diff options
Diffstat (limited to 'issues')
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 |