#3 - updated dependencies

Author: hohonuuli

project/Dependencies.scala

@@ -2,7 +2,7 @@ import sbt._
 
 object Dependencies {
 
-  private val circeVersion = "0.14.1"
+  private val circeVersion = "0.14.5"
   lazy val circeCore       = "io.circe" %% "circe-core"    % circeVersion
   lazy val circeGeneric    = "io.circe" %% "circe-generic" % circeVersion
   lazy val circeParser     = "io.circe" %% "circe-parser"  % circeVersion
@@ -18,22 +18,22 @@ object Dependencies {
   lazy val jsoniterCore =  "com.github.plokhotnyuk.jsoniter-scala" %% "jsoniter-scala-core"   % jsoniterVersion
   lazy val jsoniterMacros = "com.github.plokhotnyuk.jsoniter-scala" %% "jsoniter-scala-macros" % jsoniterVersion
 
-  lazy val logback  = "ch.qos.logback"               % "logback-classic" % "1.4.5"
+  lazy val logback  = "ch.qos.logback"               % "logback-classic" % "1.4.7"
   lazy val methanol = "com.github.mizosoft.methanol" % "methanol"        % "1.7.0"
   lazy val munit    = "org.scalameta"               %% "munit"           % "1.0.0-M7"
-  lazy val picocli  = "info.picocli"                 % "picocli"         % "4.7.1"
+  lazy val picocli  = "info.picocli"                 % "picocli"         % "4.7.3"
 
   private val scalatraVersion = "2.8.2"
   lazy val scalatra           = ("org.scalatra" %% "scalatra"      % scalatraVersion).cross(CrossVersion.for3Use2_13)
   lazy val scalatraJson       = ("org.scalatra" %% "scalatra-json" % scalatraVersion).cross(CrossVersion.for3Use2_13)
 
-  lazy val slf4jJdk     = "org.slf4j"      % "slf4j-jdk-platform-logging"   % "2.0.6"
+  lazy val slf4jJdk     = "org.slf4j"      % "slf4j-jdk-platform-logging"   % "2.0.7"
 
-  private val tapirVersion  = "1.2.8"
+  private val tapirVersion  = "1.4.0"
   lazy val tapirStubServer  = "com.softwaremill.sttp.tapir" %% "tapir-sttp-stub-server" % tapirVersion
   lazy val tapirSwagger     = "com.softwaremill.sttp.tapir" %% "tapir-swagger-ui-bundle" % tapirVersion
   lazy val tapirCirce       = "com.softwaremill.sttp.tapir" %% "tapir-json-circe" % tapirVersion
-  lazy val tapirCirceClient = "com.softwaremill.sttp.client3" %% "circe" % "3.6.2"
+  lazy val tapirCirceClient = "com.softwaremill.sttp.client3" %% "circe" % "3.8.15"
   lazy val tapirNetty       = "com.softwaremill.sttp.tapir" %% "tapir-netty-server" % tapirVersion
   lazy val tapirVertx       = "com.softwaremill.sttp.tapir" %% "tapir-vertx-server" % tapirVersion
       // "com.typesafe.scala-logging" %% "scala-logging" % "3.9.4",
@@ -43,6 +43,6 @@ object Dependencies {
 
 
   lazy val typesafeConfig = "com.typesafe"   % "config"          % "1.4.2"
-  lazy val zio            = "dev.zio"       %% "zio"             % "2.0.6"
+  lazy val zio            = "dev.zio"       %% "zio"             % "2.0.13"
 
 }

src/main/scala/org/fathomnet/worms/Main.scala

@@ -33,7 +33,6 @@ import org.fathomnet.worms.io.extended.CombineTrees.combine
 import org.fathomnet.worms.io.extended.CombineTrees
 import org.fathomnet.worms.io.extended.ExtendedLoader
 
-
 @Command(
   description = Array("The Worms Server"),
   name = "main",
@@ -42,19 +41,24 @@ import org.fathomnet.worms.io.extended.ExtendedLoader
 )
 class MainRunner extends Callable[Int]:
 
