Dump genenetwork database
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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


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.


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.


See bugs and tasks in BUGS.org.