- GN Markdown Editor Integration
issue opened on Jun 07 2024 by Alexander_Kabui, last updated on Aug 22 2024 by Alexander_Kabui; 9 of 10 tasks done
...2 for line\n test 3 for new line\n ## real markdown two test\n",
"hash": "<commit_sha>"
}
```
In case of an error, the expected response is:
```json
{
"error": "<error_type>",
"msg": "<error_reason>"...
- 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
...[root@lily conf]# /usr/sbin/httpd -V
Server version: Apache/2.2.3
Server built: Sep 16 2014 11:05:09
Server's Module Magic Number: 20051115:3
Server loaded: APR 1.2.7, APR-Util 1.2.7
Compiled...
- 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
...M430v2 (Jun06) PDNN 1436869_at Shh sonic hedgehog (hedgehog) mid distal 3' UTR 5 28.457155 9.279090909090911 12.7711275309832 rs8253327 0.306...
- GN1 github problem
issue opened on Dec 17 2022 by Pjotr Prins
...using up to 128 threads
Compressing objects: 100% (21/21), done.
Writing objects: 100% (23/23), 118.03 MiB | 23.15 MiB/s, done.
Total 23 (delta 20), reused 3 (delta 2)
remote: Resolving deltas: 100%...
- 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...
- Apps
issue opened on Nov 19 2024 by Pjotr Prins, last updated 5 weeks ago by Pjotr Prins; 33 of 74 tasks done
...//git.genenetwork.org/gn-machines/tree/gn/services/mouse-longevity.scm
gaeta:~/iwrk/deploy/gn-machines$ guix system container -L . -L ~/guix-bioinformatics --verbosity=3 test-r-container.scm -L ~/iwrk/...
- Penguin2 RAID 5
issue opened on Feb 28 2025 by Pjotr Prins
...contains 3 disks:
```
root@penguin2:~# cat /proc/mdstat
md0 : active raid5 sdb1[1] sda1[0] sdg1[4]
/dev/md0 33T 27T 4.2T 87% /export
```
using /dev/sda,sdb,sdg
The current root and swap...
- 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
...genenetwork.org/show_trait?trait_id=5581148&dataset=UMUTAffyExon_0209_RMA
```
GeneNetwork 2.11-rc2 https://fallback.genenetwork.org/run_mapping (10:01AM UTC Mar 22, 2024)
Traceback (most recent...
- 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
...GN2#755
=> https://github.com/genenetwork/genenetwork2/pull/753 GN2#753
=> https://github.com/genenetwork/genenetwork2/pull/751 GN2#751
=> https://github.com/genenetwork/genenetwork2/pull/747 GN2#747...
- 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
...may take a while. And when guix starts building lots of software it may be necessary to configure a substitute server (we use guix.genenetwork.org) adding --substitute-urls="http://guix.genenetwork...
- 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
...@Millak found this one:
=> http://www.genenetwork.org/tutorial/ppt/html/webqtl_demo2_part1.ppt.htm
```
GeneNetwork tux01:gene:2.11-rc2-production-1e421a063 http://www.genenetwork.org/tutorial/...
- Fallbacks and backups
issue opened on Aug 31 2021 by Pjotr Prins, last updated on Jun 28 2024 by Pjotr Prins; 3 of 25 tasks done
...it hadn't been down for months, but that is a different story).
As we are introducing an external sheepdog server we may give it a DNS entry as sheepdog.genenetwork.org.
=> http://sheepdog.genenetwork...
- 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...
- 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...
- 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...
- 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...
- Annotation
issue opened on Sep 14 2022 by Pjotr Prins, last updated on Mar 14 2023 by Arun Isaac; 0 of 5 tasks done
.../genenetwork/genenetwork2/blob/df36cc808e21202075d32559c9f295087bd8aee2/wqflask/base/trait.py#L528-L597
where max LRS locus position is fetched for traits
=> https://github.com/genenetwork/genenetwork2/...
- 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
...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 has no attribute 'query_for_group'...
- Wrong CSV in ITP_10001 longevity dataset
✓ issue opened on Apr 11 2022 by BonfaceKilz, last updated on Apr 12 2022 by BonfaceKilz
...similar) software resulted in data that seems jumbled up.
### Tue 12 Apr 2022 13:33:31 EAT
The relevant fixes:
=> https://github.com/genenetwork/genenetwork2/pull/697
=> https://github.com/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).
- 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...
- Parsing genotyfiles
issue opened on Jul 11 2023 by Alexander_Kabui
...GENOTYPE_FILES and extract sample_listx
for entire parsing code refer to:
=> https://github.com/genenetwork/genenetwork3/blob/main/gn3/db/genotypes.py
* Linked to issue
=> https://issues.genenetwork...
- 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...
- Zoomed mapping result are empty for certain traits
issue opened on Apr 11 2022 by Zachary Sloan, last updated on Apr 13 2022 by Zachary Sloan
...trait, if you zoom into a range for a specific Chromosome by clicking the top pink bar ("8x expanded WebQTL map") no points are displayed: https://genenetwork.org/show_trait?trait_id=NM_029911&dataset...
- 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
...they are not logged in.
* [x] Implement a redirect to the correct resource after users log in.
## Notes
See this PR for commits that fixes this:
=> https://github.com/genenetwork/genenetwork2/pull/875
- 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...
- Marker covariates implemented wrong in rqtl_wrapper.R
issue opened on Sep 22 2021 by Zachary Sloan, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
- 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...
- Capture state of phenotypes in a HASH
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
.../genenetwork/genenetwork2/issues/551 From GitHub
To represent the state of the database we need to start using HASH values or UUIDs. For phenotypes we should create these for phenotype columns within...
- 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...
- Fix GN1 Network Graph
issue opened on Sep 15 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
.../
genenetwork/genenetwork1/commit/88a6cb549cc318a961325666aed06f3196a5475d Commenting out functionality
Reverting on that code still won't show the image contained in
```
<img border="0" alt="the graph"...
- Investigate and Fix `rm` Command in `rqtl` Logs
issue opened on Jan 08 2025 by Alexander_Kabui, last updated on Jan 09 2025 by Munyoki Kilyungi; 4 of 6 tasks done
.../genenetwork/genenetwork3/blob/main/scripts/rqtl_wrapper.R
The issue is that, upon analyzing the logs for `rqtl`, we see that an `rm` command is unexpectedly invoked:
```
sh: line 1: rm: command not...
- Designing an issue tracker on gemini
✓ issue opened on Jul 25 2021 by Pjotr Prins, last updated on Feb 02 2022 by Pjotr Prins
...file E-mails as issues ourselves.
Key point is that the issue tracker is meant to track issues owned by the project.
## Example
I added a first issue here:
=> https://github.com/genenetwork/gn-gemtext-...
- Fetch trait data using genofiles
issue opened on Jul 11 2023 by Alexander_Kabui, last updated on Jul 13 2023 by Alexander_Kabui; 2 of 3 tasks done
...since Genenetwork database does not have all genotype files when fetching sample data use genotypes to fetch trat data given a dataset and the trait
Having fetched the sample names of a given group...