check point

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

@@ -73,6 +73,7 @@ object AppConfig {
         user = Config.getString("database.user"),
         password = Config.getString("database.password"),
         driver = Config.getString("database.driver"),
+        queryView = Config.getString("database.query.view")
     )
 }
 
@@ -87,7 +88,8 @@ case class DatabaseConfig(
     url: String,
     user: String,
     password: String,
-    driver: String
+    driver: String,
+    queryView: String
 ):
     def newConnection(): java.sql.Connection =
         Class.forName(driver)

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

@@ -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

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

@@ -63,7 +63,8 @@ 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/controllers/AnnotationController.scala

@@ -249,7 +249,7 @@ class AnnotationController(
 
     def create(annotation: Annotation)(using ec: ExecutionContext): Future[Seq[Annotation]] =
         val entity = annotation.toEntity
-        val dao = daoFactory.newImagedMomentDAO()
+        val dao    = daoFactory.newImagedMomentDAO()
         val future = dao.runTransaction(d => {
 //            d.create(entity)
 //            Annotation.fromImagedMoment(entity, true)
@@ -259,7 +259,6 @@ class AnnotationController(
         future.onComplete(_ => dao.close())
         future
 
-
     /** Bulk create annotations
       * @param annotations
       *   THe annotations to create

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

@@ -0,0 +1,42 @@
+/*
+ * Copyright 2017 Monterey Bay Aquarium Research Institute
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.mbari.annosaurus.controllers
+
+import org.mbari.annosaurus.DatabaseConfig
+import org.mbari.annosaurus.domain.QueryRequest
+import org.mbari.annosaurus.repository.query.{
+    Constraint,
+    Constraints,
+    JDBC,
+    QueryResults,
+    QueryService
+}
+
+class QueryController(databaseConfig: DatabaseConfig, viewName: String) {
+
+    private lazy val queryService = new QueryService(databaseConfig, viewName)
+
+    def count(constraints: Constraints): Either[Throwable, Int] =
+        queryService.count(constraints)
+
+    def query(queryRequest: QueryRequest): Either[Throwable, QueryResults] =
+        queryService.query(queryRequest.querySelects, queryRequest.constraints)
+
+    def listColumns(): Either[Throwable, Seq[JDBC.Metadata]] =
+        queryService.jdbc.listColumnsMetadata(viewName)
+
+}

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

@@ -18,14 +18,18 @@ package org.mbari.annosaurus.domain
 
 import java.util.UUID
 
-/**
- * Update multiple observations at once
- * @param observationUuids The UUIDs of the observations to update
- * @param concept The new concept
- * @param observer The new observer
- * @param activity The new activity
- * @param group The new group
- */
+/** Update multiple observations at once
+  * @param observationUuids
+  *   The UUIDs of the observations to update
+  * @param concept
+  *   The new concept
+  * @param observer
+  *   The new observer
+  * @param activity
+  *   The new activity
+  * @param group
+  *   The new group
+  */
 case class ObservationsUpdate(
     observationUuids: Seq[UUID],
     concept: Option[String] = None,

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

@@ -0,0 +1,24 @@
+/*
+ * Copyright 2017 Monterey Bay Aquarium Research Institute
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.mbari.annosaurus.domain
+
+import org.mbari.annosaurus.repository.query.Constraints
+
+case class QueryRequest(
+    querySelects: Seq[String],
+    constraints: Constraints
+)

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

@@ -24,6 +24,7 @@ import org.mbari.annosaurus.etc.circe.CirceCodecs
 import org.mbari.annosaurus.etc.circe.CirceCodecs.{*, given}
 import org.mbari.annosaurus.etc.jwt.JwtService
 import org.mbari.annosaurus.etc.jdk.Logging.given
+import org.mbari.annosaurus.repository.query.{Constraint, Constraints}
 
