diff options
78 files changed, 495 insertions, 44 deletions
diff --git a/issues/binderlite/add-configuration-to-set-server-name.gmi b/issues/binderlite/add-configuration-to-set-server-name.gmi index d54997c..4181f17 100644 --- a/issues/binderlite/add-configuration-to-set-server-name.gmi +++ b/issues/binderlite/add-configuration-to-set-server-name.gmi @@ -1,8 +1,14 @@ # Add configuration to set server name +## Tags + * assigned: jgart +* type: feature-request +* status: unclear +* priority: high +* keywords: binderlite, notebooks, configuration -* feature +## Description Let's use environment variables as configuration diff --git a/issues/binderlite/add-regex-to-prevent-user-from-inputting-invalid-url.gmi b/issues/binderlite/add-regex-to-prevent-user-from-inputting-invalid-url.gmi index 035fb76..4640c1c 100644 --- a/issues/binderlite/add-regex-to-prevent-user-from-inputting-invalid-url.gmi +++ b/issues/binderlite/add-regex-to-prevent-user-from-inputting-invalid-url.gmi @@ -1,6 +1,13 @@ -* bug +# Add Regular Expression to Prevent Invalid Input +## Tags +* type: bug * assigned: jgart +* status: unclear +* keywords: binderlite, notebooks +* priority: high + +## Description Add regex to the html form to prevent the user from submitting an invalid git repo url or other string. diff --git a/issues/binderlite/ansi2html_terminal_user_feedback.gmi b/issues/binderlite/ansi2html_terminal_user_feedback.gmi index 969448a..c0cba55 100644 --- a/issues/binderlite/ansi2html_terminal_user_feedback.gmi +++ b/issues/binderlite/ansi2html_terminal_user_feedback.gmi @@ -1,8 +1,12 @@ # ansi2html terminal user feedback -* ongoing -* feature-request +* status: ongoing, in progress +* type: feature-request * assigned: jgart +* priority: medium +* keywords: binderlite, notebooks, ansi2html + +## Description https://builds.sr.ht/~sircmpwn/job/610711 diff --git a/issues/binderlite/finds-unknown-package-in-manifest.gmi b/issues/binderlite/finds-unknown-package-in-manifest.gmi index 1bcba39..cf1d25b 100644 --- a/issues/binderlite/finds-unknown-package-in-manifest.gmi +++ b/issues/binderlite/finds-unknown-package-in-manifest.gmi @@ -30,4 +30,10 @@ Or, should channels be managed by the sysadmin only for security reasons? It's probably a security risk since a guix channel can pull in arbitrary packaged code that might not be audited or fully trusted. -* bug +## Tags + +* type: bug +* assigned: jgart +* status: unclear +* keywords: binderlite, notebooks +* priority: high diff --git a/issues/binderlite/integrate-styling-with-gn2.gmi b/issues/binderlite/integrate-styling-with-gn2.gmi index dc158fa..e2d5843 100644 --- a/issues/binderlite/integrate-styling-with-gn2.gmi +++ b/issues/binderlite/integrate-styling-with-gn2.gmi @@ -1,7 +1,12 @@ # Integrate styling of app with GN2 -* ongoing +* status: ongoing, in progress * assigned: jgart +* type: bug +* priority: medium +* keywords: binderlite, notebooks, styling, UI + +## Description Currently using antiweb for styling with modifications. diff --git a/issues/binderlite/kernel-dying.gmi b/issues/binderlite/kernel-dying.gmi index 07017f2..25008de 100644 --- a/issues/binderlite/kernel-dying.gmi +++ b/issues/binderlite/kernel-dying.gmi @@ -1,5 +1,15 @@ # R Kernel Dying +## Tags + +* assigned: jgart +* type: bug +* priority: high +* status: unclear +* keywords: R + +## Core Dump + ``` [I 08:45:24.502 NotebookApp] Writing notebook-signing key to /home/jgart/.local/share/jupyter/notebook_secret [W 08:45:24.515 NotebookApp] Notebook 2020-05-08/solberg-rat-analysis.ipynb is not trusted diff --git a/issues/binderlite/return-canned-text-if-notebook-description-returns-none.gmi b/issues/binderlite/return-canned-text-if-notebook-description-returns-none.gmi index 49f5d3f..b734f5c 100644 --- a/issues/binderlite/return-canned-text-if-notebook-description-returns-none.gmi +++ b/issues/binderlite/return-canned-text-if-notebook-description-returns-none.gmi @@ -1,7 +1,13 @@ # Return canned text if notebook description returns none -* bug? +## Tags +* type: bug * assigned: jgart +* priority: high +* status: in progress +* keywords: binderlite, notebooks + +## Description Notebooks that do not have a description will use python's `None` value as the project's description. @@ -23,3 +29,7 @@ if notebook.description == None: ``` WDYT? + +### 2022-03-16 fredm + +I like the first one better diff --git a/issues/binderlite/use-root-file.gmi b/issues/binderlite/use-root-file.gmi index 21a7ac5..aa2978c 100644 --- a/issues/binderlite/use-root-file.gmi +++ b/issues/binderlite/use-root-file.gmi @@ -1,4 +1,18 @@ - # guix shell --root +# Guix: Using guix shell with root file + +## Tags + +* assigned: jgart +* type: unclear +* status: unclear +* priority: low +* keywords: guix, guix shell, root file + +## Description + +``` +guix shell --root +``` Let's benchmark and test these options to see if it helps the