Lincbrain WebKNOSSOS upstream sync #15

* make login, registration and forgot password view more responsive to mobile devices - includes adding a link back to login for password reset view * make dashboard dataset view less awful * add changelog entry

…o LINC

* allow viewing a mapping * WIP: enable setting default active mappings in default view configuration * add default active mapping to default view configuration - add config settings to dataset settings default view config tab - auto load initial default mapping * fix bottom margin of layer settings - was broken in view mode with multiple segmentation layers; the "Save View Config..." Button had no spacing to towards * fix having the mapping settings enabled for layers with default mapping * WIP: move default mapping store proeprty to dataset layer config - undo moving mapping selection to a shared component * moved default active mapping from separate select to view config layer config - Also added validation check whether the mapping exists in the dataset view config settings * allow saving no default active mapping from view mode & model init to new dataset config version * rename defaultMapping to mapping * cache available mappings fetched from backend when checking config in dataset settings * remove logging statements * clean up * add changelog entry * apply pr feedback

* fix animation modal color layer validation * changelog * rename variable * apply pr feedback * improve error message of uint24 layers in animation modal --------- Co-authored-by: Michael Büßemeyer <[email protected]>

* validate BB size to be larger then 0 * changelog * appy PR feedback

Co-authored-by: MichaelBuessemeyer <[email protected]>

* default state wording to indicate loading * update nml tests --------- Co-authored-by: Michael Büßemeyer <[email protected]>

* Remove suggestion route * Remove WKWDataFormat * Lint * wip remove in frontend * unify readInboxDataSource * remove datasource suggestion - but keep isEditMode prop due to onboarding process needing this prop * remove left over code line linking to dataset import and clean up code * remove unused imports in backend * always show edit settings for datasets the user can edit * remove unused type * er-add dataset actions (show error & delete dataset) for broken datasets in dataset table * adapt wording in messages * add changelog entry * update migrationguide,changelog,docs --------- Co-authored-by: Florian M <[email protected]> Co-authored-by: Michael Büßemeyer <[email protected]> Co-authored-by: Florian M <[email protected]>

… split-off segments (scalableminds#7877) * combine custom names of merged agglomerates & transfer custom name to split off segment * add changelog entry * also keep custom name in split from all neighbors action * Update CHANGELOG.unreleased.md Co-authored-by: Philipp Otto <[email protected]> --------- Co-authored-by: Philipp Otto <[email protected]>

…calableminds#7887) * correctly use base mapping in FullMeshRequest when forwarding from TS to DS * changelog --------- Co-authored-by: MichaelBuessemeyer <[email protected]>

…7889) * Fix dataset composition when only one dataset is used * update changelog

* WIP: adding unit setting to datasource settings * WIP: backend: voxel size as object * WIP: Adding unit to dataset scale [ci skip] - make keep the base unit internally to nm - use configured unit for 3d space / voxel space - WIP: post fix all relevant function with Nm or Vx depending on their unit to make this as explicit as possible * finish migrating to new datasetscale format [ci skip] - current state: broken; nothing is rendered * adjust nml schema to backend changes * Fix initial dataset loading with scale in mircometers - add a lot of debugging output for testing [ci skip] * Fix td viewport camera init ( calulate in datasource unit not always in nm) - [ci skip] - Dont ignore far plane calculation * undo accidental semantic change * support conversion between larger and smaller units in 1d-3d - Full support for uncommon units is missing for 2d and 3d * format 1d length units in datasource unit to avoid precision loss * WIP: Support formatting for 2d and 3d values without always converting to nm [ci skip] * unify format function to work with multi dimensional values and not only in 1d && fix lots of tests [ci skip] * finish writing more tests for format utils * include all unit format in the datasource json validation in the frontend * Add support to convert to cm - WIP: Fix tests now that cm is supported * Add tests for uncommon units [ci skip] * rename "datasourceUnit" to "unit" everywhere * WIP: remove complex tests and add example based tests [ci skip] * add more format utils tests and fix some tests * fix / remove introduced todos of this pr * remove debugging console.logs * fix datasets e2e test * redo: use shorter decimals in scalebar * WIP: voxel unit support backend * fix vx distance calculation of shortest path between nodes * improve previous vx length calculation fix * use voxel size unit in more spots * schema, evolutions * snapshots * rename LengthUnit to Unit in frontend * further clean up of frontend code * more code cleanup frontend * update datasource json frontend validation * add changelog entry * log warning in case a mesh is loaded whose scale does not match the dataset's scale * bump api version to 7, drop 1 and 2 * document that ad-hoc meshing uses voxel size factor only * unused imports * WIP: use ngff units during explore * read ngff voxel size unit during explore * implement backend pr feedback part 1 * update nml spec snapshot * report unit in ngff streaming. change composeRequest to expect full voxel size with unit * format * unused import * Fix uploading zipped tiff (should set needsConversion=true) * changelog * rephrase code comment * WIP apply feedback * Add unit to params of wkw conversion job for dataset upload * apply pr feedback * fix adhoc mesh computation * rename datasetScale to voxelSize in frontend And remove datasetScale/voxelSize uniform from shaders as it was unused * power-of-two check on all mag dimensions * adapt voxelSize to nanometer for worker for now * use term REST API in changelog after all * use long lengthUnit names as default format * snapshots * migrate frontend to use long unit names except for format utils * rename UnitShortMap to LongUnitToShortUnitMap * fix flycam reducer tests --------- Co-authored-by: Florian M <[email protected]> Co-authored-by: Florian M <[email protected]>

* update to Typescript v5.5.0 * update typescript to version 5.5.x * changelog * apply PR feedback * fix formatting

scalableminds#7896) This reverts commit b6930e5.

…set (scalableminds#7893)

* mark json mappings as deprecated in docs * undo changes in application.conf

* fix not being able to save dataset settings due to diffing object with undefined resulting in an access error * add changelog entry

…calableminds#7890) * improve case handling of segment group child mesh visibility changing options * remove "All" from menu item text * add changelog entry * Update frontend/javascripts/oxalis/view/right-border-tabs/segments_tab/segments_view.tsx Co-authored-by: Philipp Otto <[email protected]> * apply pr feedback --------- Co-authored-by: Philipp Otto <[email protected]>

* Fix progress bar in brain spinner * fix typo in CSS var --------- Co-authored-by: Tom Herold <[email protected]>

… in getDerivedStateFromProps (scalableminds#7905)

) * Revert "Revert "Support other units than nm for datasets (scalableminds#7783)" (scalableminds#7896)" This reverts commit f874f68. * always pass short unit version to findBestUnitForFormatting * in zarr streaming served datasource-properties.json, use old voxel size format * make typing for UnitDimension / findBestUnitForFormatting more strict * make type of unit param for adjustUnitToDimension more restrictive --------- Co-authored-by: Michael Büßemeyer <[email protected]>

