- A linter for gnbug
✓ issue opened on Oct 28 2021 by jgart, last updated on Jul 06 2022 by Arun Isaac
...among other things:
* what tags to display
* colouring of said tags
* maybe what tags to allow (for those that need to restrict allowed tags)
The tags could be parsed into a hashmap or an associative...
- Add HTML Page for ProbeSet Page
✓ issue opened on Dec 14 2023 by Munyoki Kilyungi, last updated on Jan 09 2024 by Munyoki Kilyungi
...query=tag%3Avirtuoso Add GeneList to Metadata
Remaining work is to display this work in GN2.
## Resolution
Some minor updates were done to fix how gene-symbols are transformed. See: 1ea6e2dd7655...
- Add convenience templates
✓ issue opened on Oct 28 2021 by jgart, last updated on Jul 11 2022 by Arun Isaac
I was thinking of an interface like the following:
```
gnbug report feature-request "New feature: IPFS Downloads"
```
Or expressed as generic command parameters:
```
command subcommand tag(s) title...
- Cleanup GN2 Base HTML File
✓ issue opened on Sep 23 2024 by Alexander_Kabui, last updated on Oct 16 2024 by Alexander_Kabui; 3 of 3 tasks done
...(e.g., tags)
* [x] Inherit from index page for all gn2 templates
## Notes
See the PR that seeks to fix this:
=> https://github.com/genenetwork/genenetwork2/pull/877
## Notes 26/09/2024
It was agreed...
- Designing an issue tracker on gemini
✓ issue opened on Jul 25 2021 by Pjotr Prins, last updated on Feb 02 2022 by Pjotr Prins
...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 :)
## Tracking information
Git can do all of that. A viewer may benefit...
- Data Uploads: Zero Representation
✓ issue opened on Feb 08 2022 by BonfaceKilz, last updated on Nov 11 2022 by Munyoki Kilyungi
...Zero Representation
## Tags
* assigned: bonfacem
* type: bug
* priority: high
* status: closed
* keywords: data uploads
### Introduction
When editing data, given the following data:
```
Strain Name...
- Fix Xapian search bug
✓ issue opened on Jun 07 2024 by Zachary Sloan, last updated on Oct 17 2024 by Zachary Sloan
...bug
## Tags
* assigned: zsloan
* priority: high
* type: search
* status: closed
* keywords: xapian, gn2, gn3
## Description
Currently all Xapian searches that aren't just simple individual terms fail.
- Upload GeneWiki RDF metadata to CD
✓ issue opened on Apr 17 2023 by Munyoki Kilyungi, last updated on Apr 18 2023 by Munyoki Kilyungi
Upload GeneWiki RDF metadata to CD
## Tags
* assigned: bonfacem
* keywords: generif, metadata, RDF
Following this:
=> /topics/our-virtuoso-instances.gmi Our Virtuoso Instances
I've tried loading ttl...
- Uninformative error when batch submitting unknown strains
✓ issue opened on May 05 2022 by BonfaceKilz, last updated on Apr 18 2023 by Munyoki Kilyungi
Uninformative error when batch submitting unknown strains
# Tags
* assigned: bonfacem,zachs
* keywords: metatadata
* priority: medium
* closed
## Description
When batch submitting temporary traits...
- 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
Unable to open new tab for mapping/ correlations with Chrome
## Tags
* assigned: bonfacem
* type: bug
* status: unclear
* priority: medium
* keywords: mapping, correlation, google chrome, UI...
- Editing traits for BXDs is failing for "%" substitution
✓ issue opened on Nov 09 2022 by Munyoki Kilyungi, last updated on Apr 18 2023 by Munyoki Kilyungi
...Tags
* assigned: bonfacem
* type: bug
* priority: high
* closed
In the screenshot below, a user tried to change the word "percent" to the symbol "%".
=> /pictures/percent-failure.png
Submitting...
- Trait Page Errors on CD
✓ issue opened on Nov 22 2022 by Frederick Muriuki Muriithi, last updated on Dec 18 2023 by Frederick Muriuki Muriithi
...Errors on CD
## Tags
* type: bug
* priority: critical, high
* status: closed, completed
* keywords: trait page
* assigned:
## Description
A few examples of pages that fail on CD, but work as expected...
- Timeout in CD
✓ issue opened on Jul 22 2022 by Arun Isaac, last updated on Aug 17 2022 by Arun Isaac
Timeout in CD
* tags: cd
* assigned: aruni
The timeout of the reverse proxy in the genenetwork CD should be increased from the default 1 minute to 5 minutes. This is a kludge, but needs to be done...
- MySQLdb._exceptions.OperationalError: (1040, 'Too many connections')
✓ issue opened on Aug 29 2022 by Munyoki Kilyungi, last updated on Sep 05 2022 by Alexander_Kabui; 2 of 2 tasks done
MySQLdb._exceptions.OperationalError: (1040, 'Too many connections')
## Tags
* assigned: bonfacem, fredm, aruni
* type: bug
* keywords: mysql, database
## Tasks
* [x] Figure out root cause
* [x] Send...
- issues/sorting-correlation-nan-vals.gmi
✓ issue opened on Nov 28 2022 by AlexanderKabui, last updated on May 29 2024 by Alexander_Kabui
Tags
* type: bug
* assigned:alexm
* priority: medium
* status: closed, done, completed
* keywords: correlations, sorting,nan
## Description
sorting floats (correlation values) where
some cases have...
- Re-use JWTs in gn3
✓ issue opened on Apr 30 2024 by Munyoki Kilyungi
Re-use JWTs in gn3
* assigned: bonfacem
* tags: critical
## Description
We move auth related functionality to GN2. Auth is currently in used by the LLM app, and the editing metadata work.
Resolved...
- Sample Data not Appearing in Phenotype-Editing Page
✓ issue opened on Jul 12 2023 by Frederick Muriuki Muriithi, last updated on Jul 12 2023 by Frederick Muriuki Muriithi
...not Appearing in Phenotype-Editing Page
## Tags
* assigned: fredm
* priority: urgent
* type: bug
* keywords: editing, phenotype, phenotype editing
* status: closed
## Description
On clicking the "Edit"...
- Rework Fetching Settings
✓ issue opened on Sep 25 2022 by Munyoki Kilyungi, last updated on Oct 11 2023 by Munyoki Kilyungi
...zsloan, alex, fredm
* priority: low
* status: closed
* tags: refactor
In GN2, We fetch all our settings from the "wqflask.utility.tools". This module contains many functions that are only used once.
- Try out Auth Code Locally
✓ issue opened on Apr 21 2023 by Munyoki Kilyungi, last updated on Oct 11 2023 by Munyoki Kilyungi; 2 of 2 tasks done
...Locally
## Tags
* assigned: bonfacem
* type: review
## Description
Have a look at Fred's Auth code and in particular:
* [X] Set it up in a local development environment.
* [X] Improve documentation if...
- Document redis data
✓ issue opened on Nov 27 2021 by BonfaceKilz, last updated on Apr 18 2023 by Munyoki Kilyungi
...hard for contributors to work out how to modify some things. For
example, PJ would want to add himself to the editors group. Doing
this was non-trivial for him.
## Tags
* type: bug
* priority: low...
- Redirect HTTP to HTTPS
✓ issue opened on Jul 31 2021 by Arun Isaac, last updated on Jun 24 2022 by Frederick Muriuki Muriithi
Redirect HTTP to HTTPS
## Tags
* assigned: ??
* keywords: http, https
* status: closed, completed
* priority: medium
All http://genenetwork.org URIs should redirect to https://genenetwork.org URIs.
- Redesign Global Search Design
✓ issue opened on Sep 26 2024 by Alexander_Kabui, last updated on Oct 16 2024 by Alexander_Kabui; 2 of 2 tasks done
Redesign Global Search Design
## Tags
* assigned: alexm, zac
* keywords: global search, design, HTML
* type: enhancement
* status: closed, completed, done
## Description
Rob suggested we model...
- Fix Flash Messages
✓ issue opened on Jan 05 2024 by Frederick Muriuki Muriithi, last updated on Jul 03 2024 by Frederick Muriuki Muriithi
...Tags
* assigned: fredm
* priority: low
* type: bug
* status: closed, completed, fixed
* keywords: flask, flash
## Description
The
```
{% with messages = get_flashed_messages(with_categories=true)...
- Enumerating all QC checks
✓ issue opened on Nov 19 2021 by jgart, last updated on Jul 20 2022 by Frederick Muriuki Muriithi
ume
# Enumerating all QC checks
We need to enumerate all QC checks and platforms that we want to test against.
## Tags
* assigned: fredm, jgart, arthur
* status: closed
* type: feature-request...
- Big File Upload Fails
✓ issue opened on Jan 17 2023 by Frederick Muriuki Muriithi, last updated on Nov 28 2023 by Frederick Muriuki Muriithi
...Fails
## Tags
* assigned: fredm
* priority: high
* type: bug
* status: closed, completed
* keywords: qc, quality control
## Description
Trying to upload big files (>= 500MB) fails quietly, dropping...
