From ccfeb71ef2a25a479c083051acc0ebb7436e421b Mon Sep 17 00:00:00 2001 From: Ellen Spertus Date: Tue, 7 Aug 2018 12:06:40 -0700 Subject: Removed HBaseCrossrefScore{Job,Test} and references thereto. --- .../scala/sandcrawler/HBaseCrossrefScoreTest.scala | 293 --------------------- 1 file changed, 293 deletions(-) delete mode 100644 scalding/src/test/scala/sandcrawler/HBaseCrossrefScoreTest.scala (limited to 'scalding/src/test/scala') 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": "<>", - "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 - */ -} -- cgit v1.2.3