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Diffstat (limited to 'README.md')
| -rw-r--r-- | README.md | 24 |
1 files changed, 14 insertions, 10 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 @@ -74,22 +78,22 @@ Here's a sample *conn.scm*. ## Dump the database -Then, to dump the database to \~/data/dump, run +Then, to dump the database to \~/data/dump, run inside shell -``` shell -$ guix shell -m manifest.scm -- ./pre-inst-env ./examples/dump-dataset-metadata.scm conn.scm ~/data/dump-data/ +```sh +./pre-inst-env ./examples/dump-species-metadata.scm ../conn.scm ~/tmp ``` -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. +``` shell +$ guix shell -m manifest.scm -- ./pre-inst-env ./examples/dump-dataset-metadata.scm ../conn.scm ~/tmp +``` ## 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 |