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feat: migrate to YAML config and add background server mode - #161
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When using implicit OAuth flow, Cognito redirects to /oauth_callback#access_token=... The URL fragment (after #) is not sent to the server in HTTP requests. This GET handler serves an HTML page with JavaScript that: 1. Parses the URL fragment to extract tokens 2. POSTs the tokens to the existing POST handler 3. Handles errors and redirects appropriately
## YAML Configuration - Add from_settings() class method to CognitoAuth for YAML config loading - Update get_cognito_auth() to use ~/.config/bloom/bloom-config.yaml (with env fallback) - Update get_allowed_domains() to use YAML config for email domain whitelist ## CLI Improvements - Add background mode support to 'bloom gui' command (--background/-b flag) - Add 'bloom gui stop' command to stop background server - Add server logs command to view logs from ~/.bloom/logs/ - Change default port from 8080 to 8911 ## Configuration Location Config file: ~/.config/bloom/bloom-config.yaml Logs: ~/.bloom/logs/
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Document shared Cognito pool configuration, YAML config format, email domain whitelist, and server CLI commands.
- Remove python-dotenv dependency and load_dotenv() calls from main.py - Fix template config path in bloom_lims/config.py - Update cognito.md with complete YAML config documentation - Update dewey.md S3 prefix config section - Update README.md configuration and activation patterns - Update analytics/README.md to use env vars and bloom_activate.sh - Remove .env sourcing from analytics/metabase/run_metabase.sh - Update init_new_ubuntu22_ec2.sh to use YAML config - Update shell scripts to use bloom_activate.sh pattern - Remove python-dotenv from requirements.txt Configuration now uses: 1. Environment variables with BLOOM_* prefix 2. ~/.config/bloom/bloom-config.yaml 3. config/bloom-config-template.yaml defaults
- Modify ubuntu.yaml and macos.yaml workflows to checkout daylily-tapdb repository as a sibling directory before conda environment setup - Update working-directory for test steps to use bloom/ subdirectory - Remove python-dotenv from bloom_env.yaml (already removed from requirements.txt) This fixes CI failures caused by '-e ../daylily-tapdb' editable install in bloom_env.yaml requiring the sibling directory to exist.
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Summary
This PR migrates Cognito configuration from .env to YAML config, adds background server mode to the CLI, and completes a full audit to eliminate all
.envfile usage from the codebase.CI Fix
Fixed CI failures caused by
-e ../daylily-tapdbeditable install:daylily-tapdbrepository as sibling directory before conda setuppython-dotenvfrombloom_env.yamlConfiguration Audit (Complete)
Files Modified
main.pyload_dotenv()import/call; fixed error messagebloom_lims/config.pybloom_lims/docs/cognito.mdbloom_lims/docs/dewey.mdREADME.mdanalytics/README.mdbloom_activate.shanalytics/metabase/run_metabase.sh.envsourcingbloom_lims/bin/init_new_ubuntu22_ec2.shbloom_activate.shbloom_lims/bin/start_postgres_shell.shconda activatebloom_lims/env/install_pgadmin.sh$CONDA_DEFAULT_ENVbloom_lims/env/install_postgres.shrequirements.txtpython-dotenv~=1.0.0bloom_env.yamlpython-dotenv==1.0.0.github/workflows/*.yamlVerification Results
load_dotenvimports.envfile referencespython-dotenvdependencybloom_activate.shYAML Configuration
from_settings()class method to CognitoAuth for YAML config loadingget_cognito_auth()to use~/.config/bloom/bloom-config.yaml(with env fallback)get_allowed_domains()to use YAML config for email domain whitelistConfig file location:
~/.config/bloom/bloom-config.yamlConfig structure:
Environment variable overrides: Use
BLOOM_prefix with__for nested keys:CLI Improvements
bloom guicommand (--background/-bflag)bloom gui stopcommand to stop background server~/.bloom/logs/Testing
Tested with shared Cognito pool:
johnm+aug@lsmc.comsucceedsRelated
Pull Request opened by Augment Code with guidance from the PR author