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| -rw-r--r-- | topics/systems/virtuoso.gmi | 49 |
1 files changed, 49 insertions, 0 deletions
diff --git a/topics/systems/virtuoso.gmi b/topics/systems/virtuoso.gmi index 1a6b8b9..e9d841d 100644 --- a/topics/systems/virtuoso.gmi +++ b/topics/systems/virtuoso.gmi @@ -153,3 +153,52 @@ When virtuoso has just been started up with a clean state (that is, the virtuoso =>https://github.com/genenetwork/dump-genenetwork-database/commit/8f60fde7f5499e5ffe352d7ae98a2de34a91b89f Retry uploading to virtuoso (commit from dump-genenetwork-database repo) formerly (https://git.genenetwork.org/arunisaac/dump-genenetwork-database/commit/8f60fde7f5499e5ffe352d7ae98a2de34a91b89f) + +## Dumping data from a MySQL database + +To dump data into a ttl file, first make sure that you are in the guix environment in the "dump-genenetwork-database" repository + +=> https://github.com/genenetwork/dump-genenetwork-database/ Dump Genenetwork Database + +Next, drop into a development environment with: + +``` +$ guix shell +``` + +Build the sources: + +``` +$ make +``` + +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. + +``` +((sql-username . "root") + (sql-password . "root") + (sql-database . "db_webqtl_s") + (sql-host . "localhost") + (sql-port . 3306) + (virtuoso-port . 8891) + (virtuoso-username . "dba") + (virtuoso-password . "dba") + (sparql-scheme . http) + (sparql-host . "localhost") + (sparql-port . 8892)) +``` + +Then, to dump the database to \~/data/dump, run: + +``` +$ ./pre-inst-env ./dump.scm conn.scm ~/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. + +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. + +``` +$ rapper --input turtle --count ~/data/dump/dump.ttl +$ ./pre-inst-env ./load-rdf.scm conn.scm ~/data/dump/dump.ttl +``` |