- 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, db connections, medium priority, from github
## Description
=> https://github.com/genenetwork/genenetwork2/issues/418 From GitHub
Global search '*' causes loads of aborted connections...
- 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
.../genenetwork/genenetwork2/issues/395
### Description
After an update using the latest datatables from GUIX from
=> https://github.com/genenetwork/genenetwork2/pull/394 #394,
the genotype search results...
- 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).
- 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
...server. If you entered the URL manually please check your spelling and try again.
```
## Tasks
* [x] code to search for broken links in web pages
* [x] run gn2 on CI as a background task to search...
- 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 Annotate traits page with 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...
- 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
...genenetwork.org/test/index.html
Now a php version
=> http://gn1-pjotr.genenetwork.org/test/index.php
works after setting
```
# CUSTOM: Add PHP 5 parsing (via CGI) handler and action
ScriptAlias /local-...
- 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...
- Slow query
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
.../genenetwork/genenetwork2/issues/419 From GitHub
These queries take 3 minutes and are pretty insane!
```
Query_time: 187.220555 Lock_time: 0.075028 Rows_sent: 71 Rows_examined: 21265516
Query_time...
- 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
...calculating correlation:
(GeneNetwork error: 'NoneType' object is not iterable)
```
GeneNetwork tux01:gene:2.11-rc2-production-283af77a7 http://www.genenetwork.org/corr_compute ( 2:39PM UTC Feb 19...
- 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
...GeneNetwork tux01:gene:2.11-rc2-testing-73131a84f http://www.genenetwork.org/collections/view?uc_id=a7e8dce1-f6a3-464d-85eb-e5a7696ce0b6 (12:12PM UTC Mar 01, 2021)
Traceback (most...
- Multi-trait heat map failed
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
...to Ap3m2 in the hippocampus.
Selected "Heat Map"
```
GeneNetwork tux01:gene:2.11-rc2-production-2abbf82b4 http://gn2.genenetwork.org/heatmap (11:25AM UTC Sep 17, 2019)
reaper: the length of the strain...
- BXD102xBXD077F1 Error
✓ issue opened on Mar 22 2022 by Frederick Muriuki Muriithi, last updated on Apr 07 2022 by Zachary Sloan
...the error:
> GeneNetwork tux01:gene:2.11-rc2-testing-c16e361c4
> 'BXD102xBXD077F1' (error)
>
> Is this a server issue? Thanks!
>
> jacs123
> It is this https://www.genenetwork.org/show_trait?trait_id...
- csv export meta data are not commented out
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
.../genenetwork/genenetwork2/issues/594 From GitHub
csv export data can't be read using the example R code
The csv looks like this:
```
Phenotype ID: 11320
Phenotype URL: http://genenetwork.org/show_trait...
- Error when attempt to zoom to a chromosome after mapping a PCA trait
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
...GeneNetwork tux01:gene:2.11-rc2-production-5c6be7a36 http://gn2.genenetwork.org/run_mapping ( 5:57PM UTC Aug 22, 2019)
Traceback (most recent call last):
File "/usr/local/guix-profiles/...
- '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
...clicking the correlate button. This produced the error below:
GeneNetwork tux01:gene:2.11-rc2-staging-427071fc7 http://www.genenetwork.org/corr_compute (12:29PM UTC Jul 16, 2021)
'TempDataSet' object...
- 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
...https://github.com/genenetwork/genenetwork2/issues/399 From GitHub
Based off
=> https://github.com/genenetwork/genenetwork2/pull/394 Pull Request #394.
I'd need to spec this further later
* closed
- GN1 annotation page broken
issue opened on Dec 23 2022 by Pjotr Prins
...com/genenetwork/genenetwork2/issues/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...