-  @Opt(names = Array("-p", "--port"), description = Array("The server port. Default is ${DEFAULT-VALUE}"))
+  @Opt(
+    names = Array("-p", "--port"),
+    description = Array("The server port. Default is ${DEFAULT-VALUE}")
+  )
   private var port: Int = Option(System.getenv("WORMS_PORT")).map(_.toInt).getOrElse(8080)
 
   // "/Users/brian/Downloads/worms"
   @Parameters(index = "0", description = Array("Path to the WoRMS data file directory"))
   var path: Path = _
 
-  @Parameters(index = "1..*", 
+  @Parameters(
+    index = "1..*",
     description = Array(
       "Paths to extra tree files (CSV with 3 columns: id, parentId, names).  [Optional]",
       "These will becombined with the main WoRMS tree. This will create a new root (object)",
       "All the nodes from these files will have synthetic aphiaIds with negative values."
-      ))
+    )
+  )
   var treeFiles: Array[Path] = Array.empty[Path]
 
   override def call(): Int =
@@ -123,15 +127,11 @@ object Main:
     WormsLoader.load(wormsDir).map { root =>
       if (treeFiles.nonEmpty)
         // Our new base. We use 0 as aphiaId so that the real aphiaIds are not incremented when the trees are combined
-        val newRoot = WormsNode("object", "", 0L, Nil, Nil)                
-        val newBranches = treeFiles.flatMap(ExtendedLoader.load(_)).toSeq
-        val trees = root +: newBranches
+        val newRoot      = WormsNode("object", "", 0L, Nil, Nil)
+        val newBranches  = treeFiles.flatMap(ExtendedLoader.load(_)).toSeq
+        val trees        = root +: newBranches
         val combinedRoot = CombineTrees.combine(newRoot, trees, root.maxAphiaId)
         // We need to reset the aphiaId to -1 so that it's obivious that the root is not a real aphiaId
         combinedRoot.copy(aphiaId = -1L)
-
-      else
-        root
+      else root
     }
-
-

src/main/scala/org/fathomnet/worms/StateController.scala

@@ -140,11 +140,10 @@ object StateController:
 
   def taxaByNameStartingWith(prefix: String): Either[ErrorMsg, List[SimpleWormsNode]] =
     def search(data: Data): List[SimpleWormsNode] =
-      data.names
+      data
+        .names
         .filter(_.toLowerCase.startsWith(prefix.toLowerCase))
         .flatMap(data.findNodeByName)
         .map(_.simple)
         .toList
     runSearch(search)
-
-

src/main/scala/org/fathomnet/worms/WormsNode.scala

@@ -42,8 +42,8 @@ final case class WormsNode(
     (this.name +: this.alternateNames.sorted).toSeq
 
   /**
-    * A version of this node with no children
-    */
+   * A version of this node with no children
+   */
   lazy val simple: SimpleWormsNode = SimpleWormsNode(
     name = this.name,
     rank = this.rank,

src/main/scala/org/fathomnet/worms/api/TaxaEndpoints.scala

@@ -89,15 +89,18 @@ class TaxaEndpoints(using ec: ExecutionContext) extends Endpoints:
   val taxaChildrenServerEndpoint: ServerEndpoint[Any, Future] =
     taxaChildren.serverLogic((name: String) => Future(StateController.childTaxa(name)))
 
-  val taxaQueryStartswith: PublicEndpoint[String, ErrorMsg, List[SimpleWormsNode], Any] = baseEndpoint
-    .get
-    .in("taxa" / "query" / "startswith")
-    .in(path[String]("prefix"))
-    .out(jsonBody[List[SimpleWormsNode]])
-    .description("Returns a list of taxa that start with the given prefix.")
+  val taxaQueryStartswith: PublicEndpoint[String, ErrorMsg, List[SimpleWormsNode], Any] =
+    baseEndpoint
+      .get
+      .in("taxa" / "query" / "startswith")
+      .in(path[String]("prefix"))
+      .out(jsonBody[List[SimpleWormsNode]])
+      .description("Returns a list of taxa that start with the given prefix.")
 
