologies.json")); - typologiesMapping = new Gson().fromJson(tt, Map.class); - } catch (final Exception e) { - logger.error("loading typologies", e); - } - } - - public static final String PID_TYPES = "dnet:pid_types"; - - public static Oaf generatePublicationActionsFromDump(final JsonObject rootElement, final String setName) { - - if (!isValid(rootElement/*, context*/)) { return null; } - - Publication publication = new Publication(); - - final DataInfo dataInfo = new DataInfo(); - dataInfo.setDeletedbyinference(false); - dataInfo.setInferred(false); - dataInfo.setTrust("0.9"); - dataInfo.setProvenanceaction( - mapQualifier( - "sysimport:actionset:orcidworks-no-doi", - "sysimport:actionset:orcidworks-no-doi", - "dnet:provenanceActions", - "dnet:provenanceActions")); - publication.setDataInfo(dataInfo); - - publication.setLastupdatetimestamp(new Date().getTime()); - - publication.setDateofcollection("2019-10-22"); - publication.setDateoftransformation(DumpToActionsUtility.now_ISO8601()); - - // Adding external ids - externalIds.keySet().stream() - .forEach(jsonExtId -> { - final String classid = externalIds.get(jsonExtId.toLowerCase()).getValue(); - final String classname = externalIds.get(jsonExtId.toLowerCase()).getKey(); - final String extId = getStringValue(rootElement, jsonExtId); - if (StringUtils.isNotBlank(extId)) { - publication.getExternalReference().add( - convertExtRef(extId, classid, classname, "dnet:pid_types", "dnet:pid_types")); - } - }); - - // Adding source -// final String source = getStringValue(rootElement, "source"); -// if (StringUtils.isNotBlank(source)) { -// metadata.addSource(StringField.newBuilder().setValue(source).build()); -// } - - // Adding titles - final List titles = createRepeatedField(rootElement, "titles"); - if (titles==null || titles.isEmpty()) { -// context.incrementCounter("filtered", "title_not_found", 1); - return null; - } - Qualifier q = mapQualifier("main title","main title","dnet:dataCite_title","dnet:dataCite_title"); - publication.setTitle( - titles - .stream() - .map(t -> { - return mapStructuredProperty(t, q, null); - }) - .collect(Collectors.toList())); - // Adding identifier - final String id = getStringValue(rootElement, "id"); - String sourceId = null; - if (id != null) { - publication.setOriginalId(Arrays.asList(id)); - sourceId = String.format("50|%s" + SEPARATOR + "%s", orcidPREFIX, DHPUtils.md5(id.toLowerCase())); - } else { - String mergedTitle = titles.stream().map(Object::toString).collect(Collectors.joining(",")); - sourceId = String.format("50|%s" + SEPARATOR + "%s", orcidPREFIX, DHPUtils.md5(mergedTitle.toLowerCase())); - } - publication.setId(sourceId); - - // Adding relevant date - settingRelevantDate(rootElement, publication, "publication_date", "issued", true); - - // Adding collectedfrom - publication.setCollectedfrom(Arrays.asList(createCollectedFrom())); - - // Adding type - final String type = getStringValue(rootElement, "type"); - String cobjValue = ""; - if (StringUtils.isNotBlank(type)) { - publication.setResourcetype(mapQualifier(type, type, "dnet:dataCite_resource", "dnet:dataCite_resource")); - - final String typeValue = typologiesMapping.get(type).get("value"); - cobjValue = typologiesMapping.get(type).get("cobj"); - final Instance instance = new Instance(); - - // Adding hostedby - instance.setHostedby(createHostedBy()); - - // Adding url - final List urls = createRepeatedField(rootElement, "urls"); - if (urls!=null && !urls.isEmpty()) { - instance.setUrl(urls); - } - - final String pubDate = getPublicationDate(rootElement, "publication_date"); - if (StringUtils.isNotBlank(pubDate)) { - instance.setDateofacceptance(mapStringField(pubDate, null)); - } - - instance.setCollectedfrom(createCollectedFrom()); - - // Adding accessright - instance.setAccessright(mapQualifier("UNKNOWN", "UNKNOWN", "dnet:access_modes", "dnet:access_modes")); - - // Adding type - instance.setInstancetype(mapQualifier(cobjValue, typeValue, "dnet:publication_resource", "dnet:publication_resource")); - - publication.setInstance(Arrays.asList(instance)); - } else { -// context.incrementCounter("filtered", "type_not_found", 1); - return null; - } - - // Adding authors - final List authors = createAuthors(rootElement); - if (authors != null && authors.size() > 0) { - publication.setAuthor(authors); - } else { -// context.incrementCounter("filtered", "author_not_found", 1); - return null; - } - String classValue = getDefaultResulttype(cobjValue); - publication.setResulttype(mapQualifier(classValue, classValue,"dnet:result_typologies", "dnet:result_typologies")); - return publication; - } - - public static List createAuthors(final JsonObject root) { - - final String authorsJSONFieldName = "authors"; - - if (root.has(authorsJSONFieldName) && root.get(authorsJSONFieldName).isJsonArray()) { - - final List authors = new ArrayList<>(); - final JsonArray jsonAuthors = root.getAsJsonArray(authorsJSONFieldName); - int firstCounter = 0; - int defaultCounter = 0; - int rank = 1; - int currentRank = 0; - - for (final JsonElement item : jsonAuthors) { - final JsonObject jsonAuthor = item.getAsJsonObject(); - final Author author = new Author(); - if (item.isJsonObject()) { - final String surname = getStringValue(jsonAuthor, "surname"); - final String name = getStringValue(jsonAuthor, "name"); - final String oid = getStringValue(jsonAuthor, "oid"); - final String seq = getStringValue(jsonAuthor, "seq"); - if (StringUtils.isNotBlank(seq)) { - if (seq.equals("first")) { - firstCounter += 1; - rank = firstCounter; - - } else if (seq.equals("additional")) { - rank = currentRank + 1; - } else { - defaultCounter += 1; - rank = defaultCounter; - } - } - - if (StringUtils.isNotBlank(oid)) { - author.setPid(Arrays.asList(mapAuthorId(oid))); - author.setFullname(name + " " + surname); - if (StringUtils.isNotBlank(name)) { - author.setName(name); - } - if (StringUtils.isNotBlank(surname)) { - author.setSurname(surname); - } - } else { - String fullname = ""; - if (StringUtils.isNotBlank(name)) { - fullname = name; - } else { - if (StringUtils.isNotBlank(surname)) { - fullname = surname; - } - } - PacePerson p = new PacePerson(fullname, false); - if (p.isAccurate()) { - author.setName(p.getNormalisedFirstName()); - author.setSurname(p.getNormalisedSurname()); - author.setFullname(p.getNormalisedFullname()); - } - else { - author.setFullname(fullname); - } - } - } - author.setRank(rank); - authors.add(author); - currentRank = rank; - } - return authors; - - } - return null; - } - - private static List createRepeatedField(final JsonObject rootElement, final String fieldName) { - if (!rootElement.has(fieldName)) { return null; } - if (rootElement.has(fieldName) && rootElement.get(fieldName).isJsonNull()) { return null; } - if (rootElement.get(fieldName).isJsonArray()) { - if (!isValidJsonArray(rootElement, fieldName)) { return null; } - return getArrayValues(rootElement, fieldName); - } else { - String field = getStringValue(rootElement, fieldName); - return Arrays.asList(cleanField(field)); - } - } - - private static String cleanField(String value) { - if (value != null && !value.isEmpty() && value.charAt(0) == '"' && value.charAt(value.length() - 1) == '"') { - value = value.substring(1, value.length() - 1); - } - return value; - } - - private static void settingRelevantDate(final JsonObject rootElement, - final Publication publication, - final String jsonKey, - final String dictionaryKey, - final boolean addToDateOfAcceptance) { - - final String pubDate = getPublicationDate(rootElement, "publication_date"); - if (StringUtils.isNotBlank(pubDate)) { - if (addToDateOfAcceptance) { - publication.setDateofacceptance(mapStringField(pubDate, null)); - } - Qualifier q = mapQualifier(dictionaryKey,dictionaryKey,"dnet:dataCite_date","dnet:dataCite_date"); - publication.setRelevantdate( - Arrays.asList(pubDate) - .stream() - .map(r -> { - return mapStructuredProperty(r, q, null); - }) - .collect(Collectors.toList())); - } - } - - private static String getPublicationDate(final JsonObject rootElement, - final String jsonKey) { - - final JsonObject pubDateJson = rootElement.getAsJsonObject(jsonKey); - if (pubDateJson == null) { return null; } - final String year = getStringValue(pubDateJson, "year"); - final String month = getStringValue(pubDateJson, "month"); - final String day = getStringValue(pubDateJson, "day"); - - if (StringUtils.isBlank(year)) { return null; } - String pubDate = "".concat(year); - if (StringUtils.isNotBlank(month)) { - pubDate = pubDate.concat("-" + month); - if (StringUtils.isNotBlank(day)) { - pubDate = pubDate.concat("-" + day); - } else { - pubDate += "-01"; - } - } else { - pubDate += "-01-01"; - } - if (isValidDate(pubDate)) { return pubDate; } - return null; - } - - protected static boolean isValid(final JsonObject rootElement/*, final Reporter context*/) { - - final String type = getStringValue(rootElement, "type"); - if (!typologiesMapping.containsKey(type)) { -// context.incrementCounter("filtered", "unknowntype_" + type, 1); - return false; - } - - if (!isValidJsonArray(rootElement, "titles")) { -// context.incrementCounter("filtered", "invalid_title", 1); - return false; - } - return true; - } - - private static boolean isValidJsonArray(final JsonObject rootElement, final String fieldName) { - if (!rootElement.has(fieldName)) { return false; } - final JsonElement jsonElement = rootElement.get(fieldName); - if (jsonElement.isJsonNull()) { return false; } - if (jsonElement.isJsonArray()) { - final JsonArray jsonArray = jsonElement.getAsJsonArray(); - if (jsonArray.isJsonNull()) { return false; } - if (jsonArray.get(0).isJsonNull()) { return false; } - } - return true; - } - - private static Qualifier mapQualifier(String classId, String className, String schemeId, String schemeName) { - final Qualifier qualifier = new Qualifier(); - qualifier.setClassid(classId); - qualifier.setClassname(className); - qualifier.setSchemeid(schemeId); - qualifier.setSchemename(schemeName); - return qualifier; - } - - private static ExternalReference convertExtRef(String extId, String classId, String className, String schemeId, String schemeName) { - ExternalReference ex = new ExternalReference(); - ex.setRefidentifier(extId); - ex.setQualifier(mapQualifier(classId, className, schemeId, schemeName )); - return ex; - } - - private static StructuredProperty mapStructuredProperty(String value, Qualifier qualifier, DataInfo dataInfo) { - if (value == null | StringUtils.isBlank(value)) { - return null; - } - - final StructuredProperty structuredProperty = new StructuredProperty(); - structuredProperty.setValue(value); - structuredProperty.setQualifier(qualifier); - structuredProperty.setDataInfo(dataInfo); - return structuredProperty; - } - - private static Field mapStringField(String value, DataInfo dataInfo) { - if (value == null || StringUtils.isBlank(value)) { - return null; - } - - final Field stringField = new Field<>(); - stringField.setValue(value); - stringField.setDataInfo(dataInfo); - return stringField; - } - - private static KeyValue createCollectedFrom() { - KeyValue cf = new KeyValue(); - cf.setValue(ORCID); - cf.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + "806360c771262b4d6770e7cdf04b5c5a"); - return cf; - } - - private static KeyValue createHostedBy() { - KeyValue hb = new KeyValue(); - hb.setValue("Unknown Repository"); - hb.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + "55045bd2a65019fd8e6741a755395c8c"); - return hb; - } - - private static StructuredProperty mapAuthorId(String orcidId) { - final StructuredProperty sp = new StructuredProperty(); - sp.setValue(orcidId); - final Qualifier q = new Qualifier(); - q.setClassid("ORCID"); - q.setClassname("ORCID"); - sp.setQualifier(q); - return sp; - } -} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java new file mode 100644 index 000000000..dc03767ec --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java @@ -0,0 +1,456 @@ + +package eu.dnetlib.doiboost.orcidnodoi.oaf; + +import static eu.dnetlib.doiboost.orcidnodoi.util.DumpToActionsUtility.*; + +import java.util.*; +import java.util.stream.Collectors; + +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.google.gson.Gson; +import com.google.gson.JsonArray; +import com.google.gson.JsonElement; +import com.google.gson.JsonObject; + +import eu.dnetlib.dhp.common.PacePerson; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.utils.DHPUtils; +import eu.dnetlib.doiboost.orcidnodoi.util.DumpToActionsUtility; +import eu.dnetlib.doiboost.orcidnodoi.util.Pair; + +public class PublicationToOaf { + + static Logger logger = LoggerFactory.getLogger(PublicationToOaf.class); + + public static final String ORCID = "ORCID"; + public final static String orcidPREFIX = "orcid_______"; + public static final String OPENAIRE_PREFIX = "openaire____"; + public static final String SEPARATOR = "::"; + + private static Map> datasources = new HashMap>() { + + { + put(ORCID.toLowerCase(), new Pair<>(ORCID, OPENAIRE_PREFIX + SEPARATOR + "orcid")); + + } + }; + + // json external id will be mapped to oaf:pid/@classid Map to oaf:pid/@classname + private static Map> externalIds = new HashMap>() { + + { + put("ark".toLowerCase(), new Pair<>("ark", "ark")); + put("arxiv".toLowerCase(), new Pair<>("arxiv", "arXiv")); + put("pmc".toLowerCase(), new Pair<>("pmc", "pmc")); + put("pmid".toLowerCase(), new Pair<>("pmid", "pmid")); + put("source-work-id".toLowerCase(), new Pair<>("orcidworkid", "orcidworkid")); + put("urn".toLowerCase(), new Pair<>("urn", "urn")); + } + }; + + static Map> typologiesMapping; + + static { + try { + final String tt = IOUtils + .toString( + PublicationToOaf.class + .getResourceAsStream( + "/eu/dnetlib/dhp/doiboost/orcidnodoi/mappings/typologies.json")); + typologiesMapping = new Gson().fromJson(tt, Map.class); + } catch (final Exception e) { + logger.error("loading typologies", e); + } + } + + public static final String PID_TYPES = "dnet:pid_types"; + + public static Oaf generatePublicationActionsFromDump(final JsonObject rootElement) { + + logger.debug("generatePublicationActionsFromDump ..."); + if (!isValid(rootElement/* , context */)) { + logger.error("publication not valid"); + return null; + } + + Publication publication = new Publication(); + + final DataInfo dataInfo = new DataInfo(); + dataInfo.setDeletedbyinference(false); + dataInfo.setInferred(false); + dataInfo.setTrust("0.9"); + dataInfo + .setProvenanceaction( + mapQualifier( + "sysimport:actionset:orcidworks-no-doi", + "sysimport:actionset:orcidworks-no-doi", + "dnet:provenanceActions", + "dnet:provenanceActions")); + publication.setDataInfo(dataInfo); + + publication.setLastupdatetimestamp(new Date().getTime()); + + publication.setDateofcollection("2019-10-22"); + publication.setDateoftransformation(DumpToActionsUtility.now_ISO8601()); + + // Adding external ids + externalIds + .keySet() + .stream() + .forEach(jsonExtId -> { + final String classid = externalIds.get(jsonExtId.toLowerCase()).getValue(); + final String classname = externalIds.get(jsonExtId.toLowerCase()).getKey(); + final String extId = getStringValue(rootElement, jsonExtId); + if (StringUtils.isNotBlank(extId)) { + publication + .getExternalReference() + .add( + convertExtRef(extId, classid, classname, "dnet:pid_types", "dnet:pid_types")); + } + }); + + // Adding source + final String source = getStringValue(rootElement, "sourceName"); + if (StringUtils.isNotBlank(source)) { + publication.setSource(Arrays.asList(mapStringField(source, null))); + } + + // Adding titles + final List titles = createRepeatedField(rootElement, "titles"); + if (titles == null || titles.isEmpty()) { + logger.error("titles not found"); +// context.incrementCounter("filtered", "title_not_found", 1); + return null; + } + Qualifier q = mapQualifier("main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title"); + publication + .setTitle( + titles + .stream() + .map(t -> { + return mapStructuredProperty(t, q, null); + }) + .collect(Collectors.toList())); + // Adding identifier + final String id = getStringValue(rootElement, "id"); + String sourceId = null; + if (id != null) { + publication.setOriginalId(Arrays.asList(id)); + sourceId = String.format("50|%s" + SEPARATOR + "%s", orcidPREFIX, DHPUtils.md5(id.toLowerCase())); + } else { + String mergedTitle = titles.stream().map(Object::toString).collect(Collectors.joining(",")); + sourceId = String.format("50|%s" + SEPARATOR + "%s", orcidPREFIX, DHPUtils.md5(mergedTitle.toLowerCase())); + } + publication.setId(sourceId); + + // Adding relevant date + settingRelevantDate(rootElement, publication, "publication_date", "issued", true); + + // Adding collectedfrom + publication.setCollectedfrom(Arrays.asList(createCollectedFrom())); + + // Adding type + final String type = getStringValue(rootElement, "type"); + String cobjValue = ""; + if (StringUtils.isNotBlank(type)) { + publication.setResourcetype(mapQualifier(type, type, "dnet:dataCite_resource", "dnet:dataCite_resource")); + + final String typeValue = typologiesMapping.get(type).get("value"); + cobjValue = typologiesMapping.get(type).get("cobj"); + final Instance instance = new Instance(); + + // Adding hostedby + instance.setHostedby(createHostedBy()); + + // Adding url + final List urls = createRepeatedField(rootElement, "urls"); + if (urls != null && !urls.isEmpty()) { + instance.setUrl(urls); + } + + final String pubDate = getPublicationDate(rootElement, "publication_date"); + if (StringUtils.isNotBlank(pubDate)) { + instance.setDateofacceptance(mapStringField(pubDate, null)); + } + + instance.setCollectedfrom(createCollectedFrom()); + + // Adding accessright + instance.setAccessright(mapQualifier("UNKNOWN", "UNKNOWN", "dnet:access_modes", "dnet:access_modes")); + + // Adding type + instance + .setInstancetype( + mapQualifier(cobjValue, typeValue, "dnet:publication_resource", "dnet:publication_resource")); + + publication.setInstance(Arrays.asList(instance)); + } else { + logger.error("type not found"); +// context.incrementCounter("filtered", "type_not_found", 1); + return null; + } + + // Adding authors + final List authors = createAuthors(rootElement); + if (authors != null && authors.size() > 0) { + publication.setAuthor(authors); + } else { + logger.error("authors not found"); +// context.incrementCounter("filtered", "author_not_found", 1); + return null; + } + String classValue = getDefaultResulttype(cobjValue); + publication + .setResulttype(mapQualifier(classValue, classValue, "dnet:result_typologies", "dnet:result_typologies")); + return publication; + } + + public static List createAuthors(final JsonObject root) { + + final String authorsJSONFieldName = "contributors"; + + if (root.has(authorsJSONFieldName) && root.get(authorsJSONFieldName).isJsonArray()) { + + final List authors = new ArrayList<>(); + final JsonArray jsonAuthors = root.getAsJsonArray(authorsJSONFieldName); + int firstCounter = 0; + int defaultCounter = 0; + int rank = 1; + int currentRank = 0; + + for (final JsonElement item : jsonAuthors) { + final JsonObject jsonAuthor = item.getAsJsonObject(); + final Author author = new Author(); + if (item.isJsonObject()) { + final String creditname = getStringValue(jsonAuthor, "creditName"); + final String surname = getStringValue(jsonAuthor, "surname"); + final String name = getStringValue(jsonAuthor, "name"); + final String oid = getStringValue(jsonAuthor, "oid"); + final String seq = getStringValue(jsonAuthor, "sequence"); + if (StringUtils.isNotBlank(seq)) { + if (seq.equals("first")) { + firstCounter += 1; + rank = firstCounter; + + } else if (seq.equals("additional")) { + rank = currentRank + 1; + } else { + defaultCounter += 1; + rank = defaultCounter; + } + } + if (StringUtils.isNotBlank(oid)) { + author.setPid(Arrays.asList(mapAuthorId(oid))); + author.setFullname(name + " " + surname); + if (StringUtils.isNotBlank(name)) { + author.setName(name); + } + if (StringUtils.isNotBlank(surname)) { + author.setSurname(surname); + } + } else { + PacePerson p = new PacePerson(creditname, false); + if (p.isAccurate()) { + author.setName(p.getNormalisedFirstName()); + author.setSurname(p.getNormalisedSurname()); + author.setFullname(p.getNormalisedFullname()); + } else { + author.setFullname(creditname); + } + } + } + author.setRank(rank); + authors.add(author); + currentRank = rank; + } + return authors; + + } + return null; + } + + private static List createRepeatedField(final JsonObject rootElement, final String fieldName) { + if (!rootElement.has(fieldName)) { + return null; + } + if (rootElement.has(fieldName) && rootElement.get(fieldName).isJsonNull()) { + return null; + } + if (rootElement.get(fieldName).isJsonArray()) { + if (!isValidJsonArray(rootElement, fieldName)) { + return null; + } + return getArrayValues(rootElement, fieldName); + } else { + String field = getStringValue(rootElement, fieldName); + return Arrays.asList(cleanField(field)); + } + } + + private static String cleanField(String value) { + if (value != null && !value.isEmpty() && value.charAt(0) == '"' && value.charAt(value.length() - 1) == '"') { + value = value.substring(1, value.length() - 1); + } + return value; + } + + private static void settingRelevantDate(final JsonObject rootElement, + final Publication publication, + final String jsonKey, + final String dictionaryKey, + final boolean addToDateOfAcceptance) { + + final String pubDate = getPublicationDate(rootElement, "publication_date"); + if (StringUtils.isNotBlank(pubDate)) { + if (addToDateOfAcceptance) { + publication.setDateofacceptance(mapStringField(pubDate, null)); + } + Qualifier q = mapQualifier(dictionaryKey, dictionaryKey, "dnet:dataCite_date", "dnet:dataCite_date"); + publication + .setRelevantdate( + Arrays + .asList(pubDate) + .stream() + .map(r -> { + return mapStructuredProperty(r, q, null); + }) + .collect(Collectors.toList())); + } + } + + private static String getPublicationDate(final JsonObject rootElement, + final String jsonKey) { + + final JsonObject pubDateJson = rootElement.getAsJsonObject(jsonKey); + if (pubDateJson == null) { + return null; + } + final String year = getStringValue(pubDateJson, "year"); + final String month = getStringValue(pubDateJson, "month"); + final String day = getStringValue(pubDateJson, "day"); + + if (StringUtils.isBlank(year)) { + return null; + } + String pubDate = "".concat(year); + if (StringUtils.isNotBlank(month)) { + pubDate = pubDate.concat("-" + month); + if (StringUtils.isNotBlank(day)) { + pubDate = pubDate.concat("-" + day); + } else { + pubDate += "-01"; + } + } else { + pubDate += "-01-01"; + } + if (isValidDate(pubDate)) { + return pubDate; + } + return null; + } + + protected static boolean isValid(final JsonObject rootElement/* , final Reporter context */) { + + final String type = getStringValue(rootElement, "type"); + if (!typologiesMapping.containsKey(type)) { + logger.error("unknowntype_" + type); +// context.incrementCounter("filtered", "unknowntype_" + type, 1); + return false; + } + + if (!isValidJsonArray(rootElement, "titles")) { + logger.error("invalid_title"); +// context.incrementCounter("filtered", "invalid_title", 1); + return false; + } + return true; + } + + private static boolean isValidJsonArray(final JsonObject rootElement, final String fieldName) { + if (!rootElement.has(fieldName)) { + return false; + } + final JsonElement jsonElement = rootElement.get(fieldName); + if (jsonElement.isJsonNull()) { + return false; + } + if (jsonElement.isJsonArray()) { + final JsonArray jsonArray = jsonElement.getAsJsonArray(); + if (jsonArray.isJsonNull()) { + return false; + } + if (jsonArray.get(0).isJsonNull()) { + return false; + } + } + return true; + } + + private static Qualifier mapQualifier(String classId, String className, String schemeId, String schemeName) { + final Qualifier qualifier = new Qualifier(); + qualifier.setClassid(classId); + qualifier.setClassname(className); + qualifier.setSchemeid(schemeId); + qualifier.setSchemename(schemeName); + return qualifier; + } + + private static ExternalReference convertExtRef(String extId, String classId, String className, String schemeId, + String schemeName) { + ExternalReference ex = new ExternalReference(); + ex.setRefidentifier(extId); + ex.setQualifier(mapQualifier(classId, className, schemeId, schemeName)); + return ex; + } + + private static StructuredProperty mapStructuredProperty(String value, Qualifier qualifier, DataInfo dataInfo) { + if (value == null | StringUtils.isBlank(value)) { + return null; + } + + final StructuredProperty structuredProperty = new StructuredProperty(); + structuredProperty.setValue(value); + structuredProperty.setQualifier(qualifier); + structuredProperty.setDataInfo(dataInfo); + return structuredProperty; + } + + private static Field mapStringField(String value, DataInfo dataInfo) { + if (value == null || StringUtils.isBlank(value)) { + return null; + } + + final Field stringField = new Field<>(); + stringField.setValue(value); + stringField.setDataInfo(dataInfo); + return stringField; + } + + private static KeyValue createCollectedFrom() { + KeyValue cf = new KeyValue(); + cf.setValue(ORCID); + cf.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + "806360c771262b4d6770e7cdf04b5c5a"); + return cf; + } + + private static KeyValue createHostedBy() { + KeyValue hb = new KeyValue(); + hb.setValue("Unknown Repository"); + hb.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + "55045bd2a65019fd8e6741a755395c8c"); + return hb; + } + + private static StructuredProperty mapAuthorId(String orcidId) { + final StructuredProperty sp = new StructuredProperty(); + sp.setValue(orcidId); + final Qualifier q = new Qualifier(); + q.setClassid("ORCID"); + q.setClassname("ORCID"); + sp.setQualifier(q); + return sp; + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/util/DumpToActionsUtility.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/util/DumpToActionsUtility.java index c460f6299..9b9f3c8b2 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/util/DumpToActionsUtility.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/util/DumpToActionsUtility.java @@ -1,107 +1,109 @@ -package eu.dnetlib.doiboost.orcidnodoi.util; -import com.google.gson.JsonArray; -import com.google.gson.JsonObject; -import org.apache.commons.lang3.StringUtils; +package eu.dnetlib.doiboost.orcidnodoi.util; import java.text.SimpleDateFormat; import java.util.*; +import org.apache.commons.lang3.StringUtils; + +import com.google.gson.JsonArray; +import com.google.gson.JsonObject; + public class DumpToActionsUtility { - private static final SimpleDateFormat ISO8601FORMAT = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ssZ", Locale.US); + private static final SimpleDateFormat ISO8601FORMAT = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ssZ", Locale.US); - public static String getStringValue(final JsonObject root, final String key) { - if (root.has(key) && !root.get(key).isJsonNull()) - return root.get(key).getAsString(); - return null; - } + public static String getStringValue(final JsonObject root, final String key) { + if (root.has(key) && !root.get(key).isJsonNull()) + return root.get(key).getAsString(); + return null; + } - public static List getArrayValues(final JsonObject root, final String key) { - if (root.has(key) && root.get(key).isJsonArray()) { - final JsonArray asJsonArray = root.get(key).getAsJsonArray(); - final List result = new ArrayList<>(); + public static List getArrayValues(final JsonObject root, final String key) { + if (root.has(key) && root.get(key).isJsonArray()) { + final JsonArray asJsonArray = root.get(key).getAsJsonArray(); + final List result = new ArrayList<>(); + asJsonArray.forEach(it -> { + if (StringUtils.isNotBlank(it.getAsString())) { + result.add(it.getAsString()); + } + }); + return result; + } + return new ArrayList<>(); + } - asJsonArray.forEach(it -> { - if (StringUtils.isNotBlank(it.getAsString())) { - result.add(it.getAsString()); - } - }); - return result; - } - return new ArrayList<>(); - } - public static List getArrayObjects(final JsonObject root, final String key) { - if (root.has(key) && root.get(key).isJsonArray()) { - final JsonArray asJsonArray = root.get(key).getAsJsonArray(); - final List result = new ArrayList<>(); - asJsonArray.forEach(it -> { - if (it.getAsJsonObject() != null) { - result.add(it.getAsJsonObject()); - } - }); - return result; - } - return new ArrayList<>(); - } + public static List getArrayObjects(final JsonObject root, final String key) { + if (root.has(key) && root.get(key).isJsonArray()) { + final JsonArray asJsonArray = root.get(key).getAsJsonArray(); + final List result = new ArrayList<>(); + asJsonArray.forEach(it -> { + if (it.getAsJsonObject() != null) { + result.add(it.getAsJsonObject()); + } + }); + return result; + } + return new ArrayList<>(); + } - public static boolean isValidDate(final String date) { - return date.matches("\\d{4}-\\d{2}-\\d{2}"); - } + public static boolean isValidDate(final String date) { + return date.matches("\\d{4}-\\d{2}-\\d{2}"); + } - public static String now_ISO8601() { // NOPMD - String result; - synchronized (ISO8601FORMAT) { - result = ISO8601FORMAT.format(new Date()); - } - //convert YYYYMMDDTHH:mm:ss+HH00 into YYYYMMDDTHH:mm:ss+HH:00 - //- note the added colon for the Timezone - return result.substring(0, result.length() - 2) + ":" + result.substring(result.length() - 2); - } + public static String now_ISO8601() { // NOPMD + String result; + synchronized (ISO8601FORMAT) { + result = ISO8601FORMAT.format(new Date()); + } + // convert YYYYMMDDTHH:mm:ss+HH00 into YYYYMMDDTHH:mm:ss+HH:00 + // - note the added colon for the Timezone + return result.substring(0, result.length() - 2) + ":" + result.substring(result.length() - 2); + } - public static String getDefaultResulttype(final String cobjcategory) { - switch (cobjcategory) { - case "0029": - return "software"; - case "0021": - case "0024": - case "0025": - case "0030": - return "dataset"; - case "0000": - case "0010": - case "0018": - case "0020": - case "0022": - case "0023": - case "0026": - case "0027": - case "0028": - case "0037": - return "other"; - case "0001": - case "0002": - case "0004": - case "0005": - case "0006": - case "0007": - case "0008": - case "0009": - case "0011": - case "0012": - case "0013": - case "0014": - case "0015": - case "0016": - case "0017": - case "0019": - case "0031": - case "0032": - return "publication"; - default: - return "publication"; - } - } + public static String getDefaultResulttype(final String cobjcategory) { + switch (cobjcategory) { + case "0029": + return "software"; + case "0021": + case "0024": + case "0025": + case "0030": + return "dataset"; + case "0000": + case "0010": + case "0018": + case "0020": + case "0022": + case "0023": + case "0026": + case "0027": + case "0028": + case "0037": + return "other"; + case "0001": + case "0002": + case "0004": + case "0005": + case "0006": + case "0007": + case "0008": + case "0009": + case "0011": + case "0012": + case "0013": + case "0014": + case "0015": + case "0016": + case "0017": + case "0019": + case "0031": + case "0032": + return "publication"; + default: + return "publication"; + } + } } diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/util/Pair.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/util/Pair.java index 58c09af60..8883d00f5 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/util/Pair.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/util/Pair.java @@ -1,30 +1,32 @@ + package eu.dnetlib.doiboost.orcidnodoi.util; public class Pair { - private K k; + private K k; - private V v; + private V v; - public Pair(K k, V v) { - this.k = k; - this.v = v; - } + public Pair(K k, V v) { + this.k = k; + this.v = v; + } - public K getKey() { - return k; - } + public K getKey() { + return k; + } - public V getValue() { - return v; - } + public V getValue() { + return v; + } - @Override - public boolean equals(Object obj) { - if (obj instanceof Pair) { - Pair tmp = (Pair) obj; - return k.equals(tmp.getKey()) && v.equals(tmp.getValue()); - } else return false; - } + @Override + public boolean equals(Object obj) { + if (obj instanceof Pair) { + Pair tmp = (Pair) obj; + return k.equals(tmp.getKey()) && v.equals(tmp.getValue()); + } else + return false; + } } diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/OrcidClientTest.java b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/OrcidClientTest.java index 75f857ca4..8b50f2d8f 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/OrcidClientTest.java +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/OrcidClientTest.java @@ -54,7 +54,7 @@ public class OrcidClientTest { } // @Test - public void testLambdaFileParser() throws Exception { + private void testLambdaFileParser() throws Exception { try (BufferedReader br = new BufferedReader( new InputStreamReader(this.getClass().getResourceAsStream("last_modified.csv")))) { String line; diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/PublicationToOafTest.java b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/PublicationToOafTest.java new file mode 100644 index 000000000..4d04e1a16 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/PublicationToOafTest.java @@ -0,0 +1,76 @@ + +package eu.dnetlib.doiboost.orcidnodoi; + +import static org.junit.jupiter.api.Assertions.*; + +import org.apache.commons.io.IOUtils; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.google.gson.JsonElement; +import com.google.gson.JsonParser; + +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.doiboost.orcidnodoi.oaf.PublicationToOaf; + +public class PublicationToOafTest { + + private static final Logger logger = LoggerFactory.getLogger(PublicationToOafTest.class); + + @Test +// @Ignore + public void convertOafPublicationTest() throws Exception { + String jsonPublication = IOUtils + .toString( + PublicationToOafTest.class.getResourceAsStream("publication.json")); + JsonElement j = new JsonParser().parse(jsonPublication); + logger.info("json publication loaded: " + j.toString()); + Publication oafPublication = (Publication) PublicationToOaf + .generatePublicationActionsFromDump(j.getAsJsonObject()); + assertNotNull(oafPublication.getId()); + assertNotNull(oafPublication.getOriginalId()); + assertEquals(oafPublication.getOriginalId().get(0), "60153327"); + logger.info("oafPublication.getId(): " + oafPublication.getId()); + assertEquals( + oafPublication.getTitle().get(0).getValue(), + "Evaluation of a percutaneous optical fibre glucose sensor (FiberSense) across the glycemic range with rapid glucoseexcursions using the glucose clamp"); + assertNotNull(oafPublication.getLastupdatetimestamp()); + assertNotNull(oafPublication.getDateofcollection()); + assertNotNull(oafPublication.getDateoftransformation()); + assertTrue(oafPublication.getAuthor().size() == 7); + oafPublication.getAuthor().forEach(a -> { + assertNotNull(a.getFullname()); + assertNotNull(a.getRank()); + logger.info("a.getFullname(): " + a.getFullname()); + if (a.getName() != null) { + logger.info("a.getName(): " + a.getName()); + } + if (a.getSurname() != null) { + logger.info("a.getSurname(): " + a.getSurname()); + } + logger.info("a.getRank(): " + a.getRank()); + if (a.getPid() != null) { + logger.info("a.getPid(): " + a.getPid().get(0).getValue()); + } + + }); + assertNotNull(oafPublication.getCollectedfrom()); + if (oafPublication.getSource() != null) { + logger.info((oafPublication.getSource().get(0).getValue())); + } + if (oafPublication.getExternalReference() != null) { + oafPublication.getExternalReference().forEach(e -> { + assertNotNull(e.getRefidentifier()); + assertEquals(e.getQualifier().getSchemeid(), "dnet:pid_types"); + }); + } + assertNotNull(oafPublication.getInstance()); + oafPublication.getInstance().forEach(i -> { + assertNotNull(i.getInstancetype().getClassid()); + logger.info("i.getInstancetype().getClassid(): " + i.getInstancetype().getClassid()); + assertNotNull(i.getInstancetype().getClassname()); + logger.info("i.getInstancetype().getClassname(): " + i.getInstancetype().getClassname()); + }); + } +} diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/xml/OrcidNoDoiTest.java b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/xml/OrcidNoDoiTest.java index 6a5faddbd..d426b01f1 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/xml/OrcidNoDoiTest.java +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/xml/OrcidNoDoiTest.java @@ -95,7 +95,8 @@ public class OrcidNoDoiTest { } @Test - public void authorMatchTest() throws Exception { + @Ignore + private void authorMatchTest() throws Exception { logger.info("running authorSimpleMatchTest ...."); String orcidWork = "activity_work_0000-0003-2760-1191-similarity.xml"; AuthorData author = new AuthorData(); diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/publication.json b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/publication.json new file mode 100644 index 000000000..579e12f2e --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/publication.json @@ -0,0 +1 @@ +{"oid":"0000-0002-4147-3387","id":"60153327","sourceName":"The Chinese University of Hong Kong","type":"conference-paper","titles":["Evaluation of a percutaneous optical fibre glucose sensor (FiberSense) across the glycemic range with rapid glucoseexcursions using the glucose clamp"],"extIds":[{"type":"wosuid","value":"000425015800225","relationShip":"self"},{"type":"other-id","value":"441f521e-ab19-448d-ba32-83157b348ada","relationShip":"self"}],"publicationDates":[],"contributors":[{"sequence":"1","oid":"0000-0002-4147-3387","name":"Elaine","surname":"Chow","creditName":"Elaine Chow"},{"sequence":"2","creditName":"Victor Tsui"},{"sequence":"3","creditName":"Achim Müller"},{"sequence":"4","creditName":"Vincy Lee"},{"sequence":"5","creditName":"Lucia Krivánekova"},{"sequence":"6","creditName":"Roland Krivánek"},{"sequence":"7","creditName":"Juliana CN Chan"}]} \ No newline at end of file From ca37d3427bc4bfe05932c9231e11ccdfb98752f2 Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Fri, 3 Jul 2020 23:30:31 +0200 Subject: [PATCH 07/37] separate workflow to parse orcid summaries, activities and generate dataset with no doi publications; test --- .../orcid/OrcidAuthorsDOIsDataGen.java | 8 +- .../doiboost/orcid/OrcidDSManager.java | 14 +- .../doiboost/orcid/OrcidDownloader.java | 8 +- .../orcidnodoi/ActivitiesDumpReader.java | 6 +- .../orcidnodoi/GenOrcidAuthorWork.java | 3 +- .../SparkGenEnrichedOrcidWorks.java | 18 +- .../orcidnodoi/oaf/PublicationToOaf.java | 9 +- .../doiboost/create_orcid_authors_data.json | 2 +- .../create_orcid_authors_dois_data.json | 2 +- .../dhp/doiboost/download_orcid_data.json | 2 +- .../oozie_app/workflow.xml | 497 +---------------- .../dhp/doiboost/orcid/oozie_app/workflow.xml | 44 +- .../oozie_app/config-default.xml | 31 ++ .../orcid_activities/oozie_app/workflow.xml | 514 ++++++++++++++++++ .../oozie_app/config-default.xml | 22 + .../orcid_summaries/oozie_app/workflow.xml | 68 +++ .../doiboost/orcid/OrcidClientTest.java | 29 +- .../orcidnodoi/PublicationToOafTest.java | 5 +- .../orcidnodoi/xml/OrcidNoDoiTest.java | 4 +- .../xml/activity_work_0000-0002-2536-4498.xml | 72 +++ 20 files changed, 815 insertions(+), 543 deletions(-) create mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_activities/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_activities/oozie_app/workflow.xml create mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_summaries/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_summaries/oozie_app/workflow.xml create mode 100644 dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/xml/activity_work_0000-0002-2536-4498.xml diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidAuthorsDOIsDataGen.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidAuthorsDOIsDataGen.java index 70528a8f6..2ec4fe59d 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidAuthorsDOIsDataGen.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidAuthorsDOIsDataGen.java @@ -25,8 +25,8 @@ public class OrcidAuthorsDOIsDataGen extends OrcidDSManager { public void generateAuthorsDOIsData() throws Exception { Configuration conf = initConfigurationObject(); FileSystem fs = initFileSystemObject(conf); - String tarGzUri = hdfsServerUri.concat(hdfsOrcidDefaultPath).concat(activitiesFileNameTarGz); - Path outputPath = new Path(hdfsServerUri.concat(hdfsOrcidDefaultPath).concat(outputAuthorsDOIsPath)); + String tarGzUri = hdfsServerUri.concat(workingPath).concat(activitiesFileNameTarGz); + Path outputPath = new Path(hdfsServerUri.concat(workingPath).concat(outputAuthorsDOIsPath)); ActivitiesDecompressor.parseGzActivities(conf, tarGzUri, outputPath); } @@ -41,8 +41,8 @@ public class OrcidAuthorsDOIsDataGen extends OrcidDSManager { hdfsServerUri = parser.get("hdfsServerUri"); Log.info("HDFS URI: " + hdfsServerUri); - hdfsOrcidDefaultPath = parser.get("hdfsOrcidDefaultPath"); - Log.info("Default Path: " + hdfsOrcidDefaultPath); + workingPath = parser.get("workingPath"); + Log.info("Default Path: " + workingPath); activitiesFileNameTarGz = parser.get("activitiesFileNameTarGz"); Log.info("Activities File Name: " + activitiesFileNameTarGz); outputAuthorsDOIsPath = parser.get("outputAuthorsDOIsPath"); diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDSManager.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDSManager.java index 4f846bdf3..aa61c0117 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDSManager.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDSManager.java @@ -15,7 +15,7 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser; public class OrcidDSManager { protected String hdfsServerUri; - protected String hdfsOrcidDefaultPath; + protected String workingPath; private String summariesFileNameTarGz; private String outputAuthorsPath; @@ -28,10 +28,10 @@ public class OrcidDSManager { public void generateAuthors() throws Exception { Configuration conf = initConfigurationObject(); FileSystem fs = initFileSystemObject(conf); - String tarGzUri = hdfsServerUri.concat(hdfsOrcidDefaultPath).concat(summariesFileNameTarGz); + String tarGzUri = hdfsServerUri.concat(workingPath).concat(summariesFileNameTarGz); Path outputPath = new Path( hdfsServerUri - .concat(hdfsOrcidDefaultPath) + .concat(workingPath) .concat(outputAuthorsPath) .concat("authors.seq")); SummariesDecompressor.parseGzSummaries(conf, tarGzUri, outputPath); @@ -41,7 +41,7 @@ public class OrcidDSManager { // ====== Init HDFS File System Object Configuration conf = new Configuration(); // Set FileSystem URI - conf.set("fs.defaultFS", hdfsServerUri.concat(hdfsOrcidDefaultPath)); + conf.set("fs.defaultFS", hdfsServerUri.concat(workingPath)); // Because of Maven conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName()); conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName()); @@ -52,7 +52,7 @@ public class OrcidDSManager { // Get the filesystem - HDFS FileSystem fs = null; try { - fs = FileSystem.get(URI.create(hdfsServerUri.concat(hdfsOrcidDefaultPath)), conf); + fs = FileSystem.get(URI.create(hdfsServerUri.concat(workingPath)), conf); } catch (IOException e) { // TODO Auto-generated catch block e.printStackTrace(); @@ -71,8 +71,8 @@ public class OrcidDSManager { hdfsServerUri = parser.get("hdfsServerUri"); Log.info("HDFS URI: " + hdfsServerUri); - hdfsOrcidDefaultPath = parser.get("hdfsOrcidDefaultPath"); - Log.info("Default Path: " + hdfsOrcidDefaultPath); + workingPath = parser.get("workingPath"); + Log.info("Working Path: " + workingPath); summariesFileNameTarGz = parser.get("summariesFileNameTarGz"); Log.info("Summaries File Name: " + summariesFileNameTarGz); outputAuthorsPath = parser.get("outputAuthorsPath"); diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDownloader.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDownloader.java index 2e1a199da..762d8aecd 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDownloader.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDownloader.java @@ -69,12 +69,12 @@ public class OrcidDownloader extends OrcidDSManager { long startDownload = 0; Configuration conf = initConfigurationObject(); FileSystem fs = initFileSystemObject(conf); - String lambdaFileUri = hdfsServerUri.concat(hdfsOrcidDefaultPath).concat(lambdaFileName); + String lambdaFileUri = hdfsServerUri.concat(workingPath).concat(lambdaFileName); Path hdfsreadpath = new Path(lambdaFileUri); FSDataInputStream lambdaFileStream = fs.open(hdfsreadpath); Path hdfsoutputPath = new Path( hdfsServerUri - .concat(hdfsOrcidDefaultPath) + .concat(workingPath) .concat(outputPath) .concat("orcid_records.seq")); @@ -176,8 +176,8 @@ public class OrcidDownloader extends OrcidDSManager { hdfsServerUri = parser.get("hdfsServerUri"); Log.info("HDFS URI: " + hdfsServerUri); - hdfsOrcidDefaultPath = parser.get("hdfsOrcidDefaultPath"); - Log.info("Default Path: " + hdfsOrcidDefaultPath); + workingPath = parser.get("workingPath"); + Log.info("Default Path: " + workingPath); lambdaFileName = parser.get("lambdaFileName"); Log.info("Lambda File Name: " + lambdaFileName); outputPath = parser.get("outputPath"); diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/ActivitiesDumpReader.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/ActivitiesDumpReader.java index bf63568d8..807f52972 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/ActivitiesDumpReader.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/ActivitiesDumpReader.java @@ -26,8 +26,8 @@ import eu.dnetlib.doiboost.orcidnodoi.xml.XMLRecordParserNoDoi; public class ActivitiesDumpReader { - private static final int MAX_XML_WORKS_PARSED = 100; - private static final int XML_WORKS_PARSED_COUNTER_LOG_INTERVAL = 10; + private static final int MAX_XML_WORKS_PARSED = -1; + private static final int XML_WORKS_PARSED_COUNTER_LOG_INTERVAL = 100000; public static void parseGzActivities(Configuration conf, String inputUri, Path outputPath) throws Exception { @@ -127,7 +127,7 @@ public class ActivitiesDumpReader { Log .warn( "Parsing work from tar archive and xml work: " + filename + " " + e.getMessage()); - Log.warn(e); +// Log.warn(e); } if ((counter % XML_WORKS_PARSED_COUNTER_LOG_INTERVAL) == 0) { diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/GenOrcidAuthorWork.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/GenOrcidAuthorWork.java index 8dcee796c..041424ba9 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/GenOrcidAuthorWork.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/GenOrcidAuthorWork.java @@ -16,7 +16,7 @@ public class GenOrcidAuthorWork extends OrcidDSManager { private String activitiesFileNameTarGz; private String outputWorksPath; - private String workingPath; +// private String workingPath; public static void main(String[] args) throws IOException, Exception { GenOrcidAuthorWork genOrcidAuthorWork = new GenOrcidAuthorWork(); @@ -45,7 +45,6 @@ public class GenOrcidAuthorWork extends OrcidDSManager { Log.info("HDFS URI: " + hdfsServerUri); workingPath = parser.get("workingPath"); Log.info("Working Path: " + workingPath); - hdfsOrcidDefaultPath = workingPath; activitiesFileNameTarGz = parser.get("activitiesFileNameTarGz"); Log.info("Activities File Name: " + activitiesFileNameTarGz); outputWorksPath = parser.get("outputWorksPath"); diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java index ae1e4dae6..b0b989463 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java @@ -16,6 +16,7 @@ import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -24,9 +25,11 @@ import com.google.gson.JsonElement; import com.google.gson.JsonParser; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.oaf.Publication; import eu.dnetlib.doiboost.orcid.json.JsonHelper; import eu.dnetlib.doiboost.orcid.model.AuthorData; import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi; +import eu.dnetlib.doiboost.orcidnodoi.oaf.PublicationToOaf; import eu.dnetlib.doiboost.orcidnodoi.similarity.AuthorMatcher; import scala.Tuple2; @@ -59,7 +62,7 @@ public class SparkGenEnrichedOrcidWorks { JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaPairRDD summariesRDD = sc - .sequenceFile(workingPath + "../orcid_summaries/output/authors.seq", Text.class, Text.class); + .sequenceFile(workingPath + "summaries/output/authors.seq", Text.class, Text.class); Dataset summariesDataset = spark .createDataset( summariesRDD.map(seq -> loadAuthorFromJson(seq._1(), seq._2())).rdd(), @@ -89,8 +92,19 @@ public class SparkGenEnrichedOrcidWorks { .filter(Objects::nonNull) .toJavaRDD(); logger.info("Works enriched data created: " + enrichedWorksRDD.count()); - enrichedWorksRDD.repartition(10).saveAsTextFile(workingPath + outputEnrichedWorksPath); + enrichedWorksRDD.saveAsTextFile(workingPath + outputEnrichedWorksPath); logger.info("Works enriched data saved"); + JavaRDD> oafPublicationRDD = enrichedWorksRDD.map(e -> { + JsonElement j = new JsonParser().parse(e._2()); + return new Tuple2<>(e._1(), (Publication) PublicationToOaf + .generatePublicationActionsFromDump(j.getAsJsonObject())); + }); + + Dataset> publicationDataset = spark + .createDataset( + oafPublicationRDD.repartition(1).rdd(), + Encoders.tuple(Encoders.STRING(), Encoders.bean(Publication.class))); + publicationDataset.write().mode(SaveMode.Overwrite).save(workingPath + "no_doi_dataset/output"); }); } diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java index dc03767ec..19bfe0f30 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java @@ -172,7 +172,7 @@ public class PublicationToOaf { instance.setUrl(urls); } - final String pubDate = getPublicationDate(rootElement, "publication_date"); + final String pubDate = getPublicationDate(rootElement, "publicationDates"); if (StringUtils.isNotBlank(pubDate)) { instance.setDateofacceptance(mapStringField(pubDate, null)); } @@ -325,7 +325,12 @@ public class PublicationToOaf { private static String getPublicationDate(final JsonObject rootElement, final String jsonKey) { - final JsonObject pubDateJson = rootElement.getAsJsonObject(jsonKey); + JsonObject pubDateJson = null; + try { + pubDateJson = rootElement.getAsJsonObject(jsonKey); + } catch (Exception e) { + return null; + } if (pubDateJson == null) { return null; } diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/create_orcid_authors_data.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/create_orcid_authors_data.json index bf992b508..6f213e415 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/create_orcid_authors_data.json +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/create_orcid_authors_data.json @@ -1,6 +1,6 @@ [ {"paramName":"n", "paramLongName":"hdfsServerUri", "paramDescription": "the server uri", "paramRequired": true}, - {"paramName":"d", "paramLongName":"hdfsOrcidDefaultPath", "paramDescription": "the default work path", "paramRequired": true}, + {"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the default work path", "paramRequired": true}, {"paramName":"f", "paramLongName":"summariesFileNameTarGz", "paramDescription": "the name of the summaries orcid file", "paramRequired": true}, {"paramName":"o", "paramLongName":"outputAuthorsPath", "paramDescription": "the relative folder of the sequencial file to write", "paramRequired": true} ] \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/create_orcid_authors_dois_data.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/create_orcid_authors_dois_data.json index 131c30125..b2f0fdeda 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/create_orcid_authors_dois_data.json +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/create_orcid_authors_dois_data.json @@ -1,6 +1,6 @@ [ {"paramName":"n", "paramLongName":"hdfsServerUri", "paramDescription": "the server uri", "paramRequired": true}, - {"paramName":"d", "paramLongName":"hdfsOrcidDefaultPath", "paramDescription": "the default work path", "paramRequired": true}, + {"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the default work path", "paramRequired": true}, {"paramName":"f", "paramLongName":"activitiesFileNameTarGz", "paramDescription": "the name of the activities orcid file", "paramRequired": true}, {"paramName":"o", "paramLongName":"outputAuthorsDOIsPath", "paramDescription": "the relative folder of the sequencial file to write", "paramRequired": true} ] \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/download_orcid_data.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/download_orcid_data.json index 444e487f7..8c69b168b 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/download_orcid_data.json +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/download_orcid_data.json @@ -1,6 +1,6 @@ [ {"paramName":"n", "paramLongName":"hdfsServerUri", "paramDescription": "the server uri", "paramRequired": true}, - {"paramName":"d", "paramLongName":"hdfsOrcidDefaultPath", "paramDescription": "the default work path", "paramRequired": true}, + {"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the default work path", "paramRequired": true}, {"paramName":"f", "paramLongName":"lambdaFileName", "paramDescription": "the name of the lambda file", "paramRequired": true}, {"paramName":"o", "paramLongName":"outputPath", "paramDescription": "the relative folder of the sequencial file to write", "paramRequired": true}, {"paramName":"t", "paramLongName":"token", "paramDescription": "token to grant access", "paramRequired": true} diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works/oozie_app/workflow.xml index df5e0e76f..a60af8b45 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works/oozie_app/workflow.xml @@ -1,75 +1,9 @@ - workingPath_activities + workingPath the working dir base path - - shell_cmd_0 - wget -O /tmp/ORCID_2019_activites_0.tar.gz https://orcid.figshare.com/ndownloader/files/18017660 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_0.tar.gz /data/orcid_activities/ORCID_2019_activites_0.tar.gz ; rm -f /tmp/ORCID_2019_activites_0.tar.gz - - the shell command that downloads and puts to hdfs orcid activity file 0 - - - shell_cmd_1 - wget -O /tmp/ORCID_2019_activites_1.tar.gz https://orcid.figshare.com/ndownloader/files/18017675 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_1.tar.gz /data/orcid_activities/ORCID_2019_activites_1.tar.gz ; rm -f /tmp/ORCID_2019_activites_1.tar.gz - - the shell command that downloads and puts to hdfs orcid activity file 1 - - - shell_cmd_2 - wget -O /tmp/ORCID_2019_activites_2.tar.gz https://orcid.figshare.com/ndownloader/files/18017717 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_2.tar.gz /data/orcid_activities/ORCID_2019_activites_2.tar.gz ; rm -f /tmp/ORCID_2019_activites_2.tar.gz - - the shell command that downloads and puts to hdfs orcid activity file 2 - - - shell_cmd_3 - wget -O /tmp/ORCID_2019_activites_3.tar.gz https://orcid.figshare.com/ndownloader/files/18017765 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_3.tar.gz /data/orcid_activities/ORCID_2019_activites_3.tar.gz ; rm -f /tmp/ORCID_2019_activites_3.tar.gz - - the shell command that downloads and puts to hdfs orcid activity file 3 - - - shell_cmd_4 - wget -O /tmp/ORCID_2019_activites_4.tar.gz https://orcid.figshare.com/ndownloader/files/18017831 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_4.tar.gz /data/orcid_activities/ORCID_2019_activites_4.tar.gz ; rm -f /tmp/ORCID_2019_activites_4.tar.gz - - the shell command that downloads and puts to hdfs orcid activity file 4 - - - shell_cmd_5 - wget -O /tmp/ORCID_2019_activites_5.tar.gz https://orcid.figshare.com/ndownloader/files/18017987 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_5.tar.gz /data/orcid_activities/ORCID_2019_activites_5.tar.gz ; rm -f /tmp/ORCID_2019_activites_5.tar.gz - - the shell command that downloads and puts to hdfs orcid activity file 5 - - - shell_cmd_6 - wget -O /tmp/ORCID_2019_activites_6.tar.gz https://orcid.figshare.com/ndownloader/files/18018053 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_6.tar.gz /data/orcid_activities/ORCID_2019_activites_6.tar.gz ; rm -f /tmp/ORCID_2019_activites_6.tar.gz - - the shell command that downloads and puts to hdfs orcid activity file 6 - - - shell_cmd_7 - wget -O /tmp/ORCID_2019_activites_7.tar.gz https://orcid.figshare.com/ndownloader/files/18018023 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_7.tar.gz /data/orcid_activities/ORCID_2019_activites_7.tar.gz ; rm -f /tmp/ORCID_2019_activites_7.tar.gz - - the shell command that downloads and puts to hdfs orcid activity file 7 - - - shell_cmd_8 - wget -O /tmp/ORCID_2019_activites_8.tar.gz https://orcid.figshare.com/ndownloader/files/18018248 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_8.tar.gz /data/orcid_activities/ORCID_2019_activites_8.tar.gz ; rm -f /tmp/ORCID_2019_activites_8.tar.gz - - the shell command that downloads and puts to hdfs orcid activity file 8 - - - shell_cmd_9 - wget -O /tmp/ORCID_2019_activites_9.tar.gz https://orcid.figshare.com/ndownloader/files/18018029 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_9.tar.gz /data/orcid_activities/ORCID_2019_activites_9.tar.gz ; rm -f /tmp/ORCID_2019_activites_9.tar.gz - - the shell command that downloads and puts to hdfs orcid activity file 9 - - - shell_cmd_X - wget -O /tmp/ORCID_2019_activites_X.tar.gz https://orcid.figshare.com/ndownloader/files/18018182 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_X.tar.gz /data/orcid_activities/ORCID_2019_activites_X.tar.gz ; rm -f /tmp/ORCID_2019_activites_X.tar.gz - - the shell command that downloads and puts to hdfs orcid activity file X - @@ -80,436 +14,11 @@ - - + - + - - - - - - - - - - - - - - - - - - - ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_0.tar.gz'))} - - - - - - - - ${jobTracker} - ${nameNode} - bash - -c - ${shell_cmd_0} - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork - -w${workingPath_activities}/ - -n${nameNode} - -fORCID_2019_activites_0.tar.gz - -owno_doi_works/works_0.seq - -oewno_doi_enriched_works/ - - - - - - - - - ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_1.tar.gz'))} - - - - - - - - ${jobTracker} - ${nameNode} - bash - -c - ${shell_cmd_1} - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork - -w${workingPath_activities}/ - -n${nameNode} - -fORCID_2019_activites_1.tar.gz - -owno_doi_works/works_1.seq - -oewno_doi_enriched_works/ - - - - - - - - - ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_2.tar.gz'))} - - - - - - - - ${jobTracker} - ${nameNode} - bash - -c - ${shell_cmd_2} - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork - -w${workingPath_activities}/ - -n${nameNode} - -fORCID_2019_activites_2.tar.gz - -owno_doi_works/works_2.seq - -oewno_doi_enriched_works/ - - - - - - - - - ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_3.tar.gz'))} - - - - - - - - ${jobTracker} - ${nameNode} - bash - -c - ${shell_cmd_3} - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork - -w${workingPath_activities}/ - -n${nameNode} - -fORCID_2019_activites_3.tar.gz - -owno_doi_works/works_3.seq - -oewno_doi_enriched_works/ - - - - - - - - - ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_4.tar.gz'))} - - - - - - - - ${jobTracker} - ${nameNode} - bash - -c - ${shell_cmd_4} - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork - -w${workingPath_activities}/ - -n${nameNode} - -fORCID_2019_activites_4.tar.gz - -owno_doi_works/works_4.seq - -oewno_doi_enriched_works/ - - - - - - - - - ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_5.tar.gz'))} - - - - - - - - ${jobTracker} - ${nameNode} - bash - -c - ${shell_cmd_5} - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork - -w${workingPath_activities}/ - -n${nameNode} - -fORCID_2019_activites_5.tar.gz - -owno_doi_works/works_5.seq - -oewno_doi_enriched_works/ - - - - - - - - - ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_6.tar.gz'))} - - - - - - - - ${jobTracker} - ${nameNode} - bash - -c - ${shell_cmd_6} - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork - -w${workingPath_activities}/ - -n${nameNode} - -fORCID_2019_activites_6.tar.gz - -owno_doi_works/works_6.seq - -oewno_doi_enriched_works/ - - - - - - - - - - ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_7.tar.gz'))} - - - - - - - - ${jobTracker} - ${nameNode} - bash - -c - ${shell_cmd_7} - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork - -w${workingPath_activities}/ - -n${nameNode} - -fORCID_2019_activites_7.tar.gz - -owno_doi_works/works_7.seq - -oewno_doi_enriched_works/ - - - - - - - - - ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_8.tar.gz'))} - - - - - - - - ${jobTracker} - ${nameNode} - bash - -c - ${shell_cmd_8} - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork - -w${workingPath_activities}/ - -n${nameNode} - -fORCID_2019_activites_8.tar.gz - -owno_doi_works/works_8.seq - -oewno_doi_enriched_works/ - - - - - - - - - ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_9.tar.gz'))} - - - - - - - - ${jobTracker} - ${nameNode} - bash - -c - ${shell_cmd_9} - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork - -w${workingPath_activities}/ - -n${nameNode} - -fORCID_2019_activites_9.tar.gz - -owno_doi_works/works_9.seq - -oewno_doi_enriched_works/ - - - - - - - - - ${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_X.tar.gz'))} - - - - - - - - ${jobTracker} - ${nameNode} - bash - -c - ${shell_cmd_X} - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork - -w${workingPath_activities}/ - -n${nameNode} - -fORCID_2019_activites_X.tar.gz - -owno_doi_works/works_X.seq - -oewno_doi_enriched_works/ - - - - - - diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid/oozie_app/workflow.xml index 7a8d04187..51e00dc0f 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid/oozie_app/workflow.xml @@ -1,9 +1,15 @@ - + workingPath the working dir base path + + shell_cmd_0 + wget -O /tmp/ORCID_2019_summaries.tar.gz https://orcid.figshare.com/ndownloader/files/18017633 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_summaries.tar.gz /data/orcid_activities/ORCID_2019_summaries.tar.gz ; rm -f /tmp/ORCID_2019_summaries.tar.gz + + the shell command that downloads and puts to hdfs orcid summaries + @@ -15,24 +21,44 @@ - - + + - + + + + + + + + ${fs:exists(concat(workingPath,'/ORCID_2019_summaries.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_0} + + + - - - + ${jobTracker} ${nameNode} eu.dnetlib.doiboost.orcid.OrcidDSManager - -d${workingPath}/ + -w${workingPath}/ -n${nameNode} -fORCID_2019_summaries.tar.gz - -ooutput/ + -osummaries/output/ diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_activities/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_activities/oozie_app/config-default.xml new file mode 100644 index 000000000..3068562d0 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_activities/oozie_app/config-default.xml @@ -0,0 +1,31 @@ + + + oozie.action.sharelib.for.java + spark2 + + + oozie.launcher.mapreduce.user.classpath.first + true + + + oozie.launcher.mapreduce.map.java.opts + -Xmx4g + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_activities/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_activities/oozie_app/workflow.xml new file mode 100644 index 000000000..8f9a5123e --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_activities/oozie_app/workflow.xml @@ -0,0 +1,514 @@ + + + + workingPath + the working dir base path + + + shell_cmd_0 + wget -O /tmp/ORCID_2019_activites_0.tar.gz https://orcid.figshare.com/ndownloader/files/18017660 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_0.tar.gz /data/orcid_activities/ORCID_2019_activites_0.tar.gz ; rm -f /tmp/ORCID_2019_activites_0.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file 0 + + + shell_cmd_1 + wget -O /tmp/ORCID_2019_activites_1.tar.gz https://orcid.figshare.com/ndownloader/files/18017675 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_1.tar.gz /data/orcid_activities/ORCID_2019_activites_1.tar.gz ; rm -f /tmp/ORCID_2019_activites_1.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file 1 + + + shell_cmd_2 + wget -O /tmp/ORCID_2019_activites_2.tar.gz https://orcid.figshare.com/ndownloader/files/18017717 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_2.tar.gz /data/orcid_activities/ORCID_2019_activites_2.tar.gz ; rm -f /tmp/ORCID_2019_activites_2.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file 2 + + + shell_cmd_3 + wget -O /tmp/ORCID_2019_activites_3.tar.gz https://orcid.figshare.com/ndownloader/files/18017765 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_3.tar.gz /data/orcid_activities/ORCID_2019_activites_3.tar.gz ; rm -f /tmp/ORCID_2019_activites_3.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file 3 + + + shell_cmd_4 + wget -O /tmp/ORCID_2019_activites_4.tar.gz https://orcid.figshare.com/ndownloader/files/18017831 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_4.tar.gz /data/orcid_activities/ORCID_2019_activites_4.tar.gz ; rm -f /tmp/ORCID_2019_activites_4.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file 4 + + + shell_cmd_5 + wget -O /tmp/ORCID_2019_activites_5.tar.gz https://orcid.figshare.com/ndownloader/files/18017987 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_5.tar.gz /data/orcid_activities/ORCID_2019_activites_5.tar.gz ; rm -f /tmp/ORCID_2019_activites_5.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file 5 + + + shell_cmd_6 + wget -O /tmp/ORCID_2019_activites_6.tar.gz https://orcid.figshare.com/ndownloader/files/18018053 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_6.tar.gz /data/orcid_activities/ORCID_2019_activites_6.tar.gz ; rm -f /tmp/ORCID_2019_activites_6.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file 6 + + + shell_cmd_7 + wget -O /tmp/ORCID_2019_activites_7.tar.gz https://orcid.figshare.com/ndownloader/files/18018023 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_7.tar.gz /data/orcid_activities/ORCID_2019_activites_7.tar.gz ; rm -f /tmp/ORCID_2019_activites_7.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file 7 + + + shell_cmd_8 + wget -O /tmp/ORCID_2019_activites_8.tar.gz https://orcid.figshare.com/ndownloader/files/18018248 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_8.tar.gz /data/orcid_activities/ORCID_2019_activites_8.tar.gz ; rm -f /tmp/ORCID_2019_activites_8.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file 8 + + + shell_cmd_9 + wget -O /tmp/ORCID_2019_activites_9.tar.gz https://orcid.figshare.com/ndownloader/files/18018029 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_9.tar.gz /data/orcid_activities/ORCID_2019_activites_9.tar.gz ; rm -f /tmp/ORCID_2019_activites_9.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file 9 + + + shell_cmd_X + wget -O /tmp/ORCID_2019_activites_X.tar.gz https://orcid.figshare.com/ndownloader/files/18018182 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_X.tar.gz /data/orcid_activities/ORCID_2019_activites_X.tar.gz ; rm -f /tmp/ORCID_2019_activites_X.tar.gz + + the shell command that downloads and puts to hdfs orcid activity file X + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + + + + + + + + + + + + + + + + + + + + ${fs:exists(concat(workingPath,'/ORCID_2019_activites_0.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_0} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork + -w${workingPath}/ + -n${nameNode} + -fORCID_2019_activites_0.tar.gz + -owno_doi_works/works_0.seq + -oewno_doi_enriched_works/ + + + + + + + + + ${fs:exists(concat(workingPath,'/ORCID_2019_activites_1.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_1} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork + -w${workingPath}/ + -n${nameNode} + -fORCID_2019_activites_1.tar.gz + -owno_doi_works/works_1.seq + -oewno_doi_enriched_works/ + + + + + + + + + ${fs:exists(concat(workingPath,'/ORCID_2019_activites_2.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_2} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork + -w${workingPath}/ + -n${nameNode} + -fORCID_2019_activites_2.tar.gz + -owno_doi_works/works_2.seq + -oewno_doi_enriched_works/ + + + + + + + + + ${fs:exists(concat(workingPath,'/ORCID_2019_activites_3.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_3} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork + -w${workingPath}/ + -n${nameNode} + -fORCID_2019_activites_3.tar.gz + -owno_doi_works/works_3.seq + -oewno_doi_enriched_works/ + + + + + + + + + ${fs:exists(concat(workingPath,'/ORCID_2019_activites_4.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_4} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork + -w${workingPath}/ + -n${nameNode} + -fORCID_2019_activites_4.tar.gz + -owno_doi_works/works_4.seq + -oewno_doi_enriched_works/ + + + + + + + + + ${fs:exists(concat(workingPath,'/ORCID_2019_activites_5.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_5} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork + -w${workingPath}/ + -n${nameNode} + -fORCID_2019_activites_5.tar.gz + -owno_doi_works/works_5.seq + -oewno_doi_enriched_works/ + + + + + + + + + ${fs:exists(concat(workingPath,'/ORCID_2019_activites_6.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_6} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork + -w${workingPath}/ + -n${nameNode} + -fORCID_2019_activites_6.tar.gz + -owno_doi_works/works_6.seq + -oewno_doi_enriched_works/ + + + + + + + + + + ${fs:exists(concat(workingPath,'/ORCID_2019_activites_7.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_7} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork + -w${workingPath}/ + -n${nameNode} + -fORCID_2019_activites_7.tar.gz + -owno_doi_works/works_7.seq + -oewno_doi_enriched_works/ + + + + + + + + + ${fs:exists(concat(workingPath,'/ORCID_2019_activites_8.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_8} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork + -w${workingPath}/ + -n${nameNode} + -fORCID_2019_activites_8.tar.gz + -owno_doi_works/works_8.seq + -oewno_doi_enriched_works/ + + + + + + + + + ${fs:exists(concat(workingPath,'/ORCID_2019_activites_9.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_9} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork + -w${workingPath}/ + -n${nameNode} + -fORCID_2019_activites_9.tar.gz + -owno_doi_works/works_9.seq + -oewno_doi_enriched_works/ + + + + + + + + + ${fs:exists(concat(workingPath,'/ORCID_2019_activites_X.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_X} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork + -w${workingPath}/ + -n${nameNode} + -fORCID_2019_activites_X.tar.gz + -owno_doi_works/works_X.seq + -oewno_doi_enriched_works/ + + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_summaries/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_summaries/oozie_app/config-default.xml new file mode 100644 index 000000000..e77dd09c9 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_summaries/oozie_app/config-default.xml @@ -0,0 +1,22 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + oozie.launcher.mapreduce.user.classpath.first + true + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_summaries/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_summaries/oozie_app/workflow.xml new file mode 100644 index 000000000..3362cc67b --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_summaries/oozie_app/workflow.xml @@ -0,0 +1,68 @@ + + + + workingPath + the working dir base path + + + shell_cmd_0 + wget -O /tmp/ORCID_2019_summaries.tar.gz https://orcid.figshare.com/ndownloader/files/18017633 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_summaries.tar.gz /data/orcid_activities/ORCID_2019_summaries.tar.gz ; rm -f /tmp/ORCID_2019_summaries.tar.gz + + the shell command that downloads and puts to hdfs orcid summaries + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + + + + + + + ${fs:exists(concat(workingPath,'/ORCID_2019_summaries.tar.gz'))} + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd_0} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcid.OrcidDSManager + -w${workingPath}/ + -n${nameNode} + -fORCID_2019_summaries.tar.gz + -osummaries/output/ + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/OrcidClientTest.java b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/OrcidClientTest.java index 8b50f2d8f..5e0f91ecd 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/OrcidClientTest.java +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/OrcidClientTest.java @@ -3,9 +3,8 @@ package eu.dnetlib.doiboost.orcid; import static org.junit.jupiter.api.Assertions.assertTrue; -import java.io.BufferedReader; -import java.io.IOException; -import java.io.InputStreamReader; +import java.io.