Merge upstream changes from webknossos upstream main #33
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* add debug logging for dataset list route * add extensive logging to listGrouped method of DatasetController * dont log full objects * restore logging full object except for user objects --------- Co-authored-by: Michael Büßemeyer <[email protected]> Co-authored-by: Florian M <[email protected]>
Co-authored-by: Michael Büßemeyer <[email protected]>
…nds#8249) * fix permisson error in listGrouped in list datasets route * add changelog entry --------- Co-authored-by: Michael Büßemeyer <[email protected]>
) * sync dataset name with datasource in add remote view * add changelog entry * make syncing simple to advanced tab more robust * add comment explaining when syncing datasetNames is needed and when not * use TS nullish coalescing operator instead of if * make missing occurences of syncDataSourceFields also sync dataset name --------- Co-authored-by: Michael Büßemeyer <[email protected]>
* add missing isValidNewName legacy route * add changelog entry --------- Co-authored-by: Michael Büßemeyer <[email protected]>
…ab (scalableminds#8229) * add DS extent to tooltip * add changelog * use formatVoxels to format no voxels * include error handling for largest numbers * remove safeMultiply * fix capitalization
* rename local vars in ai_model_list_view, create_explorative_modal, model_initialization, api_latest and plane_material_factory * rename to mag up to volume interpolation saga * continue renaming local vars * rename more occurences of resolution to mag * change ServerNode resolution to mag * remove shader code edit * fix test: rename resolution to mag in volumetracing saga spec * rename resolution in create node action * rename resolution to mag in DataLayer type * revert shader code edit * add changelog * rename resolution to mag in MutableNode and add type checking file for skeletontracingreducer test * change dummy trees to test compatibility of backend and frontend CreadeNodeAction * fix createnode method * rename resolution to magnification in shader relevant code * address review: revert one change and rename resInfo * lint * refresh annotations e2e snapshot --------- Co-authored-by: Michael Büßemeyer <[email protected]>
* add debug logging for dataset list route * add extensive logging to listGrouped method of DatasetController * dont log full objects * restore logging full object except for user objects * re add extensive logging for debugging * re add global access context to finding organizations in DSController.listGrouped --------- Co-authored-by: Michael Büßemeyer <[email protected]> Co-authored-by: Florian M <[email protected]>
* remove superfluous toasts * more layout fixes etc * update changelog * fix initial progress when uploading more than one dataset in the same screen * improve isFinishing state with a dedicated spinner (without overlay)
* remove too dark tree colors from hand coded array * update changelog * fix test * update colors again * fix that circles in front of tree names touched the border of the highlighted background * revert changes in spec * also take sahils wish into account
…calableminds#8244) * disallow empty annotation layer names and names starting with a '.' * add changelog entry * move new annotation layer validation rules to validateReadableLayerName --------- Co-authored-by: Michael Büßemeyer <[email protected]>
…#8218) * Add key in volumetracing to store if volume bucket data has changed * show warning in context menu for loading precomputed meshes when bucket data has changed * avoid unnecessary rerenders in context menu * ensure SET_VOLUME_BUCKET_DATA_HAS_CHANGED is dispatched when buckets are changed * add missing file * fix linting * rename load_mesh_menu_item_label file * use action creator instead of hardcoding action * fix that volumeBucketDataHashChanged was not handled when the server sent it * add comments * update snapshots * add changelog entry * remove unintentional changelog entry * change action property from layerName to tracingId --------- Co-authored-by: Philipp Otto <[email protected]> Co-authored-by: Philipp Otto <[email protected]> Co-authored-by: Michael Büßemeyer <[email protected]>
…yment (scalableminds#8240) * update pg_isready args to database configuration * update changelog
