diff --git a/.github/workflows/e2e_wsl.yml b/.github/workflows/e2e_wsl.yml index d6f1594..bc891dd 100644 --- a/.github/workflows/e2e_wsl.yml +++ b/.github/workflows/e2e_wsl.yml @@ -15,20 +15,9 @@ jobs: with: node-version: lts/* cache: 'npm' - - - name: Enable WSL - run: | - curl -L "https://cloud-images.ubuntu.com/releases/jammy/release/ubuntu-22.04-server-cloudimg-amd64-root.tar.xz" -o ubuntu-22.04.tar.xz - wsl --import glacier . ubuntu-22.04.tar.xz - - name: Install dependencies inside WSL - run: | - wsl bash -lc "sudo apt-get update" - wsl bash -lc "sudo apt-get install -y openjdk-17-jre curl unzip" - - name: Install Nextflow inside WSL - run: | - wsl bash -lc "curl -s https://get.nextflow.io | bash" - wsl bash -lc "sudo mv nextflow /usr/local/bin/" - + - name: Setup WSL + shell: pwsh + run: ./scripts/wsl-setup.ps1 - name: Install dependencies run: npm ci - name: Install Playwright Browsers diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index ed566ae..358af27 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -27,7 +27,7 @@ jobs: uses: actions/setup-java@v5 with: distribution: 'temurin' - java-version: '25' + java-version: '21' - name: Setup Node.js uses: actions/setup-node@v4 diff --git a/.gitignore b/.gitignore index 74c5831..9bb10fa 100644 --- a/.gitignore +++ b/.gitignore @@ -1,4 +1,5 @@ bundle +tests/test-data/instances* # Logs logs diff --git a/api-server/index.js b/api-server/index.js index a7356c4..41f61e9 100644 --- a/api-server/index.js +++ b/api-server/index.js @@ -38,7 +38,7 @@ async function call(fcn, ...args) { } app.post('/api/create-workflow-instance', async (req, res) => - post_response(res, collection.createWorkflowInstance(req.body.workflow_id)) + post_response(res, collection.createWorkflowInstance(req.body.workflow_id, req.body.version)) ); app.post('/api/run-workflow', async (req, res) => @@ -97,15 +97,76 @@ app.post('/api/get-available-profiles', async (req, res) => ); app.post('/api/clone-repo', async (req, res) => - post_response(res, collection.cloneRepo(req.body.repoUrl, req.body.ver)) + post_response(res, call(collection.cloneRepo.bind(collection), req.body.repoUrl, req.body.ver)) +); + +app.post('/api/is-repo-installed', async (req, res) => + post_response( + res, + call(collection.isRepoInstalled.bind(collection), req.body.repoUrl, req.body.ver) + ) ); app.post('/api/sync-repo', async (req, res) => post_response(res, collection.syncRepo(req.body.repo)) ); -app.post('/api/get-collections', async (req, res) => - post_response(res, collection.getCollections()) +app.post('/api/add-catalogue', async (req, res) => + post_response(res, call(collection.addCatalogue.bind(collection), req.body.repoUrl, req.body.ver)) +); + +app.post('/api/remove-catalogue', async (req, res) => + post_response(res, collection.removeCatalogue(req.body.catalogue_name)) +); + +app.post('/api/remove-catalogue-section', async (req, res) => + post_response( + res, + collection.removeCatalogueSection(req.body.catalogue_name, req.body.section_name) + ) +); + +app.post('/api/remove-catalogue-workflow', async (req, res) => + post_response( + res, + collection.removeCatalogueWorkflow( + req.body.catalogue_name, + req.body.section_name, + req.body.workflow_name + ) + ) +); + +app.post('/api/update-catalogue-workflow', async (req, res) => + post_response( + res, + collection.updateCatalogueWorkflow( + req.body.catalogue_name, + req.body.section_name, + req.body.workflow_name + ) + ) +); + +app.post('/api/get-catalogues', async (req, res) => + post_response(res, call(collection.getCatalogues.bind(collection))) +); + +app.post('/api/add-user-workflow', async (req, res) => + post_response( + res, + call( + collection.addUserWorkflow.bind(collection), + req.body.name, + req.body.repoUrl, + req.body.ver, + req.body.section + ) + ) +); + +app.post('/api/get-collection-repos', async (req, res) => + post_response(res, collection.getCollectionRepos()) ); app.post('/api/get-collections-path', async (req, res) => @@ -136,18 +197,6 @@ app.post('/api/get-workflow-schema', async (req, res) => post_response(res, collection.getWorkflowSchema(req.body.repoPath)) ); -app.post('/api/get-projects-list', async (req, res) => - post_response(res, collection.getProjectsList()) -); - -app.post('/api/add-project', async (req, res) => - post_response(res, collection.addProject(req.body.repoPath)) -); - -app.post('/api/remove-project', async (req, res) => - post_response(res, collection.removeProject(req.body.project)) -); - app.post('/api/get-installable-repos-list', async (req, res) => post_response(res, collection.getInstallableReposList()) ); @@ -164,10 +213,12 @@ app.post('/api/get-workflow-information', async (req, res) => post_response(res, collection.getWorkflowInformation(req.body.instance)) ); -app.post('/api/settings-get', async (req, res) => post_response(res, collection.settingsGet())); +app.post('/api/settings-get', async (req, res) => + post_response(res, collection.settingsGet(req.body.key)) +); app.post('/api/settings-set', async (req, res) => - post_response(res, collection.settingsSet(req.body.value)) + post_response(res, collection.settingsSet(req.body.key, req.body.value)) ); app.post('/api/open-web-page', async (req, res) => diff --git a/eslint.config.js b/eslint.config.js index 79d9862..8023d83 100644 --- a/eslint.config.js +++ b/eslint.config.js @@ -3,11 +3,16 @@ import react from 'eslint-plugin-react'; import reactHooks from 'eslint-plugin-react-hooks'; import jsxA11y from 'eslint-plugin-jsx-a11y'; import prettier from 'eslint-config-prettier'; +import tsParser from '@typescript-eslint/parser'; +import tsPlugin from '@typescript-eslint/eslint-plugin'; +import importPlugin from 'eslint-plugin-import'; +import { createTypeScriptImportResolver } from 'eslint-import-resolver-typescript'; +import unusedImports from 'eslint-plugin-unused-imports'; export default [ // Global ignore block { - ignores: ['node_modules', 'public', 'coverage'] + ignores: ['node_modules', 'public', 'coverage', 'dist'] }, // Vite config (ESM) @@ -16,15 +21,27 @@ export default [ languageOptions: { ecmaVersion: 'latest', sourceType: 'module' + }, + settings: { + 'import-x/resolver-next': [ + createTypeScriptImportResolver({ + project: 'src' + }) + ] } }, - // Backend (ESM) + // Backend (Node / ESM + TypeScript) { - files: ['src/main/**/*.{js,jsx}', 'src/preload/**/*.{js,jsx}', 'vite.config.js'], + files: ['src/main/**/*.{js,jsx,ts,tsx}', 'src/preload/**/*.{js,jsx,ts,tsx}', 'vite.config.js'], languageOptions: { ecmaVersion: 'latest', sourceType: 'module', + parser: tsParser, + parserOptions: { + ecmaVersion: 'latest', + sourceType: 'module' + }, globals: { require: 'readonly', module: 'readonly', @@ -32,16 +49,66 @@ export default [ process: 'readonly', URL: 'readonly' } + }, + plugins: { + '@typescript-eslint': tsPlugin, + import: importPlugin, + 'unused-imports': unusedImports, + 'jsx-a11y': jsxA11y + }, + settings: { + 'import/resolver': { + typescript: { + /* project: './tsconfig.json' or backend tsconfig */ + } + } + }, + rules: { + 'no-unused-vars': 'off', // JS core rule off + '@typescript-eslint/no-unused-vars': [ + 'warn', + { + vars: 'all', + args: 'after-used', + ignoreRestSiblings: true + } + ], + + 'unused-imports/no-unused-imports': 'warn', + 'unused-imports/no-unused-vars': 'off', + + // backend-specific import rules: + // allow devDependencies in scripts/tests but not in src + 'import/no-extraneous-dependencies': [ + 'error', + { + devDependencies: [ + 'test/**', + 'tests/**', + '**/*.test.{js,jsx,ts,tsx}', + 'scripts/**', + 'build/**', + 'tools/**' + ], + optionalDependencies: false, + peerDependencies: false + } + ], + + 'import/no-unresolved': 'error' } }, // Frontend (ESM + React) { - files: ['src/renderer/**/*.{js,jsx}'], + files: ['src/renderer/**/*.{js,jsx,ts,tsx}'], languageOptions: { ecmaVersion: 'latest', sourceType: 'module', + parser: tsParser, parserOptions: { + ecmaVersion: 'latest', + sourceType: 'module', ecmaFeatures: { jsx: true } }, globals: { @@ -53,15 +120,44 @@ export default [ plugins: { react, 'react-hooks': reactHooks, - 'jsx-a11y': jsxA11y - }, - rules: { - 'react/react-in-jsx-scope': 'off' + 'jsx-a11y': jsxA11y, + '@typescript-eslint': tsPlugin, + import: importPlugin, + 'unused-imports': unusedImports }, settings: { - react: { - version: 'detect' + react: { version: 'detect' }, + 'import/resolver': { + typescript: { + /* project: './tsconfig.json' if needed */ + } } + }, + rules: { + 'react/react-in-jsx-scope': 'off', + + 'no-unused-vars': 'off', // JS core rule off + '@typescript-eslint/no-unused-vars': [ + 'warn', + { + vars: 'all', + args: 'after-used', + ignoreRestSiblings: true + } + ], + + // unused-imports plugin (detects & can auto-fix unused imports) + 'unused-imports/no-unused-imports': 'warn', + 'unused-imports/no-unused-vars': 'off', + + // helpful import resolution rules + 'import/no-unresolved': 'error', + 'import/no-extraneous-dependencies': [ + 'error', + { + devDependencies: ['**/*.test.*', 'test/**', 'tests/**', 'scripts/**'] + } + ] } } ]; diff --git a/package-lock.json b/package-lock.json index 80c3312..26d2f31 100644 --- a/package-lock.json +++ b/package-lock.json @@ -16,11 +16,15 @@ "@jsonforms/react": "^3.7.0-alpha.1", "@mui/icons-material": "^7.2.0", "@mui/material": "^7.2.0", + "@mui/system": "^7.3.7", + "@vitejs/plugin-react": "^4.6.0", "ajv": "^8.17.1", "ansi-to-html": "^0.7.2", "dockerode": "^4.0.7", "dompurify": "^3.2.7", + "electron": "^37.3.1", "electron-store": "8.2.0", + "hast-util-sanitize": "^5.0.2", "i18next": "^25.5.2", "i18next-browser-languagedetector": "^8.2.0", "i18next-resources-to-backend": "^1.2.1", @@ -39,25 +43,28 @@ "slash": "^5.1.0", "typescript": "^5.9.3", "unique-names-generator": "^4.7.1", - "unist-util-visit": "^5.0.0" + "unist-util-visit": "^5.0.0", + "vite": "^7.1.11" }, "devDependencies": { "@playwright/test": "^1.56.1", "@types/dockerode": "^3.3.42", "@types/js-yaml": "^4.0.9", "@types/node": "^24.0.12", - "@vitejs/plugin-react": "^4.6.0", + "@typescript-eslint/eslint-plugin": "^8.54.0", + "@typescript-eslint/parser": "^8.54.0", "@vitest/coverage-v8": "^3.2.4", "css.escape": "^1.5.1", - "electron": "^37.3.1", "electron-builder": "^26.0.12", "eslint": "^9.30.1", "eslint-config-prettier": "^10.1.5", + "eslint-import-resolver-typescript": "^4.4.4", + "eslint-plugin-import": "^2.32.0", "eslint-plugin-jsx-a11y": "^6.10.2", "eslint-plugin-react": "^7.37.5", "eslint-plugin-react-hooks": "^5.2.0", + "eslint-plugin-unused-imports": "^4.3.0", "prettier": "^3.6.2", - "vite": "^7.1.11", "vitest": "^3.2.4" } }, @@ -76,9 +83,9 @@ } }, "node_modules/@babel/code-frame": { - "version": "7.28.6", - "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.28.6.tgz", - "integrity": "sha512-JYgintcMjRiCvS8mMECzaEn+m3PfoQiyqukOMCCVQtoJGYJw8j/8LBJEiqkHLkfwCcs74E3pbAUFNg7d9VNJ+Q==", + "version": "7.29.0", + "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.29.0.tgz", + "integrity": "sha512-9NhCeYjq9+3uxgdtp20LSiJXJvN0FeCtNGpJxuMFZ1Kv3cWUNb6DOhJwUvcVCzKGR66cw4njwM6hrJLqgOwbcw==", "license": "MIT", "dependencies": { "@babel/helper-validator-identifier": "^7.28.5", @@ -90,31 +97,29 @@ } }, "node_modules/@babel/compat-data": { - "version": "7.28.6", - "resolved": "https://registry.npmjs.org/@babel/compat-data/-/compat-data-7.28.6.tgz", - "integrity": "sha512-2lfu57JtzctfIrcGMz992hyLlByuzgIk58+hhGCxjKZ3rWI82NnVLjXcaTqkI2NvlcvOskZaiZ5kjUALo3Lpxg==", - "dev": true, + "version": "7.29.0", + "resolved": "https://registry.npmjs.org/@babel/compat-data/-/compat-data-7.29.0.tgz", + "integrity": "sha512-T1NCJqT/j9+cn8fvkt7jtwbLBfLC/1y1c7NtCeXFRgzGTsafi68MRv8yzkYSapBnFA6L3U2VSc02ciDzoAJhJg==", "license": "MIT", "engines": { "node": ">=6.9.0" } }, "node_modules/@babel/core": { - "version": "7.28.6", - "resolved": "https://registry.npmjs.org/@babel/core/-/core-7.28.6.tgz", - "integrity": "sha512-H3mcG6ZDLTlYfaSNi0iOKkigqMFvkTKlGUYlD8GW7nNOYRrevuA46iTypPyv+06V3fEmvvazfntkBU34L0azAw==", - "dev": true, + "version": "7.29.0", + "resolved": "https://registry.npmjs.org/@babel/core/-/core-7.29.0.tgz", + "integrity": "sha512-CGOfOJqWjg2qW/Mb6zNsDm+u5vFQ8DxXfbM09z69p5Z6+mE1ikP2jUXw+j42Pf1XTYED2Rni5f95npYeuwMDQA==", "license": "MIT", "dependencies": { - "@babel/code-frame": "^7.28.6", - "@babel/generator": "^7.28.6", + "@babel/code-frame": "^7.29.0", + "@babel/generator": "^7.29.0", "@babel/helper-compilation-targets": "^7.28.6", "@babel/helper-module-transforms": "^7.28.6", "@babel/helpers": "^7.28.6", - "@babel/parser": "^7.28.6", + "@babel/parser": "^7.29.0", "@babel/template": "^7.28.6", - "@babel/traverse": "^7.28.6", - "@babel/types": "^7.28.6", + "@babel/traverse": "^7.29.0", + "@babel/types": "^7.29.0", "@jridgewell/remapping": "^2.3.5", "convert-source-map": "^2.0.0", "debug": "^4.1.0", @@ -134,17 +139,25 @@ "version": "2.0.0", "resolved": 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"sha512-vSH118/wwM/pLR38g/Sgk05sNtro6TlTJKuiMXDaZqPUfjTFcudpCOt00IhOfj+1BFAX+UFAlzCU+6WXr3GLFQ==", "license": "MIT", "dependencies": { - "@babel/parser": "^7.28.6", - "@babel/types": "^7.28.6", + "@babel/parser": "^7.29.0", + "@babel/types": "^7.29.0", "@jridgewell/gen-mapping": "^0.3.12", "@jridgewell/trace-mapping": "^0.3.28", "jsesc": "^3.0.2" @@ -157,7 +170,6 @@ "version": "7.28.6", "resolved": "https://registry.npmjs.org/@babel/helper-compilation-targets/-/helper-compilation-targets-7.28.6.tgz", "integrity": "sha512-JYtls3hqi15fcx5GaSNL7SCTJ2MNmjrkHXg4FSpOA/grxK8KwyZ5bubHsCq8FXCkua6xhuaaBit+3b7+VZRfcA==", - "dev": true, "license": "MIT", "dependencies": { "@babel/compat-data": "^7.28.6", @@ -170,6 +182,15 @@ "node": ">=6.9.0" } }, + "node_modules/@babel/helper-compilation-targets/node_modules/semver": { + "version": "6.3.1", + "resolved": "https://registry.npmjs.org/semver/-/semver-6.3.1.tgz", + "integrity": "sha512-BR7VvDCVHO+q2xBEWskxS6DJE1qRnb7DxzUrogb71CWoSficBxYsiAGd+Kl0mmq/MprG9yArRkyrQxTO6XjMzA==", + "license": "ISC", + "bin": { + "semver": "bin/semver.js" + } + }, "node_modules/@babel/helper-globals": { "version": "7.28.0", "resolved": "https://registry.npmjs.org/@babel/helper-globals/-/helper-globals-7.28.0.tgz", @@ -196,7 +217,6 @@ "version": "7.28.6", "resolved": "https://registry.npmjs.org/@babel/helper-module-transforms/-/helper-module-transforms-7.28.6.tgz", "integrity": "sha512-67oXFAYr2cDLDVGLXTEABjdBJZ6drElUSI7WKp70NrpyISso3plG9SAGEF6y7zbha/wOzUByWWTJvEDVNIUGcA==", - "dev": true, "license": "MIT", "dependencies": { "@babel/helper-module-imports": "^7.28.6", @@ -214,7 +234,6 @@ "version": "7.28.6", "resolved": "https://registry.npmjs.org/@babel/helper-plugin-utils/-/helper-plugin-utils-7.28.6.tgz", "integrity": "sha512-S9gzZ/bz83GRysI7gAD4wPT/AI3uCnY+9xn+Mx/KPs2JwHJIz1W8PZkg2cqyt3RNOBM8ejcXhV6y8Og7ly/Dug==", - "dev": true, "license": "MIT", "engines": { "node": ">=6.9.0" @@ -242,7 +261,6 @@ "version": "7.27.1", "resolved": "https://registry.npmjs.org/@babel/helper-validator-option/-/helper-validator-option-7.27.1.tgz", "integrity": "sha512-YvjJow9FxbhFFKDSuFnVCe2WxXk1zWc22fFePVNEaWJEu8IrZVlda6N0uHwzZrUM1il7NC9Mlp4MaJYbYd9JSg==", - "dev": true, "license": "MIT", "engines": { "node": ">=6.9.0" @@ -252,7 +270,6 @@ "version": "7.28.6", "resolved": "https://registry.npmjs.org/@babel/helpers/-/helpers-7.28.6.tgz", "integrity": "sha512-xOBvwq86HHdB7WUDTfKfT/Vuxh7gElQ+Sfti2Cy6yIWNW05P8iUslOVcZ4/sKbE+/jQaukQAdz/gf3724kYdqw==", - "dev": true, "license": "MIT", "dependencies": { "@babel/template": "^7.28.6", @@ -263,12 +280,12 @@ } }, "node_modules/@babel/parser": { - "version": "7.28.6", - "resolved": "https://registry.npmjs.org/@babel/parser/-/parser-7.28.6.tgz", - "integrity": "sha512-TeR9zWR18BvbfPmGbLampPMW+uW1NZnJlRuuHso8i87QZNq2JRF9i6RgxRqtEq+wQGsS19NNTWr2duhnE49mfQ==", + "version": "7.29.0", + "resolved": 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+ "strip-bom": "^3.0.0" + } + }, + "node_modules/tsconfig-paths/node_modules/json5": { + "version": "1.0.2", + "resolved": "https://registry.npmjs.org/json5/-/json5-1.0.2.tgz", + "integrity": "sha512-g1MWMLBiz8FKi1e4w0UyVL3w+iJceWAFBAaBnnGKOpNa5f8TLktkbre1+s6oICydWAm+HRUGTmI+//xv2hvXYA==", + "dev": true, + "license": "MIT", + "dependencies": { + "minimist": "^1.2.0" + }, + "bin": { + "json5": "lib/cli.js" + } + }, + "node_modules/tslib": { + "version": "2.8.1", + "resolved": "https://registry.npmjs.org/tslib/-/tslib-2.8.1.tgz", + "integrity": "sha512-oJFu94HQb+KVduSUQL7wnpmqnfmLsOA/nAh6b6EH0wCEoK0/mPeXU6c3wKDV83MkOuHPRHtSXKKU99IBazS/2w==", + "dev": true, + "license": "0BSD", + "optional": true + }, "node_modules/tweetnacl": { "version": "0.14.5", "resolved": "https://registry.npmjs.org/tweetnacl/-/tweetnacl-0.14.5.tgz", @@ -12909,9 +13608,9 @@ } }, "node_modules/unist-util-visit": { - "version": "5.0.0", - "resolved": "https://registry.npmjs.org/unist-util-visit/-/unist-util-visit-5.0.0.tgz", - "integrity": "sha512-MR04uvD+07cwl/yhVuVWAtw+3GOR/knlL55Nd/wAdblk27GCVt3lqpTivy/tkJcZoNPzTwS1Y+KMojlLDhoTzg==", + "version": "5.1.0", + "resolved": "https://registry.npmjs.org/unist-util-visit/-/unist-util-visit-5.1.0.tgz", + "integrity": "sha512-m+vIdyeCOpdr/QeQCu2EzxX/ohgS8KbnPDgFni4dQsfSCtpz8UqDyY5GjRru8PDKuYn7Fq19j1CQ+nJSsGKOzg==", "license": "MIT", "dependencies": { "@types/unist": "^3.0.0", @@ -12941,17 +13640,50 @@ "version": "0.1.2", "resolved": "https://registry.npmjs.org/universalify/-/universalify-0.1.2.tgz", "integrity": "sha512-rBJeI5CXAlmy1pV+617WB9J63U6XcazHHF2f2dbJix4XzpUF0RS3Zbj0FGIOCAva5P/d/GBOYaACQ1w+0azUkg==", - "dev": true, "license": "MIT", "engines": { "node": ">= 4.0.0" } }, + "node_modules/unrs-resolver": { + "version": "1.11.1", + "resolved": "https://registry.npmjs.org/unrs-resolver/-/unrs-resolver-1.11.1.tgz", + "integrity": "sha512-bSjt9pjaEBnNiGgc9rUiHGKv5l4/TGzDmYw3RhnkJGtLhbnnA/5qJj7x3dNDCRx/PJxu774LlH8lCOlB4hEfKg==", + "dev": true, + "hasInstallScript": true, + "license": "MIT", + "dependencies": { + "napi-postinstall": "^0.3.0" + }, + "funding": { + "url": "https://opencollective.com/unrs-resolver" + }, + "optionalDependencies": { + "@unrs/resolver-binding-android-arm-eabi": "1.11.1", + "@unrs/resolver-binding-android-arm64": "1.11.1", + "@unrs/resolver-binding-darwin-arm64": "1.11.1", + "@unrs/resolver-binding-darwin-x64": "1.11.1", + "@unrs/resolver-binding-freebsd-x64": "1.11.1", + "@unrs/resolver-binding-linux-arm-gnueabihf": "1.11.1", + "@unrs/resolver-binding-linux-arm-musleabihf": "1.11.1", + "@unrs/resolver-binding-linux-arm64-gnu": "1.11.1", + "@unrs/resolver-binding-linux-arm64-musl": "1.11.1", + "@unrs/resolver-binding-linux-ppc64-gnu": "1.11.1", + "@unrs/resolver-binding-linux-riscv64-gnu": "1.11.1", + "@unrs/resolver-binding-linux-riscv64-musl": "1.11.1", + "@unrs/resolver-binding-linux-s390x-gnu": "1.11.1", + "@unrs/resolver-binding-linux-x64-gnu": "1.11.1", + "@unrs/resolver-binding-linux-x64-musl": "1.11.1", + "@unrs/resolver-binding-wasm32-wasi": "1.11.1", + "@unrs/resolver-binding-win32-arm64-msvc": "1.11.1", + "@unrs/resolver-binding-win32-ia32-msvc": "1.11.1", + "@unrs/resolver-binding-win32-x64-msvc": "1.11.1" + } + }, "node_modules/update-browserslist-db": { "version": "1.2.3", "resolved": "https://registry.npmjs.org/update-browserslist-db/-/update-browserslist-db-1.2.3.tgz", "integrity": "sha512-Js0m9cx+qOgDxo0eMiFGEueWztz+d4+M3rGlmKPT+T4IS/jP4ylw3Nwpu6cpTTP8R1MAC1kF4VbdLt3ARf209w==", - "dev": true, "funding": [ { "type": "opencollective", @@ -13086,7 +13818,6 @@ "version": "7.3.1", "resolved": "https://registry.npmjs.org/vite/-/vite-7.3.1.tgz", "integrity": "sha512-w+N7Hifpc3gRjZ63vYBXA56dvvRlNWRczTdmCBBa+CotUzAPf5b7YMdMR/8CQoeYE5LX3W4wj6RYTgonm1b9DA==", - "dev": true, "license": "MIT", "dependencies": { "esbuild": "^0.27.0", @@ -13184,7 +13915,6 @@ "version": "2.3.3", "resolved": "https://registry.npmjs.org/fsevents/-/fsevents-2.3.3.tgz", "integrity": "sha512-5xoDfX+fL7faATnagmWPpbFtwh/R77WmMMqqHGS65C3vvB0YHrgF+B1YmZ3441tMj5n63k0212XNoJwzlhffQw==", - "dev": true, "hasInstallScript": true, "license": "MIT", "optional": true, @@ -13493,14 +14223,12 @@ "version": "3.1.1", "resolved": "https://registry.npmjs.org/yallist/-/yallist-3.1.1.tgz", "integrity": "sha512-a4UGQaWPH59mOXUYnAG2ewncQS4i4F43Tv3JoAM+s2VDAmS9NsK8GpDMLrCHPksFT7h3K6TOoUNn2pb7RoXx4g==", - "dev": true, "license": "ISC" }, "node_modules/yaml": { "version": "2.8.2", "resolved": "https://registry.npmjs.org/yaml/-/yaml-2.8.2.tgz", "integrity": "sha512-mplynKqc1C2hTVYxd0PU2xQAc22TI1vShAYGksCCfxbn/dFwnHTNi1bvYsBTkhdUNtGIf5xNOg938rrSSYvS9A==", - "dev": true, "license": "ISC", "optional": true, "peer": true, @@ -13545,7 +14273,6 @@ "version": "2.10.0", "resolved": "https://registry.npmjs.org/yauzl/-/yauzl-2.10.0.tgz", "integrity": "sha512-p4a9I6X6nu6IhoGmBqAcbJy1mlC4j27vEPZX9F4L4/vZT3Lyq1VkFHw/V/PUcB9Buo+DG3iHkT0x3Qya58zc3g==", - "dev": true, "license": "MIT", "dependencies": { "buffer-crc32": "~0.2.3", diff --git a/package.json b/package.json index 26c5861..2acee8c 100644 --- a/package.json +++ b/package.json @@ -59,18 +59,20 @@ "@types/dockerode": "^3.3.42", "@types/js-yaml": "^4.0.9", "@types/node": "^24.0.12", - "@vitejs/plugin-react": "^4.6.0", + "@typescript-eslint/eslint-plugin": "^8.54.0", + "@typescript-eslint/parser": "^8.54.0", "@vitest/coverage-v8": "^3.2.4", "css.escape": "^1.5.1", - "electron": "^37.3.1", "electron-builder": "^26.0.12", "eslint": "^9.30.1", "eslint-config-prettier": "^10.1.5", + "eslint-import-resolver-typescript": "^4.4.4", + "eslint-plugin-import": "^2.32.0", "eslint-plugin-jsx-a11y": "^6.10.2", "eslint-plugin-react": "^7.37.5", "eslint-plugin-react-hooks": "^5.2.0", + "eslint-plugin-unused-imports": "^4.3.0", "prettier": "^3.6.2", - "vite": "^7.1.11", "vitest": "^3.2.4" }, "dependencies": { @@ -81,11 +83,15 @@ "@jsonforms/react": "^3.7.0-alpha.1", "@mui/icons-material": "^7.2.0", "@mui/material": "^7.2.0", + "@mui/system": "^7.3.7", + "@vitejs/plugin-react": "^4.6.0", "ajv": "^8.17.1", "ansi-to-html": "^0.7.2", "dockerode": "^4.0.7", "dompurify": "^3.2.7", + "electron": "^37.3.1", "electron-store": "8.2.0", + "hast-util-sanitize": "^5.0.2", "i18next": "^25.5.2", "i18next-browser-languagedetector": "^8.2.0", "i18next-resources-to-backend": "^1.2.1", @@ -104,6 +110,7 @@ "slash": "^5.1.0", "typescript": "^5.9.3", "unique-names-generator": "^4.7.1", - "unist-util-visit": "^5.0.0" + "unist-util-visit": "^5.0.0", + "vite": "^7.1.11" } } diff --git a/scripts/prepare_bundle.js b/scripts/prepare_bundle.js index f3acf1d..8e75bce 100644 --- a/scripts/prepare_bundle.js +++ b/scripts/prepare_bundle.js @@ -21,7 +21,8 @@ import { fileURLToPath } from 'url'; const __filename = fileURLToPath(import.meta.url); const __dirname = path.dirname(__filename); -const JAVA_VERSION = process.env.JAVA_VERSION || '25'; +const bundle_full_jre = false; +const JAVA_VERSION = process.env.JAVA_VERSION || '21'; const NXF_URL = process.env.NXF_URL || 'https://www.nextflow.io/releases/v25.10.2/nextflow-25.10.2-one.jar'; @@ -81,6 +82,34 @@ function downloadFile(url, destPath) { }); } +function detectJavaHome(javaCmd = 'java') { + try { + // java -XshowSettings:properties prints " java.home = /path" + const out = runOutput(`${javaCmd} -XshowSettings:properties -version 2>&1`); + const m = out.match(/^\s*java\.home = (.+)$/m); + if (m && m[1]) return m[1].trim(); + } catch (e) { + // fallback: try `which java` -> resolve path -> go up two directories + try { + const whichJava = runOutput('which java').trim(); + if (whichJava) { + // On many systems 'which java' returns the wrapper; try readlink -f + try { + const resolved = runOutput(`readlink -f ${whichJava}`).trim(); + if (resolved) { + // java binary lives in .../bin/java -> java.home is parent dir + return path.dirname(path.dirname(resolved)); + } + } catch (e2) { + // fallback to dirname(dirname(whichJava)) + return path.dirname(path.dirname(whichJava)); + } + } + } catch {} + } + return null; +} + async function main() { try { // SCRIPT_DIR logic: assume script is at scripts/prepare_bundle.js @@ -118,75 +147,160 @@ async function main() { // Prepare Java runtime const jreDir = path.join(bundleDir, 'jre'); if (!fileExists(jreDir)) { - log('Preparing Java runtime...'); - - // Ensure jdeps exists - try { - execSync('jdeps --version', { stdio: 'ignore' }); - } catch (e) { - throw new Error( - 'jdeps not found in PATH. Please install a JDK that includes jdeps and jlink.' - ); - } + if (bundle_full_jre) { + // --- Copy full JRE --- - log('Determining Java dependencies (jdeps)...'); - - // Run jdeps similar to: jdeps --multi-release $JAVA_VERSION -summary nextflow.jar | awk '/->/ {print $NF}' | grep -E '^(java\.|jdk\.)' | sort -u | paste -sd, - - const jdepsCmd = `jdeps --multi-release ${JAVA_VERSION} -summary "${nextflowJar}"`; - const jdepsOut = runOutput(jdepsCmd); - // Parse lines containing '->' and extract right-most token, then filter java./jdk. - const modules = jdepsOut - .split(/\r?\n/) - .map((l) => l.trim()) - .filter((l) => l.includes('->')) - .map((l) => { - // take last token - const parts = l.split(/\s+/); - return parts[parts.length - 1]; - }) - .filter((m) => /^java\.|^jdk\./.test(m)) - .filter(Boolean); + log('Bundling full system JRE into the app...'); - const uniqueModules = Array.from(new Set(modules)).sort(); - if (uniqueModules.length === 0) { - log('Warning: no java/jdk modules found by jdeps. Falling back to "java.base".'); - } - const MODULES = uniqueModules.length > 0 ? uniqueModules.join(',') : 'java.base'; - log('Required modules:', MODULES); - - // Ensure jlink exists - try { - execSync('jlink --version', { stdio: 'ignore' }); - } catch (e) { - throw new Error('jlink not found in PATH. Please install a JDK that includes jlink.'); - } + // allow an override for reproducible packaging + const JAVA_CMD = process.env.SYSTEM_JAVA || 'java'; + const javaHome = detectJavaHome(JAVA_CMD); + if (!javaHome) { + throw new Error( + 'Could not detect system JAVA_HOME. Set SYSTEM_JAVA env or ensure `java` is on PATH.' + ); + } + log('Detected java.home:', javaHome); - log('Creating minimal Java runtime (jlink)...'); - // Build jlink command: jlink --add-modules "$MODULES" --strip-debug --compress zip-6 --no-header-files --no-man-pages --output ./jre - const jlinkCmd = [ - 'jlink', - `--add-modules "${MODULES}"`, - '--strip-debug', - '--compress', - 'zip-6', - '--no-header-files', - '--no-man-pages', - `--output "${jreDir}"` - ].join(' '); - - run(jlinkCmd); - - log('Minimal Java runtime created.'); - - // Smoke test: run jre/bin/java -jar nextflow.jar info - const javaBin = path.join(jreDir, 'bin', 'java'); - if (!fileExists(javaBin)) { - throw new Error(`Expected java executable not found at ${javaBin}`); - } + // Copy the full JRE/JDK directory into bundle/jre + // Prefer Node's fs.cpSync (Node 16+). Fallback to system 'cp -a' or rsync. + try { + // Ensure destination parent exists + fs.mkdirSync(jreDir, { recursive: true }); + try { + // Node >= 16: use fs.cpSync for recursive copy + if (fs.cpSync) { + log('Copying JRE using fs.cpSync (fast)...'); + fs.cpSync(javaHome, jreDir, { recursive: true }); + } else { + throw new Error('fs.cpSync not available'); + } + } catch (copyErr) { + log('fs.cpSync failed or not available, falling back to system copy (cp -a)...'); + // Use POSIX cp -a (works on macOS/Linux) + run(`cp -a "${javaHome}" "${jreDir}"`); + } + } catch (copyError) { + err( + 'Failed to copy JRE into bundle:', + copyError && copyError.message ? copyError.message : copyError + ); + throw copyError; + } + + // Normalize: in some JDKs javaHome may be the JDK root (e.g. .../Contents/Home). + // Ensure bin/java exists. + let javaBin = path.join(jreDir, 'bin', 'java'); + if (!fileExists(javaBin)) { + // If the copied tree contains 'jre' inside, try that + const alt = path.join(jreDir, 'jre', 'bin', 'java'); + if (fileExists(alt)) { + javaBin = alt; + } else { + // sometimes JDK home has 'bin/java' but copy created nested structure; search + const found = runOutput( + `find "${jreDir}" -type f -name java -print -quit 2>/dev/null` + ).trim(); + if (found) javaBin = found; + } + } - log('Running smoke test...'); - run(`"${javaBin}" -jar "${nextflowJar}" info`); - log('Smoke test completed successfully.'); + if (!fileExists(javaBin)) { + throw new Error(`Expected java executable not found in copied JRE. Searched: ${javaBin}`); + } + + // Make sure java binary is executable + try { + fs.chmodSync(javaBin, 0o755); + } catch (e) { + // ignore if chmod fails due to permissions on packaging system + } + + log('Bundled java binary at:', javaBin); + log('Running smoke test with bundled JRE...'); + run(`"${javaBin}" -jar "${nextflowJar}" info`); + log('Smoke test completed successfully (full JRE).'); + } else { + // --- Minimal JRE --- + + log('Preparing minimal Java runtime...'); + + // Ensure jdeps exists + try { + execSync('jdeps --version', { stdio: 'ignore' }); + } catch (e) { + throw new Error( + 'jdeps not found in PATH. Please install a JDK that includes jdeps and jlink.' + ); + } + + log('Determining Java dependencies (jdeps)...'); + + // Run jdeps similar to: jdeps --multi-release $JAVA_VERSION -summary nextflow.jar | awk '/->/ {print $NF}' | grep -E '^(java\.|jdk\.)' | sort -u | paste -sd, - + const jdepsCmd = `jdeps --multi-release ${JAVA_VERSION} -summary "${nextflowJar}"`; + const jdepsOut = runOutput(jdepsCmd); + // Parse lines containing '->' and extract right-most token, then filter java./jdk. + const modules = jdepsOut + .split(/\r?\n/) + .map((l) => l.trim()) + .filter((l) => l.includes('->')) + .map((l) => { + // take last token + const parts = l.split(/\s+/); + return parts[parts.length - 1]; + }) + .filter((m) => /^java\.|^jdk\./.test(m)) + .filter(Boolean); + + modules.push('java.base'); + modules.push('java.net.http'); + modules.push('jdk.crypto.ec'); + modules.push('jdk.crypto.cryptoki'); + modules.push('java.security.jgss'); + modules.push('java.naming'); + modules.push('java.xml'); + + const uniqueModules = Array.from(new Set(modules)).sort(); + if (uniqueModules.length === 0) { + log('Warning: no java/jdk modules found by jdeps. Falling back to "java.base".'); + } + const MODULES = uniqueModules.length > 0 ? uniqueModules.join(',') : 'java.base'; + log('Required modules:', MODULES); + + // Ensure jlink exists + try { + execSync('jlink --version', { stdio: 'ignore' }); + } catch (e) { + throw new Error('jlink not found in PATH. Please install a JDK that includes jlink.'); + } + + log('Creating minimal Java runtime (jlink)...'); + // Build jlink command: jlink --add-modules "$MODULES" --strip-debug --compress zip-6 --no-header-files --no-man-pages --output ./jre + const jlinkCmd = [ + 'jlink', + `--add-modules "${MODULES}"`, + '--strip-debug', + '--compress', + 'zip-6', + '--no-header-files', + '--no-man-pages', + `--output "${jreDir}"` + ].join(' '); + + run(jlinkCmd); + + log('Minimal Java runtime created.'); + + // Smoke test: run jre/bin/java -jar nextflow.jar info + const javaBin = path.join(jreDir, 'bin', 'java'); + if (!fileExists(javaBin)) { + throw new Error(`Expected java executable not found at ${javaBin}`); + } + + log('Running smoke test...'); + run(`"${javaBin}" -jar "${nextflowJar}" info`); + log('Smoke test completed successfully.'); + } } else { log('Java runtime already exists. Skipping preparation.'); } diff --git a/scripts/wsl-setup.ps1 b/scripts/wsl-setup.ps1 new file mode 100644 index 0000000..6f9fcfc --- /dev/null +++ b/scripts/wsl-setup.ps1 @@ -0,0 +1,42 @@ +#!/usr/bin/env pwsh + +wsl.exe --version +wsl.exe --list + +mkdir "$env:USERPROFILE\glacier\wsl" -Force +curl.exe -L "https://cloud-images.ubuntu.com/releases/jammy/release/ubuntu-22.04-server-cloudimg-amd64-root.tar.xz" -o "$env:USERPROFILE\glacier\wsl\ubuntu-22.04.tar.xz" + +wsl.exe --import build "$env:USERPROFILE\glacier\wsl" "$env:USERPROFILE\glacier\wsl\ubuntu-22.04.tar.xz" + +wsl.exe -d build -u root -- apt update +wsl.exe -d build -u root -- apt upgrade -y +wsl.exe -d build -u root -- apt install -y docker.io openjdk-17-jre-headless +wsl.exe -d build -u root -- java -version + +wsl.exe -d build -u root -- useradd -m -s /bin/bash user +wsl.exe -d build -u root -- bash -c "echo 'user:user' | chpasswd" +wsl.exe -d build -u root -- bash -c "echo -e '[boot]\nsystemd=true\n[user]\ndefault=user' > /etc/wsl.conf" +wsl.exe -d build -u root -- usermod -aG docker user +wsl.exe -d build -u root -- bash -c "sed -i 's/127.0.1.1.