diff options
39 files changed, 265 insertions, 32 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 diff --git a/tasks/pjotrp.gmi b/tasks/pjotrp.gmi index f6554fd..0c1d056 100644 --- a/tasks/pjotrp.gmi +++ b/tasks/pjotrp.gmi @@ -3,6 +3,13 @@ ## Tags * kanban: pjotrp +* assigned: pjotrp +* status: unclear +* keywords: pjotrp, to remove + +## Notes + +The tasks here should probably be broken out into appropriately tagged issues, where they have not - they can be found and filtered out with tissue (formerly gnbug). ## Tasks 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). |