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* adding custom data to basic bar charts * fixing context selection bug * more bug fixes * Refactor multi selection adapter - Add optional `diffSubtypes` to `IMultiSelectionAdapter` - Remove `ReprovisynMultiSelectionAdapter` - Add generics to `MultiSelectionAdapter` - Comment functions of `MultiSelectionAdapter` * Replace `PromiseLike` with `Promise` + async/await See also https://masteringjs.io/tutorials/fundamentals/promise-resolve * Replace `() => IContext` with `IContext` Unecessary convoluted call * Remove `waitForIt` promise from selection adapter - Add and refactor return types `Promise<any>` to `Promise<void>` - Switch to async/await where possible - await `removeDynamicColumns` before `addDynamicColumns` -> previously it was not waited for the removal * Add unit tests for SelectionAdapter * adding parameters check on use effect * removing outdated todo * Update context inside selection adapter * fixing default params value * builds * fixing bar selection * making bar click removal work * code improvements * fixing uncontrolled error * removing zooming on bar charts * adding promise to fix typing * pr suggestions/cleanup * prepare next development version 15.0.1-SNAPSHOT * Added build-storybook to build script (#733) * Added build-storybook to build script * Add tdp_core/dist alias to the storybook webpack config * updated version of storybook (#736) Co-authored-by: Moritz Heckmann <[email protected]> Co-authored-by: dvmoritzschoefl <[email protected]> Co-authored-by: Moritz Heckmann <[email protected]> * Fix eslint for AggregateTypeSelected Probably a missing type cast in PR #729 * Remove await `this.built` in `withoutTracking()` Waiting for `this.built` will never resolve/terminate and show an infite loading icon. Reason: `this.built` is created with `build()` in line 355 and it is only resolved after the `build()` call is complete. With the changes to the selection adapter the `this.selectionAdapter.selectionChanged` now returns a valid promise. Previously, `context.add()` did not return it's promise (see 919cfb2#diff-f0f07e4a6ac30a813315b152545245d4cf26830e01b701f3e82ff7b5c22363a7R18). Now, we are waiting until all dynamic columns are added. The circle closes when we add the columns which calls `withoutTracking()` which in-turn is waiting for the resolved `this.built` promise. As far as I can see, we always call `withoutTracking` on a built/resolved ranking view. In the other places (line 377 and 400) we have a dedicated `await this.built;` before triggering changes to dynamic columns. In my tests adding and removing columns via score and selection adapter worked as before. I also tested reloading the page and checked the result of the session. In all cases it looks the same as before. * use `useRef` instead of `useSyncedRef` * Add Storybook stories for custom buttons (#708) * create first storybook for button styles * add story for single button * change background * linting * fix background * add additional kind of buttons * typing * add functions for buttons into stories * started chaning source of button * finish Button storybook docu * linting problems * linting * styling of code * change style to UI * add comments * Added build-storybook to build script * Add tdp_core/dist alias to the storybook webpack config * added outline buttons, adjusted layout to not contain margin inside a story, added link to styleguide Co-authored-by: Michael Puehringer <[email protected]> Co-authored-by: Moritz Heckmann <[email protected]> * added cypress run script to package json (#738) Co-authored-by: Moritz Heckmann <[email protected]> * Add exception handler middleware (#723) * Add exception handler middleware * Extract default logging config and set it on server startup Co-authored-by: dvtschachinger <[email protected]> * address PR comments * Initial visyn_scripts integration * Update storybook script to storybook:build * adding description to axis labels (#744) * Add NODE_OPTIONS=--max_old_space_size=4096 to storybook scripts (#746) * Add NODE_OPTIONS=--max_old_space_size=4096 to storybook scripts * Update build script to include storybook:build * Update cache key * Fix `ARankingView` typings of `rebuild` and `reloadData` (#749) * prepare next dev version * Fixed return value of logout of ALB security store (#751) * Fix incorrect route for server buildInfo.json (#752) * Export initialize.ts for external Storybook instance (#753) * Migrated to new webpack5 visyn_scripts * Updated npm scripts * Moved entries from yo-rc to package.json * Fix SCSS warning for divide numbers using `/` (#758) Fix SCSS warning for divide numbers using / * Show selection indicator next to scroll bar in rankings (#756) Show LineUp selection indicator next to scroll bar * Prepare github changes * Update CODEOWNERS * Prepare github changes * Prepare github changes * Prepare github changes * Prepare github changes * Remove circleci * prepare next dev version * Set modal