- CD is slow
issue opened on Jul 20 2025 by Pjotr Prins, last updated on Jul 24 2025 by Pjotr Prins; 2 of 8 tasks done
...32.09. Typically, a traits page should take 8.79s. The difference: (- 37.9 32.09) = 5.8s; which explains the slowness:
```
ncall tottime percall cumtime percall filename:lineno(function)...
- Slow query
issue opened on May 27 2023 by Pjotr Prins, last updated on May 29 2023 by Pjotr Prins; 0 of 2 tasks done
...caches every data page and index page (and its grandmother) it touches. If your InnoDB Buffer Pool is too small, you could be caching pages, invalidating pages, and removing pages all in one query.
I...
- Slow query
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
Slow query
## Tags
* assigned: Uditgulati
* priority: high
* status: stalled
* keywords: slow query, from github
## Description
=> https://github.com/genenetwork/genenetwork2/issues/419 From GitHub...
- Annotate traits page with metadata from RDF
✓ issue opened on Sep 30 2022 by Munyoki Kilyungi, last updated on Dec 15 2022 by Munyoki Kilyungi; 16 of 16 tasks done
...page with metadata from RDF
* assigned: bonfacem
* priority: high
* status: in progress
* keywords: rdf, critical, metadata
Read the design-doc here:
=> /topics/add-metadata-to-trait-page
This task...
- Global search does not close connections properly (and is slow)
✓ issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Oct 14 2022 by Arun Isaac
Global search does not close connections properly (and is slow)
## Tags
* type: bug
* priority: medium
* status: stalled
* assigned: Uditgulati
* keywords: global search, db connections, medium...
- Designing an issue tracker on gemini
✓ issue opened on Jul 25 2021 by Pjotr Prins, last updated on Feb 02 2022 by Pjotr Prins
.../gn-gemtext-threads/blob/main/issues/database-not-responding.gmi
## Process
We leverage git to pull out dates and people contributions (pjotrp wrote ...) for display in a document/web page. This page...
- Sheepdog
issue opened on Nov 08 2021 by Pjotr Prins, last updated on Jul 01 2022 by Arun Isaac; 3 of 17 tasks done
...exists)
* [ ] synchronize between queues using a dump
* [ ] sheepdog_expect.rb - expect PINGs
* [ ] sheepdog_rsync.rb - test for 'total size is 0'
* [ ] sheepdog_list tag and filter switches improve...
- GN1 github problem
issue opened on Dec 17 2022 by Pjotr Prins
...rm --cached --ignore-unmatch \
MouseTissuesRWWMay08.xls' --prune-empty --tag-name-filter cat -- --all
git reflog expire --expire=now --all && git gc --prune=now --aggressive
```
Note this rewrites...
- GN1 Production
issue opened on Sep 15 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi; 3 of 8 tasks done
...pjotrp, zachs, robw
## List of outstanding issues
(see also E-mail Rob 14 Sep 2021)
* [ ] Fix annotating metadata - or do we have GN2 alternative?
=> gn1-slowness.gmi [.] Clean up tmp dirs with CRON...
- AI UI Enhancements
issue opened on Mar 01 2024 by Pjotr Prins; 0 of 3 tasks done
...GN searched for the term(s) "shh" in 754 datasets and 39,765,944 traits across 10 species
and found 1210 results that match your query.
You can filter these results by adding key words in the fields...
- Fallback issues
issue opened on Mar 22 2024 by Pjotr Prins, last updated on Apr 05 2024 by Pjotr Prins; 3 of 6 tasks done
...path, query, fragment = parse_url(url)
File "/gnu/store/a39cgbdawj9vp24nsz9q25sf9g5vda7c-profile/lib/python3.10/site-packages/urllib3/util/url.py", line 397, in parse_url
return six.raise_from...
- GN1 annotation page broken
issue opened on Dec 23 2022 by Pjotr Prins
.../421 From GitHub
=> http://gn1.genenetwork.org/webqtl/main.py?FormID=annotation The annotations page in GN1
is broken. An exception stack trace is displayed, instead of the annotations page content.
- Redirect Users to the Correct URL on Login for GN2
✓ issue opened on Sep 17 2024 by Alexander_Kabui, last updated on Oct 16 2024 by Alexander_Kabui; 2 of 2 tasks done
...then return them to the page they were trying to access before logging in, rather than sending them to the homepage. Additionally, display the message "You are required to log in" on the current page...
- GN1 annotation page broken
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Dec 17 2022 by Pjotr Prins; 0 of 2 tasks done
...page in GN1
is broken. An exception stack trace is displayed, instead of the annotations page content.
