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authorBryan Newbold <bnewbold@archive.org>2018-09-12 15:27:08 -0700
committerBryan Newbold <bnewbold@archive.org>2018-09-12 15:27:11 -0700
commite5db9bc783c1157984c160d155c44d38b84b57ce (patch)
tree2bae1f8a17e9a667ec5df8d468decb2b5b10915e
parent9d21a922386624b39b730849ab56c00a061f255f (diff)
downloadsandcrawler-e5db9bc783c1157984c160d155c44d38b84b57ce.tar.gz
sandcrawler-e5db9bc783c1157984c160d155c44d38b84b57ce.zip
hack scorejob variant with extra context joined in
This is to allow pushes to fatcat. There is probably a better way...
-rw-r--r--scalding/src/main/scala/sandcrawler/ScoreInsertable.scala86
-rw-r--r--scalding/src/test/scala/sandcrawler/ScoreInsertableJobTest.scala262
2 files changed, 348 insertions, 0 deletions
diff --git a/scalding/src/main/scala/sandcrawler/ScoreInsertable.scala b/scalding/src/main/scala/sandcrawler/ScoreInsertable.scala
new file mode 100644
index 0000000..58007fa
--- /dev/null
+++ b/scalding/src/main/scala/sandcrawler/ScoreInsertable.scala
@@ -0,0 +1,86 @@
+package sandcrawler
+
+import cascading.tuple.Fields
+import cascading.pipe.Pipe
+import com.twitter.scalding._
+import com.twitter.scalding.typed.TDsl._
+import org.apache.hadoop.hbase.io.ImmutableBytesWritable
+import org.apache.hadoop.hbase.util.Bytes
+import parallelai.spyglass.base.JobBase
+import parallelai.spyglass.hbase.HBaseConstants.SourceMode
+import parallelai.spyglass.hbase.HBasePipeConversions
+import parallelai.spyglass.hbase.HBaseSource
+
+class ScoreInsertableJob(args: Args) extends JobBase(args) {
+
+ val grobidRowCount = Stat("grobid-rows-filtered", "sandcrawler")
+ val crossrefRowCount = Stat("crossref-rows-filtered", "sandcrawler")
+ val cdxRowCount = Stat("cdx-rows", "sandcrawler")
+ val scoredRowCount = Stat("scored-rows", "sandcrawler")
+ val joinedRowCount = Stat("joined-rows", "sandcrawler")
+
+ val grobidScorable : Scorable = new GrobidScorable()
+ val crossrefScorable : Scorable = new CrossrefScorable()
+
+ val grobidPipe : TypedPipe[(String, ReduceFeatures)] = grobidScorable
+ .getInputPipe(args)
+ .map { r =>
+ grobidRowCount.inc
+ r
+ }
+ val crossrefPipe : TypedPipe[(String, ReduceFeatures)] = crossrefScorable
+ .getInputPipe(args)
+ .map { r =>
+ crossrefRowCount.inc
+ r
+ }
+ val cdxPipe : TypedPipe[(String, String, String, Long)] = ScoreInsertableJob.getHBaseCdxSource(args("hbase-table"), args("zookeeper-hosts"))
+ .read
+ .toTypedPipe[(ImmutableBytesWritable,ImmutableBytesWritable,ImmutableBytesWritable,ImmutableBytesWritable)](new Fields("key", "cdx", "mime", "size"))
+ .filter { case (_, cdx, mime, size) => cdx != null && mime != null && size != null }
+ .map { case (key, cdx, mime, size) =>
+ (Bytes.toString(key.copyBytes()),
+ Bytes.toString(cdx.copyBytes()),
+ Bytes.toString(mime.copyBytes()),
+ Bytes.toLong(size.copyBytes()))
+ }
+ .map { r =>
+ cdxRowCount.inc
+ r
+ }
+
+ val scoredPipe = grobidPipe
+ .addTrap(TypedTsv(args("output") + ".trapped"))
+ .join(crossrefPipe)
+ .map { case (slug, (grobidFeatures, crossrefFeatures)) =>
+ scoredRowCount.inc
+ //val (slug : String, (grobidFeatures: ReduceFeatures, crossrefFeatures: ReduceFeatures)) = entry
+ // Not ever Empty, I promise
+ val key = Scorable.getStringOption(Scorable.jsonToMap(grobidFeatures.json), "sha1").orNull
+ (key, new ReduceOutput(
+ slug,
+ Scorable.computeSimilarity(grobidFeatures, crossrefFeatures),
+ grobidFeatures.json,
+ crossrefFeatures.json))
+ }
+ .map { case (key, entry) => (key, entry.slug, entry.score, entry.json1, entry.json2) }
+ .groupBy { case (key, _, _, _, _) => key }
+
+ // TypedTsv doesn't work over case classes.
