feat(backend): add users table with GitHub sync and internal IDs

backend/src/main/kotlin/org/genspectrum/dashboardsbackend/api/Collection.kt

@@ -21,7 +21,7 @@ import kotlin.time.Instant
 data class Collection(
     val id: Long,
     val name: String,
-    val ownedBy: String,
+    val ownedBy: Long,
     val organism: String,
     val description: String?,
     val variants: List<Variant>,

backend/src/main/kotlin/org/genspectrum/dashboardsbackend/api/User.kt

@@ -0,0 +1,16 @@
+package org.genspectrum.dashboardsbackend.api
+
+import kotlin.time.Instant
+
+data class User(
+    val id: Long,
+    val githubId: String?,
+    val name: String,
+    val email: String?,
+    val createdAt: Instant,
+    val updatedAt: Instant,
+)
+
+data class UserSyncRequest(val githubId: String, val name: String, val email: String?)
+
+data class PublicUser(val id: Long, val name: String)

backend/src/main/kotlin/org/genspectrum/dashboardsbackend/controller/CollectionsController.kt

@@ -26,7 +26,7 @@ class CollectionsController(private val collectionModel: CollectionModel) {
         description = "Returns collections filtered by optional userId and/or organism parameters.",
     )
     fun getCollections(
-        @RequestParam(required = false) userId: String?,
+        @RequestParam(required = false) userId: Long?,
         @RequestParam(required = false) organism: String?,
     ): List<Collection> = collectionModel.getCollections(
         userId = userId,
@@ -50,7 +50,7 @@ class CollectionsController(private val collectionModel: CollectionModel) {
     )
     fun postCollection(
         @RequestBody collection: CollectionRequest,
-        @UserIdParameter @RequestParam userId: String,
+        @UserIdParameter @RequestParam userId: Long,
     ): Collection = collectionModel.createCollection(
         request = collection,
         userId = userId,
@@ -65,7 +65,7 @@ class CollectionsController(private val collectionModel: CollectionModel) {
     fun putCollection(
         @RequestBody collection: CollectionUpdate,
         @Parameter(description = "The ID of the collection", example = "1") @PathVariable id: Long,
-        @UserIdParameter @RequestParam userId: String,
+        @UserIdParameter @RequestParam userId: Long,
     ): Collection = collectionModel.putCollection(id, collection, userId)
 
     @DeleteMapping("/collections/{id}")
@@ -76,6 +76,6 @@ class CollectionsController(private val collectionModel: CollectionModel) {
     )
     fun deleteCollection(
         @Parameter(description = "The ID of the collection", example = "1") @PathVariable id: Long,
-        @UserIdParameter @RequestParam userId: String,
+        @UserIdParameter @RequestParam userId: Long,
     ) = collectionModel.deleteCollection(id, userId)
 }

backend/src/main/kotlin/org/genspectrum/dashboardsbackend/controller/SubscriptionsController.kt

@@ -36,7 +36,7 @@ class SubscriptionsController(
     )
     fun getSubscription(
         @IdParameter @PathVariable id: String,
-        @UserIdParameter @RequestParam userId: String,
+        @UserIdParameter @RequestParam userId: Long,
     ): Subscription = subscriptionModel.getSubscription(
         subscriptionId = id,
         userId = userId,
@@ -47,7 +47,7 @@ class SubscriptionsController(
         summary = "Get all subscriptions of a user",
         description = "Returns a list of all subscriptions of a user.",
     )
-    fun getSubscriptions(@UserIdParameter @RequestParam userId: String): List<Subscription> =
+    fun getSubscriptions(@UserIdParameter @RequestParam userId: Long): List<Subscription> =
         subscriptionModel.getSubscriptions(userId)
 
     @PostMapping("/subscriptions")
@@ -58,7 +58,7 @@ class SubscriptionsController(
     )
     fun postSubscriptions(
         @RequestBody subscription: SubscriptionRequest,
-        @UserIdParameter @RequestParam userId: String,
+        @UserIdParameter @RequestParam userId: Long,
     ): Subscription = subscriptionModel.postSubscriptions(
         request = subscription,
         userId = userId,
@@ -70,7 +70,7 @@ class SubscriptionsController(
         summary = "Delete a subscription",
         description = "Deletes a specific subscription of a user by its uuid.",
     )
-    fun deleteSubscription(@IdParameter @PathVariable id: String, @UserIdParameter @RequestParam userId: String) {
+    fun deleteSubscription(@IdParameter @PathVariable id: String, @UserIdParameter @RequestParam userId: Long) {
         subscriptionModel.deleteSubscription(
             subscriptionId = id,
             userId = userId,
@@ -85,7 +85,7 @@ class SubscriptionsController(
     fun putSubscription(
         @RequestBody subscription: SubscriptionUpdate,
         @IdParameter @PathVariable id: String,
-        @UserIdParameter @RequestParam userId: String,
+        @UserIdParameter @RequestParam userId: Long,
     ): Subscription = subscriptionModel.putSubscription(
         subscriptionId = id,
         subscriptionUpdate = subscription,
@@ -99,7 +99,7 @@ class SubscriptionsController(
     )
     fun evaluateTrigger(
         @IdParameter @RequestParam id: String,
-        @UserIdParameter @RequestParam userId: String,
+        @UserIdParameter @RequestParam userId: Long,
     ): TriggerEvaluationResponse {
         val triggerEvaluationResult = triggerEvaluationModel.evaluateSubscriptionTrigger(
             subscriptionId = id,