speed/times with building a new container. diff --git a/issues/deploy.gmi b/issues/deploy.gmi index 94d73ec..35e707c 100644 --- a/issues/deploy.gmi +++ b/issues/deploy.gmi @@ -13,7 +13,11 @@ settings; and removing this would make gn2 as is disfunctional. # Tags -* assigned: bonfacem +* assigned: bonfacem, fredm +* type: bug +* priority: medium +* status: in progress +* keywords: GN2, configuration, deploy # Notes diff --git a/issues/gemma/HS-Rat-crashes-gemma.gmi b/issues/gemma/HS-Rat-crashes-gemma.gmi index 5d0171a..316e1a3 100644 --- a/issues/gemma/HS-Rat-crashes-gemma.gmi +++ b/issues/gemma/HS-Rat-crashes-gemma.gmi @@ -7,6 +7,10 @@ Running GEMMA on the NSNIH dataset in Genenetwork sends the server in a tail spi ## Tags * assigned: pjotrp, zachs +* status: unclear +* type: bug +* priority: high +* keywords: gemma, crash ## Tasks diff --git a/issues/gemma/databases-getting-out-of-wack.gmi b/issues/gemma/databases-getting-out-of-wack.gmi index 5e4fc1c..a102846 100644 --- a/issues/gemma/databases-getting-out-of-wack.gmi +++ b/issues/gemma/databases-getting-out-of-wack.gmi @@ -1,10 +1,14 @@ # Databases Getting Out of Wack -## Let's use Gemma instead of Reaper +## Tags * assigned: Bonface, Zach, jgart * priority: high -* bug +* type: bug +* status: unclear +* keywords: database, gemma, reaper + +## Let's use Gemma instead of Reaper Zachary: > If we're using GEMMA, we'll need to recalculate all other trait Max LRS scores using diff --git a/issues/genenetwork/api-docs.gmi b/issues/genenetwork/api-docs.gmi index 8805cc4..e9fbc92 100644 --- a/issues/genenetwork/api-docs.gmi +++ b/issues/genenetwork/api-docs.gmi @@ -6,4 +6,5 @@ Here's a simple way that SourceHut documents their API endpoints with markdown. ## Tags -* docs +* type: documentation +* keywords: GN3 diff --git a/issues/genenetwork/environment.gmi b/issues/genenetwork/environment.gmi index 00105be..e66550f 100644 --- a/issues/genenetwork/environment.gmi +++ b/issues/genenetwork/environment.gmi @@ -9,3 +9,7 @@ It somehow got reverted and is out of date. Please see if we can get a list agai ## Tags * assigned: bonfacem +* type: bug +* status: unclear +* priority: medium +* keywords: guix, packages, environments diff --git a/issues/genenetwork/genewiki.gmi b/issues/genenetwork/genewiki.gmi index e7096dc..e0a0a00 100644 --- a/issues/genenetwork/genewiki.gmi +++ b/issues/genenetwork/genewiki.gmi @@ -19,6 +19,9 @@ with an edit button, similar to ## Tags * assigned: pjotrp, zsloan -* enhancement +* type: enhancement +* priority: medium +* status: unclear +* keywords: GN1, documentation ## Tasks diff --git a/issues/genenetwork/global-search.gmi b/issues/genenetwork/global-search.gmi index 01d9c0f..a39da80 100644 --- a/issues/genenetwork/global-search.gmi +++ b/issues/genenetwork/global-search.gmi @@ -5,6 +5,10 @@ Global search is the top bar of GN2 ## Tags * assigned: pjotrp, zsloan +* status: unclear +* priority: critical +* type: bug +* keywords: global search, BRCA2 ## Tasks diff --git a/issues/genenetwork/http-https.gmi b/issues/genenetwork/http-https.gmi index 80306bf..9777185 100644 --- a/issues/genenetwork/http-https.gmi +++ b/issues/genenetwork/http-https.gmi @@ -12,4 +12,10 @@ if ($scheme = http) { } ``` +## Tags + * assigned: pjotr, arthur, jgart +* type: bug +* priority: medium +* status: unclear +* keywords: GN2, http, https diff --git a/issues/genenetwork/proxy-hard-coded.gmi b/issues/genenetwork/proxy-hard-coded.gmi index ab4c974..f9a7b18 100644 --- a/issues/genenetwork/proxy-hard-coded.gmi +++ b/issues/genenetwork/proxy-hard-coded.gmi @@ -25,3 +25,7 @@ wqflask/utility/authentication_tools.py # Tags * assigned: bonfacem, pjotrp, zachs +* type: bug +* priority: medium +* status: unclear +* keywords: proxy, configuration, settings diff --git a/issues/genenetwork/remove-elasticsearch.gmi b/issues/genenetwork/remove-elasticsearch.gmi index c484ca1..461423f 100644 --- a/issues/genenetwork/remove-elasticsearch.gmi +++ b/issues/genenetwork/remove-elasticsearch.gmi @@ -2,6 +2,14 @@ We are no longer using that database +Seems related to + +=> ../issues/remove-elastic-search.gmi + ## Tags * assigned: bonfacem +* type: enhancement +* priority: low +* status: unclear +* keywords: elasticsearch, purge diff --git a/issues/genenetwork1/gn1-symbols.gmi b/issues/genenetwork1/gn1-symbols.gmi index ac4cf71..1bc3606 100644 --- a/issues/genenetwork1/gn1-symbols.gmi +++ b/issues/genenetwork1/gn1-symbols.gmi @@ -3,6 +3,10 @@ # Tags * assigned: pjotrp, arthurc +* type: bug +* priority: medium +* status: unclear +* keywords: GN1, symbols # Tasks diff --git a/issues/gn3-technical-debt.gmi b/issues/gn3-technical-debt.gmi index 189b756..a31012f 100644 --- a/issues/gn3-technical-debt.gmi +++ b/issues/gn3-technical-debt.gmi @@ -1,6 +1,12 @@ +# GN3: Technical Debt + ## Tags * assigned: bonfacem +* priority: medium +* status: in progress +* type: enhancement +* keywords: GN3 ### Introduction diff --git a/issues/gnbug/add-convenience-templates.gmi b/issues/gnbug/add-convenience-templates.gmi index 41eb975..29f266a 100644 --- a/issues/gnbug/add-convenience-templates.gmi +++ b/issues/gnbug/add-convenience-templates.gmi @@ -1,6 +1,14 @@ -# Add convenienve templates +# Add convenience templates -* feature-request +## Tags + +* assigned: jgart +* type: feature-request +* priority: low +* status: in progress, discussion, stalled +* keywords: tissue, gnbug + +## Description WDYT of adding a subcommand called `report` to generate a template for a bug report? diff --git a/issues/gnbug/hide-stale-issues.gmi b/issues/gnbug/hide-stale-issues.gmi index b07fc5d..3184fdc 100644 --- a/issues/gnbug/hide-stale-issues.gmi +++ b/issues/gnbug/hide-stale-issues.gmi @@ -2,4 +2,10 @@ Our list of issues are growing by the day. And, for some reason, we are not eager to close many of them. :-P This makes the command-line output long. Maybe, hide stale issues by default, and show them only if some --all flag is passed. Stale issues are tentatively defined as those issues that have been inactive for more than 6 months. +## Tags + * assigned: bonfacem, aruni +* type: enhancement, feature-request +* status: unclear +* priority: low +* keywords: tissue, gnbug diff --git a/issues/gnbug/recent-first-sort.gmi b/issues/gnbug/recent-first-sort.gmi index 229554a..983b224 100644 --- a/issues/gnbug/recent-first-sort.gmi +++ b/issues/gnbug/recent-first-sort.gmi @@ -2,7 +2,13 @@ Add a command-line option --sort=(newest-first|oldest-first) to gnbug that determines the order the issues are listed. oldest-first is useful for command-line usage where you don't want to scroll up to see the most recent issue. newest-first is useful when generating gemtext/web pages where you don't want to scroll down to see the most recent issue. +## Tags + * assigned: bonfacem +* type: enhancement, feature-request +* priority: medium +* status: stalled +* keywords: tissue, gnbug # INFO diff --git a/issues/per-service-profile-for-shepherd-services.gmi b/issues/per-service-profile-for-shepherd-services.gmi index b22448b..654a723 100644 --- a/issues/per-service-profile-for-shepherd-services.gmi +++ b/issues/per-service-profile-for-shepherd-services.gmi @@ -31,3 +31,11 @@ Currently there are a bunch of shepherd services (on Penguin2, as user shepherd) * power * rn6app * singlecell + +## Tags + +* assigned: efraim +* type: bug +* status: unclear +* priority: high +* keywords: shepherd, system administration diff --git a/issues/quality-control/enumerate-all-qc-checks.gmi b/issues/quality-control/enumerate-all-qc-checks.gmi index 2f72f24..90addc5 100644 --- a/issues/quality-control/enumerate-all-qc-checks.gmi +++ b/issues/quality-control/enumerate-all-qc-checks.gmi @@ -1,7 +1,12 @@ +ume # Enumerating all QC checks We need to enumerate all QC checks and platforms that we want to test against. -* assigned: jgart, arthur +## Tags -* in progress +* assigned: jgart, arthur +* status: in progress +* type: feature-request +* priority: high +* keywords: quality control diff --git a/issues/redis-data.gmi b/issues/redis-data.gmi index 2246c96..995ef1e 100644 --- a/issues/redis-data.gmi +++ b/issues/redis-data.gmi @@ -3,4 +3,12 @@ ATM how we store data in redis is undocumented. Without this, it's hard for contributors to work out how to modify some things. For example, PJ would want to add himself to the editors group. Doing -this was non-trivial for him.
\ No newline at end of file +this was non-trivial for him. + +## Tags + +* type: bug +* priority: high +* assigned: bonfacem +* status: unclear +* keywords: documentation, data, redis diff --git a/issues/remove-elastic-search.gmi b/issues/remove-elastic-search.gmi index af475d6..49b2385 100644 --- a/issues/remove-elastic-search.gmi +++ b/issues/remove-elastic-search.gmi @@ -7,9 +7,15 @@ in gn2. ## Tasks * assigned: bonfacekilz -* keywords: chore, done +* keywords: chore, elasticsearch +* status: done, completed, closed +* type: bug ## Notes While at it, "@depracated" was removed since it added extra noise to -the logs.
\ No newline at end of file +the logs. + +Seems related to + +=> genenetwork/remove-elasticsearch.gmi diff --git a/issues/resurrect-mechanical-rob.gmi b/issues/resurrect-mechanical-rob.gmi index 7b12f0d..bea2a78 100644 --- a/issues/resurrect-mechanical-rob.gmi +++ b/issues/resurrect-mechanical-rob.gmi @@ -2,4 +2,10 @@ We need to run Mechanical Rob tests as part of our continuous integration tests. Mechanical Rob has not been run in a while, and I'm not sure the Mechanical Rob code in the genenetwork2 repository is complete. Get it running again and document the process. +## Tags + * assigned: bonfacem, aruni +* keywords: testing, CI, CD, mechanical rob +* status: in progress +* type: enhancement +* priority: medium diff --git a/issues/slow-correlations.gmi b/issues/slow-correlations.gmi index 955800c..9f4c8c8 100644 --- a/issues/slow-correlations.gmi +++ b/issues/slow-correlations.gmi @@ -2,10 +2,15 @@ Correlations for huge data set(like the exo dataset) is very slow; and the UI crashes. -## Tasks +## Tags +* type: bug +* priority: critical * assigned: bonfacekilz, alex -* keywords: critical bug, in progress +* keywords: correlations, ui, crash +* status: in progress + +## Tasks * [ ] Caching slow queries * [ ] Server side pagination @@ -104,4 +109,4 @@ time to compute. According to Rob, GN1 does not rely on a cache. Instead it is computing from a materialized view of the database that is -intentionally designed for a fast web service.
