Merge pull request #44 from mbari-org/feature/query

Feature/query

.scalafix.conf

@@ -0,0 +1,9 @@
+rules = [
+    OrganizeImports
+]
+OrganizeImports {
+    expandRelative = true
+    groupedImports = Merge
+}
+OrganizeImports.targetDialect = Scala3
+OrganizeImports.removeUnused = true

.scalafmt.conf

@@ -1,14 +1,25 @@
-version = "3.7.14"
+version = "3.8.0"
+runner.dialect = scala3
+
 align.preset = most
+docstrings.style = Asterisk
 includeNoParensInSelectChains = true
 indent.main = 4
 indent.callSite = 4
-maxColumn = 100
+# Recommended, to not penalize `match` statements
+# indent.matchSite = 0
+maxColumn = 120
 newlines.alwaysBeforeElseAfterCurlyIf = true
+
 rewrite.rules = [
   PreferCurlyFors,
-  RedundantParens, 
+  RedundantParens,
   SortModifiers,
-  SortImports
+  Imports
 ]
-runner.dialect = scala3
+
+rewrite.imports.expand = false
+rewrite.imports.sort = original
+rewrite.scala3.convertToNewSyntax = true
+# rewrite.scala3.insertEndMarkerMinLines = 5
+rewrite.scala3.removeOptionalBraces = yes

annosaurus/src/main/resources/reference.conf

@@ -48,6 +48,9 @@ database {
   url = ${?DATABASE_URL}
   user = "sa"
   user = ${?DATABASE_USER}
+
+  query.view = ${?DATABASE_QUERY_VIEW}
+  query.view = "annotations"
   # name = "Derby"
   # name = ${?DATABASE_NAME}
   # https://docs.jboss.org/hibernate/orm/4.3/manual/en-US/html_single/#configuration-optional-dialects

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

@@ -17,23 +17,22 @@
 package org.mbari.annosaurus
 
 import com.typesafe.config.ConfigFactory
-import org.mbari.annosaurus.etc.jdk.Logging
-import org.mbari.annosaurus.etc.jdk.Logging.{*, given}
+import org.mbari.annosaurus.etc.jdk.Loggers
+import org.mbari.annosaurus.etc.jdk.Loggers.{*, given}
 import org.mbari.annosaurus.etc.jwt.JwtService
 
 import scala.util.Try
 import scala.util.control.NonFatal
 
-object AppConfig {
+object AppConfig:
 
-    private val log = Logging(getClass)
+    private val log = Loggers(getClass)
 
     val Name: String = "annosaurus"
 
-    val Version: String = {
+    val Version: String =
         val v = Try(getClass.getPackage.getImplementationVersion).getOrElse("0.0.0")
-        if (v == null) "0.0.0" else v
-    }
+        if v == null then "0.0.0" else v
 
     val Description: String = "Annotation Service"
 
@@ -56,22 +55,47 @@ object AppConfig {
     )
 
     lazy val DefaultZeroMQConfig: Option[ZeroMQConfig] =
-        try {
+        try
             val port   = Config.getInt("messaging.zeromq.port")
             val enable = Config.getBoolean("messaging.zeromq.enable")
             val topic  = Config.getString("messaging.zeromq.topic")
             Some(ZeroMQConfig(port, enable, topic))
-        }
-        catch {
+        catch
             case NonFatal(e) =>
                 log.atWarn.withCause(e).log("Failed to load ZeroMQ configuration")
                 None
-        }
-}
+
+    lazy val DefaultDatabaseConfig: DatabaseConfig = DatabaseConfig(
+        url = Config.getString("database.url"),
+        user = Config.getString("database.user"),
+        password = Config.getString("database.password"),
+        driver = Config.getString("database.driver"),
+        queryView = Config.getString("database.query.view")
+    )
 
 case class HttpConfig(
     port: Int,
     stopTimeout: Int,
     connectorIdleTimeout: Int,
     contextPath: String
 )
+
+case class DatabaseConfig(
+    url: String,
+    user: String,
+    password: String,
+    driver: String,
+    queryView: String
+):
+    lazy val dataSource                      =
+        val ds = new com.zaxxer.hikari.HikariDataSource()
+        ds.setJdbcUrl(url)
+        ds.setUsername(user)
+        ds.setPassword(password)
+        ds.setDriverClassName(driver)
+        ds.setMaximumPoolSize(AppConfig.NumberOfVertxWorkers)
+        ds
+    def newConnection(): java.sql.Connection =
+        dataSource.getConnection()
+        // Class.forName(driver)
+        // java.sql.DriverManager.getConnection(url, user, password)

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

@@ -27,7 +27,7 @@ import sttp.tapir.swagger.bundle.SwaggerInterpreter
 
 import scala.concurrent.{ExecutionContext, Future}
 
-object Endpoints {
+object Endpoints:
 