* center login forms * add changelog entry * proposal: stlye "try logging in" page like regular login page --------- Co-authored-by: Tom Herold <[email protected]>

…lableminds#7916)

* WIP pass through url param as default value to form and start to validate * auto fill URI form * WIP: try to submit second form * WIP: parse default dataset name from url * fix setting name * WIP: add hook to automatically store dataset * WIP: automatically submit second form * start to extract post upload modal * WIP: automatically import dataset * automatically store remote DS in happy path! * keep search params when redirecting back after required login * overlay brain spinner * clean up code a bit * remove console log * remove hook and use callback instead * fix theming of pw input * implement encoding and hash for remote dataset url * add tests for hash function * reroute to existing dataset * WIP: split URL better and set right DS name * pass through the successful url to DatasetAddRemoteView * improve regex * change text if we are in url import * clean up code * add changelog * WIP: address review * address review 2/2 * remove outdated comments from other PR * improve base62 encoding * add more test cases for base62 encoding * improve interface of onSuccess method and remove some obsolete null checks for url

* show segment name in context menu * long and short segment names * segment id and name in one line * Revert "segment id and name in one line" This reverts commit d4cbde4. * always truncate name to 20 letters * small code improvements * add changelog * remove emtpy line

…segmentation layer resolution (scalableminds#7921) * check for any matching resolution of the active segmentation layer before showing mesh scale mismatch error in console * add changelog entry

* enforce default newly create bounding boxes to be within dataset bounds * add first version bounding box moving * move bounding box by global data to be zoom independent * move bbox on ctrl / meta * add changelog entry * in case newly create bbox is outside of dataset bounds * add move hint to statusbar on ctrl pressed * use move mouse curser when in bbox tool and ctrl / meta is pressed * remove messages files * remove accidental pushed changes

…calableminds#7922) * Minor upgrades for backend dependencies, run codespell * changelog * bump scala and sbt --------- Co-authored-by: MichaelBuessemeyer <[email protected]>

* filter webgl context loss / isTrusted errors * fix that WebGLContextLost error should be logged instead of serialized isTrusted msg

…bleminds#7932) * add max timeout for chunks in resumable upload; use floor for rounding progress; tweak listed supported extensions * update changelog * remove rogue 'import' from UI * Update frontend/javascripts/admin/admin_rest_api.ts Co-authored-by: Florian M <[email protected]> --------- Co-authored-by: Florian M <[email protected]>

* Forbid editing other orgas public annotations * changelog

* WIP: Add recursive exporation of remote s3 layer * WIP: finish first version of recursive exploration of remote s3 layer * WIP: add gcs support * WIP: add gcs support * WIP: run explorers in parallel on same subdirectory * Code clean up (mainly extracted methods) * add local file system exploration * do not include mutableReport in requests regarding the local file system * add missing override of listDirectory of MockDataVault * some cleanup * add command to build backend parts like in CI to be ablte to detect errors before pushing * clean up code * format backend code * update docs to mention recursive exploration * add changelog entry * apply some feedback * apply some feedback; Mainly extract methods in ExploreRemoteLayerService.scala * Only let explorers of simple dataset formats explore for additional layers in sibling folders - And remove exploration of sibling folders to find additional layers * apply pr feedback * restore accidentally deleted changelog entry

* pin dockerfile to eclipse-temurin:21-jammy so that ubuntu 22.04 is used (libdraco4 is only published for that) * also update docker files for tracing and datastore

…ableminds#7911) * WIP: add option to expand and collable all children of segment group * recursively open subgroups * adjust icon, label and expand all groups on default * WIP: add two menu entries * add two menu entries and hide/show them as useful * remove comments * only collapse subgroups * remove unnecessary types and extract groupid to key conversion to method * avoid multiple calculations to get children * only add group itself to expanded if it is collapsed * add changelog * address review

* add yarn/dbtool command insert-local-datastore * typo * fix typo

* WIP: add option to expand and collapse all children of segment group * recusively open subgroups * add two menu entries and hide/show them as useful * remove comments * WIP: move expanded groups to store * WIP: allow expanding and collapsing groups again * keep state of collapsed or expanded subgroups if parents is collapsed * remove comments etc * improve comments * dont use treedata any more * persist expanded state of segment groups * fix bug that root group expansion collapsed everything * fix bug that groups are collapsed upon subgroup expansion * hopefully improve performance by updating only in getDerivedStateFromProps * improve some comments and var names, lint * improve performance * WIP: address review * add changelog * lint * add comment and rename method --------- Co-authored-by: Michael Büßemeyer <[email protected]>

* detect redundant savequeue entries and escalate to an error to prevent data corruption * provoke redundant saves by spawning setup saga twice * temporarily disable some CI checks * add UPDATE_TEMPORARY_SETTING to blacklist for action logging * Revert "temporarily disable some CI checks" This reverts commit e121983.

…lableminds#7947) * avoid object creation when segment groups are collapsed/expanded * set isExpanded to shouldBeExpanded

* the error reporting of unhandled rejections was buggy which led to too much aggregation in airbrake * temporarily disable some CI checks * revert not-on-master.sh changes

an error is an error is an error

* add first version of bbox highlighting via left click in viewports * auto scroll active bbox into view upon change * also highlight bbox when modified or created * add changelog entry * apply feedback & refactor bounding box highlighting mechanism

…calableminds#7954) * lower z-index for trashcans in remote dataset import * add changelog

* expand segment group if the are collapsed and one of their children is focused * always expand root group in segments tab * hide switcher icon for root group * add root to expanded groups again * add changelog entry * address review: initialize pathToRoot as Set * rename method