*/127.0.1.1 glacier/' /etc/hosts" + +wsl.exe -t build +wsl.exe -d build -u root -- systemctl enable docker +wsl.exe -d build -u root -- systemctl start docker +wsl.exe -d build -u user -- bash -c "curl -s https://get.nextflow.io -o ~/nextflow && chmod +x ~/nextflow" +wsl.exe -d build -u root -- mv /home/user/nextflow /usr/local/bin/ + +wsl.exe -t build + +wsl.exe -d build -- nextflow -v +wsl.exe -d build -- nextflow run hello +wsl.exe -d build -- docker run hello-world + +wsl.exe -t build +wsl.exe --export build "$env:USERPROFILE\glacier\wsl\glacier-wsl.tar" +wsl.exe --unregister build + +wsl.exe --import glacier "$env:USERPROFILE\glacier\wsl" "$env:USERPROFILE\glacier\wsl\glacier-wsl.tar" + +wsl.exe -d glacier -- nextflow -v +wsl.exe -d glacier -- nextflow run hello +wsl.exe -d glacier -- docker run hello-world diff --git a/src/locales/en/translation.json b/src/locales/en/translation.json index 933f88a..bd37e46 100644 --- a/src/locales/en/translation.json +++ b/src/locales/en/translation.json @@ -2,32 +2,63 @@ "glacier": "GLACIER", "container-started": "Container built and started with ID", "common": { + "okay": "Okay", "cancel": "Cancel" }, "sidebar": { - "hub": "Hub", "library": "Library", "instances": "Instances", "settings": "Settings" }, - "hub": { - "add-workflow-from-repository": "Add Workflow from Repository", - "repo": "Repo", - "add": "Add", - "clone": "Clone", - "clone-return-none": "Clone failed or returned nothing", - "clone-failed": "Clone operation failed", - "install": "Install", - "repo-added": "Repository added successfully", - "repo-add-failed": "Failed to add repository" - }, "library": { "local-repositories": "Local Repositories", + "install": "Install", "run": "Run", "sync": "Sync", "repo-sync-success": "Repository synced successfully", "repo-sync-failed": "Repository sync failed", - "no-repos-installed": "No repositories installed. Add a repository from the Hub to get started." + "no-repos-installed": "No repositories installed. Add a repository or catalogue to get started.", + "clone-error": "Error cloning repository", + "actions": "Actions", + "add-catalogue": "Add Catalogue", + "remove-catalogue": "Remove Catalogue", + "add-section": "Add Section", + "remove-section": "Remove Section", + "add-repository": "Add Workflow", + "remove-repository": "Remove Workflow", + "install-all-workflows": "Install All Workflows", + "check-for-updates": "Check for Updates", + "confirm-remove-catalogue": "Are you sure you want to remove this catalogue? All workflows and workflow instances will remain installed.", + "catalogue-removed-success": "Catalogue removed successfully", + "catalogue-removed-failure": "Failed to remove catalogue", + "confirm-remove-section": "Are you sure you want to remove this section from the catalogue? All workflows and workflow instances will remain installed.", + "section-removed-success": "Section removed successfully", + "section-removed-failure": "Failed to remove section", + "confirm-remove-workflow": "Are you sure you want to remove this workflow from the section?", + "workflow-removed-success": "Workflow removed successfully", + "workflow-removed-failure": "Failed to remove workflow", + "workflow-updated-success": "Workflow updated successfully", + "workflow-updated-failure": "Failed to update workflow", + "installing-workflows": "Installing workflows...", + "install-workflows-completed-with-errors": "Workflow installation completed with errors.", + "add-catalogue-dialog": { + "title": "Add Catalogue", + "description": "Enter the Github organisation, or repository to add:", + "repository-url": "Repository URL", + "error-unable-to-add": "Unable to add catalogue. Please check the URL and try again.", + "error-repo-required": "Repository URL is required." + }, + "add-workflow-dialog": { + "title": "Add Workflow", + "description": "Enter the Github repository to add:", + "repository-url": "Repository URL", + "version": "Version (branch, tag, or commit)", + "section": "Section", + "name": "Workflow name (optional)", + "error-unable-to-add": "Unable to add workflow. Please check the URL and try again.", + "error-repo-required": "Repository URL is required.", + "error-section-required": "Section is required." + } }, "instances": { "title": "Instances", @@ -101,7 +132,9 @@ "general": "General", "dark-mode": "Dark Mode", "collections-path": "Library path", - "allow-arbitrary-repo-cloning": "Allow arbitrary repository cloning", + "permit-add-catalogues": "Allow adding catalogues", + "permit-catalogue-modifications": "Allow modifying catalogues", + "permit-add-repos": "Allow adding repositories", "language-select": "Language", "visual-options": "Visual", "advanced-options": "Advanced", diff --git a/src/locales/fr/translation.json b/src/locales/fr/translation.json index 0c776d4..af5dd82 100644 --- a/src/locales/fr/translation.json +++ b/src/locales/fr/translation.json @@ -2,32 +2,63 @@ "glacier": "GLACIER", "container-started": "Conteneur construit et démarré avec l'ID", "common": { + "okay": "OK", "cancel": "Annuler" }, "sidebar": { - "hub": "Hub", "library": "Bibliothèque", "instances": "Instances", "settings": "Paramètres" }, - "hub": { - "add-workflow-from-repository": "Ajouter un flux de travail depuis un dépôt", - "repo": "Dépôt", - "add": "Ajouter", - "clone": "Cloner", - "clone-return-none": "Le clonage a échoué ou n'a rien retourné", - "clone-failed": "L'opération de clonage a échoué", - "install": "Installer", - "repo-added": "Dépôt ajouté avec succès", - "repo-add-failed": "L'ajout du dépôt a échoué" - }, "library": { "local-repositories": "Dépôts locaux", + "install": "Installer", "run": "Exécuter", "sync": "Synchroniser", "repo-sync-success": "Dépôt synchronisé avec succès", "repo-sync-failed": "La synchronisation du dépôt a échoué", - "no-repos-installed": "Aucun dépôt installé. Veuillez ajouter un dépôt depuis le Hub." + "no-repos-installed": "Aucun dépôt n’est installé. Ajoutez un dépôt ou un catalogue pour commencer.", + "clone-error": "Erreur lors du clonage du dépôt", + "actions": "Actions", + "add-catalogue": "Ajouter un catalogue", + "remove-catalogue": "Supprimer le catalogue", + "add-section": "Ajouter une section", + "remove-section": "Supprimer la section", + "add-repository": "Ajouter un dépôt", + "remove-repository": "Supprimer le dépôt", + "install-all-workflows": "Installer tous les flux de travail", + "check-for-updates": "Vérifier les mises à jour", + "confirm-remove-catalogue": "Êtes-vous sûr de vouloir supprimer ce catalogue ? Tous les flux de travail et instances de flux de travail resteront installés.", + "catalogue-removed-success": "Catalogue supprimé avec succès", + "catalogue-removed-failure": "Échec de la suppression du catalogue", + "confirm-remove-section": "Êtes-vous sûr de vouloir supprimer cette section du catalogue ? Tous les flux de travail et instances de flux de travail resteront installés.", + "section-removed-success": "Section supprimée avec succès", + "section-removed-failure": "Échec de la suppression de la section", + "confirm-remove-workflow": "Êtes-vous sûr de vouloir supprimer ce flux de travail de la section ?", + "workflow-removed-success": "Flux de travail supprimé avec succès", + "workflow-removed-failure": "Échec de la suppression du flux de travail", + "workflow-updated-success": "Flux de travail mis à jour avec succès", + "workflow-updated-failure": "Échec de la mise à jour du flux de travail", + "installing-workflows": "Installation des flux de travail...", + "install-workflows-completed-with-errors": "Installation des flux de travail terminée avec des erreurs.", + "add-catalogue-dialog": { + "title": "Ajouter un catalogue", + "description": "Entrez l'URL du catalogue à ajouter:", + "repository-url": "URL du dépôt", + "error-unable-to-add": "Impossible d'ajouter le catalogue. Veuillez vérifier l'URL et réessayer.", + "error-repo-required": "L'URL du dépôt est requise." + }, + "add-workflow-dialog": { + "title": "Ajouter un flux de travail", + "description": "Ajouter un flux de travail depuis un dépôt Github.", + "repository-url": "URL du dépôt", + "version": "Version (branche, tag ou commit)", + "section": "Section", + "name": "Nom du flux de travail (optionnel)", + "error-unable-to-add": "Impossible d'ajouter le flux de travail. Veuillez vérifier l'URL et réessayer.", + "error-repo-required": "L'URL du dépôt est requise.", + "error-section-required": "Le nom de la section est requis." + } }, "instances": { "title": "Instances", @@ -101,7 +132,9 @@ "general": "Général", "dark-mode": "Mode sombre", "collections-path": "Chemin de la bibliothèque", - "allow-arbitrary-repo-cloning": "Autoriser le clonage de dépôts arbitraires", + "permit-add-catalogues": "Autoriser l'ajout de catalogues", + "permit-catalogue-modifications": "Autoriser les modifications de catalogues", + "permit-add-repos": "Autoriser l'ajout de dépôts", "language-select": "Langue", "visual-options": "Visuelles", "advanced-options": "Avancées", diff --git a/src/main/collection.ts b/src/main/collection.ts index 388d713..6c49d22 100644 --- a/src/main/collection.ts +++ b/src/main/collection.ts @@ -10,9 +10,8 @@ import { cloneRepo, ICloneRepo, getRepoTags, getRepoBranches } from './repo.js'; import { runWorkflow } from './runner.js'; import { getEnvironmentStatus, performEnvironmentAction } from '../runners/environment.js'; import { WorkflowStatus } from '../types/types.js'; -import { EnvironmentKey } from '../types/environment.js'; import { syncRepo, getWorkflowParams, getWorkflowSchema } from './repo.js'; -import { getCollectionsPath, getDefaultCollectionsDir, locateReports } from './paths.js'; +import { getCollectionsPath, locateReports } from './paths.js'; import { settings, StoreSchema } from './settings.js'; // Should remove imports from specific runners @@ -22,7 +21,28 @@ import { parseNextflowLog } from '../runners/nextflow/nf-parse.js'; const instance_database_file = 'instances.json'; -const default_repos = ['artic-network/artic-mpxv-nf', 'artic-network/amplicon-nf']; +export interface Catalogue { + name: string; + source: string; + description?: string; + icon?: string; + scheme?: Record; + sections: CatalogueSection[]; +} + +export interface CatalogueSection { + name: string; + description?: string; + icon?: string; + scheme?: Record; + workflows: CatalogueWorkflow[]; +} + +export interface CatalogueWorkflow { + name: string; + repo: string; + version?: string; +} export enum IWorkflowType { NEXTFLOW = 'nextflow', @@ -76,8 +96,6 @@ class Workflow implements IWorkflow { url: string; versions: WorkflowVersion[]; - project: IProject | null = null; // reference to project if applicable - constructor(wf: IWorkflow) { this.id = wf.id; this.name = wf.name; @@ -156,28 +174,6 @@ class WorkflowInstance implements IWorkflowInstance { } } -// A project is a collection of workflows, mainly used for branding -export interface IProject { - id: string; - name: string; - url: string; - workflows: IWorkflow[]; -} - -class Project implements IProject { - id: string; - name: string; - url: string; - workflows: IWorkflow[]; - - constructor({ id, name, url, workflows = [] }: IProject) { - this.id = id; - this.name = name; - this.url = url; - this.workflows = workflows; - } -} - // Singleton class export class Collection { // --- Class management -------------------------------------------------------------- @@ -203,7 +199,7 @@ export class Collection { root_path: string = ''; - projects: Project[] = []; + catalogues: Catalogue[] = []; workflows: Workflow[] = []; workflow_instances: WorkflowInstance[] = []; @@ -219,11 +215,16 @@ export class Collection { return path.join(this.root_path, 'instances'); } + get catalogues_path(): string { + return path.join(this.root_path, 'catalogues'); + } + // --- Logic ------------------------------------------------------------------------- async parseCollection() { this.parseWorkflows(); this.parseInstallableRepos(); + await this.parseCatalogues(); await this.parseInstances(); } @@ -273,11 +274,7 @@ export class Collection { } } - private parseInstallableRepos() { - default_repos.forEach((repo) => { - this.addInstallableRepo(repo); - }); - } + private parseInstallableRepos() {} private async parseInstances() { // Clean existing instances @@ -356,7 +353,7 @@ export class Collection { try { process.kill(pid, 0); // Check if process is running console.log(`Instance ${instance.id} has running PID: ${pid}`); - } catch (e) { + } catch { console.log(`Instance ${instance.id} PID ${pid} is not running, updating status.`); // Remove PID from instance instance.pid = instance.pid.filter((p) => p !== pid); @@ -406,6 +403,7 @@ export class Collection { } } + // eslint-disable-next-line @typescript-eslint/no-unused-vars determineWorkflowType(folder: string): IWorkflowType { // Placeholder logic, can be improved return IWorkflowType.NEXTFLOW; @@ -428,7 +426,7 @@ export class Collection { throw new Error(`Workflow ${workflow_id} has no versions.`); } let workflow_version; - if (version === undefined) { + if (version === undefined || version === 'latest') { // Local repository workflow_version = workflow.versions[0]; } else { @@ -542,12 +540,12 @@ export class Collection { try { process.kill(-pid, sig); // signal the process group return true; - } catch (e) { + } catch { // Fallback: try the single process try { process.kill(pid, sig); return true; - } catch (_) { + } catch { return false; } } @@ -739,7 +737,7 @@ export class Collection { // Check if version already exists let version = wf.versions.find((v) => v.version === repo.version); if (version !== undefined) { - throw new Error(`Workflow ${wf_id}@${repo.version} already exists.`); + return version; } version = new WorkflowVersion({ id: `${wf_id}@${repo.version}`, @@ -760,7 +758,7 @@ export class Collection { await this.parseCollection(); } - getCollections(): IRepo[] { + getCollectionRepos(): IRepo[] { const repos: IRepo[] = []; this.workflows.forEach((wf) => { wf.versions.forEach((ver) => { @@ -861,34 +859,6 @@ export class Collection { return locateReports(instance.path); } - getProjectsList(): IProject[] { - if (this.projects.length > 0) { - return this.projects; - } - return this.projects; - } - - addProject(repoPath: string): string { - // /// Replace with repo parsing logic /// - const i = this.projects.length + 1; - this.projects.push( - new Project({ - id: i.toString(), - name: `New Project ${i}`, - url: repoPath, - workflows: [] - }) - ); - return ''; - } - - removeProject(project: IProject) { - const index = this.projects.findIndex((p) => p.id === project.id); - if (index === -1) return 'Project not found in collection.'; - this.projects.splice(index, 1); - return ''; - } - getInstallableReposList(): IRepoVersions[] { return this.installable_repos; } @@ -975,4 +945,243 @@ export class Collection { async performEnvironmentAction(key: string, action: string) { return performEnvironmentAction(key, action); } + + async parseCatalogues() { + // Clear existing catalogues + this.catalogues = []; + + // Read catalogues from catalogues path + if (!fs.existsSync(this.catalogues_path)) { + console.log(`Catalogues path ${this.catalogues_path} does not exist.`); + return; + } + const owners = fs.readdirSync(this.catalogues_path); + for (const owner of owners) { + const ownerPath = path.join(this.catalogues_path, owner); + const repoDirs = fs.readdirSync(ownerPath); + for (const repo of repoDirs) { + const repoPath = path.join(ownerPath, repo); + // Read catalogue.json + const cat_file = path.join(repoPath, 'catalogue.json'); + const cat_contents = fs.readFileSync(cat_file, 'utf-8'); + const js = JSON.parse(cat_contents); + js['source'] = `${owner}/${repo}`; + js['base_dir'] = repoPath; + // Add to catalogues + this.catalogues.push(js); + } + } + } + + async addCatalogue(url: string, version: string) { + // Clone catalogue repository and refresh catalogues list + console.log(`Cloning catalogue repository ${url} version ${version}`); + const hasSlash = url.includes('/'); + if (!hasSlash) { + url = `${url}/glacier-catalogue`; + } + const repo: ICloneRepo = await cloneRepo(url, this.catalogues_path, version); + const cat_file = path.join(repo.path, 'catalogue.json'); + const contents = fs.readFileSync(cat_file, 'utf-8'); + const js = JSON.parse(contents); + js['source'] = url; + js['base_dir'] = repo.path; + this.parseCatalogues(); // update catalogue + } + + async removeCatalogue(catalogue_name: string) { + // Remove catalogue from catalogues path + const cat = this.catalogues.find((c) => c.name === catalogue_name); + if (!cat) { + throw new Error(`Catalogue ${catalogue_name} not found.`); + } + const owner = cat.source.split('/')[0]; + const repo = cat.source.split('/')[1]; + const cat_path = path.join(this.catalogues_path, owner, repo); + fs.rmSync(cat_path, { recursive: true, force: true }); + // Refresh catalogues + this.parseCatalogues(); + } + + async removeCatalogueSection(catalogue_name: string, section_name: string) { + // Remove section from catalogue + const cat = this.catalogues.find((c) => c.name === catalogue_name); + if (!cat) { + throw new Error(`Catalogue ${catalogue_name} not found.