Merge pull request #163 from X-DataInitiative/CNAM-352-Release-1.1

Cnam 352: Release 1.1

Author: ysebiat

build.sbt

@@ -1,6 +1,6 @@
 name := "SNIIRAM-featuring"
 
-version := "1.0"
+version := "1.1"
 
 scalaVersion := "2.11.12"
 val sparkVersion = "2.3.0"

src/main/scala/fr/polytechnique/cmap/cnam/study/fall/FallMain.scala

@@ -33,10 +33,7 @@ object FallMain extends Main with FractureCodes {
 
     logger.info("Reading sources")
     import implicits.SourceReader
-    val sources = Sources.sanitizeDates(
-      Sources.sanitize(sqlContext.readSources(fallConfig.input)),
-      fallConfig.base.studyStart, fallConfig.base.studyEnd
-    )
+    val sources = Sources.sanitize(sqlContext.readSources(fallConfig.input))
     val dcir = sources.dcir.get.repartition(4000).persist()
     val mco = sources.mco.get.repartition(4000).persist()
 

src/main/scala/fr/polytechnique/cmap/cnam/study/fall/config/FallConfig.scala

@@ -31,9 +31,9 @@ object FallConfig extends FallConfigLoader with FractureCodes {
 
   /** Base fixed parameters for this study. */
   final object BaseConfig extends BaseConfig(
-    ageReferenceDate = LocalDate.of(2015, 1, 1),
-    studyStart = LocalDate.of(2015, 1, 1),
-    studyEnd = LocalDate.of(2016, 1, 1)
+    ageReferenceDate = LocalDate.of(2014, 1, 1),
+    studyStart = LocalDate.of(2014, 1, 1),
+    studyEnd = LocalDate.of(2017, 1, 1)
   )
 
   /** Fixed parameters needed for the Patients extractors. */

src/main/scala/fr/polytechnique/cmap/cnam/study/pioglitazone/PioglitazoneMain.scala

@@ -46,10 +46,7 @@ object PioglitazoneMain extends Main {
     val config = PioglitazoneConfig.load(argsMap("conf"), argsMap("env"))
 
     import implicits.SourceReader
-    val sources = Sources.sanitizeDates(
-      Sources.sanitize(sqlContext.readSources(config.input)),
-      config.base.studyStart, config.base.studyEnd
-    )
+    val sources = Sources.sanitize(sqlContext.readSources(config.input))
 
     val patients: Dataset[Patient] = new Patients(config.patients).extract(sources).cache()
     operationsMetadata += {

src/main/scala/fr/polytechnique/cmap/cnam/study/rosiglitazone/RosiglitazoneMain.scala

@@ -40,10 +40,7 @@ object RosiglitazoneMain extends Main {
 
     logger.info("Reading sources")
     import implicits.SourceReader
-    val sources = Sources.sanitizeDates(
-      Sources.sanitize(sqlContext.readSources(config.input)),
-      config.base.studyStart, config.base.studyEnd
-    )
+    val sources = Sources.sanitize(sqlContext.readSources(config.input))
 
     //Extracting Patients
     val patients: Dataset[Patient] = new Patients(config.patients).extract(sources).cache()