Release 16.2.0 (#800)

* 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* removing outdated todo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 <moritz.heckmann@datavisyn.io>

Co-authored-by: dvmoritzschoefl <77104411+dvmoritzschoefl@users.noreply.github.com>
Co-authored-by: Moritz Heckmann <moritz.heckmann@datavisyn.io>

* 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 <michael.puehringer@datavisyn.io>
Co-authored-by: Moritz Heckmann <moritz.heckmann@datavisyn.io>

* added cypress run script to package json (#738)

Co-authored-by: Moritz Heckmann <moritz.heckmann@datavisyn.io>

* Add exception handler middleware (#723)

* Add exception handler middleware

* Extract default logging config and set it on server startup

Co-authored-by: dvtschachinger <thomas.schachinger@datavisyn.io>

* 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 lineupjs@4.6.2

Co-authored-by: Moritz Heckmann <moritz.heckmann@datavisyn.io>
Co-authored-by: Holger Stitz <holger.stitz@datavisyn.io>

* 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 <holger.stitz@datavisyn.io>

* 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 <51900829+puehringer@users.noreply.github.com>

* 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
...

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* 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 <michael.puehringer@datavisyn.io>
Co-authored-by: Michael Pühringer <51900829+puehringer@users.noreply.github.com>

* Minor improvements and feedback incorporation

Co-authored-by: Holger Stitz <holger.stitz@datavisyn.io>
Co-authored-by: Michael Puehringer <michael.puehringer@datavisyn.io>
Co-authored-by: Michael Pühringer <51900829+puehringer@users.noreply.github.com>

* 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 <michael.puehringer@datavisyn.io>
Co-authored-by: Michael Pühringer <51900829+puehringer@users.noreply.github.com>

* 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 <holger.stitz@datavisyn.io>

* Remove modal element when hiding a dialog (#783)

Co-authored-by: Holger Stitz <holger.stitz@datavisyn.io>

* 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 <holger.stitz@datavisyn.io>

* Add missing dist files.

* deps: Update dependency lineupjs@4.7.0 (#793)

chore: Update dependency lineupjs@4.7.0

Co-authored-by: Michael Pühringer <51900829+puehringer@users.noreply.github.com>

* feat: Added engine parameter to onBuiltLineUp in Ranking.tsx (#788)

* feat: Add `removePlugins` method to plugin registry (#799)

Co-authored-by: Holger Stitz <holger.stitz@datavisyn.io>

* prepare release 16.2.0

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