Merge branch 'bnewbold-backfill' of git.archive.org:webgroup/sandcrawler

5 files changed, 322 insertions, 11 deletions

diff --git a/scalding/scalding-debugging.md b/scalding/scalding-debugging.md
index 9143698..404fb4d 100644
--- a/scalding/scalding-debugging.md
+++ b/scalding/scalding-debugging.md
@@ -45,6 +45,20 @@ resolved by ensuring that the `HBaseSource` constructors had exactly identical
 names and arguments (eg, table names and zookeeper quorums have to be exact
 matches).
 
+If you get:
+
+    value toTypedPipe is not a member of cascading.pipe.Pipe
+
+You probably need to:
+
+    import com.twitter.scalding.typed.TDsl._
+
+## Running Individual Tests
+
+You can run a single test matching a string glob pattern like:
+
+    sbt:sandcrawler> testOnly *CdxBackfill*
+
 ## Fields
 
 Values of type `List[Fields]` are not printed in the expected way:
diff --git a/scalding/src/main/scala/sandcrawler/CdxBackfillJob.scala b/scalding/src/main/scala/sandcrawler/CdxBackfillJob.scala
new file mode 100644
index 0000000..0251e07
--- /dev/null
+++ b/scalding/src/main/scala/sandcrawler/CdxBackfillJob.scala
@@ -0,0 +1,173 @@
+package sandcrawler
+
+import cascading.property.AppProps
+import cascading.tuple.Fields
+import cascading.pipe.joiner._
+import com.twitter.scalding._
+import com.twitter.scalding.typed.TDsl._
+import java.util.Properties
+import cascading.tap.SinkMode
+import parallelai.spyglass.base.JobBase
+import parallelai.spyglass.hbase.HBaseConstants.SourceMode
+import parallelai.spyglass.hbase.{HBaseSource, HBasePipeConversions}
+
+// Type that represents a raw parsed CDX line
+case class CdxLine(surt: String,
+                   datetime: String,
+                   url: String,
+                   mime: String,
+                   http_status: String,
+                   sha1: String,
+                   c_size: String,
+                   offset: String,
+                   warc: String)
+
+
+/**
+ *  CDX backfill:
+ *  1. parse CDX (all columns)
+ *  2. filter CDX (pdf, HTTP 200, etc)
+ *  3. source HBase (key column only)
+ *  4. left join CDX to HBase
+ *  5. filter to only those with null HBase key column
+ *  6. convert CDX fields to HBase columns
+ *  7. sink results to HBase
+ *
+ * TODO: I really mixed the Scalding "field-base" and "type-based" APIs here.
+ * Should decide on a best practice.
+ */
+class CdxBackfillJob(args: Args) extends JobBase(args) with HBasePipeConversions {
+
+  import CdxBackfillJob._
+
+  val hbaseSource = getHBaseSource(args("hbase-table"), args("zookeeper-hosts"))
+  val hbaseSink = getHBaseSink(args("hbase-table"), args("zookeeper-hosts"))
+
+  // Parse CDX lines from text file to typed pipe
+  val lines : TypedPipe[String] = TypedPipe.from(TextLine(args("cdx-input-path")))
+  val cdxLines : TypedPipe[CdxLine] = lines
+    .filter { isCdxLine }
+    .map { lineToCdxLine }
+    .filter { CdxBackfillJob.keepCdx(_) }
+
+  val cdxRows : TypedPipe[(String, String, String, String)] = cdxLines
+    .map { CdxBackfillJob.cdxLineToRow }
+
