Pipeline works, all tests pass, no scalastyle errors.

5 files changed, 12 insertions, 290 deletions

diff --git a/scalding/src/main/scala/sandcrawler/CrossrefScorable.scala b/scalding/src/main/scala/sandcrawler/CrossrefScorable.scala
index e257152..4558ee6 100644
--- a/scalding/src/main/scala/sandcrawler/CrossrefScorable.scala
+++ b/scalding/src/main/scala/sandcrawler/CrossrefScorable.scala
@@ -1,36 +1,14 @@
 package sandcrawler
 
-import cascading.flow.FlowDef
-import cascading.pipe.Pipe
-import cascading.tuple.Fields
-import com.twitter.scalding._
-import com.twitter.scalding.typed.TDsl._
-import parallelai.spyglass.hbase.HBaseConstants.SourceMode
-import parallelai.spyglass.hbase.HBasePipeConversions
-import parallelai.spyglass.hbase.HBaseSource
-import TDsl._
-import scala.util.parsing.json.JSONObject
-
-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 scala.util.parsing.json.JSONObject
 
+import cascading.flow.FlowDef
 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 CrossrefScorable extends Scorable with HBasePipeConversions {
   // TODO: Generalize args so there can be multiple Crossref pipes in one job.
@@ -50,8 +28,8 @@ object CrossrefScorable {
     Scorable.jsonToMap(json) match {
       case None => MapFeatures(Scorable.NoSlug, json)
       case Some(map) => {
-        if ((map contains "titles") && (map contains "DOI")) {
-          val titles = map("titles").asInstanceOf[List[String]]
+        if ((map contains "title") && (map contains "DOI")) {
+          val titles = map("title").asInstanceOf[List[String]]
           val doi = Scorable.getString(map, "DOI")
           if (titles.isEmpty || titles == null || doi.isEmpty || doi == null) {
             new MapFeatures(Scorable.NoSlug, json)
diff --git a/scalding/src/main/scala/sandcrawler/GrobidScorable.scala b/scalding/src/main/scala/sandcrawler/GrobidScorable.scala
index de9f51a..94b3494 100644
--- a/scalding/src/main/scala/sandcrawler/GrobidScorable.scala
+++ b/scalding/src/main/scala/sandcrawler/GrobidScorable.scala
@@ -1,15 +1,14 @@
 package sandcrawler
 
 import scala.util.parsing.json.JSONObject
+
 import cascading.flow.FlowDef
-import cascading.pipe.Pipe
 import cascading.tuple.Fields
 import com.twitter.scalding._
 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 = {
diff --git a/scalding/src/main/scala/sandcrawler/HBaseCrossrefScoreJob.scala b/scalding/src/main/scala/sandcrawler/HBaseCrossrefScoreJob.scala
deleted file mode 100644
index 018a74b..0000000
--- a/scalding/src/main/scala/sandcrawler/HBaseCrossrefScoreJob.scala
+++ /dev/null
@@ -1,218 +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
-import TDsl._
-
-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
-
-  // Here I CAN call Pipe.toTypedPipe()
-  val grobidPipe : TypedPipe[(String, String, String)] = temp
-    .fromBytesWritable(new Fields("key", "tei_json"))
-    .toTypedPipe[(String, String)]('key, 'tei_json)
-    .map { entry =>
-      val (key, json) = (entry._1, entry._2)
-      HBaseCrossrefScore.grobidToSlug(json) match {
-        case Some(slug) => (slug, key, json)
-        case None => (NoTitle, key, json)
-      }
-    }
-    .filter { entry =>
-      val (slug, _, _) = entry
-      slug != NoTitle
-    }
-
-  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 a256fa4..717b2d5 100644
--- a/scalding/src/main/scala/sandcrawler/Scorable.scala
+++ b/scalding/src/main/scala/sandcrawler/Scorable.scala
@@ -39,7 +39,7 @@ object Scorable {
   // NOTE: I could go all out and make ScorableMap a type.
   // TODO: Require year. Other features will get added here.
   def toScorableMap(title : String, year : Int = 0, doi : String = "", sha1 : String = "") : Map[String, Any] = {
-   Map("title" -> title, "year" -> year, "doi" -> doi, "sha1" -> sha1)
+    Map("title" -> title, "year" -> year, "doi" -> doi, "sha1" -> sha1)
   }
 