…ntend (scalableminds#7654) * add datastore route to list all agglomerate ids * remove unused file access * types * Apply hdf5 mappings in frontend [WIP] * Fix segment and agglomerate id mixup in proofreading saga * add route to tracingstore * edit mapping after merge and set it in redux store * Fix mapping initialization * WIP: implement split in frontend * Only load subset of mapping for segments visible 5s after page load * small fix * cleanup, time measurements, throttle mapping requests to 500ms -> currently too laggy * Update redux-saga to use throttle with effectChannels * Only refresh mapping if bucket data changed. Fix partial mapping updates after master merge. * Fix how proofreading actions update the mapping in the frontend * disable most ci checks * misc improvements * refine shouldUseDataStore logic * fix type error * fix some type errors * fix more type errors * use NumberLike type for number and bigint at various places * more NumberLike usages * fix lots of typescript errors (related to bigint and to redux) * fix more type errors * fix the last type errors * restore proper NumberLike definition and fix remaining type errors * remove unused imports * fix race condition which could cause mapping to not be properly initialized upon reload * only pass isCentered instead of centeredSegmentId to SegmentListItems * fix react warning when closing context menu for the first time * add debug code for rare scenario where segment id is not an integer * fix TS error * fix that hovered unmapped segment id would not update sometimes * avoid two map look ups * add dryUpdate step before saving proofreading update actions * undo provoking the error * make selective segment visibility in proofreading an option * fix NaN value after mapping unknown segment key * avoid parallel executions of updateHdf5Mapping and also cancel updateHdf5Mapping if wk enters a busy state to avoid using outdated values * always compare known segment ids to newest mapping instead of 'previous' one that isn't updated when doing proofreading operations * don't crash completely when segment mapping is not known yet and user initiates proofreading action * remove artificial delays * improve logging * fix ts error * remove debugging code for NaN mapped id * tweak hovering * rename MIN_CUT_AGGLOMERATE actions * adapt cutFromNeighbors to magic mapping approach * avoid roundtrip for mesh reloading by using newest mapping * tweak hovering (II) * extract code into gatherInfoForOperation * fix context menu for skeletons in 3d viewport * make agglomerate-skeleton-proofreading compatible with magic mappings * don't run rendering code for context menu when its not open * remove unused previousMappingObject * dynamically switch between local and remotely applied mappings when switching to/from proofreading tool etc. (unfortunately, buggy) * auto-reload page if dev-proxy fails * fix missing reload when disabling/re-enabling mapping (now too many reloads are performed) * extract finishMappingInitialization action * extract ensureMappingsAreLoadedAndRequestedMappingExists * rename mappingIsEditable to hasEditableMapping * introduce BucketRetrievalSource to better cancel/restart bucket watchers and reload the layer when necessary * introduce clearMappingAction * make sure that getBucketRetrievalSource doesn't create new instances all the time when multiple volume layers exist * move cuckoo modules into libs/cuckoo * use cuckoo hashing for gpu-based mapping instead of binary search (proper uint64 support needs to be tested) * add missing module * remove logging * make use of protobuf shortcut getHasEditableMapping * Update frontend/javascripts/oxalis/model/sagas/mapping_saga.ts Co-authored-by: MichaelBuessemeyer <[email protected]> * Update frontend/javascripts/oxalis/model/sagas/proofread_saga.ts Co-authored-by: MichaelBuessemeyer <[email protected]> * mappingIsEditable -> hasEditableMapping to fix compilation error * remove unnecessary braces * incorporate some pr feedback * more pr feedback * add comment to cuckoo table 64 bit * also implement cuckoo table for uint32 keys and values * fix invalid initialization of mapping texture when mapping is disabled * fix that mapping was applied twice * fix uint32 cuckoo implementation (still hardcoded to always use 32 bit) * use 64 bit look up when necessary in shader * remove unused mappingSize * avoid toolbar rerendering * only write necessary changes to cuckoo table instead of rewriting it from scratch every time * ensure diffing of previous and new mapping is fast be providing cached diff operation for which the cache is manually set by the mapping saga * eagerly compute value set when reasonable to avoid clustering of that computation and to improve FPS * add missing worker * implement maintenance of value set for entire data cube to avoid recomputation * Revert maintenance of value set because it didn't help with performance This reverts commit c7bb508. * remove todo because it was tried in c7bb508 and reverted afterwards * remove some time logging * optimize/combine some set operations (2x as fast now) * move and rename diffSets function * further optimization of set operations (in total 4x faster compared to the initial version) * remove unused code * remove superfluous parameter * add renaming todo * delete create_set_from_array webworker as it didn't show an improved FPS rate (therefore, the overhead of passing the data doesn't seem reasonable) * delete debugging code from cuckoo modules * move attemptMappingLookUp glsl code * add some comments * reactivate CI checks * remove unused code * remove obsolete imports * simplify editableMapping check * fix ts problems * fix cyclic dependencies * fix 64 bit mapping rendering * remove UI warnings that the merger mode doesn't support 64 bit, because now it does * fix linting * fix proto related tests * fix more specs * fix pullqueue spec * refactor setNumberLike in cuckoo tables and update some todo comments * remove unused route, change tracingstore mapping route to proto ListOfLong * toSet * remove unused getAgglomerateIdForSegmentId * fix rendering bug outside of viewport on some GPUs * adapt agglomeratesForSegments route to new protobuf interface * link 64-bit issue (scalableminds#6921) in todo comments * introduce mappingIsPartial uniform * mention scalableminds#7895 in todo comment * remove commented code * avoid expensive console.log for large mappings * disable most ci checks * fix incorrect hash table size and use hashCombine twice to fix poor capacity utilization due to suboptimal hash distribution * fix cuckootable rehash (did redundant work) and adapt max iterations parameter * if many inserts are done for the mapping, flush the table at the end * fix weak hashing for power-of-two table sizes * refactor diminished hash capacity tweak; clean up and extend tests so that maxing out capacity is tested, too * clean up reloadData related code in mapping_saga * fix serializing bigint to protobuf long * fix toggling of json mappings * group consecutive actions in action logger middleware; add debug logging for dispatched actions * fix that forceful disabled tool wasn't re-enabled when possible (e.g., after toggling segmentation opacity) * mention 64 bit support issue in comment * fix broken mapping of ids by sorting the input ids for the server * add comment about sorting * don't map ids dynamically in segment list view (instead segment items are created with the mapped id if a mapping exists); see scalableminds#7919 as a follow-up * test reaching critical capacity and remove todo comment * remove some todo comments regarding mapId code that might return unmapped ids if the mapping is partial (impact should be low, add comments for it) * remove more todos and fix toggling of hdf mappings when no volume tracing exists * cast to number when sorting bigint * use bigint in proofreading_saga where sensible and cast to number as late as possible (e.g., in action creators, in REST API etc) * disable more ci stuff * try to handle most ids as Number and cast to Number only when dealing with mapping object and buckets * show zoom warning for agglomerate files only when the mapping is applied remotely * fix that supervoxel highlighting of mesh stays active after leaving proofreading tool (fixes scalableminds#7867) * fix that after changing the color of a mesh via the segments tab the mesh is always highlighted after initial hover (fixes scalableminds#7845) * remove unused imports * fix proper type of values returned from getAgglomeratesForSegmentsFrom* * fix incorrect bigint check and refactor to avoid the same mistake in the future * fix unnecessary type adaption that failed on null * fix another sorting bug * integrate pr feedback * rename cuckoo table to CuckooTableVec3 * unify 64 bit todo comments * forceful -> forcefully * refactor eager value set computation * use 0s to initialize mapping uniforms * refactor/fix mapId logic for unmapped ids * fix selective visibility for alpha != 0.2 * only emit soft errors when a data value could not be mapped * fix mapping message hiding too early/never; fix disabled message in mapping UI * misc console stuff * also skip texture updates for cuckoo table when lots of unsets need to be done * show short user notification when segmentation layer is reloaded * highlight whole segment mesh on hover even when geometry is not merged (i.e., super-voxels are highlightable) if not in proofreading tool * use current mag when reading segment ids in proofreading (unless agglomerate skeletons are used) * remove last todo comments * update changelog * remove console.log * re-enable ci checks * fix linting --------- Co-authored-by: Daniel Werner <[email protected]> Co-authored-by: Charlie Meister <[email protected]> Co-authored-by: Philipp Otto <[email protected]> Co-authored-by: Philipp Otto <[email protected]> Co-authored-by: MichaelBuessemeyer <[email protected]>

