- 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...
- 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...
- 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...
- Letsencrypt
issue opened on Oct 13 2021 by Pjotr Prins, last updated on Jul 04 2023 by Pjotr Prins; 2 of 5 tasks done
...22 4 * * 3 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...
- Backup Drops
document created on Oct 27 2022 by Pjotr Prins, last updated on Feb 07 2023 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...
- CI/ CD for genetwork projects
document created on Oct 12 2022 by Munyoki Kilyungi, last updated on Jul 13 2023 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...
- GN1 github problem
issue opened on Dec 17 2022 by Pjotr Prins
...rm --cached --ignore-unmatch \
MouseTissuesRWWMay08.xls' --prune-empty --tag-name-filter cat -- --all
git reflog expire --expire=now --all && git gc --prune=now --aggressive
```
Note this rewrites...
- 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.
- 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...
- 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...
- 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, from...
- 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
Trait Page Errors on CD
## Tags
* type: bug
* priority: critical, high
* status: open
* 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 Feb 22 2023 by Pjotr Prins; 5 of 5 tasks done
Octopus sysmaintenance
# Tags
* assigned: pjotrp, efraimf, erikg
* priority: high
* status: completed, closed
* type: system administration
* keywords: systems, octopus
# Tasks
* [X] install sheepdog...
- 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...
- Machine room
issue opened on Nov 23 2021 by Pjotr Prins, last updated on Jul 01 2022 by Arun Isaac; 1 of 4 tasks done
...room
## Tags
* assign: pjotrp, dana
* type: system administration
* priority: high
* keywords: systems
* status: unclear
## Tasks
* [X] Make tux02e visible from outside
* [ ] Network switch 10Gbs...
- 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...
- issues/sorting-correlation-nan-vals.gmi
issue opened on Nov 28 2022 by AlexanderKabui
Tags
* type: bug
* assigned:alexm
* priority: medium
* status:in progress
* keywords: correlations, sorting,nan
## Description
sorting floats (correlation values) where
some cases have nan values...
- 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...
- 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"...
- Try out Auth Code Locally
issue opened on Apr 21 2023 by Munyoki Kilyungi; 0 of 2 tasks done
...Locally
## Tags
* assigned: bonfacem
* type: review
## Description
Have a look at Fred's Auth code and in particular:
* [ ] Set it up in a local development environment.
* [ ] Improve documentation if...
- Set password when virtuoso containers are rebuilt
issue opened on Jul 07 2023 by Munyoki Kilyungi
...containers are rebuilt
## Tags
* assigned: bonfacem
Whenever the virtuoso container is rebuilt, we manually have to reset the password. We should fix this by modifying the virtuoso service so...
- 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...
- 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...
- Document redis data
✓ issue opened on Nov 27 2021 by BonfaceKilz, last updated on Apr 18 2023 by Munyoki Kilyungi
Without this, it's
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...
- 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.
- 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
...Upload Fails
## Tags
* assigned: fredm
* priority: high
* type: bug
* status: open, started
* keywords: qc, quality control
## Description
Trying to upload big files (>= 500MB) fails quietly, dropping...
- 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
...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...
- 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...
- Model Menu In RDF
issue opened on Apr 18 2023 by Munyoki Kilyungi, last updated on Apr 27 2023 by Munyoki Kilyungi
Model Menu In RDF
## Tags
* assigned: bonfacem
* type: modelling
* status: in progress
* priority: high
* keywords: rdf, modelling
## Description
Read the following for more details...
- 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...
- 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...
- Integrate Feed Analyser
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Oct 12 2022 by Munyoki Kilyungi
Integrate Feed Analyser
## Tags
* assigned: bonfacem
* type: feature-request
* status: stalled
* priority: medium
* keywords: twitter, feed analyser
## Members
* bonfacem
* robw
## Description...
- Improve sparql results
issue opened on Jul 07 2023 by Munyoki Kilyungi
...Tags
* assigned: bonfacem
* type: improvement
* priority: high
* status: in progress
* keywords: RDF, SPARQL
For this query:
=> https://sparql.genenetwork.org/sparql?default-graph-uri=&qtxt=prefix%...
- Gn Markdown Editor implementation
issue opened 8 weeks ago by Alexander_Kabui, last updated 3 weeks ago by Alexander_Kabui; 4 of 5 tasks done
...//markdownlivepreview.com/
## Tags
* assigned: alexm
* type: enhancement
* status: IN PROGRESS
* keywords: markdown,editor
## Tasks
* [x] implement markdown page editor
* [x] add live preview...