- Order entries in CSV dump
✓ issue opened on Mar 20 2023 by Munyoki Kilyungi, last updated on Oct 11 2023 by Munyoki Kilyungi
...in CSV dump
## Tags
* assigned: bonfacem
* type: improvement
* keywords: csv, data
Order entries in the CSV dump according to how they are ordered in the genotype files. This way, it's consistent wrt...
- Error when loading GN2 with old pre-update session
✓ issue opened on Jun 03 2024 by Zachary Sloan, last updated on Oct 17 2024 by Zachary Sloan
...loading GN2 with old pre-update session
## Tags
* status: closed
* priority: medium
* type: bug
* assigned: zsloan, fredm
* keywords: gn-auth, gn2
## Description
Something about the recent updates...
- Move Search to Xapian
✓ issue opened on Sep 08 2023 by Munyoki Kilyungi, last updated on Jul 29 2024 by Munyoki Kilyungi
...to Xapian
## Tags
* priority: high
* keywords: xapian, search
* status: open
* assigned: bonfacem, zachs
## Description
Currently, one of our most challenging issues stems from the Python 3.10 update...
- Model Menu In RDF
✓ issue opened on Apr 18 2023 by Munyoki Kilyungi, last updated on Oct 11 2023 by Munyoki Kilyungi
Model Menu In RDF
## Tags
* assigned: bonfacem
* type: modelling
* status: closed
* priority: high
* keywords: rdf, modelling
## Description
Read the following for more details:
=> https://github.com/...
- Minor Phenotype Page UI updates
✓ issue opened on Nov 30 2023 by Munyoki Kilyungi, last updated on Dec 01 2023 by Munyoki Kilyungi; 6 of 6 tasks done
...Phenotype Page UI updates
## Tags
* assigned: bonfacem, robw, rupert
* priority: high
* type: ui
* keywords: phenotypes
## Description
These are minor updates depending on feedback from Rob and Rupert.
- Mapping figure can't be horizontally scrolled
✓ issue opened on Apr 20 2022 by Zachary Sloan, last updated on Apr 21 2022 by Zachary Sloan
...Tags
* assigned: zsloan
* priority: medium
* status: closed
* keywords: mapping
## Description
The mapping figure can't be horizontally scrolled, which is apparently annoying for people using small...
- Mapping: Haley-Knott Regression: Zooming Bug
✓ issue opened on Sep 22 2022 by Zachary Sloan, last updated on Sep 28 2022 by Alexander_Kabui
...Haley-Knott Regression: Zooming Bug
## Tags
* status: closed
* keywords: mapping, Haley-Knott Regression
* priority: medium
* type: bug
* assigned: zsloan
## Definition of terms
* ${HOST}: The host...
- Integrate Feed Analyser
✓ issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Oct 11 2023 by Munyoki Kilyungi
Integrate Feed Analyser
## Tags
* assigned: bonfacem
* type: feature-request
* status: closed
* priority: medium
* keywords: twitter, feed analyser
## Members
* bonfacem
* robw
## Description...
- Improve sparql results
✓ issue opened on Jul 07 2023 by Munyoki Kilyungi, last updated on Oct 11 2023 by Munyoki Kilyungi
...Tags
* assigned: bonfacem
* type: improvement
* priority: high
* status: closed
* keywords: RDF, SPARQL
For this query:
=> https://sparql.genenetwork.org/sparql?default-graph-uri=&qtxt=prefix%20gn%...
- Improve presentation of search results
✓ issue opened on Feb 13 2023 by Arun Isaac, last updated on Apr 04 2023 by Alexander_Kabui
Improve presentation of search results
## Tags
* assigned: arun, alexm
* status: stalled,closed
* keywords: xapian,search,UI
At the moment, we present search results in tabular form. See, for example...
- Refactoring gn-llm code and adding test modules
✓ issue opened on Jan 17 2024 by Alexander_Kabui, last updated on Sep 09 2024 by Alexander_Kabui
...modules
## Tags:
* assigned:alexm,shelby
* keywords:refactoring,llm,tests
* type: enchancements
* status: completed, closed
## Description
The task is to Refactor `gn-llm` code for improved structure...
- Implement Reference Rating for gn-llm
✓ issue opened on Jan 11 2024 by Alexander_Kabui, last updated on Sep 09 2024 by Alexander_Kabui; 2 of 2 tasks done
Implement Reference Rating for gn-llm
## Tags
* assigned: alexm,
* keywords: llm, reference, rating
* type: enhancements
* status: closed, completed
## Description
For each reference in a query...
- Integrating gn-auth with gn-llm
✓ issue opened on Jan 10 2024 by Alexander_Kabui, last updated on Sep 09 2024 by Alexander_Kabui
...gn-llm
## Tags
* assigned: alexm, Shelby
* keywords: llm, auth
* type: feature
* priority: high
* status: done, completed, closed
## Description
The main objective is to integrate gn-authentication...
- GNQA UI Enhancements
✓ issue opened on Feb 12 2024 by Alexander_Kabui, last updated on May 29 2024 by Alexander_Kabui; 1 of 1 tasks done
...Enhancements
## Tags
* Assigned: alexm
* Keywords: UI, GNQA
* Type: enhancement
* Status: completed, closed
## Description
The issue involves integrating pubmed data to references list from fahamu api.
- Implementing Efficient Database Caching for Query Responses in GN-LLM system
✓ issue opened on Jan 17 2024 by Alexander_Kabui, last updated on Sep 09 2024 by Alexander_Kabui; 3 of 3 tasks done
...system
## Tags:
* assigned: alexm,shelby
* keywords: llm,caching,database,query,response
* type: enhancements
* status: closed, done, completed
## Description:
This implementation task aims to enhance...
- Fetch Pubmed data to GNQA
✓ issue opened on Feb 12 2024 by Alexander_Kabui, last updated on Sep 09 2024 by Alexander_Kabui; 6 of 6 tasks done
...GNQA
## Tags
* assigned: alexm
* keywords: llm, pubmed, api, references
* type: enhancements
* status: completed, closed
## Description
The task is to integrate PubMed references into the GNQA system...
- Sort gnbug issues most recent first
✓ issue opened on Jan 31 2022 by Arun Isaac, last updated on Mar 22 2022 by Arun Isaac
...usage where you don't want to scroll up to see the most recent issue. newest-first is useful when generating gemtext/web pages where you don't want to scroll down to see the most recent issue.
## Tags...
- Hide stale issues in gnbug
✓ issue opened on Jan 31 2022 by Arun Isaac, last updated on Mar 22 2022 by Arun Isaac
...long. Maybe, hide stale issues by default, and show them only if some --all flag is passed. Stale issues are tentatively defined as those issues that have been inactive for more than 6 months.
## Tags...
- Add a transient interface for tissue
✓ issue opened on Mar 28 2022 by BonfaceKilz, last updated on Jul 08 2022 by Arun Isaac
...transient interface for tissue
## Tags
* type: feature-request
* keywords: linter, tissue
* assigned: bonfacem
* priority: low
## Description
Add a transient interface for GNU Emacs for tissue. Check...
- GN3: Technical Debt
✓ issue opened on Feb 08 2022 by BonfaceKilz, last updated on May 25 2022 by BonfaceKilz
...Debt
## Tags
* assigned: bonfacem
* priority: medium
* status: closed
* type: enhancement
* keywords: GN3
### Introduction
Here I log some technical debt in gn3 as a checklist.
- [x] Clean up gn3/db/...
- GN3 NGINX Timeout
✓ issue opened on Jan 15 2024 by Alexander_Kabui, last updated on Jan 25 2024 by Alexander_Kabui
...NGINX Timeout
## Tags
* Assigned: alexm
* Keywords: CD, GN3
* Status: closed
* Priority: Medium
* Type: Bug
## Description
The issue is that some requests to the GN3 API result in an nginx 504 Gateway...
- Upload Strains
✓ issue opened on Dec 06 2023 by Frederick Muriuki Muriithi, last updated on Feb 27 2024 by Frederick Muriuki Muriithi; 5 of 5 tasks done
Upload Strains
## Tags
* status: closed, completed
* assigned: fredm, zachs, zsloan, acenteno
* priority: high
* type: feature-request
* keywords: QC, quality control, strains, gn-uploader...
- Rework Test: Remove redis as Test Dependency
✓ issue opened on Oct 27 2023 by Frederick Muriuki Muriithi, last updated on Feb 27 2024 by Frederick Muriuki Muriithi
...Test: Remove redis as Test Dependency
## Tags
* assigned: fred, fredm
* status: closed, completed
* priority: medium
* keywords: gn-uploader, tests
* type: improvement
## Description
Some tests depend...
- gn-uploader container: Running wrong genenetwork2
✓ issue opened on Mar 18 2024 by Frederick Muriuki Muriithi, last updated on Sep 16 2024 by Frederick Muriuki Muriithi
...Tags
* assigned: fredm, aruni
* status: closed, completed
* priority: high
* type: bug
* keywords: guix, gn-uploader
## Description
I build the uploader container with Genenetwork2, commit b9e04ad...
