From 3e33d60aac9db78d0458876fbe987627db222bbb Mon Sep 17 00:00:00 2001
From: Ellen Spertus <ellen.spertus@gmail.com>
Date: Tue, 24 Jul 2018 11:53:58 -0700
Subject: grobidToSlug() seems to work, including parsing of valid JSON
 strings.

---
 .../scala/sandcrawler/HBaseCrossrefScoreJob.scala  | 58 +++++++++++++++++
 .../scala/sandcrawler/HBaseCrossrefScoreTest.scala | 73 ++++++++++++++++++++++
 2 files changed, 131 insertions(+)
 create mode 100644 scalding/src/main/scala/sandcrawler/HBaseCrossrefScoreJob.scala
 create mode 100644 scalding/src/test/scala/sandcrawler/HBaseCrossrefScoreTest.scala

(limited to 'scalding')

diff --git a/scalding/src/main/scala/sandcrawler/HBaseCrossrefScoreJob.scala b/scalding/src/main/scala/sandcrawler/HBaseCrossrefScoreJob.scala
new file mode 100644
index 0000000..a22af81
--- /dev/null
+++ b/scalding/src/main/scala/sandcrawler/HBaseCrossrefScoreJob.scala
@@ -0,0 +1,58 @@
+package sandcrawler
+
+import java.util.Properties
+
+import scala.util.parsing.json.JSON
+
+import cascading.tuple.Fields
+import com.twitter.scalding._
+import com.twitter.scalding.typed.TDsl._
+import org.apache.hadoop.hbase.io.ImmutableBytesWritable
+import parallelai.spyglass.base.JobBase
+import parallelai.spyglass.hbase.HBaseConstants.SourceMode
+import parallelai.spyglass.hbase.HBasePipeConversions
+
+class HBaseCrossrefScoreJob(args: Args) extends JobBase(args) with HBasePipeConversions {
+
+  // key is SHA1
+  val grobidSource = HBaseBuilder.build(
+    args("grobid-table"),
+    args("zookeeper-hosts"),
+    List("grobid0:tei_json"),
+    sourceMode = SourceMode.SCAN_ALL)
+
+  val grobidPipe = grobidSource
+   .read
+    .map('tei_json -> 'slug) {
+      json : String => HBaseCrossrefScore.grobidToSlug(json)}
+
+  /*
+  val crossrefSource = TextLine(args("input"))
+  val crossrefPipe = crossrefSource
+    .read
+    .map('line -> 'slug) {
+      json : String => crossrefToSlug(json)}
+
+
+  statusPipe.groupBy { identity }
+    .size
+    .debug
+    .write(TypedTsv[(Long,Long)](args("output")))
+   */
+}
+
+object HBaseCrossrefScore {
+  def grobidToSlug(json : String) = {
+    // https://stackoverflow.com/a/32717262/631051
+    val jsonObject = JSON.parseFull(json)
+    val globalMap = jsonObject.get.asInstanceOf[Map[String, Any]]
+    globalMap.get("title") match {
+      case Some(title) => titleToSlug(title.asInstanceOf[String])
+      case None => ""
+    }
+  }
+
+  def titleToSlug(title : String) = {
+    title.split(":")(0)
+  }
+}
diff --git a/scalding/src/test/scala/sandcrawler/HBaseCrossrefScoreTest.scala b/scalding/src/test/scala/sandcrawler/HBaseCrossrefScoreTest.scala
new file mode 100644
index 0000000..186bb70
--- /dev/null
+++ b/scalding/src/test/scala/sandcrawler/HBaseCrossrefScoreTest.scala
@@ -0,0 +1,73 @@
+package sandcrawler
+
+import cascading.tuple.Fields
+import org.scalatest._
+import parallelai.spyglass.hbase.HBaseConstants.SourceMode
+
+class HBaseCrossrefScoreTest extends FlatSpec with Matchers {
+  val GrobidString = """
+{
+  "title": "Dummy Example File",
+  "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 GrobidStringWithoutTitle = GrobidString.replace("title", "nottitle")
+
+  "titleToSlug()" should "extract the parts of titles before a colon" in {
+    val slug = HBaseCrossrefScore.titleToSlug("hello:there")
+    slug shouldBe "hello"
+  }
+  it should "extract an entire colon-less string" in {
+    val slug = HBaseCrossrefScore.titleToSlug("hello there")
+    slug shouldBe "hello there"
+  }
+
+  "grobidToSlug()" should "get the right slug for a grobid json string" in {
+    val slug = HBaseCrossrefScore.grobidToSlug(GrobidString)
+    slug shouldBe "Dummy Example File"
+  }
+
+  "grobidToSlug()" should "return empty string for a grobid json string without a title" in {
+    val slug = HBaseCrossrefScore.grobidToSlug(GrobidStringWithoutTitle)
+    slug shouldBe ""
+  }
+}
-- 
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