- Designing an issue tracker on gemini
✓ issue opened on Jul 25 2021 by Pjotr Prins, last updated on Feb 02 2022 by Pjotr Prins
...flexible, but common ones are
* request
* bug
* critical bug
* enhancement
* in progress
* testing
* later
* documentation
* help wanted
* closed
the keyword statement may have aliases, such as tag...
- AI UI Enhancements
issue opened on Mar 01 2024 by Pjotr Prins; 0 of 3 tasks done
...until a first global search is done:
* [ ] When a global search is done, before the table show a line that people can use the text search:
```
------- [search]
GN searched for the term(s) "shh" in 754...
- 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
...global search, db connections, medium priority, from github
## Description
=> https://github.com/genenetwork/genenetwork2/issues/418 From GitHub
Global search '*' causes loads of aborted connections...
- 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...
- 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...
- 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
Fix Broken Global Search UI
## Tags
* Assigned: alexm, zsloan
* Priority: high
* status: in progress
* Keyword : search, UI, bug, Refactor
* Type: UI, bug
## Description
The Global search UI layout...
- 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
...`alias`,`GenbankId`,`UniGeneId`,`Probe_Target_Description`),
```
BLOB and TEXT columns also can be indexed, but a prefix length must be given not to exceed the maximum length. In global search...
- CD is slow
issue opened on Jul 20 2025 by Pjotr Prins, last updated on Jul 24 2025 by Pjotr Prins; 2 of 8 tasks done
...Consortium M430v2 (Jun06) PDNN 1457545_at 9530036O11Rik long non-coding RNA, expressed sequence tag (EST) AK035474 with high bladder expression antisense EST 14 Kb upstream of Shh...
- Search results presentation
issue opened on Apr 04 2023 by Alexander_Kabui
Search results presentation
## Tags
* assigned: alex
* status:in progress
* keywords: UI,search
## Notes
The idea is to research and find good design for search results in global search
Currently...
- Wrong CSV in ITP_10001 longevity dataset
✓ issue opened on Apr 11 2022 by BonfaceKilz, last updated on Apr 12 2022 by BonfaceKilz
...bug
* status: closed
* priority: critical
* keywords: critical bug, in progress, metadata, phenotypes
## Description
[From Suheeta]:
"I downloaded the sample csv file for ITP_10001 to add a couple...
- 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
...question, which can override the defaults
Converted tables:
[X] - Search Results
[X] - Collection View
[X] - Collection List
[X] - Correlation Results
[X] - Global Search
[X] - Trait Page Sample Table...
- BXD102xBXD077F1 Error
✓ issue opened on Mar 22 2022 by Frederick Muriuki Muriithi, last updated on Apr 07 2022 by Zachary Sloan
...zsloan
* type: bug
* priority: critical
* status: unclear
* keywords: correlations, from github, closed
## Description
=> https://github.com/genenetwork/genenetwork2/issues/612 From GitHub
> Hi...
- 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
...please check your spelling and try again.
```
## Tasks
* [x] code to search for broken links in web pages
* [x] run gn2 on CI as a background task to search for broken links
### Notes
the bug above...
- 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
Search results for SNP looks weird
## Tags
* assigned: zsloan
* type: bug
* priority: medium
* status: in progress
* keywords: UI, SNP, from github
## Description
=> https://github.com/...
- Variant Browser seems to be using mm9
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
...bug
* status: stalled
* keywords: variant browser, mm9, from github
## Members
* acenteno
* robw
* pjotrp
## Description
=> https://github.com/genenetwork/genenetwork2/issues/581 From GitHub
When...
- 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
...the global shepherd guix profile and loading guix-bioinformatics at service start time to start their services. This is bad because:
* we aren't using per-service guix-bioinformatics worktrees, so...
- 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
...bug
* priority: critical
* keywords: GN1
* status: in progress
* kanban: pjotrp
* assigned: pjotrp, zachs, robw
## List of outstanding issues
(see also E-mail Rob 14 Sep 2021)
* [ ] Fix annotating...
- 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/genenetwork2/pull/755 GN2#755
=> https://github.com/genenetwork/genenetwork2/pull/753 GN2#753
=> https://github.com/genenetwork/genenetwork2/pull/751 GN2#751
=> https://github...
- Annotation
issue opened on Sep 14 2022 by Pjotr Prins, last updated on Mar 14 2023 by Arun Isaac; 0 of 5 tasks done
...//github.com/genenetwork/genenetwork2/blob/df36cc808e21202075d32559c9f295087bd8aee2/wqflask/wqflask/do_search.py#L819-L857 - Search queries
notably the Position Search (the most "ambitious" version...
- 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
...critical
## Tasks
* [X] fix redis queue and sheepdog server
* [X] check backups on tux01
* [ ] drop tux02 backups off-site
* [ ] backup ratspub, r/shiny, bnw, covid19, hegp, pluto services
* [ ] /etc...