- 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...
- 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...
- 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 does not return results
✓ issue opened on Mar 22 2022 by Frederick Muriuki Muriithi, last updated on Oct 14 2022 by Arun Isaac
...Tags
* priority: critical
* type: bug
* assigned: zsloan, pjotrp
* status: unclear
* keywords: global search, from github
## Description
=> https://github.com/genenetwork/genenetwork2/issues/629...
- 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...
- Genotype Metadata
issue opened on Nov 29 2022 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...
- 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 $GNRoot/web/tmp -mmin +100 -exec rm -rfv...
- Marker mapping
✓ issue opened on Sep 15 2021 by Pjotr Prins, last updated on Dec 17 2022 by Pjotr Prins
.../MarkerRegressionPage.py", line 438, in GenReport
qtlresults = _genotype.regression(strains = _strains, trait = _vals)
AttributeError: 'genotype' object has no attribute 'regression'
```
## Tags...
- Remove everything elastic search
✓ issue opened on Oct 22 2021 by Pjotr Prins, last updated on Apr 01 2022 by BonfaceKilz
.../remove-elastic-search.gmi
## Tags
* assigned: bonfacem
* type: enhancement
* priority: low
* status: closed, done
* keywords: elasticsearch, purge
### Notes
Removed in #44bf8ee and #03caa57a in GN2.
- Marker covariates implemented wrong in rqtl_wrapper.R
issue opened on Sep 22 2021 by Zachary Sloan, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...covariates in rqtl_wrapper.R is wrong. For the time being,
I've removed this option. Currently just waiting on Danny to get back to me with the fix (which I'll then add to rqtl_wrapper.R)
## Tags...
- Arthur mentioned last meet that GeneNetwork2 does not redirect http urls to https.
issue opened on Dec 05 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...https.
He'd like http to redirect to https.
http://genenetwork.org/ -> https://genenetwork.org/
# nginx snippet
```
if ($scheme = http) {
return 301 https://$server_name$request_uri;
}
```
## Tags...
- 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 Mar 16 2022 by Frederick Muriuki Muriithi
...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 Apr 07 2023 by Pjotr Prins
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...
- Scree Plot appears to be incorrect
issue opened on May 19 2022 by Zachary Sloan, last updated on Jun 15 2022 by BonfaceKilz
...to verify 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...
- 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
Fix Missing Genotype Files for GEMMA
## Tags
* assigned:
* priority: medium
* type: bug
* status: pending
* keywords: gemma, technical debt
## Description
Run GEMMA (under "Mapping Tools")...
- 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...
- 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 MR Failing Tests
issue opened 3 weeks ago by Munyoki Kilyungi, last updated 3 weeks ago by Munyoki Kilyungi
...Failing MR Failing Tests
## Tags
* priority: high
* status: open
* assigned: bonfacem
## Description
MR fails because of a python-flask/requests issue. Everytime you issue a GET request to the server...
- 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 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...
- 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
Failing Tests
## Tags
* assigned: zsloan, alex
* type: bug
* priority: critical
* status: completed, done
* keywords: genenetwork2, tests failure
## Description
The following changes are causing the...
- 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
...Database
## Tags
* type: feature request
* status: closed
* assigned: fredm
* keywords: editing, metadata audit
* priority: high
## Description
The rejected diffs will be maintained, but will simply...
- 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...
- 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...
- 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
Create a new UI language for gn2
## Tags
* assigned: robw, zachs, bonfacem
* type: ui
* status: unclear
* priority: low
* keywords: ui
## Introduction
New UI keeps spring up in the genenetwork eco-...
- Create Traits Endpoints in RDF
✓ issue opened on May 18 2023 by Munyoki Kilyungi, last updated on Jun 19 2023 by Munyoki Kilyungi; 3 of 3 tasks done
Create Traits Endpoints in RDF
## Tags
* assigned: bonfacem
* type: feature
* status: closed
Create end-points that query RDF for the following:
* [x] Phenotypes: (prefix "phenotype:" "<http...
- Correlations: 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...
- 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
...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...
- 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
Enable User Masquerade
## Tags
* assigned: fredm, zsloan, zachs
* priority: medium
* status: closed, completed
* keywords: authentication, authorisation, oauth2
* type: feature request
## Description...
- 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...
- 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...
