diff options
Diffstat (limited to 'scalding/src/main/scala')
| -rw-r--r-- | scalding/src/main/scala/sandcrawler/GrobidScorable.scala | 8 | ||||
| -rw-r--r-- | scalding/src/main/scala/sandcrawler/HBaseCrossrefScoreJob.scala | 216 |
2 files changed, 5 insertions, 219 deletions
diff --git a/scalding/src/main/scala/sandcrawler/GrobidScorable.scala b/scalding/src/main/scala/sandcrawler/GrobidScorable.scala index 25e5985..bf36855 100644 --- a/scalding/src/main/scala/sandcrawler/GrobidScorable.scala +++ b/scalding/src/main/scala/sandcrawler/GrobidScorable.scala @@ -12,9 +12,11 @@ import parallelai.spyglass.hbase.HBaseSource class GrobidScorable extends Scorable with HBasePipeConversions { def getFeaturesPipe(args : Args)(implicit flowDef : FlowDef, mode : Mode) = { // TODO: Clean up code after debugging. - val grobidSource = HBaseCrossrefScore.getHBaseSource( + val grobidSource = HBaseBuilder.build( args("hbase-table"), - args("zookeeper-hosts")) + args("zookeeper-hosts"), + List("grobid0:tei_json"), + SourceMode.SCAN_ALL) // val pipe0 : Pipe = grobidSource.read // val grobidPipe : TypedPipe[MapFeatures] = pipe0 @@ -26,7 +28,7 @@ class GrobidScorable extends Scorable with HBasePipeConversions { .toTypedPipe[(String, String)](new Fields("key", "tei_json")) .map { entry => val (key : String, json : String) = (entry._1, entry._2) - HBaseCrossrefScore.grobidToSlug(json) match { + GrobidScorable.grobidToSlug(json) match { case Some(slug) => new MapFeatures(slug, json) case None => new MapFeatures(Scorable.NoSlug, json) } diff --git a/scalding/src/main/scala/sandcrawler/HBaseCrossrefScoreJob.scala b/scalding/src/main/scala/sandcrawler/HBaseCrossrefScoreJob.scala deleted file mode 100644 index 2fbb19f..0000000 --- a/scalding/src/main/scala/sandcrawler/HBaseCrossrefScoreJob.scala +++ /dev/null @@ -1,216 +0,0 @@ -package sandcrawler - -import java.text.Normalizer -import java.util.Arrays -import java.util.Properties -import java.util.regex.Pattern - -import scala.math -import scala.util.parsing.json.JSON - -import cascading.tuple.Fields -import com.twitter.scalding._ -import com.twitter.scalding.typed.CoGrouped -import com.twitter.scalding.typed.Grouped -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 HBaseCrossrefScoreJob(args: Args) extends JobBase(args) with HBasePipeConversions { - val NoTitle = "NO TITLE" // Used for slug if title is empty or unparseable - - // key is SHA1 - val grobidSource = HBaseCrossrefScore.getHBaseSource( - args("hbase-table"), - args("zookeeper-hosts")) - - val pipe0 : cascading.pipe.Pipe = grobidSource.read - val grobidPipe : TypedPipe[(String, String, String)] = pipe0 - .fromBytesWritable(new Fields("key", "tei_json")) - // .debug // Should be 4 tuples for mocked data - .toTypedPipe[(String, String)]('key, 'tei_json) - .map { entry => - val (key, json) = (entry._1, entry._2) - // TODO: Consider passing forward only a subset of JSON. - HBaseCrossrefScore.grobidToSlug(json) match { - case Some(slug) => (slug, key, json) - case None => (NoTitle, key, json) - } - } - .filter { entry => - val (slug, _, _) = entry - slug != NoTitle - } -// .debug // SHould be 3 tuples for mocked data - - val grobidGroup = grobidPipe - .groupBy { case (slug, key, json) => slug } - - val crossrefSource = TextLine(args("crossref-input")) - val crossrefPipe : TypedPipe[(String, String)] = crossrefSource - .read - // .debug // Should be 4 tuples for mocked data - .toTypedPipe[String]('line) - .map{ json : String => - HBaseCrossrefScore.crossrefToSlug(json) match { - case Some(slug) => (slug, json) - case None => (NoTitle, json) - } - } - .filter { entry => - val (slug, json) = entry - slug != NoTitle - } - - val crossrefGroup = crossrefPipe - .groupBy { case (slug, json) => slug } - - val theJoin : CoGrouped[String, ((String, String, String), (String, String))] = - grobidGroup.join(crossrefGroup) - - theJoin.map{ entry => - val (slug : String, - ((slug0: String, sha1 : String, grobidJson : String), - (slug1 : String, crossrefJson : String))) = entry - HBaseCrossrefScore.computeOutput(sha1, grobidJson, crossrefJson)} - // Output: score, sha1, doi, grobid title, crossref title - .write(TypedTsv[(Int, String, String, String, String)](args("output"))) -} - -object HBaseCrossrefScore { - def getHBaseSource(hbaseTable: String, zookeeperHosts: String) : HBaseSource = HBaseBuilder.build( - hbaseTable, // HBase Table Name - zookeeperHosts, // HBase Zookeeper server (to get runtime config info; can be array?) - List("grobid0:tei_json"), - SourceMode.SCAN_ALL) - - 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 grobidToSlug(json : String) : Option[String] = { - jsonToMap(json) match { - case None => None - case Some(map) => { - if (map contains "title") { - titleToSlug(map("title").asInstanceOf[String]) - } else { - None - } - } - } - } - - def crossrefToSlug(json : String) : Option[String] = { - jsonToMap(json) match { - case None => None - case Some(map) => { - if (map contains "title") { - // TODO: Don't ignore titles after the first. - titleToSlug(map("title").asInstanceOf[List[String]](0)) - } else { - None - } - } - } - } - - def titleToSlug(title : String) : Option[String] = { - val slug = removeAccents(title).split(":")(0).toLowerCase() - if (slug.isEmpty) { - None - } else { - Some(slug) - } - } - - val MaxScore = 1000 - - def computeOutput(sha1 : String, grobidJson : String, crossrefJson : String) : - // (score, sha1, doi, grobidTitle, crossrefTitle) - (Int, String, String, String, String) = { - jsonToMap(grobidJson) match { - case None => (0, "", "", "", "") // This can't happen, because grobidJson already validated in earlier stage - case Some(grobid) => { - val grobidTitle = grobid("title").asInstanceOf[String].toLowerCase() - - jsonToMap(crossrefJson) match { - case None => (0, "", "", "", "") // This can't happen, because crossrefJson already validated in earlier stage - case Some(crossref) => { - val crossrefTitle = crossref("title").asInstanceOf[List[String]](0).toLowerCase() - - (similarity(removeAccents(grobidTitle), removeAccents(crossrefTitle)), - sha1, - crossref("DOI").asInstanceOf[String], - "'" + grobidTitle + "'", - "'" + crossrefTitle + "'") - } - } - } - } - } - - // 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("") - } - - // Adapted from: https://stackoverflow.com/a/16018452/631051 - def similarity(s1 : String, s2 : String) : Int = { - 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. - MaxScore - } else { - (longer.length - stringDistance(longer, shorter)) * MaxScore / longer.length - } - } - - // 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 ) - } -} - |