Merge pull request #5 from databrickslabs/release

Minor adjustments to test suite & build

Author: pohlposition

build.sbt

@@ -10,7 +10,7 @@ import sbt.nio.Keys._
 lazy val scala212 = "2.12.8"
 lazy val scala211 = "2.11.12"
 
-lazy val sparkVersion = sys.env.getOrElse("SPARK_VERSION", "3.0.0")
+lazy val sparkVersion = sys.env.getOrElse("SPARK_VERSION", "3.0.1")
 
 def majorMinorVersion(version: String): String = {
   StringUtils.ordinalIndexOf(version, ".", 2) match {
@@ -158,7 +158,7 @@ lazy val sparkClasspath = taskKey[String]("sparkClasspath")
 lazy val sparkHome = taskKey[String]("sparkHome")
 
 // Publish to Bintray
-ThisBuild / description := "An open-source toolkit for large-scale genomic analysis"
+ThisBuild / description := "An open-source toolkit for large-scale EHR processing"
 ThisBuild / homepage := Some(url("https://databricks.com/solutions/industries/healthcare"))
 ThisBuild / scmInfo := Some(
   ScmInfo(

src/main/scala/com/databricks/labs/smolder/Message.scala

@@ -64,13 +64,16 @@ private[smolder] object Message {
     * @return Parses the message into a Message case class.
     */
   def apply(text: UTF8String): Message = {
+
+    val delim: Byte = 0x0d
+
     if (text == null) {
       null
     } else {
       val textString = text.toString
       require(textString.nonEmpty, "Received empty string.")
 
-      Message(textString.split('\n').toIterator)
+      Message(textString.split(delim.toChar).toIterator)
     }
   }
 }

src/test/scala/com/databricks/labs/smolder/MessageSuite.scala

@@ -101,8 +101,10 @@ class MessageSuite extends SmolderBaseTest {
 
   test("parse a full message, by string") {
 
+    val delim: Byte = 0x0d
+
     val file = testFile("single_record.hl7")
-    val lines = Source.fromFile(file).getLines().mkString("\n")
+    val lines = Source.fromFile(file).getLines().mkString(delim.toChar.toString)
 
     val message = Message(UTF8String.fromString(lines))
 

src/test/scala/com/databricks/labs/smolder/functionsSuite.scala

@@ -30,7 +30,9 @@ class functionsSuite extends SmolderBaseTest {
       .wholeTextFiles(file)
       .map(p => TextFile(p._1, p._2)))
 
-    val hl7Df = df.select(parse_hl7_message(df("value")).alias("hl7"))
+    val cleanDF  = df.select(regexp_replace(df("value"), "\n", "\r").alias("clean"))
+
+    val hl7Df = cleanDF.select(parse_hl7_message(cleanDF("clean")).alias("hl7"))
 
     assert(hl7Df.count() === 1)
     assert(hl7Df.selectExpr("explode(hl7.segments)").count() === 3)
@@ -59,7 +61,8 @@ class functionsSuite extends SmolderBaseTest {
       .wholeTextFiles(file)
       .map(p => TextFile(p._1, p._2)))
 
-    val hl7Df = df.select(parse_hl7_message(df("value")).alias("hl7"))
+    val cleanDF  = df.select(regexp_replace(df("value"), "\n", "\r").alias("clean"))
+    val hl7Df = cleanDF.select(parse_hl7_message(cleanDF("clean")).alias("hl7"))
 
     val evnType = hl7Df.select(segment_field("EVN", 0, col("hl7.segments"))
       .alias("type"))