Merge branch 'refactoring' into 'master'

Refactoring to add, use, and test class HBaseBuilder to eliminate duplicated code and facilitate HBaseSource creation

See merge request webgroup/sandcrawler!1

4 files changed, 101 insertions, 20 deletions

diff --git a/scalding/src/main/scala/sandcrawler/HBaseBuilder.scala b/scalding/src/main/scala/sandcrawler/HBaseBuilder.scala
new file mode 100644
index 0000000..87cc0cb
--- /dev/null
+++ b/scalding/src/main/scala/sandcrawler/HBaseBuilder.scala
@@ -0,0 +1,46 @@
+package sandcrawler
+
+import cascading.tuple.Fields
+import parallelai.spyglass.hbase.HBaseConstants.SourceMode
+import parallelai.spyglass.hbase.HBaseSource
+import scala._
+
+object HBaseBuilder {
+  // map from column families to column names
+  val schema = Map("f" -> List("c"),
+    "file" -> List("size", "mime", "cdx"),
+    "grobid0" -> List("status_code", "quality", "status", "tei_xml", "tei_json", "metadata"),
+    "match0" -> List("status", "doi", "info"))
+  val inverseSchema = {for ((k,vs) <- schema; v <-vs) yield (k + ":" + v)}.toList
+
+  // The argument should be a comma-separated list of family:column, such as "f:c, file:size".
+  @throws(classOf[IllegalArgumentException])
+  def parseColSpec(colSpecs: List[String]) : (List[String], List[Fields]) = {
+    // Verify that all column specifiers are legal.
+    for (colSpec <- colSpecs) {
+      if (!(inverseSchema contains colSpec)) {
+        throw new IllegalArgumentException("No such column: " + colSpec)
+      }
+      val pair = colSpec split(":")
+      if (colSpec.split(":").length != 2) {
+        throw new IllegalArgumentException("Bad column specifier " + colSpec + 
+          " (specifiers should be family:name)")
+      }
+    }
+
+    // Produce and return a tuple containing:
+    // 1. A list of column families.
+    // 2. A corresponding list of Fields, each containing column names.
+    val groupMap: Map[String, List[String]] = colSpecs.groupBy(c => (c split ":")(0))
+    val families = groupMap.keys.toList
+    val groupedColNames : List[List[String]] = families map {fam => {
+        val cols = {groupMap(fam).map(v => v.split(":")(1))}
+        cols}}
+    (families, groupedColNames.map({fields => new Fields(fields : _*)}))
+  }
+
+  def build(table: String, server: String, colSpec: List[String], sourceMode: SourceMode, keyList: List[String] = List("key")) = {
+    val (families, fields) = parseColSpec(colSpec)
+    new HBaseSource(table, server, new Fields("key"), families, fields, sourceMode = sourceMode, keyList = keyList)
+  }
+}
diff --git a/scalding/src/main/scala/sandcrawler/HBaseRowCountJob.scala b/scalding/src/main/scala/sandcrawler/HBaseRowCountJob.scala
index d47fe60..9d074ab 100644
--- a/scalding/src/main/scala/sandcrawler/HBaseRowCountJob.scala
+++ b/scalding/src/main/scala/sandcrawler/HBaseRowCountJob.scala
@@ -16,17 +16,17 @@ class HBaseRowCountJob(args: Args) extends JobBase(args) with HBasePipeConversio
 
   val output = args("output")
 
