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-rw-r--r--issues/authorisation.gmi3
-rw-r--r--issues/binderlite/show_template_for_when_git_url_is_not_found.gmi9
-rw-r--r--issues/cant-use-guix-bioinformatics-with-guix-pull.gmi8
-rw-r--r--issues/correlations-time-out.gmi9
-rw-r--r--issues/data/MIKK-panel.gmi3
-rw-r--r--issues/database-not-responding.gmi5
-rw-r--r--issues/fetch-sample-data.gmi10
-rw-r--r--issues/fix-broken-builds-in-gn2-and-gn3.gmi3
-rw-r--r--issues/gemma/multivariate_gemma_hangs-issue243.gmi10
-rw-r--r--issues/genecup-running-as-root.gmi10
-rw-r--r--issues/genenetwork/issue-404-in-logs.gmi6
-rw-r--r--issues/genenetwork/marker_covariates_in_rqtl.gmi7
-rw-r--r--issues/genenetwork1/gn1-mapping-broken.gmi6
-rw-r--r--issues/genenetwork1/gn1-network-graph.gmi8
-rw-r--r--issues/genenetwork1/gn1-pairscan.gmi7
-rw-r--r--issues/genenetwork1/gn1-production-system-issues.gmi8
-rw-r--r--issues/genenetwork1/gn1-slowness.gmi9
-rw-r--r--issues/gnbug/add-linter.gmi29
-rw-r--r--issues/redirect-http-to-https.gmi6
-rw-r--r--issues/systems/tux01-hard-disk-crash.gmi2
20 files changed, 137 insertions, 21 deletions
diff --git a/issues/authorisation.gmi b/issues/authorisation.gmi
index 0adac56..9a17985 100644
--- a/issues/authorisation.gmi
+++ b/issues/authorisation.gmi
@@ -12,6 +12,9 @@ clean up authorisation.
# Tags
* assigned: bonfacem, pjotrp, zachs
+* keywords: authorisation
+* status: in progress, stalled
+* priority: medium
# TODO
diff --git a/issues/binderlite/show_template_for_when_git_url_is_not_found.gmi b/issues/binderlite/show_template_for_when_git_url_is_not_found.gmi
index 257c4d3..07fdb0e 100644
--- a/issues/binderlite/show_template_for_when_git_url_is_not_found.gmi
+++ b/issues/binderlite/show_template_for_when_git_url_is_not_found.gmi
@@ -1,5 +1,12 @@
-* bug
+# Show Template for when Git URL is not Found
+
+## Tags
+
+* type: bug
* assigned: jgart
+* priority: medium
+* keywords: binderlite, template
+## Description
Let's add a template for when a url fails because the user entered the wrong
url or the resource is not available.
diff --git a/issues/cant-use-guix-bioinformatics-with-guix-pull.gmi b/issues/cant-use-guix-bioinformatics-with-guix-pull.gmi
index 8000f7b..1a8d102 100644
--- a/issues/cant-use-guix-bioinformatics-with-guix-pull.gmi
+++ b/issues/cant-use-guix-bioinformatics-with-guix-pull.gmi
@@ -4,6 +4,14 @@ Without this we can't:
* programatically and reproducably use the repository to cherry-pick commits that work with shepherd services
+## Tags
+
+* assigned: Efraim
+* type: bug
+* keywords: guix-bioinformatics
+* status: unclear
+* priority: medium
+
## TODO:
* Adjust the genenetwork2 package to no longer break running `guix pull` with this repository in channels.scm
diff --git a/issues/correlations-time-out.gmi b/issues/correlations-time-out.gmi
index 58ee624..4d0a317 100644
--- a/issues/correlations-time-out.gmi
+++ b/issues/correlations-time-out.gmi
@@ -6,10 +6,15 @@ We are seeing errors with correlations which happen for the larger requests, suc
It looks like correlations don't finish - and worse the running processes take a significant chunk of RAM, around 10GB each. Eventually they disappear.
