diff options
10 files changed, 135 insertions, 100 deletions
diff --git a/scalding/build.sbt b/scalding/build.sbt index 2addd60..d477399 100644 --- a/scalding/build.sbt +++ b/scalding/build.sbt @@ -20,6 +20,13 @@ lazy val root = (project in file(".")). scalaSourceFiles.filterNot(_.getAbsolutePath.contains(dirNameToExclude)) }, + (scalastyleSources in Test) := { + // all .scala files in "src/test/scala" + val scalaSourceFiles = ((scalaSource in Test).value ** "*.scala").get + val dirNameToExclude = "/example/" + scalaSourceFiles.filterNot(_.getAbsolutePath.contains(dirNameToExclude)) + }, + name := "sandcrawler", resolvers += "conjars.org" at "http://conjars.org/repo", diff --git a/scalding/src/test/scala/sandcrawler/CrossrefScorableTest.scala b/scalding/src/test/scala/sandcrawler/CrossrefScorableTest.scala index 75be03e..e171dba 100644 --- a/scalding/src/test/scala/sandcrawler/CrossrefScorableTest.scala +++ b/scalding/src/test/scala/sandcrawler/CrossrefScorableTest.scala @@ -2,72 +2,77 @@ package sandcrawler import cascading.tuple.Fields import cascading.tuple.Tuple -import com.twitter.scalding.{JobTest, TextLine, TypedTsv, TupleConversions} +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 CrossrefScorableTest extends FlatSpec with Matchers { + // 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" : { "$numberLong" : "820454400000" } }, +{ "_id" : { "$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 ] ] }, + "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" : { "$numberLong" : "1027609781000" } }, - "page" : "186-187", - "source" : "Crossref", - "is-referenced-by-count" : 0, + "type" : "journal-article", + "created" : { "date-parts" : [ [ 2002, 7, 25 ] ], + "date-time" : "2002-07-25T15:09:41Z", + "timestamp" : { "$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" ], + "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-type" : "text/xml", "content-version" : "vor", - "intended-application" : "text-mining" }, + "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-type" : "text/plain", "content-version" : "vor", - "intended-application" : "text-mining" } ], - "deposited" : { "date-parts" : [ [ 2015, 9, 3 ] ], - "date-time" : "2015-09-03T10:03:43Z", - "timestamp" : { "$numberLong" : "1441274623000" } }, - "score" : 1, - "issued" : { "date-parts" : [ [ 1996 ] ] }, - "references-count" : 0, - "alternative-id" : [ "0987-7983(96)87729-2" ], - "URL" : "http://dx.doi.org/10.1016/0987-7983(96)87729-2", - "ISSN" : [ "0987-7983" ], - "issn-type" : [ { "value" : "0987-7983", "type" : "print" } ], + "intended-application" : "text-mining" } ], + "deposited" : { "date-parts" : [ [ 2015, 9, 3 ] ], + "date-time" : "2015-09-03T10:03:43Z", + "timestamp" : { "$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>>", "Some Title") val CrossrefStringWithoutTitle = CrossrefString.replace("title", "nottitle") val MalformedCrossrefString = CrossrefString.replace("}", "") // Unit tests "CrossrefScorable.jsonToMapFeatures()" should "handle invalid JSON" in { - val result = CrossrefScorable.jsonToMapFeatures(MalformedCrossrefString) + val result = CrossrefScorable.jsonToMapFeatures(MalformedCrossrefString) result.slug shouldBe Scorable.NoSlug } diff --git a/scalding/src/test/scala/sandcrawler/GrobidScorableTest.scala b/scalding/src/test/scala/sandcrawler/GrobidScorableTest.scala index 4b958b9..661824b 100644 --- a/scalding/src/test/scala/sandcrawler/GrobidScorableTest.scala +++ b/scalding/src/test/scala/sandcrawler/GrobidScorableTest.scala @@ -2,7 +2,10 @@ package sandcrawler import cascading.tuple.Fields import cascading.tuple.Tuple -import com.twitter.scalding.