diff options
| -rw-r--r-- | scalding/scalding-debugging.md | 14 | ||||
| -rw-r--r-- | scalding/src/main/scala/sandcrawler/CdxBackfillJob.scala | 173 | ||||
| -rw-r--r-- | scalding/src/main/scala/sandcrawler/HBaseBuilder.scala | 7 | ||||
| -rw-r--r-- | scalding/src/test/scala/sandcrawler/CdxBackfillJob.scala | 117 | ||||
| -rw-r--r-- | scalding/src/test/scala/sandcrawler/HBaseStatusCountTest.scala | 22 |
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 |