- Quality Control Project
✓ issue opened on Nov 19 2021 by Arthur Centeno, last updated on Jul 20 2022 by Frederick Muriuki Muriithi
...data.
QC should be embedded functionality of the data uploader that Bonface has written.
* Upload data through REST API - it goes into a temp dir for a user (data is in
escrow) - Bonface wrote...
- Provide Page/Link for/to Uploaded Data
issue opened on Jul 10 2024 by Frederick Muriuki Muriithi
...gn-uploader, uploader, data dashboard
## Description
Once a user has uploaded their data, provide them with a landing page/dashboard for the data they have uploaded, with details on what that data...
- 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
...the upload of data, doing the bare minimum in terms of quality control. In this document, we detail the quality control checks that are required to be run against the uploaded data, to ensure the data...
- Temporary Traits Access Concerns
issue opened on Aug 03 2023 by Frederick Muriuki Muriithi
...uploadeh data or the data used in the correlation matrix could be, in some cases, sensitive data. Making the temporary traits always publicly visible could lead to leaking the data, especially if the...
- New Privileges: Samples Ordering
issue opened on Sep 19 2024 by Frederick Muriuki Muriithi
...opposed to a data curator role).
This allows us to have users that are "data curators" that we can offload some of the data curation work to (e.g. @flisso, @suheeta etc.).
We would then, restrict the...
- Link Authentication/Authorisation
issue opened on Jun 24 2024 by Frederick Muriuki Muriithi
...auth system, by default, will deny anyone/everyone access to any data that is not linked to a resource and which no user has any roles allowing them access to the data.
We, currently, assign such data...
- Paginate Resources Page
issue opened on Jul 27 2023 by Frederick Muriuki Muriithi
...have too many data items linked, which leads to the page freezing when loaded.
Pagination will help aleviate the issue in those situations.
We also need to add a search of sorts for the data within...
- 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
...heading in the first row MUST appear in the first row ONLY ONE time
* no empty data cells
* no data cells with spurious characters like `eeeee`, `5.555iloveguix`, etc...
* decimal numbers must conform...
- Clean up Authorisation
✓ issue opened on Nov 19 2021 by BonfaceKilz, last updated on Dec 04 2023 by Frederick Muriuki Muriithi; 4 of 4 tasks done
...probeset data. Get data from the genotype file and work out how to update the values from the database.
* [X] Every resource needs to have the 3 fields set for the group-mask and default-mask: "data"...
- Feature Request: Create Test Accounts
issue opened on Sep 16 2024 by Frederick Muriuki Muriithi, last updated on Sep 17 2024 by Frederick Muriuki Muriithi
...deleted.
* What happens to any data uploaded by these accounts? They should probably not upload data meant to be permanent. All their data might need to be deleted along with the temporary accounts.
- Quality Control Checks
✓ issue opened on Nov 17 2021 by jgart, last updated on Jul 20 2022 by Frederick Muriuki Muriithi
...Strain names should prefer long form:
B6 -> C57BL/6
D2 -> DBA/2
3. Probeset IDs that don't have any values should be pruned:
For example an Affymetrix data set might have ~28,000 entries and the data...
- 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
...was a myopic view of the data uploader, and needs to be expanded significantly. The user will need to specify the species for the data they wish to upload before being allowed to upload. That implies...
- 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
...strains into populations/tissue etc.
## TODO
* [x] UI to select species
* [x] UI to select or create a grouping for the strains (think InbredSet)
* [x] UI to select the CSV file with the strains data...
- Replace Redis with SQL
issue opened 7 weeks ago by Frederick Muriuki Muriithi
...one of the many SQL databases (we'll probably use SQLite3 anyway), which are more standardised, and easier to migrate data from and to. It has the added advantage that we can open multiple connections...
- UI Design
✓ issue opened on Dec 01 2021 by jgart, last updated on Jul 20 2022 by Frederick Muriuki Muriithi
Input/Receive Data in UI (drag and drop/upload submit form)
2. Select Mouse
"What type of Group are you using?"
> (AKXD, BXH, Mouse Diversity Panel, BXD)
3. "What is your platform?"
> (Aff, Ilumina...