backend/src/main/kotlin/org/genspectrum/dashboardsbackend/controller/UsersController.kt

@@ -0,0 +1,30 @@
+package org.genspectrum.dashboardsbackend.controller
+
+import io.swagger.v3.oas.annotations.Operation
+import org.genspectrum.dashboardsbackend.api.PublicUser
+import org.genspectrum.dashboardsbackend.api.User
+import org.genspectrum.dashboardsbackend.api.UserSyncRequest
+import org.genspectrum.dashboardsbackend.model.user.UserModel
+import org.springframework.http.MediaType
+import org.springframework.web.bind.annotation.GetMapping
+import org.springframework.web.bind.annotation.PathVariable
+import org.springframework.web.bind.annotation.PostMapping
+import org.springframework.web.bind.annotation.RequestBody
+import org.springframework.web.bind.annotation.RestController
+
+@RestController
+class UsersController(private val userModel: UserModel) {
+    @PostMapping("/users/sync", produces = [MediaType.APPLICATION_JSON_VALUE])
+    @Operation(
+        summary = "Sync user from external auth provider",
+        description = "Upserts a user record by github_id. Returns the user with their internal ID.",
+    )
+    fun syncUser(@RequestBody request: UserSyncRequest): User = userModel.syncUser(request)
+
+    @GetMapping("/users/{id}", produces = [MediaType.APPLICATION_JSON_VALUE])
+    @Operation(
+        summary = "Get user by internal ID",
+        description = "Returns public user info by internal UUID.",
+    )
+    fun getUser(@PathVariable id: Long): PublicUser = userModel.getUser(id)
+}

backend/src/main/kotlin/org/genspectrum/dashboardsbackend/model/collection/CollectionModel.kt

@@ -10,6 +10,7 @@ import org.genspectrum.dashboardsbackend.config.DashboardsConfig
 import org.genspectrum.dashboardsbackend.controller.BadRequestException
 import org.genspectrum.dashboardsbackend.controller.ForbiddenException
 import org.genspectrum.dashboardsbackend.controller.NotFoundException
+import org.genspectrum.dashboardsbackend.util.now
 import org.jetbrains.exposed.v1.core.Op
 import org.jetbrains.exposed.v1.core.and
 import org.jetbrains.exposed.v1.core.eq
@@ -18,19 +19,12 @@ import org.jetbrains.exposed.v1.core.notInList
 import org.jetbrains.exposed.v1.jdbc.deleteWhere
 import org.springframework.stereotype.Service
 import org.springframework.transaction.annotation.Transactional
-import kotlin.time.Clock
 import kotlin.time.Instant
 
 @Service
 @Transactional
 class CollectionModel(private val dashboardsConfig: DashboardsConfig) {
-    // Truncate to milliseconds to avoid mismatches between the in-memory value
-    // we return and what is read back from the DB.
-    private fun now(): Instant = Clock.System.now().run {
-        Instant.fromEpochMilliseconds(toEpochMilliseconds())
-    }
-
-    fun getCollections(userId: String?, organism: String?): List<Collection> {
+    fun getCollections(userId: Long?, organism: String?): List<Collection> {
         if (organism != null) {
             dashboardsConfig.validateIsValidOrganism(organism)
             dashboardsConfig.validateCollectionsEnabled(organism)
@@ -81,7 +75,7 @@ class CollectionModel(private val dashboardsConfig: DashboardsConfig) {
         return entity.toCollection()
     }
 
-    fun createCollection(request: CollectionRequest, userId: String): Collection {
+    fun createCollection(request: CollectionRequest, userId: Long): Collection {
         dashboardsConfig.validateIsValidOrganism(request.organism)
         dashboardsConfig.validateCollectionsEnabled(request.organism)
 
@@ -113,7 +107,7 @@ class CollectionModel(private val dashboardsConfig: DashboardsConfig) {
         )
     }
 
