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[tests] Add unit test for FeaturesTableRepositoryDAO
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Ludovic Claude
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Dec 31, 2018
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,50 @@ | ||
| /* | ||
| * Copyright (C) 2017 LREN CHUV for Human Brain Project | ||
| * | ||
| * This program is free software: you can redistribute it and/or modify | ||
| * it under the terms of the GNU Affero General Public License as | ||
| * published by the Free Software Foundation, either version 3 of the | ||
| * License, or (at your option) any later version. | ||
| * | ||
| * This program is distributed in the hope that it will be useful, | ||
| * but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| * GNU Affero General Public License for more details. | ||
| * | ||
| * You should have received a copy of the GNU Affero General Public License | ||
| * along with this program. If not, see <http://www.gnu.org/licenses/>. | ||
| */ | ||
|
|
||
| package ch.chuv.lren.woken.dao | ||
| import java.sql.Connection | ||
|
|
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| import acolyte.jdbc.{ AbstractCompositeHandler, AcolyteDSL, ConnectionHandler } | ||
| import cats.effect.{ ContextShift, IO, Resource } | ||
| import cats.effect.internals.IOContextShift | ||
| import doobie.util.ExecutionContexts | ||
| import doobie.util.transactor.Transactor | ||
|
|
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| trait DAOTest[DAO <: Repository] { | ||
|
|
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| def withRepository(sqlHandler: AbstractCompositeHandler[_], | ||
| mkDAO: Transactor[IO] => DAO)(testCode: DAO => Any): Unit = { | ||
|
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| val conn: Connection = AcolyteDSL.connection(sqlHandler) | ||
| implicit val cs: ContextShift[IO] = IOContextShift.global | ||
|
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| // Resource yielding a Transactor[IO] wrapping the given `Connection` | ||
| def transactor(c: Connection): Resource[IO, Transactor[IO]] = | ||
| ExecutionContexts.cachedThreadPool[IO].flatMap { te => | ||
| val t: Transactor[IO] = Transactor.fromConnection[IO](c, te) | ||
| Resource.liftF(t.configure(_ => IO.pure(t))) | ||
| } | ||
|
|
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| transactor(conn) | ||
| .use { tr => | ||
| val dao = mkDAO(tr) | ||
| IO.delay(testCode(dao)) | ||
| } | ||
| .unsafeRunSync() | ||
| } | ||
|
|
||
| } |
147 changes: 147 additions & 0 deletions
147
src/test/scala/ch/chuv/lren/woken/dao/FeaturesTableRepositoryDAOTest.scala
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,147 @@ | ||
| /* | ||
| * Copyright (C) 2017 LREN CHUV for Human Brain Project | ||
| * | ||
| * This program is free software: you can redistribute it and/or modify | ||
| * it under the terms of the GNU Affero General Public License as | ||
| * published by the Free Software Foundation, either version 3 of the | ||
| * License, or (at your option) any later version. | ||
| * | ||
| * This program is distributed in the hope that it will be useful, | ||
| * but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| * GNU Affero General Public License for more details. | ||
| * | ||
| * You should have received a copy of the GNU Affero General Public License | ||
| * along with this program. If not, see <http://www.gnu.org/licenses/>. | ||
| */ | ||
|
|
||
| package ch.chuv.lren.woken.dao | ||
|
|
||
| import acolyte.jdbc._ | ||
| import acolyte.jdbc.RowLists.{ rowList1, rowList2 } | ||
| import acolyte.jdbc.Implicits._ | ||
| import cats.effect.IO | ||
| import ch.chuv.lren.woken.core.model.database.TableColumn | ||
| import ch.chuv.lren.woken.messages.datasets.DatasetId | ||
| import ch.chuv.lren.woken.messages.query.filters._ | ||
| import ch.chuv.lren.woken.messages.variables.SqlType | ||
| import org.scalatest.{ Matchers, WordSpec } | ||
|
|
||
| class FeaturesTableRepositoryDAOTest | ||
| extends WordSpec | ||
| with Matchers | ||
| with DAOTest[FeaturesTableRepositoryDAO[IO]] | ||
