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WormBase / pseudoace

Modelling the WormBase ACeDB database in datomic.
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Feature/patching #80

Closed mgrbyte closed 4 years ago

mgrbyte commented 4 years ago

This adds the ability to patch the datomic database from ACeDB file input as per the PATCHES directory on the FTP server.

There are two new CLI sub-commands:

Examples of running:

clojure -A:datomic-pro -m pseudoace.cli apply-patches --url datomic:ddb-local://localhost:8000/wormbase/WS266 --patches-ftp-url ftp://ftp.ebi.ac.uk/pub/databases/wormbase/releases/WS270/acedb/PATCHES -v

I've also updated this repository to use clojure CLI tools (deps.edn) for everything, inline with how most other clojure projects are going; accordingly the release script (scripts/bundle-release.sh) and the README have changed for deploying and running tests.

Documentation/example to be added to this repository's wiki for patching.