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biopet.biopet
Commit f3963eee authored by Peter van 't Hof's avatar Peter van 't Hof
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Adding a lot of testing to summaryDB

parent 5c5cb42d
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Showing with 218 additions and 2 deletions
biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/db/SummaryDb.scala
View file @ f3963eee
......@@ -414,7 +414,7 @@ class SummaryDb(val db: Database) extends Closeable {
}
/** Returns all [[Files]] with the given criteria */
def getFiles(runId: Option[Int] = None, pipeline: Option[Either[Int, String]] = None, module: Option[Option[Either[Int, String]]],
def getFiles(runId: Option[Int] = None, pipeline: Option[Either[Int, String]] = None, module: Option[Option[Either[Int, String]]] = None,
sample: Option[Option[Either[Int, String]]] = None, library: Option[Option[Either[Int, String]]] = None,
key: Option[String] = None): Future[Seq[Schema.File]] = {
db.run(filesFilter(runId, pipeline, module, sample, library, key).result)
......
biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/summary/db/SummaryDbTest.scala
View file @ f3963eee
......@@ -15,6 +15,116 @@ import scala.concurrent.duration.Duration
*/
class SummaryDbTest extends TestNGSuite with Matchers {
@Test
def testRuns: Unit = {
val dbFile = File.createTempFile("summary.", ".db")
dbFile.deleteOnExit()
val db = SummaryDb.openSqliteSummary(dbFile)
db.createTables()
val date = new Date(System.currentTimeMillis())
Await.result(db.getRuns(), Duration.Inf) shouldBe empty
val runId = Await.result(db.createRun("name", "dir", "version", "hash", date), Duration.Inf)
Await.result(db.getRuns(), Duration.Inf) shouldBe Seq(Schema.Run(runId, "name", "dir", "version", "hash", date))
val runId2 = Await.result(db.createRun("name", "dir", "version", "hash", date), Duration.Inf)
Await.result(db.getRuns(), Duration.Inf) shouldBe Seq(Schema.Run(runId, "name", "dir", "version", "hash", date), Schema.Run(runId2, "name", "dir", "version", "hash", date))
db.close()
}
@Test
def testSamples: Unit = {
val dbFile = File.createTempFile("summary.", ".db")
dbFile.deleteOnExit()
val db = SummaryDb.openSqliteSummary(dbFile)
db.createTables()
val date = new Date(System.currentTimeMillis())
val runId = Await.result(db.createRun("name", "dir", "version", "hash", date), Duration.Inf)
Await.result(db.getSamples(), Duration.Inf) shouldBe empty
val sampleId = Await.result(db.createSample("test_sample", runId), Duration.Inf)
Await.result(db.getSamples(), Duration.Inf) shouldBe Seq(Schema.Sample(sampleId, "test_sample", runId, None))
Await.result(db.getSampleName(sampleId), Duration.Inf) shouldBe Some("test_sample")
Await.result(db.getSampleId(runId, "test_sample"), Duration.Inf) shouldBe Some(sampleId)
Await.result(db.getSampleTags(sampleId), Duration.Inf) shouldBe None
val sampleId2 = Await.result(db.createSample("test_sample2", runId, Some("""{"test": "test"}""")), Duration.Inf)
Await.result(db.getSampleTags(sampleId2), Duration.Inf) shouldBe Some(Map("test" -> "test"))
Await.result(db.getSamples(), Duration.Inf) shouldBe Seq(Schema.Sample(sampleId, "test_sample", runId, None), Schema.Sample(sampleId2, "test_sample2", runId, Some("""{"test": "test"}""")))
db.close()
}
@Test
def testLibraries: Unit = {
val dbFile = File.createTempFile("summary.", ".db")
dbFile.deleteOnExit()
val db = SummaryDb.openSqliteSummary(dbFile)
db.createTables()
val date = new Date(System.currentTimeMillis())
val runId = Await.result(db.createRun("name", "dir", "version", "hash", date), Duration.Inf)
val sampleId = Await.result(db.createSample("test_sample", runId), Duration.Inf)
Await.result(db.getLibraries(), Duration.Inf) shouldBe empty
val libraryId = Await.result(db.createLibrary("test_lib", runId, sampleId), Duration.Inf)
Await.result(db.getLibraries(), Duration.Inf) shouldBe Seq(Schema.Library(libraryId, "test_lib", runId, sampleId, None))