{JobTest, TextLine, TypedTsv, TupleConversions} +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._ @@ -62,7 +65,7 @@ class GrobidScorableTest extends FlatSpec with Matchers { // Unit tests "GrobidScorable.jsonToMapFeatures()" should "handle invalid JSON" in { - val result = GrobidScorable.jsonToMapFeatures(Key, MalformedGrobidString) + val result = GrobidScorable.jsonToMapFeatures(Key, MalformedGrobidString) result.slug shouldBe Scorable.NoSlug } diff --git a/scalding/src/test/scala/sandcrawler/HBaseBuilderTest.scala b/scalding/src/test/scala/sandcrawler/HBaseBuilderTest.scala index 603a4c7..c61cb22 100644 --- a/scalding/src/test/scala/sandcrawler/HBaseBuilderTest.scala +++ b/scalding/src/test/scala/sandcrawler/HBaseBuilderTest.scala @@ -22,6 +22,7 @@ class HBaseBuilderTest extends FlatSpec with Matchers { fields should have length 0 } + //scalastyle:off no.whitespace.before.left.bracket it should "throw IllegalArgumentException on malformed input" in { a [IllegalArgumentException] should be thrownBy { HBaseBuilder.parseColSpecs(List("file_size")) diff --git a/scalding/src/test/scala/sandcrawler/HBaseMimeCountTest.scala b/scalding/src/test/scala/sandcrawler/HBaseMimeCountTest.scala index fde2290..d6d283f 100644 --- a/scalding/src/test/scala/sandcrawler/HBaseMimeCountTest.scala +++ b/scalding/src/test/scala/sandcrawler/HBaseMimeCountTest.scala @@ -1,15 +1,18 @@ package sandcrawler -import cascading.tuple.{Tuple, Fields} -import com.twitter.scalding.{JobTest, Tsv, TupleConversions} +import cascading.tuple.Fields +import cascading.tuple.Tuple +import com.twitter.scalding.JobTest +import com.twitter.scalding.Tsv +import com.twitter.scalding.TupleConversions import org.apache.hadoop.hbase.io.ImmutableBytesWritable import org.apache.hadoop.hbase.util.Bytes import org.junit.runner.RunWith import org.scalatest.FunSpec import org.scalatest.junit.JUnitRunner import org.slf4j.LoggerFactory -import parallelai.spyglass.hbase.HBaseSource import parallelai.spyglass.hbase.HBaseConstants.SourceMode +import parallelai.spyglass.hbase.HBaseSource import scala._ @RunWith(classOf[JUnitRunner]) diff --git a/scalding/src/test/scala/sandcrawler/HBaseRowCountTest.scala b/scalding/src/test/scala/sandcrawler/HBaseRowCountTest.scala index 3424a36..c4ca5aa 100644 --- a/scalding/src/test/scala/sandcrawler/HBaseRowCountTest.scala +++ b/scalding/src/test/scala/sandcrawler/HBaseRowCountTest.scala @@ -1,15 +1,18 @@ package sandcrawler -import cascading.tuple.{Tuple, Fields} -import com.twitter.scalding.{JobTest, Tsv, TupleConversions} +import cascading.tuple.Fields +import cascading.tuple.Tuple +import com.twitter.scalding.JobTest +import com.twitter.scalding.Tsv +import com.twitter.scalding.TupleConversions import org.apache.hadoop.hbase.io.ImmutableBytesWritable import org.apache.hadoop.hbase.util.Bytes import org.junit.runner.RunWith import org.scalatest.FunSpec import org.scalatest.junit.JUnitRunner import org.slf4j.LoggerFactory -import parallelai.spyglass.hbase.HBaseSource import parallelai.spyglass.hbase.HBaseConstants.SourceMode +import parallelai.spyglass.hbase.HBaseSource import scala._ /** @@ -47,12 +50,10 @@ class HBaseRowCountTest extends FunSpec with TupleConversions { outputBuffer => it("should return the test data provided.") { - println("outputBuffer.size => " + outputBuffer.size) assert(outputBuffer.size === 1) } it("should return the correct count") { - println("raw output => " + outputBuffer) assert(outputBuffer(0).getObject(0) === 8) } } diff --git a/scalding/src/test/scala/sandcrawler/HBaseStatusCountTest.scala b/scalding/src/test/scala/sandcrawler/HBaseStatusCountTest.scala index 8a71f31..fe3ff21 100644 --- a/scalding/src/test/scala/sandcrawler/HBaseStatusCountTest.scala +++ b/scalding/src/test/scala/sandcrawler/HBaseStatusCountTest.scala @@ -1,15 +1,19 @@ package sandcrawler -import cascading.tuple.{Tuple, Fields} -import com.twitter.scalding.{JobTest, Tsv, TypedTsv, TupleConversions} +import cascading.tuple.Fields +import cascading.tuple.Tuple +import com.twitter.scalding.JobTest +import com.twitter.scalding.Tsv +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.junit.runner.RunWith import org.scalatest.FunSpec import org.scalatest.junit.JUnitRunner import org.slf4j.LoggerFactory -import parallelai.spyglass.hbase.HBaseSource import parallelai.spyglass.hbase.HBaseConstants.SourceMode +import parallelai.spyglass.hbase.HBaseSource import scala._ @RunWith(classOf[JUnitRunner]) diff --git a/scalding/src/test/scala/sandcrawler/ScorableFeaturesTest.scala b/scalding/src/test/scala/sandcrawler/ScorableFeaturesTest.scala