`); + } + const section_index = cat.sections.findIndex((s) => s.name === section_name); + if (section_index === -1) { + throw new Error(`Section ${section_name} not found in catalogue ${catalogue_name}.`); + } + cat.sections.splice(section_index, 1); + // Save to catalogues path + const owner = cat.source.split('/')[0]; + const repo = cat.source.split('/')[1]; + const cat_path = path.join(this.catalogues_path, owner, repo, 'catalogue.json'); + fs.writeFileSync(cat_path, JSON.stringify(cat, null, 2)); + // Refresh catalogues + this.parseCatalogues(); + } + + async removeCatalogueWorkflow( + catalogue_name: string, + section_name: string, + workflow_name: string + ) { + // Remove workflow from catalogue section + const cat = this.catalogues.find((c) => c.name === catalogue_name); + if (!cat) { + throw new Error(`Catalogue ${catalogue_name} not found.`); + } + const section = cat.sections.find((s) => s.name === section_name); + if (!section) { + throw new Error(`Section ${section_name} not found in catalogue ${catalogue_name}.`); + } + const workflow_index = section.workflows.findIndex((w) => w.name === workflow_name); + if (workflow_index === -1) { + throw new Error( + `Workflow ${workflow_name} not found in section ${section_name} of catalogue ${catalogue_name}.` + ); + } + section.workflows.splice(workflow_index, 1); + // Save to catalogues path + const owner = cat.source.split('/')[0]; + const repo = cat.source.split('/')[1]; + const cat_path = path.join(this.catalogues_path, owner, repo, 'catalogue.json'); + fs.writeFileSync(cat_path, JSON.stringify(cat, null, 2)); + // Refresh catalogues + this.parseCatalogues(); + } + + async updateCatalogueWorkflow( + catalogue_name: string, + section_name: string, + workflow_name: string + ) { + // Update workflow in catalogue section by re-fetching tags/branches + const cat = this.catalogues.find((c) => c.name === catalogue_name); + if (!cat) { + throw new Error(`Catalogue ${catalogue_name} not found.`); + } + const section = cat.sections.find((s) => s.name === section_name); + if (!section) { + throw new Error(`Section ${section_name} not found in catalogue ${catalogue_name}.`); + } + const workflow = section.workflows.find((w) => w.name === workflow_name); + if (!workflow) { + throw new Error( + `Workflow ${workflow_name} not found in section ${section_name} of catalogue ${catalogue_name}.` + ); + } + // Re-fetch tags and branches + const tags = await getRepoTags(workflow.repo); + const branches = await getRepoBranches(workflow.repo); + const all_versions = tags.concat(branches); + if (all_versions.length === 0) { + throw new Error(`No tags or branches found for repository: ${workflow.repo}`); + } + // Update version if current version not found + if (workflow.version !== 'latest' && !all_versions.includes(workflow.version || '')) { + workflow.version = all_versions[0]; + } + // Save to catalogues path + const owner = cat.source.split('/')[0]; + const repo = cat.source.split('/')[1]; + const cat_path = path.join(this.catalogues_path, owner, repo, 'catalogue.json'); + fs.writeFileSync(cat_path, JSON.stringify(cat, null, 2)); + // Refresh catalogues + this.parseCatalogues(); + } + + async addUserWorkflow(name: string, url: string, version: string, section: string) { + if (!name) { + name = url.split('/')[1]; + } + if (!section) { + section = 'My Workflows'; + } + if (!version) { + version = 'latest'; + } + // Verify that repository url exists + const tags = await getRepoTags(url); + const branches = await getRepoBranches(url); + const all_versions = tags.concat(branches); + if (all_versions.length === 0) { + throw new Error(`No tags or branches found for repository: ${url}`); + } + if (version !== 'latest' && !all_versions.includes(version)) { + throw new Error( + `Version ${version} not found for repository: ${url}. Available versions: ${all_versions.join( + ', ' + )}` + ); + } + // Add workflow to catalogue + const user_cat_path = path.join( + this.catalogues_path, + 'user_collection', + 'store', + 'catalogue.json' + ); + let user_catalogue: Catalogue; + if (fs.existsSync(user_cat_path)) { + // Read existing catalogue + const contents = fs.readFileSync(user_cat_path, 'utf-8'); + user_catalogue = JSON.parse(contents); + } else { + // Create new catalogue + user_catalogue = { + name: 'User collection', + source: 'local', + sections: [] + }; + } + // Find (or create) section + let user_section = user_catalogue.sections.find((sec) => sec.name === section); + if (!user_section) { + user_section = { + name: section, + workflows: [] + }; + user_catalogue.sections.push(user_section); + } + user_section.workflows.push({ + name: name, + repo: url, + version: version + }); + // Save to catalogues path + this.ensurePathExists(path.dirname(user_cat_path)); + fs.writeFileSync(user_cat_path, JSON.stringify(user_catalogue, null, 2)); + // Refresh catalogues + this.parseCatalogues(); + } + + async getCatalogues() { + return this.catalogues; + } + + async isRepoInstalled(url: string, version: string): Promise { + const owner = url.split('/')[0]; + const repo = url.split('/')[1]; + const wf = this.workflows.find((wf) => wf.id === `${owner}/${repo}`); + if (!wf) { + return ''; + } + if (version === 'latest') { + // Any version installed + if (wf.versions.length > 0) { + return wf.versions[0].version || ''; + } else { + return ''; + } + } + const ver = wf.versions.find((v) => v.version === version); + if (ver) { + return ver.version || ''; + } else { + return ''; + } + } } diff --git a/src/main/ipc-handlers.ts b/src/main/ipc-handlers.ts index ab03083..0ed0886 100644 --- a/src/main/ipc-handlers.ts +++ b/src/main/ipc-handlers.ts @@ -1,7 +1,3 @@ -import fs from 'fs'; -import path from 'path'; -import git from 'isomorphic-git'; -import http from 'isomorphic-git/http/node/index.cjs'; import { ipcMain } from 'electron'; import { Collection } from './collection.js'; import { StoreSchema } from './settings.js'; @@ -22,6 +18,29 @@ async function call(fcn: any, ...args: any[]): Promise> { } export function registerIpcHandlers() { + const redirect = { + 'run-workflow': collection.runWorkflow.bind(collection), + 'get-catalogues': collection.getCatalogues.bind(collection), + 'add-catalogue': collection.addCatalogue.bind(collection), + 'remove-catalogue': collection.removeCatalogue.bind(collection), + 'remove-catalogue-section': collection.removeCatalogueSection.bind(collection), + 'remove-catalogue-workflow': collection.removeCatalogueWorkflow.bind(collection), + 'update-catalogue-workflow': collection.updateCatalogueWorkflow.bind(collection), + 'add-user-workflow': collection.addUserWorkflow.bind(collection), + 'clone-repo': collection.cloneRepo.bind(collection), + 'is-repo-installed': collection.isRepoInstalled.bind(collection) + }; + + for (const [channel, fcn] of Object.entries(redirect)) { + ipcMain.handle(channel, async (event, ...args) => { + return call(fcn, ...args); + }); + } + + /* + * Legacy call format - update to use call() for consistent error handling + */ + ipcMain.handle( 'create-workflow-instance', async (event, workflow_id: string, version: string) => { @@ -81,10 +100,6 @@ export function registerIpcHandlers() { return collection.getAvailableProfiles(instance); }); - ipcMain.handle('clone-repo', async (event, repoUrl, ver) => { - return await collection.cloneRepo(repoUrl, ver); - }); - ipcMain.handle('get-collections-path', () => { return collection.getCollectionsPath(); }); @@ -93,12 +108,8 @@ export function registerIpcHandlers() { return collection.setCollectionsPath(path); }); - ipcMain.handle('get-collections', async () => { - return collection.getCollections(); - }); - - ipcMain.handle('run-workflow', async (event, ...args) => { - return call(collection.runWorkflow.bind(collection), ...args); + ipcMain.handle('get-collection-repos', async () => { + return collection.getCollectionRepos(); }); ipcMain.handle('sync-repo', async (event, path: string) => { @@ -113,19 +124,7 @@ export function registerIpcHandlers() { return collection.getWorkflowSchema(repoPath); }); - ipcMain.handle('get-projects-list', async (event) => { - return collection.getProjectsList(); - }); - - ipcMain.handle('add-project', async (event, repoPath) => { - return collection.addProject(repoPath); - }); - - ipcMain.handle('remove-project', async (event, project) => { - return collection.removeProject(project); - }); - - ipcMain.handle('get-installable-repos-list', async (event) => { + ipcMain.handle('get-installable-repos-list', async () => { return collection.getInstallableReposList(); }); diff --git a/src/main/main.ts b/src/main/main.ts index 7174d00..3addbdd 100644 --- a/src/main/main.ts +++ b/src/main/main.ts @@ -1,5 +1,4 @@ import { app, screen, BrowserWindow, ipcMain, dialog } from 'electron'; -import * as fs from 'fs'; import * as path from 'path'; import { fileURLToPath } from 'url'; import { registerIpcHandlers } from './ipc-handlers.js'; diff --git a/src/main/paths.ts b/src/main/paths.ts index 755da79..6a8794a 100644 --- a/src/main/paths.ts +++ b/src/main/paths.ts @@ -3,7 +3,6 @@ import path from 'path'; // import { userDataDir } from 'platformdirs'; import fs from 'fs'; import store from './store.js'; -import { IRepo } from './types'; export function getDefaultCollectionsDir(): string { const homeDir = os.homedir(); diff --git a/src/main/preload.ts b/src/main/preload.ts index 88faf03..03a0757 100644 --- a/src/main/preload.ts +++ b/src/main/preload.ts @@ -28,9 +28,24 @@ contextBridge.exposeInMainWorld('electronAPI', { getAvailableProfiles: (instance: any) => ipcRenderer.invoke('get-available-profiles', instance), cloneRepo: (repoUrl: string, ver: string) => ipcRenderer.invoke('clone-repo', repoUrl, ver), + isRepoInstalled: (repoUrl: string, ver: string) => + ipcRenderer.invoke('is-repo-installed', repoUrl, ver), getCollectionsPath: () => ipcRenderer.invoke('get-collections-path'), setCollectionsPath: (path: string) => ipcRenderer.invoke('set-collections-path', path), - getCollections: () => ipcRenderer.invoke('get-collections'), + getCollectionRepos: () => ipcRenderer.invoke('get-collection-repos'), + addCatalogue: (repoUrl: string, version: string) => + ipcRenderer.invoke('add-catalogue', repoUrl, version), + removeCatalogue: (catalogue_name: string) => + ipcRenderer.invoke('remove-catalogue', catalogue_name), + removeCatalogueSection: (catalogue_name: string, section_name: string) => + ipcRenderer.invoke('remove-catalogue-section', catalogue_name, section_name), + removeCatalogueWorkflow: (catalogue_name: string, section_name: string, workflow_name: string) => + ipcRenderer.invoke('remove-catalogue-workflow', catalogue_name, section_name, workflow_name), + updateCatalogueWorkflow: (catalogue_name: string, section_name: string, workflow_name: string) => + ipcRenderer.invoke('update-catalogue-workflow', catalogue_name, section_name, workflow_name), + getCatalogues: () => ipcRenderer.invoke('get-catalogues'), + addUserWorkflow: (name: string, repoUrl: string, version: string, section: string) => + ipcRenderer.invoke('add-user-workflow', name, repoUrl, version, section), syncRepo: (repo: string) => ipcRenderer.invoke('sync-repo', repo), getWorkflowParams: (repoPath: string) => ipcRenderer.invoke('get-workflow-params', repoPath), pickFile: (filters?: Electron.FileFilter[]) => ipcRenderer.invoke('pick-file', { filters }), @@ -38,9 +53,6 @@ contextBridge.exposeInMainWorld('electronAPI', { pickFileOrDirectory: (options: Electron.OpenDialogOptions) => ipcRenderer.invoke('pick-file-or-directory', options), getWorkflowSchema: (repoPath: string) => ipcRenderer.invoke('get-workflow-schema', repoPath), - getProjectsList: () => ipcRenderer.invoke('get-projects-list'), - addProject: (repoPath: string) => ipcRenderer.invoke('add-project', repoPath), - removeProject: (project: any) => ipcRenderer.invoke('remove-project', project), getInstallableReposList: () => ipcRenderer.invoke('get-installable-repos-list'), addInstallableRepo: (repoUrl: string) => ipcRenderer.invoke('add-installable-repo', repoUrl), getWorkflowInformation: (instance: any) => diff --git a/src/main/repo.ts b/src/main/repo.ts index 183b928..85676d1 100644 --- a/src/main/repo.ts +++ b/src/main/repo.ts @@ -1,10 +1,8 @@ -import { getDefaultCollectionsDir } from './paths.js'; import * as fs from 'fs'; import * as path from 'path'; import yaml from 'js-yaml'; import git from 'isomorphic-git'; import http from 'isomorphic-git/http/node'; -import { IRepo } from './types.js'; import { uniqueNamesGenerator, adjectives, animals } from 'unique-names-generator'; interface WorkflowData { @@ -55,24 +53,43 @@ export async function cloneRepo( // Determine the version to clone let version = ver || (await getDefaultBranch(url)); - if (version === null || version === '') { - version = 'main'; // Fallback + if (version === null || version === '' || version === 'latest') { + const tags = (await getRepoTags(url)) || []; + if (tags.length === 0) { + version = 'main'; + } else { + version = tags[0]; + } } // Determine and create the target directory const targetDir = path.join(workflowDir, owner, repo + '@' + version); + if (fs.existsSync(targetDir)) { + return { + owner: owner, + repo: repo, + version: version, + url: url, + path: targetDir + } as ICloneRepo; + } fs.mkdirSync(targetDir, { recursive: true }); // Clone - await git.clone({ - fs, - http, - dir: targetDir, - url: url, - ref: version, // branch or tag - singleBranch: true, - depth: 1 - }); + try { + await git.clone({ + fs, + http, + dir: targetDir, + url: url, + ref: version, // branch or tag + singleBranch: true, + depth: 1 + }); + } catch (err: unknown) { + fs.rmSync(targetDir, { recursive: true, force: true }); // Clean up on failure + throw err; + } return { owner: owner, @@ -124,22 +141,22 @@ export async function deleteRepo(repoPath: string) { } export async function getRepoTags(url: string) { - const { owner, repo, url: full_url } = parseRepoUrl(url); + const { url: full_url } = parseRepoUrl(url); try { const info = await git.getRemoteInfo({ http, url: full_url }); return Object.keys(info.refs.tags).reverse(); - } catch (err) { + } catch { console.info(`Failed to fetch tags from ${url}`); return []; } } export async function getRepoBranches(url: string) { - const { owner, repo, url: full_url } = parseRepoUrl(url); + const { url: full_url } = parseRepoUrl(url); try { const info = await git.getRemoteInfo({ http, url: full_url }); return Object.keys(info.refs.heads); - } catch (err) { + } catch { console.info(`Failed to fetch branches from ${url}`); return []; } diff --git a/src/main/runner.ts b/src/main/runner.ts index 0c1a755..bfd1f20 100644 --- a/src/main/runner.ts +++ b/src/main/runner.ts @@ -1,9 +1,3 @@ -import * as os from 'os'; -import * as path from 'path'; -import * as fs_sync from 'fs'; -import { IRepo } from './types'; -import { spawn } from 'child_process'; -import { Readable, Duplex } from 'stream'; import { promises as fs } from 'fs'; import { IWorkflowInstance, IWorkflowParams } from './collection.js'; import { diff --git a/src/main/store.ts b/src/main/store.ts index ba43128..834ea2e 100644 --- a/src/main/store.ts +++ b/src/main/store.ts @@ -3,7 +3,10 @@ import Store from 'electron-store'; // Keep in sync with types/settings.js export interface StoreSchema { collectionsPath: string; - disableProjects: boolean; + darkMode: boolean; + permitAddCatalogues: boolean; + permitCatalogueModifications: boolean; + permitAddRepos: boolean; disableSchemaValidation: boolean; } @@ -13,7 +16,19 @@ const store = new Store({ type: 'string', default: '' }, - disableProjects: { + darkMode: { + type: 'boolean', + default: false + }, + permitAddCatalogues: { + type: 'boolean', + default: true + }, + permitCatalogueModifications: { + type: 'boolean', + default: true + }, + permitAddRepos: { type: 'boolean', default: true }, diff --git a/src/renderer/pages/Hub.tsx b/src/renderer/pages/Hub.tsx deleted file mode 100644 index 7946a57..0000000 --- a/src/renderer/pages/Hub.tsx +++ /dev/null @@ -1,197 +0,0 @@ -import React, { useEffect, useState } from 'react'; -import { - Button, - Container, - Paper, - Stack, - TextField, - Typography, - Box, - Grid, - Select, - Snackbar, - Alert, - MenuItem -} from '@mui/material'; -import CircularProgress from '@mui/material/CircularProgress'; -import { API } from '../services/api.js'; -import { useTranslation } from 'react-i18next'; - -export