Merge branch 'bnewbold-scoring-patches' into 'master'

Patches on top of scoring-refactor branch (Crossref/GROBID matching work)

See merge request webgroup/sandcrawler!15

10 files changed, 651 insertions, 12 deletions

diff --git a/scalding/src/test/scala/sandcrawler/CrossrefScorableTest.scala b/scalding/src/test/scala/sandcrawler/CrossrefScorableTest.scala
new file mode 100644
index 0000000..1789d1a
--- /dev/null
+++ b/scalding/src/test/scala/sandcrawler/CrossrefScorableTest.scala
@@ -0,0 +1,100 @@
+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 CrossrefScorableTest extends FlatSpec with Matchers {
+  // scalastyle:off
+  val CrossrefString =
+"""
+{ "_id" : { "$oid" : "5a553d5988a035a45bf50ed3" },
+  "indexed" : { "date-parts" : [ [ 2017, 10, 23 ] ],
+    "date-time" : "2017-10-23T17:19:16Z",
+    "timestamp" : { "$numberLong" : "1508779156477" } },
+  "reference-count" : 0,
+  "publisher" : "Elsevier BV",
+  "issue" : "3",
+  "license" : [ { "URL" : "http://www.elsevier.com/tdm/userlicense/1.0/",
+                    "start" : { "date-parts" : [ [ 1996, 1, 1 ] ],
+                                "date-time" : "1996-01-01T00:00:00Z",
+                                "timestamp" : { "$numberLong" : "820454400000" } },
+                                "delay-in-days" : 0, "content-version" : "tdm" }],
+  "content-domain" : { "domain" : [], "crossmark-restriction" : false },
+  "published-print" : { "date-parts" : [ [ 1996 ] ] },
+  "DOI" : "<<DOI>>",
+  "type" : "journal-article",
+  "created" : { "date-parts" : [ [ 2002, 7, 25 ] ],
+    "date-time" : "2002-07-25T15:09:41Z",
+    "timestamp" : { "$numberLong" : "1027609781000" } },
+  "page" : "186-187",
+  "source" : "Crossref",
+  "is-referenced-by-count" : 0,
+  "title" : [ "<<TITLE>>" ],
+  "prefix" : "10.1016",
+  "volume" : "9",
+  "author" : [ { "given" : "W", "family" : "Gaier", "affiliation" : [] } ],
+  "member" : "78",
+  "container-title" : [ "Journal de Pédiatrie et de Puériculture" ],
+  "link" : [ { "URL" :  "http://api.elsevier.com/content/article/PII:0987-7983(96)87729-2?httpAccept=text/xml",
+               "content-type" : "text/xml",
+                 "content-version" : "vor",
+                 "intended-application" : "text-mining" },
+               { "URL" :
+  "http://api.elsevier.com/content/article/PII:0987-7983(96)87729-2?httpAccept=text/plain",
+                 "content-type" : "text/plain",
+                 "content-version" : "vor",
+                 "intended-application" : "text-mining" } ],
+  "deposited" : { "date-parts" : [ [ 2015, 9, 3 ] ],
+                  "date-time" : "2015-09-03T10:03:43Z",
+                  "timestamp" : { "$numberLong" : "1441274623000" } },
+  "score" : 1,
+  "issued" : { "date-parts" : [ [ 1996 ] ] },
+  "references-count" : 0,
+  "alternative-id" : [ "0987-7983(96)87729-2" ],
+  "URL" : "http://dx.doi.org/10.1016/0987-7983(96)87729-2",
+  "ISSN" : [ "0987-7983" ],
+  "issn-type" : [ { "value" : "0987-7983", "type" : "print" } ],
+  "subject" : [ "Pediatrics, Perinatology, and Child Health" ]
+}
+"""
+  // scalastyle:on
+  val CrossrefStringWithTitle = CrossrefString.replace("<<TITLE>>", "Some Title")
+  val CrossrefStringWithEmptyTitle = CrossrefString.replace("<<TITLE>>", "")
+  val CrossrefStringWithoutTitle = CrossrefString.replace("title", "nottitle")
+  val MalformedCrossrefString = CrossrefString.replace("}", "")
+
+  // Unit tests
+  "CrossrefScorable.jsonToMapFeatures()" should "handle invalid JSON" in {
+    val result = CrossrefScorable.jsonToMapFeatures(MalformedCrossrefString)
+    result.slug shouldBe Scorable.NoSlug
+  }
+
+  it should "handle missing title" in {
+    val result = CrossrefScorable.jsonToMapFeatures(CrossrefStringWithoutTitle)
+    result.slug shouldBe Scorable.NoSlug
+  }
+
