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authorEllen Spertus <ellen.spertus@gmail.com>2018-08-14 19:12:46 -0700
committerEllen Spertus <ellen.spertus@gmail.com>2018-08-14 19:12:46 -0700
commitd1833985ee4359733ff880a1e0aa75e60a3bc76d (patch)
treeaa87f14898eeb5af8834fe3ad21cc2012c6d3169
parentb4f1acce5eccbb56291f82906d9c01534c7f1506 (diff)
downloadsandcrawler-d1833985ee4359733ff880a1e0aa75e60a3bc76d.tar.gz
sandcrawler-d1833985ee4359733ff880a1e0aa75e60a3bc76d.zip
Now ignores grobid entries with status other than 200.
-rw-r--r--scalding/src/main/scala/sandcrawler/GrobidScorable.scala10
-rw-r--r--scalding/src/test/scala/sandcrawler/HBaseStatusCountTest.scala2
-rw-r--r--scalding/src/test/scala/sandcrawler/ScoreJobTest.scala47
3 files changed, 39 insertions, 20 deletions
diff --git a/scalding/src/main/scala/sandcrawler/GrobidScorable.scala b/scalding/src/main/scala/sandcrawler/GrobidScorable.scala
index 5ba7d58..c319fe6 100644
--- a/scalding/src/main/scala/sandcrawler/GrobidScorable.scala
+++ b/scalding/src/main/scala/sandcrawler/GrobidScorable.scala
@@ -11,6 +11,8 @@ 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"))
@@ -19,15 +21,17 @@ class GrobidScorable extends Scorable with HBasePipeConversions {
def getFeaturesPipe(args : Args)(implicit mode : Mode, flowDef : FlowDef) : TypedPipe[MapFeatures] = {
getSource(args)
.read
- .fromBytesWritable(new Fields("key", "tei_json"))
- .toTypedPipe[(String, String)](new Fields("key", "tei_json"))
+ .fromBytesWritable(new Fields("key", "tei_json", "status_code"))
+ .toTypedPipe[(String, String, Int)](new Fields("key", "tei_json", "status_code"))
+ // 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"), SourceMode.SCAN_ALL)
+ HBaseBuilder.build(table, host, List("grobid0:tei_json", "grobid0:status_code"), SourceMode.SCAN_ALL)
}
def jsonToMapFeatures(key : String, json : String) : MapFeatures = {
diff --git a/scalding/src/test/scala/sandcrawler/HBaseStatusCountTest.scala b/scalding/src/test/scala/sandcrawler/HBaseStatusCountTest.scala
index d7689cd..8a71f31 100644
--- a/scalding/src/test/scala/sandcrawler/HBaseStatusCountTest.scala
+++ b/scalding/src/test/scala/sandcrawler/HBaseStatusCountTest.scala
@@ -25,7 +25,7 @@ class HBaseStatusCountTest extends FunSpec with TupleConversions {
val statusType1Bytes = Bytes.toBytes(statusType1)
val statusType2Bytes = Bytes.toBytes(statusType2)
- val sampleData = List(
+ val sampleData : List[List[Array[Byte]]] = List(
List(Bytes.toBytes("sha1:K2DKSSVTXWPRMFDTWSTCQW3RVWRIOV3Q"), statusType1Bytes),
List(Bytes.toBytes("sha1:C3YNNEGH5WAG5ZAAXWAEBNXJWT6CZ3WU"), statusType1Bytes),
List(Bytes.toBytes("sha1:SDKUVHC3YNNEGH5WAG5ZAAXWAEBNX4WT"), statusType2Bytes),
diff --git a/scalding/src/test/scala/sandcrawler/ScoreJobTest.scala b/scalding/src/test/scala/sandcrawler/ScoreJobTest.scala
index f0b411f..e72eb7a 100644
--- a/scalding/src/test/scala/sandcrawler/ScoreJobTest.scala
+++ b/scalding/src/test/scala/sandcrawler/ScoreJobTest.scala
@@ -9,7 +9,7 @@ import org.scalatest._
import parallelai.spyglass.hbase.HBaseConstants.SourceMode
class ScoreJobTest extends FlatSpec with Matchers {
- val GrobidString = """
+ val JsonString = """
{
"title": "<<TITLE>>",
"authors": [
