M3-122: prepping release

mbari-org · Jun 12, 2020 · fc9c32c · fc9c32c
1 parent 5db4c8e
commit fc9c32c
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Showing 47 changed files with 1,325 additions and 917 deletions.
diff --git a/build.sbt b/build.sbt
@@ -1,41 +1,46 @@
 val akkaVersion         = "2.4.7"
-val auth0Version        = "3.10.2"
+val auth0Version        = "3.10.3"
 val codecVersion        = "1.14"
 val configVersion       = "1.4.0"
 val derbyVersion        = "10.15.2.0"
-val eclipselinkVersion  = "2.7.6"
+val eclipselinkVersion  = "2.7.7"
 val gsonJavatimeVersion = "1.1.1"
 val gsonVersion         = "2.8.6"
 val h2Version           = "1.4.200"
-val hikariVersion       = "3.4.2"
+val hikariVersion       = "3.4.5"
 val jansiVersion        = "1.18"
-val javamelodyVersion   = "1.82.0"
-val jettyVersion        = "9.4.27.v20200227"
-val jsonVersion         = "3.6.7"
+val javamelodyVersion   = "1.83.0"
+val jettyVersion        = "9.4.30.v20200611"
+val jsonVersion         = "3.6.8"
 val jtaVersion          = "1.1"
 val jtdsVersion         = "1.3.1"
 val junitVersion        = "4.13"
-val logbackVersion      = "1.2.3"
+val logbackVersion      = "1.3.0-alpha4"
 val oracleVersion       = "19.3.0.0"
-val postgresqlVersion   = "42.2.11"
-val rxjavaVersion       = "3.0.1"
-val scalatestVersion    = "3.1.1"
+val postgresqlVersion   = "42.2.14"
+val rxjavaVersion       = "3.0.4"
+val scalatestVersion    = "3.1.2"
 val scalatraVersion     = "2.7.0"
 val scilubeVersion      = "2.0.7.jre11"
 val servletVersion      = "4.0.1"
-val slf4jVersion        = "1.7.30"
+val slf4jVersion        = "1.8.0-beta4"
 val sqlserverVersion    = "8.2.2.jre11"
 val uuidgenVersion      = "0.1.3"
 val vcr4jVersion        = "4.0.2"
 val zeromqVersion       = "0.5.2"
 
 Global / onChangedBuildSource := ReloadOnSourceChanges
 
+addCommandAlias(
+  "fix",
+  "clean;scalafix RemoveUnused;scalafix LeakingImplicitClassVal;scalafmtAll;compile"
+)
+
 lazy val buildSettings = Seq(
   organization := "org.mbari.vars",
-  version := "0.6.3",
-  scalaVersion in ThisBuild := "2.13.1",
-  crossScalaVersions := Seq("2.13.1"),
+  version := "0.7.0",
+  scalaVersion in ThisBuild := "2.13.2",
+  crossScalaVersions := Seq("2.13.2"),
   organizationName := "Monterey Bay Aquarium Research Institute",
   startYear := Some(2017),
   licenses += ("Apache-2.0", new URL(
@@ -63,15 +68,30 @@ lazy val dependencySettings = Seq(
 )
 
 lazy val optionSettings = Seq(
+  semanticdbEnabled := true, // enable SemanticDB,
+  semanticdbVersion := scalafixSemanticdb.revision,
   scalacOptions ++= Seq(
-    "-deprecation",
+    "-deprecation", // Emit warning and location for usages of deprecated APIs.
     "-encoding",
-    "UTF-8", // yes, this is 2 args
-    "-feature",
+    "UTF-8",         // yes, this is 2 args. Specify character encoding used by source files.
+    "-explaintypes", // Explain type errors in more detail.
+    "-feature",      // Emit warning and location for usages of features that should be imported explicitly.
     "-language:existentials",
+    "-language:higherKinds",
     "-language:implicitConversions",
     "-unchecked",
-    "-Xlint"
+    "-Xlint",
+    "-Yrangepos",              // required by SemanticDB compiler plugin
+    "-Ywarn-dead-code",        // Warn when dead code is identified.
+    "-Ywarn-extra-implicit",   // Warn when more than one implicit parameter section is defined.
+    "-Ywarn-numeric-widen",    // Warn when numerics are widened.
+    "-Ywarn-unused:implicits", // Warn if an implicit parameter is unused.
+    "-Ywarn-unused:imports",   // Warn if an import selector is not referenced.
+    "-Ywarn-unused:locals",    // Warn if a local definition is unused.
+    "-Ywarn-unused:params",    // Warn if a value parameter is unused.
+    "-Ywarn-unused:patvars",   // Warn if a variable bound in a pattern is unused.
+    "-Ywarn-unused:privates",  // Warn if a private member is unused.
+    "-Ywarn-value-discard"     // Warn when non-Unit expression results are unused.
   ),
   javacOptions ++= Seq("-target", "11", "-source", "11"),
   updateOptions := updateOptions.value.withCachedResolution(true)