- Check Genotypes in the Database for R/qtl2 Uploads
✓ issue opened on Jun 26 2024 by Frederick Muriuki Muriithi, last updated on Jul 01 2024 by Frederick Muriuki Muriithi
Check Genotypes in the Database for R/qtl2 Uploads
## Tags
* type: bug
* assigned: fredm
* priority: high
* status: closed, completed, fixed
* keywords: gn-uploader, uploader, upload, genotypes, geno...
- Send out Confimation Emails on Registration
✓ issue opened on Feb 27 2024 by Frederick Muriuki Muriithi, last updated on Sep 16 2024 by Frederick Muriuki Muriithi
Send out Confimation Emails on Registration
## Tags
* status: closed, completed
* assigned: fredm
* priority: medium
* type: feature request, feature-request
* keywords: gn-auth, email, user...
- Resources: Duplicates in Resources List
✓ issue opened on Oct 03 2024 by Frederick Muriuki Muriithi, last updated on Oct 03 2024 by Frederick Muriuki Muriithi
Resources: Duplicates in Resources List
## Tags
* type: bug
* status: closed
* priority: medium
* assigned: fredm, zachs, zsloan
* keywords: gn-auth, auth, authorisation, resources
## Reproduce
* Go...
- Remove bcrypt as a Dependency
✓ issue opened on Oct 27 2023 by Frederick Muriuki Muriithi, last updated on Nov 28 2023 by Frederick Muriuki Muriithi
...Dependency
## Tags
* assigned: fred, fredm
* status: closed, completed
* priority: low
* keywords: gn-auth, dependencies
* type: improvement
## Description
BCrypt has been superceded by better systems...
- Implement "Refresh Token" Feature for JWTs
✓ issue opened on Apr 26 2024 by Frederick Muriuki Muriithi, last updated on Jun 26 2024 by Frederick Muriuki Muriithi
...JWTs
## Tags
* status: closed, completed, fixed
* priority: high
* assigned: fredm, bonfacem
* type: feature-request, bug
* keywords: gn-auth, token, refresh token, jwt
## Description
We have recently...
- 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
Redirect Users to the Correct URL on Login for GN2
## Tags
* assigned: alexm
* priority: medium
* status: in progress
* keywords: gn-auth, auth, redirect, login, completed, closed, done...
- E-Mail Verification
✓ issue opened on Jun 04 2024 by Zachary Sloan, last updated on Sep 16 2024 by Frederick Muriuki Muriithi
E-Mail Verification
## Tags
* status: closed, completed
* priority: medium
* type: enhancement
* assigned: fredm, zsloan
* keywords: gn-auth, oauth2, email
## Description
When setting up e-mail...
- Global search doesn't seem to return phenotype traits
✓ issue opened on Nov 11 2022 by Zachary Sloan, last updated on Mar 14 2023 by Zachary Sloan
...search doesn't seem to return phenotype traits
## Tags
* priority: high
* type: bug
* assigned: zsloan, aruni
* status: closed
* keywords: global search, phenotypes
## Description
For a search like...
- Global Search: Unhandled Error
✓ issue opened on Mar 04 2024 by Frederick Muriuki Muriithi, last updated on Sep 16 2024 by Frederick Muriuki Muriithi
Global Search: Unhandled Error
## Tags
* assigned: aruni, fredm
* priority: high
* type: bug
* status: closed
* keywords: global search, gn2, genenetwork2
## Description
=> https://github.com/...
- 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...
- The * Search for Genotypes Not Working
✓ issue opened on Sep 17 2024 by Zachary Sloan, last updated on Oct 17 2024 by Zachary Sloan
...Working
## Tags
* type: bug
* priority: medium
* status: closed
* assigned: zsloan
* keywords: bug, search
## Description
Currently * searches for genotypes return no results, even when data exists.
- Genotype Metadata
✓ issue opened on Nov 29 2022 by Munyoki Kilyungi, last updated on Oct 11 2023 by Munyoki Kilyungi
...Tags
* assigned: bonfacem
* type: feature
* priority: medium
## Description
At the moment, you can only edit phenotype and probeset metadata. We also need to put in place a way of editing genotype...
- Add HTML Page for Genotypes
✓ issue opened on Jan 09 2024 by Munyoki Kilyungi, last updated on Jan 10 2024 by Munyoki Kilyungi
Add HTML Page for Genotypes
## Tags
* assigned: bonfacem
* priority: high
* type: ui
* keywords: virtuoso
* status: closed
## Description
Create HTML frontend for Genotype metadata.
## Resolution...
- Genotype correlations only returning results from first chromosome
✓ issue opened on Oct 21 2022 by Zachary Sloan, last updated on Nov 29 2023 by Zachary Sloan
...only returning results from first chromosome
## Tags
* assigned: fredm, alexm, zsloan
* type: bug
* priority: high
* status: closed
* keywords: correlations
## Description
=> http://gn2-zach...
- Marker mapping
✓ issue opened on Sep 15 2021 by Pjotr Prins, last updated on Dec 17 2022 by Pjotr Prins
.../MarkerRegressionPage.py", line 438, in GenReport
qtlresults = _genotype.regression(strains = _strains, trait = _vals)
AttributeError: 'genotype' object has no attribute 'regression'
```
## Tags...
- Setup Mailing on Tux04
✓ issue opened on Oct 28 2024 by Frederick Muriuki Muriithi, last updated on Oct 28 2024 by Frederick Muriuki Muriithi
Setup Mailing on Tux04
## Tags
* type: bug
* status: closed
* assigned: fredm
* priority: critical
* interested: pjotrp, zsloan
* keywords: production, container, tux04
## Description
We use emails...
- Remove everything elastic search
✓ issue opened on Oct 22 2021 by Pjotr Prins, last updated on Apr 01 2022 by BonfaceKilz
.../remove-elastic-search.gmi
## Tags
* assigned: bonfacem
* type: enhancement
* priority: low
* status: closed, done
* keywords: elasticsearch, purge
### Notes
Removed in #44bf8ee and #03caa57a in GN2.
- Proxy has hard coded URLs
✓ issue opened on Oct 22 2021 by Pjotr Prins, last updated on Apr 18 2023 by Munyoki Kilyungi
.../utility/authentication_tools.py
39: the_url = "http://localhost:8080/available?resource={}&user={}".format(
96: the_url = "http://localhost:8080/available?resource={}&user={}".format(
```
# Tags...
- Handle Temporary Directories in the Container
✓ issue opened on Nov 01 2024 by Frederick Muriuki Muriithi, last updated on Nov 05 2024 by Frederick Muriuki Muriithi
...Temporary Directories in the Container
## Tags
* type: feature
* assigned: fredm
* priority: critical
* status: closed, completed
* keywords: production, container, tux04
* interested: alexk, aruni...
- Global search problems
✓ issue opened on Aug 26 2022 by Pjotr Prins, last updated on Oct 14 2022 by Arun Isaac; 1 of 2 tasks done
...the top bar of GN2.
Note we are replacing search with xapian. So this is less important.
## Tags
* assigned: pjotrp, zsloan
* status: later
* priority: low
* type: bug
* keywords: global search, BRCA2...
- Need Guix packages
✓ issue opened on Mar 12 2022 by Pjotr Prins, last updated on Oct 11 2023 by Munyoki Kilyungi
...the guix packages:
=> https://genenetwork.org/environments/
It somehow got reverted and is out of date. Please see if we can get a list again that does not slow down the installation process.
## Tags...
- Bug: Incorrect code for GN2 generic error handler
✓ issue opened on May 28 2024 by Alexander_Kabui, last updated on May 29 2024 by Alexander_Kabui
...GN2 generic error handler
## Tags
* type: bug
* priority: medium
* status: closed
* assigned: alexm
* keywords: errors, Exceptions, gn2, Bug
## Description
The GN2 generic error handler returns a `200`...
- Fix Failing GN2 tests
✓ issue opened on Jan 12 2024 by Munyoki Kilyungi, last updated on Jan 15 2024 by Munyoki Kilyungi
...GN2 tests
## Tags
* assigned: bonfacem, alexm
* priority: medium
* type: CI
* keywords: CI
## Description
We have failing tests, staring from:
=> https://ci.genenetwork.org/jobs/genenetwork2/995...
- Fix Failing MR Failing Tests
✓ issue opened on Sep 13 2023 by Munyoki Kilyungi, last updated on Oct 11 2023 by Munyoki Kilyungi
...MR Failing Tests
## Tags
* priority: high
* status: closed
* assigned: bonfacem
## Description
MR fails because of a python-flask/requests issue. Everytime you issue a GET request to the server you...
- Fix some display issue with the Correlation Results table (plus add column resizing)
✓ issue opened on May 11 2022 by Zachary Sloan, last updated on Nov 22 2022 by Zachary Sloan
...to reproduce this)
Since these issues don't appear to occur in the search results table, I'm going to try to just use the same code for both tables (which includes adding resizable columns).
## Tags...
- Fix Collection Export
✓ issue opened on Apr 20 2022 by Zachary Sloan, last updated on Apr 21 2022 by Zachary Sloan
...Collection Export
## Tags
* assigned: zsloan
* type: bug
* priority: high
* status: closed
* keywords: collections
## Description
The export function from "collection" has not been working for a while.
