- 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
...in progress
* keywords: UI, SNP, from github
## Description
=> https://github.com/genenetwork/genenetwork2/issues/395
### Description
After an update using the latest datatables from GUIX from...
- 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
...in Guix GN1. No mention of PHP in either.
For simplicity we may switch to php-cgi
=> https://stackoverflow.com/questions/28823252/installing-php-5-3-29-from-sources-on-ubuntu-14-with-apache-2-module...
- 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...
- 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
...genenetwork.org/tutorial/ppt/html/webqtl_demo2_part1.ppt.htm
```
GeneNetwork tux01:gene:2.11-rc2-production-1e421a063 http://www.genenetwork.org/tutorial/ppt/html/webqtl_demo2_part1.ppt.htm (11...
- 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...
- Error when attempt to zoom to a chromosome after mapping a PCA trait
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
...I produced a PCA trait in GN2, I could map fine, but when I selected a particular chromosome I got the following error:
```
GeneNetwork tux01:gene:2.11-rc2-production-5c6be7a36 http://gn2.genenetwork...
- 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...
- 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...
- csv export meta data are not commented out
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
...Goldowitz D, Chesler EJ"
Title: High-throughput behavioral phenotyping in the expanded panel of BXD recombinant inbred strains
"Journal: Genes, Brain & Behavior"
Dataset Link: http://gn1.genenetwork...
- '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
...in init
dataset.query_for_group)
Hi Rob and Zachary,
Thanks for getting back so quickly. There is no urgency for me. I managed
to upload the trait as a batch file in the old version of genenetwork.
- 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).
- 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
.../genenetwork/genenetwork2/issues/612 From GitHub
> Hi,
>
> There is an error when I click on Compute in Calculate Correlations. It does not load the correlations. This is the error:
> GeneNetwork tux01...
- 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...
- 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...
- 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...