- 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...
- Sheepdog
issue opened on Nov 08 2021 by Pjotr Prins, last updated on Jul 01 2022 by Arun Isaac; 3 of 17 tasks done
...Tags
* assigned: pjotrp
* type: enhancement
* status: in progress, halted
* priority: medium
* keywords: system, sheepdog
## Tasks
* [X] add locking functionality for tags - added borg with-lock...
- CI/ CD for genetwork projects
document created on Oct 12 2022 by Munyoki Kilyungi, last updated on Feb 27 2024 by Pjotr Prins
...reuse container from staging; tag container as a release container
* Deploy container to production
* Generate documentation for tagged commit
* Generate guix declaration for re-generating the release...
- 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 8 weeks ago by Alexander_Kabui, last updated 5 weeks ago 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...
- Using curl
document created on Dec 23 2022 by Pjotr Prins
..."2310010I16Rik"
sheepdog_run.rb -c "curl \"$URL\"|grep -i $FIND" --tag "wild-card-search-$URL" $*
```
## POST fetch
Post fetches are a bit harder. First use firefox console and click of Debugger tab.
- Capture state of phenotypes in a HASH
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
...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 them here, for their evaluation...
- Backup Drops
document created on Oct 27 2022 by Pjotr Prins, last updated on Feb 18 2024 by Pjotr Prins
...-v --tag "drop-mount-dropserver" -c "sshfs -o IdentityFile=~/.ssh/id_ecdsa_backup bacchus@dropserver:/ ~/mnt/this"
sheepdog_run.rb -h rabbit --always -v --tag "drop-rsync-dropserver" -c "rsync -vrltDP...
- Letsencrypt
issue opened on Oct 13 2021 by Pjotr Prins, last updated on Jul 04 2023 by Pjotr Prins; 2 of 5 tasks done
...sheepdog_run.rb -c '/usr/bin/certbot renew --quiet' --always --tag CERTBOT >> ~/cron.log 2>&1
```
Add certificate
```
certbot certonly --nginx --agree-tos --preferred-challenges http -d ucscbrowser...
- Update RDF Generation and Ingress to Virtuoso
issue opened 5 weeks ago by Munyoki Kilyungi, last updated 4 weeks ago by Munyoki Kilyungi
Update RDF Generation and Ingress to Virtuoso
## Tags
* assigned: bonfacem
* priority: high
* tags: in-progress
* deadline: 2024-10-23 Wed
We need to update Virtuoso in production. At the moment...
- GN1 github problem
issue opened on Dec 17 2022 by Pjotr Prins
...--tree-filter 'rm -f web/images/upload/MouseTissuesRWWMay08.xls' HEAD
git filter-branch --force --index-filter 'git rm --cached --ignore-unmatch \
MouseTissuesRWWMay08.xls' --prune-empty --tag-name-...
- Add mouse data-set
issue opened on Jun 30 2022 by BonfaceKilz, last updated on Apr 18 2023 by Munyoki Kilyungi; 0 of 4 tasks done
...tag data by "animal.no." and "sex". So for a male version of "CC001" with animal number 1, we have "CC001_m_1". This is a problem---storing TS data---that Rob/Suheeta have highlighted in the past.
- 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
...Markdown Editor Integration
## Tags
* assigned: alexm
* status: in progress
* priority: high
* tags: markdown, integration, guile
## Notes
This is a to-do list to integrate the GN Markdown editor into...
- Designing an issue tracker on gemini
✓ issue opened on Jul 25 2021 by Pjotr Prins, last updated on Feb 02 2022 by Pjotr Prins
...testing
* later
* documentation
* help wanted
* closed
the keyword statement may have aliases, such as tag and kanban. To undo a keyword simply remove them from the file.
Can't think of anything...
- 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 5 weeks ago 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.
- Variant Browser seems to be using mm9
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
Variant Browser seems to be using mm9
## Tags
* assigned:
* priority: unclear
* type: bug
* status: stalled
* keywords: variant browser, mm9, from github
## Members
* acenteno
* robw
* pjotrp...
- 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...
- Troubleshoot response inconsistencies for GN-llm
issue opened on Jan 10 2024 by Alexander_Kabui
...-llm
## Tags
* Assigned: Alex, SoloShelby
* Priority: High
* Type: LLM
* Keywords: LLM
* Status: In Progress
# Description
There are discrepancies when asking questions on Qnqa using Fahamu. Sometimes...
- 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
...substitution
## 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...
- 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...
- Tux01 hard disk crash
issue opened on Sep 29 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...One spinning disk crashed on Sept. 26th. It was used for Arthur's HOME and backups.
# Tags
* assigned: pjotrp
* priority: medium
* status: in progress
* keywords: system, tux01, hard disk crash
# Info...
- Octopus sysmaintenance
issue opened on Oct 12 2021 by Pjotr Prins, last updated on Oct 31 2023 by Pjotr Prins; 0 of 8 tasks done
...new machines to Octopus and get fiber optic network going with @andreag. See also
=> ../../topics/systemtopics/systems/hpcs/hpc/octopus-maintenance
# Tags
* assigned: pjotrp, efraimf, erikg, andreag...
- Clean Up
issue opened on Jan 02 2022 by Pjotr Prins, last updated on Jul 01 2022 by Arun Isaac
...Up
## Tags
* assigned: pjotrp, robw
* status: unclear
* priority: unclear
* type: database administration
* keywords: database, mariadb
## Description
Find all larger tables
```
SELECT TABLE_SCHEMA...
- ProbeSE
issue opened on Dec 30 2021 by Pjotr Prins, last updated on Jul 01 2022 by Arun Isaac
ProbeSE
## Tags
* assigned: pjotrp
* status: unclear
* priority: medium
* type: enhancement
* keywords: database, mariadb, innodb, ProbeSE
## Description
Zach pointed out that ProbeSE is used on GN1...
- Support searching using SNP names
issue opened on Feb 15 2023 by Arun Isaac
...searching using SNP names
* tags: enhancement
SNPs are named in an rs### form (for example, rs429358).
=> https://en.wikipedia.org/wiki/Single-nucleotide_polymorphism#Nomenclature
We should permit...
- StrainId wrong
issue opened on May 07 2024 by Pjotr Prins
...wrong
# Tags
* assigned: arthurc
* type: bug
* status: unknown
# Info
When I do:
```
MariaDB [db_webqtl]> SELECT StrainId,Strain.Name FROM Strain, StrainXRef WHERE StrainXRef.StrainId = Strain.Id...
- 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...
- Set Up gn-guile in tux02
issue opened on Aug 29 2024 by Munyoki Kilyungi, last updated 4 weeks ago by Munyoki Kilyungi; 3 of 3 tasks done
Set Up gn-guile in tux02
## Tags
* assigned: bonfacem
* priority: high
* status: in-progress
* deadline: 2024-10-23 Wed
## Tasks
* [-] Create gn-guile container.
* [X] Merge gn2 UI PR.
- Search results presentation
issue opened on Apr 04 2023 by Alexander_Kabui
...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 the results are...
- 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
...looks weird
## Tags
* assigned: zsloan
* type: bug
* priority: medium
* status: in progress
* keywords: UI, SNP, from github
## Description
=> https://github.com/genenetwork/genenetwork2/issues/395...
- Search Improvements: capital insensitive search for RIF+WIKI; Examples
issue opened on Mar 14 2023 by Arun Isaac, last updated on Aug 16 2024 by Munyoki Kilyungi
...Improvements: capital insensitive search for RIF+WIKI; Examples
## Tags
* assigned: bonfacem, rookie101
* priority: high
* type: ops
* keywords: virtuoso
## Description
RIF search is finally working...
- 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"...
- sample data caching bug
issue opened on Feb 11 2022 by Zachary Sloan, last updated on Mar 14 2023 by Arun Isaac
...few days (maybe later today).
The relevant caching code is here - https://github.com/genenetwork/genenetwork2/blob/2c22e593c59a9b4f9129a2e669443709d9c5154a/wqflask/base/data_set.py#L1288-L1317
# Tags...
- Rework Fetching Settings
✓ issue opened on Sep 25 2022 by Munyoki Kilyungi, last updated on Oct 11 2023 by Munyoki Kilyungi
...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. As an example, consider this function which...
- 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...
- Set password when virtuoso containers are rebuilt
issue opened on Jul 07 2023 by Munyoki Kilyungi, last updated on Jul 29 2024 by Munyoki Kilyungi
...when virtuoso containers are rebuilt
## Tags
* assigned: bonfacem
* status: stalled
Whenever the virtuoso container is rebuilt, we manually have to reset the password. We should fix this by modifying...
- 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...
- Replace Neo4J with Virtuoso
issue opened 4 weeks ago by Munyoki Kilyungi
Replace Neo4J with Virtuoso
## Tags
* assigned: bonfacem, soloshelby
* deadline: 2024-10-25 Fri
Currently, the RAG ingests TTL files into Neo4J. Replace this with Virtuoso.
- Gn3 network dependency
issue opened on Mar 18 2022 by Alexander Kabui, last updated on Jul 08 2022 by Alexander_Kabui; 0 of 2 tasks done
...while sending requests from gn3 from gn2
for tools like ctl and wgcna users run into network
errors if the gn3 server is down or other issues.Idea
is to use gn3 as library to avoid the above
## Tags...
- Remove References to Old gn-auth code
issue opened on Feb 21 2024 by Munyoki Kilyungi, last updated on Jul 29 2024 by Munyoki Kilyungi
Remove References to Old gn-auth code
## Tags
* assigned: bonfacem
* keywords: auth
* status: stalled
## Description
We still reference the old Racket gn-auth code. We should deprecate...
- 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 8 weeks ago by Alexander_Kabui, last updated 5 weeks ago 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 the...
- A Listing of Features and/or Bugs without Dedicated Issues
issue opened on Feb 16 2024 by Frederick Muriuki Muriithi; 1 of 1 tasks done
.../or Bugs without Dedicated Issues
## Tags
* type: listing
* status: open
* assigned: fredm
* priority: high
* keywords: listing, bug, feature
## Description
This is a listing of non-critical features...
- 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...
- Provide Link to Register User on Sign-In Page
issue opened on Feb 27 2024 by Frederick Muriuki Muriithi, last updated on Feb 27 2024 by Frederick Muriuki Muriithi
...Link to Register User on Sign-In Page
## Tags
* type: bug
* status: open
* assigned: fredm
* priority: medium
* keywords: register user, gn-auth, genenetwork
## Description
Provide a link allowing...
- Prevent Weak Passwords
issue opened on Feb 27 2024 by Frederick Muriuki Muriithi
Prevent Weak Passwords
## Tags
* status: open
* assigned: fredm
* priority: medium
* keywords: security, password, gn-auth
* type: feature-request, feature request
## Description
=> https://matrix.to/...
