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Diffstat (limited to 'topics/systems')
-rw-r--r-- | topics/systems/virtuoso.gmi | 68 |
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diff --git a/topics/systems/virtuoso.gmi b/topics/systems/virtuoso.gmi index b85ab86..548481b 100644 --- a/topics/systems/virtuoso.gmi +++ b/topics/systems/virtuoso.gmi @@ -170,6 +170,74 @@ guix shell -N virtuoso-ose -m manifest.scm -- ./pre-inst-env ./load-rdf.scm conn => https://github.com/genenetwork/dump-genenetwork-database/blob/master/conn.scm Example conn.scm +### Bulk Loading Data + +Virtuoso has access to the folder: /export/data/genenetwork-virtuoso/. As such, place all the turtle files for bulk uploads here. To bulk load data: + +First make sure that all the data is deleted: + +``` +$ isql +SQL> DELETE FROM rdf_quad WHERE g = iri_to_id('http://genenetwork.org'); +``` + +Use isql to register all the title files: + +``` +SQL> ld_dir('/var/lib/data', '*.ttl', 'http://genenetwork.org'); +``` + + +You can check the table DB.DBA.load_list to check the list of datasets registered for loading.: + +``` +SQL> SELECT * FROM DB.DBA.load_list; +``` + +In case you want to empty the list: + +``` +DELETE FROM DB.DBA.load_list WHERE ll_file='*.ttl'; +``` + +Perform the bulk load of all data by running: + +``` +SQL> rdf_loader_run(); +``` + +Commit the bulk loaded data to the Virtuoso database file by running: + +``` +checkpoint; +``` + +Run a query to make sure that indeed you have loaded data E.g. + +``` +SPARQL +PREFIX gn: <http://genenetwork.org/id/> + +SELECT * FROM <http://genenetwork.org> WHERE { +gn:Mus_musculus ?p ?o. +}; +``` + +In case you want to get a list of all queries: + +``` +SPARQL +SELECT DISTINCT ?g + WHERE { GRAPH ?g {?s ?p ?o} } +ORDER BY ?g; +``` + +Other resources: + +=> https://vos.openlinksw.com/owiki/wiki/VOS/VirtBulkRDFLoader Bulk Loading RDF Source Files into one or more Graph IRIs + +=> https://vos.openlinksw.com/owiki/wiki/VOS/VirtBulkRDFLoaderExampleSingle VOS.VirtBulkRDFLoaderExampleSingle + ## Dumping to RDF from the GeneNetwork MySQL database See also |