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Package vulnerability audit dec 2024 (#190)
* Updated python docker images to gracefuly stop since they now start in the primary process in a container, through taking over execution of the entrypoint script via a command; * Increased python-multipart pacakge version to avoid vulnerability; * increased eslint's version to remove dependency which has vulnerability; this required upgrading the eslint configuration within rosalution to use the new flat file configuration. It is temporarily tuned to be close to the existing code base linting however, the team will review and revise linting guidelines when we gather soon. * @stylistic/[email protected] requires 20.9 & higher; after investigating, in order to avoid the vulnerably also being inside the docker images, need to upgrade to both alpine3.21 & 23.4.; * Linting upgrade for eslint to 9.16 for system tests & some updates to corresponding tests. * Resolved unit test text formatting issue; updated system test package.json to indicate its of type module for JavaScript. * Updated system test with finicky rendering of context menus for test * Upping vite to 6.0.3 to resolve vulnerabilities and update its dependencies that have vulnerabilities * Updated to support attaching genbank .gb files * Forced package resolutions to avoid the vulnerabilities
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,3 @@ | ||
| FROM mongo:5.0.9 as production-stage | ||
| FROM mongo:5.0.9 AS production-stage | ||
| COPY --chmod=0777 ./initial-seed/initial-db-seed.sh /docker-entrypoint-initdb.d/initial-db-seed.sh | ||
| COPY ./initial-seed/ /tmp/fixtures/initial-seed/ |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,113 @@ | ||
| import stylistic from '@stylistic/eslint-plugin-js'; | ||
|
|
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| export default [{ | ||
| plugins: { | ||
| '@stylistic/js': stylistic, | ||
| }, | ||
| rules: { | ||
| // Possible Errors | ||
| 'no-cond-assign': 'off', | ||
| 'no-irregular-whitespace': 'error', | ||
| 'no-unexpected-multiline': 'error', | ||
|
|
||
| // Best Practices | ||
| 'curly': ['error', 'multi-line'], | ||
| 'guard-for-in': 'error', | ||
| 'no-caller': 'error', | ||
| 'no-extend-native': 'error', | ||
| 'no-extra-bind': 'error', | ||
| 'no-invalid-this': 'off', | ||
| 'no-multi-str': 'error', | ||
| 'no-new-wrappers': 'error', | ||
| 'no-throw-literal': 'error', | ||
| 'no-with': 'error', | ||
| 'prefer-promise-reject-errors': 'error', | ||
|
|
||
| // Variables | ||
| 'no-unused-vars': ['error', {args: 'none'}], | ||
|
|
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| // Stylistic | ||
| '@stylistic/js/array-bracket-newline': 'off', | ||
| '@stylistic/js/array-bracket-spacing': ['error', 'never'], | ||
| '@stylistic/js/array-element-newline': 'off', | ||
| '@stylistic/js/block-spacing': ['error', 'never'], | ||
| '@stylistic/js/brace-style': 'error', | ||
| 'camelcase': ['error', {properties: 'never'}], | ||
| '@stylistic/js/comma-dangle': ['error', 'always-multiline'], | ||
| '@stylistic/js/comma-spacing': 'error', | ||
| '@stylistic/js/comma-style': 'error', | ||
| '@stylistic/js/computed-property-spacing': 'error', | ||
| '@stylistic/js/eol-last': 'error', | ||
| '@stylistic/js/func-call-spacing': 'error', | ||
| '@stylistic/js/indent': [ | ||
| 'error', 2, { | ||
| 'CallExpression': { | ||
| 'arguments': 2, | ||
| }, | ||
| 'FunctionDeclaration': { | ||
| 'body': 1, | ||
| 'parameters': 2, | ||
| }, | ||
| 'FunctionExpression': { | ||
| 'body': 1, | ||
| 'parameters': 2, | ||
| }, | ||
| 'MemberExpression': 2, | ||
| 'ObjectExpression': 1, | ||
| 'SwitchCase': 1, | ||
| 'ignoredNodes': [ | ||
| 'ConditionalExpression', | ||
| ], | ||
| }, | ||
| ], | ||
| '@stylistic/js/key-spacing': 'error', | ||
| '@stylistic/js/keyword-spacing': 'error', | ||
| '@stylistic/js/linebreak-style': 'error', | ||
| '@stylistic/js/max-len': ['error', { | ||
| code: 120, | ||
| tabWidth: 2, | ||
| ignoreUrls: true, | ||
| ignorePattern: 'goog.(module|require)', | ||
