- csv export meta data are not commented out
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
csv export meta data are not commented out
## Tags
* assigned: zsloan
* priority: high
* type: bug
* status: unclear
* keywords: CSV, from github, meta data
## Description...
- Search results for SNP looks weird
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Oct 12 2022 by Munyoki Kilyungi
...bug
* priority: medium
* status: in progress
* keywords: UI, SNP, from github
## Description
=> https://github.com/genenetwork/genenetwork2/issues/395
### Description
After an update using the latest...
- 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 data and index pages. MyISAM only caches index pages.
Just in this area alone, MyISAM does not waste time caching data. That's because it's not designed to cache data. InnoDB caches every data...
- Adding principal component to collection returns an error
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Apr 07 2022 by Alexander Kabui
...bug
* keywords: collections, from github
## Members
* rupertoverall
## Description
=> https://github.com/genenetwork/genenetwork2/issues/559 From GitHub
### Describe the bug
When calcuating principal...
- 'TempDataSet' object has no attribute 'query_for_group' (error)
✓ issue opened on Mar 22 2022 by Frederick Muriuki Muriithi, last updated on Sep 28 2022 by Alexander_Kabui
...as a batch file in the old version of genenetwork.
The trait data that I tried to upload and check on GN2 was the
median-lateral position of the representation of visual space on V1. It was
old data...
- Multi-trait heat map failed
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
Multi-trait heat map failed
## Tags
* assigned: zsloan
* type: bug
* priority: medium
* status: stalled
* keywords: heatmap, from github
## Members
* zsloan
* pjotrp
* echesler
## Description...
- Automatically find broken links on GN2
✓ issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Oct 12 2022 by Munyoki Kilyungi; 2 of 2 tasks done
...links in web pages
* [x] run gn2 on CI as a background task to search for broken links
### Notes
the bug above no longer exists.
gn2 CI runs on the background after for any push
raises an error if...
- 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
...metadata from RDF
Work on dumping RDF has already been done in:
=> https://github.com/genenetwork/dump-genenetwork-database dump-genenetwork-database
Also, vector/matrix data should be put in lmdb...
- Variant Browser seems to be using mm9
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
...in the search box at http://www.genenetwork.org/snp_browser, but the results are for the same coordinates in mm9 (see screenshot).
The example is for a search for 'Snx6' (chr12 54.746356 - 54.795662).
- 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
...-08-15 2:53:58 140273206434560 [Warning] Aborted connection 45219 to db: 'db_webqtl' user: 'webqtlout' host: '127.0.0.1' (CLOSE_CONNECTION)
```
generating 6Mb of log file info.
In fact, every row in...
- correlation error: 'NoneType' object is not iterable
✓ issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Apr 13 2022 by Alexander Kabui
...Feb 19, 2020)
'NoneType' object is not iterable (error)
File "/export/local/home/gn2/production/gene/wqflask/wqflask/correlation/show_corr_results.py", line 473, in process_samples
for sample in...
- Error when attempt to zoom to a chromosome after mapping a PCA trait
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
...bug
* priority: high
* status: unclear
* keywords: PCA, from github, high priority
## Description
=> https://github.com/genenetwork/genenetwork2/issues/367 From GitHub
When I produced a PCA trait in...
- Unable to open new tab for mapping/ correlations with Chrome
✓ issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Apr 18 2023 by Munyoki Kilyungi
Unable to open new tab for mapping/ correlations with Chrome
## Tags
* assigned: bonfacem
* type: bug
* status: unclear
* priority: medium
* keywords: mapping, correlation, google chrome, UI...
- GN1 annotation page broken
issue opened on Dec 23 2022 by Pjotr Prins
...bug
* keywords: GN1, genenetwork1, annotation, from github
## Description
=> https://github.com/genenetwork/genenetwork2/issues/421 From GitHub
=> http://gn1.genenetwork.org/webqtl/main.py?FormID...
- BXD102xBXD077F1 Error
✓ issue opened on Mar 22 2022 by Frederick Muriuki Muriithi, last updated on Apr 07 2022 by Zachary Sloan
...bug
* priority: critical
* status: unclear
* keywords: correlations, from github, closed
## Description
=> https://github.com/genenetwork/genenetwork2/issues/612 From GitHub
> Hi,
>
> There is an...
- 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
...have ?php are in ./infoshare. Try
```
gn1@tux01:~/production/gnshare/gn-pjotr-test$ grep '?php' -r > phpfiles.txt
```
they end in .htm and .html so we need to wire that together.
So adding a test in...
- Fetch trait names for phenotypes
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
..."Central nervous system, behavior, learning and memory: Morris water maze search-time preference, amount of time spent in the trained quadrant of the pool minus mean time in the alternative quadrants...