{"id":19749523,"url":"https://github.com/mskcc/igo-sample-qc-backend","last_synced_at":"2026-06-16T07:31:10.612Z","repository":{"id":39842770,"uuid":"199043851","full_name":"mskcc/igo-sample-qc-backend","owner":"mskcc","description":null,"archived":false,"fork":false,"pushed_at":"2023-11-28T21:49:20.000Z","size":228,"stargazers_count":1,"open_issues_count":8,"forks_count":1,"subscribers_count":8,"default_branch":"main","last_synced_at":"2025-07-08T21:48:42.989Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/mskcc.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2019-07-26T15:50:53.000Z","updated_at":"2021-11-04T14:12:43.000Z","dependencies_parsed_at":"2023-11-28T22:43:26.739Z","dependency_job_id":null,"html_url":"https://github.com/mskcc/igo-sample-qc-backend","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/mskcc/igo-sample-qc-backend","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Figo-sample-qc-backend","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Figo-sample-qc-backend/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Figo-sample-qc-backend/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Figo-sample-qc-backend/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mskcc","download_url":"https://codeload.github.com/mskcc/igo-sample-qc-backend/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Figo-sample-qc-backend/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":34394371,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-06-16T02:00:06.860Z","response_time":126,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-12T02:27:05.208Z","updated_at":"2026-06-16T07:31:10.593Z","avatar_url":"https://github.com/mskcc.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Sample QC Backend\n\n## Deploying on a server \u003cbr\u003e\nClone the repository to a path under your local folder. \nPull the changes you wish to deploy.\nMove them over to the corresponding file under `/srv/www/sample-qc/sample-qc-backend/` and then restart uwsgi with \n```\ndzdo systemctl restart uwsgi\n```\n\nSample QC backend runs on Python. You will have to follow this set up if it's your first time running this project locally.\n\n## Basic Setup Instructions \u003cbr\u003e\n\n**Install python3 and pip3** \u003cbr\u003e\n```\n$ brew install python\n```\n```\n$ brew install pip3\n```\n\n**Get mySQL running on your machine** \u003cbr\u003e\n```\n$ brew install mysql\n```\nYou'll then need to start your mySQL server (this will keep it running in the background on your machine) \u003cbr\u003e\n```\n$ brew services start mysql\n```\nFirst time downloads, you'll want to securely set up the mySQL server by running \u003cbr\u003e\n```\n$ mysql_secure_installation\n```\nFollow the prompts and set up your root password \u003cbr\u003e\nAt this point, you can connect to your mySQL server with the following command \u003cbr\u003e\n```\n$ mysql -u root -p\n```\nNOTE: you can also use mySQL Workbench for a UI to manipulate your db \u003cbr\u003e\n\n**Set up your Virtual Environment** \u003cbr\u003e\n```\n$ pip3 install virtualenv\n```\nMake sure you `cd` into `igo-sample-qc-backend` in your terminal, then run the following cmd to setup the VE locally \u003cbr\u003e\n```\n$ virtualenv venv\n```\nActivate the venv \u003cbr\u003e\n```\n$ source venv/bin/activate\n```\nYou should now see `(venv)` appear at the beginning of your terminal prompt indicating that you are working inside the virtualenv \u003cbr\u003e\nCheck out [this setup walk through](https://sourabhbajaj.com/mac-setup/Python/virtualenv.html) for additional steps/options \u003cbr\u003e\n\n**Set up config file** \u003cbr\u003e\nCreate a new file at root level of this project called `secret_config.py` \u003cbr\u003e\nTo get fields needed for this config, consult a fellow dev :) but the most important field needed in this config is a `SQLALCHEMY_DATABASE_URI` field that matches a user in your local mySQL instance.\u003cbr\u003e\nExample field: \u003cbr\u003e\n```\nSQLALCHEMY_DATABASE_URI = \"mysql+pymysql://sample_qc_dev_user1:napkinWatermelon1Dev!@localhost:3306/dev_sample_qc\"\n```\n\nHow to create mySQL users and grant privileges (do this within `mysql\u003e` server):\n```\n# CREATE USER 'sample_qc_dev_user'@'localhost' IDENTIFIED BY 'napkinWatermelon1Dev!';\n# GRANT ALL PRIVILEGES ON dev_sample_qc.* TO 'sample_qc_dev_user'@'localhost';\n```\n\n[Look here for more info on how you can add/remove users from your MySQL server](https://sebhastian.com/mysql-error-1396/)\n\n**Install project packages**\u003cbr\u003e\n(this is usually only for the first run) \u003cbr\u003e\n```\n$ pip3 install -r requirements.txt\n```\n\n**Start the python server** \u003cbr\u003e\n```\n$ python3 run.py\n```\nNOTE: You might run into an error that `uwsgi` is not defined. To run locally, you might have to comment out all references to `uwsgi`  in the `qc_report.py` file\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmskcc%2Figo-sample-qc-backend","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmskcc%2Figo-sample-qc-backend","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmskcc%2Figo-sample-qc-backend/lists"}