{"id":29639159,"url":"https://github.com/neotomadb/taxoninsertion","last_synced_at":"2025-07-21T20:08:22.252Z","repository":{"id":279701645,"uuid":"939668660","full_name":"NeotomaDB/taxoninsertion","owner":"NeotomaDB","description":"A package to bulk upload taxonomic data (beetles in this case) from Family/genus/species info.","archived":false,"fork":false,"pushed_at":"2025-05-21T21:31:23.000Z","size":39,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":4,"default_branch":"main","last_synced_at":"2025-05-21T21:36:47.000Z","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":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/NeotomaDB.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":"code_of_conduct.md","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":"2025-02-26T23:00:10.000Z","updated_at":"2025-05-21T21:31:26.000Z","dependencies_parsed_at":"2025-02-27T00:29:27.380Z","dependency_job_id":null,"html_url":"https://github.com/NeotomaDB/taxoninsertion","commit_stats":null,"previous_names":["neotomadb/taxoninsertion"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/NeotomaDB/taxoninsertion","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NeotomaDB%2Ftaxoninsertion","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NeotomaDB%2Ftaxoninsertion/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NeotomaDB%2Ftaxoninsertion/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NeotomaDB%2Ftaxoninsertion/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/NeotomaDB","download_url":"https://codeload.github.com/NeotomaDB/taxoninsertion/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NeotomaDB%2Ftaxoninsertion/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":266371486,"owners_count":23918862,"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","status":"online","status_checked_at":"2025-07-21T11:47:31.412Z","response_time":64,"last_error":null,"robots_txt_status":null,"robots_txt_updated_at":null,"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":"2025-07-21T20:08:17.527Z","updated_at":"2025-07-21T20:08:22.242Z","avatar_url":"https://github.com/NeotomaDB.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![NSF-2410965](https://img.shields.io/badge/NSF-2410965-blue.svg)](https://www.nsf.gov/awardsearch/showAward?AWD_ID=2410965\u0026HistoricalAwards=false)\n[![NSF-2410961](https://img.shields.io/badge/NSF-2410961-blue.svg)](https://www.nsf.gov/awardsearch/showAward?AWD_ID=2410961\u0026HistoricalAwards=false)\n\n[![DOI](https://zenodo.org/badge/939668660.svg)](https://doi.org/10.5281/zenodo.15485153)\n\n# Taxon Insertion in Neotoma\n\nThis is a package intended to help support both bulk and individual taxon insertion in Neotoma.\n\nWhat the package does:\n\n1. Connects to the Neotoma Paleoecology Database (both main and tank).\n2. Takes a taxon name and checks the name with GBIF and NCBI.\n3. Finds the appropriate insertion point within Neotoma for insertion.\n4. Returns a set of rows to be inserted into Neotoma to support the new taxonname.\n5. Inserts new rows into Neotoma.\n6. Supports rollback and commit features.\n\n## Contributors\n\n* [Simon Goring](http://goring.org): University of Wisconsin - Madison [![orcid](https://img.shields.io/badge/orcid-0000--0002--2700--4605-brightgreen.svg)](https://orcid.org/0000-0002-2700-4605)\n\n## Using this Repository\n\nSecrets to connect to the database are in an \"ignored\" file named `.env`. It should have the format:\n\n```bash\nDBAUTH={\"host\":\"localhost\",\"port\":5432,\"user\":\"postgres\",\"password\":\"postgres\",\"dbname\":\"neotoma\"}\n```\n\nThe repository uses the `uv` package manager to help manage dependencies and ensure a stable development platform. To use this repository, first clone the repository locally, and then, run `uv init` to install all neccessary packages. Once the packages are installed, the script `testing_beetles.py` can be run using `uv run testing_beetles.py`.\n\nThe script may be slow to run because it must interact with the Neotoma database (and could interact with GBIF and NCBI if wanted).\n\n## Current Expected Input and Output\n\nThe script in this repository is designed to work with a CSV file provided by the [BUGSCep](https://bugscep.com/) research data group. That CSV has the format:\n\n```csv\nCODE,FAMILY,GENUS,SPECIES,AUTHORITY,epithet,neotoma_path,gbifid,ncbi_id,taxonRank,taxonomicStatus,ncbi_lineage_names\n```\n\nThe `testing_beetles.py` file parses this document row by row and returns a similar CSV, with the additional columns `familyid`, `genusid`, and `speciesid`, with the associated Neotoma taxon IDs.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fneotomadb%2Ftaxoninsertion","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fneotomadb%2Ftaxoninsertion","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fneotomadb%2Ftaxoninsertion/lists"}