Merge branch 'master' into ak-docker-tag

scalableminds · Jun 19, 2024 · 8bd7a91 · 8bd7a91
2 parents 48cd515 + c36b647
commit 8bd7a91
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diff --git a/CHANGELOG.unreleased.md b/CHANGELOG.unreleased.md
@@ -11,12 +11,14 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 [Commits](https://github.com/scalableminds/webknossos/compare/24.06.0...HEAD)
 
 ### Added
+- Added that proofreading merge actions reuse custom names of segments. A merge action now combines the potenial existing custom names of both segments and a split-action copies the custom name to the split-off segment. [#7877](https://github.com/scalableminds/webknossos/pull/7877)
 - Added the option for the owner to lock explorative annotations. Locked annotations cannot be modified by any user. An annotation can be locked in the annotations table and when viewing the annotation via the navbar dropdown menu. [#7801](https://github.com/scalableminds/webknossos/pull/7801)
 - Added the option to set a default mapping for a dataset in the dataset view configuration. The default mapping is loaded when the dataset is opened and the user / url does not configure something else. [#7858](https://github.com/scalableminds/webknossos/pull/7858)
 - Uploading an annotation into a dataset that it was not created for now also works if the dataset is in a different organization. [#7816](https://github.com/scalableminds/webknossos/pull/7816)
 - When downloading + reuploading an annotation that is based on a segmentation layer with active mapping, that mapping is now still be selected after the reupload. [#7822](https://github.com/scalableminds/webknossos/pull/7822)
 - In the Voxelytics workflow list, the name of the WEBKNOSSOS user who started the job is displayed. [#7794](https://github.com/scalableminds/webknossos/pull/7795)
 - Start an alignment job (aligns the section in a dataset) via the "AI Analysis" button. [#7820](https://github.com/scalableminds/webknossos/pull/7820)
+- Added additional validation for the animation job modal. Bounding boxes must be larger then zero. [#7883](https://github.com/scalableminds/webknossos/pull/7883)
 
 ### Changed
 - The "WEBKNOSSOS Changelog" modal now lazily loads its content potentially speeding up the initial loading time of WEBKNOSSOS and thus improving the UX. [#7843](https://github.com/scalableminds/webknossos/pull/7843)
@@ -30,7 +32,9 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 - Fixed a bug where brushing on a fallback segmentation with active mapping and with segment index file would lead to failed saves. [#7833](https://github.com/scalableminds/webknossos/pull/7833)
 - Fixed a bug where sometimes old mismatching javascript code would be served after upgrades. [#7854](https://github.com/scalableminds/webknossos/pull/7854)
 - Fixed a bug where dataset uploads of zipped tiff data via the UI would be rejected. [#7856](https://github.com/scalableminds/webknossos/pull/7856)
+- Fixed a bug with incorrect valiation of layer names in the animation modal. [#7882](https://github.com/scalableminds/webknossos/pull/7882)
 
 ### Removed
+- If the datasource-properties.json file for a dataset is missing or contains errors, WEBKNOSSOS no longer attempts to guess its contents from the raw data. Exploring remote datasets will still create the file. [#7697](https://github.com/scalableminds/webknossos/pull/7697)
 
 ### Breaking Changes
diff --git a/MIGRATIONS.unreleased.md b/MIGRATIONS.unreleased.md
@@ -8,12 +8,12 @@ User-facing changes are documented in the [changelog](CHANGELOG.released.md).
 ## Unreleased
 [Commits](https://github.com/scalableminds/webknossos/compare/24.06.0...HEAD)
 
-- The datastore config field `datastore.cache.dataCube.maxEntries` is no longer used an can be removed.
-
+- The datastore config field `datastore.cache.dataCube.maxEntries` is no longer used an can be removed. [#7818](https://github.com/scalableminds/webknossos/pull/7818)
 - If your setup contains webknossos-workers, you may want to add the newly available job `align_sections` to the `supportedJobCommands` of your workers. Make sure you deploy the latest webknossos-worker release. [#7820](https://github.com/scalableminds/webknossos/pull/7820)
+- If you place WKW datasets directly on disk, a datasource-properties.json is now required, as WEBKNOSSOS no longer guesses its contents from the raw data. Standard dataset creation methods, e.g. with the WEBKNOSSOS CLI or python libs will already automatically this metadata file. [#7697](https://github.com/scalableminds/webknossos/pull/7697)
 
 ### Postgres Evolutions:
 
 - [114-ai-models.sql](conf/evolutions/114-ai-models.sql)
 - [115-annotation-locked-by-user.sql](conf/evolutions/115-annotation-locked-by-user.sql)
-- [116-drop-overtimemailinglist.sql](conf/evolutions/116-drop-overtimemailinglist.sql)
+- [116-drop-overtimemailinglist.sql](conf/evolutions/116-drop-overtimemailinglist.sql)
diff --git a/docs/data_formats.md b/docs/data_formats.md
@@ -126,9 +126,8 @@ The term "magnifications" is used synonymously for resolutions throughout the UI
 At the moment, WebKnossos guarantees correct rendering of data with non-uniform resolution factors only if the z-component between two resolutions changes by a factor of 1 or 2.
 
