Age | Commit message (Expand) | Author |
2025-07-14 | Handle case where authorisation is already set up. | Frederick Muriuki Muriithi |
2025-07-14 | Restore original names and instead ignore specific linter errors. | Frederick Muriuki Muriithi |
2025-07-14 | Fix linting issues. | Frederick Muriuki Muriithi |
2025-07-14 | Provide timeouts for requests calls. | Frederick Muriuki Muriithi |
2025-07-14 | Remove unused script•••The bulk edit feature is no longer supported in the uploader.
| Frederick Muriuki Muriithi |
2025-07-14 | Fix imports•••Remove unused imports, update old imports to newer forms and add
missing imports.
| Frederick Muriuki Muriithi |
2025-07-02 | Compute the means while doing the cross-refences. | Frederick Muriuki Muriithi |
2025-07-01 | Ignore any optional files that are not provided. | Frederick Muriuki Muriithi |
2025-06-26 | Add cross-reference IDs to job as metadata. | Frederick Muriuki Muriithi |
2025-06-26 | BugFix: Logical bug - files have already been "untransposed".•••The `read_csv_file_headers` function can read headings from
non-transposed or transposed file, depending on the value of a flag.
The bug was passing the value of the `*_transposed` flag from the
control file, even after any transposed files have been
"untransposed".
This commit passes an explicit `False` value, and adds a comment to
note the fix.
| Frederick Muriuki Muriithi |
2025-06-26 | Convert to tuple to allow indexing. | Frederick Muriuki Muriithi |
2025-06-26 | Replace first field header with standard "id" header. | Frederick Muriuki Muriithi |
2025-06-26 | Pass in the field separator, and comment char while reading file•••Pass in the field separator character to split the fields
correctly. Also pass in the comment character to safely ignore any
comment lines.
| Frederick Muriuki Muriithi |
2025-06-17 | Allow users to provide transposed files. | Frederick Muriuki Muriithi |
2025-06-10 | Pass on the publication to the next job. | Frederick Muriuki Muriithi |
2025-06-10 | Change message level. | Frederick Muriuki Muriithi |
2025-06-09 | Fix minor bug. | Frederick Muriuki Muriithi |
2025-06-09 | Run the authorisation update requests. | Frederick Muriuki Muriithi |
2025-06-09 | Compute the data_link_ids from the request results. | Frederick Muriuki Muriithi |
2025-06-09 | Fix bug in data for creating a new resource. | Frederick Muriuki Muriithi |
2025-06-09 | Compute request data for …/data/link/phenotypes endpoint. | Frederick Muriuki Muriithi |
2025-06-09 | Add debug logging to track process. | Frederick Muriuki Muriithi |
2025-06-09 | Fix return: Don't use `RETURNING *`.•••Fetching the results of the insert query with `RETURNING *` does not
work as expected with MySQLdb. This commit, thus, returns the
explicitly computed values instead.
| Frederick Muriuki Muriithi |
2025-06-05 | Break up long lines. | Frederick Muriuki Muriithi |
2025-06-05 | `update_auth()` scaffolding•••Add untested scaffolding for how the `update_auth()` function will
work. Include notes to help with figuring the feature out.
| Frederick Muriuki Muriithi |
2025-06-05 | Only update authorisation after all data is entered.•••Pull the auth update function out of the database connection
contextmanager to prevent any problems with an auth update from
causing a rollback of all the data.
We can always manually update the authorisation later, therefore, we
do not want a failure in that causing the (potentially) time-consuming
data entry process from being rolled back.
| Frederick Muriuki Muriithi |
2025-06-03 | Add more logging to track progress. | Frederick Muriuki Muriithi |
2025-06-03 | Save data with `LOAD DATA INFILE …` query•••To help speed up the saving of the data (for really huge files) into
the database, use the `LOAD DATA INFILE …` command if available, and
if not fallback to the one using raw queries.
| Frederick Muriuki Muriithi |
2025-06-03 | Extract building of data items into helper function. | Frederick Muriuki Muriithi |
2025-06-03 | Memory saving: Don't reload saved data•••We already have all the data in memory, so we do not need to reload it
and keep yet another copy.
| Frederick Muriuki Muriithi |
2025-06-02 | Compute data in files lazily. | Frederick Muriuki Muriithi |
2025-06-02 | Process NA-strings in the worker script. | Frederick Muriuki Muriithi |
2025-06-02 | Update placeholder function•••We'll probably provide a token to use to update the authorisation for
the new data.
The commit also explicitly raises a `NotImplement` exception for now.
| Frederick Muriuki Muriithi |
2025-06-02 | Add missing import. | Frederick Muriuki Muriithi |
2025-06-02 | Fix bug: Compute data correctly. Replace N/A strings with NoneType. | Frederick Muriuki Muriithi |
2025-06-02 | Add some debugging statements. | Frederick Muriuki Muriithi |
2025-06-02 | Pass the phenotypes name-to-id map to functions. | Frederick Muriuki Muriithi |
2025-06-02 | Compute the map from a phenotype's name to its ID. | Frederick Muriuki Muriithi |
2025-05-30 | Refactor: Extract common pattern into separate function•••Extract the common pattern into a separate, more generalized function
and pass the new function the data it requires to perform its tasks
for the different file types.
| Frederick Muriuki Muriithi |
2025-05-30 | Add typing to load_data function and invoke it. | Frederick Muriuki Muriithi |
2025-05-30 | Save standard errors and counts. | Frederick Muriuki Muriithi |
2025-05-30 | Get the species, population and dataset. | Frederick Muriuki Muriithi |
2025-05-30 | Add more tables to lock list. | Frederick Muriuki Muriithi |
2025-05-30 | Fix query: Add missing field and parameter. | Frederick Muriuki Muriithi |
2025-05-30 | Fix function names. | Frederick Muriuki Muriithi |
2025-05-30 | Fix processing of numerical data to save to the database. | Frederick Muriuki Muriithi |
2025-05-30 | Fix file paths: append the path to the extraction directory. | Frederick Muriuki Muriithi |
2025-05-30 | Refactor out common `__row_to_dataitems__` function. | Frederick Muriuki Muriithi |
2025-05-28 | Bug: Fix actual data value, not result set. | Frederick Muriuki Muriithi |
2025-05-28 | Bug: Add missing commas. | Frederick Muriuki Muriithi |