diff options
Diffstat (limited to 'scalding/src/main')
6 files changed, 359 insertions, 0 deletions
diff --git a/scalding/src/main/scala/sandcrawler/CrossrefScorable.scala b/scalding/src/main/scala/sandcrawler/CrossrefScorable.scala new file mode 100644 index 0000000..ff8201a --- /dev/null +++ b/scalding/src/main/scala/sandcrawler/CrossrefScorable.scala @@ -0,0 +1,47 @@ +package sandcrawler + +import scala.math +import scala.util.parsing.json.JSON +import scala.util.parsing.json.JSONObject + +import cascading.flow.FlowDef +import cascading.tuple.Fields +import com.twitter.scalding._ +import com.twitter.scalding.typed.TDsl._ +import parallelai.spyglass.hbase.HBasePipeConversions + +class CrossrefScorable extends Scorable with HBasePipeConversions { + // TODO: Generalize args so there can be multiple Crossref pipes in one job. + def getSource(args : Args) : Source = { + TextLine(args("crossref-input")) + } + + def getFeaturesPipe(args : Args)(implicit mode : Mode, flowDef : FlowDef) : TypedPipe[MapFeatures] = { + getSource(args).read + .toTypedPipe[String](new Fields("line")) + .map { CrossrefScorable.jsonToMapFeatures(_) } + } +} + +object CrossrefScorable { + def jsonToMapFeatures(json : String) : MapFeatures = { + Scorable.jsonToMap(json) match { + case None => MapFeatures(Scorable.NoSlug, json) + case Some(map) => { + if ((map contains "title") && (map contains "DOI")) { + val titles = map("title").asInstanceOf[List[String]] + val doi = Scorable.getString(map, "DOI") + if (titles.isEmpty || titles == null || doi.isEmpty || doi == null) { + new MapFeatures(Scorable.NoSlug, json) + } else { + // bnewbold: not checking that titles(0) is non-null/non-empty; case would be, in JSON, "title": [ null ] + val sf : ScorableFeatures = new ScorableFeatures(title=titles(0), doi=doi) + new MapFeatures(sf.toSlug, sf.toString) + } + } else { + new MapFeatures(Scorable.NoSlug, json) + } + } + } + } +} diff --git a/scalding/src/main/scala/sandcrawler/GrobidScorable.scala b/scalding/src/main/scala/sandcrawler/GrobidScorable.scala new file mode 100644 index 0000000..9a09e05 --- /dev/null +++ b/scalding/src/main/scala/sandcrawler/GrobidScorable.scala @@ -0,0 +1,56 @@ +package sandcrawler + +import scala.util.parsing.json.JSONObject + +import cascading.flow.FlowDef +import cascading.tuple.Fields +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.hbase.HBaseConstants.SourceMode +import parallelai.spyglass.hbase.HBasePipeConversions +import parallelai.spyglass.hbase.HBaseSource + +class GrobidScorable extends Scorable with HBasePipeConversions { + val StatusOK = 200 + + def getSource(args : Args) : Source = { + // TODO: Generalize args so there can be multiple grobid pipes in one job. + GrobidScorable.getHBaseSource(args("hbase-table"), args("zookeeper-hosts")) + } + + def getFeaturesPipe(args : Args)(implicit mode : Mode, flowDef : FlowDef) : TypedPipe[MapFeatures] = { + getSource(args) + .read + // Can't just "fromBytesWritable" because we have multiple types? + .toTypedPipe[(ImmutableBytesWritable,ImmutableBytesWritable,ImmutableBytesWritable)](new Fields("key", "tei_json", "status_code")) + .filter { case (_, tei_json, status_code) => tei_json != null && status_code != null } + .map { case (key, tei_json, status_code) => + (Bytes.toString(key.copyBytes()), Bytes.toString(tei_json.copyBytes()), Bytes.toLong(status_code.copyBytes())) + } + // TODO: Should I combine next two stages for efficiency? + .collect { case (key, json, StatusOK) => (key, json) } + .map { entry : (String, String) => GrobidScorable.jsonToMapFeatures(entry._1, entry._2) } + } +} + +object GrobidScorable { + def getHBaseSource(table : String, host : String) : HBaseSource = { + HBaseBuilder.build(table, host, List("grobid0:tei_json", "grobid0:status_code"), SourceMode.SCAN_ALL) + } + + def jsonToMapFeatures(key : String, json : String) : MapFeatures = { + Scorable.jsonToMap(json) match { + case None => MapFeatures(Scorable.NoSlug, json) + case Some(map) => { + if (map contains "title") { + new ScorableFeatures(Scorable.getString(map, "title"), sha1=key).toMapFeatures + } else { + MapFeatures(Scorable.NoSlug, json) + } + } + } + } +} + diff --git a/scalding/src/main/scala/sandcrawler/Scorable.scala b/scalding/src/main/scala/sandcrawler/Scorable.scala new file mode 100644 index 0000000..9b9c633 --- /dev/null +++ b/scalding/src/main/scala/sandcrawler/Scorable.scala @@ -0,0 +1,79 @@ +package sandcrawler + +import scala.math +import scala.util.parsing.json.JSON +import scala.util.parsing.json.JSONObject + +import cascading.flow.FlowDef +import com.twitter.scalding._ +import com.twitter.scalding.typed.TDsl._ + +case class MapFeatures(slug : String, json : String) +case class ReduceFeatures(json : String) +case class ReduceOutput(val slug : String, score : Int, json1 : String, json2 : String) + +abstract class Scorable { + def getInputPipe(args : Args)(implicit mode : Mode, flowDef : FlowDef) : TypedPipe[(String, ReduceFeatures)] = + { + getFeaturesPipe(args) + .filter { entry => Scorable.isValidSlug(entry.slug) } + .groupBy { case MapFeatures(slug, json) => slug } + .map { tuple => + val (slug : String, features : MapFeatures) = tuple + (slug, ReduceFeatures(features.json)) + } + } + + // abstract methods + def getSource(args : Args) : Source + def getFeaturesPipe(args : Args)(implicit mode : Mode, flowDef : FlowDef) : TypedPipe[MapFeatures] +} + +object Scorable { + val NoSlug = "NO SLUG" // Used for slug if title is empty or unparseable + + def isValidSlug(slug : String) : Boolean = { + slug != NoSlug + } + + def jsonToMap(json : String) : Option[Map[String, Any]] = { + // https://stackoverflow.com/a/32717262/631051 + val jsonObject = JSON.parseFull(json) + if (jsonObject == None) { + None + } else { + Some(jsonObject.get.asInstanceOf[Map[String, Any]]) + } + } + + def getStringOption(optionalMap : Option[Map[String, Any]], key : String) : Option[String] = { + optionalMap match { + case None => None + case Some(map) => if (map contains key) Some(map(key).asInstanceOf[String]) else None + } + } + + // Caller is responsible for ensuring that key is a String in map. + // TODO: Add and handle ClassCastException + def getString(map : Map[String, Any], key : String) : String = { + assert(map contains key) + map(key).asInstanceOf[String] + } + + val MaxScore = 1000 + + def computeSimilarity(features1 : ReduceFeatures, features2 : ReduceFeatures) : Int = { + val json1 = jsonToMap(features1.json) + val json2 = jsonToMap(features2.json) + getStringOption(json1, "title") match { + case None => 0 + case Some(title1) => { + getStringOption(json2, "title") match { + case None => 0 + case Some(title2) => + (StringUtilities.similarity(title1, title2) * MaxScore).toInt + } + } + } + } +} diff --git a/scalding/src/main/scala/sandcrawler/ScorableFeatures.scala b/scalding/src/main/scala/sandcrawler/ScorableFeatures.scala new file mode 100644 index 0000000..8ed3369 --- /dev/null +++ b/scalding/src/main/scala/sandcrawler/ScorableFeatures.scala @@ -0,0 +1,44 @@ +package sandcrawler + +import scala.util.parsing.json.JSONObject + + +// Contains features needed to make slug and to score (in combination +// with a second ScorableFeatures). +class ScorableFeatures(title : String, year: Int = 0, doi : String = "", sha1: String = "") { + + val slugBlacklist = Set( "abbreviations", "abstract", "acknowledgements", + "article", "authorreply", "authorsreply", "bookreview", "bookreviews", + "casereport", "commentary", "commentaryon", "commenton", "commentto", + "contents", "correspondence", "dedication", "editorialadvisoryboard", + "focus", "hypothesis", "inbrief", "introduction", "introductiontotheissue", + "lettertotheeditor", "listofabbreviations", "note", "overview", "preface", + "references", "results", "review", "reviewarticle", "summary", "title", + "name") + + def toMap() : Map[String, Any] = { + Map("title" -> (if (title == null) "" else title), + "year" -> year, + "doi" -> (if (doi == null) "" else doi), + "sha1" -> (if (sha1 == null) "" else sha1)) + } + + override def toString() : String = { + JSONObject(toMap()).toString + } + + def toSlug() : String = { + if (title == null) { + Scorable.NoSlug + } else { + val unaccented = StringUtilities.removeAccents(title) + // Remove punctuation + val slug = StringUtilities.removePunctuation((unaccented.toLowerCase())).replaceAll("\\s", "") + if (slug.isEmpty || slug == null || (slugBlacklist contains slug)) Scorable.NoSlug else slug + } + } + + def toMapFeatures = { + MapFeatures(toSlug, toString) + } +} diff --git a/scalding/src/main/scala/sandcrawler/ScoreJob.scala b/scalding/src/main/scala/sandcrawler/ScoreJob.scala new file mode 