+  it should "handle empty title" in {
+    val result = CrossrefScorable.jsonToMapFeatures(CrossrefStringWithEmptyTitle)
+    result.slug shouldBe Scorable.NoSlug
+  }
+
+  it should "handle valid input" in {
+    val result = CrossrefScorable.jsonToMapFeatures(CrossrefStringWithTitle)
+    result.slug shouldBe "sometitle"
+    Scorable.jsonToMap(result.json) match {
+      case None => fail()
+      case Some(map) => {
+        map("title").asInstanceOf[String] shouldBe "Some Title"
+      }
+    }
+  }
+}
diff --git a/scalding/src/test/scala/sandcrawler/GrobidScorableTest.scala b/scalding/src/test/scala/sandcrawler/GrobidScorableTest.scala
new file mode 100644
index 0000000..661824b
--- /dev/null
+++ b/scalding/src/test/scala/sandcrawler/GrobidScorableTest.scala
@@ -0,0 +1,88 @@
+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 GrobidScorableTest extends FlatSpec with Matchers {
+  val GrobidString = """
+{
+  "title": "<<TITLE>>",
+  "authors": [
+    {"name": "Brewster Kahle"},
+    {"name": "J Doe"}
+  ],
+  "journal": {
+    "name": "Dummy Example File. Journal of Fake News. pp. 1-2. ISSN 1234-5678",
+    "eissn": null,
+    "issn": null,
+    "issue": null,
+    "publisher": null,
+    "volume": null
+  },
+  "date": "2000",
+  "doi": null,
+  "citations": [
+    { "authors": [{"name": "A Seaperson"}],
+      "date": "2001",
+      "id": "b0",
+      "index": 0,
+      "issue": null,
+      "journal": "Letters in the Alphabet",
+      "publisher": null,
+      "title": "Everything is Wonderful",
+      "url": null,
+      "volume": "20"},
+    { "authors": [],
+      "date": "2011-03-28",
+      "id": "b1",
+      "index": 1,
+      "issue": null,
+      "journal": "The Dictionary",
+      "publisher": null,
+      "title": "All about Facts",
+      "url": null,
+      "volume": "14"}
+  ],
+  "abstract": "Everything you ever wanted to know about nothing",
+  "body": "Introduction \nEverything starts somewhere, as somebody [1]  once said. \n\n In Depth \n Meat \nYou know, for kids. \n Potatos \nQED.",
+  "acknowledgement": null,
+  "annex": null
+}
+"""
+  val GrobidStringWithTitle = GrobidString.replace("<<TITLE>>", "Dummy Example File")
+  val GrobidStringWithoutTitle = GrobidString.replace("title", "nottitle")
+  val MalformedGrobidString = GrobidString.replace("}", "")
+  val Key = "Dummy Key"
+
+  // Unit tests
+
+  "GrobidScorable.jsonToMapFeatures()" should "handle invalid JSON" in {
+    val result = GrobidScorable.jsonToMapFeatures(Key, MalformedGrobidString)
+    result.slug shouldBe Scorable.NoSlug
+  }
+
+  it should "handle missing title" in {
+    val result = GrobidScorable.jsonToMapFeatures(Key, GrobidStringWithoutTitle)
+    result.slug shouldBe Scorable.NoSlug
+  }
+
+  it should "handle valid input" in {
+    val result = GrobidScorable.jsonToMapFeatures(Key, GrobidStringWithTitle)
+    result.slug shouldBe "dummyexamplefile"
+    Scorable.jsonToMap(result.json) match {
+      case None => fail()
+      case Some(map) => {
+        map should contain key "title"
+        map("title").asInstanceOf[String] shouldBe "Dummy Example File"
+      }
+    }
+  }
+}
diff --git a/scalding/src/test/scala/sandcrawler/HBaseBuilderTest.scala b/scalding/src/test/scala/sandcrawler/HBaseBuilderTest.scala
index 603a4c7..c61cb22 100644
--- a/scalding/src/test/scala/sandcrawler/HBaseBuilderTest.scala
+++ b/scalding/src/test/scala/sandcrawler/HBaseBuilderTest.scala
@@ -22,6 +22,7 @@ class HBaseBuilderTest extends FlatSpec with Matchers {
     fields should have length 0
   }
 
+  //scalastyle:off no.whitespace.before.left.bracket
   it should "throw IllegalArgumentException on malformed input" in {
     a [IllegalArgumentException] should be thrownBy {
       HBaseBuilder.parseColSpecs(List("file_size"))