@@ -54,9 +54,9 @@ class ScoreJobTest extends FlatSpec with Matchers {
"annex": null
}
"""
- val GrobidStringWithTitle = GrobidString.replace("<<TITLE>>", "Dummy Example File")
- val GrobidStringWithoutTitle = GrobidString.replace("title", "nottitle")
- val MalformedGrobidString = GrobidString.replace("}", "")
+ val JsonStringWithTitle = JsonString.replace("<<TITLE>>", "Dummy Example File")
+ val JsonStringWithoutTitle = JsonString.replace("title", "nottitle")
+ val MalformedJsonString = JsonString.replace("}", "")
val CrossrefString =
"""
@@ -124,21 +124,36 @@ class ScoreJobTest extends FlatSpec with Matchers {
val input = "/tmp/testInput"
val (testTable, testHost) = ("test-table", "dummy-host:2181")
- val Sha1Strings = List(
+ val Sha1Strings : List[String] = List(
"sha1:K2DKSSVTXWPRMFDTWSTCQW3RVWRIOV3Q",
"sha1:C3YNNEGH5WAG5ZAAXWAEBNXJWT6CZ3WU",
"sha1:SDKUVHC3YNNEGH5WAG5ZAAXWAEBNX4WT",
- "sha1:35985C3YNNEGH5WAG5ZAAXWAEBNXJW56")
+ "sha1:35985C3YNNEGH5WAG5ZAAXWAEBNXJW56",
+ "sha1:93187A85273589347598473894839443",
+ "sha1:024937534094897039547e9824382943")
- val GrobidStrings = List(
- GrobidString.replace("<<TITLE>>", "Title 1"),
- GrobidString.replace("<<TITLE>>", "Title 2: TNG"),
- GrobidString.replace("<<TITLE>>", "Title 3: The Sequel"),
- MalformedGrobidString)
+ val JsonStrings : List[String] = List(
+ JsonString.replace("<<TITLE>>", "Title 1"),
+ JsonString.replace("<<TITLE>>", "Title 2: TNG"),
+ JsonString.replace("<<TITLE>>", "Title 3: The Sequel"),
+ // This will have bad status.
+ JsonString.replace("<<TITLE>>", "Title 1"),
+ MalformedJsonString,
+ // This will have bad status.
+ JsonString.replace("<<TITLE>>", "Title 2")
+ )
- val GrobidSampleData = (Sha1Strings zip GrobidStrings)
- .map{case(s, g) =>
- List(Bytes.toBytes(s), Bytes.toBytes(g))}
+ val Ok = Bytes.toBytes("200")
+ val Bad = Bytes.toBytes("404")
+
+ val SampleData : List[List[Array[Byte]]] = List(
+ List(Bytes.toBytes(Sha1Strings(0)), Bytes.toBytes(JsonStrings(0)), Ok),
+ List(Bytes.toBytes(Sha1Strings(1)), Bytes.toBytes(JsonStrings(1)), Ok),
+ List(Bytes.toBytes(Sha1Strings(2)), Bytes.toBytes(JsonStrings(2)), Ok),
+ List(Bytes.toBytes(Sha1Strings(3)), Bytes.toBytes(JsonStrings(3)), Bad),
+ List(Bytes.toBytes(Sha1Strings(4)), Bytes.toBytes(JsonStrings(4)), Ok),
+ List(Bytes.toBytes(Sha1Strings(5)), Bytes.toBytes(JsonStrings(5)), Bad)
+ )
JobTest("sandcrawler.ScoreJob")
.arg("test", "")
@@ -149,7 +164,7 @@ class ScoreJobTest extends FlatSpec with Matchers {
.arg("crossref-input", input)
.arg("debug", "true")
.source[Tuple](GrobidScorable.getHBaseSource(testTable, testHost),
- GrobidSampleData.map(l => new Tuple(l.map(s => {new ImmutableBytesWritable(s)}):_*)))
+ SampleData.map(l => new Tuple(l.map(s => {new ImmutableBytesWritable(s)}):_*)))
.source(TextLine(input), List(
0 -> CrossrefStrings(0),
1 -> CrossrefStrings(1),
@@ -181,7 +196,7 @@ class ScoreJobTest extends FlatSpec with Matchers {
def bundle(slug : String, grobidIndex : Int, crossrefIndex : Int) = {
val mf1 : MapFeatures = GrobidScorable.jsonToMapFeatures(
Sha1Strings(grobidIndex),
- GrobidStrings(grobidIndex))
+ JsonStrings(grobidIndex))
val mf2 : MapFeatures = CrossrefScorable.jsonToMapFeatures(
CrossrefStrings(crossrefIndex))
val score = Scorable.computeSimilarity(