Implement WebAuthn #8109
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Implement WebAuthn #8109
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* Fewer hdf5 reads when loading precomputed meshes * changelog * implement pr feedback
* build wrapper around slider to allow change on wheel event * refactor slider wrapper into one component * on double click, reset slider to default value * pass through step size * add default values to sliders for layer settings tab * add default for slider in conntectome setting and lint * add default slider values for controls and rendering settings tab, toolbar view and starting job modal * defaults for sliders in create explorative, dataset setting viewconfig, download modal and quickselect settings * add more defaults to sliders * improve condition onWheel for range slider * fix restrictresolutionslider * pass through wheelFactor from NumericSliderSetting * fix sliders with small ranges * fix disabled sliders * add changelog * address review * renaming var all the way * improve typing and default setting for slider step
…utputSegmentationLayerName param (#8118) Co-authored-by: Michael Büßemeyer <[email protected]>
* fix shape in zarr.json in zarr3 streaming * remove comment to make code DRYer * use default mag when creating zarr3 header file in bucket sink * add changelog entry * Update CHANGELOG.unreleased.md * Update CHANGELOG.unreleased.md --------- Co-authored-by: Michael Büßemeyer <[email protected]> Co-authored-by: Florian M <[email protected]>
* fix search behavior for comments tab * formatting * fix comment sorting --------- Co-authored-by: MichaelBuessemeyer <[email protected]>
Co-authored-by: Florian M <[email protected]>
* WIP restructured docs * restructure more pages into sub pages * fix all image references * restructured docs into more pages * update keyboardshortcuts with key highlgihting syntax * fix many cross-page links * fix more links * fix links etc * moar fixed links * more link repairs * apply albane's changes * fix links etc * moar fixed links * more link repairs * update gitignore * fixed links * added albane's images * gitignore
* fix skeleton search * add changelog entry * also expand parent segment groups on segment search --------- Co-authored-by: Michael Büßemeyer <[email protected]>
* sort mags before streaming them via zarr streaming * add changelog & remove unused import * format backend * apply review feedback * format backend --------- Co-authored-by: Michael Büßemeyer <[email protected]> Co-authored-by: Florian M <[email protected]>
* extend segment search to default name used in segments list * add changelog entry --------- Co-authored-by: Michael Büßemeyer <[email protected]>
* convert circleci nightly workflow to github action * try iwthout docker image and node action * exclude deployement during debugging * CI * CI * CI * CI * CI * CI * CI * CI * cleanup * wait for deployment * apply PR feedback * replace puppeteer with puppeteer-core for light install * changelog
* convert wkorg nightly screenshot test from CircleCI to GitHub actions * CI * changelog
* start to replace term resolution * rename resolution to mag in backend where possible * rename resolution restrictions * rename resolution info to mag info * rename in dataset accessor, a.o. * rename in frontend code * rename in docs * rename node resolution to mag * adjust mag slider * fix tests * add explaining sentences * refresh snapshots * improve explanation in info tab and status bar * adapt param name * remove application conf edits * lint * rename columns + table in sql, add migration * adapt test db after schema change * changelog * slightly adjust changelog entry to lower expectations * adjust docs and revert some changes * adjust neuroglancer docs * Update webknossos-tracingstore/app/com/scalableminds/webknossos/tracingstore/tracings/volume/VolumeTracingDownsampling.scala Co-authored-by: MichaelBuessemeyer <[email protected]> * address review * fix previous version in db evolution * adjust version in schema.sql * also adapt schema version in reversion * adjust form names * adjust get params for /createExplorational * remove unused messages --------- Co-authored-by: Florian M <[email protected]> Co-authored-by: Florian M <[email protected]> Co-authored-by: MichaelBuessemeyer <[email protected]> Co-authored-by: Tom Herold <[email protected]>
Co-authored-by: MichaelBuessemeyer <[email protected]>
Bumps [cross-spawn](https://github.com/moxystudio/node-cross-spawn) from 7.0.3 to 7.0.6. - [Changelog](https://github.com/moxystudio/node-cross-spawn/blob/master/CHANGELOG.md) - [Commits](moxystudio/node-cross-spawn@v7.0.3...v7.0.6) --- updated-dependencies: - dependency-name: cross-spawn 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: Florian M <[email protected]> Co-authored-by: Philipp Otto <[email protected]>