   def toScorableJson(title : String, year : Int, doi : String = "", sha1 : String = "") : String = {
diff --git a/scalding/src/main/scala/sandcrawler/ScoreJob.scala b/scalding/src/main/scala/sandcrawler/ScoreJob.scala
index 386b367..75d45e9 100644
--- a/scalding/src/main/scala/sandcrawler/ScoreJob.scala
+++ b/scalding/src/main/scala/sandcrawler/ScoreJob.scala
@@ -1,16 +1,12 @@
 package sandcrawler
 
-import cascading.flow.FlowDef
-import cascading.tuple.Fields
-import com.twitter.scalding.{Args,Source,TextLine,TypedPipe, TypedTsv}
-//import com.twitter.scalding.source.TypedText
-import parallelai.spyglass.base.JobBase
-import parallelai.spyglass.hbase.HBasePipeConversions
-import parallelai.spyglass.hbase.HBaseSource
-import com.twitter.scalding.{ Dsl, RichPipe, IterableSource, TupleSetter, TupleConverter }
 import cascading.pipe.Pipe
+import com.twitter.scalding.Args
+import com.twitter.scalding.TypedPipe
+import com.twitter.scalding.TypedTsv
+import parallelai.spyglass.base.JobBase
 
-class ScoreJob(args: Args) extends JobBase(args) { //with HBasePipeConversions {
+class ScoreJob(args: Args) extends JobBase(args) {
   // TODO: Instantiate any subclass of Scorable specified in args.
   val sc1 : Scorable = new GrobidScorable()
   val sc2 : Scorable = new CrossrefScorable()
@@ -27,10 +23,10 @@ class ScoreJob(args: Args) extends JobBase(args) { //with HBasePipeConversions {
   }
   //TypedTsv doesn't work over case classes.
     .map { entry => (entry.slug, entry.score, entry.json1, entry.json2) }
-
     .write(TypedTsv[(String, Int, String, String)](args("output")))
 }
 
+/*
 // Ugly hack to get non-String information into ScoreJob above.
 object ScoreJob {
   var scorable1 : Option[Scorable] = None
@@ -57,38 +53,5 @@ object ScoreJob {
       case None => null
     }
   }
-
-  /*
-  implicit def sourceToRichPipe(src: Source): RichPipe = new RichPipe(src.read)
-
-  // This converts an Iterable into a Pipe or RichPipe with index (int-based) fields
-  implicit def toPipe[T](iter: Iterable[T])(implicit set: TupleSetter[T], conv: TupleConverter[T]): Pipe =
-    IterableSource[T](iter)(set, conv).read
-
-  implicit def iterableToRichPipe[T](iter: Iterable[T])(implicit set: TupleSetter[T], conv: TupleConverter[T]): RichPipe =
-    RichPipe(toPipe(iter)(set, conv))
-
-  // Provide args as an implicit val for extensions such as the Checkpoint extension.
-//  implicit protected def _implicitJobArgs: Args = args
-
-  def getFeaturesPipe1(pipe : cascading.pipe.Pipe) : TypedPipe[String] = {
-    pipe
-    // The next line gives an error: value toTypedPipe is not a member of cascading.pipe.Pipe
-      .toTypedPipe[String](new Fields("line"))
-  }
-
-  def getFeaturesPipe(pipe : cascading.pipe.Pipe) : TypedPipe[MapFeatures] = {
-    pipe
-      .fromBytesWritable(new Fields("key", "tei_json"))
-    // I needed to change symbols to strings when I pulled this out of ScoreJob.
-      .toTypedPipe[(String, String)](new Fields("key", "tei_json"))
-      .map { entry =>
-        val (key : String, json : String) = (entry._1, entry._2)
-        GrobidScorable.grobidToSlug(json) match {
-          case Some(slug) => new MapFeatures(slug, json)
-          case None => new MapFeatures(Scorable.NoSlug, json)
-        }
-      }
-  }
- */
 }
+ */