- Fix Case Attribute Work (Same Columns)
✓ issue opened on Apr 06 2022 by BonfaceKilz, last updated on Oct 12 2022 by Munyoki Kilyungi; 9 of 9 tasks done
...Tags
* assigned: bonfacem
* type: bug
* keywords: case attributes, data editing
## Tasks
* [x] Parse things in "brackets"
* [x] When editing columns with the same header:
* [x] Check whether...
- Failing Tests
✓ issue opened on Aug 03 2022 by Frederick Muriuki Muriithi, last updated on Sep 20 2022 by Alexander_Kabui
...Tags
* assigned: zsloan, alex
* type: bug
* priority: critical
* status: completed, done
* keywords: genenetwork2, tests failure
## Description
The following changes are causing the tests to fail...
- Troubleshoot CD Menu Failure
✓ issue opened on Apr 21 2023 by Munyoki Kilyungi, last updated on Apr 26 2023 by Munyoki Kilyungi
Troubleshoot CD Menu Failure
## Tags
* assigned: bonfacem
* type: modelling
* status: stalled
## Description
The menu in CD fails. This is because the database in CD is out of sync with the one in...
- Enter key in global search field
✓ issue opened on Feb 13 2023 by Arun Isaac, last updated on Apr 04 2023 by Alexander_Kabui
...field
## Tags
* assigned: alex
* status: completed, closed
* keywords: search,UI
## Notes
In the home page, putting in a search query in the global search field and pressing the Enter key takes us to...
- Show "Edit" Button for All Users
✓ issue opened on Jul 24 2023 by Frederick Muriuki Muriithi, last updated on Jul 24 2023 by Frederick Muriuki Muriithi
...Tags
* type: feature request
* assigned: fredm
* priority: high
* keywords: editing
* status: closed
## Description
Show the "Edit" button for all users, but only allow users with the appropriate...
- Delete Rejected Diffs from Database
✓ issue opened on Jul 25 2023 by Frederick Muriuki Muriithi, last updated on Jul 25 2023 by Frederick Muriuki Muriithi
Delete Rejected Diffs from Database
## Tags
* type: feature request
* status: closed
* assigned: fredm
* keywords: editing, metadata audit
* priority: high
## Description
The rejected diffs will...
- Do Bulk Query for Correlation Results' Display
✓ issue opened on Oct 21 2022 by Frederick Muriuki Muriithi, last updated on Oct 24 2022 by Frederick Muriuki Muriithi
Do Bulk Query for Correlation Results' Display
## Tags
* assigned: fredm
* priority: high
* status: closed
* keywords: correlations, bulk queries, optimisation
* type: enhancement, optimisation...
- Give Examples of Fetching GeneRIF Metadata in Sparql
✓ issue opened on Apr 04 2023 by Munyoki Kilyungi, last updated on May 18 2023 by Munyoki Kilyungi
Give Examples of Fetching GeneRIF Metadata in Sparql
## Tags
* assigned: bonfacem
* type: documentation
* keywords: generif, metadata, RDF
## Tasks
* Upload GeneRIF data in Tux02.
* Give example...
- Dataset Queried Twice
✓ issue opened on Oct 20 2022 by Frederick Muriuki Muriithi, last updated on Nov 21 2022 by AlexanderKabui
Dataset Queried Twice
## Tags
* assigned: alexm
* type: bug
* priority: medium
* keywords: performance enhancement, optimisation
* status: closed ,complete
## Description
In the function...
- Create a new UI language for gn2
✓ issue opened on Apr 18 2022 by BonfaceKilz, last updated on Oct 11 2023 by Munyoki Kilyungi
Create a new UI language for gn2
## Tags
* assigned: robw, zachs, bonfacem
* type: ui
* status: unclear
* priority: low
* keywords: ui
## Introduction
New UI keeps spring up in the genenetwork eco-...
- Create Traits Endpoints in RDF
✓ issue opened on May 18 2023 by Munyoki Kilyungi, last updated on Jun 19 2023 by Munyoki Kilyungi; 3 of 3 tasks done
Create Traits Endpoints in RDF
## Tags
* assigned: bonfacem
* type: feature
* status: closed
Create end-points that query RDF for the following:
* [x] Phenotypes: (prefix "phenotype:" "<http...
- Correlations are wrongly always using all samples
✓ issue opened on Oct 21 2022 by Zachary Sloan, last updated on Nov 22 2022 by Frederick Muriuki Muriithi
Correlations are wrongly always using all samples
## Tags
* assigned: fredm, zsloan, alexm
* type: bug
* priority: high
* status: closed, completed
* keywords: correlations
## Description
Do any BXD...
- 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
...iterable
## Tags
* type: bug
* priority: high
* status: closed, completed
* keywords: correlations, from github, high priority
## Description
=> https://github.com/genenetwork/genenetwork2/issues/374...
- Fix Case Attribute Work (Consecutive CRUD applications)
✓ issue opened on Apr 06 2022 by BonfaceKilz, last updated on Apr 18 2023 by Munyoki Kilyungi; 0 of 2 tasks done
...Tags
* assigned: bonfacem
* status: stalled
* type: bug
* keywords: case attributes, data editing
* priority: medium
## Tasks
* [ ] Consecutive inserts with same values
* [ ] Consecutive deletions...
- Collections Count Bug
✓ issue opened on Dec 18 2023 by Frederick Muriuki Muriithi, last updated on Dec 18 2023 by Frederick Muriuki Muriithi
...Count Bug
## Tags
* assigned: fredm
* priority: medium
* type: bug
* status: closed, completed
* keywords: collections
## Description
If the user creates even a single collection, a default collection...
- GN3 API Configurations on CD
✓ issue opened on Jan 08 2024 by Alexander_Kabui, last updated on Jan 08 2024 by Alexander_Kabui
...Tags
* assigned: alexm, Bonfacem
* keywords: configurations, CD, API, genenetwork3
* type: bug
* priority: high
* status: closed, completed
## Description
The issue arises in GN3 when the Gunicorn...
- Broken Indexing
✓ issue opened on May 03 2023 by Munyoki Kilyungi, last updated on Oct 11 2023 by Munyoki Kilyungi
Broken Indexing
## Tags
* assigned: bonfacem, alex, fredm
* type: CD
* priority: high
* keywords: xapian, search
## Description
Broken Search from:
=> https://ci.genenetwork.org/jobs/genenetwork3-...
- Use "Authorisation Code Flow" for Authentication
✓ issue opened on May 08 2023 by Frederick Muriuki Muriithi, last updated on May 22 2023 by Frederick Muriuki Muriithi
Use "Authorisation Code Flow" for Authentication
## Tags
* assigned: fredm
* priority: critical
* status: closed, completed
* keywords: authentication, authorisation, oauth2, authorisation code flow...
- Enable User Masquerade
✓ issue opened on May 22 2023 by Frederick Muriuki Muriithi, last updated on May 23 2023 by Frederick Muriuki Muriithi
...Tags
* assigned: fredm, zsloan, zachs
* priority: medium
* status: closed, completed
* keywords: authentication, authorisation, oauth2
* type: feature request
## Description
To enable debug...
- Build Registration Page for OAuth2 Clients
✓ issue opened on Dec 22 2022 by Frederick Muriuki Muriithi, last updated on May 30 2023 by Frederick Muriuki Muriithi
Build Registration Page for OAuth2 Clients
## Tags
* assigned: fredm, zsloan, zachs
* priority: high
* status: closed, completed
* keywords: authentication, authorisation, oauth2
* type: feature...
- Reset/Forgot Password Feature for GN2
✓ issue opened on May 15 2024 by Munyoki Kilyungi, last updated on Sep 16 2024 by Frederick Muriuki Muriithi
...Tags
* assigned: fredm
* priority: critical
* status: closed
* keywords: gn-auth, auth, reset password
* type: feature-request
## Description
Should a user forget his/her password, there's no clear...
- Add "Target" (Y) Column in Partial Correlations Selection Table
✓ issue opened on Apr 22 2022 by Frederick Muriuki Muriithi, last updated on May 26 2022 by Frederick Muriuki Muriithi
..."Target" (Y) Column in Partial Correlations Selection Table
## Tags
* assigned: fredm
* priority: medium
* type: migration, feature-request
* status: closed, completed
* keywords: partial correlations...
- Add search syntax hints to web UI
✓ issue opened on Feb 15 2023 by Arun Isaac, last updated on Apr 04 2023 by Alexander_Kabui
...hints to web UI
## Tags
* assigned: alexm
* status: completed, closed
* keywords: xapian,search,UI
The web UI of the global search should hint at the supported search syntax. For example, see how mumi...
- Improve Logging in GN3 RDF endpoints
✓ issue opened on Feb 10 2024 by Munyoki Kilyungi, last updated on Feb 14 2024 by Munyoki Kilyungi
...endpoints
## Tags
* assigned: bonfacem
* priority: high
* type: API
* keywords: RDF, gn3
## Description
Right now troubleshooting RDF endpoints as mentioned in:
=> issues/non-deterministic-gn3-setup-...