+  val existingKeys : TypedPipe[String] = hbaseSource
+    .read
+    .toTypedPipe[String]('key)
+
+  // filters out all the lines that have an existing SHA1 key in HBase
+  // the groupBy statements are to select key values to join on
+  val newRows : TypedPipe[(String, String, String, String)] = existingKeys
+    .groupBy( identity )
+    .rightJoin(cdxRows.groupBy(_._1))
+    .toTypedPipe
+    .debug
+    .collect { case (_, (None, row)) => row }
+    .debug
+
+  // convert to tuple form and write out into HBase
+  newRows
+    .toPipe('key, 'c, 'cdx, 'mime)
+    .toBytesWritable( new Fields("key", "c", "cdx", "mime") )
+    .write(hbaseSink)
+
+    // XXX:
+    //.toPipe("all")
+    //.mapTo('all -> ('key, 'c, 'cdx, 'mime)) { x : (String, String, String, String) => x }
+
+}
+
+object CdxBackfillJob {
+
+  def getHBaseSource(hbase_table: String, zookeeper_hosts: String) : HBaseSource = {
+    return HBaseBuilder.build(
+      hbase_table,
+      zookeeper_hosts,
+      List("file:size"), // not actually needed
+      SourceMode.SCAN_ALL)
+  }
+
+  def getHBaseSink(hbase_table: String, zookeeper_hosts: String) : HBaseSource = {
+    return HBaseBuilder.buildSink(
+      hbase_table,
+      zookeeper_hosts,
+      List("f:c", "file:cdx", "file:mime"),
+      SinkMode.UPDATE)
+  }
+
+  def normalizeMime(raw: String) : String = {
+
+    val NORMAL_MIME = List("application/pdf",
+                           "application/postscript",
+                           "text/html",
+                           "text/xml")
+
+    val lower = raw.toLowerCase()
+    NORMAL_MIME.foreach(norm =>
+      if (lower.startsWith(norm)) {
+        return norm
+      }
+    )
+
+    // Common special cases
+    if (lower.startsWith("application/xml")) {
+      return "text/xml"
+    }
+    if (lower.startsWith("application/x-pdf")) {
+      return "application/pdf"
+    }
+    return lower
+
+  }
+
+  def isCdxLine(line: String) : Boolean = {
+    // malformated or non-CDX11 lines
+    !(line.startsWith("#") || line.startsWith(" ") || line.startsWith("filedesc") ||
+      line.split(" ").size != 11)
+  }
+
+  def keepCdx(line: CdxLine) : Boolean = {
+    // TODO: sha1.isalnum() and c_size.isdigit() and offset.isdigit() and dt.isdigit()
+    if (line.http_status != "200" || line.sha1.size != 32) {
+      return false
+    }
+    // TODO: '-' in (line.surt, line.datetime, line.url, line.mime, line.c_size, line.offset, line.warc)
+    return true
+  }
+
+  // Returns (key, f:c, file:cdx, file:mime), all as strings, which is close to
+  // how they will be inserted into HBase
+  def cdxLineToRow(line: CdxLine) : (String, String, String, String) = {
+
+    val key = "sha1:" + line.sha1
+
+    val warcFile = line.warc.split('/')(1)
+
+    // Read CDX-style datetime and conver to ISO 8601 with second resolution
+    val dtFormat = new java.text.SimpleDateFormat("yyyyMMddHHmmss")
+    val isoFormat = new java.text.SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss'Z'")
+    // TODO: timezones? UTC to UTC, so I don't think so.
