A community-driven list of Specify integrations, software, and resources developed by the community.
Please see the official Specify code repositories at https://github.com/specify.
Taxa Tree Generator - A tool for creating taxon tree files for import via the Specify WorkBench based on source data from GBIF, WoRMS, Catalogue of Life, and ITIS. It is especially useful during conversions. Users often request trees along with a list of names, such as families, genera, or species, and we use that list to select the appropriate names and ranks.
Specify7-Api-Demo by @melton-jason: Currently in Specify 7, there is not an easy way using the frontend interface (or the WorkBench component) to mass-import synonymized Taxa. This demo aims to create an application that reads a CSV file with taxonomic information to upload new taxa to a Specify 7 instance and update existing taxa with the latest data from the file.
Sp7APIToolbox by NHMDenmark - Aimes to gather different code classes, named tools, for interacting with the Specify7 API allowing for bulk actions. For the time being it will run from a command line and can be run directly in a development environment. Pending needs, a fully functional release may be published eventually, perhaps even with a graphical user interface.
SpecifyUtilities: A mishmash of scripts developed by the Natural Science Collections Facility for doing various things in Specify, including batch copying queries from one user to several others, extracting data in Darwin Core format, updating catalog numbers, updating parasite hosts, updating synonyms, etc. See importBRAHMS8Checklist for importing a flat taxon file and constructing full names for plants. Scripts DO NOT use the API, so beware!
specify-sort-views: Sometimes the XML files that define the Specify forms are a bit untidy, so this formats and sorts the views/viewdefs alphabetically to make them easier to work with. Nice to do this with a new Specify instance before starting on form customization.
specify-sql: a set of SQL queries I used to quickly get information directly from the database while troubleshooting, migrating, etc.
specify-api-js-client: An OLD repo for getting started with the Specify API, mainly getting the access token, in Javascript. May well no longer work...
Specify 7 Test Panel - A powerful utility to manage and deploy a cluster of Specify 7 instances for testing with automatic deployment, authentication and a test panel for setting configuration. Used internally at Specify.
nca-data-migrator:
A script written to migrate a relatively large collection (> 80 000 collection object records) to Specify,
because the workbench was just too slow. Intended for initial migration only, does not use the API. On a
local instance migrates all records in ~4 minutes. Can be tweaked to work with other datasets by updating
mappings.py, although you'll need to add additional table classes under db and update importdata.py
if you're importing data into additional tables. Some scripts are a bit messy and may not work, e.g.
updatesynonyms, which was intended to use World Spider Catalog, but was abandoned in dispair when it was
discovered that WSC taxon identifiers are moved when names are synonymized. Please CLONE and not FORK
this repo for migrations on other collections.