* Redirect rather than proxy to about page * migration guide * use 301 MOVED_PERMANENTLY * for / use SEE_OTHER, otherwise MOVED_PERMANENTLY
* Use match shorthand DataLayerWithMagLocators.mapped * spelling in changelog.released
* WIP: add rotations settings for each axis * WIP: first version allowing to set a rotation for each layer * reduce rotation max to 270 degrees as 0 == 360 * keep axis rotation as put in by the user * WIP: allow multiple transformations per layer * remove combining affine transformations only * fix flycam dummy matrix * clean up * WIP: make rotation setting for complete dataset & add translation to origin and back * add debugging code & notes for bug that no data layer are transformed according to affine matrix coordTransform * fix rotation seting by using storing transformations in row major order - and some code clean up * WIP: allow multiple layer to be rendered natively * finish allowing to toggle all transformations off and on - also always translate by dataset bounding box and not by layer bounding box for consistent rotation results * fix transformations for annotations * fix linting * undo change to save natively rendered layer names. Instead only save a single one. - in case layers have the same transformation, the automatic inverse of the natively rendered layer (applied to all other layers) will cancel out the layers transformation - and fixing the code according to the logic of only saving one native layer * fix rendering transforms for volume layers without fallback & fix init datasetconfig when nativelyRenderedLayerName is not present in current view / dataset * clean up code for pr review * add changelog entry * apply pr feedback * adjust logic when toggling transformations is allowed according to discussion & refactoring * - rename file with transformation accessors - fix & refactor positional change when toggling natively rendered layer - only toggling natively rendered layer name when layer is rendered natively and has not transforms configured * apply minifeedback fro coderabbit * fix cyclic dependency * organize imports * fix auto merge errors * fix hovered segment id highlighting when volume layer is rendered with transforms * orga imports * avoid magic number when expecting length of transformation which is rotation only * remove additional use of magic number * fix applying segmentation layer transform to hovered cell highlighting * use position in volume layer space when retrieving segmentation id from a position * do not allow to toggle transformations on layers that cannot have a transform configured --------- Co-authored-by: Michael Büßemeyer <[email protected]>
Probably an accidental import. It's not compatible across JDKs.
* adds certificate public key * add certificate validation * add certificate validation * fix proofreading message * format backend * fix frontend * fix wording * fix snapshots * fix typos and improve verification * styling * rename file * include expiration date * use formatted date * unify with application conf naming * format backend * fix typecheck tests * improve comments * do not block if server is down * apply frontend feedback * increase certificate cache time * apply backend feedback * rename proofreading enabling var * add new image * format backend * fix single sign on * make certificate route accessible to unauthorized users * fix image sizing * Update app/security/CertificateValidationService.scala Co-authored-by: frcroth <[email protected]> --------- Co-authored-by: Michael Büßemeyer <[email protected]> Co-authored-by: MichaelBuessemeyer <[email protected]> Co-authored-by: frcroth <[email protected]>
* prototype that merger mode is allowed when null-mapping is locked * clean up * update changelog * remove unused import
* WIP: Log slow RPC requests * WIP add duration formatting * format duration * unify duration logging * adapt format * use Instant in TempFileService * merge with existing Formatter * since * 2 minutes threshold * better date formatting, use Instant in more places * better error message for ConfigRreader, use Long for durations * replace try/catch with getOrElse * unused import * replace string ops by if/elseif/else, name magic numbers, add test for >Int.MaxValue * fix typo in reversion comment --------- Co-authored-by: MichaelBuessemeyer <[email protected]>