*; +import java.nio.file.Files; import java.text.ParseException; import java.text.SimpleDateFormat; import java.util.Arrays; @@ -20,6 +19,7 @@ import org.apache.http.impl.client.HttpClients; import org.junit.jupiter.api.Test; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import jdk.nashorn.internal.ir.annotations.Ignore; public class OrcidClientTest { final String orcidId = "0000-0001-7291-3210"; @@ -32,11 +32,20 @@ public class OrcidClientTest { String lastUpdate = "2019-09-30 00:00:00"; String shortDate = "2020-05-06 16:06:11"; -// curl -i -H "Accept: application/vnd.orcid+xml" +// curl -i -H "Accept: application/vnd.orcid+xml" // -H 'Authorization: Bearer 78fdb232-7105-4086-8570-e153f4198e3d' // 'https://api.orcid.org/v3.0/0000-0001-7291-3210/record' - public String testDownloadRecord(String orcidId) throws Exception { + @Test + public void downloadTest() throws Exception { + String record = testDownloadRecord("0000-0002-2536-4498"); + File f = new File("/tmp/downloaded_0000-0002-2536-4498.xml"); + OutputStream outStream = new FileOutputStream(f); + IOUtils.write(record.getBytes(), outStream); + System.out.println("saved to tmp"); + } + + private String testDownloadRecord(String orcidId) throws Exception { try (CloseableHttpClient client = HttpClients.createDefault()) { HttpGet httpGet = new HttpGet("https://api.orcid.org/v3.0/" + orcidId + "/record"); httpGet.addHeader("Accept", "application/vnd.orcid+xml"); @@ -100,7 +109,7 @@ public class OrcidClientTest { } // @Test - public void getRecordDatestamp() throws ParseException { + private void getRecordDatestamp() throws ParseException { Date toRetrieveDateDt = new SimpleDateFormat(DATE_FORMAT).parse(toRetrieveDate); Date toNotRetrieveDateDt = new SimpleDateFormat(DATE_FORMAT).parse(toNotRetrieveDate); Date lastUpdateDt = new SimpleDateFormat(DATE_FORMAT).parse(lastUpdate); @@ -108,7 +117,7 @@ public class OrcidClientTest { assertTrue(!toNotRetrieveDateDt.after(lastUpdateDt)); } - public void testDate(String value) throws ParseException { + private void testDate(String value) throws ParseException { System.out.println(value.toString()); if (value.length() != 19) { value = value.substring(0, 19); @@ -118,14 +127,16 @@ public class OrcidClientTest { } // @Test - public void testModifiedDate() throws ParseException { + @Ignore + private void testModifiedDate() throws ParseException { testDate(toRetrieveDate); testDate(toNotRetrieveDate); testDate(shortDate); } // @Test - public void testReadBase64CompressedRecord() throws Exception { + @Ignore + private void testReadBase64CompressedRecord() throws Exception { final String base64CompressedRecord = IOUtils .toString(getClass().getResourceAsStream("0000-0001-6645-509X.compressed.base64")); final String recordFromSeqFile = ArgumentApplicationParser.decompressValue(base64CompressedRecord); diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/PublicationToOafTest.java b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/PublicationToOafTest.java index 4d04e1a16..39f78522f 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/PublicationToOafTest.java +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/PublicationToOafTest.java @@ -13,14 +13,15 @@ import com.google.gson.JsonParser; import eu.dnetlib.dhp.schema.oaf.Publication; import eu.dnetlib.doiboost.orcidnodoi.oaf.PublicationToOaf; +import jdk.nashorn.internal.ir.annotations.Ignore; public class PublicationToOafTest { private static final Logger logger = LoggerFactory.getLogger(PublicationToOafTest.class); @Test -// @Ignore - public void convertOafPublicationTest() throws Exception { + @Ignore + private void convertOafPublicationTest() throws Exception { String jsonPublication = IOUtils .toString( PublicationToOafTest.class.getResourceAsStream("publication.json")); diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/xml/OrcidNoDoiTest.java b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/xml/OrcidNoDoiTest.java index d426b01f1..ca91a242a 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/xml/OrcidNoDoiTest.java +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/xml/OrcidNoDoiTest.java @@ -42,12 +42,12 @@ public class OrcidNoDoiTest { @Test @Ignore - private void readPublicationFieldsTest() + public void readPublicationFieldsTest() throws IOException, XPathEvalException, XPathParseException, NavException, VtdException, ParseException { logger.info("running loadPublicationFieldsTest ...."); String xml = IOUtils .toString( - OrcidNoDoiTest.class.getResourceAsStream("activity_work_0000-0003-2760-1191.xml")); + OrcidNoDoiTest.class.getResourceAsStream("activity_work_0000-0002-2536-4498.xml")); if (xml == null) { logger.info("Resource not found"); diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/xml/activity_work_0000-0002-2536-4498.xml b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/xml/activity_work_0000-0002-2536-4498.xml new file mode 100644 index 000000000..43d3b2351 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/xml/activity_work_0000-0002-2536-4498.xml @@ -0,0 +1,72 @@ + + + 2019-10-22T03:18:13.755Z + 2020-06-17T11:07:13.703Z + + + https://orcid.org/client/0000-0001-8607-8906 + 0000-0001-8607-8906 + orcid.org + + INSPIRE-HEP + + + Measurement of the $t\bar{t}$ production cross-section and lepton differential distributions in $e\mu$ dilepton events from $pp$ collisions at $\sqrt{s}=13$ TeV with the ATLAS detector + + + + other-id + 1759875 + 1759875 + http://inspirehep.net/record/1759875 + self + + + doi + 10.1140/epjc/s10052-020-7907-9 + 10.1140/epjc/s10052-020-7907-9 + http://dx.doi.org/10.1140/epjc/s10052-020-7907-9 + self + + + arxiv + 1910.08819 + arXiv:1910.08819 + http://arxiv.org/abs/1910.08819 + self + + + http://inspirehep.net/record/1759875 + journal-article + + 2020 + 06 + 12 + + Eur.Phys.J.C + From c82b15b5f4817348d446fbf53f8337a5e3601085 Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Tue, 28 Jul 2020 15:23:52 +0200 Subject: [PATCH 08/37] migrate configuration to ocean, fix publication dataset creation --- .../SparkGenEnrichedOrcidWorks.java | 13 ++-- .../oozie_app/config-default.xml | 31 --------- .../oozie_app/workflow.xml | 68 ++++++++++++++++--- .../orcid/xml/XMLRecordParserTest.java | 6 +- 4 files changed, 68 insertions(+), 50 deletions(-) delete mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works/oozie_app/config-default.xml diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java index b0b989463..b24e71615 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java @@ -91,19 +91,18 @@ public class SparkGenEnrichedOrcidWorks { Encoders.tuple(Encoders.STRING(), Encoders.STRING())) .filter(Objects::nonNull) .toJavaRDD(); - logger.info("Works enriched data created: " + enrichedWorksRDD.count()); enrichedWorksRDD.saveAsTextFile(workingPath + outputEnrichedWorksPath); logger.info("Works enriched data saved"); - JavaRDD> oafPublicationRDD = enrichedWorksRDD.map(e -> { + JavaRDD oafPublicationRDD = enrichedWorksRDD.map(e -> { JsonElement j = new JsonParser().parse(e._2()); - return new Tuple2<>(e._1(), (Publication) PublicationToOaf - .generatePublicationActionsFromDump(j.getAsJsonObject())); - }); + return (Publication) PublicationToOaf + .generatePublicationActionsFromDump(j.getAsJsonObject()); + }).filter(p -> p != null); - Dataset> publicationDataset = spark + Dataset publicationDataset = spark .createDataset( oafPublicationRDD.repartition(1).rdd(), - Encoders.tuple(Encoders.STRING(), Encoders.bean(Publication.class))); + Encoders.bean(Publication.class)); publicationDataset.write().mode(SaveMode.Overwrite).save(workingPath + "no_doi_dataset/output"); }); } diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works/oozie_app/config-default.xml deleted file mode 100644 index 3068562d0..000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works/oozie_app/config-default.xml +++ /dev/null @@ -1,31 +0,0 @@ - - - oozie.action.sharelib.for.java - spark2 - - - oozie.launcher.mapreduce.user.classpath.first - true - - - oozie.launcher.mapreduce.map.java.opts - -Xmx4g - - - jobTracker - yarnRM - - - nameNode - hdfs://nameservice1 - - - - oozie.use.system.libpath - true - - - oozie.action.sharelib.for.spark - spark2 - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works/oozie_app/workflow.xml index a60af8b45..faed3104a 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works/oozie_app/workflow.xml @@ -1,11 +1,56 @@ - + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + workingPath the working dir base path + + ${jobTracker} + ${nameNode} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + @@ -16,20 +61,25 @@ - + - + - ${jobTracker} - ${nameNode} - yarn + yarn-cluster cluster - Gen_Enriched_Orcid_Works + GenOrcidNoDoiDataset eu.dnetlib.doiboost.orcidnodoi.SparkGenEnrichedOrcidWorks - dhp-doiboost-1.2.4-SNAPSHOT.jar - --num-executors 10 --conf spark.yarn.jars="hdfs://hadoop-rm1.garr-pa1.d4science.org:8020/user/oozie/share/lib/lib_20180405103059/spark2" --executor-memory=${sparkExecutorMemory} --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} + dhp-doiboost-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} -w${workingPath}/ -n${nameNode} diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParserTest.java b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParserTest.java index 4d8237f77..5bf6f27b9 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParserTest.java +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParserTest.java @@ -12,7 +12,7 @@ import eu.dnetlib.doiboost.orcid.model.WorkData; public class XMLRecordParserTest { @Test - public void testOrcidAuthorDataXMLParser() throws Exception { + private void testOrcidAuthorDataXMLParser() throws Exception { String xml = IOUtils.toString(this.getClass().getResourceAsStream("summary_0000-0001-6828-479X.xml")); @@ -27,7 +27,7 @@ public class XMLRecordParserTest { } @Test - public void testOrcidXMLErrorRecordParser() throws Exception { + private void testOrcidXMLErrorRecordParser() throws Exception { String xml = IOUtils.toString(this.getClass().getResourceAsStream("summary_error.xml")); @@ -40,7 +40,7 @@ public class XMLRecordParserTest { } @Test - public void testOrcidWorkDataXMLParser() throws Exception { + private void testOrcidWorkDataXMLParser() throws Exception { String xml = IOUtils .toString( From 196f36c6edd10203ff304e7cd122b3b679593618 Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Thu, 30 Jul 2020 13:38:33 +0200 Subject: [PATCH 09/37] fix publication dataset creation --- .../SparkGenEnrichedOrcidWorks.java | 47 +++++-- .../orcidnodoi/oaf/PublicationToOaf.java | 117 +++++++++++++----- .../orcidnodoi/PublicationToOafTest.java | 3 +- 3 files changed, 128 insertions(+), 39 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java index b24e71615..cae5a168f 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java @@ -17,10 +17,12 @@ import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; +import org.apache.spark.util.LongAccumulator; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import com.google.gson.Gson; +import com.google.gson.GsonBuilder; import com.google.gson.JsonElement; import com.google.gson.JsonParser; @@ -93,17 +95,48 @@ public class SparkGenEnrichedOrcidWorks { .toJavaRDD(); enrichedWorksRDD.saveAsTextFile(workingPath + outputEnrichedWorksPath); logger.info("Works enriched data saved"); - JavaRDD oafPublicationRDD = enrichedWorksRDD.map(e -> { - JsonElement j = new JsonParser().parse(e._2()); - return (Publication) PublicationToOaf - .generatePublicationActionsFromDump(j.getAsJsonObject()); - }).filter(p -> p != null); + + final LongAccumulator parsedPublications = spark.sparkContext().longAccumulator("parsedPublications"); + final LongAccumulator enrichedPublications = spark + .sparkContext() + .longAccumulator("enrichedPublications"); + final LongAccumulator errorsGeneric = spark.sparkContext().longAccumulator("errorsGeneric"); + final LongAccumulator errorsInvalidTitle = spark.sparkContext().longAccumulator("errorsInvalidTitle"); + final LongAccumulator errorsNotFoundAuthors = spark + .sparkContext() + .longAccumulator("errorsNotFoundAuthors"); + final LongAccumulator errorsInvalidType = spark.sparkContext().longAccumulator("errorsInvalidType"); + final PublicationToOaf publicationToOaf = new PublicationToOaf( + parsedPublications, + enrichedPublications, + errorsGeneric, + errorsInvalidTitle, + errorsNotFoundAuthors, + errorsInvalidType); + JavaRDD oafPublicationRDD = enrichedWorksRDD + .map( + e -> { + return (Publication) publicationToOaf + .generatePublicationActionsFromJson(e._2()); + }) + .filter(p -> p != null); Dataset publicationDataset = spark .createDataset( - oafPublicationRDD.repartition(1).rdd(), + oafPublicationRDD.rdd(), Encoders.bean(Publication.class)); - publicationDataset.write().mode(SaveMode.Overwrite).save(workingPath + "no_doi_dataset/output"); + publicationDataset + .write() + .format("parquet") + .mode(SaveMode.Overwrite) + .save(workingPath + "no_doi_dataset/output"); + + logger.info("parsedPublications: " + parsedPublications.value().toString()); + logger.info("enrichedPublications: " + enrichedPublications.value().toString()); + logger.info("errorsGeneric: " + errorsGeneric.value().toString()); + logger.info("errorsInvalidTitle: " + errorsInvalidTitle.value().toString()); + logger.info("errorsNotFoundAuthors: " + errorsNotFoundAuthors.value().toString()); + logger.info("errorsInvalidType: " + errorsInvalidType.value().toString()); }); } diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java index 19bfe0f30..448fa9a74 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java @@ -3,18 +3,17 @@ package eu.dnetlib.doiboost.orcidnodoi.oaf; import static eu.dnetlib.doiboost.orcidnodoi.util.DumpToActionsUtility.*; +import java.io.Serializable; import java.util.*; import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; +import org.apache.spark.util.LongAccumulator; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import com.google.gson.Gson; -import com.google.gson.JsonArray; -import com.google.gson.JsonElement; -import com.google.gson.JsonObject; +import com.google.gson.*; import eu.dnetlib.dhp.common.PacePerson; import eu.dnetlib.dhp.schema.oaf.*; @@ -22,7 +21,7 @@ import eu.dnetlib.dhp.utils.DHPUtils; import eu.dnetlib.doiboost.orcidnodoi.util.DumpToActionsUtility; import eu.dnetlib.doiboost.orcidnodoi.util.Pair; -public class PublicationToOaf { +public class PublicationToOaf implements Serializable { static Logger logger = LoggerFactory.getLogger(PublicationToOaf.class); @@ -31,6 +30,37 @@ public class PublicationToOaf { public static final String OPENAIRE_PREFIX = "openaire____"; public static final String SEPARATOR = "::"; + private final LongAccumulator parsedPublications; + private final LongAccumulator enrichedPublications; + private final LongAccumulator errorsGeneric; + private final LongAccumulator errorsInvalidTitle; + private final LongAccumulator errorsNotFoundAuthors; + private final LongAccumulator errorsInvalidType; + + public PublicationToOaf( + LongAccumulator parsedPublications, + LongAccumulator enrichedPublications, + LongAccumulator errorsGeneric, + LongAccumulator errorsInvalidTitle, + LongAccumulator errorsNotFoundAuthors, + LongAccumulator errorsInvalidType) { + this.parsedPublications = parsedPublications; + this.enrichedPublications = enrichedPublications; + this.errorsGeneric = errorsGeneric; + this.errorsInvalidTitle = errorsInvalidTitle; + this.errorsNotFoundAuthors = errorsNotFoundAuthors; + this.errorsInvalidType = errorsInvalidType; + } + + public PublicationToOaf() { + this.parsedPublications = null; + this.enrichedPublications = null; + this.errorsGeneric = null; + this.errorsInvalidTitle = null; + this.errorsNotFoundAuthors = null; + this.errorsInvalidType = null; + } + private static Map> datasources = new HashMap>() { { @@ -69,11 +99,27 @@ public class PublicationToOaf { public static final String PID_TYPES = "dnet:pid_types"; - public static Oaf generatePublicationActionsFromDump(final JsonObject rootElement) { + public Oaf generatePublicationActionsFromJson(final String json) { + try { + if (parsedPublications != null) { + parsedPublications.add(1); + } + JsonElement jElement = new JsonParser().parse(json); + JsonObject jObject = jElement.getAsJsonObject(); + return generatePublicationActionsFromDump(jObject); + } catch (Throwable t) { + logger.error("creating publication: " + t.getMessage()); + if (errorsGeneric != null) { + errorsGeneric.add(1); + } + return null; + } + } + + public Oaf generatePublicationActionsFromDump(final JsonObject rootElement) { logger.debug("generatePublicationActionsFromDump ..."); - if (!isValid(rootElement/* , context */)) { - logger.error("publication not valid"); + if (!isValid(rootElement)) { return null; } @@ -122,8 +168,9 @@ public class PublicationToOaf { // Adding titles final List titles = createRepeatedField(rootElement, "titles"); if (titles == null || titles.isEmpty()) { - logger.error("titles not found"); -// context.incrementCounter("filtered", "title_not_found", 1); + if (errorsInvalidTitle != null) { + errorsInvalidTitle.add(1); + } return null; } Qualifier q = mapQualifier("main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title"); @@ -189,8 +236,9 @@ public class PublicationToOaf { publication.setInstance(Arrays.asList(instance)); } else { - logger.error("type not found"); -// context.incrementCounter("filtered", "type_not_found", 1); + if (errorsInvalidType != null) { + errorsInvalidType.add(1); + } return null; } @@ -199,17 +247,21 @@ public class PublicationToOaf { if (authors != null && authors.size() > 0) { publication.setAuthor(authors); } else { - logger.error("authors not found"); -// context.incrementCounter("filtered", "author_not_found", 1); + if (errorsNotFoundAuthors != null) { + errorsNotFoundAuthors.add(1); + } return null; } String classValue = getDefaultResulttype(cobjValue); publication .setResulttype(mapQualifier(classValue, classValue, "dnet:result_typologies", "dnet:result_typologies")); + if (enrichedPublications != null) { + enrichedPublications.add(1); + } return publication; } - public static List createAuthors(final JsonObject root) { + public List createAuthors(final JsonObject root) { final String authorsJSONFieldName = "contributors"; @@ -273,7 +325,7 @@ public class PublicationToOaf { return null; } - private static List createRepeatedField(final JsonObject rootElement, final String fieldName) { + private List createRepeatedField(final JsonObject rootElement, final String fieldName) { if (!rootElement.has(fieldName)) { return null; } @@ -291,14 +343,14 @@ public class PublicationToOaf { } } - private static String cleanField(String value) { + private String cleanField(String value) { if (value != null && !value.isEmpty() && value.charAt(0) == '"' && value.charAt(value.length() - 1) == '"') { value = value.substring(1, value.length() - 1); } return value; } - private static void settingRelevantDate(final JsonObject rootElement, + private void settingRelevantDate(final JsonObject rootElement, final Publication publication, final String jsonKey, final String dictionaryKey, @@ -322,7 +374,7 @@ public class PublicationToOaf { } } - private static String getPublicationDate(final JsonObject rootElement, + private String getPublicationDate(final JsonObject rootElement, final String jsonKey) { JsonObject pubDateJson = null; @@ -358,24 +410,27 @@ public class PublicationToOaf { return null; } - protected static boolean isValid(final JsonObject rootElement/* , final Reporter context */) { + protected boolean isValid(final JsonObject rootElement/* , final Reporter context */) { final String type = getStringValue(rootElement, "type"); if (!typologiesMapping.containsKey(type)) { logger.error("unknowntype_" + type); -// context.incrementCounter("filtered", "unknowntype_" + type, 1); + if (errorsInvalidType != null) { + errorsInvalidType.add(1); + } return false; } if (!isValidJsonArray(rootElement, "titles")) { - logger.error("invalid_title"); -// context.incrementCounter("filtered", "invalid_title", 1); + if (errorsInvalidTitle != null) { + errorsInvalidTitle.add(1); + } return false; } return true; } - private static boolean isValidJsonArray(final JsonObject rootElement, final String fieldName) { + private boolean isValidJsonArray(final JsonObject rootElement, final String fieldName) { if (!rootElement.has(fieldName)) { return false; } @@ -395,7 +450,7 @@ public class PublicationToOaf { return true; } - private static Qualifier mapQualifier(String classId, String className, String schemeId, String schemeName) { + private Qualifier mapQualifier(String classId, String className, String schemeId, String schemeName) { final Qualifier qualifier = new Qualifier(); qualifier.setClassid(classId); qualifier.setClassname(className); @@ -404,7 +459,7 @@ public class PublicationToOaf { return qualifier; } - private static ExternalReference convertExtRef(String extId, String classId, String className, String schemeId, + private ExternalReference convertExtRef(String extId, String classId, String className, String schemeId, String schemeName) { ExternalReference ex = new ExternalReference(); ex.setRefidentifier(extId); @@ -412,7 +467,7 @@ public class PublicationToOaf { return ex; } - private static StructuredProperty mapStructuredProperty(String value, Qualifier qualifier, DataInfo dataInfo) { + private StructuredProperty mapStructuredProperty(String value, Qualifier qualifier, DataInfo dataInfo) { if (value == null | StringUtils.isBlank(value)) { return null; } @@ -424,7 +479,7 @@ public class PublicationToOaf { return structuredProperty; } - private static Field mapStringField(String value, DataInfo dataInfo) { + private Field mapStringField(String value, DataInfo dataInfo) { if (value == null || StringUtils.isBlank(value)) { return null; } @@ -435,21 +490,21 @@ public class PublicationToOaf { return stringField; } - private static KeyValue createCollectedFrom() { + private KeyValue createCollectedFrom() { KeyValue cf = new KeyValue(); cf.setValue(ORCID); cf.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + "806360c771262b4d6770e7cdf04b5c5a"); return cf; } - private static KeyValue createHostedBy() { + private KeyValue createHostedBy() { KeyValue hb = new KeyValue(); hb.setValue("Unknown Repository"); hb.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + "55045bd2a65019fd8e6741a755395c8c"); return hb; } - private static StructuredProperty mapAuthorId(String orcidId) { + private StructuredProperty mapAuthorId(String orcidId) { final StructuredProperty sp = new StructuredProperty(); sp.setValue(orcidId); final Qualifier q = new Qualifier(); diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/PublicationToOafTest.java b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/PublicationToOafTest.java index 39f78522f..01e26dcb4 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/PublicationToOafTest.java +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/PublicationToOafTest.java @@ -27,7 +27,8 @@ public class PublicationToOafTest { PublicationToOafTest.class.getResourceAsStream("publication.json")); JsonElement j = new JsonParser().parse(jsonPublication); logger.info("json publication loaded: " + j.toString()); - Publication oafPublication = (Publication) PublicationToOaf + PublicationToOaf publicationToOaf = new PublicationToOaf(); + Publication oafPublication = (Publication) publicationToOaf .generatePublicationActionsFromDump(j.getAsJsonObject()); assertNotNull(oafPublication.getId()); assertNotNull(oafPublication.getOriginalId()); From 0377b40fbad56c0dd75fb7c8287488a4f63ceffe Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Thu, 30 Jul 2020 18:38:07 +0200 Subject: [PATCH 10/37] output to one parquet file --- .../doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java | 2 +- .../doiboost/orcidnodoi/oaf/PublicationToOaf.java | 9 +++++++-- 2 files changed, 8 insertions(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java index cae5a168f..dea597cbb 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java @@ -123,7 +123,7 @@ public class SparkGenEnrichedOrcidWorks { Dataset publicationDataset = spark .createDataset( - oafPublicationRDD.rdd(), + oafPublicationRDD.repartition(1).rdd(), Encoders.bean(Publication.class)); publicationDataset .write() diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java index 448fa9a74..503df67ff 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java @@ -16,6 +16,7 @@ import org.slf4j.LoggerFactory; import com.google.gson.*; import eu.dnetlib.dhp.common.PacePerson; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.utils.DHPUtils; import eu.dnetlib.doiboost.orcidnodoi.util.DumpToActionsUtility; @@ -217,6 +218,8 @@ public class PublicationToOaf implements Serializable { final List urls = createRepeatedField(rootElement, "urls"); if (urls != null && !urls.isEmpty()) { instance.setUrl(urls); + } else { + dataInfo.setInvisible(true); } final String pubDate = getPublicationDate(rootElement, "publicationDates"); @@ -508,8 +511,10 @@ public class PublicationToOaf implements Serializable { final StructuredProperty sp = new StructuredProperty(); sp.setValue(orcidId); final Qualifier q = new Qualifier(); - q.setClassid("ORCID"); - q.setClassname("ORCID"); + q.setClassid(ORCID.toLowerCase()); + q.setClassname(ORCID.toLowerCase()); + q.setSchemeid(ModelConstants.DNET_PID_TYPES); + q.setSchemename(ModelConstants.DNET_PID_TYPES); sp.setQualifier(q); return sp; } From 538f299767d433ba17681ab82f4b7a32bfb24a2c Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Mon, 14 Sep 2020 12:35:16 +0200 Subject: [PATCH 11/37] merged --- .../dhp/broker/oa/IndexNotificationsJob.java | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java index cb7acb46d..792a2354a 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java @@ -47,8 +47,9 @@ public class IndexNotificationsJob { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString(IndexNotificationsJob.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/index_notifications.json"))); + .toString( + IndexNotificationsJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/index_notifications.json"))); parser.parseArgument(args); final SparkConf conf = new SparkConf(); @@ -116,7 +117,8 @@ public class IndexNotificationsJob { final long date) { final List list = subscriptions .stream() - .filter(s -> StringUtils.isBlank(s.getTopic()) || s.getTopic().equals("*") || s.getTopic().equals(e.getTopic())) + .filter( + s -> StringUtils.isBlank(s.getTopic()) || s.getTopic().equals("*") || s.getTopic().equals(e.getTopic())) .filter(s -> verifyConditions(e.getMap(), s.conditionsAsMap())) .map(s -> generateNotification(s, e, date)) .collect(Collectors.toList()); @@ -147,15 +149,18 @@ public class IndexNotificationsJob { if (conditions.containsKey("trust") && !SubscriptionUtils - .verifyFloatRange(map.getTrust(), conditions.get("trust").get(0).getValue(), conditions.get("trust").get(0).getOtherValue())) { + .verifyFloatRange( + map.getTrust(), conditions.get("trust").get(0).getValue(), + conditions.get("trust").get(0).getOtherValue())) { return false; } if (conditions.containsKey("targetDateofacceptance") && !conditions .get("targetDateofacceptance") .stream() - .anyMatch(c -> SubscriptionUtils - .verifyDateRange(map.getTargetDateofacceptance(), c.getValue(), c.getOtherValue()))) { + .anyMatch( + c -> SubscriptionUtils + .verifyDateRange(map.getTargetDateofacceptance(), c.getValue(), c.getOtherValue()))) { return false; } From 9e8e7fe6ef24dbf6a004190cf86cbc623c8b8d21 Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Tue, 15 Sep 2020 11:32:49 +0200 Subject: [PATCH 12/37] add comments --- .../java/eu/dnetlib/doiboost/orcid/model/AuthorData.java | 4 ++++ .../dnetlib/doiboost/orcidnodoi/ActivitiesDumpReader.java | 6 +++++- .../dnetlib/doiboost/orcidnodoi/GenOrcidAuthorWork.java | 6 +++++- .../doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java | 5 ++++- .../eu/dnetlib/doiboost/orcidnodoi/json/JsonWriter.java | 4 ++++ .../eu/dnetlib/doiboost/orcidnodoi/model/Contributor.java | 4 ++++ .../eu/dnetlib/doiboost/orcidnodoi/model/ExternalId.java | 4 ++++ .../doiboost/orcidnodoi/model/PublicationDate.java | 4 ++++ .../dnetlib/doiboost/orcidnodoi/model/WorkDataNoDoi.java | 4 ++++ .../dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java | 5 ++++- .../doiboost/orcidnodoi/similarity/AuthorMatcher.java | 8 ++++++++ .../doiboost/orcidnodoi/util/DumpToActionsUtility.java | 4 ++++ .../doiboost/orcidnodoi/xml/XMLRecordParserNoDoi.java | 4 ++++ 13 files changed, 58 insertions(+), 4 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/model/AuthorData.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/model/AuthorData.java index 87f1f65c8..e0624509b 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/model/AuthorData.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/model/AuthorData.java @@ -3,6 +3,10 @@ package eu.dnetlib.doiboost.orcid.model; import java.io.Serializable; +/** + * This class models the data that are retrieved from orcid publication + */ + public class AuthorData implements Serializable { private String oid; diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/ActivitiesDumpReader.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/ActivitiesDumpReader.java index 807f52972..d852a7023 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/ActivitiesDumpReader.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/ActivitiesDumpReader.java @@ -20,10 +20,14 @@ import org.apache.hadoop.io.compress.CompressionCodecFactory; import org.mortbay.log.Log; import eu.dnetlib.doiboost.orcid.json.JsonHelper; -import eu.dnetlib.doiboost.orcidnodoi.json.JsonWriter; import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi; import eu.dnetlib.doiboost.orcidnodoi.xml.XMLRecordParserNoDoi; +/** + * This class write on hdfs one sequence file, the key is an orcid identifier and the + * value is an orcid publication in json format + */ + public class ActivitiesDumpReader { private static final int MAX_XML_WORKS_PARSED = -1; diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/GenOrcidAuthorWork.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/GenOrcidAuthorWork.java index 041424ba9..d32e6d945 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/GenOrcidAuthorWork.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/GenOrcidAuthorWork.java @@ -12,11 +12,15 @@ import org.mortbay.log.Log; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.doiboost.orcid.OrcidDSManager; +/** + * This job generates one sequence file, the key is an orcid identifier and the + * value is an orcid publication in json format + */ + public class GenOrcidAuthorWork extends OrcidDSManager { private String activitiesFileNameTarGz; private String outputWorksPath; -// private String workingPath; public static void main(String[] args) throws IOException, Exception { GenOrcidAuthorWork genOrcidAuthorWork = new GenOrcidAuthorWork(); diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java index dea597cbb..b984ee2b2 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java @@ -22,7 +22,6 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; import com.google.gson.Gson; -import com.google.gson.GsonBuilder; import com.google.gson.JsonElement; import com.google.gson.JsonParser; @@ -35,6 +34,10 @@ import eu.dnetlib.doiboost.orcidnodoi.oaf.PublicationToOaf; import eu.dnetlib.doiboost.orcidnodoi.similarity.AuthorMatcher; import scala.Tuple2; +/** + * This spark job generates one parquet file, containing orcid publications dataset + */ + public class SparkGenEnrichedOrcidWorks { static Logger logger = LoggerFactory.getLogger(SparkGenEnrichedOrcidWorks.class); diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/json/JsonWriter.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/json/JsonWriter.java index 7f7e3a10a..363cb13e6 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/json/JsonWriter.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/json/JsonWriter.java @@ -6,6 +6,10 @@ import com.google.gson.JsonObject; import eu.dnetlib.doiboost.orcid.model.AuthorData; import eu.dnetlib.doiboost.orcid.model.WorkData; +/** + * This class converts an object to json and viceversa + */ + public class JsonWriter { public static String create(AuthorData authorData) { diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/Contributor.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/Contributor.java index 8a170de09..9a8651c85 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/Contributor.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/Contributor.java @@ -5,6 +5,10 @@ import java.io.Serializable; import eu.dnetlib.doiboost.orcid.model.AuthorData; +/** + * This class models the data related to a contributor, that are retrieved from an orcid publication + */ + public class Contributor extends AuthorData implements Serializable { private String sequence; private String role; diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/ExternalId.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/ExternalId.java index 865e54ae3..7fe50ce25 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/ExternalId.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/ExternalId.java @@ -1,6 +1,10 @@ package eu.dnetlib.doiboost.orcidnodoi.model; +/** + * This class models the data related to external id, that are retrieved from an orcid publication + */ + public class ExternalId { private String type; private String value; diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/PublicationDate.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/PublicationDate.java index 9282a80ba..5f794d8eb 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/PublicationDate.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/PublicationDate.java @@ -1,6 +1,10 @@ package eu.dnetlib.doiboost.orcidnodoi.model; +/** + * This class models the data related to a publication date, that are retrieved from an orcid publication + */ + public class PublicationDate { private String year; private String month; diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/WorkDataNoDoi.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/WorkDataNoDoi.java index 5756521e7..58f992d12 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/WorkDataNoDoi.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/WorkDataNoDoi.java @@ -4,6 +4,10 @@ package eu.dnetlib.doiboost.orcidnodoi.model; import java.io.Serializable; import java.util.List; +/** + * This class models the data that are retrieved from orcid publication + */ + public class WorkDataNoDoi implements Serializable { private String oid; diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java index 503df67ff..4d1408470 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java @@ -22,6 +22,10 @@ import eu.dnetlib.dhp.utils.DHPUtils; import eu.dnetlib.doiboost.orcidnodoi.util.DumpToActionsUtility; import eu.dnetlib.doiboost.orcidnodoi.util.Pair; +/** + * This class converts an orcid publication from json format to oaf + */ + public class PublicationToOaf implements Serializable { static Logger logger = LoggerFactory.getLogger(PublicationToOaf.class); @@ -119,7 +123,6 @@ public class PublicationToOaf implements Serializable { public Oaf generatePublicationActionsFromDump(final JsonObject rootElement) { - logger.debug("generatePublicationActionsFromDump ..."); if (!isValid(rootElement)) { return null; } diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/similarity/AuthorMatcher.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/similarity/AuthorMatcher.java index 1e4c38bef..88c84ee89 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/similarity/AuthorMatcher.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/similarity/AuthorMatcher.java @@ -21,6 +21,14 @@ import eu.dnetlib.doiboost.orcid.model.AuthorData; import eu.dnetlib.doiboost.orcidnodoi.model.Contributor; import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi; +/** + * This class is used for searching from a list of publication contributors a + * specific author making a similarity check on both name and surname of the + * author with the credit name of each contributor of the list; as soon as + * the match is found (if exist) author informations are used to enrich the + * matched contribuotr inside contributors list + */ + public class AuthorMatcher { private static final Logger logger = LoggerFactory.getLogger(AuthorMatcher.class); diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/util/DumpToActionsUtility.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/util/DumpToActionsUtility.java index 9b9f3c8b2..ea4e58c44 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/util/DumpToActionsUtility.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/util/DumpToActionsUtility.java @@ -9,6 +9,10 @@ import org.apache.commons.lang3.StringUtils; import com.google.gson.JsonArray; import com.google.gson.JsonObject; +/** + * Utility class + */ + public class DumpToActionsUtility { private static final SimpleDateFormat ISO8601FORMAT = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ssZ", Locale.US); diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/xml/XMLRecordParserNoDoi.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/xml/XMLRecordParserNoDoi.java index ae96a322f..c5c115551 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/xml/XMLRecordParserNoDoi.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/xml/XMLRecordParserNoDoi.java @@ -17,6 +17,10 @@ import eu.dnetlib.doiboost.orcidnodoi.model.ExternalId; import eu.dnetlib.doiboost.orcidnodoi.model.PublicationDate; import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi; +/** + * This class is used for parsing xml data with vtd parser + */ + public class XMLRecordParserNoDoi { private static final Logger logger = LoggerFactory.getLogger(XMLRecordParserNoDoi.class); From fefbcfb10682728a499ad6181e83519f66b708a7 Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Tue, 22 Sep 2020 10:20:25 +0200 Subject: [PATCH 13/37] dependency version moved to main pom (PR review) --- dhp-workflows/dhp-doiboost/pom.xml | 2 +- pom.xml | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-doiboost/pom.xml b/dhp-workflows/dhp-doiboost/pom.xml index e9768be7e..357a57367 100644 --- a/dhp-workflows/dhp-doiboost/pom.xml +++ b/dhp-workflows/dhp-doiboost/pom.xml @@ -87,7 +87,7 @@ org.apache.commons commons-text - 1.8 + ${common.text.version} diff --git a/pom.xml b/pom.xml index e88e1d51b..9897c8abe 100644 --- a/pom.xml +++ b/pom.xml @@ -669,5 +669,6 @@ 1.1 3.5.3 4.13.0 + 1.8 From a97ad20c7bd7725ee513694d9b00aae0a19b19d2 Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Tue, 22 Sep 2020 10:46:34 +0200 Subject: [PATCH 14/37] exception is now propagated (PR review) --- .../java/eu/dnetlib/doiboost/orcid/OrcidDSManager.java | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDSManager.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDSManager.java index aa61c0117..8ebeab2e5 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDSManager.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDSManager.java @@ -48,15 +48,10 @@ public class OrcidDSManager { return conf; } - protected FileSystem initFileSystemObject(Configuration conf) { + protected FileSystem initFileSystemObject(Configuration conf) throws IOException { // Get the filesystem - HDFS FileSystem fs = null; - try { - fs = FileSystem.get(URI.create(hdfsServerUri.concat(workingPath)), conf); - } catch (IOException e) { - // TODO Auto-generated catch block - e.printStackTrace(); - } + fs = FileSystem.get(URI.create(hdfsServerUri.concat(workingPath)), conf); return fs; } From ab083f9946a219396b0099f29d67d7c492eec126 Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Thu, 22 Oct 2020 14:02:32 +0200 Subject: [PATCH 15/37] propagate exception on parsing work (PR request) --- .../dnetlib/doiboost/orcidnodoi/ActivitiesDumpReader.java | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/ActivitiesDumpReader.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/ActivitiesDumpReader.java index d852a7023..c73e1efd1 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/ActivitiesDumpReader.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/ActivitiesDumpReader.java @@ -128,10 +128,7 @@ public class ActivitiesDumpReader { } } } catch (Exception e) { - Log - .warn( - "Parsing work from tar archive and xml work: " + filename + " " + e.getMessage()); -// Log.warn(e); + throw new Exception(filename, e); } if ((counter % XML_WORKS_PARSED_COUNTER_LOG_INTERVAL) == 0) { @@ -143,7 +140,7 @@ public class ActivitiesDumpReader { } } } - } catch (IOException e) { + } catch (Exception e) { Log.warn("Parsing work from gzip archive: " + e.getMessage()); Log.warn(e); throw new RuntimeException(e); From c295c71ca0c77f5b3aed5817a872d9c9da77aade Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Thu, 22 Oct 2020 14:07:26 +0200 Subject: [PATCH 16/37] added comment --- .../src/main/java/eu/dnetlib/doiboost/orcid/OrcidDSManager.java | 1 + 1 file changed, 1 insertion(+) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDSManager.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDSManager.java index 8ebeab2e5..b62ad370e 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDSManager.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDSManager.java @@ -50,6 +50,7 @@ public class OrcidDSManager { protected FileSystem initFileSystemObject(Configuration conf) throws IOException { // Get the filesystem - HDFS + // if there is an exception, it will be propagate FileSystem fs = null; fs = FileSystem.get(URI.create(hdfsServerUri.concat(workingPath)), conf); return fs; From c3114ba0aeaada891ff13de4c3e4f6469b40ba99 Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Thu, 22 Oct 2020 14:21:31 +0200 Subject: [PATCH 17/37] replaced null as return value with a more safe empty string --- .../dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java index b984ee2b2..24f0f7a87 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java @@ -167,6 +167,6 @@ public class SparkGenEnrichedOrcidWorks { return name.getAsString(); } } - return null; + return new String(""); } } From 846ba3087310024cf3e28fb2c88f10259323f5f6 Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Thu, 22 Oct 2020 14:36:18 +0200 Subject: [PATCH 18/37] if typologies mapping fails, an exception will be propagated --- .../eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java index 4d1408470..deb83723b 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java @@ -97,8 +97,8 @@ public class PublicationToOaf implements Serializable { .getResourceAsStream( "/eu/dnetlib/dhp/doiboost/orcidnodoi/mappings/typologies.json")); typologiesMapping = new Gson().fromJson(tt, Map.class); - } catch (final Exception e) { - logger.error("loading typologies", e); + } catch (Exception e) { + throw new RuntimeException("loading typologies", e); } } From c58db1c8eab65e0e4ad7d27b7bbc5f815961f050 Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Thu, 22 Oct 2020 15:11:02 +0200 Subject: [PATCH 19/37] added filter on null value after map function --- .../eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java index deb83723b..63979d1af 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java @@ -185,6 +185,7 @@ public class PublicationToOaf implements Serializable { .map(t -> { return mapStructuredProperty(t, q, null); }) + .filter(s -> s!=null) .collect(Collectors.toList())); // Adding identifier final String id = getStringValue(rootElement, "id"); @@ -376,7 +377,7 @@ public class PublicationToOaf implements Serializable { .map(r -> { return mapStructuredProperty(r, q, null); }) - .collect(Collectors.toList())); + .filter(s -> s!=null).collect(Collectors.toList())); } } From 1139d6568d392b61e97c12ce1ceac9b2a59b42e2 Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Thu, 22 Oct 2020 15:32:26 +0200 Subject: [PATCH 20/37] replaced null value with a more safe empty string as return value --- .../dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java | 8 +++++++- .../doiboost/orcidnodoi/util/DumpToActionsUtility.java | 2 +- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java index 63979d1af..136356161 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java @@ -166,7 +166,13 @@ public class PublicationToOaf implements Serializable { // Adding source final String source = getStringValue(rootElement, "sourceName"); if (StringUtils.isNotBlank(source)) { - publication.setSource(Arrays.asList(mapStringField(source, null))); + Field sourceField = mapStringField(source, null); + if (sourceField==null) { + publication.setSource(null); + } + else { + publication.setSource(Arrays.asList(sourceField)); + } } // Adding titles diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/util/DumpToActionsUtility.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/util/DumpToActionsUtility.java index ea4e58c44..8096c4e8e 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/util/DumpToActionsUtility.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/util/DumpToActionsUtility.java @@ -20,7 +20,7 @@ public class DumpToActionsUtility { public static String getStringValue(final JsonObject root, final String key) { if (root.has(key) && !root.get(key).isJsonNull()) return root.get(key).getAsString(); - return null; + return new String(""); } public static List getArrayValues(final JsonObject root, final String key) { From a38ab57062955b425c1fec90875c16a6954fb83d Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Thu, 22 Oct 2020 15:43:50 +0200 Subject: [PATCH 21/37] let run test methods --- .../eu/dnetlib/doiboost/orcidnodoi/xml/OrcidNoDoiTest.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/xml/OrcidNoDoiTest.java b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/xml/OrcidNoDoiTest.java index ca91a242a..bf5aba99b 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/xml/OrcidNoDoiTest.java +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/xml/OrcidNoDoiTest.java @@ -41,7 +41,7 @@ public class OrcidNoDoiTest { String orcidIdA = "0000-0003-2760-1191"; @Test - @Ignore +// @Ignore public void readPublicationFieldsTest() throws IOException, XPathEvalException, XPathParseException, NavException, VtdException, ParseException { logger.info("running loadPublicationFieldsTest ...."); @@ -95,7 +95,7 @@ public class OrcidNoDoiTest { } @Test - @Ignore +// @Ignore private void authorMatchTest() throws Exception { logger.info("running authorSimpleMatchTest ...."); String orcidWork = "activity_work_0000-0003-2760-1191-similarity.xml"; From b0290dbcb7728da0b447d38953702ab681bb1ce0 Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Thu, 22 Oct 2020 16:20:46 +0200 Subject: [PATCH 22/37] moved all dependencies version to main pom.xml --- dhp-workflows/dhp-doiboost/pom.xml | 4 ++-- pom.xml | 2 ++ 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/pom.xml b/dhp-workflows/dhp-doiboost/pom.xml index 357a57367..b81299cd1 100644 --- a/dhp-workflows/dhp-doiboost/pom.xml +++ b/dhp-workflows/dhp-doiboost/pom.xml @@ -14,7 +14,7 @@ net.alchim31.maven scala-maven-plugin - 4.0.1 + ${net.alchim31.maven.version} scala-compile-first @@ -51,7 +51,7 @@ org.apache.httpcomponents httpclient - 4.3.4 + ${org.apache.httpcomponents.version} eu.dnetlib.dhp diff --git a/pom.xml b/pom.xml index 9897c8abe..bae53fcc0 100644 --- a/pom.xml +++ b/pom.xml @@ -670,5 +670,7 @@ 3.5.3 4.13.0 1.8 + 4.3.4 + 4.0.1 From 210a50e4f486c195b627d462e64d8ee10c3dc70e Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Thu, 22 Oct 2020 16:24:42 +0200 Subject: [PATCH 23/37] replaced null value --- .../doiboost/orcidnodoi/oaf/PublicationToOaf.java | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java index 136356161..ece59c3f1 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java @@ -167,10 +167,9 @@ public class PublicationToOaf implements Serializable { final String source = getStringValue(rootElement, "sourceName"); if (StringUtils.isNotBlank(source)) { Field sourceField = mapStringField(source, null); - if (sourceField==null) { + if (sourceField == null) { publication.setSource(null); - } - else { + } else { publication.setSource(Arrays.asList(sourceField)); } } @@ -191,7 +190,7 @@ public class PublicationToOaf implements Serializable { .map(t -> { return mapStructuredProperty(t, q, null); }) - .filter(s -> s!=null) + .filter(s -> s != null) .collect(Collectors.toList())); // Adding identifier final String id = getStringValue(rootElement, "id"); @@ -383,7 +382,8 @@ public class PublicationToOaf implements Serializable { .map(r -> { return mapStructuredProperty(r, q, null); }) - .filter(s -> s!=null).collect(Collectors.toList())); + .filter(s -> s != null) + .collect(Collectors.toList())); } } From 6bc7dbeca76e94f6cb00725aa50753d61d122952 Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Fri, 6 Nov 2020 13:47:50 +0100 Subject: [PATCH 24/37] first version of dataset successful generated from orcid dump 2020 --- dhp-workflows/dhp-doiboost/pom.xml | 2 - .../doiboost/orcid/OrcidDSManager.java | 2 +- .../orcidnodoi/ActivitiesDumpReader.java | 4 +- .../orcidnodoi/GenOrcidAuthorWork.java | 2 +- .../SparkGenEnrichedOrcidWorks.java | 8 +- .../orcidnodoi/similarity/AuthorMatcher.java | 4 +- .../orcidnodoi/xml/XMLRecordParserNoDoi.java | 53 +++--- ... => gen_orcid_authors_from_summaries.json} | 0 ...en_orcid_works-no-doi_from_activities.json | 7 + .../orcid/oozie_app/config-default.xml | 42 ----- .../dhp/doiboost/orcid/oozie_app/workflow.xml | 67 -------- .../oozie_app/config-default.xml | 2 +- .../orcid_activities/oozie_app/workflow.xml | 156 +++++++++++------- .../oozie_app/config-default.xml | 4 + .../orcid_summaries/oozie_app/workflow.xml | 14 +- .../oozie_app/workflow.xml | 4 +- .../doiboost/orcid/OrcidClientTest.java | 4 +- .../orcidnodoi/xml/OrcidNoDoiTest.java | 60 ++++++- ..._work_0000-0003-2760-1191_contributors.xml | 101 ++++++++++++ pom.xml | 12 ++ 20 files changed, 320 insertions(+), 228 deletions(-) rename dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/{create_orcid_authors_data.json => gen_orcid_authors_from_summaries.json} (100%) create mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_orcid_works-no-doi_from_activities.json delete mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid/oozie_app/config-default.xml delete mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid/oozie_app/workflow.xml rename dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/{gen_enriched_orcid_works => orcidnodoi}/oozie_app/workflow.xml (95%) create mode 100644 dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/xml/activity_work_0000-0003-2760-1191_contributors.xml diff --git a/dhp-workflows/dhp-doiboost/pom.xml b/dhp-workflows/dhp-doiboost/pom.xml index b81299cd1..624dd7b31 100644 --- a/dhp-workflows/dhp-doiboost/pom.xml +++ b/dhp-workflows/dhp-doiboost/pom.xml @@ -51,7 +51,6 @@ org.apache.httpcomponents httpclient - ${org.apache.httpcomponents.version} eu.dnetlib.dhp @@ -87,7 +86,6 @@ org.apache.commons commons-text - ${common.text.version} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDSManager.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDSManager.java index b62ad370e..bf13db021 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDSManager.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDSManager.java @@ -62,7 +62,7 @@ public class OrcidDSManager { .toString( OrcidDSManager.class .getResourceAsStream( - "/eu/dnetlib/dhp/doiboost/create_orcid_authors_data.json"))); + "/eu/dnetlib/dhp/doiboost/gen_orcid_authors_from_summaries.json"))); parser.parseArgument(args); hdfsServerUri = parser.get("hdfsServerUri"); diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/ActivitiesDumpReader.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/ActivitiesDumpReader.java index c73e1efd1..c2cfafd87 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/ActivitiesDumpReader.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/ActivitiesDumpReader.java @@ -73,7 +73,7 @@ public class ActivitiesDumpReader { SequenceFile.Writer.valueClass(Text.class))) { while ((entry = tais.getNextTarEntry()) != null) { String filename = entry.getName(); - + StringBuffer buffer = new StringBuffer(); try { if (entry.isDirectory() || !filename.contains("works")) { @@ -83,7 +83,7 @@ public class ActivitiesDumpReader { BufferedReader br = new BufferedReader(new InputStreamReader(tais)); // Read directly from // tarInput String line; - StringBuffer buffer = new StringBuffer(); + buffer = new StringBuffer(); while ((line = br.readLine()) != null) { buffer.append(line); } diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/GenOrcidAuthorWork.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/GenOrcidAuthorWork.java index d32e6d945..d3e9aeaef 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/GenOrcidAuthorWork.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/GenOrcidAuthorWork.java @@ -42,7 +42,7 @@ public class GenOrcidAuthorWork extends OrcidDSManager { .toString( GenOrcidAuthorWork.class .getResourceAsStream( - "/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works_parameters.json"))); + "/eu/dnetlib/dhp/doiboost/gen_orcid_works-no-doi_from_activities.json"))); parser.parseArgument(args); hdfsServerUri = parser.get("hdfsServerUri"); diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java index 24f0f7a87..691ca3eee 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java @@ -67,7 +67,7 @@ public class SparkGenEnrichedOrcidWorks { JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaPairRDD summariesRDD = sc - .sequenceFile(workingPath + "summaries/output/authors.seq", Text.class, Text.class); + .sequenceFile(workingPath + "authors/authors.seq", Text.class, Text.class); Dataset summariesDataset = spark .createDataset( summariesRDD.map(seq -> loadAuthorFromJson(seq._1(), seq._2())).rdd(), @@ -96,8 +96,8 @@ public class SparkGenEnrichedOrcidWorks { Encoders.tuple(Encoders.STRING(), Encoders.STRING())) .filter(Objects::nonNull) .toJavaRDD(); - enrichedWorksRDD.saveAsTextFile(workingPath + outputEnrichedWorksPath); - logger.info("Works enriched data saved"); +// enrichedWorksRDD.saveAsTextFile(workingPath + outputEnrichedWorksPath); + logger.info("Enriched works RDD ready."); final LongAccumulator parsedPublications = spark.sparkContext().longAccumulator("parsedPublications"); final LongAccumulator enrichedPublications = spark @@ -132,7 +132,7 @@ public class SparkGenEnrichedOrcidWorks { .write() .format("parquet") .mode(SaveMode.Overwrite) - .save(workingPath + "no_doi_dataset/output"); + .save(workingPath + outputEnrichedWorksPath); logger.info("parsedPublications: " + parsedPublications.value().toString()); logger.info("enrichedPublications: " + enrichedPublications.value().toString()); diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/similarity/AuthorMatcher.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/similarity/AuthorMatcher.java index 88c84ee89..6a1468f4c 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/similarity/AuthorMatcher.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/similarity/AuthorMatcher.java @@ -5,6 +5,7 @@ import java.io.IOException; import java.text.Normalizer; import java.util.*; +import org.apache.commons.lang3.StringUtils; import org.apache.commons.text.similarity.JaroWinklerSimilarity; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -40,7 +41,7 @@ public class AuthorMatcher { int matchCounter = 0; List matchCounters = Arrays.asList(matchCounter); Contributor contributor = null; - contributors.forEach(c -> { + contributors.stream().filter(c -> !StringUtils.isBlank(c.getCreditName())).forEach(c -> { if (simpleMatch(c.getCreditName(), author.getName()) || simpleMatch(c.getCreditName(), author.getSurname()) || simpleMatch(c.getCreditName(), author.getOtherName())) { @@ -54,6 +55,7 @@ public class AuthorMatcher { Optional optCon = contributors .stream() .filter(c -> c.isSimpleMatch()) + .filter(c -> !StringUtils.isBlank(c.getCreditName())) .map(c -> { c.setScore(bestMatch(author.getName(), author.getSurname(), c.getCreditName())); return c; diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/xml/XMLRecordParserNoDoi.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/xml/XMLRecordParserNoDoi.java index c5c115551..f4b093402 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/xml/XMLRecordParserNoDoi.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/xml/XMLRecordParserNoDoi.java @@ -183,39 +183,34 @@ public class XMLRecordParserNoDoi { private static List getContributors(VTDGen vg, VTDNav vn, AutoPilot ap) throws XPathParseException, NavException, XPathEvalException { List contributors = new ArrayList(); - int nameIndex = 0; - ap.selectXPath("//work:contributor/work:credit-name"); + ap.selectXPath("//work:contributors/work:contributor"); while (ap.evalXPath() != -1) { Contributor contributor = new Contributor(); - int t = vn.getText(); - if (t >= 0) { - contributor.setCreditName(vn.toNormalizedString(t)); - contributors.add(nameIndex, contributor); - nameIndex++; + if (vn.toElement(VTDNav.FIRST_CHILD, "work:credit-name")) { + int val = vn.getText(); + if (val != -1) { + contributor.setCreditName(vn.toNormalizedString(val)); + } + vn.toElement(VTDNav.PARENT); } - } - if (contributors.size() == 0) { - return contributors; - } - - int sequenceIndex = 0; - ap.selectXPath("//work:contributor/work:contributor-attributes/work:contributor-sequence"); - while (ap.evalXPath() != -1) { - int t = vn.getText(); - if (t >= 0) { - contributors.get(sequenceIndex).setSequence(vn.toNormalizedString(t)); - sequenceIndex++; - } - } - - int roleIndex = 0; - ap.selectXPath("//work:contributor/work:contributor-attributes/work:contributor-role"); - while (ap.evalXPath() != -1) { - int t = vn.getText(); - if (t >= 0) { - contributors.get(roleIndex).setRole(vn.toNormalizedString(t)); - roleIndex++; + if (vn.toElement(VTDNav.FIRST_CHILD, "work:contributor-attributes")) { + if (vn.toElement(VTDNav.FIRST_CHILD, "work:contributor-sequence")) { + int val = vn.getText(); + if (val != -1) { + contributor.setSequence(vn.toNormalizedString(val)); + } + vn.toElement(VTDNav.PARENT); + } + if (vn.toElement(VTDNav.FIRST_CHILD, "work:contributor-role")) { + int val = vn.getText(); + if (val != -1) { + contributor.setRole(vn.toNormalizedString(val)); + } + vn.toElement(VTDNav.PARENT); + } + vn.toElement(VTDNav.PARENT); } + contributors.add(contributor); } return contributors; } diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/create_orcid_authors_data.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_orcid_authors_from_summaries.json similarity index 100% rename from dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/create_orcid_authors_data.json rename to dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_orcid_authors_from_summaries.json diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_orcid_works-no-doi_from_activities.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_orcid_works-no-doi_from_activities.json new file mode 100644 index 000000000..c3a8f92ec --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_orcid_works-no-doi_from_activities.json @@ -0,0 +1,7 @@ +[ + {"paramName":"n", "paramLongName":"hdfsServerUri", "paramDescription": "the server uri", "paramRequired": true}, + {"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the default work path", "paramRequired": true}, + {"paramName":"f", "paramLongName":"activitiesFileNameTarGz", "paramDescription": "the name of the activities orcid file", "paramRequired": true}, + {"paramName":"ow", "paramLongName":"outputWorksPath", "paramDescription": "the relative folder of the sequencial file to write", "paramRequired": true}, + {"paramName":"oew", "paramLongName":"outputEnrichedWorksPath", "paramDescription": "the relative folder of the sequencial file to write the data", "paramRequired": true} +] \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid/oozie_app/config-default.xml deleted file mode 100644 index fe14bb8cb..000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid/oozie_app/config-default.xml +++ /dev/null @@ -1,42 +0,0 @@ - - - jobTracker - hadoop-rm3.garr-pa1.d4science.org:8032 - - - nameNode - hdfs://hadoop-rm1.garr-pa1.d4science.org:8020 - - - oozie.use.system.libpath - true - - - oozie.action.sharelib.for.spark - spark2 - - - oozie.launcher.mapreduce.user.classpath.first - true - - - hive_metastore_uris - thrift://hadoop-edge2.garr-pa1.d4science.org:9083 - - - spark2YarnHistoryServerAddress - http://hadoop-edge1.garr-pa1.d4science.org:18089/ - - - spark2EventLogDir - /user/spark/spark2ApplicationHistory - - - spark2ExtraListeners - "com.cloudera.spark.lineage.NavigatorAppListener" - - - spark2SqlQueryExecutionListeners - "com.cloudera.spark.lineage.NavigatorQueryListener" - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid/oozie_app/workflow.xml deleted file mode 100644 index 51e00dc0f..000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid/oozie_app/workflow.xml +++ /dev/null @@ -1,67 +0,0 @@ - - - - workingPath - the working dir base path - - - shell_cmd_0 - wget -O /tmp/ORCID_2019_summaries.tar.gz https://orcid.figshare.com/ndownloader/files/18017633 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_summaries.tar.gz /data/orcid_activities/ORCID_2019_summaries.tar.gz ; rm -f /tmp/ORCID_2019_summaries.tar.gz - - the shell command that downloads and puts to hdfs orcid summaries - - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - - - - - - - - - - - ${fs:exists(concat(workingPath,'/ORCID_2019_summaries.tar.gz'))} - - - - - - - - ${jobTracker} - ${nameNode} - bash - -c - ${shell_cmd_0} - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcid.OrcidDSManager - -w${workingPath}/ - -n${nameNode} - -fORCID_2019_summaries.tar.gz - -osummaries/output/ - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_activities/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_activities/oozie_app/config-default.xml index 3068562d0..05fe6d014 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_activities/oozie_app/config-default.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_activities/oozie_app/config-default.xml @@ -9,7 +9,7 @@ oozie.launcher.mapreduce.map.java.opts - -Xmx4g + -Xmx2g jobTracker diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_activities/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_activities/oozie_app/workflow.xml index 8f9a5123e..ea4d33296 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_activities/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_activities/oozie_app/workflow.xml @@ -1,4 +1,4 @@ - + workingPath @@ -6,70 +6,70 @@ shell_cmd_0 - wget -O /tmp/ORCID_2019_activites_0.tar.gz https://orcid.figshare.com/ndownloader/files/18017660 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_0.tar.gz /data/orcid_activities/ORCID_2019_activites_0.tar.gz ; rm -f /tmp/ORCID_2019_activites_0.tar.gz + wget -O /tmp/ORCID_2020_10_activites_0.tar.gz https://orcid.figshare.com/ndownloader/files/25002232 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_0.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_0.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_0.tar.gz the shell command that downloads and puts to hdfs orcid activity file 0 shell_cmd_1 - wget -O /tmp/ORCID_2019_activites_1.tar.gz https://orcid.figshare.com/ndownloader/files/18017675 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_1.tar.gz /data/orcid_activities/ORCID_2019_activites_1.tar.gz ; rm -f /tmp/ORCID_2019_activites_1.tar.gz + wget -O /tmp/ORCID_2020_10_activites_1.tar.gz https://orcid.figshare.com/ndownloader/files/25002088 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_1.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_1.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_1.tar.gz the shell command that downloads and puts to hdfs orcid activity file 1 shell_cmd_2 - wget -O /tmp/ORCID_2019_activites_2.tar.gz https://orcid.figshare.com/ndownloader/files/18017717 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_2.tar.gz /data/orcid_activities/ORCID_2019_activites_2.tar.gz ; rm -f /tmp/ORCID_2019_activites_2.tar.gz + wget -O /tmp/ORCID_2020_10_activites_2.tar.gz https://orcid.figshare.com/ndownloader/files/25000596 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_2.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_2.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_2.tar.gz the shell command that downloads and puts to hdfs orcid activity file 2 shell_cmd_3 - wget -O /tmp/ORCID_2019_activites_3.tar.gz https://orcid.figshare.com/ndownloader/files/18017765 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_3.tar.gz /data/orcid_activities/ORCID_2019_activites_3.tar.gz ; rm -f /tmp/ORCID_2019_activites_3.tar.gz + wget -O /tmp/ORCID_2020_10_activites_3.tar.gz https://orcid.figshare.com/ndownloader/files/25015150 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_3.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_3.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_3.tar.gz the shell command that downloads and puts to hdfs orcid activity file 3 - + shell_cmd_4 - wget -O /tmp/ORCID_2019_activites_4.tar.gz https://orcid.figshare.com/ndownloader/files/18017831 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_4.tar.gz /data/orcid_activities/ORCID_2019_activites_4.tar.gz ; rm -f /tmp/ORCID_2019_activites_4.tar.gz + wget -O /tmp/ORCID_2020_10_activites_4.tar.gz https://orcid.figshare.com/ndownloader/files/25033643 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_4.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_4.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_4.tar.gz the shell command that downloads and puts to hdfs orcid activity file 4 - + shell_cmd_5 - wget -O /tmp/ORCID_2019_activites_5.tar.gz https://orcid.figshare.com/ndownloader/files/18017987 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_5.tar.gz /data/orcid_activities/ORCID_2019_activites_5.tar.gz ; rm -f /tmp/ORCID_2019_activites_5.tar.gz + wget -O /tmp/ORCID_2020_10_activites_5.tar.gz https://orcid.figshare.com/ndownloader/files/25005483 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_5.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_5.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_5.tar.gz the shell command that downloads and puts to hdfs orcid activity file 5 - + shell_cmd_6 - wget -O /tmp/ORCID_2019_activites_6.tar.gz https://orcid.figshare.com/ndownloader/files/18018053 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_6.tar.gz /data/orcid_activities/ORCID_2019_activites_6.tar.gz ; rm -f /tmp/ORCID_2019_activites_6.tar.gz + wget -O /tmp/ORCID_2020_10_activites_6.tar.gz https://orcid.figshare.com/ndownloader/files/25005425 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_6.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_6.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_6.tar.gz the shell command that downloads and puts to hdfs orcid activity file 6 shell_cmd_7 - wget -O /tmp/ORCID_2019_activites_7.tar.gz https://orcid.figshare.com/ndownloader/files/18018023 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_7.tar.gz /data/orcid_activities/ORCID_2019_activites_7.tar.gz ; rm -f /tmp/ORCID_2019_activites_7.tar.gz + wget -O /tmp/ORCID_2020_10_activites_7.tar.gz https://orcid.figshare.com/ndownloader/files/25012016 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_7.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_7.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_7.tar.gz the shell command that downloads and puts to hdfs orcid activity file 7 shell_cmd_8 - wget -O /tmp/ORCID_2019_activites_8.tar.gz https://orcid.figshare.com/ndownloader/files/18018248 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_8.tar.gz /data/orcid_activities/ORCID_2019_activites_8.tar.gz ; rm -f /tmp/ORCID_2019_activites_8.tar.gz + wget -O /tmp/ORCID_2020_10_activites_8.tar.gz https://orcid.figshare.com/ndownloader/files/25012079 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_8.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_8.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_8.tar.gz the shell command that downloads and puts to hdfs orcid activity file 8 shell_cmd_9 - wget -O /tmp/ORCID_2019_activites_9.tar.gz https://orcid.figshare.com/ndownloader/files/18018029 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_9.tar.gz /data/orcid_activities/ORCID_2019_activites_9.tar.gz ; rm -f /tmp/ORCID_2019_activites_9.tar.gz + wget -O /tmp/ORCID_2020_10_activites_9.tar.gz https://orcid.figshare.com/ndownloader/files/25010727 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_9.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_9.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_9.tar.gz the shell command that downloads and puts to hdfs orcid activity file 9 - + shell_cmd_X - wget -O /tmp/ORCID_2019_activites_X.tar.gz https://orcid.figshare.com/ndownloader/files/18018182 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_X.tar.gz /data/orcid_activities/ORCID_2019_activites_X.tar.gz ; rm -f /tmp/ORCID_2019_activites_X.tar.gz + wget -O /tmp/ORCID_2020_10_activites_X.tar.gz https://orcid.figshare.com/ndownloader/files/25011025 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_X.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_X.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_X.tar.gz the shell command that downloads and puts to hdfs orcid activity file X - + @@ -82,11 +82,11 @@ - + - + @@ -102,8 +102,8 @@ - - ${fs:exists(concat(workingPath,'/ORCID_2019_activites_0.tar.gz'))} + + ${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_0.tar.gz'))} @@ -118,7 +118,7 @@ ${shell_cmd_0} - + @@ -129,7 +129,7 @@ eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork -w${workingPath}/ -n${nameNode} - -fORCID_2019_activites_0.tar.gz + -fORCID_2020_10_activites_0.tar.gz -owno_doi_works/works_0.seq -oewno_doi_enriched_works/ @@ -139,8 +139,8 @@ - - ${fs:exists(concat(workingPath,'/ORCID_2019_activites_1.tar.gz'))} + + ${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_1.tar.gz'))} @@ -155,7 +155,7 @@ ${shell_cmd_1} - + @@ -166,7 +166,7 @@ eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork -w${workingPath}/ -n${nameNode} - -fORCID_2019_activites_1.tar.gz + -fORCID_2020_10_activites_1.tar.gz -owno_doi_works/works_1.seq -oewno_doi_enriched_works/ @@ -176,8 +176,8 @@ - - ${fs:exists(concat(workingPath,'/ORCID_2019_activites_2.tar.gz'))} + + ${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_2.tar.gz'))} @@ -192,7 +192,7 @@ ${shell_cmd_2} - + @@ -203,7 +203,7 @@ eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork -w${workingPath}/ -n${nameNode} - -fORCID_2019_activites_2.tar.gz + -fORCID_2020_10_activites_2.tar.gz -owno_doi_works/works_2.seq -oewno_doi_enriched_works/ @@ -213,8 +213,8 @@ - - ${fs:exists(concat(workingPath,'/ORCID_2019_activites_3.tar.gz'))} + + ${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_3.tar.gz'))} @@ -229,7 +229,7 @@ ${shell_cmd_3} - + @@ -240,7 +240,7 @@ eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork -w${workingPath}/ -n${nameNode} - -fORCID_2019_activites_3.tar.gz + -fORCID_2020_10_activites_3.tar.gz -owno_doi_works/works_3.seq -oewno_doi_enriched_works/ @@ -250,8 +250,8 @@ - - ${fs:exists(concat(workingPath,'/ORCID_2019_activites_4.tar.gz'))} + + ${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_4.tar.gz'))} @@ -266,7 +266,7 @@ ${shell_cmd_4} - + @@ -277,7 +277,7 @@ eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork -w${workingPath}/ -n${nameNode} - -fORCID_2019_activites_4.tar.gz + -fORCID_2020_10_activites_4.tar.gz -owno_doi_works/works_4.seq -oewno_doi_enriched_works/ @@ -287,8 +287,8 @@ - - ${fs:exists(concat(workingPath,'/ORCID_2019_activites_5.tar.gz'))} + + ${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_5.tar.gz'))} @@ -303,7 +303,7 @@ ${shell_cmd_5} - + @@ -314,7 +314,7 @@ eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork -w${workingPath}/ -n${nameNode} - -fORCID_2019_activites_5.tar.gz + -fORCID_2020_10_activites_5.tar.gz -owno_doi_works/works_5.seq -oewno_doi_enriched_works/ @@ -324,8 +324,8 @@ - - ${fs:exists(concat(workingPath,'/ORCID_2019_activites_6.tar.gz'))} + + ${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_6.tar.gz'))} @@ -340,7 +340,7 @@ ${shell_cmd_6} - + @@ -351,7 +351,7 @@ eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork -w${workingPath}/ -n${nameNode} - -fORCID_2019_activites_6.tar.gz + -fORCID_2020_10_activites_6.tar.gz -owno_doi_works/works_6.seq -oewno_doi_enriched_works/ @@ -362,8 +362,8 @@ - - ${fs:exists(concat(workingPath,'/ORCID_2019_activites_7.tar.gz'))} + + ${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_7.tar.gz'))} @@ -378,7 +378,7 @@ ${shell_cmd_7} - + @@ -389,7 +389,7 @@ eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork -w${workingPath}/ -n${nameNode} - -fORCID_2019_activites_7.tar.gz + -fORCID_2020_10_activites_7.tar.gz -owno_doi_works/works_7.seq -oewno_doi_enriched_works/ @@ -399,8 +399,8 @@ - - ${fs:exists(concat(workingPath,'/ORCID_2019_activites_8.tar.gz'))} + + ${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_8.tar.gz'))} @@ -415,7 +415,7 @@ ${shell_cmd_8} - + @@ -426,7 +426,7 @@ eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork -w${workingPath}/ -n${nameNode} - -fORCID_2019_activites_8.tar.gz + -fORCID_2020_10_activites_8.tar.gz -owno_doi_works/works_8.seq -oewno_doi_enriched_works/ @@ -436,8 +436,8 @@ - - ${fs:exists(concat(workingPath,'/ORCID_2019_activites_9.tar.gz'))} + + ${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_9.tar.gz'))} @@ -452,7 +452,7 @@ ${shell_cmd_9} - + @@ -463,7 +463,7 @@ eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork -w${workingPath}/ -n${nameNode} - -fORCID_2019_activites_9.tar.gz + -fORCID_2020_10_activites_9.tar.gz -owno_doi_works/works_9.seq -oewno_doi_enriched_works/ @@ -473,8 +473,8 @@ - - ${fs:exists(concat(workingPath,'/ORCID_2019_activites_X.tar.gz'))} + + ${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_X.tar.gz'))} @@ -489,7 +489,7 @@ ${shell_cmd_X} - + @@ -500,7 +500,7 @@ eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork -w${workingPath}/ -n${nameNode} - -fORCID_2019_activites_X.tar.gz + -fORCID_2020_10_activites_X.tar.gz -owno_doi_works/works_X.seq -oewno_doi_enriched_works/ @@ -508,7 +508,35 @@ + + + + + + + + + + + + + + + + - + + + + + + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_summaries/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_summaries/oozie_app/config-default.xml index e77dd09c9..e1829e847 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_summaries/oozie_app/config-default.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_summaries/oozie_app/config-default.xml @@ -19,4 +19,8 @@ oozie.launcher.mapreduce.user.classpath.first true + + oozie.launcher.mapreduce.map.java.opts + -Xmx16g + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_summaries/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_summaries/oozie_app/workflow.xml index 3362cc67b..8517f35ee 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_summaries/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_summaries/oozie_app/workflow.xml @@ -1,4 +1,4 @@ - + workingPath @@ -6,7 +6,7 @@ shell_cmd_0 - wget -O /tmp/ORCID_2019_summaries.tar.gz https://orcid.figshare.com/ndownloader/files/18017633 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_summaries.tar.gz /data/orcid_activities/ORCID_2019_summaries.tar.gz ; rm -f /tmp/ORCID_2019_summaries.tar.gz + wget -O /tmp/ORCID_2020_10_summaries.tar.gz https://orcid.figshare.com/ndownloader/files/25032905 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_summaries.tar.gz /data/orcid_activities_2020/ORCID_2020_10_summaries.tar.gz ; rm -f /tmp/ORCID_2020_10_summaries.tar.gz the shell command that downloads and puts to hdfs orcid summaries @@ -21,8 +21,8 @@ - - + + @@ -31,7 +31,7 @@ - ${fs:exists(concat(workingPath,'/ORCID_2019_summaries.tar.gz'))} + ${fs:exists(concat(workingPath,'/ORCID_2020_10_summaries.tar.gz'))} @@ -57,8 +57,8 @@ eu.dnetlib.doiboost.orcid.OrcidDSManager -w${workingPath}/ -n${nameNode} - -fORCID_2019_summaries.tar.gz - -osummaries/output/ + -fORCID_2020_10_summaries.tar.gz + -oauthors/ diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcidnodoi/oozie_app/workflow.xml similarity index 95% rename from dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works/oozie_app/workflow.xml rename to dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcidnodoi/oozie_app/workflow.xml index faed3104a..6cec48a6d 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcidnodoi/oozie_app/workflow.xml @@ -59,7 +59,7 @@ - + @@ -85,7 +85,7 @@ -n${nameNode} -f- -owno_doi_works/ - -oewno_doi_enriched_works/output + -oewno_doi_dataset diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/OrcidClientTest.java b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/OrcidClientTest.java index 5e0f91ecd..774475626 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/OrcidClientTest.java +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/OrcidClientTest.java @@ -38,8 +38,8 @@ public class OrcidClientTest { @Test public void downloadTest() throws Exception { - String record = testDownloadRecord("0000-0002-2536-4498"); - File f = new File("/tmp/downloaded_0000-0002-2536-4498.xml"); + String record = testDownloadRecord("0000-0001-6163-2042"); + File f = new File("/tmp/downloaded_0000-0001-6163-2042.xml"); OutputStream outStream = new FileOutputStream(f); IOUtils.write(record.getBytes(), outStream); System.out.println("saved to tmp"); diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/xml/OrcidNoDoiTest.java b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/xml/OrcidNoDoiTest.java index bf5aba99b..fa2980ac4 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/xml/OrcidNoDoiTest.java +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/xml/OrcidNoDoiTest.java @@ -2,15 +2,20 @@ package eu.dnetlib.doiboost.orcidnodoi.xml; import static org.junit.jupiter.api.Assertions.assertNotNull; +import static org.junit.jupiter.api.Assertions.assertTrue; import java.io.IOException; import java.text.Normalizer; import java.util.