* WIP: Use java s3 client v2 * credential providers * compiler errors * scratch out correct exception type * undo application.conf changes * wip: add more s3 datavault tess * fix range header * test for file listing * test dir listing * localhost is not amazon * default region US_EAST_1 * content encoding * fix and test encoding * changelog * use renaming imports rather than fully qualified identifiers

* More compact repeated logging * unused import * Update webknossos-tracingstore/app/com/scalableminds/webknossos/tracingstore/controllers/Application.scala Co-authored-by: MichaelBuessemeyer <[email protected]> --------- Co-authored-by: MichaelBuessemeyer <[email protected]>

* WIP: disable AI analysis for 2D and ND datasets * improve 2D and ND check * disable start job button if dataformat is not supported * improve code structure * simplify logic whether AI job can be started based on data format of color layer * add toast for warning about wrong DS format * blacklist uint24 * remove bool negotiation * add changelog * remove application.conf edits * put tooltip to var instead of function * address review * lint

…minds#7949) * misc improvements for restoring an older version via the UI * wording * remove sleep * tweak margin * use utility css class * revert constant

* support reading zstd-compressed zarr2 datasets * changelog

…leminds#7902) * WIP: Allow supplying full workflow yaml for infer_with_model job * fix request logging rounding error * show workflow yaml editor (collapsed by default) when configuring inference for custom models * remove new_segmentation_layer_name param * Add default workflow to custom model inference * only use custom workflow if advanced collapse is enabled & make enabling more explicit via using a checkbox * remove option to specify output segmentation layer name * reset application.conf * rename job param * rename workflow template file and rename its imported var to full caps --------- Co-authored-by: Philipp Otto <[email protected]> Co-authored-by: Michael Büßemeyer <[email protected]>

Bumps [braces](https://github.com/micromatch/braces) from 3.0.2 to 3.0.3. - [Changelog](https://github.com/micromatch/braces/blob/master/CHANGELOG.md) - [Commits](micromatch/braces@3.0.2...3.0.3) --- updated-dependencies: - dependency-name: braces 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]>

…scalableminds#7902)" (scalableminds#7972) This reverts commit 24e1e00.

* pass unit to wkw conversion job * improve typing in upload view & replace scale with voxelSizeFactor * add changelog entry * rename job param to be more explicit part of the voxel size

) * refactor tree hierarchy view as functional component * WIP refacator as antd <Tree> * restore checkbox and expaneded keys * restored expand/collapse all behaviors * re-use <DotIcon> components but with rgba values * restore search * fix drag and drop for single tree * fix multi select * remove react-sortable-tree library * updated styling and text wrap * make tree height/width smaller * collapse sup groups * added shift selection to skeleton tree * updated changelog * Update frontend/javascripts/oxalis/view/right-border-tabs/skeleton_tab_view.tsx Co-authored-by: MichaelBuessemeyer <[email protected]> * Update frontend/javascripts/oxalis/view/right-border-tabs/tree_hierarchy_view_helpers.ts Co-authored-by: MichaelBuessemeyer <[email protected]> * Update frontend/javascripts/oxalis/view/right-border-tabs/tree_hierarchy_view.tsx Co-authored-by: MichaelBuessemeyer <[email protected]> * Update frontend/javascripts/oxalis/view/right-border-tabs/tree_hierarchy_view.tsx Co-authored-by: MichaelBuessemeyer <[email protected]> * apply PR feedback * fix tooltip * add autofocus to tree search * fix active tree updates highlighting tree * fix shift selection * fix crash on tree deletion * apply darker background colors for trees in dark mode * disable node drag icon * disabled checkboxes for empty groups * use darker colors for <Tree> components in dark mode * fix multi select drag and drop * formatting * fix CSS alignment of tree checkboxes * use antd themeing instead of CSS overrides * format * Persist skeleton group expansion state (scalableminds#7939) * move skeleton expanded/collapsed group state to store * WIP: expand and collapse all skeleton groups * fix expand/collapse skeleton groups * expand group if tree is dropped * clean up code * lint * address review * address review 2/2 * remove console.log * lint * add small condition for ondrop * persist isExpanded state in backend * make groups default expanded if field is absent in nml (backend only) * make groups default expanded if for written nmls (backend only) * fix backend treegroup update action tests * add isExpanded to frontend nml support * update snapshots * omit object creation in var * omit useless return statement in map * add isExpanded prop to tree groups in backend testing fixtures (dummies) * add test to backend nml test to test properly setting default to expanded * add changelog * WIP: address review * fix bug where drag and drop of empty groups was failing * remove comment --------- Co-authored-by: Michael Büßemeyer <[email protected]> Co-authored-by: Philipp Otto <[email protected]> * fix tree sorting * fix off-by-one error in shift select * override <Tree> scroll handle in dark mode * use scrollTo(auto) * format * fix typo --------- Co-authored-by: MichaelBuessemeyer <[email protected]> Co-authored-by: Philipp Otto <[email protected]> Co-authored-by: Charlie Meister <[email protected]> Co-authored-by: Michael Büßemeyer <[email protected]> Co-authored-by: Philipp Otto <[email protected]>

* assert gzip in wkorg nightly for buckets and assets * [tmp] run wkorg nightly on push * only request one bucket in test * fix tmp nightly config * provoke error * don't provoke error anymore * restore original ci

* WIP: try autosizer * WIP: use antd virtual table * recover table layout * combine autosizer and antd virtual table; fix width * add changelog * make the scroll height of virtual table a bit smaller than the surrounding div --------- Co-authored-by: Philipp Otto <[email protected]>

…alableminds#7975) * dont fill segment if editable mapping is active * fix that some context menu entries were shown without segmentation layer * clean up code and reuse disabledVolumeInfo * add changelog * address review

…bleminds#7967) * Allow alignment job to take matches from skeleton into account * Use url parameters instead of request body json, check for empty trees * Update changelog * Beautify --------- Co-authored-by: MichaelBuessemeyer <[email protected]>

