Update scalafmt-core to 3.9.9

.git-blame-ignore-revs

@@ -3,3 +3,6 @@
 
 # Scala Steward: Reformat with scalafmt 3.6.0
 df858b0ea7cc4743ec9c78cee1486ad91de1dbd4
+
+# Scala Steward: Reformat with scalafmt 3.9.9
+aa0891ef4a981f567bc7c8c827a934d5583e77ce

.scalafmt.conf

@@ -13,5 +13,5 @@ optIn.breakChainOnFirstMethodDot = false
 align.openParenDefnSite          = false
 project.git                      = true
 assumeStandardLibraryStripMargin = true
-version                          = 3.6.1
+version                          = 3.9.9
 runner.dialect                   = scala213

modules/auth/src/main/scala/de/proteinevolution/auth/dao/UserDao.scala

@@ -108,7 +108,7 @@ class UserDao @Inject() (
         User.ACCOUNT_TYPE          -> AccountType.REGISTEREDUSER.toInt,
         User.DELETION_WARNING_SENT -> false,
         User.CONNECTED             -> false,
-        User.DATE_LAST_LOGIN -> BSONDocument(
+        User.DATE_LAST_LOGIN       -> BSONDocument(
           "$lt" -> BSONDateTime(warnRegistratedUserAfterLoginDate.toInstant.toEpochMilli)
         )
       )

modules/auth/src/main/scala/de/proteinevolution/auth/services/UserSessionService.scala

@@ -53,7 +53,7 @@ class UserSessionService @Inject() (
       // cache related stuff should remain in the project where the cache is bound
       userCache.get[User](sessionID) match {
         case Some(user) => fuccess(user)
-        case None => // session not known yet in cache
+        case None       => // session not known yet in cache
           val newSessionData = SessionData(
             ip = MurmurHash3.stringHash(request.remoteAddress).toString,
             userAgent = request.headers.get(Http.HeaderNames.USER_AGENT).getOrElse("Not specified"),

modules/backend/src/main/scala/de/proteinevolution/backend/controllers/BackendController.scala

@@ -101,7 +101,7 @@ final class BackendController @Inject() (
   def setMaintenanceState(): Action[Json] = userAction(circe.json) { implicit request =>
     if (request.user.isSuperuser) {
       request.body.asObject match {
-        case None => BadRequest
+        case None        => BadRequest
         case Some(value) =>
           maintenanceMessage = value("message").get.asString.orElse(Some("")).get
           maintenanceSubmitBlocked = value("submitBlocked").get.asBoolean.orElse(Some(false)).get

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

modules/common/src/main/scala/de/proteinevolution/common/models/util/ZonedDateTimeHelper.scala

@@ -23,8 +23,8 @@ import reactivemongo.api.bson.BSONDateTime
 
 object ZonedDateTimeHelper {
 
-  final val dateTimeFormatter: DateTimeFormatter = DateTimeFormatter.ofPattern("dd.MM.yyyy HH:mm:ss O")
-  final val defaultZoneID: ZoneId                = ZoneId.systemDefault()
+  final val dateTimeFormatter: DateTimeFormatter        = DateTimeFormatter.ofPattern("dd.MM.yyyy HH:mm:ss O")
+  final val defaultZoneID: ZoneId                       = ZoneId.systemDefault()
   def getZDT(bsonDateTime: BSONDateTime): ZonedDateTime = {
     Instant.ofEpochMilli(bsonDateTime.value).atZone(defaultZoneID)
   }

modules/common/src/main/scala/de/proteinevolution/common/parsers/FASTA.scala

@@ -140,7 +140,7 @@ object FASTA {
     private[FASTA] def parse(input: String): Option[FASTA] = {
       parseAll(sequence, input) match {
         case Success(es, _) => Some(FASTA(List(Entry("empty header", es))))
-        case _ =>
+        case _              =>
           parseAll(entries, input) match {
             case Success(es, _) => Some(FASTA(es))
             case _              => None

