Devcontainer setup to work with seed data.

.devcontainer/config/.genologicsrc

@@ -0,0 +1,4 @@
+[genologics]
+BASEURI=http://localhost:8443
+USERNAME=fake_user
+PASSWORD=fake_password

.devcontainer/config/lims_backend_cred.yaml

@@ -0,0 +1,4 @@
+# Fake LIMS backend credentials for local development
+baseuri: http://localhost:8443
+username: fake_user
+password: fake_password

.devcontainer/config/settings.yaml

@@ -0,0 +1,73 @@
+# Local development settings for genomics-status
+# Uses the CouchDB container from docker-compose
+
+couch_server: http://admin:admin@couchdb:5984
+username: admin
+password: admin
+port: 9761
+redirect_uri: http://localhost:9761/login
+cookie_secret: dev-cookie-secret-not-for-production
+
+# CouchDB URL - use 'couchdb' hostname for docker network
+couch_url: http://couchdb:5984
+
+# Font Awesome - using free version CDN for dev
+font_awesome_url: https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.0/js/all.min.js
+
+# LIMS backend credentials location
+lims_backend_credential_location: /workspace/.devcontainer/config/lims_backend_cred.yaml
+
+# Order portal - not needed for local dev
+order_portal_credential_location: /workspace/.devcontainer/config/orderportal_cred.yaml
+
+# Google OAuth - disabled in testing_mode
+google_oauth:
+    key: fake-google-oauth-key
+    secret: fake-google-oauth-secret
+
+# Zendesk - not needed for local dev
+zendesk:
+    url: https://example.zendesk.com
+    username: fake@example.com
+    token: fake-zendesk-token
+
+contact_person: dev@localhost
+
+# Instruments - empty for local dev
+instruments:
+    HiSeq:
+        DEV001: Dev-HiSeq
+    MiSeq:
+        DEV002: Dev-MiSeq
+
+# Slack - not needed for local dev
+slack:
+    token: fake-slack-token
+
+# Jira - not needed for local dev
+jira:
+    url: https://example.atlassian.net
+    user: fake@example.com
+    api_token: fake-jira-token
+    project_key: DEV
+
+# Suggestion box log
+sb_log: suggestion_box.log
+
+# PSUL log - not needed for local dev
+psul_log: /tmp/lims2db_projects.log
+
+# Charon - not needed for local dev
+charon:
+    url: https://example.com
+    api_token: fake-charon-token
+
+# LIMS Dashboard
+lims_dashboard_url: http://localhost:8080
+
+# Server status - empty for local dev
+server_status:
+    instruments: {}
+
+# Reports path
+reports_path: /tmp/reports

.devcontainer/devcontainer.json

@@ -1,32 +1,40 @@
-// For format details, see https://aka.ms/devcontainer.json. For config options, see the
-// README at: https://github.com/devcontainers/templates/tree/main/src/docker-existing-dockerfile
 {
     "name": "Genomics Status",
-    "build": {
-        // Sets the run context to one level up instead of the .devcontainer folder.
-        "context": "..",
-        // Update the 'dockerFile' property if you aren't using the standard 'Dockerfile' filename.
-        "dockerfile": "../Dockerfile"
-    },
+    "dockerComposeFile": "docker-compose.yml",
+    "service": "genomics-status",
+    "workspaceMounts": [
+        "source=${localWorkspaceFolder},target=/workspace,type=bind",
+        "source=${localWorkspaceFolder}/../StatusDB_seed_data,target=/StatusDB_seed_data,type=bind"
+    ],
+    "workspaceFolder": "/workspace",
+
+    "initializeCommand": "bash -c 'if [ ! -d ../StatusDB_seed_data ]; then echo \"Cloning StatusDB_seed_data...\"; git clone https://github.com/SciLifeLab/StatusDB_seed_data.git ../StatusDB_seed_data; else echo \"StatusDB_seed_data already exists\"; fi'",
     "features": {},
+
     "customizations": {
         "vscode": {
             "extensions": [
                 "charliermarsh.ruff",
                 "ms-python.python",
-                "Tobermory.es6-string-html" 
+                "Tobermory.es6-string-html"
             ]
         }
     },
-    // Use 'forwardPorts' to make a list of ports inside the container available locally.
-    "forwardPorts": [9761],
+
+    "forwardPorts": [9761, 5984],
+    "portsAttributes": {
+        "9761": {
+            "label": "Genomics Status",
+            "onAutoForward": "notify"
+        },
+        "5984": {
+            "label": "CouchDB",
+            "onAutoForward": "silent"
+        }
+    },
+
     "postCreateCommand": "./.devcontainer/postCreateCommand.sh",
     "postStartCommand": "cd run_dir && python ../status_app.py --develop --testing_mode",
-    // Configure tool-specific properties.
-    // "customizations": {},
-    // Uncomment to connect as an existing user other than the container default. More info: https://aka.ms/dev-containers-non-root.
-    "remoteUser": "mambauser",
-    "mounts": [
-        "source=${localEnv:HOME}/conf,target=/home/mambauser/conf,type=bind,consistency=cached"
-    ]
-}
+
+    "remoteUser": "mambauser"
+}