diff --git a/scalding/src/test/scala/sandcrawler/HBaseMimeCountTest.scala b/scalding/src/test/scala/sandcrawler/HBaseMimeCountTest.scala
index fde2290..d6d283f 100644
--- a/scalding/src/test/scala/sandcrawler/HBaseMimeCountTest.scala
+++ b/scalding/src/test/scala/sandcrawler/HBaseMimeCountTest.scala
@@ -1,15 +1,18 @@
 package sandcrawler
 
-import cascading.tuple.{Tuple, Fields}
-import com.twitter.scalding.{JobTest, Tsv, TupleConversions}
+import cascading.tuple.Fields
+import cascading.tuple.Tuple
+import com.twitter.scalding.JobTest
+import com.twitter.scalding.Tsv
+import com.twitter.scalding.TupleConversions
 import org.apache.hadoop.hbase.io.ImmutableBytesWritable
 import org.apache.hadoop.hbase.util.Bytes
 import org.junit.runner.RunWith
 import org.scalatest.FunSpec
 import org.scalatest.junit.JUnitRunner
 import org.slf4j.LoggerFactory
-import parallelai.spyglass.hbase.HBaseSource
 import parallelai.spyglass.hbase.HBaseConstants.SourceMode
+import parallelai.spyglass.hbase.HBaseSource
 import scala._
 
 @RunWith(classOf[JUnitRunner])
diff --git a/scalding/src/test/scala/sandcrawler/HBaseRowCountTest.scala b/scalding/src/test/scala/sandcrawler/HBaseRowCountTest.scala
index 3424a36..c4ca5aa 100644
--- a/scalding/src/test/scala/sandcrawler/HBaseRowCountTest.scala
+++ b/scalding/src/test/scala/sandcrawler/HBaseRowCountTest.scala
@@ -1,15 +1,18 @@
 package sandcrawler
 
-import cascading.tuple.{Tuple, Fields}
-import com.twitter.scalding.{JobTest, Tsv, TupleConversions}
+import cascading.tuple.Fields
+import cascading.tuple.Tuple
+import com.twitter.scalding.JobTest
+import com.twitter.scalding.Tsv
+import com.twitter.scalding.TupleConversions
 import org.apache.hadoop.hbase.io.ImmutableBytesWritable
 import org.apache.hadoop.hbase.util.Bytes
 import org.junit.runner.RunWith
 import org.scalatest.FunSpec
 import org.scalatest.junit.JUnitRunner
 import org.slf4j.LoggerFactory
-import parallelai.spyglass.hbase.HBaseSource
 import parallelai.spyglass.hbase.HBaseConstants.SourceMode
+import parallelai.spyglass.hbase.HBaseSource
 import scala._
 
 /**
@@ -47,12 +50,10 @@ class HBaseRowCountTest extends FunSpec with TupleConversions {
       outputBuffer =>
 
         it("should return the test data provided.") {
-          println("outputBuffer.size => " + outputBuffer.size)
           assert(outputBuffer.size === 1)
         }
 
         it("should return the correct count") {
-          println("raw output => " + outputBuffer)
           assert(outputBuffer(0).getObject(0) === 8)
         }
     }
diff --git a/scalding/src/test/scala/sandcrawler/HBaseStatusCountTest.scala b/scalding/src/test/scala/sandcrawler/HBaseStatusCountTest.scala
index d7689cd..0da0b9c 100644
--- a/scalding/src/test/scala/sandcrawler/HBaseStatusCountTest.scala
+++ b/scalding/src/test/scala/sandcrawler/HBaseStatusCountTest.scala
@@ -1,15 +1,19 @@
 package sandcrawler
 
-import cascading.tuple.{Tuple, Fields}
-import com.twitter.scalding.{JobTest, Tsv, TypedTsv, TupleConversions}
+import cascading.tuple.Fields
+import cascading.tuple.Tuple
+import com.twitter.scalding.JobTest
+import com.twitter.scalding.Tsv
+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.junit.runner.RunWith
 import org.scalatest.FunSpec
 import org.scalatest.junit.JUnitRunner
 import org.slf4j.LoggerFactory
-import parallelai.spyglass.hbase.HBaseSource
 import parallelai.spyglass.hbase.HBaseConstants.SourceMode
+import parallelai.spyglass.hbase.HBaseSource
 import scala._
 
 @RunWith(classOf[JUnitRunner])
@@ -25,7 +29,8 @@ class HBaseStatusCountTest extends FunSpec with TupleConversions {
   val statusType1Bytes = Bytes.toBytes(statusType1)
   val statusType2Bytes = Bytes.toBytes(statusType2)
 
-  val sampleData = List(
+  val sampleData : List[List[Array[Byte]]] = List(
+    // TODO(bnewbold): now to express a null (empty value) in this list?
