refactor(worker): code quality phase 3 - centralized config and tests

.changeset/worker-code-quality-phase-3.md

@@ -0,0 +1,5 @@
+---
+'@bilbomd/worker': minor
+---
+
+Enhance worker code quality with centralized configuration and comprehensive test coverage. Extract all magic numbers to config/constants.ts (worker concurrency, polling intervals, retry settings, progress calculation). Consolidate duplicated error handling into shared helpers/errors.ts utility. Add 100% test coverage for mongo-utils.ts and workerControl.ts, plus 63% coverage for job-utils.ts (39 new tests total). Improve runPythonStep.ts coverage from 88% to 92%. Remove dead/commented code across worker files.

.claude/settings.local.json

@@ -19,7 +19,10 @@
       "Bash(pnpm -C apps/ui run test:*)",
       "Bash(pnpm -C apps/worker run test:*)",
       "Bash(gh run view:*)",
-      "Bash(gh pr checks:*)"
+      "Bash(gh pr checks:*)",
+      "Bash(pnpm -F @bilbomd/worker test:*)",
+      "Bash(gh pr view:*)",
+      "Bash(git fetch:*)"
     ]
   }
-}
+}

CLAUDE.md

@@ -91,6 +91,55 @@ pnpm changeset        # Select packages, choose semver bump, write summary
 
 Changesets are applied on merge to `main`, producing git tags and Docker image semver tags. `updateInternalDependencies: "patch"` is enabled — bumping an internal package auto-bumps dependents.
 
+### Manual Changeset Creation
+
+**IMPORTANT**: The `pnpm changeset` command is interactive and won't work in non-TTY environments (like Claude Code CLI). When this happens, create changeset files manually:
+
+1. **Create a new file** in `.changeset/` with a descriptive kebab-case name:
+   - Pattern: `.changeset/descriptive-name.md`
+   - Examples: `worker-code-quality-improvements.md`, `backend-security-fixes.md`
+
+2. **File format** (YAML front matter + description):
+   ```markdown
+   ---
+   '@bilbomd/package-name': patch|minor|major
+   ---
+
+   Brief description of changes. Focus on user/developer impact, not implementation details.
+   ```
+
+3. **Semver guidelines**:
+   - `patch` - Bug fixes, minor improvements, internal refactoring
+   - `minor` - New features, significant improvements (backwards compatible)
+   - `major` - Breaking changes
+
+4. **Examples**:
+   ```markdown
+   ---
+   '@bilbomd/worker': patch
+   ---
+
+   Improve worker reliability with graceful shutdown handling and MongoDB connection retry logic.
+   ```
+
+   ```markdown
+   ---
+   '@bilbomd/worker': minor
+   ---
+
+   Add comprehensive test coverage for critical infrastructure (mongo-utils, job-utils, workerControl). Extract magic numbers to centralized config/constants.ts. Consolidate error handling utilities.
+   ```
+
+5. **Multiple packages** (if changes affect multiple):
+   ```markdown
+   ---
+   '@bilbomd/backend': patch
+   '@bilbomd/mongodb-schema': patch
+   ---
+
+   Fix user authentication schema validation and update backend handlers.
+   ```
+
 ## Git Branch Naming Convention
 
 Use standardized branch prefixes to indicate the type of work. Branch names should use kebab-case (lowercase with hyphens).

apps/worker/src/config/constants.ts

@@ -0,0 +1,76 @@
+/**
+ * Worker configuration constants
+ *
+ * This file centralizes all magic numbers and hardcoded values used throughout
+ * the worker application to improve maintainability and configuration flexibility.
+ */
+
+// Worker concurrency settings
+export const WORKER_CONCURRENCY = {
+  NERSC: 50,
+  LOCAL: 1,
+  MOVIE: 1,
+  MULTI_MD: 1
+} as const
+
+// BullMQ lock settings (in milliseconds)
+export const LOCK_SETTINGS = {
+  DURATION: 60_000, // 1 minute
+  RENEW_TIME: 30_000 // 30 seconds
+} as const
+
+// Polling and monitoring intervals (in milliseconds)
+export const INTERVALS = {
+  TOKEN_CHECK: 300_000, // 5 minutes
+  JOB_MONITORING: 60_000, // 1 minute
+  NERSC_TASK_POLL: 2_000, // 2 seconds
+  NERSC_JOB_POLL: 60_000 // 1 minute
+} as const
+
+// NERSC API retry configuration
+export const NERSC_RETRY = {
+  MAX_ATTEMPTS: 11,
+  MAX_JOB_RETRIES: 10,
+  MAX_ITERATIONS: 1_440, // 1440 x 60s = 24 hours
+  RETRY_DELAY: 60_000 // 1 minute
+} as const
+
+// Progress calculation constants
+export const PROGRESS = {
+  MIN: 20, // Minimum progress percentage
+  MAX: 90, // Maximum progress percentage
+  SCALE_FACTOR: 70 // Scale factor for progress calculation (20% to 90%)
+} as const
+
+// Step weights for progress calculation
+export const STEP_WEIGHTS: Record<string, number> = {
+  alphafold: 20,
+  pdb2crd: 5,
+  pae: 5,
+  autorg: 5,
+  minimize: 10,
+  initfoxs: 5,
+  heat: 10,
+  md: 30,
+  dcd2pdb: 10,
+  foxs: 10,
+  multifoxs: 10,
+  copy_results_to_cfs: 5,
+  results: 3,
+  email: 1,
+  nersc_prepare_slurm_batch: 5,
+  nersc_submit_slurm_batch: 5,
+  nersc_job_status: 5,
+  nersc_copy_results_to_cfs: 5
+} as const
+
+// Server configuration
+export const SERVER = {
+  PORT: 3000
+} as const
+
+// NERSC paths
+// TODO: Make this configurable via environment variable
+export const NERSC_PATHS = {
+  SCRIPT_LOGS_DIR: '/global/homes/s/sclassen/script-logs'
+} as const

apps/worker/src/helpers/__tests__/runPythonStep.test.ts

@@ -79,4 +79,10 @@ describe('runPythonStep', () => {
     const result = await runPythonStep('a.py', 'b.yaml')
     expect(result).toEqual({ code: 42, signal: 'SIGUSR1' })
   })
+
+  it('throws error when spawn fails', async () => {
+    const spawnError = new Error('ENOENT: python binary not found')
+    setTimeout(() => mockChild.emit('error', spawnError), 10)
+    await expect(runPythonStep('a.py', 'b.yaml')).rejects.toThrow('ENOENT: python binary not found')
+  })
 })

apps/worker/src/helpers/errors.ts

@@ -0,0 +1,14 @@
+/**
+ * Error handling utilities
+ *
+ * Shared error handling functions used throughout the worker application
+ */
+
+/**
+ * Extracts a readable error message from various error types
+ *
+ * @param e - The error to extract a message from
+ * @returns A string representation of the error
+ */
+export const getErrorMessage = (e: unknown): string =>
+  e instanceof Error ? e.message : typeof e === 'string' ? e : JSON.stringify(e)