jvm 22

VEuPathDB · Apr 26, 2024 · 570f956 · 570f956
1 parent dfba113
commit 570f956
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Showing 6 changed files with 48 additions and 8 deletions.
diff --git a/build.gradle.kts b/build.gradle.kts
@@ -1,6 +1,3 @@
-import kotlinx.coroutines.Dispatchers
-import kotlinx.coroutines.launch
-import kotlinx.coroutines.runBlocking
 import org.gradle.api.tasks.testing.logging.TestExceptionFormat
 import org.gradle.api.tasks.testing.logging.TestLogEvent
 import org.jetbrains.kotlin.gradle.tasks.KotlinCompile
@@ -34,13 +31,13 @@ allprojects {
 
   tasks.withType<KotlinCompile> {
     compilerOptions {
-      jvmTarget.set(org.jetbrains.kotlin.gradle.dsl.JvmTarget.JVM_18)
+      jvmTarget.set(org.jetbrains.kotlin.gradle.dsl.JvmTarget.JVM_21)
     }
   }
 
   tasks.withType<JavaCompile> {
-    sourceCompatibility = "18"
-    targetCompatibility = "18"
+    sourceCompatibility = "21"
+    targetCompatibility = "21"
   }
 
   tasks.withType<Test> {

diff --git a/buildSrc/build.gradle.kts b/buildSrc/build.gradle.kts
@@ -1,3 +1,5 @@
+import org.jetbrains.kotlin.gradle.tasks.KotlinCompile
+
 plugins {
   kotlin("jvm") version "1.9.23"
 }
@@ -6,6 +8,10 @@ repositories {
   mavenCentral()
 }
 
+tasks.withType<KotlinCompile> {
+  compilerOptions { jvmTarget.set(org.jetbrains.kotlin.gradle.dsl.JvmTarget.JVM_21) }
+}
+
 dependencies {
   implementation("org.jetbrains.kotlinx:kotlinx-coroutines-core:1.8.0")
 }
diff --git a/lib/cache-db/src/main/kotlin/vdi/component/db/cache/model/AdminAllDatasetsRow.kt b/lib/cache-db/src/main/kotlin/vdi/component/db/cache/model/AdminAllDatasetsRow.kt
@@ -3,6 +3,7 @@ package vdi.component.db.cache.model
 import org.veupathdb.vdi.lib.common.field.DatasetID
 import org.veupathdb.vdi.lib.common.field.ProjectID
 import org.veupathdb.vdi.lib.common.field.UserID
+import org.veupathdb.vdi.lib.common.model.VDIDatasetFileInfo
 import org.veupathdb.vdi.lib.common.model.VDIDatasetVisibility
 import java.time.OffsetDateTime
 
@@ -23,4 +24,6 @@ data class AdminAllDatasetsRow(
   override val importStatus: DatasetImportStatus,
   val importMessage: String?,
   override val inserted: OffsetDateTime,
+  val uploadFiles: List<VDIDatasetFileInfo>,
+  val installFiles: List<VDIDatasetFileInfo>,
 ) : Dataset, DatasetMeta
diff --git a/lib/cache-db/src/main/kotlin/vdi/component/db/cache/sql/select/select-admin-all-datasets.kt b/lib/cache-db/src/main/kotlin/vdi/component/db/cache/sql/select/select-admin-all-datasets.kt
@@ -32,6 +32,16 @@ SELECT
   ) AS projects
 , i.status
 , s.message
+, array(
+    SELECT array[f.file_name, f.file_size]
+    FROM vdi.upload_files AS f
+    WHERE f.dataset_id = d.dataset_id
+  ) AS upload_files
+, array(
+    SELECT array[f.file_name, f.file_size]
+    FROM vdi.install_files AS f
+    WHERE f.dataset_id = d.dataset_id
+  ) AS install_files
 FROM
   vdi.datasets AS d
   INNER JOIN vdi.dataset_metadata AS m
@@ -121,6 +131,8 @@ internal fun Connection.selectAdminAllDatasets(query: AdminAllDatasetsQuery): Li
           importStatus  = it.getString("status")?.let(DatasetImportStatus::fromString) ?: DatasetImportStatus.Queued,
           importMessage = it.getString("message"),
           inserted      = it.getDateTime("inserted"),
+          uploadFiles   = it.getFileDetailList("upload_files"),
+          installFiles  = it.getFileDetailList("install_files"),
         )
       }
     }

