2021-10-15 15:00:15 +02:00
|
|
|
package eu.dnetlib.dhp.sx.bio.pubmed
|
2021-05-04 14:54:12 +02:00
|
|
|
|
|
|
|
import scala.xml.MetaData
|
2020-07-10 14:44:50 +02:00
|
|
|
import scala.xml.pull.{EvElemEnd, EvElemStart, EvText, XMLEventReader}
|
2021-11-15 14:32:01 +01:00
|
|
|
|
2022-01-11 16:57:48 +01:00
|
|
|
/** @param xml
|
|
|
|
*/
|
|
|
|
class PMParser(xml: XMLEventReader) extends Iterator[PMArticle] {
|
2021-11-15 14:32:01 +01:00
|
|
|
|
2022-01-11 16:57:48 +01:00
|
|
|
var currentArticle: PMArticle = generateNextArticle()
|
2020-07-10 14:44:50 +02:00
|
|
|
|
2022-01-11 16:57:48 +01:00
|
|
|
override def hasNext: Boolean = currentArticle != null
|
2020-07-10 14:44:50 +02:00
|
|
|
|
|
|
|
override def next(): PMArticle = {
|
|
|
|
val tmp = currentArticle
|
|
|
|
currentArticle = generateNextArticle()
|
|
|
|
tmp
|
|
|
|
}
|
|
|
|
|
2022-01-11 16:57:48 +01:00
|
|
|
def extractAttributes(attrs: MetaData, key: String): String = {
|
2021-05-04 14:54:12 +02:00
|
|
|
|
|
|
|
val res = attrs.get(key)
|
|
|
|
if (res.isDefined) {
|
2022-01-11 16:57:48 +01:00
|
|
|
val s = res.get
|
2021-05-04 14:54:12 +02:00
|
|
|
if (s != null && s.nonEmpty)
|
|
|
|
s.head.text
|
|
|
|
else
|
|
|
|
null
|
2022-01-11 16:57:48 +01:00
|
|
|
} else null
|
2021-05-04 14:54:12 +02:00
|
|
|
}
|
|
|
|
|
2022-01-11 16:57:48 +01:00
|
|
|
def validate_Date(year: String, month: String, day: String): String = {
|
2021-05-04 14:54:12 +02:00
|
|
|
try {
|
|
|
|
f"${year.toInt}-${month.toInt}%02d-${day.toInt}%02d"
|
|
|
|
|
|
|
|
} catch {
|
2022-01-11 16:57:48 +01:00
|
|
|
case _: Throwable => null
|
2021-05-04 14:54:12 +02:00
|
|
|
}
|
|
|
|
}
|
2020-07-10 14:44:50 +02:00
|
|
|
|
2022-01-11 16:57:48 +01:00
|
|
|
def generateNextArticle(): PMArticle = {
|
2021-05-04 14:54:12 +02:00
|
|
|
|
2022-01-11 16:57:48 +01:00
|
|
|
var currentSubject: PMSubject = null
|
2020-07-10 14:44:50 +02:00
|
|
|
var currentAuthor: PMAuthor = null
|
|
|
|
var currentJournal: PMJournal = null
|
2021-05-04 14:54:12 +02:00
|
|
|
var currentGrant: PMGrant = null
|
2020-07-10 14:44:50 +02:00
|
|
|
var currNode: String = null
|
|
|
|
var currentYear = "0"
|
|
|
|
var currentMonth = "01"
|
|
|
|
var currentDay = "01"
|
2022-01-11 16:57:48 +01:00
|
|
|
var currentArticleType: String = null
|
2020-07-10 14:44:50 +02:00
|
|
|
|
|
|
|
while (xml.hasNext) {
|
|
|
|
xml.next match {
|
2021-05-04 14:54:12 +02:00
|
|
|
case EvElemStart(_, label, attrs, _) =>
|
2020-07-10 14:44:50 +02:00
|
|
|
currNode = label
|
2021-05-04 14:54:12 +02:00
|
|
|
|
2020-07-10 14:44:50 +02:00
|
|
|
label match {
|
|
|
|
case "PubmedArticle" => currentArticle = new PMArticle
|
2022-01-11 16:57:48 +01:00
|
|
|
case "Author" => currentAuthor = new PMAuthor
|
|
|
|
case "Journal" => currentJournal = new PMJournal
|
|
|
|
case "Grant" => currentGrant = new PMGrant
|
2021-05-04 14:54:12 +02:00
|
|
|
case "PublicationType" | "DescriptorName" =>
|
|
|
|
currentSubject = new PMSubject
|
|
|
|
currentSubject.setMeshId(extractAttributes(attrs, "UI"))
|
2022-01-11 16:57:48 +01:00
|
|
|
case "ArticleId" => currentArticleType = extractAttributes(attrs, "IdType")
|
|
|
|
case _ =>
|
