- 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 github problem
issue opened on Dec 17 2022 by Pjotr Prins
...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% (20/20)...
- Penguin2 RAID 5
issue opened 8 weeks ago by Pjotr Prins
...RAID 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...
- 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...
- Apps
issue opened on Nov 19 2024 by Pjotr Prins, last updated 5 weeks ago by Pjotr Prins; 33 of 74 tasks done
...reboot (systemd)
=> https://bnw.genenetwork.org/
* [+] bnw [container] (yan cui and rob)
* [X] - fire up service
* [X] - add sheepdog monitor
* [X] - add link in GN2
* [ ] - add banner for GeneNetwork...
- 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
...GN3#104
=> https://github.com/genenetwork/genenetwork3/pull/101 GN3#101
=> https://github.com/genenetwork/genenetwork2/pull/757 GN2#757
=> https://github.com/genenetwork/genenetwork2/pull/756 GN2#756...
- 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
...use guix.genenetwork.org) adding --substitute-urls="http://guix.genenetwork.org https://ci.guix.info".
### Mariadb (est. 1-2 hours)
Set up a global Mariadb
```
guix package -i mariadb -p /usr/local/...
- 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...
- 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/...
- 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/...
- 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...
- 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
- 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
- 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...