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| -rw-r--r-- | README.md | 40 |
1 files changed, 38 insertions, 2 deletions
@@ -24,7 +24,13 @@ with the appropriate values. (sql-password . "<sql-password-here>") (sql-database . "<sql-database-name-here>") (sql-host . "<sql-hostname-here>") - (sql-port . <sql-port-here>)) + (sql-port . <sql-port-here>) + (virtuoso-port . <virtuoso-port-here>) + (virtuoso-username . "<virtuoso-username-here>") + (virtuoso-password . "<virtuoso-password-here>") + (sparql-scheme . <sparql-endpoint-scheme-here>) + (sparql-host . "<sparql-endpoint-hostname-here>") + (sparql-port . <sparql-endpoint-port-here>)) ``` Then, to dump the database to \~/data/dump, run @@ -34,7 +40,37 @@ $ ./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. +penguin2 where disk space and bandwidth are not significant +constraints. + +Then, load the dumped RDF into virtuoso. This will load the dumped RDF +into the `http://genenetwork.org` graph, and will delete all +pre-existing data in that graph. + +``` shell +$ ./pre-inst-env ./load-rdf.scm conn.scm ~/data/dump/dump.ttl +``` + +Now, you may query virtuoso to visualize the SQL and RDF schema. + +``` shell +$ ./pre-inst-env ./visualize-schema.scm conn.scm +``` + +This will output graphviz dot files `sql.dot` and `rdf.dot` describing +the schema. Render them into SVG images like so. + +``` shell +$ dot -Tsvg -osql.svg sql.dot +$ dot -Tsvg -ordf.svg rdf.dot +``` + +Or, peruse them interactively with `xdot`. + +``` shell +$ xdot sql.dot +$ xdot rdf.dot +``` # Contributing |