- 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
...global search query.
## Indices
ProbeSet has a large number of columns, indices and full text indices(!)
## Nailing it down
The obvious thing to try is to reduce the query and see what speeds it up...
- 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 does not close connections properly (and is slow)
## Tags
* type: bug
* priority: medium
* status: stalled
* assigned: Uditgulati
* keywords: global search, db connections, medium...
- 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
...curl, try
```
curl -G https://query.wikidata.org/sparql -H "Accept: application/json; charset=utf-8" --data-urlencode query="SELECT DISTINCT * where {
wd:Q158695 wdt:P225 ?o .
} limit 5"
{
"head"...
- 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...
- 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
...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...
- 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 Mar 23 2022 by Frederick Muriuki Muriithi
Slow query
## Tags
* assigned: Uditgulati
* priority: high
* status: stalled
* keywords: slow query, from github
## Description
=> https://github.com/genenetwork/genenetwork2/issues/419 From GitHub...
- 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...
- 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...
- 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...
- 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
My findings are: federated queries can be slow (querying wikidata took as long as 5-30 seconds). As such, a better strategy would be to write scripts to enrich our dataset from other data sources...
- Fetch trait names for phenotypes
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
...query returns detailed information for transcript expression traits, but not for traits from the 'Publish' database.
### Describe the solution you'd like
For example, downloading the data as CSV via...
- Variant Browser seems to be using mm9
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
...do not match the query.
Searching for a gene gives correct coordinates in the search box at http://www.genenetwork.org/snp_browser, but the results are for the same coordinates in mm9 (see screenshot).
- 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
...pjotrp, zachs, robw
## List of outstanding issues
(see also E-mail Rob 14 Sep 2021)
* [ ] Fix annotating metadata - or do we have GN2 alternative?
=> gn1-slowness.gmi [.] Clean up tmp dirs with CRON...
- 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
...make search easy and to disambiguate terms.
### Describe alternatives you've considered
Modelling everything in MariaDB. The problem with that is that we have
redundant data and complexity increases...
- 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...
- 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
...hard to also enable for other species)
[ ] Make it display an arrow depending on the strand (whether the query strand matches the reference
[ ] Store the homology chain file data differently (keeping...
- 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...
- 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 GN2 look off.
Here's how it looked like in the past:
=> https://user-images.githubusercontent.com/11820306/82554424-8e0ac600-9b6e-11ea-9a50-f53506eb44a5.png Screen Shot 2020-05-20...
- 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/...
- 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...
- Annotation
issue opened on Sep 14 2022 by Pjotr Prins, last updated on Mar 14 2023 by Arun Isaac; 0 of 5 tasks done
.../do_search.py#L819-L857 - Search queries
notably the Position Search (the most "ambitious" version of this would allow for querying based off of different assemblies, but I can't think of a good way...
- 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
...entered the URL manually 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...
- 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...
- 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
...path, query, fragment = parse_url(url)
File "/gnu/store/a39cgbdawj9vp24nsz9q25sf9g5vda7c-profile/lib/python3.10/site-packages/urllib3/util/url.py", line 397, in parse_url
return six.raise_from...
- Add the option to save traits uploaded with the Submit Trait option
issue opened on Jul 19 2022 by Zachary Sloan
...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" trait (that is saved in Redis for a limited...
- 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
...Genoset and Publish data types
### Publish Dataset
Example for phenotype fetching data for phenotype 35
```sql
SELECT A.Sample, A.Value, A.SE, A.Count, B.CaseAttributes FROM
(SELECT DISTINCT st.Name...
- Allow analyses to be done between traits from "individuals" groups and their corresponding "main" group
issue opened on Jul 21 2022 by Zachary Sloan
...data, meta-data
# Description
Currently you can't do an analysis beween traits from the "main" BXD group and traits from any of the BXD individuals groups, but it should technically be possible to do...
- csv export meta data are not commented out
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
...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: 11320...
- '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
...data that I tried to upload and check on GN2 was the
median-lateral position of the representation of visual space on V1. It was
old data that we had, but never uploaded, because we were investigating...
- Wrong CSV in ITP_10001 longevity dataset
✓ issue opened on Apr 11 2022 by BonfaceKilz, last updated on Apr 12 2022 by BonfaceKilz
...that data for use, they were not being stripped out. As a consequence, opening the csv file in Excel (or similar) software resulted in data that seems jumbled up.
### Tue 12 Apr 2022 13:33:31 EAT...
- 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
...expected, see the `edit page` link/button at
=> http://gemini.thebird.nl/gemini/genenetwork/gn-gemtext-threads/topics/data-uploads/editing-data.gmi
noting how it drops you straight into editting the...
- 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
...backups
* [ ] mount bacchus on HPC
## Backup and restore
We are using borg for backing up data. Borg is excellent at deduplication and compression of data and is pretty fast too. Incremental copies...
- 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
...@gmail.com",
"username": "test",
"commit_message": "init commit",
"prev_commit": "7cbfc40d98b49a64e98e7cd562f373053d0325bd"
}'
```
It expects the following data in JSON format:
* `content` (the data...
- Multi-trait heat map failed
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
...trimmed_values)
IndexError: reaper: the length of the strain list and the value list are different,
```
One of my traits had missing data, deselecting this trait fixed the problem. Record 20761.
- Capture state of phenotypes in a HASH
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
...hash can be computed over data that is streamed over the REST API - so people van validate client side (as a feature).
This mentions RDF - which I think
* aruni
was involved in. I (fredm) have tagged...
- 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
...'BXD Aged hippocampus individual data' dataset (GN712).
### Expected behavior
The PC should be treated as a normal trait and added to the collection.
### Screenshots
Environment setup (please complete...
- Linking genotype files to datasets
issue opened on Jul 07 2023 by Alexander_Kabui, last updated on Jul 11 2023 by Alexander_Kabui
...data fetch all possible groups in a dataset then use that to fetch all linked genofiles
As an example example the dataset HC_M2_0606_P is of type Probeset and linked groups for this dataset include...