2020-07-10 14:44:50 +02:00
|
|
|
}
|
|
|
|
case EvElemEnd(_, label) =>
|
|
|
|
label match {
|
|
|
|
case "PubmedArticle" => return currentArticle
|
2022-01-11 16:57:48 +01:00
|
|
|
case "Author" => currentArticle.getAuthors.add(currentAuthor)
|
|
|
|
case "Journal" => currentArticle.setJournal(currentJournal)
|
|
|
|
case "Grant" => currentArticle.getGrants.add(currentGrant)
|
|
|
|
case "PubMedPubDate" =>
|
|
|
|
if (currentArticle.getDate == null)
|
|
|
|
currentArticle.setDate(validate_Date(currentYear, currentMonth, currentDay))
|
|
|
|
case "PubDate" => currentJournal.setDate(s"$currentYear-$currentMonth-$currentDay")
|
|
|
|
case "DescriptorName" => currentArticle.getSubjects.add(currentSubject)
|
|
|
|
case "PublicationType" => currentArticle.getPublicationTypes.add(currentSubject)
|
|
|
|
case _ =>
|
2020-07-10 14:44:50 +02:00
|
|
|
}
|
|
|
|
case EvText(text) =>
|
2022-01-11 16:57:48 +01:00
|
|
|
if (currNode != null && text.trim.nonEmpty)
|
2020-07-10 14:44:50 +02:00
|
|
|
currNode match {
|
|
|
|
case "ArticleTitle" => {
|
2022-01-11 16:57:48 +01:00
|
|
|
if (currentArticle.getTitle == null)
|
2020-07-10 14:44:50 +02:00
|
|
|
currentArticle.setTitle(text.trim)
|
|
|
|
else
|
|
|
|
currentArticle.setTitle(currentArticle.getTitle + text.trim)
|
|
|
|
}
|
|
|
|
case "AbstractText" => {
|
2022-01-11 16:57:48 +01:00
|
|
|
if (currentArticle.getDescription == null)
|
2020-07-10 14:44:50 +02:00
|
|
|
currentArticle.setDescription(text.trim)
|
|
|
|
else
|
|
|
|
currentArticle.setDescription(currentArticle.getDescription + text.trim)
|
|
|
|
}
|
|
|
|
case "PMID" => currentArticle.setPmid(text.trim)
|
2022-01-11 16:57:48 +01:00
|
|
|
case "ArticleId" =>
|
|
|
|
if ("doi".equalsIgnoreCase(currentArticleType)) currentArticle.setDoi(text.trim)
|
|
|
|
case "Language" => currentArticle.setLanguage(text.trim)
|
|
|
|
case "ISSN" => currentJournal.setIssn(text.trim)
|
|
|
|
case "GrantID" => currentGrant.setGrantID(text.trim)
|
|
|
|
case "Agency" => currentGrant.setAgency(text.trim)
|
|
|
|
case "Country" => if (currentGrant != null) currentGrant.setCountry(text.trim)
|
|
|
|
case "Year" => currentYear = text.trim
|
|
|
|
case "Month" => currentMonth = text.trim
|
|
|
|
case "Day" => currentDay = text.trim
|
|
|
|
case "Volume" => currentJournal.setVolume(text.trim)
|
|
|
|
case "Issue" => currentJournal.setIssue(text.trim)
|
2021-05-04 14:54:12 +02:00
|
|
|
case "PublicationType" | "DescriptorName" => currentSubject.setValue(text.trim)
|
2020-07-10 14:44:50 +02:00
|
|
|
case "LastName" => {
|
|
|
|
if (currentAuthor != null)
|
|
|
|
currentAuthor.setLastName(text.trim)
|
|
|
|
}
|
2022-01-11 16:57:48 +01:00
|
|
|
case "ForeName" =>
|
|
|
|
if (currentAuthor != null)
|
|
|
|
currentAuthor.setForeName(text.trim)
|
2020-07-10 14:44:50 +02:00
|
|
|
case "Title" =>
|
2022-01-11 16:57:48 +01:00
|
|
|
if (currentJournal.getTitle == null)
|
2020-07-10 14:44:50 +02:00
|
|
|
currentJournal.setTitle(text.trim)
|
|
|
|
else
|
|
|
|
currentJournal.setTitle(currentJournal.getTitle + text.trim)
|
|
|
|
case _ =>
|
|
|
|
|
|
|
|
}
|
|
|
|
case _ =>
|
|
|
|
}
|
|
|
|
|
|
|
|
}
|
|
|
|
null
|
|
|
|
}
|
|
|
|
}
|