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package sandcrawler
import java.text.Normalizer
import java.util.Arrays
import java.util.Properties
import java.util.regex.Pattern
import scala.math
import scala.util.parsing.json.JSON
import cascading.tuple.Fields
import com.twitter.scalding._
import com.twitter.scalding.typed.CoGrouped
import com.twitter.scalding.typed.Grouped
import com.twitter.scalding.typed.TDsl._
import org.apache.hadoop.hbase.io.ImmutableBytesWritable
import org.apache.hadoop.hbase.util.Bytes
import parallelai.spyglass.base.JobBase
import parallelai.spyglass.hbase.HBaseConstants.SourceMode
import parallelai.spyglass.hbase.HBasePipeConversions
import parallelai.spyglass.hbase.HBaseSource
class HBaseCrossrefScoreJob(args: Args) extends JobBase(args) with HBasePipeConversions {
val NoTitle = "NO TITLE" // Used for slug if title is empty or unparseable
// key is SHA1
val grobidSource = HBaseCrossrefScore.getHBaseSource(
args("hbase-table"),
args("zookeeper-hosts"))
val grobidPipe : TypedPipe[(String, String, String)] = grobidSource
.read
.fromBytesWritable(new Fields("key", "tei_json"))
// .debug // Should be 4 tuples for mocked data
.toTypedPipe[(String, String)]('key, 'tei_json)
.map { entry =>
val (key, json) = (entry._1, entry._2)
// TODO: Consider passing forward only a subset of JSON.
HBaseCrossrefScore.grobidToSlug(json) match {
case Some(slug) => (slug, key, json)
case None => (NoTitle, key, json)
}
}
.filter { entry =>
val (slug, _, _) = entry
slug != NoTitle
}
// .debug // SHould be 3 tuples for mocked data
val grobidGroup = grobidPipe
.groupBy { case (slug, key, json) => slug }
val crossrefSource = TextLine(args("crossref-input"))
val crossrefPipe : TypedPipe[(String, String)] = crossrefSource
.read
// .debug // Should be 4 tuples for mocked data
.toTypedPipe[String]('line)
.map{ json : String =>
HBaseCrossrefScore.crossrefToSlug(json) match {
case Some(slug) => (slug, json)
case None => (NoTitle, json)
}
}
.filter { entry =>
val (slug, json) = entry
slug != NoTitle
}
val crossrefGroup = crossrefPipe
.groupBy { case (slug, json) => slug }
val theJoin : CoGrouped[String, ((String, String, String), (String, String))] =
grobidGroup.join(crossrefGroup)
theJoin.map{ entry =>
val (slug : String,
((slug0: String, sha1 : String, grobidJson : String),
(slug1 : String, crossrefJson : String))) = entry
HBaseCrossrefScore.computeOutput(sha1, grobidJson, crossrefJson)}
// Output: score, sha1, doi, grobid title, crossref title
.write(TypedTsv[(Int, String, String, String, String)](args("output")))
}
object HBaseCrossrefScore {
def getHBaseSource(hbaseTable: String, zookeeperHosts: String) : HBaseSource = HBaseBuilder.build(
hbaseTable, // HBase Table Name
zookeeperHosts, // HBase Zookeeper server (to get runtime config info; can be array?)
List("grobid0:tei_json"),
SourceMode.SCAN_ALL)
def jsonToMap(json : String) : Option[Map[String, Any]] = {
// https://stackoverflow.com/a/32717262/631051
val jsonObject = JSON.parseFull(json)
if (jsonObject == None) {
None
} else {
Some(jsonObject.get.asInstanceOf[Map[String, Any]])
}
}
def grobidToSlug(json : String) : Option[String] = {
jsonToMap(json) match {
case None => None
case Some(map) => {
if (map contains "title") {
titleToSlug(map("title").asInstanceOf[String])
} else {
None
}
}
}
}
def crossrefToSlug(json : String) : Option[String] = {
jsonToMap(json) match {
case None => None
case Some(map) => {
if (map contains "title") {
// TODO: Don't ignore titles after the first.
titleToSlug(map("title").asInstanceOf[List[String]](0))
} else {
None
}
}
}
}
def titleToSlug(title : String) : Option[String] = {
val slug = removeAccents(title).split(":")(0).toLowerCase()
if (slug.isEmpty) {
None
} else {
Some(slug)
}
}
val MaxScore = 1000
def computeOutput(sha1 : String, grobidJson : String, crossrefJson : String) :
// (score, sha1, doi, grobidTitle, crossrefTitle)
(Int, String, String, String, String) = {
jsonToMap(grobidJson) match {
case None => (0, "", "", "", "") // This can't happen, because grobidJson already validated in earlier stage
case Some(grobid) => {
val grobidTitle = grobid("title").asInstanceOf[String].toLowerCase()
jsonToMap(crossrefJson) match {
case None => (0, "", "", "", "") // This can't happen, because crossrefJson already validated in earlier stage
case Some(crossref) => {
val crossrefTitle = crossref("title").asInstanceOf[List[String]](0).toLowerCase()
(similarity(removeAccents(grobidTitle), removeAccents(crossrefTitle)),
sha1,
crossref("DOI").asInstanceOf[String],
"'" + grobidTitle + "'",
"'" + crossrefTitle + "'")
}
}
}
}
}
// Adapted from https://git-wip-us.apache.org/repos/asf?p=commons-lang.git;a=blob;f=src/main/java/org/apache/commons/lang3/StringUtils.java;h=1d7b9b99335865a88c509339f700ce71ce2c71f2;hb=HEAD#l934
def removeAccents(s : String) : String = {
val replacements = Map(
'\u0141' -> 'L',
'\u0142' -> 'l', // Letter ell
'\u00d8' -> 'O',
'\u00f8' -> 'o'
)
val sb = new StringBuilder(Normalizer.normalize(s, Normalizer.Form.NFD))
for (i <- 0 to sb.length - 1) {
for (key <- replacements.keys) {
if (sb(i) == key) {
sb.deleteCharAt(i);
sb.insert(i, replacements(key))
}
}
}
val pattern = Pattern.compile("\\p{InCombiningDiacriticalMarks}+")
pattern.matcher(sb).replaceAll("")
}
// Adapted from: https://stackoverflow.com/a/16018452/631051
def similarity(s1 : String, s2 : String) : Int = {
val longer : String = if (s1.length > s2.length) s1 else s2
val shorter : String = if (s1.length > s2.length) s2 else s1
if (longer.length == 0) {
// Both strings are empty.
MaxScore
} else {
(longer.length - stringDistance(longer, shorter)) * MaxScore / longer.length
}
}
// Source: // https://oldfashionedsoftware.com/2009/11/19/string-distance-and-refactoring-in-scala/
def stringDistance(s1: String, s2: String): Int = {
val memo = scala.collection.mutable.Map[(List[Char],List[Char]),Int]()
def min(a:Int, b:Int, c:Int) = Math.min( Math.min( a, b ), c)
def sd(s1: List[Char], s2: List[Char]): Int = {
if (!memo.contains((s1, s2))) {
memo((s1,s2)) = (s1, s2) match {
case (_, Nil) => s1.length
case (Nil, _) => s2.length
case (c1::t1, c2::t2) =>
min( sd(t1,s2) + 1, sd(s1,t2) + 1,
sd(t1,t2) + (if (c1==c2) 0 else 1) )
}
}
memo((s1,s2))
}
sd( s1.toList, s2.toList )
}
}
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