*; +import javax.validation.constraints.AssertTrue; + import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.commons.text.similarity.JaccardSimilarity; import org.apache.commons.text.similarity.JaroWinklerSimilarity; import org.junit.jupiter.api.Test; +import org.mortbay.log.Log; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -41,7 +46,6 @@ public class OrcidNoDoiTest { String orcidIdA = "0000-0003-2760-1191"; @Test -// @Ignore public void readPublicationFieldsTest() throws IOException, XPathEvalException, XPathParseException, NavException, VtdException, ParseException { logger.info("running loadPublicationFieldsTest ...."); @@ -95,8 +99,7 @@ public class OrcidNoDoiTest { } @Test -// @Ignore - private void authorMatchTest() throws Exception { + public void authorMatchTest() throws Exception { logger.info("running authorSimpleMatchTest ...."); String orcidWork = "activity_work_0000-0003-2760-1191-similarity.xml"; AuthorData author = new AuthorData(); @@ -121,9 +124,60 @@ public class OrcidNoDoiTest { logger.error("parsing xml", e); } assertNotNull(workData); + + Contributor a = workData.getContributors().get(0); + assertTrue(a.getCreditName().equals("Abdel-Dayem K")); + AuthorMatcher.match(author, workData.getContributors()); GsonBuilder builder = new GsonBuilder(); Gson gson = builder.create(); logger.info(gson.toJson(workData)); + + assertTrue(workData.getContributors().size() == 6); + Contributor c = workData.getContributors().get(0); + assertTrue(c.getOid().equals("0000-0003-2760-1191")); + assertTrue(c.getName().equals("Khairy")); + assertTrue(c.getSurname().equals("Abdel Dayem")); + assertTrue(c.getCreditName().equals("Abdel-Dayem K")); + } + + @Test + public void readContributorsTest() + throws IOException, XPathEvalException, XPathParseException, NavException, VtdException, ParseException { + logger.info("running loadPublicationFieldsTest ...."); + String xml = IOUtils + .toString( + OrcidNoDoiTest.class.getResourceAsStream("activity_work_0000-0003-2760-1191_contributors.xml")); + + if (xml == null) { + logger.info("Resource not found"); + } + XMLRecordParserNoDoi p = new XMLRecordParserNoDoi(); + if (p == null) { + logger.info("XMLRecordParserNoDoi null"); + } + WorkDataNoDoi workData = null; + try { + workData = p.VTDParseWorkData(xml.getBytes()); + } catch (Exception e) { + logger.error("parsing xml", e); + } + assertNotNull(workData.getContributors()); + assertTrue(workData.getContributors().size() == 5); + assertTrue(StringUtils.isBlank(workData.getContributors().get(0).getCreditName())); + assertTrue(workData.getContributors().get(0).getSequence().equals("seq0")); + assertTrue(workData.getContributors().get(0).getRole().equals("role0")); + assertTrue(workData.getContributors().get(1).getCreditName().equals("creditname1")); + assertTrue(StringUtils.isBlank(workData.getContributors().get(1).getSequence())); + assertTrue(StringUtils.isBlank(workData.getContributors().get(1).getRole())); + assertTrue(workData.getContributors().get(2).getCreditName().equals("creditname2")); + assertTrue(workData.getContributors().get(2).getSequence().equals("seq2")); + assertTrue(StringUtils.isBlank(workData.getContributors().get(2).getRole())); + assertTrue(workData.getContributors().get(3).getCreditName().equals("creditname3")); + assertTrue(StringUtils.isBlank(workData.getContributors().get(3).getSequence())); + assertTrue(workData.getContributors().get(3).getRole().equals("role3")); + assertTrue(StringUtils.isBlank(workData.getContributors().get(4).getCreditName())); + assertTrue(workData.getContributors().get(4).getSequence().equals("seq4")); + assertTrue(workData.getContributors().get(4).getRole().equals("role4")); } } diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/xml/activity_work_0000-0003-2760-1191_contributors.xml b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/xml/activity_work_0000-0003-2760-1191_contributors.xml new file mode 100644 index 000000000..26e64aeda --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/xml/activity_work_0000-0003-2760-1191_contributors.xml @@ -0,0 +1,101 @@ + + + 2016-12-12T23:02:05.233Z + 2016-12-13T09:08:16.412Z + + + https://orcid.org/0000-0002-9157-3431 + 0000-0002-9157-3431 + orcid.org + + Europe PubMed Central + + + Cutoff Value of Admission N-Terminal Pro-Brain Natriuretic Peptide Which + Predicts Poor Myocardial Perfusion after Primary Percutaneous Coronary Intervention for + ST-Segment-Elevation Myocardial Infarction. + + + formatted-unspecified + Abdel-Dayem K, Eweda II, El-Sherbiny A, Dimitry MO, Nammas W, Acta + Cardiologica Sinica, 2016, vol. 32, no. 6, pp. 649-655, 2016 + + journal-article + + 2016 + 11 + + + + pmid + 27899851 + 27899851 + self + + + pmc + PMC5126442 + PMC5126442 + self + + + http://europepmc.org/abstract/med/27899851 + + + + seq0 + role0 + + + + creditname1 + + + creditname2 + + seq2 + + + + + creditname3 + + + role3 + + + + + + seq4 + role4 + + + + diff --git a/pom.xml b/pom.xml index d64de01ac..3629e2f1b 100644 --- a/pom.xml +++ b/pom.xml @@ -458,6 +458,18 @@ ${jsonschemagenerator.version} + + org.apache.commons + commons-text + ${common.text.version} + + + + org.apache.httpcomponents + httpclient + ${org.apache.httpcomponents.version} + + From 1513174d7ec367222c063ba47095ee7ca4897e99 Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Tue, 10 Nov 2020 11:44:55 +0100 Subject: [PATCH 25/37] added further test case --- .../SparkGenEnrichedOrcidWorks.java | 2 +- .../orcidnodoi/similarity/AuthorMatcher.java | 50 +++-- .../orcidnodoi/xml/OrcidNoDoiTest.java | 181 ++++++++++++++++-- .../xml/activity_work_0000-0003-2760-1191.xml | 2 +- 4 files changed, 202 insertions(+), 33 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java index 691ca3eee..40cd212da 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java @@ -96,7 +96,7 @@ public class SparkGenEnrichedOrcidWorks { Encoders.tuple(Encoders.STRING(), Encoders.STRING())) .filter(Objects::nonNull) .toJavaRDD(); -// enrichedWorksRDD.saveAsTextFile(workingPath + outputEnrichedWorksPath); + enrichedWorksRDD.saveAsTextFile(workingPath + "enrichedWorksText/"); logger.info("Enriched works RDD ready."); final LongAccumulator parsedPublications = spark.sparkContext().longAccumulator("parsedPublications"); diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/similarity/AuthorMatcher.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/similarity/AuthorMatcher.java index 6a1468f4c..2f86820fb 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/similarity/AuthorMatcher.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/similarity/AuthorMatcher.java @@ -33,7 +33,7 @@ import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi; public class AuthorMatcher { private static final Logger logger = LoggerFactory.getLogger(AuthorMatcher.class); - private static final Double threshold = 0.8; + public static final Double threshold = 0.8; public static void match(AuthorData author, List contributors) throws IOException, XPathEvalException, XPathParseException, NavException, VtdException, ParseException { @@ -41,16 +41,35 @@ public class AuthorMatcher { int matchCounter = 0; List matchCounters = Arrays.asList(matchCounter); Contributor contributor = null; - contributors.stream().filter(c -> !StringUtils.isBlank(c.getCreditName())).forEach(c -> { - if (simpleMatch(c.getCreditName(), author.getName()) || - simpleMatch(c.getCreditName(), author.getSurname()) || - simpleMatch(c.getCreditName(), author.getOtherName())) { - matchCounters.set(0, matchCounters.get(0) + 1); - c.setSimpleMatch(true); - } - }); + contributors + .stream() + .filter(c -> !StringUtils.isBlank(c.getCreditName())) + .forEach(c -> { + if (simpleMatch(c.getCreditName(), author.getName()) || + simpleMatch(c.getCreditName(), author.getSurname()) || + simpleMatch(c.getCreditName(), author.getOtherName())) { + matchCounters.set(0, matchCounters.get(0) + 1); + c.setSimpleMatch(true); + } + }); if (matchCounters.get(0) == 1) { updateAuthorsSimpleMatch(contributors, author); + } else if (matchCounters.get(0) == 0) { + Optional optCon = contributors + .stream() + .filter(c -> !StringUtils.isBlank(c.getCreditName())) + .map(c -> { + c.setScore(bestMatch(author.getName(), author.getSurname(), c.getCreditName())); + return c; + }) + .filter(c -> c.getScore() >= threshold) + .max(Comparator.comparing(c -> c.getScore())); + Contributor bestMatchContributor = null; + if (optCon.isPresent()) { + bestMatchContributor = optCon.get(); + bestMatchContributor.setBestMatch(true); + updateAuthorsSimilarityMatch(contributors, author); + } } else if (matchCounters.get(0) > 1) { Optional optCon = contributors .stream() @@ -68,19 +87,18 @@ public class AuthorMatcher { bestMatchContributor.setBestMatch(true); updateAuthorsSimilarityMatch(contributors, author); } - } } - private static boolean simpleMatch(String name, String searchValue) { + public static boolean simpleMatch(String name, String searchValue) { if (searchValue == null) { return false; } return normalize(name).contains(normalize(searchValue)); } - private static Double bestMatch(String authorSurname, String authorName, String contributor) { + public static Double bestMatch(String authorSurname, String authorName, String contributor) { String[] contributorSplitted = contributor.split(" "); if (contributorSplitted.length == 0) { return 0.0; @@ -106,7 +124,7 @@ public class AuthorMatcher { return sm2; } - private static Double similarity(String nameA, String surnameA, String nameB, String surnameB) { + public static Double similarity(String nameA, String surnameA, String nameB, String surnameB) { Double score = similarityJaroWinkler(nameA, surnameA, nameB, surnameB); return score; } @@ -115,7 +133,7 @@ public class AuthorMatcher { return new JaroWinklerSimilarity().apply(normalize(parse(nameA, surnameA)), normalize(parse(nameB, surnameB))); } - private static String normalize(final String s) { + public static String normalize(final String s) { if (s == null) { return new String(""); } @@ -140,7 +158,7 @@ public class AuthorMatcher { return surname + " " + name; } - private static void updateAuthorsSimpleMatch(List contributors, AuthorData author) { + public static void updateAuthorsSimpleMatch(List contributors, AuthorData author) { contributors.forEach(c -> { if (c.isSimpleMatch()) { c.setName(author.getName()); @@ -151,7 +169,7 @@ public class AuthorMatcher { updateRanks(contributors); } - private static void updateAuthorsSimilarityMatch(List contributors, AuthorData author) { + public static void updateAuthorsSimilarityMatch(List contributors, AuthorData author) { contributors .stream() .filter(c -> c.isBestMatch()) diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/xml/OrcidNoDoiTest.java b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/xml/OrcidNoDoiTest.java index fa2980ac4..c2c4ed5e1 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/xml/OrcidNoDoiTest.java +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/xml/OrcidNoDoiTest.java @@ -38,12 +38,9 @@ public class OrcidNoDoiTest { private static final Logger logger = LoggerFactory.getLogger(OrcidNoDoiTest.class); - String nameA = "Khairy"; - String surnameA = "Abdel Dayem"; - String otherNameA = "Dayem MKA"; - String nameB = "K"; - String surnameB = "Abdel-Dayem"; - String orcidIdA = "0000-0003-2760-1191"; + static String nameA = "Khairy"; + static String surnameA = "Abdel Dayem"; + static String orcidIdA = "0000-0003-2760-1191"; @Test public void readPublicationFieldsTest() @@ -99,7 +96,7 @@ public class OrcidNoDoiTest { } @Test - public void authorMatchTest() throws Exception { + public void authorDoubleMatchTest() throws Exception { logger.info("running authorSimpleMatchTest ...."); String orcidWork = "activity_work_0000-0003-2760-1191-similarity.xml"; AuthorData author = new AuthorData(); @@ -129,16 +126,8 @@ public class OrcidNoDoiTest { assertTrue(a.getCreditName().equals("Abdel-Dayem K")); AuthorMatcher.match(author, workData.getContributors()); - GsonBuilder builder = new GsonBuilder(); - Gson gson = builder.create(); - logger.info(gson.toJson(workData)); assertTrue(workData.getContributors().size() == 6); - Contributor c = workData.getContributors().get(0); - assertTrue(c.getOid().equals("0000-0003-2760-1191")); - assertTrue(c.getName().equals("Khairy")); - assertTrue(c.getSurname().equals("Abdel Dayem")); - assertTrue(c.getCreditName().equals("Abdel-Dayem K")); } @Test @@ -180,4 +169,166 @@ public class OrcidNoDoiTest { assertTrue(workData.getContributors().get(4).getSequence().equals("seq4")); assertTrue(workData.getContributors().get(4).getRole().equals("role4")); } + + @Test + public void authorSimpleMatchTest() throws Exception { + String orcidWork = "activity_work_0000-0002-5982-8983.xml"; + AuthorData author = new AuthorData(); + author.setName("Parkhouse"); + author.setSurname("H."); + author.setOid("0000-0002-5982-8983"); + String xml = IOUtils + .toString( + OrcidNoDoiTest.class.getResourceAsStream(orcidWork)); + + if (xml == null) { + logger.info("Resource not found"); + } + XMLRecordParserNoDoi p = new XMLRecordParserNoDoi(); + if (p == null) { + logger.info("XMLRecordParserNoDoi null"); + } + WorkDataNoDoi workData = null; + try { + workData = p.VTDParseWorkData(xml.getBytes()); + } catch (Exception e) { + logger.error("parsing xml", e); + } + assertNotNull(workData); + + Contributor a = workData.getContributors().get(0); + assertTrue(a.getCreditName().equals("Parkhouse, H.")); + + AuthorMatcher.match(author, workData.getContributors()); + + assertTrue(workData.getContributors().size() == 2); + Contributor c = workData.getContributors().get(0); + assertTrue(c.getOid().equals("0000-0002-5982-8983")); + assertTrue(c.getName().equals("Parkhouse")); + assertTrue(c.getSurname().equals("H.")); + assertTrue(c.getCreditName().equals("Parkhouse, H.")); + } + + @Test + public void match() { + + AuthorData author = new AuthorData(); + author.setName("Joe"); + author.setSurname("Dodge"); + author.setOid("0000-1111-2222-3333"); + Contributor contributor = new Contributor(); + contributor.setCreditName("Joe Dodge"); + List contributors = Arrays.asList(contributor); + AuthorMatcher am = new AuthorMatcher(); + int matchCounter = 0; + List matchCounters = Arrays.asList(matchCounter); + contributors + .stream() + .filter(c -> !StringUtils.isBlank(c.getCreditName())) + .forEach(c -> { + if (am.simpleMatch(c.getCreditName(), author.getName()) || + am.simpleMatch(c.getCreditName(), author.getSurname()) || + am.simpleMatch(c.getCreditName(), author.getOtherName())) { + matchCounters.set(0, matchCounters.get(0) + 1); + c.setSimpleMatch(true); + } + }); + + assertTrue(matchCounters.get(0) == 1); + am.updateAuthorsSimpleMatch(contributors, author); + assertTrue(contributors.get(0).getName().equals("Joe")); + assertTrue(contributors.get(0).getSurname().equals("Dodge")); + assertTrue(contributors.get(0).getCreditName().equals("Joe Dodge")); + assertTrue(contributors.get(0).getOid().equals("0000-1111-2222-3333")); + + AuthorData authorX = new AuthorData(); + authorX.setName(nameA); + authorX.setSurname(surnameA); + authorX.setOid(orcidIdA); + Contributor contributorA = new Contributor(); + contributorA.setCreditName("Abdel-Dayem Khai"); + Contributor contributorB = new Contributor(); + contributorB.setCreditName("Abdel-Dayem Fake"); + List contributorList = new ArrayList<>(); + contributorList.add(contributorA); + contributorList.add(contributorB); + int matchCounter2 = 0; + List matchCounters2 = Arrays.asList(matchCounter2); + contributorList + .stream() + .filter(c -> !StringUtils.isBlank(c.getCreditName())) + .forEach(c -> { + if (am.simpleMatch(c.getCreditName(), authorX.getName()) || + am.simpleMatch(c.getCreditName(), authorX.getSurname()) || + am.simpleMatch(c.getCreditName(), authorX.getOtherName())) { + int currentCounter = matchCounters2.get(0); + currentCounter += 1; + matchCounters2.set(0, currentCounter); + c.setSimpleMatch(true); + } + }); + + assertTrue(matchCounters2.get(0) == 2); + assertTrue(contributorList.get(0).isSimpleMatch()); + assertTrue(contributorList.get(1).isSimpleMatch()); + + Optional optCon = contributorList + .stream() + .filter(c -> c.isSimpleMatch()) + .filter(c -> !StringUtils.isBlank(c.getCreditName())) + .map(c -> { + c.setScore(am.bestMatch(authorX.getName(), authorX.getSurname(), c.getCreditName())); + return c; + }) + .filter(c -> c.getScore() >= AuthorMatcher.threshold) + .max(Comparator.comparing(c -> c.getScore())); + assertTrue(optCon.isPresent()); + + final Contributor bestMatchContributor = optCon.get(); + bestMatchContributor.setBestMatch(true); + assertTrue(bestMatchContributor.getCreditName().equals("Abdel-Dayem Khai")); + assertTrue(contributorList.get(0).isBestMatch()); + assertTrue(!contributorList.get(1).isBestMatch()); + am.updateAuthorsSimilarityMatch(contributorList, authorX); + assertTrue(contributorList.get(0).getName().equals(nameA)); + assertTrue(contributorList.get(0).getSurname().equals(surnameA)); + assertTrue(contributorList.get(0).getCreditName().equals("Abdel-Dayem Khai")); + assertTrue(contributorList.get(0).getOid().equals(orcidIdA)); + assertTrue(StringUtils.isBlank(contributorList.get(1).getOid())); + } + + @Test + public void authorBestMatchTest() throws Exception { + String name = "Khairy"; + String surname = "Abdel Dayem"; + String orcidWork = "activity_work_0000-0003-2760-1191.xml"; + AuthorData author = new AuthorData(); + author.setName(name); + author.setSurname(surname); + author.setOid(orcidIdA); + String xml = IOUtils + .toString( + OrcidNoDoiTest.class.getResourceAsStream(orcidWork)); + + if (xml == null) { + logger.info("Resource not found"); + } + XMLRecordParserNoDoi p = new XMLRecordParserNoDoi(); + if (p == null) { + logger.info("XMLRecordParserNoDoi null"); + } + WorkDataNoDoi workData = null; + try { + workData = p.VTDParseWorkData(xml.getBytes()); + } catch (Exception e) { + logger.error("parsing xml", e); + } + AuthorMatcher.match(author, workData.getContributors()); + assertTrue(workData.getContributors().size() == 5); + List c = workData.getContributors(); + assertTrue(c.get(0).getName().equals(name)); + assertTrue(c.get(0).getSurname().equals(surname)); + assertTrue(c.get(0).getCreditName().equals("Khair Abde Daye")); + assertTrue(c.get(0).getOid().equals(orcidIdA)); + } } diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/xml/activity_work_0000-0003-2760-1191.xml b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/xml/activity_work_0000-0003-2760-1191.xml index 485f4f8e8..83752b145 100644 --- a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/xml/activity_work_0000-0003-2760-1191.xml +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/xml/activity_work_0000-0003-2760-1191.xml @@ -68,7 +68,7 @@ http://europepmc.org/abstract/med/27899851 - Abdel-Dayem K + Khair Abde Daye first author From 1f861f2b0de77d6a693c5d5144696409c32592a7 Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Wed, 11 Nov 2020 17:38:50 +0100 Subject: [PATCH 26/37] now wf output is a sequence file with the format seq("eu.dnetlib.dhp.schema.oaf.Publication",eu.dnetlib.dhp.schema.action.AtomicActions) --- .../SparkGenEnrichedOrcidWorks.java | 62 ++++++++++--------- 1 file changed, 33 insertions(+), 29 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java index 40cd212da..7f715fa7d 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java @@ -1,14 +1,21 @@ package eu.dnetlib.doiboost.orcidnodoi; -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.IOException; -import java.util.Objects; -import java.util.Optional; - +import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.gson.Gson; +import com.google.gson.JsonElement; +import com.google.gson.JsonParser; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.action.AtomicAction; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.doiboost.orcid.json.JsonHelper; +import eu.dnetlib.doiboost.orcid.model.AuthorData; +import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi; +import eu.dnetlib.doiboost.orcidnodoi.oaf.PublicationToOaf; +import eu.dnetlib.doiboost.orcidnodoi.similarity.AuthorMatcher; import org.apache.commons.io.IOUtils; import org.apache.hadoop.io.Text; +import org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaPairRDD; import org.apache.spark.api.java.JavaRDD; @@ -16,24 +23,17 @@ import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SaveMode; import org.apache.spark.util.LongAccumulator; import org.slf4j.Logger; import org.slf4j.LoggerFactory; - -import com.google.gson.Gson; -import com.google.gson.JsonElement; -import com.google.gson.JsonParser; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.doiboost.orcid.json.JsonHelper; -import eu.dnetlib.doiboost.orcid.model.AuthorData; -import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi; -import eu.dnetlib.doiboost.orcidnodoi.oaf.PublicationToOaf; -import eu.dnetlib.doiboost.orcidnodoi.similarity.AuthorMatcher; import scala.Tuple2; +import java.io.IOException; +import java.util.Objects; +import java.util.Optional; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + /** * This spark job generates one parquet file, containing orcid publications dataset */ @@ -42,6 +42,8 @@ public class SparkGenEnrichedOrcidWorks { static Logger logger = LoggerFactory.getLogger(SparkGenEnrichedOrcidWorks.class); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + public static void main(String[] args) throws IOException, Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( @@ -58,6 +60,7 @@ public class SparkGenEnrichedOrcidWorks { final String workingPath = parser.get("workingPath"); final String outputEnrichedWorksPath = parser.get("outputEnrichedWorksPath"); final String outputWorksPath = parser.get("outputWorksPath"); + final String hdfsServerUri = parser.get("hdfsServerUri"); SparkConf conf = new SparkConf(); runWithSparkSession( @@ -96,7 +99,6 @@ public class SparkGenEnrichedOrcidWorks { Encoders.tuple(Encoders.STRING(), Encoders.STRING())) .filter(Objects::nonNull) .toJavaRDD(); - enrichedWorksRDD.saveAsTextFile(workingPath + "enrichedWorksText/"); logger.info("Enriched works RDD ready."); final LongAccumulator parsedPublications = spark.sparkContext().longAccumulator("parsedPublications"); @@ -124,15 +126,17 @@ public class SparkGenEnrichedOrcidWorks { }) .filter(p -> p != null); - Dataset publicationDataset = spark - .createDataset( - oafPublicationRDD.repartition(1).rdd(), - Encoders.bean(Publication.class)); - publicationDataset - .write() - .format("parquet") - .mode(SaveMode.Overwrite) - .save(workingPath + outputEnrichedWorksPath); + oafPublicationRDD + .mapToPair( + p -> new Tuple2<>(p.getClass().toString(), + OBJECT_MAPPER.writeValueAsString(new AtomicAction<>(Publication.class, (Publication) p)))) + .mapToPair(t -> new Tuple2(new Text(t._1()), new Text(t._2()))) + .saveAsNewAPIHadoopFile( + workingPath.concat(outputEnrichedWorksPath), + Text.class, + Text.class, + SequenceFileOutputFormat.class, + sc.hadoopConfiguration()); logger.info("parsedPublications: " + parsedPublications.value().toString()); logger.info("enrichedPublications: " + enrichedPublications.value().toString()); From 13f28fa225d248e080c13d99694c3069826b3184 Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Thu, 12 Nov 2020 17:43:32 +0100 Subject: [PATCH 27/37] moved AuthorData to dhp-schemas; added other names to author data --- .../dnetlib/dhp/schema/orcid}/AuthorData.java | 18 +- .../orcid/SparkGenerateDoiAuthorList.java | 5 +- .../doiboost/orcid/SummariesDecompressor.java | 7 +- .../doiboost/orcid/xml/XMLRecordParser.java | 8 +- .../SparkGenEnrichedOrcidWorks.java | 38 +- .../doiboost/orcidnodoi/json/JsonWriter.java | 19 +- .../orcidnodoi/model/Contributor.java | 2 +- .../orcidnodoi/similarity/AuthorMatcher.java | 11 +- .../oozie_app/config-default.xml | 2 +- .../orcid/xml/XMLRecordParserTest.java | 21 +- .../orcidnodoi/xml/OrcidNoDoiTest.java | 12 +- .../orcid/xml/record_8888-8888-8888-8880.xml | 770 ++++++++++++++++++ .../summary_0000-0001-5109-1000_othername.xml | 196 +++++ 13 files changed, 1053 insertions(+), 56 deletions(-) rename {dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/model => dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid}/AuthorData.java (71%) create mode 100644 dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/xml/record_8888-8888-8888-8880.xml create mode 100644 dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/xml/summary_0000-0001-5109-1000_othername.xml diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/model/AuthorData.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/AuthorData.java similarity index 71% rename from dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/model/AuthorData.java rename to dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/AuthorData.java index e0624509b..6c94cdb13 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/model/AuthorData.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/AuthorData.java @@ -1,7 +1,10 @@ -package eu.dnetlib.doiboost.orcid.model; +package eu.dnetlib.dhp.schema.orcid; import java.io.Serializable; +import java.util.List; + +import com.google.common.collect.Lists; /** * This class models the data that are retrieved from orcid publication @@ -13,8 +16,8 @@ public class AuthorData implements Serializable { private String name; private String surname; private String creditName; - private String otherName; private String errorCode; + private List otherNames; public String getErrorCode() { return errorCode; @@ -56,11 +59,14 @@ public class AuthorData implements Serializable { this.oid = oid; } - public String getOtherName() { - return otherName; + public List getOtherNames() { + return otherNames; } - public void setOtherName(String otherName) { - this.otherName = otherName; + public void setOtherNames(List otherNames) { + if (this.otherNames == null) { + this.otherNames = Lists.newArrayList(); + } + this.otherNames = otherNames; } } diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkGenerateDoiAuthorList.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkGenerateDoiAuthorList.java index b4239bba2..011c153ec 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkGenerateDoiAuthorList.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkGenerateDoiAuthorList.java @@ -13,9 +13,6 @@ import java.util.stream.Stream; import org.apache.commons.io.IOUtils; import org.apache.hadoop.io.Text; -import org.apache.hadoop.io.compress.GzipCodec; -import org.apache.hadoop.mapreduce.Job; -import org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaPairRDD; import org.apache.spark.api.java.JavaRDD; @@ -33,7 +30,7 @@ import com.google.gson.JsonElement; import com.google.gson.JsonParser; import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.doiboost.orcid.model.AuthorData; +import eu.dnetlib.dhp.schema.orcid.AuthorData; import eu.dnetlib.doiboost.orcid.model.WorkData; import scala.Tuple2; diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SummariesDecompressor.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SummariesDecompressor.java index 29d72ed0b..d1b2a1d73 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SummariesDecompressor.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SummariesDecompressor.java @@ -19,7 +19,7 @@ import org.apache.hadoop.io.compress.CompressionCodec; import org.apache.hadoop.io.compress.CompressionCodecFactory; import org.mortbay.log.Log; -import eu.dnetlib.doiboost.orcid.model.AuthorData; +import eu.dnetlib.dhp.schema.orcid.AuthorData; import eu.dnetlib.doiboost.orcid.xml.XMLRecordParser; import eu.dnetlib.doiboost.orcidnodoi.json.JsonWriter; @@ -56,6 +56,7 @@ public class SummariesDecompressor { int nameFound = 0; int surnameFound = 0; int creditNameFound = 0; + int otherNamesFound = 0; int errorFromOrcidFound = 0; int xmlParserErrorFound = 0; try (TarArchiveInputStream tais = new TarArchiveInputStream(gzipInputStream)) { @@ -117,6 +118,9 @@ public class SummariesDecompressor { if (authorData.getCreditName() != null) { creditNameFound += 1; } + if (authorData.getOtherNames() != null && authorData.getOtherNames().size() > 1) { + otherNamesFound += authorData.getOtherNames().size(); + } } else { Log.warn("Data not retrievable [" + entry.getName() + "] " + buffer.toString()); @@ -152,6 +156,7 @@ public class SummariesDecompressor { Log.info("Name found: " + nameFound); Log.info("Surname found: " + surnameFound); Log.info("Credit name found: " + creditNameFound); + Log.info("Other names found: " + otherNamesFound); Log.info("Error from Orcid found: " + errorFromOrcidFound); Log.info("Error parsing xml record found: " + xmlParserErrorFound); } diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParser.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParser.java index 2e43f4d3e..a807cf132 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParser.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParser.java @@ -14,7 +14,7 @@ import com.ximpleware.VTDNav; import eu.dnetlib.dhp.parser.utility.VtdException; import eu.dnetlib.dhp.parser.utility.VtdUtilityParser; -import eu.dnetlib.doiboost.orcid.model.AuthorData; +import eu.dnetlib.dhp.schema.orcid.AuthorData; import eu.dnetlib.doiboost.orcid.model.WorkData; public class XMLRecordParser { @@ -81,6 +81,12 @@ public class XMLRecordParser { if (!creditNames.isEmpty()) { authorData.setCreditName(creditNames.get(0)); } + + final List otherNames = VtdUtilityParser.getTextValue(ap, vn, "//other-name:content"); + if (!otherNames.isEmpty()) { + authorData.setOtherNames(otherNames); + } + return authorData; } diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java index 7f715fa7d..cc65b0b4f 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java @@ -1,18 +1,12 @@ package eu.dnetlib.doiboost.orcidnodoi; -import com.fasterxml.jackson.databind.ObjectMapper; -import com.google.gson.Gson; -import com.google.gson.JsonElement; -import com.google.gson.JsonParser; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.schema.action.AtomicAction; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.doiboost.orcid.json.JsonHelper; -import eu.dnetlib.doiboost.orcid.model.AuthorData; -import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi; -import eu.dnetlib.doiboost.orcidnodoi.oaf.PublicationToOaf; -import eu.dnetlib.doiboost.orcidnodoi.similarity.AuthorMatcher; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.IOException; +import java.util.Objects; +import java.util.Optional; + import org.apache.commons.io.IOUtils; import org.apache.hadoop.io.Text; import org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat; @@ -26,14 +20,22 @@ import org.apache.spark.sql.Encoders; import org.apache.spark.util.LongAccumulator; import org.slf4j.Logger; import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.gson.Gson; +import com.google.gson.JsonElement; +import com.google.gson.JsonParser; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.action.AtomicAction; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.orcid.AuthorData; +import eu.dnetlib.doiboost.orcid.json.JsonHelper; +import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi; +import eu.dnetlib.doiboost.orcidnodoi.oaf.PublicationToOaf; +import eu.dnetlib.doiboost.orcidnodoi.similarity.AuthorMatcher; import scala.Tuple2; -import java.io.IOException; -import java.util.Objects; -import java.util.Optional; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - /** * This spark job generates one parquet file, containing orcid publications dataset */ diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/json/JsonWriter.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/json/JsonWriter.java index 363cb13e6..982fb6316 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/json/JsonWriter.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/json/JsonWriter.java @@ -1,9 +1,12 @@ package eu.dnetlib.doiboost.orcidnodoi.json; +import com.fasterxml.jackson.annotation.JsonInclude; +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; import com.google.gson.JsonObject; -import eu.dnetlib.doiboost.orcid.model.AuthorData; +import eu.dnetlib.dhp.schema.orcid.AuthorData; import eu.dnetlib.doiboost.orcid.model.WorkData; /** @@ -12,15 +15,11 @@ import eu.dnetlib.doiboost.orcid.model.WorkData; public class JsonWriter { - public static String create(AuthorData authorData) { - JsonObject author = new JsonObject(); - author.addProperty("oid", authorData.getOid()); - author.addProperty("name", authorData.getName()); - author.addProperty("surname", authorData.getSurname()); - if (authorData.getCreditName() != null) { - author.addProperty("creditname", authorData.getCreditName()); - } - return author.toString(); + public static final com.fasterxml.jackson.databind.ObjectMapper OBJECT_MAPPER = new ObjectMapper() + .setSerializationInclusion(JsonInclude.Include.NON_NULL);; + + public static String create(AuthorData authorData) throws JsonProcessingException { + return OBJECT_MAPPER.writeValueAsString(authorData); } public static String create(WorkData workData) { diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/Contributor.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/Contributor.java index 9a8651c85..9222c1cc4 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/Contributor.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/model/Contributor.java @@ -3,7 +3,7 @@ package eu.dnetlib.doiboost.orcidnodoi.model; import java.io.Serializable; -import eu.dnetlib.doiboost.orcid.model.AuthorData; +import eu.dnetlib.dhp.schema.orcid.AuthorData; /** * This class models the data related to a contributor, that are retrieved from an orcid publication diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/similarity/AuthorMatcher.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/similarity/AuthorMatcher.java index 2f86820fb..c0f617868 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/similarity/AuthorMatcher.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/similarity/AuthorMatcher.java @@ -18,7 +18,7 @@ import com.ximpleware.XPathEvalException; import com.ximpleware.XPathParseException; import eu.dnetlib.dhp.parser.utility.VtdException; -import eu.dnetlib.doiboost.orcid.model.AuthorData; +import eu.dnetlib.dhp.schema.orcid.AuthorData; import eu.dnetlib.doiboost.orcidnodoi.model.Contributor; import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi; @@ -47,7 +47,7 @@ public class AuthorMatcher { .forEach(c -> { if (simpleMatch(c.getCreditName(), author.getName()) || simpleMatch(c.getCreditName(), author.getSurname()) || - simpleMatch(c.getCreditName(), author.getOtherName())) { + simpleMatchOnOtherNames(c.getCreditName(), author.getOtherNames())) { matchCounters.set(0, matchCounters.get(0) + 1); c.setSimpleMatch(true); } @@ -91,6 +91,13 @@ public class AuthorMatcher { } + public static boolean simpleMatchOnOtherNames(String name, List otherNames) { + if (otherNames == null || (otherNames != null && otherNames.isEmpty())) { + return false; + } + return otherNames.stream().filter(o -> simpleMatch(name, o)).count() > 0; + } + public static boolean simpleMatch(String name, String searchValue) { if (searchValue == null) { return false; diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_summaries/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_summaries/oozie_app/config-default.xml index e1829e847..191654378 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_summaries/oozie_app/config-default.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_summaries/oozie_app/config-default.xml @@ -21,6 +21,6 @@ oozie.launcher.mapreduce.map.java.opts - -Xmx16g + -Xmx8g \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParserTest.java b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParserTest.java index 5bf6f27b9..b7be5e5cd 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParserTest.java +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParserTest.java @@ -2,12 +2,14 @@ package eu.dnetlib.doiboost.orcid.xml; import static org.junit.jupiter.api.Assertions.assertNotNull; +import static org.junit.jupiter.api.Assertions.assertTrue; import org.apache.commons.io.IOUtils; import org.junit.jupiter.api.Test; -import eu.dnetlib.doiboost.orcid.model.AuthorData; +import eu.dnetlib.dhp.schema.orcid.AuthorData; import eu.dnetlib.doiboost.orcid.model.WorkData; +import eu.dnetlib.doiboost.orcidnodoi.json.JsonWriter; public class XMLRecordParserTest { @@ -55,4 +57,21 @@ public class XMLRecordParserTest { assertNotNull(workData.getDoi()); System.out.println("doi: " + workData.getDoi()); } + + @Test + public void testOrcidOtherNamesXMLParser() throws Exception { + + String xml = IOUtils + .toString( + this.getClass().getResourceAsStream("summary_0000-0001-5109-1000_othername.xml")); + + XMLRecordParser p = new XMLRecordParser(); + + AuthorData authorData = XMLRecordParser.VTDParseAuthorData(xml.getBytes()); + assertNotNull(authorData); + assertNotNull(authorData.getOtherNames()); + assertTrue(authorData.getOtherNames().get(0).equals("Andrew C. Porteus")); + String jsonData = JsonWriter.create(authorData); + assertNotNull(jsonData); + } } diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/xml/OrcidNoDoiTest.java b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/xml/OrcidNoDoiTest.java index c2c4ed5e1..948e5b094 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/xml/OrcidNoDoiTest.java +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/xml/OrcidNoDoiTest.java @@ -5,34 +5,24 @@ import static org.junit.jupiter.api.Assertions.assertNotNull; import static org.junit.jupiter.api.Assertions.assertTrue; import java.io.IOException; -import java.text.Normalizer; import java.util.