- Add genotype file paths to RDF
issue opened on Jun 19 2023 by Munyoki Kilyungi
...paths to RDF
## Tags
* assigned: bonfacem
* type: bug
* status: open, in progress
In Penguin2, genotype files are located in: /export/data/genenetwork/genotype_files/genotype. Each genotype files has...
- 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...
- 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...
- issues/add-bulklmm-feature.gmi
issue opened on Jun 27 2023 by GregFa
BulkLMM integration
## Tags
* assigned: pjotrp
* type: feature
* priority: high
## Description
Integrate BulkLMM in GeneNetwork. The first step is to test the command line interface to BulkLMM in...
- 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
BXD102xBXD077F1 Error
## Tags
* assigned: zsloan
* type: bug
* priority: critical
* status: unclear
* keywords: correlations, from github, closed
## Description
=> https://github.com/...
- 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 Mar 16 2022 by Frederick Muriuki Muriithi
...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
* type...
- Using pudb with pytest
document created on Dec 21 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...pudb with pytest
```
pytest --pdbcls pudb.debugger:Debugger --pdb --capture=no
```
=> https://documen.tician.de/pudb/starting.html?highlight=pytest#usage-with-pytest
## Tags
* type: documentation...
- Profiling Python code
document created on Dec 22 2021 by Frederick Muriuki Muriithi, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...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...
- Reproducibility
document created on Oct 04 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...managing or thinking about reproducibility
https://github.com/fonsp/Pluto.jl#built-in-package-manager
https://mybinder.readthedocs.io/en/latest/tutorials/reproducibility.html#pin-dependencies
## Tags...
- port map
document created on Sep 20 2021 by jgart, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
port map
|-----|-----------|
|port |service |
|-----|-----------|
|80 |nginx |
|8989 |binderlite |
|xxxx |jupyter(s) |
## Tags
* type: documentation
* keywords: documentation, port map
- Julia Pluto
document created on Aug 31 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...Tags
* type: documentation
* status: unclear
## Pluto in a Guix container
We run Pluto in a container. It allows for self-install of Julia packages:
```
guix environment -L ~/guix-past/modules/ -L...
- Guix Containers
document created on Oct 01 2021 by jgart, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
Guix Containers
## Tags
* type: bug
* assigned: jgart
* status: unclear
* priority: medium
* keywords: notebooks, guix, containers
## Bugs
guix container exec command does not currently work:
http...
- CLI Features
document created on Oct 12 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...Tags
* assigned: jgart
* priority: low
* status: unclear
* type: feature-request
* keywords: bindelite, notebooks
## Admin
* Clear Database
## User
* Upload Notebooks
* List Notebooks
* Download...
- LMM Notes
document created on Aug 13 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...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...
- 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...
- 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 Mar 16 2022 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: unclear...
- Replace Hard coded authentication with gn-proxy
document created on Mar 14 2022 by Frederick Muriuki Muriithi, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...Hard coded authentication with gn-proxy
## Tags
* assigned: bonfacem
* priority: medium
* type: enhancement
* status: in progress
* keywords: authentication, gn-proxy
## Description
Originally in the...
- 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...
- Genotype correlations only returning results from first chromosome
issue opened on Oct 21 2022 by Zachary Sloan
...only returning results from first chromosome
## Tags
* assigned: fredm, alexm, zsloan
* type: bug
* priority: high
* status: ongoing
* keywords: correlations
## Description
=> http://gn2-zach...
- 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...
- Upload GeneWiki RDF metadata to CD
✓ issue opened on Apr 17 2023 by Munyoki Kilyungi, last updated on Apr 18 2023 by Munyoki Kilyungi
...to CD
## Tags
* assigned: bonfacem
* keywords: generif, metadata, RDF
Following this:
=> /topics/our-virtuoso-instances.gmi Our Virtuoso Instances
I've tried loading ttl files in our CD in tux02.
- 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...
- 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...
- Move Search to Xapian
issue opened 3 weeks ago 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...
- Make Partial Correlations Table Searchable
issue opened on Apr 22 2022 by Frederick Muriuki Muriithi
...Table Searchable
## Tags
* assigned: fredm
* priority: medium
* type: migration, feature-request
* status: pending
* keywords: partial correlations, datatables
## Description
@robw notes, correctly...
- 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...
- 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...
- Running pudb From an External Environment
document created on Dec 22 2021 by Frederick Muriuki Muriithi, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...--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...
- 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...
- 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.
- 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)...
- 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...