| with FeaturesTableTestSupport { | ||
|
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| val wokenRepository = new WokenInMemoryRepository[IO]() | ||
|
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| val sampleTableHandler: ScalaCompositeHandler = AcolyteDSL.handleStatement | ||
| .withQueryDetection("^SELECT ") // regex test from beginning | ||
| .withQueryHandler { e: QueryExecution => | ||
| e.sql.trim match { | ||
|
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| case """SELECT count(*) FROM "Sample"""" => | ||
| rowList1(classOf[Int]) :+ 99 | ||
|
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| case """SELECT count(*) FROM "Sample" WHERE "score_test1" >= 2 AND "cognitive_task2" < 9""" => | ||
| rowList1(classOf[Int]) :+ 5 | ||
|
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| case """SELECT "college_math" , count(*) FROM "Sample" GROUP BY "college_math"""" => | ||
| (rowList2(classOf[String], classOf[Int]) | ||
| :+ ("0", 47) // tuple as row | ||
| :+ ("1", 52)) | ||
|
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| case """SELECT "college_math" , count(*) FROM "Sample" WHERE "score_test1" >= 2 GROUP BY "college_math"""" => | ||
| (rowList2(classOf[String], classOf[Int]) | ||
| :+ ("0", 12) // tuple as row | ||
| :+ ("1", 22)) | ||
|
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| case _ => throw new IllegalArgumentException(s"Unhandled $e") | ||
| } | ||
| } | ||
|
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| val cdeTableHandler: ScalaCompositeHandler = AcolyteDSL.handleStatement | ||
| .withQueryDetection("^SELECT ") // regex test from beginning | ||
| .withQueryHandler { e: QueryExecution => | ||
| e.sql.trim match { | ||
|
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| case """SELECT count(*) FROM "cde_features_a" WHERE "dataset" = ?""" | ||
| if e.parameters == List(DefinedParameter("datasetA", ParameterMetaData.Str)) => | ||
| rowList1(classOf[Int]) :+ 5 | ||
|
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| case _ => throw new IllegalArgumentException(s"Unhandled $e") | ||
| } | ||
| } | ||
|
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| "FeaturesTableRepositoryDAO" should { | ||
|
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| "count all records in the table" in withRepository( | ||
| sampleTableHandler, | ||
| xa => new FeaturesTableRepositoryDAO[IO](xa, sampleTable, sampleHeaders, wokenRepository) | ||
| ) { dao => | ||
| dao.count.unsafeRunSync() shouldBe 99 | ||
| } | ||
|
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| "count all records matching a dataset for a table without a dataset column" in withRepository( | ||
| sampleTableHandler, | ||
| xa => new FeaturesTableRepositoryDAO[IO](xa, sampleTable, sampleHeaders, wokenRepository) | ||
| ) { dao => | ||
| dao.count(DatasetId(sampleTable.table.name)).unsafeRunSync() shouldBe 99 | ||
| dao.count(DatasetId("other")).unsafeRunSync() shouldBe 0 | ||
| } | ||
|
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| "count all records matching a dataset for a table with a dataset column" in withRepository( | ||
| cdeTableHandler, | ||
| xa => new FeaturesTableRepositoryDAO[IO](xa, cdeTable, cdeHeaders, wokenRepository) | ||
| ) { dao => | ||
| dao.count(DatasetId("datasetA")).unsafeRunSync() shouldBe 5 | ||
| } | ||
|
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| "count all records matching a filter" in withRepository( | ||
| sampleTableHandler, | ||
| xa => new FeaturesTableRepositoryDAO[IO](xa, sampleTable, sampleHeaders, wokenRepository) | ||
| ) { dao => | ||
| val filter = CompoundFilterRule( | ||
| Condition.and, | ||
| rules = List( | ||
| SingleFilterRule("score_test1", | ||
| "score_test1", | ||
| "number", | ||
| InputType.number, | ||
| Operator.greaterOrEqual, | ||
| List("2")), | ||
| SingleFilterRule("cognitive_task2", | ||
| "cognitive_task2", | ||
| "number", | ||
| InputType.number, | ||
| Operator.less, | ||
| List("9")) | ||
| ) | ||
| ) | ||
| dao.count(None).unsafeRunSync() shouldBe 99 | ||
| dao.count(Some(filter)).unsafeRunSync() shouldBe 5 | ||
| } | ||
|