default function HubPage({ - repoUrl, - setRepoUrl, - targetDir, - drawerOpen, - setTargetDir, - setFolderPath, - allowArbitraryRepoCloning, - logMessage, - setView -}) { - const { t } = useTranslation(); - - const [installedRepos, setInstalledRepos] = useState([]); - const [open, setOpen] = useState(false); - const [repos, setRepos] = useState([]); - - const updateInstalledRepos = async () => { - API.getCollections().then((list) => { - setInstalledRepos(list); - }); - }; - - const getInstallableRepos = () => { - API.getInstallableReposList().then((repos) => { - repos.forEach((repo) => { - repo.installing = false; - }); - setRepos(repos); - }); - }; - - useEffect(() => { - getInstallableRepos(); - updateInstalledRepos(); - }, []); - - const addRepo = (repoUrl: string) => { - API.addInstallableRepo(repoUrl) - .then(() => { - logMessage(t('hub.repo-added'), 'success'); - getInstallableRepos(); - }) - .catch((err) => { - console.error(err); - logMessage(`${t('hub.repo-add-failed')}`, 'error'); - }); - }; - - const setInstallationState = (repoUrl: string, version: string, installing: boolean) => { - const newRepos = repos.map((repo) => - repo.url === repoUrl && repo.version === version ? { ...repo, installing: installing } : repo - ); - setRepos(newRepos); - }; - - const cloneRepo = async (repoUrl: string, version: string) => { - // Clone repository - setInstallationState(repoUrl, version, true); - try { - const result = await API.cloneRepo(repoUrl, version); - if (result?.path) { - setTargetDir(result.path); - setFolderPath(result.path); - logMessage(`Cloned ${result.name} to ${result.path}`, 'success'); - setView('library'); - } else { - logMessage(t('hub.clone-return-none'), 'error'); - } - } catch (err) { - console.error(err); - logMessage(t('hub.clone-failed'), 'error'); - } - setInstallationState(repoUrl, version, false); - updateInstalledRepos(); - }; - - const isRepoInstalled = (repoUrl: string, version: string) => { - return installedRepos.some((repo) => repo.url === repoUrl && repo.version === version); - }; - - const onChangeRepoVersion = (repo, newVersion) => { - const updatedRepos = repos.map((r) => (r.url === repo.url ? { ...r, version: newVersion } : r)); - setRepos(updatedRepos); - }; - - return ( - - {' '} - {/* extra space for fixed log */} - - {allowArbitraryRepoCloning && ( - - - {t('hub.add-workflow-from-repository')} - - - {t('hub.repo')}: - setRepoUrl(e.target.value)} - size="small" - fullWidth - /> - - - {targetDir && ( - - {targetDir} - - )} - - )} - - {repos.length === 0 ? ( - - No installable workflows. - - ) : ( - - {repos.map((repo) => ( - - - - {repo.name} - - - - - - - - ))} - - )} - - - ); -} diff --git a/src/renderer/pages/Instances.tsx b/src/renderer/pages/Instances.tsx index 87a662f..8a663ee 100644 --- a/src/renderer/pages/Instances.tsx +++ b/src/renderer/pages/Instances.tsx @@ -1,16 +1,5 @@ -import React, { useState, useEffect, useMemo } from 'react'; -import { - Box, - Container, - Paper, - Stack, - Tabs, - Tab, - TextField, - Typography, - Button, - Alert -} from '@mui/material'; +import React, { useState, useEffect } from 'react'; +import { Box, Container, Paper, Typography, Button } from '@mui/material'; import Table from '@mui/material/Table'; import TableBody from '@mui/material/TableBody'; import TableCell from '@mui/material/TableCell'; @@ -20,20 +9,12 @@ import TableRow from '@mui/material/TableRow'; import Tooltip from '@mui/material/Tooltip'; import MonitorPage from './Monitor/Monitor'; import ParametersPage from './Parameters/Parameters'; -import { JsonForms } from '@jsonforms/react'; -import List from '@mui/material/List'; -import ListItem from '@mui/material/ListItem'; -import ListItemText from '@mui/material/ListItemText'; -import ListItemButton from '@mui/material/ListItemButton'; -import ListItemAvatar from '@mui/material/ListItemAvatar'; -import Avatar from '@mui/material/Avatar'; import CreatedIcon from '@mui/icons-material/PlayCircle'; import ClosedIcon from '@mui/icons-material/PlayCircle'; import RunningIcon from '@mui/icons-material/Update'; import QuestionMarkIcon from '@mui/icons-material/QuestionMark'; import CompletedIcon from '@mui/icons-material/CheckCircle'; import FailedIcon from '@mui/icons-material/Error'; -import DeleteIcon from '@mui/icons-material/Delete'; import IconButton from '@mui/material/IconButton'; import { API } from '../services/api.js'; import { useTranslation } from 'react-i18next'; @@ -119,9 +100,9 @@ const InstanceList = ({ rows, setItem, instancesList, refreshInstancesList }) => {row.workflow} - handleDeleteInstance(row.name)}> - - + ))} @@ -143,12 +124,6 @@ export default function InstancesPage({ const [rows, setRows] = useState([]); - const onLaunch = async (instance, params) => { - API.runWorkflow(instance, params, {}).then(() => { - logMessage(`Launched workflow ${instance.name}`); - }); - }; - useEffect(() => { setRows( instancesList.map((item) => diff --git a/src/renderer/pages/Library.tsx b/src/renderer/pages/Library.tsx deleted file mode 100644 index a296281..0000000 --- a/src/renderer/pages/Library.tsx +++ /dev/null @@ -1,120 +0,0 @@ -import React, { useEffect, useState } from 'react'; -import { - Button, - Container, - Paper, - Stack, - TextField, - Typography, - Box, - Grid, - Select, - Snackbar, - MenuItem, - Alert, - Link -} from '@mui/material'; -import { useTranslation } from 'react-i18next'; -import { API } from '../services/api.js'; - -export default function LibraryPage({ - repoUrl, - setRepoUrl, - targetDir, - drawerOpen, - setTargetDir, - setFolderPath, - addToInstancesList, - logMessage, - setView -}) { - const { t } = useTranslation(); - - const [repos, setRepos] = useState([]); - const [open, setOpen] = useState(false); - - const getRepos = async () => { - const list = await API.getCollections(); - const enriched = await Promise.all( - list.map(async (repo) => { - const info = await API.getWorkflowInformation(repo); - return { - ...repo, - info: { - ...(repo.info ?? {}), - title: info.title || repo.name, - description: info.description || '' - } - }; - }) - ); - setRepos(enriched); - }; - - useEffect(() => { - getRepos(); - }, []); - - const onClickSync = async (repo) => { - try { - const result = await API.syncRepo(repo.path); - if (result?.status === 'ok') { - logMessage(t('library.repo-sync-success'), 'success'); - } else { - throw new Error(result?.message || t('library.repo-sync-failed')); - } - } catch (err) { - console.error(err); - logMessage(t('library.repo-sync-failed'), 'error'); - } - }; - - return ( - - {' '} - {/* extra space for fixed log */} - - - {repos.map((repo) => ( - /* @ts-ignore */ - - - {repo.info.title} - - {repo.name} @ {repo.version} - - {repo.info.description} - - - - - - - - ))} - - - {repos.length === 0 && ( - - - {t('library.no-repos-installed')} - - - )} - - ); -} diff --git a/src/renderer/pages/Library/ActionMenu.tsx b/src/renderer/pages/Library/ActionMenu.tsx new file mode 100644 index 0000000..1dab0bb --- /dev/null +++ b/src/renderer/pages/Library/ActionMenu.tsx @@ -0,0 +1,109 @@ +import React, { useState } from 'react'; +import { Button, Box, Menu, MenuItem } from '@mui/material'; +import { useTranslation } from 'react-i18next'; +import QueryAddCatalogueDialog from './QueryAddCatalogueDialog'; +import QueryAddWorkflowDialog from './QueryAddWorkflowDialog'; +import { API } from '../../services/api.js'; + +export default function ActionMenu({ setCatalogues, permitAddCatalogues, permitAddRepos }) { + const { t } = useTranslation(); + const [showQueryCatalogueDialog, setShowQueryCatalogueDialog] = useState(false); + const [showQueryRepositoryDialog, setShowQueryRepositoryDialog] = useState(false); + const [anchorEl, setAnchorEl] = useState(null); + const menuIsOpen = Boolean(anchorEl); + + const handleMenuOpen = (event) => { + setAnchorEl(event.currentTarget); + }; + + const handleMenuClose = () => { + setAnchorEl(null); + }; + + const handleDialogClose = () => { + setShowQueryCatalogueDialog(false); + setShowQueryRepositoryDialog(false); + handleMenuClose(); + }; + + const addCatalogue = async (repo, version) => { + return API.addCatalogue(repo, version).then((result) => { + if (result.ok) { + return API.getCatalogues().then((result) => { + if (result.ok) { + setCatalogues(result.data); + } else { + throw new Error(result.error.message); + } + }); + } else { + throw new Error(result.error.message); + } + }); + }; + + const addUserWorkflow = async (name, url, version, section) => { + return API.addUserWorkflow(name, url, version, section).then((result) => { + if (result.ok) { + return API.getCatalogues().then((result) => { + if (result.ok) { + setCatalogues(result.data); + } else { + throw new Error(result.error.message); + } + }); + } else { + throw new Error(result.error.message); + } + }); + handleDialogClose(); + }; + + const display = permitAddCatalogues || permitAddRepos; + return ( + + {display && ( + <> + + + {permitAddCatalogues && ( + setShowQueryCatalogueDialog(true)} + disabled={!permitAddCatalogues} + > + {t('library.add-catalogue')} + + )} + {permitAddRepos && ( + setShowQueryRepositoryDialog(true)} + disabled={!permitAddRepos} + > + {t('library.add-repository')} + + )} + + + + + )} + + ); +} diff --git a/src/renderer/pages/Library/Library.tsx b/src/renderer/pages/Library/Library.tsx new file mode 100644 index 0000000..ed03b9a --- /dev/null +++ b/src/renderer/pages/Library/Library.tsx @@ -0,0 +1,581 @@ +import React, { useEffect, useState } from 'react'; +import { useTheme } from '@mui/material/styles'; +import { + Button, + Container, + IconButton, + Paper, + Stack, + Typography, + Box, + Grid, + Menu, + MenuItem +} from '@mui/material'; +import { useTranslation } from 'react-i18next'; +import ActionMenu from './ActionMenu'; +import ProgressDialog from './ProgressDialog'; +import MoreVertIcon from '@mui/icons-material/MoreVert'; +import { API } from '../../services/api.js'; + +const resolveHttpUrl = (path, source) => { + if (!path) return null; + if (path.startsWith('http://') || path.startsWith('https://')) { + return path; + } + if (source) { + return `${source.replace(/\/$/, '')}/${path.replace(/^\//, '')}`; + } + // Fallback + return path; +}; + +function WorkflowCard({ + workflow, + deleteWorkflow, + updateWorkflow, + scheme, + createWorkflowInstance, + refresh, + setRefresh, + logMessage +}) { + const { t } = useTranslation(); + + const [anchorEl, setAnchorEl] = useState(null); + const [isRepoInstalled, setIsRepoInstalled] = useState(false); + const [versionInstalled, setVersionInstalled] = useState(''); + const [loading, setLoading] = useState(false); + const menuIsOpen = Boolean(anchorEl); + + workflow['id'] = workflow['repo']; + workflow['version'] = workflow['version'] ?? 'latest'; + + const checkRepoInstalled = () => + API.isRepoInstalled(workflow.repo, workflow.version).then((result) => { + if (result.ok) { + const installed_version = result.data; + if (installed_version) { + setVersionInstalled(installed_version); + setIsRepoInstalled(true); + setLoading(false); + } + } else { + setIsRepoInstalled(false); + } + }); + + useEffect(() => { + checkRepoInstalled(); + }, [refresh]); + + const cloneRepo = async () => { + setLoading(true); + const result = await API.cloneRepo(workflow.repo, workflow.version); + if (result.ok) { + setLoading(false); + setRefresh(!refresh); + logMessage(`Cloned ${result.data.name} to ${result.data.path}`, 'success'); + } else { + setLoading(false); + setRefresh(!refresh); + logMessage(`${t('library.clone-error')} (${result.error.message})`, 'error'); + } + }; + + const runWorkflow = () => { + createWorkflowInstance(workflow); + }; + + const handleMenuOpen = (event) => { + setAnchorEl(event.currentTarget); + }; + + const handleMenuClose = () => { + setAnchorEl(null); + }; + + const handleDeleteWorkflow = async () => { + deleteWorkflow(); + handleMenuClose(); + }; + + const checkForUpdates = async () => { + updateWorkflow(); + handleMenuClose(); + }; + + return ( + + + {workflow.name} + + + + + + + {t('library.remove-repository')} + {workflow['version'] === 'latest' && isRepoInstalled && ( + {t('library.check-for-updates')} + )} + + + + {workflow.version}{' '} + {isRepoInstalled && workflow.version === 'latest' && `(${versionInstalled})`} + + + + {isRepoInstalled ? ( + + ) : ( + + )} + + + ); +} + +function SectionCard({ + section, + deleteSection, + deleteWorkflow, + updateWorkflow, + scheme, + source, + createWorkflowInstance, + permitCatalogueModifications, + refresh, + setRefresh, + installAllWorkflows, + logMessage +}) { + const { t } = useTranslation(); + const [anchorEl, setAnchorEl] = useState(null); + const menuIsOpen = Boolean(anchorEl); + + const handleMenuOpen = (event) => { + setAnchorEl(event.currentTarget); + }; + + const handleMenuClose = () => { + setAnchorEl(null); + }; + + const queueInstallWorkflows = async () => { + let workflows = section?.workflows || []; + await installAllWorkflows( + workflows.map((workflow) => ({ + id: `${workflow.repo}@${workflow.version}`, + repo: workflow.repo, + version: workflow.version + })) + ); + setRefresh(!refresh); + handleMenuClose(); + }; + + const handleDeleteSection = async () => { + deleteSection(); + handleMenuClose(); + }; + + return ( + + + {section?.icon && ( + { + e.currentTarget.style.display = 'none'; + }} + /> + )} + + + {section.name} + + {section.description && ( + + {section.description} + + )} + + {permitCatalogueModifications && ( + <> + + + + + + + + {t('library.install-all-workflows')} + + {t('library.remove-section')} + + + )} + + + {(section?.workflows || []).map((workflow) => ( + + deleteWorkflow(workflow)} + updateWorkflow={() => updateWorkflow(workflow)} + scheme={scheme} + createWorkflowInstance={createWorkflowInstance} + refresh={refresh} + setRefresh={setRefresh} + logMessage={logMessage} + /> + + ))} + + + ); +} + +function CatalogueCard({ + catalogue, + deleteCatalogue, + deleteSection, + deleteWorkflow, + updateWorkflow, + createWorkflowInstance, + permitCatalogueModifications, + refresh, + setRefresh, + installAllWorkflows, + logMessage +}) { + const { t } = useTranslation(); + const theme = useTheme(); + const [anchorEl, setAnchorEl] = useState(null); + const menuIsOpen = Boolean(anchorEl); + + const handleMenuOpen = (event) => { + setAnchorEl(event.currentTarget); + }; + + const handleMenuClose = () => { + setAnchorEl(null); + }; + + const queueInstallWorkflows = async () => { + let workflows = []; + for (const section of catalogue.sections || []) { + for (const workflow of section.workflows || []) { + workflows.push({ + id: `${workflow.repo}@${workflow.version}`, + repo: workflow.repo, + version: workflow.version + }); + } + } + await installAllWorkflows(workflows); + setRefresh(!refresh); + handleMenuClose(); + }; + + const handleDeleteCatalogue = async () => { + deleteCatalogue(); + handleMenuClose(); + }; + + const checkForUpdates = async () => { + await API.syncRepo(catalogue?.['base_dir']); + handleMenuClose(); + }; + + return ( + + + {catalogue?.icon && ( + { + e.currentTarget.style.display = 'none'; + }} + /> + )} + + {catalogue.name} + {catalogue.description && ( + {catalogue.description} + )} + + {permitCatalogueModifications && ( + <> + + + + + + + + {t('library.install-all-workflows')} + + {t('library.remove-catalogue')} + {catalogue?.name !== 'User collection' && ( + {t('library.check-for-updates')} + )} + + + )} + + + {(catalogue?.sections || []).map((section) => ( + deleteSection(section)} + deleteWorkflow={(workflow) => deleteWorkflow(section, workflow)} + updateWorkflow={(workflow) => updateWorkflow(section, workflow)} + scheme={catalogue?.scheme || {}} + source={catalogue?.