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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 ScoreJobTest 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("}", "")
// 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)))
// TODO: Make less yucky.
ScoreJob.setScorable1(new CrossrefScorable())
ScoreJob.setScorable2(new GrobidScorable())
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),
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[(String, Int, String, String)](TypedTsv[(String, Int, String, String)](output)) {
// Grobid titles and slugs (in parentheses):
// Title 1 (title1)
// Title 2: TNG (title2)
// Title 3: The Sequel (title3)
// crossref titles and slugs (in parentheses):
// Title 1: TNG (title1)
// Title 1: TNG 2 (title1)
// Title 1: TNG 3 (title1)
// Title 2 Rebooted (title2rebooted)
// Join should have 3 "title1" slugs and 1 "title2" slug
outputBuffer =>
"The pipeline" should "return a 4-element list" in {
outputBuffer should have length 4
}
/*
it should "return the right first entry" in {
outputBuffer(0) shouldBe ReduceOutput("slug", 50, "",
"")
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
}
|
