Merge branch 'master' of github.com:scalableminds/webknossos into rel…

…ease-24.12.0
scalableminds · Dec 6, 2024 · 309722e · 309722e
2 parents 8c43a66 + 2bdc9eb
commit 309722e
Show file tree

Hide file tree

Showing 300 changed files with 4,596 additions and 3,950 deletions.
diff --git a/CHANGELOG.released.md b/CHANGELOG.released.md
@@ -474,7 +474,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 ### Fixed
 - Fixed that some segment (group) actions were not properly disabled for non-editable segmentation layers. [#7207](https://github.com/scalableminds/webknossos/issues/7207)
 - Fixed a bug where data from zarr2 datasets that have a channel axis was broken. [#7374](https://github.com/scalableminds/webknossos/pull/7374)
-- Fixed a bug which changed the cursor position while editing the name of a tree or the comment of a node. [#7390](#https://github.com/scalableminds/webknossos/pull/7390)
+- Fixed a bug which changed the cursor position while editing the name of a tree or the comment of a node. [#7390](https://github.com/scalableminds/webknossos/pull/7390)
 - Streaming sharded zarr3 datasets from servers which do not respond with Accept-Ranges header is now possible. [#7392](https://github.com/scalableminds/webknossos/pull/7392)
 
 ## [23.10.2](https://github.com/scalableminds/webknossos/releases/tag/23.10.2) - 2023-09-26

diff --git a/CHANGELOG.unreleased.md b/CHANGELOG.unreleased.md
@@ -11,11 +11,24 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 [Commits](https://github.com/scalableminds/webknossos/compare/24.12.0...HEAD)
 
 ### Added
+- Added the total volume of a dataset to a tooltip in the dataset info tab. [#8229](https://github.com/scalableminds/webknossos/pull/8229)
 
 ### Changed
+- Renamed "resolution" to "magnification" in more places within the codebase, including local variables. [#8168](https://github.com/scalableminds/webknossos/pull/8168)
+- Datasets can now be renamed and can have duplicate names. [#8075](https://github.com/scalableminds/webknossos/pull/8075)
+- Improved the default colors for skeleton trees. [#8228](https://github.com/scalableminds/webknossos/pull/8228)
+- Allowed to train an AI model using differently sized bounding boxes. We recommend all bounding boxes to have equal dimensions or to have dimensions which are multiples of the smallest bounding box. [#8222](https://github.com/scalableminds/webknossos/pull/8222)
 
 ### Fixed
+- Fixed that listing datasets with the `api/datasets` route without compression failed due to missing permissions regarding public datasets. [#8249](https://github.com/scalableminds/webknossos/pull/8249)
+- Fixed that the frontend did not ensure a minium length for annotation layer names. Moreover, names starting with a `.` are also disallowed now. [#8244](https://github.com/scalableminds/webknossos/pull/8244)
+- Fixed a bug where in the add remote dataset view the dataset name setting was not in sync with the datasource setting of the advanced tab making the form not submittable. [#8245](https://github.com/scalableminds/webknossos/pull/8245)
+- Fix read and update dataset route for versions 8 and lower. [#8263](https://github.com/scalableminds/webknossos/pull/8263)
+- Added missing legacy support for `isValidNewName` route. [#8252](https://github.com/scalableminds/webknossos/pull/8252)
+- Fixed some layout issues in the upload view. [#8231](https://github.com/scalableminds/webknossos/pull/8231)
+- Fixed `FATAL: role "postgres" does not exist` error message in Docker compose. [#8240](https://github.com/scalableminds/webknossos/pull/8240)
 
 ### Removed
+- Removed support for HTTP API versions 3 and 4. [#8075](https://github.com/scalableminds/webknossos/pull/8075)
 
 ### Breaking Changes
diff --git a/MIGRATIONS.unreleased.md b/MIGRATIONS.unreleased.md
@@ -7,5 +7,7 @@ User-facing changes are documented in the [changelog](CHANGELOG.released.md).
 
 ## Unreleased
 [Commits](https://github.com/scalableminds/webknossos/compare/24.12.0...HEAD)
+- Removed support for HTTP API versions 3 and 4. [#8075](https://github.com/scalableminds/webknossos/pull/8075)
 
 ### Postgres Evolutions:
+- [124-decouple-dataset-directory-from-name](conf/evolutions/124-decouple-dataset-directory-from-name)
diff --git a/app/controllers/AiModelController.scala b/app/controllers/AiModelController.scala
@@ -12,7 +12,7 @@ import play.api.libs.json.{Json, OFormat}
 import play.api.mvc.{Action, AnyContent, PlayBodyParsers}
 import play.silhouette.api.Silhouette
 import security.WkEnv
-import utils.ObjectId
+import com.scalableminds.util.objectid.ObjectId
 
 import javax.inject.Inject
 import scala.concurrent.ExecutionContext
@@ -42,7 +42,7 @@ object RunTrainingParameters {
 
