From b7c5f2aed32a7edc19fbe716f3415e86c39705af Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Wed, 7 Dec 2022 15:54:14 -0600
Subject: Virtuoso updates

---
 topics/systems/update-production-tux01.gmi | 51 ++++++++++++++++++++++++++++++
 topics/systems/virtuoso.gmi                |  2 +-
 2 files changed, 52 insertions(+), 1 deletion(-)
 create mode 100644 topics/systems/update-production-tux01.gmi

(limited to 'topics/systems')

diff --git a/topics/systems/update-production-tux01.gmi b/topics/systems/update-production-tux01.gmi
new file mode 100644
index 0000000..ea99527
--- /dev/null
+++ b/topics/systems/update-production-tux01.gmi
@@ -0,0 +1,51 @@
+# Update production
+
+In this document we describe the specific steps required to update production.
+
+# Virtuoso RDF
+
+Once we have an RDF dump of the database in a file 'data.ttl' we can test it for correctness with:
+
+```
+tux01:~$ rapper --input turtle --count  dump.ttl
+rapper: Parsing URI file:///home/wrk/dump.ttl with parser turtle
+rapper: Parsing returned 652395 triples
+```
+
+Test the virtuoso endpoint with
+
+```
+curl http://localhost:8892/sparql
+```
+
+Then, upload it to a virtuoso SPARQL endpoint running at port 8892
+
+```
+curl -v -X PUT --digest -u dba:password -T data.ttl -G http://localhost:8892/sparql-graph-crud-auth --data-urlencode graph=http://genenetwork.org
+```
+
+To test
+
+```
+curl "http://localhost:8892/sparql?default-graph-uri=&query=prefix+gn%3A+%3Chttp%3A%2F%2Fgenenetwork.org%2F%3E+%0D%0A%0D%0ASELECT+distinct+*+WHERE+%7B%3Fu++gn%3AbinomialName+%3Fo%7D&format=application%2Fsparql-results%2Bjson&timeout=0&signal_void=on"
+```
+
+and you should see the data:
+
+```js
+      {
+        "u": {
+          "type": "uri",
+          "value": "http://genenetwork.org/inbredSet_srxshrspf2"
+        },
+        "o": {
+          "type": "literal",
+          "value": "UIOWA SRxSHRSP F2"
+        }
+      },
+      ...
+```
+
+For more information see
+
+=> ./virtuoso.gmi Virtuoso setup documentation
diff --git a/topics/systems/virtuoso.gmi b/topics/systems/virtuoso.gmi
index 3f608b5..bdfd14e 100644
--- a/topics/systems/virtuoso.gmi
+++ b/topics/systems/virtuoso.gmi
@@ -134,7 +134,7 @@ We recap the same here.
 When uploading data, the virtuoso server often does not report errors properly. It simply freezes up. So, it is very helpful to validate your RDF before uploading. For this, use rapper from the raptor2 package. To validate data.ttl, a turtle file, run
 ```
 rapper --input turtle --count data.ttl
-rapper: Parsing URI file:///home/wrk/dump.ttl with parser turtle
+rapper: Parsing URI file: data.ttl with parser turtle
 rapper: Parsing returned 652395 triples
 ```
 Then, upload it to a virtuoso SPARQL endpoint running at port 8892
-- 
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