diff --git a/project/plugins.sbt b/project/plugins.sbt
@@ -1,10 +1,10 @@
-addSbtPlugin("ch.epfl.scala"     % "sbt-scalafix"                 % "0.9.4")
+addSbtPlugin("ch.epfl.scala"     % "sbt-scalafix"                 % "0.9.17")
 addSbtPlugin("com.earldouglas"   % "xsbt-web-plugin"              % "4.1.0")
 addSbtPlugin("com.github.atais"  % "sbt-eclipselink-static-weave" % "0.1.1")
-addSbtPlugin("com.timushev.sbt"  % "sbt-updates"                  % "0.5.0")
+addSbtPlugin("com.timushev.sbt"  % "sbt-updates"                  % "0.5.1")
 addSbtPlugin("com.typesafe.sbt"  % "sbt-git"                      % "1.0.0")
-addSbtPlugin("de.heikoseeberger" % "sbt-header"                   % "5.4.0")
-addSbtPlugin("org.scalameta"     % "sbt-scalafmt"                 % "2.3.2")
+addSbtPlugin("de.heikoseeberger" % "sbt-header"                   % "5.5.0")
+addSbtPlugin("org.scalameta"     % "sbt-scalafmt"                 % "2.4.0")
 addSbtPlugin("org.scalastyle"    %% "scalastyle-sbt-plugin"       % "1.0.0")
 addSbtPlugin("org.xerial.sbt"    % "sbt-pack"                     % "0.12")
 

diff --git a/src/main/scala/JettyMain.scala b/src/main/scala/JettyMain.scala
@@ -23,7 +23,6 @@ import org.eclipse.jetty.webapp.WebAppContext
 import org.mbari.vars.annotation.Constants
 import org.mbari.vars.annotation.messaging.zeromq.ZeroMQPublisher
 import org.scalatra.servlet.ScalatraListener
-import org.slf4j.LoggerFactory
 
 object JettyMain {
 

diff --git a/src/main/scala/ScalatraBootstrap.scala b/src/main/scala/ScalatraBootstrap.scala
@@ -16,14 +16,11 @@
 
 import java.util.concurrent.Executors
 
-import com.typesafe.config.ConfigFactory
 import javax.servlet.ServletContext
-import org.mbari.vars.annotation.{AppConfig, Constants}
 import org.mbari.vars.annotation.api.v1._
 import org.mbari.vars.annotation.api.v2._
 import org.mbari.vars.annotation.controllers._
 import org.mbari.vars.annotation.dao.jpa.JPADAOFactory
-import org.mbari.vars.annotation.messaging.zeromq.ZeroMQPublisher
 import org.scalatra.LifeCycle
 import org.slf4j.LoggerFactory
 

diff --git a/src/main/scala/org/mbari/vars/annotation/AppConfig.scala b/src/main/scala/org/mbari/vars/annotation/AppConfig.scala
@@ -16,7 +16,7 @@
 
 package org.mbari.vars.annotation
 
-import com.typesafe.config.{Config, ConfigFactory}
+import com.typesafe.config.Config
 import org.slf4j.LoggerFactory
 
