Merge branch 'main' of https://github.com/genenetwork/gn-gemtext-threads into main

3 files changed, 48 insertions, 13 deletions

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.
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/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.