So I'm very (extremely) new to Databases and slick and scala, so I was using the example code from their documentation at http://slick.typesafe.com/doc/3.0.0/gettingstarted.html
My problem is that for some reason, I have to run a query multiple times before it returns data. I have to rerun it atleast 3-4 times before it returns results. I use a for-loop to rerun the query and they don't necessarily give me the exact same results each time either.
to create two tables as followed:
class Patients(tag: Tag) extends Table[(String, String, Int, String)](tag, "Patientss") {
def PID = column[String]("Patient Id", O.PrimaryKey)
def Gender = column[String]("Gender")
def Age = column[Int]("Age")
def Ethnicity = column[String]("Ethnicity")
def * = (PID, Gender, Age, Ethnicity)
}
val patientsss = TableQuery[Patients]
class DrugEffect(tag: Tag) extends Table[(String, String, Double)](tag, "DrugEffectss") {
def DrugID = column[String]("Drug ID", O.PrimaryKey)
def PatientID = column[String]("Patient_ID")
def DrugEffectssss = column[Double]("Drug Effect")
def * = (DrugID, PatientID, DrugEffectssss)
def Patient = foreignKey("Patient_FK", PatientID, patientsss)(_.PID)}
val d_effects = TableQuery[DrugEffect]
I then create these tables using
val create_empty = DBIO.seq((patientsss.schema ++ d_effects.schema).create)
val setup_1 = db.run(create_empty)
I have actual data in two text files, which I parse through using a buffered reader.
I store all the Drug ID's in a list creatively named DrugIds
Then, I start filling in the tables in the following way
I first fill in the Patients table:
while (switch != 1) {
val Patient = CurPatient.split("\\s+")
if (Patient(2).toUpperCase() == "NA" || (Patient(2).toFloat % 1 != 0))
age = -1
else age = Patient(2).toInt
val insertPatient: DBIO[Option[Int]] = patientsss ++= Seq(
(Patient(0), Patient(1), age, Patient(3))
)
var future = db.run(insertPatient)
CurPatient = PatientReader.readLine()
if (CurPatient == null)
switch = 1 //switch to 1
}
For the DrugEffects table, I do the following:
while (switch != 1) {
val Effect = CurEffect.split("\\s+")
for (i <- 1 until DrugIds.size - 1) {
if (Effect(i).toUpperCase() == "NA")
d_ef = -1.00
else d_ef = (Effect(i).toFloat).asInstanceOf[Double]
val insertEffect: DBIO[Option[Int]] = d_effects ++= Seq(
(DrugIds(i), Effect(0), d_ef)
)
var future2 = db.run(insertEffect)
}
CurEffect = EffectReader.readLine()
if (CurEffect == null)
switch = 1
}
Then I run a query with the following piece of code
val q1 = for {
c <- patientsss
} yield (c.PID, c.Gender, c.Age, c.Ethnicity)
db.stream(q1.result).foreach(println)
This should just give me all the data in the Patient's table, but it doesn't necessarily do that.
Sometimes, I get the following error (but not always):
java.util.concurrent.RejectedExecutionException: Task slick.backend.DatabaseComponent$DatabaseDef$$anon$3@47089c2c rejected from java.util.concurrent.ThreadPoolExecutor@6453123[Terminated, pool size = 0, active threads = 0, queued tasks = 0, completed tasks = 215]
at java.util.concurrent.ThreadPoolExecutor$AbortPolicy.rejectedExecution(ThreadPoolExecutor.java:2048)
at java.util.concurrent.ThreadPoolExecutor.reject(ThreadPoolExecutor.java:821)
at java.util.concurrent.ThreadPoolExecutor.execute(ThreadPoolExecutor.java:1372)
at scala.concurrent.impl.ExecutionContextImpl$$anon$1.execute(ExecutionContextImpl.scala:136)
at slick.backend.DatabaseComponent$DatabaseDef$class.scheduleSynchronousStreaming(DatabaseComponent.scala:253)
at slick.jdbc.JdbcBackend$DatabaseDef.scheduleSynchronousStreaming(JdbcBackend.scala:38)
at slick.backend.DatabaseComponent$BasicStreamingActionContext.restartStreaming(DatabaseComponent.scala:516)
at slick.backend.DatabaseComponent$BasicStreamingActionContext.request(DatabaseComponent.scala:531)
at slick.backend.DatabasePublisher$$anon$3$$anonfun$onNext$2.apply(DatabasePublisher.scala:50)
at slick.backend.DatabasePublisher$$anon$3$$anonfun$onNext$2.apply(DatabasePublisher.scala:49)
at scala.concurrent.impl.CallbackRunnable.run(Promise.scala:32)
at scala.concurrent.impl.ExecutionContextImpl$AdaptedForkJoinTask.exec(ExecutionContextImpl.scala:121)
at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
at scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.pollAndExecAll(ForkJoinPool.java:1253)
at scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1346)
at scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
at scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
If I run a more complex query, the data I get back is accurate to the parameters of the query, but the same problems occur, which is that the results are either duplicated or non-existent or not complete (when I rerun the query multiple times).
