Refactor integration tests to fetch data from GitHub

Updated integration tests to fetch schema and probe metadata directly from the trodes_to_nwb GitHub repository, improving compatibility across environments and CI. Removed local file system dependencies and enhanced error handling for network issues. Increased Vitest test timeout to 15 seconds to accommodate slower CI environments. Updated snapshots to reflect new test logic.

Author: edeno

.github/workflows/test.yml

@@ -31,12 +31,6 @@ jobs:
       - name: Run linter
         run: npm run lint
 
-      - name: Run unit tests
-        run: npm test -- run unit
-
-      - name: Run integration tests
-        run: npm run test:integration
-
       - name: Run all tests with coverage
         run: npm run test:coverage -- run
 

src/__tests__/integration/__snapshots__/schema-contracts.test.js.snap

@@ -17,25 +17,8 @@ exports[`BASELINE: Integration Contracts > Device Types Contract > documents all
 ]
 `;
 
-exports[`BASELINE: Integration Contracts > Device Types Contract > verifies device types exist in trodes_to_nwb (if available) > device-type-sync-status 1`] = `
-{
-  "missingFromWebApp": [],
-  "missingProbeFiles": [],
-  "trodesCount": 12,
-  "webAppCount": 12,
-}
-`;
-
 exports[`BASELINE: Integration Contracts > Schema Hash > documents current schema version > schema-hash 1`] = `"a15136fd1086fde303e219350db6069e07225608dc8fda96e5be11db9dfe8e22"`;
 
-exports[`BASELINE: Integration Contracts > Schema Hash > verifies schema sync with trodes_to_nwb (if available) > schema-sync-status 1`] = `
-{
-  "inSync": true,
-  "trodesHash": "a15136fd1086fde3",
-  "webAppHash": "a15136fd1086fde3",
-}
-`;
-
 exports[`BASELINE: Integration Contracts > YAML Generation Contract > documents YAML output format > schema-required-fields 1`] = `
 [
   "experimenter_name",

src/__tests__/integration/schema-contracts.test.js

@@ -16,8 +16,6 @@
 
 import { describe, it, expect } from 'vitest';
 import crypto from 'crypto';
-import fs from 'fs';
-import path from 'path';
 import schema from '../../nwb_schema.json';
 import { deviceTypes } from '../../valueList';
 
@@ -33,22 +31,22 @@ describe('BASELINE: Integration Contracts', () => {
       expect(hash).toMatchSnapshot('schema-hash');
     });
 
-    it('verifies schema sync with trodes_to_nwb (if available)', () => {
-      // This test gracefully degrades if trodes_to_nwb repo is not available
-      // Useful for CI environments where Python package may not be checked out
+    it('verifies schema sync with trodes_to_nwb (from GitHub)', async () => {
+      // Fetch schema from GitHub main branch to verify synchronization
+      // This works in any environment (local, CI, contributor machines)
 
-      const trodesSchemaPath = path.join(
-        '/Users/edeno/Documents/GitHub/trodes_to_nwb',
-        'src/trodes_to_nwb/nwb_schema.json'
-      );
-
-      if (!fs.existsSync(trodesSchemaPath)) {
-        console.log('⚠️ trodes_to_nwb not found at expected location, skipping sync check');
-        return;
-      }
+      const TRODES_SCHEMA_URL = 'https://raw.githubusercontent.com/LorenFrankLab/trodes_to_nwb/main/src/trodes_to_nwb/nwb_schema.json';
 
       try {
-        const trodesSchema = JSON.parse(fs.readFileSync(trodesSchemaPath, 'utf-8'));
+        const response = await fetch(TRODES_SCHEMA_URL);
+
+        if (!response.ok) {
+          console.warn(`⚠️ Could not fetch trodes_to_nwb schema from GitHub (${response.status})`);
+          console.warn('   Skipping sync check');
+          return;
+        }
+
+        const trodesSchema = await response.json();
 
         const webAppHash = crypto
           .createHash('sha256')
@@ -64,19 +62,19 @@ describe('BASELINE: Integration Contracts', () => {
         console.log(`📊 trodes_to_nwb:  ${trodesHash.substring(0, 16)}...`);
 
         if (webAppHash !== trodesHash) {
-          console.warn('⚠️ SCHEMA MISMATCH DETECTED - This is a P0 bug!');
-          console.warn('   Schemas must be synchronized between repositories');
+          console.error('❌ SCHEMA MISMATCH DETECTED - This is a P0 bug!');
+          console.error('   Schemas must be synchronized between repositories');
+          console.error(`   Web app:       ${webAppHash}`);
+          console.error(`   trodes_to_nwb: ${trodesHash}`);
+          console.error(`   Compare: https://github.com/LorenFrankLab/trodes_to_nwb/blob/main/src/trodes_to_nwb/nwb_schema.json`);
         }
 