- Pre-Cache Datasets
issue opened on Oct 24 2022 by Frederick Muriuki Muriithi
Pre-Cache Datasets
## Tags
* assigned:
* priority: medium
* type: enhancement
* status: open
* keywords: cache, optimisation
## Description
To improve the performance of the system when running...
- List of proposed changes for PCA traits/figures in Correlation Matrix page
issue opened on Jan 09 2023 by Zachary Sloan
...PCA traits/figures in Correlation Matrix page
## Tags
* type: feature, chore
* priority: medium
* assigned: zsloan
* status: in-progress
* keywords: pca, correlations
## Description
Rob proposed the...
- Parsing genotyfiles
issue opened on Jul 11 2023 by Alexander_Kabui
Parsing genotyfiles
## Tags
* assigned: alexm
* type: debug
* priority: high
* status: in progress
## Once you identify the genofile identify
the file in the GENOTYPE_FILES and extract sample_listx...
- 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 5 weeks ago 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...
- Multi-trait heat map failed
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
Multi-trait heat map failed
## Tags
* assigned: zsloan
* type: bug
* priority: medium
* status: stalled
* keywords: heatmap, from github
## Members
* zsloan
* pjotrp
* echesler
## Description...
- 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...
- Move GN Racket Rest API to GNU Guile
issue opened on Jan 08 2024 by Munyoki Kilyungi, last updated on Jul 29 2024 by Munyoki Kilyungi
...Tags
* assigned: bonfacem
* priority: medium
* type: API, metadata
* keywords: API
* status: stalled
## Description
Currently, gene aliases retrieval relies on querying the outdated GN3 Rest Server...
- 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/...
- Missing Python Module(s) for GeneNetwork3
issue opened on Sep 19 2022 by Frederick Muriuki Muriithi
...Tags
* type: bug
* priority: high
* status: open
* keywords: python-modules
## Description
Missing modules when you try launching genenetwork3 locally:
* python-typing-extensions
The module needs...
- 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.
- MGAMMA LMM
issue opened on Aug 19 2024 by Artyom Bologov; 3 of 5 tasks done
...LMM
MGamma does GWAS, which means it has to do Linear Mixed Models—both univariate and multivariate.
# Tags
* assigned: pjotrp, artyom
* type: feature
* priority: high
# Tasks
* [X] Kinship matrix...
- MGAMMA CLI
issue opened on Apr 17 2024 by Pjotr Prins, last updated on May 18 2024 by Artyom Bologov; 4 of 6 tasks done
...Tags
* assigned: pjotrp, artyom
* type: feature
* priority: high
# Tasks
* [ ] Provide sane CLI interface
* [X] Add --map-size 10M switch
* [X] Use lmdb files instead of dir
* [X] Find a way to open/...
- 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
...by clicking the top pink bar ("8x expanded WebQTL map") no points are displayed: https://genenetwork.org/show_trait?trait_id=NM_029911&dataset=UTHSC_BXD_WB_RNASeq1112
# Tags:
* source: robwwilliams...
- 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
...horizontally scrolled
## Tags
* assigned: zsloan
* priority: medium
* status: closed
* keywords: mapping
## Description
The mapping figure can't be horizontally scrolled, which is apparently annoying...
- 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...
- Make Partial Correlations Table Searchable
issue opened on Apr 22 2022 by Frederick Muriuki Muriithi
...Correlations Table Searchable
## Tags
* assigned: fredm
* priority: medium
* type: migration, feature-request
* status: pending
* keywords: partial correlations, datatables
## Description
@robw notes...
- 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...
- Xapian to Text Transformer
issue opened on Sep 09 2024 by Alexander_Kabui
...Text Transformer
## Tags
* assigned: alexm, jnduli
* keywords: llm, genenetwork2, xapian, transform
* type: feature
* status: in-progress
## Description:
Given a Xapian search query, e.g., "CYTOCHROME...
- Gn Markdown Editor implementation
issue opened on Aug 07 2023 by Alexander_Kabui, last updated on Sep 11 2023 by Alexander_Kabui; 4 of 5 tasks done
...to edit and live preview the results
also added to this is the ability to commit the changes directly to github repo:
Example of similar implementation
=> https://markdownlivepreview.com/
## Tags...
- Gn Markdown Editor implementation
issue opened on Nov 03 2023 by Alexander_Kabui; 4 of 5 tasks done
...git
## Tags
* assigned: alexm
* type: feature
* priority: high
## Tasks
* [x] implement initial apis;fetch page,edit and commit
* [x] UI: implement markdown page:editor
* [x] UI: add live preview...
- Handle "too-many-password-attempts"
issue opened on Feb 27 2024 by Frederick Muriuki Muriithi
..."too-many-password-attempts"
## Tags
* type: bug
* status: open
* assigned: fredm
* priority: medium
* keywords: security, password
## Description
=> https://matrix.to/#/!mBYtTotZGiPpHmjJnI:matrix.org/$...
- 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...
- Merge GNQA to Production
issue opened on Feb 12 2024 by Alexander_Kabui, last updated on Sep 09 2024 by Alexander_Kabui; 0 of 2 tasks done
...Tags
* assigned: alexm,
* keywords: production, GNQA, integration
## Description
GNQA is currently in continuous development and needs to
be pushed to production. We need to allow only logged-in...
- GN-LLM Integration
issue opened on Dec 12 2023 by Alexander_Kabui, last updated on Sep 09 2024 by Alexander_Kabui; 3 of 3 tasks done
...com/ShelbySolomonDarnell/GN-LLMs) into Genenetwork as a search.
For reference on the initial implementation, please visit:
=> https://github.com/ShelbySolomonDarnell/GN-LLMs
## Tags
* Assigned: alexm...
- 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
Integrating gn-auth with gn-llm
## Tags
* assigned: alexm, Shelby
* keywords: llm, auth
* type: feature
* priority: high
* status: done, completed, closed
## Description
The main objective...
- 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...
- Get GNQA Ready for evaluation
issue opened on Mar 21 2024 by Solomon Shelby, last updated on Jul 24 2024 by Solomon Shelby; 2 of 2 tasks done
...for evaluation
## Tags
* Assigned: alexm, shelbys
* Keywords: UI, GNQA, evaluation
* Type: immediate
* Status: completed
## Description
We need to publish a paper on GeneNetwork Question & Answering...
- 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
...Technical 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...
- 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...
- GN1 annotation page broken
issue opened on Dec 23 2022 by Pjotr Prins
GN1 annotation page broken
## Tags
* assigned: zsloan, pjotrp
* priority: high
* status: overdue
* type: bug
* keywords: GN1, genenetwork1, annotation, from github
## Description
=> https://github...
- rewrite sampledata fetching with genofiles using scheme
issue opened on Jul 19 2023 by Alexander_Kabui, last updated on Jul 26 2023 by Alexander_Kabui; 2 of 6 tasks done
rewrite sampledata fetching with genofiles using scheme
## Tags
* assigned: alexm,
* type: improvement
* priority: high
* status: in progress
## Notes
having identified ways to link genofiles to...
- 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
...Tags
* assigned: fred, fredm
* status: closed, completed
* priority: medium
* keywords: gn-uploader, tests
* type: improvement
## Description
Some tests depend on a running redis instance to work.
- Provide Page/Link for/to Uploaded Data
issue opened on Jul 10 2024 by Frederick Muriuki Muriithi
Provide Page/Link for/to Uploaded Data
## Tags
* status: open
* assigned: fredm
* priority: medium
* type: feature, feature request, feature-request
* keywords: gn-uploader, uploader, data dashboard...
- ProbeSet not Applicable to All Data
issue opened on Jun 20 2024 by Frederick Muriuki Muriithi
...Applicable to All Data
## Tags
* type: bug
* assigned: fredm
* status: open
* priority: high
* keywords: gn-uploader, uploader, ProbeSet
## Description
From the email from Lucia:
```
The only other...
- Link Authentication/Authorisation
issue opened on Jun 24 2024 by Frederick Muriuki Muriithi
.../Authorisation
## Tags
* status: open
* assigned: fredm
* priority: critical
* type: feature request, feature-request
* keywords: gn-uploader, gn-auth, authorisation, authentication, uploader, upload...
- 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 7 weeks ago by Frederick Muriuki Muriithi, last updated 7 weeks ago 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
...bcrypt as a Dependency
## Tags
* assigned: fred, fredm
* status: closed, completed
* priority: low
* keywords: gn-auth, dependencies
* type: improvement
## Description
BCrypt has been superceded by...
- 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 5 weeks ago 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
Global 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...
- 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 5 weeks ago 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...
- Broken Aliases
issue opened 4 weeks ago by Frederick Muriuki Muriithi, last updated 4 weeks ago by Frederick Muriuki Muriithi
...Aliases
## Tags
* type: bug
* status: open
* priority: high
* assigned: fredm
* interested: pjotrp
* keywords: aliases, aliases server
## Repository
=> https://github.com/genenetwork/gn3
## Bug Report...
- Handle OAuth Errors Better
issue opened 4 weeks ago by Frederick Muriuki Muriithi
Handle OAuth Errors Better
## Tags
* type: bug
* status: open
* priority: high
* assigned: fredm
* interested: zachs, robw
* keywords: gn2, genenetwork2, ui, user interface, oauth, oauth errors...
- GN1 symbols
issue opened on Nov 23 2021 by Pjotr Prins, last updated on Mar 16 2022 by Frederick Muriuki Muriithi; 0 of 2 tasks done
...symbols
# Tags
* assigned: pjotrp, arthurc
* type: bug
* priority: medium
* status: unclear
* keywords: GN1, symbols
# Tasks
* [ ] fix font issue
* [ ] fix linked webqtl images
# Info
The fonts differ...
- GN1 Slowness
issue opened on Sep 15 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...Tags
* assigned: ??
* type: bug
* priority: high
* keywords: GN1
## Description
GN1 needs to clean up the following
```
GNRoot="/gnshare/gn"
find $GNRoot/web/tmp -mmin +100 -exec rm -rfv...
- 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
...for that.
## Tags
* type: 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)...
- 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 3 weeks ago by Frederick Muriuki Muriithi, last updated 3 weeks ago by Frederick Muriuki Muriithi
...Tags
* type: bug
* status: closed
* assigned: fredm
* priority: critical
* interested: pjotrp, zsloan
* keywords: production, container, tux04
## Description
We use emails to verify user accounts...
- 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...
- 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
...covariates in rqtl_wrapper.R is wrong. 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...
- Arthur mentioned last meet that GeneNetwork2 does not redirect http urls to https.
issue opened on Dec 05 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...org/
# nginx snippet
```
if ($scheme = http) {
return 301 https://$server_name$request_uri;
}
```
## Tags
* assigned: pjotr, arthur, jgart
* type: bug
* priority: medium
* status: unclear...