…minds#7958) * use react-tooltip in segments tab instead of antd tooltip * fix layout issue with new tooltip * use one dropdown component for entire segment list view * clean up * also switch segment group context menu to centralized dropdown * more clean up and fix auto closing of context menu * expose disableSaving in front-end api * use FastTooltip in position view * use FastTooltip in toolbar * use FastTooltip in statusbar * remove unused imports * temporarily disable some CI checks * fix styling * DRY some code and remove commented code * also use FastTooltip for flex layout tab titles * prepare FastTooltip for more usages * change Tooltip to FastTooltip in many more places (sidebars, ButtonComponent, InputComponent etc) * use FastTooltip in dataset info tab * fix linting * expose webknossos.DEV with benchmarkMove, createManyTrees, createManySegments, showFpsMeter, debuggerIn and direct property access to api and store * use FastTooltip in scalebar and fix positioning in ViewportStatusIndicator * simplify resolution tooltip in status bar by using html prop instead of portals; also extract speedometer to avoid that the interval recalculates the entire statusbar * avoid constant re-rendering of ToolbarView * remove unnecessary connect props from MappingSettingsView * disable smoke tests * avoid re-render of save button every few seconds * add explanation to biome-ignore * remove skeletonToolHint code completely (this used to display a tooltip automatically on the toolbar for complex skeleton actions when being in legacy mode) because the status bar now does a way better job for this [ci skip] * don't update FixedExpandedTable when expandedRows 'changed' from empty array to empty array * remove perfTest code * restore ci * restore ci * use antds validation when bbox field is invalid (replacement for styled tooltip) * fix style passed to input_component * remove unused import * remove unused prop * get rid of ReactDOMServer.renderToStaticMarkup * simplify interface for using danymicRenderer with FastTooltip * add a nice docstring for FastTooltip * extract constants * add fast tooltip to async button * add full stops in settingsTooltips where it makes sense * contextmenu -> context menu * fix that switching to skeleton tab always jumped to the position of the active node * fix layouting of right sidebar-toggle button * improve typing in flex layout wrapper * also use fasttooltips in global context menu * update changelog

* WIP: Segment Anything 2 * adapt api to segmentAnythingMask * renamings * unused import * use new getSamMask route in front-end * remove onnx from webpack config * fix interpreting sam mask * temporarily disable some CI checks * allow 3d sam in backend * send full shape to sam serve * request sam masks for multiple sections * time logging in backend * fix strides for viewports * allow sam to paint outside of user provided bbox; fix some bugs * fix sam-labeling in other mags * allow to configure prediction depth via ui * add progress bar to navbar and use that for showing progress when SAM is used * clean up generate_diff_message.spec.ts * implement estimateBBoxInMask * tweak progress bar * integrate fast estimateBBoxInMask * add NUX for new sam with depth * fix error in case predictionDepth wasn't configured yet * simplify and fix calculation of targetBox * fine-tune nux * put quick select for multiple slices into same undo action * restore ci * update changelog * tmp: skip getFeatureToggles() snapshot test * remove unused findBBoxInMask * make surroundingBoundingBox comment clearer * integrate pr feedback * tweak progress bar styling * undo remaining dev related changes * update migration guide --------- Co-authored-by: Philipp Otto <[email protected]>

* move delete, go to center and export options for bounding boxes to context menu * register all segments in a bounding box * lint * add limits for segment count and bb volume * add limits for segment number and bb volume; improve styling * remove dev edits * require visible segmentation layer to register segments * register segments to seperate new group * add tooltip * add margin and add info icon for tooltip * move method * add changelog * improve changelog * WIP: address review * address review pt 2 * fix some errors that occured when solving merge conflicts * unify and fix the bbox context menu in case the annotation is not editable * improve toast message * fix that segment 0 was registered * small fixes

…eminds#7988) * create new group to set expanded skeleton groups * minor improvements * introduce new action when segment groups are expanded or collapsed * move method to helper * fix collapse/expand all action in skeleton tab * remove console.log * add changelog * hopefully fix cyclic dependency * WIP: address review * fix that nested groups can be selected * fix that root group wasnt selectable

* WIP add zarr3 streaming - Added mag/zarr.json & mag/coords route for datasets (not annotations) * manage minimal zarr3 support for viewing a dataset and viewing an annotation * add basic zarr 3 ngff v2 group header route * add zarr 3 ngff v2 group header route for annotations * merge Zarr3StreamController into ZarrStreamingController * ensure full match when parsing zarr coordinates to avoid parsing any non-numerical characters * make NgffMetadataV2 nd compatible * refactor code * remove Zarr3StreamingController.scala * minor code fixes; mostly remove unused imports * remove fixed full length match of zarr coordinate regex parsing; - wk seems to send c.0.x.y.z requests and the c at the start does not match with the regex resulting in invalid coordinate parsing * add c. as a prefix to the coordinate parsing regex as defined by the zarr spec * exclude leading c from the zarr3 coordinate parsing * apply pr feedback * remove unused imports and format code * add datasource-properties.json and dir listing routes to zarr 3 streaming * format code * add changelog entry * fix Zarr3GroupHeader json serialization format * fix backend format * Update webknossos-datastore/app/com/scalableminds/webknossos/datastore/datareaders/zarr/NgffMetadataV0_5.scala * add comments about why manual json serializer is needed --------- Co-authored-by: Norman Rzepka <[email protected]>

) This reverts commit cb1331b.

* integrate speed test * use one ContextMenuContainer for the skeleton tab (3x speed up for scroll benchmark) * remove deleteGroup wrapper * rename skeletonTrees to skeletonTreeIds; slight misc improvements * change tooltip to fasttooltip in two places * remove unnecessary connect-dependency on state.tracing in SkeletonTabView * clean up * clean up * update changelog * DRY context menu wrapper for segment and skeleton tab * DRY getNoActionsAvailableMenu * move tree and tree-group renderer into own module; also extract the functions for the context menu and hoist where possible * inline function * fix up typing after merge conflict * fix type-ahead filtering in folder-select-UI in dataset import * fix width of sharing link in share modal

* WIP add zarr3 streaming - Added mag/zarr.json & mag/coords route for datasets (not annotations) * manage minimal zarr3 support for viewing a dataset and viewing an annotation * add basic zarr 3 ngff v2 group header route * add zarr 3 ngff v2 group header route for annotations * merge Zarr3StreamController into ZarrStreamingController * ensure full match when parsing zarr coordinates to avoid parsing any non-numerical characters * make NgffMetadataV2 nd compatible * refactor code * remove Zarr3StreamingController.scala * minor code fixes; mostly remove unused imports * remove fixed full length match of zarr coordinate regex parsing; - wk seems to send c.0.x.y.z requests and the c at the start does not match with the regex resulting in invalid coordinate parsing * add c. as a prefix to the coordinate parsing regex as defined by the zarr spec * exclude leading c from the zarr3 coordinate parsing * apply pr feedback * remove unused imports and format code * add datasource-properties.json and dir listing routes to zarr 3 streaming * format code * add changelog entry * fix Zarr3GroupHeader json serialization format * fix backend format * Update webknossos-datastore/app/com/scalableminds/webknossos/datastore/datareaders/zarr/NgffMetadataV0_5.scala * add comments about why manual json serializer is needed * use chunk key encoding version 2 as zarr 2 stream also has no prefix of "c." when addressing an array * do not include a prefixed "c." when parsing coordinates -> works with zarr 2 and 3 streaming * remove outdated comment * update error message (remove hint to include a prepending "c." --------- Co-authored-by: Norman Rzepka <[email protected]>

