- 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
...an ontology exists and it looks sensible we should reuse that. If non-existent, we create our own ontology. Obviously we can't get away from adding free flow textual fields. What we want to lift out...
- 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
...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 changing...
- 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...
- Fix GN1 Network Graph
issue opened on Sep 15 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...neatoExit = os.spawnlp(os.P_WAIT, "/usr/local/bin/neato", "/usr/local/bin/neato", webqtlConfig.IMGDIR + filename, "-T", format, "-o", webqtlConfig.IMGDIR + imageFilename)
```
hard coded bin path...
- 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
.../28823252/installing-php-5-3-29-from-sources-on-ubuntu-14-with-apache-2-module
=> https://www.bobulous.org.uk/coding/apache-php-cgi.html
## Test instance of GN1
I started a test instance that listens...
- 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...
- 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
...annotation link - appears to be a hard coded redirect
* [ ] Enable time machines
* [ ] Disable all defunct URLs (needs a script)
* [X] Disable galaxy URL
* [X] Disable EC2 URL
* [X] Disable GN mailing...
- 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...
- csv export meta data are not commented out
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
...code
The csv looks like this:
```
Phenotype ID: 11320
Phenotype URL: http://genenetwork.org/show_trait?trait_id=11320&dataset=BXDPublish
Group: BXD
"Phenotype: Central nervous system"","" pharmacology""...
- 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...
- 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...
- 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
...routing_exception
NotFound: 404 Not Found: The requested URL was not found on the server. If you entered the URL manually please check your spelling and try again.
```
## Tasks
* [x] code...
- GN1 github problem
issue opened on Dec 17 2022 by Pjotr Prins
...genenetwork1 code base, so I can rewrite the git store.
```
find . -size +20M -exec ls -lh \{\} \;
-rwxr-xr-x 1 wrk wrk 263M Dec 15 15:38 ./web/images/upload/MouseTissuesRWWMay08.xls
```
Make a backup...
- 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...