- Designing an issue tracker on gemini
✓ issue opened on Jul 25 2021 by Pjotr Prins, last updated on Feb 02 2022 by Pjotr Prins
...will disconnect the git record. Therefore simple add
* closed
## Converting github issues
### Converting issues from a github issue tracker
=> https://github.com/mattduck/gh2md Github to markdown dump
- 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
...//github.com/genenetwork/genenetwork3/pull/104 GN3#104
=> https://github.com/genenetwork/genenetwork3/pull/101 GN3#101
=> https://github.com/genenetwork/genenetwork2/pull/757 GN2#757
=> https://github...
- GN1 github problem
issue opened on Dec 17 2022 by Pjotr Prins
...Large File Storage - https://git-lfs.github.com.
To github.com:genenetwork/genenetwork1.git
! [remote rejected] lily -> lily (pre-receive hook declined)
error: failed to push some refs to 'git@github...
- 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
...GN1, GN2, broken links, from github
## Members
* Millak
* pjotrp
* zsloan
* alex
* bonfacem
* robw
## Description
=> https://github.com/genenetwork/genenetwork2/issues/420 From GitHub
@Millak found...
- 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
...chrome, UI, from github
## Description
=> https://github.com/genenetwork/genenetwork2/issues/399 From GitHub
Based off
=> https://github.com/genenetwork/genenetwork2/pull/394 Pull Request #394.
I'd...
- Variant Browser seems to be using mm9
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
...stalled
* keywords: variant browser, mm9, from github
## Members
* acenteno
* robw
* pjotrp
## Description
=> https://github.com/genenetwork/genenetwork2/issues/581 From GitHub
When looking for SNPs...
- 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
...UI, SNP, from github
## Description
=> https://github.com/genenetwork/genenetwork2/issues/395
### Description
After an update using the latest datatables from GUIX from
=> https://github.com/...
- Multi-trait heat map failed
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
...from github
## Members
* zsloan
* pjotrp
* echesler
## Description
=> https://github.com/genenetwork/genenetwork2/issues/368 From GitHub
Selected multiple traits from phenotype correlations to Ap3m2...
- Gn Markdown Editor implementation
issue opened on Aug 07 2023 by Alexander_Kabui, last updated on Sep 11 2023 by Alexander_Kabui; 4 of 5 tasks done
...preview for page markdown on edit
* [] authentication(WIP)
* [x] commit changes to github repo
* [x] UI improvement
## Notes
for quick server setup refer to the documentation below:
=> https://github...
- GN1 annotation page broken
issue opened on Dec 23 2022 by Pjotr Prins
...github
## Description
=> https://github.com/genenetwork/genenetwork2/issues/421 From GitHub
=> http://gn1.genenetwork.org/webqtl/main.py?FormID=annotation The annotations page in GN1
is broken. An...
- 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
...github
## Description
=> https://github.com/genenetwork/genenetwork2/issues/418 From GitHub
Global search '*' causes loads of aborted connections... I mean
```
2020-08-15 2:53:58 140273206434560...
- Fetch trait names for phenotypes
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
...github
## Members
* robw
* rupertoverall
## Description
=> https://github.com/genenetwork/genenetwork2/issues/564 From GitHub
The 'Fetch Trait Info' query returns detailed information for transcript...
- 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
...github, high priority
## Description
=> https://github.com/genenetwork/genenetwork2/issues/374 From GitHub
Dear Developer,
When calculating correlation:
(GeneNetwork error: 'NoneType' object is not...
- BXD102xBXD077F1 Error
✓ issue opened on Mar 22 2022 by Frederick Muriuki Muriithi, last updated on Apr 07 2022 by Zachary Sloan
...github, closed
## Description
=> https://github.com/genenetwork/genenetwork2/issues/612 From GitHub
> Hi,
>
> There is an error when I click on Compute in Calculate Correlations. It does not load...
- csv export meta data are not commented out
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
...github, meta data
## Description
=> https://github.com/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...
- Annotation
issue opened on Sep 14 2022 by Pjotr Prins, last updated on Mar 14 2023 by Arun Isaac; 0 of 5 tasks done
.../End)
=> https://github.com/genenetwork/genenetwork2/blob/df36cc808e21202075d32559c9f295087bd8aee2/wqflask/base/trait.py#L528-L597
where max LRS locus position is fetched for traits
=> https://github...
- Error when attempt to zoom to a chromosome after mapping a PCA trait
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
...from github, high priority
## Description
=> https://github.com/genenetwork/genenetwork2/issues/367 From GitHub
When I produced a PCA trait in GN2, I could map fine, but when I selected a particular...