diff --git a/lib/cache-db/src/main/kotlin/vdi/component/db/cache/util/jdbc.kt b/lib/cache-db/src/main/kotlin/vdi/component/db/cache/util/jdbc.kt
@@ -3,6 +3,8 @@ package vdi.component.db.cache.util
 import org.veupathdb.vdi.lib.common.field.DatasetID
 import org.veupathdb.vdi.lib.common.field.ProjectID
 import org.veupathdb.vdi.lib.common.field.UserID
+import org.veupathdb.vdi.lib.common.model.VDIDatasetFileInfo
+import org.veupathdb.vdi.lib.common.model.VDIDatasetFileInfoImpl
 import java.sql.Connection
 import java.sql.PreparedStatement
 import java.sql.ResultSet
@@ -75,6 +77,23 @@ internal inline fun ResultSet.getUserID(column: String) = UserID(getString(colum
 @Suppress("NOTHING_TO_INLINE")
 internal inline fun ResultSet.getDateTime(column: String) = getObject(column, OffsetDateTime::class.java)
 
+/**
+ * Parses a postgres array containing 2-value sub-arrays that contain a file
+ * name and file size.
+ *
+ * Expected format:
+ * ```json
+ * [
+ *   ["some_file.txt", 12345],
+ *   ["other_file.tsv", 34244]
+ * ]
+ * ```
+ */
+@Suppress("NOTHING_TO_INLINE")
+internal inline fun ResultSet.getFileDetailList(column: String): List<VDIDatasetFileInfo> =
+  arrayMap(column) { it.getArray(2).resultSet.map { VDIDatasetFileInfoImpl(it.getString(2), it.getLong(3)) } }
+    .reduce { a, b -> (a as MutableList).addAll(b); a }
+
 /**
  * Iterates over the results in the result set, calling the given function on
  * each row in the [ResultSet].
@@ -105,4 +124,7 @@ internal inline fun ResultSet.forEach(fn: (rs: ResultSet) -> Unit) {
 internal inline fun <T> ResultSet.map(fn: (rs: ResultSet) -> T): List<T> =
   with(ArrayList<T>(16)) { this@map.forEach { add(fn(it)) }; this }
 
+internal inline fun <T> ResultSet.arrayMap(column: String, fn: (rs: ResultSet) -> T): List<T> =
+  with(ArrayList<T>(16)) { this@arrayMap.forEach { getArray(column).resultSet.forEach { add(fn(it)) } }; this }
+
 // endregion ResultSet
diff --git a/...rest-service/src/main/kotlin/org/veupathdb/service/vdi/service/admin/list-all-datasets.kt b/...rest-service/src/main/kotlin/org/veupathdb/service/vdi/service/admin/list-all-datasets.kt
@@ -27,7 +27,7 @@ internal fun listAllDatasets(
     includeDeleted ?: false,
   )
 
-  val totalCount = vdi.component.db.cache.CacheDB().selectAdminAllDatasetCount(query)
+  val totalCount = CacheDB().selectAdminAllDatasetCount(query)
 
   if (totalCount == 0u) {
     return AllDatasetsListResponse(
@@ -36,7 +36,7 @@ internal fun listAllDatasets(
     )
   }
 
-  val cacheDBResults = vdi.component.db.cache.CacheDB().selectAdminAllDatasets(query)
+  val cacheDBResults = CacheDB().selectAdminAllDatasets(query)
   val appDBResults = getAppDBStatuses(cacheDBResults)
 
   return AllDatasetsListResponse(