['base_dir']} + createWorkflowInstance={createWorkflowInstance} + permitCatalogueModifications={permitCatalogueModifications} + refresh={refresh} + setRefresh={setRefresh} + installAllWorkflows={installAllWorkflows} + logMessage={logMessage} + /> + ))} + + + ); +} + +export default function LibraryPage({ + createWorkflowInstance, + permitAddCatalogues, + permitCatalogueModifications, + permitAddRepos, + logMessage +}) { + const { t } = useTranslation(); + const [catalogues, setCatalogues] = useState([]); + const [refresh, setRefresh] = useState(false); + + const [progressCount, setProgressCount] = useState(0); + const [progressValue, setProgressValue] = useState(0); + + const getCatalogues = async () => { + API.getCatalogues().then((result) => { + if (result.ok) { + setCatalogues(result.data); + } + }); + }; + + useEffect(() => { + getCatalogues(); + }, []); + + const deleteCatalogue = async (catalogue) => { + if (!window.confirm(t('library.confirm-remove-catalogue', { name: catalogue.name }))) { + return; + } + API.removeCatalogue(catalogue.name).then((result) => { + if (result.ok) { + logMessage(t('library.catalogue-removed-success', { name: catalogue.name }), 'success'); + getCatalogues(); + } else { + logMessage(t('library.catalogue-removed-failure', { name: catalogue.name }), 'error'); + } + }); + }; + + const deleteSection = async (catalogue, section) => { + if (!window.confirm(t('library.confirm-remove-section', { name: section.name }))) { + return; + } + API.removeCatalogueSection(catalogue.name, section.name).then((result) => { + if (result.ok) { + logMessage(t('library.section-removed-success', { name: section.name }), 'success'); + getCatalogues(); + } else { + logMessage(t('library.section-removed-failure', { name: section.name }), 'error'); + } + }); + }; + + const deleteWorkflow = (catalogue, section, workflow) => { + if (!window.confirm(t('library.confirm-remove-workflow', { name: workflow.name }))) { + return; + } + API.removeCatalogueWorkflow(catalogue.name, section.name, workflow.name).then((result) => { + if (result.ok) { + logMessage(t('library.workflow-removed-success', { name: workflow.name }), 'success'); + getCatalogues(); + } else { + logMessage(t('library.workflow-removed-failure', { name: workflow.name }), 'error'); + } + }); + }; + + const updateWorkflow = (catalogue, section, workflow) => { + API.updateCatalogueWorkflow(catalogue.name, section.name, workflow.name).then((result) => { + if (result.ok) { + logMessage(t('library.workflow-updated-success', { name: workflow.name }), 'success'); + getCatalogues(); + } else { + logMessage(t('library.workflow-updated-failure', { name: workflow.name }), 'error'); + } + }); + }; + + const installAllWorkflows = async (workflows) => { + // Remove duplicates + workflows = workflows.filter( + (workflow, index, self) => index === self.findIndex((w) => w.id === workflow.id) + ); + // Clone + setProgressValue(0); + setProgressCount(workflows.length); + const failed_list = []; + for (const workflow of workflows) { + const result = await API.cloneRepo(workflow.repo, workflow.version); + if (!result.ok) { + failed_list.push(workflow.id); + } + setProgressValue((prev) => prev + 1); + } + setProgressCount(0); + setProgressValue(0); + if (failed_list.length > 0) { + const failed_str = failed_list.join(', '); + logMessage(`${t('library.install-workflows-completed-with-errors')}: ${failed_str}`, 'error'); + } + setRefresh(!refresh); + }; + + return ( + + + 0} + title={t('library.installing-workflows')} + value={progressValue} + total={progressCount} + /> + + {(catalogues || []).map((catalogue) => ( + deleteCatalogue(catalogue)} + deleteSection={(section) => deleteSection(catalogue, section)} + deleteWorkflow={(section, workflow) => deleteWorkflow(catalogue, section, workflow)} + updateWorkflow={(section, workflow) => updateWorkflow(catalogue, section, workflow)} + createWorkflowInstance={createWorkflowInstance} + permitCatalogueModifications={permitCatalogueModifications} + refresh={refresh} + setRefresh={setRefresh} + installAllWorkflows={installAllWorkflows} + logMessage={logMessage} + /> + ))} + + {catalogues.length === 0 && ( + + + {t('library.no-repos-installed')} + + + )} + + ); +} diff --git a/src/renderer/pages/Library/ProgressDialog.tsx b/src/renderer/pages/Library/ProgressDialog.tsx new file mode 100644 index 0000000..cb9c137 --- /dev/null +++ b/src/renderer/pages/Library/ProgressDialog.tsx @@ -0,0 +1,48 @@ +import React, { useEffect } from 'react'; +import { + Dialog, + DialogTitle, + DialogContent, + DialogContentText, + Box, + LinearProgress +} from '@mui/material'; + +type ProgressDialogProps = { + open: boolean; + title: string; + message?: string; + value: number; + total: number; +}; + +export default function ProgressDialog({ + open, + title, + message, + value, + total +}: ProgressDialogProps) { + const [progress, setProgress] = React.useState(0); + + useEffect(() => { + if (total > 0) { + const calculatedProgress = (value / total) * 100; + setProgress(calculatedProgress); + } else { + setProgress(0); + } + }, [value, total]); + + return ( + + {title} + + {message && {message}} + + + + + + ); +} diff --git a/src/renderer/pages/Library/QueryAddCatalogueDialog.tsx b/src/renderer/pages/Library/QueryAddCatalogueDialog.tsx new file mode 100644 index 0000000..e83ca01 --- /dev/null +++ b/src/renderer/pages/Library/QueryAddCatalogueDialog.tsx @@ -0,0 +1,91 @@ +import React, { useEffect } from 'react'; +import { + Alert, + Button, + Dialog, + DialogTitle, + DialogContent, + DialogActions, + FormControl, + Typography, + TextField +} from '@mui/material'; +import { useTranslation } from 'react-i18next'; + +export default function QueryAddCatalogueDialog({ open, action, onClose }) { + const { t } = useTranslation(); + + const [repo, setRepo] = React.useState(''); + const [loading, setLoading] = React.useState(false); + const [error, setError] = React.useState(null); + + const handleLaunch = async () => { + // Validate inputs + if (!repo) { + setError(t('library.add-catalogue-dialog.error-repo-required')); + return; + } + // Perform action + const version = ''; + setLoading(true); + action(repo, version) + .then(() => { + // close the dialog after action is completed successfully + setLoading(false); + onClose(); + }) + .catch(() => { + setLoading(false); + setError(t('library.add-catalogue-dialog.error-unable-to-add')); + }); + }; + + useEffect(() => { + // Reset state when dialog is opened + setRepo(''); + setError(null); + }, [open]); + + return ( + +
{ + e.preventDefault(); + handleLaunch(); + }} + > + + {t('library.add-catalogue-dialog.title')} + + + + + {t('library.add-catalogue-dialog.description')} + + + {error && ( + + {error} + + )} + + + setRepo(e.target.value)} + autoFocus + /> + + + + + + + +
+ + ); +} diff --git a/src/renderer/pages/Library/QueryAddWorkflowDialog.tsx b/src/renderer/pages/Library/QueryAddWorkflowDialog.tsx new file mode 100644 index 0000000..b3bd781 --- /dev/null +++ b/src/renderer/pages/Library/QueryAddWorkflowDialog.tsx @@ -0,0 +1,136 @@ +import React, { useEffect } from 'react'; +import { + Alert, + Button, + Dialog, + DialogTitle, + DialogContent, + DialogActions, + FormControl, + Typography, + TextField +} from '@mui/material'; +import { useTranslation } from 'react-i18next'; + +export default function QueryAddWorkflowDialog({ open, action, onClose }) { + const { t } = useTranslation(); + + const default_version = 'latest'; + const default_section = 'My Workflows'; + + const [name, setName] = React.useState(''); + const [repo, setRepo] = React.useState(''); + const [version, setVersion] = React.useState(default_version); + const [section, setSection] = React.useState(default_section); + + const [loading, setLoading] = React.useState(false); + const [error, setError] = React.useState(null); + + const handleLaunch = async () => { + // Validate inputs + if (!repo) { + setError(t('library.add-workflow-dialog.error-repo-required')); + return; + } + if (!section) { + setError(t('library.add-workflow-dialog.error-section-required')); + return; + } + // Perform the action + setLoading(true); + action(name, repo, version, section) + .then(() => { + // close the dialog after action is completed successfully + setLoading(false); + onClose(); + }) + .catch((error) => { + setLoading(false); + setError(`${t('library.add-workflow-dialog.error-unable-to-add')} +(${error.message})`); + }); + }; + + useEffect(() => { + // Reset state when dialog is opened + setName(''); + setRepo(''); + setVersion(default_version); + setSection(default_section); + setError(null); + }, [open]); + + return ( + +
{ + e.preventDefault(); + handleLaunch(); + }} + > + + {t('library.add-workflow-dialog.title')} + + + + + {t('library.add-workflow-dialog.description')} + + + {error && ( + + {error} + + )} + + + setRepo(e.target.value)} + autoFocus + /> + + + + setVersion(e.target.value)} + /> + + + + setName(e.target.value)} + /> + + + + setSection(e.target.value)} + /> + + + + + + + +
+ + ); +} diff --git a/src/renderer/pages/Main.tsx b/src/renderer/pages/Main.tsx index a39ba9c..8dc3f54 100644 --- a/src/renderer/pages/Main.tsx +++ b/src/renderer/pages/Main.tsx @@ -1,81 +1,43 @@ -import React, { useState, useEffect, useMemo } from 'react'; -import { uniqueNamesGenerator, adjectives, animals } from 'unique-names-generator'; +import React, { useState, useEffect } from 'react'; import { - AppBar, Box, - Button, Drawer, - IconButton, List, ListItem, ListItemText, - Stack, - TextField, Typography, Snackbar, Paper, Alert } from '@mui/material'; import { Panel, PanelGroup, PanelResizeHandle } from 'react-resizable-panels'; -import Toolbar from '@mui/material/Toolbar'; -import MenuIcon from '@mui/icons-material/Menu'; -import HubIcon from '@mui/icons-material/Hub'; import LibraryIcon from '@mui/icons-material/Apps'; import InstancesIcon from '@mui/icons-material/Storage'; import SettingsIcon from '@mui/icons-material/Settings'; import ListItemIcon from '@mui/material/ListItemIcon'; -import Select from '@mui/material/Select'; -import MenuItem from '@mui/material/MenuItem'; +import ListItemButton from '@mui/material/ListItemButton'; import { useTranslation } from 'react-i18next'; -import HubPage from './Hub'; -import LibraryPage from './Library'; +import LibraryPage from './Library/Library'; import InstancesPage from './Instances'; import SettingsPage from './Settings/Settings'; -import TitleBar from './TitleBar'; +import { SettingsKey } from '../../types/settings.js'; import { API } from '../services/api.js'; -const defaultRepoUrl = 'jsbrittain/workflow-runner-testworkflow'; -const defaultImageName = 'testworkflow'; - -type navbar_page = 'hub' | 'library' | 'instances' | 'settings'; +type navbar_page = 'library' | 'instances' | 'settings'; type severityLevels = 'info' | 'success' | 'warning' | 'error'; -// Quick function to predict target directory based on repo URL and base collections path -// Replace this with a call to the backend -const computeTargetDir = (repoUrl, basePath) => { - try { - if (repoUrl.includes('://')) { - const url = new URL(repoUrl); - const [owner, repo] = url.pathname - .replace(/^\//, '') - .replace(/\.git$/, '') - .split('/'); - return `${basePath}/workflows/${owner}/${repo}`; - } else if (repoUrl.includes('/')) { - const [owner, repo] = repoUrl.replace(/\.git$/, '').split('/'); - return `${basePath}/workflows/${owner}/${repo}`; - } - } catch { - return ''; - } -}; - export default function MainPage({ darkMode, setDarkMode }) { const { t } = useTranslation(); - const [repoUrl, setRepoUrl] = useState(defaultRepoUrl); const [collectionsPath, setCollectionsPath] = useState(''); - const [allowArbitraryRepoCloning, setAllowArbitraryRepoCloning] = useState(true); - const [targetDir, setTargetDir] = useState(''); - const [folderPath, setFolderPath] = useState(''); - const [imageName, setImageName] = useState(defaultImageName); - const [output, setOutput] = useState(''); - const [drawerOpen, setDrawerOpen] = useState(false); - const [view, setView] = useState('hub'); + const [permitAddCatalogues, setPermitAddCatalogues] = useState(true); + const [permitCatalogueModifications, setPermitCatalogueModifications] = useState(true); + const [permitAddRepos, setPermitAddRepos] = useState(true); + const [drawerOpen] = useState(true); + const [view, setView] = useState('library'); const [instancesList, setInstancesList] = useState([]); const [log, setLog] = useState([]); - const [projectsList, setProjectsList] = useState([]); const [severity, setSeverity] = useState('info'); const [message, setMessage] = useState(''); const [open, setOpen] = useState(false); @@ -92,57 +54,24 @@ export default function MainPage({ darkMode, setDarkMode }) { }); }; - const getProjectsList = async () => { - const all_project = { - id: 'all', - name: 'All', - url: undefined, - workflows: [] - }; - API.getProjectsList().then((projects) => { - setProjectsList([all_project, ...projects]); - }); - }; - useEffect(() => { (async () => { + API.settingsGet(SettingsKey.PermitAddCatalogues).then((result) => { + setPermitAddCatalogues(result); + }); + API.settingsGet(SettingsKey.PermitCatalogueModifications).then((result) => { + setPermitCatalogueModifications(result); + }); + API.settingsGet(SettingsKey.PermitAddRepos).then((result) => { + setPermitAddRepos(result); + }); const path = await API.getCollectionsPath(); setCollectionsPath(path); refreshInstancesList(); - getProjectsList(); })(); }, []); - useEffect(() => { - const predictedPath = computeTargetDir(repoUrl, collectionsPath); - setTargetDir(predictedPath); - }, [repoUrl, collectionsPath]); - - const handlePathChange = (e) => { - const value = e.target.value; - setCollectionsPath(value); - API.setCollectionsPath(value); - }; - - const handleList = async () => { - const containers = await API.listContainers(); - setOutput(JSON.stringify(containers, null, 2)); - }; - - const generateUniqueName = (baseName, queue) => { - let newName = ''; - const existingNames = new Set(queue.map((item) => item.name)); - do { - newName = uniqueNamesGenerator({ - dictionaries: [adjectives, animals], - separator: '-', - length: 2 - }); - } while (existingNames.has(newName)); - return newName; - }; - - const addToInstancesList = async (repo) => { + const createWorkflowInstance = async (repo) => { const workflow_id = repo.id; API.createWorkflowInstance(workflow_id, repo.version).then((instance) => { setInstancesList((prev) => { @@ -163,21 +92,14 @@ export default function MainPage({ darkMode, setDarkMode }) { return ( - - theme.transitions.create('width', { @@ -187,37 +109,57 @@ export default function MainPage({ darkMode, setDarkMode }) { } }} > - - setView('hub')}> - - - - {drawerOpen && } - - setView('library')}> - - - - {drawerOpen && } + ({ + '& .MuiListItemButton-root.Mui-selected': { + boxShadow: `inset 4px 0 0 ${theme.palette.primary.main}`, + '& .MuiListItemIcon-root': { + color: theme.palette.primary.main + }, + '&:hover': { + backgroundColor: theme.palette.action.selected + } + } + })} + > + + setView('library')} + > + + + + {drawerOpen && } + - { - setItem(''); - setView('instances'); - }} - > - - - - {drawerOpen && } + + { + setItem(''); + setView('instances'); + }} + > + + + + {drawerOpen && } + - setView('settings')}> - - - - {drawerOpen && } + + setView('settings')} + > + + + + {drawerOpen && } + @@ -229,30 +171,13 @@ export default function MainPage({ darkMode, setDarkMode }) { sx={{ width: '100%', height: '100%', overflowY: 'auto', minHeight: 0, p: 3 }} square > - - {view === 'hub' ? ( - - ) : view === 'library' ? ( + {view === 'library' ? ( ) : view === 'instances' ? ( ) : null} diff --git a/src/renderer/pages/Monitor/HeaderMenu.tsx b/src/renderer/pages/Monitor/HeaderMenu.tsx index ee69e0e..4278ce6 100644 --- a/src/renderer/pages/Monitor/HeaderMenu.tsx +++ b/src/renderer/pages/Monitor/HeaderMenu.tsx @@ -1,48 +1,14 @@ -import React, { useEffect } from 'react'; -import { Box, Tabs, Tab, Paper, Typography } from '@mui/material'; +import React from 'react'; +import { Box, Typography } from '@mui/material'; import Button from '@mui/material/Button'; import Menu from '@mui/material/Menu'; import MenuItem from '@mui/material/MenuItem'; -import IconButton from '@mui/material/IconButton'; -import DoneIcon from '@mui/icons-material/Done'; -import CancelIcon from '@mui/icons-material/Cancel'; -import RefreshIcon from '@mui/icons-material/Refresh'; -import AnsiLog from '../AnsiLog.js'; import { API } from '../../services/api.js'; import { useTranslation } from 'react-i18next'; -import FolderOutlinedIcon from '@mui/icons-material/FolderOutlined'; -import DescriptionOutlinedIcon from '@mui/icons-material/DescriptionOutlined'; - -interface TabPanelProps { - children?: React.ReactNode; - index: number; - value: number; -} - -function TabPanel(props: TabPanelProps) { - const { children, value, index, ...other } = props; - return ( - - ); -} - -const SECOND = 1000; - -const STATUS_ICONS = { - created: , - starting: , - submitted: , - completed: , - error: -}; export default function HeaderMenu({ instance, logMessage }) { const { t } = useTranslation(); const [anchorEl, setAnchorEl] = React.useState(null); - const [processRunning, setProcessRunning] = React.useState(true); // ####### check if the process is running - const [processHasRunHistory, setProcessHasRunHistory] = React.useState(true); // ####### check if the process has run history const handleExecutionActionsMenuClose = () => { setAnchorEl(null); @@ -64,7 +30,7 @@ export default function HeaderMenu({ instance, logMessage }) { if (!window.confirm(t('monitor.execution.resume-confirm'))) { return; } - const id = await API.runWorkflow(instance, {}, { resume: true }); + await API.runWorkflow(instance, {}, { resume: true }); logMessage(`${t('monitor.execution.resuming')}: ${instance.id}.