- Add GeneRIF page
✓ issue opened on Apr 14 2023 by Munyoki Kilyungi, last updated on Apr 18 2023 by Munyoki Kilyungi
...page
## Tags
* assigned: bonfacem
* type: feature
* keywords: generif, metadata, RDF
## Tasks
* Create an endpoint in GN3 that queries virtuoso for generif metadata
* Create a page to show generif...
- 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
...to Tissue
## Tags
* assigned: aruni
* priority: medium
* type: feature-request, enhancement
* status: open, in progress
* keywords: tissue, edit issue
## Description
Add an `Edit Issue` link on each...
- Add Documentation For Set Up and Data Retrieval For AI Repo
✓ issue opened on Dec 01 2023 by Munyoki Kilyungi, last updated on Jul 29 2024 by Munyoki Kilyungi
...Data Retrieval For AI Repo
## Tags
* assigned: bonfacem, soloshelby
* priority: high
* type: ui
* keywords: phenotypes
## Description
* Improve the guix documentation for the AI repo.
* Sharing TTL...
- issues/add-collection-import.gmi
✓ issue opened on Apr 29 2022 by Zachary Sloan, last updated on Mar 14 2023 by Arun Isaac
...Tags
* assigned: zsloan
* type: bug
* priority: medium
* status: closed
* keywords: collections
## Description
One feature from GN1 that is still missing from GN2 is the ability to export/import...
- DOL group mapping issues
✓ issue opened on Apr 07 2022 by Zachary Sloan, last updated on Apr 20 2022 by Zachary Sloan
...Tags
* assigned: zsloan
* type: bug
* priority: medium
* status: closed
* keywords: mapping
## Description
After generating the genotype files for the Diversity Outbred Lung (DOL) group for Jacco...
- BXD102xBXD077F1 Error
✓ issue opened on Mar 22 2022 by Frederick Muriuki Muriithi, last updated on Apr 07 2022 by Zachary Sloan
...Tags
* assigned: zsloan
* type: bug
* priority: critical
* status: unclear
* keywords: correlations, from github, closed
## Description
=> https://github.com/genenetwork/genenetwork2/issues/612...
- Notify a user after a minor change
✓ issue opened on Nov 09 2022 by Munyoki Kilyungi, last updated on Nov 11 2022 by Munyoki Kilyungi
Notify a user after a minor change
## Tags
* assigned: bonfacem
* type: ui, refactor, enhancement
* priority: medium
## Description
When the user submits a change of a trait in GN it looks like this...
- Edit OAuth2 Clients
✓ issue opened on Apr 24 2024 by Frederick Muriuki Muriithi, last updated on May 02 2024 by Frederick Muriuki Muriithi
...OAuth2 Clients
## Tags
* status: closed, completed
* priority: high
* type: enhancement
* assigned: fredm
* keywords: gn-auth, issue, oauth2
## Description
With the recent updates to use JWT in place...
- Move Uploader to tux02
✓ issue opened on Mar 12 2024 by Frederick Muriuki Muriithi, last updated on Jul 03 2024 by Frederick Muriuki Muriithi; 3 of 3 tasks done
...tux02
## Tags
* type: migration
* assigned: fredm
* priority: high
* status: closed, completed, fixed
* keywords: gn-uploader, guix, container, deploy
## Databases
### MariaDB
To avoid corrupting the...
- Broken continuous deployment
✓ issue opened on Jul 06 2022 by Arun Isaac, last updated on Jul 11 2022 by Frederick Muriuki Muriithi
...aruni
* tags: critical
The continuous deployment (CD) of GeneNetwork2 at https://gn2dev.genenetwork.org/ is broken. Even with all javascript enabled, none of the menu items load. The error message...
- Upload probeset metadata
✓ issue opened on Jun 19 2023 by Munyoki Kilyungi, last updated on Jun 26 2023 by Munyoki Kilyungi
...Tags
* assigned: bonfacem
* type: bug
* status: closed
Probeset metadata is the only significant metadata that remains to be uploaded. Uploading using SPARQL'S endpoint (either using CURL or the...
- UI Design
✓ issue opened on Dec 01 2021 by jgart, last updated on Jul 20 2022 by Frederick Muriuki Muriithi
...have the wrong format for the strain name."
"Here's our format of how your dataset should look like."
> ProbeSetID Strains ...
"Inbred Set ID 1 is the same as BXD"
> These are the strains: ...
## Tags...
- Remove Extra Partial Correlations Options
✓ issue opened on May 16 2022 by Frederick Muriuki Muriithi, last updated on Nov 22 2022 by Frederick Muriuki Muriithi
Remove Extra Partial Correlations Options
## Tags
* assigned: fredm
* keywords: partial correlations
* status: closed, completed
* type: bug
* priority: high
## Description
When running the partial...
- Data Integrity for Table Identifiers
✓ issue opened on Apr 16 2024 by Frederick Muriuki Muriithi, last updated on Apr 17 2024 by Frederick Muriuki Muriithi
...Table Identifiers
## Tags
* type: bug
* assigned: fredm
* priority: critical
* status: closed, completed
* keywords: data integrity, mariadb, gn-uploader
## Description
The use of
```
SELECT MAX(Id)...
- QC: Fix Integration Tests
✓ issue opened on Jan 09 2024 by Frederick Muriuki Muriithi, last updated on Feb 27 2024 by Frederick Muriuki Muriithi
...Integration Tests
## Tags
* assigned: fredm
* priority: medium
* status: closed, completed
* keywords: quality control, qc, tests, gn-uploader
* type: bug
## Description
Tests that require that Redis...
- Migrate to Python3.10
✓ issue opened on Jul 12 2023 by Frederick Muriuki Muriithi, last updated on Oct 11 2023 by Munyoki Kilyungi; 0 of 1 tasks done
...to Python3.10
## Tags
* priority: high
* keywords: python3.10
* status: closed
* assigned: bonfacem, fredm, alex, zachs
## Description
Migrate the application(s) over to Python3.10.
The sections below...
- Editing Case Attribute
✓ issue opened on Mar 16 2023 by Munyoki Kilyungi, last updated on Apr 18 2023 by Munyoki Kilyungi
...Attribute
## Tags
* assigned: bonfacem
* type: bug
* keywords: case attributes, data editing
The Metadata and Data Editing Form has several issues that need to be addressed to improve user experience...
- Missing CI/CD Definitions for "Service" Daemons
✓ issue opened on May 16 2022 by Frederick Muriuki Muriithi, last updated on May 16 2022 by Frederick Muriuki Muriithi; 1 of 1 tasks done
Missing CI/CD Definitions for "Service" Daemons
## Tags
* keywords: ci-cd, service daemons, GN3
* status: closed
* priority: medium
* type: bug
* assigned: fredm
## Description
The ~sheepdog/worker...
- gn-uploader: Resume Upload
✓ issue opened on Jun 24 2024 by Frederick Muriuki Muriithi, last updated on Jul 03 2024 by Frederick Muriuki Muriithi; 4 of 4 tasks done
...Resume Upload
## Tags
* status: closed, completed, fixed
* priority: medium
* assigned: fredm, flisso
* type: feature request, feature-request
* keywords: gn-uploader, uploader, upload, resume upload...
- Correlations fail for at least some ProbeSet datasets (as the target dataset)
✓ issue opened on Oct 17 2022 by Zachary Sloan, last updated on Nov 22 2022 by Frederick Muriuki Muriithi
...Tags
* type: bug
* priority: high
* status: closed, completed
* keywords: correlations
## Description
Go to
=> https://genenetwork.org/show_trait?trait_id=P40630_SWEEQMAEVGR_2&dataset=EPFL-ETHZ-...
- Make Existing Data Public View by Default
✓ issue opened on May 24 2023 by Frederick Muriuki Muriithi, last updated on Dec 18 2023 by Frederick Muriuki Muriithi
Make Existing Data Public View by Default
## Tags
* assigned: fredm, zsloan, zachs
* priority: medium
* status: closed, completed
* keywords: authentication, authorisation, oauth2, data migration...
- Sort by Attributes
✓ issue opened on May 31 2024 by Frederick Muriuki Muriithi, last updated on May 31 2024 by Zachary Sloan
...by Attributes
## Tags
* assigned: zachs, fredm
* type: feature-request, feature request
* priority: high
* status: closed
* keywords: genenetwork2, sorting, attributes
## Description
From the email...
- Temp traits don't seem to be handled by the authorization system
✓ issue opened on Jul 28 2023 by Zachary Sloan, last updated on Feb 27 2024 by Frederick Muriuki Muriithi
Temp traits don't seem to be handled by the authorization system
## Tags
* assigned: fredm, zsloan
* priority: high
* status: closed, completed
* keywords: authentication, authorisation, oauth2, temp-...
- Quality Control Checks
✓ issue opened on Nov 17 2021 by jgart, last updated on Jul 20 2022 by Frederick Muriuki Muriithi
...the same capitalization style.
10. Assesing Phenotypes for normality with Shapiro-Wilk Test.
11. Check for annotations file.
12. Check for CRLF.
13. Check for UTF-8 encoding.
## Tags
* assigned: fredm...