 case class RunInferenceParameters(annotationId: Option[ObjectId],
                                   aiModelId: ObjectId,
-                                  datasetName: String,
+                                  datasetDirectoryName: String,
                                   organizationId: String,
                                   colorLayerName: String,
                                   boundingBox: String,
@@ -147,7 +147,7 @@ class AiModelController @Inject()(
         jobCommand = JobCommand.train_model
         commandArgs = Json.obj(
           "training_annotations" -> Json.toJson(trainingAnnotations),
-          "organization_name" -> organization._id,
+          "organization_id" -> organization._id,
           "model_id" -> modelId,
           "custom_workflow_provided_by_user" -> request.body.workflowYaml
         )
@@ -180,21 +180,19 @@ class AiModelController @Inject()(
           "organization.notFound",
           request.body.organizationId)
         _ <- bool2Fox(request.identity._organization == organization._id) ?~> "job.runInference.notAllowed.organization" ~> FORBIDDEN
-        dataset <- datasetDAO.findOneByNameAndOrganization(request.body.datasetName, organization._id) ?~> Messages(
-          "dataset.notFound",
-          request.body.datasetName)
+        dataset <- datasetDAO.findOneByDirectoryNameAndOrganization(request.body.datasetDirectoryName, organization._id)
         dataStore <- dataStoreDAO.findOneByName(dataset._dataStore) ?~> "dataStore.notFound"
         _ <- aiModelDAO.findOne(request.body.aiModelId) ?~> "aiModel.notFound"
         _ <- datasetService.assertValidDatasetName(request.body.newDatasetName)
-        _ <- datasetService.assertNewDatasetName(request.body.newDatasetName, organization._id)
         jobCommand = JobCommand.infer_with_model
         boundingBox <- BoundingBox.fromLiteral(request.body.boundingBox).toFox
         commandArgs = Json.obj(
-          "organization_name" -> organization._id,
+          "organization_id" -> organization._id,
           "dataset_name" -> dataset.name,
           "color_layer_name" -> request.body.colorLayerName,
           "bounding_box" -> boundingBox.toLiteral,
           "model_id" -> request.body.aiModelId,
+          "dataset_directory_name" -> request.body.datasetDirectoryName,
           "new_dataset_name" -> request.body.newDatasetName,
           "custom_workflow_provided_by_user" -> request.body.workflowYaml
         )

diff --git a/app/controllers/AnnotationController.scala b/app/controllers/AnnotationController.scala
@@ -4,6 +4,7 @@ import org.apache.pekko.util.Timeout
 import play.silhouette.api.Silhouette
 import com.scalableminds.util.accesscontext.{DBAccessContext, GlobalAccessContext}
 import com.scalableminds.util.geometry.BoundingBox
+import com.scalableminds.util.objectid.ObjectId
 import com.scalableminds.util.time.Instant
 import com.scalableminds.util.tools.{Fox, FoxImplicits}
 import com.scalableminds.webknossos.datastore.models.annotation.AnnotationLayerType.AnnotationLayerType
@@ -34,7 +35,7 @@ import play.api.libs.json._
 import play.api.mvc.{Action, AnyContent, PlayBodyParsers}
 import security.{URLSharing, UserAwareRequestLogging, WkEnv}
 import telemetry.SlackNotificationService
-import utils.{ObjectId, WkConf}
+import utils.WkConf
 
 import javax.inject.Inject
 import scala.concurrent.ExecutionContext
@@ -242,15 +243,11 @@ class AnnotationController @Inject()(
       } yield result
     }
 
-  def createExplorational(organizationId: String, datasetName: String): Action[List[AnnotationLayerParameters]] =
+  def createExplorational(datasetId: String): Action[List[AnnotationLayerParameters]] =
     sil.SecuredAction.async(validateJson[List[AnnotationLayerParameters]]) { implicit request =>
       for {
-        organization <- organizationDAO.findOne(organizationId)(GlobalAccessContext) ?~> Messages(
-          "organization.notFound",
-          organizationId) ~> NOT_FOUND
-        dataset <- datasetDAO.findOneByNameAndOrganization(datasetName, organization._id) ?~> Messages(
-          "dataset.notFound",
-          datasetName) ~> NOT_FOUND
+        datasetIdValidated <- ObjectId.fromString(datasetId)
+        dataset <- datasetDAO.findOne(datasetIdValidated) ?~> Messages("dataset.notFound", datasetIdValidated) ~> NOT_FOUND
         annotation <- annotationService.createExplorationalFor(
           request.identity,
           dataset._id,
@@ -262,19 +259,12 @@ class AnnotationController @Inject()(
       } yield JsonOk(json)
     }
 
-  def getSandbox(organization: String,
-                 datasetName: String,
-                 typ: String,
-                 sharingToken: Option[String]): Action[AnyContent] =
+  def getSandbox(datasetId: String, typ: String, sharingToken: Option[String]): Action[AnyContent] =
     sil.UserAwareAction.async { implicit request =>
       val ctx = URLSharing.fallbackTokenAccessContext(sharingToken) // users with dataset sharing token may also get a sandbox annotation
       for {
-        organization <- organizationDAO.findOne(organization)(GlobalAccessContext) ?~> Messages(
-          "organization.notFound",
-          organization) ~> NOT_FOUND
-        dataset <- datasetDAO.findOneByNameAndOrganization(datasetName, organization._id)(ctx) ?~> Messages(
-          "dataset.notFound",
-          datasetName) ~> NOT_FOUND
+        datasetIdValidated <- ObjectId.fromString(datasetId)
+        dataset <- datasetDAO.findOne(datasetIdValidated)(ctx) ?~> Messages("dataset.notFound", datasetIdValidated) ~> NOT_FOUND
         tracingType <- TracingType.fromString(typ).toFox
         _ <- bool2Fox(tracingType == TracingType.skeleton) ?~> "annotation.sandbox.skeletonOnly"
         annotation = Annotation(