…ds#7998) * rename setWaypoint to handleCreateNode in arbitrary controller * rename setWaypoint to handleNodeCreation * refactor * implement createNode in api_latest; refactor to allow better parameteriziation; fix that centering node did not work when new node was not activated * refactor getActiveNode accessor to not use a Maybe * refactor getActiveTree accessor to not use a Maybe * update changelog * remove unused import * allow to pass additionalCoordinates when creating nodes via API * set skipCenteringAnimationInThirdDimension to false when using api

…lse (scalableminds#8008) * detect neuroglancer precomputed and n5 datasets as needsConversion=false * changelog

…calableminds#8009) * fix registering segments in bbox for segmentations with missing mag1 * update changelog

* upgrade ant icons to 5.4 * remove iconfont * changelog * reformat package.json --------- Co-authored-by: Philipp Otto <[email protected]>

* backend: add support for point interaction * format backend * fix buffer size calculation of buffer sent to torchserve * support point interaction with sam-based quick select * tmp enable SAM and disable most of ci * improve comments * update nux text * tweak width of nux * incorporate feedback * undo tmp changes * fix busy-mutex violated * make backend accept sam bboxes with width / height less than 1024 * refactor a bit (e.g.,DEV flags) * use a local bounding box for SAM by default (can be toggled via webknossos.DEV.flags.sam.useLocalMask = false) * tune busy blocking msg * refactor WkDevFlags further * remove unused import * tmp: disable some ci steps * update comment in backend about torchserver request params * fix that the padding could make the bbox too large * use viewport extent in correct mag as minimum for mask size * Revert "tmp: disable some ci steps" This reverts commit 8362003. * also mention clicking in quick select tooltip (and docs) * update changelog * add tooltip with hints for sam * improve styling of hint * improve tooltip text --------- Co-authored-by: Philipp Otto <[email protected]> Co-authored-by: Philipp Otto <[email protected]>

…inds#8006) * add links for skipped tasks in voxelytics workflow reports * changelog * comments * styling * add evolution and comment --------- Co-authored-by: Florian M <[email protected]>

* Bump fossildb, backend deps, run codespell * changelog

…s#8015) * keep asset timestamps from filesystem when building jar * undo application.conf edits

* update husky for faster post-checkout * remove yarn prepare * undo formatting changes to package.json * remove unused yarn command

…odel job (scalableminds#7902)" (scalableminds#7972)" (scalableminds#8017) This reverts commit 97ef1d1.

* use tps instead of affine in compose * temporarily disable some CI checks * always sort trees when composing datasets with landmarks * add UI checkbox for affine vs tps * fix that p tag cannot contain ul * also sort nodes by id * fix inverted TPS transform creation when loading dataset; add more comments * render dataset description as markdown in dashboard; update dataset description after composing * fix mean error formatting in description * disable TPS checkbox for now * restore ci * update changelog * make optInfoOut writing independent from IS_TESTING * ask user for landmark augmentation when affine estimation fails; assert >= landmarks; test tps creation eagerly etc * move allowThinPlateSplines into wk dev flags * Update frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx Co-authored-by: MichaelBuessemeyer <[email protected]> * move guardedWithErrorToast fn * format * fix cyclic dependency --------- Co-authored-by: MichaelBuessemeyer <[email protected]>

…ableminds#7976) * add missing parameters to conversion between wk layer to zarr layer * format code * fix axes indexing when exporting datasource json in zarr v2 streaming * remove accidental comment in datastore routes file * fix axis order when writing datasource-properties.json for nd datasets * properly map additional coordinates to existing additional axes * apply feedback * fix datasource properties json of zarr3 annoation streaming sending wrong format version for volume annotation layers * format backend --------- Co-authored-by: Florian M <[email protected]>

…scalableminds#8011)

…scalableminds#8012) * Move to new voxel size format in zarr-streaming datasource-properties.json * changelog

…ing to comments tab (scalableminds#8022) * fix active tree's comments not getting scrolled into view when switching to comments tab * add changelog entry * remove outdated comment in schema.sql * scroll to top

* fix wrong react import * update changelog

* temporarily disable some CI checks * bump 5 to 30 * set limit to 16 * try to fix sam masks for long depths if segment is moving in xy * Revert "temporarily disable some CI checks" This reverts commit feae116. * update changelog * cross link constants

…eminds#7981) * implement test route checking if chunk is present * WIP: Implement ongoing uploads listing route * implement first version of robust resumable upload * update build backend script command to remove autogenerated message files * fix frontend typing * refactor code * format backend * fix test file route * clear uploadId after successful upload in frontend; reenable checking for duplicate dataset names when not continuing an upload * format backend * apply feedback * fix expected format from backend when requesting ongoinguploads * apply feedback * remove unused import * consistent renaming to unfinished uploads * add sanity check that file names must be equal to initial upload * do not require same order of files * include file names in error to make searching for these file more easy and less guessy * fix "files not matching initial upload try" error message * add changelog entry --------- Co-authored-by: Michael Büßemeyer <[email protected]>

* update deps to ract v17 * refactor antd table columns as arrays instead of react elements * fix dayjs types * update more packages * fix linting * undo any changes related to SortableTree lib * remove enyzme adapter for react 16 * format with 4 spaces * fix type imports * updated cahngelog * removed duplicate keys * remove enzyme component testing framework * move e2e-setup.ts out of enzyme folder * pr feedback --------- Co-authored-by: Philipp Otto <[email protected]>

) * save some io when loading oversegmentation meshfiles * remove time logging * format