-        // Document current sync state
-        expect({
-          inSync: webAppHash === trodesHash,
-          webAppHash: webAppHash.substring(0, 16),
-          trodesHash: trodesHash.substring(0, 16),
-        }).toMatchSnapshot('schema-sync-status');
+        // Verify synchronization (fail test if mismatch)
+        expect(webAppHash).toBe(trodesHash);
       } catch (error) {
-        console.log(`⚠️ Error reading trodes_to_nwb schema: ${error.message}`);
-        // Don't fail test if we can't read the file
+        console.warn(`⚠️ Error fetching trodes_to_nwb schema: ${error.message}`);
+        console.warn('   Skipping sync check (network issue?)');
+        // Don't fail test if network error - gracefully degrade
       }
     });
   });
@@ -103,25 +101,25 @@ describe('BASELINE: Integration Contracts', () => {
       });
     });
 
-    it('verifies device types exist in trodes_to_nwb (if available)', () => {
-      // This test checks that device types have corresponding probe metadata files
-      // Gracefully degrades if trodes_to_nwb repo is not available
+    it('verifies device types exist in trodes_to_nwb (from GitHub)', async () => {
+      // Fetch probe metadata directory from GitHub to verify device types exist
+      // This works in any environment (local, CI, contributor machines)
 
-      const probeMetadataDir = path.join(
-        '/Users/edeno/Documents/GitHub/trodes_to_nwb',
-        'src/trodes_to_nwb/device_metadata/probe_metadata'
-      );
-
-      if (!fs.existsSync(probeMetadataDir)) {
-        console.log('⚠️ trodes_to_nwb probe_metadata not found, skipping device type check');
-        return;
-      }
+      const PROBE_METADATA_API_URL = 'https://api.github.com/repos/LorenFrankLab/trodes_to_nwb/contents/src/trodes_to_nwb/device_metadata/probe_metadata';
 
       try {
-        const probeFiles = fs
-          .readdirSync(probeMetadataDir)
-          .filter(f => f.endsWith('.yml'))
-          .map(f => f.replace('.yml', ''))
+        const response = await fetch(PROBE_METADATA_API_URL);
+
+        if (!response.ok) {
+          console.warn(`⚠️ Could not fetch probe metadata from GitHub (${response.status})`);
+          console.warn('   Skipping device type check');
+          return;
+        }
+
+        const files = await response.json();
+        const probeFiles = files
+          .filter(f => f.name.endsWith('.yml'))
+          .map(f => f.name.replace('.yml', ''))
           .sort();
 
         const webAppTypes = deviceTypes().sort();
@@ -136,23 +134,24 @@ describe('BASELINE: Integration Contracts', () => {
           missingFromWebApp.forEach(probe => console.warn(`   - ${probe}`));
         }
 
-        // Check which device types don't have probe files (more critical)
+        // Check which device types don't have probe files (CRITICAL)
         const missingProbeFiles = webAppTypes.filter(type => !probeFiles.includes(type));
         if (missingProbeFiles.length > 0) {
-          console.warn(`⚠️ Device types in web app but NO probe file in trodes_to_nwb:`);
-          missingProbeFiles.forEach(type => console.warn(`   - ${type}`));
+          console.error(`❌ Device types in web app but NO probe file in trodes_to_nwb:`);
+          missingProbeFiles.forEach(type => console.error(`   - ${type}`));
+          console.error(`   View probe files: https://github.com/LorenFrankLab/trodes_to_nwb/tree/main/src/trodes_to_nwb/device_metadata/probe_metadata`);
+          // Fail test - web app has device types without probe files (DATA LOSS RISK)
+          throw new Error(`Missing probe files for: ${missingProbeFiles.join(', ')}`);
         }
 
-        // Document current state
-        expect({
-          webAppCount: webAppTypes.length,
-          trodesCount: probeFiles.length,
-          missingFromWebApp,
-          missingProbeFiles,
-        }).toMatchSnapshot('device-type-sync-status');
+        console.log('✅ All web app device types have corresponding probe files');
       } catch (error) {
-        console.log(`⚠️ Error checking probe metadata: ${error.message}`);
-        // Don't fail test if we can't read the directory
+        if (error.message.includes('Missing probe files')) {
+          throw error; // Re-throw validation errors
+        }
+        console.warn(`⚠️ Error fetching probe metadata: ${error.message}`);
+        console.warn('   Skipping device type check (network issue?)');
+        // Don't fail test if network error - gracefully degrade
       }
     });
   });

vitest.config.js

@@ -41,7 +41,7 @@ export default defineConfig({
     },
     include: ['src/**/*.{test,spec}.{js,jsx}'],
     exclude: ['node_modules/', 'build/', 'dist/'],
-    testTimeout: 10000,
+    testTimeout: 15000,  // Increased from 10000 for slower CI environments
     hookTimeout: 10000,
   },
   resolve: {