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| "count records grouped by a field" in withRepository( | ||
| sampleTableHandler, | ||
| xa => new FeaturesTableRepositoryDAO[IO](xa, sampleTable, sampleHeaders, wokenRepository) | ||
| ) { dao => | ||
| dao.countGroupBy(TableColumn("college_math", SqlType.int), None).unsafeRunSync() shouldBe Map( | ||
| "0" -> 47, | ||
| "1" -> 52 | ||
| ) | ||
|
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| val filter = SingleFilterRule("score_test1", | ||
| "score_test1", | ||
| "number", | ||
| InputType.number, | ||
| Operator.greaterOrEqual, | ||
| List("2")) | ||
|
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| dao | ||
| .countGroupBy(TableColumn("college_math", SqlType.int), Some(filter)) | ||
| .unsafeRunSync() shouldBe Map("0" -> 12, "1" -> 22) | ||
| } | ||
|
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| } | ||
| } |
73 changes: 73 additions & 0 deletions
73
src/test/scala/ch/chuv/lren/woken/dao/FeaturesTableTestSupport.scala
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,73 @@ | ||
| /* | ||
| * Copyright (C) 2017 LREN CHUV for Human Brain Project | ||
| * | ||
| * This program is free software: you can redistribute it and/or modify | ||
| * it under the terms of the GNU Affero General Public License as | ||
| * published by the Free Software Foundation, either version 3 of the | ||
| * License, or (at your option) any later version. | ||
| * | ||
| * This program is distributed in the hope that it will be useful, | ||
| * but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| * GNU Affero General Public License for more details. | ||
| * | ||
| * You should have received a copy of the GNU Affero General Public License | ||
| * along with this program. If not, see <http://www.gnu.org/licenses/>. | ||
| */ | ||
|
|
||
| package ch.chuv.lren.woken.dao | ||
| import ch.chuv.lren.woken.core.model.database.{ FeaturesTableDescription, TableColumn, TableId } | ||
| import ch.chuv.lren.woken.messages.variables.SqlType | ||
| import spray.json.{ JsNumber, JsObject, JsString } | ||
|
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| trait FeaturesTableTestSupport { | ||
|
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| val database = "features_db" | ||
| val sampleTable = FeaturesTableDescription(TableId(database, None, "Sample"), | ||
| Nil, | ||
| None, | ||
| validateSchema = false, | ||
| None, | ||
| 0.67) | ||
| val sampleHeaders = List( | ||
| TableColumn("ID", SqlType.int), | ||
| TableColumn("stress_before_test1", SqlType.numeric), | ||
| TableColumn("score_test1", SqlType.numeric), | ||
| TableColumn("IQ", SqlType.numeric), | ||
| TableColumn("cognitive_task2", SqlType.numeric), | ||
| TableColumn("practice_task2", SqlType.numeric), | ||
| TableColumn("response_time_task2", SqlType.numeric), | ||
| TableColumn("college_math", SqlType.numeric), | ||
| TableColumn("score_math_course1", SqlType.numeric), | ||
| TableColumn("score_math_course2", SqlType.numeric) | ||
| ) | ||
|
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| val sampleData = List( | ||
| JsObject("ID" -> JsNumber(1), | ||
| "stress_before_test1" -> JsNumber(2.0), | ||
| "score_test1" -> JsNumber(1.0)) | ||
| ) | ||
|
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| val cdeTable = FeaturesTableDescription( | ||
| TableId(database, None, "cde_features_a"), | ||
| List(TableColumn("subjectcode", SqlType.varchar)), | ||
| Some(TableColumn("dataset", SqlType.varchar)), | ||
| validateSchema = false, | ||
| None, | ||
| 0.67 | ||
| ) | ||
| val cdeHeaders = List( | ||
| TableColumn("subjectcode", SqlType.varchar), | ||
| TableColumn("apoe4", SqlType.int), | ||
| TableColumn("lefthippocampus", SqlType.numeric), | ||
| TableColumn("dataset", SqlType.varchar) | ||
| ) | ||
|
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| val cdeData = List( | ||
| JsObject("subjectcode" -> JsString("p001"), | ||
| "apoe4" -> JsNumber(2), | ||
| "lefthippocampus" -> JsNumber(1.37), | ||
| "dataset" -> JsString("desd-synthdata")) | ||
| ) | ||
|
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| } |
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