FatcatScorable and ScoreSelfFatcat job

3 files changed, 334 insertions, 0 deletions

diff --git a/scalding/src/main/scala/sandcrawler/FatcatScorable.scala b/scalding/src/main/scala/sandcrawler/FatcatScorable.scala
new file mode 100644
index 0000000..cffc2c0
--- /dev/null
+++ b/scalding/src/main/scala/sandcrawler/FatcatScorable.scala
@@ -0,0 +1,131 @@
+package sandcrawler
+
+import scala.math
+import scala.util.parsing.json.JSON
+import scala.util.parsing.json.JSONArray
+import scala.util.parsing.json.JSONObject
+
+import cascading.flow.FlowDef
+import cascading.tuple.Fields
+import com.twitter.scalding._
+import com.twitter.scalding.typed.TDsl._
+import parallelai.spyglass.hbase.HBasePipeConversions
+
+class FatcatScorable extends Scorable with HBasePipeConversions {
+
+  def getSource(args : Args) : Source = {
+    TextLine(args("fatcat-release-input"))
+  }
+
+  def getFeaturesPipe(args : Args)(implicit mode : Mode, flowDef : FlowDef) : TypedPipe[Option[MapFeatures]] = {
+    getSource(args).read
+      .toTypedPipe[String](new Fields("line"))
+      .filter { FatcatScorable.keepRecord(_) }
+      .map { FatcatScorable.jsonToMapFeatures(_) }
+  }
+}
+
+object FatcatScorable {
+
+  // Note; removed ReleaseType filtering
+
+  def keepRecord(json : String) : Boolean = {
+    Scorable.jsonToMap(json) match {
+      case None => false
+      case Some(map) => {
+        mapToTitle(map) match {
+          case None => false
+          case Some(title) => title.length <= Scorable.MaxTitleLength
+        }
+      }
+    }
+  }
+
+  // Returns None if title is null, empty, or too long.
+  def mapToTitle(map : Map[String, Any]) : Option[String] = {
+    def getTitle : Option[String] = {
+      if (map contains "title") {
+        val title = map("title").asInstanceOf[String]
+        if (title == null || title.isEmpty) None else Some(title)
+      } else {
+        None
+      }
+    }
+
+    def getSubtitle : Option[String] = {
+      if (map contains "subtitle") {
+        val subtitle = map("subtitle").asInstanceOf[String]
+        if (subtitle == null || subtitle.isEmpty) {
+          None
+        } else {
+          Some(subtitle)
+        }
+      } else {
+        None
+      }
+    }
+
+    getTitle match {
+      case None => None
+      case Some(baseTitle) => {
+        if (baseTitle == null) {
+          None
+        } else {
+          getSubtitle match {
+            case None => Some(baseTitle)
+            case Some(baseSubtitle) => Some(baseTitle.concat(":".concat(baseSubtitle)))
+          }
+        }
+      }
+    }
+  }
+
+  def mapToAuthorList(map : Map[String, Any]) : List[String] = {
+    if (map contains "contribs") {
+      val objArray = map("contribs").asInstanceOf[List[Any]].map(e => e.asInstanceOf[Map[String,Any]])
+      // TODO(bnewbold): better name stuff... contrib.surname, creator.surname,
+      // or raw_name split to last
+      objArray
+        .filter(e => e contains "raw_name")
+        .map(e => e.get("raw_name").get.asInstanceOf[String])
+    } else {
+      List()
+    }
+  }
+
+  def mapToYear(map : Map[String, Any]) : Option[Int] = {
+    map.get("release_year") match {
+      case None => None
+      case Some(year) => {
+        Some(year.asInstanceOf[Double].toInt)
+      }
+    }
+  }
+
+  def jsonToMapFeatures(json : String) : Option[MapFeatures] = {
+    def makeMapFeatures(title : String, doi : String, fatcat_release: String, fatcat_work : String, authors : List[String], year : Int, contentType : String) : Option[MapFeatures] = {
+      // NOTE: not doing any filtering here!
