- 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
...map") no points are displayed: https://genenetwork.org/show_trait?trait_id=NM_029911&dataset=UTHSC_BXD_WB_RNASeq1112
# Tags:
* source: robwwilliams
* type: mapping user interface display failure...
- Sheepdog
issue opened on Nov 08 2021 by Pjotr Prins, last updated on Jul 01 2022 by Arun Isaac; 3 of 17 tasks done
...rb - test for 'total size is 0'
* [ ] sheepdog_list tag and filter switches improve behaviour
* [ ] add sheepdog_web_monitor - currently using plain curl
* [X] borg: set user/group after backup...
- Add track for showing which regions in mouse/rat correspond to human regions to the mapping figure
issue opened on Jul 21 2022 by Zachary Sloan, last updated on Sep 14 2022 by Pjotr Prins
...in progress
* keywords: mapping
I currently have it displaying regions in mouse with text and a UCSC genome browser link to the corresponding human region as a track for the mapping figure.
# TODO
[X]...
- Designing an issue tracker on gemini
✓ issue opened on Jul 25 2021 by Pjotr Prins, last updated on Feb 02 2022 by Pjotr Prins
...in progress
* testing
* later
* documentation
* 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...
- 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...
- 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
...logging in, rather than sending them to the homepage. Additionally, display the message "You are required to log in" on the current page instead of on the homepage.
## Tasks
* [x] Redirect users...
- 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
...patches for review
## Display the metadata in GN2 as HTML
* [x] Display the metadata as part of GN2 web-page. This data is stored as HTML. How do work around this WRT displaying in a UI friendly way?
- 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
...stdout.
run_id: Unique ID to identify the process.
Returns:
A dictionary with the results, indicating success or failure.
"""
cmd.append(" && rm") # Injecting potentially...
- Search results presentation
issue opened on Apr 04 2023 by Alexander_Kabui
...displayed in tabular form and too many columns are presented to user overlapping the page
Design should be simple and eye catching to user
links to suggesetd designs:
=> https://www.ncbi.nlm.nih.gov/...
- 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
...TUX01_BORG_GN2_HOME-20210830-04:00-Mon
```
## Get backups running on fallback
Recently epysode was reinstated after hardware failure. I took the opportunity to reinstall the machine. The backups are...
- Allow analyses to be done between traits from "individuals" groups and their corresponding "main" group
issue opened on Jul 21 2022 by Zachary Sloan
These mappings could be stored in a simple JSON file.
The "main" group trait(s) could then have their sample data converted to the sample list of the "individuals" group, provided the mappings...
- Capture state of phenotypes in a HASH
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
...dataset - i.e. the column one uses for mapping. @zsloan this is metadata and I suggest we use RDF so we can have a historic view of changes in datasets. A change can be described as table - mapped to...
- 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
...-r--r-- 1 root root 10M Apr 2 07:03 4OJCzmGV.cross
-rw-r--r-- 1 root root 10M Apr 2 07:03 6cExgwkd.cross
```
# Purescript browser buttons not showing (fixed)
The following button does not display...
- 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
...progress
* keywords: tables, javascript
# Description
Currently most DataTables are drawn independently, so each separate page has its own DataTables initialization code. This results in inconsistency...
- Annotation
issue opened on Sep 14 2022 by Pjotr Prins, last updated on Mar 14 2023 by Arun Isaac; 0 of 5 tasks done
...open, in progress
* keywords: mapping, architecture
# TODO
* [ ] Point out where annotation is used in code (@zsloan)
* [ ] Come up with a storage model to replace the existing Mariadb tables (pjotrp...
- Fix GN1 Network Graph
issue opened on Sep 15 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...that
displays the graph itself
652: body += ''' <p>This graph took %s seconds to generate with the <a href="http://www.research.att.com/sw/tools/graphviz/" class="normalsize" target="_blank">...
- 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
...(about an hour)
```
root@tux02:/export3/backup/tux01/borg# borg extract borg-tux01::borg-backup-mariadb-20211024-03:09-Sun --progress
```
Next move the dir to fast storage.
#### Symlink /var/lib/mysql...
- 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
...past:
=> https://user-images.githubusercontent.com/11820306/82554424-8e0ac600-9b6e-11ea-9a50-f53506eb44a5.png Screen Shot 2020-05-20 at 10 01 10 PM
Here's how it looks like now:
https://user-images...
- AI UI Enhancements
issue opened on Mar 01 2024 by Pjotr Prins; 0 of 3 tasks done
...In Progress
## Description
This issue addresses user feedback received during the testing phase of GNQA on CD. The following improvements are required
## Tasks
* [ ] Only show the link when a user...
- Troubleshoot response inconsistencies for GN-llm
issue opened on Jan 10 2024 by Alexander_Kabui
...Progress
# Description
There are discrepancies when asking questions on Qnqa using Fahamu. Sometimes, responses take too long, and related queries with differing sentence structures may result in no...
- 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
...PROGRESS
* keywords: markdown,editor
## Tasks
* [x] implement markdown page editor
* [x] add live preview for page markdown on edit
* [] authentication(WIP)
* [x] commit changes to github repo
* [x]...
- 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
...open, in progress
* keywords: tissue, edit issue
## Description
Add an `Edit Issue` link on each issue that drops the user in the forge's (currently GitHub) editting mode for the selected file.