- Handle Temporary Directories in the Container
✓ issue opened 3 weeks ago by Frederick Muriuki Muriithi, last updated 2 weeks ago 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
Global search problems
Global search is 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...
- Genenetwork2 Configurations
issue opened on Jun 15 2023 by Frederick Muriuki Muriithi, last updated on Jun 28 2023 by Frederick Muriuki Muriithi
...Tags
* assigned: fredm
* priority: normal
* status: open
* keywords: configuration, config, gn2, genenetwork, genenetwork2
* type: bug
## Description
The configuration file should only ever contain...
- 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...
- Document API endpoints for GeneNetwork3
issue opened on Mar 04 2022 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...API endpoints for GeneNetwork3
Here's a simple way that SourceHut documents their API endpoints with markdown.
=> https://git.sr.ht/~sircmpwn/sr.ht-docs/tree/master/builds.sr.ht/api.md
## Tags...
- Add LICENSE page to GN2
issue opened on Dec 12 2022 by Pjotr Prins
...LICENSE page to GN2
GN1 has a nice license page
=> http://gn1.genenetwork.org/conditionsofUse.html
we should copy that on GN2.
## Tags
* assigned: zsloan, pjotrp
* priority: medium
* type: enhancement...
- LMM precomputed scores
issue opened on Mar 16 2023 by Pjotr Prins, last updated on May 07 2024 by Pjotr Prins; 0 of 1 tasks done
LMM precomputed scores
Here we will track introducing a new precomputation of scores for GN. Interestingly, this ties in with our xapian search and fast querying of value ranges.
# Tags...
- Spam Entries in Auth (Production)
issue opened on Mar 07 2024 by Munyoki Kilyungi
...Tags
* assigned: fredm
* keywords: auth
## Description
We have spam entries in gn-auth in production in the groups table:
```
b59229de-2fce-4a3d-82f1-d9eeee9b7009|Business For Sale Adelaide...
- Scree Plot appears to be incorrect
issue opened on May 19 2022 by Zachary Sloan, last updated on Jun 15 2022 by BonfaceKilz
...GN2's Scree Plot).
See
=> https://gist.github.com/sens/195214c1833d435b3406fa55abf2b6f4 Jupyter notebook
for a demo on what it should look like using the GN API.
## Tags
* assigned: zsloan, alexm...
- Fix Missing Genotype Files for GEMMA
issue opened on Sep 13 2022 by Frederick Muriuki Muriithi, last updated on Sep 20 2022 by Frederick Muriuki Muriithi; 1 of 3 tasks done
...Tags
* assigned:
* priority: medium
* type: bug
* status: pending
* keywords: gemma, technical debt
## Description
Run GEMMA (under "Mapping Tools") for
=> https://cd.genenetwork.org/show_trait...
- Correlations are not including f1 parents
issue opened on Nov 07 2022 by AlexanderKabui, last updated on Nov 22 2022 by Frederick Muriuki Muriithi
...f1 parents
## Tags
* assigned:alexm,zsloan
* type:bug
* priority: high
* status:ongoing
* keywords: correlation,f1
## Description
Correlations should be including parents/F1s among the samples...
- Long samplenames overflow in Haplotype Analyst
issue opened on Nov 11 2022 by Zachary Sloan
Long samplenames overflow in Haplotype Analyst
## Tags
* priority: medium
* type: UI
* assigned: zsloan
* status: ongoing
* keywords: global search, phenotypes
## Description
For any BXD mapping...
- 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`...
- issues/fix-genotype-filename-HSNIH-Palmer.gmi
issue opened on Jun 27 2023 by GregFa
...filename HSNIH-Palmer
## Tags
* assigned: pjotrp
* type: bug fix
* priority: high
## Description
When using the Rest API to get the groups for "rat", it mentions the group HSNIH-Palmer.
But the REST...
- 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
Fix Failing 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...
- 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...
- Fetch trait names for phenotypes
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
Fetch trait names for phenotypes
## Tags
* assigned:
* status: pending
* priority: unclear
* type: feature-request, enhancement
* keywords: phenotype, from github
## Members
* robw
* rupertoverall...
- Add Cis-Trans plot
issue opened on Apr 07 2023 by Pjotr Prins
Add Cis-Trans plot
After we complete precompute we should add Cis-Trans plots for eQTL datasets.
See also
=> ../../topics/systems/mariadb/precompute-mapping-input-data.gmi
# Tags
* assigned: zsloan...
- 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 Last Edited
issue opened on Jul 24 2023 by Frederick Muriuki Muriithi
Show Last Edited
## Tags
* type: feature request
* priority: medium
* assigned: fredm
* keywords: editing
* status: open
## Description
Following the GNSoC Plenary meeting of Thursday, 20 July 2023...
- 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
...Diffs from Database
## Tags
* type: feature request
* status: closed
* assigned: fredm
* keywords: editing, metadata audit
* priority: high
## Description
The rejected diffs will be maintained, but...
- Edit Dataset Metadata
issue opened on Jan 10 2024 by Munyoki Kilyungi, last updated on Jul 29 2024 by Munyoki Kilyungi; 4 of 6 tasks done
...Tags
* assigned: bonfacem
* priority: high
* type: editing
* status: stalled
* keywords: metadata editing
## Description
Currently, we can only showcase dataset metadata. This task involves adding...
- 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
=> https...
- Database Migrations
issue opened on Oct 19 2022 by Frederick Muriuki Muriithi
...Tags
* assigned:
* type: feature
* priority: high
* keywords: database migrations
* status: pending
## Description
There might need to be some form of database migration to help keep the
* schema...
- Medaka Inbred Kiyosu-Karlsruhe (MIKK) Panel
issue opened on Sep 22 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...route is nasty and probably error prone. bcftools same, same. Arthur, if you copy the VCF files to tux01 and tell me when and where, I can have a go at setting up a tool chain we/you can use.
## Tags...
- Add the option to save traits uploaded with the Submit Trait option
issue opened on Jul 19 2022 by Zachary Sloan
...save traits uploaded with the Submit Trait option
# Tags
* assigned: zsloan
* priority: medium
* type: feature-request
* status: open, in progress
* keywords: data, meta-data
# Description
Current the...
- issues/custom_data_for_scatterplot.gmi
issue opened on Mar 09 2023 by Zachary Sloan
...Tags
* assigned: zsloan
* type: feature
* priority: high
* status: in-progress
* keywords: scatterplot, correlation
## Description
Currently the correlation scatterplot just takes the two trait/...
- 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...
- Create Custom RIF XAPIAN Index
issue opened 5 weeks ago by Munyoki Kilyungi, last updated 4 weeks ago by Munyoki Kilyungi
Create Custom RIF XAPIAN Index
## Tags
* assigned: bonfacem
* priority: medium
* status: in-progress
* deadline: 2024-10-23 Wed
## Description
Given the GN Wiki search page:
=> https://cd.genenetwork...
- Correlations: Fewer Results than Expected
issue opened on Nov 22 2022 by Frederick Muriuki Muriithi
...Tags
* type: bug
* priority: critical
* status: open
* assigned: zsloan, zachs
* keywords: correlations
## Description
Doing a search for top 500 covariates and get this instead—the top 435.
- 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
...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...
- Correlations timing out for "UMUTAffy Hippocampus Exon (Feb09) RMA" correlations (and probably some others)
issue opened on Oct 17 2022 by Zachary Sloan, last updated on Nov 22 2022 by Frederick Muriuki Muriithi
Correlations timing out for "UMUTAffy Hippocampus Exon (Feb09) RMA" correlations (and probably some others)
## Tags
* assigned: fredm, zsloan, alexm
* type: bug
* priority: high
* status: ongoing...
- 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...
- 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
...we don't have a guix-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...
- Broken Indexing
✓ issue opened on May 03 2023 by Munyoki Kilyungi, last updated on Oct 11 2023 by Munyoki Kilyungi
...Indexing
## Tags
* assigned: bonfacem, alex, fredm
* type: CD
* priority: high
* keywords: xapian, search
## Description
Broken Search from:
=> https://ci.genenetwork.org/jobs/genenetwork3-build-...
- Guix: Using guix shell with root file
issue opened on Jan 27 2022 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...Tags
* assigned: jgart
* type: unclear
* status: unclear
* priority: low
* keywords: guix, guix shell, root file
## Description
```
guix shell --root
```
Let's benchmark and test these options to...
- Show Template for when Git URL is not Found
issue opened on Sep 28 2021 by jgart, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...not Found
## Tags
* type: bug
* assigned: jgart
* priority: medium
* keywords: binderlite, template
## Description
Let's add a template for when a url fails because the user entered the wrong
url or...
- 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...
- Add Regular Expression to Prevent Invalid Input
issue opened on Oct 01 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
Add Regular Expression to Prevent Invalid Input
## Tags
* type: bug
* assigned: jgart
* status: unclear
* keywords: binderlite, notebooks
* priority: high
## Description
Add regex to the html form to...
- Add configuration to set server name
issue opened on Nov 10 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...to set server name
## Tags
* assigned: jgart
* type: feature-request
* status: unclear
* priority: high
* keywords: binderlite, notebooks, configuration
## Description
Let's use environment variables...
- 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...
- UI issues/improvements
issue opened on Jul 26 2023 by Zachary Sloan
.../improvements
## Tags
* assigned: fredm, zsloan
* priority: medium
* status: open
* keywords: authentication, authorisation, oauth2, resources, ui
* type: feature-request
## Description
Linking data...
- Paginate Resources Page
issue opened on Jul 27 2023 by Frederick Muriuki Muriithi
Paginate Resources Page
## Tags
* priority: medium
* status: open
* assigned: fredm, zachs
* keywords: resources, data linking, auth
* type: feature request
## Description
Some of the Resources have...
- 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 of...
- 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...
- Various UI issues raised by Rob (8/19/2024)
issue opened on Aug 19 2024 by Zachary Sloan, last updated on Sep 18 2024 by Zachary Sloan; 12 of 13 tasks done
...raised by Rob (8/19/2024)
# Tags
* assigned: zsloan
* keywords: user-interface
* priority: medium
* open
## Tasks
* [X] Fix collection encoding issue
* [X] Don't import empty collections (like the...
- Add Case Attributes to RDF
issue opened on Sep 03 2024 by Munyoki Kilyungi
Add Case Attributes to RDF
## Tags
* assigned: bonfacem
* priority: high
* status: open
## Description
Add case attributes and their metadata into RDF.
- 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...
- issues/add-pluto-notebooks.gmi
issue opened on Jun 27 2023 by GregFa
...Pluto Notebooks
## Tags
* assigned: pjotrp
* type: feature
* priority: high
## Description
Host Pluto Notebooks in GeneNetwork. As a proof of concept, we host:
=> https://notebooks.one/ notebooks.one...
