Added unit tests

oni/src/main/scala/org/mbari/oni/AppConfig.scala

@@ -12,6 +12,9 @@ import scala.util.Try
 import org.mbari.oni.jpa.EntityManagerFactories
 import jakarta.persistence.EntityManagerFactory
 
+/**
+  * Parse configuration info from reference.conf and application.conf
+  */
 object AppConfig:
 
     val Config = ConfigFactory.load()

oni/src/main/scala/org/mbari/oni/Endpoints.scala

@@ -8,7 +8,18 @@
 package org.mbari.oni
 
 import jakarta.persistence.EntityManagerFactory
-import org.mbari.oni.endpoints.{AuthorizationEndpoints, ConceptEndpoints, ConceptNameEndpoints, HealthEndpoints, HistoryEndpoints, LinkEndpoints, PhylogenyEndpoints, PrefNodeEndpoints, ReferenceEndpoints, UserAccountEndpoints}
+import org.mbari.oni.endpoints.{
+    AuthorizationEndpoints,
+    ConceptEndpoints,
+    ConceptNameEndpoints,
+    HealthEndpoints,
+    HistoryEndpoints,
+    LinkEndpoints,
+    PhylogenyEndpoints,
+    PrefNodeEndpoints,
+    ReferenceEndpoints,
+    UserAccountEndpoints
+}
 import org.mbari.oni.etc.jwt.JwtService
 import org.mbari.oni.jdbc.FastPhylogenyService
 import sttp.tapir.server.ServerEndpoint
@@ -27,23 +38,24 @@ object Endpoints:
         val config = AppConfig.DefaultJwtConfig
         JwtService(config.issuer, config.apiKey, config.signingSecret)
 
-    given ExecutionContext = ExecutionContext.fromExecutorService(Executors.newFixedThreadPool(AppConfig.NumberOfThreads))
+    given ExecutionContext =
+        ExecutionContext.fromExecutorService(Executors.newFixedThreadPool(AppConfig.NumberOfThreads))
 
     val entityMangerFactory: EntityManagerFactory = AppConfig.DefaultEntityManagerFactory
 
     val phylogenyEndpoints: PhylogenyEndpoints = PhylogenyEndpoints(entityMangerFactory)
 
-    val authorizationEndpoints: AuthorizationEndpoints = AuthorizationEndpoints(entityMangerFactory)
-    val conceptEndpoints: ConceptEndpoints             = ConceptEndpoints(entityMangerFactory)
-    val conceptNameEndpoints: ConceptNameEndpoints     = ConceptNameEndpoints(entityMangerFactory)
-    val healthEndpoints: HealthEndpoints               = HealthEndpoints()
-    val historyEndpoints: HistoryEndpoints             = HistoryEndpoints(entityMangerFactory, phylogenyEndpoints.service)
-    val linkEndpoints: LinkEndpoints                   = LinkEndpoints(entityMangerFactory)
+    val authorizationEndpoints: AuthorizationEndpoints     = AuthorizationEndpoints(entityMangerFactory)
+    val conceptEndpoints: ConceptEndpoints                 = ConceptEndpoints(entityMangerFactory)
+    val conceptNameEndpoints: ConceptNameEndpoints         = ConceptNameEndpoints(entityMangerFactory)
+    val healthEndpoints: HealthEndpoints                   = HealthEndpoints()
+    val historyEndpoints: HistoryEndpoints                 = HistoryEndpoints(entityMangerFactory, phylogenyEndpoints.service)
+    val linkEndpoints: LinkEndpoints                       = LinkEndpoints(entityMangerFactory)
     val linkRealizationEndpoints: LinkRealizationEndpoints = LinkRealizationEndpoints(entityMangerFactory)
     val linkTemplateEndpoints: LinkTemplateEndpoints       = LinkTemplateEndpoints(entityMangerFactory)
-    val prefNodeEndpoints: PrefNodeEndpoints           = PrefNodeEndpoints(entityMangerFactory)
-    val referenceEndpoints: ReferenceEndpoints         = ReferenceEndpoints(entityMangerFactory)
-    val userAccountEndpoints: UserAccountEndpoints     = UserAccountEndpoints(entityMangerFactory)
+    val prefNodeEndpoints: PrefNodeEndpoints               = PrefNodeEndpoints(entityMangerFactory)
+    val referenceEndpoints: ReferenceEndpoints             = ReferenceEndpoints(entityMangerFactory)
+    val userAccountEndpoints: UserAccountEndpoints         = UserAccountEndpoints(entityMangerFactory)
 
     val endpoints: List[ServerEndpoint[Any, Future]] = List(
         authorizationEndpoints,

oni/src/main/scala/org/mbari/oni/Main.scala

@@ -19,6 +19,9 @@ import io.vertx.core.VertxOptions
 import scala.concurrent.Await
 import scala.concurrent.duration.Duration
 