- Tux01 hard disk crash
issue opened on Sep 29 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...fortunately we have a BORG_BORG backup (a backup of the backup):
```
epysode:/export/backup$ borg extract --progress borg-borg::BORG_BORG_TUX01-Saturday-20210925-07:12:04
```
We are adding a new 4TB...
- 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
...user, in our case from auth)
* `commit_message`
If the request succeeds, the response should be:
```json
{
"status": "201",
"message": "Committed file successfully",
"content": "Test for new user\n...
- Each shepherd service needs its own guix profile.
issue opened on Nov 03 2021 by Efraim Flashner, last updated on Jun 21 2024 by Pjotr Prins
...a guix shell/environment:
* bnw
* cronjob-gitea
* cronjob-pubmed (genecup)
* genecup
* gitea
* ipfs
* power
* rn6app
* singlecell
## Tags
* assigned: efraim, pjotrp
* type: bug
* status: in progress...
- Wrong CSV in ITP_10001 longevity dataset
✓ issue opened on Apr 11 2022 by BonfaceKilz, last updated on Apr 12 2022 by BonfaceKilz
...progress, metadata, phenotypes
## Description
[From Suheeta]:
"I downloaded the sample csv file for ITP_10001 to add a couple of attributes to it. What I see is that the csv file is somewhat messed up.
- Branding and front-end-services
issue opened on Jun 14 2023 by Pjotr Prins; 0 of 1 tasks done
...specific datasets
* + [ ] Show specific publications
* + [ ] Show specific twitter feed
# Tags
* assigned: pjotrp
* type: feature
* priority: high
* status: in progress
* keywords: website, branding
- 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
...--progress /export2/backup/tux01/borg-tux01::borg-backup-mariadb-20220815-03:13-Mon
```
Extracting 430Gb takes about 90 minutes.
Now make sure mariadb is stopped. Copy the database to fast storage.
- Report invalid search queries passed to the search API
issue opened on Feb 15 2023 by Arun Isaac, last updated on Apr 04 2023 by Alexander_Kabui
...progress
genenetwork2 offloads search to the genenetwork3 search API. When there is an error in the genenetwork3 API call, genenetwork2 has no idea what went wrong and cannot produce a good stacktrace.
- Parsing genotyfiles
issue opened on Jul 11 2023 by Alexander_Kabui
Parsing genotyfiles
## Tags
* assigned: alexm
* type: debug
* priority: high
* status: in progress
## Once you identify the genofile identify
the file in the GENOTYPE_FILES and extract sample_listx...
- 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
...in progress
## Notes
having identified ways to link genofiles to Dataset
and fetching sample data and case attributes using them
we need to integrate the components intoa fully working module...
- 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
...waiting on Danny to get back to me with the fix (which I'll then add to rqtl_wrapper.R)
## Tags
* type: bug
* assigned: zsloan, danny
* status: in progress, halted
* keywords: marker covariates...
- 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
...in progress
* Keyword : search, UI, bug, Refactor
* Type: UI, bug
## Description
The Global search UI layout is broken on certain browser versions.
This issue was reported to occur for **Firefox...
- Add the option to save traits uploaded with the Submit Trait option
issue opened on Jul 19 2022 by Zachary Sloan
...-request
* status: open, in progress
* keywords: data, meta-data
# Description
Current the Submit Trait feature only allows for trait data (submitted as just a string of values) to be saved as a "temp"...
- 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
I think we should move to ssh keys and cgit. The latter has to run in a container, ideally.
## Tags
* assigned: efraimf, pjotrp
* type: bug
* keywords: guix-bioinformatics
* status: in progress...
- Return canned text if notebook description returns none
issue opened on Oct 28 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
Return canned text if notebook description returns none
## Tags
* type: bug
* assigned: jgart
* priority: high
* status: in progress
* keywords: binderlite, notebooks
## Description
Notebooks that do...
- Integrate styling of app with GN2
issue opened on Oct 28 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...in progress
* assigned: jgart
* type: bug
* priority: medium
* keywords: binderlite, notebooks, styling, UI
## Description
Currently using antiweb for styling with modifications.
=> https://git.sr.ht/~...
- Penguin2 RAID 5
issue opened 8 weeks ago by Pjotr Prins
...progress
# Description
The current 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/...
- Apps
issue opened on Nov 19 2024 by Pjotr Prins, last updated 5 weeks ago by Pjotr Prins; 33 of 74 tasks done
...in progress
* priority: medium
* keywords: system, sheepdog, shepherd
# Tasks
* [ ] Get services running
* [ ] Move guix shell into containers
* [ ] Make sure the container starts up on reboot and/or...
- Linking genotype files to datasets
issue opened on Jul 07 2023 by Alexander_Kabui, last updated on Jul 11 2023 by Alexander_Kabui
...in progress
## Notes
A dataset can have multiple groups. In order to fetch all possible sample data fetch all possible groups in a dataset then use that to fetch all linked genofiles
As an example...
- 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
...progress
## Notes
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...
- Slow query
issue opened on May 27 2023 by Pjotr Prins, last updated on May 29 2023 by Pjotr Prins; 0 of 2 tasks done
...in progress
* keywords: slow query
# Tasks
* [ ] upgrade mariadb on production
* [ ] switch character type on ProbeSet table from latin1/utf8mb3 to utf8mb4 (and any other tables) - depends on mariadb...