- Add option to directly link to mapping results
issue opened on Jan 19 2023 by Zachary Sloan
Add option to directly link to mapping results
## Tags
* assigned: zsloan
* keywords: mapping
* priority: medium
## Description
Currently it's not possible to link to mapping results, so I'm adding a...
- 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 genotype file paths to RDF
issue opened on Jun 19 2023 by Munyoki Kilyungi, last updated on Jul 29 2024 by Munyoki Kilyungi
...file paths to RDF
## Tags
* assigned: bonfacem
* type: bug
* status: stalled
In Penguin2, genotype files are located in: /export/data/genenetwork/genotype_files/genotype. Each genotype files has an...
- 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...
- GeneNetwork CLI
document created on Sep 20 2021 by jgart, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...CLI
## Tags
* assigned: ??
* type: feature-request
* priority: low
* keywords: command-line interface, CLI
## Description
It would be great for GeneNetwork to have a nice command line client for doing...
- Add button to delete an entire dataset in gn2
document created on Sep 08 2021 by BonfaceKilz, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...delete an entire dataset in gn2
## Tags
* assigned: ??
* type: bug
* keywords: ui, dangerous feature, status: unclear
## Description
An interface for deleting data existed in gn1 but is not present in...
- Using pudb
document created on Dec 21 2021 by jgart, last updated on Dec 03 2023 by Pjotr Prins
...interface
> as Python’s built-in pdb module. Just replace pdb with pudb. (One
> exception: run is called runstatement.)
=> https://docs.python.org/3/library/pdb.html?highlight=pdb#module-pdb
## Tags...
- Running pudb From an External Environment
document created on Dec 03 2023 by Pjotr Prins
...--load=guix.scm
4) Inside the container, run the debugger with something like:
* env PYTHONPATH="${PYTHONPATH}:${HOME}/pudb_env/lib/python3.8/site-packages" ... python3 -m pudb script.py
## Tags...
- Using pudb with pytest
document created on Dec 21 2021 by jgart, last updated on Dec 03 2023 by Pjotr Prins
Using pudb with pytest
```
pytest --pdbcls pudb.debugger:Debugger --pdb --capture=no
```
=> https://documen.tician.de/pudb/starting.html?highlight=pytest#usage-with-pytest
## Tags...
- Profiling Python code
document created on Dec 03 2023 by Pjotr Prins
...e.g.
* env [various-env-vars] python3 -m cProfile the-script.py 2>error.log 1>performance.log
which should help will separating errors from the performance data, for easier analysis
## Tags...
- Jupyter notebooks
document created on Sep 01 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
Jupyter notebooks
## Tags
* type: documentation
* keywords: documentation, jupyter, notebooks
* status: unclear
## Run with GNU Guix
Jupyter notebooks can be installed in a profile
```
~/opt/guix-...
- LMM Notes
document created on Aug 13 2021 by Pjotr Prins, last updated on Jan 08 2024 by Solomon Shelby
...Tags
* assigned: ??
* keywords: LMM
* status: unclear
* priority: low
## Time series data
FlxQTL by Saunak Sen can handle time series data in an (genetic) LMM
context. They have to be measured...
- Defining a scheme sexp comment with a reader macro
document created on Feb 02 2022 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...-character #\# #\; (lambda (s c n) c n (read s t nil t) (values)))
CL-USER(2): (+ 3 (+ 2 3) 1)
9
CL-USER(3): (+ 3 #;(+ 2 3) 1)
4
```
Special thanks to Ed Langley on #common-lisp:matrix.org.
## Tags...
- Debugging Lisp
document created on Dec 22 2021 by Pjotr Prins, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...provided by Common Lisp
Some links
=> https://malisper.me/debugging-lisp-part-1-recompilation/ Debug Common Lisp (CL)
=> https://www.youtube.com/watch?v=bl8jQ2wRh6k Video on CL web development
## Tags...
- Common LISP: sly
document created on Jan 29 2022 by Pjotr Prins, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
Common LISP: sly
This document will collect some resources on sly
## Tags
* type: documentation
* keywords: common-lisp, sly, emacs
## Resources
=> https://joaotavora.github.io/sly/ SLY User Manual
- Common LISP: Notes
document created on Feb 09 2022 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...com/nonguix/nonguix/-/blob/master/nongnu/packages/emacs.scm#L26 clhs
## Getting Help / Asking Questions
### Libera Chat
```
#clschool
#commonlisp
```
### Matrix
```
#common-lisp:matrix.org
```
## Tags...
- Non-Clustered and Flippable Heatmaps
document created on Oct 01 2021 by Frederick Muriuki Muriithi, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...be possible to flip the heatmap orientation from horizontal to vertical and vice-versa
* It should be possible to generate a heatmap with no dendrograms
## Members
* fredm
* pjotr
* zsloan
## Tags...
- Indicating Heterozygosity
document created on Jun 20 2024 by Frederick Muriuki Muriithi, last updated on Jun 20 2024 by Frederick Muriuki Muriithi
Indicating Heterozygosity
## Tags
* status: ongoing
* assigned: fredm, zachs, acenteno
* type: documentation
* priority: medium
* keywords: doc, documentation, heterozygous, hererozygosity...
- Genome Details
document created on Jul 01 2024 by Frederick Muriuki Muriithi
...know where this fits
## Tags
* type: documentation, doc, docs
* assigned: fredm
* priority: docs
* status: open
* keywords: gn-uploader, uploader, genome
## Location
### centiMorgan (cM)
We no longer...
- Ideas and References
document created on Nov 22 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
Ideas and References
=> gemini://drewdevault.com/2021/11/15/Reframing-gemini.gmi Reframing the philosophy of Gemini
## Tags
* type: documentation
* keywords: documentation, gemini
- gemtext cheatsheet
document created on Dec 21 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
gemtext cheatsheet
=> gemini://gemini.circumlunar.space/docs/cheatsheet.gmi
=> https://gemini.circumlunar.space/docs/cheatsheet.gmi proxy
## Tags
* type: documentation
* keywords: gemini
- GeneNetwork documentation
document created on Nov 16 2021 by Pjotr Prins, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
.../gn-docs/blob/master/general/help/facilities.md
the markdown is rendered on github, which makes it easy to edit for most users, so it should be the default.
## Tags
* assigned: pjotrp
* status: unclear...
- Deploy GeneNetwork
document created on Jan 18 2023 by Arun Isaac, last updated on Aug 27 2024 by Frederick Muriuki Muriithi
...Tags
* type: doc, docs, documentation
* keywords: deploy, deployment, deploying, guix, guix container, guix system container
* status: in progress
# Description
This page attempts to document the...
- Data Uploads: Reversing a Diff
document created on Feb 03 2022 by BonfaceKilz, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...Reversing a Diff
## Tags
* assigned: bonfacem, zachs
* status: unclear
* type: enhancement
* priority: high
* keywords: data uploads
### Introduction
Given a diff file, we should be able to reverse...
- Put user info in the a/c name in the menu
document created on Mar 14 2022 by Frederick Muriuki Muriithi, last updated on Dec 04 2023 by Frederick Muriuki Muriithi
Put user info in the a/c name in the menu
When the user signs in to GN2, there is no info on the account name in the menu.
## Tags
* assigned: bonfacem
* priority: medium
* status: closed, completed...
- Replace Hard coded authentication with gn-proxy
document created on Mar 14 2022 by Frederick Muriuki Muriithi, last updated on Dec 04 2023 by Frederick Muriuki Muriithi
...Hard coded authentication with gn-proxy
## Tags
* assigned: bonfacem
* priority: medium
* type: enhancement
* status: closed, completed
* keywords: authentication, gn-proxy
## Description
Originally...
- COVID-19
document created on Nov 14 2021 by Pjotr Prins, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
COVID-19
We are setting up a Cloud HPC for COVID-19 using Arvados as the underlying infrastructure.
## Tasks
=> https://github.com/yatisht/usher Fast phylogeny
## Tags
* assigned: pjotrp...
- Handle Configuration Files
issue opened on Dec 03 2021 by BonfaceKilz, last updated on Oct 12 2022 by Munyoki Kilyungi
...imports whenever we use blueprints. Unfortunately, a huge chunk of the code base uses "utility/tools.py" to get configuration settings; and removing this would make gn2 as is disfunctional.
# Tags...
- 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...
- Adding Terminal Output
document created on Aug 07 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...As GN3 (REST) API handles calling external tools it kinda make sense to handle the terminal output page through GN3 and communicate through websockets. But first I'll do a Sinatra test run.
## Tags...
- Simplify `dataset.py` in GeneNetwork2
issue opened on Sep 13 2022 by Frederick Muriuki Muriithi
Simplify `dataset.py` in GeneNetwork2
## Tags
* assigned:
* priority: medium
* type: bug
* status: pending
* keywords: technical debt
## Description
The entire file
=>https://github.com/genenetwork/...
- Broken continuous deployment
✓ issue opened on Jul 06 2022 by Arun Isaac, last updated on Jul 11 2022 by Frederick Muriuki Muriithi
...deployment
* assigned: 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.
- Add search, select and export to datatables table
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
Add search, select and export to datatables table
## Tags
* assigned: bonfacem, zsloan
* priority: low
* type: feature-request
* status: unclear
* keywords: datatables, UI, low...
- 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...
- 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
...code
# Tags
* assigned: zsloan
* priority: medium
* type: refactor
* status: open, in progress
* keywords: tables, javascript
# Description
Currently most DataTables are drawn independently, so each...
- 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...
- Rating System: No Indication for Login Requirement
issue opened on Jul 24 2024 by Solomon Shelby
Rating System: No Indication for Login Requirement
## Tags
* type: bug
* status: open
* priority: medium
* assigned: alex, shelby
* keywords: gnqna, user experience, UX
## Description
=> https://cd...
- csv export meta data are not commented out
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
...commented out
## Tags
* assigned: zsloan
* priority: high
* type: bug
* status: unclear
* keywords: CSV, from github, meta data
## Description
=> https://github.com/genenetwork/genenetwork2/issues/594...
- 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
Data Integrity for Table Identifiers
## Tags
* type: bug
* assigned: fredm
* priority: critical
* status: closed, completed
* keywords: data integrity, mariadb, gn-uploader
## Description
The use of...
- Generate Heatmaps Failing
issue opened 5 weeks ago by Frederick Muriuki Muriithi
Generate Heatmaps Failing
## Tags
* type: bug
* status: open
* priority: medium
* assigned: fredm, zachs, zsloan
* keywords: genenetwork3, gn3, GN3, heatmaps
## Reproduce
* Go to https://genenetwork...
- Bug with linking data
issue opened on Jul 26 2023 by Zachary Sloan, last updated on Oct 19 2023 by Frederick Muriuki Muriithi
...with linking data
## Tags
* assigned: fredm, zsloan
* priority: high
* status: open
* keywords: authentication, authorisation, oauth2, xapian
* type: bug
## Description
While trying to link some newly-...