+      val sf : ScorableFeatures = ScorableFeatures.create(title=title, authors=authors, doi=doi, fatcat_release=fatcat_release, fatcat_work=fatcat_work, year=year)
+      sf.toSlug match {
+        case None => None
+        case Some(slug) => Some(MapFeatures(slug, sf.toString))
+      }
+    }
+    Scorable.jsonToMap(json) match {
+      case None => None
+      case Some(map) =>
+        mapToTitle(map) match {
+          case None => None
+          case Some(title) => makeMapFeatures(
+            title=title,
+            // TODO: doi=Scorable.getString(map, "doi"),
+            doi=null,
+            fatcat_release=Scorable.getString(map, "ident"),
+            fatcat_work=Scorable.getString(map, "work_id"),
+            authors=mapToAuthorList(map),
+            year=mapToYear(map).getOrElse(0),
+            contentType=map.get("type").map(e => e.asInstanceOf[String]).getOrElse("MISSING-CONTENT-TYPE"))
+        }
+    }
+  }
+}
diff --git a/scalding/src/main/scala/sandcrawler/ScoreSelfFatcat.scala b/scalding/src/main/scala/sandcrawler/ScoreSelfFatcat.scala
new file mode 100644
index 0000000..d1a94fe
--- /dev/null
+++ b/scalding/src/main/scala/sandcrawler/ScoreSelfFatcat.scala
@@ -0,0 +1,43 @@
+package sandcrawler
+
+import cascading.pipe.Pipe
+import com.twitter.scalding.Args
+import com.twitter.scalding.Stat
+import com.twitter.scalding.TypedPipe
+import com.twitter.scalding.TypedTsv
+import parallelai.spyglass.base.JobBase
+
+class ScoreSelfFatcatJob(args: Args) extends JobBase(args) {
+
+  val fatcatRowCount = Stat("fatcat-rows-filtered", "sandcrawler")
+  val joinedRowCount = Stat("joined-rows", "sandcrawler")
+
+  val fatcatScorable : Scorable = new FatcatScorable()
+  val fatcatPipe : TypedPipe[(String, ReduceFeatures)] = fatcatScorable
+    .getInputPipe(args)
+    .map { r =>
+      fatcatRowCount.inc
+      r
+    }
+
+  val joinedPipe = fatcatPipe
+    .addTrap(TypedTsv(args("output") + ".trapped"))
+    .join(fatcatPipe)
+
+  // TypedTsv doesn't work over case classes.
+  joinedPipe
+    // filter out trivial self-matches (releases are identical)
+    .filter { case (slug, (fatcatFeaturesLeft, fatcatFeaturesRight)) =>
+      Scorable.selfMatchable(fatcatFeaturesLeft, fatcatFeaturesRight)
+    }
+    .map { case (slug, (fatcatFeaturesLeft, fatcatFeaturesRight)) =>
+      joinedRowCount.inc
+      new ReduceOutput(
+        slug,
+        Scorable.computeSimilarity(fatcatFeaturesLeft, fatcatFeaturesRight),
+        fatcatFeaturesLeft.json,
+        fatcatFeaturesRight.json)
+    }
+    .map { entry => (entry.slug, entry.score, entry.json1, entry.json2) }
+    .write(TypedTsv[(String, Int, String, String)](args("output")))
+}
diff --git a/scalding/src/test/scala/sandcrawler/FatcatScorableTest.scala b/scalding/src/test/scala/sandcrawler/FatcatScorableTest.scala
new file mode 100644
index 0000000..823e14a
--- /dev/null
+++ b/scalding/src/test/scala/sandcrawler/FatcatScorableTest.scala
@@ -0,0 +1,160 @@
+package sandcrawler
+
+import cascading.tuple.Fields
+import cascading.tuple.Tuple
+import com.twitter.scalding.JobTest
+import com.twitter.scalding.TextLine
+import com.twitter.scalding.TupleConversions
+import com.twitter.scalding.TypedTsv
+import org.apache.hadoop.hbase.io.ImmutableBytesWritable
+import org.apache.hadoop.hbase.util.Bytes
+import org.scalatest._
+import parallelai.spyglass.hbase.HBaseConstants.SourceMode
+
+class FatcatScorableTest extends FlatSpec with Matchers {
+  // scalastyle:off
+  val FatcatString =
+"""
+{
+  "abstracts": [],
+  "refs": [],
+  "contribs": [
+    {
+      "index": 0,
+      "raw_name": "W Gaier",
+      "surname": "Gaier",
+      "role": "author",
+      "extra": {
+        "seq": "first"
+      }
+    }
+  ],
+  "publisher": "Elsevier BV",
+  "pages": "186-187",
+  "ext_ids": {
+    "doi": "<<DOI>>"
+  },
+  "release_year": 1996,
+  "release_stage": "published",
+  "release_type": "article-journal",
+  "container_id": "3nccslsn5jez3ixrp5skjyjxu4",
+  "title": "<<TITLE>>",
+  "state": "active",
+  "ident": "pnri57u66ffytigdmyybbmouni",
+  "work_id": "tdmqnfzm2nggrhfwzasyegvpyu",
+  "revision": "e50bd04e-d0d4-4ee7-b7a4-6b4f079de154",
+  "extra": {
+    "crossref": {
+      "alternative-id": [
+        "0987-7983(96)87729-2"
+      ],
+      "type": "journal-article"
+    }
+  }
+}
+""".replace("<<DOI>>", "10.123/aBc")
+  // scalastyle:on
+  val FatcatStringWithGoodTitle = FatcatString.replace("<<TITLE>>", "Some Title")
+  val FatcatStringWithMaximumTitle = FatcatString.replace("<<TITLE>>", "T" * Scorable.MaxTitleLength)
+  val FatcatStringWithExcessiveTitle = FatcatString.replace("<<TITLE>>", "T" * Scorable.MaxTitleLength + "0")