\ No newline at end of file +intentionally designed for a fast web service. diff --git a/issues/zero-repr-in-data-upload.gmi b/issues/zero-repr-in-data-upload.gmi index b283add..f8143e8 100644 --- a/issues/zero-repr-in-data-upload.gmi +++ b/issues/zero-repr-in-data-upload.gmi @@ -1,6 +1,12 @@ +# Data Uploads: Zero Representation + ## Tags * assigned: bonfacem +* type: bug +* priority: high +* status: in progress +* keywords: data uploads ### Introduction diff --git a/tasks/dana.gmi b/tasks/dana.gmi index 51f33b6..4463d1a 100644 --- a/tasks/dana.gmi +++ b/tasks/dana.gmi @@ -3,6 +3,10 @@ ## Tags * assigned: dana, pjotrp +* priority: medium +* type: system administration +* status: unclear +* keywords: system administration, octopus, gateway, tux02, tux01 ## Tasks diff --git a/tasks/zsloan.gmi b/tasks/zsloan.gmi index 7e60240..30cba44 100644 --- a/tasks/zsloan.gmi +++ b/tasks/zsloan.gmi @@ -3,6 +3,9 @@ ## Tags * assigned: zsloan +* keywords: global search, genewiki +* status: unclear +* priority: unclear ## Tasks diff --git a/topics/arvados/covid19.gmi b/topics/arvados/covid19.gmi index be96605..48bd028 100644 --- a/topics/arvados/covid19.gmi +++ b/topics/arvados/covid19.gmi @@ -5,3 +5,11 @@ We are setting up a Cloud HPC for COVID-19 using Arvados as the underlying infra ## Tasks => https://github.com/yatisht/usher Fast phylogeny + +## Tags + +* assigned: pjotrp +* priority: unclear +* type: system administration +* status: unclear +* keywords: covid-19, systems, arvados diff --git a/topics/authentication/replace-hard-coded-auth-with-gn-proxy.gmi b/topics/authentication/replace-hard-coded-auth-with-gn-proxy.gmi index f066399..05ccb53 100644 --- a/topics/authentication/replace-hard-coded-auth-with-gn-proxy.gmi +++ b/topics/authentication/replace-hard-coded-auth-with-gn-proxy.gmi @@ -2,9 +2,14 @@ ## Tags -* assigned: ?? +* assigned: bonfacem * priority: medium -* status: unclear +* type: enhancement +* status: in progress * keywords: authentication, gn-proxy ## Description + +Originally in the now deleted file `topics/authentication/auth.gmi` which was originally created by BonfaceKilz. + +Assigned to bonfacem for better description, and further work/reassignment as appropriate diff --git a/topics/authentication/user-info.gmi b/topics/authentication/user-info.gmi index c5723af..6a1bc33 100644 --- a/topics/authentication/user-info.gmi +++ b/topics/authentication/user-info.gmi @@ -4,7 +4,8 @@ When the user signs in to GN2, there is no info on the account name in the menu. ## Tags -* assigned: ?? +* assigned: bonfacem * priority: medium * status: unclear +* type: bug * keywords: authentication, user info diff --git a/topics/cli/weechat.gmi b/topics/cli/weechat.gmi index b6fc062..337f3c9 100644 --- a/topics/cli/weechat.gmi +++ b/topics/cli/weechat.gmi @@ -1,5 +1,10 @@ # Weechat +## Tags + +* type: documentation +* keywords: cli, weechat, documentation + Weechat is a very versatile terminal chat that can handle IRC, Matrix and Slack. ## Weechat install + slack diff --git a/topics/data-uploads/inserting-data.gmi b/topics/data-uploads/inserting-data.gmi index 33b500c..5c79808 100644 --- a/topics/data-uploads/inserting-data.gmi +++ b/topics/data-uploads/inserting-data.gmi @@ -1,6 +1,12 @@ +# Data Uploads: Inserting Data + ## Tags * assigned: bonfacem, zachs +* type: bug +* priority: high +* status: in progress +* keywords: data uploads ### Introduction @@ -160,4 +166,4 @@ MariaDB [db_webqtl]> select * from Strain where Id=66086; - There are 1000s of mice with computable genomes that have never been born yet. Can we compute their phenotype? This is as difficult as - getting to Mars.