- Markdown docs
issue opened on Sep 10 2022 by Pjotr Prins
...to edit this garbage
> file that is about 10 years old. Love to update it.
> Is there a way to force line wraps at some practical length?
## Tags
* assigned: pjotrp, zsloan, robw, arthurc...
- MGAMMA Convert
issue opened on Apr 17 2024 by Pjotr Prins, last updated on May 18 2024 by Artyom Bologov; 7 of 11 tasks done
Tags
* assigned: pjotrp, artyom
* type: feature
* priority: high
# Tasks
* [X] Store genotypes as floats instead of doubles in lmdb
* [X] Required for the above: rework the type system in guile-gsl...
- 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...
- Paths in Flask Application
document created on Sep 11 2024 by Frederick Muriuki Muriithi
Paths in Flask Application
## Tags
* type: doc, docs, documentation
* assigned: fredm
* keywords: application paths, flask, absolute path, relative path
## Content
Always build and use absolute paths...
- R/qtl2
document created 6 weeks ago by Pjotr Prins
...Tags
* assigned: pjotrp, alexm
* priority: high
* type: enhancement
* status: open
* keywords: database, gemma, reaper, rqtl2
# Description
R/qtl2 handles multi-parent populations, such as DO, HS...
- Temporary Traits Access Concerns
issue opened on Aug 03 2023 by Frederick Muriuki Muriithi
...Access Concerns
## Tags
* type: feature request
* priority: medium
* status: open
* assigned: fredm, zachs
* keywords: temp traits, temporary traits, access control
## Description
The temporary traits...
- 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...
- Shapiro Wilk Test
document created on Nov 24 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...orderNorm function to
perform Ordered Quantile normalization43 on all phenotypes. QTL
--
A quantitative trait variant in Gabra2 underlies increased methamphetamine stimulant sensitivity
```
## Tags...
- Allow analyses to be done between traits from "individuals" groups and their corresponding "main" group
issue opened on Jul 21 2022 by Zachary Sloan
..."main" group
# Tags
* assigned: zsloan
* priority: medium
* type: feature-request
* status: open, in progress
* keywords: data, meta-data
# Description
Currently you can't do an analysis beween traits...
- 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...
- New Privileges: Samples Ordering
issue opened on Sep 19 2024 by Frederick Muriuki Muriithi
New Privileges: Samples Ordering
## Tags
* status: open
* assigned: fredm
* interested: @zachs, @jnduli, @flisso
* priority: medium
* type: feature-request, feature request
* keywords: gn-auth, auth...
- 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
...Data Public View by Default
## Tags
* assigned: fredm, zsloan, zachs
* priority: medium
* status: closed, completed
* keywords: authentication, authorisation, oauth2, data migration
* type: migration...
- Decouple Tasks in Correlations Results Display
issue opened on Oct 24 2022 by Frederick Muriuki Muriithi, last updated on Nov 25 2022 by Frederick Muriuki Muriithi
Decouple Tasks in Correlations Results Display
## Tags
* type: bug
* priority: medium
* assigned: alexm
* keywords: correlations
* status: ongoing
## Description
=> https://github.com/genenetwork/...
- 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...
- Explanation of how Sample Lists are handled in GN2 (and may be handled moving forward)
issue opened on Sep 19 2024 by Zachary Sloan
Explanation of how Sample Lists are handled in GN2 (and may be handled moving forward)
## Tags
* status: open
* assigned: fredm, zsloan
* priority: medium
* type: documentation
* keywords: strains...
- 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-...
- Bug when a user quickly clicks "Compute" for mapping on the trait page
issue opened on Feb 06 2023 by Zachary Sloan, last updated on Feb 13 2023 by Zachary Sloan
...clicks "Compute" for mapping on the trait page
## Tags
* assigned: zsloan
* type: bug
* priority: high
* status: completed
* keywords: mapping, trait-page
## Description
The user sometimes gets a 405...
- 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 4 weeks ago by Frederick Muriuki Muriithi, last updated 2 weeks ago 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.
- Speed Up QC on R/qtl2 Bundles
issue opened on Jun 24 2024 by Frederick Muriuki Muriithi
.../qtl2 Bundles
## Tags
## Description
The default format for the CSV files in a R/qtl2 bundle is:
```
matrix of individuals × (markers/phenotypes/covariates/phenotype covariates/etc.)
```
(A) (f/F)ile...
- Database: `ProbeSetSE` Schema Bug
issue opened on Mar 22 2024 by Frederick Muriuki Muriithi, last updated on Mar 22 2024 by Frederick Muriuki Muriithi
...Schema Bug
## Tags
* type: bug
* priority: critical
* status: open
* keywords: database, mariadb, schema
* assigned:
## Description
The schemas are defined as follows:
```
MariaDB [db_webqtl]> DESC...
- When binderlite finds an unkown package in a guix manifest
issue opened on Oct 01 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...be managed by the sysadmin only for security reasons?
It's probably a security risk since a guix channel can pull in arbitrary
packaged code that might not be audited or fully trusted.
## Tags
* type...
- 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
...Tags
* type: bug
* priority: critical
* assigned: fredm, acenteno
* keywords: QC, quality control, samples, strains, cases, gn-uploader
* status: closed, completed
## Description
I discovered a...
- 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...
- Markdown Editing Service: Not Deployed
issue opened 4 weeks ago by Frederick Muriuki Muriithi, last updated 3 weeks ago by Frederick Muriuki Muriithi
Markdown Editing Service: Not Deployed
## Tags
* type: bug
* status: open
* assigned: fredm
* priority: critical
* keywords: production, container, tux04
* interested: alexk, aruni, bonfacem, fredm...
- 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...
- Editing Phenotypes
document created on Jul 07 2023 by Frederick Muriuki Muriithi, last updated on Jul 12 2023 by Frederick Muriuki Muriithi
...Phenotypes
## Tags
* keyword: editing phenotypes
## Introduction
There is old code for editing phenotypes in place, but it was not in use. The main aim at this point is to fix any bugs and adapt it to...
- Annotation
issue opened on Sep 14 2022 by Pjotr Prins, last updated on Mar 14 2023 by Arun Isaac; 0 of 5 tasks done
...genomes. Here we track a next generation annotation system which will support versions of annotation with a matching reference genome. In the future we'll build this out with pangenome support.
# Tags...
- GN-AUTH FAQ
document created on Aug 19 2024 by John Nduli, last updated on Aug 19 2024 by John Nduli
...-AUTH FAQ
## Tags
* type: docs, documentation
* status: ongoing, open
* keywords: authentication, authorisation, docs, documentation
* author: @jnduli
## Quick configuration for local development
Save...
- 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
Add track for showing which regions in mouse/rat correspond to human regions to the mapping figure
# Tags
* assigned: zsloan
* priority: medium
* type: feature-request
* status: open, in progress...
- NGINX Configuration Notes
document created on Jun 01 2023 by Zachary Sloan
...Notes
## Tags
* type: info, documentation
* keywords: nginx, configurations
## Use of proxy_redirect (in this case for authentication, which runs on GN3 through a GN2 URI)
In this case GN3 (which runs...
- GN3 Error Handling
document created on May 28 2024 by Alexander_Kabui
...Handling
## Tags
* type: docs, documentation
* status: open, ongoing
* keywords: gn3, error_handling, exceptions, docs, documentation
## Introduction
This documentation explains how GN3 handles errors...
- Mapping Error
issue opened on Jul 03 2024 by Frederick Muriuki Muriithi, last updated on Jul 03 2024 by Zachary Sloan
Mapping Error
## Tags
* type: bug
* status: open
* priority: medium
* assigned: zachs, fredm, flisso
* keywords: gn2, genenetwork2, genenetwork 2, mapping
## Reproduction
* Go to https://staging...
- 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
...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 for a...
- 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
...in External Process
## Tags
* assigned: fredm
* type: feature
* priority: high
* keywords: correlations, asynchronous jobs, external process
* status: completed, closed
## Description
Currently...
- Error when attempt to zoom to a chromosome after mapping a PCA trait
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
Error when attempt to zoom to a chromosome after mapping a PCA trait
## Tags
* assigned: zsloan
* type: bug
* priority: high
* status: unclear
* keywords: PCA, from github, high...
- 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...
- 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
Adding principal component to collection returns an error
## Tags
* assigned: alex
* status: unclear
* priority: high
* type: bug
* keywords: collections, from github
## Members
* rupertoverall...
- Lisp For Schemers
document created on Dec 29 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...Schemers
## Tags
* type: documentation
* keywords: LISP, Scheme, iota, loop, iterate
## iota
### In Scheme
```
scheme@(guile-user)> (iota 12)
$1 = (0 1 2 3 4 5 6 7 8 9 10 11)
```
### In Common Lisp...
- AI UI Enhancements
issue opened on Mar 01 2024 by Pjotr Prins; 0 of 3 tasks done
AI UI Enhancements
## Tags
* Assigned: alexm, shelbys
* Keywords: UI, GNQA
* Type: critical
* Status: In Progress
## Description
This issue addresses user feedback received during the testing phase...
- BNW interface for GN2
document created on Oct 18 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...at this point.
## Tags
* type: bug
* priority: high
* assigned: pjotrp
* status: in progress
* keywords: BNW
## Todo
The current output reads:
```
<title>Opening BNW</title>
<form method="post" action...
- Genotypes, Assemblies, Markers and GeneNetwork
document created 8 weeks ago by Frederick Muriuki Muriithi
...Tags
* type: documentation, docs, doc
* keywords: genotype, assembly, markers, data, database, genenetwork, uploader
## Markers
```
The marker is the SNP…
— Rob (Paraphrased)
```
SNPs (Single...
- Types of Data in GeneNetwork
document created on Jul 02 2024 by Frederick Muriuki Muriithi, last updated on Jul 10 2024 by Frederick Muriuki Muriithi
Types of Data in GeneNetwork
## Tags
* assigned:
* priority:
* status: open
* type: documentation
* keywords: gn-uploader, uploader, genenetwork, documentation, doc, docs, data, data type, types of...
- 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...
- Adding Platforms
document created on Apr 04 2024 by Frederick Muriuki Muriithi, last updated on Apr 24 2024 by Frederick Muriuki Muriithi
Adding Platforms
## Tags
* status: open
* priority: medium
* type: documentation
* assigned: fredm, flisso, acenteno
* keywords: doc, documentation, platform, gn-uploader, uploader, adding data...
- 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...
- Weechat
document created on Nov 04 2021 by Pjotr Prins, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...Tags
* type: documentation
* keywords: cli, weechat, documentation
Weechat is a very versatile terminal chat that can handle IRC, Matrix and Slack.
