Merge branch 'master' into delete-workflow-reports

Author: frcroth

CHANGELOG.unreleased.md

@@ -16,6 +16,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 - Most sliders have been improved: Wheeling above a slider now changes its value and double-clicking its knob resets it to its default value. [#8095](https://github.com/scalableminds/webknossos/pull/8095)
 - It is now possible to search for unnamed segments with the full default name instead of only their id. [#8133](https://github.com/scalableminds/webknossos/pull/8133)
 - Increased loading speed for precomputed meshes. [#8110](https://github.com/scalableminds/webknossos/pull/8110)
+- Added a button to the search popover in the skeleton and segment tab to select all matching non-group results. [#8123](https://github.com/scalableminds/webknossos/pull/8123)
 - Unified wording in UI and code: “Magnification”/“mag” is now used in place of “Resolution“ most of the time, compare [https://docs.webknossos.org/webknossos/terminology.html](terminology document). [#8111](https://github.com/scalableminds/webknossos/pull/8111)
 - Added support for adding remote OME-Zarr NGFF version 0.5 datasets. [#8122](https://github.com/scalableminds/webknossos/pull/8122)
 - Workflow reports may be deleted. [#8156](https://github.com/scalableminds/webknossos/pull/8156)
@@ -28,6 +29,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 
 ### Fixed
 - Fixed a bug during dataset upload in case the configured `datastore.baseFolder` is an absolute path. [#8098](https://github.com/scalableminds/webknossos/pull/8098) [#8103](https://github.com/scalableminds/webknossos/pull/8103)
+- Fixed bbox export menu item [#8152](https://github.com/scalableminds/webknossos/pull/8152)
 - When trying to save an annotation opened via a link including a sharing token, the token is automatically discarded in case it is insufficient for update actions but the users token is. [#8139](https://github.com/scalableminds/webknossos/pull/8139)
 - Fixed that the skeleton search did not automatically expand groups that contained the selected tree [#8129](https://github.com/scalableminds/webknossos/pull/8129)
 - Fixed a bug that zarr streaming version 3 returned the shape of mag (1, 1, 1) / the finest mag for all mags. [#8116](https://github.com/scalableminds/webknossos/pull/8116)

MIGRATIONS.unreleased.md

@@ -12,3 +12,4 @@ User-facing changes are documented in the [changelog](CHANGELOG.released.md).
 
 - [121-worker-name.sql](conf/evolutions/121-worker-name.sql)
 - [122-resolution-to-mag.sql](conf/evolutions/122-resolution-to-mag.sql)
+- [123-more-model-categories.sql](conf/evolutions/123-more-model-categories.sql)

app/controllers/AiModelController.scala

@@ -57,6 +57,16 @@ object UpdateAiModelParameters {
   implicit val jsonFormat: OFormat[UpdateAiModelParameters] = Json.format[UpdateAiModelParameters]
 }
 
+case class RegisterAiModelParameters(id: ObjectId, // must be a valid MongoDB ObjectId
+                                     dataStoreName: String,
+                                     name: String,
+                                     comment: Option[String],
+                                     category: Option[AiModelCategory])
+
+object RegisterAiModelParameters {
+  implicit val jsonFormat: OFormat[RegisterAiModelParameters] = Json.format[RegisterAiModelParameters]
+}
+
 class AiModelController @Inject()(
     aiModelDAO: AiModelDAO,
     aiModelService: AiModelService,
@@ -209,6 +219,28 @@ class AiModelController @Inject()(
       } yield Ok(jsResult)
     }
 
+  def registerAiModel: Action[RegisterAiModelParameters] =
+    sil.SecuredAction.async(validateJson[RegisterAiModelParameters]) { implicit request =>
+      for {
+        _ <- userService.assertIsSuperUser(request.identity)
+        _ <- dataStoreDAO.findOneByName(request.body.dataStoreName) ?~> "dataStore.notFound"
+        _ <- aiModelDAO.findOne(request.body.id).reverse ?~> "aiModel.id.taken"
+        _ <- aiModelDAO.findOneByName(request.body.name).reverse ?~> "aiModel.name.taken"
+        _ <- aiModelDAO.insertOne(
+          AiModel(
+            request.body.id,
+            _organization = request.identity._organization,
+            request.body.dataStoreName,
+            request.identity._id,
+            None,
+            List.empty,
+            request.body.name,
+            request.body.comment,
+            request.body.category
+          ))
+      } yield Ok
+    }
+
   def deleteAiModel(aiModelId: String): Action[AnyContent] =
     sil.SecuredAction.async { implicit request =>
       for {

app/models/aimodels/AiModel.scala

@@ -144,4 +144,11 @@ class AiModelDAO @Inject()(sqlClient: SqlClient)(implicit ec: ExecutionContext)
         q"UPDATE webknossos.aiModels SET name = ${a.name}, comment = ${a.comment}, modified = ${a.modified} WHERE _id = ${a._id}".asUpdate)
     } yield ()
 
