Undid changes that did not belong in this branch.

3 files changed, 0 insertions, 304 deletions

diff --git a/scalding/scalding-debugging.md b/scalding/scalding-debugging.md
index 404fb4d..9143698 100644
--- a/scalding/scalding-debugging.md
+++ b/scalding/scalding-debugging.md
@@ -45,20 +45,6 @@ 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
deleted file mode 100644
index 0251e07..0000000
--- a/scalding/src/main/scala/sandcrawler/CdxBackfillJob.scala
+++ /dev/null
@@ -1,173 +0,0 @@
-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/test/scala/sandcrawler/CdxBackfillJob.scala b/scalding/src/test/scala/sandcrawler/CdxBackfillJob.scala
deleted file mode 100644
index de94494..0000000
--- a/scalding/src/test/scala/sandcrawler/CdxBackfillJob.scala
+++ /dev/null
@@ -1,117 +0,0 @@
-
-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
-}