…lableminds#8035) Co-authored-by: Michael Büßemeyer <[email protected]>

* Add dataset metadata input to details view in dashboard * update docs * Improve mobile support of views (scalableminds#7876) * make login, registration and forgot password view more responsive to mobile devices - includes adding a link back to login for password reset view * make dashboard dataset view less awful * add changelog entry * Mapping in default view config (scalableminds#7858) * allow viewing a mapping * WIP: enable setting default active mappings in default view configuration * add default active mapping to default view configuration - add config settings to dataset settings default view config tab - auto load initial default mapping * fix bottom margin of layer settings - was broken in view mode with multiple segmentation layers; the "Save View Config..." Button had no spacing to towards * fix having the mapping settings enabled for layers with default mapping * WIP: move default mapping store proeprty to dataset layer config - undo moving mapping selection to a shared component * moved default active mapping from separate select to view config layer config - Also added validation check whether the mapping exists in the dataset view config settings * allow saving no default active mapping from view mode & model init to new dataset config version * rename defaultMapping to mapping * cache available mappings fetched from backend when checking config in dataset settings * remove logging statements * clean up * add changelog entry * apply pr feedback * Fix animation modal color layer validation (scalableminds#7882) * fix animation modal color layer validation * changelog * rename variable * apply pr feedback * improve error message of uint24 layers in animation modal --------- Co-authored-by: Michael Büßemeyer <[email protected]> * Validate animation job bounding box (scalableminds#7883) * validate BB size to be larger then 0 * changelog * appy PR feedback * force serialization of dataset details prop in compact version of dataset * WIP adding details to folder * First version metadata support for folders * fix folder listing query * finish frontend support for folder metadata * default to undefined columnKey and not null to potentially prevent frontend dataset filtering - reason: ll.530 checks for sortedInfo.columnKey == null and columnKey is per default "" which makes this check fail and thus the chained map will never be executed * add evolution * update test db init data & folder snapshot test & bump schema version * remove unused import * also blur on property input * only support / show current error * improve css * WIP: use new json schema to save dataset & folder details and re-style metadata table * fix backend to work with new type of details dataset / folder field & WIP restyling of metadata / details table * WIP: improve dataset details table styling and add support for different types * details table for folders and datasets version 2 * WIP: adapt migration to new details format * uncomment ci tests * mini migration fix * - rename details to metadata * fix schema * remove unused backend imports * only update metadata set of metadata table when folder / dataset changes * ensure flushing updates on unmount of metadata table & increase debounce time * remove accidental change * WIP apply styling feedback & refactor handling metadataentry type * remove unused css * keep old dataset while updating & refetching in the dataset details view * remove unused code as search support for metadata entries is currently not planned * do not include metadata in dataset compact version * Fix Dataset refetching - also update datasetById when updating a dataset in the dashboard - Avoid spinner when updating metadata - Avoid unnecessary updates by guarding the debounced flush against not having pending calls to the debounced function * have fix width for metadata table cell contents to ensure consistent table column width and consistent layout - Ignore adding new metadata entry when there is already an empty one to avoid showing an error * enable selecting current folder of folder tree view as active details element * do not have initial empty metadata row * WIP: Apply styling update * Finish next version * hopefully fix flickering bug in when two different metadata updates have a cyclic race against each other * Only have default metadata on species, brainRegion & acquisition when creating a publication * also fill full metadata table width in case of an empty table * allow changing prop name although it is a duplicate; do not save metadata in case it has errors * clean up code for review * add changelog & migration entry; rename evolution * also rename revision; add comments to revision; remove dev logging * Apply PR Feedback * move metadata table to own file * only update when metadata changed & refactor code * fix updating the wrong dataset or folder with the newest metadata version of the table * allow multiple error rows & only update local metadata set if new folder/dataset or update failed - Try forcing dropdown menu to stay open during update -> does not work atm :/ * update preview image * fix color layer / segmentation layer switchero bug * remove periodic autosave an replace with explicit save via button or autosave when changing focused dataset / folder * re add auto saving mechanism and do not have nested components to avoid frequent remounting * update snapshots * refactor code & remove `useWillUnmount` which sent outdated metadata update to the backend breaking the whole metadata feature. * remove unnecessary dependency from useEffect accidentally added in a different pr * include metadata in full dataset update route * fix full update dataset route for metadata support * remove option to update tags (as they will no longer be rendered in the frontend) * remove index from initial metdata added to datasets with publication * apply pr feedback (testing pending) * lint frontend * do not send updates while a row of the metadata table is focused - Also: Use up-to-date metadata value on unmount effect (previously the inital value was sent to the server) * avoid lost isSaving updates due to changes to `focusedRow` state while updating. Due to changes to `focusedRow` while saving the previously used isMounted boolean was set to false when changed during the update post to the backend and thus the update to isSaving never got through the guarding. => Now it is explicitly tracked via a custom hook to avoid this scenario * fix sending double updates on unmount * apply pr feedback * migrate existing tags into metadata * remove unwanted additional wrapping array around migrated tags in metadata value entry * add undo migrating tags to metadata to revision * fix revision schema * give delete metadata entry button some more space; align key input to top & center delete button * update schema migration version * apply feedback * readd tag support in frontend (and backend) * fix backend * make metadata non nullable * update snapshots tests * fix metadatatype type definition * fix reversion against default null values of re-added details column --------- Co-authored-by: Tom Herold <[email protected]> Co-authored-by: Florian M <[email protected]> Co-authored-by: Philipp Otto <[email protected]> Co-authored-by: Michael Büßemeyer <[email protected]> Co-authored-by: Florian M <[email protected]>

* Update ava to v4.3 * update ava to v5.3.1 * Update ava to v6.1.3. Fix e2e tests and snapshots. * readd mistakenly removed code * Ignore changed lastActivity property in one test. It is unclear why it changes - the test are executed serially and the db is reset before.

* WIP: make organization name its id, drop the mongo id * more usages * Update LokiClient.scala * fix compiler errors after merge * prune scala usages of organizationName * fix migration guide * prune frontend usages of organizationName * prune frontend usages of organization.name * fix data type of orga references * sql check, fix delete organization * WIP: Add migration and revision * format backend * enable backend to parse old analytics schema for ingest events * format backend * update schema version * finish first version of migration and revision * fix schema & migration - give explicit name to constraints to make the name more consistent and less implicit * add migration for analyticsEvents' eventProperties * add organizationName to LinkedLayerIdentifier to make it backwards compatible * add legacy route to list datasets supporting the old get param organizationName when filtering for specific datasets & bump api version * dont use direct get on box and throw jserror when no orgaid or organame is defined in analytics event * format backend * remove comments from evolution files & fix schema version * fix migration, remove old now duplicate unique index * readd unique contraint in reversion * in reversion: migrate local join orga, open dataset & uplaod dataset back * in reversion: fix fk constraints and views * in reversion: fix user infos view * migrate new code pulled in by merge to use orgaId and not name * format backend * update schema version & include warning in reversion * rename organizationDisplayName to organizationName * add changelog entry * add migration entry * remove auto generated message files for data and tracingstore * update e2e db fixtures / initial db data * rename left over orgDisplayName variable to orgName * update snapshots to use new e2e your name last names * fix typo and format code * more relaxed analytics json reads * drop default for id column * add missing redirect to versioned.routes * rename migration, undo changing worker job args --------- Co-authored-by: Norman Rzepka <[email protected]> Co-authored-by: Michael Büßemeyer <[email protected]> Co-authored-by: Michael Büßemeyer <[email protected]>