* unify logging * cleanup * init fossildb migration * update frontend to newest annotation stats schema and fix typing & linting * include annotation stats per layer in time tracking api response json * continue if a layer’s stats couldn’t be updated * add some function stubs to migration * wip migration: read annotations from postgres * fetch annotation info from postgres * iterate on migration * wip migrate updates * migrate updates in stupid concat strategy * migrate skeleton + volume proto * restructure migration code * cleanup * add two frontend TODO comments * migration: renamings for update actions, insert actionTracingId * migration: add generaetd code * migration: set tracing proto fields, create annotationProto * migrate volume buckets * migration: annotation layer name, volume segment index * migrate editable mapping distributed elements * migration: remove morton index, migrate editablemappinginfo objects * migration: switch from orjson to msgspec * migration: add cli args, actually write to target fossilDB * parallelize, add postgres connection parameter * avoid redundant calls in task creation (regression introduced in cba70af) * migration: humanize time diff add previous-start argument * migration: wip handle compacted update actions, add error logging + counting * fix removeAllButLastUpdateTracingAction * adapt some todo comments * change renameTracing to use old editAnnotation route * more comments * fix merge conflicts * fix types for editAnnotation * handle UpdatTdCamera updates, migration: mark more as compacted * fix parsing CompactVolumeUpdateActions * fix migration for proofreading, add some more error messages to backend * when initializing an annotation in the front-end use annotation.version for that * remove max handling of versions * wip: allow updating annotation name from dashboard * migration use passed pg password, add ETR, remove debug logging * fix version handling in model initialization etc * adapt the types so that update actions that need isolation cannot be grouped with others * remove downsampling feature volume annotations * use editableMappingId == volumeTracingId constraint * fix deletion of layer * fix importVolumeData * improve labels for proofreading entries in version restore view * remove/fix some more todo comments * pass tracingId directly to update actions instead of magically adding it later to some (but not all) actions * get rid of unused-tracing-id and superfluous passing of relevant tracing ids * fix stuck 'Activating Mapping' message * do not include name in annotationProto and updateAnnotationMetadata action. make description non-optional, emptystring means empty * add version parameter to editableMapping agglomerateIdsForSegments * option to count versions * migration: add verbose flag, log also to file * add error for missing layers * migration: randomize order with md5 hash * get rid of tracing.version in frontend * fix linting * remove remaining version properties * fix save saga spec * fix skeletontracing saga spec * mock annotation proto in specs * fix wkstore adapter spec * fix more incorrectly passed transactionIds; fix save_reducer spec * fix last frontend tests ™️ * fix linting * format backend * WIP: migration: merge updates in a less naive way * incorporate version parameter in agglomeratesForSegments route; refactor some GET parameters in api module * migration: iron out reverts, merge updates by timestamp * migration: adapt to changed annotationProto format * small cleanup in migration * fix version restore preview for editable mappings * fix that restoring to another version broke the loading of mesh files * fix ordering in updateActionLog * migration: wip select which to materialize * reload page when switching to a version in the version restore view that has different layers (including debugging code because it does not work properly) * revert temporary sorting fix in FE * respect earliestAccessibleVersion in version restore view * fix editing of annotation name * fix that newest version was also requested even when no annotation exists (e.g., in dashboard or in DS view mode) * fix tooltip for segment stats * require passing annotationid to some tracingstore routes * Revert "require passing annotationid to some tracingstore routes" This reverts commit 856f11b. * introduce skeletonMayHavePendingUpdates property to annotation proto to handle special case in migration * Revert "Revert "require passing annotationid to some tracingstore routes"" This reverts commit f24d123. * set skeletonMayHavePendingUpdates to None after applying updates * migration: set the bool only where it makes sense * migration: set earliest_accessible_version for editable mapping annotations * don't fail on loading addSegmentIndex and compactVolumeActions * checkpoints for migration * cleanup in migration * pass annotationId to routes that require it (back-end cannot find the annotation on version restore, though) * also require annotation id in volume data request * fix annotationId