forked from D-Net/dnet-hadoop
updated pubmed
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c00be646f3
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714b71bd21
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@ -33,7 +33,6 @@ object SparkCreateBaselineDataFrame {
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implicit val PMJEncoder: Encoder[PMJournal] = Encoders.kryo(classOf[PMJournal])
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implicit val PMAEncoder: Encoder[PMAuthor] = Encoders.kryo(classOf[PMAuthor])
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val k: RDD[(String, String)] = sc.wholeTextFiles(s"$workingPath/baseline",2000)
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val ds:Dataset[PMArticle] = spark.createDataset(k.filter(i => i._1.endsWith(".gz")).flatMap(i =>{
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val xml = new XMLEventReader(Source.fromBytes(i._2.getBytes()))
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new PMParser(xml)
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@ -8,10 +8,33 @@ import java.util.List;
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public class PMArticle implements Serializable {
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private String pmid;
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private String doi;
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private String date;
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private PMJournal journal;
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private String title;
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private String description;
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private String language;
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private final List<PMSubject> subjects = new ArrayList<>();
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private final List<PMSubject> publicationTypes = new ArrayList<>();
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public List<PMSubject> getPublicationTypes() {
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return publicationTypes;
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}
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private final List<PMGrant> grants = new ArrayList<>();
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public List<PMGrant> getGrants() {
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return grants;
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}
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public String getDoi() {
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return doi;
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}
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public void setDoi(String doi) {
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this.doi = doi;
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}
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private List<PMAuthor> authors = new ArrayList<>();
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public String getPmid() {
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@ -61,4 +84,16 @@ public class PMArticle implements Serializable {
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public void setAuthors(List<PMAuthor> authors) {
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this.authors = authors;
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}
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public List<PMSubject> getSubjects() {
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return subjects;
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}
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public String getLanguage() {
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return language;
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}
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public void setLanguage(String language) {
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this.language = language;
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}
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}
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@ -0,0 +1,42 @@
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package eu.dnetlib.dhp.sx.ebi.model;
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public class PMGrant {
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private String grantID;
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private String agency;
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private String country;
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public PMGrant() {
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}
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public PMGrant(String grantID, String agency, String country) {
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this.grantID = grantID;
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this.agency = agency;
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this.country = country;
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}
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public String getGrantID() {
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return grantID;
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}
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public void setGrantID(String grantID) {
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this.grantID = grantID;
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}
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public String getAgency() {
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return agency;
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}
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public void setAgency(String agency) {
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this.agency = agency;
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}
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public String getCountry() {
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return country;
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}
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public void setCountry(String country) {
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this.country = country;
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}
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}
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@ -1,4 +1,6 @@
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package eu.dnetlib.dhp.sx.ebi.model
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import scala.xml.MetaData
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import scala.xml.pull.{EvElemEnd, EvElemStart, EvText, XMLEventReader}
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class PMParser(xml:XMLEventReader) extends Iterator[PMArticle] {
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@ -12,24 +14,61 @@ class PMParser(xml:XMLEventReader) extends Iterator[PMArticle] {
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tmp
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}
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def extractAttributes(attrs:MetaData, key:String):String = {
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val res = attrs.get(key)
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if (res.isDefined) {
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val s =res.get
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if (s != null && s.nonEmpty)
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s.head.text
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else
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null
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}
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else null
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}
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def validate_Date(year:String, month:String, day:String):String = {
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try {
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f"${year.toInt}-${month.toInt}%02d-${day.toInt}%02d"
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} catch {
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case _: Throwable =>null
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}
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}
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def generateNextArticle():PMArticle = {
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var currentSubject:PMSubject = null
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var currentAuthor: PMAuthor = null
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var currentJournal: PMJournal = null
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var currentGrant: PMGrant = null
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var currNode: String = null
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var currentYear = "0"
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var currentMonth = "01"
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var currentDay = "01"
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var currentArticleType:String = null
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while (xml.hasNext) {
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xml.next match {
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case EvElemStart(_, label, _, _) =>
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case EvElemStart(_, label, attrs, _) =>
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currNode = label
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label match {
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case "PubmedArticle" => currentArticle = new PMArticle
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case "Author" => currentAuthor = new PMAuthor
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case "Journal" => currentJournal = new PMJournal
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case "Grant" => currentGrant = new PMGrant
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case "PublicationType" | "DescriptorName" =>
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currentSubject = new PMSubject
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currentSubject.setMeshId(extractAttributes(attrs, "UI"))
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case "ArticleId" => currentArticleType = extractAttributes(attrs,"IdType")
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case _ =>
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}
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case EvElemEnd(_, label) =>
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@ -37,8 +76,12 @@ class PMParser(xml:XMLEventReader) extends Iterator[PMArticle] {
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case "PubmedArticle" => return currentArticle
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case "Author" => currentArticle.getAuthors.add(currentAuthor)
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case "Journal" => currentArticle.setJournal(currentJournal)
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case "DateCompleted" => currentArticle.setDate(s"$currentYear-$currentMonth-$currentDay")
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case "Grant" => currentArticle.getGrants.add(currentGrant)
