{"id":22313867,"url":"https://github.com/ctb/2021-sourmash-jsonrpc","last_synced_at":"2025-07-06T20:07:27.848Z","repository":{"id":66659492,"uuid":"380815155","full_name":"ctb/2021-sourmash-jsonrpc","owner":"ctb","description":"A simple JSON RPC client/server setup for sourmash databases","archived":false,"fork":false,"pushed_at":"2021-06-27T19:13:20.000Z","size":43,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"latest","last_synced_at":"2025-06-10T23:05:13.516Z","etag":null,"topics":["sourmash"],"latest_commit_sha":null,"homepage":"","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/ctb.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":"2021-06-27T18:48:23.000Z","updated_at":"2022-02-06T12:11:41.000Z","dependencies_parsed_at":"2023-03-27T11:47:07.762Z","dependency_job_id":null,"html_url":"https://github.com/ctb/2021-sourmash-jsonrpc","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/ctb/2021-sourmash-jsonrpc","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ctb%2F2021-sourmash-jsonrpc","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ctb%2F2021-sourmash-jsonrpc/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ctb%2F2021-sourmash-jsonrpc/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ctb%2F2021-sourmash-jsonrpc/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ctb","download_url":"https://codeload.github.com/ctb/2021-sourmash-jsonrpc/tar.gz/refs/heads/latest","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ctb%2F2021-sourmash-jsonrpc/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":263966170,"owners_count":23536814,"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":["sourmash"],"created_at":"2024-12-03T22:08:25.204Z","updated_at":"2025-07-06T20:07:27.816Z","avatar_url":"https://github.com/ctb.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# a simple sourmash search server, plus client plugin\n\nA simple (and still quite hacky) sourmash client/server search.\n\nSee\n[sourmash#1484](https://github.com/sourmash-bio/sourmash/issues/1484)\nfor some info.\n\n## Quickstart\n\nYou'll need to have sourmash installed already, using the branch from\n[PR #1644](https://github.com/sourmash-bio/sourmash/pull/1644).\n\nThen, run the following.\n\n### Installation:\n\n```\n# install necessary packages\npip install jsonrpcserver\npip install \"jsonrpcclient[requests]\"\n```\n\n### Server side:\n\nStart a server on localhost:5000, running in the background:\n```\nexport PYTHONPATH=.\n./sourmash-server ./podar-ref/1.sig.gz \u0026\n```\n\n### Client side\n\n```\nexport PYTHONPATH=.\nsourmash search ./podar-ref/1.sig.gz http://localhost:5000/\n```\n\nand then you should see\n```\n== This is sourmash version 4.1.3.dev16+g9dbd8b5. ==\n== Please cite Brown and Irber (2016), doi:10.21105/joss.00027. ==\n\nselecting specified query k=31\nloaded query: CP001941.1 Aciduliprofundum bo... (k=31, DNA)\nloaded 1 databases.\n\n1 matches:\nsimilarity   match\n----------   -----\n100.0%       CP001941.1 Aciduliprofundum boonei T469, complete genome\n```\n\n## Notes\n\n\n### Some details\n\n* Over in\n  [PR #1644](https://github.com/sourmash-bio/sourmash/pull/1644), we\n  inject a \"remote index\" loader in sourmash_args. That's what handles the\n  http URL on the command line. Ugly, but works for now :).\n* The sourmash-server code can serve any sourmash database - so, SBT,\n  LCA, pathlist, zipfile, directory, or signature file. Use a pathlist\n  if you want to serve multiple indexes as a single database.\n  \n### Limitations:\n\n* Only the 'find' method works, so 'search' and 'gather' and 'prefetch' but\n  not much else.\n* Signature retrieval doesn't work, except with search.\n* Picklists do not yet work, either.\n* One big and invisible gotcha for 'gather' is that the prefetch stage is\n  done remotely, and then the gather is done locally. This is straightforward\n  to fix.\n* Only 50 results are returned at the moment.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fctb%2F2021-sourmash-jsonrpc","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fctb%2F2021-sourmash-jsonrpc","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fctb%2F2021-sourmash-jsonrpc/lists"}