diff options
| -rw-r--r-- | README.md | 17 | ||||
| -rw-r--r-- | conn.scm | 4 |
2 files changed, 10 insertions, 11 deletions
@@ -3,9 +3,7 @@ badge](https://ci.genenetwork.org/badge/dump-genenetwork-database-tests.svg)](ht [](https://ci.genenetwork.org/jobs/dump-genenetwork-database) -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. +This repository contains code to dump the metadata in the GeneNetwork relational database to RDF. It requires a connection to a SQL server. # Using @@ -15,6 +13,12 @@ Drop into a development environment with $ guix shell -m manifest.scm ``` +If the path is not picked up add + +``` +export PATH=$GUIX_ENVIRONMENT/bin:$PATH +``` + Build the sources. ``` shell @@ -79,17 +83,12 @@ Then, to dump the database to \~/data/dump, run ``` shell $ guix shell -m manifest.scm -- ./pre-inst-env ./examples/dump-dataset-metadata.scm conn.scm ~/data/dump-data/ ``` - -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. - ## Validate and load dump Then, validate the dumped RDF using `rapper` and load it into virtuoso. This will load the dumped RDF into the `http://genenetwork.org` graph, and will delete all pre-existing data -in that graph. +in that graph (FIXME) ``` shell $ guix shell -m manifest.scm -- rapper --input turtle --count ~/data/dump/dump.ttl @@ -1,11 +1,11 @@ ((sql-username . "webqtlout") - (sql-password . "webqtlout") + (sql-password . "*") (sql-database . "db_webqtl") (sql-host . "localhost") (sql-port . 3306) (virtuoso-port . 8891) (virtuoso-username . "dba") - (virtuoso-password . "dba") + (virtuoso-password . "*") (sparql-scheme . http) (sparql-host . "localhost") (sparql-port . 8892) |