+    val dtIso = isoFormat.format(dtFormat.parse(line.datetime))
+
+    // warc_file = warc.split('/')[-1]
+    // dt_iso = datetime.strptime(dt, "%Y%m%d%H%M%S").isoformat()
+    // f:c = dict(u=url, d=dt_iso, f=warc_file, o=int(offset), c=1)
+
+    // This is the "f:c" field. 'i' intentionally not set
+    val heritrixInfo = ""
+
+    // file:cdx = dict(surt=surt, dt=dt, url=url, c_size=int(c_size),
+    //                 offset=int(offset), warc=warc)
+    val fileCdx = ""
+    (key, heritrixInfo, fileCdx, line.mime)
+  }
+
+  def lineToCdxLine(line: String) : CdxLine = {
+    val raw = line.split("\\s+")
+    // surt, datetime, url, mime, http_status, sha1, SKIP, SKIP, c_size, offset, warc
+    CdxLine(raw(0), raw(1), raw(2), raw(3), raw(4), raw(5), raw(8), raw(9), raw(10))
+  }
+
+}
diff --git a/scalding/src/main/scala/sandcrawler/HBaseBuilder.scala b/scalding/src/main/scala/sandcrawler/HBaseBuilder.scala
index b271def..fd04f2e 100644
--- a/scalding/src/main/scala/sandcrawler/HBaseBuilder.scala
+++ b/scalding/src/main/scala/sandcrawler/HBaseBuilder.scala
@@ -1,6 +1,8 @@
 package sandcrawler
 
 import cascading.tuple.Fields
+import parallelai.spyglass.base.JobBase
+import cascading.tap.SinkMode
 import parallelai.spyglass.hbase.HBaseConstants.SourceMode
 import parallelai.spyglass.hbase.HBaseSource
 import scala._
@@ -48,4 +50,9 @@ object HBaseBuilder {
     val (families, fields) = parseColSpecs(colSpecs)
     new HBaseSource(table, server, new Fields("key"), families, fields, sourceMode = sourceMode, keyList = keyList)
   }
+
+  def buildSink(table: String, server: String, colSpecs: List[String], sinkMode: SinkMode, keyList: List[String] = List("key")) : HBaseSource = {
+    val (families, fields) = parseColSpecs(colSpecs)
+    new HBaseSource(table, server, new Fields("key"), families, fields, sinkMode = sinkMode)
+  }
 }
diff --git a/scalding/src/test/scala/sandcrawler/CdxBackfillJob.scala b/scalding/src/test/scala/sandcrawler/CdxBackfillJob.scala
new file mode 100644
index 0000000..de94494
--- /dev/null
+++ b/scalding/src/test/scala/sandcrawler/CdxBackfillJob.scala
@@ -0,0 +1,117 @@
+
+package sandcrawler
+
+import org.scalatest._
+import cascading.tuple.{Tuple, Fields}
+import com.twitter.scalding.{JobTest, Tsv, TypedTsv, TupleConversions, TextLine}
+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
+
+class CdxBackfillTest extends FlatSpec with Matchers {
+
+  import CdxBackfillJob._
+
+  it should "normalize mimetypes" in {
+    assert(CdxBackfillJob.normalizeMime("asdf") === "asdf")
+    assert(CdxBackfillJob.normalizeMime("application/pdf") === "application/pdf")
+    assert(CdxBackfillJob.normalizeMime("application/pdf+journal") === "application/pdf")
+    assert(CdxBackfillJob.normalizeMime("Application/PDF") === "application/pdf")
+    assert(CdxBackfillJob.normalizeMime("application/p") === "application/p")
+    assert(CdxBackfillJob.normalizeMime("application/xml+stuff") === "text/xml")
+    assert(CdxBackfillJob.normalizeMime("application/x-pdf") === "application/pdf")
+    assert(CdxBackfillJob.normalizeMime("application/x-html") === "application/x-html")
+  }
+
+  it should "filter CDX lines" in {
+    assert(true === keepCdx(lineToCdxLine(
