diff options
Diffstat (limited to 'topics/systems')
-rw-r--r-- | topics/systems/fallbacks-and-backups.gmi | 6 | ||||
-rw-r--r-- | topics/systems/gn-services.gmi | 8 | ||||
-rw-r--r-- | topics/systems/sheepdog.gmi | 5 | ||||
-rw-r--r-- | topics/systems/shepherd.gmi | 14 | ||||
-rw-r--r-- | topics/systems/virtuoso.gmi | 13 |
5 files changed, 40 insertions, 6 deletions
diff --git a/topics/systems/fallbacks-and-backups.gmi b/topics/systems/fallbacks-and-backups.gmi index 302a8af..1a22db9 100644 --- a/topics/systems/fallbacks-and-backups.gmi +++ b/topics/systems/fallbacks-and-backups.gmi @@ -4,9 +4,11 @@ As a hurricane is barreling towards our machine room in Memphis we are checking ## Tags -* enhancement -* deploy +* type: enhancement * assigned: pjotrp +* keywords: systems, fallback, backup, deploy +* status: in progress +* priority: critical ## Tasks diff --git a/topics/systems/gn-services.gmi b/topics/systems/gn-services.gmi index 334bb5c..6f9f7fd 100644 --- a/topics/systems/gn-services.gmi +++ b/topics/systems/gn-services.gmi @@ -1,5 +1,13 @@ # GN Services +## Tags + +* type: documentation +* status: in progress +* keywords: gn services, documentation + +## Description + In addition to gn1 and gn2 we have 3 running gn3 services: 1. gn-proxy - deployed as gn3 user in production diff --git a/topics/systems/sheepdog.gmi b/topics/systems/sheepdog.gmi index 137a5dd..5285553 100644 --- a/topics/systems/sheepdog.gmi +++ b/topics/systems/sheepdog.gmi @@ -8,7 +8,10 @@ that need resolving at some point. ## Tags * assigned: pjotrp -* enhancement +* type: enhancement +* status: in progress, halted +* priority: medium +* keywords: system, sheepdog ## Tasks diff --git a/topics/systems/shepherd.gmi b/topics/systems/shepherd.gmi index 5f9ca4f..ea5f10b 100644 --- a/topics/systems/shepherd.gmi +++ b/topics/systems/shepherd.gmi @@ -1,5 +1,15 @@ # Shepherd +## Tags + +* assigned: ?? +* type: documentation +* keywords: system, shepherd +* status: unclear +* priority: unclear + +## Description + On Debian based systems we run shepherd as a shepherd user. The service gets started up through systemd: ``` @@ -18,3 +28,7 @@ WantedBy=multi-user.target ``` => https://git.genenetwork.org/efraim/shepherd-services Running shepherd services + +## Notes + +This seems to be documentation, and not necessarily a task, issue or enhancement to be worked on diff --git a/topics/systems/virtuoso.gmi b/topics/systems/virtuoso.gmi index 187f961..05819e1 100644 --- a/topics/systems/virtuoso.gmi +++ b/topics/systems/virtuoso.gmi @@ -1,5 +1,12 @@ # Running Virtuoso +## Tags + +* type: documentation +* status: unclear + +## Description + 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 @@ -17,7 +24,7 @@ guix environment --ad-hoc virtuoso-ose -- virtuoso-t -f The database is initialized from 'penguin2:/export/virtuoso/var/lib/virtuoso/db/virtuoso.ini' -## Running a new instance +### Running a new instance For testing we want to run a temporary instance. Let's start from the virtuoso.ini file: @@ -58,7 +65,7 @@ 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 +### Uploading data with CURL To upload RDF I use rapper to validate the data. First delete the existing graph with something like @@ -76,7 +83,7 @@ Where BioHackrXiv is the name of the graph (in this example). A python version c => https://github.com/pubseq/bh20-seq-resource/blob/master/scripts/update_virtuoso/check_for_updates.py -## Virtuoso.ini +### Virtuoso.ini What changed in $HOME/services/virtuoso/virtuoso.ini |