-  val hbs = new HBaseSource(
-    //"table_name",
-    //"quorum_name:2181",
-    "wbgrp-journal-extract-0-qa",     // HBase Table Name
-    "mtrcs-zk1.us.archive.org:2181",  // HBase Zookeeper server (to get runtime config info; can be array?)
-    new Fields("key"),
-    List("file"),
-    List(new Fields("size", "mimetype")),
-    sourceMode = SourceMode.SCAN_ALL)
+  HBaseRowCountJob.getHBaseSource
     .read
     .debug
     .groupAll { _.size('count) }
     .write(Tsv(output))
 }
+
+object HBaseRowCountJob {
+  def getHBaseSource = HBaseBuilder.build(
+    "wbgrp-journal-extract-0-qa",     // HBase Table Name
+    "mtrcs-zk1.us.archive.org:2181",  // HBase Zookeeper server (to get runtime config info; can be array?)
+    List("file:size", "file:mime"),
+    SourceMode.SCAN_ALL)
+}
diff --git a/scalding/src/test/scala/sandcrawler/HBaseBuilderTest.scala b/scalding/src/test/scala/sandcrawler/HBaseBuilderTest.scala
new file mode 100644
index 0000000..b45751d
--- /dev/null
+++ b/scalding/src/test/scala/sandcrawler/HBaseBuilderTest.scala
@@ -0,0 +1,43 @@
+package example
+
+import cascading.tuple.Fields
+import org.scalatest._
+import sandcrawler.HBaseBuilder
+
+class HBaseBuilderTest extends FlatSpec with Matchers {
+  "parseColSpec()" should "work on legal nontrivial input" in {
+    val (fams, fields) = HBaseBuilder.parseColSpec(List("file:size", "file:cdx", "match0:status"))
+    fams should have length 2
+    fields should have length 2
+    val fileIndex = fams.indexOf("file")
+    fileIndex should not be -1
+    fields(fileIndex) should be (new Fields("size", "cdx"))
+    val match0Index = fams.indexOf("match0")
+    match0Index should not be -1
+    fields(match0Index) should be (new Fields("status"))
+  }
+
+  it should "work on empty input" in {
+    val (fams, fields) = HBaseBuilder.parseColSpec(List())
+    fams should have length 0
+    fields should have length 0
+  }
+
+  it should "throw IllegalArgumentException on malformed input" in {
+    a [IllegalArgumentException] should be thrownBy {
+      HBaseBuilder.parseColSpec(List("file_size"))
+    }
+  }
+
+  it should "throw IllegalArgumentException on nonexistent family" in {
+    a [IllegalArgumentException] should be thrownBy {
+      HBaseBuilder.parseColSpec(List("foo:bar"))
+    }
+  }
+
+  it should "throw IllegalArgumentException on nonexistent column" in {
+    a [IllegalArgumentException] should be thrownBy {
+      HBaseBuilder.parseColSpec(List("file:bar"))
+    }
+  }
+}
diff --git a/scalding/src/test/scala/sandcrawler/HBaseRowCountTest.scala b/scalding/src/test/scala/sandcrawler/HBaseRowCountTest.scala
index 94b3740..abb017c 100644
--- a/scalding/src/test/scala/sandcrawler/HBaseRowCountTest.scala
+++ b/scalding/src/test/scala/sandcrawler/HBaseRowCountTest.scala
@@ -12,6 +12,7 @@ import scala._
 import com.twitter.scalding.Tsv
 import parallelai.spyglass.hbase.HBaseSource
 import parallelai.spyglass.hbase.HBaseConstants.SourceMode
+import sandcrawler.HBaseRowCountJob
 
 /**
  * Example of how to define tests for HBaseSource
@@ -39,18 +40,9 @@ class HBaseRowCountTest extends FunSpec with TupleConversions {
     .arg("app.conf.path", "app.conf")
     .arg("output", output)
     .arg("debug", "true")
-    .source[Tuple](
-    new HBaseSource(
-      //"table_name",
-      //"quorum_name:2181",
-      "wbgrp-journal-extract-0-qa",
-      "mtrcs-zk1.us.archive.org:2181",
-      new Fields("key"),
-      List("file"),
-      List(new Fields("size", "mimetype")),
-      sourceMode = SourceMode.SCAN_ALL),
+    .source[Tuple](HBaseRowCountJob.getHBaseSource,
       sampleData.map(l => new Tuple(l.map(s => {new ImmutableBytesWritable(Bytes.toBytes(s))}):_*)))
-    .sink[Tuple](Tsv(output)) {
+      .sink[Tuple](Tsv(output)) {
       outputBuffer =>
 
         it("should return the test data provided.") {