- Jupyter notebooks
document created on Sep 01 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...notebooks
## Tags
* type: documentation
* keywords: documentation, jupyter, notebooks
* status: unclear
## Run with GNU Guix
Jupyter notebooks can be installed in a profile
```
~/opt/guix-latest/bin/...
- 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
...(1040, 'Too many connections')
## Tags
* assigned: bonfacem, fredm, aruni
* type: bug
* keywords: mysql, database
## Tasks
* [x] Figure out root cause
* [x] Send patch
## Description
See the strack...
- Rework Fetching Settings
issue opened on Sep 25 2022 by Munyoki Kilyungi, last updated on Oct 12 2022 by Munyoki Kilyungi
...stalled
* 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...
- 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...
- 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...
- 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...
- Bug with linking data
issue opened on Jul 26 2023 by Zachary Sloan
...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-...
- Remove externally loaded JS
issue opened on Apr 18 2022 by BonfaceKilz, last updated on Apr 18 2023 by Munyoki Kilyungi
Remove externally loaded JS
## Tags
* assigned: alex
* type: ui, enhancement
* status: stalled
* priority: medium
* keywords: ui, guix
## Description
`jquery-ui` is still loaded from a CDN. This...
- 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...
- 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/...
- Broken continuous deployment
✓ issue opened on Jul 06 2022 by Arun Isaac, last updated on Jul 11 2022 by Frederick Muriuki Muriithi
...aruni
* tags: critical
The continuous deployment (CD) of GeneNetwork2 at https://gn2dev.genenetwork.org/ is broken. Even with all javascript enabled, none of the menu items load. The error message...
- 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
...metadata
## 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...
- 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...
- 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...
- Rework Resources
issue opened 4 weeks ago by Frederick Muriuki Muriithi
Rework Resources
## Tags
* assigned: fredm
* status: open
* priority: medium
* type: refactor, feature request, design change
* keywords: auth, authorisation, resources, design change
## Description...
- Markdown docs
issue opened on Sep 10 2022 by Pjotr Prins
...am logged in but do not seem to have permissions 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...
- Migrate to Python3.10
issue opened on Jul 12 2023 by Frederick Muriuki Muriithi, last updated 3 weeks ago by Munyoki Kilyungi; 0 of 1 tasks done
...Python3.10
## Tags
* priority: high
* keywords: python3.10
* status: open
* assigned: bonfacem, fredm, alex, zachs
## Description
Migrate the application(s) over to Python3.10.
The sections below will...
- 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...
- Make Existing Data Public View by Default
issue opened on May 24 2023 by Frederick Muriuki Muriithi
...Existing Data Public View by Default
## Tags
* assigned: fredm, zsloan, zachs
* priority: medium
* status: open
* keywords: authentication, authorisation, oauth2, data migration
* type: migration...
- 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
Allow analyses to be done between traits from "individuals" groups and their corresponding "main" group
# Tags
* assigned: zsloan
* priority: medium
* type: feature-request
* status: open, in...
- 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-...
- 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/...
- Temp traits don't seem to be handled by the authorization system
issue opened on Jul 28 2023 by Zachary Sloan, last updated on Aug 02 2023 by Frederick Muriuki Muriithi
...handled by the authorization system
## Tags
* assigned: fredm, zsloan
* priority: high
* status: open
* keywords: authentication, authorisation, oauth2, temp-traits
* type: bug
## Description
Trying...
- Conflating `dataset_id` with `inbred_set_id`
issue opened on Jul 18 2023 by Frederick Muriuki Muriithi, last updated on Jul 18 2023 by Frederick Muriuki Muriithi
Conflating `dataset_id` with `inbred_set_id`
## Tags
* type: bug
* status: open
* assigned: fredm, bonz
* keywords: editing
* priority: critical
## Description
The existing code that handles editing...
- 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...
- 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...
- Each shepherd service needs its own guix profile.
issue opened on Nov 03 2021 by Efraim Flashner, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...probably OK)
## Services which already have their own profile:
* bnw
* cronjob-gitea
* cronjob-pubmed (genecup)
* genecup
* gitea
* ipfs
* power
* rn6app
* singlecell
## Tags
* assigned: efraim...
- 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...
- Buggy Use of `urllib.parse.urljoin`
issue opened on Jul 25 2022 by Frederick Muriuki Muriithi
Buggy Use of `urllib.parse.urljoin`
## Tags
* type: bug
* priority: low
* assigned: fredm
* status: pending
* keywords: url
## Description
The
=> https://docs.python.org/3/library/urllib.parse.html#...