 Most users do not create these metadata files manually.
-WEBKNOSSOS can infer most of these properties automatically, except for `scale` and `largestSegmentId`.
-During the data import process, WEBKNOSSOS will ask for the necessary properties.
 When using the [WEBKNOSSOS CLI](http://docs.webknossos.org/cli), a metadata file is automatically generated. Alternatively, you can create and edit WEBKNOSSOS datasets using the [WEBKNOSSOS Python library](https://github.com/scalableminds/webknossos-libs/).
+During the data import process, WEBKNOSSOS will ask for the necessary properties.
 
 [See below for the full specification](#dataset-metadata-specification).
 

diff --git a/frontend/javascripts/admin/admin_rest_api.ts b/frontend/javascripts/admin/admin_rest_api.ts
@@ -11,7 +11,6 @@ import type {
   APIBuildInfo,
   APIConnectomeFile,
   APIDataSource,
-  APIDataSourceWithMessages,
   APIDataStore,
   APIDataset,
   APIDatasetId,
@@ -1116,16 +1115,6 @@ export async function getDatasets(
   return datasets;
 }
 
-export function getDatasetDatasource(
-  dataset: APIMaybeUnimportedDataset,
-): Promise<APIDataSourceWithMessages> {
-  return doWithToken((token) =>
-    Request.receiveJSON(
-      `${dataset.dataStore.url}/data/datasets/${dataset.owningOrganization}/${dataset.name}?token=${token}`,
-    ),
-  );
-}
-
 export function readDatasetDatasource(dataset: APIDataset): Promise<APIDataSource> {
   return doWithToken((token) =>
     Request.receiveJSON(

diff --git a/frontend/javascripts/admin/dataset/dataset_add_view.tsx b/frontend/javascripts/admin/dataset/dataset_add_view.tsx
@@ -96,7 +96,7 @@ function DatasetAddView({ history }: RouteComponentProps) {
                   View the Dataset
                 </Button>
                 <Button
-                  onClick={() => history.push(`/datasets/${organization}/${datasetName}/import`)}
+                  onClick={() => history.push(`/datasets/${organization}/${datasetName}/edit`)}
                 >
                   Go to Dataset Settings
                 </Button>

diff --git a/frontend/javascripts/admin/dataset/dataset_upload_view.tsx b/frontend/javascripts/admin/dataset/dataset_upload_view.tsx
@@ -725,12 +725,12 @@ class DatasetUploadView extends React.Component<PropsWithFormAndRouter, State> {
                 rules={[
                   {
                     required: this.state.needsConversion,
-                    message: "Please provide a scale for the dataset.",
+                    message: "Please provide a voxel size for the dataset.",
                   },
                   {
                     validator: syncValidator(
                       (value: Vector3) => value?.every((el) => el > 0),
-                      "Each component of the scale must be larger than 0.",
+                      "Each component of the voxel size must be larger than 0.",
                     ),
                   },
                 ]}

diff --git a/frontend/javascripts/dashboard/advanced_dataset/dataset_action_view.tsx b/frontend/javascripts/dashboard/advanced_dataset/dataset_action_view.tsx
@@ -3,7 +3,6 @@ import {
   EllipsisOutlined,
   EyeOutlined,
   LoadingOutlined,
-  PlusCircleOutlined,
   PlusOutlined,
   ReloadOutlined,
   SettingOutlined,
@@ -18,9 +17,9 @@ import Toast from "libs/toast";
 import messages from "messages";
 import CreateExplorativeModal from "dashboard/advanced_dataset/create_explorative_modal";
 import { MenuProps, Modal, Typography } from "antd";
+import { useState } from "react";
 import { confirmAsync } from "dashboard/dataset/helper_components";
 import { useQueryClient } from "@tanstack/react-query";
-import { useState } from "react";
 