…leminds#8263) * fix legacy support for outdated displayName field of datasets * add changelog entry * remove directoryName from serialized dataset json format in legacy routes --------- Co-authored-by: Michael Büßemeyer <[email protected]>
* Revert "Re-Add debug logging for ds listing (scalableminds#8251)" This reverts commit 0a2afa4. * add some error message * Update app/models/dataset/DataStore.scala Co-authored-by: Florian M <[email protected]> --------- Co-authored-by: Michael Büßemeyer <[email protected]> Co-authored-by: Florian M <[email protected]>
…-properties.json` file (scalableminds#8268) * fix already upload of zarr datasets with alread existing datasource-properties.json * undo changes to exploreLocalDatasource in upload service * add changelog entry --------- Co-authored-by: Michael Büßemeyer <[email protected]>
* allow dollar in layer and dataset name * only allow $ layer names, not dataset names * add changelog entry * allow $ in annotation layer names * add schema version reversion to db reversion & rename var * fix dataset setting form validation errors * set timeout fixing form validation error to 0 ms --------- Co-authored-by: Michael Büßemeyer <[email protected]>
* add switch orga to legacy routes * fix pattern matching for annotation in orga switching mechanism * add assertion that directoryName and organizationId must be defined together * simplify assertion in backend * undo changes except for making AsyncRedirect a functional component * include successful disambiguation request even in case orga is not correct * add changelog entry * fix backend formatting * move code checking if ds is accessible via orga switching to separate service * fix imports * rename to AccessibleBySwitchingService * remove unused import --------- Co-authored-by: Michael Büßemeyer <[email protected]>
…calableminds#8271) * Data loading: save mem + cpu by re-using allocated fill-value chunks * changelog
* updated documentation on team assignments * update docs on toolbar * added toolbar icons to docs * added icon images for volume annotations * added icons for volume tool modifiers * more keyboard shortcuts highlighting * rephrasing for volume annotation tools * updated docs * Update docs/ui/toolbar.md Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> * Update docs/ui/toolbar.md Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> * more markdown formatting * Update docs/skeleton_annotation/tools.md Co-authored-by: Philipp Otto <[email protected]> * Update docs/volume_annotation/tools.md Co-authored-by: Philipp Otto <[email protected]> * Update docs/ui/toolbar.md Co-authored-by: Philipp Otto <[email protected]> * Update docs/users/new_users.md Co-authored-by: Philipp Otto <[email protected]> * Update docs/volume_annotation/tools.md Co-authored-by: Philipp Otto <[email protected]> * applied PR feedback * more PR feedback --------- Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> Co-authored-by: Philipp Otto <[email protected]>
…otation (scalableminds#8273) * only show locked banner if current user is in organization of the annotation * remove debugger statements * add changelog entry --------- Co-authored-by: Michael Büßemeyer <[email protected]>
…ack (scalableminds#8277) * Fix nml upload with only ds name set by using user's orga as fallback * add changelog entry * apply feedback * fix test compilation --------- Co-authored-by: Michael Büßemeyer <[email protected]>
…leminds#8280) * fix appending task bbox to user bbox in annotation nml upload * add changelog entry --------- Co-authored-by: Michael Büßemeyer <[email protected]>
…8253) * set move bbox cursor in bbox tool without moving mouse * improve code structure by extracting method * remove unnecessary code * add cursor update to tool specific key handlers * pass keyup map to input ts * remove console logs * improve arg names * add changelog * make some methods static members of BoundingBoxKeybindings
Bumps [nanoid](https://github.com/ai/nanoid) from 3.3.2 to 3.3.8. - [Release notes](https://github.com/ai/nanoid/releases) - [Changelog](https://github.com/ai/nanoid/blob/main/CHANGELOG.md) - [Commits](ai/nanoid@3.3.2...3.3.8) --- updated-dependencies: - dependency-name: nanoid dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Philipp Otto <[email protected]>
* auto-width for mapping dropdown * update changelog
…" (scalableminds#8572) This reverts commit 7275b8b.