- Containerising Production: Issues
✓ issue opened on Oct 26 2024 by Frederick Muriuki Muriithi, last updated on Nov 05 2024 by Frederick Muriuki Muriithi; 1 of 1 tasks done
Containerising Production: Issues
## Tags
* type: bug
* assigned: fredm
* priority: critical
* status: closed, completed
* keywords: production, container, tux04
* interested: alexk, aruni, bonfacem...
- Remove externally loaded JS
✓ issue opened on Apr 18 2022 by BonfaceKilz, last updated on Feb 28 2024 by Alexander_Kabui; 3 of 3 tasks done
Remove externally loaded JS
## Tags
* assigned: alex
* type: ui, enhancement
* status: closed, completed
* priority: medium
* keywords: ui, guix
## Description
`jquery-ui` is still loaded from a CDN.
- Read Samples/Cases/Individuals From Database
✓ issue opened on Jan 20 2024 by Frederick Muriuki Muriithi, last updated on Feb 27 2024 by Frederick Muriuki Muriithi
Read Samples/Cases/Individuals From Database
## Tags
* type: bug
* priority: critical
* assigned: fredm, acenteno
* keywords: QC, quality control, samples, strains, cases, gn-uploader...
- Move Data Endpoints from GN2 to GN3
✓ issue opened on Nov 03 2023 by Frederick Muriuki Muriithi, last updated on Nov 03 2023 by Frederick Muriuki Muriithi
...Tags
* assigned: fredm
* priority: medium
* type: feature-request
* status: closed
* keywords: API
## Description
GN3 is the API server, but currently (as of Friday 03 November 2023 at 11:11AM +03...
- Conflating `dataset_id` with `inbred_set_id`
✓ issue opened on Jul 18 2023 by Frederick Muriuki Muriithi, last updated on Nov 28 2023 by Frederick Muriuki Muriithi
Conflating `dataset_id` with `inbred_set_id`
## Tags
* type: bug
* status: closed
* assigned: fredm, bonz
* keywords: editing
* priority: critical
## Description
The issue described here should no...
- Fix Broken UTF-8 characters in our Database
✓ issue opened on Nov 29 2022 by Munyoki Kilyungi, last updated on Aug 29 2023 by Munyoki Kilyungi
...in our Database
## Tags
* assigned: bonfacem, arthur
* type: database
* priority: high
## Description
We have jumbled up text in our database and this has been the case for years. It's impractical...
- Run Correlations in External Process
✓ issue opened on Oct 19 2022 by Frederick Muriuki Muriithi, last updated on Oct 31 2022 by Frederick Muriuki Muriithi
Run Correlations in External Process
## Tags
* assigned: fredm
* type: feature
* priority: high
* keywords: correlations, asynchronous jobs, external process
* status: completed, closed...
- Replace sqlalchemy with MySQLdb
✓ issue opened on Aug 29 2022 by Munyoki Kilyungi, last updated on Sep 08 2022 by Munyoki Kilyungi
...Tags
* assigned: bonfacem, zachs
* type: refactor
* priority: medium
## Description
Connections that use sqlalchemy are the only placen in GN2 where connections remain "open" indefinitely until a...
- Autogenerate documentation: trees, and labels
✓ issue opened on Jun 23 2023 by Munyoki Kilyungi, last updated on Oct 11 2023 by Munyoki Kilyungi
Autogenerate documentation: trees, and labels
# Tags
* assigned: bonfacem
* type: feature, NextGenDatabases
* priority: high
* keywords: RDF, GNSOC2023
See this
=> https://github.com/genenetwork/dump-...
- Error Handling: External Errors
✓ issue opened on Jan 29 2024 by Frederick Muriuki Muriithi, last updated on Sep 16 2024 by Frederick Muriuki Muriithi
...Handling: External Errors
## Tags
* assigned: fredm
* status: closed
* type: bug
* priority: high
* keywords: error handling
## Description
We have been consistently moving a lot of our features out...
- Miscellaneous UI issues
✓ issue opened on Apr 08 2022 by Zachary Sloan, last updated on Aug 08 2022 by Munyoki Kilyungi
Tags
* type: ui
* keywords: user-interface
* assigned: zachs, ethan, bonfacem
* status: closed
* priority: low
## TODO
- [X] Change following drop-down menu items:
* Diversity Outbred -> DO Gatti...
- Buggy Use of `urllib.parse.urljoin`
✓ issue opened on Jul 25 2022 by Frederick Muriuki Muriithi, last updated on Nov 28 2023 by Frederick Muriuki Muriithi
Buggy Use of `urllib.parse.urljoin`
## Tags
* type: bug
* priority: low
* assigned: fredm
* status: closed, completed
* keywords: url
## Description
This issue was circumvented by ensuring all the...
- Rework Resources
✓ issue opened on Sep 06 2023 by Frederick Muriuki Muriithi, last updated on Feb 27 2024 by Frederick Muriuki Muriithi; 2 of 3 tasks done
Rework Resources
## Tags
* assigned: fredm
* status: closed, completed
* priority: medium
* type: refactor, feature request, design change
* keywords: auth, authorisation, resources, design change...
- Import Collections Pop-up Bug
✓ issue opened on Dec 12 2023 by Zachary Sloan, last updated on Dec 18 2023 by Frederick Muriuki Muriithi
Import Collections Pop-up Bug
## Tags
* assigned: fredm, zachs
* priority: urgent
* type: bug
* status: closed, completed
* keywords: collections
## Description
If you create collections while logged-...
- Quality Control Project
✓ issue opened on Nov 19 2021 by Arthur Centeno, last updated on Jul 20 2022 by Frederick Muriuki Muriithi
...could run QC through the REST API too. That would allow it to
be run from R and Python and Jupyter notebooks. Make it part of GN3.
The tricky part is still how the data is handled in escrow.
## Tags...
- Improve Menu Generation and Move it to GN3
✓ issue opened on May 16 2022 by Frederick Muriuki Muriithi, last updated on Jun 23 2022 by Frederick Muriuki Muriithi; 2 of 3 tasks done
Improve Menu Generation and Move it to GN3
## Tags
* assigned: fredm
* type: bug
* priority: medium
* status: closed, completed
* keywords: menu generation, GN2, GN3
## Description
The
=> https...
- Fix Opaque Errors
✓ issue opened on Feb 12 2024 by Frederick Muriuki Muriithi, last updated on Feb 27 2024 by Frederick Muriuki Muriithi
...Opaque Errors
## Tags
* status: closed, completed
* assigned: fredm
* type: bug
* priority: high
* keywords: opaque errors, errors, UX, user experience, gn-uploader
## Description
This issue is meant...
- GN3 Setup on tux01 - Non-Deterministic Behavior
✓ issue opened on Jan 15 2024 by Munyoki Kilyungi, last updated on Feb 10 2024 by Munyoki Kilyungi
...Setup on tux01 - Non-Deterministic Behavior
## Tags
* assigned: bonfacem, zachs
* priority: high
* type: ops, guix
* keywords: gn3
* status: closed
## Description
Zach and Munyoki attempted to set up...
- 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
Automatically find broken links on GN2
## Tags
* assigned: zsloan, alex
* type: bug
* priority: medium
* status: completed, closed
* keywords: GN1, GN2, broken links, from github
## Members
* Millak...
- genecup is currently running as root on penguin2.
✓ issue opened on Aug 15 2021 by Efraim Flashner, last updated on Jun 21 2024 by Pjotr Prins
Tags
* assigned: Efraim
* type: failure
* keywords: genecup, penguin2
* status: closed
* priority: high
## Notes
* It is unclear if the environmental-variables in the shepherd service are carried...
- Troubleshoot https://luna.genenetwork.org/ai/ asking questions
✓ issue opened on Jan 04 2024 by Munyoki Kilyungi, last updated on Jan 04 2024 by Munyoki Kilyungi
...org/ai/ asking questions
## Tags
* assigned: bonfacem, soloshelby
* priority: high
* type: llm
* keywords: llm
* status: closed
## Description
We have the following stack-trace in https://luna...
- Dump GeneWiki Metadata
✓ issue opened on Mar 16 2023 by Munyoki Kilyungi, last updated on Apr 04 2023 by Munyoki Kilyungi
...Tags
* assigned: bonfacem
* type: feature
* keywords: metadata, RDF
Dump the tables:
* GeneRIF
* GeneRIF_BASIC
## Resources
=> https://www.w3.org/TR/rdf-schema/ RDF Schema 1.1
=> https://www...
- Coupling current_app and db_utils
✓ issue opened on Apr 04 2023 by Frederick Muriuki Muriithi, last updated on Apr 15 2023 by Frederick Muriuki Muriithi
Coupling current_app and db_utils
## Tags
* assigned: fredm, aruni
* priority: high
* type: bug
* status: closed, completed, fixed
* keywords: bug, configurations
## Description
=> https://github.com/...