modules/jobs/src/main/scala/de/proteinevolution/jobs/actors/JobActor.scala

@@ -75,8 +75,8 @@ 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 Tick: Cancellable = {
+  private val fetchLatestInterval = 500.millis
+  private val Tick: Cancellable   = {
     // scheduler should use the system dispatcher
     context.system.scheduler.scheduleWithFixedDelay(Duration.Zero, fetchLatestInterval, self, UpdateLog)(
       context.system.dispatcher
@@ -109,7 +109,7 @@ class JobActor @Inject() (
   private def getCurrentExecutionContext(jobID: String): Option[ExecutionContext] = {
     currentExecutionContexts.get(jobID) match {
       case Some(executionContext) => Some(executionContext)
-      case None =>
+      case None                   =>
         if ((constants.jobPath / jobID).exists) {
           val executionContext = ExecutionContext(constants.jobPath / jobID, reOpen = true)
           currentExecutionContexts = currentExecutionContexts.updated(jobID, executionContext)
@@ -196,7 +196,7 @@ class JobActor @Inject() (
     jobDao.updateJobStatus(job.jobID, job.status).map { _ =>
       val jobLog = currentJobLogs.get(job.jobID) match {
         case Some(jobEventLog) => jobEventLog.addJobStateEvent(job.status)
-        case None =>
+        case None              =>
           JobEventLog(
             jobID = job.jobID,
             toolName = job.tool,
@@ -355,7 +355,7 @@ class JobActor @Inject() (
         .getCurrentJob(jobID)
         .flatMap {
           case Some(job) => fuccess(Some(job))
-          case None =>
+          case None      =>
             if (verbose)
               log.info(
                 s"[JobActor[$jobActorNumber].Delete] jobID $jobID not found in current jobs. Loading job from DB."

modules/jobs/src/main/scala/de/proteinevolution/jobs/controllers/FileController.scala

@@ -40,7 +40,7 @@ class FileController @Inject() (
     with ContentTypes {
 
   def getStructureFile(accession: String): Action[AnyContent] = Action { implicit request =>
-    val db = LinkUtil.identifyDatabase(accession)
+    val db     = LinkUtil.identifyDatabase(accession)
     val ending = db match {
       case "scop"   => "pdb"
       case "ecod"   => "pdb"

modules/jobs/src/main/scala/de/proteinevolution/jobs/controllers/JobGetController.scala

@@ -57,7 +57,7 @@ class JobGetController @Inject() (
 
   def suggestJobsForQuery(queryString: String): Action[AnyContent] =
     userAction.async { implicit request =>
-      val user = request.user
+      val user              = request.user
       val tools: List[Tool] = toolConfig.values
         .unsafeRunSync()
         .values

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

modules/jobs/src/main/scala/de/proteinevolution/jobs/controllers/SubmissionController.scala

@@ -60,11 +60,13 @@ class SubmissionController @Inject() (
           Unauthorized
         } else {
           request.body.asObject match {
-            case None => BadRequest
+            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
           }
@@ -91,7 +93,7 @@ class SubmissionController @Inject() (
 
   def submitJob(toolName: String): Action[Json] = userAction(circe.json).async { implicit request =>
     request.body.asObject match {
-      case None => fuccess(BadRequest)
+      case None      => fuccess(BadRequest)
       case Some(obj) =>
         val parts: Iterable[(String, String)] = for {
           (key, json) <- obj.toIterable

modules/jobs/src/main/scala/de/proteinevolution/jobs/results/HmmerHSP.scala

@@ -62,7 +62,7 @@ case class HmmerHSP(
       "hitLen"          -> hit_len.asJson,
       "observedDomains" -> domain_obs_num.asJson,
       "agree"           -> midline.asJson,
-      "query" -> Map(
+      "query"           -> Map(
         "start" -> query_start.asJson,
         "end"   -> query_end.asJson,
         "seq"   -> query_seq.asJson

modules/jobs/src/main/scala/de/proteinevolution/jobs/results/LinkUtil.scala

@@ -80,7 +80,7 @@ object LinkUtil {
       case "ecod"    => val idEcod = id.slice(5, 14); generateLink(ecodBaseLink, idEcod, id)
       case "cath"    => val idCath = id.slice(5, 12); generateLink(cathBaseLink, idCath, id)
       case "phrog"   => val idPhrog = id.replaceAll("phrog_", ""); generateLink(phrogBaseLink, idPhrog, id)
-      case "keggoc" =>
+      case "keggoc"  =>
         val idKeggoc = id.split("OC.").last; generateLink(keggocBaseLink, idKeggoc, id)
 