     List(Bytes.toBytes("sha1:K2DKSSVTXWPRMFDTWSTCQW3RVWRIOV3Q"), statusType1Bytes),
     List(Bytes.toBytes("sha1:C3YNNEGH5WAG5ZAAXWAEBNXJWT6CZ3WU"), statusType1Bytes),
     List(Bytes.toBytes("sha1:SDKUVHC3YNNEGH5WAG5ZAAXWAEBNX4WT"), statusType2Bytes),
diff --git a/scalding/src/test/scala/sandcrawler/ScorableFeaturesTest.scala b/scalding/src/test/scala/sandcrawler/ScorableFeaturesTest.scala
new file mode 100644
index 0000000..80d92aa
--- /dev/null
+++ b/scalding/src/test/scala/sandcrawler/ScorableFeaturesTest.scala
@@ -0,0 +1,57 @@
+package sandcrawler
+
+import org.scalatest._
+
+// scalastyle:off null
+class ScorableFeaturesTest extends FlatSpec with Matchers {
+  private def titleToSlug(s : String) : String = {
+    new ScorableFeatures(title = s).toSlug
+  }
+
+  "toMapFeatures()" should "work with gnarly inputs" in {
+    new ScorableFeatures(title = null).toMapFeatures
+    new ScorableFeatures(title = "something", doi = null, sha1 = null, year = 123).toMapFeatures
+  }
+
+  "mapToSlug()" should "extract the parts of titles before a colon" in {
+    titleToSlug("HELLO:there") shouldBe "hellothere"
+  }
+
+  it should "extract an entire colon-less string" in {
+    titleToSlug("hello THERE") shouldBe "hellothere"
+  }
+
+  it should "return Scorable.NoSlug if given empty string" in {
+    titleToSlug("") shouldBe Scorable.NoSlug
+  }
+
+  it should "return Scorable.NoSlug if given null" in {
+    titleToSlug(null) shouldBe Scorable.NoSlug
+  }
+
+  it should "strip punctuation" in {
+    titleToSlug("HELLO!:the:re") shouldBe "hellothere"
+    titleToSlug("a:b:c") shouldBe "abc"
+    titleToSlug(
+      "If you're happy and you know it, clap your hands!") shouldBe "ifyourehappyandyouknowitclapyourhands"
+    titleToSlug(":;\"\'") shouldBe Scorable.NoSlug
+  }
+
+  it should "filter stub titles" in {
+    titleToSlug("abstract") shouldBe Scorable.NoSlug
+    titleToSlug("title!") shouldBe Scorable.NoSlug
+    titleToSlug("a real title which is not on blacklist") shouldBe "arealtitlewhichisnotonblacklist"
+  }
+
+  it should "strip special characters" in {
+    titleToSlug(":;!',|\"\'`.#?!-@*/\\=+~%$^{}()[]<>-_") shouldBe Scorable.NoSlug
+    // TODO: titleToSlug("©™₨№…") shouldBe Scorable.NoSlug
+    // TODO: titleToSlug("πµΣσ") shouldBe Scorable.NoSlug
+  }
+
+  it should "remove whitespace" in {
+    titleToSlug("foo bar : baz ::") shouldBe "foobarbaz"
+    titleToSlug("\na\t:b:c") shouldBe "abc"
+    titleToSlug("\n \t \r  ") shouldBe Scorable.NoSlug
+  }
+}
diff --git a/scalding/src/test/scala/sandcrawler/ScorableTest.scala b/scalding/src/test/scala/sandcrawler/ScorableTest.scala
new file mode 100644
index 0000000..f63bef8
--- /dev/null
+++ b/scalding/src/test/scala/sandcrawler/ScorableTest.scala
@@ -0,0 +1,73 @@
+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 ScorableTest extends FlatSpec with Matchers {
+  val JsonString = """
+{
+  "title": "<<TITLE>>",
+  "authors": [
+    {"name": "Brewster Kahle"},
+    {"name": "J Doe"}
+  ],
+  "journal": {
+    "name": "Dummy Example File. Journal of Fake News. pp. 1-2. ISSN 1234-5678",
+    "eissn": null,
+    "issn": null,
+    "issue": null,
+    "publisher": null,
+    "volume": null
+  },
+  "date": "2000",
+  "doi": null,
+  "citations": [
+    { "authors": [{"name": "A Seaperson"}],
+      "date": "2001",
+      "id": "b0",
+      "index": 0,
+      "issue": null,