- Add GeneList to Metadata
✓ issue opened on Dec 13 2023 by Munyoki Kilyungi, last updated on Dec 20 2023 by Munyoki Kilyungi
...Tags
* assigned: bonfacem
* priority: high
* type: RDF
* keywords: virtuoso
## Description:
=> https://www.gene-list.com/about About GeneList
The GeneList table in GN fetches metadata about given...
- Wrong CSV in ITP_10001 longevity dataset
✓ issue opened on Apr 11 2022 by BonfaceKilz, last updated on Apr 12 2022 by BonfaceKilz
...ITP_10001 longevity dataset
## Tags
* assigned: bonfacem
* type: bug
* status: closed
* priority: critical
* keywords: critical bug, in progress, metadata, phenotypes
## Description
[From Suheeta]:
"I...
- Implementing parallel correlation with rust
✓ issue opened on Apr 25 2022 by Alexander Kabui, last updated on Jul 11 2023 by Alexander_Kabui; 12 of 15 tasks done
Implementing parallel correlation with rust
### Notes
In an attempt to speed the current gn2 correlation
we are doing an reimplentation in rust to support
parralel computation
## Tags
* assigned:alem...
- test1-auth.genenetwork.org Can't Find Templates
✓ issue opened on Mar 02 2024 by Frederick Muriuki Muriithi, last updated on Jun 26 2024 by Frederick Muriuki Muriithi
...Tags
* assigned: fredm, aruni
* priority: critical
* status: closed, completed, fixed
* type: bug
* keywords: gn-auth, deployment, test1
## Description
The new (as of 2024-02-03T14:20+03:00UTC)...
- Modelling Phenotype Data
✓ issue opened on Aug 08 2023 by Munyoki Kilyungi, last updated on Oct 11 2023 by Munyoki Kilyungi
...feel secure.
* For private data, expose the pre-publication data.
* Pre, post, published data with a tag of whether private or public and share with Rob/Arthur (in ms word).
* Full time expert curator.
- Correlations time out
✓ issue opened on Aug 06 2021 by Pjotr Prins, last updated on Nov 22 2022 by Frederick Muriuki Muriithi; 2 of 3 tasks done
...It looks like correlations don't finish - and worse the running processes take a significant chunk of RAM, around 10GB each. Eventually they disappear.
## Tags
* assigned: pjotrp, zachs, alexm...
- Configurations
✓ issue opened on Jun 05 2023 by Frederick Muriuki Muriithi, last updated on Sep 16 2024 by Frederick Muriuki Muriithi
...Tags
* assigned: aruni, fredm
* priority: normal
* status: closed, completed
* keywords: CI, CD, configuration, config
* type: bug
## Description
There are configurations that change depending...
- Migrate User Accounts from Redis to new Auth DB
✓ issue opened on Dec 22 2022 by Frederick Muriuki Muriithi, last updated on May 22 2023 by Frederick Muriuki Muriithi
...DB
## Tags
* assigned: fredm, zsloan, zachs
* priority: high
* status: closed, wontfix
* keywords: authentication, authorisation, oauth2
* type: feature request
## Description
After some discussion...
- Handling Resource Links in ProbeSet Page
✓ issue opened on Nov 22 2023 by Munyoki Kilyungi, last updated on Dec 14 2023 by Munyoki Kilyungi
...Tags
* assigned: bonfacem
* priority: high
* type: RDF
* keywords: virtuoso
## Description:
During the finalization of the UI for endpoints, specifically the probeset page, modifications were made...
- Unresponsive Virtuoso in CD
✓ issue opened on Apr 02 2024 by Munyoki Kilyungi
...bonfacem
* tags: critical
## Description
In CD, when you navigate to a datasets page, say:
=> https://cd.genenetwork.org/datasets/BXDPublish /datasets/BXDPublish
you get the following stack trace...
- Quality Control of Data in Uploaded R/qtl2 Bundles
✓ issue opened on Feb 02 2024 by Frederick Muriuki Muriithi, last updated on Sep 16 2024 by Frederick Muriuki Muriithi; 10 of 15 tasks done
...Tags
* assigned: fredm, acenteno
* status: closed, completed
* type: feature request
* priority: medium
* keywords: quality control, QC, R/qtl2 bundle
## Description
Currently (2024-02-02T05:41+03...
- Problem With Roles: Privilege Escalation
✓ issue opened on Jun 06 2024 by Frederick Muriuki Muriithi, last updated on Jul 03 2024 by Frederick Muriuki Muriithi; 8 of 8 tasks done
...Roles: Privilege Escalation
## Tags
* type: bug
* priority: critical
* assigned: fredm, zachs
* status: closed, completed, fixed
* keywords: gn-auth, authorisation, authorization, roles, privileges...
- Xapian Search Results not Quite as Expected
✓ issue opened on Mar 25 2023 by Frederick Muriuki Muriithi, last updated on Mar 31 2023 by Arun Isaac
...Search Results not Quite as Expected
## Tags
* type: bug
* assigned: arun, fredm
* priority: medium
* status:
* keywords: xapian, search
## Description
The following is a list of failing examples...
- metadata caching bug
✓ issue opened on Mar 18 2022 by Alexander Kabui, last updated on Dec 23 2022 by Pjotr Prins; 2 of 2 tasks done
...-python-3.9.6/lib/python3.9/json/decoder.py", line 340, in decode
raise JSONDecodeError("Extra data", s, end)
json.decoder.JSONDecodeError: Extra data: line 1 column 6765450 (char 6765449)
## Tags...
- issues/fetch-sample-data.gmi
✓ issue opened on Aug 09 2021 by BonfaceKilz, last updated on May 25 2022 by BonfaceKilz
Tags
* assigned: bonifacem
* keywords: sample data, GN2, GN3
* status: closed
* priority: medium
#### Fetch all Sample Data
Currently we fetch all the sample data using this function:
```
def...
- Error when fetching SNPs in a search page
✓ issue opened on Sep 28 2022 by Munyoki Kilyungi, last updated on Apr 18 2023 by Munyoki Kilyungi
Error when fetching SNPs in a search page
Wed 28 Sep 2022 17:45:01 EAT
* assigned: zachs, bonfacem
* tags: critical
* priority: high
* closed
## Steps to reproduce
* Consider this search page...
- Add to Collection Error
✓ issue opened on Oct 09 2023 by Frederick Muriuki Muriithi, last updated on Nov 28 2023 by Frederick Muriuki Muriithi
Add to Collection Error
## Tags
* assigned: fredm, zachs
* priority: urgent
* type: bug
* status: closed, completed
* keywords: collections
## Description
Go to the following correlation results...
- Better Logging
✓ issue opened on Aug 23 2022 by Munyoki Kilyungi, last updated on Oct 12 2022 by Munyoki Kilyungi
...Tags
* type: enhancement
* keywords: deployment, 404
* assigned: bonfacem, pjotrp
* priority: low
## Introduction
=> https://flask.palletsprojects.com/en/2.0.x/errorhandling/
Some of those 404's in...
- Case Attribute Editing Problems
✓ issue opened on May 02 2022 by Zachary Sloan, last updated on Mar 20 2023 by Munyoki Kilyungi
...manually added them to the CaseAttribute table (with (id,name) of (48, 'MBS2022') and (49, 'DA2022') respectively), but they weren't added when I submitted a CSV with those two extra columns.
## Tags...
- Migrate User Collections
✓ issue opened on May 08 2023 by Frederick Muriuki Muriithi, last updated on May 22 2023 by Frederick Muriuki Muriithi
...Tags
* assigned: zachs, fredm
* priority: critical
* status: closed, completed
* keywords: authentication, authorisation, oauth2, user collections
* type: bug
## Description
With the successful...
- GEMMA output differs from R/qtl2
✓ issue opened on Aug 01 2024 by Pjotr Prins, last updated on Sep 20 2024 by Pjotr Prins
...differs from R/qtl2
# Tags
* assigned: pjotrp, davea
* priority: high
* type: bug, enhancement
* status: closed
* keywords: database, gemma, reaper, rqtl2
# Description
When running trait BXD_21526...
- 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
Capture Data on the BXDs in RDF
## Tags
* assigned: bonfacem, pjotrp, zsloan
* priority: high
* status: unclear
* type: feature-request, enhancement
* keywords: RDF, BXD, REST, from github, high...
- Phenotype Correlation Error
✓ issue opened on Sep 28 2022 by Zachary Sloan, last updated on Nov 28 2023 by Frederick Muriuki Muriithi
...bugs
this code that does preprocessing of data needs to be modified
thats is :-
* Tissue correlation data
* top n sample correlation data
* top n tissue correlation data
## Tags
* assigned: alexm...
- Bug when using HTMX Ajax Post request
✓ issue opened on May 14 2024 by Alexander_Kabui, last updated on May 28 2024 by Alexander_Kabui
...HTMX Ajax Post request
## Tags
* type: bug
* priority: high
* status: complete, closed
* assigned: alexm
* keywords: htmx, error, javascript, api
## Description
The issue occurs when you send a post...
- UI Frontend for RDF
✓ issue opened on Oct 11 2023 by Munyoki Kilyungi, last updated on Mar 06 2024 by Munyoki Kilyungi
UI Frontend for RDF
## Tags
* assigned: bonfacem
* type: issue
### Motivation
We have GN Metadata in RDF already. Right now, it's only accessible through a SPARQL endpoint, and it's not benefiting...
