| Age | Commit message (Expand) | Author |
|---|
| 2024-11-22 | Use gn-libs code for db connection....Use the code in gn-libs to connect to the database, rather than a
local module.
| Frederick Muriuki Muriithi |
| 2024-07-25 | Rename module: qc_app --> uploader | Frederick Muriuki Muriithi |
| 2024-03-29 | Quiet linter. | Frederick Muriuki Muriithi |
| 2024-03-22 | Notify user if identifiers are not consistent. | Frederick Muriuki Muriithi |
| 2024-03-22 | Map names in files to names in database. | Frederick Muriuki Muriithi |
| 2024-03-22 | Fix linting issue. | Frederick Muriuki Muriithi |
| 2024-03-20 | Fix bug: correctly merge standard-error values in file to data in db...`read_datavalues(…)` function returns a dict of the form:
```
{
ProbeSetName01: ({…}, …),
ProbeSetName02: ({…}, …),
︙
}
```
Previously, the generator would thus try to index into the keys of the
datavalues, which were strings, leading to an error.
This commit changes the generator to return the values of the
datavalues dict as a flattened list of values.
| Frederick Muriuki Muriithi |
| 2024-02-28 | Fix bug: fetch from cursor, not return from cursor.execute(…)load-raw-data-no-parsing | Frederick Muriuki Muriithi |
| 2024-02-12 | Provide better error messaging...Provide a better error message that can help the user figure out what
they did wrong and fix it for themselves instead of the older, cryptic
and extremely unhelpful error message.
| Frederick Muriuki Muriithi |
| 2024-01-15 | Update imports: `take` was moved to different package. | Frederick Muriuki Muriithi |
| 2023-12-20 | Fix ID column key...Fix the wrong assumption that the ID key will always be
"ProbeSetID". The key for the ID column could change from study to
study or dataset to dataset.
| Frederick Muriuki Muriithi |
| 2023-11-30 | Bug: Fix insertion error...Fix a bug that was causing the data insertion to fail.
| Frederick Muriuki Muriithi |
| 2023-11-30 | Fix errors caught by pylint and mypy. | Frederick Muriuki Muriithi |
| 2023-11-15 | Log out DB errors even when handled...Log out any DB errors that occur to help with tracking and debugging
failures.
| Frederick Muriuki Muriithi |
| 2023-11-15 | Remove debugging statement. | Frederick Muriuki Muriithi |
| 2023-11-15 | Bug: Insert ProbeSets before average data and cross-refs...Insert the ProbeSets first before inserting the average data and
cross-referencing it.
| Frederick Muriuki Muriithi |
| 2023-11-15 | mypy: Fix typing errors. | Frederick Muriuki Muriithi |
| 2023-11-15 | Linting: Fix linting errors. | Frederick Muriuki Muriithi |
| 2023-10-30 | Prevent overwrite. Avoid inserting same probeset multiple times....* Avoid overwriting existing data by adding a random string to the
name of the ProbeSet
* Read ProbeSet names separately from the means for the strains, to
avoid entering the same ProbeSet record over and over with varying
names.
| Frederick Muriuki Muriithi |
| 2023-10-18 | Link to `ProbeSet.Id` in XRef Table...The "ProbeSetId" value in the file is actually stored in the database
in the `ProbeSet.Name` field, whereas the `ProbeSetXRef` table
actually uses the `ProbeSet.Id` value to define the
relationships. This commit fixes that issue.
| Frederick Muriuki Muriithi |
| 2023-10-16 | Fix bug: Insert ProbeSets if they do not exist. | Frederick Muriuki Muriithi |
| 2023-10-16 | Fix bug: Provide the platform_id to `insert_means` | Frederick Muriuki Muriithi |
| 2023-10-16 | Fix bug: parsing fields from query. | Frederick Muriuki Muriithi |
| 2022-08-05 | Update job status. Display stdout and stderr outputs...* Display the status of the job, as it is running
* Display STDERR output if an error occurs
* Display STDOUT output as job is running and on successful completion
of the job
| Frederick Muriuki Muriithi |
| 2022-08-04 | Format queries for output. Get rid of extraneous output. | Frederick Muriuki Muriithi |
| 2022-07-19 | Save standard error data. Fix linting and typing errors. | Frederick Muriuki Muriithi |
| 2022-07-19 | Implement data insertion (averages/means)...* quality_control/file_utils.py (new file): extract common file
utilities.
* quality_control/parsing.py (refactor): extract common file
utilities.
* scripts/insert_data.py: Implement data insertion for averages/means
| Frederick Muriuki Muriithi |
