- issues/fetch-sample-data.gmi
✓ issue opened on Aug 09 2021 by BonfaceKilz, last updated on May 25 2022 by BonfaceKilz
...keywords: sample data, GN2, GN3
* status: closed
* priority: medium
#### Fetch all Sample Data
Currently we fetch all the sample data using this function:
```
def get_trait_csv_sample_data(conn: Any...
- Editing Phenotypes
document created on Jul 07 2023 by Frederick Muriuki Muriithi, last updated on Jul 12 2023 by Frederick Muriuki Muriithi
...page
* Approve or reject the diffs
## Notes
* Sample data editing is only available for phenotype traits. You cannot edit sample data for genotype or probeset traits
* Removing values for sample data...
- sample data caching bug
issue opened on Feb 11 2022 by Zachary Sloan, last updated on Mar 14 2023 by Arun Isaac
sample data caching bug
When we cache sample data (mainly for features like correlations), it doesn't take into account changes in the sample list (which is derived from the .geno file).
While...
- 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
...sample data and case attributes for Publish using the parsed genofiles
```sql
SELECT
Strain.Name, GenoData.value, GenoSE.error, GenoData.Id
FROM
(GenoData, GenoFreeze, Strain, Geno, GenoXRef)...
- Dump sample data to LMDB
issue opened on Dec 15 2022 by Munyoki Kilyungi, last updated on Mar 06 2024 by Munyoki Kilyungi; 0 of 5 tasks done
...sample data in LMDB, allowing it to be accessed quickly in GN2/3 via RDF, which will decouple the data from the python-base classes/objects it is associated with, significantly improving sample data...
- Export Uploaded Data to LMDB and RDF Stores
issue opened on Nov 03 2023 by Frederick Muriuki Muriithi, last updated on Oct 20 2025 by Frederick Muriuki Muriithi; 0 of 6 tasks done
...work.
## Exporting Sample Data
We can export the sample (numeric) data to LMDB with the "dataset->lmdb" project[3].
The project (as of 2023-11-14T10:12+03:00UTC) does not define an installable binary/...
- Data Uploads: Inserting Data
document created on Jan 27 2022 by BonfaceKilz, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...Editing sample data from a published phenotype
- Deleting sample data from published phenotypes
- Inserting data from strains that already exist in a ".geno" file
However, one of our beta users ran...
- Pre-Cache Datasets
issue opened on Oct 24 2022 by Frederick Muriuki Muriithi
...cache files based on dates for latest changes without deleting older cache files -- we could look into whether this is possible.
## Related Issues
=> /issues/sample-data-caching-problem Sample Data...
- 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
...On clicking the "Edit" button in the traits' page (/show_trait?...), the sample data is supposed to appear at the bottom of the page for editing. This is not happening locally.
## Troubleshooting...
- issues/custom_data_for_scatterplot.gmi
issue opened on Mar 09 2023 by Zachary Sloan
...any edits to sample data a user does for correlations are not reflected in the scatterplots.
I'm thinking of dealing with this similarly to the way I dealt with the mapping links - just using the hash...
- rewrite sampledata fetching with genofiles using scheme
issue opened on Jul 19 2023 by Alexander_Kabui, last updated on Sep 01 2025 by Alexander_Kabui; 2 of 6 tasks done
...fetching sample data and case attributes using them
we need to integrate the components intoa fully working module
This is in turn be used to dump data to lmdb
We chose scheme to accomplish the task...
- Allow analyses to be done between traits from "individuals" groups and their corresponding "main" group
issue opened on Jul 21 2022 by Zachary Sloan
...-LongevityPublish). These mappings could be stored in a simple JSON file.
The "main" group trait(s) could then have their sample data converted to the sample list of the "individuals" group, provided...
- MariaDB Database Architecture
document created on Jun 29 2024 by Pjotr Prins, last updated on Feb 24 2025 by Pjotr Prins
...reflect the relationship between these groups*
* As far as the database is concerned, there is no distinction between strain means and individual sample data - they're all rows in the ProbeSetData/...