       case _ => id
@@ -116,7 +116,7 @@ object LinkUtil {
       case prokaryoticProteasomeNameReg(_) => links += generateLink(ncbiProteinBaseLink, idNcbi, "NCBI Fasta")
       case pdbNameReg(_)                   => links += generateLink(pdbeBaseLink, idPdb, "PDBe")
       case pfamNameReg(_)                  => links += generateLink(cddBaseLink, idCDD, "CDD")
-      case alphafolddbNameReg(_) =>
+      case alphafolddbNameReg(_)           =>
         links += generateLink(uniprotBaseLink, idAlphaFold, "UniProt")
         links += generateLink(uniprotBaseLink, idAlphaFold + ".fasta", "UniProt FASTA")
       case uniprotNameReg(_) =>

modules/jobs/src/main/scala/de/proteinevolution/jobs/results/PLMBlastHSP.scala

@@ -53,7 +53,7 @@ case class PLMBlastHSP(
       "eval"     -> eValue.asJson,
       "bitScore" -> (identScore * 100).round.asJson,
       "hitLen"   -> hit_len.asJson,
-      "query" -> Map(
+      "query"    -> Map(
         "start" -> query_start.asJson,
         "end"   -> query_end.asJson
       ).asJson,

modules/jobs/src/main/scala/de/proteinevolution/jobs/results/PSIBlastHSP.scala

@@ -71,7 +71,7 @@ case class PSIBlastHSP(
       "refLen"    -> ref_len.asJson,
       "hitLen"    -> hit_len.asJson,
       "agree"     -> midLine.asJson,
-      "query" -> Map(
+      "query"     -> Map(
         "start" -> query_start.asJson,
         "end"   -> query_end.asJson,
         "seq"   -> query_seq.asJson

modules/jobs/src/main/scala/de/proteinevolution/jobs/services/HHService.scala

@@ -42,7 +42,7 @@ class HHService @Inject() (
       tool <- toolFinder.getTool(jobID)
     } yield (json, tool)).map {
       case (json, tool) => resultFiles.parseResult(tool, json)
-      case _ =>
+      case _            =>
         val error = "parsing result json failed."
         logger.error(error)
         Left(DecodingFailure(error, Nil))

modules/jobs/src/main/scala/de/proteinevolution/jobs/services/JobDispatcher.scala

@@ -54,10 +54,10 @@ final class JobDispatcher @Inject() (
       EitherT.leftT(JobSubmitError.ModellerKeyInvalid)
     } else {
       for {
-        generatedId <- generateJobId(parts)
-        _           <- validateJobId(generatedId)
-        _           <- checkNotAlreadyTaken(generatedId)
-        job         <- EitherT.pure[Future, JobSubmitError](generateJob(toolName, generatedId, parts, user))
+        generatedId     <- generateJobId(parts)
+        _               <- validateJobId(generatedId)
+        _               <- checkNotAlreadyTaken(generatedId)
+        job             <- EitherT.pure[Future, JobSubmitError](generateJob(toolName, generatedId, parts, user))
         isFromInstitute <- EitherT.pure[Future, JobSubmitError](
           user.userData.map(_.eMail).getOrElse("").matches("[email protected]")
         )
@@ -114,7 +114,7 @@ final class JobDispatcher @Inject() (
       form: Map[String, String],
       user: User
   ): Job = {
-    val now = ZonedDateTime.now
+    val now            = ZonedDateTime.now
     val dateDeletionOn = now.plusDays(
       if (user.isRegistered) constants.jobDeletionRegistered.toLong
       else constants.jobDeletion.toLong

modules/jobs/src/main/scala/de/proteinevolution/jobs/services/ProcessService.scala

@@ -82,7 +82,7 @@ final class ProcessService @Inject() (
           val generateAlignmentScript = (scriptPath + "/generateAlignment.sh").toFile // HHPRED, HHBLITS alnEval
           val retrieveFullSeq         = (scriptPath + "/retrieveFullSeq.sh").toFile
           val retrieveAlnEval         = (scriptPath + "/retrieveAlnEval.sh").toFile   // Hmmer & PSIBLAST alnEval
-          val retrieveFullSeqHHblits =
+          val retrieveFullSeqHHblits  =
             (scriptPath + "/retrieveFullSeqHHblits.sh").toFile // why so little abstractions ???
 
           val fullEvalAccs: () => String =
@@ -94,15 +94,15 @@ final class ProcessService @Inject() (
                 "%s ".format(result.HSPS(num - 1).accession)
               }.mkString
 