Await.result(db.getLibraryName(libraryId), Duration.Inf) shouldBe Some("test_lib")
Await.result(db.getLibraryId(runId, sampleId, "test_lib"), Duration.Inf) shouldBe Some(libraryId)
Await.result(db.getLibraryTags(sampleId), Duration.Inf) shouldBe None
val sampleId2 = Await.result(db.createLibrary("test_lib2", runId, sampleId, Some("""{"test": "test"}""")), Duration.Inf)
Await.result(db.getLibraryTags(sampleId2), Duration.Inf) shouldBe Some(Map("test" -> "test"))
Await.result(db.getLibraries(), Duration.Inf) shouldBe Seq(Schema.Library(sampleId, "test_lib", runId, sampleId, None), Schema.Library(sampleId2, "test_lib2", runId, sampleId, Some("""{"test": "test"}""")))
db.close()
}
@Test
def testPipelines: Unit = {
val dbFile = File.createTempFile("summary.", ".db")
dbFile.deleteOnExit()
val db = SummaryDb.openSqliteSummary(dbFile)
db.createTables()
val date = new Date(System.currentTimeMillis())
val runId = Await.result(db.createRun("name", "dir", "version", "hash", date), Duration.Inf)
Await.result(db.getPipelines(), Duration.Inf) shouldBe empty
val pipelineId = Await.result(db.createPipeline("test", runId), Duration.Inf)
Await.result(db.getPipelines(), Duration.Inf) shouldBe Seq(Schema.Pipeline(pipelineId, "test", runId))
Await.result(db.getPipelineId(runId, "test"), Duration.Inf) shouldBe Some(pipelineId)
Await.result(db.createPipeline("test", runId), Duration.Inf) shouldBe pipelineId
Await.result(db.getPipelines(), Duration.Inf) shouldBe Seq(Schema.Pipeline(pipelineId, "test", runId))
db.close()
}
@Test
def testModules: Unit = {
val dbFile = File.createTempFile("summary.", ".db")
dbFile.deleteOnExit()
val db = SummaryDb.openSqliteSummary(dbFile)
db.createTables()
val date = new Date(System.currentTimeMillis())
val runId = Await.result(db.createRun("name", "dir", "version", "hash", date), Duration.Inf)
val pipelineId = Await.result(db.createPipeline("test", runId), Duration.Inf)
Await.result(db.getModules(), Duration.Inf) shouldBe empty
val moduleId = Await.result(db.createModule("test", runId, pipelineId), Duration.Inf)
Await.result(db.getmoduleId(runId, "test", pipelineId), Duration.Inf) shouldBe Some(moduleId)
Await.result(db.getModules(), Duration.Inf) shouldBe Seq(Schema.Module(pipelineId, "test", runId, pipelineId))
Await.result(db.createModule("test", runId, pipelineId), Duration.Inf) shouldBe pipelineId
Await.result(db.getModules(), Duration.Inf) shouldBe Seq(Schema.Module(pipelineId, "test", runId, pipelineId))
db.close()
}
@Test
def testSettings: Unit = {
val dbFile = File.createTempFile("summary.", ".db")
......@@ -23,13 +133,85 @@ class SummaryDbTest extends TestNGSuite with Matchers {
db.createTables()
Await.result(db.createOrUpdateSetting(0, 0, None, None, None, """{"content": "test" }"""), Duration.Inf)
val bla = Await.result(db.getSettings(Some(0)), Duration.Inf)
Await.result(db.getSetting(0, Left(0), None, None, None), Duration.Inf) shouldBe Some(Map("content" -> "test"))
Await.result(db.createOrUpdateSetting(0, 0, None, None, None, """{"content": "test2" }"""), Duration.Inf)
Await.result(db.getSetting(0, Left(0), None, None, None), Duration.Inf) shouldBe Some(Map("content" -> "test2"))
db.close()
}
@Test
def testSettingKeys: Unit = {
val dbFile = File.createTempFile("summary.", ".db")
dbFile.deleteOnExit()
val db = SummaryDb.openSqliteSummary(dbFile)
db.createTables()
Await.result(db.createOrUpdateSetting(0, 0, Some(0), Some(0), Some(0),
"""
|{
|"content": "test",
|"content2": {
| "key": "value"
|}
| }""".stripMargin), Duration.Inf)
db.getSettingKeys(0, Left(0), Some(Left(0)), Some(Left(0)), Some(Left(0)), keyValues = Map()) shouldBe Map()
db.getSettingKeys(0, Left(0), Some(Left(0)), Some(Left(0)), Some(Left(0)), keyValues = Map("content" -> List("content"))) shouldBe Map("content" -> Some("test"))
db.getSettingKeys(0, Left(0), Some(Left(0)), Some(Left(0)), Some(Left(0)), keyValues = Map("content" -> List("content2", "key"))) shouldBe Map("content" -> Some("value"))
db.close()
}
@Test
def testSettingsForSamples: Unit = {
