{"id":23032995,"url":"https://github.com/jervenbolleman/sapfhir-cli","last_synced_at":"2025-04-02T21:43:00.088Z","repository":{"id":144952218,"uuid":"319753582","full_name":"JervenBolleman/sapfhir-cli","owner":"JervenBolleman","description":"A CLI tool to query GFA1 files with SPARQL","archived":false,"fork":false,"pushed_at":"2024-03-27T20:38:34.000Z","size":40,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-02-08T12:15:31.153Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Java","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/JervenBolleman.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}},"created_at":"2020-12-08T20:30:55.000Z","updated_at":"2022-01-10T13:42:09.000Z","dependencies_parsed_at":null,"dependency_job_id":"5d58f440-86a1-4882-babb-ebed5954d015","html_url":"https://github.com/JervenBolleman/sapfhir-cli","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JervenBolleman%2Fsapfhir-cli","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JervenBolleman%2Fsapfhir-cli/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JervenBolleman%2Fsapfhir-cli/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JervenBolleman%2Fsapfhir-cli/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/JervenBolleman","download_url":"https://codeload.github.com/JervenBolleman/sapfhir-cli/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":246899637,"owners_count":20851893,"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":"2024-12-15T15:56:49.756Z","updated_at":"2025-04-02T21:43:00.042Z","avatar_url":"https://github.com/JervenBolleman.png","language":"Java","funding_links":[],"categories":[],"sub_categories":[],"readme":"# SapFhir-CLI\n\nJoin genomic variation graphs with public data or internal medical data e.g. FHIR.\nby having a FAIR data access, using W3C sparql as a standard protocol.\n\nThis is a command line tool to quickly test the concept.\n\n\n# Building\n\nYou need local checkouts of \n\n[handlegraph4j](https://github.com/JervenBolleman/handlegraph4j)\n[handlegraph4jGFA](https://github.com/JervenBolleman/handlegraph4jGFA)\n[handlegraph4jRDF](https://github.com/JervenBolleman/handlegraph4jRDF)\n[handlegraph4j-simple](https://github.com/JervenBolleman/handlegraph4j-simple)\n[sapfhir](https://github.com/JervenBolleman/sapfhir)\n\nBuild them with maven on java 11+\n\n```\nfor i in handlegraph4j handlegraph4jGFA handlegraph4jRDF handlegraph4j-simple sapfhir\ncd $i\n    mvn install\ncd ..\n```\n\n```\nmvn package\n```\n\n# Run\n\n```\njava -jar target/sapfhir-cli-0.2-SNAPSHOT-jar-with-dependencies.jar \\\n    --gfa ~/git/odgi/test/t.gfa \\\n    -Xmx12g \\\n    \"PREFIX vg:\u003chttp://biohackathon.org/resource/vg#\u003e SELECT ?path WHERE {?path a vg:Path}\"\n```\n\n# Status\n\nThis is a [RDF4j](https://rdf4j.org/) SAIL implementation that can take any handlegraph4j \nimplementation and represent it as a [W3C sparql 1.1](https://www.w3.org/TR/sparql11-query/) endpoint. \n\nIt is believed to be functionally complete.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjervenbolleman%2Fsapfhir-cli","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjervenbolleman%2Fsapfhir-cli","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjervenbolleman%2Fsapfhir-cli/lists"}