- 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
...broken links
### Notes
the bug above no longer exists.
gn2 CI runs on the background after for any push
raises an error if any broken link is found
On gn2 web pages all missing links that are found...
- 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
...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...
- 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...
- 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
...(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, 2020)
'NoneType' object...
- 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/...
- 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
...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 data...
- '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...
- 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).
- 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
- 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...
- 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
...com/genenetwork/genenetwork2/issues/418 From GitHub
Global search '*' causes loads of aborted connections... I mean
```
2020-08-15 2:53:58 140273206434560 [Warning] Aborted connection 45219 to db...
- Fetch trait names for phenotypes
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
...robw
* rupertoverall
## Description
=> https://github.com/genenetwork/genenetwork2/issues/564 From GitHub
The 'Fetch Trait Info' query returns detailed information for transcript expression traits...