1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
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
}
|