param for data route * use annotation id also for access request * fix switched ids * adapt e2e tests * unused import * fix that version restore view didnt open when loading a version that had no skeleton layer; also use ensureWkReady in most places instead of actively waiting on wk-ready action * remove unused imports * use toasts related to proofreading undo * add custom start time argument to migration * set editableMappingsMayHavePendingUpdates in migration * fetch extra editable mapping updates if needed * fix downloading older volumes. changelog + migration guide. * fix assertion in volume download * remove debug logging * fix typing and CI * fix requesting volume data from older version * if allDataZip is requested with annotationId, use that one also for the access check * fix test * clean up editAnnotation * rename to getUnversionedAnnotationInformation * fix annotation stats and linting * fix superfluous request with empty annotation id * fix type check test * resnap freshshots * add e2e test for updating metadata * clean up typing of update actions * update todo comment * unused import * save one lookup of annotationProto * fix sandbox view * more verbose bucket loading errors, include Failure message * set editableMappingsMayHavePendingUpdates to None after are updates are applied * implement migrationf feedback part1 * Update MIGRATIONS.unreleased.md Co-authored-by: Norman Rzepka <[email protected]> * wip: clean-up older migration run in case of reverts. use new fossilDB putMultipleVersions * migration: fix cleanup of previous, use multi-version put * pin versions in requirements.txt * iterate on migration guide * bump fossildb version to 0.1.33 (master_504) * migration: fix mapping id lookup * rename type to typ in AnnotationLayerProto and DeleteLayerAnnotationAction * fix applying extraSkeletonActions on older requested annotation versions * remove debug logging * WIP: switch migration from threading to multiprocessing * re-add isViewOnlyChange for skeleton actions where it got lost * reformat comment for TokenContext Co-authored-by: MichaelBuessemeyer <[email protected]> * unify function naming in RpcRequest * fix userToken param, remove stateless services from Singleton list * rename some functions, remove unused imports * fix bucketMutatingActions lookup, rename emptystring to empty string * reorder functions in AnnotationWithTracings * correctly clear editableMappings map, fix typo * rename + rephrase some things for pr feedback * add some error messages for editable mapping routes * add comment on merging editable mappings, move up saveSkeleton call in mergedFromIds * Remove superfluous empty list in SequenceUtils.splitAndIsolate * extract EditableMappingMergeService * incorporate pr feedback * extract actionTracingId in spec * remove unused updateActionStatistics route * remove superfluous for/yield * fix merge conflicts * Revert "WIP: switch migration from threading to multiprocessing" This reverts commit a8babc0. * refresh snapshots after merge * WIP: make migration faster using multi-get/put * prepare merge for import sorting pr * fix merge related problems * make biome ignore some type imports because it produces invalid syntax, otherwise * more batching for migration * include actionTracingId, actionTimestamp in compact action writes * Fix annotation duplicate * decrease batch sizes to avoid grpc message size limits * Fix viewing compound annotations * improve test for regroupByIsolationSensitiveActions, add ordering assertion * bump fossildb to 0.1.34/master__510 * clear all tracings when initialization is (re-)initialized and put initialization actions into a special batch action to avoid inconsistent inbetween-states * block UI when previewing or restoring to another version * fix brushing by waiting for init volume action * fix that the actual restore button was missing in the version restore view (only download was possible); fix achieved by moving isWkReady to store and conditioning the view on that * additional logging if verbose * use version parameter when requesting mapping (frontend and backend) * store initialAllowUpdate so that we can clearly revert that boolean after closing the version restore view * add some error messages, migration: attempt with lower batch size for segment index * auto-expand version group that contains the current version * fix closing version restore view when the currently previewed version has a different layer set from the newest version * lint * when reverting distributed elements of volumetracings/editableMappings, handle the layer not existing before the revert * incorporate pr feedback * rename function (pr feedback) * fix ordering of extra updates * append rather than