- GeneNetwork Uploader Requirements
document created on Feb 22 2024 by Frederick Muriuki Muriithi, last updated on Feb 22 2024 by Frederick Muriuki Muriithi
...include sample data. If user specifies a GEO platform ID, we could fetch such details and auto-populate relevant tables, perhaps. We'd (well, mostly I, Fred) need to figure out whether NCBI provides...
- Editing Case-Attributes
document created on Jul 07 2023 by Frederick Muriuki Muriithi, last updated on Sep 09 2024 by Munyoki Kilyungi
...@zachs: Implement case-attributes editing in GN3 that correctly models case-attributes at the group-level. CRUD operations with the correct authorization. People who can edit sample data should not...
- Editing Trait Metadata and Sample Data
document created on Jul 07 2023 by Frederick Muriuki Muriithi, last updated on Jul 25 2023 by Frederick Muriuki Muriithi
...Sample Data
## Priority Ordering for Editing Work
=> /topics/editing/phenotypes Phenotype Editing
=> /topics/editing/case_attributes Case Attributes Editing
=> /topics/editing/info_files Info-Files...
- Add Metadata To The Trait Page (RDF)
document created on Sep 28 2022 by Munyoki Kilyungi, last updated on Dec 03 2023 by Pjotr Prins
...(RDF)
Fri 30 Sep 2022 11:48:41 EAT
## Introduction
We are migrating the GN2 relational database to a plain text and RDF database. Matrix-like data (E.g. fetching sample data for a given data) will...
- Some Historical Context
document created on Jul 05 2022 by BonfaceKilz
...specifically refers to a grouping of traits. It's easy to confuse that with individual GN traits (which can best be defined as a single set of sample data). So Time Series (TS) data would consist...
- 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
.../tmp/gn2/gn2/ProbeSetFreezeId_886_EPFL/ETHZ BXD Liver Proteome CD-HFD (Nov19)' (error)
```
This obviously has something to do with the sample data files, though not sure what yet.
### 2022-10-18
I...
- Add option to directly link to mapping results
issue opened on Jan 19 2023 by Zachary Sloan
...to allow other people to see your results.
The way I'm currently doing this is to link an ID (generated as a hash from the mapping inputs) with JSON of all the options/sample-data/filenames. A URL...
- Brittle Fix for Editing Metadata
issue opened on Aug 02 2023 by Frederick Muriuki Muriithi
...L273-L276 awkwardly detects changes to sample data
----
The problem with the javascript code above is that it is hacky and the solutions are brittle. For example
* marking the field as changed on blur...
- Materialised Views for Correlations
✓ issue opened on Oct 19 2022 by Frederick Muriuki Muriithi, last updated on Dec 19 2022 by Frederick Muriuki Muriithi
...Tables
* Geno
* ProbeSet
* Phenotype
* Temp
#### Sample Data
* GenoData and GenoSE
* ProbeSetData and ProbeSetSE
* PublishData and PublishSE
* TempData
There might also need to be materialised views...
- Linking genotype files to datasets
issue opened on Jul 07 2023 by Alexander_Kabui, last updated on Jul 11 2023 by Alexander_Kabui
...can have multiple groups. In order to fetch all possible sample data fetch all possible groups in a dataset then use that to fetch all linked genofiles
As an example example the dataset HC_M2_0606_P...
- 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
Historical reasons for the "pre-*" field e.g. pre-publication was explained in detail. They are there to mark a sort of "confidential" not-yet-ready data.
* The word "sample data file" is confusing...
- GNSoC 2023
document created on Jun 21 2023 by Pjotr Prins, last updated on Aug 24 2023 by Pjotr Prins
...-gen-databases/design-doc Design doc
### Week 1
* RDF dumps
* Parsing S-exp -> markdown
* Hashing tables (Fred)
- automated updates
* Some progress on sample data from SQL -> lmdb (Alex)
* Next week...
- Precompute mapping input data
document created on Apr 23 2025 by Pjotr Prins, last updated on Jul 29 2025 by Pjotr Prins
.../wqflask/api/router.py
Fetch traits and sample data API (we may use this!)
### wqflask/wqflask/show_trait/show_trait.py
Same.
### The following are a punch of scripts:
* scripts/insert_expression_data...