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-rw-r--r--topics/bnw/GN2-BNW-data-transfer.gmi5
-rw-r--r--topics/data-uploads/editing-data.gmi3
-rw-r--r--topics/gn1-migration-to-gn2/clustering.gmi2
-rw-r--r--topics/lmms/lmm-notes.gmi7
-rw-r--r--topics/notebooks/binding-lite.gmi7
-rw-r--r--topics/notebooks/guix-containers.gmi8
-rw-r--r--topics/notebooks/jupyter.gmi6
-rw-r--r--topics/notebooks/pluto.gmi5
-rw-r--r--topics/notebooks/port-map.gmi6
-rw-r--r--topics/notebooks/user-stories.gmi8
-rw-r--r--topics/systems/fallbacks-and-backups.gmi6
-rw-r--r--topics/systems/gn-services.gmi8
-rw-r--r--topics/systems/sheepdog.gmi5
-rw-r--r--topics/systems/shepherd.gmi14
-rw-r--r--topics/systems/virtuoso.gmi13
-rw-r--r--topics/ui/adding-delete-button.gmi12
-rw-r--r--topics/ui/adding-terminal-output.gmi7
-rw-r--r--topics/ui/gn3-api-cli.gmi10
18 files changed, 121 insertions, 11 deletions
diff --git a/topics/bnw/GN2-BNW-data-transfer.gmi b/topics/bnw/GN2-BNW-data-transfer.gmi
index e4ef6d0..20789a3 100644
--- a/topics/bnw/GN2-BNW-data-transfer.gmi
+++ b/topics/bnw/GN2-BNW-data-transfer.gmi
@@ -4,8 +4,11 @@ The BNW interface is broken at this point.
## Tags
-* bug
+* type: bug
+* priority: high
* assigned: pjotrp
+* status: in progress
+* keywords: BNW
## Todo
diff --git a/topics/data-uploads/editing-data.gmi b/topics/data-uploads/editing-data.gmi
index 6ae2015..e5050d7 100644
--- a/topics/data-uploads/editing-data.gmi
+++ b/topics/data-uploads/editing-data.gmi
@@ -1,6 +1,9 @@
## Tags
* assigned: bonfacem
+* keywords: metadata
+* status: unclear
+* priority: medium
### Introduction
diff --git a/topics/gn1-migration-to-gn2/clustering.gmi b/topics/gn1-migration-to-gn2/clustering.gmi
index 5202ab2..e354bff 100644
--- a/topics/gn1-migration-to-gn2/clustering.gmi
+++ b/topics/gn1-migration-to-gn2/clustering.gmi
@@ -22,6 +22,8 @@ Next click on 'Cluster traits' and 'Redraw' map. This is the one we want in GN3/
## Tags
* assigned: fredm
+* keywords: GN1, GN3, clustering, heatmaps
+* status: completed, deployed
## Useful links
diff --git a/topics/lmms/lmm-notes.gmi b/topics/lmms/lmm-notes.gmi
index e905687..2b8de0e 100644
--- a/topics/lmms/lmm-notes.gmi
+++ b/topics/lmms/lmm-notes.gmi
@@ -1,5 +1,12 @@
# LMM Notes
+### Tags
+
+* assigned: ??
+* keywords: LMM
+* status: unclear
+* priority: low
+
## Time series data
FlxQTL by Saunak Sen can handle time series data in an (genetic) LMM
diff --git a/topics/notebooks/binding-lite.gmi b/topics/notebooks/binding-lite.gmi
index cc818d7..e90f8fd 100644
--- a/topics/notebooks/binding-lite.gmi
+++ b/topics/notebooks/binding-lite.gmi
@@ -2,6 +2,13 @@
Binder and Cocalc are tools for deploying Jupyter notebooks, R/shiny notebooks and Pluto notebooks. These binding tools do a lot more and do not leverage GNU Guix lightweight container infrastructure. In this project we want to create a binding-lite.