* fix that representativeMagForVertexAlignment uniform was not updated when transforms were toggled * also work with dynamically changed transform value * slim down boilerplate * update changelog
Co-authored-by: Florian M <[email protected]>
* tmp: prototype tps surface for splitting segments * temporarily disable some CI checks * also implement delauny and splines approach * add missing saga * change default to splines * experiment with automatic ordering of points and flipping * fix typo * show spline on each section; don't cross surface in floodfill * fix some stuff * allow to continously place skeleton nodes like in a draw tool * prototype workflow mode * start introducing tool workspaces * some clean up * fix ts errors * linting * only generate bent surface when split workspace is active * remove lots of unused code (from old delauney and tps based approaches) * don't show edges if tree was created in split-workspace; more clean up * rename some stuff * linting * move file * fix bug * wip: add badge dot to workspace dropdown * fix missing type import * refactor annotation tool enums * remove AnnotationToolType in favor of AnnotationTool * rename control classes to ....ToolController; clean up tool label code * linting * make use of hasOverwriteCapabilities properties etc * rename tool workspace to toolkit * use toolkit collection in toolbar * fix cycling of tools * fix some cyclic imports * fix more cyclic dependencies and multiple bugs * tune toolkit view * clean up * lint * ensure that changing active toolkit won't leave a tool activated that is not available anymore * refactor disable/re-enable tool logic to saga * lint * remove verb-nurbs * remove unnecessary global * fix yarn.lock (hopefully) * fix tests * improve typing * merge tool saga into annotation tool saga * fix one tool spec; skip the other one for now * misc fixes for new skeleton brush mode * fix tool cycling in view mode * further clean up * more clean up * update changelog * automatically switch to default toolkit if in view mode * sort imports * make 2D floodfills possible on single section with new split boundary; tell user what's wrong when using floodfill in split-toolkit * forbid floodfill in other viewports if split toolkit is active * update surface on create tree and undo/redo * hide edges automatically for the active tree when the split tool is active and restore the edges visibility again later * fix spec * wip: indicator for different tool behavior * remove commented code * Update frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx Co-authored-by: MichaelBuessemeyer <[email protected]> * incorporate feedback * listen to more actions * add comments * debounce saga * iterate on ui * use fake enums for toolkit strings * clean up getPoints parameter * update docs * fix incorrect highlighting when measurement tool is active * refactor switch statement to record look up * remove superfluous hint in tooltip * add skeleton pen mode to docs * Update docs/proofreading/split_segments_toolkit.md Co-authored-by: Tom Herold <[email protected]> * Update docs/skeleton_annotation/tools.md Co-authored-by: Tom Herold <[email protected]> * Update docs/proofreading/split_segments_toolkit.md Co-authored-by: Tom Herold <[email protected]> * Update docs/proofreading/split_segments_toolkit.md Co-authored-by: Tom Herold <[email protected]> * Update docs/proofreading/split_segments_toolkit.md Co-authored-by: Tom Herold <[email protected]> * Update docs/proofreading/split_segments_toolkit.md Co-authored-by: Tom Herold <[email protected]> * use ordered list in docs * proof-read -> proofread; misc * pr feedback * split toolbar_view into several files and move into action-bar/tools subfolder --------- Co-authored-by: MichaelBuessemeyer <[email protected]> Co-authored-by: Tom Herold <[email protected]>
scalableminds#8574) * reduce page size for fetching version log to help against max string limits * update changelog
* use GITHUB_REF_NAME for push events * Revert "use GITHUB_REF_NAME for push events" This reverts commit 7bf6f69. * push docker tags only for branches --------- Co-authored-by: Florian M <[email protected]>
* rename view task type button and add tooltip * changelog
* replace docker compose script in yarn * update default postgres port * map redis port to 6381 * remove redis from docker-env * use ephermal postgres volume * add script to refresh screenshots * fix scripts * add missing env variables
…lableminds#8493) * fix coloring and spacing of icon in ai list view * makes bboxes and meshes rotate according to transformation settings * remove unused meshes root group * add utility function to iterate over each mesh group * fix applying transforms for meshes * move mesh mag scale into outer group again * Apply PR feedback (function renaming, wording and more) * refactor scene controller a bit to make hierarchy more obvious * get rid of group helper * transform bboxes according to attached tracing and meshes according to active segmentation layer * fix frontend tests * fix adding layer manually via advanced dataset settings tab * make meshes visible dependent on layer visibility * add missing mesh lights * fix removing meshes * use reuseInstanceOnEquality to cache visible segmentation layer names * fix precomputed mesh loading (context of yield calls was missing) * format frontend * fix import sorting in frontend
* Fix documentation link * Update `View Modes` page * Update changelog --------- Co-authored-by: Tom Herold <[email protected]> Co-authored-by: Philipp Otto <[email protected]>
* fix broken proofreading tool links in docs * html -> md --------- Co-authored-by: Tom Herold <[email protected]>
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