- Fix GN1 Network Graph
issue opened on Sep 15 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
Fix GN1 Network Graph
Status: the network graph works on production. PDF output is empty, however.
## Tags
* type: bug
* priority: high
* keywords: GN1, Network Graph
* status: in progress
* kanban...
- GN1 Production
issue opened on Sep 15 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi; 3 of 8 tasks done
...EC2 URL
* [X] Disable GN mailing list URL
=> ./gn1-pairscan.gmi [x] Pairscan not working
=> ./gn1-network-graph.gmi [X] Fix network graph (it does not display image)
* [ ] Disable all defunct URLs
- GN1 github problem
issue opened on Dec 17 2022 by Pjotr Prins
...rm --cached --ignore-unmatch \
MouseTissuesRWWMay08.xls' --prune-empty --tag-name-filter cat -- --all
git reflog expire --expire=now --all && git gc --prune=now --aggressive
```
Note this rewrites...
- Apps
issue opened on Nov 19 2024 by Pjotr Prins, last updated 5 weeks ago by Pjotr Prins; 33 of 74 tasks done
...error after above upgrade:
```
no slot of name "counts" for this object of class
```
and the code needs to be updated:
=> https://github.com/satijalab/seurat/issues/8804
The 4 year old code lives at...
- Sheepdog
issue opened on Nov 08 2021 by Pjotr Prins, last updated on Jul 01 2022 by Arun Isaac; 3 of 17 tasks done
...exists)
* [ ] synchronize between queues using a dump
* [ ] sheepdog_expect.rb - expect PINGs
* [ ] sheepdog_rsync.rb - test for 'total size is 0'
* [ ] sheepdog_list tag and filter switches improve...
- 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
...are pretty straightforward. With GN2 the complexity has increased a lot because of interacting services and a larger dependency graph.
Here I track what it takes today to install a fallback instance...
- Designing an issue tracker on gemini
✓ issue opened on Jul 25 2021 by Pjotr Prins, last updated on Feb 02 2022 by Pjotr Prins
...help wanted
* closed
the keyword statement may have aliases, such as tag and kanban. To undo a keyword simply remove them from the file.
Can't think of anything more to add to make it really useful...
- Tux02 Production
issue opened on Oct 07 2021 by Pjotr Prins, last updated on Dec 14 2022 by Pjotr Prins; 17 of 22 tasks done
...-1.3.0-9.f743f20
* [X] set up nginx (Debian)
* [X] test ipmi console (172.23.30.40)
* [X] test ports (nginx)
* [?] set up network for external tux02e.uthsc.edu (128.169.4.52)
* [X] set up deployment...
- Enable all DataTables to call the same code
issue opened on Jul 26 2022 by Zachary Sloan, last updated on Jul 27 2022 by Zachary Sloan
...each separate page has its own DataTables initialization code. This results in inconsistency with features (like some tables having resizable columns and others not) and a lot of duplicated code.
I'm...
- Annotation
issue opened on Sep 14 2022 by Pjotr Prins, last updated on Mar 14 2023 by Arun Isaac; 0 of 5 tasks done
...replace existing code
* [ ] Replace all code to allow for selecting versions
# Notes
=> https://github.com/genenetwork/genenetwork2/blob/testing/wqflask/wqflask/interval_analyst/GeneUtil.py GeneList...
- 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
...
code is
```
<div class="qtlcharts" id="chart_container">
<div id="pairscan_chart"></div>
</div>
```
The problem is with Karl's D3 panels, we get an error 'TypeError: d3.scaleLinear...
- 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...
- 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
...and chromosome 7, it will show up first in the chromosome 7 result file even if its position is 122Mb. This causes a problem in the mapping display code, since the loop is set to break when the marker...
- 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
...integrate the components 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...
- Fix Broken Global Search UI
issue opened on Jan 07 2025 by Alexander_Kabui, last updated on Jan 07 2025 by Alexander_Kabui; 0 of 2 tasks done
...certain browser versions.
This issue was reported to occur for **Firefox Version 128.3.1** ESR Version.
The root cause of the problem is unclear,
but after reviewing the global search UI code,
the...
- Allow analyses to be done between traits from "individuals" groups and their corresponding "main" group
issue opened on Jul 21 2022 by Zachary Sloan
...so as long as there's a mapping of individuals with their respective strains.
My idea to enable this is to have some code (probably as a decorator function) that, prior to an analysis, checks if there...
- 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
...the genofiles
```
### TODOS
* [x] indentify all required fields for this
* [x] code implementation
* [ ] handling null values
## Documentation for Probeset,Genoset and Publish data types
### Publish...
- 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
...line 1: rm: command not found
```
The actual code for GeneNetwork3 is:
```python
def run_process(cmd, output_file, run_id):
"""Function to execute an external process and capture the stdout...