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Add nix-infra-machine
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Ruben Hensen
@@ -0,0 +1,309 @@
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# Beiwe Backend package
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# A Django-based smartphone digital phenotyping research platform backend
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#
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# Using jhsware fork which adds environment variable support for Celery configuration
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# (CELERY_MANAGER_IP and CELERY_PASSWORD instead of manager_ip file)
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#
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# To update to a new version:
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# 1. Update the rev to the new commit hash
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# 2. Run: nix-prefetch-url --unpack https://github.com/jhsware/beiwe-backend/archive/<NEW_COMMIT>.tar.gz
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# 3. Update the hash with the output from step 2
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{
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lib,
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stdenv,
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fetchFromGitHub,
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fetchPypi,
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python312,
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python312Packages,
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postgresql,
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# Custom parameters
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rev ? "93be878", # jhsware fork with env var support for Celery
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}:
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let
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# Known version hashes
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# To add a new version, run:
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# nix-prefetch-url --unpack https://github.com/jhsware/beiwe-backend/archive/<COMMIT>.tar.gz
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versionHashes = {
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# jhsware fork with CELERY_MANAGER_IP and CELERY_PASSWORD env var support
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"93be878" = {
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srcHash = "sha256-marYxVINxgW0X9x+xoHL7bdRYEgm+4q+O1CF5WXeZGg=";
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};
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# Original onnela-lab version (for reference)
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"6bb5363" = {
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srcHash = "sha256-EeD+I3mWC81mhmlO9cKzRrArDLKVBmqhZjgJI8+geu0=";
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};
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};
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hashes = versionHashes.${rev} or (throw ''
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beiwe-backend revision ${rev} is not supported.
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Supported revisions: ${builtins.concatStringsSep ", " (builtins.attrNames versionHashes)}
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To add support for revision ${rev}:
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1. Get source hash: nix-prefetch-url --unpack https://github.com/jhsware/beiwe-backend/archive/${rev}.tar.gz
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2. Add entry to versionHashes in app_modules/_unstable/beiwe-backend/package.nix
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'');
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# Build cronutils from PyPI (not available in nixpkgs)
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cronutils = python312Packages.buildPythonPackage rec {
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pname = "cronutils";
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version = "0.4.2";
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format = "setuptools";
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src = fetchPypi {
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inherit pname version;
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hash = "sha256-SFHkQ9NltAyWArArkFpSBIJF3gMoXbxHEXreM1SEPUY=";
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};
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propagatedBuildInputs = with python312Packages; [
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sentry-sdk
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];
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# Tests require network access
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doCheck = false;
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pythonImportsCheck = [ "cronutils" ];
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meta = with lib; {
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description = "Utilities for cron jobs including error handling";
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homepage = "https://pypi.org/project/cronutils/";
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license = licenses.mit;
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};
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};
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# Build beiwe-forest from GitHub (Forest analysis library)
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# See: https://github.com/onnela-lab/forest
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# Note: pip install git+https://github.com/onnela-lab/forest
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beiweForest = python312Packages.buildPythonPackage rec {
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pname = "forest";
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version = "unstable-2024-12-01";
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format = "pyproject";
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src = fetchFromGitHub {
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owner = "onnela-lab";
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repo = "forest";
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rev = "develop"; # Main development branch
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hash = "sha256-t+oq/jfJUmWCs0XzrN+xciYc3lz4oPiO8V8qfj3iTJA=";
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};
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nativeBuildInputs = with python312Packages; [
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setuptools
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];
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propagatedBuildInputs = with python312Packages; [
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# Core data science
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numpy
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pandas
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scipy
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scikit-learn
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# Time/date utilities
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pytz
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holidays
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timezonefinder
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# GIS/mapping
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shapely
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pyproj
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# Audio processing (for voice analysis)
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librosa
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# HTTP/API
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requests
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ratelimit
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];
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# Some optional dependencies not in nixpkgs (openrouteservice, ssqueezepy)
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# Disable strict runtime deps check to allow partial functionality
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pythonRelaxDeps = true;
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pythonRemoveDeps = [ "openrouteservice" "ssqueezepy" ];
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# Tests require data files
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doCheck = false;
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pythonImportsCheck = [ "forest" ];
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meta = with lib; {
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description = "Forest library for analyzing Beiwe digital phenotyping data";
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homepage = "https://github.com/onnela-lab/forest";
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license = licenses.bsd3;
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};
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};
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# Python environment with all dependencies from requirements.txt
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pythonEnv = python312.withPackages (ps: with ps; [
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# Django and web framework
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django
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django-extensions
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django-timezone-field # Provides timezone_field module
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gunicorn
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jinja2
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# Database - using psycopg (v3) as specified in requirements.txt
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psycopg
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# AWS/S3 support
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boto3
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# Celery for task queue