+/**
+  * Launches Oni
+  */
 object Main:
 
     def main(args: Array[String]): Unit =

oni/src/main/scala/org/mbari/oni/OniException.scala

@@ -7,6 +7,9 @@
 
 package org.mbari.oni
 
+/**
+  * Defines custom exceptions used by Oni
+  */
 sealed trait OniException extends Throwable
 
 trait NotFoundException extends OniException

oni/src/main/scala/org/mbari/oni/domain/AuthorizationSC.scala

@@ -7,6 +7,12 @@
 
 package org.mbari.oni.domain
 
+/**
+  * Authorization information as snake_case
+  *
+  * @param token_type Typically it will be `Beaerer`
+  * @param access_token For Oni this will be a JWT
+  */
 final case class AuthorizationSC(token_type: String, access_token: String)
 
 object AuthorizationSC:

oni/src/main/scala/org/mbari/oni/domain/Concept.scala

@@ -11,6 +11,16 @@ import org.mbari.oni.jpa.entities.ConceptEntity
 import org.mbari.oni.etc.jdk.Numbers.*
 import scala.jdk.CollectionConverters.*
 
+/**
+  * A node in the knoweldgebase tree
+  *
+  * @param name The primary, or accepted, name of the concept
+  * @param rank The pyhologenetic rank
+  * @param alternativeNames Synonyms, common names, or former names
+  * @param children Child concepts of this concept
+  * @param aphiaId The WoRMS AphiaID
+  * @param id The database id
+  */
 case class Concept(
     name: String,
     rank: Option[String] = None,
@@ -19,18 +29,38 @@ case class Concept(
     aphiaId: Option[Long] = None,
     id: Option[Long] = None
 ):
+
+    /**
+      * Checks is this concept uses the provided name
+      *
+      * @param n The name to check
+      * @return true if this concept's name or alternative names contain this
+      *         name. false if it does not.
+      */
     def containsName(n: String): Boolean = name.equals(n) ||
         alternativeNames.contains(n)
 
+    /**
+      * All names applicable to this concept. THe first name will
+      * be the primary name.
+      */
     lazy val names: Seq[String] = name +: alternativeNames
 
+    /**
+      * A sorted list all names applicable to this concept and 
+      * all of it's descendants.
+      */
     lazy val descendantNames: Seq[String] = descendants
         .flatMap(_.names)
         .toSeq
         .sorted
 
+    /**
+      * A list of all of this concepts descendants
+      */
     lazy val descendants: Set[Concept] = children.toSet.flatMap(_.descendants) + this
 
+
     lazy val flatten: Seq[Concept] = Seq(this) ++ children.flatMap(_.flatten)
 
 object Concept:

oni/src/main/scala/org/mbari/oni/domain/ConceptMetadata.scala

@@ -12,6 +12,7 @@ import org.mbari.oni.jpa.entities.ConceptEntity
 import org.mbari.oni.etc.jdk.Numbers.*
 
 /**
+ * Detailed information about a concept
  * @author
  *   Brian Schlining
  * @since 2016-11-17T15:54:00

oni/src/main/scala/org/mbari/oni/etc/jdk/CloseableLock.scala

@@ -9,6 +9,9 @@ package org.mbari.oni.etc.jdk
 
 import java.util.concurrent.locks.ReentrantLock
 
+/**
+  * An auto-closeable lock. Use in a try-with-resources block to ensure the lock is released.
+  */
 class CloseableLock extends ReentrantLock with AutoCloseable {
 
     def lockAndGet: CloseableLock = {

oni/src/main/scala/org/mbari/oni/etc/jdk/Colors.scala

@@ -11,6 +11,13 @@ import java.awt.Color
 
 class Colors:
 