   val taxaQueryStartswithEndpoint: ServerEndpoint[Any, Future] =
-    taxaQueryStartswith.serverLogic((prefix: String) => Future(StateController.taxaByNameStartingWith(prefix)))
+    taxaQueryStartswith.serverLogic((prefix: String) =>
+      Future(StateController.taxaByNameStartingWith(prefix))
+    )
 
   val all: List[ServerEndpoint[Any, Future]] = List(
     taxaDescendantsServerEndpoint,

src/main/scala/org/fathomnet/worms/io/extended/CombineTrees.scala

@@ -8,37 +8,34 @@ package org.fathomnet.worms.io.extended
 
 import org.fathomnet.worms.WormsNode
 
-
-
 object CombineTrees:
-  
-/**
-  * Combine a sequence of trees into a single tree. It adjust the Aphia IDs of the
-  * combined tree so that they are unique. The inteneded usage is that the
-  * rootNode have a low aphiaId (0), then add the WormS tree first.
-  * Then the worms aphiaId's will not be changed. Ony the subsequent trees will
-  * have their aphiaId's incremented and then multiplied by -1 so that all fake 
-  * aphiaId's are negative.
-  *
-  * @param rootNode The root node of the tree to add the other trees to
-  * @param trees The trees to add
-  * @param maxAphiaId The maximum aphiaId of the original WoRMS tree. Only aphiaId's
-  *                  greater than this value will be flipped to negative so that they 
-  *                 are not confused with real aphiaId's.
-  * @return The combined tree
-  */
-  def combine(rootNode: WormsNode,  trees: Seq[WormsNode], maxAphiaId: Long): WormsNode = 
+
+  /**
+   * Combine a sequence of trees into a single tree. It adjust the Aphia IDs of the combined tree so
+   * that they are unique. The inteneded usage is that the rootNode have a low aphiaId (0), then add
+   * the WormS tree first. Then the worms aphiaId's will not be changed. Ony the subsequent trees
+   * will have their aphiaId's incremented and then multiplied by -1 so that all fake aphiaId's are
+   * negative.
+   *
+   * @param rootNode
+   *   The root node of the tree to add the other trees to
+   * @param trees
+   *   The trees to add
+   * @param maxAphiaId
+   *   The maximum aphiaId of the original WoRMS tree. Only aphiaId's greater than this value will
+   *   be flipped to negative so that they are not confused with real aphiaId's.
+   * @return
+   *   The combined tree
+   */
+  def combine(rootNode: WormsNode, trees: Seq[WormsNode], maxAphiaId: Long): WormsNode =
     var root = rootNode
-    trees.foreach(t => {
-      root = add(root, t, root.maxAphiaId)
-    })
+    trees.foreach(t => root = add(root, t, root.maxAphiaId))
     flipFakeAphiaId(root, maxAphiaId)
 
-  def add(rootNode: WormsNode, tree: WormsNode, maxAphiaId: Long): WormsNode = 
-    val node = incrementAphiaId(tree, maxAphiaId)
+  def add(rootNode: WormsNode, tree: WormsNode, maxAphiaId: Long): WormsNode =
+    val node     = incrementAphiaId(tree, maxAphiaId)
     val children = rootNode.children :+ node
     rootNode.copy(children = children)
-    
 
   def incrementAphiaId(node: WormsNode, maxAphiaId: Long): WormsNode =
     node.copy(
@@ -47,18 +44,18 @@ object CombineTrees:
     )
 
   /**
-    * Flip the aphiaId of all nodes that have aphiaId > maxAphiaId so that
-    * fake aphiaId's are negative.
-    *
-    * @param node The node to flip
-    * @param maxAphiaId The maximum aphiaId of the original tree
-    * @return A new tree with fake aphiaId's flipped to negative
-    */
+   * Flip the aphiaId of all nodes that have aphiaId > maxAphiaId so that fake aphiaId's are
+   * negative.
+   *
+   * @param node
+   *   The node to flip
+   * @param maxAphiaId
+   *   The maximum aphiaId of the original tree
+   * @return
+   *   A new tree with fake aphiaId's flipped to negative
+   */
   def flipFakeAphiaId(node: WormsNode, maxAphiaId: Long): WormsNode =
     node.copy(
       aphiaId = if (node.aphiaId > maxAphiaId) -node.aphiaId else node.aphiaId,
       children = node.children.map(n => flipFakeAphiaId(n, maxAphiaId))
     )
-
-  
-