+ val joinedPipe = scoredPipe
+ .join(cdxPipe.groupBy { case (key, _, _, _) => key })
+ .map { case (key, ((_, slug, score, left, right), (_, cdx, mime, size))) => (key, slug, score, left, right, cdx, mime, size) }
+ .write(TypedTsv[(String, String, Int, String, String, String, String, Long)](args("output")))
+}
+
+object ScoreInsertableJob {
+
+ // eg, "wbgrp-journal-extract-0-qa",7 "mtrcs-zk1.us.archive.org:2181"
+ def getHBaseCdxSource(hbaseTable: String, zookeeperHosts: String) : HBaseSource = {
+ HBaseBuilder.build(
+ hbaseTable,
+ zookeeperHosts,
+ List("file:cdx", "file:mime", "file:size"),
+ SourceMode.SCAN_ALL)
+ }
+}
diff --git a/scalding/src/test/scala/sandcrawler/ScoreInsertableJobTest.scala b/scalding/src/test/scala/sandcrawler/ScoreInsertableJobTest.scala
new file mode 100644
index 0000000..5393f10
--- /dev/null
+++ b/scalding/src/test/scala/sandcrawler/ScoreInsertableJobTest.scala
@@ -0,0 +1,262 @@
+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 ScoreInsertableJobTest 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 TooLongOfTitle = "X" * Scorable.MaxTitleLength + "Y" // arbitrary long string
+ val TooShortOfTitle = "X" * (ScorableFeatures.MinSlugLength - 1)
+ 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"),
+ CrossrefString.replace("<<TITLE>>", TooLongOfTitle).replace("<<DOI>>", "DOI-1"),
+ CrossrefString.replace("<<TITLE>>", TooShortOfTitle).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",
+ "sha1:93229759932857982837892347893892",
+ "sha1:83229759932857982837892347893892")
+
+ val JsonStrings : List[String] = List(
+ JsonString.replace("<<TITLE>>", "Title 1: The Original"),
+ JsonString.replace("<<TITLE>>", "Title 2: TNG"),
+ JsonString.replace("<<TITLE>>", "Title 3: The Sequel"),
+ // This will have bad status.
+ JsonString.replace("<<TITLE>>", "Title 1: The Original"),
+ MalformedJsonString,
+ // This will have bad status.
+ JsonString.replace("<<TITLE>>", "Title 2: Not TNG"),
+ // These are in both sources but have bad titles
+ JsonString.replace("<<TITLE>>", TooLongOfTitle),
+ JsonString.replace("<<TITLE>>", TooShortOfTitle)
+ )
+
+ // 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, Ok, Ok)
+
+ 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)}):_*) }
+
+ // scalastyle:off null
+ // Add example of lines without GROBID data
+ // scalastyle:off null
+ val SampleData = SampleDataHead :+ new Tuple(
+ new ImmutableBytesWritable(Bytes.toBytes("sha1:35985C3YNNEGH5WAG5ZAA88888888888")), null, null)
+ // scalastyle:on null
+
+ val CdxList: List[String] = List("{}", "{}", "{}", "{}", "{}", "{}", "{}", "{}" )
+ val MimeList: List[String] = List("application/pdf", "application/pdf", "application/pdf",
+ "application/pdf", "application/pdf", "application/pdf", "application/pdf",
+ "application/pdf")
+ val SizeList: List[Long] = List(1,2,3,4,5,6,7,8)
+
+ // Can zip 3 lists, but not 4... so we recursively zip
+ val SampleCdxData : List[Tuple] = ((Sha1Strings, CdxList).zipped.toList, (MimeList, SizeList).zipped.toList)
+ .zipped
+ .toList
+ .map { case ((sha: String, cdx: String), (mime: String, size: Long)) => List(Bytes.toBytes(sha), Bytes.toBytes(cdx), Bytes.toBytes(mime), Bytes.toBytes(size)) }
+ .map { l => new Tuple(l.map(s => {new ImmutableBytesWritable(s)}):_*) }
+
+ JobTest("sandcrawler.ScoreInsertableJob")
+ .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[Tuple](ScoreInsertableJob.getHBaseCdxSource(testTable, testHost), SampleCdxData)
+ .source(TextLine(input), List(
+ 0 -> CrossrefStrings(0),
+ 1 -> CrossrefStrings(1),
+ 2 -> CrossrefStrings(2),
+ 3 -> CrossrefStrings(3),
+ 4 -> CrossrefStrings(4),
+ 4 -> CrossrefStrings(5)))
+ .sink[(String, ReduceFeatures)](TypedTsv[(String, ReduceFeatures)](output + ".trapped")) { _ => () }
+ .sink[(String, String, Int, String, String, String, String, Long)](TypedTsv[(String, String, Int, String, String, String, String, Long)](output)) {
+ // Grobid titles and slugs (in parentheses):
+ // Title 1 (title1)
+ // Title 2: TNG (title2tng)
+ // Title 3: The Sequel (title3thesequel)
+ // <too long of a title>
+ // <too short of a title>
+ // crossref titles and slugs (in parentheses):
+ // Title 2: TNG (title2tng)
+ // Title 1: TNG 2A (title1tng2a)
+ // Title 1: TNG 3 (title1tng3)
+ // Title 2: Rebooted (title2rebooted)
+ // <too long of a title>
+ // <too short of a title>
+ // 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(_._2)
+ 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 mfg : Option[MapFeatures] = GrobidScorable.jsonToMapFeatures(
+ Sha1Strings(grobidIndex),
+ JsonStrings(grobidIndex))
+ val mfc : Option[MapFeatures] = CrossrefScorable.jsonToMapFeatures(CrossrefStrings(crossrefIndex))
+ if (mfg.isEmpty || mfc.isEmpty) {
+ fail()
+ } else {
+ val score = Scorable.computeSimilarity(
+ ReduceFeatures(mfg.get.json),
+ ReduceFeatures(mfc.get.json))
+ (slug, score, mfg.get.json, mfc.get.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
+}