val dbFile = File.createTempFile("summary.", ".db")
dbFile.deleteOnExit()
val db = SummaryDb.openSqliteSummary(dbFile)
db.createTables()
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,
"""
|{
|"content": "test",
|"content2": {
| "key": "value"
|}
| }""".stripMargin), Duration.Inf)
db.getSettingsForSamples(0, Left(0), Some(Left(0)), keyValues = Map()) shouldBe Map(0 -> Map())
db.getSettingsForSamples(0, Left(0), Some(Left(0)), keyValues = Map("content" -> List("content"))) shouldBe Map(0 -> Map("content" -> Some("test")))
db.close()
}
@Test
def testSettingsForLibraries: Unit = {
val dbFile = File.createTempFile("summary.", ".db")
dbFile.deleteOnExit()
val db = SummaryDb.openSqliteSummary(dbFile)
db.createTables()
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), Some(libraryId),
"""
|{
|"content": "test",
|"content2": {
| "key": "value"
|}
| }""".stripMargin), Duration.Inf)
db.getSettingsForLibraries(0, Left(0), Some(Left(0)), keyValues = Map()) shouldBe Map((0, 0) -> Map())
db.getSettingsForLibraries(0, Left(0), Some(Left(0)), keyValues = Map("content" -> List("content"))) shouldBe Map((0, 0) -> Map("content" -> Some("test")))
db.close()
}
@Test
def testStats: Unit = {
val dbFile = File.createTempFile("summary.", ".db")
......@@ -43,14 +225,19 @@ class SummaryDbTest extends TestNGSuite with Matchers {
val sampleId = Await.result(db.createSample("test_sample", runId), Duration.Inf)
val libraryId = Await.result(db.createLibrary("test_library", runId, sampleId), Duration.Inf)
Await.result(db.getStatsSize(), Duration.Inf) shouldBe 0
Await.result(db.createOrUpdateStat(runId, pipelineId, None, None, None, """{"content": "test" }"""), Duration.Inf)
Await.result(db.getStat(runId, Left(pipelineId), None, None, None), Duration.Inf) shouldBe Some(Map("content" -> "test"))
Await.result(db.getStatsSize(), Duration.Inf) shouldBe 1
Await.result(db.createOrUpdateStat(runId, pipelineId, None, None, None, """{"content": "test2" }"""), Duration.Inf)
Await.result(db.getStat(runId, Left(pipelineId), None, None, None), Duration.Inf) shouldBe Some(Map("content" -> "test2"))
Await.result(db.getStatsSize(), Duration.Inf) shouldBe 1
// Test join queries
Await.result(db.createOrUpdateStat(runId, pipelineId, Some(moduleId), Some(sampleId), Some(libraryId), """{"content": "test3" }"""), Duration.Inf)
Await.result(db.getStat(runId, Right("test_pipeline"), Some(Right("test_module")), Some(Right("test_sample")), Some(Right("test_library"))), Duration.Inf) shouldBe Some(Map("content" -> "test3"))
Await.result(db.getStatsSize(), Duration.Inf) shouldBe 2
db.close()
}
......@@ -128,6 +315,35 @@ class SummaryDbTest extends TestNGSuite with Matchers {
db.close()
}
@Test
def testFiles: Unit = {
val dbFile = File.createTempFile("summary.", ".db")
dbFile.deleteOnExit()
val db = SummaryDb.openSqliteSummary(dbFile)
db.createTables()
val runId = Await.result(db.createRun("test", "", "", "", new Date(System.currentTimeMillis())), Duration.Inf)
val pipelineId = Await.result(db.createPipeline("test_pipeline", runId), Duration.Inf)
val moduleId = Await.result(db.createModule("test_module", runId, pipelineId), 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)
Await.result(db.createOrUpdateFile(runId, pipelineId, None, None, None, "key", "path", "md5", 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.getFiles(), Duration.Inf) shouldBe Seq(Schema.File(0,0,None,None,None,"key","path","md5",false,1))
Await.result(db.createOrUpdateFile(runId, pipelineId, None, None, None, "key", "path2", "md5", 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.getFiles(), Duration.Inf) shouldBe Seq(Schema.File(0,0,None,None,None,"key","path2","md5",false,1))
// 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.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.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))
db.close()
}
@Test
def testExecutable: Unit = {
val dbFile = File.createTempFile("summary.", ".db")
......
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