135 lines
5.3 KiB
Scala
135 lines
5.3 KiB
Scala
package eu.dnetlib.dhp.sx.bio.pubmed
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import scala.xml.MetaData
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import scala.xml.pull.{EvElemEnd, EvElemStart, EvText, XMLEventReader}
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/** @param xml
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*/
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class PMParser(xml: XMLEventReader) extends Iterator[PMArticle] {
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var currentArticle: PMArticle = generateNextArticle()
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override def hasNext: Boolean = currentArticle != null
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override def next(): PMArticle = {
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val tmp = currentArticle
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currentArticle = generateNextArticle()
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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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} 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, 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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label match {
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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 "Grant" => currentArticle.getGrants.add(currentGrant)
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case "PubMedPubDate" =>
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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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if (currNode != null && text.trim.nonEmpty)
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currNode match {
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case "ArticleTitle" => {
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if (currentArticle.getTitle == null)
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currentArticle.setTitle(text.trim)
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else
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currentArticle.setTitle(currentArticle.getTitle + text.trim)
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}
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case "AbstractText" => {
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if (currentArticle.getDescription == null)
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currentArticle.setDescription(text.trim)
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else
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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" =>
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if ("doi".equalsIgnoreCase(currentArticleType)) currentArticle.setDoi(text.trim)
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if ("pmc".equalsIgnoreCase(currentArticleType)) currentArticle.setPmcId(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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}
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case "ForeName" =>
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if (currentAuthor != null)
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currentAuthor.setForeName(text.trim)
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case "Title" =>
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if (currentJournal.getTitle == null)
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currentJournal.setTitle(text.trim)
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else
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currentJournal.setTitle(currentJournal.getTitle + text.trim)
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case _ =>
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}
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case _ =>
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}
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}
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null
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}
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}
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