Removed HBaseCrossrefScore{Job,Test} and references thereto.

1 files changed, 0 insertions, 293 deletions

diff --git a/scalding/src/test/scala/sandcrawler/HBaseCrossrefScoreTest.scala b/scalding/src/test/scala/sandcrawler/HBaseCrossrefScoreTest.scala
deleted file mode 100644
index ebe7dc0..0000000
--- a/scalding/src/test/scala/sandcrawler/HBaseCrossrefScoreTest.scala
+++ /dev/null
@@ -1,293 +0,0 @@
-package sandcrawler
-
-import cascading.tuple.Fields
-import cascading.tuple.Tuple
-import com.twitter.scalding.{JobTest, TextLine, TypedTsv, TupleConversions}
-import org.apache.hadoop.hbase.io.ImmutableBytesWritable
-import org.apache.hadoop.hbase.util.Bytes
-import org.scalatest._
-import parallelai.spyglass.hbase.HBaseConstants.SourceMode
-
-class HBaseCrossrefScoreTest 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 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" ]
-}
-"""
-  val CrossrefStringWithTitle = CrossrefString.replace("<<TITLE>>", "SomeTitle")
-  val CrossrefStringWithoutTitle = CrossrefString.replace("title", "nottitle")
-  val MalformedCrossrefString = CrossrefString.replace("}", "")
-
-  // Unit tests
-
-  "titleToSlug()" should "extract the parts of titles before a colon" in {
-    val slug = HBaseCrossrefScore.titleToSlug("HELLO:there")
-    slug should contain ("hello")
-  }
-
-  it should "extract an entire colon-less string" in {
-    val slug = HBaseCrossrefScore.titleToSlug("hello THERE")
-    slug should contain ("hello there")
-  }
-
-  it should "return None if given empty string" in {
-    HBaseCrossrefScore.titleToSlug("") shouldBe None
-  }
-
-  "grobidToSlug()" should "get the right slug for a grobid json string" in {
-    val slug = HBaseCrossrefScore.grobidToSlug(GrobidStringWithTitle)
-    slug should contain ("dummy example file")
-  }
-
-  it should "return None if given json string without title" in {
-    val slug = HBaseCrossrefScore.grobidToSlug(GrobidStringWithoutTitle)
-    slug shouldBe None
-  }
-
-  it should "return None if given a malformed json string" in {
-    val slug = HBaseCrossrefScore.grobidToSlug(MalformedGrobidString)
-    slug shouldBe None
-  }
-
-  it should "return None if given an empty json string" in {
-    val slug = HBaseCrossrefScore.grobidToSlug("")
-    slug shouldBe None
-  }
-
-  "crossrefToSlug()" should "get the right slug for a crossref json string" in {
-    val slug = HBaseCrossrefScore.crossrefToSlug(CrossrefStringWithTitle)
-    slug should contain ("sometitle")
-  }
-
-  it should "return None if given json string without title" in {
-    val slug = HBaseCrossrefScore.grobidToSlug(CrossrefStringWithoutTitle)
-    slug shouldBe None
-  }
-
-  it should "return None if given a malformed json string" in {
-    val slug = HBaseCrossrefScore.grobidToSlug(MalformedCrossrefString)
-    slug shouldBe None
-  }
-
-  "removeAccents()" should "handle the empty string" in {
-    HBaseCrossrefScore.removeAccents("") shouldBe ""
-  }
-
-  it should "not change a string with unaccented characters" in {
-    HBaseCrossrefScore.removeAccents("abc123") shouldBe "abc123"
-  }
-
-  it should "remove accents from Ls" in {
-    HBaseCrossrefScore.removeAccents("E\u0141\u0142en") shouldBe "ELlen"
-  }
-
-  it should "remove accents from Es without changing case" in {
-    val result = HBaseCrossrefScore.removeAccents("\u00e9")
-    result should have length 1
-    result shouldBe "e"
-  }
-
-  it should "convert the ø in Soren" in {
-    HBaseCrossrefScore.removeAccents("Søren") shouldBe "Soren"
-    HBaseCrossrefScore.removeAccents("SØREN") shouldBe "SOREN"
-  }
-
-  // Tests adapted from https://oldfashionedsoftware.com/2009/11/19/string-distance-and-refactoring-in-scala/
-  "stringDistance" should "work on empty strings" in {
-    HBaseCrossrefScore.stringDistance("", "") shouldBe 0
-    HBaseCrossrefScore.stringDistance("a", "") shouldBe 1
-    HBaseCrossrefScore.stringDistance("", "a") shouldBe 1
-    HBaseCrossrefScore.stringDistance("abc", "") shouldBe 3
-    HBaseCrossrefScore.stringDistance("", "abc") shouldBe 3
-  }
-
-  it should "work on equal strings" in {