*; -import javax.validation.constraints.AssertTrue; - import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.commons.text.similarity.JaccardSimilarity; -import org.apache.commons.text.similarity.JaroWinklerSimilarity; import org.junit.jupiter.api.Test; -import org.mortbay.log.Log; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import com.google.gson.Gson; -import com.google.gson.GsonBuilder; import com.ximpleware.NavException; import com.ximpleware.ParseException; import com.ximpleware.XPathEvalException; import com.ximpleware.XPathParseException; import eu.dnetlib.dhp.parser.utility.VtdException; -import eu.dnetlib.dhp.schema.oaf.Author; -import eu.dnetlib.doiboost.orcid.model.AuthorData; +import eu.dnetlib.dhp.schema.orcid.AuthorData; import eu.dnetlib.doiboost.orcidnodoi.model.Contributor; import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi; import eu.dnetlib.doiboost.orcidnodoi.similarity.AuthorMatcher; -import jdk.nashorn.internal.ir.annotations.Ignore; public class OrcidNoDoiTest { diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/xml/record_8888-8888-8888-8880.xml b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/xml/record_8888-8888-8888-8880.xml new file mode 100644 index 000000000..7abc2f35a --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/xml/record_8888-8888-8888-8880.xml @@ -0,0 +1,770 @@ + + + + https://orcid.org/8888-8888-8888-8880 + 8888-8888-8888-8880 + orcid.org + + + zh_CN + + + API + 2001-12-31T12:00:00 + 2001-12-31T12:00:00 + 2001-12-31T12:00:00 + true + + + https://orcid.org/8888-8888-8888-8880 + 8888-8888-8888-8880 + orcid.org + + + + 2001-12-31T12:00:00 + true + true + + + 2001-12-31T12:00:00 + + 2001-12-31T12:00:00 + give-names + family-name + credit-name + + + 2001-12-31T12:00:00 + + 2001-12-31T12:00:00 + 2001-12-31T12:00:00 + + + https://orcid.org/8888-8888-8888-8880 + 8888-8888-8888-8880 + orcid.org + + + + other-name-1 + + + + 2001-12-31T12:00:00 + 2001-12-31T12:00:00 + biography + + + 2001-12-31T12:00:00 + + 2001-12-31T12:00:00 + 2001-12-31T12:00:00 + + + https://orcid.org/8888-8888-8888-8880 + 8888-8888-8888-8880 + orcid.org + + + + url-name-1 + http://url.com/ + + + + 2001-12-31T12:00:00 + + 2001-12-31T12:00:00 + 2001-12-31T12:00:00 + + + https://orcid.org/8888-8888-8888-8880 + 8888-8888-8888-8880 + orcid.org + + + + user1@email.com + + + + 2001-12-31T12:00:00 + + 2001-12-31T12:00:00 + 2001-12-31T12:00:00 + + + https://orcid.org/8888-8888-8888-8880 + 8888-8888-8888-8880 + orcid.org + + + + US + + + + 2001-12-31T12:00:00 + + 2001-12-31T12:00:00 + 2001-12-31T12:00:00 + + + https://orcid.org/8888-8888-8888-8880 + 8888-8888-8888-8880 + orcid.org + + + + keyword1 + + + + 2001-12-31T12:00:00 + + 2001-12-31T12:00:00 + 2001-12-31T12:00:00 + + + https://orcid.org/8888-8888-8888-8880 + 8888-8888-8888-8880 + orcid.org + + + + type-1 + value-1 + http://url.com/1 + self + + + + + 2001-12-31T12:00:00 + + 2001-12-31T12:00:00 + + 2001-12-31T12:00:00 + + + + agr + external-id-value + + http://orcid.org + part-of + + + + 2001-12-31T12:00:00 + 2001-12-31T12:00:00 + + + https://orcid.org/8888-8888-8888-8880 + 8888-8888-8888-8880 + orcid.org + + + + distinction:department-name + distinction:role-title + + 1948 + 02 + 02 + + + 1948 + 02 + 02 + + + distinction-org + + common:city + common:region + AF + + + common:disambiguated-organization-identifier-distinction + GRID + + + + + + + 2001-12-31T12:00:00 + + 2001-12-31T12:00:00 + + + + agr + external-id-value + + http://orcid.org + part-of + + + + 2001-12-31T12:00:00 + 2001-12-31T12:00:00 + + + https://orcid.org/8888-8888-8888-8880 + 8888-8888-8888-8880 + orcid.org + + + + education:department-name + education:role-title + + 1948 + 02 + 02 + + + 2019 + 01 + 01 + + + education-org + + common:city + common:region + AF + + + common:disambiguated-organization-identifier-education + GRID + + + + + + + 2001-12-31T12:00:00 + + 2001-12-31T12:00:00 + + + + agr + external-id-value + + http://orcid.org + part-of + + + + 2001-12-31T12:00:00 + 2001-12-31T12:00:00 + + + https://orcid.org/8888-8888-8888-8880 + 8888-8888-8888-8880 + orcid.org + + + + employment:department-name + employment:role-title + + 1948 + 02 + 02 + + + 2025 + + + employment-org + + common:city + common:region + AF + + + common:disambiguated-organization-identifier-employment + GRID + + + + + + + 2001-12-31T12:00:00 + + 2001-12-31T12:00:00 + + + grant_number + external-id-value-1 + + + + 2001-12-31T12:00:00 + 2001-12-31T12:00:00 + + + https://orcid.org/8888-8888-8888-8880 + 8888-8888-8888-8880 + orcid.org + + + + + common:title + common:translated-title + + + + grant_number + external-id-value-1 + http://tempuri.org + self + + + grant + + 1948 + 02 + 02 + + + 1948 + 02 + 02 + + + common:name + + common:city + common:region + AF + + + common:disambiguated-organization-identifier-funding + FUNDREF + + + + + + + 2001-12-31T12:00:00 + + 2001-12-31T12:00:00 + + + + agr + external-id-value + + http://orcid.org + part-of + + + + 2001-12-31T12:00:00 + 2001-12-31T12:00:00 + + + https://orcid.org/8888-8888-8888-8880 + 8888-8888-8888-8880 + orcid.org + + + + invited-position:department-name + invited-position:role-title + + 2019 + 01 + 01 + + + 2025 + 01 + 01 + + + invited-position-org + + common:city + common:region + AF + + + common:disambiguated-organization-identifier-invited-position + GRID + + + + + + + 2001-12-31T12:00:00 + + 2001-12-31T12:00:00 + + + + agr + external-id-value + + http://orcid.org + part-of + + + + 2001-12-31T12:00:00 + 2001-12-31T12:00:00 + + + https://orcid.org/8888-8888-8888-8880 + 8888-8888-8888-8880 + orcid.org + + + + membership:department-name + membership:role-title + + 1948 + 02 + 02 + + + membership-org + + common:city + common:region + AF + + + common:disambiguated-organization-identifier-membership + RINGGOLD + + + + + + + 2001-12-31T12:00:00 + + 2001-12-31T12:00:00 + + + something + external-id-value + http://orcid.org + self + + + + 2001-12-31T12:00:00 + + + something + external-id-value + + http://orcid.org + self + + + + 2001-12-31T12:00:00 + 2001-12-31T12:00:00 + + + https://orcid.org/client/APP-9999999999999901 + APP-9999999999999901 + orcid.org + + + + reviewer + + + something + external-id-value + http://orcid.org + self + + + http://orcid.org + review + + 1948 + 02 + 02 + + orcid-generated:12345 + + common:name + + common:city + common:region + AF + + + common:disambiguated-organization-identifier-peer-review + RINGGOLD + + + + + + + + 2001-12-31T12:00:00 + + 2001-12-31T12:00:00 + + + + agr + external-id-value + + http://orcid.org + part-of + + + + 2001-12-31T12:00:00 + 2001-12-31T12:00:00 + + + https://orcid.org/8888-8888-8888-8880 + 8888-8888-8888-8880 + orcid.org + + + + qualification:department-name + qualification:role-title + + 1948 + 02 + 02 + + + 2025 + 12 + + + qualification-org + + common:city + common:region + AF + + + common:disambiguated-organization-identifier-qualification + RINGGOLD + + + + + + + 2017-01-18T15:06:05.147-06:00 + + 2017-01-18T15:03:56.856-06:00 + + + proposal_id + 123456 + self + + + + + 2015-06-25T16:01:12.718Z + 2017-09-08T13:31:19.987Z + + + + https://orcid.org/0000-0000-0000-0000 + 0000-0000-0000-0000 + orcid.org + + XSEDE ORCID integration + + + + + Giant Laser Award + + + + XSEDE + + city + region + US + + + XX + grid + + + + + + proposal_id + 123456 + self + + + + 1999 + 02 + 02 + + + 2012 + 02 + 02 + + http://xsede.org/GiantLaserAward + + + + + + 2001-12-31T12:00:00 + + 2001-12-31T12:00:00 + + + + agr + external-id-value + + http://orcid.org + part-of + + + + 2001-12-31T12:00:00 + 2001-12-31T12:00:00 + + + https://orcid.org/8888-8888-8888-8880 + 8888-8888-8888-8880 + orcid.org + + + + service:department-name + service:role-title + + 1948 + 02 + 02 + + + service-org + + common:city + common:region + AF + + + common:disambiguated-organization-identifier-service + RINGGOLD + + + + + + + 2001-12-31T12:00:00 + + 2001-12-31T12:00:00 + + + agr + external-id-value + http://orcid.org + part-of + + + + 2001-12-31T12:00:00 + 2001-12-31T12:00:00 + + + https://orcid.org/client/8888-8888-8888-8880 + 8888-8888-8888-8880 + orcid.org + + + + + common:title + + common:translated-title + + + + agr + external-id-value + http://tempuri.org + self + + + artistic-performance + + 1948 + 02 + 02 + + Procedia Computer Science + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/xml/summary_0000-0001-5109-1000_othername.xml b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/xml/summary_0000-0001-5109-1000_othername.xml new file mode 100644 index 000000000..43bc96b8c --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/xml/summary_0000-0001-5109-1000_othername.xml @@ -0,0 +1,196 @@ + + + + https://orcid.org/0000-0001-5109-1000 + 0000-0001-5109-1000 + orcid.org + + + en + + + Member-referred + 2019-05-01T13:04:57.507Z + 2019-05-01T13:59:54.268Z + true + true + true + + + 2019-05-01T13:45:47.727Z + + 2019-05-01T13:04:57.507Z + 2019-05-01T13:04:57.740Z + Andrew + Porteus + + + 2019-05-01T13:44:57.072Z + + 2019-05-01T13:44:57.072Z + 2019-05-01T13:44:57.072Z + + + https://orcid.org/0000-0001-5109-1000 + 0000-0001-5109-1000 + orcid.org + + Andrew Porteus + + Andrew C. Porteus + + + + 2019-05-01T13:59:54.263Z + 2019-05-01T13:59:54.263Z + Retired Librarian + + + 2019-05-01T13:45:47.727Z + + 2019-05-01T13:45:47.727Z + 2019-05-01T13:45:47.727Z + + + https://orcid.org/0000-0001-5109-1000 + 0000-0001-5109-1000 + orcid.org + + Andrew Porteus + + Niagara Falls Poetry Project + http://niagarapoetry.ca + + + + + 2019-05-01T13:45:09.764Z + + 2019-05-01T13:45:09.764Z + 2019-05-01T13:45:09.764Z + + + https://orcid.org/0000-0001-5109-1000 + 0000-0001-5109-1000 + orcid.org + + Andrew Porteus + + CA + + + + + + + 2019-05-01T13:57:45.787Z + + + 2019-05-01T13:15:26.102Z + + 2019-05-01T13:15:26.102Z + + + 2019-05-01T13:15:26.102Z + 2019-05-01T13:15:26.102Z + + + https://orcid.org/0000-0001-5109-1000 + 0000-0001-5109-1000 + orcid.org + + Andrew Porteus + + Library Technician Diploma + + 1976 + 09 + + + 1978 + 05 + + + Niagara College + + Welland + ON + CA + + + 125147 + RINGGOLD + + + + + + + + + + + + 2019-05-01T13:19:49.021Z + + 2019-05-01T13:19:49.021Z + + + 2019-05-01T13:19:49.021Z + 2019-05-01T13:19:49.021Z + + + https://orcid.org/0000-0001-5109-1000 + 0000-0001-5109-1000 + orcid.org + + Andrew Porteus + + Communication, Film & Popular Culture + Master's Candidate + + 2018 + 09 + + + Brock University + + Saint Catharines + ON + CA + + + 7497 + RINGGOLD + + + + + + + \ No newline at end of file From 9a2fa9dc2f45f030ca358621ddbbd51a4be3bf2c Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Fri, 13 Nov 2020 10:25:34 +0100 Subject: [PATCH 28/37] added test for other names parsing from summaries dump --- .../orcidnodoi/xml/OrcidNoDoiTest.java | 28 +++++++++++++++++-- 1 file changed, 26 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/xml/OrcidNoDoiTest.java b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/xml/OrcidNoDoiTest.java index 948e5b094..1f77197ab 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/xml/OrcidNoDoiTest.java +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/xml/OrcidNoDoiTest.java @@ -13,6 +13,7 @@ import org.junit.jupiter.api.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import com.google.common.collect.Lists; import com.ximpleware.NavException; import com.ximpleware.ParseException; import com.ximpleware.XPathEvalException; @@ -218,7 +219,7 @@ public class OrcidNoDoiTest { .forEach(c -> { if (am.simpleMatch(c.getCreditName(), author.getName()) || am.simpleMatch(c.getCreditName(), author.getSurname()) || - am.simpleMatch(c.getCreditName(), author.getOtherName())) { + am.simpleMatchOnOtherNames(c.getCreditName(), author.getOtherNames())) { matchCounters.set(0, matchCounters.get(0) + 1); c.setSimpleMatch(true); } @@ -250,7 +251,7 @@ public class OrcidNoDoiTest { .forEach(c -> { if (am.simpleMatch(c.getCreditName(), authorX.getName()) || am.simpleMatch(c.getCreditName(), authorX.getSurname()) || - am.simpleMatch(c.getCreditName(), authorX.getOtherName())) { + am.simpleMatchOnOtherNames(c.getCreditName(), author.getOtherNames())) { int currentCounter = matchCounters2.get(0); currentCounter += 1; matchCounters2.set(0, currentCounter); @@ -321,4 +322,27 @@ public class OrcidNoDoiTest { assertTrue(c.get(0).getCreditName().equals("Khair Abde Daye")); assertTrue(c.get(0).getOid().equals(orcidIdA)); } + + @Test + public void otherNamesMatchTest() + throws VtdException, ParseException, IOException, XPathEvalException, NavException, XPathParseException { + + AuthorData author = new AuthorData(); + author.setName("Joe"); + author.setSurname("Dodge"); + author.setOid("0000-1111-2222-3333"); + String otherName1 = new String("Joe Dr. Dodge"); + String otherName2 = new String("XY"); + List others = Lists.newArrayList(); + others.add(otherName1); + others.add(otherName2); + author.setOtherNames(others); + Contributor contributor = new Contributor(); + contributor.setCreditName("XY"); + List contributors = Arrays.asList(contributor); + AuthorMatcher.match(author, contributors); + assertTrue(contributors.get(0).getName().equals("Joe")); + assertTrue(contributors.get(0).getSurname().equals("Dodge")); + assertTrue(contributors.get(0).getOid().equals("0000-1111-2222-3333")); + } } From 005f849674c93f44e9a3e66b86211dd8f38f8919 Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Fri, 13 Nov 2020 12:45:31 +0100 Subject: [PATCH 29/37] added compression to output dataset --- .../dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java | 2 ++ 1 file changed, 2 insertions(+) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java index cc65b0b4f..a92d534d8 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java @@ -128,6 +128,8 @@ public class SparkGenEnrichedOrcidWorks { }) .filter(p -> p != null); + sc.hadoopConfiguration().set("mapreduce.output.fileoutputformat.compress", "true"); + oafPublicationRDD .mapToPair( p -> new Tuple2<>(p.getClass().toString(), From c0c2e05eae56c3dad6e111177d88f1959b654d2e Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Tue, 17 Nov 2020 18:23:12 +0100 Subject: [PATCH 30/37] added wf to extracting authors and works xml data from orcid dump to hdfs; added wf to download the lamda file (containing last orcid update informations) from orcid to hdfs --- .../orcid/ActivitiesDecompressor.java | 61 +++++ .../orcid/ExtractXMLActivitiesData.java | 54 ++++ .../orcid/ExtractXMLSummariesData.java | 56 +++++ .../doiboost/orcid/SummariesDecompressor.java | 64 +++++ .../doiboost/orcid/xml/XMLRecordParser.java | 31 +++ .../orcid_download/oozie_app/workflow.xml | 45 ---- .../oozie_app/workflow.xml | 232 ++++++++++++++++++ .../oozie_app/config-default.xml | 26 ++ .../oozie_app/workflow.xml | 40 +++ .../oozie_app/config-default.xml | 0 .../oozie_app/workflow.xml | 64 +++++ 11 files changed, 628 insertions(+), 45 deletions(-) create mode 100644 dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ExtractXMLActivitiesData.java create mode 100644 dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ExtractXMLSummariesData.java delete mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_download/oozie_app/workflow.xml create mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_extract_xml_activities/oozie_app/workflow.xml create mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_extract_xml_summaries/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_extract_xml_summaries/oozie_app/workflow.xml rename dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/{orcid_download => orcid_updates_download}/oozie_app/config-default.xml (100%) create mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_updates_download/oozie_app/workflow.xml diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ActivitiesDecompressor.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ActivitiesDecompressor.java index 02d2b267b..420c363ec 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ActivitiesDecompressor.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ActivitiesDecompressor.java @@ -17,6 +17,7 @@ import org.apache.hadoop.io.SequenceFile; import org.apache.hadoop.io.Text; import org.apache.hadoop.io.compress.CompressionCodec; import org.apache.hadoop.io.compress.CompressionCodecFactory; +import org.apache.hadoop.io.compress.GzipCodec; import org.mortbay.log.Log; import eu.dnetlib.doiboost.orcid.model.WorkData; @@ -143,4 +144,64 @@ public class ActivitiesDecompressor { Log.info("Error from Orcid found: " + errorFromOrcidFound); Log.info("Error parsing xml work found: " + xmlParserErrorFound); } + + public static void extractXML(Configuration conf, String inputUri, Path outputPath) + throws Exception { + String uri = inputUri; + FileSystem fs = FileSystem.get(URI.create(uri), conf); + Path inputPath = new Path(uri); + CompressionCodecFactory factory = new CompressionCodecFactory(conf); + CompressionCodec codec = factory.getCodec(inputPath); + if (codec == null) { + System.err.println("No codec found for " + uri); + System.exit(1); + } + CompressionCodecFactory.removeSuffix(uri, codec.getDefaultExtension()); + InputStream gzipInputStream = null; + try { + gzipInputStream = codec.createInputStream(fs.open(inputPath)); + int counter = 0; + try (TarArchiveInputStream tais = new TarArchiveInputStream(gzipInputStream)) { + TarArchiveEntry entry = null; + try (SequenceFile.Writer writer = SequenceFile + .createWriter( + conf, + SequenceFile.Writer.file(outputPath), + SequenceFile.Writer.keyClass(Text.class), + SequenceFile.Writer.valueClass(Text.class), + SequenceFile.Writer.compression(SequenceFile.CompressionType.BLOCK, new GzipCodec()))) { + while ((entry = tais.getNextTarEntry()) != null) { + String filename = entry.getName(); + if (entry.isDirectory() || !filename.contains("works")) { + } else { + counter++; + BufferedReader br = new BufferedReader(new InputStreamReader(tais)); + String line; + StringBuffer buffer = new StringBuffer(); + while ((line = br.readLine()) != null) { + buffer.append(line); + } + String xml = buffer.toString(); + String[] filenameParts = filename.split("/"); + final Text key = new Text( + XMLRecordParser + .retrieveOrcidIdFromActivity( + xml.getBytes(), filenameParts[filenameParts.length - 1])); + final Text value = new Text(xml); + writer.append(key, value); + if ((counter % 100000) == 0) { + Log.info("Current xml works extracted: " + counter); + } + } + } + } + } + Log.info("Activities extraction completed"); + Log.info("Total XML works parsed: " + counter); + } finally { + Log.debug("Closing gzip stream"); + IOUtils.closeStream(gzipInputStream); + } + } + } diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ExtractXMLActivitiesData.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ExtractXMLActivitiesData.java new file mode 100644 index 000000000..c834efa20 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ExtractXMLActivitiesData.java @@ -0,0 +1,54 @@ + +package eu.dnetlib.doiboost.orcid; + +import java.io.IOException; + +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.mortbay.log.Log; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork; + +public class ExtractXMLActivitiesData extends OrcidDSManager { + private String outputWorksPath; + private String activitiesFileNameTarGz; + + public static void main(String[] args) throws IOException, Exception { + ExtractXMLActivitiesData extractXMLActivitiesData = new ExtractXMLActivitiesData(); + extractXMLActivitiesData.loadArgs(args); + extractXMLActivitiesData.extractWorks(); + } + + private void loadArgs(String[] args) throws IOException, Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + GenOrcidAuthorWork.class + .getResourceAsStream( + "/eu/dnetlib/dhp/doiboost/gen_orcid_works-no-doi_from_activities.json"))); + parser.parseArgument(args); + + hdfsServerUri = parser.get("hdfsServerUri"); + Log.info("HDFS URI: " + hdfsServerUri); + workingPath = parser.get("workingPath"); + Log.info("Working Path: " + workingPath); + activitiesFileNameTarGz = parser.get("activitiesFileNameTarGz"); + Log.info("Activities File Name: " + activitiesFileNameTarGz); + outputWorksPath = parser.get("outputWorksPath"); + Log.info("Output Author Work Data: " + outputWorksPath); + } + + private void extractWorks() throws Exception { + Configuration conf = initConfigurationObject(); + FileSystem fs = initFileSystemObject(conf); + String tarGzUri = hdfsServerUri.concat(workingPath).concat(activitiesFileNameTarGz); + Path outputPath = new Path( + hdfsServerUri + .concat(workingPath) + .concat(outputWorksPath)); + ActivitiesDecompressor.extractXML(conf, tarGzUri, outputPath); + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ExtractXMLSummariesData.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ExtractXMLSummariesData.java new file mode 100644 index 000000000..843889108 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ExtractXMLSummariesData.java @@ -0,0 +1,56 @@ + +package eu.dnetlib.doiboost.orcid; + +import java.io.IOException; + +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.mortbay.log.Log; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork; + +public class ExtractXMLSummariesData extends OrcidDSManager { + + private String outputAuthorsPath; + private String summariesFileNameTarGz; + + public static void main(String[] args) throws IOException, Exception { + ExtractXMLSummariesData extractXMLSummariesData = new ExtractXMLSummariesData(); + extractXMLSummariesData.loadArgs(args); + extractXMLSummariesData.extractAuthors(); + } + + private void loadArgs(String[] args) throws IOException, Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + GenOrcidAuthorWork.class + .getResourceAsStream( + "/eu/dnetlib/dhp/doiboost/gen_orcid_authors_from_summaries.json"))); + parser.parseArgument(args); + + hdfsServerUri = parser.get("hdfsServerUri"); + Log.info("HDFS URI: " + hdfsServerUri); + workingPath = parser.get("workingPath"); + Log.info("Working Path: " + workingPath); + summariesFileNameTarGz = parser.get("summariesFileNameTarGz"); + Log.info("Summaries File Name: " + summariesFileNameTarGz); + outputAuthorsPath = parser.get("outputAuthorsPath"); + Log.info("Output Authors Data: " + outputAuthorsPath); + } + + public void extractAuthors() throws Exception { + Configuration conf = initConfigurationObject(); + FileSystem fs = initFileSystemObject(conf); + String tarGzUri = hdfsServerUri.concat(workingPath).concat(summariesFileNameTarGz); + Path outputPath = new Path( + hdfsServerUri + .concat(workingPath) + .concat(outputAuthorsPath) + .concat("xml_authors.seq")); + SummariesDecompressor.extractXML(conf, tarGzUri, outputPath); + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SummariesDecompressor.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SummariesDecompressor.java index d1b2a1d73..c16899977 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SummariesDecompressor.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SummariesDecompressor.java @@ -17,6 +17,7 @@ import org.apache.hadoop.io.SequenceFile; import org.apache.hadoop.io.Text; import org.apache.hadoop.io.compress.CompressionCodec; import org.apache.hadoop.io.compress.CompressionCodecFactory; +import org.apache.hadoop.io.compress.GzipCodec; import org.mortbay.log.Log; import eu.dnetlib.dhp.schema.orcid.AuthorData; @@ -160,4 +161,67 @@ public class SummariesDecompressor { Log.info("Error from Orcid found: " + errorFromOrcidFound); Log.info("Error parsing xml record found: " + xmlParserErrorFound); } + + public static void extractXML(Configuration conf, String inputUri, Path outputPath) + throws Exception { + String uri = inputUri; + FileSystem fs = FileSystem.get(URI.create(uri), conf); + Path inputPath = new Path(uri); + CompressionCodecFactory factory = new CompressionCodecFactory(conf); + CompressionCodec codec = factory.getCodec(inputPath); + if (codec == null) { + System.err.println("No codec found for " + uri); + System.exit(1); + } + CompressionCodecFactory.removeSuffix(uri, codec.getDefaultExtension()); + InputStream gzipInputStream = null; + try { + gzipInputStream = codec.createInputStream(fs.open(inputPath)); + int counter = 0; + try (TarArchiveInputStream tais = new TarArchiveInputStream(gzipInputStream)) { + TarArchiveEntry entry = null; + CompressionCodec Codec = new GzipCodec(); + org.apache.hadoop.io.SequenceFile.Writer.Option optCom = SequenceFile.Writer + .compression(SequenceFile.CompressionType.RECORD, Codec); + try (SequenceFile.Writer writer = SequenceFile + .createWriter( + conf, + SequenceFile.Writer.file(outputPath), + SequenceFile.Writer.keyClass(Text.class), + SequenceFile.Writer.valueClass(Text.class), optCom)) { + while ((entry = tais.getNextTarEntry()) != null) { + String filename = entry.getName(); + if (entry.isDirectory()) { + Log.debug("Directory entry name: " + entry.getName()); + } else { + Log.debug("XML record entry name: " + entry.getName()); + counter++; + BufferedReader br = new BufferedReader(new InputStreamReader(tais)); + String line; + StringBuffer buffer = new StringBuffer(); + while ((line = br.readLine()) != null) { + buffer.append(line); + } + String xml = buffer.toString(); + final Text key = new Text( + XMLRecordParser + .retrieveOrcidIdFromSummary( + xml.getBytes(), filename.split("/")[2].substring(0, 19))); + final Text value = new Text(xml); + writer.append(key, value); + } + if ((counter % 100000) == 0) { + Log.info("Current xml records extracted: " + counter); + } + } + } + } + Log.info("Summaries extract completed"); + Log.info("Total XML records parsed: " + counter); + + } finally { + Log.debug("Closing gzip stream"); + IOUtils.closeStream(gzipInputStream); + } + } } diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParser.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParser.java index a807cf132..cc9abb621 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParser.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParser.java @@ -4,6 +4,8 @@ package eu.dnetlib.doiboost.orcid.xml; import java.util.Arrays; import java.util.List; +import org.mortbay.log.Log; + import com.ximpleware.AutoPilot; import com.ximpleware.EOFException; import com.ximpleware.EncodingException; @@ -126,4 +128,33 @@ public class XMLRecordParser { } return workData; } + + public static String retrieveOrcidIdFromSummary(byte[] bytes, String defaultValue) + throws VtdException, ParseException { + return retrieveOrcidId(bytes, defaultValue, NS_RECORD, NS_RECORD_URL, "//record:record", "path").substring(1); + } + + public static String retrieveOrcidIdFromActivity(byte[] bytes, String defaultValue) + throws VtdException, ParseException { + return retrieveOrcidId(bytes, defaultValue, NS_WORK, NS_WORK_URL, "//work:work", "put-code"); + } + + private static String retrieveOrcidId(byte[] bytes, String defaultValue, String ns, String nsUrl, String xpath, + String idAttributeName) + throws VtdException, ParseException { + final VTDGen vg = new VTDGen(); + vg.setDoc(bytes); + vg.parse(true); + final VTDNav vn = vg.getNav(); + final AutoPilot ap = new AutoPilot(vn); + ap.declareXPathNameSpace(ns, nsUrl); + List recordNodes = VtdUtilityParser + .getTextValuesWithAttributes( + ap, vn, xpath, Arrays.asList(idAttributeName)); + if (!recordNodes.isEmpty()) { + return (recordNodes.get(0).getAttributes().get(idAttributeName)); + } + Log.info("id not found - default: " + defaultValue); + return defaultValue; + } } diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_download/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_download/oozie_app/workflow.xml deleted file mode 100644 index 1f9adeb4d..000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_download/oozie_app/workflow.xml +++ /dev/null @@ -1,45 +0,0 @@ - - - - workingPathOrcid - the working dir base path - - - token - access token - - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - - - - - - - - - - ${jobTracker} - ${nameNode} - eu.dnetlib.doiboost.orcid.OrcidDownloader - -d${workingPathOrcid}/ - -n${nameNode} - -flast_modified.csv - -odownload/ - -t${token} - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_extract_xml_activities/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_extract_xml_activities/oozie_app/workflow.xml new file mode 100644 index 000000000..6f629c754 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_extract_xml_activities/oozie_app/workflow.xml @@ -0,0 +1,232 @@ + + + + workingPath + the working dir base path + + + + + ${jobTracker} + ${nameNode} + + + oozie.action.sharelib.for.java + ${oozieActionShareLibForSpark2} + + + oozie.launcher.mapreduce.user.classpath.first + true + + + oozie.launcher.mapreduce.map.java.opts + -Xmx2g + + + oozie.use.system.libpath + true + + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + + + + + + + + + + + + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData + -w${workingPath}/ + -n${nameNode} + -fORCID_2020_10_activites_0.tar.gz + -owxml/works/xml_works_0.seq + -oew--- + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData + -w${workingPath}/ + -n${nameNode} + -fORCID_2020_10_activites_1.tar.gz + -owxml/works/xml_works_1.seq + -oew--- + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData + -w${workingPath}/ + -n${nameNode} + -fORCID_2020_10_activites_2.tar.gz + -owxml/works/xml_works_2.seq + -oew--- + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData + -w${workingPath}/ + -n${nameNode} + -fORCID_2020_10_activites_3.tar.gz + -owxml/works/xml_works_3.seq + -oew--- + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData + -w${workingPath}/ + -n${nameNode} + -fORCID_2020_10_activites_4.tar.gz + -owxml/works/xml_works_4.seq + -oew--- + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData + -w${workingPath}/ + -n${nameNode} + -fORCID_2020_10_activites_5.tar.gz + -owxml/works/xml_works_5.seq + -oew--- + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData + -w${workingPath}/ + -n${nameNode} + -fORCID_2020_10_activites_6.tar.gz + -owxml/works/xml_works_6.seq + -oew--- + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData + -w${workingPath}/ + -n${nameNode} + -fORCID_2020_10_activites_7.tar.gz + -owxml/works/xml_works_7.seq + -oew--- + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData + -w${workingPath}/ + -n${nameNode} + -fORCID_2020_10_activites_8.tar.gz + -owxml/works/xml_works_8.seq + -oew--- + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData + -w${workingPath}/ + -n${nameNode} + -fORCID_2020_10_activites_9.tar.gz + -owxml/works/xml_works_9.seq + -oew--- + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcid.ExtractXMLActivitiesData + -w${workingPath}/ + -n${nameNode} + -fORCID_2020_10_activites_X.tar.gz + -owxml/works/xml_works_X.seq + -oew--- + + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_extract_xml_summaries/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_extract_xml_summaries/oozie_app/config-default.xml new file mode 100644 index 000000000..191654378 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_extract_xml_summaries/oozie_app/config-default.xml @@ -0,0 +1,26 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + oozie.launcher.mapreduce.user.classpath.first + true + + + oozie.launcher.mapreduce.map.java.opts + -Xmx8g + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_extract_xml_summaries/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_extract_xml_summaries/oozie_app/workflow.xml new file mode 100644 index 000000000..68d468ab3 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_extract_xml_summaries/oozie_app/workflow.xml @@ -0,0 +1,40 @@ + + + + workingPath + the working dir base path + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcid.ExtractXMLSummariesData + -w${workingPath}/ + -n${nameNode} + -fORCID_2020_10_summaries.tar.gz + -oxml/authors/ + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_download/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_updates_download/oozie_app/config-default.xml similarity index 100% rename from dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_download/oozie_app/config-default.xml rename to dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_updates_download/oozie_app/config-default.xml diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_updates_download/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_updates_download/oozie_app/workflow.xml new file mode 100644 index 000000000..a3daab116 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_updates_download/oozie_app/workflow.xml @@ -0,0 +1,64 @@ + + + + workingPath + the working dir base path + + + token + access token + + + shell_cmd + wget -O /tmp/last_modified.csv.tar http://74804fb637bd8e2fba5b-e0a029c2f87486cddec3b416996a6057.r3.cf1.rackcdn.com/last_modified.csv.tar ; hdfs dfs -copyFromLocal /tmp/last_modified.csv.tar /data/orcid_activities_2020/last_modified.csv.tar ; rm -f /tmp/last_modified.csv.tar + + the shell command that downloads the lambda file from orcid containing last orcid update informations + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + + + + + + ${jobTracker} + ${nameNode} + bash + -c + ${shell_cmd} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.doiboost.orcid.OrcidDownloader + -d${workingPathOrcid}/ + -n${nameNode} + -flast_modified.csv + -odownload/ + -t${token} + + + + + + + \ No newline at end of file From 97c8111847a148fb738c593136d16934c6be15cf Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Mon, 23 Nov 2020 09:49:22 +0100 Subject: [PATCH 31/37] action to convert lambda file in seq file; spark action to download updated authors --- .../doiboost/orcid/OrcidDownloader.java | 185 +++++++++--------- .../orcid/SparkDownloadOrcidAuthors.java | 166 ++++++++++++++++ .../orcid/SparkGenLastModifiedSeq.java | 99 ++++++++++ .../orcid/SparkOrcidGenerateAuthors.java | 165 ---------------- .../orcid/SparkPartitionLambdaFile.java | 50 ----- .../orcid/model/DownloadedRecordData.java | 14 +- .../gen_orcid_authors_parameters.json | 4 - .../oozie_app/config-default.xml | 22 --- .../orcid_gen_authors/oozie_app/workflow.xml | 83 -------- .../oozie_app/workflow.xml | 122 +++++++++++- .../doiboost/orcid/OrcidClientTest.java | 139 +++++++++++-- .../0000-0001-6645-509X.compressed.base64 | 1 - .../0000-0003-3028-6161.compressed.base64 | 1 + 13 files changed, 608 insertions(+), 443 deletions(-) create mode 100644 dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkDownloadOrcidAuthors.java create mode 100644 dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkGenLastModifiedSeq.java delete mode 100644 dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkOrcidGenerateAuthors.java delete mode 100644 dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkPartitionLambdaFile.java delete mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_orcid_authors_parameters.json delete mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_gen_authors/oozie_app/config-default.xml delete mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_gen_authors/oozie_app/workflow.xml delete mode 100644 dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/0000-0001-6645-509X.compressed.base64 create mode 100644 dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/0000-0003-3028-6161.compressed.base64 diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDownloader.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDownloader.java index 762d8aecd..be727ab9f 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDownloader.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDownloader.java @@ -1,14 +1,15 @@ package eu.dnetlib.doiboost.orcid; -import java.io.BufferedReader; -import java.io.IOException; -import java.io.InputStreamReader; +import java.io.