diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs index 4be937d471..08e23c8b90 100644 --- a/.git-blame-ignore-revs +++ b/.git-blame-ignore-revs @@ -3,3 +3,6 @@ # Scala Steward: Reformat with scalafmt 3.6.0 df858b0ea7cc4743ec9c78cee1486ad91de1dbd4 + +# Scala Steward: Reformat with scalafmt 3.9.6 +2697072fd81618af89bf76500edfc52ab11b55b0 diff --git a/.scalafmt.conf b/.scalafmt.conf index ace08b0c38..08d3ff9ced 100644 --- a/.scalafmt.conf +++ b/.scalafmt.conf @@ -13,5 +13,5 @@ optIn.breakChainOnFirstMethodDot = false align.openParenDefnSite = false project.git = true assumeStandardLibraryStripMargin = true -version = 3.6.1 +version = 3.9.6 runner.dialect = scala213 diff --git a/modules/common/src/main/scala/de/proteinevolution/common/models/ConstantsV2.scala b/modules/common/src/main/scala/de/proteinevolution/common/models/ConstantsV2.scala index 260b15b0c4..c1a0017899 100644 --- a/modules/common/src/main/scala/de/proteinevolution/common/models/ConstantsV2.scala +++ b/modules/common/src/main/scala/de/proteinevolution/common/models/ConstantsV2.scala @@ -57,10 +57,10 @@ class ConstantsV2 @Inject() (config: Configuration) { // Job deletion settings /** Sweeps at this time after server start */ - final val jobDeletionDelay: FiniteDuration = 10 minutes + final val jobDeletionDelay: FiniteDuration = 10.minutes /** Sweeps in this interval */ - final val jobDeletionInterval: FiniteDuration = 3 hours + final val jobDeletionInterval: FiniteDuration = 3.hours /** all jobs of registered users that are older than the given number are permanently deleted everywhere */ final val jobDeletionRegistered: Int = 90 @@ -73,10 +73,10 @@ class ConstantsV2 @Inject() (config: Configuration) { // User Deletion settings /** Sweeps at this time after server start */ - final val userDeletionDelay: FiniteDuration = 70 minutes + final val userDeletionDelay: FiniteDuration = 70.minutes /** Sweeps in this interval */ - final val userDeletionInterval: FiniteDuration = 3 hours + final val userDeletionInterval: FiniteDuration = 3.hours /** Sending an eMail to the user this many days before the deletion */ final val userDeletionWarning: Int = 14 // days @@ -89,7 +89,7 @@ class ConstantsV2 @Inject() (config: Configuration) { // qstat long polling in order to detect zombie jobs, not used for cluster load calc anymore /** Interval of the qstat requests */ - final val pollingInterval: FiniteDuration = 5 minutes + final val pollingInterval: FiniteDuration = 5.minutes /** The marker for 100% load capacity */ final val loadPercentageMarker: Int = 32 // Jobs diff --git a/modules/jobs/src/main/scala/de/proteinevolution/jobs/actors/JobActor.scala b/modules/jobs/src/main/scala/de/proteinevolution/jobs/actors/JobActor.scala index 9433b13e0a..a207d75896 100644 --- a/modules/jobs/src/main/scala/de/proteinevolution/jobs/actors/JobActor.scala +++ b/modules/jobs/src/main/scala/de/proteinevolution/jobs/actors/JobActor.scala @@ -75,7 +75,7 @@ class JobActor @Inject() ( @volatile private var currentJobLogs: Map[String, JobEventLog] = Map.empty[String, JobEventLog] @volatile private var currentExecutionContexts: Map[String, ExecutionContext] = Map.empty[String, ExecutionContext] - private val fetchLatestInterval = 500 millis + private val fetchLatestInterval = 500.millis private val Tick: Cancellable = { // scheduler should use the system dispatcher context.system.scheduler.scheduleWithFixedDelay(Duration.Zero, fetchLatestInterval, self, UpdateLog)( diff --git a/modules/jobs/src/main/scala/de/proteinevolution/jobs/controllers/ResultsController.scala