100644 index 0000000..75d45e9 --- /dev/null +++ b/scalding/src/main/scala/sandcrawler/ScoreJob.scala @@ -0,0 +1,57 @@ +package sandcrawler + +import cascading.pipe.Pipe +import com.twitter.scalding.Args +import com.twitter.scalding.TypedPipe +import com.twitter.scalding.TypedTsv +import parallelai.spyglass.base.JobBase + +class ScoreJob(args: Args) extends JobBase(args) { + // TODO: Instantiate any subclass of Scorable specified in args. + val sc1 : Scorable = new GrobidScorable() + val sc2 : Scorable = new CrossrefScorable() + val pipe1 : TypedPipe[(String, ReduceFeatures)] = sc1.getInputPipe(args) + val pipe2 : TypedPipe[(String, ReduceFeatures)] = sc2.getInputPipe(args) + + pipe1.join(pipe2).map { entry => + val (slug : String, (features1 : ReduceFeatures, features2 : ReduceFeatures)) = entry + new ReduceOutput( + slug, + Scorable.computeSimilarity(features1, features2), + features1.json, + features2.json) + } + //TypedTsv doesn't work over case classes. + .map { entry => (entry.slug, entry.score, entry.json1, entry.json2) } + .write(TypedTsv[(String, Int, String, String)](args("output"))) +} + +/* +// Ugly hack to get non-String information into ScoreJob above. +object ScoreJob { + var scorable1 : Option[Scorable] = None + var scorable2 : Option[Scorable] = None + + def setScorable1(s : Scorable) { + scorable1 = Some(s) + } + + def getScorable1() : Scorable = { + scorable1 match { + case Some(s) => s + case None => null + } + } + + def setScorable2(s: Scorable) { + scorable2 = Some(s) + } + + def getScorable2() : Scorable = { + scorable2 match { + case Some(s) => s + case None => null + } + } +} + */ diff --git a/scalding/src/main/scala/sandcrawler/StringUtilities.scala b/scalding/src/main/scala/sandcrawler/StringUtilities.scala new file mode 100644 index 0000000..2745875 --- /dev/null +++ b/scalding/src/main/scala/sandcrawler/StringUtilities.scala @@ -0,0 +1,76 @@ +package sandcrawler + +import java.text.Normalizer +import java.util.regex.Pattern + +object StringUtilities { + // bnewbold: I propose that we: + // 1. keep only \p{Ideographic}, \p{Alphabetic}, and \p{Digit} + // 2. strip accents + // 3. "lower-case" (unicode-aware) + // 4. do any final custom/manual mappings + // + // We should check (test) that null bytes are handled, in addition to other + // more obvious characters + + // Adapted from https://git-wip-us.apache.org/repos/asf?p=commons-lang.git;a=blob;f=src/main/java/org/apache/commons/lang3/StringUtils.java;h=1d7b9b99335865a88c509339f700ce71ce2c71f2;hb=HEAD#l934 + def removeAccents(s : String) : String = { + val replacements = Map( + '\u0141' -> 'L', + '\u0142' -> 'l', // Letter ell + '\u00d8' -> 'O', + '\u00f8' -> 'o' + ) + val sb = new StringBuilder(Normalizer.normalize(s, Normalizer.Form.NFD)) + for (i <- 0 to sb.length - 1) { + for (key <- replacements.keys) { + if (sb(i) == key) { + sb.deleteCharAt(i); + sb.insert(i, replacements(key)) + } + } + } + val pattern = Pattern.compile("\\p{InCombiningDiacriticalMarks}+") + pattern.matcher(sb).replaceAll("") + } + + // Source: https://stackoverflow.com/a/30076541/631051 + def removePunctuation(s: String) : String = { + s.replaceAll("""[\p{Punct}]""", "") + } + + // Adapted from: https://stackoverflow.com/a/16018452/631051 + def similarity(s1a : String, s2a : String) : Double = { + val (s1, s2) = (removeAccents(removePunctuation(s1a)), + removeAccents(removePunctuation(s2a))) + val longer : String = if (s1.length > s2.length) s1 else s2 + val shorter : String = if (s1.length > s2.length) s2 else s1 + if (longer.length == 0) { + // Both strings are empty. + 1 + } else { + (longer.length - stringDistance(longer, shorter)) / longer.length.toDouble + } + } + + // Source: https://oldfashionedsoftware.com/2009/11/19/string-distance-and-refactoring-in-scala/ + def stringDistance(s1: String, s2: String): Int = { + val memo = scala.collection.mutable.Map[(List[Char],List[Char]),Int]() + def min(a:Int, b:Int, c:Int) = Math.min( Math.min( a, b ), c) + def sd(s1: List[Char], s2: List[Char]): Int = { + if (!memo.contains((s1, s2))) { + memo((s1,s2)) = (s1, s2) match { + case (_, Nil) => s1.length + case (Nil, _) => s2.length + case (c1::t1, c2::t2) => + min( sd(t1,s2) + 1, sd(s1,t2) + 1, + sd(t1,t2) + (if (c1==c2) 0 else 1) ) + } + } + memo((s1,s2)) + } + + sd( s1.toList, s2.toList ) + } +} + |