+  def findOneByName(name: String)(implicit ctx: DBAccessContext): Fox[AiModel] =
+    for {
+      accessQuery <- readAccessQuery
+      r <- run(q"SELECT $columns FROM $existingCollectionName WHERE name = $name AND $accessQuery".as[AimodelsRow])
+      parsed <- parseFirst(r, name)
+    } yield parsed
+
 }

app/models/aimodels/AiModelCategory.scala

@@ -4,5 +4,5 @@ import com.scalableminds.util.enumeration.ExtendedEnumeration
 
 object AiModelCategory extends ExtendedEnumeration {
   type AiModelCategory = Value
-  val em_neurons, em_nuclei = Value
+  val em_neurons, em_nuclei, em_synapses, em_neuron_types, em_cell_organelles = Value
 }

app/utils/sql/SQLDAO.scala

@@ -47,7 +47,7 @@ abstract class SQLDAO[C, R, X <: AbstractTable[R]] @Inject()(sqlClient: SqlClien
       case Some(r) =>
         parse(r) ?~> ("sql: could not parse database row for object" + id)
       case _ =>
-        Fox.failure("sql: could not find object " + id)
+        Fox.empty
     }.flatten
 
   @nowarn // suppress warning about unused implicit ctx, as it is used in subclasses

app/views/mail/jobFailedUploadConvert.scala.html

@@ -11,9 +11,9 @@
 
 <p>Here are some tips for uploading and converting datasets:
 <ul>
-  <li><a href="https://docs.webknossos.org/webknossos/data_formats.html">See the document on supported files formats</a></li>
+  <li><a href="https://docs.webknossos.org/webknossos/data/index.html">See the document on supported files formats</a></li>
   <li><a href="https://docs.webknossos.org/webknossos-py/index.html">Try our Python library for uploading datasets</a></li>
-  <li><a href="https://docs.webknossos.org/webknossos/datasets.html#working-with-zarr-neuroglancer-precomputed-and-n5-datasets">Try streaming your data as Zarr, Neuroglancer, or N5 files instead of uploading</a></li>
+  <li><a href="https://docs.webknossos.org/webknossos/data/streaming.html">Try streaming your data as Zarr, Neuroglancer, or N5 files instead of uploading</a></li>
 </ul>
 </p>
 

app/views/mail/jobSuccessfulSegmentation.scala.html

@@ -38,7 +38,7 @@
 </div>
 
 <p>
-  Do you want to make corrections to the automated segmentation? Use the easy-to-use, built-in <a href="https://docs.webknossos.org/webknossos/proof_reading.html#proofreading-tool">proof-reading tools in WEBKNOSSOS</a> (requires Power plan).
+  Do you want to make corrections to the automated segmentation? Use the easy-to-use, built-in <a href="https://docs.webknossos.org/webknossos/proofreading/tools.html">proof-reading tools in WEBKNOSSOS</a> (requires Power plan).
 </p>
 <div style="text-align: center; margin-bottom: 20px;">
   <img src="https://static.webknossos.org/mails/email-proofreading-preview.600.jpg" 

conf/evolutions/123-more-model-categories.sql

@@ -0,0 +1,11 @@
+
+-- no transaction here, since ALTER TYPE ... ADD cannot run inside a transaction block
+
+do $$ begin ASSERT (select schemaVersion from webknossos.releaseInformation) = 122, 'Previous schema version mismatch'; end; $$ LANGUAGE plpgsql;
+
+ALTER TYPE webknossos.AI_MODEL_CATEGORY ADD VALUE 'em_synapses';
+ALTER TYPE webknossos.AI_MODEL_CATEGORY ADD VALUE 'em_neuron_types';
+ALTER TYPE webknossos.AI_MODEL_CATEGORY ADD VALUE 'em_cell_organelles';
+
+UPDATE webknossos.releaseInformation SET schemaVersion = 123;
+

conf/evolutions/reversions/123-more-model-categories.sql

@@ -0,0 +1,11 @@
+START TRANSACTION;
+
+do $$ begin ASSERT (select schemaVersion from webknossos.releaseInformation) = 123, 'Previous schema version mismatch'; end; $$ LANGUAGE plpgsql;
+
+-- removing enum values is not supported in postgres, see https://www.postgresql.org/docs/current/datatype-enum.html#DATATYPE-ENUM-IMPLEMENTATION-DETAILS
+
+UPDATE webknossos.aiModels SET isDeleted = TRUE WHERE category IN ('em_synapses', 'em_neuron_types', 'em_cell_organelles');
+
+UPDATE webknossos.releaseInformation SET schemaVersion = 122;
+
+COMMIT TRANSACTION;