prepend, pendingAnnotationupdates have higher version numbers * add explaining comment * put editable mapping updates to correct id when merging annotations * rephrase migration guide * fix duplicate updates if addLayer is in the history * don't access dataSource.id.name (fixes toast when previewing older version) * clear potential get variables after closing version restore view * refactor how allowUpdate is reset; fix incorrectly captured initialAllowUpdate value in useWillUnmount * restore modified condition * use UnsupportedOperationException in VolumeTracingLayer * format * unused import * fix type error --------- Co-authored-by: Michael Büßemeyer <[email protected]> Co-authored-by: Philipp Otto <[email protected]> Co-authored-by: Norman Rzepka <[email protected]> Co-authored-by: MichaelBuessemeyer <[email protected]>
… timestamps (#8357) * In UAV migration, respect timezone when comparing annotation modified timestamps * fix off-by-one error in progress logging * Update migration.py
* do not drop all tress of other type when merging trees * improve skeleton tests * add another test testing that trees of diffrent types are not merged * add changelog entry --------- Co-authored-by: Michael Büßemeyer <[email protected]>
* more verbose error message when duplicating updates fails * undo provoking error
…aset settings"" (#8355) * Revert "Revert "Allow permanent dataset layer rotation in dataset settings (#…" This reverts commit e20c218. * fix add remote dataset view --------- Co-authored-by: Michael Büßemeyer <[email protected]>
* Update MIGRATIONS.released.md * Update MIGRATIONS.released.md Co-authored-by: Florian M <[email protected]> --------- Co-authored-by: Florian M <[email protected]>
* Set actionTracingId to tracingId for editableMappingUpdates * fix sql syntax * include annotation id * wip repair update actions script * wip fetch relevant updates * iterate on repariring updates * put updated updates * skip the reverse, the order in which we deal with the update groups doesnt matter here * undo application.conf change
…acted update action writes (#8367) * Fix merging editable mappings where self-merge is generated; fix compacted update action writes * Update application.conf * changelog * Apply suggestions from code review Co-authored-by: MichaelBuessemeyer <[email protected]> --------- Co-authored-by: MichaelBuessemeyer <[email protected]>
* added new inputs for model evaluation * run formatter * updated changelog * add support for displaying annotation links instead of datasets * Update CHANGELOG.unreleased.md Co-authored-by: MichaelBuessemeyer <[email protected]> * adapt to feedback * update antd to allow form.field to set its own layout * Update frontend/javascripts/admin/api/jobs.ts Co-authored-by: MichaelBuessemeyer <[email protected]> * apply some of the requested changes * yarn fix-frontend * add assertion for annotationId * change variable name in error message * remove changes in application.conf * actually undo changes in application.conf * format frontend * apply feedback * fix drag handle alignment --------- Co-authored-by: MichaelBuessemeyer <[email protected]> Co-authored-by: Michael Büßemeyer <[email protected]>
…boxes (#8364) * Fix segment registering in coarser mags for non-mag-aligned bounding boxes * update changelog
* show measurement tool in view mode * lint and remove console log * improve code structure and change position of buttons in action bar * add changelog * fix spelling * fix that actions were falsely available in read-only annotations * allow to set tools in ui reducer * complete case distinction in reducer * remove default value and optional param * address review
* add error handling * remove unused imports * improve structure of try catch clause * add changelog * add margin * remove typo * move other api calls outside of try catch block * add another function call to try and catch because failure would lead to blank screen * move all methods to try catch block * improve styling
* added various WK workflow tutorials to docs * added TIL videos to docs * fix url seperator
* fix that slider could be scrolled to NaN * only scroll slider on focus * remove console logs * WIP: prevent parent scrolling * improve onWheel method * fix resetting to default on log sliders * add event listener with useEffect * remove event listener * add changelog * improve changelog wording * WIP: address review * fix opacity default for segmentation layers * disable text select when slider is focused * improve if clause
* support reading blosc-compressed data chunks with autoshuffle * changelog * Update CHANGELOG.unreleased.md
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(Please delete unneeded items, merge only when none are left open)