- Invalid Token Error
✓ issue opened on Aug 25 2023 by Zachary Sloan, last updated on Aug 31 2023 by Frederick Muriuki Muriithi
Invalid Token Error
## Tags
* assigned: fredm, zsloan
* type: bug
* priority: high
* status: closed, completed, resolved
* keywords: authentication
## Description
A while after logging in, users (who...
- GNQA Integration to Global Search Design Proposal
✓ issue opened on Sep 02 2024 by Alexander_Kabui, last updated on Oct 16 2024 by Alexander_Kabui; 9 of 9 tasks done
...Tags
* assigned: jnduli, alexm
* keywords: llm, genenetwork2
* type: feature
* status: complete, closed, done
## Description
This document outlines the design proposal for integrating GNQA into...
- GN1 Pairscan
✓ issue opened on Sep 15 2021 by Pjotr Prins, last updated on Dec 17 2022 by Pjotr Prins
...py", line 79, in ?
from pairScan import DirectPlotPage
File "/gnshare/gn/web/webqtl/cmdLine/../pairScan/DirectPlotPage.py", line 32,
in ?
import direct
ImportError: No module named direct
```
# Tags...
- '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
'TempDataSet' object has no attribute 'query_for_group' (error)
## Tags
* assigned: alex
* priority: high
* type: bug
* status: closed
* keywords: TempDataSet, from github
## Description
=> https...
- gemma-wrapper has incomplete files
✓ issue opened on Nov 14 2021 by Pjotr Prins, last updated on Feb 17 2022 by Pjotr Prins; 2 of 2 tasks done
...it can happen a cached file is incomplete and never updated again. The problem appears when GNU parallel is invoked and hits an error. The task here is to make gemma-wrapper transactional.
## Tags...
- Virtuoso: Shutdown Clears Data
✓ issue opened on Oct 28 2024 by Frederick Muriuki Muriithi, last updated on Oct 30 2024 by Frederick Muriuki Muriithi
...Shutdown Clears Data
## Tags
* type: bug
* assigned: fredm
* priority: critical
* status: closed, completed
* interested: bonfacem, pjotrp, zsloan
* keywords: production, container, tux04, virtuoso...
- Set-up Virtuoso+Xapian on Production
✓ issue opened on Nov 22 2023 by Munyoki Kilyungi, last updated on Oct 28 2024 by Frederick Muriuki Muriithi; 1 of 1 tasks done
...Tags
* assigned: bonfacem, zachs, fredm
* priority: high
* type: ops
* keywords: virtuoso
## Description
We already have virtuoso set-up in tux02. Right now, to be able to interact with RDF...
- Haley-Knott Regression Mapping Error
✓ issue opened on Sep 11 2024 by Frederick Muriuki Muriithi
Haley-Knott Regression Mapping Error
## Tags
* type: bug
* status: closed, completed
* priority: high
* assigned: fredm
* keywords: gn2, genenetwork2, genenetwork 2, mapping, haley-knott...
- Materialised Views for Correlations
✓ issue opened on Oct 19 2022 by Frederick Muriuki Muriithi, last updated on Dec 19 2022 by Frederick Muriuki Muriithi
Materialised Views for Correlations
## Tags
* assigned: alex, fred, zachs
* type: feature, improvement
* priority: high
* keywords: correlations, materialised views, optimisation...
- Edit RIF Metadata in GN2
✓ issue opened on Jul 29 2024 by Munyoki Kilyungi, last updated on Oct 15 2024 by Munyoki Kilyungi; 15 of 15 tasks done
...Tags
* assigned: bonfacem, jnduli
* priority: high
* status: closed
## Tasks
### Viewing
* [X] API: Get WIKI/RIF by symbol from rdf.
> GET /wiki/<symbol>
```
[{
"symbol": "XXXX",
"reason"...
- R/qtl JSONDecodeError
✓ issue opened on Dec 23 2022 by Pjotr Prins, last updated on Dec 24 2022 by Pjotr Prins; 3 of 3 tasks done
...informative message
* [X] Log in error log
* [X] Add test regressions
These have been fixed by Zach and Pjotr
## Tags
* status: closed
## Info
Now qtlreaper works. That suggests a problem with R. Zach...
- GeneNetwork2: Account Registration Error
✓ issue opened on Mar 19 2024 by Frederick Muriuki Muriithi, last updated on Sep 16 2024 by Frederick Muriuki Muriithi
...Tags
* type: bug
* priority: critical
* assigned: zachs, zsloan, fredm
* status: closed, completed
* keywords: genenetwork2, account management, user, registration
## Description
When one attempts...
- tux01 running out of RAM
✓ issue opened on Sep 03 2022 by Pjotr Prins, last updated on May 03 2024 by Pjotr Prins; 1 of 6 tasks done
...RAM
Tux01 ran out of steam.
## Tags
* assigned: pjotrp, zsloan
* type: systems
* keywords: database
* status: closed
* priority: medium
## Tasks
* [X] post-mortem (see below)
* [ ] free up disk space...
- Login issues with gn-auth
✓ issue opened on Mar 01 2024 by Pjotr Prins, last updated on Jul 03 2024 by Frederick Muriuki Muriithi
Login issues with gn-auth
# Tags
* type: bug
* assigned: fredm
* priority: critical
* status: closed, completed, fixed
* keywords: gn-auth, auth, authorisation, authentication, registration...
- guix build gn-uploader: error
✓ issue opened on Mar 13 2024 by Frederick Muriuki Muriithi, last updated on Mar 18 2024 by Frederick Muriuki Muriithi
...Tags
* assigned: fredm, aruni
* status: closed
* priority: critical
* type: bug
* keywords: guix, gn-uploader
## Description
Trying to build `gn-uploader` with
> $ guix build -L /home/frederick/...
- Rewrite qc and qc-uploads in Python3
✓ issue opened on Apr 11 2022 by Frederick Muriuki Muriithi, last updated on Nov 28 2023 by Frederick Muriuki Muriithi
Rewrite qc and qc-uploads in Python3
## Tags
* type: rewrite
* priority: high
* assigned: fredm
* status: closed, completed
* keywords: quality control
## Description
Since the quality control...
- Clean up Authorisation
✓ issue opened on Nov 19 2021 by BonfaceKilz, last updated on Dec 04 2023 by Frederick Muriuki Muriithi; 4 of 4 tasks done
...Atm genenetwork2's handling of authorisation is a bit clunky; Since @Bonface is working on the data data up-loader, and it requires authorisation, this is a good time to clean up authorisation.
# Tags...
- Slow Correlations and UI crashes
✓ issue opened on Oct 18 2021 by BonfaceKilz, last updated on Jul 08 2022 by Alexander_Kabui
...and UI crashes
Correlation in gn2 has regressed when compared gn1
Issue experienced by users include
* Correlation being slow
* Browser crush and timeout for huge datasets like (exo dataset)
## Tags...
- Automated Testing
✓ issue opened on Feb 10 2022 by Frederick Muriuki Muriithi, last updated on Oct 12 2022 by Munyoki Kilyungi; 0 of 10 tasks done
Automated Testing
## Tags
* assigned: fredm, bonfacem, alex
* priority: medium
* type: enhancement
* keywords: testing, CI, CD
## Introduction
As part of the
=> ../systems/ci-cd.gmi CI/CD effort...
- Cannot Edit Metadata of BXD Traits Effectively
✓ issue opened on Apr 28 2022 by BonfaceKilz, last updated on Apr 18 2023 by Munyoki Kilyungi; 10 of 12 tasks done
...Traits Effectively
# Tags
* assigned: bonfacem
* keywords: metadata
* priority: high
* closed
## Tasks
* [ ] I cannot edit the PMID number
* [ ] There is inadequate feedback on whether or not changes...
- Genenetwork3 Effective UID
✓ issue opened on Jun 05 2023 by Frederick Muriuki Muriithi, last updated on Jun 09 2023 by Frederick Muriuki Muriithi
...Effective UID
## Tags
* assigned: aruni, fredm
* priority: critical
* status: closed, completed
* keywords: CI, CD, Effective UID, Genenetwork3, GN3
* type: bug
## Description
The issue was...
- Editing Metadata [Improvements to Make]
✓ issue opened on Mar 31 2022 by BonfaceKilz, last updated on Apr 18 2023 by Munyoki Kilyungi; 7 of 11 tasks done
...Make]
## Tags
* assigned: bonfacem, zachs, robw
* type: ui
* priority: high
* keywords: metadata, phenotypes
* closed
## Tasks
This is closely related to:
=> /issues/edit-metadata-bugs
### mRNA assay/...
- Python Requests Error in Container
✓ issue opened on Nov 01 2024 by Frederick Muriuki Muriithi, last updated on Nov 07 2024 by Frederick Muriuki Muriithi
...Tags
* type: bug
* assigned: fredm
* priority: critical
* status: closed, completed, fixed
* interested: alexk, aruni, bonfacem, pjotrp, zsloan
* keywords: production, container, tux04, python...