- 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
...collections, from github
## Members
* rupertoverall
## Description
=> https://github.com/genenetwork/genenetwork2/issues/559 From GitHub
### Describe the bug
When calcuating principal components...
- Wrong CSV in ITP_10001 longevity dataset
✓ issue opened on Apr 11 2022 by BonfaceKilz, last updated on Apr 12 2022 by BonfaceKilz
...Excel (or 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/...
- Slow query
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
...from github
## Description
=> https://github.com/genenetwork/genenetwork2/issues/419 From GitHub
These queries take 3 minutes and are pretty insane!
```
Query_time: 187.220555 Lock_time: 0.075028...
- rewrite sampledata fetching with genofiles using scheme
issue opened on Jul 19 2023 by Alexander_Kabui, last updated on Jul 26 2023 by Alexander_Kabui; 2 of 6 tasks done
...intoa fully working module
This is in turn be used to dump data to lmdb
We chose scheme to accomplish the task
See code:
=> https://github.com/BonfaceKilz/gn-data-vault.git
=> https://github.com/...
- Capture state of phenotypes in a HASH
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
...REST, UI
## Description
=> https://github.com/genenetwork/genenetwork2/issues/551 From GitHub
To represent the state of the database we need to start using HASH values or UUIDs. For phenotypes...
- 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
...annotation, from github
## Tasks
* [ ] Fix PHP view
* [ ] Fix CKEDITOR
## Description
Turns out that it is a PHP page that is not working. Also CKEDITOR is not visible.
=> https://github.com/...
- '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
...TempDataSet, from github
## Description
=> https://github.com/genenetwork/genenetwork2/issues/592 From GitHub
After successful entry of new BXD trait data (both my own data and the example BXD set...
- 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
...github, high priority
## Description
### Is your feature request related to a problem? Please describe.
We aim to capture metadata on the BXDs in RDF which will make querying
metadata fairly trivial.
- Apps
issue opened on Nov 19 2024 by Pjotr Prins, last updated 5 weeks ago by Pjotr Prins; 33 of 74 tasks done
...//github.com/satijalab/seurat/issues/8804
The 4 year old code lives at
=> https://github.com/genenetwork/singleCellRshiny
and it looks like lines like these need to be updated:
=> https://github.com/...
- 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
.../gene/aliases/Shh
["Hx","ShhNC","9530036O11Rik","Dsh","Hhg1","Hxl3","M100081","ShhNC"]
```
### Authentication proxy
The proxy also needs to run.
```
su gn2
cd ~/gn3_production
git clone https://github...
- Sheepdog
issue opened on Nov 08 2021 by Pjotr Prins, last updated on Jul 01 2022 by Arun Isaac; 3 of 17 tasks done
Sheepdog
I have written sheepdog to keep track of backups etc. Here are some issues
that need resolving at some point.
=> https://github.com/pjotrp/deploy...
- Parsing genotyfiles
issue opened on Jul 11 2023 by Alexander_Kabui
...the genofile identify
the file in the GENOTYPE_FILES and extract sample_listx
for entire parsing code refer to:
=> https://github.com/genenetwork/genenetwork3/blob/main/gn3/db/genotypes.py
* Linked...
- 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
...Redirect users to the login page if 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...
- Using guix-bioinformatics in a channels.scm file
issue opened on Aug 15 2021 by Efraim Flashner, last updated on Oct 09 2022 by Pjotr Prins
...a channels.scm file
channels.scm works fine. Only problem is that we don't have a guix-bioinformatics git server that is *not* gitlab or github.
I think we should move to ssh keys and cgit. The latter...
- 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
...forge's (currently GitHub) editting mode for the selected file.
For an example of what is expected, see the `edit page` link/button at
=> http://gemini.thebird.nl/gemini/genenetwork/gn-gemtext-threads/...
- Fix GN1 Network Graph
issue opened on Sep 15 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...//
github.com/genenetwork/genenetwork1/commit/88a6cb549cc318a961325666aed06f3196a5475d Commenting out functionality
Reverting on that code still won't show the image contained in
```
<img border="0"...
- 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
...the actual JS through github. The page
=> https://d3js.org/getting-started
has links to
=> https://d3js.org/d3.v7.js
=> https://d3js.org/d3.v7.min.js
We can't use those because the SHA may change. So...
- 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
...Recently epysode was reinstated after hardware failure. I took the opportunity to reinstall the machine. The backups are described in the repo (genenetwork org members have access)
=> https://github...
- 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
...//github.com/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...
- 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
...screenshots:
=> https://github.com/genenetwork/genenetwork2/pull/854
Genenetwork2 consumes the endpoint for the GN-Editor. Authentication is required to prevent access by malicious users and bots.
The...