+      "edu,upenn,ldc)/sites/www.ldc.upenn.edu/files/medar2009-large-arabic-broadcast-collection.pdf 20170828233154 https://www.ldc.upenn.edu/sites/www.ldc.upenn.edu/files/medar2009-large-arabic-broadcast-collection.pdf application/pdf 200 WL3FEA62TEU4F52Y5DOVQ62VET4QJW7G - - 210251 931661233 SEMSCHOLAR-PDF-CRAWL-2017-08-04-20170828231135742-00000-00009-wbgrp-svc284/SEMSCHOLAR-PDF-CRAWL-2017-08-04-20170828232253025-00005-3480~wbgrp-svc284.us.archive.org~8443.warc.gz")))
+    // redirect
+    assert(false === keepCdx(lineToCdxLine(
+      "edu,upenn,ldc)/sites/www.ldc.upenn.edu/files/medar2009-large-arabic-broadcast-collection.pdf 20170828233154 https://www.ldc.upenn.edu/sites/www.ldc.upenn.edu/files/medar2009-large-arabic-broadcast-collection.pdf application/pdf 301 WL3FEA62TEU4F52Y5DOVQ62VET4QJW7G - - 210251 931661233 SEMSCHOLAR-PDF-CRAWL-2017-08-04-20170828231135742-00000-00009-wbgrp-svc284/SEMSCHOLAR-PDF-CRAWL-2017-08-04-20170828232253025-00005-3480~wbgrp-svc284.us.archive.org~8443.warc.gz")))
+  }
+
+  it should "know what CDX lines are" in {
+    assert(true === isCdxLine(
+      "edu,upenn,ldc)/sites/www.ldc.upenn.edu/files/medar2009-large-arabic-broadcast-collection.pdf 20170828233154 https://www.ldc.upenn.edu/sites/www.ldc.upenn.edu/files/medar2009-large-arabic-broadcast-collection.pdf application/pdf 200 WL3FEA62TEU4F52Y5DOVQ62VET4QJW7G - - 210251 931661233 SEMSCHOLAR-PDF-CRAWL-2017-08-04-20170828231135742-00000-00009-wbgrp-svc284/SEMSCHOLAR-PDF-CRAWL-2017-08-04-20170828232253025-00005-3480~wbgrp-svc284.us.archive.org~8443.warc.gz"))
+    assert(false === isCdxLine(""))
+    assert(false === isCdxLine(
+      " edu,upenn,ldc)/sites/www.ldc.upenn.edu/files/medar2009-large-arabic-broadcast-collection.pdf 20170828233154 https://www.ldc.upenn.edu/sites/www.ldc.upenn.edu/files/medar2009-large-arabic-broadcast-collection.pdf application/pdf 200 WL3FEA62TEU4F52Y5DOVQ62VET4QJW7G - - 210251 931661233 SEMSCHOLAR-PDF-CRAWL-2017-08-04-20170828231135742-00000-00009-wbgrp-svc284/SEMSCHOLAR-PDF-CRAWL-2017-08-04-20170828232253025-00005-3480~wbgrp-svc284.us.archive.org~8443.warc.gz"))
+    assert(false === isCdxLine(
+      "#edu,upenn,ldc)/sites/www.ldc.upenn.edu/files/medar2009-large-arabic-broadcast-collection.pdf 20170828233154 https://www.ldc.upenn.edu/sites/www.ldc.upenn.edu/files/medar2009-large-arabic-broadcast-collection.pdf application/pdf 200 WL3FEA62TEU4F52Y5DOVQ62VET4QJW7G - - 210251 931661233 SEMSCHOLAR-PDF-CRAWL-2017-08-04-20170828231135742-00000-00009-wbgrp-svc284/SEMSCHOLAR-PDF-CRAWL-2017-08-04-20170828232253025-00005-3480~wbgrp-svc284.us.archive.org~8443.warc.gz"))
+    // missing two fields
+    assert(false === isCdxLine(
+      "edu,upenn,ldc)/sites/www.ldc.upenn.edu/files/medar2009-large-arabic-broadcast-collection.pdf 20170828233154 https://www.ldc.upenn.edu/sites/www.ldc.upenn.edu/files/medar2009-large-arabic-broadcast-collection.pdf application/pdf 200 WL3FEA62TEU4F52Y5DOVQ62VET4QJW7G 210251 931661233 SEMSCHOLAR-PDF-CRAWL-2017-08-04-20170828231135742-00000-00009-wbgrp-svc284/SEMSCHOLAR-PDF-CRAWL-2017-08-04-20170828232253025-00005-3480~wbgrp-svc284.us.archive.org~8443.warc.gz"))
+    // extra field
+    assert(false === isCdxLine(