+      "journal": "Letters in the Alphabet",
+      "publisher": null,
+      "title": "Everything is Wonderful",
+      "url": null,
+      "volume": "20"},
+    { "authors": [],
+      "date": "2011-03-28",
+      "id": "b1",
+      "index": 1,
+      "issue": null,
+      "journal": "The Dictionary",
+      "publisher": null,
+      "title": "All about Facts",
+      "url": null,
+      "volume": "14"}
+  ],
+  "abstract": "Everything you ever wanted to know about nothing",
+  "body": "Introduction \nEverything starts somewhere, as somebody [1]  once said. \n\n In Depth \n Meat \nYou know, for kids. \n Potatos \nQED.",
+  "acknowledgement": null,
+  "annex": null
+}
+"""
+  "jsonToMap()" should "return a map, given a legal JSON string" in {
+    Scorable.jsonToMap(JsonString) should not be (None)
+  }
+
+  it should "return None, given illegal JSON" in {
+    Scorable.jsonToMap("illegal{,json{{") should be (None)
+  }
+
+  "computeOutput()" should "return Scorable.MaxScore if given identical ReduceFeatures" in {
+    val score = Scorable.computeSimilarity(
+      new ReduceFeatures(JsonString), new ReduceFeatures(JsonString))
+    score shouldBe Scorable.MaxScore
+  }
+}
diff --git a/scalding/src/test/scala/sandcrawler/ScoreJobTest.scala b/scalding/src/test/scala/sandcrawler/ScoreJobTest.scala
new file mode 100644
index 0000000..f92ba31
--- /dev/null
+++ b/scalding/src/test/scala/sandcrawler/ScoreJobTest.scala
@@ -0,0 +1,226 @@
+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 ScoreJobTest extends FlatSpec with Matchers {
+  //scalastyle:off
+  val JsonString = """
+{
+  "title": "<<TITLE>>",
+  "authors": [
+    {"name": "Brewster Kahle"},
+    {"name": "J Doe"}
+  ],
+  "journal": {
+    "name": "Dummy Example File. Journal of Fake News. pp. 1-2. ISSN 1234-5678",
+    "eissn": null,
+    "issn": null,
+    "issue": null,
+    "publisher": null,
+    "volume": null
+  },
+  "date": "2000",
+  "doi": null,
+  "citations": [
+    { "authors": [{"name": "A Seaperson"}],
+      "date": "2001",
+      "id": "b0",
+      "index": 0,
+      "issue": null,
+      "journal": "Letters in the Alphabet",
+      "publisher": null,
+      "title": "Everything is Wonderful",
+      "url": null,
+      "volume": "20"},
+    { "authors": [],
+      "date": "2011-03-28",
+      "id": "b1",
+      "index": 1,
+      "issue": null,
+      "journal": "The Dictionary",
+      "publisher": null,
+      "title": "All about Facts",
+      "url": null,
+      "volume": "14"}
+  ],
+  "abstract": "Everything you ever wanted to know about nothing",
+  "body": "Introduction \nEverything starts somewhere, as somebody [1]  once said. \n\n In Depth \n Meat \nYou know, for kids. \n Potatos \nQED.",
+  "acknowledgement": null,
+  "annex": null
+}
+"""
+  // scalastyle:on
+  val JsonStringWithTitle = JsonString.replace("<<TITLE>>", "Dummy Example File")
+  val JsonStringWithoutTitle = JsonString.replace("title", "nottitle")
+  val MalformedJsonString = JsonString.replace("}", "")
+
+  // scalastyle:off
+  val CrossrefString =
+"""
+{ "_id" : { "$oid" : "5a553d5988a035a45bf50ed3" },
+  "indexed" : { "date-parts" : [ [ 2017, 10, 23 ] ],
+    "date-time" : "2017-10-23T17:19:16Z",
+    "timestamp" : { "$numberLong" : "1508779156477" } },
+  "reference-count" : 0,
+  "publisher" : "Elsevier BV",
+  "issue" : "3",
+  "license" : [ { "URL" : "http://www.elsevier.com/tdm/userlicense/1.0/",