+    /**
+     * Converts any string to a hex color. The color is generated from the hash code of the string.
+     * @param s
+     *   The string to convert
+     * @return
+     *   The hex color
+     */
     def stringToHexColor(s: String): String =
         val c = intToRGBA(s.hashCode)
         f"#${c.getRed}%02X${c.getGreen}%02X${c.getBlue}%02X" // ignore alpha. Sharktopoda won't parse colors with alpha

oni/src/main/scala/org/mbari/oni/etc/jdk/Files.scala

@@ -12,6 +12,7 @@ import java.nio.file.Path
 import scala.util.Using
 
 import java.nio.file.Files as JFiles
+import java.io.BufferedInputStream
 
 object Files:
 
@@ -25,7 +26,7 @@ object Files:
     def concatenate(files: Seq[Path], output: Path): Unit =
         Using(BufferedOutputStream(JFiles.newOutputStream(output))) { out =>
             files.foreach { file =>
-                Using(JFiles.newInputStream(file)) { in =>
+                Using(BufferedInputStream(JFiles.newInputStream(file))) { in =>
                     val buffer    = new Array[Byte](1024)
                     var bytesRead = in.read(buffer)
                     while bytesRead != -1 do

oni/src/main/scala/org/mbari/oni/etc/jdk/Instants.scala

@@ -22,6 +22,16 @@ object Instants:
     val CompactTimeFormatterNs: DateTimeFormatter =
         DateTimeFormatter.ofPattern("yyyyMMdd'T'HHmmss.SSSSSSX").withZone(utcZone)
 
+    /**
+     * Parse a string into an Instant. The string can be in any of the following formats:
+     *   - yyyyMMdd'T'HHmmssX
+     *   - yyyyMMdd'T'HHmmss.SSSX
+     *   - yyyyMMdd'T'HHmmss.SSSSSSX
+     *   - yyyy-MM-dd'T'HH:mm:ssX
+     *
+     * @param s
+     * @return
+     */
     def parseIso8601(s: String): Either[Throwable, Instant] =
         val tried = Try(Instant.from(CompactTimeFormatter.parse(s))) orElse
             Try(Instant.from(TimeFormatter.parse(s))) orElse

oni/src/main/scala/org/mbari/oni/etc/jdk/JdbcTypes.scala

@@ -20,11 +20,11 @@ object JdbcTypes:
      * the JdbcRepository and associatited SQL classes.
      */
     extension (obj: Object)
-        def asDouble: Option[Double]   = doubleConverter(obj)
-        def asFloat: Option[Float]     = floatConverter(obj)
+        def asDouble: Option[Double]   = Numbers.doubleConverter(obj)
+        def asFloat: Option[Float]     = Numbers.floatConverter(obj)
         def asInstant: Option[Instant] = instantConverter(obj)
-        def asInt: Option[Int]         = intConverter(obj)
-        def asLong: Option[Long]       = longConverter(obj)
+        def asInt: Option[Int]         = Numbers.intConverter(obj)
+        def asLong: Option[Long]       = Numbers.longConverter(obj)
         def asString: Option[String]   = stringConverter(obj)
         def asUrl: Option[URL]         = urlConverter(obj)
         def asUUID: Option[UUID]       = uuidConverter(obj)
@@ -42,41 +42,14 @@ object JdbcTypes:
             case null      => None
             case u: UUID   => Some(u)
             case s: String => Try(UUID.fromString(s)).toOption // TODO this could swallow errors
+            case _         => None
 
     def stringConverter(obj: Object): Option[String] =
         obj match
             case null      => None
             case s: String => Some(s)
             case _         => Some(obj.toString)
 
-    def doubleConverter(obj: Object): Option[Double] =
-        obj match
-            case null      => None
-            case n: Number => Some(n.doubleValue())
-            case s: String => Try(s.toDouble).toOption
-            case _         => None
-
-    def floatConverter(obj: Object): Option[Float] =
-        obj match
-            case null      => None
-            case n: Number => Some(n.floatValue())
-            case s: String => Try(s.toFloat).toOption
-            case _         => None
-
-    def longConverter(obj: Object): Option[Long] =
-        obj match
-            case null      => None
-            case n: Number => Some(n.longValue())
-            case s: String => Try(s.toLong).toOption
-            case _         => None
-
-    def intConverter(obj: Object): Option[Int] =
-        obj match
-            case null      => None
-            case n: Number => Some(n.intValue())
-            case s: String => Try(s.toInt).toOption
-            case _         => None
-
     def urlConverter(obj: Object): Option[URL] =
         obj match
             case null      => None

