Fixed rank issue

mbari-org · May 13, 2024 · 8092a25 · 8092a25
1 parent fab3c8e
commit 8092a25
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Showing 3 changed files with 28 additions and 10 deletions.
diff --git a/oni/src/main/scala/org/mbari/oni/jdbc/MutableConcept.scala b/oni/src/main/scala/org/mbari/oni/jdbc/MutableConcept.scala
@@ -104,8 +104,11 @@ object MutableConcept {
                 }
             })
 
+            if (concept.rank.isEmpty && row.rank.isDefined) {
+                concept.rank = row.rank
+            }
+
             val cn = CName(row.name, row.nameType)
-            concept.rank = row.rank
             concept.names = concept.names :+ cn
 
         }

diff --git a/oni/src/test/scala/org/mbari/oni/jdbc/MutableConceptSuite.scala b/oni/src/test/scala/org/mbari/oni/jdbc/MutableConceptSuite.scala
@@ -1,3 +1,10 @@
+/*
+ * Copyright (c) Monterey Bay Aquarium Research Institute 2024
+ *
+ * oni code is non-public software. Unauthorized copying of this file,
+ * via any medium is strictly prohibited. Proprietary and confidential. 
+ */
+
 package org.mbari.oni.jdbc
 
 import org.mbari.oni.domain.ConceptNameTypes
@@ -18,7 +25,7 @@ class MutableConceptSuite extends munit.FunSuite {
                 `- 7 - child7
     */
     val rows = Seq(
-        ConceptRow(1, None, "root"),
+        ConceptRow(1, None, "root", rankLevel = Some("super"), rankName = Some("family")),
         ConceptRow(1, None, "object", nameType = ConceptNameTypes.ALTERNATE.getType),
         ConceptRow(2, Some(1), "child2"),
         ConceptRow(3, Some(1), "child3"),
@@ -28,22 +35,29 @@ class MutableConceptSuite extends munit.FunSuite {
         ConceptRow(7, Some(3), "child7"),
         ConceptRow(8, Some(4), "child8"),
         ConceptRow(9, Some(4), "child9"),
-        ConceptRow(10, Some(9), "child10")
+        ConceptRow(10, Some(9), "child10", nameType = ConceptNameTypes.PRIMARY.getType),
+        ConceptRow(10, Some(9), "child10a", nameType = ConceptNameTypes.ALTERNATE.getType),
+        ConceptRow(10, Some(9), "child10s", nameType = ConceptNameTypes.SYNONYM.getType, rankLevel = Some("sub"), rankName = Some("species")),
+        ConceptRow(10, Some(9), "child10c", nameType = ConceptNameTypes.COMMON.getType),
+        ConceptRow(10, Some(9), "child10f", nameType = ConceptNameTypes.FORMER.getType)
     )
 
+    val (rootOpt, nodes) = MutableConcept.toTree(rows)
+
+
+
     test("toTree") {
-        val (rootOpt, nodes) = MutableConcept.toTree(rows)
         assert(rootOpt.isDefined)
         val root = rootOpt.get
         assertEquals(root.id.get, 1L)
         assertEquals(root.children.size, 2)
         assertEquals(nodes.size, 10)
         assertEquals(root.primaryName, Some("root"))
         assertEquals(root.names.map(_.name).sorted, Seq("object", "root"))
+        assertEquals(root.rank, Some("superfamily"))
     }
 
     test("root") {
-        val (rootOpt, nodes) = MutableConcept.toTree(rows)
         val root = rootOpt.get
         val child2 = root.children.head
         val child4 = child2.children.head
@@ -61,7 +75,6 @@ class MutableConceptSuite extends munit.FunSuite {
     }
 
     test("copyUp") {
-        val (rootOpt, nodes) = MutableConcept.toTree(rows)
         val child9 = nodes.find(_.id.get == 9).get
         val child9Copy = child9.copyUp()
         assertEquals(child9Copy.id, child9.id)
@@ -73,15 +86,16 @@ class MutableConceptSuite extends munit.FunSuite {
     }
 
     test("toImmutable") {
-        val (rootOpt, nodes) = MutableConcept.toTree(rows)
         val root = rootOpt.get
         val concept = root.toImmutable
         assertEquals(concept.name, "root")
-        assertEquals(concept.rank, None)
+        assertEquals(concept.rank, Some("superfamily"))
         assertEquals(concept.alternativeNames, Seq("object"))
         assertEquals(concept.children.size, 2)
         assertEquals(concept.children.head.name, "child2")
         assertEquals(concept.children(1).name, "child3")
+        assertEquals(concept.descendants.size, 10)
+        assertEquals(concept.descendantNames.size, 15)
     }
 
 }
diff --git a/project/Dependencies.scala b/project/Dependencies.scala
@@ -28,7 +28,7 @@ object Dependencies {
     lazy val scilube     = "org.mbari.scilube"      %% "scilube"                    % "3.0.1"
     lazy val slf4jSystem = "org.slf4j"               % "slf4j-jdk-platform-logging" % "2.0.13"
 
-    private val tapirVersion = "1.10.6"
+    private val tapirVersion = "1.10.7"
     lazy val tapirCirce      = "com.softwaremill.sttp.tapir" %% "tapir-json-circe"         % tapirVersion
     lazy val tapirHelidon    = "com.softwaremill.sttp.tapir" %% "tapir-nima-server"        % tapirVersion
     lazy val tapirPrometheus = "com.softwaremill.sttp.tapir" %% "tapir-prometheus-metrics" % tapirVersion
@@ -37,7 +37,8 @@ object Dependencies {
     lazy val tapirVertex     = "com.softwaremill.sttp.tapir" %% "tapir-vertx-server"       % tapirVersion
 
     lazy val tapirSttpCirce          = "com.softwaremill.sttp.client3" %% "circe"          % "3.9.6"
-    val testcontainersVersion        = "1.19.7"
+
+    val testcontainersVersion        = "1.19.8"
     lazy val testcontainersCore      = "org.testcontainers"             % "testcontainers" % testcontainersVersion
     lazy val testcontainersJdbc      = "org.testcontainers"             % "jdbc"           % testcontainersVersion
     lazy val testcontainersSqlserver = "org.testcontainers"             % "mssqlserver"    % testcontainersVersion