 const disabledStyle: React.CSSProperties = {
   pointerEvents: "none",
@@ -193,18 +192,31 @@ function DatasetActionView(props: Props) {
       style={disabledWhenReloadingStyle}
       type="link"
     >
-      {isReloading ? <LoadingOutlined /> : <ReloadOutlined className="icon-margin-right" />}
+      {isReloading ? (
+        <LoadingOutlined className="icon-margin-right" />
+      ) : (
+        <ReloadOutlined className="icon-margin-right" />
+      )}
       Reload
     </a>
   );
-  const importLink = (
-    <div className="dataset-table-actions">
-      <Link
-        to={`/datasets/${dataset.owningOrganization}/${dataset.name}/import`}
-        className="import-dataset"
+  const datasetSettingsLink = (
+    <>
+      <LinkWithDisabled
+        to={`/datasets/${dataset.owningOrganization}/${dataset.name}/edit`}
+        title="Open Dataset Settings"
+        disabled={isReloading}
       >
-        <PlusCircleOutlined className="icon-margin-right" />
-        Import
+        <SettingOutlined className="icon-margin-right" />
+        Settings
+      </LinkWithDisabled>
+    </>
+  );
+  const brokenDatasetActions = (
+    <div className="dataset-table-actions">
+      <Link to={`/datasets/${dataset.owningOrganization}/${dataset.name}/edit`}>
+        <SettingOutlined className="icon-margin-right" />
+        Settings
       </Link>
       {reloadLink}
       <a
@@ -236,41 +248,35 @@ function DatasetActionView(props: Props) {
       ) : null}
     </div>
   );
+
+  const activeDatasetActions = (
+    <>
+      {" "}
+      <NewAnnotationLink
+        dataset={dataset}
+        isReloading={isReloading}
+        isCreateExplorativeModalVisible={isCreateExplorativeModalVisible}
+        onShowCreateExplorativeModal={() => setIsCreateExplorativeModalVisible(true)}
+        onCloseCreateExplorativeModal={() => setIsCreateExplorativeModalVisible(false)}
+      />
+      <LinkWithDisabled
+        to={`/datasets/${dataset.owningOrganization}/${dataset.name}/view`}
+        title="View Dataset"
+        disabled={isReloading}
+      >
+        <EyeOutlined className="icon-margin-right" />
+        View
+      </LinkWithDisabled>
+      {dataset.isEditable ? datasetSettingsLink : null}
+      {reloadLink}
+    </>
+  );
   return (
     <div>
-      {dataset.isEditable && !dataset.isActive ? importLink : null}
-      {dataset.isActive ? (
-        <div className="dataset-table-actions nowrap">
-          <NewAnnotationLink
-            dataset={dataset}
-            isReloading={isReloading}
-            isCreateExplorativeModalVisible={isCreateExplorativeModalVisible}
-            onShowCreateExplorativeModal={() => setIsCreateExplorativeModalVisible(true)}
-            onCloseCreateExplorativeModal={() => setIsCreateExplorativeModalVisible(false)}
-          />
-          <LinkWithDisabled
-            to={`/datasets/${dataset.owningOrganization}/${dataset.name}/view`}
-            title="View Dataset"
-            disabled={isReloading}
-          >
-            <EyeOutlined className="icon-margin-right" />
-            View
-          </LinkWithDisabled>
-          {dataset.isEditable ? (
-            <React.Fragment>
-              <LinkWithDisabled
-                to={`/datasets/${dataset.owningOrganization}/${dataset.name}/edit`}
-                title="Open Dataset Settings"
-                disabled={isReloading}
-              >
-                <SettingOutlined className="icon-margin-right" />
-                Settings
-              </LinkWithDisabled>
-              {reloadLink}
-            </React.Fragment>
-          ) : null}
-        </div>
-      ) : null}
+      {dataset.isEditable && !dataset.isActive ? brokenDatasetActions : null}
+      <div className="dataset-table-actions nowrap">
+        {dataset.isActive ? activeDatasetActions : null}
+      </div>
     </div>
   );
 }
@@ -330,7 +336,7 @@ export function getDatasetActionContextMenu({
             },
           }
         : null,
-      dataset.isEditable && dataset.isActive
+      dataset.isEditable
         ? {
             key: "edit",
             label: "Open Settings",
@@ -340,15 +346,6 @@ export function getDatasetActionContextMenu({
           }
         : null,
 
-      dataset.isEditable && !dataset.isActive
-        ? {
-            key: "import",
-            label: "Import",
-            onClick: () => {
-              window.location.href = `/datasets/${dataset.owningOrganization}/${dataset.name}/import`;
-            },
-          }
-        : null,
       {
         key: "reload",
         label: "Reload",

diff --git a/frontend/javascripts/dashboard/dataset/dataset_settings_data_tab.tsx b/frontend/javascripts/dashboard/dataset/dataset_settings_data_tab.tsx
@@ -64,14 +64,12 @@ export default function DatasetSettingsDataTab({
   form,
   activeDataSourceEditMode,
   onChange,
-  additionalAlert,
   dataset,
 }: {
   allowRenamingDataset: boolean;
   form: FormInstance;
   activeDataSourceEditMode: "simple" | "advanced";
   onChange: (arg0: "simple" | "advanced") => void;
-  additionalAlert?: React.ReactNode | null | undefined;
   dataset?: APIDataset | null | undefined;
 }) {
   // Using the return value of useWatch for the `dataSource` var
@@ -113,8 +111,6 @@ export default function DatasetSettingsDataTab({
         </Tooltip>
       </div>
 
-      {additionalAlert}
-
       <Hideable hidden={activeDataSourceEditMode !== "simple"}>
         <RetryingErrorBoundary>
           <SimpleDatasetForm
@@ -217,12 +213,12 @@ function SimpleDatasetForm({
                   rules={[
                     {
                       required: true,
-                      message: "Please provide a scale for the dataset.",
+                      message: "Please provide a voxel size for the dataset.",
                     },
                     {
                       validator: syncValidator(
                         (value: Vector3) => value?.every((el) => el > 0),
-                        "Each component of the scale must be greater than 0",
+                        "Each component of the voxel size must be greater than 0",
                       ),
                     },
                   ]}