\ No newline at end of file + getting to Mars. diff --git a/topics/data-uploads/reverse-from-file.gmi b/topics/data-uploads/reverse-from-file.gmi index f7eb028..9e368db 100644 --- a/topics/data-uploads/reverse-from-file.gmi +++ b/topics/data-uploads/reverse-from-file.gmi @@ -1,8 +1,13 @@ +# Data Uploads: Reversing a Diff + ## Tags * assigned: bonfacem, zachs +* status: unclear +* type: enhancement +* priority: high +* keywords: data uploads ### Introduction -Given a diff file, we should be able to reverse the operations that -were ran on it. +Given a diff file, we should be able to reverse the operations that were ran on it. diff --git a/topics/documentation/gn-documentation.gmi b/topics/documentation/gn-documentation.gmi index 653a1a4..9cf729d 100644 --- a/topics/documentation/gn-documentation.gmi +++ b/topics/documentation/gn-documentation.gmi @@ -13,6 +13,10 @@ the markdown is rendered on github, which makes it easy to edit for most users, ## Tags * assigned: pjotrp +* status: unclear +* type: documentation +* priority: high +* keywords: documentation, wiki ## Tasks diff --git a/topics/documentation/gn-hacking-documentation.gmi b/topics/documentation/gn-hacking-documentation.gmi index 93898b2..60b34a3 100644 --- a/topics/documentation/gn-hacking-documentation.gmi +++ b/topics/documentation/gn-hacking-documentation.gmi @@ -11,6 +11,10 @@ The goal of this document is to encourage and track the documentation that assis ## Tags * assigned: fredm +* type: documentation +* status: in progress +* priority: medium +* keywords: traits, datasets, hacking ## Unifying Principles diff --git a/topics/gemini/cheatsheet.gmi b/topics/gemini/cheatsheet.gmi index b2158ea..58b4000 100644 --- a/topics/gemini/cheatsheet.gmi +++ b/topics/gemini/cheatsheet.gmi @@ -3,3 +3,8 @@ => gemini://gemini.circumlunar.space/docs/cheatsheet.gmi => https://gemini.circumlunar.space/docs/cheatsheet.gmi proxy + +## Tags + +* type: documentation +* keywords: gemini diff --git a/topics/gemini/ideas_and_references.gmi b/topics/gemini/ideas_and_references.gmi index dfb026d..d28f85c 100644 --- a/topics/gemini/ideas_and_references.gmi +++ b/topics/gemini/ideas_and_references.gmi @@ -1,3 +1,8 @@ -Ideas and References +# Ideas and References => gemini://drewdevault.com/2021/11/15/Reframing-gemini.gmi Reframing the philosophy of Gemini + +## Tags + +* type: documentation +* keywords: documentation, gemini diff --git a/topics/gn1-migration-to-gn2/non-clustered-heatmaps-and-flipping.gmi b/topics/gn1-migration-to-gn2/non-clustered-heatmaps-and-flipping.gmi index 0fbdabc..e87628f 100644 --- a/topics/gn1-migration-to-gn2/non-clustered-heatmaps-and-flipping.gmi +++ b/topics/gn1-migration-to-gn2/non-clustered-heatmaps-and-flipping.gmi @@ -19,5 +19,6 @@ During the presentation meeting on 2021-10-01, Rob requested that the heatmaps h ## Tags -* feature +* type: feature-request * assigned: fredm, zsloan +* status: closed, completed diff --git a/topics/gn1-migration-to-gn2/partial-correlations.gmi b/topics/gn1-migration-to-gn2/partial-correlations.gmi index 8ddb783..ceba819 100644 --- a/topics/gn1-migration-to-gn2/partial-correlations.gmi +++ b/topics/gn1-migration-to-gn2/partial-correlations.gmi @@ -27,7 +27,10 @@ That gives you a list of hits. ## Tags * assigned: fredm, zsloan, robw -* migration, in progress, deployed, under test +* keywords: migration, partial correlations, GN3, GN1 +* status: in progress, deployed, under test +* type: feature-migration +* priority: medium ## Notes diff --git a/topics/lisp/common-lisp-notes.gmi b/topics/lisp/common-lisp-notes.gmi index eca6c3d..cf48013 100644 --- a/topics/lisp/common-lisp-notes.gmi +++ b/topics/lisp/common-lisp-notes.gmi @@ -1,34 +1,40 @@ -# List of common lisp packages: +# Common LISP: Notes + +## List of common lisp packages: => https://github.com/CodyReichert/awesome-cl -# Books +## Books http://cliki.net/Lisp+Books -# Practice +## Practice https://github.com/google/lisp-koans https://exercism.io/tracks/common-lisp -# Documentation +## Documentation The nonguix channel provides an emacs package for the Common Lisp HyperSpec: => https://gitlab.com/nonguix/nonguix/-/blob/master/nongnu/packages/emacs.scm#L26 clhs -# Getting Help / Asking Questions +## Getting Help / Asking Questions -## Libera Chat +### Libera Chat ``` #clschool #commonlisp ``` -## Matrix +### Matrix ``` #common-lisp:matrix.org ``` +## Tags + +* type: documentation +* keywords: LISP, common-lisp, packages diff --git a/topics/lisp/common-lisp-sly.gmi b/topics/lisp/common-lisp-sly.gmi index e69de29..494d821 100644 --- a/topics/lisp/common-lisp-sly.gmi +++ b/topics/lisp/common-lisp-sly.gmi @@ -0,0 +1,12 @@ +# Common LISP: sly + +This document will collect some resources on sly + +## Tags + +* type: documentation +* keywords: common-lisp, sly, emacs + +## Resources + +=> https://joaotavora.github.io/sly/ SLY User Manual diff --git a/topics/lisp/debugging.gmi b/topics/lisp/debugging.gmi index a3565c6..2945e0c 100644 --- a/topics/lisp/debugging.gmi +++ b/topics/lisp/debugging.gmi @@ -7,3 +7,8 @@ Some links => https://malisper.me/debugging-lisp-part-1-recompilation/ Debug Common Lisp (CL) => https://www.youtube.com/watch?v=bl8jQ2wRh6k Video on CL web development + +## Tags + +* type: documentation +* keywords: LISP, debugging diff --git a/topics/lisp/define-condition.gmi b/topics/lisp/define-condition.gmi index 59d3f56..e6891d6 100644 --- a/topics/lisp/define-condition.gmi +++ b/topics/lisp/define-condition.gmi @@ -72,3 +72,9 @@ Why is condition handling special in common lisp compared to other languages? => https://lispcookbook.github.io/cl-cookbook/error_handling.html define-condition in the cl-cookbook => https://www.nhplace.com/kent/Papers/Condition-Handling-2001.html Condition Handling in the Lisp Language Family => https://gigamonkeys.com/book/beyond-exception-handling-conditions-and-restarts.html Conditions and Restarts + + +## Tags + +* type: documentation +* keywords: LISP, condition handling diff --git a/topics/lisp/lisp4schemers.gmi b/topics/lisp/lisp4schemers.gmi index f0ee1af..a385890 100644 --- a/topics/lisp/lisp4schemers.gmi +++ b/topics/lisp/lisp4schemers.gmi @@ -1,5 +1,10 @@ # Lisp For Schemers +## Tags + +* type: documentation +* keywords: LISP, Scheme, iota, loop, iterate + ## iota ### In Scheme diff --git a/topics/lisp/tips-and-tricks.gmi b/topics/lisp/tips-and-tricks.gmi index 792980b..024d865 100644 --- a/topics/lisp/tips-and-tricks.gmi +++ b/topics/lisp/tips-and-tricks.gmi @@ -14,3 +14,8 @@ CL-USER(3): (+ 3 #;(+ 2 3) 1) ``` Special thanks to Ed Langley on #common-lisp:matrix.org. + +## Tags + +* type: documentation +* keywords: lisp, scheme, tips, tricks diff --git a/topics/notebooks/binderlite-cli.gmi b/topics/notebooks/binderlite-cli.gmi index fede6f4..81e6db8 100644 --- a/topics/notebooks/binderlite-cli.gmi +++ b/topics/notebooks/binderlite-cli.gmi @@ -1,5 +1,13 @@ # CLI Features +## Tags + +* assigned: jgart +* priority: low +* status: unclear +* type: feature-request +* keywords: bindelite, notebooks + ## Admin * Clear Database diff --git a/topics/notebooks/reproducibility.gmi b/topics/notebooks/reproducibility.gmi index 8d565a1..7219539 100644 --- a/topics/notebooks/reproducibility.gmi +++ b/topics/notebooks/reproducibility.gmi @@ -14,3 +14,9 @@ https://github.com/fonsp/Pluto.jl#built-in-package-manager https://mybinder.readthedocs.io/en/latest/tutorials/reproducibility.html#pin-dependencies +## Tags + +* type: documentation +* priority: medium +* assigned: jgart +* keywords: documentation, notebooks, reproducibility, guix diff --git a/topics/profiling_python_code.gmi b/topics/profiling_python_code.gmi index d7f9ea0..9052364 100644 --- a/topics/profiling_python_code.gmi +++ b/topics/profiling_python_code.gmi @@ -20,3 +20,9 @@ The output can be redirected, e.g. * env [various-env-vars] python3 -m cProfile the-script.py 2>error.log 1>performance.log which should help will separating errors from the performance data, for easier analysis + + +## Tags + +* type: documentation +* keywords: profiling, python diff --git a/topics/pudb/pytest-pudb.gmi b/topics/pudb/pytest-pudb.gmi index 5a979c0..4a9b685 100644 --- a/topics/pudb/pytest-pudb.gmi +++ b/topics/pudb/pytest-pudb.gmi @@ -5,3 +5,8 @@ pytest --pdbcls pudb.debugger:Debugger --pdb --capture=no ``` => https://documen.tician.de/pudb/starting.html?highlight=pytest#usage-with-pytest + +## Tags + +* type: documentation +* keywords: pudb, pytest diff --git a/topics/pudb/using-pudb.gmi b/topics/pudb/using-pudb.gmi index 877a700..7cac743 100644 --- a/topics/pudb/using-pudb.gmi +++ b/topics/pudb/using-pudb.gmi @@ -19,3 +19,8 @@ The standard pdb docs should work for pudb with one small exception. > exception: run is called runstatement.) => https://docs.python.org/3/library/pdb.html?highlight=pdb#module-pdb + +## Tags + +* type: documentation +* keywords: pudb diff --git a/topics/quality-control/qc-checks.gmi b/topics/quality-control/qc-checks.gmi index 0d04625..dc18f94 100644 --- a/topics/quality-control/qc-checks.gmi +++ b/topics/quality-control/qc-checks.gmi @@ -45,3 +45,11 @@ is allowed into the GeneNetwork will be 22,000 entries. 12. Check for CRLF. 13. Check for UTF-8 encoding. + +## Tags + +* assigned: jgart +* type: feature-request +* priority: high +* status: unclear +* keywords: quality control diff --git a/topics/quality-control/qc.gmi b/topics/quality-control/qc.gmi index 96c4604..7b5d1e4 100644 --- a/topics/quality-control/qc.gmi +++ b/topics/quality-control/qc.gmi @@ -31,3 +31,11 @@ Note we could run QC through the REST API too. That would allow it to be run from R and Python and Jupyter notebooks. Make it part of GN3. The tricky part is still how the data is handled in escrow. + +## Tags + +* assigned: jgart +* priority: high +* type: feature-request +* status: in progress, beta +* keywords: quality control diff --git a/topics/quality-control/shapiro-wilk-test.gmi b/topics/quality-control/shapiro-wilk-test.gmi index b1bdbfd..352dc5b 100644 --- a/topics/quality-control/shapiro-wilk-test.gmi +++ b/topics/quality-control/shapiro-wilk-test.gmi @@ -31,3 +31,8 @@ perform Ordered Quantile normalization43 on all phenotypes. QTL -- A quantitative trait variant in Gabra2 underlies increased methamphetamine stimulant sensitivity ``` + +## Tags + +* type: documentation +* keywords: documentation, Shapiro Wilk test diff --git a/topics/quality-control/ui-design.gmi b/topics/quality-control/ui-design.gmi index 84f7748..029a2b8 100644 --- a/topics/quality-control/ui-design.gmi +++ b/topics/quality-control/ui-design.gmi @@ -39,3 +39,11 @@ dataset so that we can inspect it." "Inbred Set ID 1 is the same as BXD" > These are the strains: ... + +## Tags + +* assigned: jgart +* type: feature-request +* status: unclear +* priority: medium +* keywords: UI, quality control diff --git a/topics/running_pudb_from_external_environment.gmi b/topics/running_pudb_from_external_environment.gmi index be9bf14..a533e22 100644 --- a/topics/running_pudb_from_external_environment.gmi +++ b/topics/running_pudb_from_external_environment.gmi @@ -1,5 +1,7 @@ # Running pudb From an External Environment +This documentation is now obsolete since pudb was added as a package in GNU Guix + Currently (22nd December 2021), it is a tad difficult to get pudb running under the various guix environments without having to update a lot of stuff. This documents a workaround that seems to work for me (@fredm). ## GeneNetwork3 @@ -20,3 +22,9 @@ Currently (22nd December 2021), it is a tad difficult to get pudb running under 4) Inside the container, run the debugger with something like: * env PYTHONPATH="${PYTHONPATH}:${HOME}/pudb_env/lib/python3.8/site-packages" ... python3 -m pudb script.py + +## Tags + +* type: documentation +* keywords: pudb +* status: obsolete diff --git a/topics/systems/bbb.gmi b/topics/systems/bbb.gmi index 9ef54a3..73582e6 100644 --- a/topics/systems/bbb.gmi +++ b/topics/systems/bbb.gmi @@ -1,4 +1,9 @@ -# BBB +# BigBlueButton + +## Tags + +* type: documentation +* keywords: BigBlueButton ## BASH script to install BigBlueButton in 30 minutes. diff --git a/topics/systems/ci-cd.gmi b/topics/systems/ci-cd.gmi index cc12069..a5e00b6 100644 --- a/topics/systems/ci-cd.gmi +++ b/topics/systems/ci-cd.gmi @@ -13,7 +13,10 @@ deployment cycle to help with quick iteration of the code. ## Tags * assigned: bonfacem, fredm, efraimf, aruni -* deployment +* keywords: deployment, CI, CD, testing +* status: in progress +* priority: high +* type: enhancement ## Tasks diff --git a/topics/systems/decommission-machines.gmi b/topics/systems/decommission-machines.gmi index 92614ad..496f23f 100644 --- a/topics/systems/decommission-machines.gmi +++ b/topics/systems/decommission-machines.gmi @@ -3,6 +3,10 @@ # Tags * assigned: pjotrp, arthurc, dana +* priority: high +* keywords: systems +* type: system administration +* status: unclear # Tasks diff --git a/topics/systems/gn1-time-machines.gmi b/topics/systems/gn1-time-machines.gmi index 1154a5e..0029016 100644 --- a/topics/systems/gn1-time-machines.gmi +++ b/topics/systems/gn1-time-machines.gmi @@ -39,6 +39,10 @@ so you can see all the different versions. The matching code bases should be the ## Tags * assigned: pjotrp, efraimf +* priority: high +* status: unclear +* type: system administration +* keywords: systems ## Tasks diff --git a/topics/systems/letsencrypt.gmi b/topics/systems/letsencrypt.gmi index feb4f48..bafae55 100644 --- a/topics/systems/letsencrypt.gmi +++ b/topics/systems/letsencrypt.gmi @@ -3,7 +3,9 @@ ## Tags * assigned: pjotr -* bug +* type: bug +* priority: critical +* status: completed, done, closed ## Tasks diff --git a/topics/systems/machine-room.gmi b/topics/systems/machine-room.gmi index d75883a..28d9921 100644 --- a/topics/systems/machine-room.gmi +++ b/topics/systems/machine-room.gmi @@ -3,6 +3,10 @@ ## Tags * assign: pjotrp, dana +* type: system administration +* priority: high +* keywords: systems +* status: unclear ## Tasks diff --git a/topics/systems/mariadb/ProbeData.gmi b/topics/systems/mariadb/ProbeData.gmi index b613784..c339571 100644 --- a/topics/systems/mariadb/ProbeData.gmi +++ b/topics/systems/mariadb/ProbeData.gmi @@ -1,4 +1,14 @@ +# ProbeData +## Tags + +* assigned: pjotrp, aruni +* status: unclear +* priority: medium +* type: enhancement +* keywords: database, mariadb, innodb, ProbeData + +## Description Probe level data is used to examine the correlation structure among the N probes that have the same nominal target. Sometimes several probes diff --git a/topics/systems/mariadb/ProbeSE.gmi b/topics/systems/mariadb/ProbeSE.gmi index f9aa670..2c36514 100644 --- a/topics/systems/mariadb/ProbeSE.gmi +++ b/topics/systems/mariadb/ProbeSE.gmi @@ -1,3 +1,15 @@ +# ProbeSE + +## Tags + +* assigned: pjotrp +* status: unclear +* priority: medium +* type: enhancement +* keywords: database, mariadb, innodb, ProbeSE + +## Description + Zach pointed out that ProbeSE is used on GN1 with => http://gn1.genenetwork.org/webqtl/main.py?FormID=showProbeInfo&database=HC_M2_0606_P&ProbeSetID=1427571_at&CellID=None&RISet=BXD&incparentsf1=ON diff --git a/topics/systems/mariadb/ProbeSetData.gmi b/topics/systems/mariadb/ProbeSetData.gmi index 63e7912..672b64c 