`); }; @@ -121,24 +87,16 @@ export default function HeaderMenu({ instance, logMessage }) { anchorOrigin={{ vertical: 'top', horizontal: 'left' }} transformOrigin={{ vertical: 'top', horizontal: 'left' }} > - handleExecutionCancel()} disabled={!processRunning}> + handleExecutionCancel()}> {t('monitor.execution.cancel')} - handleExecutionResume()} - disabled={processRunning && processHasRunHistory} - > + handleExecutionResume()}> {t('monitor.execution.resume')} - handleExecutionRestart()} - disabled={!processHasRunHistory} - > + handleExecutionRestart()}> {t('monitor.execution.restart')} - handleExecutionKill()} disabled={!processRunning}> + handleExecutionKill()}> {t('monitor.execution.kill')} diff --git a/src/renderer/pages/Monitor/HtmlReports.tsx b/src/renderer/pages/Monitor/HtmlReports.tsx index 347fb0a..993bd22 100644 --- a/src/renderer/pages/Monitor/HtmlReports.tsx +++ b/src/renderer/pages/Monitor/HtmlReports.tsx @@ -1,22 +1,10 @@ -import React, { useEffect } from 'react'; -import { Box, Tabs, Tab, Paper, Typography } from '@mui/material'; -import Button from '@mui/material/Button'; -import Menu from '@mui/material/Menu'; +import React from 'react'; +import { Box, Typography } from '@mui/material'; import MenuItem from '@mui/material/MenuItem'; import Select from '@mui/material/Select'; -import IconButton from '@mui/material/IconButton'; -import DoneIcon from '@mui/icons-material/Done'; -import CancelIcon from '@mui/icons-material/Cancel'; -import RefreshIcon from '@mui/icons-material/Refresh'; import FormControl from '@mui/material/FormControl'; -import AnsiLog from './AnsiLog.js'; import { API } from '../../services/api.js'; import { useTranslation } from 'react-i18next'; -import FolderOutlinedIcon from '@mui/icons-material/FolderOutlined'; -import DescriptionOutlinedIcon from '@mui/icons-material/DescriptionOutlined'; - -import HeaderMenu from './HeaderMenu'; -import ProgressTracker from './ProgressTracker'; export default function HtmlReports({ instance }) { const { t } = useTranslation(); diff --git a/src/renderer/pages/Monitor/Logs.tsx b/src/renderer/pages/Monitor/Logs.tsx index d307817..418a4dd 100644 --- a/src/renderer/pages/Monitor/Logs.tsx +++ b/src/renderer/pages/Monitor/Logs.tsx @@ -1,21 +1,7 @@ -import React, { useEffect } from 'react'; -import { Box, Tabs, Tab, Paper, Typography } from '@mui/material'; -import Button from '@mui/material/Button'; -import Menu from '@mui/material/Menu'; -import MenuItem from '@mui/material/MenuItem'; -import IconButton from '@mui/material/IconButton'; -import DoneIcon from '@mui/icons-material/Done'; -import CancelIcon from '@mui/icons-material/Cancel'; -import RefreshIcon from '@mui/icons-material/Refresh'; +import React from 'react'; +import { Box, Tabs, Tab, Paper } from '@mui/material'; import AnsiLog from './AnsiLog.js'; -import HtmlReports from './HtmlReports.js'; -import { API } from '../../services/api.js'; import { useTranslation } from 'react-i18next'; -import FolderOutlinedIcon from '@mui/icons-material/FolderOutlined'; -import DescriptionOutlinedIcon from '@mui/icons-material/DescriptionOutlined'; - -import HeaderMenu from './HeaderMenu'; -import ProgressTracker from './ProgressTracker'; interface TabPanelProps { children?: React.ReactNode; @@ -32,14 +18,10 @@ function TabPanel(props: TabPanelProps) { ); } -const SECOND = 1000; - -export default function LogsPage({ instance, stdOut, stdErr, nextflowLog, logMessage }) { +export default function LogsPage({ stdOut, stdErr, nextflowLog }) { const { t } = useTranslation(); - const [nextflowProgress, setNextflowProgress] = React.useState(''); const [tabSelected, setTabSelected] = React.useState(0); - const [workflowStatus, setWorkflowStatus] = React.useState('unknown'); const handleTabChange = (event, newValue) => { setTabSelected(newValue); diff --git a/src/renderer/pages/Monitor/Monitor.tsx b/src/renderer/pages/Monitor/Monitor.tsx index 28a96a3..41e2341 100644 --- a/src/renderer/pages/Monitor/Monitor.tsx +++ b/src/renderer/pages/Monitor/Monitor.tsx @@ -1,19 +1,9 @@ import React, { useEffect } from 'react'; -import { Box, Tabs, Tab, Paper, Typography } from '@mui/material'; -import Button from '@mui/material/Button'; -import Menu from '@mui/material/Menu'; -import MenuItem from '@mui/material/MenuItem'; -import IconButton from '@mui/material/IconButton'; -import DoneIcon from '@mui/icons-material/Done'; -import CancelIcon from '@mui/icons-material/Cancel'; -import RefreshIcon from '@mui/icons-material/Refresh'; -import AnsiLog from './AnsiLog.js'; +import { Box, Tabs, Tab, Paper } from '@mui/material'; import HtmlReports from './HtmlReports.js'; import LogsPage from './Logs.js'; import { API } from '../../services/api.js'; import { useTranslation } from 'react-i18next'; -import FolderOutlinedIcon from '@mui/icons-material/FolderOutlined'; -import DescriptionOutlinedIcon from '@mui/icons-material/DescriptionOutlined'; import HeaderMenu from './HeaderMenu'; import ProgressTracker from './ProgressTracker'; @@ -35,14 +25,6 @@ function TabPanel(props: TabPanelProps) { const SECOND = 1000; -const STATUS_ICONS = { - created: , - starting: , - submitted: , - completed: , - error: -}; - export default function MonitorPage({ instance, logMessage }) { const { t } = useTranslation(); @@ -115,13 +97,7 @@ export default function MonitorPage({ instance, logMessage }) { - + ); diff --git a/src/renderer/pages/Monitor/ProgressTracker.tsx b/src/renderer/pages/Monitor/ProgressTracker.tsx index 752c2b2..879499d 100644 --- a/src/renderer/pages/Monitor/ProgressTracker.tsx +++ b/src/renderer/pages/Monitor/ProgressTracker.tsx @@ -1,8 +1,5 @@ import React, { useEffect } from 'react'; -import { Box, Tabs, Tab, Paper, Typography } from '@mui/material'; -import Button from '@mui/material/Button'; -import Menu from '@mui/material/Menu'; -import MenuItem from '@mui/material/MenuItem'; +import { Box, Typography } from '@mui/material'; import IconButton from '@mui/material/IconButton'; import DoneIcon from '@mui/icons-material/Done'; import CancelIcon from '@mui/icons-material/Cancel'; @@ -55,7 +52,7 @@ export default function ProgressTracker({ instance, nextflowProgress, workflowSt return () => clearInterval(interval); }, [showWork]); - const FormatWorkflowStatus = ({ workflowStatus: string }) => { + const FormatWorkflowStatus = ({ workflowStatus }: { workflowStatus: string }) => { let color_palette = 'info'; if (workflowStatus === WorkflowStatus.Failed) { color_palette = 'error'; diff --git a/src/renderer/pages/Parameters/FilePathControl.tsx b/src/renderer/pages/Parameters/FilePathControl.tsx index 46bd6cc..050d7f0 100644 --- a/src/renderer/pages/Parameters/FilePathControl.tsx +++ b/src/renderer/pages/Parameters/FilePathControl.tsx @@ -47,7 +47,6 @@ function InnerFilePathControl(props: ControlProps) { (uischema as any)?.options?.description ?? schema?.description ?? (schema as any)?.help_text; const showDesc = !isDescriptionHidden(visible, description, config); - const accept = (uischema as any)?.options?.accept as string | undefined; type PickerMode = 'file' | 'directory' | 'both'; diff --git a/src/renderer/pages/Parameters/Parameters.tsx b/src/renderer/pages/Parameters/Parameters.tsx index a1430fc..09dcfc3 100644 --- a/src/renderer/pages/Parameters/Parameters.tsx +++ b/src/renderer/pages/Parameters/Parameters.tsx @@ -1,26 +1,6 @@ import React, { useState, useEffect, useMemo } from 'react'; -import { - Box, - Container, - Paper, - Stack, - Tabs, - Tab, - TextField, - Typography, - Button, - Alert -} from '@mui/material'; +import { Box, Paper, Stack, Tabs, Tab, Typography, Button } from '@mui/material'; import { JsonForms } from '@jsonforms/react'; -import List from '@mui/material/List'; -import ListItem from '@mui/material/ListItem'; -import ListItemText from '@mui/material/ListItemText'; -import ListItemButton from '@mui/material/ListItemButton'; -import ListItemAvatar from '@mui/material/ListItemAvatar'; -import Avatar from '@mui/material/Avatar'; -import NotStartedIcon from '@mui/icons-material/NotStarted'; -import DeleteIcon from '@mui/icons-material/Delete'; -import IconButton from '@mui/material/IconButton'; import Ajv, { ErrorObject } from 'ajv'; // ajv is also used by jsonforms import { buildUISchema } from './buildUISchema'; import { renderers } from './renderers'; @@ -72,19 +52,18 @@ export default function ParametersPage({ instance, refreshInstancesList, logMess const profile = params['profile'] || default_profile; delete call_params['profile']; // Return PID on success - const res = await API.runWorkflow(instance, call_params, { profile: profile }); - if (!res.ok) { - logMessage(`Error launching workflow: ${res.error.message || 'Unknown error'}`, 'error'); + const result = await API.runWorkflow(instance, call_params, { profile: profile }); + if (!result.ok) { + logMessage(`Error launching workflow: ${result.error.message || 'Unknown error'}`, 'error'); return; } - const id = res.data as number; logMessage(`Launched workflow ${instance.name}`); refreshInstancesList(); }; const onTestLaunchWorkflow = async (testProfiles) => { const test_profiles_str = testProfiles.join(','); - const id = await API.runWorkflow(instance, {}, { profile: test_profiles_str }); + await API.runWorkflow(instance, {}, { profile: test_profiles_str }); logMessage(`Launched test workflow ${instance.name}`); refreshInstancesList(); }; @@ -216,7 +195,7 @@ export default function ParametersPage({ instance, refreshInstancesList, logMess uischema={uischema} data={params} renderers={renderers} - onChange={({ data, errors }) => setParams(data)} + onChange={({ data }) => setParams(data)} ajv={disableSchemaValidation ? undefined : ajv} /> ) : ( diff --git a/src/renderer/pages/Settings/Environment.tsx b/src/renderer/pages/Settings/Environment.tsx index d2faa57..d96e684 100644 --- a/src/renderer/pages/Settings/Environment.tsx +++ b/src/renderer/pages/Settings/Environment.tsx @@ -5,7 +5,7 @@ import { EnvironmentKey } from '../../../types/environment.js'; import { useTranslation } from 'react-i18next'; export default function EnvironmentPage() { - const { t, i18n } = useTranslation(); + const { t } = useTranslation(); const [nextflowStatus, setNextflowStatus] = React.useState([]); const [performingAction, setPerformingAction] = React.useState(null); @@ -21,7 +21,7 @@ export default function EnvironmentPage() { const handlePerformAction = async (id: string) => { setPerformingAction(id); - API.performEnvironmentAction(EnvironmentKey.Nextflow, id).then((msg) => { + API.performEnvironmentAction(EnvironmentKey.Nextflow, id).then(() => { getEnvironmentStatus(); // refresh status after action setPerformingAction(null); }); @@ -39,7 +39,7 @@ export default function EnvironmentPage() { {item.description} - {(item?.actions || []).map((action, actionIndex) => ( + {(item?.actions || []).map((action) => ( diff --git a/src/renderer/pages/Settings/ProjectsList.tsx b/src/renderer/pages/Settings/ProjectsList.tsx deleted file mode 100644 index e920bca..0000000 --- a/src/renderer/pages/Settings/ProjectsList.tsx +++ /dev/null @@ -1,88 +0,0 @@ -import React from 'react'; -import { - Container, - Box, - Button, - Typography, - Switch, - FormControlLabel, - TextField, - Select, - MenuItem, - Paper, - IconButton -} from '@mui/material'; -import DeleteIcon from '@mui/icons-material/Delete'; -import { useTranslation } from 'react-i18next'; -import { API } from '../../services/api.js'; - -export default function ProjectsList({ projectsList, getProjectsList, logMessage }) { - const { t } = useTranslation(); - const [projectUrl, setProjectUrl] = React.useState(''); - - const onClickRemoveProject = (project) => { - API.removeProject(project).then((msg) => { - if (msg) { - logMessage(`${t('settings.projects.remove-failure')}: ${msg}`, 'error'); - } else { - getProjectsList(); - } - }); - }; - - const onClickAddProject = () => { - API.addProject(projectUrl).then((msg) => { - if (!msg) { - // success - getProjectsList(); - setProjectUrl(''); - } else { - logMessage(`${t('settings.projects.add-failure')}: ${msg}`, 'error'); - } - }); - }; - - const onKeyDownUrl = (e) => { - if (e.key === 'Enter') { - onClickAddProject(); - } - }; - - return ( - - {projectsList.map((project, index) => { - if (project.name === 'All' || project.url === undefined) return null; - return ( - - - {project.name || t('settings.projects.unnamed')} - {project.url} - - onClickRemoveProject(project)}> - - - - ); - })} - - {projectsList.length < 2 && ( - - {t('settings.projects.no-projects')} - - )} - - setProjectUrl(e.target.value)} - onKeyDown={onKeyDownUrl} - /> - - - - ); -} diff --git a/src/renderer/pages/Settings/Settings.tsx b/src/renderer/pages/Settings/Settings.tsx index ef02051..9e8c901 100644 --- a/src/renderer/pages/Settings/Settings.tsx +++ b/src/renderer/pages/Settings/Settings.tsx @@ -1,7 +1,6 @@ import React, { useEffect } from 'react'; import { Box, - Container, Typography, Switch, FormControlLabel, @@ -13,12 +12,10 @@ import { Tab, Tabs } from '@mui/material'; -import ProjectsList from './ProjectsList.js'; import EnvironmentPage from './Environment.js'; import LicensesPage from './Licenses.js'; import { API } from '../../services/api.js'; import { SettingsKey } from '../../../types/settings.js'; -import { EnvironmentKey } from '../../../types/environment.js'; import { useTranslation } from 'react-i18next'; export default function SettingsPage({ @@ -26,20 +23,19 @@ export default function SettingsPage({ setDarkMode, collectionsPath, setCollectionsPath, - allowArbitraryRepoCloning, - setAllowArbitraryRepoCloning, - projectsList, - getProjectsList, - logMessage + permitAddCatalogues, + setPermitAddCatalogues, + permitCatalogueModifications, + setPermitCatalogueModifications, + permitAddRepos, + setPermitAddRepos }) { const { t, i18n } = useTranslation(); const pathRef = React.useRef(null); const [language, setLanguage] = React.useState(i18n.language || 'en'); const [tabValue, setTabValue] = React.useState(0); - const [disableProjects, setDisableProjects] = React.useState(false); const [disableSchemaValidation, setDisableSchemaValidation] = React.useState(false); - const [nextflowStatus, setNextflowStatus] = React.useState([]); const handlePathKeyDown = (e) => { if (e.key === 'Enter') { @@ -64,9 +60,24 @@ export default function SettingsPage({ i18n.changeLanguage(newLang); }; - const handleDisableProjects = (value) => { - setDisableProjects(value); - API.settingsSet(SettingsKey.DisableProjects, value); + const handlePermitAddCatalogues = (value) => { + setPermitAddCatalogues(value); + API.settingsSet(SettingsKey.PermitAddCatalogues, value); + }; + + const handlePermitCatalogueModifications = (value) => { + setPermitCatalogueModifications(value); + API.settingsSet(SettingsKey.PermitCatalogueModifications, value); + }; + + const handlePermitAddRepos = (value) => { + setPermitAddRepos(value); + API.settingsSet(SettingsKey.PermitAddRepos, value); + }; + + const handleDarkMode = (value) => { + setDarkMode(value); + API.settingsSet(SettingsKey.DarkMode, value); }; const handleDisableSchemaValidation = (value) => { @@ -75,14 +86,20 @@ export default function SettingsPage({ }; useEffect(() => { - API.settingsGet(SettingsKey.DisableSchemaValidation).then((value) => { - setDisableSchemaValidation(value); + API.settingsGet(SettingsKey.DarkMode).then((value) => { + setDarkMode(value); + }); + API.settingsGet(SettingsKey.PermitAddCatalogues).then((value) => { + setPermitAddCatalogues(value); }); - API.settingsGet(SettingsKey.DisableProjects).then((value) => { - setDisableProjects(value); + API.settingsGet(SettingsKey.PermitCatalogueModifications).then((value) => { + setPermitCatalogueModifications(value); }); - API.getEnvironmentStatus(EnvironmentKey.Nextflow).then((status) => { - setNextflowStatus(status); + API.settingsGet(SettingsKey.PermitAddRepos).then((value) => { + setPermitAddRepos(value); + }); + API.settingsGet(SettingsKey.DisableSchemaValidation).then((value) => { + setDisableSchemaValidation(value); }); if (pathRef.current && document.activeElement !