New Treatments endpoint and bump to 5.0.0-alpha4

Author: tverbeiren

build.sbt

@@ -2,15 +2,15 @@ name := "LuciusAPI"
 
 import aether.AetherKeys._
 
-version in ThisBuild := "5.0.0-alpha2"
+version in ThisBuild := "5.0.0-alpha4"
 
 scalaVersion := "2.11.12"
 
 resolvers += Resolver.githubPackages("data-intuitive")
 resolvers += "Artifactory" at "https://sparkjobserver.jfrog.io/artifactory/jobserver/"
 
 libraryDependencies ++= Seq(
-  "com.data-intuitive" %% "luciuscore"        % "4.0.1-SNAPSHOT",
+  "com.data-intuitive" %% "luciuscore"        % "4.0.5",
   "spark.jobserver"    %% "job-server-api"    % "0.11.1"     % "provided",
   "spark.jobserver"    %% "job-server-extras" % "0.11.1"     % "provided",
   "org.scalactic"      %% "scalactic"         % "3.0.7"      % "test"    ,

src/main/scala/com/dataintuitive/luciusapi/Common.scala

@@ -167,6 +167,14 @@ object Common extends Serializable {
       Try(config.getString("limit").toInt).getOrElse(default)
     }
 
+    def optParamLike(config: Config, default: List[String] = Nil): List[String] = {
+      Try(config.getString("like").split(" ").toList).getOrElse(default)
+    }
+
+    def optParamTrtType(config: Config, default: List[String] = Nil): List[String] = {
+      Try(config.getString("trtType").split(" ").toList).getOrElse(default)
+    }
+
     def optParamFeatures(config: Config, default: List[String] = List(".*")): List[String] = {
       Try(config.getString("features").toString.split(" ").toList).getOrElse(default)
     }

src/main/scala/com/dataintuitive/luciusapi/treatments.scala

@@ -0,0 +1,73 @@
+package com.dataintuitive.luciusapi
+
+import com.dataintuitive.luciuscore._
+import genes._
+import api._
+
+import Common.ParamHandlers._
+
+import spark.jobserver.api.{JobEnvironment, SingleProblem, ValidationProblem}
+import spark.jobserver._
+
+import scala.util.Try
+import org.scalactic._
+import Accumulation._
+import com.typesafe.config.Config
+
+import org.apache.spark.sql.SparkSession
+import org.apache.spark.sql.Dataset
+
+/**
+  * Returns a list of treatments and corresponding samples matching a query, optionally with a limit on the number of results.
+  *
+  * Input:
+  *
+  * - __`query`__: Depending on the pattern, a regexp match or `startsWith` is applied (mandatory)
+  *
+  * - __`version`__: v1, v2 or t1 (optional, default is `v1`)
+  *
+  * - __`limit`__: The result size is limited to this number (optional, default is 10)
+  */
+object treatments extends SparkSessionJob with NamedObjectSupport {
+
+  import Treatments._
+
+  type JobData = Treatments.JobData
+  type JobOutput = collection.Map[String, Any]
+
+  override def validate(sparkSession: SparkSession,
+                        runtime: JobEnvironment,
+                        config: Config): JobData Or Every[ValidationProblem] = {
+
+    val version = validVersion(config)
+    val db = getDB(runtime)
+    val flatDb = getFlatDB(runtime)
+    val genes = getGenes(runtime)
+
+    val compoundQuery = paramCompoundQ(config)
+    val limit = optParamLimit(config)
+    val trtType = optParamTrtType(config)
+    val like = optParamLike(config)
+
+    val cachedData = withGood(db, flatDb, genes) { CachedData(_, _, _) }
+    val specificData = withGood(compoundQuery) { SpecificData(_, limit, like, trtType) }
+
+    withGood(version, cachedData, specificData) { JobData(_, _, _) }
+
+  }
+
+  override def runJob(sparkSession: SparkSession,
+                      runtime: JobEnvironment,
+                      data: JobData): JobOutput = {
+
+    implicit val thisSession = sparkSession
+
+    Map(
+      "info" -> Treatments.infoMsg,
+      "header" -> Treatments.header(data),
+      "data" -> Treatments.result(data)
+    )
+
+  }
+
+}