+                    "start" : { "date-parts" : [ [ 1996, 1, 1 ] ],
+                                "date-time" : "1996-01-01T00:00:00Z",
+                                "timestamp" : { "$numberLong" : "820454400000" } },
+                                "delay-in-days" : 0, "content-version" : "tdm" }],
+  "content-domain" : { "domain" : [], "crossmark-restriction" : false },
+  "published-print" : { "date-parts" : [ [ 1996 ] ] },
+  "DOI" : "<<DOI>>",
+  "type" : "journal-article",
+  "created" : { "date-parts" : [ [ 2002, 7, 25 ] ],
+    "date-time" : "2002-07-25T15:09:41Z",
+    "timestamp" : { "$numberLong" : "1027609781000" } },
+  "page" : "186-187",
+  "source" : "Crossref",
+  "is-referenced-by-count" : 0,
+  "title" : [ "<<TITLE>>" ],
+  "prefix" : "10.1016",
+  "volume" : "9",
+  "author" : [ { "given" : "W", "family" : "Gaier", "affiliation" : [] } ],
+  "member" : "78",
+  "container-title" : [ "Journal de Pédiatrie et de Puériculture" ],
+  "link" : [ { "URL" :  "http://api.elsevier.com/content/article/PII:0987-7983(96)87729-2?httpAccept=text/xml",
+               "content-type" : "text/xml",
+               "content-version" : "vor",
+               "intended-application" : "text-mining" },
+               { "URL" :
+  "http://api.elsevier.com/content/article/PII:0987-7983(96)87729-2?httpAccept=text/plain",
+                 "content-type" : "text/plain",
+                 "content-version" : "vor",
+                 "intended-application" : "text-mining" } ],
+  "deposited" : { "date-parts" : [ [ 2015, 9, 3 ] ],
+                  "date-time" : "2015-09-03T10:03:43Z",
+                  "timestamp" : { "$numberLong" : "1441274623000" } },
+  "score" : 1,
+  "issued" : { "date-parts" : [ [ 1996 ] ] },
+  "references-count" : 0,
+  "alternative-id" : [ "0987-7983(96)87729-2" ],
+  "URL" : "http://dx.doi.org/10.1016/0987-7983(96)87729-2",
+  "ISSN" : [ "0987-7983" ],
+  "issn-type" : [ { "value" : "0987-7983", "type" : "print" } ],
+  "subject" : [ "Pediatrics, Perinatology, and Child Health" ]
+}
+"""
+  // scalastyle:on
+  val CrossrefStringWithTitle = CrossrefString.replace("<<TITLE>>", "SomeTitle")
+  val CrossrefStringWithoutTitle = CrossrefString.replace("title", "nottitle")
+  val MalformedCrossrefString = CrossrefString.replace("}", "")
+  val CrossrefStrings = List(
+    CrossrefString.replace("<<TITLE>>", "Title 2: TNG").replace("<<DOI>>", "DOI-0"),
+    CrossrefString.replace("<<TITLE>>", "Title 1: TNG 2A").replace("<<DOI>>", "DOI-0.5"),
+    CrossrefString.replace("<<TITLE>>", "Title 1: TNG 3").replace("<<DOI>>", "DOI-0.75"),
+    CrossrefString.replace("<<TITLE>>", "Title 2: Rebooted").replace("<<DOI>>", "DOI-1"))
+
+  //  Pipeline tests
+  val output = "/tmp/testOutput"
+  val input = "/tmp/testInput"
+  val (testTable, testHost) = ("test-table", "dummy-host:2181")
+
+  val Sha1Strings : List[String] = List(
+    "sha1:K2DKSSVTXWPRMFDTWSTCQW3RVWRIOV3Q",
+    "sha1:C3YNNEGH5WAG5ZAAXWAEBNXJWT6CZ3WU",
+    "sha1:SDKUVHC3YNNEGH5WAG5ZAAXWAEBNX4WT",
+    "sha1:35985C3YNNEGH5WAG5ZAAXWAEBNXJW56",
+    "sha1:93187A85273589347598473894839443",
+    "sha1:024937534094897039547e9824382943")
+
+  val JsonStrings : List[String] = List(
+    JsonString.replace("<<TITLE>>", "Title 1"),
+    JsonString.replace("<<TITLE>>", "Title 2: TNG"),
+    JsonString.replace("<<TITLE>>", "Title 3: The Sequel"),
+    // This will have bad status.
