{"id":21318780,"url":"https://github.com/sydney-informatics-hub/gen3-data-dictionary-dev","last_synced_at":"2025-03-15T22:14:53.018Z","repository":{"id":237622857,"uuid":"788756991","full_name":"Sydney-Informatics-Hub/Gen3-data-dictionary-dev","owner":"Sydney-Informatics-Hub","description":null,"archived":false,"fork":false,"pushed_at":"2024-08-16T01:35:39.000Z","size":172,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":5,"default_branch":"main","last_synced_at":"2025-01-22T11:12:55.346Z","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/Sydney-Informatics-Hub.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":"2024-04-19T02:50:13.000Z","updated_at":"2024-08-16T01:35:41.000Z","dependencies_parsed_at":"2024-06-27T04:54:00.555Z","dependency_job_id":"cbe7776f-aaa2-4d9e-825a-36f061ca9021","html_url":"https://github.com/Sydney-Informatics-Hub/Gen3-data-dictionary-dev","commit_stats":null,"previous_names":["sydney-informatics-hub/gen3-data-dictionary-dev"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Sydney-Informatics-Hub%2FGen3-data-dictionary-dev","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Sydney-Informatics-Hub%2FGen3-data-dictionary-dev/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Sydney-Informatics-Hub%2FGen3-data-dictionary-dev/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Sydney-Informatics-Hub%2FGen3-data-dictionary-dev/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Sydney-Informatics-Hub","download_url":"https://codeload.github.com/Sydney-Informatics-Hub/Gen3-data-dictionary-dev/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243796741,"owners_count":20349264,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","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":"2024-11-21T19:22:33.721Z","updated_at":"2025-03-15T22:14:52.997Z","avatar_url":"https://github.com/Sydney-Informatics-Hub.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Gen3-data-dictionary-dev\n\nThis repository contains dev notes and instructions for how to create and manage a Gen3 data dictionary using the [Australian BioCommons Gen3 Schema Dev tools](https://github.com/AustralianBioCommons/gen3schemadev) and [UMCCR-dictionary](https://github.com/AustralianBioCommons/umccr-dictionary) for USyd use cases.  \n\n## Set up and tooling\n\nRun notebooks provided here with [PyCharm community edition](https://www.jetbrains.com/pycharm/download) or VScode. \n\n## Generate the schema DAG\n\nSee [USyd gen3 data dictionary repo](https://github.com/Sydney-Informatics-Hub/usyd-gen3-data-dictionary). \n\n1. Get a copy of the code \n\n```bash\ngit submodule add https://github.com/Sydney-Informatics-Hub/usyd-gen3-data-dictionary usyd-gen3-data-dictionary\ngit submodule add https://github.com/AustralianBioCommons/gen3schemadev.git gen3schemadev \n```\n\n2. Launch containers. Need to have Docker desktop installed to run the following commands: \n\n```bash\ncd ./usyd-gen3-data-dictionary \u0026\u0026 git pull\nmake pull # pull updates/dependencies for project\nmake up # spin up containers \nmake ps # display status of containers\n```\n\n3. Refactor the yamls into json \n\n```bash \ncp -r ../dictionary/thyroid dictionary/.\nmake compile program=thyroid # write schema to json \nmake validate program=thyroid # do validation checks\n```\n\n4. Generate and visualise the DAG \n\n```bash\nopen http://localhost:8080/#schema/thyroid.json\n```","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsydney-informatics-hub%2Fgen3-data-dictionary-dev","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsydney-informatics-hub%2Fgen3-data-dictionary-dev","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsydney-informatics-hub%2Fgen3-data-dictionary-dev/lists"}