diff options
Diffstat (limited to 'issues')
| -rw-r--r-- | issues/set-up-virtuoso-on-production.gmi | 50 |
1 files changed, 30 insertions, 20 deletions
diff --git a/issues/set-up-virtuoso-on-production.gmi b/issues/set-up-virtuoso-on-production.gmi index 14a8575..a4dd21c 100644 --- a/issues/set-up-virtuoso-on-production.gmi +++ b/issues/set-up-virtuoso-on-production.gmi @@ -27,17 +27,17 @@ Note where the virtuoso data directory is mapped from the "production.sh" script ### Generating the TTL Files -* Run "generate-ttl-files" to generate the TTL files: +=> https://git.genenetwork.org/gn-transform-databases/tree/generate-ttl-files.scm Run "generate-ttl-files" to generate the TTL files: ``` time guix shell guile-dbi -m manifest.scm -- ./generate-ttl-files.scm --settings conn-dev.scm --output /export2/guix-containers/genenetwork-development/var/lib/virtuoso --documentation /tmp/doc-directory ``` -=> https://git.genenetwork.org/gn-transform-databases/tree/generate-ttl-files.scm generate-ttl-files.scm +* [Recommended] Alternatively, copy over the TTL files (in Tux02) to the correct shared directory in the container: -* (Recommended) Alternatively, copy over the TTL files (in Tux02) to the correct shared directory in the container ("--share=/export2/guix-containers/genenetwork-development/var/lib/virtuoso=/var/lib/virtuoso"): - -> cp /home/bonfacem/ttl-files/*ttl /export2/guix-containers/genenetwork/var/lib/virtuoso/ +``` +cp /home/bonfacem/ttl-files/*ttl /export2/guix-containers/genenetwork/var/lib/virtuoso/ +``` ### Loading the TTL Files @@ -53,23 +53,28 @@ time guix shell guile-dbi -m manifest.scm -- ./generate-ttl-files.scm --settings * Get into isql: -> guix shell virtuoso-ose -- isql 7892 - +``` +guix shell virtuoso-ose -- isql 7892 +``` * Make sure that no pre-existing files exist in "DB.DBA.LOAD_LIST": -> SQL> select * from DB.DBA.LOAD_LIST; -> SQL> delete from DB.DBA.load_list; - +``` +SQL> select * from DB.DBA.LOAD_LIST; +SQL> delete from DB.DBA.load_list; +``` * Delete the genenetwork graph: -> SQL> DELETE FROM rdf_quad WHERE g = iri_to_id('http://genenetwork.org'); +``` +SQL> DELETE FROM rdf_quad WHERE g = iri_to_id('http://genenetwork.org'); +``` * Load all the TTL files (This takes some time): -> SQL> ld_dir('/var/lib/virtuoso', '*.ttl', 'http://genenetwork.org'); -> SQL> rdf_loader_run(); -> SQL> CHECKPOINT; - +``` +SQL> ld_dir('/var/lib/virtuoso', '*.ttl', 'http://genenetwork.org'); +SQL> rdf_loader_run(); +SQL> CHECKPOINT; +``` * Verify you have some RDF data by running: ``` @@ -93,18 +98,23 @@ SELECT * WHERE { > SPARQL_ENDPOINT="http://localhost:7893/sparql" -## Generating the Xapian Index +## HOWTO: Generating the Xapian Index * Make sure you are using the correct guix profile or that you have your PYTHONPATH pointing to the GN3 repository. * Generate the Xapian Index using "genenetwork3/scripts/create-xapian-index" against the correct output directory (The build takes around 71 minutes on an SSD Drive): -> time python index-genenetwork create-xapian-index /export/data/genenetwork-xapian/ mysql://<user>:<password>@localhost/db_webqtl http://localhost:7893/sparql - +``` +time python index-genenetwork create-xapian-index \ +/export/data/genenetwork-xapian/ \ +mysql://<user>:<password>@localhost/db_webqtl \ +http://localhost:7893/sparql +``` * After the build, you can verify that the index works by: -> guix shell xapian -- xapian-delve /export/data/genenetwork-xapian/ - +``` +guix shell xapian -- xapian-delve /export/data/genenetwork-xapian/ +``` * Update GN3 configuration files to point to the right Xapian path: > XAPIAN_DB_PATH="/export/data/genenetwork-xapian/" |