+      "edu,upenn,ldc)/sites/www.ldc.upenn.edu/files/medar2009-large-arabic-broadcast-collection.pdf 20170828233154 https://www.ldc.upenn.edu/sites/www.ldc.upenn.edu/files/medar2009-large-arabic-broadcast-collection.pdf application/pdf 200 WL3FEA62TEU4F52Y5DOVQ62VET4QJW7G - - 210251 931661233 SEMSCHOLAR-PDF-CRAWL-2017-08-04-20170828231135742-00000-00009-wbgrp-svc284/SEMSCHOLAR-PDF-CRAWL-2017-08-04-20170828232253025-00005-3480~wbgrp-svc284.us.archive.org~8443.warc.gz -"))
+  }
+
+  it should "execute lineToRow" in {
+    cdxLineToRow(lineToCdxLine(
+      "edu,upenn,ldc)/sites/www.ldc.upenn.edu/files/medar2009-large-arabic-broadcast-collection.pdf 20170828233154 https://www.ldc.upenn.edu/sites/www.ldc.upenn.edu/files/medar2009-large-arabic-broadcast-collection.pdf application/pdf 200 WL3FEA62TEU4F52Y5DOVQ62VET4QJW7G - - 210251 931661233 SEMSCHOLAR-PDF-CRAWL-2017-08-04-20170828231135742-00000-00009-wbgrp-svc284/SEMSCHOLAR-PDF-CRAWL-2017-08-04-20170828232253025-00005-3480~wbgrp-svc284.us.archive.org~8443.warc.gz"))
+  }
+
+}
+
+@RunWith(classOf[JUnitRunner])
+class CdxBackfillJobTest extends FunSpec with TupleConversions {
+
+  val output = "/tmp/testOutput"
+  val (testTable, testHost, testCdxFile) = ("test-table", "dummy-host:2181", "test_file.cdx")
+
+  val log = LoggerFactory.getLogger(this.getClass.getName)
+
+  val dummySizeBytes = Bytes.toBytes(100)
+
+  val sampleData = List(
+    List(Bytes.toBytes("sha1:K2DKSSVTXWPRMFDTWSTCQW3RVWRIOV3Q"), dummySizeBytes),
+    List(Bytes.toBytes("sha1:C3YNNEGH5WAG5ZAAXWAEBNXJWT6CZ3WU"), dummySizeBytes),
+    List(Bytes.toBytes("sha1:SDKUVHC3YNNEGH5WAG5ZAAXWAEBNX4WT"), dummySizeBytes),
+    List(Bytes.toBytes("sha1:095893C3YNNEGH5WAG5ZAAXWAEBNXJWT"), dummySizeBytes)
+  )
+  val sampleCdxLines = List(
+    // clean line
+    "edu,upenn,ldc)/sites/www.ldc.upenn.edu/files/medar2009-large-arabic-broadcast-collection.pdf 20170828233154 https://www.ldc.upenn.edu/sites/www.ldc.upenn.edu/files/medar2009-large-arabic-broadcast-collection.pdf application/pdf 200 WL3FEA62TEU4F52Y5DOVQ62VET4QJW7G - - 210251 931661233 SEMSCHOLAR-PDF-CRAWL-2017-08-04-20170828231135742-00000-00009-wbgrp-svc284/SEMSCHOLAR-PDF-CRAWL-2017-08-04-20170828232253025-00005-3480~wbgrp-svc284.us.archive.org~8443.warc.gz",
+    // has existing SHA1
+    "edu,upenn,ldc)/sites/www.ldc.upenn.edu/files/medar2009-large-arabic-broadcast-collection.pdf 20170828233154 https://www.ldc.upenn.edu/sites/www.ldc.upenn.edu/files/medar2009-large-arabic-broadcast-collection.pdf application/pdf 200 C3YNNEGH5WAG5ZAAXWAEBNXJWT6CZ3WU - - 210251 931661233 SEMSCHOLAR-PDF-CRAWL-2017-08-04-20170828231135742-00000-00009-wbgrp-svc284/SEMSCHOLAR-PDF-CRAWL-2017-08-04-20170828232253025-00005-3480~wbgrp-svc284.us.archive.org~8443.warc.gz",
+    // HTTP status code
+    "edu,upenn,ldc)/sites/www.ldc.upenn.edu/files/medar2009-large-arabic-broadcast-collection.pdf 20170828233154 https://www.ldc.upenn.edu/sites/www.ldc.upenn.edu/files/medar2009-large-arabic-broadcast-collection.pdf application/pdf 301 WL3FEA62TEU4F52Y5DOVQ62VET4QJW7G - - 210251 931661233 SEMSCHOLAR-PDF-CRAWL-2017-08-04-20170828231135742-00000-00009-wbgrp-svc284/SEMSCHOLAR-PDF-CRAWL-2017-08-04-20170828232253025-00005-3480~wbgrp-svc284.us.archive.org~8443.warc.gz",