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celery
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# Error tracking and monitoring
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sentry-sdk
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cronutils # Custom package built above
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# Firebase (push notifications)
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firebase-admin
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# Security and crypto
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pycryptodomex # Note: pycryptodomex not pycryptodome
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pyotp
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bleach
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# Serialization
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orjson
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# Date/time utilities
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python-dateutil
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pytz
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# Compression - pyzstd provides "import pyzstd" (jhsware fork uses pyzstd)
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pyzstd
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# Data analysis
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numpy
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pandas
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scipy
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scikit-learn
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beiweForest # Custom package - provides "import forest"
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# Other utilities
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requests
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rcssmin
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pypng
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pyqrcode
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# Development/debugging
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ipython
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mypy
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]);
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in
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stdenv.mkDerivation {
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pname = "beiwe-backend";
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version = rev;
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src = fetchFromGitHub {
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owner = "jhsware"; # Fork with env var support for Celery
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repo = "beiwe-backend";
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inherit rev;
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hash = hashes.srcHash;
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};
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buildInputs = [
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pythonEnv
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postgresql
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];
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# No build phase needed - this is a Python application
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dontBuild = true;
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# Patch Django settings to support DATABASE_SSLMODE environment variable
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# This allows controlling PostgreSQL SSL mode via environment variable
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postPatch = ''
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# Find the Django settings file and patch the database configuration
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# to include sslmode from environment variable
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# Add sslmode support to database configuration
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# This sed command finds the DATABASES dict and adds OPTIONS with sslmode
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if [ -f config/django_settings.py ]; then
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echo "Patching config/django_settings.py for DATABASE_SSLMODE support..."
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# Add import for os at the top if not already there
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if ! grep -q "^import os" config/django_settings.py; then
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sed -i '1i import os' config/django_settings.py
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fi
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# Append code to add sslmode to database options at the end of the file
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cat >> config/django_settings.py << 'SSLPATCH'
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# Patched by nix-infra-machine: Add DATABASE_SSLMODE support
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# This allows setting PostgreSQL sslmode via environment variable
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_db_sslmode = os.environ.get('DATABASE_SSLMODE', os.environ.get('PGSSLMODE', 'prefer'))
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if 'default' in DATABASES:
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if 'OPTIONS' not in DATABASES['default']:
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DATABASES['default']['OPTIONS'] = {}
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DATABASES['default']['OPTIONS']['sslmode'] = _db_sslmode
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SSLPATCH
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echo "Patched database settings for sslmode support"
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else
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echo "Warning: config/django_settings.py not found, skipping sslmode patch"
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fi
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'';
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installPhase = ''
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runHook preInstall
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# Create directory structure
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mkdir -p $out/lib/beiwe-backend
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mkdir -p $out/bin
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# Copy all source files
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cp -r . $out/lib/beiwe-backend/
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# Create wrapper scripts
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cat > $out/bin/beiwe-manage <<EOF
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#!/usr/bin/env bash
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cd $out/lib/beiwe-backend
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exec ${pythonEnv}/bin/python manage.py "\$@"
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EOF
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chmod +x $out/bin/beiwe-manage
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cat > $out/bin/beiwe-gunicorn <<EOF
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#!/usr/bin/env bash
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cd $out/lib/beiwe-backend
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exec ${pythonEnv}/bin/gunicorn "\$@"
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EOF
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chmod +x $out/bin/beiwe-gunicorn
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cat > $out/bin/beiwe-celery <<EOF
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#!/usr/bin/env bash
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cd $out/lib/beiwe-backend
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exec ${pythonEnv}/bin/celery "\$@"
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EOF
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chmod +x $out/bin/beiwe-celery
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runHook postInstall
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'';
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meta = {
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description = "Beiwe - smartphone-based digital phenotyping research platform backend";
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longDescription = ''
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The Beiwe Research Platform collects high-throughput smartphone-based
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digital phenotyping data including spatial trajectories (GPS), physical
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activity patterns (accelerometer/gyroscope), social networks and
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communication dynamics (call/text logs), and voice samples.
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This package provides the Django-based backend server that supports:
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- Web-based study management portal
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- API endpoints for iOS/Android mobile apps
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- Data processing pipelines
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This is the jhsware fork which adds environment variable support for
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Celery configuration (CELERY_MANAGER_IP and CELERY_PASSWORD).
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Patched by nix-infra-machine to support DATABASE_SSLMODE environment
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variable for controlling PostgreSQL SSL mode.
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'';
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homepage = "https://github.com/jhsware/beiwe-backend";
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license = lib.licenses.bsd3;
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platforms = lib.platforms.unix;
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};
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}
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