 import scala.concurrent.ExecutionContext
 import scala.concurrent.Future
@@ -118,6 +119,19 @@ trait Endpoints:
     implicit lazy val sURL: Schema[URL]                                                 = Schema.string
     implicit lazy val sInstant: Schema[Instant]                                         = Schema.string
     implicit lazy val sBulkAnnotationSc: Schema[BulkAnnotationSC]                       = Schema.derived[BulkAnnotationSC]
+    implicit lazy val sConstraintDate: Schema[Constraint.Date]                          = Schema.derived[Constraint.Date]
+    implicit lazy val sConstraintInString: Schema[Constraint.In[String]]                =
+        Schema.derived[Constraint.In[String]]
+    implicit lazy val sConstraintLike: Schema[Constraint.Like]                          = Schema.derived[Constraint.Like]
+    implicit lazy val sConstraintMax: Schema[Constraint.Max]                            = Schema.derived[Constraint.Max]
+    implicit lazy val sConstraintMin: Schema[Constraint.Min]                            = Schema.derived[Constraint.Min]
+    implicit lazy val sConstraintMinMax: Schema[Constraint.MinMax]                      =
+        Schema.derived[Constraint.MinMax]
+    implicit lazy val sConstraintIsNull: Schema[Constraint.IsNull]                      =
+        Schema.derived[Constraint.IsNull]
+    implicit lazy val sConstraint: Schema[Constraint]                                   = Schema.string
+    implicit lazy val sConstraints: Schema[Constraints]                                 = Schema.derived[Constraints]
+    implicit lazy val sQueryRequest: Schema[QueryRequest]                               = Schema.derived[QueryRequest]
 //    given Schema[Option[URL]]                              = Schema.string
 //    implicit lazy val sOptCAD: Schema[Option[CachedAncillaryDatumSC]]                     = Schema.derived[Option[CachedAncillaryDatumSC]]
 //    implicit lazy val sOptDouble: Schema[Option[Double]]                                 = Schema.derived[Option[Double]]
@@ -139,6 +153,15 @@ trait Endpoints:
                 log.atError.withCause(exception).log("Error")
                 Success(Left(ServerError(exception.getMessage)))
 
+    def handleEitherAsync[T](
+        f: => Either[Throwable, T]
+    )(using ec: ExecutionContext): Future[Either[ErrorMsg, T]] =
+        Future {
+            f match
+                case Right(value) => Right(value)
+                case Left(e)      => Left(ServerError(e.getMessage))
+        }
+
     def handleOption[T](f: Future[Option[T]])(using
         ec: ExecutionContext
     ): Future[Either[ErrorMsg, T]] =

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

@@ -335,7 +335,9 @@ class FastAnnotationEndpoints(jdbcRepository: JdbcRepository)(using
             .in(paging)
             .out(jsonBody[Seq[UUID]])
             .name("findImageMomentUuidsByConcept")
-            .description("Find the UUIDS of image moments by concept. Only include image moments with images. Sorted by recorded timestamp.")
+            .description(
+                "Find the UUIDS of image moments by concept. Only include image moments with images. Sorted by recorded timestamp."
+            )
             .tag(tag)
 
     val findImagedMomentUuidsByConceptImpl: ServerEndpoint[Any, Future] =
@@ -363,7 +365,9 @@ class FastAnnotationEndpoints(jdbcRepository: JdbcRepository)(using
             .in(paging)
             .out(jsonBody[Seq[UUID]])
             .name("findImagedMomentUuidsByToConcept")
-            .description("Find image moment UUIDs by to concept. Only include image moments with images. Sorted by recorded timestamp.")
+            .description(
+                "Find image moment UUIDs by to concept. Only include image moments with images. Sorted by recorded timestamp."
+            )
             .tag(tag)
 
     val findImagedMomentUuidsByToConceptImpl: ServerEndpoint[Any, Future] =

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

@@ -59,7 +59,9 @@ class ImagedMomentEndpoints(controller: ImagedMomentController)(using
             .in(jsonBody[MoveImagedMoments])
             .out(jsonBody[Count])
             .name("bulkMove")
-            .description("Bulk move imaged moments to a new video reference. JSON request can be camelCase or snake_case")
+            .description(
+                "Bulk move imaged moments to a new video reference. JSON request can be camelCase or snake_case"
+            )
             .tag(tag)
 