-## Tasks
+## Tags
* assigned: pjotrp, zachs
-* keywords: critical bug, in progress
+* keywords: correlations, time out
+* type: bug
+* status: in progress
+* priority: critical
+
+## Tasks
* [X] Set up OOM killer
* [X] Prevent many GN2 threads taking too much RAM
diff --git a/issues/data/MIKK-panel.gmi b/issues/data/MIKK-panel.gmi
index 672835d..819d483 100644
--- a/issues/data/MIKK-panel.gmi
+++ b/issues/data/MIKK-panel.gmi
@@ -19,3 +19,6 @@ Genotyping from VCF
## Tags
* assigned: pjotrp, acenteno
+* type: data
+* status: unclear
+* keywords: data, Medaka, MIKK
diff --git a/issues/database-not-responding.gmi b/issues/database-not-responding.gmi
index cb7c600..f9ae8b2 100644
--- a/issues/database-not-responding.gmi
+++ b/issues/database-not-responding.gmi
@@ -7,7 +7,10 @@ Also it is better to use mydumper, mydumper locks MyISAM tables and does not loc
## Tags
* assigned: pjotrp, zsloan
-* bug
+* type: bug
+* keywords: database
+* status: unclear
+* priority: high
## Tasks
diff --git a/issues/fetch-sample-data.gmi b/issues/fetch-sample-data.gmi
index c467925..70c3ea1 100644
--- a/issues/fetch-sample-data.gmi
+++ b/issues/fetch-sample-data.gmi
@@ -1,4 +1,12 @@
-#
+#
+
+### Tags
+
+* assigned: bonifacem
+* keywords: sample data, GN2, GN3
+* status: unclear
+* priority: medium
+
#### Fetch all Sample Data
Currently we fetch all the sample data using this function:
diff --git a/issues/fix-broken-builds-in-gn2-and-gn3.gmi b/issues/fix-broken-builds-in-gn2-and-gn3.gmi
index 831b80d..0c2f898 100644
--- a/issues/fix-broken-builds-in-gn2-and-gn3.gmi
+++ b/issues/fix-broken-builds-in-gn2-and-gn3.gmi
@@ -8,6 +8,9 @@ Note: Pjotr made the build work again. Pushed to guix-bioinformatics.
## Tasks
* assigned: bonfacekilz, efraim
+* type: failure
+* status: complete, closed
+* keywords: build
### Notes
diff --git a/issues/gemma/multivariate_gemma_hangs-issue243.gmi b/issues/gemma/multivariate_gemma_hangs-issue243.gmi
index 7eea489..a30f461 100644
--- a/issues/gemma/multivariate_gemma_hangs-issue243.gmi
+++ b/issues/gemma/multivariate_gemma_hangs-issue243.gmi
@@ -1,5 +1,15 @@
# Multivariate GEMMA hangs (issue 243)
+## Tags
+
+* assigned: ??
+* type: failure
+* keywords: GEMMA
+* status: unclear
+* priority: high
+
+## Description
+
=> https://github.com/genetics-statistics/GEMMA/issues/243
The simulated dataset was generated. Benjamin Chu writes: I think the main problem might be how I did the simulation. I believe it was something like
diff --git a/issues/genecup-running-as-root.gmi b/issues/genecup-running-as-root.gmi
index f1898c8..c48924f 100644
--- a/issues/genecup-running-as-root.gmi
+++ b/issues/genecup-running-as-root.gmi
@@ -25,6 +25,16 @@ A number of changes to different types of shepherd services (exec-command, make-
=> https://git.genenetwork.org/efraim/shepherd-services/commit/b3c96077c2ae3ebda05eb53d81fa6e377a55132d The commit to make genecup run in a guix environment, using shepherd.
+## Tags
+
+
+
+* assigned: Efraim
+* type: failure
+* keywords: genecup, penguin2
+* status: unclear
+* priority: high
+
## Notes
* It is unclear if the environmental-variables in the shepherd service are carried over to the shell script, but it seems not
diff --git a/issues/genenetwork/issue-404-in-logs.gmi b/issues/genenetwork/issue-404-in-logs.gmi
index 8dbde62..70ce499 100644
--- a/issues/genenetwork/issue-404-in-logs.gmi
+++ b/issues/genenetwork/issue-404-in-logs.gmi
@@ -4,9 +4,11 @@ We get many 404's in GN logs. Can we rewire that so no log entries appear as a f
## Tags
-* enhancement
-* deployment
+* type: enhancement
+* keywords: deployment, 404
* assigned: bonfacem, pjotrp
+* status: unclear
+* priority: low
## Notes
diff --git a/issues/genenetwork/marker_covariates_in_rqtl.gmi b/issues/genenetwork/marker_covariates_in_rqtl.gmi
index 799701f..82b9147 100644
--- a/issues/genenetwork/marker_covariates_in_rqtl.gmi
+++ b/issues/genenetwork/marker_covariates_in_rqtl.gmi
@@ -5,5 +5,8 @@ I've removed this option. Currently just waiting on Danny to get back to me with
## Tags
-* bug
-* assigned: zsloan
+* type: bug
+* assigned: zsloan, danny
+* status: in progress, halted
+* keywords: marker covariates
+* priority: medium
diff --git a/issues/genenetwork1/gn1-mapping-broken.gmi b/issues/genenetwork1/gn1-mapping-broken.gmi
index 6a32053..525f65e 100644
--- a/issues/genenetwork1/gn1-mapping-broken.gmi
+++ b/issues/genenetwork1/gn1-mapping-broken.gmi
@@ -16,4 +16,8 @@ AttributeError: 'genotype' object has no attribute 'regression'
## Tags
* assigned: zachs, pjotrp
-* bug
+* type: bug
+* priority: high
+* status: unclear
+* keywords: marker
+* status: unclear
diff --git a/issues/genenetwork1/gn1-network-graph.gmi b/issues/genenetwork1/gn1-network-graph.gmi
index 4011ecc..f66221c 100644
--- a/issues/genenetwork1/gn1-network-graph.gmi
+++ b/issues/genenetwork1/gn1-network-graph.gmi
@@ -4,10 +4,12 @@ Status: the network graph works on production. PDF output is empty, however.
