Merge pull request #372 from VEuPathDB/371-dependency-table

Add dataset_dependencies table queries for app db
VEuPathDB · Feb 10, 2025 · f45ae93 · f45ae93
2 parents ef016ec + 39d375b
commit f45ae93
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diff --git a/lib/app-db/src/main/kotlin/vdi/component/db/app/AppDBTransaction.kt b/lib/app-db/src/main/kotlin/vdi/component/db/app/AppDBTransaction.kt
@@ -101,6 +101,8 @@ interface AppDBTransaction : AppDBAccessor, AutoCloseable {
 
   fun deleteDatasetOrganisms(datasetID: DatasetID)
 
+  fun deleteDatasetDependencies(datasetID: DatasetID)
+
   /**
    * Deletes a specific visibility record for a target dataset and user.
    *
@@ -196,6 +198,8 @@ interface AppDBTransaction : AppDBAccessor, AutoCloseable {
 
   fun insertDatasetOrganisms(datasetID: DatasetID, organisms: Collection<String>)
 
+  fun insertDatasetDependencies(datasetID: DatasetID, dependencies: Collection<VDIDatasetDependency>)
+
   // endregion Insert Operations
 
   // region Update Operations

diff --git a/lib/app-db/src/main/kotlin/vdi/component/db/app/AppDBTransactionImpl.kt b/lib/app-db/src/main/kotlin/vdi/component/db/app/AppDBTransactionImpl.kt
@@ -94,6 +94,11 @@ class AppDBTransactionImpl(
     connection.deleteDatasetOrganisms(schema, datasetID)
   }
 
+  override fun deleteDatasetDependencies(datasetID: DatasetID) {
+    log.debug("deleting dataset dependency records for dataset {}", datasetID)
+    connection.deleteDatasetDependencies(schema, datasetID)
+  }
+
   override fun insertDataset(dataset: DatasetRecord) {
     log.debug("inserting dataset record for dataset {}", dataset.datasetID)
     connection.insertDataset(schema, dataset)
@@ -183,6 +188,11 @@ class AppDBTransactionImpl(
     connection.insertDatasetOrganisms(schema, datasetID, organisms)
   }
 
+  override fun insertDatasetDependencies(datasetID: DatasetID, dependencies: Collection<VDIDatasetDependency>) {
+    log.debug("inserting {} dependency records for dataset {}", dependencies.size, datasetID)
+    connection.insertDatasetDependencies(schema, datasetID, dependencies)
+  }
+
   override fun updateDataset(dataset: DatasetRecord) {
     log.debug("updating dataset record for dataset {}", dataset.datasetID)
     connection.updateDataset(schema, dataset)

diff --git a/lib/app-db/src/main/kotlin/vdi/component/db/app/sql/delete/delete-dataset-dependencies.kt b/lib/app-db/src/main/kotlin/vdi/component/db/app/sql/delete/delete-dataset-dependencies.kt
@@ -0,0 +1,17 @@
+package vdi.component.db.app.sql.delete
+
+import org.veupathdb.vdi.lib.common.field.DatasetID
+import vdi.component.db.app.sql.preparedUpdate
+import java.sql.Connection
+
+private fun sql(schema: String) =
+// language=oracle
+"""
+DELETE FROM
+  ${schema}.dataset_dependency
+WHERE
+  dataset_id = ?
+"""
+
+internal fun Connection.deleteDatasetDependencies(schema: String, datasetID: DatasetID) =
+  preparedUpdate(sql(schema)) { setString(1, datasetID.toString()) }
diff --git a/lib/app-db/src/main/kotlin/vdi/component/db/app/sql/insert/insert-dataset-dependencies.kt b/lib/app-db/src/main/kotlin/vdi/component/db/app/sql/insert/insert-dataset-dependencies.kt
@@ -0,0 +1,35 @@
+package vdi.component.db.app.sql.insert
+
+import org.veupathdb.vdi.lib.common.field.DatasetID
+import org.veupathdb.vdi.lib.common.model.VDIDatasetDependency
+import vdi.component.db.app.sql.preparedBatchUpdate
+import vdi.component.db.app.sql.setDatasetID
+import java.sql.Connection
+
+
+private fun sql(schema: String) =
+// language=oracle
+  """
+INSERT INTO
+  ${schema}.dataset_dependency (
+    dataset_id
+  , identifier
+  , display_name
+  , version
+  )
+VALUES
+  (?, ?, ?, ?)
+"""
+
+internal fun Connection.insertDatasetDependencies(
+  schema: String,
+  datasetID: DatasetID,
+  dependencies: Collection<VDIDatasetDependency>,
+) {
+  preparedBatchUpdate(sql(schema), dependencies) {
+    setDatasetID(1, datasetID)
+    setString(2, it.identifier)
+    setString(3, it.displayName)
+    setString(4, it.version)
+  }
+}
diff --git a/lib/pruner/src/main/kotlin/vdi/component/pruner/Pruner.kt b/lib/pruner/src/main/kotlin/vdi/component/pruner/Pruner.kt
@@ -207,6 +207,7 @@ object Pruner {
       it.deleteDatasetHyperlinks(datasetID)
       it.deleteDatasetPublications(datasetID)
       it.deleteDatasetOrganisms(datasetID)
+      it.deleteDatasetDependencies(datasetID)
       it.deleteDatasetMeta(datasetID)
       it.deleteDataset(datasetID)
     }

diff --git a/lib/reconciler/src/main/kotlin/vdi/lib/reconciler/AppDBTarget.kt b/lib/reconciler/src/main/kotlin/vdi/lib/reconciler/AppDBTarget.kt
@@ -57,6 +57,7 @@ internal class AppDBTarget(override val name: String, private val projectID: Str
         it.deleteDatasetHyperlinks(dataset.datasetID)
         it.deleteDatasetPublications(dataset.datasetID)
         it.deleteDatasetOrganisms(dataset.datasetID)
+        it.deleteDatasetDependencies(dataset.datasetID)
         it.deleteDatasetMeta(dataset.datasetID)
         it.deleteDataset(dataset.datasetID)
       }

diff --git a/service/lane/update-meta/src/main/kotlin/vdi/lane/meta/UpdateMetaTriggerHandlerImpl.kt b/service/lane/update-meta/src/main/kotlin/vdi/lane/meta/UpdateMetaTriggerHandlerImpl.kt
@@ -361,6 +361,7 @@ internal class UpdateMetaTriggerHandlerImpl(
     try {
       insertDataset(record)
       insertDatasetVisibility(datasetID, meta.owner)
+      insertDatasetDependencies(datasetID, meta.dependencies)
 
       upsertInstallMetaMessage(datasetID, InstallStatus.Running)