- 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...
- 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...
- Fix Broken UTF-8 characters in our Database
✓ issue opened on Nov 29 2022 by Munyoki Kilyungi, last updated 5 weeks ago 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...
- 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...
- 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...
- 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...
- Autogenerate documentation: trees, and labels
issue opened on Jun 23 2023 by Munyoki Kilyungi, last updated on Jul 05 2023 by Munyoki Kilyungi
Autogenerate documentation: trees, and labels
# Tags
* assigned: bonfacem
* type: feature, NextGenDatabases
* priority: high
* status: in progress
* keywords: RDF, GNSOC2023
See this
=> https...
- 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...
- 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...
- MariaDB
document created on Oct 26 2021 by Pjotr Prins, last updated on Jul 06 2022 by Arun Isaac
...Here we capture some common actions
## Tags
* type: info, documentation
* keywords: mariadb, systems
## Check the transaction logs
Start the client and:
```
MariaDB [db_webqtl]> show binary logs...
- 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...
- 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...
- genecup is currently running as root on penguin2.
issue opened on Aug 15 2021 by Efraim Flashner, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
Tags
* assigned: Efraim
* type: failure
* keywords: genecup, penguin2
* status: unclear
* priority: high
## Notes
* It is unclear if the environmental-variables in the shepherd service are carried...
- 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...
- 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 7 weeks ago 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...
- 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...
- 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...
- Decommission machines
issue opened on Oct 06 2021 by Pjotr Prins, last updated 10 days ago 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...
- Shepherd
document created on Aug 27 2021 by Pjotr Prins, last updated on Feb 22 2023 by Pjotr Prins
...Tags
* assigned: pjotrp, efraimf
* type: documentation
* keywords: system, shepherd
* status: wip
* priority: unclear
## Quick overview
Shepherd runs in systemd as a shepherd user
```
systemctl...
- 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/...
- Configurations
issue opened on Jun 05 2023 by Frederick Muriuki Muriithi, last updated on Jun 09 2023 by Frederick Muriuki Muriithi
Configurations
## Tags
* assigned: aruni, fredm
* priority: normal
* status: open
* keywords: CI, CD, configuration, config
* type: bug
## Description
There are configurations that change depending...
- 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/...
- 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...
- 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...
- 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...
- 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
Migrate User Accounts from Redis to new Auth DB
## Tags
* assigned: fredm, zsloan, zachs
* priority: high
* status: closed, wontfix
* keywords: authentication, authorisation, oauth2
* type: feature...
- Modelling Phenotype Data
issue opened 8 weeks ago by Munyoki Kilyungi, last updated 7 weeks ago 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.
- 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/...
- 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...
- Fallbacks and backups
issue opened on Aug 31 2021 by Pjotr Prins, last updated on Apr 25 2023 by Munyoki Kilyungi; 19 of 24 tasks done
...so I replaced it with a bare metal server which earns itself (if it hadn't been down for months, but that is a different story).
See also
=> /topics/systems/restore-backups Restore Backups
## Tags...
- issues/fetch-sample-data.gmi
✓ issue opened on Aug 09 2021 by BonfaceKilz, last updated on May 25 2022 by BonfaceKilz
Tags
* assigned: bonifacem
* keywords: sample data, GN2, GN3
* status: closed
* priority: medium
#### Fetch all Sample Data
Currently we fetch all the sample data using this function:
```
def...
- Error when fetching SNPs in a search page
✓ issue opened on Sep 28 2022 by Munyoki Kilyungi, last updated on Apr 18 2023 by Munyoki Kilyungi
Error when fetching SNPs in a search page
Wed 28 Sep 2022 17:45:01 EAT
* assigned: zachs, bonfacem
* tags: critical
* priority: high
* closed
## Steps to reproduce
* Consider this search page...
- 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...
- 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 Sep 30 2022 by Munyoki Kilyungi
...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
...Tags
* assigned: alexm
* priority: high
* status: ongoing
* keywords: correlations,fewer results
## Description
in some cases correlaton return fewer number of results
than are required
an example...
- GN1 metadata
issue opened on Dec 09 2022 by Pjotr Prins; 0 of 3 tasks done
...it shows a missing PHP.
The problem can be replitated by logging into GN1 and selecting a dataset. Hit the info button and 'edit' next.
