Commit 93d26ab8 authored by Peter van 't Hof's avatar Peter van 't Hof

Fixing code warnings

parent f3963eee
...@@ -11,12 +11,13 @@ import scala.concurrent.Await ...@@ -11,12 +11,13 @@ import scala.concurrent.Await
import scala.concurrent.duration.Duration import scala.concurrent.duration.Duration
/** /**
* Testing voor [[SummaryDb]]
* Created by pjvanthof on 14/02/2017. * Created by pjvanthof on 14/02/2017.
*/ */
class SummaryDbTest extends TestNGSuite with Matchers { class SummaryDbTest extends TestNGSuite with Matchers {
@Test @Test
def testRuns: Unit = { def testRuns(): Unit = {
val dbFile = File.createTempFile("summary.", ".db") val dbFile = File.createTempFile("summary.", ".db")
dbFile.deleteOnExit() dbFile.deleteOnExit()
val db = SummaryDb.openSqliteSummary(dbFile) val db = SummaryDb.openSqliteSummary(dbFile)
...@@ -34,7 +35,7 @@ class SummaryDbTest extends TestNGSuite with Matchers { ...@@ -34,7 +35,7 @@ class SummaryDbTest extends TestNGSuite with Matchers {
} }
@Test @Test
def testSamples: Unit = { def testSamples(): Unit = {
val dbFile = File.createTempFile("summary.", ".db") val dbFile = File.createTempFile("summary.", ".db")
dbFile.deleteOnExit() dbFile.deleteOnExit()
val db = SummaryDb.openSqliteSummary(dbFile) val db = SummaryDb.openSqliteSummary(dbFile)
...@@ -58,7 +59,7 @@ class SummaryDbTest extends TestNGSuite with Matchers { ...@@ -58,7 +59,7 @@ class SummaryDbTest extends TestNGSuite with Matchers {
} }
@Test @Test
def testLibraries: Unit = { def testLibraries(): Unit = {
val dbFile = File.createTempFile("summary.", ".db") val dbFile = File.createTempFile("summary.", ".db")
dbFile.deleteOnExit() dbFile.deleteOnExit()
val db = SummaryDb.openSqliteSummary(dbFile) val db = SummaryDb.openSqliteSummary(dbFile)
...@@ -85,7 +86,7 @@ class SummaryDbTest extends TestNGSuite with Matchers { ...@@ -85,7 +86,7 @@ class SummaryDbTest extends TestNGSuite with Matchers {
} }
@Test @Test
def testPipelines: Unit = { def testPipelines(): Unit = {
val dbFile = File.createTempFile("summary.", ".db") val dbFile = File.createTempFile("summary.", ".db")
dbFile.deleteOnExit() dbFile.deleteOnExit()
val db = SummaryDb.openSqliteSummary(dbFile) val db = SummaryDb.openSqliteSummary(dbFile)
...@@ -105,7 +106,7 @@ class SummaryDbTest extends TestNGSuite with Matchers { ...@@ -105,7 +106,7 @@ class SummaryDbTest extends TestNGSuite with Matchers {
} }
@Test @Test
def testModules: Unit = { def testModules(): Unit = {
val dbFile = File.createTempFile("summary.", ".db") val dbFile = File.createTempFile("summary.", ".db")
dbFile.deleteOnExit() dbFile.deleteOnExit()
val db = SummaryDb.openSqliteSummary(dbFile) val db = SummaryDb.openSqliteSummary(dbFile)
...@@ -126,7 +127,7 @@ class SummaryDbTest extends TestNGSuite with Matchers { ...@@ -126,7 +127,7 @@ class SummaryDbTest extends TestNGSuite with Matchers {
} }
@Test @Test
def testSettings: Unit = { def testSettings(): Unit = {
val dbFile = File.createTempFile("summary.", ".db") val dbFile = File.createTempFile("summary.", ".db")
dbFile.deleteOnExit() dbFile.deleteOnExit()
val db = SummaryDb.openSqliteSummary(dbFile) val db = SummaryDb.openSqliteSummary(dbFile)
...@@ -140,7 +141,7 @@ class SummaryDbTest extends TestNGSuite with Matchers { ...@@ -140,7 +141,7 @@ class SummaryDbTest extends TestNGSuite with Matchers {
} }
@Test @Test
def testSettingKeys: Unit = { def testSettingKeys(): Unit = {
val dbFile = File.createTempFile("summary.", ".db") val dbFile = File.createTempFile("summary.", ".db")
dbFile.deleteOnExit() dbFile.deleteOnExit()
val db = SummaryDb.openSqliteSummary(dbFile) val db = SummaryDb.openSqliteSummary(dbFile)
...@@ -163,14 +164,13 @@ class SummaryDbTest extends TestNGSuite with Matchers { ...@@ -163,14 +164,13 @@ class SummaryDbTest extends TestNGSuite with Matchers {
} }
@Test @Test
def testSettingsForSamples: Unit = { def testSettingsForSamples(): Unit = {
val dbFile = File.createTempFile("summary.", ".db") val dbFile = File.createTempFile("summary.", ".db")
dbFile.deleteOnExit() dbFile.deleteOnExit()
val db = SummaryDb.openSqliteSummary(dbFile) val db = SummaryDb.openSqliteSummary(dbFile)