+    JsonString.replace("<<TITLE>>", "Title 1"),
+    MalformedJsonString,
+    // This will have bad status.
+    JsonString.replace("<<TITLE>>", "Title 2")
+  )
+
+  // bnewbold: status codes aren't strings, they are uint64
+  val Ok : Long = 200
+  val Bad : Long = 400
+  val StatusCodes = List(Ok, Ok, Ok, Bad, Ok, Bad)
+
+  val SampleDataHead : List[Tuple] = (Sha1Strings, JsonStrings, StatusCodes)
+    .zipped
+    .toList
+    .map { case (sha, json, status) => List(Bytes.toBytes(sha), Bytes.toBytes(json), Bytes.toBytes(status)) }
+    .map { l => new Tuple(l.map(s => {new ImmutableBytesWritable(s)}):_*) }
+
+  // Add example of lines without GROBID data
+  val SampleData = SampleDataHead :+ new Tuple(
+    new ImmutableBytesWritable(Bytes.toBytes("sha1:35985C3YNNEGH5WAG5ZAA88888888888")), null, null)
+
+  JobTest("sandcrawler.ScoreJob")
+    .arg("test", "")
+    .arg("app.conf.path", "app.conf")
+    .arg("output", output)
+    .arg("hbase-table", testTable)
+    .arg("zookeeper-hosts", testHost)
+    .arg("crossref-input", input)
+    .arg("debug", "true")
+    .source[Tuple](GrobidScorable.getHBaseSource(testTable, testHost), SampleData)
+    .source(TextLine(input), List(
+      0 -> CrossrefStrings(0),
+      1 -> CrossrefStrings(1),
+      2 -> CrossrefStrings(2),
+      3 -> CrossrefStrings(3)))
+    .sink[(String, Int, String, String)](TypedTsv[(String, Int, String, String)](output)) {
+      // Grobid titles and slugs (in parentheses):
+      //   Title 1                       (title1)
+      //   Title 2: TNG                  (title2tng)
+      //   Title 3: The Sequel           (title3thesequel)
+      // crossref titles and slugs (in parentheses):
+      //   Title 2: TNG                  (title2tng)
+      //   Title 1: TNG 2A               (title1tng2a)
+      //   Title 1: TNG 3                (title1tng3)
+      //   Title 2: Rebooted             (title2rebooted)
+      // XXX: Join should have 3 "title1" slugs and 1 "title2tng" slug
+      outputBuffer =>
+      "The pipeline" should "return a 1-element list" in {
+        outputBuffer should have length 1
+      }
+
+      it should "has right # of entries with each slug" in {
+        val slugs = outputBuffer.map(_._1)
+        val countMap : Map[String, Int] = slugs.groupBy(identity).mapValues(_.size)
+        // XXX: countMap("title1") shouldBe 3
+        countMap("title2tng") shouldBe 1
+      }
+
+      def bundle(slug : String, grobidIndex : Int, crossrefIndex : Int) : (String, Int, String, String) = {
+        val mf1 : MapFeatures = GrobidScorable.jsonToMapFeatures(
+          Sha1Strings(grobidIndex),
+          JsonStrings(grobidIndex))
+        val mf2 : MapFeatures = CrossrefScorable.jsonToMapFeatures(
+          CrossrefStrings(crossrefIndex))
+        val score = Scorable.computeSimilarity(
+          ReduceFeatures(mf1.json),
+          ReduceFeatures(mf2.json))
+        (slug, score, mf1.json, mf2.json)
+      }
+
+      it should "have right output values" in {
+        //outputBuffer.exists(_ == bundle("title1", 0, 0))
+        //outputBuffer.exists(_ == bundle("title1", 0, 2))
+        //outputBuffer.exists(_ == bundle("title1", 0, 1))
+        outputBuffer.exists(_ == bundle("title2tng", 1, 3))
+      }
+    }
+    .run
+    .finish
+}
diff --git a/scalding/src/test/scala/sandcrawler/StringUtilitiesTest.scala b/scalding/src/test/scala/sandcrawler/StringUtilitiesTest.scala
new file mode 100644
index 0000000..410819b
--- /dev/null
+++ b/scalding/src/test/scala/sandcrawler/StringUtilitiesTest.scala