b/modules/jobs/src/main/scala/de/proteinevolution/jobs/controllers/ResultsController.scala index 9d5a0d24bd..87793b3387 100644 --- a/modules/jobs/src/main/scala/de/proteinevolution/jobs/controllers/ResultsController.scala +++ b/modules/jobs/src/main/scala/de/proteinevolution/jobs/controllers/ResultsController.scala @@ -71,8 +71,9 @@ final class ResultsController @Inject() ( // access allowed to job (for { json <- EitherT.liftF(resultFiles.getResults(jobID)) - r <- EitherT - .fromEither[Future](json.hcursor.downField(resultField.getOrElse("alignment")).as[AlignmentResult]) + r <- EitherT.fromEither[Future]( + json.hcursor.downField(resultField.getOrElse("alignment")).as[AlignmentResult] + ) } yield r).value.map { case Right(r) => val l = r.alignment.length diff --git a/modules/jobs/src/main/scala/de/proteinevolution/jobs/controllers/SubmissionController.scala b/modules/jobs/src/main/scala/de/proteinevolution/jobs/controllers/SubmissionController.scala index 09112c5d2d..37fb352cfc 100644 --- a/modules/jobs/src/main/scala/de/proteinevolution/jobs/controllers/SubmissionController.scala +++ b/modules/jobs/src/main/scala/de/proteinevolution/jobs/controllers/SubmissionController.scala @@ -63,8 +63,10 @@ class SubmissionController @Inject() ( case None => BadRequest case Some(obj) => if (obj.contains("isPublic")) { - jobActorAccess - .sendToJobActor(jobID, SetJobPublic(jobID, obj("isPublic").get.asBoolean.getOrElse(false))) + jobActorAccess.sendToJobActor( + jobID, + SetJobPublic(jobID, obj("isPublic").get.asBoolean.getOrElse(false)) + ) } Ok } diff --git a/modules/statistics/src/main/scala/de/proteinevolution/statistics/UserStatistic.scala b/modules/statistics/src/main/scala/de/proteinevolution/statistics/UserStatistic.scala index e69de29bb2..8b13789179 100644 --- a/modules/statistics/src/main/scala/de/proteinevolution/statistics/UserStatistic.scala +++ b/modules/statistics/src/main/scala/de/proteinevolution/statistics/UserStatistic.scala @@ -0,0 +1 @@ + diff --git a/modules/tools/src/main/scala/de/proteinevolution/tools/parameters/ParamAccess.scala b/modules/tools/src/main/scala/de/proteinevolution/tools/parameters/ParamAccess.scala index 5d7215acb4..120d14bd4f 100644 --- a/modules/tools/src/main/scala/de/proteinevolution/tools/parameters/ParamAccess.scala +++ b/modules/tools/src/main/scala/de/proteinevolution/tools/parameters/ParamAccess.scala @@ -93,14 +93,12 @@ class ParamAccess @Inject() (tel: TEL) { case "COSINE_PERCENTILE_CUTOFF" => select("cosine_percentile_cutoff", default = Some("70")) case "ALIGNMENT_CUTOFF" => select("alignment_cutoff", default = Some("0.30")) case "WIN_LEN" => select("win_len", default = Some("15")) - case "MERGE_HITS" => select("merge_hits", default = Some("1")) - case "PLM_ALN_MODE" => select("plm_aln_mode", default = Some("loc")) - case "SPAN" => select("span", default = Some("25")) - case "SIGMA_FACTOR" => select("sigma_factor", default = Some("2")) - case "BFACTOR" => select("bfactor", default = Some("2")) - case "PLM_GAP_EXT" => select("plm_gap_ext", default = Some("0.5")) - - + case "MERGE_HITS" => select("merge_hits", default = Some("1")) + case "PLM_ALN_MODE" => select("plm_aln_mode", default = Some("loc")) + case "SPAN" => select("span", default = Some("25")) + case "SIGMA_FACTOR" => select("sigma_factor", default = Some("2")) + case "BFACTOR" => select("bfactor", default = Some("2")) + case "PLM_GAP_EXT" => select("plm_gap_ext", default = Some("0.5")) // HHpred case "TWOTEXTALIGNMENT" =>