index 7ec0c4d..f9c30a2 100644 --- a/scalding/src/test/scala/sandcrawler/ScorableFeaturesTest.scala +++ b/scalding/src/test/scala/sandcrawler/ScorableFeaturesTest.scala @@ -2,6 +2,7 @@ package sandcrawler import org.scalatest._ +// scalastyle:off null class ScorableFeaturesTest extends FlatSpec with Matchers { private def titleToSlug(s : String) : String = { new ScorableFeatures(title = s).toSlug diff --git a/scalding/src/test/scala/sandcrawler/ScorableTest.scala b/scalding/src/test/scala/sandcrawler/ScorableTest.scala index fd44f57..f63bef8 100644 --- a/scalding/src/test/scala/sandcrawler/ScorableTest.scala +++ b/scalding/src/test/scala/sandcrawler/ScorableTest.scala @@ -2,7 +2,10 @@ package sandcrawler import cascading.tuple.Fields import cascading.tuple.Tuple -import com.twitter.scalding.{JobTest, TextLine, TypedTsv, TupleConversions} +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._ diff --git a/scalding/src/test/scala/sandcrawler/ScoreJobTest.scala b/scalding/src/test/scala/sandcrawler/ScoreJobTest.scala index 1c6ae83..34081a5 100644 --- a/scalding/src/test/scala/sandcrawler/ScoreJobTest.scala +++ b/scalding/src/test/scala/sandcrawler/ScoreJobTest.scala @@ -2,13 +2,17 @@ package sandcrawler import cascading.tuple.Fields import cascading.tuple.Tuple -import com.twitter.scalding.{JobTest, TextLine, TypedTsv, TupleConversions} +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>>", @@ -54,62 +58,65 @@ class ScoreJobTest extends FlatSpec with Matchers { "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" : { "$numberLong" : "820454400000" } }, +{ "_id" : { "$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 ] ] }, + "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" : { "$numberLong" : "1027609781000" } }, - "page" : "186-187", - "source" : "Crossref", - "is-referenced-by-count" : 0, + "type" : "journal-article", + "created" : { "date-parts" : [ [ 2002, 7, 25 ] ], + "date-time" : "2002-07-25T15:09:41Z", + "timestamp" : { "$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" ], + "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" }, + "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-type" : "text/plain", "content-version" : "vor", - "intended-application" : "text-mining" } ], - "deposited" : { "date-parts" : [ [ 2015, 9, 3 ] ], - "date-time" : "2015-09-03T10:03:43Z", - "timestamp" : { "$numberLong" : "1441274623000" } }, - "score" : 1, - "issued" : { "date-parts" : [ [ 1996 ] ] }, - "references-count" : 0, - "alternative-id" : [ "0987-7983(96)87729-2" ], - "URL" : "http://dx.doi.org/10.1016/0987-7983(96)87729-2", - "ISSN" : [ "0987-7983" ], - "issn-type" : [ { "value" : "0987-7983", "type" : "print" } ], + "intended-application" : "text-mining" } ], + "deposited" : { "date-parts" : [ [ 2015, 9, 3 ] ], + "date-time" : "2015-09-03T10:03:43Z", + "timestamp" : { "$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("}", "") @@ -168,7 +175,7 @@ class ScoreJobTest extends FlatSpec with Matchers { 2 -> CrossrefStrings(2), 3 -> CrossrefStrings(3))) .sink[(String, Int, String, String)](TypedTsv[(String, Int, String, String)](output)) { - // Grobid titles and slugs (in parentheses): + // Grobid titles and slugs (in parentheses): // Title 1 (title1) // Title 2: TNG (title2) // Title 3: The Sequel (title3) @@ -178,7 +185,7 @@ class ScoreJobTest extends FlatSpec with Matchers { // Title 1: TNG 3 (title1) // Title 2: Rebooted (title2) // Join should have 3 "title1" slugs and 1 "title2" slug - outputBuffer => + outputBuffer => "The pipeline" should "return a 4-element list" in { outputBuffer should have length 4 } @@ -190,9 +197,9 @@ class ScoreJobTest extends FlatSpec with Matchers { countMap("title2") shouldBe 1 } - def bundle(slug : String, grobidIndex : Int, crossrefIndex : Int) = { + def bundle(slug : String, grobidIndex : Int, crossrefIndex : Int) : (String, Int, String, String) = { val mf1 : MapFeatures = GrobidScorable.jsonToMapFeatures( - Sha1Strings(grobidIndex), + Sha1Strings(grobidIndex), JsonStrings(grobidIndex)) val mf2 : MapFeatures = CrossrefScorable.jsonToMapFeatures( CrossrefStrings(crossrefIndex)) |