db.createTables() db.createTables()
val sampleId = Await.result(db.createSample("test_sample", 0), Duration.Inf) val sampleId = Await.result(db.createSample("test_sample", 0), Duration.Inf)
val libraryId = Await.result(db.createLibrary("test_library", 0, sampleId), Duration.Inf)
Await.result(db.createOrUpdateSetting(0, 0, Some(0), Some(sampleId), None, Await.result(db.createOrUpdateSetting(0, 0, Some(0), Some(sampleId), None,
""" """
...@@ -188,7 +188,7 @@ class SummaryDbTest extends TestNGSuite with Matchers { ...@@ -188,7 +188,7 @@ class SummaryDbTest extends TestNGSuite with Matchers {
} }
@Test @Test
def testSettingsForLibraries: Unit = { def testSettingsForLibraries(): Unit = {
val dbFile = File.createTempFile("summary.", ".db") val dbFile = File.createTempFile("summary.", ".db")
dbFile.deleteOnExit() dbFile.deleteOnExit()
val db = SummaryDb.openSqliteSummary(dbFile) val db = SummaryDb.openSqliteSummary(dbFile)
...@@ -213,7 +213,7 @@ class SummaryDbTest extends TestNGSuite with Matchers { ...@@ -213,7 +213,7 @@ class SummaryDbTest extends TestNGSuite with Matchers {
} }
@Test @Test
def testStats: Unit = { def testStats(): Unit = {
val dbFile = File.createTempFile("summary.", ".db") val dbFile = File.createTempFile("summary.", ".db")
dbFile.deleteOnExit() dbFile.deleteOnExit()
val db = SummaryDb.openSqliteSummary(dbFile) val db = SummaryDb.openSqliteSummary(dbFile)
...@@ -243,7 +243,7 @@ class SummaryDbTest extends TestNGSuite with Matchers { ...@@ -243,7 +243,7 @@ class SummaryDbTest extends TestNGSuite with Matchers {
} }
@Test @Test
def testStatKeys: Unit = { def testStatKeys(): Unit = {
val dbFile = File.createTempFile("summary.", ".db") val dbFile = File.createTempFile("summary.", ".db")
dbFile.deleteOnExit() dbFile.deleteOnExit()
val db = SummaryDb.openSqliteSummary(dbFile) val db = SummaryDb.openSqliteSummary(dbFile)
...@@ -266,14 +266,13 @@ class SummaryDbTest extends TestNGSuite with Matchers { ...@@ -266,14 +266,13 @@ class SummaryDbTest extends TestNGSuite with Matchers {
} }
@Test @Test
def testStatsForSamples: Unit = { def testStatsForSamples(): Unit = {
val dbFile = File.createTempFile("summary.", ".db") val dbFile = File.createTempFile("summary.", ".db")
dbFile.deleteOnExit() dbFile.deleteOnExit()
val db = SummaryDb.openSqliteSummary(dbFile) val db = SummaryDb.openSqliteSummary(dbFile)
db.createTables() db.createTables()
val sampleId = Await.result(db.createSample("test_sample", 0), Duration.Inf) val sampleId = Await.result(db.createSample("test_sample", 0), Duration.Inf)
val libraryId = Await.result(db.createLibrary("test_library", 0, sampleId), Duration.Inf)
Await.result(db.createOrUpdateStat(0, 0, Some(0), Some(sampleId), None, Await.result(db.createOrUpdateStat(0, 0, Some(0), Some(sampleId), None,
""" """
...@@ -291,7 +290,7 @@ class SummaryDbTest extends TestNGSuite with Matchers { ...@@ -291,7 +290,7 @@ class SummaryDbTest extends TestNGSuite with Matchers {
} }
@Test @Test
def testStatsForLibraries: Unit = { def testStatsForLibraries(): Unit = {
val dbFile = File.createTempFile("summary.", ".db") val dbFile = File.createTempFile("summary.", ".db")
dbFile.deleteOnExit() dbFile.deleteOnExit()
val db = SummaryDb.openSqliteSummary(dbFile) val db = SummaryDb.openSqliteSummary(dbFile)
...@@ -316,7 +315,7 @@ class SummaryDbTest extends TestNGSuite with Matchers { ...@@ -316,7 +315,7 @@ class SummaryDbTest extends TestNGSuite with Matchers {
} }
@Test @Test
def testFiles: Unit = { def testFiles(): Unit = {
val dbFile = File.createTempFile("summary.", ".db") val dbFile = File.createTempFile("summary.", ".db")
dbFile.deleteOnExit() dbFile.deleteOnExit()
val db = SummaryDb.openSqliteSummary(dbFile) val db = SummaryDb.openSqliteSummary(dbFile)
...@@ -328,31 +327,30 @@ class SummaryDbTest extends TestNGSuite with Matchers { ...@@ -328,31 +327,30 @@ class SummaryDbTest extends TestNGSuite with Matchers {
val sampleId = Await.result(db.createSample("test_sample", runId), Duration.Inf) val sampleId = Await.result(db.createSample("test_sample", runId), Duration.Inf)
