Dump genenetwork database
You can not select more than 25 topics Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
Arun Isaac d78b6dea84
Eval macro helper functions at macro expansion time.
4 weeks ago
dump Add dumped? field to <column> type. 1 month ago
.dir-locals.el Introduce syntax-let abstraction. 1 month ago
BUGS.org BUGS: Add "Dump table and field annotations to RDF" bug. 1 month ago
README.org README: Execute dump.scm directly without invoking guile. 1 month ago
dump.scm Eval macro helper functions at macro expansion time. 4 weeks ago
guix.scm Add guile-sparql to Guix manifest. 1 month ago
pre-inst-env Add pre-inst-env. 1 month ago
tests.scm Add tests. 1 month ago
visualize-schema.scm Make visualize-schema executable. 1 month ago

README.org

The GeneNetwork database is being migrated from a relational database to a plain text and RDF database. This repository contains code to dump the relational database to plain text.

Using

Drop into a development environment with

  $ guix shell -m guix.scm

Describe the database connection parameters in a file conn.scm file as shown below. Take care to replace the placeholders within angle brackets with the appropriate values.

  ((username . "<username-here>")
   (password . "<password-here>")
   (database . "<database-name-here>")
   (host . "<hostname-here>")
   (port . <port-here>))

Then, to dump the database, run

  $ ./pre-inst-env ./dump.scm

The database will be dumped to ~/data/dump/. Make sure there is enough free space! It's best to dump the database on penguin2 where disk space and bandwidth are not significant constraints.

Contributing

See bugs and tasks in BUGS.org.