From 0c81484eb1d5862f990f6b44ac1df480c3fcc9d9 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Fri, 24 Mar 2023 10:45:54 +0100
Subject: Info on dumping database to RDF

---
 topics/systems/virtuoso.gmi | 47 +++++----------------------------------------
 1 file changed, 5 insertions(+), 42 deletions(-)

(limited to 'topics/systems/virtuoso.gmi')

diff --git a/topics/systems/virtuoso.gmi b/topics/systems/virtuoso.gmi
index f84603f..1665f43 100644
--- a/topics/systems/virtuoso.gmi
+++ b/topics/systems/virtuoso.gmi
@@ -158,49 +158,12 @@ When virtuoso has just been started up with a clean state (that is, the virtuoso
 
 ## 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 -m manifest.scm
-```
-
-Build the sources:
-
-```
-$ make
-```
+See also
 
-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.
+=> ../RDF/genenetwork-sql-database-to-rdf.gmi
 
-```
-((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.
+To dump data into a ttl file, first make sure that you are in the guix environment in the "dump-genenetwork-database" repository
 
-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.
+=> https://github.com/genenetwork/dump-genenetwork-database/ Dump Genenetwork Database
 
-```
-$ rapper --input turtle --count ~/data/dump/dump.ttl
-$ ./pre-inst-env ./load-rdf.scm conn.scm ~/data/dump/dump.ttl
-```
+See the README for instructions.
-- 
cgit v1.2.3