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-rw-r--r--scalding/src/main/scala/sandcrawler/GrobidScorable.scala8
-rw-r--r--scalding/src/main/scala/sandcrawler/HBaseCrossrefScoreJob.scala216
2 files changed, 5 insertions, 219 deletions
diff --git a/scalding/src/main/scala/sandcrawler/GrobidScorable.scala b/scalding/src/main/scala/sandcrawler/GrobidScorable.scala
index 25e5985..bf36855 100644
--- a/scalding/src/main/scala/sandcrawler/GrobidScorable.scala
+++ b/scalding/src/main/scala/sandcrawler/GrobidScorable.scala
@@ -12,9 +12,11 @@ import parallelai.spyglass.hbase.HBaseSource
class GrobidScorable extends Scorable with HBasePipeConversions {
def getFeaturesPipe(args : Args)(implicit flowDef : FlowDef, mode : Mode) = {
// TODO: Clean up code after debugging.
- val grobidSource = HBaseCrossrefScore.getHBaseSource(
+ val grobidSource = HBaseBuilder.build(
args("hbase-table"),
- args("zookeeper-hosts"))
+ args("zookeeper-hosts"),
+ List("grobid0:tei_json"),
+ SourceMode.SCAN_ALL)
// val pipe0 : Pipe = grobidSource.read
// val grobidPipe : TypedPipe[MapFeatures] = pipe0
@@ -26,7 +28,7 @@ class GrobidScorable extends Scorable with HBasePipeConversions {
.toTypedPipe[(String, String)](new Fields("key", "tei_json"))
.map { entry =>
val (key : String, json : String) = (entry._1, entry._2)
- HBaseCrossrefScore.grobidToSlug(json) match {
+ GrobidScorable.grobidToSlug(json) match {
case Some(slug) => new MapFeatures(slug, json)
case None => new MapFeatures(Scorable.NoSlug, json)
}
diff --git a/scalding/src/main/scala/sandcrawler/HBaseCrossrefScoreJob.scala b/scalding/src/main/scala/sandcrawler/HBaseCrossrefScoreJob.scala
deleted file mode 100644
index 2fbb19f..0000000
--- a/scalding/src/main/scala/sandcrawler/HBaseCrossrefScoreJob.scala
+++ /dev/null
@@ -1,216 +0,0 @@
-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 pipe0 : cascading.pipe.Pipe = grobidSource.read
- val grobidPipe : TypedPipe[(String, String, String)] = pipe0
- .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 )
- }
-}
-
generated by cgit v1.2.3 (git 2.39.1) at 2024-11-27 15:15:10 +0000