-    fun deleteCollection(id: Long, userId: String) {
+    fun deleteCollection(id: Long, userId: Long) {
         // Find with ownership check
         val entity = CollectionEntity.findForUser(id, userId)
             ?: throw ForbiddenException("Collection $id not found or you don't have permission to delete it")
@@ -122,7 +116,7 @@ class CollectionModel(private val dashboardsConfig: DashboardsConfig) {
         entity.delete()
     }
 
-    fun putCollection(id: Long, update: CollectionUpdate, userId: String): Collection {
+    fun putCollection(id: Long, update: CollectionUpdate, userId: Long): Collection {
         val collectionEntity = CollectionEntity.findForUser(id, userId)
             ?: throw ForbiddenException("Collection $id not found or you don't have permission to update it")
         dashboardsConfig.validateCollectionsEnabled(collectionEntity.organism)

backend/src/main/kotlin/org/genspectrum/dashboardsbackend/model/collection/CollectionTable.kt

@@ -11,7 +11,7 @@ const val COLLECTION_TABLE = "collections_table"
 
 object CollectionTable : LongIdTable(COLLECTION_TABLE) {
     val name = text("name")
-    val ownedBy = varchar("owned_by", 255)
+    val ownedBy = long("owned_by")
     val organism = varchar("organism", 255)
     val description = text("description").nullable()
     val createdAt = timestamp("created_at")
@@ -20,7 +20,7 @@ object CollectionTable : LongIdTable(COLLECTION_TABLE) {
 
 class CollectionEntity(id: EntityID<Long>) : LongEntity(id) {
     companion object : LongEntityClass<CollectionEntity>(CollectionTable) {
-        fun findForUser(id: Long, userId: String) = findById(id)
+        fun findForUser(id: Long, userId: Long) = findById(id)
             ?.takeIf { it.ownedBy == userId }
     }
 

backend/src/main/kotlin/org/genspectrum/dashboardsbackend/model/subscription/SubscriptionModel.kt

@@ -13,18 +13,18 @@ import org.springframework.transaction.annotation.Transactional
 @Service
 @Transactional
 class SubscriptionModel(private val dashboardsConfig: DashboardsConfig) {
-    fun getSubscription(subscriptionId: String, userId: String): Subscription =
+    fun getSubscription(subscriptionId: String, userId: Long): Subscription =
         SubscriptionEntity.findForUser(convertToUuid(subscriptionId), userId)
             ?.toSubscription()
             ?: throw NotFoundException("Subscription $subscriptionId not found")
 
-    fun getSubscriptions(userId: String): List<Subscription> = SubscriptionEntity.find {
+    fun getSubscriptions(userId: Long): List<Subscription> = SubscriptionEntity.find {
         SubscriptionTable.userId eq userId
     }.map {
         it.toSubscription()
     }
 
-    fun postSubscriptions(request: SubscriptionRequest, userId: String): Subscription {
+    fun postSubscriptions(request: SubscriptionRequest, userId: Long): Subscription {
         dashboardsConfig.validateIsValidOrganism(request.organism)
 
         return SubscriptionEntity
@@ -40,14 +40,14 @@ class SubscriptionModel(private val dashboardsConfig: DashboardsConfig) {
             .toSubscription()
     }
 
-    fun deleteSubscription(subscriptionId: String, userId: String) {
+    fun deleteSubscription(subscriptionId: String, userId: Long) {
         val subscription = SubscriptionEntity.findForUser(convertToUuid(subscriptionId), userId)
             ?: throw NotFoundException("Subscription $subscriptionId not found")
 
         subscription.delete()
     }
 
-    fun putSubscription(subscriptionId: String, subscriptionUpdate: SubscriptionUpdate, userId: String): Subscription {
+    fun putSubscription(subscriptionId: String, subscriptionUpdate: SubscriptionUpdate, userId: Long): Subscription {
         subscriptionUpdate.organism?.also { dashboardsConfig.validateIsValidOrganism(it) }
 
         val subscription = SubscriptionEntity.findForUser(convertToUuid(subscriptionId), userId)

backend/src/main/kotlin/org/genspectrum/dashboardsbackend/model/subscription/SubscriptionTable.kt

@@ -17,12 +17,12 @@ object SubscriptionTable : UUIDTable(SUBSCRIPTION_TABLE) {
     val organism = varchar("organism", 255)
     val dateWindow = varchar("date_window", 255)
     val trigger = jacksonSerializableJsonb<Trigger>("trigger")
-    val userId = varchar("user_id", 255)
+    val userId = long("user_id")
 }
 
 class SubscriptionEntity(id: EntityID<UUID>) : UUIDEntity(id) {
     companion object : UUIDEntityClass<SubscriptionEntity>(SubscriptionTable) {
-        fun findForUser(id: UUID, userId: String) = findById(id)
+        fun findForUser(id: UUID, userId: Long) = findById(id)
             ?.takeIf { it.userId == userId }
     }
 

backend/src/main/kotlin/org/genspectrum/dashboardsbackend/model/triggerevaluation/TriggerEvaluationModel.kt