100644 --- a/topics/systems/mariadb/ProbeSetData.gmi +++ b/topics/systems/mariadb/ProbeSetData.gmi @@ -1,5 +1,15 @@ # ProbeSetData +## Tags + +* assigned: pjotrp +* status: unclear +* priority: medium +* type: enhancement +* keywords: database, mariadb, innodb + +## Description + This is by far the largest table (~200Gb). I need to add disk space to be able to host it on the NVME and move stuff around. Final move is GN2 code and we have over 400Gb free. This time I failed porting to InnoDB. Next time: diff --git a/topics/systems/mariadb/ProbeSetXRef.gmi b/topics/systems/mariadb/ProbeSetXRef.gmi index d8981a5..cdf08f4 100644 --- a/topics/systems/mariadb/ProbeSetXRef.gmi +++ b/topics/systems/mariadb/ProbeSetXRef.gmi @@ -1,3 +1,13 @@ +# ProbeSetXRef + +## Tags + +* keywords: ProbeSetXRef, database, mariadb, innodb +* type: enhancement, documentation +* assigned: pjotrp +* status: unclear +* priority: medium + ## Table ProbeSetXRef Juggling indexes and transforming to InnoDB led to a massive speed increase for typical ProbeSetXRef queries. Global search for brca2 went down from 13s to 4s! Try diff --git a/topics/systems/mariadb/cleanup.gmi b/topics/systems/mariadb/cleanup.gmi index c034fbc..0639e40 100644 --- a/topics/systems/mariadb/cleanup.gmi +++ b/topics/systems/mariadb/cleanup.gmi @@ -1,4 +1,14 @@ +# Clean Up +## Tags + +* assigned: pjotrp, robw +* status: unclear +* priority: unclear +* type: database administration +* keywords: database, mariadb + +## Description Find all larger tables diff --git a/topics/systems/mariadb/mariadb.gmi b/topics/systems/mariadb/mariadb.gmi index c2c927b..0cbd0e7 100644 --- a/topics/systems/mariadb/mariadb.gmi +++ b/topics/systems/mariadb/mariadb.gmi @@ -4,7 +4,8 @@ Here we capture some common actions ## Tags -* info +* type: info, documentation +* keywords: mariadb, systems ## Check the transaction logs diff --git a/topics/systems/mariadb/move-to-innodb.gmi b/topics/systems/mariadb/move-to-innodb.gmi index b29173e..134a50a 100644 --- a/topics/systems/mariadb/move-to-innodb.gmi +++ b/topics/systems/mariadb/move-to-innodb.gmi @@ -1,3 +1,5 @@ +# MariaDB: Move to InnoDB Engine + We are going to move from myisam to innodb. Penguin2 has been happily running innodb for some time. Main problem are fulltext columns, the text from Trello is captured below. This is for the following tables @@ -581,3 +583,12 @@ On Penguin2 we are already runing ProbeSetData as ``` which is pretty massive! It includes the index, which is 180G, so the difference is not that great. Also we should try a 4kb page size. Also make sure to enable innodb_file_per_table. + + +## Tags + +* assigned: pjotr +* type: enhancement, documentation +* status: unclear +* priority: medium +* keywords: database, mariadb, innodb diff --git a/topics/systems/octopus.gmi b/topics/systems/octopus.gmi index 0929a65..1420865 100644 --- a/topics/systems/octopus.gmi +++ b/topics/systems/octopus.gmi @@ -3,6 +3,10 @@ # Tags * assigned: pjotrp, efraimf, erikg +* priority: high +* status: completed, closed +* type: system administration +* keywords: systems, octopus # Tasks diff --git a/topics/systems/reboot-tux01-tux02.gmi b/topics/systems/reboot-tux01-tux02.gmi index afed594..3186a0d 100644 --- a/topics/systems/reboot-tux01-tux02.gmi +++ b/topics/systems/reboot-tux01-tux02.gmi @@ -44,3 +44,11 @@ The Linux kernel shows some fixes that are not on Tux01 yet => https://lkml.org/lkml/2021/2/17/970 In our case a simple reboot worked, fortunately. + +## Tags + +* assigned: pjotrp +* status: unclear +* priority: medium +* type: system administration +* keywords: systems, tux01, tux02, production diff --git a/topics/systems/tux02-production.gmi b/topics/systems/tux02-production.gmi index 3a0a3c7..0b698ab 100644 --- a/topics/systems/tux02-production.gmi +++ b/topics/systems/tux02-production.gmi @@ -5,6 +5,10 @@ We are going to move production to tux02 - tux01 will be the staging machine. Th ## Tags * assigned: pjotrp +* status: in progress +* priority: medium +* type: system administration +* keywords: systems, tux02, production ## Tasks diff --git a/topics/testing/automated-testing.gmi b/topics/testing/automated-testing.gmi index 378a641..615d3ff 100644 --- a/topics/testing/automated-testing.gmi +++ b/topics/testing/automated-testing.gmi @@ -2,7 +2,11 @@ ## Tags -* assigned: fredm bonfacem alex +* assigned: fredm, bonfacem, alex +* status: in progress +* priority: medium +* type: enhancement +* keywords: testing, CI, CD ## Introduction diff --git a/topics/testing/genenetwork-checklist.gmi b/topics/testing/genenetwork-checklist.gmi index ba19733..8d7e01c 100644 --- a/topics/testing/genenetwork-checklist.gmi +++ b/topics/testing/genenetwork-checklist.gmi @@ -5,6 +5,8 @@ This is the checklist to run through when testing GN2. ## Tags * assigned: pjotrp +* type: documentation +* keywords: documentation, testing, checklist ## Tasks |