## Weechat install + slack
Arun has packaged...
- GN2 Integration with LLM search using cached results
issue opened on Aug 26 2024 by John Nduli, last updated on Sep 09 2024 by Alexander_Kabui; 2 of 6 tasks done
...using cached results
## Tags
* assigned: jnduli, alexm, bmunyoki
* keywords: llm, genenetwork2
* type: enhancement
* status: open
## Description
We'd like to include LLM searches integrated into our...
- 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...
- Logging Handler Improvements for GN3
issue opened on Jun 11 2024 by John Nduli
Logging Handler Improvements for GN3
## Tags
* assigned: jnduli
* priority: low
* type: enhancement
## Goal
Our logs help us fix problems without the need for LOG_LEVEL=DEBUG
## Background
When...
- CLI Script to Generate Text Files
issue opened on Dec 19 2022 by Frederick Muriuki Muriithi, last updated on Jan 23 2023 by Alexander_Kabui
...Tags
* assigned: alexm
* type: feature, improvement
* priority: high
* keywords: correlations, materialised views, optimisation, script
* status: inprogress
## Description
This issue supercedes the...
- MariaDB
document created on Oct 26 2021 by Pjotr Prins, last updated on Feb 20 2024 by Pjotr Prins
...below and
=> topics/deploy/installation
# Tags
* type: info, documentation
* keywords: mariadb, systems
# Check the transaction logs
Start the client and:
```
MariaDB [db_webqtl]> show binary logs...
- 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...
- Cool Interfaces We Should Emulate
issue opened on Apr 13 2022 by BonfaceKilz, last updated on Apr 14 2022 by BonfaceKilz
Cool Interfaces We Should Emulate
## Tags
* assigned: bonfacem, zachs, robw
* type: ui
* status: stalled
* priority: low
* keywords: ui
## Description
[From RW]
We have talked about upgrading our...
- Improving Metadata Audit
document created on Jul 25 2023 by Frederick Muriuki Muriithi, last updated on Aug 11 2023 by Frederick Muriuki Muriithi
...Tags
* assigned: fredm
* priority: high
* keywords: editing, metadata, metadata audit
* type: documentation
* status: open
## Introduction
There is an existing metadata audit system that tracks the...
- Check for Mandatory Settings
issue opened 5 weeks ago by Frederick Muriuki Muriithi; 0 of 3 tasks done
...for Mandatory Settings
## Tags
* status: open
* priority: high
* type: bug, improvement
* interested: fredm, bonz
* assigned: jnduli, rookie101
* keywords: GN3, gn3, genenetwork3, settings, config...
- 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...
- Decommission machines
issue opened on Oct 06 2021 by Pjotr Prins, last updated on Sep 22 2023 by Pjotr Prins; 11 of 22 tasks done
...Tags
* assigned: pjotrp, arthurc, dana
* priority: high
* keywords: systems
* type: system administration
* status: unclear
# Tasks
## Running (OK)
* rabbit is used for backups (R815 - 2010 model...
- 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
.../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.genenetwork...
- Brittle Fix for Editing Metadata
issue opened on Aug 02 2023 by Frederick Muriuki Muriithi
Brittle Fix for Editing Metadata
## Tags
* type: bug
* priority: high
* assigned: fredm, zachs, bonz
* keywords: metadata, editing
* status: open
## Description
=> https://github.com/genenetwork/...
- Dump GeneWiki Metadata
✓ issue opened on Mar 16 2023 by Munyoki Kilyungi, last updated on Apr 04 2023 by Munyoki Kilyungi
...GeneWiki Metadata
## 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...
- Fallbacks
document created on Feb 18 2024 by Pjotr Prins, last updated on Apr 09 2024 by Pjotr Prins
...directories.
# Tags
* assigned: pjotrp
* priority: medium
* type: system administration
* keywords: system administration, GN, tux01, tux02, tux04, balg01
# Tasks
## Prepare backups to copy to the new...
- 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
...guix binary, acting like a time machine. It is
used to fire up a guix shell/environment:
* bnw
* cronjob-gitea
* cronjob-pubmed (genecup)
* genecup
* gitea
* ipfs
* power
* rn6app
* singlecell
## Tags...
- 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
...GeneList to Metadata
## Tags
* assigned: bonfacem
* priority: high
* type: RDF
* keywords: virtuoso
## Description:
=> https://www.gene-list.com/about About GeneList
The GeneList table in GN fetches...
- 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...
- Implementation of QTL Analysis Using r-qtl2 in GeneNetwork
document created 9 days ago by Alexander_Kabui, last updated 9 days ago by Alexander_Kabui
...Tags
* Assigned: alexm
* Keywords: RQTL, GeneNetwork2, implementation
* Type: Feature
* Status: In Progress
## Description
This document outlines the implementation of a QTL analysis tool in...
- Tasks
issue opened on Jun 27 2023 by GregFa, last updated on Apr 26 2024 by Pjotr Prins; 0 of 2 tasks done
...integration
## Tags
* assigned: pjotrp, zachs
* type: feature
* priority: high
## Description
Integrate BulkLMM in GeneNetwork. The first step is to test the command line interface to BulkLMM in...
- 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.
- Tux02 Production
issue opened on Oct 07 2021 by Pjotr Prins, last updated on Dec 14 2022 by Pjotr Prins; 17 of 22 tasks done
...staging machine. This machine is aimed to be rock solid. The idea is to have 4-6 times a year upgrades. Also we should be able to roll back on an upgrade and be able to create time machines.
## Tags...
- Branding and front-end-services
issue opened on Jun 14 2023 by Pjotr Prins; 0 of 1 tasks done
...up parallel page server
* + [ ] Handle headers and footers
* + [ ] Create portal page
* + [ ] Show specific datasets
* + [ ] Show specific publications
* + [ ] Show specific twitter feed
# Tags...
- gn-guile Configurations
issue opened 2 days ago by Frederick Muriuki Muriithi; 1 of 1 tasks done
...-guile Configurations
## Tags
* type: bug
* assigned:
* priority: high
* status: open
* keywords: gn-guile, markdown editing
* interested: alexk, bonfacem, fredm, pjotrp
## Description
=> https://git...
- BigBlueButton
document created on Mar 05 2022 by jgart, last updated on Feb 28 2023 by Pjotr Prins
...Tags
* type: documentation
* keywords: BigBlueButton
## BASH script to install BigBlueButton in 30 minutes.
https://github.com/bigbluebutton/bbb-install
```
wget -qO- https://ubuntu.bigbluebutton...
- Databases Getting Out of Wack
issue opened on Mar 03 2022 by jgart, last updated on Mar 16 2023 by Pjotr Prins
...reaper module that runs as a script:
=> https://github.com/genenetwork/genenetwork2/blob/testing/scripts/maintenance/QTL_Reaper_v6.py
We'll create a new issue:
=> lmm-precomputed-scores.gmi
## Tags...
- 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
...GTEXv8_Wbl_tpm_0220
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...
- Top 10 Things to Test
document created on Mar 28 2022 by BonfaceKilz
...10 Things to Test
## Tags
* assigned: bonfacem
* type: tests
* keywords: documentation, testing, checklist
## Introduction
Important things:
- Correctness
- Speed (fast enough)
- Reliability
Let's do...
- Rebooting the GN production machine(s)
issue opened on Jan 01 2022 by Pjotr Prins, last updated on Oct 06 2022 by Pjotr Prins; 4 of 4 tasks done
...-module-crashes-on-14G-servers/td-p/6031769
The Linux kernel shows some fixes that are not on Tux01 yet
=> https://lkml.org/lkml/2021/2/17/970
In our case a simple reboot worked, fortunately.
## Tags...
- 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 on...
- Some correlations running very slowly
issue opened on Mar 06 2023 by Zachary Sloan, last updated on Mar 07 2023 by Pjotr Prins
...very slowly
## Tags
* assigned: zsloan, pjotrp
* type: bug
* priority: high
* status: in-progress
* keywords: correlations, database
## Description
Some correlations (it specifically seems to be ones...
- 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
Unresponsive Virtuoso in CD
* assigned: bonfacem
* tags: critical
## Description
In CD, when you navigate to a datasets page, say:
=> https://cd.genenetwork.org/datasets/BXDPublish /datasets/...
- Apps
issue opened 44 hours ago by Pjotr Prins, last updated 22 hours ago by Pjotr Prins; 6 of 15 tasks done
Apps
GeneNetwork.org retains a number of apps. Currently they are managed by shepherd as `guix shell` services, but we should really move them to system containers.
# Tags
* assigned: pjotrp
* type...
- 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...
- ProbeData
issue opened on Dec 30 2021 by Pjotr Prins, last updated on Mar 14 2023 by Arun Isaac
ProbeData
## Tags
* assigned: pjotrp
* status: unclear
* priority: medium
* type: enhancement
* keywords: database, mariadb, innodb, ProbeData
## Description
Probe level data is used to examine the...
- GN1 Time machines
issue opened on Oct 07 2021 by Pjotr Prins, last updated on Jul 01 2022 by Arun Isaac
...sudo 33730812 Wed, 2017-04-12 17:06:40 export/backup/artemis/mysql/gn_db_20180228/Geno.MYD
```
so you can see all the different versions. The matching code bases should be there too.
## Tags...
- 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...
- GN Services
document created on Sep 15 2021 by Pjotr Prins, last updated on Dec 23 2022 by Pjotr Prins
...Tags
* type: documentation
* status: in progress
* keywords: gn services, documentation
# Description
First make sure to have a stable guix checkout. E.g.
```
gn3@tux01:~/production/gn-proxy$ /home/...
- 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
...Quite as Expected
## Tags
* type: bug
* assigned: arun, fredm
* priority: medium
* status:
* keywords: xapian, search
## Description
The following is a list of failing examples of search, with notes...
- 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...
- Fix GN1 Network Graph
issue opened on Sep 15 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
Tags
* type: bug
* priority: high
* keywords: GN1, Network Graph
* status: in progress
* kanban: pjotrp
* assigned: pjotrp, zachs
## Tracking
To reproduce this bug: select a 'shopping basket' and...
- Shepherd
document created on Aug 27 2021 by Pjotr Prins, last updated on Dec 02 2023 by Pjotr Prins
...(on Debian).
# Tags
* assigned: pjotrp, efraimf
* type: documentation
* keywords: system, shepherd
* status: wip
* priority: normal
# Issues
* [ ] Currently guix system is started up using sudo as a...
- 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...
- Feature Request: Create Test Accounts
issue opened on Sep 16 2024 by Frederick Muriuki Muriithi, last updated on Sep 17 2024 by Frederick Muriuki Muriithi
...Tags
* assigned: fredm, alex
* status: open
* type: feature request, feature-request
* priority: medium
* keywords: gn-auth, auth, test accounts
## Description
From the requests on Matrix:
@alexm...