@@ -0,0 +1,85 @@
+package sandcrawler
+
+import org.scalatest._
+
+class StringUtilitiesTest extends FlatSpec with Matchers {
+  "removeAccents()" should "handle the empty string" in {
+    StringUtilities.removeAccents("") shouldBe ""
+  }
+
+  it should "not change a string with unaccented characters" in {
+    StringUtilities.removeAccents("abc123") shouldBe "abc123"
+  }
+
+  it should "remove accents from Ls" in {
+    StringUtilities.removeAccents("E\u0141\u0142en") shouldBe "ELlen"
+  }
+
+  it should "remove accents from Es without changing case" in {
+    val result = StringUtilities.removeAccents("\u00e9")
+    result should have length 1
+    result shouldBe "e"
+  }
+
+  it should "convert the ø in Soren" in {
+    StringUtilities.removeAccents("Søren") shouldBe "Soren"
+    StringUtilities.removeAccents("SØREN") shouldBe "SOREN"
+  }
+
+  "removePunctuation" should "work on the empty string" in {
+    StringUtilities.removePunctuation("") shouldBe ""
+  }
+
+  it should "work on non-empty text strings" in {
+    StringUtilities.removePunctuation("Hello, world!") shouldBe "Hello world"
+    StringUtilities.removePunctuation(":-)") shouldBe ""
+    StringUtilities.removePunctuation("<<---a---b--->") shouldBe "ab"
+  }
+
+  // Tests adapted from https://oldfashionedsoftware.com/2009/11/19/string-distance-and-refactoring-in-scala/
+  "stringDistance" should "work on empty strings" in {
+    StringUtilities.stringDistance("", "") shouldBe 0
+    StringUtilities.stringDistance("a", "") shouldBe 1
+    StringUtilities.stringDistance("", "a") shouldBe 1
+    StringUtilities.stringDistance("abc", "") shouldBe 3
+    StringUtilities.stringDistance("", "abc") shouldBe 3
+  }
+
+  it should "work on equal strings" in {
+    StringUtilities.stringDistance("", "") shouldBe 0
+    StringUtilities.stringDistance("a", "a") shouldBe 0
+    StringUtilities.stringDistance("abc", "abc") shouldBe 0
+  }
+
+  it should "work where only inserts are needed" in {
+    StringUtilities.stringDistance("", "a") shouldBe 1
+    StringUtilities.stringDistance("a", "ab") shouldBe 1
+    StringUtilities.stringDistance("b", "ab") shouldBe 1
+    StringUtilities.stringDistance("ac", "abc") shouldBe 1
+    StringUtilities.stringDistance("abcdefg", "xabxcdxxefxgx") shouldBe 6
+  }
+
+  it should "work where only deletes are needed" in {
+    StringUtilities.stringDistance( "a", "") shouldBe 1
+    StringUtilities.stringDistance( "ab", "a") shouldBe 1
+    StringUtilities.stringDistance( "ab", "b") shouldBe 1
+    StringUtilities.stringDistance("abc", "ac") shouldBe 1
+    StringUtilities.stringDistance("xabxcdxxefxgx", "abcdefg") shouldBe 6
+  }
+
+  it should "work where only substitutions are needed" in {
+    StringUtilities.stringDistance(  "a",   "b") shouldBe 1
+    StringUtilities.stringDistance( "ab",  "ac") shouldBe 1
+    StringUtilities.stringDistance( "ac",  "bc") shouldBe 1
+    StringUtilities.stringDistance("abc", "axc") shouldBe 1
+    StringUtilities.stringDistance("xabxcdxxefxgx", "1ab2cd34ef5g6") shouldBe 6
+  }
+
+  it should "work where many operations are needed" in {
+    StringUtilities.stringDistance("example", "samples") shouldBe 3
+    StringUtilities.stringDistance("sturgeon", "urgently") shouldBe 6
+    StringUtilities.stringDistance("levenshtein", "frankenstein") shouldBe 6
+    StringUtilities.stringDistance("distance", "difference") shouldBe 5
+    StringUtilities.stringDistance("java was neat", "scala is great") shouldBe 7
+  }
+}