## Tags
-* bug
-* in progress
-* assigned: pjotrp, zachs
+* type: bug
+* priority: high
+* keywords: GN1, Network Graph
+* status: in progress
* kanban: pjotrp
+* assigned: pjotrp, zachs
## Tracking
diff --git a/issues/genenetwork1/gn1-pairscan.gmi b/issues/genenetwork1/gn1-pairscan.gmi
index fea14e9..f58c6b3 100644
--- a/issues/genenetwork1/gn1-pairscan.gmi
+++ b/issues/genenetwork1/gn1-pairscan.gmi
@@ -16,10 +16,11 @@ ImportError: No module named direct
# Tags
-* critical bug
-* missing dependency
-* binary blob
+* type: bug
+* priority: critical
+* keywords: missing dependency, binary blob, GN1
* assigned: pjotrp
+* status: unclear
# Notes
diff --git a/issues/genenetwork1/gn1-production-system-issues.gmi b/issues/genenetwork1/gn1-production-system-issues.gmi
index 0edef5a..0353cd5 100644
--- a/issues/genenetwork1/gn1-production-system-issues.gmi
+++ b/issues/genenetwork1/gn1-production-system-issues.gmi
@@ -6,10 +6,12 @@ This list does not include stuff that needs to be ported to GN2(!). See the GN2
## Tags
-* critical bug
-* in progress
-* assigned: pjotrp, zachs, robw
+* type: bug
+* priority: critical
+* keywords: GN1
+* status: in progress
* kanban: pjotrp
+* assigned: pjotrp, zachs, robw
## List of outstanding issues
(see also E-mail Rob 14 Sep 2021)
diff --git a/issues/genenetwork1/gn1-slowness.gmi b/issues/genenetwork1/gn1-slowness.gmi
index d632f7c..6e60c3c 100644
--- a/issues/genenetwork1/gn1-slowness.gmi
+++ b/issues/genenetwork1/gn1-slowness.gmi
@@ -1,5 +1,14 @@
# GN1 Slowness
+## Tags
+
+* assigned: ??
+* type: bug
+* priority: high
+* keywords: GN1
+
+## Description
+
GN1 needs to clean up the following
```
diff --git a/issues/gnbug/add-linter.gmi b/issues/gnbug/add-linter.gmi
index 1a8a301..3d2d5bd 100644
--- a/issues/gnbug/add-linter.gmi
+++ b/issues/gnbug/add-linter.gmi
@@ -1,7 +1,14 @@
# A linter for gnbug
-* feature-request
-* gnbug
+## Tags
+
+* type: feature-request
+* keywords: gnbug, linter, tissue
+* assigned: ??
+* priority: low
+* status: under discussion
+
+## Description
Should gnbug have a linter?
@@ -22,3 +29,21 @@ If we'd like to "keep the text as unstructured and unrestrictive as possible" I'
fine with that too.
I was just worried about using "invalid" tags. Now, I know it's ok :)
+
+### 2022-03-14
+
+I am thinking tissue (formerly gnbug) should deal with a list of tags of the form:
+
+```
+* key: value[, value, ...]
+```
+
+and each instance of the issue tracker can have some config file that defines, among other things:
+
+* what tags to display
+* colouring of said tags
+* maybe what tags to allow (for those that need to restrict allowed tags)
+
+The tags could be parsed into a hashmap or an associative list, or any other similarly useful datatype, from which the values would be read for display.
+
+Tissue could determine what the context is (CLI, web, etc) and using the config, figure out what tags to display and how
diff --git a/issues/redirect-http-to-https.gmi b/issues/redirect-http-to-https.gmi
index 52cf583..9526b23 100644
--- a/issues/redirect-http-to-https.gmi
+++ b/issues/redirect-http-to-https.gmi
@@ -1,5 +1,11 @@
# Redirect HTTP to HTTPS
+## Tags
+* assigned: ??
+* keywords: http, https
+* status: unclear
+* priority: medium
+
All http://genenetwork.org URIs should redirect to https://genenetwork.org URIs. This should be done on the HTTP server (nginx) config. Currently, if the user enters the HTTP site on their browser, they stay on the HTTP site.
> Note the issue is that we get errors on an automatic redirect. Needs some work.
diff --git a/issues/systems/tux01-hard-disk-crash.gmi b/issues/systems/tux01-hard-disk-crash.gmi
index b7616ee..294024c 100644
--- a/issues/systems/tux01-hard-disk-crash.gmi
+++ b/issues/systems/tux01-hard-disk-crash.gmi
@@ -6,6 +6,8 @@ One spinning disk crashed on Sept. 26th. It was used for Arthur's HOME and backu
* assigned: pjotrp
* priority: medium
+* status: in progress
+* keywords: system, tux01, hard disk crash
# Info
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-26 03:21:27 +0000