== pathRef.current) { pathRef.current.value = collectionsPath ?? ''; @@ -125,11 +142,6 @@ export default function SettingsPage({ sx={{ borderRight: 1, borderColor: 'divider' }} > - @@ -148,34 +160,46 @@ export default function SettingsPage({ onBlur={handlePathBlur} sx={{ mt: 2 }} /> - setAllowArbitraryRepoCloning(!allowArbitraryRepoCloning)} + id="settings-permit-add-catalogues" + checked={permitAddCatalogues} + onChange={() => handlePermitAddCatalogues(!permitAddCatalogues)} /> } - label={t('settings.allow-arbitrary-repo-cloning')} + label={t('settings.permit-add-catalogues')} /> - - - - handlePermitCatalogueModifications(!permitCatalogueModifications)} + /> + } + label={t('settings.permit-catalogue-modifications')} + /> + handlePermitAddRepos(!permitAddRepos)} + /> + } + label={t('settings.permit-add-repos')} /> - + setDarkMode(!darkMode)} />} + control={ handleDarkMode(!darkMode)} />} label={t('settings.dark-mode')} /> - + onChangeProject(e.target.value)} - size="small" - > - {projectsList.map((proj, index) => ( - {proj.name} - ))} - - )} diff --git a/src/renderer/services/api.ts b/src/renderer/services/api.ts index 90a828f..b64967e 100644 --- a/src/renderer/services/api.ts +++ b/src/renderer/services/api.ts @@ -25,10 +25,21 @@ const electronAPI = isElectron getWorkLog: (instance, workID, logType) => window.electronAPI.getWorkLog(instance, workID, logType), getAvailableProfiles: (instance) => window.electronAPI.getAvailableProfiles(instance), - cloneRepo: (repoUrl, ver) => window.electronAPI.cloneRepo(repoUrl, ver), + isRepoInstalled: (repoUrl, ver) => window.electronAPI.isRepoInstalled(repoUrl, ver), syncRepo: (repo) => window.electronAPI.syncRepo(repo), - getCollections: () => window.electronAPI.getCollections(), + addCatalogue: (repoUrl, ver) => window.electronAPI.addCatalogue(repoUrl, ver), + removeCatalogue: (catalogue_name) => window.electronAPI.removeCatalogue(catalogue_name), + removeCatalogueSection: (catalogue_name, section_name) => + window.electronAPI.removeCatalogueSection(catalogue_name, section_name), + removeCatalogueWorkflow: (catalogue_name, section_name, workflow_name) => + window.electronAPI.removeCatalogueWorkflow(catalogue_name, section_name, workflow_name), + updateCatalogueWorkflow: (catalogue_name, section_name, workflow_name) => + window.electronAPI.updateCatalogueWorkflow(catalogue_name, section_name, workflow_name), + getCatalogues: () => window.electronAPI.getCatalogues(), + addUserWorkflow: (name, repoUrl, ver, section) => + window.electronAPI.addUserWorkflow(name, repoUrl, ver, section), + getCollectionRepos: () => window.electronAPI.getCollectionRepos(), getCollectionsPath: () => window.electronAPI.getCollectionsPath(), setCollectionsPath: (path) => window.electronAPI.setCollectionsPath(path), getContainerLogs: (containerId) => window.electronAPI.getContainerLogs(containerId), @@ -36,9 +47,6 @@ const electronAPI = isElectron deleteRepo: (repoPath) => window.electronAPI.deleteRepo(repoPath), getWorkflowParams: (repoPath) => window.electronAPI.getWorkflowParams(repoPath), getWorkflowSchema: (repoPath) => window.electronAPI.getWorkflowSchema(repoPath), - getProjectsList: () => window.electronAPI.getProjectsList(), - addProject: (repoPath) => window.electronAPI.addProject(repoPath), - removeProject: (project) => window.electronAPI.removeProject(project), getInstallableReposList: () => window.electronAPI.getInstallableReposList(), addInstallableRepo: (repoUrl) => window.electronAPI.addInstallableRepo(repoUrl), getWorkflowInformation: (instance) => window.electronAPI.getWorkflowInformation(instance), @@ -60,7 +68,8 @@ const httpDispatch = async (endpoint, method = 'GET', body = null) => { } const res = await fetch(endpoint, options); if (!res.ok) throw new Error(`HTTP error at ${endpoint}, status: ${res.status}`); - return res.json(); + const js = res.json(); + return js; }; const httpAPI = { @@ -96,8 +105,31 @@ const httpAPI = { getAvailableProfiles: async (instance) => httpDispatch('/api/get-available-profiles', 'POST', { instance }), cloneRepo: async (repoUrl, ver) => httpDispatch('/api/clone-repo', 'POST', { repoUrl, ver }), + isRepoInstalled: async (repoUrl, ver) => + httpDispatch('/api/is-repo-installed', 'POST', { repoUrl, ver }), syncRepo: async (repo) => httpDispatch('/api/sync-repo', 'POST', { repo }), - getCollections: async () => httpDispatch('/api/get-collections', 'POST', {}), + addCatalogue: async (repoUrl, ver) => + httpDispatch('/api/add-catalogue', 'POST', { repoUrl, ver }), + removeCatalogue: async (catalogue_name) => + httpDispatch('/api/remove-catalogue', 'POST', { catalogue_name }), + removeCatalogueSection: async (catalogue_name, section_name) => + httpDispatch('/api/remove-catalogue-section', 'POST', { catalogue_name, section_name }), + removeCatalogueWorkflow: async (catalogue_name, section_name, workflow_name) => + httpDispatch('/api/remove-catalogue-workflow', 'POST', { + catalogue_name, + section_name, + workflow_name + }), + updateCatalogueWorkflow: async (catalogue_name, section_name, workflow_name) => + httpDispatch('/api/update-catalogue-workflow', 'POST', { + catalogue_name, + section_name, + workflow_name + }), + getCatalogues: async () => httpDispatch('/api/get-catalogues', 'POST', {}), + addUserWorkflow: async (name, repoUrl, ver, section) => + httpDispatch('/api/add-user-workflow', 'POST', { name, repoUrl, ver, section }), + getCollectionRepos: async () => httpDispatch('/api/get-collection-repos', 'POST', {}), getCollectionsPath: async () => httpDispatch('/api/get-collections-path', 'POST', {}), setCollectionsPath: async (path) => httpDispatch('/api/set-collections-path', 'POST', { path }), getContainerLogs: async (containerId) => @@ -109,9 +141,6 @@ const httpAPI = { httpDispatch('/api/get-workflow-params', 'POST', { repoPath }), getWorkflowSchema: async (repoPath) => httpDispatch('/api/get-workflow-schema', 'POST', { repoPath }), - getProjectsList: async () => httpDispatch('/api/get-projects-list', 'POST', {}), - addProject: async (repoPath) => httpDispatch('/api/add-project', 'POST', { repoPath }), - removeProject: async (project) => httpDispatch('/api/remove-project', 'POST', { project }), getInstallableReposList: async () => httpDispatch('/api/get-installable-repos-list', 'POST', {}), addInstallableRepo: async (repoUrl) => httpDispatch('/api/add-installable-repo', 'POST', { repoUrl }), diff --git a/src/runners/nextflow/nextflow.ts b/src/runners/nextflow/nextflow.ts index fd25646..968f309 100644 --- a/src/runners/nextflow/nextflow.ts +++ b/src/runners/nextflow/nextflow.ts @@ -19,7 +19,12 @@ export interface IRunWorkflowOpts { const is_windows = process.platform === 'win32'; const toPosixPath = (base: string) => { - return slash(base).replace('C:', '/mnt/c'); + return slash( + base.replace( + /^([A-Za-z]):\\/, + (_, drive) => `/mnt/${drive.toLowerCase()}/` + ) + ); }; const resolvePath = (base: string, name: string) => { @@ -205,12 +210,34 @@ export async function runWorkflow( '-Dcapsule.trampoline', '-Dcom.sun.security.enableAIAcaIssuers=true', '-Djava.awt.headless=true', + + // performance '-XX:+TieredCompilation', '-XX:TieredStopAtLevel=1', + + // Native access + '--enable-native-access=ALL-UNNAMED', + + // Core reflection (Groovy / Nextflow) '--add-opens=java.base/java.lang=ALL-UNNAMED', + '--add-opens=java.base/java.lang.reflect=ALL-UNNAMED', '--add-opens=java.base/java.io=ALL-UNNAMED', - '--enable-native-access=ALL-UNNAMED', - '--sun-misc-unsafe-memory-access=allow' + + // Collections / Kryo serializers + '--add-opens=java.base/java.util=ALL-UNNAMED', + '--add-opens=java.base/java.util.concurrent=ALL-UNNAMED', + + // FileSystemProvider injection + '--add-opens=java.base/java.nio.file.spi=ALL-UNNAMED', + '--add-exports=java.base/java.nio.file.spi=ALL-UNNAMED', + + // FTP support (Nextflow HTTP/FTP provider) + '--add-exports=java.base/sun.net.www.protocol.ftp=ALL-UNNAMED', + '--add-opens=java.base/sun.net.www.protocol.ftp=ALL-UNNAMED', + + // Internal memory access + '--add-exports=java.base/jdk.internal.misc=ALL-UNNAMED', + '--add-opens=java.base/jdk.internal.misc=ALL-UNNAMED' ]; console.log(`Spawning nextflow with command: nextflow ${cmd.join(' ')} from ${instancePath}`); diff --git a/src/types/settings.ts b/src/types/settings.ts index 7585dbb..d1f29ec 100644 --- a/src/types/settings.ts +++ b/src/types/settings.ts @@ -1,7 +1,10 @@ // Keep in sync with main/store.js export const SettingsKey = { CollectionsPath: 'collectionsPath', - DisableProjects: 'disableProjects', + DarkMode: 'darkMode', + PermitAddCatalogues: 'permitAddCatalogues', + PermitCatalogueModifications: 'permitCatalogueModifications', + PermitAddRepos: 'permitAddRepos', DisableSchemaValidation: 'disableSchemaValidation' } as const; diff --git a/tests/e2e/fixtures.ts b/tests/e2e/fixtures.ts index a763c3d..e5a722a 100644 --- a/tests/e2e/fixtures.ts +++ b/tests/e2e/fixtures.ts @@ -7,11 +7,24 @@ type Fixtures = { export const test = base.extend({ page: async ({ browser, page }, use, testInfo) => { if (testInfo.project.name.includes('Electron')) { + + // Electron mode + const electronApp: ElectronApplication = await electron.launch({ args: ['.', '--fullscreen', '--no-sandbox'] }); + + // Capture main process stdout/stderr + const proc = await electronApp.process(); + proc.stdout.on('data', (chunk) => process.stdout.write(`[main] ${chunk}`)); + proc.stderr.on('data', (chunk) => process.stderr.write(`[main:error] ${chunk}`)); + const win = await electronApp.firstWindow(); + // Capture renderer console + win.on('console', (msg) => console.log(`[renderer:${msg.type()}] ${msg.text()}`)); + win.on('pageerror', (err) => console.error(`[renderer:error] ${err}`)); + await electronApp.evaluate(({ BrowserWindow }) => { const win = BrowserWindow.getAllWindows()[0]; win.setBounds({ width: 1024, height: 768 }); diff --git a/tests/e2e/ui.spec.ts b/tests/e2e/ui.spec.ts index e97e89f..a84fb62 100644 --- a/tests/e2e/ui.spec.ts +++ b/tests/e2e/ui.spec.ts @@ -39,6 +39,12 @@ test('clone a repository', async ({ page }) => { const library_path = path.resolve(path.join(glacier_path, 'library')); fs.mkdirSync(library_path, { recursive: true }); // rebuild await page.fill('#settings-collections-path', `${library_path}`); + await page.locator('#settings-collections-path').blur(); + + // Ensure repositories and catalogues can be modified in settings + await page.check('#settings-permit-add-catalogues'); + await page.check('#settings-permit-catalogue-modifications'); + await page.check('#settings-permit-add-repos'); // Use English language for this test await page.click('#settings-language-panel'); @@ -49,46 +55,27 @@ test('clone a repository', async ({ page }) => { // Check that the Library is empty await page.click('#sidebar-library-button'); - expect(await page.locator('[id^="collections-sync-"]').count()).toBe(0); - - // --- Navigate to Hub page - await page.click('#sidebar-hub-button'); + await expect(page.getByText('No repositories installed.')).toBeVisible({ timeout: TIMEOUT_10s }); // Add repository const repo_owner = 'jsbrittain'; const repo_name = 'workflow-runner-test-nextflow'; - await page.fill('#collections-repo-url', `${repo_owner}/${repo_name}`); - await page.click('#collections-add-button'); - await page.waitForSelector('#hub-install-workflow-runner-test-nextflow', { - timeout: TIMEOUT_10s - }); - - // Clone the new repository - await page.click('#hub-install-workflow-runner-test-nextflow'); - // --- Navigate to Library page - await page.click('#sidebar-library-button'); - for (let i = 0; i < 30; i++) { - if ((await page.locator(`[id="collections-sync-${cssEscape(repo_name)}"]`).count()) == 1) { - break; - } - await page.reload(); - await page.waitForLoadState('networkidle'); - await page.click('#sidebar-library-button'); - await page.waitForTimeout(1000); - } - - // Find the cloned workflow - await expect(page.locator('h6').filter({ hasText: 'workflow-runner-test-nextflow' })).toBeVisible( - { timeout: TIMEOUT_10s } - ); - - // Sync the repository - await page.click(`#collections-sync-${cssEscape(repo_name)}`); - await waitForLogLine(page, 'Repository synced'); + // Click Actions menu button + await page.click('#library-actions-menu-button'); + await page.click('#library-actions-menu-add-repo'); + // Fill in repo details + await page.fill('#query-add-workflow-repo-url', `${repo_owner}/${repo_name}`); + await page.fill('#query-add-workflow-repo-version', 'main'); + await page.click('#query-add-workflow-dialog-okay-button'); + // Wait for workflow to be added + await expect(page.getByText('User collection')).toBeVisible({ timeout: TIMEOUT_10s }); + await expect(page.getByText(repo_name)).toBeVisible({ timeout: TIMEOUT_10s }); + // Click Install (clone the repository) + await page.click(`#install-${cssEscape(repo_name)}`); // Create an instance of the workflow (redirects to Parameters page) - await page.click(`#collections-run-${cssEscape(repo_name)}`); + await page.click(`#run-${cssEscape(repo_name)}`); // 'Launch Workflow' button should now be visible await expect(page.getByRole('button', { name: 'Launch Workflow' })).toBeVisible({ timeout: TIMEOUT_10s @@ -96,43 +83,22 @@ test('clone a repository', async ({ page }) => { }); test('launch local workflow', async ({ page }) => { - const local_workflow_path = path.resolve( - path.join(__dirname, '..', 'test-data', 'sleep@undefined') - ); + const local_collections_path = path.resolve(path.join(__dirname, '..', 'test-data')); // Navigate to Settings page await page.click('#sidebar-settings-button'); // Get the library path await page.click('#settings-general-panel'); - const library_path = await page.inputValue('#settings-collections-path'); - const dest_path = path.join(library_path, 'workflows', 'local', 'sleep@undefined'); - - // Copy the local workflow to the library path - fs.cpSync(local_workflow_path, dest_path, { recursive: true }); - - // Check folder exists - if (!fs.existsSync(dest_path)) { - throw new Error(`Failed to copy local workflow to library: ${dest_path}`); - } - - // Force refresh of workflows (change collections-path twice) - await page.fill('#settings-collections-path', library_path + '_temp'); - await page.locator('#settings-collections-path').blur(); // trigger change event - await page.fill('#settings-collections-path', library_path); + await page.fill('#settings-collections-path', `${local_collections_path}`); await page.locator('#settings-collections-path').blur(); // --- Navigate to Library page await page.click('#sidebar-library-button'); const repo_name = 'sleep'; - // Find the cloned workflow - await expect(page.locator('h6').filter({ hasText: repo_name })).toBeVisible({ - timeout: TIMEOUT_10s - }); - // Create an instance of the workflow (redirects to Parameters page) - await page.click(`#collections-run-${cssEscape(repo_name)}`); + await page.click(`#run-${cssEscape(repo_name)}`); // Default display is Description, switch to Parameters tab await page.click('#parameters-params-tab'); diff --git a/tests/test-data/catalogues/user_collection/store/catalogue.json b/tests/test-data/catalogues/user_collection/store/catalogue.json new file mode 100644 index 0000000..9de4286 --- /dev/null +++ b/tests/test-data/catalogues/user_collection/store/catalogue.json @@ -0,0 +1,16 @@ +{ + "name": "User collection", + "source": "local", + "sections": [ + { + "name": "My Workflows", + "workflows": [ + { + "name": "sleep", + "repo": "glacier/sleep", + "version": "main" + } + ] + } + ] +} diff --git a/tests/test-data/sleep@undefined/main.nf b/tests/test-data/workflows/glacier/sleep@main/main.nf similarity index 100% rename from tests/test-data/sleep@undefined/main.nf rename to tests/test-data/workflows/glacier/sleep@main/main.nf diff --git a/tests/test-data/sleep@undefined/nextflow_schema.json b/tests/test-data/workflows/glacier/sleep@main/nextflow_schema.json similarity index 100% rename from tests/test-data/sleep@undefined/nextflow_schema.json rename to tests/test-data/workflows/glacier/sleep@main/nextflow_schema.json diff --git a/tests/test-data/sleep@undefined/params.json b/tests/test-data/workflows/glacier/sleep@main/params.json similarity index 100% rename from tests/test-data/sleep@undefined/params.json rename to tests/test-data/workflows/glacier/sleep@main/params.json