*; import java.text.SimpleDateFormat; import java.util.Arrays; import java.util.Date; import java.util.List; +import org.apache.commons.compress.archivers.tar.TarArchiveEntry; +import org.apache.commons.compress.archivers.tar.TarArchiveInputStream; +import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream; import org.apache.commons.io.IOUtils; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.fs.FSDataInputStream; @@ -16,6 +17,7 @@ import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.Path; import org.apache.hadoop.io.SequenceFile; import org.apache.hadoop.io.Text; +import org.apache.hadoop.io.compress.GzipCodec; import org.apache.http.client.methods.CloseableHttpResponse; import org.apache.http.client.methods.HttpGet; import org.apache.http.impl.client.CloseableHttpClient; @@ -27,10 +29,10 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser; public class OrcidDownloader extends OrcidDSManager { static final int REQ_LIMIT = 24; -// static final int REQ_MAX_TEST = 100; - static final int RECORD_PARSED_COUNTER_LOG_INTERVAL = 10000; + static final int REQ_MAX_TEST = -1; + static final int RECORD_PARSED_COUNTER_LOG_INTERVAL = 500; static final String DATE_FORMAT = "yyyy-MM-dd HH:mm:ss"; - static final String lastUpdate = "2019-09-30 00:00:00"; + static final String lastUpdate = "2020-09-29 00:00:00"; private String lambdaFileName; private String outputPath; private String token; @@ -41,7 +43,7 @@ public class OrcidDownloader extends OrcidDSManager { orcidDownloader.parseLambdaFile(); } - private String downloadRecord(String orcidId) { + private String downloadRecord(String orcidId) throws IOException { try (CloseableHttpClient client = HttpClients.createDefault()) { HttpGet httpGet = new HttpGet("https://api.orcid.org/v3.0/" + orcidId + "/record"); httpGet.addHeader("Accept", "application/vnd.orcid+xml"); @@ -49,17 +51,23 @@ public class OrcidDownloader extends OrcidDSManager { CloseableHttpResponse response = client.execute(httpGet); if (response.getStatusLine().getStatusCode() != 200) { Log - .warn( + .info( "Downloading " + orcidId + " status code: " + response.getStatusLine().getStatusCode()); return new String(""); } - return IOUtils.toString(response.getEntity().getContent()); - - } catch (Throwable e) { - Log.warn("Downloading " + orcidId, e.getMessage()); - +// return IOUtils.toString(response.getEntity().getContent()); + return xmlStreamToString(response.getEntity().getContent()); } - return new String(""); + } + + private String xmlStreamToString(InputStream xmlStream) throws IOException { + BufferedReader br = new BufferedReader(new InputStreamReader(xmlStream)); + String line; + StringBuffer buffer = new StringBuffer(); + while ((line = br.readLine()) != null) { + buffer.append(line); + } + return buffer.toString(); } public void parseLambdaFile() throws Exception { @@ -76,90 +84,87 @@ public class OrcidDownloader extends OrcidDSManager { hdfsServerUri .concat(workingPath) .concat(outputPath) - .concat("orcid_records.seq")); - - try (SequenceFile.Writer writer = SequenceFile - .createWriter( - conf, - SequenceFile.Writer.file(hdfsoutputPath), - SequenceFile.Writer.keyClass(Text.class), - SequenceFile.Writer.valueClass(Text.class))) { - - try (BufferedReader br = new BufferedReader(new InputStreamReader(lambdaFileStream))) { - String line; - int nReqTmp = 0; + .concat("updated_xml_authors.seq")); + try (TarArchiveInputStream tais = new TarArchiveInputStream( + new GzipCompressorInputStream(lambdaFileStream))) { + TarArchiveEntry entry = null; + StringBuilder sb = new StringBuilder(); + try (SequenceFile.Writer writer = SequenceFile + .createWriter( + conf, + SequenceFile.Writer.file(hdfsoutputPath), + SequenceFile.Writer.keyClass(Text.class), + SequenceFile.Writer.valueClass(Text.class), + SequenceFile.Writer.compression(SequenceFile.CompressionType.BLOCK, new GzipCodec()))) { startDownload = System.currentTimeMillis(); - long startReqTmp = System.currentTimeMillis(); - while ((line = br.readLine()) != null) { - parsedRecordsCounter++; - // skip headers line - if (parsedRecordsCounter == 1) { - continue; - } - String[] values = line.split(","); - List recordInfo = Arrays.asList(values); - String orcidId = recordInfo.get(0); - if (isModified(orcidId, recordInfo.get(3))) { - String record = downloadRecord(orcidId); - downloadedRecordsCounter++; - if (!record.isEmpty()) { - String compressRecord = ArgumentApplicationParser.compressArgument(record); - final Text key = new Text(recordInfo.get(0)); - final Text value = new Text(compressRecord); - - try { + while ((entry = tais.getNextTarEntry()) != null) { + BufferedReader br = new BufferedReader(new InputStreamReader(tais)); // Read directly from tarInput + String line; + while ((line = br.readLine()) != null) { + String[] values = line.split(","); + List recordInfo = Arrays.asList(values); + int nReqTmp = 0; + long startReqTmp = System.currentTimeMillis(); + // skip headers line + if (parsedRecordsCounter == 0) { + parsedRecordsCounter++; + continue; + } + parsedRecordsCounter++; + String orcidId = recordInfo.get(0); + if (isModified(orcidId, recordInfo.get(3))) { + String record = downloadRecord(orcidId); + downloadedRecordsCounter++; + if (!record.isEmpty()) { +// String compressRecord = ArgumentApplicationParser.compressArgument(record); + final Text key = new Text(recordInfo.get(0)); + final Text value = new Text(record); writer.append(key, value); savedRecordsCounter++; - } catch (IOException e) { - Log.warn("Writing to sequence file: " + e.getMessage()); - Log.warn(e); - throw new RuntimeException(e); + } + } else { + break; + } + long endReq = System.currentTimeMillis(); + nReqTmp++; + if (nReqTmp == REQ_LIMIT) { + long reqSessionDuration = endReq - startReqTmp; + if (reqSessionDuration <= 1000) { + Log + .info( + "\nreqSessionDuration: " + + reqSessionDuration + + " nReqTmp: " + + nReqTmp + + " wait ...."); + Thread.sleep(1000 - reqSessionDuration); + } else { + nReqTmp = 0; + startReqTmp = System.currentTimeMillis(); + } + } + if ((parsedRecordsCounter % RECORD_PARSED_COUNTER_LOG_INTERVAL) == 0) { + Log + .info( + "Current parsed: " + + parsedRecordsCounter + + " downloaded: " + + downloadedRecordsCounter + + " saved: " + + savedRecordsCounter); + if (REQ_MAX_TEST != -1 && parsedRecordsCounter > REQ_MAX_TEST) { + break; } } } - long endReq = System.currentTimeMillis(); - nReqTmp++; - if (nReqTmp == REQ_LIMIT) { - long reqSessionDuration = endReq - startReqTmp; - if (reqSessionDuration <= 1000) { - Log - .warn( - "\nreqSessionDuration: " - + reqSessionDuration - + " nReqTmp: " - + nReqTmp - + " wait ...."); - Thread.sleep(1000 - reqSessionDuration); - } else { - nReqTmp = 0; - startReqTmp = System.currentTimeMillis(); - } - } - -// if (parsedRecordsCounter > REQ_MAX_TEST) { -// break; -// } - if ((parsedRecordsCounter % RECORD_PARSED_COUNTER_LOG_INTERVAL) == 0) { - Log - .info( - "Current parsed: " - + parsedRecordsCounter - + " downloaded: " - + downloadedRecordsCounter - + " saved: " - + savedRecordsCounter); -// if (parsedRecordsCounter > REQ_MAX_TEST) { -// break; -// } - } + long endDownload = System.currentTimeMillis(); + long downloadTime = endDownload - startDownload; + Log.info("Download time: " + ((downloadTime / 1000) / 60) + " minutes"); } - long endDownload = System.currentTimeMillis(); - long downloadTime = endDownload - startDownload; - Log.info("Download time: " + ((downloadTime / 1000) / 60) + " minutes"); } } - lambdaFileStream.close(); Log.info("Download started at: " + new Date(startDownload).toString()); + Log.info("Download ended at: " + new Date(System.currentTimeMillis()).toString()); Log.info("Parsed Records Counter: " + parsedRecordsCounter); Log.info("Downloaded Records Counter: " + downloadedRecordsCounter); Log.info("Saved Records Counter: " + savedRecordsCounter); @@ -185,7 +190,7 @@ public class OrcidDownloader extends OrcidDSManager { token = parser.get("token"); } - private boolean isModified(String orcidId, String modifiedDate) { + public boolean isModified(String orcidId, String modifiedDate) { Date modifiedDateDt = null; Date lastUpdateDt = null; try { @@ -195,7 +200,7 @@ public class OrcidDownloader extends OrcidDSManager { modifiedDateDt = new SimpleDateFormat(DATE_FORMAT).parse(modifiedDate); lastUpdateDt = new SimpleDateFormat(DATE_FORMAT).parse(lastUpdate); } catch (Exception e) { - Log.warn("[" + orcidId + "] Parsing date: ", e.getMessage()); + Log.info("[" + orcidId + "] Parsing date: ", e.getMessage()); return true; } return modifiedDateDt.after(lastUpdateDt); diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkDownloadOrcidAuthors.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkDownloadOrcidAuthors.java new file mode 100644 index 000000000..850a654d4 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkDownloadOrcidAuthors.java @@ -0,0 +1,166 @@ + +package eu.dnetlib.doiboost.orcid; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.IOException; +import java.text.SimpleDateFormat; +import java.util.Date; +import java.util.List; +import java.util.Optional; + +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.io.Text; +import org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat; +import org.apache.http.client.methods.CloseableHttpResponse; +import org.apache.http.client.methods.HttpGet; +import org.apache.http.impl.client.CloseableHttpClient; +import org.apache.http.impl.client.HttpClients; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaPairRDD; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.Function; +import org.apache.spark.util.LongAccumulator; +import org.mortbay.log.Log; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.doiboost.orcid.model.DownloadedRecordData; +import scala.Tuple2; + +public class SparkDownloadOrcidAuthors { + + static Logger logger = LoggerFactory.getLogger(SparkDownloadOrcidAuthors.class); + static final String DATE_FORMAT = "yyyy-MM-dd HH:mm:ss"; + static final String lastUpdate = "2020-09-29 00:00:00"; + + public static void main(String[] args) throws IOException, Exception { + + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + SparkDownloadOrcidAuthors.class + .getResourceAsStream( + "/eu/dnetlib/dhp/doiboost/download_orcid_data.json"))); + parser.parseArgument(args); + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + logger.info("isSparkSessionManaged: {}", isSparkSessionManaged); + final String workingPath = parser.get("workingPath"); + logger.info("workingPath: ", workingPath); + final String outputPath = parser.get("outputPath"); + logger.info("outputPath: ", outputPath); + final String token = parser.get("token"); + final String lambdaFileName = parser.get("lambdaFileName"); + logger.info("lambdaFileName: ", lambdaFileName); + + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + LongAccumulator parsedRecordsAcc = spark.sparkContext().longAccumulator("parsedRecords"); + LongAccumulator modifiedRecordsAcc = spark.sparkContext().longAccumulator("modifiedRecords"); + LongAccumulator downloadedRecordsAcc = spark.sparkContext().longAccumulator("downloadedRecords"); + + logger.info("Retrieving data from lamda sequence file"); + JavaPairRDD lamdaFileRDD = sc + .sequenceFile(workingPath + lambdaFileName, Text.class, Text.class); + logger.info("Data retrieved: " + lamdaFileRDD.count()); + + Function, Boolean> isModifiedAfterFilter = data -> { + String orcidId = data._1().toString(); + String lastModifiedDate = data._2().toString(); + parsedRecordsAcc.add(1); + if (isModified(orcidId, lastModifiedDate)) { + modifiedRecordsAcc.add(1); + return true; + } + return false; + }; + + Function, Tuple2> downloadRecordFunction = data -> { + String orcidId = data._1().toString(); + String lastModifiedDate = data._2().toString(); + final DownloadedRecordData downloaded = new DownloadedRecordData(); + downloaded.setOrcidId(orcidId); + downloaded.setLastModifiedDate(lastModifiedDate); + try (CloseableHttpClient client = HttpClients.createDefault()) { + HttpGet httpGet = new HttpGet("https://api.orcid.org/v3.0/" + orcidId + "/record"); + httpGet.addHeader("Accept", "application/vnd.orcid+xml"); + httpGet.addHeader("Authorization", String.format("Bearer %s", token)); + CloseableHttpResponse response = client.execute(httpGet); + int statusCode = response.getStatusLine().getStatusCode(); + downloaded.setStatusCode(statusCode); + if (statusCode != 200) { + logger + .info( + "Downloading " + orcidId + " status code: " + + response.getStatusLine().getStatusCode()); + return downloaded.toTuple2(); + } + downloadedRecordsAcc.add(1); + long currentDownloaded = downloadedRecordsAcc.value(); + if ((currentDownloaded % 10000) == 0) { + logger.info("Current downloaded: " + currentDownloaded); + } + downloaded + .setCompressedData( + ArgumentApplicationParser + .compressArgument(IOUtils.toString(response.getEntity().getContent()))); + } catch (Throwable e) { + logger.info("Downloading " + orcidId, e.getMessage()); + downloaded.setErrorMessage(e.getMessage()); + return downloaded.toTuple2(); + } + return downloaded.toTuple2(); + }; + + sc.hadoopConfiguration().set("mapreduce.output.fileoutputformat.compress", "true"); + + logger.info("Start execution ..."); +// List> sampleList = lamdaFileRDD.take(500); +// JavaRDD> sampleRDD = sc.parallelize(sampleList); +// sampleRDD + JavaPairRDD authorsModifiedRDD = lamdaFileRDD + .filter(isModifiedAfterFilter); + logger.info("Authors modified count: " + authorsModifiedRDD.count()); + logger.info("Start downloading ..."); + authorsModifiedRDD + .map(downloadRecordFunction) + .mapToPair(t -> new Tuple2(new Text(t._1()), new Text(t._2()))) + .saveAsNewAPIHadoopFile( + workingPath.concat(outputPath), + Text.class, + Text.class, + SequenceFileOutputFormat.class, + sc.hadoopConfiguration()); + logger.info("parsedRecordsAcc: " + parsedRecordsAcc.value().toString()); + logger.info("modifiedRecordsAcc: " + modifiedRecordsAcc.value().toString()); + logger.info("downloadedRecordsAcc: " + downloadedRecordsAcc.value().toString()); + }); + + } + + private static boolean isModified(String orcidId, String modifiedDate) { + Date modifiedDateDt = null; + Date lastUpdateDt = null; + try { + if (modifiedDate.length() != 19) { + modifiedDate = modifiedDate.substring(0, 19); + } + modifiedDateDt = new SimpleDateFormat(DATE_FORMAT).parse(modifiedDate); + lastUpdateDt = new SimpleDateFormat(DATE_FORMAT).parse(lastUpdate); + } catch (Exception e) { + logger.info("[" + orcidId + "] Parsing date: ", e.getMessage()); + return true; + } + return modifiedDateDt.after(lastUpdateDt); + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkGenLastModifiedSeq.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkGenLastModifiedSeq.java new file mode 100644 index 000000000..f710635ab --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkGenLastModifiedSeq.java @@ -0,0 +1,99 @@ + +package eu.dnetlib.doiboost.orcid; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.BufferedReader; +import java.io.IOException; +import java.io.InputStreamReader; +import java.net.URI; +import java.util.Arrays; +import java.util.List; +import java.util.Optional; + +import org.apache.commons.compress.archivers.tar.TarArchiveEntry; +import org.apache.commons.compress.archivers.tar.TarArchiveInputStream; +import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream; +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FSDataInputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.apache.hadoop.io.SequenceFile; +import org.apache.hadoop.io.Text; +import org.apache.hadoop.io.compress.GzipCodec; +import org.apache.spark.SparkConf; +import org.mortbay.log.Log; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; + +public class SparkGenLastModifiedSeq { + private static String hdfsServerUri; + private static String workingPath; + private static String outputPath; + private static String lambdaFileName; + + public static void main(String[] args) throws IOException, Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + SparkGenLastModifiedSeq.class + .getResourceAsStream( + "/eu/dnetlib/dhp/doiboost/download_orcid_data.json"))); + parser.parseArgument(args); + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + hdfsServerUri = parser.get("hdfsServerUri"); + workingPath = parser.get("workingPath"); + outputPath = parser.get("outputPath"); + lambdaFileName = parser.get("lambdaFileName"); + String lambdaFileUri = hdfsServerUri.concat(workingPath).concat(lambdaFileName); + + SparkConf sparkConf = new SparkConf(); + runWithSparkSession( + sparkConf, + isSparkSessionManaged, + spark -> { + int rowsNum = 0; + Path output = new Path( + hdfsServerUri + .concat(workingPath) + .concat(outputPath)); + Path hdfsreadpath = new Path(lambdaFileUri); + Configuration conf = new Configuration(); + conf.set("fs.defaultFS", hdfsServerUri.concat(workingPath)); + conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName()); + conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName()); + FileSystem fs = FileSystem.get(URI.create(hdfsServerUri.concat(workingPath)), conf); + FSDataInputStream lambdaFileStream = fs.open(hdfsreadpath); + try (TarArchiveInputStream tais = new TarArchiveInputStream( + new GzipCompressorInputStream(lambdaFileStream))) { + TarArchiveEntry entry = null; + try (SequenceFile.Writer writer = SequenceFile + .createWriter( + conf, + SequenceFile.Writer.file(output), + SequenceFile.Writer.keyClass(Text.class), + SequenceFile.Writer.valueClass(Text.class), + SequenceFile.Writer.compression(SequenceFile.CompressionType.BLOCK, new GzipCodec()))) { + while ((entry = tais.getNextTarEntry()) != null) { + BufferedReader br = new BufferedReader(new InputStreamReader(tais)); + String line; + while ((line = br.readLine()) != null) { + String[] values = line.split(","); + List recordInfo = Arrays.asList(values); + String orcidId = recordInfo.get(0); + final Text key = new Text(orcidId); + final Text value = new Text(recordInfo.get(3)); + writer.append(key, value); + rowsNum++; + } + } + } + } + Log.info("Saved rows from lamda csv tar file: " + rowsNum); + }); + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkOrcidGenerateAuthors.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkOrcidGenerateAuthors.java deleted file mode 100644 index 4e18ab840..000000000 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkOrcidGenerateAuthors.java +++ /dev/null @@ -1,165 +0,0 @@ - -package eu.dnetlib.doiboost.orcid; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.IOException; -import java.text.SimpleDateFormat; -import java.util.Date; -import java.util.List; -import java.util.Optional; - -import org.apache.commons.io.IOUtils; -import org.apache.hadoop.io.Text; -import org.apache.http.client.methods.CloseableHttpResponse; -import org.apache.http.client.methods.HttpGet; -import org.apache.http.impl.client.CloseableHttpClient; -import org.apache.http.impl.client.HttpClients; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.function.Function; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.util.LongAccumulator; -import org.mortbay.log.Log; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.doiboost.orcid.model.DownloadedRecordData; -import scala.Tuple2; - -public class SparkOrcidGenerateAuthors { - - static final String DATE_FORMAT = "yyyy-MM-dd HH:mm:ss"; - static final String lastUpdate = "2019-09-30 00:00:00"; - - public static void main(String[] args) throws IOException, Exception { - Logger logger = LoggerFactory.getLogger(SparkOrcidGenerateAuthors.class); - logger.info("[ SparkOrcidGenerateAuthors STARTED]"); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - SparkOrcidGenerateAuthors.class - .getResourceAsStream( - "/eu/dnetlib/dhp/doiboost/gen_orcid_authors_parameters.json"))); - parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - logger.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String workingPath = parser.get("workingPath"); - logger.info("workingPath: ", workingPath); - final String outputAuthorsPath = parser.get("outputAuthorsPath"); - logger.info("outputAuthorsPath: ", outputAuthorsPath); - final String token = parser.get("token"); - - SparkConf conf = new SparkConf(); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - LongAccumulator parsedRecordsAcc = sc.sc().longAccumulator("parsedRecords"); - LongAccumulator modifiedRecordsAcc = sc.sc().longAccumulator("modifiedRecords"); - LongAccumulator downloadedRecordsAcc = sc.sc().longAccumulator("downloadedRecords"); - LongAccumulator alreadyDownloadedRecords = sc.sc().longAccumulator("alreadyDownloadedRecords"); - JavaRDD lamdaFileRDD = sc.textFile(workingPath + "lamdafiles"); - - JavaRDD downloadedRDD = sc.textFile(workingPath + "downloaded"); - Function getOrcidIdFunction = line -> { - try { - String[] values = line.split(","); - return values[0].substring(1); - } catch (Exception e) { - return new String(""); - } - }; - List downloadedRecords = downloadedRDD.map(getOrcidIdFunction).collect(); - - Function isModifiedAfterFilter = line -> { - String[] values = line.split(","); - String orcidId = values[0]; - parsedRecordsAcc.add(1); - if (isModified(orcidId, values[3])) { - modifiedRecordsAcc.add(1); - return true; - } - return false; - }; - Function isNotDownloadedFilter = line -> { - String[] values = line.split(","); - String orcidId = values[0]; - if (downloadedRecords.contains(orcidId)) { - alreadyDownloadedRecords.add(1); - return false; - } - return true; - }; - Function> downloadRecordFunction = line -> { - String[] values = line.split(","); - String orcidId = values[0]; - String modifiedDate = values[3]; - return downloadRecord(orcidId, modifiedDate, token, downloadedRecordsAcc); - }; - - lamdaFileRDD - .filter(isModifiedAfterFilter) - .filter(isNotDownloadedFilter) - .map(downloadRecordFunction) - .rdd() - .saveAsTextFile(workingPath.concat(outputAuthorsPath)); - }); - - } - - private static boolean isModified(String orcidId, String modifiedDate) { - Date modifiedDateDt = null; - Date lastUpdateDt = null; - try { - if (modifiedDate.length() != 19) { - modifiedDate = modifiedDate.substring(0, 19); - } - modifiedDateDt = new SimpleDateFormat(DATE_FORMAT).parse(modifiedDate); - lastUpdateDt = new SimpleDateFormat(DATE_FORMAT).parse(lastUpdate); - } catch (Exception e) { - Log.warn("[" + orcidId + "] Parsing date: ", e.getMessage()); - return true; - } - return modifiedDateDt.after(lastUpdateDt); - } - - private static Tuple2 downloadRecord(String orcidId, String modifiedDate, String token, - LongAccumulator downloadedRecordsAcc) { - final DownloadedRecordData data = new DownloadedRecordData(); - data.setOrcidId(orcidId); - data.setModifiedDate(modifiedDate); - try (CloseableHttpClient client = HttpClients.createDefault()) { - HttpGet httpGet = new HttpGet("https://api.orcid.org/v3.0/" + orcidId + "/record"); - httpGet.addHeader("Accept", "application/vnd.orcid+xml"); - httpGet.addHeader("Authorization", String.format("Bearer %s", token)); - CloseableHttpResponse response = client.execute(httpGet); - int statusCode = response.getStatusLine().getStatusCode(); - data.setStatusCode(statusCode); - if (statusCode != 200) { - Log - .warn( - "Downloading " + orcidId + " status code: " + response.getStatusLine().getStatusCode()); - return data.toTuple2(); - } - downloadedRecordsAcc.add(1); - data - .setCompressedData( - ArgumentApplicationParser.compressArgument(IOUtils.toString(response.getEntity().getContent()))); - } catch (Throwable e) { - Log.warn("Downloading " + orcidId, e.getMessage()); - data.setErrorMessage(e.getMessage()); - return data.toTuple2(); - } - return data.toTuple2(); - } -} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkPartitionLambdaFile.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkPartitionLambdaFile.java deleted file mode 100644 index ca6f0f6c4..000000000 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkPartitionLambdaFile.java +++ /dev/null @@ -1,50 +0,0 @@ - -package eu.dnetlib.doiboost.orcid; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.IOException; -import java.util.Optional; - -import org.apache.commons.io.IOUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; - -public class SparkPartitionLambdaFile { - - public static void main(String[] args) throws IOException, Exception { - Logger logger = LoggerFactory.getLogger(SparkOrcidGenerateAuthors.class); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - SparkOrcidGenerateAuthors.class - .getResourceAsStream( - "/eu/dnetlib/dhp/doiboost/gen_orcid_authors_parameters.json"))); - parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - final String workingPath = parser.get("workingPath"); - - SparkConf conf = new SparkConf(); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD lamdaFileRDD = sc.textFile(workingPath + "last_modified.csv"); - - lamdaFileRDD - .repartition(20) - .saveAsTextFile(workingPath.concat("lamdafiles")); - }); - } - -} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/model/DownloadedRecordData.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/model/DownloadedRecordData.java index f66ef82a2..da1a79b19 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/model/DownloadedRecordData.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/model/DownloadedRecordData.java @@ -3,8 +3,6 @@ package eu.dnetlib.doiboost.orcid.model; import java.io.Serializable; -import org.apache.hadoop.io.Text; - import com.google.gson.JsonObject; import scala.Tuple2; @@ -12,7 +10,7 @@ import scala.Tuple2; public class DownloadedRecordData implements Serializable { private String orcidId; - private String modifiedDate; + private String lastModifiedDate; private String statusCode; private String compressedData; private String errorMessage; @@ -20,7 +18,7 @@ public class DownloadedRecordData implements Serializable { public Tuple2 toTuple2() { JsonObject data = new JsonObject(); data.addProperty("statusCode", getStatusCode()); - data.addProperty("modifiedDate", getModifiedDate()); + data.addProperty("lastModifiedDate", getLastModifiedDate()); if (getCompressedData() != null) { data.addProperty("compressedData", getCompressedData()); } @@ -66,11 +64,11 @@ public class DownloadedRecordData implements Serializable { this.compressedData = compressedData; } - public String getModifiedDate() { - return modifiedDate; + public String getLastModifiedDate() { + return lastModifiedDate; } - public void setModifiedDate(String modifiedDate) { - this.modifiedDate = modifiedDate; + public void setLastModifiedDate(String lastModifiedDate) { + this.lastModifiedDate = lastModifiedDate; } } diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_orcid_authors_parameters.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_orcid_authors_parameters.json deleted file mode 100644 index 35bfe1b41..000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_orcid_authors_parameters.json +++ /dev/null @@ -1,4 +0,0 @@ -[{"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the working path", "paramRequired": true}, - {"paramName":"t", "paramLongName":"token", "paramDescription": "token to grant access", "paramRequired": true}, - {"paramName":"o", "paramLongName":"outputAuthorsPath", "paramDescription": "the relative folder of the sequencial file to write the authors data", "paramRequired": true} -] \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_gen_authors/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_gen_authors/oozie_app/config-default.xml deleted file mode 100644 index a720e7592..000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_gen_authors/oozie_app/config-default.xml +++ /dev/null @@ -1,22 +0,0 @@ - - - jobTracker - hadoop-rm3.garr-pa1.d4science.org:8032 - - - nameNode - hdfs://hadoop-rm1.garr-pa1.d4science.org:8020 - - - queueName - default - - - oozie.use.system.libpath - true - - - oozie.action.sharelib.for.spark - spark2 - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_gen_authors/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_gen_authors/oozie_app/workflow.xml deleted file mode 100644 index 7ebc5f0a0..000000000 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_gen_authors/oozie_app/workflow.xml +++ /dev/null @@ -1,83 +0,0 @@ - - - - workingPath - the working dir base path - - - token - access token - - - sparkDriverMemory - memory for driver process - - - sparkExecutorMemory - memory for individual executor - - - sparkExecutorCores - number of cores used by single executor - - - outputPath - the working dir base path - - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - - - - - - - - - ${jobTracker} - ${nameNode} - yarn - cluster - Split_Lambda_File - eu.dnetlib.doiboost.orcid.SparkPartitionLambdaFile - dhp-doiboost-1.2.1-SNAPSHOT.jar - --num-executors 24 --conf spark.yarn.jars="hdfs://hadoop-rm1.garr-pa1.d4science.org:8020/user/oozie/share/lib/lib_20180405103059/spark2" --executor-memory=${sparkExecutorMemory} --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} - - -w${workingPath}/ - -oauthors/ - -t${token} - - - - - - - - ${jobTracker} - ${nameNode} - yarn - cluster - Gen_Orcid_Authors - eu.dnetlib.doiboost.orcid.SparkOrcidGenerateAuthors - dhp-doiboost-1.2.1-SNAPSHOT.jar - --num-executors 20 --conf spark.yarn.jars="hdfs://hadoop-rm1.garr-pa1.d4science.org:8020/user/oozie/share/lib/lib_20180405103059/spark2" --executor-memory=${sparkExecutorMemory} --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} - - -w${workingPath}/ - -oauthors/ - -t${token} - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_updates_download/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_updates_download/oozie_app/workflow.xml index a3daab116..5f728d35b 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_updates_download/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_updates_download/oozie_app/workflow.xml @@ -14,9 +14,63 @@ the shell command that downloads the lambda file from orcid containing last orcid update informations + + sparkExecutorNumber + 20 + + + sparkDriverMemory + 7G + memory for driver process + + + sparkExecutorMemory + 2G + memory for individual executor + + + sparkExecutorCores + 1 + number of cores used by single executor + + + spark2MaxExecutors + 20 + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + - - + + + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + @@ -26,6 +80,7 @@ + @@ -41,24 +96,77 @@ ${shell_cmd} - + - + ${jobTracker} ${nameNode} eu.dnetlib.doiboost.orcid.OrcidDownloader - -d${workingPathOrcid}/ + -w${workingPath}/ -n${nameNode} - -flast_modified.csv - -odownload/ + -flast_modified.csv.tar + -odownloads/ -t${token} + + + + yarn-cluster + cluster + GenLastModifiedSeq + eu.dnetlib.doiboost.orcid.SparkGenLastModifiedSeq + dhp-doiboost-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + + -w${workingPath}/ + -n${nameNode} + -flast_modified.csv.tar + -olast_modified.seq + -t- + + + + + + + + yarn-cluster + cluster + DownloadOrcidAuthors + eu.dnetlib.doiboost.orcid.SparkDownloadOrcidAuthors + dhp-doiboost-${projectVersion}.jar + + --num-executors=${sparkExecutorNumber} + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + + -w${workingPath}/ + -n${nameNode} + -flast_modified.seq + -odownloads/updated_authors + -t${token} + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/OrcidClientTest.java b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/OrcidClientTest.java index 774475626..d6ce99f1c 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/OrcidClientTest.java +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/OrcidClientTest.java @@ -5,17 +5,24 @@ import static org.junit.jupiter.api.Assertions.assertTrue; import java.io.*; import java.nio.file.Files; +import java.nio.file.Path; +import java.nio.file.Paths; +import java.nio.file.StandardOpenOption; import java.text.ParseException; import java.text.SimpleDateFormat; import java.util.Arrays; import java.util.Date; import java.util.List; +import org.apache.commons.compress.archivers.tar.TarArchiveEntry; +import org.apache.commons.compress.archivers.tar.TarArchiveInputStream; +import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream; import org.apache.commons.io.IOUtils; import org.apache.http.client.methods.CloseableHttpResponse; import org.apache.http.client.methods.HttpGet; import org.apache.http.impl.client.CloseableHttpClient; import org.apache.http.impl.client.HttpClients; +import org.apache.spark.sql.catalyst.expressions.objects.AssertNotNull; import org.junit.jupiter.api.Test; import eu.dnetlib.dhp.application.ArgumentApplicationParser; @@ -37,12 +44,49 @@ public class OrcidClientTest { // 'https://api.orcid.org/v3.0/0000-0001-7291-3210/record' @Test - public void downloadTest() throws Exception { - String record = testDownloadRecord("0000-0001-6163-2042"); - File f = new File("/tmp/downloaded_0000-0001-6163-2042.xml"); + private void multipleDownloadTest() throws Exception { + int toDownload = 1; + long start = System.currentTimeMillis(); + OrcidDownloader downloader = new OrcidDownloader(); + TarArchiveInputStream input = new TarArchiveInputStream( + new GzipCompressorInputStream(new FileInputStream("/tmp/last_modified.csv.tar"))); + TarArchiveEntry entry = input.getNextTarEntry(); + BufferedReader br = null; + StringBuilder sb = new StringBuilder(); + int rowNum = 0; + int entryNum = 0; + int modified = 0; + while (entry != null) { + br = new BufferedReader(new InputStreamReader(input)); // Read directly from tarInput + String line; + while ((line = br.readLine()) != null) { + String[] values = line.toString().split(","); + List recordInfo = Arrays.asList(values); + String orcidId = recordInfo.get(0); + if (downloader.isModified(orcidId, recordInfo.get(3))) { + downloadTest(orcidId); + modified++; + } + rowNum++; + if (modified > toDownload) { + break; + } + } + entryNum++; + entry = input.getNextTarEntry(); + } + long end = System.currentTimeMillis(); + logToFile("start test: " + new Date(start).toString()); + logToFile("end test: " + new Date(end).toString()); + } + + @Test + private void downloadTest(String orcid) throws Exception { + String record = testDownloadRecord(orcid); + String filename = "/tmp/downloaded_".concat(orcid).concat(".xml"); + File f = new File(filename); OutputStream outStream = new FileOutputStream(f); IOUtils.write(record.getBytes(), outStream); - System.out.println("saved to tmp"); } private String testDownloadRecord(String orcidId) throws Exception { @@ -50,7 +94,9 @@ public class OrcidClientTest { HttpGet httpGet = new HttpGet("https://api.orcid.org/v3.0/" + orcidId + "/record"); httpGet.addHeader("Accept", "application/vnd.orcid+xml"); httpGet.addHeader("Authorization", "Bearer 78fdb232-7105-4086-8570-e153f4198e3d"); + logToFile("start connection: " + new Date(System.currentTimeMillis()).toString()); CloseableHttpResponse response = client.execute(httpGet); + logToFile("end connection: " + new Date(System.currentTimeMillis()).toString()); if (response.getStatusLine().getStatusCode() != 200) { System.out .println("Downloading " + orcidId + " status code: " + response.getStatusLine().getStatusCode()); @@ -62,7 +108,7 @@ public class OrcidClientTest { return new String(""); } -// @Test + // @Test private void testLambdaFileParser() throws Exception { try (BufferedReader br = new BufferedReader( new InputStreamReader(this.getClass().getResourceAsStream("last_modified.csv")))) { @@ -108,7 +154,7 @@ public class OrcidClientTest { } } -// @Test + // @Test private void getRecordDatestamp() throws ParseException { Date toRetrieveDateDt = new SimpleDateFormat(DATE_FORMAT).parse(toRetrieveDate); Date toNotRetrieveDateDt = new SimpleDateFormat(DATE_FORMAT).parse(toNotRetrieveDate); @@ -126,7 +172,7 @@ public class OrcidClientTest { System.out.println(valueDt.toString()); } -// @Test + // @Test @Ignore private void testModifiedDate() throws ParseException { testDate(toRetrieveDate); @@ -134,14 +180,81 @@ public class OrcidClientTest { testDate(shortDate); } -// @Test - @Ignore - private void testReadBase64CompressedRecord() throws Exception { + @Test + public void testReadBase64CompressedRecord() throws Exception { final String base64CompressedRecord = IOUtils - .toString(getClass().getResourceAsStream("0000-0001-6645-509X.compressed.base64")); + .toString(getClass().getResourceAsStream("0000-0003-3028-6161.compressed.base64")); final String recordFromSeqFile = ArgumentApplicationParser.decompressValue(base64CompressedRecord); - System.out.println(recordFromSeqFile); - final String downloadedRecord = testDownloadRecord("0000-0001-6645-509X"); + logToFile("\n\ndownloaded \n\n" + recordFromSeqFile); + final String downloadedRecord = testDownloadRecord("0000-0003-3028-6161"); assertTrue(recordFromSeqFile.equals(downloadedRecord)); } + + @Test + private void lambdaFileReaderTest() throws Exception { + TarArchiveInputStream input = new TarArchiveInputStream( + new GzipCompressorInputStream(new FileInputStream("/develop/last_modified.csv.tar"))); + TarArchiveEntry entry = input.getNextTarEntry(); + BufferedReader br = null; + StringBuilder sb = new StringBuilder(); + int rowNum = 0; + int entryNum = 0; + while (entry != null) { + br = new BufferedReader(new InputStreamReader(input)); // Read directly from tarInput + String line; + while ((line = br.readLine()) != null) { + String[] values = line.toString().split(","); + List recordInfo = Arrays.asList(values); + assertTrue(recordInfo.size() == 4); + + rowNum++; + if (rowNum == 1) { + assertTrue(recordInfo.get(3).equals("last_modified")); + } else if (rowNum == 2) { + assertTrue(recordInfo.get(0).equals("0000-0002-0499-7333")); + } + } + entryNum++; + assertTrue(entryNum == 1); + entry = input.getNextTarEntry(); + } + } + + @Test + private void lambdaFileCounterTest() throws Exception { + final String lastUpdate = "2020-09-29 00:00:00"; + OrcidDownloader downloader = new OrcidDownloader(); + TarArchiveInputStream input = new TarArchiveInputStream( + new GzipCompressorInputStream(new FileInputStream("/tmp/last_modified.csv.tar"))); + TarArchiveEntry entry = input.getNextTarEntry(); + BufferedReader br = null; + StringBuilder sb = new StringBuilder(); + int rowNum = 0; + int entryNum = 0; + int modified = 0; + while (entry != null) { + br = new BufferedReader(new InputStreamReader(input)); // Read directly from tarInput + String line; + while ((line = br.readLine()) != null) { + String[] values = line.toString().split(","); + List recordInfo = Arrays.asList(values); + String orcidId = recordInfo.get(0); + if (downloader.isModified(orcidId, recordInfo.get(3))) { + modified++; + } + rowNum++; + } + entryNum++; + entry = input.getNextTarEntry(); + } + logToFile("rowNum: " + rowNum); + logToFile("modified: " + modified); + } + + private void logToFile(String log) + throws IOException { + log = log.concat("\n"); + Path path = Paths.get("/tmp/orcid_log.txt"); + Files.write(path, log.getBytes(), StandardOpenOption.APPEND); + } } diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/0000-0001-6645-509X.compressed.base64 b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/0000-0001-6645-509X.compressed.base64 deleted file mode 100644 index 1b088e061..000000000 --- a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/0000-0001-6645-509X.compressed.base64 +++ /dev/null @@ -1 +0,0 @@ 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\ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/0000-0003-3028-6161.compressed.base64 b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/0000-0003-3028-6161.compressed.base64 new file mode 100644 index 000000000..8dc3d32ad --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/0000-0003-3028-6161.compressed.base64 @@ -0,0 +1 @@ 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 \ No newline at end of file From 5c17e768b26789df1e8bf120eeebab93854a716e Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Mon, 23 Nov 2020 16:01:23 +0100 Subject: [PATCH 32/37] set wf configuration with spark.dynamicAllocation.maxExecutors 20 over 20 input partitions --- .../orcid/SparkDownloadOrcidAuthors.java | 39 +++++++++++++------ .../oozie_app/workflow.xml | 4 +- 2 files changed, 29 insertions(+), 14 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkDownloadOrcidAuthors.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkDownloadOrcidAuthors.java index 850a654d4..68f44541a 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkDownloadOrcidAuthors.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkDownloadOrcidAuthors.java @@ -65,9 +65,14 @@ public class SparkDownloadOrcidAuthors { spark -> { JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - LongAccumulator parsedRecordsAcc = spark.sparkContext().longAccumulator("parsedRecords"); - LongAccumulator modifiedRecordsAcc = spark.sparkContext().longAccumulator("modifiedRecords"); - LongAccumulator downloadedRecordsAcc = spark.sparkContext().longAccumulator("downloadedRecords"); + LongAccumulator parsedRecordsAcc = spark.sparkContext().longAccumulator("parsed_records"); + LongAccumulator modifiedRecordsAcc = spark.sparkContext().longAccumulator("to_download_records"); + LongAccumulator downloadedRecordsAcc = spark.sparkContext().longAccumulator("downloaded_records"); + LongAccumulator errorHTTP403Acc = spark.sparkContext().longAccumulator("error_HTTP_403"); + LongAccumulator errorHTTP409Acc = spark.sparkContext().longAccumulator("error_HTTP_409"); + LongAccumulator errorHTTP503Acc = spark.sparkContext().longAccumulator("error_HTTP_503"); + LongAccumulator errorHTTP525Acc = spark.sparkContext().longAccumulator("error_HTTP_525"); + LongAccumulator errorHTTPGenericAcc = spark.sparkContext().longAccumulator("error_HTTP_Generic"); logger.info("Retrieving data from lamda sequence file"); JavaPairRDD lamdaFileRDD = sc @@ -99,6 +104,18 @@ public class SparkDownloadOrcidAuthors { int statusCode = response.getStatusLine().getStatusCode(); downloaded.setStatusCode(statusCode); if (statusCode != 200) { + switch (statusCode) { + case 403: + errorHTTP403Acc.add(1); + case 409: + errorHTTP409Acc.add(1); + case 503: + errorHTTP503Acc.add(1); + case 525: + errorHTTP525Acc.add(1); + default: + errorHTTPGenericAcc.add(1); + } logger .info( "Downloading " + orcidId + " status code: " @@ -106,10 +123,6 @@ public class SparkDownloadOrcidAuthors { return downloaded.toTuple2(); } downloadedRecordsAcc.add(1); - long currentDownloaded = downloadedRecordsAcc.value(); - if ((currentDownloaded % 10000) == 0) { - logger.info("Current downloaded: " + currentDownloaded); - } downloaded .setCompressedData( ArgumentApplicationParser @@ -125,14 +138,11 @@ public class SparkDownloadOrcidAuthors { sc.hadoopConfiguration().set("mapreduce.output.fileoutputformat.compress", "true"); logger.info("Start execution ..."); -// List> sampleList = lamdaFileRDD.take(500); -// JavaRDD> sampleRDD = sc.parallelize(sampleList); -// sampleRDD - JavaPairRDD authorsModifiedRDD = lamdaFileRDD - .filter(isModifiedAfterFilter); + JavaPairRDD authorsModifiedRDD = lamdaFileRDD.filter(isModifiedAfterFilter); logger.info("Authors modified count: " + authorsModifiedRDD.count()); logger.info("Start downloading ..."); authorsModifiedRDD + .repartition(20) .map(downloadRecordFunction) .mapToPair(t -> new Tuple2(new Text(t._1()), new Text(t._2()))) .saveAsNewAPIHadoopFile( @@ -144,6 +154,11 @@ public class SparkDownloadOrcidAuthors { logger.info("parsedRecordsAcc: " + parsedRecordsAcc.value().toString()); logger.info("modifiedRecordsAcc: " + modifiedRecordsAcc.value().toString()); logger.info("downloadedRecordsAcc: " + downloadedRecordsAcc.value().toString()); + logger.info("errorHTTP403Acc: " + errorHTTP403Acc.value().toString()); + logger.info("errorHTTP409Acc: " + errorHTTP409Acc.value().toString()); + logger.info("errorHTTP503Acc: " + errorHTTP503Acc.value().toString()); + logger.info("errorHTTP525Acc: " + errorHTTP525Acc.value().toString()); + logger.info("errorHTTPGenericAcc: " + errorHTTPGenericAcc.value().toString()); }); } diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_updates_download/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_updates_download/oozie_app/workflow.xml index 5f728d35b..1c2a7b588 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_updates_download/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_updates_download/oozie_app/workflow.xml @@ -149,9 +149,9 @@ eu.dnetlib.doiboost.orcid.SparkDownloadOrcidAuthors dhp-doiboost-${projectVersion}.jar - --num-executors=${sparkExecutorNumber} + --conf spark.dynamicAllocation.enabled=true + --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors} --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.extraListeners=${spark2ExtraListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} From 99a086f0c68f17489e4b39e32e9fbbb24418b21d Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Tue, 24 Nov 2020 17:49:32 +0100 Subject: [PATCH 33/37] max concurrent executors set to 10, according to ORCID Director of Technology mail request --- .../orcid/SparkDownloadOrcidAuthors.java | 17 +++++-- .../oozie_app/workflow.xml | 6 +-- .../doiboost/orcid/OrcidClientTest.java | 47 +++++++++++++++++-- 3 files changed, 57 insertions(+), 13 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkDownloadOrcidAuthors.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkDownloadOrcidAuthors.java index 68f44541a..598835a00 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkDownloadOrcidAuthors.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkDownloadOrcidAuthors.java @@ -100,7 +100,13 @@ public class SparkDownloadOrcidAuthors { HttpGet httpGet = new HttpGet("https://api.orcid.org/v3.0/" + orcidId + "/record"); httpGet.addHeader("Accept", "application/vnd.orcid+xml"); httpGet.addHeader("Authorization", String.format("Bearer %s", token)); + long startReq = System.currentTimeMillis(); CloseableHttpResponse response = client.execute(httpGet); + long endReq = System.currentTimeMillis(); + long reqTime = endReq - startReq; + if (reqTime < 1000) { + Thread.sleep(1000 - reqTime); + } int statusCode = response.getStatusLine().getStatusCode(); downloaded.setStatusCode(statusCode); if (statusCode != 200) { @@ -111,15 +117,16 @@ public class SparkDownloadOrcidAuthors { errorHTTP409Acc.add(1); case 503: errorHTTP503Acc.add(1); + throw new RuntimeException("Orcid request rate limit reached (HTTP 503)"); case 525: errorHTTP525Acc.add(1); default: errorHTTPGenericAcc.add(1); + logger + .info( + "Downloading " + orcidId + " status code: " + + response.getStatusLine().getStatusCode()); } - logger - .info( - "Downloading " + orcidId + " status code: " - + response.getStatusLine().getStatusCode()); return downloaded.toTuple2(); } downloadedRecordsAcc.add(1); @@ -142,7 +149,7 @@ public class SparkDownloadOrcidAuthors { logger.info("Authors modified count: " + authorsModifiedRDD.count()); logger.info("Start downloading ..."); authorsModifiedRDD - .repartition(20) + .repartition(10) .map(downloadRecordFunction) .mapToPair(t -> new Tuple2(new Text(t._1()), new Text(t._2()))) .saveAsNewAPIHadoopFile( diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_updates_download/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_updates_download/oozie_app/workflow.xml index 1c2a7b588..b9383558c 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_updates_download/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_updates_download/oozie_app/workflow.xml @@ -14,10 +14,6 @@ the shell command that downloads the lambda file from orcid containing last orcid update informations - - sparkExecutorNumber - 20 - sparkDriverMemory 7G @@ -35,7 +31,7 @@ spark2MaxExecutors - 20 + 10 oozieActionShareLibForSpark2 diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/OrcidClientTest.java b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/OrcidClientTest.java index d6ce99f1c..66a7badb7 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/OrcidClientTest.java +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/OrcidClientTest.java @@ -10,6 +10,9 @@ import java.nio.file.Paths; import java.nio.file.StandardOpenOption; import java.text.ParseException; import java.text.SimpleDateFormat; +import java.time.Duration; +import java.time.LocalDateTime; +import java.time.temporal.TemporalUnit; import java.util.Arrays; import java.util.Date; import java.util.List; @@ -24,6 +27,7 @@ import org.apache.http.impl.client.CloseableHttpClient; import org.apache.http.impl.client.HttpClients; import org.apache.spark.sql.catalyst.expressions.objects.AssertNotNull; import org.junit.jupiter.api.Test; +import org.mortbay.log.Log; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import jdk.nashorn.internal.ir.annotations.Ignore; @@ -45,7 +49,7 @@ public class OrcidClientTest { @Test private void multipleDownloadTest() throws Exception { - int toDownload = 1; + int toDownload = 10; long start = System.currentTimeMillis(); OrcidDownloader downloader = new OrcidDownloader(); TarArchiveInputStream input = new TarArchiveInputStream( @@ -64,7 +68,7 @@ public class OrcidClientTest { List recordInfo = Arrays.asList(values); String orcidId = recordInfo.get(0); if (downloader.isModified(orcidId, recordInfo.get(3))) { - downloadTest(orcidId); + slowedDownDownload(orcidId); modified++; } rowNum++; @@ -181,7 +185,7 @@ public class OrcidClientTest { } @Test - public void testReadBase64CompressedRecord() throws Exception { + private void testReadBase64CompressedRecord() throws Exception { final String base64CompressedRecord = IOUtils .toString(getClass().getResourceAsStream("0000-0003-3028-6161.compressed.base64")); final String recordFromSeqFile = ArgumentApplicationParser.decompressValue(base64CompressedRecord); @@ -257,4 +261,41 @@ public class OrcidClientTest { Path path = Paths.get("/tmp/orcid_log.txt"); Files.write(path, log.getBytes(), StandardOpenOption.APPEND); } + + @Test + private void slowedDownDownloadTest() throws Exception { + String orcid = "0000-0001-5496-1243"; + String record = slowedDownDownload(orcid); + String filename = "/tmp/downloaded_".concat(orcid).concat(".xml"); + File f = new File(filename); + OutputStream outStream = new FileOutputStream(f); + IOUtils.write(record.getBytes(), outStream); + } + + private String slowedDownDownload(String orcidId) throws Exception { + try (CloseableHttpClient client = HttpClients.createDefault()) { + HttpGet httpGet = new HttpGet("https://api.orcid.org/v3.0/" + orcidId + "/record"); + httpGet.addHeader("Accept", "application/vnd.orcid+xml"); + httpGet.addHeader("Authorization", "Bearer 78fdb232-7105-4086-8570-e153f4198e3d"); + long start = System.currentTimeMillis(); + CloseableHttpResponse response = client.execute(httpGet); + long endReq = System.currentTimeMillis(); + long reqSessionDuration = endReq - start; + logToFile("req time (millisec): " + reqSessionDuration); + if (reqSessionDuration < 1000) { + logToFile("wait ...."); + Thread.sleep(1000 - reqSessionDuration); + } + long end = System.currentTimeMillis(); + long total = end - start; + logToFile("total time (millisec): " + total); + if (response.getStatusLine().getStatusCode() != 200) { + logToFile("Downloading " + orcidId + " status code: " + response.getStatusLine().getStatusCode()); + } + return IOUtils.toString(response.getEntity().getContent()); + } catch (Throwable e) { + e.printStackTrace(); + } + return new String(""); + } } From 40c4559e923c5e2f0124477dc8deb8bfe2ef22d5 Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Mon, 30 Nov 2020 14:19:22 +0100 Subject: [PATCH 34/37] added datainfo on authors pid with "sysimport:crosswalk:entityregistry", --- .../doiboost/orcidnodoi/oaf/PublicationToOaf.java | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java index ece59c3f1..18fecc6c2 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java @@ -144,7 +144,7 @@ public class PublicationToOaf implements Serializable { publication.setLastupdatetimestamp(new Date().getTime()); - publication.setDateofcollection("2019-10-22"); + publication.setDateofcollection("2020-10-14"); publication.setDateoftransformation(DumpToActionsUtility.now_ISO8601()); // Adding external ids @@ -526,6 +526,18 @@ public class PublicationToOaf implements Serializable { q.setSchemeid(ModelConstants.DNET_PID_TYPES); q.setSchemename(ModelConstants.DNET_PID_TYPES); sp.setQualifier(q); + final DataInfo dataInfo = new DataInfo(); + dataInfo.setDeletedbyinference(false); + dataInfo.setInferred(false); + dataInfo.setTrust("0.9"); + dataInfo + .setProvenanceaction( + mapQualifier( + "sysimport:crosswalk:entityregistry", + "Harvested", + "dnet:provenanceActions", + "dnet:provenanceActions")); + sp.setDataInfo(dataInfo); return sp; } } From a417624670aa1b1908c8e3a40ee457bf45241112 Mon Sep 17 00:00:00 2001 From: Alessia Bardi Date: Wed, 2 Dec 2020 10:15:26 +0100 Subject: [PATCH 35/37] tests for raw graph mapping --- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 17 +++ .../dnetlib/dhp/oa/graph/raw/oaf-bologna.xml | 115 ++++++++++++++++++ .../eu/dnetlib/dhp/oa/graph/raw/textgrid.xml | 24 ++-- 3 files changed, 145 insertions(+), 11 deletions(-) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf-bologna.xml diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index 2d4cccdfb..46cb1a535 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -358,6 +358,23 @@ public class MappersTest { System.out.println(p.getTitle().get(0).getValue()); } + @Test + void testBologna() throws IOException { + final String xml = IOUtils.toString(getClass().getResourceAsStream("oaf-bologna.xml")); + final List list = new OafToOafMapper(vocs, false).processMdRecord(xml); + + System.out.println("***************"); + System.out.println(new ObjectMapper().writeValueAsString(list)); + System.out.println("***************"); + + final Publication p = (Publication) list.get(0); + assertValidId(p.getId()); + assertValidId(p.getCollectedfrom().get(0).getKey()); + System.out.println(p.getTitle().get(0).getValue()); + assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue())); + System.out.println(p.getTitle().get(0).getValue()); + } + private void assertValidId(final String id) { assertEquals(49, id.length()); assertEquals('|', id.charAt(2)); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf-bologna.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf-bologna.xml new file mode 100644 index 000000000..296a2fe94 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf-bologna.xml @@ -0,0 +1,115 @@ + + +
+ od_________3::4f7038e665fdd3800297735f087a530c + oai:amsacta.unibo.it:6382 + + + + + + 2020-05-21T05:26:15.93Z + 2020-08-01T11:06:26.977Z + od_________3 +
+ + CONSOLE Project - Deliverable 5.1 - "Guidelines for Community of Practice (CoP) + management at local level" + Blanco-Velázquez, Francisco José + Runge, Tania + Anaya-Romero, María + 2020-05-11 + The Community of Practice (CoP) is foreseen to play a key role in boosting + innovation in the effective and long-lasting delivery of agri-environmental-climate + public goods (AECPGs). The CONSOLE CoP will be organized around practitioners + experienced in the provision of AECPGs and those interested in it and will be nourished + throughout the project lifetime. In line with the definition of Wenger1 the CoP is + defined as a group of people (the community) who share a common interest and who learn + how to perform better through regular interaction and exchange of experiences. The idea + is to set up a pan-European CoP with national and/or local (regional) sub-groups managed + by the CONSOLE partners with the aim of developing improved and novel contract solutions + in collaboration with its members. This document sets out: (a) the purpose and + objectives of the CoP in CONSOLE, (b) the setting up and management of the CoP at + European, national and local level, (c) the process for motivating individuals to + participate. The CONSOLE CoP is intended to facilitate knowledge exchange and mutual + learning, mainly through virtual contacts. Participation in the CoP is based on sharing + and reciprocity principle. A core objective of these guidelines is to ensure a sound + management and facilitation of the CoP by all CONSOLE partners in view of optimizing the + input from CoP members in the project activities. Members within a national or local + CONSOLE CoP are: 1) CONSOLE partners; 2) practitioners, mainly farmers and foresters, + who test and implement practically the contractual models, and 3) experts, that may have + punctual interventions in the CoP. A vibrant CoP with active involvement of its members + is crucial for the assessment and testing of improved and novel voluntary measures for + the delivery of AECPGs. For each of the CONSOLE countries one national contact person is + nominated to take over the role as national focal point for the CoP activities in his + country and to serve as facilitator of the CoP. These facilitators are responsible to + ensure participation along the various project tasks foreseen within several WPs and to + overcome potential language barriers. The national contact person may be supported by + other CONSOLE partners from his country for local activities. At local level the CoP + benefits from existing contacts of CONSOLE partners to practitioners, including the + experts interviewed for the case studies analysis within WP2. The forming/development of + a CoP requires promoting exchanges taking on board the interests and needs of the actors + involved and to animate them to share their expertise. Collaborative learning within the + CoP supported by dedicated training activities will be crucial to ensure the intended + major transition towards smarter AECPGs-related practices in Europe. These guidelines + focus on the identification of the various tasks where CoP participation is foreseen at + local (regional) level and to provide support for the identification of potential + members. In the deliverable D5.2 “Guidelines for testing the solutions catalogue by CoP + and partners” further details about the involvement of the CoP will be + provided. + application/pdf + http://amsacta.unibo.it/6382/ + eng + info:eu-repo/grantAgreement/EC/H2020/817949/EU/CONtract SOLutions for Effective + and lasting delivery of agri-environmental-climate public goods by EU agriculture and + forestry/CONSOLE + info:eu-repo/semantics/altIdentifier/doi/10.6092/unibo/amsacta/6382 + info:eu-repo/semantics/reference/url/https://console-project.eu/ + Blanco-Velázquez, Francisco José ; Runge, Tania ; Anaya-Romero, María (2020) + CONSOLE Project - Deliverable 5.1 - "Guidelines for Community of Practice (CoP) + management at local level". p. 21. DOI 10.6092/unibo/amsacta/6382 + <http://doi.org/10.6092/unibo/amsacta/6382>. + AGR/01 Economia ed estimo rurale + SECS-S/01 Statistica + info:eu-repo/semantics/book + info:eu-repo/semantics/publishedVersion + 0002 + 2020-05-11 + corda__h2020::817949 + + opendoar____::3 + OPEN + + + 10.6092/unibo/amsacta/6382 + + + + + + http%3A%2F%2Famsacta.unibo.it%2Fcgi%2Fopenaire3 + oai:amsacta.unibo.it:6382 + 2020-05-13T09:27:00Z + http://www.openarchives.org/OAI/2.0/oai_dc/ + + + + false + false + 0.9 + + + + + diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/textgrid.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/textgrid.xml index d6970ab3e..eddbc1ec4 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/textgrid.xml +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/textgrid.xml @@ -1,23 +1,24 @@ - + + xmlns:dri="http://www.driver-repository.eu/namespace/dri" + xmlns:prov="http://www.openarchives.org/OAI/2.0/provenance" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> r3f52792889d::000051aa1f61d77d2c0b340091f8024e textgrid:q9cv.0 2020-11-17T09:34:11.128+01:00 r3f52792889d textgrid:q9cv.0 2012-01-21T13:35:20Z - 2020-11-17T09:46:21.551+01:00 + 2020-11-17T19:08:56.703+01:00 + xmlns:dri="http://www.driver-repository.eu/namespace/dri" + xmlns:prov="http://www.openarchives.org/OAI/2.0/provenance" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> hdl:11858/00-1734-0000-0003-7664-F @@ -46,8 +47,8 @@ 2012-01-21T13:35:20Z - - textgrid:q9cv.0 + + textgrid:q9cv.0 http://hdl.handle.net/hdl:11858/00-1734-0000-0003-7664-F @@ -83,7 +84,7 @@ hdl:11858/00-1734-0000-0003-7664-F 0021 0002 - 2012-01-01 + 2012-01-21 OPEN http://creativecommons.org/licenses/by/3.0/de/legalcode und @@ -91,7 +92,8 @@ + xmlns:dri="http://www.driver-repository.eu/namespace/dri" + xmlns:prov="http://www.openarchives.org/OAI/2.0/provenance" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> https%3A%2F%2Fdev.textgridlab.org%2F1.0%2Ftgoaipmh%2Foai From 2d15667b4a49b8de59683650614b5027df547da6 Mon Sep 17 00:00:00 2001 From: Alessia Bardi Date: Wed, 2 Dec 2020 10:16:26 +0100 Subject: [PATCH 36/37] testing XML generation from json object (case AMS ACTA) --- .../oa/provision/XmlRecordFactoryTest.java | 39 +- .../dnetlib/dhp/oa/provision/oaf-bologna.json | 379 ++++++++++++++++++ 2 files changed, 416 insertions(+), 2 deletions(-) create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/oaf-bologna.json diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java index 992ab26e8..619df7716 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java @@ -5,8 +5,15 @@ import static org.junit.jupiter.api.Assertions.*; import java.io.IOException; import java.io.StringReader; +import java.util.List; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.OafEntity; +import eu.dnetlib.dhp.schema.oaf.OafMapperUtils; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; import org.dom4j.Document; import org.dom4j.DocumentException; import org.dom4j.io.SAXReader; @@ -19,9 +26,10 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.oa.provision.model.JoinedEntity; import eu.dnetlib.dhp.oa.provision.utils.ContextMapper; import eu.dnetlib.dhp.oa.provision.utils.XmlRecordFactory; +import org.mockito.Mock; //TODO to enable it we need to update the joined_entity.json test file -@Disabled +//@Disabled public class XmlRecordFactoryTest { private static final String otherDsTypeId = "scholarcomminfra,infospace,pubsrepository::mock,entityregistry,entityregistry::projects,entityregistry::repositories,websource"; @@ -35,10 +43,35 @@ public class XmlRecordFactoryTest { JoinedEntity je = new ObjectMapper().readValue(json, JoinedEntity.class); assertNotNull(je); + Document doc = buildXml(je); + ////TODO specific test assertion on doc + } + + + + @Test + void testBologna() throws IOException, DocumentException { + final String json = IOUtils.toString(getClass().getResourceAsStream("oaf-bologna.json")); + Publication oaf = new ObjectMapper().readValue(json, Publication.class); + assertNotNull(oaf); + JoinedEntity je = new JoinedEntity(); + je.setEntity(oaf); + assertNotNull(je); + + Document doc = buildXml(je); + //TODO specific test assertion on doc + + System.out.println(doc.asXML()); + + + + } + + private Document buildXml(JoinedEntity je) throws DocumentException { ContextMapper contextMapper = new ContextMapper(); XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false, XmlConverterJob.schemaLocation, - otherDsTypeId); + otherDsTypeId); String xml = xmlRecordFactory.build(je); @@ -49,5 +82,7 @@ public class XmlRecordFactoryTest { assertNotNull(doc); // TODO add assertions based of values extracted from the XML record + + return doc; } } diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/oaf-bologna.json b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/oaf-bologna.json new file mode 100644 index 000000000..3bb7d5b68 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/oaf-bologna.json @@ -0,0 +1,379 @@ + + { + "collectedfrom": [ + { + "key": "10|opendoar____::eccbc87e4b5ce2fe28308fd9f2a7baf3", + "value": "AMS Acta", + "dataInfo": null + } + ], + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.9", + "inferenceprovenance": "", + "provenanceaction": { + "classid": "sysimport:crosswalk:repository", + "classname": "sysimport:crosswalk:repository", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + }, + "lastupdatetimestamp": 1606898557407, + "id": "50|od_________3::4f7038e665fdd3800297735f087a530c", + "originalId": [ + "oai:amsacta.unibo.it:6382" + ], + "pid": [ + { + "value": "10.6092/unibo/amsacta/6382", + "qualifier": { + "classid": "doi", + "classname": "doi", + "schemeid": "dnet:pid_types", + "schemename": "dnet:pid_types" + }, + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.9", + "inferenceprovenance": "", + "provenanceaction": { + "classid": "sysimport:crosswalk:repository", + "classname": "sysimport:crosswalk:repository", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + } + ], + "dateofcollection": "", + "dateoftransformation": "2020-08-01T11:06:26.977Z", + "extraInfo": [], + "oaiprovenance": { + "originDescription": { + "harvestDate": "2020-05-21T05:26:15.93Z", + "altered": true, + "baseURL": "http%3A%2F%2Famsacta.unibo.it%2Fcgi%2Fopenaire3", + "identifier": "oai:amsacta.unibo.it:6382", + "datestamp": "2020-05-13T09:27:00Z", + "metadataNamespace": "http://www.openarchives.org/OAI/2.0/oai_dc/" + } + }, + "measures": null, + "author": [ + { + "fullname": "Blanco-Velázquez, Francisco José", + "name": "Francisco José", + "surname": "Blanco-Velázquez", + "rank": 1, + "pid": [], + "affiliation": null + }, + { + "fullname": "Runge, Tania", + "name": "Tania", + "surname": "Runge", + "rank": 2, + "pid": [], + "affiliation": null + }, + { + "fullname": "Anaya-Romero, María", + "name": "María", + "surname": "Anaya-Romero", + "rank": 3, + "pid": [], + "affiliation": null + } + ], + "resulttype": { + "classid": "publication", + "classname": "publication", + "schemeid": "dnet:result_typologies", + "schemename": "dnet:result_typologies" + }, + "language": { + "classid": "eng", + "classname": "English", + "schemeid": "dnet:languages", + "schemename": "dnet:languages" + }, + "country": [], + "subject": [ + { + "value": "AGR/01 Economia ed estimo rurale", + "qualifier": { + "classid": "keyword", + "classname": "keyword", + "schemeid": "dnet:result_subject", + "schemename": "dnet:result_subject" + }, + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.9", + "inferenceprovenance": "", + "provenanceaction": { + "classid": "sysimport:crosswalk:repository", + "classname": "sysimport:crosswalk:repository", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + { + "value": "SECS-S/01 Statistica", + "qualifier": { + "classid": "keyword", + "classname": "keyword", + "schemeid": "dnet:result_subject", + "schemename": "dnet:result_subject" + }, + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.9", + "inferenceprovenance": "", + "provenanceaction": { + "classid": "sysimport:crosswalk:repository", + "classname": "sysimport:crosswalk:repository", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + } + ], + "title": [ + { + "value": "CONSOLE Project - Deliverable 5.1 - \"Guidelines for Community of Practice (CoP)\n management at local level\"", + "qualifier": { + "classid": "main title", + "classname": "main title", + "schemeid": "dnet:dataCite_title", + "schemename": "dnet:dataCite_title" + }, + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.9", + "inferenceprovenance": "", + "provenanceaction": { + "classid": "sysimport:crosswalk:repository", + "classname": "sysimport:crosswalk:repository", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + } + ], + "relevantdate": [], + "description": [ + { + "value": "The Community of Practice (CoP) is foreseen to play a key role in boosting\n innovation in the effective and long-lasting delivery of agri-environmental-climate\n public goods (AECPGs). The CONSOLE CoP will be organized around practitioners\n experienced in the provision of AECPGs and those interested in it and will be nourished\n throughout the project lifetime. In line with the definition of Wenger1 the CoP is\n defined as a group of people (the community) who share a common interest and who learn\n how to perform better through regular interaction and exchange of experiences. The idea\n is to set up a pan-European CoP with national and/or local (regional) sub-groups managed\n by the CONSOLE partners with the aim of developing improved and novel contract solutions\n in collaboration with its members. This document sets out: (a) the purpose and\n objectives of the CoP in CONSOLE, (b) the setting up and management of the CoP at\n European, national and local level, (c) the process for motivating individuals to\n participate. The CONSOLE CoP is intended to facilitate knowledge exchange and mutual\n learning, mainly through virtual contacts. Participation in the CoP is based on sharing\n and reciprocity principle. A core objective of these guidelines is to ensure a sound\n management and facilitation of the CoP by all CONSOLE partners in view of optimizing the\n input from CoP members in the project activities. Members within a national or local\n CONSOLE CoP are: 1) CONSOLE partners; 2) practitioners, mainly farmers and foresters,\n who test and implement practically the contractual models, and 3) experts, that may have\n punctual interventions in the CoP. A vibrant CoP with active involvement of its members\n is crucial for the assessment and testing of improved and novel voluntary measures for\n the delivery of AECPGs. For each of the CONSOLE countries one national contact person is\n nominated to take over the role as national focal point for the CoP activities in his\n country and to serve as facilitator of the CoP. These facilitators are responsible to\n ensure participation along the various project tasks foreseen within several WPs and to\n overcome potential language barriers. The national contact person may be supported by\n other CONSOLE partners from his country for local activities. At local level the CoP\n benefits from existing contacts of CONSOLE partners to practitioners, including the\n experts interviewed for the case studies analysis within WP2. The forming/development of\n a CoP requires promoting exchanges taking on board the interests and needs of the actors\n involved and to animate them to share their expertise. Collaborative learning within the\n CoP supported by dedicated training activities will be crucial to ensure the intended\n major transition towards smarter AECPGs-related practices in Europe. These guidelines\n focus on the identification of the various tasks where CoP participation is foreseen at\n local (regional) level and to provide support for the identification of potential\n members. In the deliverable D5.2 “Guidelines for testing the solutions catalogue by CoP\n and partners” further details about the involvement of the CoP will be\n provided.", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.9", + "inferenceprovenance": "", + "provenanceaction": { + "classid": "sysimport:crosswalk:repository", + "classname": "sysimport:crosswalk:repository", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + } + ], + "dateofacceptance": { + "value": "2020-05-11", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.9", + "inferenceprovenance": "", + "provenanceaction": { + "classid": "sysimport:crosswalk:repository", + "classname": "sysimport:crosswalk:repository", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + "publisher": null, + "embargoenddate": null, + "source": [ + { + "value": "Blanco-Velázquez, Francisco José ; Runge, Tania ; Anaya-Romero, María (2020)\n CONSOLE Project - Deliverable 5.1 - \"Guidelines for Community of Practice (CoP)\n management at local level\". p. 21. DOI 10.6092/unibo/amsacta/6382\n .", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.9", + "inferenceprovenance": "", + "provenanceaction": { + "classid": "sysimport:crosswalk:repository", + "classname": "sysimport:crosswalk:repository", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + } + ], + "fulltext": [], + "format": [ + { + "value": "application/pdf", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.9", + "inferenceprovenance": "", + "provenanceaction": { + "classid": "sysimport:crosswalk:repository", + "classname": "sysimport:crosswalk:repository", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + } + ], + "contributor": [], + "resourcetype": null, + "coverage": [], + "bestaccessright": { + "classid": "OPEN", + "classname": "Open Access", + "schemeid": "dnet:access_modes", + "schemename": "dnet:access_modes" + }, + "context": [], + "externalReference": [], + "instance": [ + { + "license": null, + "accessright": { + "classid": "OPEN", + "classname": "Open Access", + "schemeid": "dnet:access_modes", + "schemename": "dnet:access_modes" + }, + "instancetype": { + "classid": "0002", + "classname": "Book", + "schemeid": "dnet:publication_resource", + "schemename": "dnet:publication_resource" + }, + "hostedby": { + "key": "10|opendoar____::eccbc87e4b5ce2fe28308fd9f2a7baf3", + "value": "AMS Acta", + "dataInfo": null + }, + "url": [ + "http://amsacta.unibo.it/6382/" + ], + "distributionlocation": "", + "collectedfrom": { + "key": "10|opendoar____::eccbc87e4b5ce2fe28308fd9f2a7baf3", + "value": "AMS Acta", + "dataInfo": null + }, + "dateofacceptance": { + "value": "2020-05-11", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.9", + "inferenceprovenance": "", + "provenanceaction": { + "classid": "sysimport:crosswalk:repository", + "classname": "sysimport:crosswalk:repository", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + "processingchargeamount": null, + "processingchargecurrency": null, + "refereed": { + "classid": "UNKNOWN", + "classname": "Unknown", + "schemeid": "dnet:review_levels", + "schemename": "dnet:review_levels" + } + } + ], + "journal": null + }, + { + "collectedfrom": [ + { + "key": "10|opendoar____::eccbc87e4b5ce2fe28308fd9f2a7baf3", + "value": "AMS Acta", + "dataInfo": null + } + ], + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.9", + "inferenceprovenance": "", + "provenanceaction": { + "classid": "sysimport:crosswalk:repository", + "classname": "sysimport:crosswalk:repository", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + }, + "lastupdatetimestamp": 1606898557407, + "relType": "resultProject", + "subRelType": "outcome", + "relClass": "isProducedBy", + "source": "50|od_________3::4f7038e665fdd3800297735f087a530c", + "target": "40|corda__h2020::79a0e16c122c9a18eb60e4a5e64b620d", + "validated": null, + "validationDate": null, + "properties": [] + }, + { + "collectedfrom": [ + { + "key": "10|opendoar____::eccbc87e4b5ce2fe28308fd9f2a7baf3", + "value": "AMS Acta", + "dataInfo": null + } + ], + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.9", + "inferenceprovenance": "", + "provenanceaction": { + "classid": "sysimport:crosswalk:repository", + "classname": "sysimport:crosswalk:repository", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + }, + "lastupdatetimestamp": 1606898557407, + "relType": "resultProject", + "subRelType": "outcome", + "relClass": "produces", + "source": "40|corda__h2020::79a0e16c122c9a18eb60e4a5e64b620d", + "target": "50|od_________3::4f7038e665fdd3800297735f087a530c", + "validated": null, + "validationDate": null, + "properties": [] + } + From 57f448b7a423030f7d745e80a6fc7100ed480e57 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 2 Dec 2020 10:44:05 +0100 Subject: [PATCH 37/37] graph cleaning workflow separate orcid_pending from orcid, depending on the author pid provenance --- .../dhp/schema/common/ModelConstants.java | 3 +++ .../dhp/oa/graph/clean/CleaningFunctions.java | 25 ++++++++++++++++++- .../eu/dnetlib/dhp/oa/graph/clean/result.json | 22 ++++++++++++++++ .../eu/dnetlib/dhp/oa/graph/clean/terms.txt | 1 + 4 files changed, 50 insertions(+), 1 deletion(-) diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java index d759f0d55..0b4d29c8e 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java @@ -7,6 +7,9 @@ import eu.dnetlib.dhp.schema.oaf.Qualifier; public class ModelConstants { + public static final String ORCID = "orcid"; + public static final String ORCID_PENDING = "orcid_pending"; + public static final String DNET_SUBJECT_TYPOLOGIES = "dnet:subject_classification_typologies"; public static final String DNET_RESULT_TYPOLOGIES = "dnet:result_typologies"; public static final String DNET_PUBLICATION_RESOURCE = "dnet:publication_resource"; diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java index 5155d0242..945f717bb 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java @@ -189,6 +189,14 @@ public class CleaningFunctions { author.setRank(i++); } } + + final Set collectedFrom = Optional + .ofNullable(r.getCollectedfrom()) + .map(c -> c.stream() + .map(KeyValue::getKey) + .collect(Collectors.toCollection(HashSet::new))) + .orElse(new HashSet<>()); + for (Author a : r.getAuthor()) { if (Objects.isNull(a.getPid())) { a.setPid(Lists.newArrayList()); @@ -201,13 +209,28 @@ public class CleaningFunctions { .filter(p -> Objects.nonNull(p.getQualifier())) .filter(p -> StringUtils.isNotBlank(p.getValue())) .map(p -> { + // hack to distinguish orcid from orcid_pending + String pidProvenance = Optional + .ofNullable(p.getDataInfo()) + .map(d -> Optional + .ofNullable(d.getProvenanceaction()) + .map(Qualifier::getClassid) + .orElse("")) + .orElse(""); + if (pidProvenance.equals(ModelConstants.SYSIMPORT_CROSSWALK_ENTITYREGISTRY)) { + p.getQualifier().setClassid(ModelConstants.ORCID); + } else { + p.getQualifier().setClassid(ModelConstants.ORCID_PENDING); + } p.setValue(p.getValue().trim().replaceAll(ORCID_PREFIX_REGEX, "")); return p; }) .collect( Collectors .toMap( - StructuredProperty::getValue, Function.identity(), (p1, p2) -> p1, + p -> p.getQualifier().getClassid() + p.getValue(), + Function.identity(), + (p1, p2) -> p1, LinkedHashMap::new)) .values() .stream() diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json index 5c903cd0e..e746d236e 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json @@ -49,6 +49,28 @@ "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, diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt index 93cc00eca..67c070d1d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt @@ -1031,6 +1031,7 @@ dnet:pid_types @=@ dnet:pid_types @=@ jprn @=@ JPRN Identifier dnet:pid_types @=@ dnet:pid_types @=@ mag_id @=@ Microsoft Academic Graph Identifier dnet:pid_types @=@ dnet:pid_types @=@ oai @=@ Open Archives Initiative dnet:pid_types @=@ dnet:pid_types @=@ orcid @=@ Open Researcher and Contributor ID +dnet:pid_types @=@ dnet:pid_types @=@ orcid_pending @=@ Open Researcher and Contributor ID dnet:pid_types @=@ dnet:pid_types @=@ PANGAEA @=@ PANGAEA dnet:pid_types @=@ dnet:pid_types @=@ epo_nr_epodoc @=@ Patent application number in EPODOC format dnet:pid_types @=@ dnet:pid_types @=@ UNKNOWN @=@ UNKNOWN