+    // not CDX (prefixed with hash)
+    "#edu,upenn,ldc)/sites/www.ldc.upenn.edu/files/medar2009-large-arabic-broadcast-collection.pdf 20170828233154 https://www.ldc.upenn.edu/sites/www.ldc.upenn.edu/files/medar2009-large-arabic-broadcast-collection.pdf application/pdf 200 WL3FEA62TEU4F52Y5DOVQ62VET4QJW7G - - 210251 931661233 SEMSCHOLAR-PDF-CRAWL-2017-08-04-20170828231135742-00000-00009-wbgrp-svc284/SEMSCHOLAR-PDF-CRAWL-2017-08-04-20170828232253025-00005-3480~wbgrp-svc284.us.archive.org~8443.warc.gz"
+  )
+
+  JobTest("sandcrawler.CdxBackfillJob")
+    .arg("test", "")
+    .arg("app.conf.path", "app.conf")
+    .arg("output", output)
+    .arg("hbase-table", testTable)
+    .arg("zookeeper-hosts", testHost)
+    .arg("cdx-input-path", testCdxFile)
+    .arg("debug", "true")
+    .source[Tuple](CdxBackfillJob.getHBaseSource(testTable, testHost),
+      sampleData.map(l => new Tuple(l.map(s => {new ImmutableBytesWritable(s)}):_*)))
+    .source[String](TextLine(testCdxFile), sampleCdxLines)
+    .sink[Tuple](CdxBackfillJob.getHBaseSink(testTable, testHost)) {
+      outputBuffer =>
+
+        it("should return a 1-element list (after join).") {
+        // XXX:
+          assert(outputBuffer.size === 1)
+        }
+
+        // Convert List[Tuple] to Map[Long, Long].
+        val counts = outputBuffer.map(t => (t.getLong(0), t.getLong(1))).toMap
+        it("should have the appropriate number of each status type") {
+        // XXX:
+          assert(counts(1) == 3)
+        }
+      }
+    .run
+    .finish
+}
diff --git a/scalding/src/test/scala/sandcrawler/HBaseStatusCountTest.scala b/scalding/src/test/scala/sandcrawler/HBaseStatusCountTest.scala
index 11ab1d0..d7689cd 100644
--- a/scalding/src/test/scala/sandcrawler/HBaseStatusCountTest.scala
+++ b/scalding/src/test/scala/sandcrawler/HBaseStatusCountTest.scala
@@ -48,18 +48,18 @@ class HBaseStatusCountTest extends FunSpec with TupleConversions {
     .arg("debug", "true")
     .source[Tuple](HBaseCountJob.getHBaseSource(testTable, testHost, "grobid0:status_code"),
       sampleData.map(l => new Tuple(l.map(s => {new ImmutableBytesWritable(s)}):_*)))
-      .sink[Tuple](TypedTsv[(Long, Long)](output)) {
-        outputBuffer =>
-        it("should return a 2-element list.") {
-          assert(outputBuffer.size === 2)
-        }
+    .sink[Tuple](TypedTsv[(Long, Long)](output)) {
+      outputBuffer =>
+      it("should return a 2-element list.") {
+        assert(outputBuffer.size === 2)
+      }
 
-        // Convert List[Tuple] to Map[Long, Long].
-        val counts = outputBuffer.map(t => (t.getLong(0), t.getLong(1))).toMap
-        it("should have the appropriate number of each status type") {
-          assert(counts(statusType1) == statusType1Count)
-          assert(counts(statusType2) == statusType2Count)
-        }
+      // Convert List[Tuple] to Map[Long, Long].
+      val counts = outputBuffer.map(t => (t.getLong(0), t.getLong(1))).toMap
+      it("should have the appropriate number of each status type") {
+        assert(counts(statusType1) == statusType1Count)
+        assert(counts(statusType2) == statusType2Count)
+      }
     }
     .run
     .finish