WIP

4 files changed, 226 insertions, 5 deletions

diff --git a/scalding/src/main/scala/sandcrawler/CrossrefScorable.scala b/scalding/src/main/scala/sandcrawler/CrossrefScorable.scala
index 249c9ab..9842122 100644
--- a/scalding/src/main/scala/sandcrawler/CrossrefScorable.scala
+++ b/scalding/src/main/scala/sandcrawler/CrossrefScorable.scala
@@ -8,8 +8,9 @@ import com.twitter.scalding.typed.TDsl._
 import parallelai.spyglass.hbase.HBaseConstants.SourceMode
 import parallelai.spyglass.hbase.HBasePipeConversions
 import parallelai.spyglass.hbase.HBaseSource
+import TDsl._
 
-class CrossrefScorable extends Scorable {
+class CrossrefScorable extends Scorable with HBasePipeConversions {
   // TODO: Generalize args so there can be multiple Grobid pipes in one job.
   def getSource(args : Args) : Source = {
     TextLine(args("crossref-input"))
diff --git a/scalding/src/main/scala/sandcrawler/GrobidScorable.scala b/scalding/src/main/scala/sandcrawler/GrobidScorable.scala
index 5c6b140..51e40f9 100644
--- a/scalding/src/main/scala/sandcrawler/GrobidScorable.scala
+++ b/scalding/src/main/scala/sandcrawler/GrobidScorable.scala
@@ -8,6 +8,7 @@ import com.twitter.scalding.typed.TDsl._
 import parallelai.spyglass.hbase.HBaseConstants.SourceMode
 import parallelai.spyglass.hbase.HBasePipeConversions
 import parallelai.spyglass.hbase.HBaseSource
+import TDsl._
 
 class GrobidScorable extends Scorable with HBasePipeConversions {
   def getSource(args : Args) : Source = {
@@ -15,10 +16,10 @@ class GrobidScorable extends Scorable with HBasePipeConversions {
     GrobidScorable.getHBaseSource(args("hbase-table"), args("zookeeper-hosts"))
   }
 
-  def getFeaturesPipe(pipe : Pipe) : TypedPipe[MapFeatures] = {
+  def getFeaturesPipe(pipe : cascading.pipe.Pipe) : TypedPipe[MapFeatures] = {
     pipe
       .fromBytesWritable(new Fields("key", "tei_json"))
-      .toTypedPipe[(String, String)](new Fields("key", "tei_json"))
+      .toTypedPipe[(String, String)](new Fields('key, 'tei_json))
       .map { entry =>
         val (key : String, json : String) = (entry._1, entry._2)
         GrobidScorable.grobidToSlug(json) match {
diff --git a/scalding/src/main/scala/sandcrawler/HBaseCrossrefScoreJob.scala b/scalding/src/main/scala/sandcrawler/HBaseCrossrefScoreJob.scala
new file mode 100644
index 0000000..725474d
--- /dev/null
+++ b/scalding/src/main/scala/sandcrawler/HBaseCrossrefScoreJob.scala
@@ -0,0 +1,218 @@
+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 temp : cascading.pipe.Pipe = grobidSource
+    .read
+    .fromBytesWritable(new Fields("key", "tei_json"))
+  val grobidPipe : TypedPipe[(String, String, String)] = temp
+    //  .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 temp2 : cascading.pipe.Pipe = crossrefSource.read
+  val crossrefPipe : TypedPipe[(String, String)] = temp2
+    //    .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 )
+  }
+}
+
diff --git a/scalding/src/main/scala/sandcrawler/Scorable.scala b/scalding/src/main/scala/sandcrawler/Scorable.scala
index 92b61bc..bd03d57 100644
--- a/scalding/src/main/scala/sandcrawler/Scorable.scala
+++ b/scalding/src/main/scala/sandcrawler/Scorable.scala
@@ -6,13 +6,14 @@ import scala.util.parsing.json.JSON
 import cascading.flow.FlowDef
 import com.twitter.scalding._
 import com.twitter.scalding.typed.TDsl._
+import TDsl._
 
 case class MapFeatures(slug : String, json : String)
 case class ReduceFeatures(json : String)
 case class ReduceOutput(val slug : String,  score : Int, json1 : String, json2 : String)
 
 abstract class Scorable {
-  def getInputPipe(pipe : Pipe) : TypedPipe[(String, ReduceFeatures)] =
+  def getInputPipe(pipe : cascading.pipe.Pipe) : TypedPipe[(String, ReduceFeatures)] =
   {
     getFeaturesPipe(pipe)
       .filter { entry => Scorable.isValidSlug(entry.slug) }
@@ -25,7 +26,7 @@ abstract class Scorable {
 
   // abstract methods
   def getSource(args : Args) : Source
-  def getFeaturesPipe(pipe : Pipe) : TypedPipe[MapFeatures]
+  def getFeaturesPipe(pipe : cascading.pipe.Pipe) : TypedPipe[MapFeatures]
 }
 
 object Scorable {