+## Tags
+
+* keywords: binder, jupyter, notebooks
+* status: unclear
+* priority: medium
+* assigned: jgart, pjotrp
+
## Members
* jgart
diff --git a/topics/notebooks/guix-containers.gmi b/topics/notebooks/guix-containers.gmi
index b2c51b4..134acc1 100644
--- a/topics/notebooks/guix-containers.gmi
+++ b/topics/notebooks/guix-containers.gmi
@@ -1,5 +1,13 @@
# Guix Containers
+## Tags
+
+* type: bug
+* assigned: jgart
+* status: unclear
+* priority: medium
+* keywords: notebooks, guix, containers
+
## Bugs
guix container exec command does not currently work:
diff --git a/topics/notebooks/jupyter.gmi b/topics/notebooks/jupyter.gmi
index 357f2fc..ef2df46 100644
--- a/topics/notebooks/jupyter.gmi
+++ b/topics/notebooks/jupyter.gmi
@@ -1,5 +1,11 @@
# Jupyter notebooks
+## Tags
+
+* type: documentation
+* keywords: documentation, jupyter, notebooks
+* status: unclear
+
## Run with GNU Guix
Jupyter notebooks can be installed in a profile
diff --git a/topics/notebooks/pluto.gmi b/topics/notebooks/pluto.gmi
index 30b5d8d..b924020 100644
--- a/topics/notebooks/pluto.gmi
+++ b/topics/notebooks/pluto.gmi
@@ -1,5 +1,10 @@
# Julia Pluto
+## Tags
+
+* type: documentation
+* status: unclear
+
## Pluto in a Guix container
We run Pluto in a container. It allows for self-install of Julia packages:
diff --git a/topics/notebooks/port-map.gmi b/topics/notebooks/port-map.gmi
index c8426e3..4a7d680 100644
--- a/topics/notebooks/port-map.gmi
+++ b/topics/notebooks/port-map.gmi
@@ -6,3 +6,9 @@
|80 |nginx |
|8989 |binderlite |
|xxxx |jupyter(s) |
+
+
+## Tags
+
+* type: documentation
+* keywords: documentation, port map
diff --git a/topics/notebooks/user-stories.gmi b/topics/notebooks/user-stories.gmi
index 22f9398..013ee48 100644
--- a/topics/notebooks/user-stories.gmi
+++ b/topics/notebooks/user-stories.gmi
@@ -1,5 +1,13 @@
# Next Steps
+## Tags
+
+* assigned: jgart
+* type: enhancement
+* keywords: notebooks, jupyter
+* status: unclear
+
+## Description
Whenever we start a notebook let's generate an id (put the id in a db or in memory start) and then accept the id as
part of the route to get to the notebook.
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
diff --git a/topics/ui/adding-delete-button.gmi b/topics/ui/adding-delete-button.gmi
index 872c8e2..63df679 100644
--- a/topics/ui/adding-delete-button.gmi
+++ b/topics/ui/adding-delete-button.gmi
@@ -1,5 +1,11 @@
# Add button to delete an entire dataset in gn2
-An interface for deleting data existed in gn1 but is not present in
-gn1. This is something that should be added once the authorisation
-work is finalised.
+## Tags
+
+* assigned: ??
+* type: bug
+* keywords: ui, dangerous feature, status: unclear
+
+## Description
+
+An interface for deleting data existed in gn1 but is not present in gn2. This is something that should be added once the authorisation work is finalised.
diff --git a/topics/ui/adding-terminal-output.gmi b/topics/ui/adding-terminal-output.gmi
index a3e3350..afe4e9b 100644
--- a/topics/ui/adding-terminal-output.gmi
+++ b/topics/ui/adding-terminal-output.gmi
@@ -6,6 +6,13 @@ GeneNetwork runs external tools. We would like to have an option for (advanced)
As GN3 (REST) API handles calling external tools it kinda make sense to handle the terminal output page through GN3 and communicate through websockets. But first I'll do a Sinatra test run.
+## Tags
+
+* assigned: ??
+* keywords: GN3, terminal, CLI
+* status: unclear
+* priority: low
+
## possible xtermjs alternative
=> https://github.com/joewalnes/websocketd possible xtermjs alternative
diff --git a/topics/ui/gn3-api-cli.gmi b/topics/ui/gn3-api-cli.gmi
index cbb0887..1bea97c 100644
--- a/topics/ui/gn3-api-cli.gmi
+++ b/topics/ui/gn3-api-cli.gmi
@@ -1,5 +1,13 @@
-# Genetwork CLI
+# GeneNetwork CLI
+## Tags
+
+* assigned: ??
+* type: feature-request
+* priority: low
+* keywords: command-line interface, CLI
+
+## Description
It would be great for GeneNetwork to have a nice command line client for doing
most if not all the things you can do with the html interface (GN2) and/or the
API (GN3).
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-10 06:43:36 +0000