- Quality Control of Data in Uploaded R/qtl2 Bundles
✓ issue opened on Feb 02 2024 by Frederick Muriuki Muriithi, last updated on Sep 16 2024 by Frederick Muriuki Muriithi; 10 of 15 tasks done
...Control File
* [x] MUST exist in bundle
* [x] One and only one control file in the bundle
* [x] Defaults for control data are auto-provided by code
* [x] Every file listed in control file MUST exist...
- Rewrite qc and qc-uploads in Python3
✓ issue opened on Apr 11 2022 by Frederick Muriuki Muriithi, last updated on Nov 28 2023 by Frederick Muriuki Muriithi
...-control/gene-symbols Mappings between representations of symbol names
=> /issues/quality-control/qc-checks Some checks to run against files
=> /issues/quality-control/qc Notes on original QC App ideas...
- Quality Control Checks
✓ issue opened on Nov 17 2021 by jgart, last updated on Jul 20 2022 by Frederick Muriuki Muriithi
...Control Checks
1. ProbeSetId (Affymetrix format):
We favour using Illumina, Affimetrix, and other platform formats.
Custom formats require a new annotation file to be created.
We usually use Ensemble...
- Quality Control Project
✓ issue opened on Nov 19 2021 by Arthur Centeno, last updated on Jul 20 2022 by Frederick Muriuki Muriithi
Quality Control Project
Develop an app with a web interface to automate the job of cleaning tsv data
files for entry. The app would be used by a group of users on a network to
upload data.
QC should...
- Enumerating all QC checks
✓ issue opened on Nov 19 2021 by jgart, last updated on Jul 20 2022 by Frederick Muriuki Muriithi
...to enumerate all QC checks and platforms that we want to test against.
## Tags
* assigned: fredm, jgart, arthur
* status: closed
* type: feature-request
* priority: high
* keywords: quality control
- Big File Upload Fails
✓ issue opened on Jan 17 2023 by Frederick Muriuki Muriithi, last updated on Nov 28 2023 by Frederick Muriuki Muriithi
...qc, quality control
## Description
Trying to upload big files (>= 500MB) fails quietly, dropping the user back to the home page.
### Troubleshooting
This issue is reproducible on https://bioart.io/...
- UI Design
✓ issue opened on Dec 01 2021 by jgart, last updated on Jul 20 2022 by Frederick Muriuki Muriithi
"Inbred Set ID 1 is the same as BXD"
> These are the strains: ...
## Tags
* assigned: fredm, jgart
* type: feature-request
* status: closed
* priority: medium
* keywords: UI, quality control
- QC: Fix Integration Tests
✓ issue opened on Jan 09 2024 by Frederick Muriuki Muriithi, last updated on Feb 27 2024 by Frederick Muriuki Muriithi
...control, qc, tests, gn-uploader
* type: bug
## Description
Tests that require that Redis be present in order to run, fail due to the statement
```
command = [shutil.which("redis-server"), "--port"...
- Read Samples/Cases/Individuals From Database
✓ issue opened on Jan 20 2024 by Frederick Muriuki Muriithi, last updated on Feb 27 2024 by Frederick Muriuki Muriithi
...control, samples, strains, cases, gn-uploader
* status: closed, completed
## Description
I discovered a
=> https://gitlab.com/fredmanglis/gnqc_py/-/blob/6200a60eb6f04a5d50bfe0ad366674dc49a08119/...
- Upload Strains
✓ issue opened on Dec 06 2023 by Frederick Muriuki Muriithi, last updated on Feb 27 2024 by Frederick Muriuki Muriithi; 5 of 5 tasks done
...QC, quality control, strains, gn-uploader
## Description
Currently, the uploader simply fails when it encounters unknown strains in the files being uploaded.
This issue will track the implementation...