.devcontainer/docker-compose.yml

@@ -0,0 +1,46 @@
+services:
+  couchdb:
+    # For local development, build from sibling repo:
+    build:
+      context: ../../StatusDB_seed_data
+      dockerfile: Dockerfile
+    # For production, use published image:
+    # image: ghcr.io/scilifelab/statusdb_seed_data:latest
+    environment:
+      - COUCHDB_USER=admin
+      - COUCHDB_PASSWORD=admin
+    volumes:
+      - couchdb-data:/opt/couchdb/data
+    ports:
+      - "5984:5984"
+    networks:
+      - genomics-status-network
+    healthcheck:
+      test: ["CMD", "curl", "-f", "http://localhost:5984/_up"]
+      interval: 5s
+      timeout: 5s
+      retries: 10
+      start_period: 10s
+
+  genomics-status:
+    build:
+      context: ..
+      dockerfile: Dockerfile
+    volumes:
+      - ..:/workspace:cached
+      - ../../StatusDB_seed_data:/StatusDB_seed_data:cached
+    ports:
+      - "9761:9761"
+    networks:
+      - genomics-status-network
+    depends_on:
+      couchdb:
+        condition: service_healthy
+    working_dir: /workspace/run_dir
+    command: sleep infinity
+
+volumes:
+  couchdb-data:
+
+networks:
+  genomics-status-network:

.devcontainer/postCreateCommand.sh

@@ -4,6 +4,31 @@
 
 echo $PATH
 
+# Install the package in development mode
+cd /workspace
 python -m pip install -e .
-ln -s /home/mambauser/conf/.genologicsrc /home/mambauser/.genologicsrc
-ln -s /home/mambauser/conf/genosqlrc.yaml /home/mambauser/.genosqlrc.yaml
+
+# Set up config files for local development
+# Link settings.yaml to run_dir
+ln -sf /workspace/.devcontainer/config/settings.yaml /workspace/run_dir/settings.yaml
+
+# Link .genologicsrc to home directory (where genologics library looks for it)
+ln -sf /workspace/.devcontainer/config/.genologicsrc /home/mambauser/.genologicsrc
+
+# Link genosqlrc.yaml to home directory (where genologics_sql library looks for it)
+ln -sf /workspace/.devcontainer/config/.genosqlrc.yaml /home/mambauser/.genosqlrc.yaml
+
+# If user has their own conf directory mounted, prefer those configs
+if [ -d /home/mambauser/conf ]; then
+    [ -f /home/mambauser/conf/.genologicsrc ] && ln -sf /home/mambauser/conf/.genologicsrc /home/mambauser/.genologicsrc
+    [ -f /home/mambauser/conf/genosqlrc.yaml ] && ln -sf /home/mambauser/conf/genosqlrc.yaml /home/mambauser/.genosqlrc.yaml
+    [ -f /home/mambauser/conf/settings.yaml ] && ln -sf /home/mambauser/conf/settings.yaml /workspace/run_dir/settings.yaml
+fi
+
+echo ""
+echo "=== Development Environment Ready ==="
+echo "CouchDB:         http://localhost:5984"
+echo "CouchDB UI:      http://localhost:5984/_utils"
+echo "CouchDB creds:   admin / admin"
+echo "Genomics Status: http://localhost:9761 (after starting)"
+echo "====================================="