-    HBaseCrossrefScore.stringDistance("", "") shouldBe 0
-    HBaseCrossrefScore.stringDistance("a", "a") shouldBe 0
-    HBaseCrossrefScore.stringDistance("abc", "abc") shouldBe 0
-  }
-
-  it should "work where only inserts are needed" in {
-    HBaseCrossrefScore.stringDistance("", "a") shouldBe 1
-    HBaseCrossrefScore.stringDistance("a", "ab") shouldBe 1
-    HBaseCrossrefScore.stringDistance("b", "ab") shouldBe 1
-    HBaseCrossrefScore.stringDistance("ac", "abc") shouldBe 1
-    HBaseCrossrefScore.stringDistance("abcdefg", "xabxcdxxefxgx") shouldBe 6
-  }
-
-  it should "work where only deletes are needed" in {
-    HBaseCrossrefScore.stringDistance( "a", "") shouldBe 1
-    HBaseCrossrefScore.stringDistance( "ab", "a") shouldBe 1
-    HBaseCrossrefScore.stringDistance( "ab", "b") shouldBe 1
-    HBaseCrossrefScore.stringDistance("abc", "ac") shouldBe 1
-    HBaseCrossrefScore.stringDistance("xabxcdxxefxgx", "abcdefg") shouldBe 6
-  }
-
-  it should "work where only substitutions are needed" in {
-    HBaseCrossrefScore.stringDistance(  "a",   "b") shouldBe 1
-    HBaseCrossrefScore.stringDistance( "ab",  "ac") shouldBe 1
-    HBaseCrossrefScore.stringDistance( "ac",  "bc") shouldBe 1
-    HBaseCrossrefScore.stringDistance("abc", "axc") shouldBe 1
-    HBaseCrossrefScore.stringDistance("xabxcdxxefxgx", "1ab2cd34ef5g6") shouldBe 6
-  }
-
-  it should "work where many operations are needed" in {
-    HBaseCrossrefScore.stringDistance("example", "samples") shouldBe 3
-    HBaseCrossrefScore.stringDistance("sturgeon", "urgently") shouldBe 6
-    HBaseCrossrefScore.stringDistance("levenshtein", "frankenstein") shouldBe 6
-    HBaseCrossrefScore.stringDistance("distance", "difference") shouldBe 5
-    HBaseCrossrefScore.stringDistance("java was neat", "scala is great") shouldBe 7
-  }
-
-  //  Pipeline tests
-  val output = "/tmp/testOutput"
-  val input = "/tmp/testInput"
-  val (testTable, testHost) = ("test-table", "dummy-host:2181")
-
-  val grobidSampleData = List(
-    List(Bytes.toBytes("sha1:K2DKSSVTXWPRMFDTWSTCQW3RVWRIOV3Q"),
-      Bytes.toBytes(GrobidString.replace("<<TITLE>>", "Title 1"))),
-    List(Bytes.toBytes("sha1:C3YNNEGH5WAG5ZAAXWAEBNXJWT6CZ3WU"),
-      Bytes.toBytes(GrobidString.replace("<<TITLE>>", "Title 2: TNG"))),
-    List(Bytes.toBytes("sha1:SDKUVHC3YNNEGH5WAG5ZAAXWAEBNX4WT"),
-      Bytes.toBytes(GrobidString.replace("<<TITLE>>", "Title 3: The Sequel"))),
-    List(Bytes.toBytes("sha1:35985C3YNNEGH5WAG5ZAAXWAEBNXJW56"), 
-      Bytes.toBytes(MalformedGrobidString)))
-
-  JobTest("sandcrawler.HBaseCrossrefScoreJob")
-    .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](HBaseCrossrefScore.getHBaseSource(testTable, testHost),
-      grobidSampleData.map(l => new Tuple(l.map(s => {new ImmutableBytesWritable(s)}):_*)))
-    .source(TextLine(input), List(
-      0 -> CrossrefString.replace("<<TITLE>>", "Title 1: TNG").replace("<<DOI>>", "DOI-0"),
-      1 -> CrossrefString.replace("<<TITLE>>", "Title 1: TNG 2").replace("<<DOI>>", "DOI-0.5"),
-      2 -> CrossrefString.replace("<<TITLE>>", "Title 1: TNG 3").replace("<<DOI>>", "DOI-0.75"),
-      3 -> CrossrefString.replace("<<TITLE>>", "Title 2: Rebooted").replace("<<DOI>>", "DOI-1")))
-    .sink[(Int, String, String, String, String)](TypedTsv[(Int,
-    String, String, String, String)](output)) {
-      // Grobid titles: 
-      //   "Title 1", "Title 2: TNG", "Title 3: The Sequel"
-      // crossref slugs: 
-      //   "Title 1: TNG", "Title 1: TNG 2", "Title 1: TNG 3", "Title 2 Rebooted"
-      // Join should have 3 "Title  1" slugs and 1 "Title 2" slug
-      outputBuffer =>
-      "The pipeline" should "return a 4-element list" in {
-        outputBuffer should have length 4
-      }
-
-      it should "return the right first entry" in {
-        val (slug, slug0, slug1, sha1, grobidJson, crossrefJson) = outputBuffer(0)
-        slug shouldBe "title 1"
-        slug shouldBe slug0
-        slug shouldBe slug1
-        sha1 shouldBe new String(grobidSampleData(0)(0), "UTF-8")
-        grobidJson shouldBe new String(grobidSampleData(0)(1), "UTF-8")
-      }
-    }
-    .run
-    .finish
- */
-}