val libraryId = Await.result(db.createLibrary("test_library", runId, sampleId), Duration.Inf) val libraryId = Await.result(db.createLibrary("test_library", runId, sampleId), Duration.Inf)
Await.result(db.createOrUpdateFile(runId, pipelineId, None, None, None, "key", "path", "md5", false, 1), Duration.Inf) Await.result(db.createOrUpdateFile(runId, pipelineId, None, None, None, "key", "path", "md5", link = false, 1), Duration.Inf)
Await.result(db.getFile(runId, Left(pipelineId), None, None, None, "key"), Duration.Inf) shouldBe Some(Schema.File(0,0,None,None,None,"key","path","md5",false,1)) Await.result(db.getFile(runId, Left(pipelineId), None, None, None, "key"), Duration.Inf) shouldBe Some(Schema.File(0,0,None,None,None,"key","path","md5",link = false,1))
Await.result(db.getFiles(), Duration.Inf) shouldBe Seq(Schema.File(0,0,None,None,None,"key","path","md5",false,1)) Await.result(db.getFiles(), Duration.Inf) shouldBe Seq(Schema.File(0,0,None,None,None,"key","path","md5",link = false,1))
Await.result(db.createOrUpdateFile(runId, pipelineId, None, None, None, "key", "path2", "md5", false, 1), Duration.Inf) Await.result(db.createOrUpdateFile(runId, pipelineId, None, None, None, "key", "path2", "md5", link = false, 1), Duration.Inf)
Await.result(db.getFile(runId, Left(pipelineId), None, None, None, "key"), Duration.Inf) shouldBe Some(Schema.File(0,0,None,None,None,"key","path2","md5",false,1)) Await.result(db.getFile(runId, Left(pipelineId), None, None, None, "key"), Duration.Inf) shouldBe Some(Schema.File(0,0,None,None,None,"key","path2","md5",link = false,1))
Await.result(db.getFiles(), Duration.Inf) shouldBe Seq(Schema.File(0,0,None,None,None,"key","path2","md5",false,1)) Await.result(db.getFiles(), Duration.Inf) shouldBe Seq(Schema.File(0,0,None,None,None,"key","path2","md5",link = false,1))
// Test join queries // Test join queries
Await.result(db.createOrUpdateFile(runId, pipelineId, Some(moduleId), Some(sampleId), Some(libraryId), "key", "path3", "md5", false, 1), Duration.Inf) Await.result(db.createOrUpdateFile(runId, pipelineId, Some(moduleId), Some(sampleId), Some(libraryId), "key", "path3", "md5", link = false, 1), Duration.Inf)
Await.result(db.getFile(runId, Right("test_pipeline"), Some(Right("test_module")), Some(Right("test_sample")), Some(Right("test_library")), "key"), Duration.Inf) shouldBe Some(Schema.File(0,0,Some(moduleId), Some(sampleId), Some(libraryId),"key","path3","md5",false,1)) Await.result(db.getFile(runId, Right("test_pipeline"), Some(Right("test_module")), Some(Right("test_sample")), Some(Right("test_library")), "key"), Duration.Inf) shouldBe Some(Schema.File(0,0,Some(moduleId), Some(sampleId), Some(libraryId),"key","path3","md5",link = false,1))
Await.result(db.getFiles(), Duration.Inf) shouldBe Seq(Schema.File(0,0,None,None,None,"key","path2","md5",false,1), Schema.File(0,0,Some(moduleId), Some(sampleId), Some(libraryId),"key","path3","md5",false,1)) Await.result(db.getFiles(), Duration.Inf) shouldBe Seq(Schema.File(0,0,None,None,None,"key","path2","md5",link = false,1), Schema.File(0,0,Some(moduleId), Some(sampleId), Some(libraryId),"key","path3","md5",link = false,1))
db.close() db.close()
} }
@Test @Test
def testExecutable: Unit = { def testExecutable(): Unit = {
val dbFile = File.createTempFile("summary.", ".db") val dbFile = File.createTempFile("summary.", ".db")
dbFile.deleteOnExit() dbFile.deleteOnExit()
val db = SummaryDb.openSqliteSummary(dbFile) val db = SummaryDb.openSqliteSummary(dbFile)
db.createTables() db.createTables()
Await.result(db.createOrUpdateExecutable(0, "name"), Duration.Inf) Await.result(db.createOrUpdateExecutable(0, "name"), Duration.Inf)
val bla1 = Await.result(db.getExecutables(Some(0)), Duration.Inf)
Await.result(db.createOrUpdateExecutable(0, "name", Some("test")), Duration.Inf) Await.result(db.createOrUpdateExecutable(0, "name", Some("test")), Duration.Inf)
Await.result(db.getExecutables(Some(0)), Duration.Inf).head shouldBe Schema.Executable(0, "name", Some("test")) Await.result(db.getExecutables(Some(0)), Duration.Inf).head shouldBe Schema.Executable(0, "name", Some("test"))
db.close() db.close()
......
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