CLAUDE.md

@@ -0,0 +1,123 @@
+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Overview
+
+Genomics Status is a Tornado web application for visualizing NGI Stockholm operations at SciLifeLab. It interfaces with StatusDB (CouchDB) for metadata storage and Genologics LIMS for laboratory information.
+
+## Development Commands
+
+### Running the Application
+
+```bash
+# From the run_dir directory
+cd run_dir
+python ../status_app.py --testing_mode
+
+# With auto-reload for development
+python ../status_app.py --develop --testing_mode
+
+# Custom port
+python ../status_app.py --testing_mode --port=9762
+```
+
+The `--testing_mode` flag disables Google OAuth authentication. The app runs on port 9761 by default.
+
+### Dev Container
+
+The project supports VS Code Dev Containers. When using Dev Containers:
+- Ports 9761 (app) and 5984 (CouchDB) are forwarded
+- The app auto-starts with `--develop --testing_mode`
+
+### Linting
+
+```bash
+ruff check .                    # Check for issues
+ruff check --fix .              # Auto-fix issues
+ruff format .                   # Format code
+```
+
+Ruff is configured in `pyproject.toml` with rules for pycodestyle, Pyflakes, isort, and pyupgrade.
+
+### Running Tests
+
+Tests use nose and require a running server:
+```bash
+# Start the server first, then in another terminal:
+cd tests
+nosetests test_integration.py
+```
+
+Tests are in the `tests/` directory and require `tests/test_items.yaml` for test data.
+
+## Architecture
+
+### Request Flow
+
+1. Browser requests a page (e.g., `/projects/all`)
+2. Tornado routes to the appropriate Handler class
+3. Handler renders a template from `run_dir/design/` with server-side data
+4. Template makes JavaScript calls to the REST API (`/api/v1/...`)
+5. API handlers query CouchDB and return JSON
+6. Client-side JavaScript builds the UI
+
+### Code Structure
+
+- `status_app.py` - Main application entry point, defines all URL routes and initializes the Tornado Application
+- `status/` - Handler modules organized by feature:
+  - `util.py` - Base handler classes (`SafeHandler`, `UnsafeHandler`, `BaseHandler`)
+  - `projects.py`, `flowcells.py`, etc. - Feature-specific handlers
+- `run_dir/` - Runtime directory (must run app from here):
+  - `design/` - Tornado HTML templates
+  - `static/` - CSS, JavaScript, images
+  - `settings.yaml` - Configuration (not in repo)
+
+### Handler Inheritance
+
+- `BaseHandler` - Base class with authentication, error handling
+- `SafeHandler(BaseHandler)` - Requires authentication (use `@tornado.web.authenticated`)
+- `UnsafeHandler(BaseHandler)` - No authentication required
+- `SafeSocketHandler` - WebSocket with authentication
+
+### Database Access
+
+The app uses IBM Cloudant SDK to connect to CouchDB:
+```python
+# Available via self.application.cloudant in handlers
+self.application.cloudant.post_view(db="...", ddoc="...", view="...", ...)
+self.application.cloudant.get_document(db="...", doc_id="...")
+```
+
+Key databases: `projects`, `flowcells`, `worksets`, `gs_users`, `gs_configs`, `server_status`
+
+### API Pattern
+
+API handlers typically:
+1. Inherit from `SafeHandler` or `UnsafeHandler`
+2. Implement `get()`, `post()`, or `put()` methods
+3. Set `Content-type: application/json` header
+4. Return JSON via `self.write(json.dumps(data))`
+
+### Templates
+
+Templates use Tornado's templating with embedded Python:
+- `{% ... %}` for control structures
+- `{{ ... }}` for expressions
+- Templates access `gs_globals`, `user`, and handler-passed variables
+
+## Configuration
+
+Required config files in `run_dir/`:
+- `settings.yaml` - Main config (CouchDB, OAuth, Zendesk, Jira, Slack)
+- `.genologicsrc` - LIMS API credentials
+- `orderportal_cred.yaml` - Order portal API token
+
+## User Roles
+
+Defined in `status/util.py`:
+- `admin` - Full admin access
+- `pricing_admin` - Manage pricing
+- `sample_requirements_admin` - Manage sample requirements
+- `proj_coord` - Project coordinator
+- `api_user` - JWT-authenticated API access

run_dir/static/js/projects.js

@@ -490,7 +490,7 @@ function load_presets() {
     if (!jQuery.isEmptyObject(user_presets)) {
       for (var preset in user_presets) {
         userDefPresetsDropdown+='<li><a href="#" class="clickDropdownGetValue dropdown-item" style="cursor:pointer;" data-value="'+preset+'"> '+preset+'</a></li>';
-        allPresetsDropdownMod+='<li><a href="#" class="clickDropdownGetValue dropdown-item" style="cursor:pointer;" data-value="'+preset+'" data-origin="userdefined"">'+preset+'</a></li>';
+        allPresetsDropdownMod+='<li><a href="#" class="clickDropdownGetValue dropdown-item" style="cursor:pointer;" data-value="'+preset+'" data-origin="userdefined">'+preset+'</a></li>';
       }
     }
     userDefPresetsDropdown+='</ul>';