- 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...
- Linking genotype files to datasets
issue opened on Jul 07 2023 by Alexander_Kabui, last updated on Jul 11 2023 by Alexander_Kabui
Linking genotype files to datasets
## Tags
* assigned: alexm
* type: debug
* priority: high
* status: in progress
## Notes
A dataset can have multiple groups. In order to fetch all possible sample...
- 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...
- Correlation results wrong for certain traits/datasets
issue opened on Dec 12 2022 by Zachary Sloan, last updated on Dec 22 2022 by Zachary Sloan
...wrong for certain traits/datasets
## Tags
* assigned: alexm, zsloan, fredm
* priority: high
* status: ongoing
* keywords: correlations
## Description
(Note that this uses the update to using GN! text...
- Adding Species
document created on Apr 24 2024 by Frederick Muriuki Muriithi, last updated on Apr 24 2024 by Frederick Muriuki Muriithi
Adding Species
## Tags
* status: open
* priority: medium
* type: documentation
* assigned: fredm, flisso, acenteno
* keywords: doc, documentation, platform, gn-uploader, uploader, adding data...
- 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
Migrate User Collections
## Tags
* assigned: zachs, fredm
* priority: critical
* status: closed, completed
* keywords: authentication, authorisation, oauth2, user collections
* type: bug...
- Add Metadata To The Trait Page (RDF)
document created on Sep 28 2022 by Munyoki Kilyungi, last updated on Dec 03 2023 by Pjotr Prins
...and contributors.
* Add metadata as links, tooltips, or html <summary> tag to the relevant html section(s).
## Resources
=> https://www.linkedin.com/pulse/six-secret-sparql-ninja-tricks-kurt-cagle/
- Correlations: Returning Fewer Results
issue opened on Nov 07 2022 by AlexanderKabui, last updated on Nov 25 2022 by Zachary Sloan
...Returning Fewer Results
## Tags
* assigned: alexm
* priority: high
* status: ongoing
* keywords: correlations,fewer results
## Description
in some cases correlaton return fewer number of results
than...
- GN1 metadata
issue opened on Dec 09 2022 by Pjotr Prins; 0 of 3 tasks done
...be replitated by logging into GN1 and selecting a dataset. Hit the info button and 'edit' next.
## Tags
* assigned: pjotrp
* priority: high
* status: overdue
* type: bug
* keywords: GN1, genenetwork1...
- Mechanical Rob
document created on Aug 23 2022 by Arun Isaac, last updated on Aug 16 2024 by Munyoki Kilyungi
...Tags
* type: documentation, docs
* assigned: bonfacem, rookie101, fredm
* priority: medium
* status: open
* keywords: tests, testing, mechanical-rob
## What is Mechanical Rob?
Mechanical Rob is our...
- Genewiki conversion
issue opened on Aug 26 2022 by Pjotr Prins, last updated on Sep 05 2022 by Alexander_Kabui; 0 of 3 tasks done
...in that repository and (2) create a rendered page that is found through
=> https://genenetwork.org/doc/genes/BRCA2
with an edit button, similar to
=> http://genenetwork.org/facilities/
## Tags...
- 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...
- Can't Masquarade as another user as a system admin
issue opened on May 15 2024 by Munyoki Kilyungi
...tags: critical
Right now you can't masquared as another user. Here's the trace:
```
GeneNetwork 2.11-rc2 https://qa.genenetwork.org/oauth2/user/masquerade ( 3:38PM UTC May 15, 2024)
Traceback...
- 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...
- 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
...sheepdog server we may give it a DNS entry as sheepdog.genenetwork.org.
=> http://sheepdog.genenetwork.org/sheepdog/index.html
See also
=> /topics/systems/restore-backups Restore Backups
## Tags...
- Dump sample data to LMDB
issue opened on Dec 15 2022 by Munyoki Kilyungi, last updated on Mar 06 2024 by Munyoki Kilyungi; 0 of 5 tasks done
...probesets
* [ ] genotypes
* [ ] GN2/3 Integration
For RDF:
https://issues.genenetwork.org/search?query=assigned%3ABonfaceKilz+AND+tag%3Ain-progress+AND+priority%3Ahigh+AND+is%3Aopen&type=open-...
- Uploading Samples
issue opened on Sep 18 2024 by Frederick Muriuki Muriithi, last updated on Sep 19 2024 by Frederick Muriuki Muriithi
Uploading Samples
## Tags
* status: open
* assigned: fredm
* interested: acenteno, zachs, flisso
* priority: high
* type: feature-request
* keywords: gn-uploader, uploader, samples, strains...
- Invoking SQLite3: CLI
document created on Mar 30 2024 by Frederick Muriuki Muriithi
...Tags
* status:
* assigned:
* priority:
* type: documentation
* keywords: doc, documentation, sqlite, sqlite3
## TLDR
At minimum, always invoke sqlite with "PRAGMA foreign_keys = ON;" as follows...
- 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...
- UM-HET3 Timing: Slow
issue opened 4 weeks ago by Frederick Muriuki Muriithi, last updated 4 weeks ago by Frederick Muriuki Muriithi
UM-HET3 Timing: Slow
## Tags
* type: bug
* status: open
* assigned: fredm
* priority: critical
* interested: fredm, pjotrp, zsloan
* keywords: production, container, tux04, UM-HET3
## Description
In...
- Tux04/Tux05 disk issues
issue opened on May 03 2024 by Pjotr Prins, last updated 3 days ago by Pjotr Prins
...-boot-partition
# Tags
* assigned: pjotrp, aruni
* type: systems
* keywords: hardware
* status: unclear
* priority: medium
# Info
```
journalctl |grep mega
May 01 01:40:45 tux04 smartd[2440]: Device...
- Phenotype Naming Conventions
document created on Nov 23 2022 by Munyoki Kilyungi, last updated on Dec 03 2023 by Pjotr Prins
...programmatically add further tags such as year of publication (last two digits).
3. We have to decide on a format that WE IMPOSE. For better or for worse, we are apparently one of the major curators...
- GNQA Integration to Global Search Design Proposal
✓ issue opened on Sep 02 2024 by Alexander_Kabui, last updated 5 weeks ago by Alexander_Kabui; 9 of 9 tasks done
...Integration to Global Search Design Proposal
## Tags
* assigned: jnduli, alexm
* keywords: llm, genenetwork2
* type: feature
* status: complete, closed, done
## Description
This document outlines the...
- 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...
- Generating Key-Pairs
document created on Apr 18 2024 by Frederick Muriuki Muriithi, last updated on Apr 22 2024 by Frederick Muriuki Muriithi
...Key-Pairs
## Tags
* type: documentation
* keywords: doc, documentation, gn-auth, key-pair, jwt
## Generating the Key-Pair
If openssl is not present on your system, you need to get it. You can either...
- Virtuoso: Shutdown Clears Data
✓ issue opened 3 weeks ago by Frederick Muriuki Muriithi, last updated 3 weeks ago 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...
- GeneNetwork Services
document created 4 weeks ago by Frederick Muriuki Muriithi, last updated 3 weeks ago by Frederick Muriuki Muriithi
...Tags
* type: documentation
* keywords: documentation, docs, doc, services, genenetwork services
## GeneNetwork Core Services
GeneNetwork is composed of a number of different services. This document...
- Common Lisp Condition Handling
document created on Dec 28 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
.../Condition-Handling-2001.html Condition Handling in the Lisp Language Family
=> https://gigamonkeys.com/book/beyond-exception-handling-conditions-and-restarts.html Conditions and Restarts
## Tags...
- Handling Tissue in Uploader
issue opened on Mar 28 2024 by Frederick Muriuki Muriithi, last updated on Mar 28 2024 by Frederick Muriuki Muriithi; 2 of 2 tasks done
...Tissue in Uploader
## Tags
* status: open
* priority: high
* assigned: fredm
* type: feature-request
* keywords: gn-uploader, tissues
## Description
"ProbeSet" studies in GeneNetwork seem to be linked...
- Set-up Virtuoso+Xapian on Production
✓ issue opened on Nov 22 2023 by Munyoki Kilyungi, last updated 3 weeks ago 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, we...
- Fire up system container for GN-QA System
document created on May 13 2024 by Munyoki Kilyungi, last updated on May 13 2024 by Munyoki Kilyungi
Fire up system container for GN-QA System
# Tags
* assigned: bonfacem, alexm
The current code is a WIP. Patches will be sent after a working container is set-up. Most recent code can be found at...
- 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...
- Genenetwork2 Configurations
issue opened on Jun 14 2023 by Frederick Muriuki Muriithi, last updated on Jun 28 2023 by Frederick Muriuki Muriithi
...Configurations
## Tags
* assigned: fredm
* priority: normal
* status: open
* keywords: configuration, config, gn2, genenetwork, genenetwork2
* type: bug
## Description
The current way the...
- 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...
- Deploying Your Flask Application Under a URL Prefix With GUnicorn
document created 5 weeks ago by Frederick Muriuki Muriithi
Deploying Your Flask Application Under a URL Prefix With GUnicorn
## TAGS
* type: doc, documentation, docs
* author: fredm, zachs
* keywords: flask, gunicorn, SCRIPT_NAME, URL prefix
## Introduction...
- Edit RIF Metadata in GN2
✓ issue opened on Jul 29 2024 by Munyoki Kilyungi, last updated 5 weeks ago 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"...
- How to upgrade slurm on octopus
document created on Aug 29 2024 by Arun Isaac, last updated 5 weeks ago by Arun Isaac
...is safe to upgrade version 18.08 to 19.05 or 20.02, but not to 20.11 or later. This compatibility information is in the RELEASE_NOTES file of the slurm git repo with the git tag corresponding to the...
- Data Uploads: Inserting Data
document created on Jan 27 2022 by BonfaceKilz, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...Tags
* assigned: bonfacem, zachs
* type: bug
* priority: high
* status: in progress
* keywords: data uploads
### Introduction
The current uploader work documented in `editing-data.gmi` only caters...
- Export Uploaded Data to LMDB and RDF Stores
issue opened on Nov 03 2023 by Frederick Muriuki Muriithi, last updated on Nov 14 2023 by Frederick Muriuki Muriithi; 0 of 6 tasks done
...RDF Stores
## Tags
* assigned: fredm, bonz
* priority: medium
* type: feature-request
* status: open
* keywords: API, data upload
## Description
With the QC/Data Upload project nearing completion, and...
- Logging with Flask and Gunicorn
document created on Apr 15 2024 by Frederick Muriuki Muriithi
...Tags
* type: documentation
* keywords: deploy, deployment, logging, flask, gunicorn
## Logging with Flask and Gunicorn
Flask has its own output logger, `flask.logger`, which is an extension of...
- 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
...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 says there is a problem with the load path in...
- 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...