@@ -8,7 +8,7 @@ class TriggerEvaluationModel(
     private val subscriptionModel: SubscriptionModel,
     private val triggerEvaluator: TriggerEvaluator,
 ) {
-    fun evaluateSubscriptionTrigger(subscriptionId: String, userId: String) = triggerEvaluator.evaluate(
+    fun evaluateSubscriptionTrigger(subscriptionId: String, userId: Long) = triggerEvaluator.evaluate(
         subscriptionModel.getSubscription(
             subscriptionId = subscriptionId,
             userId = userId,

backend/src/main/kotlin/org/genspectrum/dashboardsbackend/model/user/UserModel.kt

@@ -0,0 +1,35 @@
+package org.genspectrum.dashboardsbackend.model.user
+
+import org.genspectrum.dashboardsbackend.api.PublicUser
+import org.genspectrum.dashboardsbackend.api.User
+import org.genspectrum.dashboardsbackend.api.UserSyncRequest
+import org.genspectrum.dashboardsbackend.controller.NotFoundException
+import org.genspectrum.dashboardsbackend.util.now
+import org.springframework.stereotype.Service
+import org.springframework.transaction.annotation.Transactional
+
+@Service
+@Transactional
+class UserModel {
+    fun syncUser(request: UserSyncRequest): User {
+        val now = now()
+        val existing = UserEntity.findByGithubId(request.githubId)
+        return if (existing != null) {
+            existing.name = request.name
+            existing.email = request.email
+            existing.updatedAt = now
+            existing.toUser()
+        } else {
+            UserEntity.new {
+                githubId = request.githubId
+                name = request.name
+                email = request.email
+                createdAt = now
+                updatedAt = now
+            }.toUser()
+        }
+    }
+
+    fun getUser(id: Long): PublicUser = UserEntity.findById(id)?.toPublicUser()
+        ?: throw NotFoundException("User $id not found")
+}

backend/src/main/kotlin/org/genspectrum/dashboardsbackend/model/user/UserTable.kt

@@ -0,0 +1,43 @@
+package org.genspectrum.dashboardsbackend.model.user
+
+import org.genspectrum.dashboardsbackend.api.PublicUser
+import org.genspectrum.dashboardsbackend.api.User
+import org.jetbrains.exposed.v1.core.dao.id.EntityID
+import org.jetbrains.exposed.v1.core.dao.id.LongIdTable
+import org.jetbrains.exposed.v1.core.eq
+import org.jetbrains.exposed.v1.dao.LongEntity
+import org.jetbrains.exposed.v1.dao.LongEntityClass
+import org.jetbrains.exposed.v1.datetime.timestamp
+
+const val USER_TABLE = "users_table"
+
+object UserTable : LongIdTable(USER_TABLE) {
+    val githubId = varchar("github_id", 255).nullable().uniqueIndex()
+    val name = varchar("name", 255)
+    val email = varchar("email", 255).nullable()
+    val createdAt = timestamp("created_at")
+    val updatedAt = timestamp("updated_at")
+}
+
+class UserEntity(id: EntityID<Long>) : LongEntity(id) {
+    companion object : LongEntityClass<UserEntity>(UserTable) {
+        fun findByGithubId(githubId: String) = find { UserTable.githubId eq githubId }.firstOrNull()
+    }
+
+    var githubId by UserTable.githubId
+    var name by UserTable.name
+    var email by UserTable.email
+    var createdAt by UserTable.createdAt
+    var updatedAt by UserTable.updatedAt
+
+    fun toPublicUser() = PublicUser(id = id.value, name = name)
+
+    fun toUser() = User(
+        id = id.value,
+        githubId = githubId,
+        name = name,
+        email = email,
+        createdAt = createdAt,
+        updatedAt = updatedAt,
+    )
+}

backend/src/main/kotlin/org/genspectrum/dashboardsbackend/util/InstantProvider.kt

@@ -0,0 +1,10 @@
+package org.genspectrum.dashboardsbackend.util
+
+import kotlin.time.Clock
+import kotlin.time.Instant
+
+// Truncate to milliseconds to avoid mismatches between the in-memory value
+// we return and what is read back from the DB.
+fun now(): Instant = Clock.System.now().run {
+    Instant.fromEpochMilliseconds(toEpochMilliseconds())
+}