focus based on tour visiblity and replace Bootstrap jQuery modal with plain JS modal (#754) * Replace BS jQuery modal with plain JS modal Caleydo/tdp_bi_bioinfodb#1371 * Refactor modal options * Replace deprecated `evt.keyCode` with `evt.key` * Set modal focus flag based on tour's visibility Also revert dialog constructor parameter to `backdrop` only again. * Resolve some dependency cycles * Upgrade to Font Awesome v6 (#732) * update to fontawesome v6 * added fontawesome scss file * add dist files * Fix icon position in sidepanel tab * Update dependency [email protected] Co-authored-by: Moritz Heckmann <[email protected]> Co-authored-by: Holger Stitz <[email protected]> * Updated modal typings in dialogs.ts to return HTMLDivElement for body (#765) * Added tsconfig.json to package.json files to allow the prepack script to build via tsc * Moved phovea_registry to src/phovea_registry.ts * Removed phovea_registry.js from package.json files * Add package-lock.json * Update build.yml * Fix Error Where FormDialog Fails to Be Instantiated (#766) check if `.tdp-tour-step-count` exists * refactor: Avoid general aside styles caused by CLUE (#763) Refactor CLUE aside styles * Avoid general `<aside>` styles * Copy general aside styles into nested panels * refactor: Improve Cypress setup and use Cypress commands.js (#757) Co-authored-by: Holger Stitz <[email protected]> * feat: CLUE support for URL query parameter + rewrite hash parameters (#762) * Replace deprecated `substr` with `substring` * Move PropertyHandler and HashProperties * Add CommonPropertyHandler + QueryPropertyHandler - Move some static functions back to the CLUEGraphManager * Add property handler options to ATDPApplication * Add destroy hook to remove event listener * Add URL property rewrite to CLUEGraphManager * Extract rewrite URL function to unit test * Add unit test for rewrite URL function * Refactor graph URL after persisting session * Fix typings in interface * Avoid property symbol only in URL string * Amend last commit to avoid empty hash only Co-authored-by: Michael Pühringer <[email protected]> * Update package.json * Update package.json * Update package.json * fix: Font Awesome import in storybook.scss (#767) * Added d3v4 alias for datavisyn-scatterplot * Switch back to prepare script as otherwise install fails with jest not found error * Removed tdp_scatterplot and old d3v4 versions (#768) * Delete dist directory * Update package.json * Update engine and prepare script * Add react resolutions and overrides * Add @types to deps instead of devDeps * Added resolutions like overrides * Fix wrongly formatted visyn_scripts git ssh link * Remove webpack as forced resolution * Move lineupjs $engine_assets variable to _variables.scss * Add yarn-3.2.2 * Change prepare to prepack * Remove yarn again * Update visyn_scripts import * Add .yarnrc.yml * Add yarn-3.2.2 * Add yarn-3.2.2 * Add webpack to overides * Replace npm run with yarn run * Switch to visyn_scripts clean * Correctly pin papaparse types * Pin core-js to 2.6.5 * Add dist/ * Added d3v3 alias for d3 * Switch from node16 to main workflows * Added d3v7 alias (#769) * Added standalone tdp_core and updated README * Override form_check to write print-color-adjust instead of color-adjust (#770) * Update README.md * fix: Prevent submit of FormDialog with `evt.preventDefault()` (#772) * Bump pyjwt from 2.1.0 to 2.4.0 (#728) Bumps [pyjwt](https://github.com/jpadilla/pyjwt) from 2.1.0 to 2.4.0. - [Release notes](https://github.com/jpadilla/pyjwt/releases) - [Changelog](https://github.com/jpadilla/pyjwt/blob/master/CHANGELOG.rst) - [Commits](jpadilla/pyjwt@2.1.0...2.4.0) --- updated-dependencies: - dependency-name: pyjwt dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Michael Pühringer <[email protected]> * Rdkit images API (#748) * Add rdkit image to router (not working? ignoring prefix/namespace?) Add api to make rdkit produce SVGs Add optional extra flavor for rdkit in setup.py Add tests (working in a standalone project) Add models for molecule parsing Add utils for rdkit-stuff * Reformat + fix imports (via make format) Add prefix/namespace-functionality to visyn_server in the same way, flask has it Cleanup tests * Make tests not run if you don't have rdkit * Fix linter errors * Change tag from default (none) to images and change docstring (from "todo move" to actual) * Make rdkit mandatory * Remove router namespace support for fastapi and add warning if it's used Remove murcko wrapper Remove unneccesary fastapi object creation Remove create_api in img_api Add app via init_app instead of via registry * Changed path form /image/ to /rdkit/ Changed kind of parameters from url params to query params, i.e. /rdkit/C -> /rdkit/?structure=C due to slashes Adapted tests Better / more correct type hints * Change to return no content (+ proper no content response code) * Fix imports * Add structured image column, renderer, and filter dialog for SMILES strings to ranking (#755) * Add molecule column + renderer for LineUp #741 * Implement fetch structured image #741 * Add SMILES renderer and column to Ranking.tsx #741 * Adapt to latest rdkit API changes * Add custom structure image filter dialog (wip) * Add loading icon + error msg to filter dialog * Remove orphan import * Fix linter warnings and improve code * Deny to set string filter * Fix lint * Fix `filter = null` case * Rename folder to `structureImage` and add index.ts * Update dist files * Add empty summary renderer Otherwise an error is thrown when switching visualizations for the smiles column * Fix lint * Nest structured image i18n strings * Set default column width for smiles column * Set row height based on smiles column width * Set min/max domain for number col domain Related to #718 The parameter default, i.e. `min = Number.NaN`, is only used if the parameter is `undefined`. However, when the parameter is `null` it does not assign `Number.NaN`. With this commit `null` and `undefined` result in `Number.NaN`. * Set default summary renderer for smiles col * StructuredImageColumn extends ValueColumn - Removes all string related dialogs and functionality (e.g., group, sort, ...) - Add rename dialog - Remove `order` to default -> in menu: rename then filter Co-authored-by: Michael Puehringer <[email protected]> Co-authored-by: Michael Pühringer <[email protected]> * Minor improvements and feedback incorporation Co-authored-by: Holger Stitz <[email protected]> Co-authored-by: Michael Puehringer <[email protected]> Co-authored-by: Michael Pühringer <[email protected]> * Pin plotly.js-dist-min to 2.12 to avoid selection error (#773) * Add test db setup fixture (#771) * Add test_db fixture * Reformatting * Simplify + fail better + test fixture * Fix weird import corner case * Fixed import order * Move test dev dependencies from requirements_dev to main, so things depending on core also have it. Also, mark both db-tests as xfail. Co-authored-by: Michael Puehringer <[email protected]> Co-authored-by: Michael Pühringer <[email protected]> * Rename test_db to postgres_db (#774) * Added no security store for static logins (#775) * Bump rdkit to 2022.3.5 (#776) * prepare next dev version * Update publish.yml * Fixing Ranking.tsx bug (#777) * adding wrapper div around ranking.tsx * moving around styles from RankingViewComponent -> Ranking * adding back tdp-busy * Fixed filtering of structure image column (#784) Co-authored-by: Holger Stitz <[email protected]> * Remove modal element when hiding a dialog (#783) Co-authored-by: Holger Stitz <[email protected]> * Improve typings for CLUE and refactor async functions (#785) * Improve typings for CLUE `graph.persist()` datavisyn/ordino_eins#525 * Fix typing of MemoryGraph.restore() * feat: Add datavisyn logo which adapts to the system scheme (#782) * types: Add `ICategory[]` to `categories` in `IServerColumn` (#794) * Add missing dist files * fix: don't initialize general vis in `ARankingView` when disabled (#796) Previously the general vis was intialized and running the background, even though it was disabled; only the button was hidden. Now the general vis not even initialized. * prepare next dev version * feat: adding Mantine `VisynApp` (#787) Co-authored-by: Holger Stitz <[email protected]> * Add missing dist files. * deps: Update dependency [email protected] (#793) chore: Update dependency [email protected] Co-authored-by: Michael Pühringer <[email protected]> * feat: Added engine parameter to onBuiltLineUp in Ranking.tsx (#788) * feat: Add `removePlugins` method to plugin registry (#799) Co-authored-by: Holger Stitz <[email protected]> * prepare next dev version * fix: Avoid `AttachmentUtils` calls when Reprovisyn feature flag is enabled (#801) Co-authored-by: Holger Stitz <[email protected]> * Add caching of users in the current request (#803) * fix: Plotly type error with `violingap` (#807) * fix: increase LineUp side panel width (#805) Closes #804 * add: missing dist files * prepare next dev version * fix: Hide login dialog after animation if logged in (#812) * fix: remove range id mapping in `rangeOf` in DB view filter (#813) * fix: remove range id mapping in DB view filter Closes Caleydo/tdp_bi_bioinfodb#1416 * fix lint * prepare next dev version * Fix missing lineup color mappings by adjusting styles (#802) Adjusted color mapping styles * Cypress and CI integration (#811) * Cypress 11 and CI integration * Enable cypress in build.yml * Delete build_nightly.yml * Add make start * Improve performance, upgrade deps and logging, remove numpy, numba, pandas (#816) * Upgrade deps and remove numpy, numba, pandas * Replace BaseHTTPMiddleware with much faster ASGI equalivalent * Increase anyio threads to 100 * Remove broken etag support * Improved logging * Switch to a2wsgi * Remove a2wsgi again * Remove greenifier extension * Bump FastAPI to 0.89.0 * Add pytest in settings.json * Set SQLAlchemy version to >= 1.4.40 and <= 1.4.46 to allow SQLModel > 0.0.6 (#819) * Loosen Flask and marshmallow-sqlalchemy