-          val tempFileName = UUID.randomUUID().toString
+          val tempFileName     = UUID.randomUUID().toString
           val (script, params) = (tool, form.forwardHitsMode, form.sequenceLengthMode) match {
             case (HHBLITS, "eval", "aln") | (HHPRED, "eval", "aln") =>
               (
                 generateAlignmentScript,
                 List(
                   "jobID"    -> jobId,
                   "filename" -> tempFileName,
-                  "numList" ->
+                  "numList"  ->
                   result.HSPS.filter(_.eValue <= form.eval).map { _.num }.mkString(" ")
                 )
               )

modules/statistics/src/main/scala/de/proteinevolution/statistics/UserStatistic.scala

@@ -0,0 +1 @@
+

modules/tel/src/main/scala/de/proteinevolution/tel/runscripts/Runscript.scala

@@ -55,7 +55,7 @@ class Runscript(files: Seq[File]) extends TELRegex with Logging {
   // Special fields to put the runscript into a larger context
 
   private case class Replacer(arguments: Seq[(String, ValidArgument)]) {
-    private var counter = -1
+    private var counter               = -1
     def apply(m: Regex.Match): String = {
       m.groupNames.foreach(s =>
         logger.debug(s)

modules/tools/src/main/scala/de/proteinevolution/tools/ToolConfig.scala

@@ -147,7 +147,7 @@ class ToolConfig @Inject() (
       validationParams
     )
     val inputGroup: Seq[String] = paramAccess.paramGroups("Input")
-    val toolParameterForm = ToolParameters(
+    val toolParameterForm       = ToolParameters(
       Seq(
         ParameterSection(
           "Input",

modules/tools/src/main/scala/de/proteinevolution/tools/parameters/ParamAccess.scala

@@ -84,7 +84,7 @@ class ParamAccess @Inject() (tel: TEL) {
     case "DIAMOND_MIN_ALN_COV" => select("diamond_min_aln_cov", default = Some("80"))
 
     // HHblits
-    case "HHBLITSDB" => select("hhblitsdb", default = Some("UniRef30"))
+    case "HHBLITSDB"         => select("hhblitsdb", default = Some("UniRef30"))
     case "HHBLITS_INCL_EVAL" =>
       select("hhblits_incl_eval", default = Some("1e-3"))
 
@@ -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" =>
@@ -125,7 +123,7 @@ class ParamAccess @Inject() (tel: TEL) {
     case "MACTHRESHOLD" => select("macthreshold", default = Some("0.3"))
 
     // HMMER
-    case "HMMER_DB" => select("hmmerdb", default = Some("alphafold_uniprot50"))
+    case "HMMER_DB"         => select("hmmerdb", default = Some("alphafold_uniprot50"))
     case "MAX_HHBLITS_ITER" =>
       select("max_hhblits_iter", default = Some("1"), onDetectedMSA = Some("0"))
 
@@ -139,7 +137,7 @@ class ParamAccess @Inject() (tel: TEL) {
       select("blast_incl_eval", default = Some("1e-3"))
 
     // Kalign
-    case "GAP_OPEN" => NumberParameter("gap_open", default = Some(11))
+    case "GAP_OPEN"     => NumberParameter("gap_open", default = Some(11))
     case "GAP_EXT_KALN" =>
       NumberParameter(
         "gap_ext_kaln",
@@ -174,8 +172,8 @@ class ParamAccess @Inject() (tel: TEL) {
     // HHrepID
     case "MSA_GEN_MAX_ITER_HHREPID" =>
       select("msa_gen_max_iter_hhrepid", default = Some("3"), onDetectedMSA = Some("0"))
-    case "SCORE_SS"           => select("score_ss", default = Some("2"))
-    case "REP_PVAL_THRESHOLD" => select("rep_pval_threshold", default = Some("1e-2"))
+    case "SCORE_SS"                => select("score_ss", default = Some("2"))
+    case "REP_PVAL_THRESHOLD"      => select("rep_pval_threshold", default = Some("1e-2"))
     case "SELF_ALN_PVAL_THRESHOLD" =>
       select("self_aln_pval_threshold", default = Some("1e-1"))
     case "MERGE_ITERS"            => select("merge_iters", default = Some("3"))
@@ -283,7 +281,7 @@ class ParamAccess @Inject() (tel: TEL) {
     case "OUT_FORMAT" => select("out_format", default = Some("fas"))
 
     // HHfilter
-    case "MAX_SEQID" => NumberParameter("max_seqid", default = Some(90))
+    case "MAX_SEQID"     => NumberParameter("max_seqid", default = Some(90))
     case "MIN_QUERY_COV" =>
       NumberParameter(
         "min_query_cov",