Release 16.0.0 (#778)

* 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was not waited for the removal * Add unit tests for SelectionAdapter * adding parameters check on use effect * removing outdated todo * Update context inside selection adapter * fixing default params value * builds * fixing bar selection * making bar click removal work * code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 release 16.0.0 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]>
datavisyn · Sep 8, 2022 · 62f7768 · 62f7768
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diff --git a/.eslintrc.js b/.eslintrc.js
@@ -1,72 +1 @@
-module.exports = {
-  root: true,
-  extends: [
-    "airbnb",
-    "airbnb-typescript",
-    "airbnb/hooks",
-    "eslint:recommended",
-    "plugin:import/recommended",
-    "plugin:react/recommended",
-    "plugin:@typescript-eslint/recommended",
-    "plugin:jest/recommended",
-    "plugin:prettier/recommended",
-    "plugin:storybook/recommended",
-  ],
-  plugins: ["react", "@typescript-eslint", "jest"],
-  ignorePatterns: ["*.js"],
-  env: {
-    browser: true,
-    es6: true,
-    jest: true
-  },
-  globals: {
-    Atomics: "readonly",
-    SharedArrayBuffer: "readonly",
-  },
-  parser: "@typescript-eslint/parser",
-  parserOptions: {
-    // Make sure eslint and VS Code use the same path for the tsconfig.json:
-    // https://github.com/typescript-eslint/typescript-eslint/issues/251
-    tsconfigRootDir: __dirname,
-    project: "./tsconfig.eslint.json"
-  },
-  rules: {
-    // Disables jsx-a11y https://github.com/import-js/eslint-plugin-import/blob/v2.25.4/docs/rules/no-webpack-loader-syntax.md
-    ...Object.keys(require('eslint-plugin-jsx-a11y').rules).reduce((acc, rule) => { acc[`jsx-a11y/${rule}`] = 'off'; return acc }, {}),
-    "class-methods-use-this":"off",
-    "linebreak-style": "off",
-    "no-continue": "off",
-    "no-multi-assign": "warn",
-    "no-nested-ternary": "off",
-    "no-param-reassign": ["error", { "props": false }],
-    "no-return-assign": "warn", 
-    "no-restricted-syntax": "off",
-    "no-plusplus": "off",
-    "no-prototype-builtins": "warn",
-    "no-minusminus": "off",
-    "no-underscore-dangle": "off",
-    "max-classes-per-file": "off",
-    "no-param-reassign": "warn",
-    "import/no-extraneous-dependencies": "off",
-    // Disable the following 2 lines because to allow webpack file-loaders syntax
-    "import/no-webpack-loader-syntax": "off",
-    "import/no-unresolved": "off",
-    "import/prefer-default-export": "off",
-    "import/order": "error",
-    "prefer-destructuring": ["warn", {"object": true, "array": false}],
-    "prefer-promise-reject-errors": "warn",
-    "prefer-spread": "warn",
-    "@typescript-eslint/ban-ts-comment": "warn",
-    "react/destructuring-assignment": "warn",
-    "react/jsx-props-no-spreading": "off",
-    "react/no-unused-class-component-methods": "warn",
-    "react/prop-types": "off",
-    "react/require-default-props": "off",
-    "react/static-property-placement": ["warn", "property assignment", {
-      childContextTypes: "static getter",
-      contextTypes: "static public field",
-      contextType: "static public field",
-      displayName: "static public field",
-    }]
-  }
-};
+module.exports = require('visyn_scripts/config/eslintrc.template')({ tsconfigRootDir: __dirname });
diff --git a/.gitignore b/.gitignore
@@ -2,9 +2,10 @@
 /.tscache
 /.eslintcache
 /.idea
+/bundles/
 /build/
 /storybook-static/
-/dist/tsBuildInfoFile
+/dist/tsconfig.tsbuildinfo
 /dist_python/
 /lib/
 *.egg-info/
@@ -27,4 +28,17 @@ node_modules/
 /src/**/*.map
 /tests/**/*.map 
 *.css
-package-lock.json
+/package-lock.json
+/yarn.lock
+
+# yarn
+.pnp.*
+.yarn/*
+!.yarn/patches
+!.yarn/plugins
+!.yarn/releases
+!.yarn/sdks
+!.yarn/versions
+
+# env
+/env/
diff --git a/.prettierrc.js b/.prettierrc.js
@@ -1,6 +1 @@
-module.exports = {
-  "endOfLine": "auto",
-  "singleQuote": true,
-  "trailingComma": "all",
-  "printWidth": 160
-};
+module.exports = require('visyn_scripts/config/prettierrc.template')
diff --git a/.yarn/releases/yarn-3.2.2.cjs b/.yarn/releases/yarn-3.2.2.cjs
diff --git a/.yarnrc.yml b/.yarnrc.yml
@@ -0,0 +1,2 @@
+yarnPath: .yarn/releases/yarn-3.2.2.cjs
+nodeLinker: node-modules
diff --git a/.yo-rc.json b/.yo-rc.json
@@ -27,9 +27,6 @@
       "redhatPackages": []
     },
     "app": "",
-    "entries": {
-      "app": "./src/index.ts"
-    },
     "libraryAliases": {
       "d3": "d3/d3"
     },

diff --git a/README.md b/README.md
@@ -8,24 +8,46 @@ Target discovery platform for exploring rankings of genes, disease models, and o
 Installation
 ------------
 
-```
-git clone https://github.com/datavisyn/tdp_core.git
+```bash
+git clone -b develop https://github.com/datavisyn/tdp_core.git  # or any other branch you want to develop in
 cd tdp_core
-npm install
+
+# Frontend
+yarn install
+
+# Backend
+python3 -m venv env  # create a new virutal environment
+source env/bin/activate  # active it
+make develop  # install all dependencies
+```
+
+Local development
+------------
+
+```bash
+# Frontend
+yarn start
+
+# Backend
+python tdp_core
 ```
 
 Testing
 -------
 
-```
-npm test
+```bash
+# Frontend
+yarn run test
+
+# Backend
+make test
 ```
 
 Building
 --------
 
 ```
-npm run build
+yarn run build
 ```
 
 

diff --git a/cypress/fixtures/example.json b/cypress/fixtures/example.json
@@ -0,0 +1,5 @@
+{
+  "name": "Using fixtures to represent data",
+  "email": "[email protected]",
+  "body": "Fixtures are a great way to mock data for responses to routes"
+}
diff --git a/cypress/plugins/index.js b/cypress/plugins/index.js
@@ -0,0 +1,22 @@
+/// <reference types="cypress" />
+// ***********************************************************
+// This example plugins/index.js can be used to load plugins
+//
+// You can change the location of this file or turn off loading
+// the plugins file with the 'pluginsFile' configuration option.
+//
+// You can read more here:
+// https://on.cypress.io/plugins-guide
+// ***********************************************************
+
+// This function is called when a project is opened or re-opened (e.g. due to
+// the project's config changing)
+
+/**
+ * @type {Cypress.PluginConfig}
+ */
+// eslint-disable-next-line no-unused-vars
+module.exports = (on, config) => {
+  // `on` is used to hook into various events Cypress emits
+  // `config` is the resolved Cypress config
+}
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		yarnPath: .yarn/releases/yarn-3.2.2.cjs
		nodeLinker: node-modules