versions for superset * Removed flake8, isort, pep8 in favor of ruff * Exclude /health from uvicorn access log * fix(storybook): upgrade to webpack5 (#810) * upgrade webpack for storybook * use webpack.config from storybook and override rules * add HtmlWebpackPlugin * Fix storybook path aliases * use latest version of storybook Co-authored-by: Michael Puehringer <[email protected]> Co-authored-by: Michael Pühringer <[email protected]> * Enable Custom Vis in LineUp (#820) * enabled custom vis in lineup * Made idField optional Co-authored-by: Moritz Heckmann <[email protected]> Co-authored-by: Michael Puehringer <[email protected]> * Enable selection in ranking vis (#821) * Add substructure filter label to dialog (#822) * Add idField to LineUpSelectionHelper * fix: show notification when score loading fails (#823) * feat: converting general vis to Mantine and add hexbin visualization (#786) Co-authored-by: Holger Stitz <[email protected]> Co-authored-by: Michael Pühringer <[email protected]> Co-authored-by: Michael Puehringer <[email protected]> * fix(vis): zoom stutter in scatter plot (#826) * fix: change vis type name to sentence case (#827) changing name * fix(cypress): health check component test (#829) fix(cypress): health check * prepare next dev version * feat: Improve visyn app with context, store awareness, ... (#824) * Improve visyn app with context, store awareness, ... * Make DummyStore a proper security store * Make Vis/Plotly lazy to strip off 10 MB of bundle size * Separate store id and ui id * Further improve header by removing unused props * Add back deprecated features like alwaysAppendDummyStore * Move plotly to own package * Added login popup to avoid losing site state * feat(vis): allow column domains to be set (#825) * converting vis component to mantine * moving sidebar into a drawer * finishing mantine conversion * bug fixing and cleanup * opening settings bar by default * adding hexbin back * adding clipping path to hexbins * fixing legend * importing vis in place in ARankingView * fixing small multiples hexbin * improving sorting speed * memoizing selection * moving packages to dev deps * adding visynApp components to core * adding dependencies * removing duplicate deps * fixing errors * removing duplicate import * debouncing slider callback * removing speed improvements (for future pr) * removing console logs * switch to debounced callback for hex slider * removing console logs * adding back scatter vis speed improvements * adding i18n * updating mantine -> peer dependencies * fixing colors bug * Remove mantine from peerDependencies * Add missing dist files * Add missing dist file * addressing pr feedback * small code fixes * added i18n for the button string * typing to any to fix plotly problem * fixing plotly type error * typing all of the layouts to any * fixing small bugs * cleaning up a lot of bad logic in hexbin * removing unnecessary logic * changed selection to be more consistent with scatterplot * improving selection consistency * more selection improvements * make categories scrollable * adding i18n * fixing error message * Fix sentence case in vis * bug fixing * moving x * fixing bugs * fixing typings, hexbin bug * linting * updating stories * small code changes * fixing pan reset problem * adding layout changes everywhere * solving bugs * fixing hexbin sidebar problem * Run `yarn run all` * bug fixing * linting * bug fixing * testing * bug fixing * removing prints * switching back to horizontal * making scroll zooming work * removing strip plots * removing prints * linting * Remove commented out code and console log * Add missing dist files * hiding setting button when sidebar disabled * moving gear icon to front * allowing domains to be set for numerical columns * cleaning up * linting * allowing undefined in domain * cleaning * fixing bug * bug * fixed axis domain bug --------- Co-authored-by: Holger Stitz <[email protected]> Co-authored-by: Michael Puehringer <[email protected]> * prepare release 17.0.0 --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dvzacharycutler <[email protected]> Co-authored-by: Holger Stitz <[email protected]> Co-authored-by: oltionchampari <[email protected]> Co-authored-by: Michael Pühringer <[email protected]> Co-authored-by: dvmoritzschoefl <[email protected]> Co-authored-by: Moritz Heckmann <[email protected]> Co-authored-by: Christian Bors <[email protected]> Co-authored-by: dvflorianengertsberger <[email protected]> Co-authored-by: Michael Puehringer <[email protected]> Co-authored-by: dvtschachinger <[email protected]> Co-authored-by: Zach Cutler <[email protected]> Co-authored-by: anita-steiner <> Co-authored-by: Anita Steiner <[email protected]> Co-authored-by: dvdanielamoitzi <[email protected]> Co-authored-by: Christian Bors <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Markus Vogl <[email protected]> Co-authored-by: Champari Oltion <[email protected]>
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