## Tags
* assigned: pjotrp
* priority: high
* status: overdue...
- 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...
- 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...
- Invalid Token Error
✓ issue opened 5 weeks ago by Zachary Sloan, last updated 5 weeks ago 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...
- Phenotype Naming Conventions
document created on Nov 23 2022 by Munyoki Kilyungi
...BW_M_6m* as the body weight of males at 6 months for 6 or more publications. Then we may need to programmatically add further tags such as year of publication (last two digits).
3. We have to decide...
- 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...
- 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...
- Genenetwork2 Configurations
issue opened on Jun 14 2023 by Frederick Muriuki Muriithi, last updated on Jun 28 2023 by Frederick Muriuki Muriithi
Genenetwork2 Configurations
## Tags
* assigned: fredm
* priority: normal
* status: open
* keywords: configuration, config, gn2, genenetwork, genenetwork2
* type: bug
## Description
The current way...
- 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...
- Next Steps
document created on Sep 09 2021 by jgart, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...Steps
## Tags
* assigned: jgart
* type: enhancement
* keywords: notebooks, jupyter
* status: unclear
## Description
Whenever we start a notebook let's generate an id (put the id in a db or in memory...
- 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...
- 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
...Give informative message
* [X] Log in error log
* [X] Add test regressions
These have been fixed by Zach and Pjotr
## Tags
* status: closed
## Info
Now qtlreaper works. That suggests a problem with R.
- Precompute mapping input data
document created on Mar 20 2023 by Pjotr Prins, last updated on Jun 14 2023 by Pjotr Prins
...functionality. Here we prepare for a new generation of functionality that introduces LMMs for compute and multiple significant scores for queries.
# Tags
* assigned: pjotrp
* type: precompute, gemma...
- tux01 running out of RAM
issue opened on Sep 03 2022 by Pjotr Prins, last updated on Sep 05 2022 by Alexander_Kabui; 1 of 6 tasks done
...RAM
Tux01 ran out of steam.
## Tags
* assigned: pjotrp, zsloan
* type: systems
* keywords: database
* status: unclear
* priority: medium
## Tasks
* [X] post-mortem (see below)
* [ ] free up disk space...
- Using PDB to Troubleshoot Python Code
document created on May 26 2022 by BonfaceKilz, last updated on May 22 2023 by Frederick Muriuki Muriithi
...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...
- Partial Correlation
document created on Oct 15 2021 by Frederick Muriuki Muriithi, last updated on May 16 2022 by Frederick Muriuki Muriithi
Pick 3 and hit 'Partial'
Put one each 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...
- Rewrite qc and qc-uploads in Python3
issue opened on Apr 11 2022 by Frederick Muriuki Muriithi, last updated on Jul 20 2022 by Frederick Muriuki Muriithi
...Tags
* type: rewrite
* priority: high
* assigned: fredm
* status: in progress
* keywords: quality control
## Description
Since the quality control application will mostly be maintained outside...
- 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 Oct 12 2022 by Munyoki Kilyungi; 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...
- Automated Testing
document created on Oct 12 2022 by Munyoki Kilyungi
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...
- 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
...Traits Effectively
# Tags
* assigned: bonfacem
* keywords: metadata
* priority: high
* closed
## Tasks
* [ ] I cannot edit the PMID number
* [ ] There is inadequate feedback on whether or not changes...
- Genenetwork3 Effective UID
✓ issue opened on Jun 05 2023 by Frederick Muriuki Muriithi, last updated on Jun 09 2023 by Frederick Muriuki Muriithi
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...
- 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/...
- 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...
- Editing Case-Attributes
document created on Jul 07 2023 by Frederick Muriuki Muriithi, last updated 4 weeks ago by Frederick Muriuki Muriithi
...Case-Attributes
## Tags
* type: document
* keywords: case-attribute, editing
* assigned: fredm, zachs, acenteno
* status: requirements gathering
## Introduction
Case-Attributes are essentially the...
- 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...
- Phenotype Correlation Error
✓ issue opened on Sep 28 2022 by Zachary Sloan, last updated on Nov 22 2022 by Frederick Muriuki Muriithi
...Tags
* assigned: alexm, fredm, zsloan
* type: bug
* keywords: correlations
* status: closed, completed
* priority: high
## Notes
* 2022-09-29: Successfully reproduced on production
* 2022-09-29...
- 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...
- 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 7 weeks ago by Munyoki Kilyungi; 0 of 6 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...