 import scala.util.Try

diff --git a/src/main/scala/org/mbari/vars/annotation/api/v1/AnnotationV1Api.scala b/src/main/scala/org/mbari/vars/annotation/api/v1/AnnotationV1Api.scala
@@ -206,7 +206,9 @@ class AnnotationV1Api(controller: AnnotationController)(implicit val executor: E
   get("/imagereference/:uuid") {
     val uuid = params
       .getAs[UUID]("uuid")
-      .getOrElse(halt(BadRequest(toJson(ErrorMsg(400, "A image reference 'uuid' parameter is required")))))
+      .getOrElse(
+        halt(BadRequest(toJson(ErrorMsg(400, "A image reference 'uuid' parameter is required"))))
+      )
     controller
       .findByImageReferenceUUID(uuid)
       .map(_.asJava)
@@ -218,11 +220,17 @@ class AnnotationV1Api(controller: AnnotationController)(implicit val executor: E
     validateRequest() // Apply API security
     val videoReferenceUUID = params
       .getAs[UUID]("video_reference_uuid")
-      .getOrElse(halt(BadRequest(toJson(ErrorMsg(400, "A 'video_reference_uuid' parameter is required")))))
+      .getOrElse(
+        halt(BadRequest(toJson(ErrorMsg(400, "A 'video_reference_uuid' parameter is required"))))
+      )
     val concept =
-      params.get("concept").getOrElse(halt(BadRequest(toJson(ErrorMsg(400, "A 'concept' parameter is required")))))
+      params
+        .get("concept")
+        .getOrElse(halt(BadRequest(toJson(ErrorMsg(400, "A 'concept' parameter is required")))))
     val observer =
-      params.get("observer").getOrElse(halt(BadRequest(toJson(ErrorMsg(400, "An 'observer' parameter is required")))))
+      params
+        .get("observer")
+        .getOrElse(halt(BadRequest(toJson(ErrorMsg(400, "An 'observer' parameter is required")))))
     val observationDate = params.getAs[Instant]("observation_timestamp").getOrElse(Instant.now())
     val timecode        = params.getAs[Timecode]("timecode")
     val elapsedTime     = params.getAs[Duration]("elapsed_time_millis")
@@ -233,9 +241,14 @@ class AnnotationV1Api(controller: AnnotationController)(implicit val executor: E
 
     if (timecode.isEmpty && elapsedTime.isEmpty && recordedDate.isEmpty) {
       halt(
-        BadRequest(toJson(ErrorMsg(400,
-          "One or more of the following indices into the video are required: timecode, elapsed_time_millis, recorded_date"
-        )))
+        BadRequest(
+          toJson(
+            ErrorMsg(
+              400,
+              "One or more of the following indices into the video are required: timecode, elapsed_time_millis, recorded_date"
+            )
+          )
+        )
       )
     }
 
@@ -266,7 +279,14 @@ class AnnotationV1Api(controller: AnnotationController)(implicit val executor: E
           .map(annos => toJson(annos.asJava))
       case _ =>
         halt(
-          BadRequest(toJson(ErrorMsg(400, "Posts to /bulk only accept JSON body (i.e. Content-Type: application/json)")))
+          BadRequest(
+            toJson(
+              ErrorMsg(
+                400,
+                "Posts to /bulk only accept JSON body (i.e. Content-Type: application/json)"
+              )
+            )
+          )
         )
     }
   }
@@ -275,7 +295,9 @@ class AnnotationV1Api(controller: AnnotationController)(implicit val executor: E
     validateRequest() // Apply API security
     val uuid = params
       .getAs[UUID]("uuid")
-      .getOrElse(halt(BadRequest(toJson(ErrorMsg(400, "An observation 'uuid' parameter is required")))))
+      .getOrElse(
+        halt(BadRequest(toJson(ErrorMsg(400, "An observation 'uuid' parameter is required"))))
+      )
     val videoReferenceUUID = params.getAs[UUID]("video_reference_uuid")
     val concept            = params.get("concept")
     val observer           = params.get("observer")
@@ -303,7 +325,11 @@ class AnnotationV1Api(controller: AnnotationController)(implicit val executor: E
       )
       .map({
         case None =>
-          halt(NotFound(toJson(ErrorMsg(404, s"An annotation with observation_uuid of $uuid was not found"))))
+          halt(
+            NotFound(
+              toJson(ErrorMsg(404, s"An annotation with observation_uuid of $uuid was not found"))
+            )
+          )
         case Some(ann) => toJson(ann)
       }) // Convert to JSON
 