     val bulkMoveImpl: ServerEndpoint[Any, Future] =

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

@@ -17,7 +17,17 @@
 package org.mbari.annosaurus.endpoints
 
 import org.mbari.annosaurus.controllers.ObservationController
-import org.mbari.annosaurus.domain.{ConceptCount, Count, CountForVideoReferenceSC, ErrorMsg, ObservationSC, ObservationUpdateSC, ObservationsUpdate, RenameConcept, RenameCountSC}
+import org.mbari.annosaurus.domain.{
+    ConceptCount,
+    Count,
+    CountForVideoReferenceSC,
+    ErrorMsg,
+    ObservationSC,
+    ObservationUpdateSC,
+    ObservationsUpdate,
+    RenameConcept,
+    RenameCountSC
+}
 import org.mbari.annosaurus.etc.jwt.JwtService
 import org.mbari.annosaurus.etc.tapir.TapirCodecs.given
 import sttp.tapir.*
@@ -320,7 +330,11 @@ class ObservationEndpoints(controller: ObservationController, jdbcRepository: Jd
         secureEndpoint
             .put
             .in(base / "bulk")
-            .in(jsonBody[ObservationsUpdate].description("Describes the parameters and uuids of the observations to update. Can be camelCase or snake_case."))
+            .in(
+                jsonBody[ObservationsUpdate].description(
+                    "Describes the parameters and uuids of the observations to update. Can be camelCase or snake_case."
+                )
+            )
             .out(jsonBody[Count].description("The number of observations updated"))
             .name("updateManyObservations")
             .description(

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

@@ -0,0 +1,78 @@
+/*
+ * Copyright 2017 Monterey Bay Aquarium Research Institute
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.mbari.annosaurus.endpoints
+
+import CustomTapirJsonCirce.*
+import org.mbari.annosaurus.controllers.QueryController
+import org.mbari.annosaurus.domain.{ErrorMsg, QueryRequest}
+import org.mbari.annosaurus.etc.circe.CirceCodecs.{*, given}
+import org.mbari.annosaurus.etc.tapir.TapirCodecs.given
+import org.mbari.annosaurus.repository.query.{JDBC, QueryResults}
+import sttp.model.StatusCode
+import sttp.tapir.*
+import sttp.tapir.generic.auto.*
+import sttp.tapir.server.ServerEndpoint
+import sttp.tapir.server.ServerEndpoint.Full
+
+import scala.util.Success
+import scala.concurrent.{ExecutionContext, Future}
+
+class QueryEndpoints(queryController: QueryController)(using executionContext: ExecutionContext)
+    extends Endpoints {
+
+    private val base = "query"
+    private val tag  = "Query"
+
+    val listColumns: Endpoint[Unit, Unit, ErrorMsg, Seq[JDBC.Metadata], Any] = openEndpoint
+        .get
+        .in(base / "columns")
+        .out(jsonBody[Seq[JDBC.Metadata]])
+        .name("listQueryColumns")
+        .description("List columns in the query view")
+        .tag(tag)
+
+    val listColumnsImpl: Full[Unit, Unit, Unit, ErrorMsg, Seq[JDBC.Metadata], Any, Future] =
+        listColumns.serverLogic(_ => handleEitherAsync(queryController.listColumns()))
+
+    val runQuery: Endpoint[Unit, QueryRequest, ErrorMsg, String, Any] =
+        openEndpoint
+            .post
+            .in(base / "run")
+            .in(jsonBody[QueryRequest])
+            .out(stringBody)
+            .out(header("Content-Type", "text/tab-separated-values"))
+            .name("runQuery")
+            .description("Run a query")
+            .tag(tag)
+
+    val runQueryImpl =
+        runQuery.serverLogic(request =>
+            handleEitherAsync(
+                queryController.query(request).map(QueryResults.toTsv).map(_.mkString("\n"))
+            )
+        )
+
+    override def all: List[Endpoint[_, _, _, _, _]] = List(
+        listColumns,
+        runQuery
+    )
+
+    override def allImpl: List[ServerEndpoint[Any, Future]] = List(
+        listColumnsImpl,
+        runQueryImpl
+    )
+}