- Editing Case-Attributes
document created on Jul 07 2023 by Frederick Muriuki Muriithi, last updated on Sep 09 2024 by Munyoki Kilyungi
...Tags
* type: document
* keywords: case-attribute, editing
* assigned: fredm, zachs, acenteno, bonfacem
* status: requirements gathering
## Introduction
Case-attributes metadata for samples. They...
- 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
# Issues...
- Using PDB to Troubleshoot Python Code
document created on Dec 03 2023 by Pjotr Prins
...Code
## Tags
* type: documentation
* keywords: debugging, python
Historically, debugging GeneNetwork code has been a bit of a pain where you would have `print' and `logging' statements to help view...
- GeneNetwork Authentication/Authorisation Architecture
document created on Dec 04 2023 by Frederick Muriuki Muriithi, last updated on Jul 25 2024 by Frederick Muriuki Muriithi
.../Authorisation Architecture
## Tags
* type: docs, documentation
* status: ongoing, open
* keywords: authentication, authorisation, architecture, docs, documentation
* author: Frederick Muriuki Muriithi...
- 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/...
- Partial Correlation
document created on Oct 15 2021 by Frederick Muriuki Muriithi, last updated on May 16 2022 by Frederick Muriuki Muriithi
...in X, Y and Z columns
And compute against database (lower half).
That gives you a list of hits.
## Members
* fredm
* pjotp
* alex
## Tags
* assigned: fredm, zsloan, robw
* keywords: migration, partial...
- 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...
- Data Upload Process
document created on Apr 30 2024 by Munyoki Kilyungi, last updated on Apr 30 2024 by Munyoki Kilyungi
...Upload Process
## Tags
* assigned: priscilla
* keywords: documentation, gn-uploader
The process of uploading data to the GeneNetwork platform began with retrieving the dataset from the Gene Network...
- GeneNetwork Hacking Documentation
document created on Mar 11 2022 by Frederick Muriuki Muriithi, last updated on Jul 18 2022 by Frederick Muriuki Muriithi
...to help with clarifying some concepts and critiquing the documentation.
The goal of this document is to encourage and track the documentation that assist with the development of the system.
## Tags...
- 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...
- 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
...page broken
## Tags
* assigned: zsloan, pjotrp
* priority: high
* status: testing
* type: bug
* keywords: GN1, genenetwork1, annotation, from github
## Tasks
* [ ] Fix PHP view
* [ ] Fix CKEDITOR...
- Precompute steps
document created on May 07 2024 by Pjotr Prins, last updated on Aug 16 2024 by Pjotr Prins
...Compute bulklmm vector
Interestingly this work coincides with Arun's work on CWL. Rather than trying to write a workflow in bash, we'll use ccwl and accompanying tools to scale up the effort.
# Tags...
- Automated Testing
document created on Oct 12 2022 by Munyoki Kilyungi, last updated on Dec 03 2023 by Pjotr Prins
Automated Testing
## Tags
* keywords: testing, CI, CD
## Introduction
As part of the
=> ../systems/ci-cd.gmi CI/CD effort
there is need for automated tests to ensure that the system is working as...
- R Kernel Dying
issue opened on Jan 17 2022 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
R Kernel Dying
## Tags
* assigned: jgart
* type: bug
* priority: high
* status: unclear
* keywords: R
## Core Dump
```
[I 08:45:24.502 NotebookApp] Writing notebook-signing key to /home/jgart/.local/...
- 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
...Tags
* assigned: bonfacem
* keywords: metadata
* priority: high
* closed
## Tasks
* [ ] I cannot edit the PMID number
* [ ] There is inadequate feedback on whether or not changes have been accepted...
- Genenetwork3 Effective UID
✓ issue opened on Jun 05 2023 by Frederick Muriuki Muriithi, last updated on Jun 09 2023 by Frederick Muriuki Muriithi
Genenetwork3 Effective UID
## Tags
* assigned: aruni, fredm
* priority: critical
* status: closed, completed
* keywords: CI, CD, Effective UID, Genenetwork3, GN3
* type: bug
## Description
The issue...
- 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
Fetch trait data using genofiles
## Tags
* assigned:alexm,
* type:improvement
* priority: high
* status: in progress
## Notes
since Genenetwork database does not have all genotype files when fetching...
- Fire up system container for GN
document created on Mar 02 2024 by Pjotr Prins, last updated on Apr 05 2024 by Pjotr Prins
Fire up system container for GN
# Tags
* assigned: pjotrp
* priority: medium
* type: system administration
* keywords: system administration, GN, tux01, tux02, tux04, balg01
# Tasks
We have the...
- Large datasets crash gemma
issue opened on Mar 12 2022 by Pjotr Prins, last updated on Mar 16 2022 by Frederick Muriuki Muriithi; 0 of 7 tasks done
...find that message). Or it may be GEMMA simply runs out of RAM and the kernel is busy cleaning up using the OOM reaper. See
=> https://lkml.iu.edu/hypermail/linux/kernel/2003.2/01012.html
## Tags...
- 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
...utf8mb4. When comparing text fields mariadb can't optimize because it is translating utf8mb3 for every comparison. Changing the table and indices to utf8mb4 or latin1 (on production) fixed it.
# Tags...
- Editing Data
document created on Nov 23 2021 by BonfaceKilz, last updated on Jul 25 2023 by Frederick Muriuki Muriithi
Editing Data
## Tags
* assigned: bonfacem
* keywords: metadata
* status: unclear
* priority: medium
### Introduction
At the moment, you can edit metadata related to a published phenotype and a...
- 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 3 weeks ago by Frederick Muriuki Muriithi, last updated 14 days ago 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...
- Deploying gn-auth
document created on Mar 04 2024 by Frederick Muriuki Muriithi, last updated on Mar 12 2024 by Frederick Muriuki Muriithi
Deploying gn-auth
## Tags
* type: doc, docs, documentation
* keywords: gn-auth, deployment
* status:
* priority:
* assigned:
## …
︙
### Run Migrations
At this point, you have a container running...
- Configuring Nginx on the Host System
document created on Aug 27 2024 by Frederick Muriuki Muriithi
Configuring Nginx on the Host System
## Tags
* type: doc, docs, documentation
* keywords: deploy, deployment, deploying, nginx, guix, guix container, guix system container
* status: in progress...
- Multivariate GEMMA hangs (issue 243)
issue opened on Aug 16 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...hangs (issue 243)
## Tags
* assigned: ??
* type: failure
* keywords: GEMMA
* status: unclear
* priority: high
## Description
=> https://github.com/genetics-statistics/GEMMA/issues/243
The simulated...
- RQTL Implementation for GeneNetwork Design Proposal
document created 5 weeks ago by Alexander_Kabui, last updated 9 days ago by Alexander_Kabui
RQTL Implementation for GeneNetwork Design Proposal
## Tags
* Assigned: alexm,
* Keywords: RQTL, GeneNetwork2, Design
* Type: Enhancements,
* Status: In Progress
## Description
This document outlines...
- 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
...also I created my own development VM in just an hour, so I don't have to mess with the fallback while others are using it.
# Tags
* type: bug
* assigned: pjotrp
* keywords: systems, fallback, deploy...
- Binding notebooks
document created on Aug 22 2021 by jgart, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...and Pluto notebooks. These binding tools do a lot more and do not leverage GNU Guix lightweight container infrastructure. In this project we want to create a binding-lite.
## Tags
* keywords: binder...
- 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
...complexity has increased a lot because of interacting services and a larger dependency graph.
Here I track what it takes today to install a fallback instance of GN2 that is 'frozen' in time.
## Tags...
- ProbeSetData
issue opened on Dec 31 2021 by Pjotr Prins, last updated on Mar 13 2023 by Pjotr Prins; 15 of 17 tasks done
...the ProbeSetData table and indices. At the end we have reduced the size by 25% and decided to keep the myisam format for this single table. In the future it may be replaced by lmdb or similar.
## Tags...
- GeneNetwork Uploader Requirements
document created on Feb 22 2024 by Frederick Muriuki Muriithi, last updated on Feb 22 2024 by Frederick Muriuki Muriithi
...Uploader Requirements
*OR*: "Reattaching the Head on Frederick's Headless-Chicken Development :-)"
## Tags
* assigned: fredm, flisso
* type: doc, requirements
* priority: high
* status: open...
- ProbeSetXRef
issue opened on Dec 29 2021 by Pjotr Prins, last updated on Jul 01 2022 by Arun Isaac
...Tags
* keywords: ProbeSetXRef, database, mariadb, innodb
* type: enhancement, documentation
* assigned: pjotrp
* status: unclear
* priority: medium
## Table ProbeSetXRef
Juggling indexes and...
- Hanging database
issue opened on Dec 21 2021 by Pjotr Prins, last updated on Mar 11 2023 by Pjotr Prins
...myisam to InnodB is the solution because it prevents full table locking.
Also it is better to use mydumper, mydumper locks MyISAM tables and does not lock InnoDB so the dump is consistent.
## Tags...
- Migrate GN1 Clustering
document created on Jul 18 2021 by Pjotr Prins, last updated on Mar 22 2022 by Frederick Muriuki Muriithi
...map' icons. Computation may take a while.
Next click on 'Cluster traits' and 'Redraw' map. This is the one we want in GN3/GN2!
=> ./heatmap.png
## Members
* fredm
* pjotr
## Kanban
* fredm
## Tags...
- MariaDB: Move to InnoDB Engine
issue opened on Dec 28 2021 by Pjotr Prins, last updated on Apr 24 2024 by Pjotr Prins; 0 of 8 tasks done
...every table
* [ ] Check for primary key
* [ ] Check fulltext fields (see below)
* [ ] Convert to innodb
* [ ] Convert to utf8mb4 and utf8mb4_general_ci
## Tags
* assigned: pjotr
* type: enhancement...
- MariaDB Database Architecture
document created on Jun 29 2024 by Pjotr Prins, last updated on Sep 02 2024 by Lisso_
...measured mRNA level, and the vendor called their assays "ProbeSets". We used this now obsolete term. Most ProbeSetData in GN1 and GN2 as of 2024 are measurments of molecular traits that can be tagged...
- Meeting Notes
document created on Jun 11 2024 by John Nduli, last updated 6 days ago by Munyoki Kilyungi
...to Haves
* @bmunyoki Nice to have tag for paper1: Fix this with Boni and get done later on/iron them out then.
* @bmunyoki fix CI job that transforms gn tables to TTL: Move this to running a cron job...
- Precompute mapping input data
document created on Mar 20 2023 by Pjotr Prins, last updated on Jun 03 2024 by Pjotr Prins
...updated traitid, i.e., DataId from ProbeSetXRef which is indexed. Before doing anything we use Locus_old to identify updates by setting it to NULL. See the header of list-traits-to-compute.scm.
# Tags...