## Info
Lily runs a PHP from 2006(!)
PHP 5.1.6 (cli) (built: Mar 18 2014 20:48:55)
Copyright (c)...
- Variant Browser seems to be using mm9
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
...do not match the query.
Searching for a gene gives correct coordinates in the search box at http://www.genenetwork.org/snp_browser, but the results are for the same coordinates in mm9 (see screenshot).
- Fetch trait names for phenotypes
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
.../564 From GitHub
The 'Fetch Trait Info' query returns detailed information for transcript expression traits, but not for traits from the 'Publish' database.
### Describe the solution you'd like
For...
- Capture Data on the BXDs in RDF
✓ issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Oct 12 2022 by Munyoki Kilyungi
...-page Add Metadata To The Trait Page (RDF)
This is currently being worked on in:
=> issues/add-metadata-to-traits-page Annotate traits page with metadata from RDF
Work on dumping RDF has already been...
- Add track for showing which regions in mouse/rat correspond to human regions to the mapping figure
issue opened on Jul 21 2022 by Zachary Sloan, last updated on Sep 14 2022 by Pjotr Prins
...showing homology across mouse/human/maybe rat (done for mouse, won't be hard to also enable for other species)
[ ] Make it display an arrow depending on the strand (whether the query strand matches...
- Enable all DataTables to call the same code
issue opened on Jul 26 2022 by Zachary Sloan, last updated on Jul 27 2022 by Zachary Sloan
...drawn independently, so each separate page has its own DataTables initialization code. This results in inconsistency with features (like some tables having resizable columns and others not) and a lot...
- Branding and front-end-services
issue opened on Jun 14 2023 by Pjotr Prins; 0 of 1 tasks done
...off a single machine.
# Tasks
* [ ] Create community server for GN4MSK
* + [ ] Fire up parallel page server
* + [ ] Handle headers and footers
* + [ ] Create portal page
* + [ ] Show specific datasets...
- Fix GN1 Network Graph
issue opened on Sep 15 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...</p> ''' % (imageName, pdfName)
```
The PDF link works but is an empty page! So something is going wrong with generating this image in an earlier step. The page says it is using GraphViz
which brings...
- Search results presentation
issue opened on Apr 04 2023 by Alexander_Kabui
...tabular form and too many columns are presented to user overlapping the page
Design should be simple and eye catching to user
links to suggesetd designs:
=> https://www.ncbi.nlm.nih.gov/genome/?term...
- Fix Broken Global Search UI
issue opened on Jan 07 2025 by Alexander_Kabui, last updated on Jan 07 2025 by Alexander_Kabui; 0 of 2 tasks done
...custom layout CSS and replace it with the Bootstrap layout for better uniformity and easier debugging.
* [ ] Modify the navbar to extend across the full width of the page on medium and small devices.
- Allow analyses to be done between traits from "individuals" groups and their corresponding "main" group
issue opened on Jul 21 2022 by Zachary Sloan
...the mappings of individuals to strains exists in the CaseAttributes tables. A Temp trait could be created for the purposes of the analysis (though this presents potential issues with trait page links).
- Add the option to save traits uploaded with the Submit Trait option
issue opened on Jul 19 2022 by Zachary Sloan
...changes/additions that should be made to this:
- Allow data to be submitted via a CSV upload
- Allow data to be saved to the DB via an "Add" (or maybe "Save") button on the trait page after submitting...
- Add an 'Edit Issue' Link to Tissue
✓ issue opened on Mar 24 2022 by Frederick Muriuki Muriithi, last updated on Apr 15 2022 by Arun Isaac
...expected, see the `edit page` link/button at
=> http://gemini.thebird.nl/gemini/genenetwork/gn-gemtext-threads/topics/data-uploads/editing-data.gmi
noting how it drops you straight into editting the...
- Wrong CSV in ITP_10001 longevity dataset
✓ issue opened on Apr 11 2022 by BonfaceKilz, last updated on Apr 12 2022 by BonfaceKilz
...case-attr page with links
## Notes
### Mon 11 Apr 2022 13:19:14 EAT:
The CSV file is technically fine. In that database, some characters are inserted with control sequences that need to be stripped...
- GN2 Time Machines
issue opened on Aug 19 2022 by Pjotr Prins, last updated on Sep 05 2022 by Alexander_Kabui; 4 of 10 tasks done
...main page and you see 'There was an error retrieving and setting the menu. Try again later.'
GN3 is a separate REST server that has its own dependencies. A bit confusingly it is also a Python module...