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case "PubMedPubDate" => if (currentArticle.getDate== null)
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currentArticle.setDate(validate_Date(currentYear,currentMonth,currentDay))
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case "PubDate" => currentJournal.setDate(s"$currentYear-$currentMonth-$currentDay")
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case "DescriptorName" => currentArticle.getSubjects.add(currentSubject)
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case "PublicationType" =>currentArticle.getPublicationTypes.add(currentSubject)
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case _ =>
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}
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case EvText(text) =>
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@ -57,12 +100,18 @@ class PMParser(xml:XMLEventReader) extends Iterator[PMArticle] {
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currentArticle.setDescription(currentArticle.getDescription + text.trim)
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}
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case "PMID" => currentArticle.setPmid(text.trim)
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case "ArticleId" => if ("doi".equalsIgnoreCase(currentArticleType)) currentArticle.setDoi(text.trim)
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case "Language" => currentArticle.setLanguage(text.trim)
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case "ISSN" => currentJournal.setIssn(text.trim)
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case "GrantID" => currentGrant.setGrantID(text.trim)
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case "Agency" => currentGrant.setAgency(text.trim)
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case "Country" => if (currentGrant != null) currentGrant.setCountry(text.trim)
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case "Year" => currentYear = text.trim
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case "Month" => currentMonth = text.trim
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case "Day" => currentDay = text.trim
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case "Volume" => currentJournal.setVolume( text.trim)
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case "Issue" => currentJournal.setIssue (text.trim)
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case "PublicationType" | "DescriptorName" => currentSubject.setValue(text.trim)
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case "LastName" => {
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if (currentAuthor != null)
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currentAuthor.setLastName(text.trim)
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@ -0,0 +1,41 @@
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package eu.dnetlib.dhp.sx.ebi.model;
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public class PMSubject {
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private String value;
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private String meshId;
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private String registryNumber;
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public PMSubject() {
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}
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public PMSubject(String value, String meshId, String registryNumber) {
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this.value = value;
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this.meshId = meshId;
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this.registryNumber = registryNumber;
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}
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public String getValue() {
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return value;
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}
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public void setValue(String value) {
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this.value = value;
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}
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public String getMeshId() {
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return meshId;
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}
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public void setMeshId(String meshId) {
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this.meshId = meshId;
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}
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public String getRegistryNumber() {
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return registryNumber;
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}
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public void setRegistryNumber(String registryNumber) {
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this.registryNumber = registryNumber;
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}
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}
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@ -5,9 +5,6 @@ import org.apache.spark.sql.{Encoder, Encoders}
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import org.json4s
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import org.json4s.DefaultFormats
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import org.json4s.jackson.JsonMethods.parse
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import java.text.SimpleDateFormat
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import java.util.Date
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import java.util.regex.Pattern
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import scala.language.postfixOps
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import scala.xml.{Elem, Node, XML}
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@ -24,7 +24,7 @@ object SparkGeneratePanagaeaDataset {
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SparkSession
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.builder()
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.config(conf)
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.appName(SparkCreateEBIDataFrame.getClass.getSimpleName)
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.appName(SparkGeneratePanagaeaDataset.getClass.getSimpleName)
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.master(parser.get("master")).getOrCreate()
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parser.getObjectMap.asScala.foreach(s => logger.info(s"${s._1} -> ${s._2}"))
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@ -0,0 +1,19 @@
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<configuration>
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<property>
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<name>jobTracker</name>
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<value>yarnRM</value>
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</property>
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<property>
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<name>nameNode</name>
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<value>hdfs://nameservice1</value>
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</property>
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<property>
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<name>oozie.use.system.libpath</name>
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<value>true</value>
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</property>
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<property>
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<name>oozie.action.sharelib.for.spark</name>
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<value>spark2</value>
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</property>
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</configuration>
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@ -0,0 +1,40 @@
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<workflow-app name="Transform_Pubmed_Workflow" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>baselineWorkingPath</name>
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<description>the Baseline Working Path</description>
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</property>
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</parameters>
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<start to="ConvertDataset"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="ConvertDataset">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Convert Baseline to Dataset</name>
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<class>eu.dnetlib.dhp.sx.ebi.SparkCreateBaselineDataFrame</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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</spark-opts>
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<arg>--workingPath</arg><arg>${baselineWorkingPath}</arg>
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<arg>--master</arg><arg>yarn</arg>
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</spark>
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<ok to="End"/>
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<error to="Kill"/>
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</action>
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<end name="End"/>
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</workflow-app>
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@ -0,0 +1,4 @@
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[
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{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
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{"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the path of the sequencial file to read", "paramRequired": true}
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]
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@ -1,16 +1,24 @@
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package eu.dnetlib.dhp.sx.ebi
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import com.fasterxml.jackson.databind.ObjectMapper
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import eu.dnetlib.dhp.sx.ebi.model.PMParser
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import org.junit.jupiter.api.Test
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import scala.io.Source
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import scala.xml.pull.XMLEventReader
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class TestEBI {
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// @Test
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@Test
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def testEBIData() = {
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SparkAddLinkUpdates.main("-mt local[*] -w /home/sandro/Downloads".split(" "))
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val inputXML = Source.fromInputStream(getClass.getResourceAsStream("pubmed.xml")).mkString
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val xml = new XMLEventReader(Source.fromBytes(inputXML.getBytes()))
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val mapper = new ObjectMapper()
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new PMParser(xml).foreach(s =>println(mapper.writeValueAsString(s)))
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