@@ -319,7 +345,14 @@ class AnnotationV1Api(controller: AnnotationController)(implicit val executor: E
           .map(annos => toJson(annos.asJava))
       case _ =>
         halt(
-          BadRequest(toJson(ErrorMsg(400, "Puts to /bulk only accept JSON body (i.e. Content-Type: application/json)")))
+          BadRequest(
+            toJson(
+              ErrorMsg(
+                400,
+                "Puts to /bulk only accept JSON body (i.e. Content-Type: application/json)"
+              )
+            )
+          )
         )
     }
   }
@@ -336,7 +369,14 @@ class AnnotationV1Api(controller: AnnotationController)(implicit val executor: E
           .map(annos => toJson(annos.asJava))
       case _ =>
         halt(
-          BadRequest(toJson(ErrorMsg(400, "Puts to tapetime only accept JSON body (i.e. Content-Type: application/json)")))
+          BadRequest(
+            toJson(
+              ErrorMsg(
+                400,
+                "Puts to tapetime only accept JSON body (i.e. Content-Type: application/json)"
+              )
+            )
+          )
         )
     }
   }

diff --git a/src/main/scala/org/mbari/vars/annotation/api/v1/AssociationV1Api.scala b/src/main/scala/org/mbari/vars/annotation/api/v1/AssociationV1Api.scala
@@ -43,11 +43,16 @@ class AssociationV1Api(controller: AssociationController)(implicit val executor:
   // Find an association
   get("/:uuid") {
     val uuid =
-      params.getAs[UUID]("uuid").getOrElse(halt(BadRequest(toJson(ErrorMsg(400, "Please provide a 'uuid' parameter")))))
+      params
+        .getAs[UUID]("uuid")
+        .getOrElse(halt(BadRequest(toJson(ErrorMsg(400, "Please provide a 'uuid' parameter")))))
     controller
       .findByUUID(uuid)
       .map({
-        case None    => halt(NotFound(toJson(ErrorMsg(400, s"An Association with a UUID of $uuid was not found"))))
+        case None =>
+          halt(
+            NotFound(toJson(ErrorMsg(400, s"An Association with a UUID of $uuid was not found")))
+          )
         case Some(v) => toJson(v)
       })
   }
@@ -58,7 +63,8 @@ class AssociationV1Api(controller: AssociationController)(implicit val executor:
       .getAs[UUID]("video_reference_uuid")
       .getOrElse(halt(BadRequest(toJson(ErrorMsg(400, "Please provide a video-reference 'uuid'")))))
     val linkName =
-      params.get("link_name")
+      params
+        .get("link_name")
         .getOrElse(halt(BadRequest(toJson(ErrorMsg(400, "A 'link_name' parameter is required")))))
     val concept = params.get("concept")
     controller
@@ -72,11 +78,12 @@ class AssociationV1Api(controller: AssociationController)(implicit val executor:
       .getAs[UUID]("observation_uuid")
       .getOrElse(halt(BadRequest(toJson(ErrorMsg(400, "Please provide an 'observation_uuid'")))))
     val linkName =
-      params.get("link_name")
+      params
+        .get("link_name")
         .getOrElse(halt(BadRequest(toJson(ErrorMsg(400, "A 'link_name' parameter is required")))))
-    val toConcept = params.get("to_concept").getOrElse(Association.TO_CONCEPT_SELF)
-    val linkValue = params.get("link_value").getOrElse(Association.LINK_VALUE_NIL)
-    val mimeType  = params.get("mime_type").getOrElse("text/plain")
+    val toConcept       = params.get("to_concept").getOrElse(Association.TO_CONCEPT_SELF)
+    val linkValue       = params.get("link_value").getOrElse(Association.LINK_VALUE_NIL)
+    val mimeType        = params.get("mime_type").getOrElse("text/plain")
     val associationUuid = params.getAs[UUID]("association_uuid")
     controller.create(uuid, linkName, toConcept, linkValue, mimeType, associationUuid).map(toJson)
   }
@@ -187,9 +194,9 @@ class AssociationV1Api(controller: AssociationController)(implicit val executor:
   post("/conceptassociations") {
     request.getHeader("Content-Type") match {
       case "application/json" =>
-        val b                         = request.body
-        val limit                     = params.getAs[Int]("limit")
-        val offset                    = params.getAs[Int]("offset")
+        val b = request.body
+        params.getAs[Int]("limit")
+        params.getAs[Int]("offset")
         val conceptAssociationRequest = fromJson(b, classOf[ConceptAssociationRequest])
         controller
           .findByConceptAssociationRequest(conceptAssociationRequest)