| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2024-02-05 | Do general bundle validation and show errors | Frederick Muriuki Muriithi | |
| * Display any and all errors on the UI * Move `validate_bundle` to QC module and refactor to use `missing_files` | |||
| 2024-02-05 | Update UI documentation | Frederick Muriuki Muriithi | |
| Improve the UI documentation by making it more explicit what each section deals with to help aleviate confusion of what the different features do. | |||
| 2024-02-02 | Bug: Specify DictCursor class to return dict-like result | Frederick Muriuki Muriithi | |
| Without specifying the `cursorclass`, the result is a tuple of the form: ((query_col01_val, query_col02_val, ...), ...) where the ellipsis specify the possibility of more than one of the previous form. We specify the DictCursor class instead so that the form changes to: ({query_col01_name: query_col01_val, ...}, ...) which allows us to pick the value we want with a string index. | |||
| 2024-01-24 | Checks: Update code and tests to ensure all checks pass. | Frederick Muriuki Muriithi | |
| 2024-01-24 | redis-prefix: update "upload samples" path | Frederick Muriuki Muriithi | |
| 2024-01-24 | redis-prefix: Update "insert data" path. | Frederick Muriuki Muriithi | |
| 2024-01-24 | redis-prefix: Update file validation code | Frederick Muriuki Muriithi | |
| Update the file validation script and routes to use the redis prefix for jobs. | |||
| 2024-01-23 | Update scripts to use redis prefix. | Frederick Muriuki Muriithi | |
| 2024-01-23 | Add prefix to redis keys | Frederick Muriuki Muriithi | |
| Since the GNQC application might find itself sharing the same redis server and/or database with other applications, add a prefix to its keys. | |||
| 2024-01-22 | UI: Fix some UI bugs. | Frederick Muriuki Muriithi | |
| 2024-01-22 | scripts: Pass in logger to get detailed updates. | Frederick Muriuki Muriithi | |
| 2024-01-22 | UI: Show progress of R/qtl2 bundle processing. | Frederick Muriuki Muriithi | |
| 2024-01-20 | Fetch sample/case names from database | Frederick Muriuki Muriithi | |
| Fetch the sample/case names from the database rather than from a static file in the repository. Issue: https://issues.genenetwork.org/issues/quality-control/read-samples-from-database-by-species | |||
| 2024-01-19 | scripts: Process R/qtl2 bundle | Frederick Muriuki Muriithi | |
| Build script to start the processing of the R/qtl2 bundle. | |||
| 2024-01-19 | UI: Present entry point for R/qtl2 bundles upload. | Frederick Muriuki Muriithi | |
| 2024-01-18 | UI: Display summary information. | Frederick Muriuki Muriithi | |
| 2024-01-18 | UI: Create new ProbeSet dataset. | Frederick Muriuki Muriithi | |
| 2024-01-18 | UI: Select from existing ProbeSet datasets. | Frederick Muriuki Muriithi | |
| 2024-01-18 | Create new ProbeSet study. | Frederick Muriuki Muriithi | |
| 2024-01-17 | UI: Select ProbeSet study. | Frederick Muriuki Muriithi | |
| 2024-01-17 | UI: Implement creating new genotype datasets. | Frederick Muriuki Muriithi | |
| 2024-01-17 | UI: Initialise summary page. | Frederick Muriuki Muriithi | |
| 2024-01-17 | Enable selecting from existing genotype datasets. | Frederick Muriuki Muriithi | |
| 2024-01-17 | Update flash-messages' categories. | Frederick Muriuki Muriithi | |
| 2024-01-16 | UI: Create UI for creating a new Genotype dataset. | Frederick Muriuki Muriithi | |
| 2024-01-16 | UI: Create UI to select from existing genotype datasets. | Frederick Muriuki Muriithi | |
| 2024-01-16 | Create intermediate step | Frederick Muriuki Muriithi | |
| We do not have the option to modify the request and then redirect with the modification in place. To go around that, this commit creates an intermediate step that informs the user of their progress, while allowing us to store the filename for future steps. | |||
| 2024-01-16 | Build a sha512 hash from the uploaded file's name and timestamp | Frederick Muriuki Muriithi | |
| Build a sha512 message digest from the file's name and the timestamp of when the file was uploaded. This ensures that the filename is URL-safe, and reduces chances of name conflicts in the upload directory which could lead to data corruption when processing the files and saving the files into the database. | |||
| 2024-01-15 | Update imports: `take` was moved to different package. | Frederick Muriuki Muriithi | |
| 2024-01-08 | Fix errors with types. | Frederick Muriuki Muriithi | |
| 2024-01-08 | Upload R/qtl2 zip bundle and check for errors. | Frederick Muriuki Muriithi | |
| 2024-01-08 | Implement "create-population" route. | Frederick Muriuki Muriithi | |
| 2024-01-08 | Implement "POST" path for "select-population" route. | Frederick Muriuki Muriithi | |
| 2024-01-08 | Use extracted functions and fix bugs | Frederick Muriuki Muriithi | |
| 2024-01-08 | Extract common database functions into a separate package. | Frederick Muriuki Muriithi | |
| 2024-01-05 | Improve styling. | Frederick Muriuki Muriithi | |
| 2024-01-05 | UI to select the population under which the data falls. | Frederick Muriuki Muriithi | |
| 2024-01-05 | Initialise R/qtl2 bundle upload path | Frederick Muriuki Muriithi | |
| Initialise the upload path for R/qtl2 bundles. This commit adds UI that allows the user to select from existing species, before proceeding to the next stage. | |||
| 2023-12-20 | Reduce table columns | Frederick Muriuki Muriithi | |
| Reduce the table columns displayed by javascript for the platforms. | |||
| 2023-12-20 | Add favicon | Frederick Muriuki Muriithi | |
| Add a favicon to reduce noise in the logs due to failed requests. | |||
| 2023-12-19 | Commit missing templates. | Frederick Muriuki Muriithi | |
| 2023-12-19 | Bug: Commit population before trying to upload data. | Frederick Muriuki Muriithi | |
| 2023-12-18 | Samples: Hook-up external async script to upload the samples. | Frederick Muriuki Muriithi | |
| 2023-12-14 | samples: Create external script and fix some bugs. | Frederick Muriuki Muriithi | |
| 2023-12-14 | Pass connection to `species_by_id` function. | Frederick Muriuki Muriithi | |
| To make `species_by_id` function reusable even outside of the application context, pass in the database connection instead of creating the connection inside the function. | |||
| 2023-12-11 | samples: Fix bugs in code saving samples to db | Frederick Muriuki Muriithi | |
| * Check whether first row in file is for headings * Break infinite loop: check batch has content * Update saving of uploaded files | |||
| 2023-12-07 | Samples: Read an save data to db. | Frederick Muriuki Muriithi | |
| 2023-12-07 | Samples: Provide preview feature. | Frederick Muriuki Muriithi | |
| 2023-12-06 | Feature: Upload Samples/Cases | Frederick Muriuki Muriithi | |
| Implements the code enabling the upload of the samples/cases to the database. | |||
| 2023-11-30 | Remove link to non-existent file. | Frederick Muriuki Muriithi | |
 |
index : gn-uploader | |
| gn-uploader: Data uploader for GeneNetwork |
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