| }], | ||
| 'new-cap': 'error', | ||
| 'no-array-constructor': 'error', | ||
| '@stylistic/js/no-mixed-spaces-and-tabs': 'error', | ||
| '@stylistic/js/no-multiple-empty-lines': ['error', {max: 2}], | ||
| 'no-new-object': 'error', | ||
| '@stylistic/js/no-tabs': 'error', | ||
| '@stylistic/js/no-trailing-spaces': 'error', | ||
| '@stylistic/js/object-curly-spacing': 'error', | ||
| 'one-var': ['error', { | ||
| var: 'never', | ||
| let: 'never', | ||
| const: 'never', | ||
| }], | ||
| '@stylistic/js/operator-linebreak': ['error', 'after'], | ||
| '@stylistic/js/padded-blocks': ['error', 'never'], | ||
| '@stylistic/js/quote-props': ['error', 'consistent'], | ||
| '@stylistic/js/quotes': ['error', 'single', {allowTemplateLiterals: true}], | ||
| '@stylistic/js/semi': 'error', | ||
| '@stylistic/js/semi-spacing': 'error', | ||
| '@stylistic/js/space-before-blocks': 'error', | ||
| '@stylistic/js/space-before-function-paren': ['error', { | ||
| asyncArrow: 'always', | ||
| anonymous: 'never', | ||
| named: 'never', | ||
| }], | ||
| '@stylistic/js/spaced-comment': ['error', 'always'], | ||
| '@stylistic/js/switch-colon-spacing': 'error', | ||
|
|
||
| // ECMA 2022 rulesets | ||
| '@stylistic/js/arrow-parens': ['error', 'always'], | ||
| 'constructor-super': 'error', | ||
| '@stylistic/js/generator-star-spacing': ['error', 'after'], | ||
| 'no-new-symbol': 'error', | ||
| 'no-this-before-super': 'error', | ||
| 'no-var': 'error', | ||
| 'prefer-const': ['error', {destructuring: 'all'}], | ||
| 'prefer-rest-params': 'error', | ||
| 'prefer-spread': 'error', | ||
| 'rest-spread-spacing': 'error', | ||
| 'yield-star-spacing': ['error', 'after'], | ||
| }, | ||
| }]; |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,71 @@ | ||
| import js from '@eslint/js'; | ||
| import pluginVue from 'eslint-plugin-vue'; | ||
| import globals from 'globals'; | ||
| import cgds from './eslint-config-cgds.js'; | ||
|
|
||
|
|
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| export default [ | ||
| { | ||
| ignores: [ | ||
| 'node_modules/**', | ||
| 'dist/**', | ||
| 'test/__mocks__/**', | ||
| ], | ||
| }, | ||
| js.configs.recommended, | ||
| // { | ||
| ...cgds, | ||
| // Temporarily setting only essential rules; will make update after team discussion | ||
| // as to which level to increase vuejs linting rules too. | ||
| ...pluginVue.configs['flat/essential'], | ||
| // files: ['src/**/*.js', 'src/**/*.vue', 'test/**/*.spec.js'], | ||
| { | ||
| languageOptions: { | ||
| sourceType: 'module', | ||
| ecmaVersion: 2022, | ||
| globals: { | ||
| ...globals.browser, | ||
| ...globals.node, | ||
| process: 'readonly', | ||
| }, | ||
| }, | ||
| }, | ||
| { | ||
| rules: { | ||
| 'vue/prop-name-casing': 'off', | ||
| 'vue/require-default-prop': 'off', | ||
| 'vue/max-attributes-per-line': ['error', { | ||
| 'singleline': { | ||
| 'max': 6, | ||
| }, | ||
| 'multiline': { | ||
| 'max': 2, | ||
| }, | ||
| }], | ||
| // Disabling error temporarilly until team can reconvence and make a decision on us moving forward regarding | ||
| // this configuration. | ||
| 'vue/html-self-closing': ['off', { | ||
| 'html': { | ||
| 'void': 'never', | ||
| 'normal': 'always', | ||
| 'component': 'always', | ||
| }, | ||
| 'svg': 'always', | ||
| 'math': 'always', | ||
| }], | ||
| // We inconsistently 2 space tab in SFC template section at the template base. | ||
| // Will update in future update to set rule and make consistent in seperate PR | ||
| // after team discussion. | ||
| 'vue/html-indent': ['off'], | ||
| // 'vue/singleline-html-element-content-newline': ['error', { | ||
| // 'ignoreWhenNoAttributes': true, | ||
| // 'ignoreWhenEmpty': true, | ||
| // 'ignores': ['pre', 'textarea', ...INLINE_ELEMENTS], | ||
| // 'externalIgnores': [] | ||
| // }], | ||
| // 'no-console': process.env.NODE_ENV === 'production' ? 'error' : 'off', | ||
| // 'no-debugger': process.env.NODE_ENV === 'production' ? 'error' : 'off', | ||
| // }, | ||
| }, | ||
| }, | ||
| ]; |
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