* WIP: fix zarr2 header in streaming * remove outdated comment from schema.sql --------- Co-authored-by: Michael Büßemeyer <[email protected]>

* try different base image * shallow clone in ci * poll more frequently in smoke tests * merge start and stop of services for the smoke tests * fix checkout * change image to ubuntu-2004:2024.05.1 * switch back to original image * switch back to original checkout * disable docker layer caching * Revert "merge start and stop of services for the smoke tests" This reverts commit 52e68d8. * Revert "switch back to original checkout" This reverts commit 31167e1. * shallow clone to cwd instead of webknossos * give name to clone ci step * merge start and stop of services for the smoke tests * attempt to spawn docker images sequentially but in the same step * use -d for docker-compose * temporarily disable ci * disable webpack cache * don't sleep before doing the very first attempt in the smoke tests * remove commented code * re-enable ci * try to build webknossos image with cache_from * temporarily disable ci * avoid re-uploading target caches when the source code did not change * set timestamps to 1.1.1970 for target/universal/stage so that docker layers can be properly cached * tmp: store target/universal/stage as artifact * call docker-compose down only once * tmp: bundle target before storing (+ early out in pipeline) * upload target.tar * also pin timestamp for target/universal and target * use directory-checksum on target/universal/stage * fix path * tmp: disable keepTimestamps in sbt * use -XDsortfiles for deterministic scala builds * -XD -> -D * use -Dsortfiles for datastore and tracingstore compilation, too * store differing jars as artifacts for inspection * fix store_artifacts paths * undo all deterministic java build related changes for now (should be done in another pr) * undo all deterministic java build related changes for now (should be done in another pr) * re-enable ci

* make file paths for reserve upload route optional * add changelog entry * apply feedback --------- Co-authored-by: Michael Büßemeyer <[email protected]>

* updated biome to v1.8 * foo * fromating? * fixed remaing biome errors * format package.json with two spaces * Update frontend/javascripts/oxalis/controller.tsx Co-authored-by: Philipp Otto <[email protected]> --------- Co-authored-by: Philipp Otto <[email protected]>

…s#8046) * remove vit_l_0b3195_decoder_quantized.onnx * remove public/images/original * avoid assets appearing twice in output jars * remove copy models instruction from webpack

* add warning if opacity is zero * improve layout, color and icon * add changelog * fix typo * remove exclamation mark --------- Co-authored-by: Philipp Otto <[email protected]>

* add missing migration to migrations guide * also fix cloning a tag in ci * fix syntax

* add new text and application.conf entry * improve styling * improve styling when wkorg shouldnt be recommended * add changelog * hopefully fix tests and improve check * remove entry for knossos format * update snapshots * fix APIFeatureToggles * update migration guide * fix line height * fix link to commits * fix link * stop event propagation for links

* fix layout of buttons in 3d viewport * fix too large margin in 3d viewport buttons * tmp: execute nightlies on push * tmp: only run xyz nightly * update screenshots for nightly * zip and upload screenshots for easier download * fix yaml syntax * fix yaml syntax * Revert "tmp: only run xyz nightly" This reverts commit 43144b9. * Revert "tmp: execute nightlies on push" This reverts commit c064579.

* update screenshots * also bundle screenshots in error case * naming

…inds#8049) * swap change color and center BB buttons * Revert "swap change color and center BB buttons" This reverts commit 6784852. * center bbox on click * fix that clicking any context menu entry centered bbox * add changelog * change cursor style for bbox row * fix that click event and cursor didnt work in padded space of bbox row --------- Co-authored-by: Philipp Otto <[email protected]>

* add focus bbox to context menu * focus on click and highlight on hover BBox in move mode * improve controls for bbox selection in move mode * improve var naming * add changelog --------- Co-authored-by: Philipp Otto <[email protected]>

* updated yarn to version 4 * update readme * update docker iamge for CI * create a tmp dir for yarn stuff during asset compilation * CI? * replace deprecated yarn --frozen-lock flag with --immutable * CI? * CI * remove yarn caching from CI * fix CI * add PR feedback * add yarn 4.4.1 to docker.dev image

* update libs to react 18.3 * update reactDom to createRoot * remove antd resolutions in package.json * update antd to version 5.17.4 * updated redux to v4.0.5 * updated react.router-dom to v5.3.4 * replace react-virtualized with react-virtualized-auto-sizer lib * replace react-sortable-hoc with dnd-kit 1/2 * replace react-sortable-hoc with dnd-kit 2/2 * fix typescript errors * updated yarn lock * updated tanstack/query * updated tanstack/query * update flex layout * update react-json-tree * fix remaining typescript errors * mock renderIndenpently in unit tests * formatting * fix unit tests * fix dark mode overwrite for flex layout * changelog * apply PR feedback for TS typing * fix dark mode layer handles * format

…n update routes (scalableminds#8069) * add assertion for no duplicated keys in dataset and folder metadata * format backend * add changelog entry * move MetadataAssertions to utils --------- Co-authored-by: Michael Büßemeyer <[email protected]>

* Script to find json mappings * skip dot dirs * add explaining comment --------- Co-authored-by: MichaelBuessemeyer <[email protected]>

…#8072) * temporarily disable ci * disable sbt and target caches * move commander into new tools/postgres/package.json; copy node_modules in dockerfile * don't copy node_modules in dockerfile because assetsGenerationTask copies whole postgres folder anyway * undo changes to docker ignore * remove last circleci caching as it did more harm than good (reproducibility and performance) * re-enable ci

Bumps [express](https://github.com/expressjs/express) from 4.18.3 to 4.21.0. - [Release notes](https://github.com/expressjs/express/releases) - [Changelog](https://github.com/expressjs/express/blob/4.21.0/History.md) - [Commits](expressjs/express@4.18.3...4.21.0) --- updated-dependencies: - dependency-name: express dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

… enough (scalableminds#7643) * Do not require binaryData dir to be writable for Compose, orga dir is enough * don't filter according to ds.allowsUpdate when composing datasets * unify writable check * Update webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/DataSourceService.scala Co-authored-by: Philipp Otto <[email protected]> --------- Co-authored-by: Philipp Otto <[email protected]> Co-authored-by: Philipp Otto <[email protected]>

Commits on Jul 5, 2024

Release 24.07.0 (scalableminds#7915 )

philippotto committed Jul 5, 2024

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Lincbrain WebKNOSSOS upstream sync #15

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Lincbrain WebKNOSSOS upstream sync #15

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