oni/src/main/scala/org/mbari/oni/etc/jdk/Loggers.scala

@@ -13,15 +13,16 @@ import java.util.function.Supplier
 
 /**
  * Add fluent logging to System.Logger. Usage:
- * {{{
- * import org.fathomnet.support.etc.jdk.Logging.{given, *}
- * given log: Logger = Sytem.getLogger("my.logger")
+ * 
+ * ```scala
+ * import org.fathomnet.support.etc.jdk.Loggers.{given, *}
+ * given log: Logger = System.getLogger("my.logger")
  *
  * log.atInfo.log("Hello World")
  * log.atInfo.withCause(new RuntimeException("Oops")).log("Hello World")
  *
  * 3.tapLog.atInfo.log(i => s"Hello World $i")
- * }}}
+ * ```
  * * @author Brian Schlining
  */
 object Loggers:

oni/src/main/scala/org/mbari/oni/jdbc/sql.scala

@@ -12,73 +12,20 @@ import java.util.UUID
 import scala.util.Try
 import java.net.URL
 import java.net.URI
+import org.mbari.oni.etc.jdk.Numbers
+import org.mbari.oni.etc.jdk.JdbcTypes
 
 /**
  * This is a collection of explicit conversions to convert from java.sql.ResultSet to various types. This is used in the
  * JdbcRepository and associatited SQL classes.
  */
 extension (obj: Object)
-    def asDouble: Option[Double]   = doubleConverter(obj)
-    def asFloat: Option[Float]     = floatConverter(obj)
-    def asInstant: Option[Instant] = instantConverter(obj)
-    def asInt: Option[Int]         = intConverter(obj)
-    def asLong: Option[Long]       = longConverter(obj)
-    def asString: Option[String]   = stringConverter(obj)
-    def asUrl: Option[URL]         = urlConverter(obj)
-    def asUUID: Option[UUID]       = uuidConverter(obj)
+    def asDouble: Option[Double]   = Numbers.doubleConverter(obj)
+    def asFloat: Option[Float]     = Numbers.floatConverter(obj)
+    def asInstant: Option[Instant] = JdbcTypes.instantConverter(obj)
+    def asInt: Option[Int]         = Numbers.intConverter(obj)
+    def asLong: Option[Long]       = Numbers.longConverter(obj)
+    def asString: Option[String]   = JdbcTypes.stringConverter(obj)
+    def asUrl: Option[URL]         = JdbcTypes.urlConverter(obj)
+    def asUUID: Option[UUID]       = JdbcTypes.uuidConverter(obj)
 
-def instantConverter(obj: Object): Option[Instant] =
-    obj match
-        case null                            => None
-        case i: Instant                      => Some(i)
-        case ts: java.sql.Timestamp          => Some(ts.toInstant)
-        case m: microsoft.sql.DateTimeOffset => Some(m.getOffsetDateTime().toInstant())
-        case _                               => None // TODO handle postgres
-
-def uuidConverter(obj: Object): Option[UUID] =
-    obj match
-        case null      => None
-        case u: UUID   => Some(u)
-        case s: String => Try(UUID.fromString(s)).toOption // TODO this could swallow errors
-
-def stringConverter(obj: Object): Option[String] =
-    obj match
-        case null      => None
-        case s: String => Some(s)
-        case _         => Some(obj.toString)
-
-def doubleConverter(obj: Object): Option[Double] =
-    obj match
-        case null      => None
-        case n: Number => Some(n.doubleValue())
-        case s: String => Try(s.toDouble).toOption
-        case _         => None
-
-def floatConverter(obj: Object): Option[Float] =
-    obj match
-        case null      => None
-        case n: Number => Some(n.floatValue())
-        case s: String => Try(s.toFloat).toOption
-        case _         => None
-
-def longConverter(obj: Object): Option[Long] =
-    obj match
-        case null      => None
-        case n: Number => Some(n.longValue())
-        case s: String => Try(s.toLong).toOption
-        case _         => None
-
-def intConverter(obj: Object): Option[Int] =
-    obj match
-        case null      => None
-        case n: Number => Some(n.intValue())
-        case s: String => Try(s.toInt).toOption
-        case _         => None
-
-def urlConverter(obj: Object): Option[URL] =
-    obj match
-        case null      => None
-        case u: URL    => Some(u)
-        case uri: URI  => Try(uri.toURL()).toOption
-        case s: String => Try(URI.create(s).toURL()).toOption
-        case _         => None