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Merged
jsbrittain merged 19 commits into from
Feb 3, 2026
Merged

Support catalogues #161

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a7c1709
Add catalogues
jsbrittain Jan 27, 2026
84272c2
Support user catalogue; highlight selected section
jsbrittain Jan 27, 2026
b1ecfc9
Enable adding collections and workflows by the user
jsbrittain Jan 28, 2026
46875a1
Add context menus to Library catalogues, sections and workflows
jsbrittain Jan 29, 2026
c2af2bf
Add permit modifying catalogues setting
jsbrittain Jan 29, 2026
e36135c
Improve linting and fix lint errors
jsbrittain Jan 29, 2026
840d33e
Update end-to-end tests for new interface
jsbrittain Jan 30, 2026
acb6950
Downgrade to JAVA 21; Support full JRE bundling
jsbrittain Jan 30, 2026
6db44d3
Update lock file
jsbrittain Feb 2, 2026
e351a1e
Implement remove workflow/section/catalogue functionality
jsbrittain Feb 2, 2026
6a81a4b
Add autofocus and keyboard Escape / Enter in cataloguedialogs
jsbrittain Feb 3, 2026
659656c
Add Library repo validation, install all, progress dialogs, repo upda…
jsbrittain Feb 3, 2026
c77ffc9
Address firefox / webkit fragility by bluring Collections path after …
jsbrittain Feb 3, 2026
5e68310
Update lock file
jsbrittain Feb 3, 2026
9d87afd
Implement more robust drive mapping when calling wsl
jsbrittain Feb 3, 2026
91ac1d8
Replace deprecated mui LoadingButton
jsbrittain Feb 3, 2026
d8652a9
Replace WSL setup in CI with powershell script
jsbrittain Feb 3, 2026
d2c838e
Improve error reporting from electron e2e tests
jsbrittain Feb 3, 2026
5daa830
Generalise WSL drive mount mapping
jsbrittain Feb 3, 2026
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17 changes: 3 additions & 14 deletions .github/workflows/e2e_wsl.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/release.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
1 change: 1 addition & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
bundle
tests/test-data/instances*

# Logs
logs
Expand Down
87 changes: 69 additions & 18 deletions api-server/index.js
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Original file line number Diff line number Diff line change
Expand Up @@ -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) =>
Expand Down Expand Up @@ -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) =>
Expand Down Expand Up @@ -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())
);
Expand All @@ -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) =>
Expand Down
116 changes: 106 additions & 10 deletions eslint.config.js
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Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand All @@ -16,32 +21,94 @@ 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',
__dirname: 'readonly',
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: {
Expand All @@ -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/**']
}
]
}
}
];
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