From b83285f518421f2e223ca6bd95332d82c270f7fa Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Tue, 23 Aug 2022 21:42:56 +0300 Subject: Update issue on 404 logs --- issues/genenetwork/issue-404-in-logs.gmi | 11 +++-------- 1 file changed, 3 insertions(+), 8 deletions(-) (limited to 'issues/genenetwork') diff --git a/issues/genenetwork/issue-404-in-logs.gmi b/issues/genenetwork/issue-404-in-logs.gmi index 0006896..8e69838 100644 --- a/issues/genenetwork/issue-404-in-logs.gmi +++ b/issues/genenetwork/issue-404-in-logs.gmi @@ -1,6 +1,4 @@ -# 404 error in logs - -We get many 404's in GN logs. Can we rewire that so no log entries appear as a full stack dump? +# Better Logging ## Tags @@ -14,12 +12,9 @@ We get many 404's in GN logs. Can we rewire that so no log entries appear as a f => https://flask.palletsprojects.com/en/2.0.x/errorhandling/ -Some of those 404's in our log -mean that we forgot to package something; for -example: +Some of those 404's in our log mean that we forgot to package something; for example: -=> -https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics/commit/e80fe4ddcf15e21004b8135cf8af34b458697f64 +=> https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics/commit/e80fe4ddcf15e21004b8135cf8af34b458697f64 Removing the 404's would prevent us from catching important errors if ever they occur. I suggest we fix the 404's; some of them have a cascading effect, like the font-awesome missing "webfonts" folder I just fixed that leads to a lot of unnecessary 404s. -- cgit v1.2.3 From dfacbce921f752098b7b3360c99b2448ce2c1bb5 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Fri, 26 Aug 2022 10:22:34 +0200 Subject: Updated tasks --- issues/genenetwork/global-search.gmi | 13 ++++++++----- tasks/ongoing.gmi | 28 ++++++++++++++++++++++++++++ tasks/zsloan.gmi | 4 +--- 3 files changed, 37 insertions(+), 8 deletions(-) create mode 100644 tasks/ongoing.gmi (limited to 'issues/genenetwork') diff --git a/issues/genenetwork/global-search.gmi b/issues/genenetwork/global-search.gmi index a39da80..156145d 100644 --- a/issues/genenetwork/global-search.gmi +++ b/issues/genenetwork/global-search.gmi @@ -1,16 +1,19 @@ # Global search problems -Global search is the top bar of GN2 +Global search is the top bar of GN2. + +Note we are replacing search with xapian. So this is less important. ## Tags * assigned: pjotrp, zsloan -* status: unclear -* priority: critical +* status: later +* priority: low * type: bug * keywords: global search, BRCA2 ## Tasks -* [ ] BRCA2 does not render results in table -* [ ] 'Brca2' with quotes gives a SQL error +* [X] BRCA2 does not render results in table +* [ ] 'Brca2' with quotes gives a SQL error, see +=> http://genenetwork.org/gsearch?type=gene&terms=%27Brca2%27 diff --git a/tasks/ongoing.gmi b/tasks/ongoing.gmi new file mode 100644 index 0000000..799f5ee --- /dev/null +++ b/tasks/ongoing.gmi @@ -0,0 +1,28 @@ +# Ongoing Work + +In this document we track ongoing work. + +## Tags + +* kanban: pjotrp +* assigned: pjotrp +* status: ongoing +* keywords: pjotrp, to remove + +## Notes + +## Tasks + +Ongoing + +* [ ] Rust correlations and materialised view (Fred, Alex) +* [ ] Fix missing GENO file (Zach, Pjotr, Gregory) +* [ ] Bringing Xapian Search to GN (Arun) +* [ ] New genotype format (Arun, Pjotr, Bonface) +* [ ] RDF and virtuoso endpoint (Bonface, Arun, Pjotr) +* [ ] Data upload and curation (Fred, Arthur) +* [ ] Deployment container for GN2 (Arun) +* [ ] GeneNetwork paper (Pjotr, Rob) +* [ ] Creating a live monitor/sanity checker for GN (Arun) +* [ ] Pangenome genotype correction with vcflib (Pjotr) +* [ ] Becoming a DOI provider (Pjotr) diff --git a/tasks/zsloan.gmi b/tasks/zsloan.gmi index 30cba44..4e425e6 100644 --- a/tasks/zsloan.gmi +++ b/tasks/zsloan.gmi @@ -3,13 +3,11 @@ ## Tags * assigned: zsloan -* keywords: global search, genewiki +* keywords: genewiki * status: unclear * priority: unclear ## Tasks -* [ ] Fix global search -=> ../issues/genenetwork/global-search.gmi fix global search * [ ] GN1 migrate genewiki pages => ../issues/genenetwork/genewiki.gmi -- cgit v1.2.3 From a6299a491b89d45c5d43d4044ecdc2e5e351cfdd Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Fri, 26 Aug 2022 05:52:42 -0500 Subject: One GeneWiki --- issues/genenetwork/genewiki.gmi | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) (limited to 'issues/genenetwork') diff --git a/issues/genenetwork/genewiki.gmi b/issues/genenetwork/genewiki.gmi index e0a0a00..ce54afb 100644 --- a/issues/genenetwork/genewiki.gmi +++ b/issues/genenetwork/genewiki.gmi @@ -25,3 +25,40 @@ with an edit button, similar to * keywords: GN1, documentation ## Tasks + +* [ ] Export Genewiki to markdown - one file per gene and store in git@github.com:genenetwork/gn-docs.git +* [ ] Format output for GN using markdown parser (similar to other docs) +* [ ] Provide edit link to github + +Later we'll add automated links to wikidata and Uniprot etc. + +## Notes + +Zach writes: How exactly do we want to store all of this? It appears to currently be +stored across three SQL tables - GeneRIF, GeneRIFXRef, and GeneCategory. +The first contains a row for each item a user adds (when displaying all +items it queries by gene symbol), and the latter two are for storing the +checkbox stuff (so there will presumably be a row in GeneRIFXRef for every +checked box for each symbol, though this isn't totally clear to me because +it's linked by GeneRIF.Id - which isn't unique - rather than GeneRIF.symbol +which is what I would have assumed). + +IIRC the issue I ran into (that isn't immediately apparent from looking at +the web page) is that it's currently stored as a list of items. There isn't +a single "free text" area - when a user edits they are either adding a new +text item with its own row in the DB or editing one of the existing items, +so I'm not sure how best to reasonably convert the current contents and +editing method to markdown. Currently it doesn't even support any sort of +user styling/formatting - users just enter basic text into a form. And if +they were converted to markdown, how would we be storing the checkbox +content? + +It's probably possible to write a script that goes through those tables and +generates a bunch of markdown files from them (one for each gene symbol, I +think?), with the list of items just being converted into a single markdown +file with those items formatted into a list. This would de-link GN1's +GeneWiki from GN2's in the future, though (since the way things are stored +would be fundamentally changed). + +Pj: That is what we want. Create a markdown file for each gene symbol. +Checklist can be part of that using markdown syntax. -- cgit v1.2.3