+  val FatcatStringWithNullTitle = FatcatString.replace("\"<<TITLE>>\"", "null")
+  val FatcatStringWithEmptyTitle = FatcatString.replace("<<TITLE>>", "")
+  val FatcatStringWithoutTitle = FatcatString.replace("title", "nottitle")
+  val MalformedFatcatString = FatcatString.replace("}", "")
+  val FatcatStringWithNoAuthors = FatcatString.replace("<<TITLE>>", "Some Valid Title").replace("contribs", "no-contribs")
+  //val FatcatStringWrongType = FatcatString.replace("<<TITLE>>", "Some Valid Title").replace("journal-article", "other")
+  //val FatcatStringNoType = FatcatString.replace("<<TITLE>>", "Some Valid Title").replace("type", "not-type")
+
+  // Unit tests
+  "FatcatScorable.jsonToMapFeatures()" should "handle invalid JSON" in {
+    FatcatScorable.jsonToMapFeatures(MalformedFatcatString) should be (None)
+  }
+
+  it should "handle missing title" in {
+    FatcatScorable.jsonToMapFeatures(FatcatStringWithoutTitle) should be (None)
+  }
+
+  it should "handle null title" in {
+    FatcatScorable.jsonToMapFeatures(FatcatStringWithNullTitle) should be (None)
+  }
+
+  it should "handle empty title" in {
+    FatcatScorable.jsonToMapFeatures(FatcatStringWithEmptyTitle) should be (None)
+  }
+
+  it should "handle subtitle" in {
+    FatcatScorable.jsonToMapFeatures(
+      """{"title": "short but not too short", "subtitle": "just right!", "ident": "pnri57u66ffytigdmyybbmouni", "work_id": "tdmqnfzm2nggrhfwzasyegvpyu", "DOI": "10.123/asdf", "type":"journal-article","contribs":[{ "raw_name" : "W Gaier", "surname" : "Gaier"}]}""") match {
+      case None => fail()
+      case Some(result) => result.slug shouldBe "shortbutnottooshortjustright"
+    }
+  }
+
+  it should "handle empty subtitle" in {
+    FatcatScorable.jsonToMapFeatures(
+      """{"title": "short but not too short", "subtitle": "", "ident": "pnri57u66ffytigdmyybbmouni", "work_id": "tdmqnfzm2nggrhfwzasyegvpyu", "DOI": "10.123/asdf", "type":"journal-article", "contribs":[{ "raw_name" : "W Gaier", "surname" : "Gaier"}]}""") match {
+      case None => fail()
+      case Some(result) => result.slug shouldBe "shortbutnottooshort"
+    }
+  }
+
+  it should "handle null subtitle" in {
+    FatcatScorable.jsonToMapFeatures(
+      """{"title": "short but not too short", "subtitle": null, "ident": "pnri57u66ffytigdmyybbmouni", "work_id": "tdmqnfzm2nggrhfwzasyegvpyu", "DOI": "10.123/asdf", "type":"journal-article", "contribs":[{ "raw_name" : "W Gaier", "surname" : "Gaier"}]}""") match {
+      case None => fail()
+      case Some(result) => result.slug shouldBe "shortbutnottooshort"
+    }
+  }
+
+  it should "handle missing authors" in {
+    // TODO: not actually removing these
+    //FatcatScorable.jsonToMapFeatures(FatcatStringWithNoAuthors) should be (None)
+    FatcatScorable.jsonToMapFeatures(FatcatStringWithNoAuthors)
+  }
+
+  it should "handle valid input" in {
+    FatcatScorable.jsonToMapFeatures(FatcatStringWithGoodTitle) match {
+      case None => fail()
+      case Some(result) => {
+        result.slug shouldBe "sometitle"
+        Scorable.jsonToMap(result.json) match {
+          case None => fail()
+          case Some(map) => {
+            map("title").asInstanceOf[String] shouldBe "Some Title"
+            //map("doi").asInstanceOf[String] shouldBe "10.123/abc"
+            map("fatcat_release").asInstanceOf[String] shouldBe "pnri57u66ffytigdmyybbmouni"
+            map("fatcat_work").asInstanceOf[String] shouldBe "tdmqnfzm2nggrhfwzasyegvpyu"
+            // TODO: full name? not just a string?
+            map("authors").asInstanceOf[List[String]] shouldBe List("W Gaier")
+            map("year").asInstanceOf[Double].toInt shouldBe 1996
+          }
+        }
+      }
+    }
+  }
+
+  "FatcatScorable.keepRecord()" should "return true for valid JSON with title" in {
+    FatcatScorable.keepRecord(FatcatStringWithGoodTitle) shouldBe true
+  }
+
+  it should "return true for valid JSON with a title of maximum permitted length" in {
+    FatcatScorable.keepRecord(FatcatStringWithMaximumTitle) shouldBe true
+  }
+
+  it should "return false for valid JSON with excessively long title" in {
+    FatcatScorable.keepRecord(FatcatStringWithExcessiveTitle) shouldBe false
+  }
+
+  it should "return false for valid JSON with null title" in {
+    FatcatScorable.keepRecord(FatcatStringWithNullTitle) shouldBe false
+  }
+
+  it should "return false for valid JSON with no title" in {
+    FatcatScorable.keepRecord(FatcatStringWithoutTitle) shouldBe false
+  }
+
+  it should "return false for invalid JSON" in {
+    FatcatScorable.keepRecord(FatcatStringWithoutTitle) shouldBe false
+  }
+
+}