- 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
...type: bug
* assigned: pjotrp
* keywords: systems, fallback, deploy
* status: in progress
* priority: critical
# Tasks
* [X] 502 timeout errors
* [X] Rqtl2 not working
* [X] 413 error
* [ ] BNW error...
- 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
...publications are in GN related to addiction and published after 2010?
We want to make search easy and to disambiguate terms.
### Describe alternatives you've considered
Modelling everything in MariaDB.
- 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
Report invalid search queries passed to the search API
* assigned: alex, arun
* tags: enhancement
* status: in progress
genenetwork2 offloads search to the genenetwork3 search API. When there is an...
- 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...
- 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
...(est. 1-2 hours)
Set up a global Mariadb
```
guix package -i mariadb -p /usr/local/guix-profiles/mariadb
```
Usually I use the Debian version to set up defaults
```
apt-get install mariadb
cd /etc/...
- 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
...bug
* keywords: collections, from github
## Members
* rupertoverall
## Description
=> https://github.com/genenetwork/genenetwork2/issues/559 From GitHub
### Describe the bug
When calcuating principal...
- Penguin2 RAID 5
issue opened on Feb 28 2025 by Pjotr Prins
...then
search --no-floppy --fs-uuid --set=root --hint-bios=hd2,msdos1 --hint-efi=hd2,msdos1 --hint-baremetal=ahci2,msdos1 7ff268df-cb90-4cbc-9d76-7fd6677b4964
else
search...
- 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
...bug
* status: unclear
* priority: medium
* keywords: mapping, correlation, google chrome, UI, from github
## Description
=> https://github.com/genenetwork/genenetwork2/issues/399 From GitHub
Based...
- Multi-trait heat map failed
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
...bug
* priority: medium
* status: stalled
* keywords: heatmap, from github
## Members
* zsloan
* pjotrp
* echesler
## Description
=> https://github.com/genenetwork/genenetwork2/issues/368 From GitHub...
- GN1 annotation page broken
issue opened on Dec 23 2022 by Pjotr Prins
...bug
* keywords: GN1, genenetwork1, annotation, from github
## Description
=> https://github.com/genenetwork/genenetwork2/issues/421 From GitHub
=> http://gn1.genenetwork.org/webqtl/main.py?FormID...
- csv export meta data are not commented out
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
...bug
* status: unclear
* keywords: CSV, from github, meta data
## Description
=> https://github.com/genenetwork/genenetwork2/issues/594 From GitHub
csv export data can't be read using the example R...
- 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
...type: bug
* priority: high
* status: closed, completed
* keywords: correlations, from github, high priority
## Description
=> https://github.com/genenetwork/genenetwork2/issues/374 From GitHub
Dear...
- Error when attempt to zoom to a chromosome after mapping a PCA trait
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
...bug
* priority: high
* status: unclear
* keywords: PCA, from github, high priority
## Description
=> https://github.com/genenetwork/genenetwork2/issues/367 From GitHub
When I produced a PCA trait...
- 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
...Bug
* status: in progress
* keywords: external, qtl, rqtl, bug, logs
## Description
For QTL analysis, we invoke the `rqtl` script as an external process through Python's `subprocess` module.
For...
- Fix GN1 Network Graph
issue opened on Sep 15 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...pjotrp, zachs
## Tracking
To reproduce this bug: select a 'shopping basket' and click on network graph. No image is shown.
We needed to revert on
=> https://github.com/genenetwork/genenetwork1/commit/...
- '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
...bug
* status: closed
* keywords: TempDataSet, from github
## Description
=> https://github.com/genenetwork/genenetwork2/issues/592 From GitHub
After successful entry of new BXD trait data (both my...
- 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
...-bioinformatics git server that is *not* gitlab or github.
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...
- 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
...bug
* keywords: GN1, genenetwork1, 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...
- Branding and front-end-services
issue opened on Jun 14 2023 by Pjotr Prins; 0 of 1 tasks done
...allow for rebranding and multiple servers of GN2 services. A community website can be created in this way with its own 'portal', dedicated search and interactive GN tooling.
To make it even more fun...
- 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
...zachs
* keywords: bug
* status: in progress
* priority: high
This issue appears to be caused by marker namees being duplicated. If a marker name appears in an earlier chromosome, it ends up displayed...
- 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
For the time being,
I've removed this option. Currently just 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...
- 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
...bug
* priority: medium
* keywords: binderlite, notebooks, styling, UI
## Description
Currently using antiweb for styling with modifications.
=> https://git.sr.ht/~sircmpwn/antiweb antiweb
Copying nav...
- 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...
- 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...
- Apps
issue opened on Nov 19 2024 by Pjotr Prins, last updated 3 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/...
- 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
...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
- 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/...
- 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...