{"id":21881220,"url":"https://github.com/wtsi-hgi/genestack-uploader","last_synced_at":"2026-04-18T19:31:58.117Z","repository":{"id":40955328,"uuid":"413893201","full_name":"wtsi-hgi/genestack-uploader","owner":"wtsi-hgi","description":"A HTTP server providing an API and a frontend for easy uploading to Genestack","archived":false,"fork":false,"pushed_at":"2023-02-16T04:42:23.000Z","size":466,"stargazers_count":1,"open_issues_count":6,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-10-29T21:49:54.647Z","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":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/wtsi-hgi.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","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":"2021-10-05T16:20:37.000Z","updated_at":"2022-07-22T11:14:45.000Z","dependencies_parsed_at":"2025-03-22T00:44:02.355Z","dependency_job_id":null,"html_url":"https://github.com/wtsi-hgi/genestack-uploader","commit_stats":null,"previous_names":[],"tags_count":7,"template":false,"template_full_name":null,"purl":"pkg:github/wtsi-hgi/genestack-uploader","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/wtsi-hgi%2Fgenestack-uploader","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/wtsi-hgi%2Fgenestack-uploader/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/wtsi-hgi%2Fgenestack-uploader/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/wtsi-hgi%2Fgenestack-uploader/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/wtsi-hgi","download_url":"https://codeload.github.com/wtsi-hgi/genestack-uploader/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/wtsi-hgi%2Fgenestack-uploader/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":31982539,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-18T17:30:12.329Z","status":"ssl_error","status_checked_at":"2026-04-18T17:29:59.069Z","response_time":103,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":"2024-11-28T09:18:11.793Z","updated_at":"2026-04-18T19:31:58.080Z","avatar_url":"https://github.com/wtsi-hgi.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Genestack Uplaoder\n\nA HTTP server providing an API and a frontend for easy uploading to Genestack\n\n## Build \u0026 Run Docker Image -- by Fei\n\n1. If any change is applied, version number (`config.py`) should be updated.\n\n```\nVERSION = \"2.4\"\n```\n\n2. `hgi-docker.sh` can build dev and production images automatically with right `frontend/.env` files. \n\nIt creates `mercury/genestack-uploader:2.4.dev` and `mercury/genestack-uploader:2.4.prod` with the appropriate configuration in the image.\n```\nsudo ./hgi-docker.sh 2.4\n```\n\nCheck built imgages\n```\nsudo docker images\nREPOSITORY                   TAG        IMAGE ID       CREATED          SIZE\nmercury/genestack-uploader   2.4.prod   ff7989cfc80c   14 minutes ago   1.3GB\nmercury/genestack-uploader   2.4.dev    2cdf3ab5dbe3   14 minutes ago   1.3GB\n\n```\n\n3. push the image to DockerHub\n\nLog in docker with mercury first. (check secrets). Then push.\n\n```\nsudo docker login\nsudo docker push mercury/genestack-uploader:2.4.dev\nsudo docker push mercury/genestack-uploader:2.4.prod\n```\n\n4. log in dev and production (details on Confluence Swarm Page)\n\n5. Update running image\n\n```\ndocker pull mercury/genestack-uploader:2.4.dev\ndocker service scale mystack_genestack-uploader=1\ndocker service scale mystack_genestack-uploader=0\ndocker service update --image=mercury/genestack-uploader:2.4.dev mystack_genestack-uploader \ndocker service scale mystack_genestack-uploader=1\n```\n\n## Running with Docker 🐳 -- by Michael\n\n1. Update `frontend/.env` and `config.py` if needed. (See `docs/spec/main-spec-updates/1.md` for discussion about base URL paths.)\n\n2. Build the image, i.e. \n\n```\ndocker build -t mercury/genestack-uploader:0.1.dev .\n```\n\nThe tagging scheme used on this project is `mercury/genestack-uploader:X.Y.{prod|dev}`, where X.Y is the version number, and the final tag is `prod` or `dev`, describing which URL is specified in `.env` and `config.py`. (This is also described in more detail in `docs/spec/main-spec-updates/1.md`.)\n\nIf deploying in the HGI environments, the script `hgi-docker.sh`, passing the argument of the verison number will build the images as we need, for example `./hgi-docker.sh 2.0` will create `mercury/genestack-uploader:2.0.dev` and `mercury/genestack-uploader:2.0.prod` with the appropriate configuration in the image.\n\n3. Run the image. You must:\n    - provide the env variable `GSSERVER` with a value of either `qc` or `default`\n    - link to config files `/root/.genestack.cfg` and `/root/.s3cfg`\n    - link SSH key files to `/root/.ssh/id_rsa_genestack` and `/root/.ssh/id_rsa_genestack.pub`\n\nOptional Environment Variables:\n    - `JOB_EXPIRY_HOURS`: defaults to `168` (hours in a week) - this is how long a job should be kept after it has completed for it to be accessed using the `/jobs/{uuid}` API endpoint\n    - `LOG_LEVEL`: one of `DEBUG`, `INFO`, `WARNING`, `ERROR`, `CRITICAL` (defaults to `INFO`) - the minimum level of logs to be reported\n\nThe app runs on port 5000 on a Docker network, so that can be used to forward it, such as in a nginx container.\n\nTo test, you can also expose port 5000, i.e.\n\n```\ndocker run -p 80:5000 -e GSSERVER=default -v /home/ubuntu/genestack-uploader/configs:/root -d --name genestack-uploader mercury/genestack-uploader:0.1.dev\n```\n\n## Version Numbering -- by Michael\n\nThere are two important version numbers to keep track of.\n\n- The version number of the `uploadtogenestack` package\n    - This is updated in the package's `setup.py` file, and is given a tag on GitLab\n    - This tag number is then used in this repositories Dockerfile to install the right version\n- The version number of this web app\n    - This is updated in `config.py` and is also reflected in the Docker image tag\n\nEnsure that these are kept up to date, as it really helps find bugs when you know which versions of each a particular image is running. The version numbers are displayed at the bottom of the homepage.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fwtsi-hgi%2Fgenestack-uploader","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fwtsi-hgi%2Fgenestack-uploader","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fwtsi-hgi%2Fgenestack-uploader/lists"}