From 384898e9977ed27e5945f4e314ff95b5a31e04b8 Mon Sep 17 00:00:00 2001 From: Scala Steward Date: Wed, 30 Apr 2025 18:20:56 +0000 Subject: [PATCH 1/3] Update scalafmt-core to 3.9.5 --- .scalafmt.conf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.scalafmt.conf b/.scalafmt.conf index ace08b0c3..1a5c349fa 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 = 3.9.5 runner.dialect = scala213 From 3b23b4a9b5f19af10334bee530b95cef3d27c0e5 Mon Sep 17 00:00:00 2001 From: Scala Steward Date: Wed, 30 Apr 2025 18:21:09 +0000 Subject: [PATCH 2/3] Reformat with scalafmt 3.9.5 Executed command: scalafmt --non-interactive --- .../common/models/ConstantsV2.scala | 10 +++++----- .../de/proteinevolution/jobs/actors/JobActor.scala | 2 +- .../jobs/controllers/ResultsController.scala | 5 +++-- .../jobs/controllers/SubmissionController.scala | 6 ++++-- .../statistics/UserStatistic.scala | 1 + .../tools/parameters/ParamAccess.scala | 14 ++++++-------- 6 files changed, 20 insertions(+), 18 deletions(-) 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 260b15b0c..c1a001789 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 9433b13e0..a207d7589 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 9d5a0d24b..87793b338 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 09112c5d2..37fb352cf 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 e69de29bb..8b1378917 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 5d7215acb..120d14bd4 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" => From 5c23484d4f670b0fc620503db458bfe5ad709466 Mon Sep 17 00:00:00 2001 From: Scala Steward Date: Wed, 30 Apr 2025 18:21:09 +0000 Subject: [PATCH 3/3] Add 'Reformat with scalafmt 3.9.5' to .git-blame-ignore-revs --- .git-blame-ignore-revs | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs index 4be937d47..0056cfb9b 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 3.9.5 +3b23b4a9b5f19af10334bee530b95cef3d27c0e5