blob: 187f9614216436c2966a2a5e278ce8169c89bcad (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
|
# Running Virtuoso
We run instances of Virtuoso for our graph databases. Virtuoso is a remarkable software and running some really large databases, including Uniprot
=> https://github.com/openlink/virtuoso-opensource
=> https://www.uniprot.org/sparql/
On Penguin2 virtuoso is running by default as a shepherd servive, see
=> ./shepherd.gmi
```
guix environment --ad-hoc virtuoso-ose -- virtuoso-t -f
```
=> https://git.genenetwork.org/efraim/shepherd-services/src/branch/master/shepherd/init.d/virtuoso.scm penguin2:/home/shepherd/shepherd-services/shepherd/init.d/virtuoso.scm
The database is initialized from 'penguin2:/export/virtuoso/var/lib/virtuoso/db/virtuoso.ini'
## Running a new instance
For testing we want to run a temporary instance. Let's start from the virtuoso.ini file:
```
mkdir -p ~/services/virtuoso
cd services/virtuoso
cp /export/virtuoso/var/lib/virtuoso/db/virtuoso.ini .
```
and edit it to change paths and ports - use non-priviliged ports(!). A full diff is below. Start the server in a screen or tmux (it may ask for creating ./db):
```
penguin2:~/services/virtuoso$ ~/.config/guix/current/bin/guix environment --ad-hoc virtuoso-ose glibc-locales
penguin2:~/services/virtuoso$ /gnu/store/9aqd4jmkafhkdm095hnmxpxzws3ym3wd-virtuoso-ose-7.2.5/bin/virtuoso-t +foreground +configfile virtuoso.ini
03:34:50 HTTP/WebDAV server online at 28890
03:34:50 Server online at 21111 (pid 57078)
```
Now the server should respond to
```
curl localhost:28890/sparql
```
and the admin interface on
```
curl localhost:28890/conductor
```
To use the service from your remote machine use ssh tunnels:
```
ssh -L 28890:127.0.0.1:28890 -f -N myname@penguin2.genenetwork.org
```
and surf to http://localhost:28890/conductor. A good time to change the default password (dba:dba)!
## Uploading data with CURL
To upload RDF I use rapper to validate the data. First delete the existing graph with something like
```
curl -v --digest --user dba:password --verbose --url -G http://localhost:28890/sparql-graph-crud-auth --data-urlencode graph=https://BioHackrXiv.org/graph -X DELETE
```
Next update the graph with
```
curl -v -X PUT --digest -u dba:password -H Content-Type:text/turtle -T test/data/biohackrxiv.ttl -G http://localhost:28890/sparql-graph-crud-auth --data-urlencode graph=https://BioHackrXiv.org/graph
```
Where BioHackrXiv is the name of the graph (in this example). A python version can be found in
=> https://github.com/pubseq/bh20-seq-resource/blob/master/scripts/update_virtuoso/check_for_updates.py
## Virtuoso.ini
What changed in $HOME/services/virtuoso/virtuoso.ini
```
+DatabaseFile = $HOME/services/virtuoso/db/virtuoso.db
+ErrorLogFile = $HOME/services/virtuoso/db/virtuoso.log
+LockFile = $HOME/services/virtuoso/db/virtuoso.lck
+TransactionFile = $HOME/services/virtuoso/db/virtuoso.trx
+xa_persistent_file = $HOME/services/virtuoso/db/virtuoso.pxa
+DatabaseFile = $HOME/services/virtuoso/db/virtuoso-temp.db
+TransactionFile = $HOME/services/virtuoso/db/virtuoso-temp.trx
-ServerPort = 1111
+ServerPort = 21111
+NumberOfBuffers = 340000
+MaxDirtyBuffers = 250000
+ServerPort = 28890
+ServerRoot = $HOME/services/virtuoso/vsp
```
|