Explain like I'm 5 if you can, or point me to a resource that can help me solve these problems
EDIT:
bjfletcher's answer worked (Thanks!), but now I have another problem:
Every now and again, the code will fail with the error:
Exception in thread "main" org.h2.jdbc.JdbcSQLException: Table "Patientss" not found; SQL statement:
insert into "Patientss" ("Patient Id","Gender","Age","Ethnicity") values (?,?,?,?) [42102-162]
at org.h2.message.DbException.getJdbcSQLException(DbException.java:329)
at org.h2.message.DbException.get(DbException.java:169)
at org.h2.message.DbException.get(DbException.java:146)
at org.h2.command.Parser.readTableOrView(Parser.java:4758)
at org.h2.command.Parser.readTableOrView(Parser.java:4736)
at org.h2.command.Parser.parseInsert(Parser.java:954)
at org.h2.command.Parser.parsePrepared(Parser.java:375)
at org.h2.command.Parser.parse(Parser.java:279)
at org.h2.command.Parser.parse(Parser.java:251)
at org.h2.command.Parser.prepareCommand(Parser.java:217)
at org.h2.engine.Session.prepareLocal(Session.java:415)
at org.h2.engine.Session.prepareCommand(Session.java:364)
at org.h2.jdbc.JdbcConnection.prepareCommand(JdbcConnection.java:1121)
at org.h2.jdbc.JdbcPreparedStatement.<init>(JdbcPreparedStatement.java:71)
at org.h2.jdbc.JdbcConnection.prepareStatement(JdbcConnection.java:267)
at slick.jdbc.JdbcBackend$SessionDef$class.prepareStatement(JdbcBackend.scala:252)
at slick.jdbc.JdbcBackend$BaseSession.prepareStatement(JdbcBackend.scala:386)
at slick.jdbc.JdbcBackend$SessionDef$class.withPreparedStatement(JdbcBackend.scala:301)
at slick.jdbc.JdbcBackend$BaseSession.withPreparedStatement(JdbcBackend.scala:386)
at slick.driver.JdbcInsertInvokerComponent$BaseInsertInvoker.preparedInsert(JdbcInsertInvokerComponent.scala:177)
at slick.driver.JdbcInsertInvokerComponent$BaseInsertInvoker$$anonfun$internalInsertAll$1.apply(JdbcInsertInvokerComponent.scala:201)
at slick.jdbc.JdbcBackend$BaseSession.withTransaction(JdbcBackend.scala:422)
at slick.driver.JdbcInsertInvokerComponent$BaseInsertInvoker.internalInsertAll(JdbcInsertInvokerComponent.scala:198)
at slick.driver.JdbcInsertInvokerComponent$BaseInsertInvoker.insertAll(JdbcInsertInvokerComponent.scala:194)
at slick.driver.JdbcInsertInvokerComponent$InsertInvokerDef$class.$plus$plus$eq(JdbcInsertInvokerComponent.scala:73)
at slick.driver.JdbcInsertInvokerComponent$BaseInsertInvoker.$plus$plus$eq(JdbcInsertInvokerComponent.scala:152)
at slick.driver.JdbcActionComponent$InsertActionComposerImpl$$anonfun$$plus$plus$eq$1.apply(JdbcActionComponent.scala:459)
at slick.driver.JdbcActionComponent$InsertActionComposerImpl$$anonfun$$plus$plus$eq$1.apply(JdbcActionComponent.scala:459)
at slick.driver.JdbcActionComponent$InsertActionComposerImpl$$anon$8.run(JdbcActionComponent.scala:449)
at slick.driver.JdbcActionComponent$InsertActionComposerImpl$$anon$8.run(JdbcActionComponent.scala:447)
at slick.backend.DatabaseComponent$DatabaseDef$$anon$2.liftedTree1$1(DatabaseComponent.scala:231)
at slick.backend.DatabaseComponent$DatabaseDef$$anon$2.run(DatabaseComponent.scala:231)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)
Doesn't happen all the time, but very often, and I have no clue what this means