     // --------------------------------
     given ExecutionContext = ExecutionContext.global
@@ -44,6 +44,10 @@ object Endpoints {
     val imageReferenceController           = new ImageReferenceController(daoFactory)
     val indexController                    = new IndexController(daoFactory)
     val observationController              = new ObservationController(daoFactory)
+    val queryController                    = new QueryController(
+        AppConfig.DefaultDatabaseConfig,
+        AppConfig.DefaultDatabaseConfig.queryView
+    )
 
     // --------------------------------
     val analysisRepository = new AnalysisRepository(daoFactory.entityManagerFactory)
@@ -67,6 +71,7 @@ object Endpoints {
     val imageReferenceEndpoints           = new ImageReferenceEndpoints(imageReferenceController)
     val indexEndpoints                    = new IndexEndpoints(indexController)
     val observationEndpoints              = new ObservationEndpoints(observationController, jdbcRepository)
+    val queryEndpoints                    = new QueryEndpoints(queryController)
 
     // --------------------------------
     // For VertX, we need to separate the non-blocking endpoints from the blocking ones
@@ -86,7 +91,8 @@ object Endpoints {
         imageEndpoints.allImpl,
         imageReferenceEndpoints.allImpl,
         indexEndpoints.allImpl,
-        observationEndpoints.allImpl
+        observationEndpoints.allImpl,
+        queryEndpoints.allImpl
     ).flatten
 
     val apiEndpoints = nonBlockingEndpoints ++ blockingEndpoints
@@ -113,5 +119,3 @@ object Endpoints {
 
     val all: List[ServerEndpoint[Any, Future]] =
         apiEndpoints ++ docEndpoints ++ List(metricsEndpoint)
-
-}

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

@@ -18,21 +18,20 @@ package org.mbari.annosaurus
 
 import io.vertx.core.{Vertx, VertxOptions}
 import io.vertx.ext.web.Router
-import org.mbari.annosaurus.etc.jdk.Logging
-import org.mbari.annosaurus.etc.jdk.Logging.{*, given}
+import org.mbari.annosaurus.etc.jdk.Loggers
+import org.mbari.annosaurus.etc.jdk.Loggers.given
 import org.mbari.annosaurus.etc.zeromq.ZeroMQPublisher
-import sttp.tapir.server.vertx.{VertxFutureServerInterpreter, VertxFutureServerOptions}
 import sttp.tapir.server.vertx.VertxFutureServerInterpreter.VertxFutureToScalaFuture
+import sttp.tapir.server.vertx.{VertxFutureServerInterpreter, VertxFutureServerOptions}
 
-import scala.concurrent.{Await, ExecutionContext, Future}
 import scala.concurrent.duration.Duration
-import scala.io.StdIn
+import scala.concurrent.{Await, ExecutionContext}
 
 object Main:
 
     // hold on to messaging objects so they don't get GC'd
     private val zmq = ZeroMQPublisher.autowire(AppConfig.DefaultZeroMQConfig)
-    private val log = Logging(this.getClass)
+    private val log = Loggers(this.getClass)
 
     def main(args: Array[String]): Unit =
 
@@ -63,7 +62,8 @@ object Main:
         val port = sys.env.get("HTTP_PORT").flatMap(_.toIntOption).getOrElse(8080)
         log.atInfo.log(s"Starting ${AppConfig.Name} v${AppConfig.Version} on port $port")
 
-        val vertx  = Vertx.vertx(new VertxOptions().setWorkerPoolSize(AppConfig.NumberOfVertxWorkers))
+        val vertx  =
+            Vertx.vertx(new VertxOptions().setWorkerPoolSize(AppConfig.NumberOfVertxWorkers))
 //        val vertx  = Vertx.vertx()
         val server = vertx.createHttpServer()
         val router = Router.router(vertx)

annosaurus/src/main/scala/org/mbari/annosaurus/PersistentObject.scala

@@ -18,15 +18,14 @@ package org.mbari.annosaurus
 
 import java.util.UUID
 
-/** We have made a design decision to always use UUIDs (aka GUIDs) as the primary key. This
-  * requirement is enforced so that external applications can rely on the use of that key. All
-  * persistent objects should implement this trait
-  *
-  * @author
-  *   Brian Schlining
-  * @since 2016-05-05T16:21:00
-  */
-trait PersistentObject {
+/**
+ * We have made a design decision to always use UUIDs (aka GUIDs) as the primary key. This requirement is enforced so
+ * that external applications can rely on the use of that key. All persistent objects should implement this trait
+ *
+ * @author
+ *   Brian Schlining
+ * @since 2016-05-05T16:21:00
+ */
+trait PersistentObject:
 
     def primaryKey: Option[UUID]
-}

annosaurus/src/main/scala/org/mbari/annosaurus/annosaurus.scala

@@ -16,8 +16,9 @@
 
 package org.mbari
 
-/** @author
-  *   Brian Schlining
-  * @since 2016-06-15T16:50:00
-  */
+/**
+ * @author
+ *   Brian Schlining
+ * @since 2016-06-15T16:50:00
+ */
 package object annosaurus {}